Interaction between HIV-1 Tat and DNA-PKcs modulates HIV transcription and class switch recombination.

PubMed

Zhang, Shi-Meng; Zhang, He; Yang, Tian-Yi; Ying, Tian-Yi; Yang, Pei-Xiang; Liu, Xiao-Dan; Tang, Sheng-Jian; Zhou, Ping-Kun

2014-01-01

HIV-1 tat targets a variety of host cell proteins to facilitate viral transcription and disrupts host cellular immunity by inducing lymphocyte apoptosis, but whether it influences humoral immunity remains unclear. Previously, our group demonstrated that tat depresses expression of DNA-PKcs, a critical component of the non-homologous end joining pathway (NHEJ) of DNA double-strand breaks repair, immunoglobulin class switch recombination (CSR) and V(D)J recombination, and sensitizes cells to ionizing radiation. In this study, we demonstrated that HIV-1 Tat down-regulates DNA-PKcs expression by directly binding to the core promoter sequence. In addition, Tat interacts with and activates the kinase activity of DNA-PKcs in a dose-dependent and DNA independent manner. Furthermore, Tat inhibits class switch recombination (CSR) at low concentrations (≤ 4 µg/ml) and stimulates CSR at high concentrations (≥ 8 µg/ml). On the other hand, low protein level and high kinase activity of DNA-PKcs promotes HIV-1 transcription, while high protein level and low kinase activity inhibit HIV-1 transcription. Co-immunoprecipitation results revealed that DNA-PKcs forms a large complex comprised of Cyclin T1, CDK9 and Tat via direct interacting with CDK9 and Tat but not Cyclin T1. Taken together, our results provide new clues that Tat regulates host humoral immunity via both transcriptional depression and kinase activation of DNA-PKcs. We also raise the possibility that inhibitors and interventions directed towards DNA-PKcs may inhibit HIV-1 transcription in AIDS patients.

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

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.

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

Ongoing In Vivo Immunoglobulin Class Switch DNA Recombination in Chronic Lymphocytic Leukemia B Cells1

PubMed Central

Cerutti, Andrea; Zan, Hong; Kim, Edmund C.; Shah, Shefali; Schattner, Elaine J.; Schaffer, András; Casali, Paolo

2015-01-01

Chronic lymphocytic leukemia (CLL) results from the expansion of malignant CD5+ B cells that usually express IgD and IgM. These leukemic cells can give rise in vivo to clonally related IgG+ or IgA+ elements. The requirements and modalities of this process remain elusive. Here we show that leukemic B cells from 14 of 20 CLLs contain the hallmarks of ongoing Ig class switch DNA recombination (CSR), including extrachromosomal switch circular DNAs and circle transcripts generated by direct Sμ→Sγ, Sμ→Sα, and Sμ→Sε as well as sequential Sγ→Sα and Sγ→Sε CSR. Similar CLL B cells express transcripts for activation-induced cytidine deaminase, a critical component of the CSR machinery, and contain germline IH-CH and mature VHDJH-CH transcripts encoded by multiple Cγ, Cα, and Cε genes. Ongoing CSR occurs in only a fraction of the CLL clone, as only small proportions of CD5+CD19+ cells express surface IgG or IgA and lack IgM and IgD. In vivo class-switching CLL B cells down-regulate switch circles and circle transcripts in vitro unless exposed to exogenous CD40 ligand and IL-4. In addition, CLL B cells that do not class switch in vivo activate the CSR machinery and secrete IgG, IgA, or IgE upon in vitro exposure to CD40 ligand and IL-4. These findings indicate that in CLL at least some members of the malignant clone actively differentiate in vivo along a pathway that induces CSR. They also suggest that this process is elicited by external stimuli, including CD40 ligand and IL-4, provided by bystander immune cells. PMID:12444172

Apurinic/Apyrimidinic Endonuclease 1 Is the Essential Nuclease during Immunoglobulin Class Switch Recombination

PubMed Central

Masani, Shahnaz; Han, Li

2013-01-01

Immunoglobulin (Ig) class switch recombination (CSR) is initiated by activation-induced cytidine deaminase (AID) that catalyzes numerous DNA cytosine deaminations within switch regions. The resulting uracils are processed by uracil base excision and/or mismatch repair enzymes that ultimately generate switch region DNA double-strand breaks (DSBs). Uracil glycosylase 2 (UNG2) is required for CSR, most likely by removing uracils to generate abasic sites. Although it is presumed that the apurinic/apyrimidinic endonuclease 1 (APE1) generates DNA strand incisions (a prerequisite for CSR) at these abasic sites, a direct test of the requirement for APE1 in CSR has been difficult because of the embryonic lethality of APE1 ablation in mice. Here, we report the successful deletion of the APE1 gene in a mouse B cell line (CH12F3) capable of robust CSR in vitro. In contrast to the general assumption that APE1 is essential for cellular viability, deletion of APE1 in CH12F3 cells has no apparent effect on cell viability or growth. Moreover, CSR in APE1-null CH12F3 cells is drastically reduced, providing direct evidence for an essential role for APE1 in switch region cleavage and CSR. Finally, deletion of AP endonuclease 2 (APE2) has no effect on CSR in either APE1-proficient or -deficient cells. PMID:23382073

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.

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

CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.

PubMed

Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

2017-05-15

B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study. Copyright © 2017 by The American Association of Immunologists, Inc.

Germinal center hypoxia potentiates immunoglobulin class switch recombination

PubMed Central

Abbott, Robert K.; Thayer, Molly; Labuda, Jasmine; Silva, Murillo; Philbrook, Phaethon; Cain, Derek W.; Kojima, Hidefumi; Hatfield, Stephen; Sethumadhavan, Shalini; Ohta, Akio; Reinherz, Ellis L.; Kelsoe, Garnett; Sitkovsky, Michail

2016-01-01

Germinal centers (GCs) are anatomic sites where B cells undergo secondary diversification to produce high affinity, class switched antibodies. We hypothesized that proliferating B cells in GCs create a hypoxic microenvironment that governs their further differentiation. Using molecular markers, we found GCs to be predominantly hypoxic. Compared to normoxia (21% O2), hypoxic culture conditions (1% O2) in vitro accelerated class switching and plasma cell formation and enhanced expression of GL-7 on B and CD4+ T cells. Reversal of GC hypoxia in vivo by breathing 60% O2 during immunization resulted in reduced frequencies of GC B cells, T follicular helper (TFH) cells and plasmacytes, as well as lower expression of ICOS on TFH. Importantly, this reversal of GC hypoxia decreased antigen-specific serum IgG1 and reduced the frequency of IgG1+ B cells within the antigen specific GC. Taken together, these observations reveal a critical role for hypoxia in GC B cell differentiation. PMID:27798169

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rev1 Recruits Ung to Switch Regions and Enhances dU Glycosylation for Immunoglobulin Class Switch DNA Recombination

PubMed Central

Zan, Hong; White, Clayton A.; Thomas, Lisa M.; Mai, Thach; Li, Guideng; Xu, Zhenming; Zhang, Jinsong; Casali, Paolo

2012-01-01

SUMMARY By diversifying the biological effector functions of antibodies, class switch DNA recombination (CSR) plays a critical role in the maturation of the immune response. It is initiated by AID-mediated dC deamination, yielding dUs, and dU glycosylation by Ung in antibody switch (S) region DNA. Here we showed that the translesion DNA synthesis polymerase Rev1 directly interacted with Ung and targeted in an AID-dependent and Ung-independent fashion the S regions undergoing CSR. Rev1–/– Ung+/+ B cells reduced Ung recruitment to S regions, DNA-dU glycosylation and CSR. This together with an S region spectrum of mutations similar to that of Rev1+/+ Ung–/– B cells suggested that Rev1 operated in the same pathway as Ung, as emphasized by further decreased CSR in Rev1–/– Msh2–/– B cells. Rescue of CSR in Rev1–/– B cells by a catalytically inactive Rev1 mutant showed that the important role of Rev1 in CSR is mediated by Rev1 scaffold, not enzymatic function. PMID:23140944

BRCT-domain protein BRIT1 influences class switch recombination

PubMed Central

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

2017-01-01

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. PMID:28724724

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.

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

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.

A transcriptional serenAID: the role of noncoding RNAs in class switch recombination

PubMed Central

Yewdell, William T.; Chaudhuri, Jayanta

2017-01-01

Abstract During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions and requires the DNA-modifying enzyme activation-induced cytidine deaminase (AID). AID-mediated DNA deamination within S regions initiates the formation of DNA double-strand breaks, which serve as biochemical beacons for downstream DNA repair pathways that coordinate the ligation of DNA breaks. Myriad factors contribute to optimal AID targeting; however, many of these factors also localize to genomic regions outside of the Igh locus. Thus, a current challenge is to explain the specific targeting of AID to the Igh locus. Recent studies have implicated noncoding RNAs in CSR, suggesting a provocative mechanism that incorporates Igh-specific factors to enable precise AID targeting. Here, we chronologically recount the rich history of noncoding RNAs functioning in CSR to provide a comprehensive context for recent and future discoveries. We present a model for the RNA-guided targeting of AID that attempts to integrate historical and recent findings, and highlight potential caveats. Lastly, we discuss testable hypotheses ripe for current experimentation, and explore promising ideas for future investigations. PMID:28535205

Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination

PubMed Central

HWANG, JOYCE K.; ALT, FREDERICK W.; YEAP, LENG-SIEW

2015-01-01

The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination. PMID:26104555

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

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.

B cell Toll-like receptors and immunoglobulin class-switch DNA recombination

PubMed Central

Pone, Egest J.; Xu, Zhenming; White, Clayton A.; Zan, Hong; Casali, Paolo

2014-01-01

Toll-like receptors (TLRs) are a family of conserved pattern recognition receptors (PRRs). Engagement of TLRs in B cells by microbe-associated molecular patterns (MAMPs) induces T-independent (TI) antibody responses and plays an important role in the early stages of T-dependent (TD) antibody responses before specific T cell help becomes available, in part by facilitating B cell entry into the germinal center reaction. The role of B cell TLRs in the antibody response is magnified by the synergy of B cell receptor (BCR) crosslinking and TLR engagement in promoting B cell proliferation and efficiently inducing immunoglobulin (Ig) class switch DNA recombination (CSR), which crucially diversifies the antibody biological effector functions. Dual engagement of TLRs and BCR can be mediated by complex MAMPs such as lipopolysaccharides (LPS), which engages TLR4 through its lipid A moiety and crosslinks the BCR through its polysaccharidic moiety (O-antigen). Dual BCR/TLR engagement induces CSR to all Ig isotypes, as directed by different cytokines, while engagement of any TLR alone induces only marginal CSR. Integration of BCR and TLR signaling results in activation of the canonical and non-canonical NF-κB pathways, induction of activation-induced cytidine deaminase (AID) and germline transcription of switch (S) regions in the IgH locus. The last two are essential events for CSR to unfold. A critical role of dual BCR/TLR engagement in induction of CSR and generation of neutralizing antibodies is emphasized by the emergence of TLR ligands as integral components of vaccines that greatly boost humoral immunity in a B cell-intrinsic fashion. Further, dual BCR/TLR engagement by complex self-antigens will result in dysregulation of AID expression and CSR in autoreactive B cells, leading to generation of isotype-switched pathogenic autoantibodies. Finally, an important aspect of dual BCR/TLR engagement is the boosting of specific antibody response to tumor antigens, as suggested by

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

Activation induced deaminase C-terminal domain links DNA breaks to end protection and repair during class switch recombination

PubMed Central

Zahn, Astrid; Eranki, Anil K.; Patenaude, Anne-Marie; Methot, Stephen P.; Fifield, Heather; Cortizas, Elena M.; Foster, Paul; Imai, Kohsuke; Durandy, Anne; Larijani, Mani; Verdun, Ramiro E.; Di Noia, Javier M.

2014-01-01

Activation-induced deaminase (AID) triggers antibody class switch recombination (CSR) in B cells by initiating DNA double strand breaks that are repaired by nonhomologous end-joining pathways. A role for AID at the repair step is unclear. We show that specific inactivation of the C-terminal AID domain encoded by exon 5 (E5) allows very efficient deamination of the AID target regions but greatly impacts the efficiency and quality of subsequent DNA repair. Specifically eliminating E5 not only precludes CSR but also, causes an atypical, enzymatic activity-dependent dominant-negative effect on CSR. Moreover, the E5 domain is required for the formation of AID-dependent Igh-cMyc chromosomal translocations. DNA breaks at the Igh switch regions induced by AID lacking E5 display defective end joining, failing to recruit DNA damage response factors and undergoing extensive end resection. These defects lead to nonproductive resolutions, such as rearrangements and homologous recombination that can antagonize CSR. Our results can explain the autosomal dominant inheritance of AID variants with truncated E5 in patients with hyper-IgM syndrome 2 and establish that AID, through the E5 domain, provides a link between DNA damage and repair during CSR. PMID:24591601

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

A role for Msh6 but not Msh3 in somatic hypermutation and class switch recombination.

PubMed

Martomo, Stella A; Yang, William W; Gearhart, Patricia J

2004-07-05

Somatic hypermutation is initiated by activation-induced cytidine deaminase (AID), and occurs in several kilobases of DNA around rearranged immunoglobulin variable (V) genes and switch (S) sites before constant genes. AID deaminates cytosine to uracil, which can produce mutations of C:G nucleotide pairs, and the mismatch repair protein Msh2 participates in generating substitutions of downstream A:T pairs. Msh2 is always found as a heterodimer with either Msh3 or Msh6, so it is important to know which one is involved. Therefore, we sequenced V and S regions from Msh3- and Msh6-deficient mice and compared mutations to those from wild-type mice. Msh6-deficient mice had fewer substitutions of A and T bases in both regions and reduced heavy chain class switching, whereas Msh3-deficient mice had normal antibody responses. This establishes a role for the Msh2-Msh6 heterodimer in hypermutation and switch recombination. When the positions of mutation were mapped, several focused peaks were found in Msh6(-/-) clones, whereas mutations were dispersed in Msh3(-/-) and wild-type clones. The peaks occurred at either G or C in WGCW motifs (W = A or T), indicating that C was mutated on both DNA strands. This suggests that AID has limited entry points into V and S regions in vivo, and subsequent mutation requires Msh2-Msh6 and DNA polymerase.

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination.

PubMed

Ribeiro de Almeida, Claudia; Dhir, Somdutta; Dhir, Ashish; Moghaddam, Amin E; Sattentau, Quentin; Meinhart, Anton; Proudfoot, Nicholas J

2018-05-17

Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

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. Copyright © 2016 by The American Association of Immunologists, Inc.

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

Hyper-IgM syndrome type 4 with a B lymphocyte–intrinsic selective deficiency in Ig class-switch recombination

PubMed Central

Imai, Kohsuke; Catalan, Nadia; Plebani, Alessandro; Maródi, László; Sanal, Özden; Kumaki, Satoru; Nagendran, Vasantha; Wood, Philip; Glastre, Catherine; Sarrot-Reynauld, Françoise; Hermine, Olivier; Forveille, Monique; Revy, Patrick; Fischer, Alain; Durandy, Anne

2003-01-01

Hyper-IgM syndrome (HIGM) is a heterogeneous condition characterized by impaired Ig class-switch recombination (CSR). The molecular defects that have so far been associated with this syndrome — which affect the CD40 ligand in HIGM type 1 (HIGM1), CD40 in HIGM3, and activation-induced cytidine deaminase (AID) in HIGM2 — do not account for all cases. We investigated the clinical and immunological characteristics of 15 patients with an unidentified form of HIGM. Although the clinical manifestations were similar to those observed in HIGM2, these patients exhibited a slightly milder HIGM syndrome with residual IgG production. We found that B cell CSR was intrinsically impaired. However, the generation of somatic hypermutations was observed in the variable region of the Ig heavy chain gene, as in control B lymphocytes. In vitro studies showed that the molecular defect responsible for this new HIGM entity (HIGM4) occurs downstream of the AID activity, as the AID gene was induced normally and AID-induced DNA double-strand breaks in the switch μ region of the Ig heavy chain locus were detected during CSR as normal. Thus, HIGM4 is probably the consequence of a selective defect either in a CSR-specific factor of the DNA repair machinery or in survival signals delivered to switched B cells. PMID:12840068

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.

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

Scaffold Functions of 14-3-3 Adaptors in B Cell Immunoglobulin Class Switch DNA Recombination

PubMed Central

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. PMID:24282540

The DSIF subunits Spt4 and Spt5 have distinct roles at various phases of immunoglobulin class switch recombination.

PubMed

Stanlie, Andre; Begum, Nasim A; Akiyama, Hideo; Honjo, Tasuku

2012-01-01

Class-switch recombination (CSR), induced by activation-induced cytidine deaminase (AID), can be divided into two phases: DNA cleavage of the switch (S) regions and the joining of the cleaved ends of the different S regions. Here, we show that the DSIF complex (Spt4 and Spt5), a transcription elongation factor, is required for CSR in a switch-proficient B cell line CH12F3-2A cells, and Spt4 and Spt5 carry out independent functions in CSR. While neither Spt4 nor Spt5 is required for transcription of S regions and AID, expression array analysis suggests that Spt4 and Spt5 regulate a distinct subset of transcripts in CH12F3-2A cells. Curiously, Spt4 is critically important in suppressing cryptic transcription initiating from the intronic Sμ region. Depletion of Spt5 reduced the H3K4me3 level and DNA cleavage at the Sα region, whereas Spt4 knockdown did not perturb the H3K4me3 status and S region cleavage. H3K4me3 modification level thus correlated well with the DNA breakage efficiency. Therefore we conclude that Spt5 plays a role similar to the histone chaperone FACT complex that regulates H3K4me3 modification and DNA cleavage in CSR. Since Spt4 is not involved in the DNA cleavage step, we suspected that Spt4 might be required for DNA repair in CSR. We examined whether Spt4 or Spt5 is essential in non-homologous end joining (NHEJ) and homologous recombination (HR) as CSR utilizes general repair pathways. Both Spt4 and Spt5 are required for NHEJ and HR as determined by assay systems using synthetic repair substrates that are actively transcribed even in the absence of Spt4 and Spt5. Taken together, Spt4 and Spt5 can function independently in multiple transcription-coupled steps of CSR.

Complex relationship between mismatch repair proteins and MBD4 during immunoglobulin class switch recombination.

PubMed

Grigera, Fernando; Bellacosa, Alfonso; Kenter, Amy L

2013-01-01

Mismatch repair (MMR) safeguards against genomic instability and is required for efficient Ig class switch recombination (CSR). Methyl CpG binding domain protein 4 (MBD4) binds to MutL homologue 1 (MLH1) and controls the post-transcriptional level of several MMR proteins, including MutS homologue 2 (MSH2). We show that in WT B cells activated for CSR, MBD4 is induced and interacts with MMR proteins, thereby implying a role for MBD4 in CSR. However, CSR is in the normal range in Mbd4 deficient mice deleted for exons 2-5 despite concomitant reduction of MSH2. We show by comparison in Msh2(+/-) B cells that a two-fold reduction of MSH2 and MBD4 proteins is correlated with impaired CSR. It is therefore surprising that CSR occurs at normal frequencies in the Mbd4 deficient B cells where MSH2 is reduced. We find that a variant Mbd4 transcript spanning exons 1,6-8 is expressed in Mbd4 deficient B cells. This transcript can be ectopically expressed and produces a truncated MBD4 peptide. Thus, the 3' end of the Mbd4 locus is not silent in Mbd4 deficient B cells and may contribute to CSR. Our findings highlight a complex relationship between MBD4 and MMR proteins in B cells and a potential reconsideration of their role in CSR.

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. © The Japanese Society for Immunology. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Fanca deficiency reduces A/T transitions in somatic hypermutation and alters class switch recombination junctions in mouse B cells

PubMed Central

Nguyen, Thuy Vy; Riou, Lydia

2014-01-01

Fanconi anemia is a rare genetic disorder that can lead to bone marrow failure, congenital abnormalities, and increased risk for leukemia and cancer. Cells with loss-of-function mutations in the FANC pathway are characterized by chromosome fragility, altered mutability, and abnormal regulation of the nonhomologous end-joining (NHEJ) pathway. Somatic hypermutation (SHM) and immunoglobulin (Ig) class switch recombination (CSR) enable B cells to produce high-affinity antibodies of various isotypes. Both processes are initiated after the generation of dG:dU mismatches by activation-induced cytidine deaminase. Whereas SHM involves an error-prone repair process that introduces novel point mutations into the Ig gene, the mismatches generated during CSR are processed to create double-stranded breaks (DSBs) in DNA, which are then repaired by the NHEJ pathway. As several lines of evidence suggest a possible role for the FANC pathway in SHM and CSR, we analyzed both processes in B cells derived from Fanca−/− mice. Here we show that Fanca is required for the induction of transition mutations at A/T residues during SHM and that despite globally normal CSR function in splenic B cells, Fanca is required during CSR to stabilize duplexes between pairs of short microhomology regions, thereby impeding short-range recombination downstream of DSB formation. PMID:24799500

Fanca deficiency reduces A/T transitions in somatic hypermutation and alters class switch recombination junctions in mouse B cells.

PubMed

Nguyen, Thuy Vy; Riou, Lydia; Aoufouchi, Saïd; Rosselli, Filippo

2014-06-02

Fanconi anemia is a rare genetic disorder that can lead to bone marrow failure, congenital abnormalities, and increased risk for leukemia and cancer. Cells with loss-of-function mutations in the FANC pathway are characterized by chromosome fragility, altered mutability, and abnormal regulation of the nonhomologous end-joining (NHEJ) pathway. Somatic hypermutation (SHM) and immunoglobulin (Ig) class switch recombination (CSR) enable B cells to produce high-affinity antibodies of various isotypes. Both processes are initiated after the generation of dG:dU mismatches by activation-induced cytidine deaminase. Whereas SHM involves an error-prone repair process that introduces novel point mutations into the Ig gene, the mismatches generated during CSR are processed to create double-stranded breaks (DSBs) in DNA, which are then repaired by the NHEJ pathway. As several lines of evidence suggest a possible role for the FANC pathway in SHM and CSR, we analyzed both processes in B cells derived from Fanca(-/-) mice. Here we show that Fanca is required for the induction of transition mutations at A/T residues during SHM and that despite globally normal CSR function in splenic B cells, Fanca is required during CSR to stabilize duplexes between pairs of short microhomology regions, thereby impeding short-range recombination downstream of DSB formation. © 2014 Nguyen et al.

AID-induced decrease in topoisomerase 1 induces DNA structural alteration and DNA cleavage for class switch recombination.

PubMed

Kobayashi, Maki; Aida, Masatoshi; Nagaoka, Hitoshi; Begum, Nasim A; Kitawaki, Yoko; Nakata, Mikiyo; Stanlie, Andre; Doi, Tomomitsu; Kato, Lucia; Okazaki, Il-mi; Shinkura, Reiko; Muramatsu, Masamichi; Kinoshita, Kazuo; Honjo, Tasuku

2009-12-29

To initiate class switch recombination (CSR) activation-induced cytidine deaminase (AID) induces staggered nick cleavage in the S region, which lies 5' to each Ig constant region gene and is rich in palindromic sequences. Topoisomerase 1 (Top1) controls the supercoiling of DNA by nicking, rotating, and religating one strand of DNA. Curiously, Top1 reduction or AID overexpression causes the genomic instability. Here, we report that the inactivation of Top1 by its specific inhibitor camptothecin drastically blocked both the S region cleavage and CSR, indicating that Top1 is responsible for the S region cleavage in CSR. Surprisingly, AID expression suppressed Top1 mRNA translation and reduced its protein level. In addition, the decrease in the Top1 protein by RNA-mediated knockdown augmented the AID-dependent S region cleavage, as well as CSR. Furthermore, Top1 reduction altered DNA structure of the Smu region. Taken together, AID-induced Top1 reduction alters S region DNA structure probably to non-B form, on which Top1 can introduce nicks but cannot religate, resulting in S region cleavage.

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. © 2016 Thomas-Claudepierre et al.

Individual Substitution Mutations in the AID C Terminus That Ablate IgH Class Switch Recombination

PubMed Central

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. PMID:26267846

Correlated Template-Switching Events during Minus-Strand DNA Synthesis: a Mechanism for High Negative Interference during Retroviral Recombination

PubMed Central

Anderson, Jeffrey A.; Teufel, Ronald J.; Yin, Philip D.; Hu, Wei-Shau

1998-01-01

Two models for the mechanism of retroviral recombination have been proposed: forced copy choice (minus-strand recombination) and strand displacement-assimilation (plus-strand recombination). Each minus-strand recombination event results in one template switch, whereas each plus-strand recombination event results in two template switches. Recombinant proviruses with one and more than one template switches were previously observed. Recombinants with one template switch were generated by minus-strand recombination, while recombinants containing more than one template switch may have been generated by plus-strand recombination or by correlated minus-strand recombination. We recently observed that retroviral recombination exhibits high negative interference whereby the frequency of recombinants containing multiple template-switching events is higher than expected. To delineate the mechanism that generates recombinants with more than one template switch, we devised a system that permits only minus-strand recombination. Two highly homologous vectors, WH204 and WH221, containing eight different restriction site markers were used. The primer binding site (PBS) of WH221 was deleted; although reverse transcription cannot initiate from WH221 RNA, it can serve as a template for DNA synthesis in heterozygotic virions. After one round of retroviral replication, the structures of the recombinant proviruses were examined. Recombinants containing two, three, four, and five template switches were observed at 1.4-, 10-, 65-, and 50-fold-higher frequencies, respectively, than expected. This indicates that minus-strand recombination events are correlated and can generate proviruses with multiple template switches efficiently. The frequencies of recombinants containing multiple template switches were similar to those observed in the previous system, which allowed both minus- and plus-strand recombination. Thus, the previously reported high negative interference during retroviral

Complex Relationship between Mismatch Repair Proteins and MBD4 during Immunoglobulin Class Switch Recombination

PubMed Central

Grigera, Fernando; Bellacosa, Alfonso; Kenter, Amy L.

2013-01-01

Mismatch repair (MMR) safeguards against genomic instability and is required for efficient Ig class switch recombination (CSR). Methyl CpG binding domain protein 4 (MBD4) binds to MutL homologue 1 (MLH1) and controls the post-transcriptional level of several MMR proteins, including MutS homologue 2 (MSH2). We show that in WT B cells activated for CSR, MBD4 is induced and interacts with MMR proteins, thereby implying a role for MBD4 in CSR. However, CSR is in the normal range in Mbd4 deficient mice deleted for exons 2–5 despite concomitant reduction of MSH2. We show by comparison in Msh2+/− B cells that a two-fold reduction of MSH2 and MBD4 proteins is correlated with impaired CSR. It is therefore surprising that CSR occurs at normal frequencies in the Mbd4 deficient B cells where MSH2 is reduced. We find that a variant Mbd4 transcript spanning exons 1,6–8 is expressed in Mbd4 deficient B cells. This transcript can be ectopically expressed and produces a truncated MBD4 peptide. Thus, the 3′ end of the Mbd4 locus is not silent in Mbd4 deficient B cells and may contribute to CSR. Our findings highlight a complex relationship between MBD4 and MMR proteins in B cells and a potential reconsideration of their role in CSR. PMID:24205214

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

PubMed

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

2013-01-31

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

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

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.

Recombination driven vacancy motion - a mechanism of memristive switching in oxides

NASA Astrophysics Data System (ADS)

Shen, Xiao; Puzyrev, Yevgeniy S.; Pantelides, Sokrates T.

2014-03-01

Wide-band gap oxides with high O deficiencies are attractive memristive materials for applications. However, the details of the defect dynamics remain elusive, especially regarding what drives the defect motion to form the conducting state. While the external field is often cited as the driving force, we report an investigation of memristive switching in polycrystalline ZnO and propose a new mechanism. Using results from density functional theory calculations, we show that the motion of O vacancies during switching to the conductive state is not driven by the electric field, but by recombination of carriers at these vacancies, which transfers energy to the defects and greatly enhances their diffusion. Such mechanism originates from the large structural change of O vacancies upon capturing electrons. In addition, contrary to the hypothesis that memristive switching in polycrystalline materials is facilitated by the defect motion along the grain boundary (GB), we show in our system the vacancies move perpendicular to the GB, attaching and detaching from it during the switching process. We call it recombination driven vacancy breathing. This work is supported by NSF Grant DMR-1207241 and NSF XSEDE grant DMR-130121.

Design and construction of a double inversion recombination switch for heritable sequential genetic memory.

PubMed

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

2008-07-30

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. 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. 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.

Antigenic Variation in the Lyme Spirochete: Insights into Recombinational Switching with a Suggested Role for Error-Prone Repair.

PubMed

Verhey, Theodore B; Castellanos, Mildred; Chaconas, George

2018-05-29

The Lyme disease spirochete, Borrelia burgdorferi, uses antigenic variation as a strategy to evade the host's acquired immune response. New variants of surface-localized VlsE are generated efficiently by unidirectional recombination from 15 unexpressed vls cassettes into the vlsE locus. Using algorithms to analyze switching from vlsE sequencing data, we characterize a population of over 45,000 inferred recombination events generated during mouse infection. We present evidence for clustering of these recombination events within the population and along the vlsE gene, a role for the direct repeats flanking the variable region in vlsE, and the importance of sequence homology in determining the location of recombination, despite RecA's dispensability. Finally, we report that non-templated sequence variation is strongly associated with recombinational switching and occurs predominantly at the 5' end of conversion tracts. This likely results from an error-prone repair mechanism operational during recombinational switching that elevates the mutation rate > 5,000-fold in switched regions. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

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

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

CMPF: class-switching minimized pathfinding in metabolic networks.

PubMed

Lim, Kevin; Wong, Limsoon

2012-01-01

The metabolic network is an aggregation of enzyme catalyzed reactions that converts one compound to another. Paths in a metabolic network are a sequence of enzymes that describe how a chemical compound of interest can be produced in a biological system. As the number of such paths is quite large, many methods have been developed to score paths so that the k-shortest paths represent the set of paths that are biologically meaningful or efficient. However, these approaches do not consider whether the sequence of enzymes can be manufactured in the same pathway/species/localization. As a result, a predicted sequence might consist of groups of enzymes that operate in distinct pathway/species/localization and may not truly reflect the events occurring within cell. We propose a path weighting method CMPF (Class-switching Minimized Pathfinder) to search for routes in a metabolic network which minimizes pathway switching. In biological terms, a pathway is a series of chemical reactions which define a specific function (e.g. glycolysis). We conjecture that routes that cross many pathways are inefficient since different pathways define different metabolic functions. In addition, native routes are also well characterized within pathways, suggesting that reasonable paths should not involve too many pathway switches. Our method can be generalized when reactions participate in a class set (e.g., pathways, species or cellular localization) so that the paths predicted have minimal class crossings. We show that our method generates k-paths that involve the least number of class switching. In addition, we also show that native paths are recoverable and alternative paths deviates less from native paths compared to other methods. This suggests that paths ranked by our method could be a way to predict paths that are likely to occur in biological systems.

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

What do somatic hypermutation and class switch recombination teach us about chronic lymphocytic leukaemia pathogenesis?

PubMed

Oppezzo, P; Dighiero, G

2005-01-01

origin. Activation induced cytidine deaminase (AID) plays a key role in SHM and class switch recombination (CSR). However, the mechanisms accounting for AID action and control of its expression remain unclear. In a recent work we have shown that in contrast to normal circulating B-cells, AID transcripts are expressed constitutively in CLL patients undergoing active CSR, but interestingly this expression occurs predominately in unmutated CLL B-cells. These data favour the view that AID protein may act differentially on CSR and SHM pathways, but the role-played by AID in both processes remains to be elucidated. Recent work indicates that AID is expressed in a small fraction of tumoral cells, which could suggest that this small fraction of cells may correspond to B-CLL cells that would have recently experienced an AID-inducing stimulus occurring in a specific microenvironment.

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…

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

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

Comparison of identical and functional Igh alleles reveals a nonessential role for Eμ in somatic hypermutation and class-switch recombination.

PubMed

Li, Fubin; Yan, Yi; Pieretti, Joyce; Feldman, Danielle A; Eckhardt, Laurel A

2010-11-15

Somatic hypermutation (SHM), coupled with Ag selection, provides a mechanism for generating Abs with high affinity for invading pathogens. Class-switch recombination (CSR) ensures that these Abs attain pathogen-appropriate effector functions. Although the enzyme critical to both processes, activation-induced cytidine deaminase, has been identified, it remains unclear which cis-elements within the Ig loci are responsible for recruiting activation-induced cytidine deaminase and promoting its activity. Studies showed that Ig gene-transcription levels are positively correlated with the frequency of SHM and CSR, making the intronic, transcriptional enhancer Eμ a likely contributor to both processes. Tests of this hypothesis yielded mixed results arising, in part, from the difficulty in studying B cell function in mice devoid of Eμ. In Eμ's absence, V(H) gene assembly is dramatically impaired, arresting B cell development. The current study circumvented this problem by modifying the murine Igh locus through simultaneous insertion of a fully assembled V(H) gene and deletion of Eμ. The behavior of this allele was compared with that of a matched allele carrying the same V(H) gene but with Eμ intact. Although IgH transcription was as great or greater on the Eμ-deficient allele, CSR and SHM were consistently, but modestly, reduced relative to the allele in which Eμ remained intact. We conclude that Eμ contributes to, but is not essential for, these complex processes and that its contribution is not as a transcriptional enhancer but, rather, is at the level of recruitment and/or activation of the SHM/CSR machinery.

Requirement of 8-mercaptoguanosine as a costimulus for IL-4-dependent mu to gamma1 class switch recombination in CD38-activated B cells.

PubMed

Tsukamoto, Yumiko; Uehara, Shoji; Mizoguchi, Chieko; Sato, Atsushi; Horikawa, Keisuke; Takatsu, Kiyoshi

2005-10-21

Mature B-2 cells expressing surface IgM and IgD proliferate upon stimulation by CD38, CD40 or lipopolysaccharide (LPS) and differentiate into IgG1-producing plasma cells in the presence of cytokines. The process of class switch recombination (CSR) from IgM to other isotypes is highly regulated by cytokines and activation-induced cytidine deaminase (AID). Blimp-1 and XBP-1 play an essential role in the terminal differentiation of switched B-2 cells to Ig-producing plasma cells. IL-5 induces AID and Blimp-1 expression in CD38- and CD40-activated B-2 cells, leading to mu to gamma1 CSR at DNA level and IgG1 production. IL-4, a well-known IgG1-inducing factor, does not induce mu to gamma1 CSR in CD38-activated B-2 cells or Blimp-1, while IL-4 induces mu to gamma1 CSR, XBP-1 expression, and IgG1 production expression in CD40-activated B-2 cells. Interestingly, the addition of 8-mercaptoguanosine (8-SGuo) with IL-4 to the culture of CD38-activated B cells can induce mu to gamma1 CSR, Blimp-1 expression, and IgG1 production. Intriguingly, 8-SGuo by itself induces AID expression in CD38-activated B cells. However, it does not induce mu to gamma1 CSR. These results imply that the mode of B-cell activation for extracellular stimulation affects the outcome of cytokine stimulation with respect to the efficiency and direction of CSR, and the requirements of the transcriptional regulator and the generation of antibody-secreting cells. Furthermore, our data suggest the requirement of additional molecules in addition to AID for CSR.

Examination of Msh6- and Msh3-deficient mice in class switching reveals overlapping and distinct roles of MutS homologues in antibody diversification.

PubMed

Li, Ziqiang; Scherer, Stefan J; Ronai, Diana; Iglesias-Ussel, Maria D; Peled, Jonathan U; Bardwell, Philip D; Zhuang, Min; Lee, KyeRyoung; Martin, Alberto; Edelmann, Winfried; Scharff, Matthew D

2004-07-05

Somatic hypermutation and class switch recombination (CSR) contribute to the somatic diversification of antibodies. It has been shown that MutS homologue (Msh)6 (in conjunction with Msh2) but not Msh3 is involved in generating A/T base substitutions in somatic hypermutation. However, their roles in CSR have not yet been reported. Here we show that Msh6(-)(/)(-) mice have a decrease in CSR, whereas Msh3(-)(/)(-) mice do not. When switch regions were analyzed for mutations, deficiency in Msh6 was associated with an increase in transition mutations at G/C basepairs, mutations at RGYW/WRCY hotspots, and a small increase in the targeting of G/C bases. In addition, Msh6(-)(/)(-) mice exhibited an increase in the targeting of recombination sites to GAGCT/GGGGT consensus repeats and hotspots in Sgamma3 but not in Smicro. In contrast to Msh2(-)(/)(-) mice, deficiency in Msh6 surprisingly did not change the characteristics of Smicro-Sgamma3 switch junctions. However, Msh6(-)(/)(-) mice exhibited a change in the positioning of Smicro and Sgamma3 junctions. Although none of these changes were seen in Msh3(-)(/)(-) mice, they had a higher percentage of large inserts in their switch junctions. Together, our data suggest that MutS homologues Msh2, Msh3, and Msh6 play overlapping and distinct roles during antibody diversification processes.

TBK1 controls IgA class switching by negatively regulating noncanonical NF-κB signaling

PubMed Central

Jin, Jin; Xiao, Yichuan; Chang, Jae-Hoon; Yu, Jiayi; Hu, Hongbo; Starr, Robyn; Brittain, George C.; Chang, Mikyoung; Cheng, Xuhong; Sun, Shao-Cong

2012-01-01

Immunoglobulin (Ig) class switching is crucial for generating antibody diversity in humoral immunity and, if deregulated, also has severe pathological consequences. How the magnitude of Ig isotype switching is controlled is still poorly understood. Here we identify TANK-binding kinase 1 (TBK1) as a pivotal negative regulator of IgA class switching. B cell-specific TBK1 ablation in mice resulted in uncontrolled production of IgA and development of nephropathy-like disease symptoms. TBK1 negatively regulated IgA class switching by attenuating noncanonical NF-κB signaling, an action that involved TBK1-mediated phosphorylation and subsequent degradation of the NF-κB-inducing kinase. These findings establish TBK1 as a pivotal negative regulator of the noncanonical NF-κB pathway and highlight a unique mechanism that controls IgA production. PMID:23023393

A class of generalized Ginzburg-Landau equations with random switching

NASA Astrophysics Data System (ADS)

Wu, Zheng; Yin, George; Lei, Dongxia

2018-09-01

This paper focuses on a class of generalized Ginzburg-Landau equations with random switching. In our formulation, the nonlinear term is allowed to have higher polynomial growth rate than the usual cubic polynomials. The random switching is modeled by a continuous-time Markov chain with a finite state space. First, an explicit solution is obtained. Then properties such as stochastic-ultimate boundedness and permanence of the solution processes are investigated. Finally, two-time-scale models are examined leading to a reduction of complexity.

Genomic Investigation Reveals Highly Conserved, Mosaic, Recombination Events Associated with Capsular Switching among Invasive Neisseria meningitidis Serogroup W Sequence Type (ST)-11 Strains.

PubMed

Mustapha, Mustapha M; Marsh, Jane W; Krauland, Mary G; Fernandez, Jorge O; de Lemos, Ana Paula S; Dunning Hotopp, Julie C; Wang, Xin; Mayer, Leonard W; Lawrence, Jeffrey G; Hiller, N Luisa; Harrison, Lee H

2016-07-03

Neisseria meningitidis is an important cause of meningococcal disease globally. Sequence type (ST)-11 clonal complex (cc11) is a hypervirulent meningococcal lineage historically associated with serogroup C capsule and is believed to have acquired the W capsule through a C to W capsular switching event. We studied the sequence of capsule gene cluster (cps) and adjoining genomic regions of 524 invasive W cc11 strains isolated globally. We identified recombination breakpoints corresponding to two distinct recombination events within W cc11: A 8.4-kb recombinant region likely acquired from W cc22 including the sialic acid/glycosyl-transferase gene, csw resulted in a C→W change in capsular phenotype and a 13.7-kb recombinant segment likely acquired from Y cc23 lineage includes 4.5 kb of cps genes and 8.2 kb downstream of the cps cluster resulting in allelic changes in capsule translocation genes. A vast majority of W cc11 strains (497/524, 94.8%) retain both recombination events as evidenced by sharing identical or very closely related capsular allelic profiles. These data suggest that the W cc11 capsular switch involved two separate recombination events and that current global W cc11 meningococcal disease is caused by strains bearing this mosaic capsular switch. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Ectopic lymphoid structures support ongoing production of class-switched autoantibodies in rheumatoid synovium.

PubMed

Humby, Frances; Bombardieri, Michele; Manzo, Antonio; Kelly, Stephen; Blades, Mark C; Kirkham, Bruce; Spencer, Jo; Pitzalis, Costantino

2009-01-13

Follicular structures resembling germinal centres (GCs) that are characterized by follicular dendritic cell (FDC) networks have long been recognized in chronically inflamed tissues in autoimmune diseases, including the synovium of rheumatoid arthritis (RA). However, it is debated whether these ectopic structures promote autoimmunity and chronic inflammation driving the production of pathogenic autoantibodies. Anti-citrullinated protein/peptide antibodies (ACPA) are highly specific markers of RA, predict a poor prognosis, and have been suggested to be pathogenic. Therefore, the main study objectives were to determine whether ectopic lymphoid structures in RA synovium: (i) express activation-induced cytidine deaminase (AID), the enzyme required for somatic hypermutation and class-switch recombination (CSR) of Ig genes; (ii) support ongoing CSR and ACPA production; and (iii) remain functional in a RA/severe combined immunodeficiency (SCID) chimera model devoid of new immune cell influx into the synovium. Using immunohistochemistry (IHC) and quantitative Taqman real-time PCR (QT-PCR) in synovial tissue from 55 patients with RA, we demonstrated that FDC+ structures invariably expressed AID with a distribution resembling secondary lymphoid organs. Further, AID+/CD21+ follicular structures were surrounded by ACPA+/CD138+ plasma cells, as demonstrated by immune reactivity to citrullinated fibrinogen. Moreover, we identified a novel subset of synovial AID+/CD20+ B cells outside GCs resembling interfollicular large B cells. In order to gain direct functional evidence that AID+ structures support CSR and in situ manufacturing of class-switched ACPA, 34 SCID mice were transplanted with RA synovium and humanely killed at 4 wk for harvesting of transplants and sera. Persistent expression of AID and Igamma-Cmu circular transcripts (identifying ongoing IgM-IgG class-switching) was observed in synovial grafts expressing FDCs/CD21L. Furthermore, synovial mRNA levels of AID were

High expression of AID and active class switch recombination might account for a more aggressive disease in unmutated CLL patients: link with an activated microenvironment in CLL disease.

PubMed

Palacios, Florencia; Moreno, Pilar; Morande, Pablo; Abreu, Cecilia; Correa, Agustín; Porro, Valentina; Landoni, Ana Ines; Gabus, Raul; Giordano, Mirta; Dighiero, Guillermo; Pritsch, Otto; Oppezzo, Pablo

2010-06-03

Interaction of chronic lymphocytic leukemia (CLL) B cells with tissue microenvironment has been suggested to favor disease progression by promoting malignant B-cell growth. Previous work has shown expression in peripheral blood (PB) of CLL B cells of activation-induced cytidine deaminase (AID) among CLL patients with an unmutated (UM) profile of immunoglobulin genes and with ongoing class switch recombination (CSR) process. Because AID expression results from interaction with activated tissue microenvironment, we speculated whether the small subset with ongoing CSR is responsible for high levels of AID expression and could be derived from this particular microenvironment. In this work, we quantified AID expression and ongoing CSR in PB of 50 CLL patients and characterized the expression of different molecules related to microenvironment interaction. Our results show that among UM patients (1) high AID expression is restricted to the subpopulation of tumoral cells ongoing CSR; (2) this small subset expresses high levels of proliferation, antiapoptotic and progression markers (Ki-67, c-myc, Bcl-2, CD49d, and CCL3/4 chemokines). Overall, this work outlines the importance of a cellular subset in PB of UM CLL patients with a poor clinical outcome, high AID levels, and ongoing CSR, whose presence might be a hallmark of a recent contact with the microenvironment.

Absence of Activation-induced Cytidine Deaminase, a Regulator of Class Switch Recombination and Hypermutation in B Cells, Suppresses Aorta Allograft Vasculopathy in Mice.

PubMed

Nakanishi, Tomonori; Xu, Xiaoyan; Wynn, Carmen; Yamada, Toshiko; Pan, Fan; Erickson, Laurie; Teo, Haeman; Nakagawa, Terry; Masunaga, Taro; Abe, Jumpei; Akamatsu, Masahiko; Tamura, Kouichi; Jiang, Hongsi

2015-08-01

Antibody-mediated rejection is caused in part by increasing circulation/production of donor-specific antibody (DSA). Activation-induced cytidine deaminase (AID) is a key regulator of class switch recombination and somatic hypermutation of immunoglobulin in B cells, yet its role in antibody-mediated transplant rejection remains unclear. We show here that AID deficiency in mice enables suppression of allograft vasculopathy (AV) after aorta transplantation, a DSA-mediated process. Splenocytes from C57BL/6 J (B6) AID(−/−) mice were used for determining in vitro proliferation responses, alloreactivity, cell surface marker expression, and antibody production. BALB/c mouse aortas were transplanted into B6 AID(−/−) mice with or without FK506 treatment. Blood and aorta grafts were harvested on day 30 after transplantation and were subjected to DSA, histological, and immunohistological analyses. The AID(−/−) splenocytes were comparable to wild type splenocytes in proliferation responses, alloreactivity, and expression of cell surface markers in vitro. However, they completely failed to produce immunoglobulin G, although they were not impaired in immunoglobulin M production relative to controls. Furthermore, BALB/c aorta grafts from B6 AID(−/−) recipient mice on day 30 after transplantation showed reduced signs of AV compared to the grafts from B6 wild type recipient mice which had severe vascular intimal hyperplasia, interstitial fibrosis, and inflammation. Treatment with FK506 produced a synergistic effect in the grafts from AID(−/−) recipients with further reduction of intimal hyperplasia and fibrosis scores. The AID deficiency inhibits DSA-mediated AV after aorta transplantation in mice. We propose that AID could be a novel molecular target for controlling antibody-mediated rejection in organ transplantation.

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

PubMed

Hartwich, Heiner; Satheesh, Somisetty V; Nothwang, Hans Gerd

2012-06-14

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

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.

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

PubMed Central

Wu, Yee Ling; Teichmann, Sarah A.

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. PMID:27994069

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

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

PubMed Central

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

2009-01-01

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. PMID:19351893

Homologous recombination occurs in a distinct retroviral subpopulation and exhibits high negative interference.

PubMed Central

Hu, W S; Bowman, E H; Delviks, K A; Pathak, V K

1997-01-01

Homologous recombination and deletions occur during retroviral replication when reverse transcriptase switches templates. While recombination occurs solely by intermolecular template switching (between copackaged RNAs), deletions can occur by an intermolecular or an intramolecular template switch (within the same RNA). To directly compare the rates of intramolecular and intermolecular template switching, two spleen necrosis virus-based vectors were constructed. Each vector contained a 110-bp direct repeat that was previously shown to delete at a high rate. The 110-bp direct repeat was flanked by two different sets of restriction site markers. These vectors were used to form heterozygotic virions containing RNAs of each parental vector, from which recombinant viruses were generated. By analyses of the markers flanking the direct repeats in recombinant and nonrecombinant proviruses, the rates of intramolecular and intermolecular template switching were determined. The results of these analyses indicate that intramolecular template switching is much more efficient than intermolecular template switching and that direct repeat deletions occur primarily through intramolecular template switching events. These studies also indicate that retroviral recombination occurs within a distinct viral subpopulation and exhibits high negative interference, whereby the selection of one recombination event increases the probability that a second recombination event will be observed. PMID:9223494

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.

Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I.

PubMed Central

Odelberg, S J; Weiss, R B; Hata, A; White, R

1995-01-01

Recombinant DNA molecules are often generated during the polymerase chain reaction (PCR) when partially homologous templates are available [e.g., see Pääbo et al. (1990) J. Biol. Chem. 265, 4718-4721]. It has been suggested that these recombinant molecules are a consequence of truncated extension products annealing to partially homologous templates on subsequent PCR cycles. However, we demonstrate here that recombinants can be generated during a single round of primer extension in the absence of subsequent heat denaturation, indicating that template-switching produces some of these recombinant molecules. Two types of template-switches were observed: (i) switches to pre-existing templates and (ii) switches to the complementary nascent strand. Recombination is reduced several fold when the complementary template strands are physically separated by attachment to streptavidin magnetic beads. This result supports the hypothesis that either the polymerase or at least one of the two extending strands switches templates during DNA synthesis and that interaction between the complementary template strands is necessary for efficient template-switching. Images PMID:7596836

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. PMID:28977829

Finite-time stabilisation of a class of switched nonlinear systems with state constraints

NASA Astrophysics Data System (ADS)

Huang, Shipei; Xiang, Zhengrong

2018-06-01

This paper investigates the finite-time stabilisation for a class of switched nonlinear systems with state constraints. Some power orders of the system are allowed to be ratios of positive even integers over odd integers. A Barrier Lyapunov function is introduced to guarantee that the state constraint is not violated at any time. Using the convex combination method and a recursive design approach, a state-dependent switching law and state feedback controllers of individual subsystems are constructed such that the closed-loop system is finite-time stable without violation of the state constraint. Two examples are provided to show the effectiveness of the proposed method.

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

PubMed

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

2018-01-23

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

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.

Adaptive tracking control for a class of stochastic switched systems

NASA Astrophysics Data System (ADS)

Zhang, Hui; Xia, Yuanqing

2018-02-01

The problem of adaptive tracking is considered for a class of stochastic switched systems, in this paper. As preliminaries, the criterion of global asymptotical practical stability in probability is first presented by the aid of common Lyapunov function method. Based on the Lyapunov stability criterion, adaptive backstepping controllers are designed to guarantee that the closed-loop system has a unique global solution, which is globally asymptotically practically stable in probability, and the tracking error in the fourth moment converges to an arbitrarily small neighbourhood of zero. Simulation examples are given to demonstrate the efficiency of the proposed schemes.

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

PubMed

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

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. 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). 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. 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 of islets.

A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination.

PubMed

León-Ortiz, Ana María; Panier, Stephanie; Sarek, Grzegorz; Vannier, Jean-Baptiste; Patel, Harshil; Campbell, Peter J; Boulton, Simon J

2018-01-18

Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses. Loss of vertebrate Rtel1 also causes a variety of unusually large and complex structural variations, including chromothripsis, breakage-fusion-bridge events, and tandem duplications with distant intra-chromosomal insertions, whose structure are consistent with a role for RTEL1 in preventing Ht-REC during break-induced replication. Our data establish Ht-REC as an unappreciated source of genome instability that underpins a novel class of complex genome rearrangements that likely arise during replication stress. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Analytical design equations for self-tuned Class-E power amplifier.

PubMed

Hu, Zhe; Troyk, Philip

2011-01-01

For many emerging neural prosthesis designs that are powered by inductive coupling, their small physical size requires large current in the extracorporeal transmitter coil, and the Class-E power amplifier topology is often used for the transmitter design. Tuning of Class-E circuits for efficient operation is difficult and a self-tuned circuit can facilitate the tuning. The coil current is sensed and used to tune the switching of the transistor switch in the Class-E circuit in order to maintain its high-efficiency operation. Although mathematically complex, the analysis and design procedure for the self-tuned Class-E circuit can be simplified due to the current feedback control, which makes the phase angle between the switching pulse and the coil current predetermined. In this paper explicit analytical design equations are derived and a detailed design procedure is presented and compared with the conventional Class-E design approaches.

Detection of isotype switch rearrangement in bulk culture by PCR.

PubMed

Max, E E; Mills, F C; Chu, C

2001-05-01

When a B lymphocyte changes from synthesizing IgM to synthesizing IgG, IgA, or IgE, this isotype switch is generally accompanied by a unique DNA rearrangement. The protocols in this unit describe two polymerase chain reaction (PCR)-based strategies for detecting switch rearrangements in bulk culture. The first involves direct PCR across the switch junctions, providing the opportunity for characterizing the recombination products by nucleotide sequence analysis; however, because of characteristics inherent to the PCR methodology this strategy cannot easily be used as a quantitative assay for recombination. A support protocol details the preparation of the 5' Su PCR probe for this protocol. The second basic protocol describes a method known as digestion-circularization PCR (DCPCR) that is more amenable to quantitation but yields no information on structure of the recombination products. Both techniques should be capable of detecting reciprocal deletion circles as well as functional recombination products remaining on the expressed chromosome.

Finite-time H∞ control for a class of discrete-time switched time-delay systems with quantized feedback

NASA Astrophysics Data System (ADS)

Song, Haiyu; Yu, Li; Zhang, Dan; Zhang, Wen-An

2012-12-01

This paper is concerned with the finite-time quantized H∞ control problem for a class of discrete-time switched time-delay systems with time-varying exogenous disturbances. By using the sector bound approach and the average dwell time method, sufficient conditions are derived for the switched system to be finite-time bounded and ensure a prescribed H∞ disturbance attenuation level, and a mode-dependent quantized state feedback controller is designed by solving an optimization problem. Two illustrative examples are provided to demonstrate the effectiveness of the proposed theoretical results.

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

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

Poliovirus RNA recombination: mechanistic studies in the absence of selection.

PubMed Central

Jarvis, T C; Kirkegaard, K

1992-01-01

Direct and quantitative detection of recombinant RNA molecules by polymerase chain reaction (PCR) provides a novel method for studying recombination in RNA viruses without selection for viable progeny. The parental poliovirus strains used in this study contained polymorphic marker loci approximately 600 bases apart; both exhibited wild-type growth characteristics. We established conditions under which the amount of PCR product was linearly proportional to the amount of input template, and the reproducibility was high. Recombinant progeny were predominantly homologous and arose at frequencies up to 2 x 10(-3). Recombination events increased in frequency throughout replication, indicating that there is no viral RNA sequestration or inhibition of recombination late in infection as proposed in earlier genetic studies. Previous studies have demonstrated that poliovirus recombination occurs by a copy-choice mechanism in which the viral polymerase switches templates during negative-strand synthesis. Varying the relative amount of input parental virus markedly altered reciprocal recombination frequencies. This, in conjunction with the kinetics data, indicated that acceptor template concentration is a determinant of template switching frequency. Since positive strands greatly outnumber negative strands throughout poliovirus infection, this would explain the bias toward recombination during negative-strand synthesis. Images PMID:1379178

Optimal control of switching time in switched stochastic systems with multi-switching times and different costs

NASA Astrophysics Data System (ADS)

Liu, Xiaomei; Li, Shengtao; Zhang, Kanjian

2017-08-01

In this paper, we solve an optimal control problem for a class of time-invariant switched stochastic systems with multi-switching times, where the objective is to minimise a cost functional with different costs defined on the states. In particular, we focus on problems in which a pre-specified sequence of active subsystems is given and the switching times are the only control variables. Based on the calculus of variation, we derive the gradient of the cost functional with respect to the switching times on an especially simple form, which can be directly used in gradient descent algorithms to locate the optimal switching instants. Finally, a numerical example is given, highlighting the validity of the proposed methodology.

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.

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.

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

Attenuating homologous recombination stimulates an AID-induced antileukemic effect

PubMed Central

Lamont, Kristin R.; Hasham, Muneer G.; Donghia, Nina M.; Branca, Jane; Chavaree, Margaret; Chase, Betsy; Breggia, Anne; Hedlund, Jacquelyn; Emery, Ivette; Cavallo, Francesca; Jasin, Maria; Rüter, Jens

2013-01-01

Activation-induced cytidine deaminase (AID) is critical in normal B cells to initiate somatic hypermutation and immunoglobulin class switch recombination. Accumulating evidence suggests that AID is also prooncogenic, inducing cancer-promoting mutations or chromosome rearrangements. In this context, we find that AID is expressed in >40% of primary human chronic lymphocytic leukemia (CLL) cases, consistent with other reports. Using a combination of human B lymphoid leukemia cells and mouse models, we now show that AID expression can be harnessed for antileukemic effect, after inhibition of the RAD51 homologous recombination (HR) factor with 4,4′-diisothiocyanatostilbene-2-2′-disulfonic acid (DIDS). As a proof of principle, we show that DIDS treatment inhibits repair of AID-initiated DNA breaks, induces apoptosis, and promotes cytotoxicity preferentially in AID-expressing human CLL. This reveals a novel antineoplastic role of AID that can be triggered by inhibition of HR, suggesting a potential new paradigm to treat AID-expressing tumors. Given the growing list of tumor types with aberrant AID expression, this novel therapeutic approach has potential to impact a significant patient population. PMID:23589568

Analysis and design of continuous class-E power amplifier at sub-nominal condition

NASA Astrophysics Data System (ADS)

Chen, Peng; Yang, Kai; Zhang, Tianliang

2017-12-01

The continuous class-E power amplifier at sub-nominal condition is proposed in this paper. The class-E power amplifier at continuous mode means it can be high efficient on a series matching networks while at sub-nominal condition means it only requires the zero-voltage-switching condition. Comparing with the classical class-E power amplifier, the proposed design method releases two additional design freedoms, which increase the class-E power amplifier's design flexibility. Also, the proposed continuous class-E power amplifier at sub-nominal condition can perform high efficiency over a broad bandwidth. The performance study of the continuous class-E power amplifier at sub-nominal condition is derived and the design procedure is summarised. The normalised switch voltage and current waveforms are investigated. Furthermore, the influences of different sub-nominal conditions on the power losses of the switch-on resistor and the output power capability are also discussed. A broadband continuous class-E power amplifier based on a Gallium Nitride (GaN) transistor is designed and testified to verify the proposed design methodology. The measurement results show, it can deliver 10-15 W output power with 64-73% power-added efficiency over 1.4-2.8 GHz.

Toll-like receptor 7 cooperates with IL-4 in activated B cells through antigen receptor or CD38 and induces class switch recombination and IgG1 production.

PubMed

Tsukamoto, Yumiko; Nagai, Yoshinori; Kariyone, Ai; Shibata, Takuma; Kaisho, Tsuneyasu; Akira, Shizuo; Miyake, Kensuke; Takatsu, Kiyoshi

2009-04-01

IL-4 and 8-mercaptoguanosine (8-SGuo) stimulation of CD38-activated B cells induces mu to gamma1 class switch recombination (CSR) at the DNA level leading to a high level of IgG1 production. Although some of signaling events initiated by IL-4 in activated B cells have been characterized, the involvement of TLR/MyD88 and Btk pathway in IL-4-dependent mu to gamma1 CSR has not been thoroughly evaluated. In this study, we characterized receptors for 8-SGuo and differential roles of 8-SGuo and IL-4 in the induction and mu to gamma1 CSR and IgG1 production. The role of TLR7 and MyD88 in 8-SGuo-induced AID expression and mu to gamma1 CSR was documented, as 8-SGuo did not act on CD38-stimulated splenic B cells from Tlr7(-/-) and Myd88(-/-) mice. CD38-activated B cells from Btk-deficient mice failed to respond to TLR7 ligands for the AID expression and CSR, indicating that Btk is also indispensable for the system. Stimulation of CD38-activated B cells with 8-SGuo induced significant AID expression and DNA double strand breaks, but IL-4 stimulation by itself did not trigger mu to gamma1 CSR. Intriguingly, the mu to gamma1 CSR in the B cells stimulated with CD38 and 8-SGuo totally depends on IL-4 stimulation. Similar results were obtained in the activated B cells through BCR and loxoribine, a well-known TLR7 ligand, in place of 8-SGuo. In vivo administration of TLR7 ligand and anti-CD38 antibody induced the generation of CD138(+) IgG1(+) cells. These results indicate that TLR7 is a receptor for 8-SGuo and plays an essential role in the AID and Blimp-1 expression; however it is not enough to complete mu to gamma1 CSR in CD38-activated B cells. IL-4 may be required for the induction of DNA repair system together with AID for the completion of CSR.

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

Origin of genetic variation: regulation of genetic recombination in the higher organisms - a theory.

PubMed

Pandey, K K

1972-01-01

loci, virtually "switches off" recombination, producing few new variations. Inbreeding produces homozygosity of these loci, resulting in certain individuals which will have a considerable number of their regulatory loci in the homozygous recessive condition and in which recombination will be "switched on", producing new variation at a high frequency. Inbreeding is thus an integrated, evolutionary system of considerable importance, and is not a degenerate "dead end", as many investigators have previously thought.The model has another compensatory function in evolution. In major loci, or in an operon, where there are structural genes and closely linked operator genes, as exemplified by the S locus, there are indications that the present model is concerned with the regulation of both structural and operator genes. The consequences of the model in the two classes of genes, however, are in direct contrast to each other: High heterozygosity which is instrumental in switching "off" recombination, and which is therefore helpful in maintaining stability in the structural gene, is conducive to functional variation of the operator gene; and high homozygosity, which is instrumental in switching "on" recombination, and which is therefore helpful in producing variation in the structural gene, is conducive to the stability of the operator gene.This model of the control of genetic variation in a specific chromosomal region is significant in development as well as in evolution, and throws light on a number of hitherto "intractable" problems peculiar to the higher organisms. For example, the model is helpful in explaining: 1) the origin of new self-incompatibility alleles in the flowering plants; 2) the impressive speciation in the waif flora (and fauna) of the oceanic islands; 3) the presence of high genetic variability in inbreeding species of plants; 4) environmentally-induced heritable variation in certain plants; and 5) the genetic mechanism of antibody diversity in animals.

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.

47 CFR 32.2210 - Central office-switching.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES Instructions for Balance Sheet Accounts § 32.2210 Central office—switching. This account shall be used by Class B companies to record the original cost of switching assets of the type and character required of Class A companies in Accounts 2211 through 2212. [67...

Immunoglobulin class switching to IgG4 in Warthin tumor and analysis of serum IgG4 levels and IgG4-positive plasma cells in the tumor.

PubMed

Aga, Mitsuharu; Kondo, Satoru; Yamada, Kazunori; Wakisaka, Naohiro; Yagi-Nakanishi, Sayaka; Tsuji, Akira; Endo, Kazuhira; Murono, Shigeyuki; Ito, Makoto; Muramatsu, Masamichi; Kawano, Mitsuhiro; Yoshizaki, Tomokazu

2014-04-01

We previously reported a case of immunoglobulin (Ig)G4-related immune inflammation in Warthin tumor. Increased serum IgG4 levels and tissue infiltration of IgG4-positive plasma cells are characteristics of IgG4-related disease (IgG4-RD), a newly emerging clinicopathological entity. However, the relationship between IgG4-RD and Warthin tumor remains to be elucidated. We aimed to investigate the involvement of systemic and local IgG4 production and class-switch recombination in Warthin tumor. We examined serum IgG4 levels and also analyzed the involvement of IgG4-positive plasma cells in Warthin tumors (18 cases) compared with those of pleomorphic adenomas (19 cases) as controls. Furthermore, in specimens of Warthin tumors (3 cases), pleomorphic adenomas (2 cases), and IgG4-RDs (2 cases), we examined messenger RNA expression of activation-induced cytidine deaminase, IgG4 germline transcripts and productive IgG4 by reverse transcription polymerase chain reaction. Serum IgG4 levels were increased in 5 of 18 Warthin tumors and not in any of the 19 pleomorphic adenomas. Infiltration of IgG4-positive plasma cells was detected in 4 Warthin tumors and none in the pleomorphic adenomas. Moreover, activation-induced cytidine deaminase, IgG4 germline transcripts, and productive IgG4 messenger RNA were found to be expressed in 2 of 3 Warthin tumors as well as IgG4-RDs by reverse transcription polymerase chain reaction, but not in pleomorphic adenomas. In conclusion, immunoglobulin class switching to IgG4 may be involved in the pathogenesis of Warthin tumor, and it is possible that certain inflammatory background with an immune reaction is involved in the pathogenesis of Warthin tumor. © 2013.

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

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.

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

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.

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)

Assessment of Recombination in the S-segment Genome of Crimean-Congo Hemorrhagic Fever Virus in Iran.

PubMed

Chinikar, Sadegh; Shah-Hosseini, Nariman; Bouzari, Saeid; Shokrgozar, Mohammad Ali; Mostafavi, Ehsan; Jalali, Tahmineh; Khakifirouz, Sahar; Groschup, Martin H; Niedrig, Matthias

2016-03-01

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. Samples were isolated from Iranian patients and those available in GenBank, and analyzed by phylogenetic and bootscan methods. 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. 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.

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

H∞ control for switched fuzzy systems via dynamic output feedback: Hybrid and switched approaches

NASA Astrophysics Data System (ADS)

Xiang, Weiming; Xiao, Jian; Iqbal, Muhammad Naveed

2013-06-01

Fuzzy T-S model has been proven to be a practical and effective way to deal with the analysis and synthesis problems for complex nonlinear systems. As for switched nonlinear system, describing its subsystems as fuzzy T-S models, namely switched fuzzy system, naturally is an alternative method to conventional control approaches. In this paper, the H∞ control problem for a class of switched fuzzy systems is addressed. Hybrid and switched design approaches are proposed with different availability of switching signal information at switching instant. The hybrid control strategy includes two parts: fuzzy controllers for subsystems and state updating controller at switching instant, and the switched control strategy contains the controllers for subsystems. It is demonstrated that the conservativeness is reduced by introducing the state updating behavior but its cost is an online prediction of switching signal. Numerical examples are given to illustrate the effectiveness of proposed approaches and compare the conservativeness of two approaches.

Site-specific genetic recombination: hops, flips, and flops.

PubMed

Sadowski, P D

1993-06-01

Genetic recombination plays a key role in the life of organisms as diverse as bacteriophages and humans. Contrary to our idea that chromosomes are stable structures, studies of recombination over the past few decades have shown that in fact DNA replicons are remarkably plastic, undergoing frequent recombination-induced rearrangements. This review summarizes our recent knowledge of the biochemistry of the two major classes of site-specific recombination: 1) transpositional recombination, and 2) conservative site-specific recombination.

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

Recombinant human basic fibroblast growth factor (bFGF) stimulates periodontal regeneration in class II furcation defects created in beagle dogs.

PubMed

Murakami, S; Takayama, S; Kitamura, M; Shimabukuro, Y; Yanagi, K; Ikezawa, K; Saho, T; Nozaki, T; Okada, H

2003-02-01

Several growth factors (or cytokines) have been recently investigated for their use as potential therapeutics for periodontal tissue regeneration. The objective of this study was to evaluate periodontal tissue regeneration, including new bone and cementum formation, following topical application of recombinant basic fibroblast growth factor (bFGF, FGF-2) to furcation class II defects. Twelve furcation class II bone defects were surgically created in six beagle dogs, then recombinant bFGF (30 micro g/site) + gelatinous carrier was topically applied to the bony defects. Six weeks after application, periodontal regeneration was analyzed. In all sites where bFGF was applied, periodontal ligament formation with new cementum deposits and new bone formation was observed histomorphometrically, in amounts greater than in the control sites. Basic FGF-applied sites exhibited significant regeneration as represented by the new bone formation rate (NBR) (83.6 +/- 14.3%), new trabecular bone formation rate (NTBR) (44.1 +/- 9.5%), and new cementum formation rate (NCR) (97.0 +/- 7.5%). In contrast, in the carrier-only sites, the NBR, NTBR, and NCR were 35.4 +/- 8.9%, 16.6 +/- 6.2%, and 37.2 +/- 15.1%, respectively. Moreover, no instances of epithelial down growth, ankylosis, or root resorption were observed in the bFGF-applied sites examined. The present results indicate that topical application of bFGF can enhance considerable periodontal regeneration in artificially created furcation class II bone defects of beagle dogs.

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

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.

Ig synthesis and class switching do not require the presence of the hs4 enhancer in the 3' IgH regulatory region.

PubMed

Vincent-Fabert, Christelle; Truffinet, Véronique; Fiancette, Remi; Cogné, Nadine; Cogné, Michel; Denizot, Yves

2009-06-01

Several studies have reported that regulatory elements located 3' of the IgH locus (namely hs3a, hs1,2, hs3b, and hs4) might play a role during class switch recombination (CSR) and Ig synthesis. While individual deletion of hs3a or hs1,2 had no effect, pairwise deletion of hs3b (an inverted copy of hs3a) and hs4 markedly affected CSR and Ig expression. Among these two elements, hs4 was tentatively presented with the master role due to its unique status within the 3' regulatory region: distal position outside repeated regions, early activation in pre-B cells, strong activity throughout B cell ontogeny. To clarify its role, we generated mice with a clean deletion of the hs4 after replacement with a floxed neo(R) cassette. Surprisingly, and as for previous deletion of hs3a or hs1,2, deletion of hs4 did not affect either in vivo CSR or the secretion level of any Ig isotype. In vitro CSR and Ig secretion in response to LPS and cytokines was not affected either. The only noticeable effects of the hs4 deletion were a decrease in the number of B splenocytes and a decreased membrane IgM expression. In conclusion, while dispensable for CSR and Ig transcription in plasma cells, hs4 mostly appears to contribute to Ig transcription in resting B lymphocytes.

Recombination and mutation of class II histocompatibility genes in wild mice.

PubMed

Wakeland, E K; Darby, B R

1983-12-01

We have compared the tryptic peptide fingerprints of the A alpha, A beta, E alpha, and E beta subunits encoded by four wild-derived H-2 complexes expressing A molecules closely related to Ak. The A molecules encoded by these Ak-related mice have A alpha and A beta subunits that differ from A alpha k and A beta k by less than 10% of their tryptic peptides. Comparisons among the four wild-derived A molecules suggested that these contemporary A alpha and A beta alleles arose by sequential mutational events from common ancestor A alpha and A beta alleles. These results suggest that A alpha and A beta may co-evolve as an A beta A alpha gene duplex in wild mice. Tryptic peptide fingerprint comparisons of the E beta gene linked to these Ak-related A beta A alpha gene duplexes indicate that two encode E beta d-like subunits, whereas another encodes an E beta s-like subunit. These results strongly suggest that the A beta A alpha duplex and E beta recombine in wild mouse populations. The significantly different evolutionary patterns exhibited by the class II genes encoding A vs E molecules are discussed.

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.

Comparative study to develop a single method for retrieving wide class of recombinant proteins from classical inclusion bodies.

PubMed

Padhiar, Arshad Ahmed; Chanda, Warren; Joseph, Thomson Patrick; Guo, Xuefang; Liu, Min; Sha, Li; Batool, Samana; Gao, Yifan; Zhang, Wei; Huang, Min; Zhong, Mintao

2018-03-01

The formation of inclusion bodies (IBs) is considered as an Achilles heel of heterologous protein expression in bacterial hosts. Wide array of techniques has been developed to recover biochemically challenging proteins from IBs. However, acquiring the active state even from the same protein family was found to be an independent of single established method. Here, we present a new strategy for the recovery of wide sub-classes of recombinant protein from harsh IBs. We found that numerous methods and their combinations for reducing IB formation and producing soluble proteins were not effective, if the inclusion bodies were harsh in nature. On the other hand, different practices with mild solubilization buffers were able to solubilize IBs completely, yet the recovery of active protein requires large screening of refolding buffers. With the integration of previously reported mild solubilization techniques, we proposed an improved method, which comprised low sarkosyl concentration, ranging from 0.05 to 0.1% coupled with slow freezing (- 1 °C/min) and fast thaw (room temperature), resulting in greater solubility and the integrity of solubilized protein. Dilution method was employed with single buffer to restore activity for every sub-class of recombinant protein. Results showed that the recovered protein's activity was significantly higher compared with traditional solubilization/refolding approach. Solubilization of IBs by the described method was proved milder in nature, which restored native-like conformation of proteins within IBs.

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

Mating-Type Genes and MAT Switching in Saccharomyces cerevisiae

PubMed Central

Haber, James E.

2012-01-01

Mating type in Saccharomyces cerevisiae is determined by two nonhomologous alleles, MATa and MATα. These sequences encode regulators of the two different haploid mating types and of the diploids formed by their conjugation. Analysis of the MATa1, MATα1, and MATα2 alleles provided one of the earliest models of cell-type specification by transcriptional activators and repressors. Remarkably, homothallic yeast cells can switch their mating type as often as every generation by a highly choreographed, site-specific homologous recombination event that replaces one MAT allele with different DNA sequences encoding the opposite MAT allele. This replacement process involves the participation of two intact but unexpressed copies of mating-type information at the heterochromatic loci, HMLα and HMRa, which are located at opposite ends of the same chromosome-encoding MAT. The study of MAT switching has yielded important insights into the control of cell lineage, the silencing of gene expression, the formation of heterochromatin, and the regulation of accessibility of the donor sequences. Real-time analysis of MAT switching has provided the most detailed description of the molecular events that occur during the homologous recombinational repair of a programmed double-strand chromosome break. PMID:22555442

Identification of a Transcriptionally Forward α Gene and Two υ Genes within the Pigeon (Columba livia) IgH Gene Locus.

PubMed

Huang, Tian; Wang, Xifeng; Si, Run; Chi, Hao; Han, Binyue; Han, Haitang; Cao, Gengsheng; Zhao, Yaofeng

2018-06-01

Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon ( Columba livia ) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as μ-α-υ1-υ2. In this article, we show that both DNA deletion and inversion may result from IgA and IgY class switching, and similar junction patterns were observed for both types of class-switch recombination. We also identified two subclasses of υ genes in pigeon, which share low sequence identity. Phylogenetic analysis suggests that divergence of the two pigeon υ genes occurred during the early stage of bird evolution. The data obtained in this study provide new insight into class-switch recombination and Ig gene evolution in birds. Copyright © 2018 by The American Association of Immunologists, Inc.

Regression of nifedipine-induced gingival hyperplasia following switch to a same class calcium channel blocker, isradipine.

PubMed

Westbrook, P; Bednarczyk, E M; Carlson, M; Sheehan, H; Bissada, N F

1997-07-01

Patients with nifedipine-induced gingival hyperplasia (GH) often require continued calcium channel blocker therapy. Switches to diltiazem and verapamil have been described; however, these drugs are of a different chemical class and present therapeutic limitations in some patients. The purpose of this study was to evaluate the effect on nifedipine-induced GH of a switch to a dihydropyridine derivative with a low incidence of GH. Fourteen patients with nifedipine-induced GH were given a medical exam and a periodontal exam. The following parameters were assessed: probing depth (PD), gingival margin (GM), gingival thickness (GT), plaque index (PI), and gingival index (GI). Intraoral photographs, study models, and a gingival biopsy for histological examination were taken. Following baseline measures, patients were randomized to continued treatment with nifedipine or an equivalent dose of isradipine in a single-blind fashion. Biweekly periodontal parameters were taken for 8 weeks. At the end of 8 weeks, some patients elected to receive 4 weeks of open label isradipine therapy, with biweekly examination continuing through the open label phase. The isradipine treatment arm showed a mean decrease in PD of 0.59 mm at week 8 (P < 0.05). No other measured parameter (GM, GT, PI, GI) was significantly changed, compared either to baseline or to the alternate treatment arm. Clinically, 60% of patients treated with isradipine exhibited a decrease in hyperplasia, while 66% of patients treated with nifedipine demonstrated an increase in hyperplasia, a significant difference (P < 0.05). When combined with open label data, patients switching therapy to isradipine exhibited an increase in GM (increase in recession) of 0.74 mm from baseline to week 12 (P < 0.05). No patients treated with isradipine exhibited an increase in gingival overgrowth. All patients exhibited adequate control of hypertension. We conclude that in hypertensive patients with nifedipine-induced GH, switching

Opc expression, LPS immunotype switch and pilin conversion contribute to serum resistance of unencapsulated meningococci.

PubMed

Hubert, Kerstin; Pawlik, Marie-Christin; Claus, Heike; Jarva, Hanna; Meri, Seppo; Vogel, Ulrich

2012-01-01

Neisseria meningitidis employs polysaccharides and outer membrane proteins to cope with human serum complement attack. To screen for factors influencing serum resistance, an assay was developed based on a colorimetric serum bactericidal assay. The screening used a genetically modified sequence type (ST)-41/44 clonal complex (cc) strain lacking LPS sialylation, polysaccharide capsule, the factor H binding protein (fHbp) and MutS, a protein of the DNA repair mechanism. After killing of >99.9% of the bacterial cells by serum treatment, the colorimetric assay was used to screen 1000 colonies, of which 35 showed enhanced serum resistance. Three mutant classes were identified. In the first class of mutants, enhanced expression of Opc was identified. Opc expression was associated with vitronectin binding and reduced membrane attack complex deposition confirming recent observations. Lipopolysaccharide (LPS) immunotype switch from immunotype L3 to L8/L1 by lgtA and lgtC phase variation represented the second class. Isogenic mutant analysis demonstrated that in ST-41/44 cc strains the L8/L1 immunotype was more serum resistant than the L3 immunotype. Consecutive analysis revealed that the immunotypes L8 and L1 were frequently observed in ST-41/44 cc isolates from both carriage and disease. Immunotype switch to L8/L1 is therefore suggested to contribute to the adaptive capacity of this meningococcal lineage. The third mutant class displayed a pilE allelic exchange associated with enhanced autoaggregation. The mutation of the C terminal hypervariable region D of PilE included a residue previously associated with increased pilus bundle formation. We suggest that autoaggregation reduced the surface area accessible to serum complement and protected from killing. The study highlights the ability of meningococci to adapt to environmental stress by phase variation and intrachromosomal recombination affecting subcapsular antigens.

Opc Expression, LPS Immunotype Switch and Pilin Conversion Contribute to Serum Resistance of Unencapsulated Meningococci

PubMed Central

Hubert, Kerstin; Pawlik, Marie-Christin; Claus, Heike; Jarva, Hanna; Meri, Seppo; Vogel, Ulrich

2012-01-01

Neisseria meningitidis employs polysaccharides and outer membrane proteins to cope with human serum complement attack. To screen for factors influencing serum resistance, an assay was developed based on a colorimetric serum bactericidal assay. The screening used a genetically modified sequence type (ST)-41/44 clonal complex (cc) strain lacking LPS sialylation, polysaccharide capsule, the factor H binding protein (fHbp) and MutS, a protein of the DNA repair mechanism. After killing of >99.9% of the bacterial cells by serum treatment, the colorimetric assay was used to screen 1000 colonies, of which 35 showed enhanced serum resistance. Three mutant classes were identified. In the first class of mutants, enhanced expression of Opc was identified. Opc expression was associated with vitronectin binding and reduced membrane attack complex deposition confirming recent observations. Lipopolysaccharide (LPS) immunotype switch from immunotype L3 to L8/L1 by lgtA and lgtC phase variation represented the second class. Isogenic mutant analysis demonstrated that in ST-41/44 cc strains the L8/L1 immunotype was more serum resistant than the L3 immunotype. Consecutive analysis revealed that the immunotypes L8 and L1 were frequently observed in ST-41/44 cc isolates from both carriage and disease. Immunotype switch to L8/L1 is therefore suggested to contribute to the adaptive capacity of this meningococcal lineage. The third mutant class displayed a pilE allelic exchange associated with enhanced autoaggregation. The mutation of the C terminal hypervariable region D of PilE included a residue previously associated with increased pilus bundle formation. We suggest that autoaggregation reduced the surface area accessible to serum complement and protected from killing. The study highlights the ability of meningococci to adapt to environmental stress by phase variation and intrachromosomal recombination affecting subcapsular antigens. PMID:23028802

Recombination and the evolution of coordinated phenotypic expression in a frequency-dependent game

PubMed Central

Arbilly, Michal; Motro, Uzi; Feldman, Marcus W.; Lotem, Arnon

2011-01-01

A long standing question in evolutionary biology concerns the maintenance of adaptive combinations of traits in the presence of recombination. This problem may be solved if positive epistasis selects for reducing the rate of recombination between such traits, but this requires sufficiently strong epistasis. Here we use a model that we developed previously to analyze a frequency-dependent strategy game in asexual populations, to study how adaptive combinations of traits may be maintained in the presence of recombination when epistasis is too weak to select for genetic linkage. Previously, in the asexual case, our model demonstrated the evolution of adaptive associations between social foraging strategies and learning rules. We verify that these adaptive associations, which are represented by different two-locus haplotypes, can easily be broken by genetic recombination. We also confirm that a modifier allele that reduces the rate of recombination fails to evolve (due to weak epistasis). However, we find that under the same conditions of weak epistasis, there is an alternative mechanism that allows association between traits to evolve. This is based on a genetic switch that responds to the presence of one social foraging allele by activating one of two alternative learning alleles that are carried by all individuals. We suggest that such coordinated phenotypic expression by genetic switches offers a general and robust mechanism for the evolution of adaptive combinations of traits in the presence of recombination. PMID:21945887

Mismatch repair proteins and AID deaminase activity are required for the dominant negative function of C terminally-deleted AID in class switching

PubMed Central

Ucher, Anna J.; Ranjit, Sanjay; Kadungure, Tatenda; Linehan, Erin K.; Khair, Lyne; Xie, Elaine; Limauro, Jennifer; Rauch, Katherina S.; Schrader, Carol E.; Stavnezer, Janet

2014-01-01

Activation-induced cytidine deaminase (AID) is essential for class switch recombination (CSR) and somatic hypermutation (SHM) of Ig genes. The AID C terminus is required for CSR but not for S region DNA DSBs during CSR, and it is not required for SHM. AID lacking the C terminus (ΔAID) is a dominant negative (DN) mutant, as human patients heterozygous for this mutant fail to undergo CSR. In agreement, we show that ΔAID is a DN mutant when expressed in AID-sufficient mouse splenic B cells. In order to have DN function,ΔAID must have deaminase activity, suggesting that its ability to induce DSBs is important for the DN function. Supporting this hypothesis, Msh2-Msh6 have previously been shown to contribute to DSB formation in S regions, and here we find that Msh2 is required for the DN activity, as ΔAID is not a DN mutant in msh2−/− cells. Our results suggest that the DNA DSBs induced by ΔAID are unable to participate in CSR, and might interfere with the ability of full-length AID to participate in CSR. We propose thatΔAID is impaired in its ability to recruit non-homologous end joining (NHEJ) repair factors, resulting in accumulation of DSBs that undergo aberrant resection. Supporting this hypothesis, we find that the S-S junctions induced by ΔAID have longer microhomologies than those induced by full-length AID. In addition, our data suggest that AID binds Sµ regions in vivo as a monomer. PMID:24973444

Investigation of the Genes Involved in Antigenic Switching at the vlsE Locus in Borrelia burgdorferi: An Essential Role for the RuvAB Branch Migrase

PubMed Central

Dresser, Ashley R.; Hardy, Pierre-Olivier; Chaconas, George

2009-01-01

Persistent infection by pathogenic organisms requires effective strategies for the defense of these organisms against the host immune response. A common strategy employed by many pathogens to escape immune recognition and clearance is to continually vary surface epitopes through recombinational shuffling of genetic information. Borrelia burgdorferi, a causative agent of Lyme borreliosis, encodes a surface-bound lipoprotein, VlsE. This protein is encoded by the vlsE locus carried at the right end of the linear plasmid lp28-1. Adjacent to the expression locus are 15 silent cassettes carrying information that is moved into the vlsE locus through segmental gene conversion events. The protein players and molecular mechanism of recombinational switching at vlsE have not been characterized. In this study, we analyzed the effect of the independent disruption of 17 genes that encode factors involved in DNA recombination, repair or replication on recombinational switching at the vlsE locus during murine infection. In Neisseria gonorrhoeae, 10 such genes have been implicated in recombinational switching at the pilE locus. Eight of these genes, including recA, are either absent from B. burgdorferi, or do not show an obvious requirement for switching at vlsE. The only genes that are required in both organisms are ruvA and ruvB, which encode subunits of a Holliday junction branch migrase. Disruption of these genes results in a dramatic decrease in vlsE recombination with a phenotype similar to that observed for lp28-1 or vls-minus spirochetes: productive infection at week 1 with clearance by day 21. In SCID mice, the persistence defect observed with ruvA and ruvB mutants was fully rescued as previously observed for vlsE-deficient B. burgdorferi. We report the requirement of the RuvAB branch migrase in recombinational switching at vlsE, the first essential factor to be identified in this process. These findings are supported by the independent work of Lin et al. in the

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.

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

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valentine, Jenny L.; Chen, Linxiao; Perregaux, Emily C.

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 highmore » 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.« less

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

DOE PAGES

Valentine, Jenny L.; Chen, Linxiao; Perregaux, Emily C.; ...

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 highmore » 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.« less

Switched Systems With Multiple Invariant Sets

DTIC Science & Technology

2015-05-06

LaSalle’s invariant set theorem [10] allow us to analyze asymptotic stability of this larger class of systems . LaSalle’s theorem and much of the... Stability and conver- gence for systems with switching equilibria, in: Proc. of the 46th IEEE Conference on Decision and Control , 2007. [8] X. Xu, G...Champaign, Urbana, Illinois 61801 Abstract This paper explores dwell time constraints on switched systems with mul- tiple, possibly disparate

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.

Output regulation control for switched stochastic delay systems with dissipative property under error-dependent switching

NASA Astrophysics Data System (ADS)

Li, L. L.; Jin, C. L.; Ge, X.

2018-01-01

In this paper, the output regulation problem with dissipative property for a class of switched stochastic delay systems is investigated, based on an error-dependent switching law. Under the assumption that none subsystem is solvable for the problem, a sufficient condition is derived by structuring multiple Lyapunov-Krasovskii functionals with respect to multiple supply rates, via designing error feedback regulators. The condition is also established when dissipative property reduces to passive property. Finally, two numerical examples are given to demonstrate the feasibility and efficiency of the present method.

47 CFR 32.6210 - Central office switching expenses.

Code of Federal Regulations, 2010 CFR

2010-10-01

... UNIFORM SYSTEM OF ACCOUNTS FOR TELECOMMUNICATIONS COMPANIES Instructions for Expense Accounts § 32.6210 Central office switching expenses. Class B telephone companies shall use this account for expenses of the type and character required of Class A companies in Accounts 6211 through 6212. [67 FR 5695, Feb. 6...

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

Specific activity of class II histone deacetylases in human breast cancer cells

PubMed Central

Duong, Vanessa; Bret, Caroline; Altucci, Lucia; Mai, Antonello; Duraffourd, Céline; Loubersac, Julie; Harmand, Pierre-Olivier; Bonnet, Sandrine; Valente, Sergio; Maudelonde, Thierry; Cavailles, Vincent; Boulle, Nathalie

2008-01-01

Although numerous studies have underlined the role of HDACs in breast physiology and tumorigenesis, little is known on the particular contribution of the various classes of HDACs in these processes. Using ERα-positive MCF-7 breast cancer cells, the effects of MC1575 and MC1568, two novel class II specific HDAC inhibitors (HDI), were analyzed on cell proliferation, apoptosis and estrogen signalling. The specificity of these HDIs was validated by measuring histone and α-tubulin acetylation and by the specific in vitro inhibition of recombinant HDAC4 using histone and non histone substrates, contrasting with the lack of inhibition of class I HDACs. In addition, MC1575 did not inhibit class I HDAC gene expression thus confirming the specific targeting of class II enzymes. Similar to TSA, MC1575 displayed a dose-dependent anti-proliferative effect and induced cell cycle arrest although this blockade occurred at a different level than TSA. Moreover, and in contrast to TSA, MC1575 had no effect on MCF-7 cells apoptosis. Interestingly, MC1575 was able to increase p2lwaf1/CIP1 mRNA levels but did not regulate the expression of other genes such as cyclin D1, p27, p14ARF, Bcl2, Baxα, Trail-R1 and -R2. Finally, MC1575 strongly induced ERβ gene expression but did not decrease ERα expression nor did it switch hydroxy-tamoxifen to an agonist activity. Altogether, these data suggest that the class II HDAC sub-family may exert specific roles in breast cancer progression and estrogen-dependence. PMID:19074835

Role of allosteric switch residue histidine 195 in maintaining active-site asymmetry in presynaptic filaments of bacteriophage T4 UvsX recombinase.

PubMed

Farb, Joshua N; Morrical, Scott W

2009-01-16

Recombinases of the highly conserved RecA/Rad51 family play central roles in homologous recombination and DNA double-stranded break repair. RecA/Rad51 enzymes form presynaptic filaments on single-stranded DNA (ssDNA) that are allosterically activated to catalyze ATPase and DNA strand-exchange reactions. Information is conveyed between DNA- and ATP-binding sites, in part, by a highly conserved glutamine residue (Gln194 in Escherichia coli RecA) that acts as an allosteric switch. The T4 UvsX protein is a divergent RecA ortholog and contains histidine (His195) in place of glutamine at the allosteric switch position. UvsX and RecA catalyze similar strand-exchange reactions, but differ in other properties. UvsX produces both ADP and AMP as products of its ssDNA-dependent ATPase activity--a property that is unique among characterized recombinases. Details of the kinetics of ssDNA-dependent ATP hydrolysis reactions indicate that UvsX-ssDNA presynaptic filaments are asymmetric and contain two classes of ATPase active sites: one that generates ADP, and another that generates AMP. Active-site asymmetry is reduced by mutations at the His195 position, since UvsX-H195Q and UvsX-H195A mutants both exhibit stronger ssDNA-dependent ATPase activity, with lower cooperativity and markedly higher ADP/AMP product ratios, than wild-type UvsX. Reduced active-site asymmetry correlates strongly with reduced ssDNA-binding affinity and DNA strand-exchange activity in both H195Q and H195A mutants. These and other results support a model in which allosteric switch residue His195 controls the formation of an asymmetric conformation of UvsX-ssDNA filaments that is active in DNA strand exchange. The implications of our findings for UvsX recombination functions, and for RecA functions in general, are discussed.

The involvement of immunoglobulin E isotype switch in scleroderma skin tissue.

PubMed

Ohtsuka, Tsutomu; Yamazaki, Soji

2005-08-01

The involvement of mast cell, which is activated by immunoglobulin E (IgE), has been reported in the formation of systemic sclerosis (SSc) abnormality. IgE is generated with isotype switch. During isotype switch, switch circles resulting from direct mu to epsilon, or from sequential mu to gamma via epsilon switching will be created. We studied whether switching occurs in SSc. We used nested polymerase chain reaction to analyze the S fragments from switch circles. Fifty-two patients with SSc, and 62 healthy women were studied. Neither of 62 normal skin tissues showed direct switch, nor sequential switch. Neither of seven normal whole blood cells showed direct switch, nor sequential switch. In 52SSc skin tissues, three (5.8%) showed direct switch, and two (3.8%) showed sequential switch. As a result, five (9.6%) of SSc skin tissue showed immunogobulin E class switch. These results were confirmed by DNA sequencing. These results demonstrated that isotype switch to the epsilon locus achieved by direct and/or sequential switch are involved in SSc skin.

Emergence of Distinct Brome Mosaic Virus Recombinants Is Determined by the Polarity of the Inoculum RNA

PubMed Central

Kwon, Sun-Jung

2012-01-01

Despite overwhelming interest in the impact exerted by recombination during evolution of RNA viruses, the relative contribution of the polarity of inoculum templates remains poorly understood. Here, by agroinfiltrating Nicotiana benthamiana leaves, we show that brome mosaic virus (BMV) replicase is competent to initiate positive-strand [(+)-strand] synthesis on an ectopically expressed RNA3 negative strand [(−) strand] and faithfully complete the replication cycle. Consequently, we sought to examine the role of RNA polarity in BMV recombination by expressing a series of replication-defective mutants of BMV RNA3 in (+) or (−) polarity. Temporal analysis of progeny sequences revealed that the genetic makeup of the primary recombinant pool is determined by the polarity of the inoculum template. When the polarity of the inoculum template was (+), the recombinant pool that accumulated during early phases of replication was a mixture of nonhomologous recombinants. These are longer than the inoculum template length, and a nascent 3′ untranslated region (UTR) of wild-type (WT) RNA1 or RNA2 was added to the input mutant RNA3 3′ UTR due to end-to-end template switching by BMV replicase during (−)-strand synthesis. In contrast, when the polarity of the inoculum was (−), the progeny contained a pool of native-length homologous recombinants generated by template switching of BMV replicase with a nascent UTR from WT RNA1 or RNA2 during (+)-strand synthesis. Repair of a point mutation caused by polymerase error occurred only when the polarity of the inoculum template was (+). These results contribute to the explanation of the functional role of RNA polarity in recombination mediated by copy choice mechanisms. PMID:22357282

Decentralized Adaptive Neural Output-Feedback DSC for Switched Large-Scale Nonlinear Systems.

PubMed

Lijun Long; Jun Zhao

2017-04-01

In this paper, for a class of switched large-scale uncertain nonlinear systems with unknown control coefficients and unmeasurable states, a switched-dynamic-surface-based decentralized adaptive neural output-feedback control approach is developed. The approach proposed extends the classical dynamic surface control (DSC) technique for nonswitched version to switched version by designing switched first-order filters, which overcomes the problem of multiple "explosion of complexity." Also, a dual common coordinates transformation of all subsystems is exploited to avoid individual coordinate transformations for subsystems that are required when applying the backstepping recursive design scheme. Nussbaum-type functions are utilized to handle the unknown control coefficients, and a switched neural network observer is constructed to estimate the unmeasurable states. Combining with the average dwell time method and backstepping and the DSC technique, decentralized adaptive neural controllers of subsystems are explicitly designed. It is proved that the approach provided can guarantee the semiglobal uniformly ultimately boundedness for all the signals in the closed-loop system under a class of switching signals with average dwell time, and the tracking errors to a small neighborhood of the origin. A two inverted pendulums system is provided to demonstrate the effectiveness of the method proposed.

Recombination at DNA replication fork barriers is not universal and is differentially regulated by Swi1.

PubMed

Pryce, David W; Ramayah, Soshila; Jaendling, Alessa; McFarlane, Ramsay J

2009-03-24

DNA replication stress has been implicated in the etiology of genetic diseases, including cancers. It has been proposed that genomic sites that inhibit or slow DNA replication fork progression possess recombination hotspot activity and can form potential fragile sites. Here we used the fission yeast, Schizosaccharomyces pombe, to demonstrate that hotspot activity is not a universal feature of replication fork barriers (RFBs), and we propose that most sites within the genome that form RFBs do not have recombination hotspot activity under nonstressed conditions. We further demonstrate that Swi1, the TIMELESS homologue, differentially controls the recombination potential of RFBs, switching between being a suppressor and an activator of recombination in a site-specific fashion.

Recombination at DNA replication fork barriers is not universal and is differentially regulated by Swi1

PubMed Central

Pryce, David W.; Ramayah, Soshila; Jaendling, Alessa; McFarlane, Ramsay J.

2009-01-01

DNA replication stress has been implicated in the etiology of genetic diseases, including cancers. It has been proposed that genomic sites that inhibit or slow DNA replication fork progression possess recombination hotspot activity and can form potential fragile sites. Here we used the fission yeast, Schizosaccharomyces pombe, to demonstrate that hotspot activity is not a universal feature of replication fork barriers (RFBs), and we propose that most sites within the genome that form RFBs do not have recombination hotspot activity under nonstressed conditions. We further demonstrate that Swi1, the TIMELESS homologue, differentially controls the recombination potential of RFBs, switching between being a suppressor and an activator of recombination in a site-specific fashion. PMID:19273851

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

Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny

PubMed Central

Kumar, Satyendra; Wuerffel, Robert; Achour, Ikbel; Lajoie, Bryan; Sen, Ranjan; Dekker, Job; Feeney, Ann J.; Kenter, Amy L.

2013-01-01

V(D)J joining is mediated by RAG recombinase during early B-lymphocyte development in the bone marrow (BM). Activation-induced deaminase initiates isotype switching in mature B cells of secondary lymphoid structures. Previous studies questioned the strict ontological partitioning of these processes. We show that pro-B cells undergo robust switching to a subset of immunoglobulin H (IgH) isotypes. Chromatin studies reveal that in pro-B cells, the spatial organization of the Igh locus may restrict switching to this subset of isotypes. We demonstrate that in the BM, V(D)J joining and switching are interchangeably inducible, providing an explanation for the hyper-IgE phenotype of Omenn syndrome. PMID:24240234

Recombination of open-f-shell tungsten ions

NASA Astrophysics Data System (ADS)

Krantz, C.; Badnell, N. R.; Müller, A.; Schippers, S.; Wolf, A.

2017-03-01

We review experimental and theoretical efforts aimed at a detailed understanding of the recombination of electrons with highly charged tungsten ions characterised by an open 4f sub-shell. Highly charged tungsten occurs as a plasma contaminant in ITER-like tokamak experiments, where it acts as an unwanted cooling agent. Modelling of the charge state populations in a plasma requires reliable thermal rate coefficients for charge-changing electron collisions. The electron recombination of medium-charged tungsten species with open 4f sub-shells is especially challenging to compute reliably. Storage-ring experiments have been conducted that yielded recombination rate coefficients at high energy resolution and well-understood systematics. Significant deviations compared to simplified, but prevalent, computational models have been found. A new class of ab initio numerical calculations has been developed that provides reliable predictions of the total plasma recombination rate coefficients for these ions.

CD8 Follicular T Cells Promote B Cell Antibody Class Switch in Autoimmune Disease.

PubMed

Valentine, Kristen M; Davini, Dan; Lawrence, Travis J; Mullins, Genevieve N; Manansala, Miguel; Al-Kuhlani, Mufadhal; Pinney, James M; Davis, Jason K; Beaudin, Anna E; Sindi, Suzanne S; Gravano, David M; Hoyer, Katrina K

2018-05-09

CD8 T cells can play both a protective and pathogenic role in inflammation and autoimmune development. Recent studies have highlighted the ability of CD8 T cells to function as T follicular helper (Tfh) cells in the germinal center in the context of infection. However, whether this phenomenon occurs in autoimmunity and contributes to autoimmune pathogenesis is largely unexplored. In this study, we show that CD8 T cells acquire a CD4 Tfh profile in the absence of functional regulatory T cells in both the IL-2-deficient and scurfy mouse models. Depletion of CD8 T cells mitigates autoimmune pathogenesis in IL-2-deficient mice. CD8 T cells express the B cell follicle-localizing chemokine receptor CXCR5, a principal Tfh transcription factor Bcl6, and the Tfh effector cytokine IL-21. CD8 T cells localize to the B cell follicle, express B cell costimulatory proteins, and promote B cell differentiation and Ab isotype class switching. These data reveal a novel contribution of autoreactive CD8 T cells to autoimmune disease, in part, through CD4 follicular-like differentiation and functionality. Copyright © 2018 by The American Association of Immunologists, Inc.

Passive Q switching and mode-locking of Er:glass lasers using VO2 mirrors

NASA Astrophysics Data System (ADS)

Pollack, S. A.; Chang, D. B.; Chudnovky, F. A.; Khakhaev, I. A.

1995-09-01

Passive Q switching of an Er:glass laser with the pulse width varying between 14 and 80 ns has been demonstrated, using three resonator vanadium-dioxide-coated (VO2) mirror samples with temperature-dependent reflectivity and differing in the reflectivity contrast. The reflectivity changes because of a phase transition from a semiconductor to a metallic state. Broad band operating characteristics of VO2 mirrors provide Q switching over a wide range of wavelengths. In addition, mode-locked pulses with much shorter time scales have been observed, due to exciton formation and recombination. A simple criterion is derived for the allowable ambient temperatures at which the Q switching operates effectively. A simple relation has also been found relating the duration of the Q-switched pulse to the contrast in reflectivities of the two mirror phases.

The immune responses in CD40-deficient mice: impaired immunoglobulin class switching and germinal center formation.

PubMed

Kawabe, T; Naka, T; Yoshida, K; Tanaka, T; Fujiwara, H; Suematsu, S; Yoshida, N; Kishimoto, T; Kikutani, H

1994-06-01

An engagement of CD40 with CD40 ligand (CD40L) expressed on activated T cells is known to provide an essential costimulatory signal to B cells in vitro. To investigate the role of CD40 in in vivo immune responses, CD40-deficient mice were generated by gene targeting. The significant reduction of CD23 expression on mature B cells and relatively decreased number of IgM bright and IgD dull B cells were observed in the mutant mice. The mutant mice mounted IgM responses but no IgG, IgA, and IgE responses to thymus-dependent (TD) antigens. However, IgG as well as IgM responses to thymus-independent (TI) antigens were normal. Furthermore, the germinal center formation was defective in the mutant mice. These results suggest that CD40 is essential for T cell-dependent immunoglobulin class switching and germinal center formation, but not for in vivo T cell-dependent IgM responses and T cell-independent antibody responses.

Ways to suppress click and pop for class D amplifiers

NASA Astrophysics Data System (ADS)

Haishi, Wang; Bo, Zhang; Jiang, Sun

2012-08-01

Undesirable audio click and pop may be generated in a speaker or headphone. Compared to linear (class A/B/AB) amplifiers, class D amplifiers that comprise of an input stage and a modulation stage are more prone to producing click and pop. This article analyzes sources that generate click and pop in class D amplifiers, and corresponding ways to suppress them. For a class D amplifier with a single-ended input, click and pop is likely to be due to two factors. One is from a voltage difference (VDIF) between the voltage of an input capacitance (VCIN) and a reference voltage (VREF) of the input stage, and the other one is from the non-linear switching during the setting up of the bias and feedback voltages/currents (BFVC) of the modulation stage. In this article, a fast charging loop is introduced into the input stage to charge VCIN to roughly near VREF. Then a correction loop further charges or discharges VCIN, substantially equalizing it with VREF. Dummy switches are introduced into the modulation stage to provide switching signals for setting up BFVC, and the power switches are disabled until the BFVC are set up successfully. A two channel single-ended class D amplifier with the above features is fabricated with 0.5 μm Bi-CMOS process. Road test and fast Fourier transform analysis indicate that there is no noticeable click and pop.

phiC31 Integrase-Mediated Site-Specific Recombination in Barley

PubMed Central

Rubtsova, Myroslava; Kumlehn, Jochen; Gils, Mario

2012-01-01

The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP), which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F1, even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity. PMID:23024817

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.

[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. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Microstructure evolution characteristics induced by oxygen vacancy generation in anatase TiO2 based resistive switching devices

NASA Astrophysics Data System (ADS)

Liu, Chen; Gao, Bin; Huang, Peng; Kang, Jinfeng

2017-03-01

In this work, first principle calculations are employed to study the microstructure characteristics of the anatase TiO2 resistive switching material associated with the generation of oxygen vacancy (V o) based nanofilaments during the switching process. The calculations indicate that both the magnéli phase Ti4O7 and V o-defect phase of anatase TiO2 may be formed with the generation of oxygen vacancies during the forming and SET processes. Based on the calculations, a new physical insight is proposed to clarify the microstructure evolution characteristics of the anatase TiO2 resistive switching material and the correlation with resistive switching behaviors. During the forming or SET process, the anatase TiO2 is first excited to a transition state with the generation of oxygen vacancies, then fully relaxes to a stable V o-defect state. This V o-defect state may either recover to the original state with the recombination of the oxygen vacancies, which causes the reversible resistive switching behavior, or further transform to a much more stable state—the magnéli phase Ti4O7, through a phase transition process with the generation of many more oxygen vacancies. The phase transition from V o- defective anatase phase to magnéli phase Ti4O7 causes the failure of the resistive switching due to the significantly reduced possibility of the reversible phase transition from the magnéli phase to the anatase phase, compared with the possibility of the recombination from the V o-defective anatase.

Observed-Based Adaptive Fuzzy Tracking Control for Switched Nonlinear Systems With Dead-Zone.

PubMed

Tong, Shaocheng; Sui, Shuai; Li, Yongming

2015-12-01

In this paper, the problem of adaptive fuzzy output-feedback control is investigated for a class of uncertain switched nonlinear systems in strict-feedback form. The considered switched systems contain unknown nonlinearities, dead-zone, and immeasurable states. Fuzzy logic systems are utilized to approximate the unknown nonlinear functions, a switched fuzzy state observer is designed and thus the immeasurable states are obtained by it. By applying the adaptive backstepping design principle and the average dwell time method, an adaptive fuzzy output-feedback tracking control approach is developed. It is proved that the proposed control approach can guarantee that all the variables in the closed-loop system are bounded under a class of switching signals with average dwell time, and also that the system output can track a given reference signal as closely as possible. The simulation results are given to check the effectiveness of the proposed approach.

Recombination rate plasticity: revealing mechanisms by design

PubMed Central

Sefick, Stephen; Rushton, Chase

2017-01-01

For over a century, scientists have known that meiotic recombination rates can vary considerably among individuals, and that environmental conditions can modify recombination rates relative to the background. A variety of external and intrinsic factors such as temperature, age, sex and starvation can elicit ‘plastic’ responses in recombination rate. The influence of recombination rate plasticity on genetic diversity of the next generation has interesting and important implications for how populations evolve. Further, many questions remain regarding the mechanisms and molecular processes that contribute to recombination rate plasticity. Here, we review 100 years of experimental work on recombination rate plasticity conducted in Drosophila melanogaster. We categorize this work into four major classes of experimental designs, which we describe via classic studies in D. melanogaster. Based on these studies, we highlight molecular mechanisms that are supported by experimental results and relate these findings to studies in other systems. We synthesize lessons learned from this model system into experimental guidelines for using recent advances in genotyping technologies, to study recombination rate plasticity in non-model organisms. Specifically, we recommend (1) using fine-scale genome-wide markers, (2) collecting time-course data, (3) including crossover distribution measurements, and (4) using mixed effects models to analyse results. To illustrate this approach, we present an application adhering to these guidelines from empirical work we conducted in Drosophila pseudoobscura. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109222

Board-to-Board Free-Space Optical Interconnections Passing through Boards for a Bookshelf-Assembled Terabit-Per-Second-Class ATM Switch.

PubMed

Hirabayashi, K; Yamamoto, T; Matsuo, S; Hino, S

1998-05-10

We propose free-space optical interconnections for a bookshelf-assembled terabit-per-second-class ATM switch. Thousands of arrayed optical beams, each having a rate of a few gigabits per second, propagate vertically to printed circuit boards, passing through some boards, and are connected to arbitrary transmitters and receivers on boards by polarization controllers and prism arrays. We describe a preliminary experiment using a 1-mm-pitch 2 x 2 beam-collimator array that uses vertical-cavity surface-emitting laser diodes. These optical interconnections can be made quite stable in terms of mechanical shock and temperature fluctuation by the attachment of reinforcing frames to the boards and use of an autoalignment system.

Improved understanding of the recombination rate at inverted p+ silicon surfaces

NASA Astrophysics Data System (ADS)

To, Alexander; Ma, Fajun; Hoex, Bram

2017-08-01

The effect of positive fixed charge on the recombination rate at SiN x -passivated p+ surfaces is studied in this work. It is shown that a high positive fixed charge on a low defect density, passivated doped surface can result in a near injection level independent lifetime in a certain injection level range. This behaviour is modelled with advanced computer simulations using Sentaurus TCAD, which replicates the measurements conditions during a photoconductance based effective minority carrier lifetime measurement. The resulting simulations show that the shape of the injection level dependent lifetime is a result of the surface recombination rate, which is non-linear due to the surfaces moving into inversion with increasing injection level. As a result, the surface recombination rate switches from being limited by electrons to holes. Equations describing the surface saturation current density, J 0s, during this regime are also derived in this work.

The N-terminal DNA-binding domain of Rad52 promotes RAD51-independent recombination in Saccharomyces cerevisiae.

PubMed Central

Tsukamoto, Mariko; Yamashita, Kentaro; Miyazaki, Toshiko; Shinohara, Miki; Shinohara, Akira

2003-01-01

In Saccharomyces cerevisiae, the Rad52 protein plays a role in both RAD51-dependent and RAD51-independent recombination pathways. We characterized a rad52 mutant, rad52-329, which lacks the C-terminal Rad51-interacting domain, and studied its role in RAD51-independent recombination. The rad52-329 mutant is completely defective in mating-type switching, but partially proficient in recombination between inverted repeats. We also analyzed the effect of the rad52-329 mutant on telomere recombination. Yeast cells lacking telomerase maintain telomere length by recombination. The rad52-329 mutant is deficient in RAD51-dependent telomere recombination, but is proficient in RAD51-independent telomere recombination. In addition, we examined the roles of other recombination genes in the telomere recombination. The RAD51-independent recombination in the rad52-329 mutant is promoted by a paralogue of Rad52, Rad59. All components of the Rad50-Mre11-Xrs2 complex are also important, but not essential, for RAD51-independent telomere recombination. Interestingly, RAD51 inhibits the RAD51-independent, RAD52-dependent telomere recombination. These findings indicate that Rad52 itself, and more precisely its N-terminal DNA-binding domain, promote an essential reaction in recombination in the absence of RAD51. PMID:14704160

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…

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…

Two-magnon bound state causes ultrafast thermally induced magnetisation switching

PubMed Central

Barker, J.; Atxitia, U.; Ostler, T. A.; Hovorka, O.; Chubykalo-Fesenko, O.; Chantrell, R. W.

2013-01-01

There has been much interest recently in the discovery of thermally induced magnetisation switching using femtosecond laser excitation, where a ferrimagnetic system can be switched deterministically without an applied magnetic field. Experimental results suggest that the reversal occurs due to intrinsic material properties, but so far the microscopic mechanism responsible for reversal has not been identified. Using computational and analytic methods we show that the switching is caused by the excitation of two-magnon bound states, the properties of which are dependent on material factors. This discovery allows us to accurately predict the onset of switching and the identification of this mechanism will allow new classes of materials to be identified or designed for memory devices in the THz regime. PMID:24253110

Two classes of ODE models with switch-like behavior.

PubMed

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

2013-12-01

In cases where the same real-world system can be modeled both by an ODE system ⅅ and a Boolean system , 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 has certain structures, consistency between ⅅ and is implied by sufficient separation of time scales in one class of our models. Namely, if the trajectories of are "one-stepping" then we prove a strong form of consistency and if has a certain monotonicity property then there is a weaker consistency between ⅅ and . These results appear to point to more general structure properties that favor consistency between ODE and Boolean models.

A dual-mode highly efficient class-E stimulator controlled by a low-Q class-E power amplifier through duty cycle.

PubMed

Chiu, Hung-Wei; Lu, Chien-Chi; Chuang, Jia-min; Lin, Wei-Tso; Lin, Chii-Wann; Kao, Ming-Chien; Lin, Mu-Lien

2013-06-01

This paper presents the design flow of two high-efficiency class-E amplifiers for the implantable electrical stimulation system. The implantable stimulator is a high-Q class-E driver that delivers a sine-wave pulsed radiofrequency (PRF) stimulation, which was verified to have a superior efficacy in pain relief to a square wave. The proposed duty-cycle-controlled class-E PRF driver designed with a high-Q factor has two operational modes that are able to achieve 100% DC-AC conversion, and involves only one switched series inductor and an unchanged parallel capacitor. The measured output amplitude under low-voltage (LV) mode using a 22% duty cycle was 0.98 V with 91% efficiency, and under high-voltage (HV) mode using a 47% duty cycle was 2.95 V with 92% efficiency. These modes were inductively controlled by a duty-cycle detector, which can detect the duty-cycle modulated signal generated from the external complementary low-Q class-E power amplifier (PA). The design methodology of the low-Q inductive interface for a non-50% duty cycle is presented. The experimental results exhibits that the 1.5-V PA that consumes DC power of 14.21 mW was able to deliver a 2.9-V sine wave to a 500 Ω load. The optimal 60% drain efficiency of the system from the PA to the load was obtained at a 10-mm coupling distance.

Variations in the electrical short-circuit current decay for recombination lifetime and velocity measurements

NASA Technical Reports Server (NTRS)

Jung, Tae-Won; Lindholm, Fredrik A.; Neugroschel, Arnost

1987-01-01

An improved measurement system for electrical short-circuit current decay is presented that extends applicability of the method to silicon solar cells having an effective lifetime as low as 1 microsec. The system uses metal/oxide/semiconductor transistors as voltage-controlled switches. Advances in theory developed here increase precision and sensitivity in the determination of the minority-carrier recombination lifetime and recombination velocity. A variation of the method, which exploits measurements made on related back-surface field and back-ohmic contact devices, further improves precision and sensitivity. The improvements are illustrated by application to 15 different silicon solar cells.

Purification of a Recombinant Glutathione Transferase from the Causative Agent of Hydatidosis, "Echinococcus granulosus"

ERIC Educational Resources Information Center

Fleitas, Andrea L.; Randall, Lía M.; Möller, Matías N.; Denicola, Ana

2016-01-01

This practical class activity was designed to introduce students to recombinant protein expression and purification. The principal goal is to shed light on basic aspects concerning recombinant protein production, in particular protein expression, chromatography methods for protein purification, and enzyme activity as a tool to evaluate purity and…

A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses.

PubMed

Henzy, Jamie E; Gifford, Robert J; Johnson, Welkin E; Coffin, John M

2014-03-01

Endogenous retroviruses (ERVs) represent ancestral sequences of modern retroviruses or their extinct relatives. The majority of ERVs cluster alongside exogenous retroviruses into two main groups based on phylogenetic analyses of the reverse transcriptase (RT) enzyme. Class I includes gammaretroviruses, and class II includes lentiviruses and alpha-, beta-, and deltaretroviruses. However, analyses of the transmembrane subunit (TM) of the envelope glycoprotein (env) gene result in a different topology for some retroviruses, suggesting recombination events in which heterologous env sequences have been acquired. We previously demonstrated that the TM sequences of five of the six genera of orthoretroviruses can be divided into three types, each of which infects a distinct set of vertebrate classes. Moreover, these classes do not always overlap the host range of the associated RT classes. Thus, recombination resulting in acquisition of a heterologous env gene could in theory facilitate cross-species transmissions across vertebrate classes, for example, from mammals to reptiles. Here we characterized a family of class II avian ERVs, "TgERV-F," that acquired a mammalian gammaretroviral env sequence. Although TgERV-F clusters near a sister clade to alpharetroviruses, its genome also has some features of betaretroviruses. We offer evidence that this unusual recombinant has circulated among several avian orders and may still have infectious members. In addition to documenting the infection of a nongalliform avian species by a mammalian retrovirus, TgERV-F also underscores the importance of env sequences in reconstructing phylogenies and supports a possible role for env swapping in allowing cross-species transmissions across wide taxonomic distances. Retroviruses can sometimes acquire an envelope gene (env) from a distantly related retrovirus. Since env is a key determinant of host range, such an event affects the host range of the recombinant virus and can lead to the creation

High Frequency PIN-Diode Switches for Radiometer Applications

NASA Technical Reports Server (NTRS)

Montes, Oliver; Dawson, Douglas E.; Kangaslahti, Pekka; Reising, Steven C.

2011-01-01

Internally calibrated radiometers are needed for ocean topography and other missions. Typically internal calibration is achieved with Dicke switching as one of the techniques. We have developed high frequency single-pole double-throw (SPDT) switches in the form of monolithic microwave integrated circuits (MMIC) that can be easily integrated into Dicke switched radiometers that utilize microstrip technology. In particular, the switches we developed can be used for a radiometer such as the one proposed for the Surface Water and Ocean Topography (SWOT) Satellite Mission whose three channels at 92, 130, and 166 GHz would allow for wet-tropospheric path delay correction near coastal zones and over land. This feat is not possible with the current Jason-class radiometers due to their lower frequency signal measurement and thus lower resolution. The MMIC chips were fabricated at NGST using their InP PIN diode process and measured at JPL using high frequency test equipment. Measurement and simulation results will be presented.

The proliferative response of cloned Peyer's patch switch T cells to syngeneic and allogeneic stimuli.

PubMed

Kawanishi, H; Ozato, K; Strober, W

1985-06-01

We previously defined a concanavalin A (Con A)-induced cloned T cell population in Peyer's patches (PP) that causes sIgM-bearing B cells to switch to sIgA-bearing B cells. In the present study we show that such IgA-specific switch T cells proliferate when exposed to syngeneic stimulator cells, i.e., the switch T cells are autoreactive. Detailed study of this phenomenon disclosed that both B cells and macrophages were capable of causing switch T cell proliferation, and in both cases, stimulation was enhanced by preactivation of the stimulator cells with lipopolysaccharide (LPS). In addition, fresh T cells can act as stimulators, but only if preactivated with Con A. Finally, it was clearly shown in blocking studies with the use of various antibodies directed at class II MHC specificities that class II MHC antigens were the stimulatory determinants. These studies suggest that IgA-specific switch T cells arise in PP as a result of autologous cell-cell interactions with activated (antigen-stimulated) B cells, macrophages, or T cells.

Development and fabrication of improved power transistor switches

NASA Technical Reports Server (NTRS)

Hower, P. L.; Chu, C. K.

1979-01-01

A new class of high-voltage power transistors was achieved by adapting present interdigitated thyristor processing techniques to the fabrication of npn Si transistors. Present devices are 2.3 cm in diameter and have V sub CEO (sus) in the range of 400 to 600V. V sub CEO (sus) = 450V devices were made with an (h sub FE)(I sub C) product of 900A at V sub CE = 2.5V. The electrical performance obtained was consistent with the predictions of an optimum design theory specifically developed for power switching transistors. The device design, wafer processing, and assembly techniques are described. Experimental measurements of the dc characteristics, forward SOA, and switching times are included. A new method of characterizing the switching performance of power transistors is proposed.

A novel pathogenic aviadenovirus from red-bellied parrots (Poicephalus rufiventris) unveils deep recombination events among avian host lineages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Shubhagata, E-mail: sdas@csu.edu.au

Competing roles of coevolution, selective pressure and recombination are an emerging interest in virus evolution. We report a novel aviadenovirus from captive red-bellied parrots (Poicephalus rufiventris) that uncovers evidence of deep recombination among aviadenoviruses. The sequence identity of the virus was most closely related to Turkey adenovirus D (42% similarity) and other adenoviruses in chickens, turkeys and pigeons. Sequencing and comparative analysis showed that the genome comprised 40,930 nucleotides containing 42 predicted open reading frames (ORFs) 19 of which had strong similarity with genes from other adenovirus species. The new genome unveiled a lineage that likely participated in deep recombinationmore » events across the genus Aviadenovirus accounting for an ancient evolutionary relationship. We hypothesize frequent host switch events and recombination among adenovirus progenitors in Galloanserae hosts caused the radiation of extant aviadenoviruses and the newly assembled Poicephalus adenovirus genome points to a potentially broader host range of these viruses among birds. - Highlights: •Shows how a single new genome can change overall phylogeny. •Reveals host switch events among adenovirus progenitors in Galloanserae hosts. •Points to a potentially broader host range of adenoviruses among birds and wildlife .« less

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

Ultrafast all-optical switching and error-free 10 Gbit/s wavelength conversion in hybrid InP-silicon on insulator nanocavities using surface quantum wells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bazin, Alexandre; Monnier, Paul; Beaudoin, Grégoire

Ultrafast switching with low energies is demonstrated using InP photonic crystal nanocavities embedding InGaAs surface quantum wells heterogeneously integrated to a silicon on insulator waveguide circuitry. Thanks to the engineered enhancement of surface non radiative recombination of carriers, switching time is obtained to be as fast as 10 ps. These hybrid nanostructures are shown to be capable of achieving systems level performance by demonstrating error free wavelength conversion at 10 Gbit/s with 6 mW switching powers.

Finite-time robust passive control for a class of switched reaction-diffusion stochastic complex dynamical networks with coupling delays and impulsive control

NASA Astrophysics Data System (ADS)

Syed Ali, M.; Yogambigai, J.; Kwon, O. M.

2018-03-01

Finite-time boundedness and finite-time passivity for a class of switched stochastic complex dynamical networks (CDNs) with coupling delays, parameter uncertainties, reaction-diffusion term and impulsive control are studied. Novel finite-time synchronisation criteria are derived based on passivity theory. This paper proposes a CDN consisting of N linearly and diffusively coupled identical reaction- diffusion neural networks. By constructing of a suitable Lyapunov-Krasovskii's functional and utilisation of Jensen's inequality and Wirtinger's inequality, new finite-time passivity criteria for the networks are established in terms of linear matrix inequalities (LMIs), which can be checked numerically using the effective LMI toolbox in MATLAB. Finally, two interesting numerical examples are given to show the effectiveness of the theoretical results.

All-optical switching in GaAs microdisk resonators by a femtosecond pump-probe technique through tapered-fiber coupling.

PubMed

Lin, Yen-Chih; Mao, Ming-Hua; Lin, You-Ru; Lin, Hao-Hsiung; Lin, Che-An; Wang, Lon A

2014-09-01

We demonstrate ultrafast all-optical switching in GaAs microdisk resonators using a femtosecond pump-probe technique through tapered-fiber coupling. The temporal tuning of the resonant modes resulted from the refractive index change due to photoexcited carrier density variation inside the GaAs microdisk resonator. Transmission through the GaAs microdisk resonator can be modulated by more than 10 dB with a switching time window of 8 ps in the switch-off operation using pumping pulses with energies as low as 17.5 pJ. The carrier lifetime was fitted to be 42 ps, much shorter than that of the bulk GaAs, typically of the order of nanoseconds. The above observation indicates that the surface recombination plays an important role in increasing the switching speed.

Crystallization of recombinant Haemophilus influenzaee (P4) acid phosphatase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ou, Zhonghui; Felts, Richard L.; Reilly, Thomas J.

2006-05-01

Lipoprotein e (P4) is a class C acid phosphatase and a potential vaccine candidate for nontypeable H. influenzae infections. This paper reports the crystallization of recombinant e (P4) and the acquisition of a 1.7 Å resolution native X-ray diffraction data set. Haemophilus influenzae infects the upper respiratory tract of humans and can cause infections of the middle ear, sinuses and bronchi. The virulence of the pathogen is thought to involve a group of surface-localized macromolecular components that mediate interactions at the host–pathogen interface. One of these components is lipoprotein e (P4), which is a class C acid phosphatase and amore » potential vaccine candidate for nontypeable H. influenzae infections. This paper reports the crystallization of recombinant e (P4) and the acquisition of a 1.7 Å resolution native X-ray diffraction data set. The space group is P4{sub 2}2{sub 1}2, with unit-cell parameters a = 65.6, c = 101.4 Å, one protein molecule per asymmetric unit and 37% solvent content. This is the first report of the crystallization of a class C acid phosphatase.« less

Runtime Support for Type-Safe Dynamic Java Classes

DTIC Science & Technology

2000-01-01

Section 4.3. For each dynamic class C, we create a proxy class, Cproxy, and an implementation class, Cimp . In order to wrap method calls, Cproxy...wrapper method (W) and a reference to the associated method body (M). W explicitly invokes M, which points to the corresponding method body in Cimp ...When C’s implementation Cimp is switched, M is updated to point to the corresponding method object in the new C imp. Cproxy also contains a reference

Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand.

PubMed

2018-02-01

Data on durability of first-line antiretroviral therapy (ART) in children with human immunodeficiency virus (HIV) are limited. We assessed time to switch to second-line therapy in 16 European countries and Thailand. Children aged <18 years initiating combination ART (≥2 nucleoside reverse transcriptase inhibitors [NRTIs] plus nonnucleoside reverse transcriptase inhibitor [NNRTI] or boosted protease inhibitor [PI]) were included. Switch to second-line was defined as (i) change across drug class (PI to NNRTI or vice versa) or within PI class plus change of ≥1 NRTI; (ii) change from single to dual PI; or (iii) addition of a new drug class. Cumulative incidence of switch was calculated with death and loss to follow-up as competing risks. Of 3668 children included, median age at ART initiation was 6.1 (interquartile range (IQR), 1.7-10.5) years. Initial regimens were 32% PI based, 34% nevirapine (NVP) based, and 33% efavirenz based. Median duration of follow-up was 5.4 (IQR, 2.9-8.3) years. Cumulative incidence of switch at 5 years was 21% (95% confidence interval, 20%-23%), with significant regional variations. Median time to switch was 30 (IQR, 16-58) months; two-thirds of switches were related to treatment failure. In multivariable analysis, older age, severe immunosuppression and higher viral load (VL) at ART start, and NVP-based initial regimens were associated with increased risk of switch. One in 5 children switched to a second-line regimen by 5 years of ART, with two-thirds failure related. Advanced HIV, older age, and NVP-based regimens were associated with increased risk of switch. © The Author(s) 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Ultralow-voltage design of graphene PN junction quantum reflective switch transistor

NASA Astrophysics Data System (ADS)

Sohier, Thibault; Yu, Bin

2011-05-01

We propose the concept of a graphene-based quantum reflective switch (QRS) for low-power logic application. With the unique electronic properties of graphene, a tilted PN junction is used to implement logic switch function with 103 ON/OFF ratio. Carriers are reflected on an electrostatically induced potential step with strong incidence-angle-dependency due to the widening of classically forbidden energies. Optimized design of the device for ultralow-voltage operating has been conducted. The device is constantly ON with a turning-off gate voltage around 180 mV using thin HfO2 as the gate dielectric. The results suggest a class of logic switch devices operating with micropower dissipation.

Global dynamics for switching systems and their extensions by linear differential equations

NASA Astrophysics Data System (ADS)

Huttinga, Zane; Cummins, Bree; Gedeon, Tomáš; Mischaikow, Konstantin

2018-03-01

Switching systems use piecewise constant nonlinearities to model gene regulatory networks. This choice provides advantages in the analysis of behavior and allows the global description of dynamics in terms of Morse graphs associated to nodes of a parameter graph. The parameter graph captures spatial characteristics of a decomposition of parameter space into domains with identical Morse graphs. However, there are many cellular processes that do not exhibit threshold-like behavior and thus are not well described by a switching system. We consider a class of extensions of switching systems formed by a mixture of switching interactions and chains of variables governed by linear differential equations. We show that the parameter graphs associated to the switching system and any of its extensions are identical. For each parameter graph node, there is an order-preserving map from the Morse graph of the switching system to the Morse graph of any of its extensions. We provide counterexamples that show why possible stronger relationships between the Morse graphs are not valid.

Global dynamics for switching systems and their extensions by linear differential equations.

PubMed

Huttinga, Zane; Cummins, Bree; Gedeon, Tomáš; Mischaikow, Konstantin

2018-03-15

Switching systems use piecewise constant nonlinearities to model gene regulatory networks. This choice provides advantages in the analysis of behavior and allows the global description of dynamics in terms of Morse graphs associated to nodes of a parameter graph. The parameter graph captures spatial characteristics of a decomposition of parameter space into domains with identical Morse graphs. However, there are many cellular processes that do not exhibit threshold-like behavior and thus are not well described by a switching system. We consider a class of extensions of switching systems formed by a mixture of switching interactions and chains of variables governed by linear differential equations. We show that the parameter graphs associated to the switching system and any of its extensions are identical. For each parameter graph node, there is an order-preserving map from the Morse graph of the switching system to the Morse graph of any of its extensions. We provide counterexamples that show why possible stronger relationships between the Morse graphs are not valid.

Leverage effect, economic policy uncertainty and realized volatility with regime switching

NASA Astrophysics Data System (ADS)

Duan, Yinying; Chen, Wang; Zeng, Qing; Liu, Zhicao

2018-03-01

In this study, we first investigate the impacts of leverage effect and economic policy uncertainty (EPU) on future volatility in the framework of regime switching. Out-of-sample results show that the HAR-RV including the leverage effect and economic policy uncertainty with regimes can achieve higher forecast accuracy than RV-type and GARCH-class models. Our robustness results further imply that these factors in the framework of regime switching can substantially improve the HAR-RV's forecast performance.

Reduced genetic distance and high replication levels increase the RNA recombination rate of hepatitis delta virus.

PubMed

Lin, Chia-Chi; Yang, Zhi-Wei; Iang, Shan-Bei; Chao, Mei

2015-01-02

Hepatitis delta virus (HDV) replication is carried out by host RNA polymerases. Since homologous inter-genotypic RNA recombination is known to occur in HDV, possibly via a replication-dependent process, we hypothesized that the degree of sequence homology and the replication level should be related to the recombination frequency in cells co-expressing two HDV sequences. To confirm this, we separately co-transfected cells with three different pairs of HDV genomic RNAs and analyzed the obtained recombinants by RT-PCR followed by restriction fragment length polymorphism and sequencing analyses. The sequence divergence between the clones ranged from 24% to less than 0.1%, and the difference in replication levels was as high as 100-fold. As expected, significant differences were observed in the recombination frequencies, which ranged from 0.5% to 47.5%. Furthermore, varying the relative amounts of parental RNA altered the dominant recombinant species produced, suggesting that template switching occurs frequently during the synthesis of genomic HDV RNA. Taken together, these data suggest that during the host RNA polymerase-driven RNA recombination of HDV, both inter- and intra-genotypic recombination events are important in shaping the genetic diversity of HDV. Copyright © 2014 Elsevier B.V. All rights reserved.

Switching Systems: Controllability and Control Design

DTIC Science & Technology

2009-04-25

controllable linear time invariant (LTI) systems ẋ = Ax+Bu are stabilizable and the stabilization can be always done by a...to control the system is bounded. As an application controllability conditions for a class of bimodal linear time invariant (LTI) systems are also...There exist a universal ( finite ) switching sequence σ such that the time varying system ẋ = A(σ)x+ B(σ)u is globally controllable . Proof: The

High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia

PubMed Central

Nedellec, Rebecca; Herbeck, Joshua T.; Hunt, Peter W.; Deeks, Steven G.; Mullins, James I.; Anton, Elizabeth D.; Reeves, Jacqueline D.

2017-01-01

Abstract Coreceptor switching from CCR5 to CXCR4 is common during chronic HIV-1 infection, but is even more common in individuals who have failed antiretroviral therapy (ART). Prior studies have suggested rapid mutation and/or recombination of HIV-1 envelope (env) genes during coreceptor switching. We compared the functional and genotypic changes in env of viruses from viremic subjects who had failed ART just before and after coreceptor switching and compared those to viruses from matched subjects without coreceptor switching. Analysis of multiple unique functional env clones from each subject revealed extensive diversity at both sample time points and rapid diversification of sequences during the 4-month interval in viruses from both 9 subjects with coreceptor switching and 15 control subjects. Only two subjects had envs with evidence of recombination. Three findings distinguished env clones from subjects with coreceptor switching from controls: (1) lower entry efficiency via CCR5; (2) longer V1/V2 regions; and (3), lower nadir CD4 T cell counts during prior years of infection. Most of these subjects harbored virus with lower replicative capacity associated with protease (PR) and/or reverse transcriptase inhibitor resistance mutations, and the extensive diversification tended to lead either to improved entry efficiency via CCR5 or the gain of entry function via CXCR4. These results suggest that R5X4 or X4 variants emerge from a diverse, low-fitness landscape shaped by chronic infection, multiple ART resistance mutations, the availability of target cells, and reduced entry efficiency via CCR5. PMID:27604829

High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia.

PubMed

Nedellec, Rebecca; Herbeck, Joshua T; Hunt, Peter W; Deeks, Steven G; Mullins, James I; Anton, Elizabeth D; Reeves, Jacqueline D; Mosier, Donald E

2017-03-01

Coreceptor switching from CCR5 to CXCR4 is common during chronic HIV-1 infection, but is even more common in individuals who have failed antiretroviral therapy (ART). Prior studies have suggested rapid mutation and/or recombination of HIV-1 envelope (env) genes during coreceptor switching. We compared the functional and genotypic changes in env of viruses from viremic subjects who had failed ART just before and after coreceptor switching and compared those to viruses from matched subjects without coreceptor switching. Analysis of multiple unique functional env clones from each subject revealed extensive diversity at both sample time points and rapid diversification of sequences during the 4-month interval in viruses from both 9 subjects with coreceptor switching and 15 control subjects. Only two subjects had envs with evidence of recombination. Three findings distinguished env clones from subjects with coreceptor switching from controls: (1) lower entry efficiency via CCR5; (2) longer V1/V2 regions; and (3), lower nadir CD4 T cell counts during prior years of infection. Most of these subjects harbored virus with lower replicative capacity associated with protease (PR) and/or reverse transcriptase inhibitor resistance mutations, and the extensive diversification tended to lead either to improved entry efficiency via CCR5 or the gain of entry function via CXCR4. These results suggest that R5X4 or X4 variants emerge from a diverse, low-fitness landscape shaped by chronic infection, multiple ART resistance mutations, the availability of target cells, and reduced entry efficiency via CCR5.

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.

Initial antihypertensive prescription and switching: a 5 year cohort study from 250,851 patients.

PubMed

Wong, Martin C S; Tam, Wilson W S; Cheung, Clement S K; Tong, Ellen L H; Sek, Antonio C H; John, George; Cheung, N T; Yan, Bryan P Y; Yu, C M; Leeder, Stephen; Griffiths, Sian

2013-01-01

Adverse effects of antihypertensive therapy incur substantial cost. We evaluated whether any major classes of antihypertensive drugs were significantly associated with switching as a proxy measure of medication side effects in a large Chinese population in Hong Kong. From a clinical database, all adult patients newly prescribed an antihypertensive mono-therapy in Hong Kong between the years 2001-2003 and 2005 were included. Those who paid only one visit, died or stayed in the cohort for <180 days after the prescription, or prescribed more than one antihypertensive agent were excluded. The factors associated with switching at 180 days were evaluated by multivariate regression analyses. Age, gender, payment status, service type, district of residence, drug class, systolic and diastolic blood pressure levels were predictor variables. From 250,851 subjects, 159,813 patients were eligible. A total of 6,163 (3.9%) switched their medications within 180 days. Patients prescribed thiazide diuretics had the highest switching rate (5.6%), followed by ACEIs (4.5%), CCBs (4.4%) and beta-blockers (3.2%). When compared with ACEIs, patients on thiazide diuretics were significantly more likely to be switchers (adjusted odds ratio [AOR] 1.49, 95% C.I. 1.31-1.69, p<0.001), whilst patients prescribed CCBs and beta-blockers were similarly likely to have switching. Following these patients up for 5 years showed that thiazide had the most marked increase in switching rate. The higher rates of switching among thiazide diuretics in this study might raise a probably greater incidence of their adverse effects in this Chinese population, yet other factors might also influence switching rates. Patients prescribed thiazide diuretics for longer term should be observed for their intolerability.

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.

Adaptive Output-Feedback Neural Control of Switched Uncertain Nonlinear Systems With Average Dwell Time.

PubMed

Long, Lijun; Zhao, Jun

2015-07-01

This paper investigates the problem of adaptive neural tracking control via output-feedback for a class of switched uncertain nonlinear systems without the measurements of the system states. The unknown control signals are approximated directly by neural networks. A novel adaptive neural control technique for the problem studied is set up by exploiting the average dwell time method and backstepping. A switched filter and different update laws are designed to reduce the conservativeness caused by adoption of a common observer and a common update law for all subsystems. The proposed controllers of subsystems guarantee that all closed-loop signals remain bounded under a class of switching signals with average dwell time, while the output tracking error converges to a small neighborhood of the origin. As an application of the proposed design method, adaptive output feedback neural tracking controllers for a mass-spring-damper system are constructed.

Structural Controllability of Temporal Networks with a Single Switching Controller

PubMed Central

Yao, Peng; Hou, Bao-Yu; Pan, Yu-Jian; Li, Xiang

2017-01-01

Temporal network, whose topology evolves with time, is an important class of complex networks. Temporal trees of a temporal network describe the necessary edges sustaining the network as well as their active time points. By a switching controller which properly selects its location with time, temporal trees are used to improve the controllability of the network. Therefore, more nodes are controlled within the limited time. Several switching strategies to efficiently select the location of the controller are designed, which are verified with synthetic and empirical temporal networks to achieve better control performance. PMID:28107538

Evaluation of four microbial Class II fructose 1,6-bisphosphate aldolase enzymes for use as biocatalysts.

PubMed

Labbé, Geneviève; de Groot, Sarah; Rasmusson, Timothy; Milojevic, Gorica; Dmitrienko, Gary I; Guillemette, J Guy

2011-12-01

Fructose 1,6-bisphosphate (FBP) aldolase has been used as biocatalyst in the synthesis of several pharmaceutical compounds such as monosaccharides and analogs. Is has been suggested that microbial metal-dependant Class II aldolases could be better industrial catalysts than mammalian Class I enzyme because of their greater stability. The Class II aldolases from four microbes were subcloned into the Escherichia coli vector pT7-7, expressed and purified to near homogeneity. The kinetic parameters, temperature stability, pH profile, and tolerance to organic solvents of the Class II enzymes were determined, and compared with the properties of the Class I aldolase from rabbit muscle. Contrary to results obtained previously with the E. coli Class II aldolase, which was reported to be more stable than the mammalian enzyme, other recombinant Class II aldolases were found to be generally less stable than the Class I enzyme, especially in the presence of organic solvents. Class II aldolase from Bacillus cereus showed higher temperature stability than the other enzymes tested, but only the Mycobacterium tuberculosis Class II aldolase had a stability comparable to the Class I mammalian enzyme under assay conditions. The turnover number of the recombinant M. tuberculosis and Magnaporthe grisea Class II type A aldolases was comparable or higher than that of the Class I enzyme. The recombinant B. cereus and Pseudomonas aeruginosa Class II type B aldolases had very low turnover numbers and low metal content, indicating that the E. coli overexpression system may not be suitable for the Class II type B aldolases from these microorganisms. Copyright © 2011 Elsevier Inc. All rights reserved.

A Collaborative, Investigative Recombinant DNA Technology Course with Laboratory

ERIC Educational Resources Information Center

Pezzementi, Leo; Johnson, Joy F.

2002-01-01

A recombinant DNA technology course was designed to promote contextual, collaborative, inquiry-based learning of science where students learn from one another and have a sense of ownership of their education. The class stressed group presentations and critical reading and discussion of scientific articles. The laboratory consisted of two research…

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

Discrete-time switching periodic adaptive control for time-varying parameters with unknown periodicity

NASA Astrophysics Data System (ADS)

Yu, Miao; Huang, Deqing; Yang, Wanqiu

2018-06-01

In this paper, we address the problem of unknown periodicity for a class of discrete-time nonlinear parametric systems without assuming any growth conditions on the nonlinearities. The unknown periodicity hides in the parametric uncertainties, which is difficult to estimate with existing techniques. By incorporating a logic-based switching mechanism, we identify the period and bound of unknown parameter simultaneously. Lyapunov-based analysis is given to demonstrate that a finite number of switchings can guarantee the asymptotic tracking for the nonlinear parametric systems. The simulation result also shows the efficacy of the proposed switching periodic adaptive control approach.

[The switch of enzyme therapy in Fabry disease].

PubMed

Riccio, Eleonora; Pisani, Antonio

2014-01-01

Fabry disease (FD) is a multiorgan X-linked lysosomal storage disorder resulted from the deficiency of the lysosomal enzyme alpha galactosidase A. It particularly affects the heart, kidneys and cerebrovascular system. The treatment options for FD patients include long-term enzyme replacement therapy (ERT). Two recombinant enzyme formulations for the ERT of FD are available on European market: agalsidase alfa and agalsidase beta. Numerous evidences in the literature have confirmed the safety and efficacy of ERT. However, to date, there have been limited comparisons between the two agents, and no firm conclusion can be drawn regarding their specific efficacy and safety. In June 2009, a viral contamination in the manufacturing process of Fabrazyme led to a global shortage of agalsidase beta. Recommendations to shift patients to the recommended dose of Replagal were published by the European Medicines Agency (EMA) for all patients receiving Fabrazyme. This offered the unique opportunity to compare, although indirectly, the two drugs evaluating any clinical modification or adverse events that occurred after the switch. Moreover, with the increased availability of agalsidase beta in the last 3 months of 2012, some of the patients who previously switched to agalsidase alfa, were switched-back and returned to full-dose agalsidase beta. This article reviews the published evidence for the clinical efficacy of the two available enzyme preparations and compare it with the experience of our center.

Solid-state switch increases switching speed

NASA Technical Reports Server (NTRS)

Mcgowan, G. F.

1966-01-01

Solid state switch for commutating capacitors in an RC commutated network increases switching speed and extends the filtering or commutating frequency spectrum well into the kilocycle region. The switch is equivalent to the standard double- pole double-throw /DPDT/ relay and is driven from digital micrologic circuits.

Preparation, Characterization and Application of Optical Switch Probes.

PubMed

Petchprayoon, Chutima; Marriott, Gerard

2010-08-01

Optical switches represent a new class of molecular probe with applications in high contrast imaging and optical manipulation of protein interactions. Small molecule, organic optical switches based on nitrospirobenzopyran (NitroBIPS) and their reactive derivatives and conjugates undergo efficient, rapid and reversible, orthogonal optically-driven transitions between a colorless spiro (SP) state and a colored merocyanine (MC) state. The excited MC-state also emits fluorescence, which serves as readout of the state of the switch. Defined optical perturbations of SP and MC generate a defined waveform of MC-fluorescence that can be isolated against unmodulated background signals by using a digital optical lock-in detection approach or to control specific dipolar interactions on proteins. The protocols describe general procedures for the synthesis and spectroscopic characterization of NitroBIPS and specifically labeled conjugates along with methods for the manipulation of dipolar interactions on proteins and imaging of the MC-state of NitroBIPS within living cells.

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.

Recombinant Clone Heterogeneity in ESCHERICHIA COLI Conjunction: Effect of Ph and Partially Replicated Recipient Deoxyribonucleic Acid

PubMed Central

Ou, Jonathan T.

1975-01-01

At pH 6.8, a substantial fraction of recombinant colonies obtained from conjugation with an HfrH donor contained multiple recombinant classes in a single colony (polygenotypic colony). In contrast, when the conjugation was performed at pH 7.6, the number of polygenotypic colonies was drastically reduced, and the recombinant colonies were predominantly monogenotypic or digenotypic. Genetic analysis revealed that the digenotypic recombinants differ in those donor markers near the origin of DNA replication but share those donor markers near the terminus. This integration pattern suggests that the formation of digenotypic recombinants involves recombination of a single copy of the exogenome with a partially replicated recipient DNA molecule. This suggestion was supported by examination of the genotype of recombinant colonies recovered from crosses with an HfrKL96 donor which was derived from HfrH but transfers its chromosome in the reverse direction. PMID:8360

The carboxy-terminal αN helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination.

PubMed

Serre, Marie-Claude; El Arnaout, Toufic; Brooks, Mark A; Durand, Dominique; Lisboa, Johnny; Lazar, Noureddine; Raynal, Bertrand; van Tilbeurgh, Herman; Quevillon-Cheruel, Sophie

2013-01-01

Tyrosine recombinases are conserved in the three kingdoms of life. Here we present the first crystal structure of a full-length archaeal tyrosine recombinase, XerA from Pyrococcus abyssi, at 3.0 Å resolution. In the absence of DNA substrate XerA crystallizes as a dimer where each monomer displays a tertiary structure similar to that of DNA-bound Tyr-recombinases. Active sites are assembled in the absence of dif except for the catalytic Tyr, which is extruded and located equidistant from each active site within the dimer. Using XerA active site mutants we demonstrate that XerA follows the classical cis-cleavage reaction, suggesting rearrangements of the C-terminal domain upon DNA binding. Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates. Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis. We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.

Plasticity of Meiotic Recombination Rates in Response to Temperature in Arabidopsis

PubMed Central

Lloyd, Andrew; Morgan, Chris; H. Franklin, F. Chris

2018-01-01

Meiotic recombination shuffles genetic information from sexual species into gametes to create novel combinations in offspring. Thus, recombination is an important factor in inheritance, adaptation, and responses to selection. However, recombination is not a static parameter; meiotic recombination rate is sensitive to variation in the environment, especially temperature. That recombination rates change in response to both increases and decreases in temperature was reported in Drosophila a century ago, and since then in several other species. But it is still unclear what the underlying mechanism is, and whether low- and high-temperature effects are mechanistically equivalent. Here, we show that, as in Drosophila, both high and low temperatures increase meiotic crossovers in Arabidopsis thaliana. We show that, from a nadir at 18°, both lower and higher temperatures increase recombination through additional class I (interfering) crossovers. However, the increase in crossovers at high and low temperatures appears to be mechanistically at least somewhat distinct, as they differ in their association with the DNA repair protein MLH1. We also find that, in contrast to what has been reported in barley, synaptonemal complex length is negatively correlated with temperature; thus, an increase in chromosome axis length may account for increased crossovers at low temperature in A. thaliana, but cannot explain the increased crossovers observed at high temperature. The plasticity of recombination has important implications for evolution and breeding, and also for the interpretation of observations of recombination rate variation among natural populations. PMID:29496746

Coexistence of minicircular and a highly rearranged mtDNA molecule suggests that recombination shapes mitochondrial genome organization.

PubMed

Mao, Meng; Austin, Andrew D; Johnson, Norman F; Dowton, Mark

2014-03-01

Recombination has been proposed as a possible mechanism to explain mitochondrial (mt) gene rearrangements, although the issue of whether mtDNA recombination occurs in animals has been controversial. In this study, we sequenced the entire mt genome of the megaspilid wasp Conostigmus sp., which possessed a highly rearranged mt genome. The sequence of the A+T-rich region contained a number of different types of repeats, similar to those reported previously in the nematode Meloidogyne javanica, in which recombination was discovered. In Conostigmus, we detected the end products of recombination: a range of minicircles. However, using isolated (cloned) fragments of the A+T-rich region, we established that some of these minicircles were found to be polymerase chain reaction (PCR) artifacts. It appears that regions with repeats are prone to PCR template switching or PCR jumping. Nevertheless, there is strong evidence that one minicircle is real, as amplification primers that straddle the putative breakpoint junction produce a single strong amplicon from genomic DNA but not from the cloned A+T-rich region. The results provide support for the direct link between recombination and mt gene rearrangement. Furthermore, we developed a model of recombination which is important for our understanding of mtDNA evolution.

Active Learning with Monty Hall in a Game Theory Class

ERIC Educational Resources Information Center

Brokaw, Alan J.; Merz, Thomas E.

2004-01-01

The authors describe a game that students can play on the first day of a game theory class. The game introduces the 4 essential elements of any game and is designed so that its sequel, also played on the first day of class, has students playing the well-known Monty Hall game, which raises the question: Should you switch doors? By implementing a…

Adaptive Backstepping-Based Neural Tracking Control for MIMO Nonlinear Switched Systems Subject to Input Delays.

PubMed

Niu, Ben; Li, Lu

2018-06-01

This brief proposes a new neural-network (NN)-based adaptive output tracking control scheme for a class of disturbed multiple-input multiple-output uncertain nonlinear switched systems with input delays. By combining the universal approximation ability of radial basis function NNs and adaptive backstepping recursive design with an improved multiple Lyapunov function (MLF) scheme, a novel adaptive neural output tracking controller design method is presented for the switched system. The feature of the developed design is that different coordinate transformations are adopted to overcome the conservativeness caused by adopting a common coordinate transformation for all subsystems. It is shown that all the variables of the resulting closed-loop system are semiglobally uniformly ultimately bounded under a class of switching signals in the presence of MLF and that the system output can follow the desired reference signal. To demonstrate the practicability of the obtained result, an adaptive neural output tracking controller is designed for a mass-spring-damper system.

Compulsory generic switching of antiepileptic drugs: high switchback rates to branded compounds compared with other drug classes.

PubMed

Andermann, Frederick; Duh, Mei Sheng; Gosselin, Antoine; Paradis, Pierre Emmanuel

2007-03-01

Compulsory generic substitution of antiepileptic drugs (AEDs) may lead to adverse effects in epilepsy patients because of seizure recurrence or increased toxicity. The study objectives were (a) to quantify and compare the switchback rates from generic to brand-name AEDs versus non-AEDs, and (b) to assess clinical implications of switching from branded Lamictal to generic lamotrigine (LTG) and whether signals exist suggesting outcome worsening. By using a public-payer pharmacy-claims database from Ontario, Canada, switchback rates from generic to branded AEDs [Lamictal, Frisium (clobazam; CLB), and Depakene (VPA; divalproex)] were calculated and compared with non-AED long-term therapies, antihyperlipidemics and antidepressants, in January 2002 through March 2006. We then assessed pharmacy utilization and AED dosage among LTG patients switching back to branded Lamictal compared with those staying on generic formulation. The 1,354 patients (403 monotherapy, 951 polytherapy) were prescribed generic LTG, of whom 12.9% switched back to Lamictal (11.7% monotherapy, 13.4% polytherapy). Switchback rates of other AEDs were approximately 20% for CLB and VPA. The switchback rates for AEDs were substantially higher than for non-AEDs (1.5-2.9%). Significant increases in LTG doses were observed after generic substitution for those who did not switch back (6.2%; p<0.0001). The average number of codispensed AEDs and non-AED drugs significantly increased (p<0.0001) after LTG generic entry, especially in the generic group. These results reflect poor acceptance of switching AEDs to generic compounds. They may also indicate increased toxicity and/or loss of seizure control associated with generic AED use.

High intralocus variability and interlocus recombination promote immunological diversity in a minimal major histocompatibility system.

PubMed

Wilson, Anthony B; Whittington, Camilla M; Bahr, Angela

2014-12-20

The genes of the major histocompatibility complex (MHC/MH) have attracted considerable scientific interest due to their exceptional levels of variability and important function as part of the adaptive immune system. Despite a large number of studies on MH class II diversity of both model and non-model organisms, most research has focused on patterns of genetic variability at individual loci, failing to capture the functional diversity of the biologically active dimeric molecule. Here, we take a systematic approach to the study of MH variation, analyzing patterns of genetic variation at MH class IIα and IIβ loci of the seahorse, which together form the immunologically active peptide binding cleft of the MH class II molecule. The seahorse carries a minimal class II system, consisting of single copies of both MH class IIα and IIβ, which are physically linked and inherited in a Mendelian fashion. Both genes are ubiquitously expressed and detectible in the brood pouch of male seahorses throughout pregnancy. Genetic variability of the two genes is high, dominated by non-synonymous variation concentrated in their peptide-binding regions. Coding variation outside these regions is negligible, a pattern thought to be driven by intra- and interlocus recombination. Despite the tight physical linkage of MH IIα and IIβ loci, recombination has produced novel composite alleles, increasing functional diversity at sites responsible for antigen recognition. Antigen recognition by the adaptive immune system of the seahorse is enhanced by high variability at both MH class IIα and IIβ loci. Strong positive selection on sites involved in pathogen recognition, coupled with high levels of intra- and interlocus recombination, produce a patchwork pattern of genetic variation driven by genetic hitchhiking. Studies focusing on variation at individual MH loci may unintentionally overlook an important component of ecologically relevant variation.

Markov switching multinomial logit model: An application to accident-injury severities.

PubMed

Malyshkina, Nataliya V; Mannering, Fred L

2009-07-01

In this study, two-state Markov switching multinomial logit models are proposed for statistical modeling of accident-injury severities. These models assume Markov switching over time between two unobserved states of roadway safety as a means of accounting for potential unobserved heterogeneity. The states are distinct in the sense that in different states accident-severity outcomes are generated by separate multinomial logit processes. To demonstrate the applicability of the approach, two-state Markov switching multinomial logit models are estimated for severity outcomes of accidents occurring on Indiana roads over a four-year time period. Bayesian inference methods and Markov Chain Monte Carlo (MCMC) simulations are used for model estimation. The estimated Markov switching models result in a superior statistical fit relative to the standard (single-state) multinomial logit models for a number of roadway classes and accident types. It is found that the more frequent state of roadway safety is correlated with better weather conditions and that the less frequent state is correlated with adverse weather conditions.

Temporal switching jitter in photoconductive switches

DOE Office of Scientific and Technical Information (OSTI.GOV)

GAUDET,JOHN A.; SKIPPER,MICHAEL C.; ABDALLA,MICHAEL D.

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.

LMI-based adaptive reliable H∞ static output feedback control against switched actuator failures

NASA Astrophysics Data System (ADS)

An, Liwei; Zhai, Ding; Dong, Jiuxiang; Zhang, Qingling

2017-08-01

This paper investigates the H∞ static output feedback (SOF) control problem for switched linear system under arbitrary switching, where the actuator failure models are considered to depend on switching signal. An active reliable control scheme is developed by combination of linear matrix inequality (LMI) method and adaptive mechanism. First, by exploiting variable substitution and Finsler's lemma, new LMI conditions are given for designing the SOF controller. Compared to the existing results, the proposed design conditions are more relaxed and can be applied to a wider class of no-fault linear systems. Then a novel adaptive mechanism is established, where the inverses of switched failure scaling factors are estimated online to accommodate the effects of actuator failure on systems. Two main difficulties arise: first is how to design the switched adaptive laws to prevent the missing of estimating information due to switching; second is how to construct a common Lyapunov function based on a switched estimate error term. It is shown that the new method can give less conservative results than that for the traditional control design with fixed gain matrices. Finally, simulation results on the HiMAT aircraft are given to show the effectiveness of the proposed approaches.

A nuclear mutation defective in mitochondrial recombination in yeast.

PubMed

Ling, F; Makishima, F; Morishima, N; Shibata, T

1995-08-15

Homologous recombination (crossing over and gene conversion) is generally essential for heritage and DNA repair, and occasionally causes DNA aberrations, in nuclei of eukaryotes. However, little is known about the roles of homologous recombination in the inheritance and stability of mitochondrial DNA which is continuously damaged by reactive oxygen species, by-products of respiration. Here, we report the first example of a nuclear recessive mutation which suggests an essential role for homologous recombination in the stable inheritance of mitochondrial DNA. For the detection of this class of mutants, we devised a novel procedure, 'mitochondrial crossing in haploid', which has enabled us to examine many mutant clones. Using this procedure, we examined mutants of Saccharomyces cerevisiae that showed an elevated UV induction of respiration-deficient mutations. We obtained a mutant that was defective in both the omega-intron homing and Endo.SceI-induced homologous gene conversion. We found that the mutant cells are temperature sensitive in the maintenance of mitochondrial DNA. A tetrad analysis indicated that elevated UV induction of respiration-deficient mutations, recombination deficiency and temperature sensitivity are all caused by a single nuclear mutation (mhr1) on chromosome XII. The pleiotropic characteristics of the mutant suggest an essential role for the MHR1 gene in DNA repair, recombination and the maintenance of DNA in mitochondria.

Ultrashort soliton switching based on coherent energy hiding.

PubMed

Romagnoli, M; Wabnitz, S; Zoccolotti, L

1991-08-15

Coherent coupling between light and atoms may be exploited for conceiving a novel class of all-optical signalprocessing devices without a direct counterpart in the continuous-wave regime. We show that the self-switching of ultrashort soliton pulses on resonance with a transition of doping centers in a slab waveguide directional coupler is based on nonlinear group-velocity (instead of the usual phase-velocity) changes.

Oxygen migration during resistance switching and failure of hafnium oxide memristors

DOE PAGES

Kumar, Suhas; Wang, Ziwen; Huang, Xiaopeng; ...

2017-03-06

While the recent establishment of the role of thermophoresis/diffusion-driven oxygen migration during resistance switching in metal oxide memristors provided critical insights required for memristor modeling, extended investigations of the role of oxygen migration during ageing and failure remain to be detailed. Such detailing will enable failure-tolerant design, which can lead to enhanced performance of memristor-based next-generation storage-class memory. Furthermore, we directly observed lateral oxygen migration using in-situ synchrotron x-ray absorption spectromicroscopy of HfO x memristors during initial resistance switching, wear over millions of switching cycles, and eventual failure, through which we determined potential physical causes of failure. Using this information,more » we reengineered devices to mitigate three failure mechanisms and demonstrated an improvement in endurance of about three orders of magnitude.« less

Study of optoelectronic switch for satellite-switched time-division multiple access

NASA Technical Reports Server (NTRS)

Su, Shing-Fong; Jou, Liz; Lenart, Joe

1987-01-01

The use of optoelectronic switching for satellite switched time division multiple access will improve the isolation and reduce the crosstalk of an IF switch matrix. The results are presented of a study on optoelectronic switching. Tasks include literature search, system requirements study, candidate switching architecture analysis, and switch model optimization. The results show that the power divided and crossbar switching architectures are good candidates for an IF switch matrix.

A non-canonical DNA structure enables homologous recombination in various genetic systems.

PubMed

Masuda, Tokiha; Ito, Yutaka; Terada, Tohru; Shibata, Takehiko; Mikawa, Tsutomu

2009-10-30

Homologous recombination, which is critical to genetic diversity, depends on homologous pairing (HP). HP is the switch from parental to recombinant base pairs, which requires expansion of inter-base pair spaces. This expansion unavoidably causes untwisting of the parental double-stranded DNA. RecA/Rad51-catalyzed ATP-dependent HP is extensively stimulated in vitro by negative supercoils, which compensates for untwisting. However, in vivo, double-stranded DNA is relaxed by bound proteins and thus is an unfavorable substrate for RecA/Rad51. In contrast, Mhr1, an ATP-independent HP protein required for yeast mitochondrial homologous recombination, catalyzes HP without the net untwisting of double-stranded DNA. Therefore, we questioned whether Mhr1 uses a novel strategy to promote HP. Here, we found that, like RecA, Mhr1 induced the extension of bound single-stranded DNA. In addition, this structure was induced by all evolutionarily and structurally distinct HP proteins so far tested, including bacterial RecO, viral RecT, and human Rad51. Thus, HP includes the common non-canonical DNA structure and uses a common core mechanism, independent of the species of HP proteins. We discuss the significance of multiple types of HP proteins.

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

49 CFR 218.103 - Hand-operated switches, including crossover switches.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Hand-operated switches, including crossover switches. 218.103 Section 218.103 Transportation Other Regulations Relating to Transportation (Continued... Equipment, Switches, and Fixed Derails § 218.103 Hand-operated switches, including crossover switches. (a)(1...

Optically-switched submillimeter-wave oscillator and radiator having a switch-to-switch propagation delay

NASA Technical Reports Server (NTRS)

Spencer, Michael G. (Inventor); Maserjian, Joseph (Inventor)

1995-01-01

A submillimeter wave-generating integrated circuit includes an array of N photoconductive switches biased across a common voltage source and an optical path difference from a common optical pulse of repetition rate f sub 0 providing a different optical delay to each of the switches. In one embodiment, each incoming pulse is applied to successive ones of the N switches with successive delays. The N switches are spaced apart with a suitable switch-to-switch spacing so as to generate at the output load or antenna radiation of a submillimeter wave frequency f on the order of N f sub 0. Preferably, the optical pulse has a repetition rate of at least 10 GHz and N is of the order of 100, so that the circuit generates radiation of frequency of the order of or greater than 1 Terahertz.

Switching control of an R/C hovercraft: stabilization and smooth switching.

PubMed

Tanaka, K; Iwasaki, M; Wang, H O

2001-01-01

This paper presents stable switching control of an radio-controlled (R/C) hovercraft that is a nonholonomic (nonlinear) system. To exactly represent its nonlinear dynamics, more importantly, to maintain controllability of the system, we newly propose a switching fuzzy model that has locally Takagi-Sugeno (T-S) fuzzy models and switches them according to states, external variables, and/or time. A switching fuzzy controller is constructed by mirroring the rule structure of the switching fuzzy model of an R/C hovercraft. We derive linear matrix inequality (LMI) conditions for ensuring the stability of the closed-loop system consisting of a switching fuzzy model and controller. Furthermore, to guarantee smooth switching of control input at switching boundaries, we also derive a smooth switching condition represented in terms of LMIs. A stable switching fuzzy controller satisfying the smooth switching condition is designed by simultaneously solving both of the LMIs. The simulation and experimental results for the trajectory control of an R/C hovercraft show the validity of the switching fuzzy model and controller design, particularly, the smooth switching condition.

Stable expression of recombinant human coagulation factor XIII in protein-free suspension culture of Chinese hamster ovary cells.

PubMed

Chun, B H; Bang, W G; Park, Y K; Woo, S K

2001-11-01

The recombinant a and bsubunits for human coagulation factor XIII were transfected into Chinese hamster ovary (CHO) cells. CHO cells were amplified and selected with methotrexate in adherent cultures containing serum, and CHO 1-62 cells were later selected in protein-free medium. To develop a recombinant factor XIII production process in a suspension culture, we have investigated the growth characteristics of CHO cells and the maintenance of factor XIII expression in the culture medium. Suspension adaptation of CHO cells was performed in protein-free medium, GC-CHO-PI, by two methods, such as serum weaning and direct switching from serum containing media to protein-free media. Although the growth of CHO cells in suspension culture was affected initially by serum depletion, cell specific productivity of factor XIII showed only minor changes by the direct switching to protein-free medium during a suspension culture. As for the long-term stability of factor XIII, CHO 1-62 cells showed a stable expression of factor XIII in protein-free condition for 1000 h. These results indicate that the CHO 1-62cells can be adapted to express recombinant human factor XIII in a stable maimer in suspension culture using a protein-free medium. Our results demonstrate that enhanced cell growth in a continuous manner is achievable for factor XIII production in a protein-free medium when a perfusion bioreactor culture system with a spin filter is employed.

Reversible solvatomagnetic switching in a single-ion magnet from an entatic state.

PubMed

Vallejo, J; Pardo, E; Viciano-Chumillas, M; Castro, I; Amorós, P; Déniz, M; Ruiz-Pérez, C; Yuste-Vivas, C; Krzystek, J; Julve, M; Lloret, F; Cano, J

2017-05-01

A vast impact on molecular nanoscience can be achieved using simple transition metal complexes as dynamic chemical systems to perform specific and selective tasks under the control of an external stimulus that switches "ON" and "OFF" their electronic properties. While the interest in single-ion magnets (SIMs) lies in their potential applications in information storage and quantum computing, the switching of their slow magnetic relaxation associated with host-guest processes is insufficiently explored. Herein, we report a unique example of a mononuclear cobalt(ii) complex in which geometrical constraints are the cause of easy and reversible water coordination and its release. As a result, a reversible and selective colour and SIM behaviour switch occurs between a "slow-relaxing" deep red anhydrous material (compound 1 ) and its "fast-relaxing" orange hydrated form (compound 2 ). The combination of this optical and magnetic switching in this new class of vapochromic and thermochromic SIMs offers fascinating possibilities for designing multifunctional molecular materials.

Numerical investigation into the injection-locking phenomena of gain switched lasers for optical frequency comb generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ó Dúill, Sean P., E-mail: sean.oduill@dcu.ie; Anandarajah, Prince M.; Zhou, Rui

2015-05-25

We present detailed numerical simulations of the laser dynamics that describe optical frequency comb formation by injection-locking a gain-switched laser. The typical rate equations for semiconductor lasers including stochastic carrier recombination and spontaneous emission suffice to show the injection-locking behavior of gain switched lasers, and we show how the optical frequency comb evolves starting from the free-running state, right through the final injection-locked state. Unlike the locking of continuous wave lasers, we show that the locking range for gain switched lasers is considerably greater because injection locking can be achieved by injecting at frequencies close to one of the combmore » lines. The quality of the comb lines is formally assessed by calculating the frequency modulation (FM)-noise spectral density and we show that under injection-locking conditions the FM-noise spectral density of the comb lines tend to that of the maser laser.« less

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

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.

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.

A Switch Is Not a Switch: Syntactically-Driven Bilingual Language Control

ERIC Educational Resources Information Center

Gollan, Tamar H.; Goldrick, Matthew

2018-01-01

The current study investigated the possibility that language switches could be relatively automatically triggered by context. "Single-word switches," in which bilinguals switched languages on a single word in midsentence and then immediately switched back, were contrasted with more complete "whole-language switches," in which…

Switching Phenomena in a System with No Switches

NASA Astrophysics Data System (ADS)

Preis, Tobias; Stanley, H. Eugene

2010-02-01

It is widely believed that switching phenomena require switches, but this is actually not true. For an intriguing variety of switching phenomena in nature, the underlying complex system abruptly changes from one state to another in a highly discontinuous fashion. For example, financial market fluctuations are characterized by many abrupt switchings creating increasing trends ("bubble formation") and decreasing trends ("financial collapse"). Such switching occurs on time scales ranging from macroscopic bubbles persisting for hundreds of days to microscopic bubbles persisting only for a few seconds. We analyze a database containing 13,991,275 German DAX Future transactions recorded with a time resolution of 10 msec. For comparison, a database providing 2,592,531 of all S&P500 daily closing prices is used. We ask whether these ubiquitous switching phenomena have quantifiable features independent of the time horizon studied. We find striking scale-free behavior of the volatility after each switching occurs. We interpret our findings as being consistent with time-dependent collective behavior of financial market participants. We test the possible universality of our result by performing a parallel analysis of fluctuations in transaction volume and time intervals between trades. We show that these financial market switching processes have properties similar to those of phase transitions. We suggest that the well-known catastrophic bubbles that occur on large time scales—such as the most recent financial crisis—are no outliers but single dramatic representatives caused by the switching between upward and downward trends on time scales varying over nine orders of magnitude from very large (≈102 days) down to very small (≈10 ms).

Meiotic recombination modulates the structure and dynamics of the synaptonemal complex during C. elegans meiosis

PubMed Central

2017-01-01

During meiotic prophase, a structure called the synaptonemal complex (SC) assembles at the interface between aligned pairs of homologous chromosomes, and crossover recombination events occur between their DNA molecules. Here we investigate the inter-relationships between these two hallmark features of the meiotic program in the nematode C. elegans, revealing dynamic properties of the SC that are modulated by recombination. We demonstrate that the SC incorporates new subunits and switches from a more highly dynamic/labile state to a more stable state as germ cells progress through the pachytene stage of meiotic prophase. We further show that the more dynamic state of the SC is prolonged in mutants where meiotic recombination is impaired. Moreover, in meiotic mutants where recombination intermediates are present in limiting numbers, SC central region subunits become preferentially stabilized on the subset of chromosome pairs that harbor a site where pro-crossover factors COSA-1 and MutSγ are concentrated. Polo-like kinase PLK-2 becomes preferentially localized to the SCs of chromosome pairs harboring recombination sites prior to the enrichment of SC central region proteins on such chromosomes, and PLK-2 is required for this enrichment to occur. Further, late pachytene nuclei in a plk-2 mutant exhibit the more highly dynamic SC state. Together our data demonstrate that crossover recombination events elicit chromosome-autonomous stabilizing effects on the SC and implicate PLK-2 in this process. We discuss how this recombination-triggered modulation of SC state might contribute to regulatory mechanisms that operate during meiosis to ensure the formation of crossovers while at the same time limiting their numbers. PMID:28339470

Observability of Automata Networks: Fixed and Switching Cases.

PubMed

Li, Rui; Hong, Yiguang; Wang, Xingyuan

2018-04-01

Automata networks are a class of fully discrete dynamical systems, which have received considerable interest in various different areas. This brief addresses the observability of automata networks and switched automata networks in a unified framework, and proposes simple necessary and sufficient conditions for observability. The results are achieved by employing methods from symbolic computation, and are suited for implementation using computer algebra systems. Several examples are presented to demonstrate the application of the results.

Development of a Competitive Binding Assay System with Recombinant Estrogen Receptors from Multiple Species

EPA Science Inventory

ABSTRACT In the current study, we developed a new system using full-length recombinant baculovirus-expressed estrogen receptors which allows for direct comparison of binding across species. Estrogen receptors representing five vertebrate classes were compared: human (hERα), quai...

SWITCH: a dynamic CRISPR tool for genome engineering and metabolic pathway control for cell factory construction in Saccharomyces cerevisiae.

PubMed

Vanegas, Katherina García; Lehka, Beata Joanna; Mortensen, Uffe Hasbro

2017-02-08

The yeast Saccharomyces cerevisiae is increasingly used as a cell factory. However, cell factory construction time is a major obstacle towards using yeast for bio-production. Hence, tools to speed up cell factory construction are desirable. In this study, we have developed a new Cas9/dCas9 based system, SWITCH, which allows Saccharomyces cerevisiae strains to iteratively alternate between a genetic engineering state and a pathway control state. Since Cas9 induced recombination events are crucial for SWITCH efficiency, we first developed a technique TAPE, which we have successfully used to address protospacer efficiency. As proof of concept of the use of SWITCH in cell factory construction, we have exploited the genetic engineering state of a SWITCH strain to insert the five genes necessary for naringenin production. Next, the naringenin cell factory was switched to the pathway control state where production was optimized by downregulating an essential gene TSC13, hence, reducing formation of a byproduct. We have successfully integrated two CRISPR tools, one for genetic engineering and one for pathway control, into one system and successfully used it for cell factory construction.

49 CFR 236.6 - Hand-operated switch equipped with switch circuit controller.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 4 2010-10-01 2010-10-01 false Hand-operated switch equipped with switch circuit..., AND APPLIANCES Rules and Instructions: All Systems General § 236.6 Hand-operated switch equipped with switch circuit controller. Hand-operated switch equipped with switch circuit controller connected to the...

49 CFR 236.6 - Hand-operated switch equipped with switch circuit controller.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 4 2013-10-01 2013-10-01 false Hand-operated switch equipped with switch circuit..., AND APPLIANCES Rules and Instructions: All Systems General § 236.6 Hand-operated switch equipped with switch circuit controller. Hand-operated switch equipped with switch circuit controller connected to the...

49 CFR 236.6 - Hand-operated switch equipped with switch circuit controller.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 4 2012-10-01 2012-10-01 false Hand-operated switch equipped with switch circuit..., AND APPLIANCES Rules and Instructions: All Systems General § 236.6 Hand-operated switch equipped with switch circuit controller. Hand-operated switch equipped with switch circuit controller connected to the...

49 CFR 236.6 - Hand-operated switch equipped with switch circuit controller.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 4 2014-10-01 2014-10-01 false Hand-operated switch equipped with switch circuit..., AND APPLIANCES Rules and Instructions: All Systems General § 236.6 Hand-operated switch equipped with switch circuit controller. Hand-operated switch equipped with switch circuit controller connected to the...

49 CFR 236.6 - Hand-operated switch equipped with switch circuit controller.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 4 2011-10-01 2011-10-01 false Hand-operated switch equipped with switch circuit..., AND APPLIANCES Rules and Instructions: All Systems General § 236.6 Hand-operated switch equipped with switch circuit controller. Hand-operated switch equipped with switch circuit controller connected to the...

Transcutaneous RF-Powered Implantable Minipump Driven by a Class-E Transmitter

PubMed Central

Moore, William H.; Holschneider, Daniel P.; Givrad, Tina K.

2007-01-01

We describe the design and testing of an inductive coupling system used to power an implantable minipump for applications in ambulating rats. A 2 MHz class-E oscillator driver powered a coil transmitter wound around a 33-cm-diameter rat cage. A receiver coil, a filtered rectifier, and a voltage-sensitive switch powered the implant. The implant DC current at the center of the primary coil (5.1 V) exceeded the level required to activate the solenoid valve in the pump. The variations of the implant current in the volume of the primary coil reflected the variations of the estimated coupling coefficient between the two coils. The pump could be activated in-vivo, while accommodating the vertical and horizontal movements of the animal. Advantages of this design include a weight reduction for the implant, an operation independent from a finite power source, and a remote activation/deactivation. PMID:16916107

Transcutaneous RF-powered implantable minipump driven by a class-E transmitter.

PubMed

Moore, William H; Holschneider, Daniel P; Givrad, Tina K; Maarek, Jean-Michel I

2006-08-01

We describe the design and testing of an inductive coupling system used to power an implantable minipump for applications in ambulating rats. A 2 MHz class-E oscillator driver powered a coil transmitter wound around a 33-cm-diameter rat cage. A receiver coil, a filtered rectifier, and a voltage-sensitive switch powered the implant. The implant DC current at the center of the primary coil (5.1 V) exceeded the level required to activate the solenoid valve in the pump. The variations of the implant current in the volume of the primary coil reflected the variations of the estimated coupling coefficient between the two coils. The pump could be activated in-vivo, while accommodating the vertical and horizontal movements of the animal. Advantages of this design include a weight reduction for the implant, an operation independent from a finite power source, and a remote activation/deactivation.

Ultrafast All-Optical Switching of Germanium-Based Flexible Metaphotonic Devices.

PubMed

Lim, Wen Xiang; Manjappa, Manukumara; Srivastava, Yogesh Kumar; Cong, Longqing; Kumar, Abhishek; MacDonald, Kevin F; Singh, Ranjan

2018-03-01

Incorporating semiconductors as active media into metamaterials offers opportunities for a wide range of dynamically switchable/tunable, technologically relevant optical functionalities enabled by strong, resonant light-matter interactions within the semiconductor. Here, a germanium-thin-film-based flexible metaphotonic device for ultrafast optical switching of terahertz radiation is experimentally demonstrated. A resonant transmission modulation depth of 90% is achieved, with an ultrafast full recovery time of 17 ps. An observed sub-picosecond decay constant of 670 fs is attributed to the presence of trap-assisted recombination sites in the thermally evaporated germanium film. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Cellular Neural Networks Based DiffServ Switch for Satellite Communication Systems

NASA Astrophysics Data System (ADS)

Tarchi, Daniele; Fantacci, Romano; Gubellini, Roberto; Pecorella, Tommaso

2003-07-01

Recent developments of Internet services and advanced compression methods has revived interest on IP based multimedia satellite communication systems. However a main problem arising here is to guarantee specific Quality of Service (QoS) constraints in order to have good performance for each traffic class.Among various QoS approach used in Internet, recently the DiffServ technique has became the most promising so- lution, mainly for its simplicity with respect to different alternatives. Moreover, in satellite communication systems, DiffServ policy computational capabilities are placed at the edge points (end-to-end philosophy); this is very important for a network constituted by one satellite link because it allows to reduce the implementation complexity of the satellite on-board equipments.The satellite switch under consideration makes use of the Multiple Input Queuing approach. Packets arrived at a switch input are stored in a shared buffer but they are logically ordered in individual queues, one for each possible output link. According to the DiffServ policy, within a same logical queue, packets are reordered in individual sub-queues according to the priority. A suitable implementation of the DiffServ policy based on a Cellular Neural Network (CNN) is proposed in the paper in order to achieve QoS requirements.The CNNs are a set of linear and nonlinear circuits connected among them that allow parallel and asynchronous computation. CNNs are a class of neural networks similar to Hopfield Neural Networks (HNN), but more flexible and suitable for solving the output contention problem, inherent of switching systems, for VLSI implementation.In this paper a CNN has been designed in order to maximize a cost functional, related to the on-board switch through- put and QoS constraints. The initial state for each neural cell is obtained looking at the presence of at least one packet from a certain input logical queue to a specific output line. The input value for each neural

Hormone Binding to Recombinant Estrogen Receptors from Human, Alligator, Quail, Salamander, and Fathead Minnow

EPA Science Inventory

In this work, a 96-well plate estrogen receptor binding assay was developed to facilitate the direct comparison of chemical binding to full-length recombinant estrogen receptors across vertebrate classes. Receptors were generated in a baculovirus expression system. This approach ...

EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

NASA Astrophysics Data System (ADS)

Weinelt, Martin; von Oppen, Felix

2012-10-01

In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on

Design and analysis of optimised class E power amplifier using shunt capacitance in the output structure

NASA Astrophysics Data System (ADS)

Hayati, Mohsen; Roshani, Sobhan; Zirak, Ali Reza

2017-05-01

In this paper, a class E power amplifier (PA) with operating frequency of 1 MHz is presented. MOSFET non-linear drain-to-source parasitic capacitance, linear external capacitance at drain-to-source port and linear shunt capacitance in the output structure are considered in design theory. One degree of freedom is added to the design of class E PA, by assuming the shunt capacitance in the output structure in the analysis. With this added design degree of freedom it is possible to achieve desired values for several parameters, such as output voltage, load resistance and operating frequency, while both zero voltage and zero derivative switching (ZVS and ZDS) conditions are satisfied. In the conventional class E PA, high value of peak switch voltage results in limitations for the design of amplifier, while in the presented structure desired specifications could be achieved with the safe margin of peak switch voltage. The results show that higher operating frequency and output voltage can also be achieved, compared to the conventional structure. PSpice software is used in order to simulate the designed circuit. The presented class E PA is designed, fabricated and measured. The measured results are in good agreement with simulation and theory results.

Recombineering: A Homologous Recombination-Based Method of Genetic Engineering

PubMed Central

Sharan, Shyam K.; Thomason, Lynn C.; Kuznetsov, Sergey G.; Court, Donald L.

2009-01-01

Recombineering is an efficient method of in vivo genetic engineering applicable to chromosomal as well as episomal replicons in E. coli. This method circumvents the need for most standard in vitro cloning techniques. Recombineering allows construction of DNA molecules with precise junctions without constraints being imposed by restriction enzyme site location. Bacteriophage homologous recombination proteins catalyze these recombineering reactions using double- and single-strand linear DNA substrates, so-called targeting constructs, introduced by electroporation. Gene knockouts, deletions and point mutations are readily made, gene tags can be inserted, and regions of bacterial artificial chromosomes (BACs) or the E. coli genome can be subcloned by gene retrieval using recombineering. Most of these constructs can be made within about a week's time. PMID:19180090

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.

Switching from computer to microcomputer architecture education

NASA Astrophysics Data System (ADS)

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

2010-03-01

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 microcomputer architecture. The authors present their strategies towards a successful crossing of boundaries between engineering disciplines. This communication aims at providing a different aspect on professional courses that are, nowadays, addressed at the expense of traditional courses.

Prevalence and patterns of antidepressant switching amongst primary care patients in the UK.

PubMed

Mars, Becky; Heron, Jon; Gunnell, David; Martin, Richard M; Thomas, Kyla H; Kessler, David

2017-05-01

Non-response to antidepressant treatment is a substantial problem in primary care, and many patients with depression require additional second-line treatments. This study aimed to examine the prevalence and patterns of antidepressant switching in the UK, and identify associated demographic and clinical factors. Cohort analysis of antidepressant prescribing data from the Clinical Practice Research Datalink, a large, anonymised UK primary care database. The sample included 262,844 patients who initiated antidepressant therapy between 1 January 2005 and 31 June 2011. 9.3% of patients switched to a different antidepressant product, with most switches (60%) occurring within 8 weeks of the index date. The proportion switching was similar for selective serotonin reuptake inhibitors (SSRIs), tricyclic antidepressants and other antidepressants (9.3%, 9.8% and 9.2%, respectively). Most switches were to an SSRI (64.5%), and this was the preferred option regardless of initial antidepressant class. Factors predictive of switching included male gender, age, and history of self-harm and psychiatric illness. Over one in every 11 patients who initiates antidepressant therapy will switch medication, suggesting that initial antidepressant treatment has been unsatisfactory. Evidence to guide choice of second-line treatment for individual patients is currently limited. Additional research comparing different pharmacological and psychological second-line treatment strategies is required in order to inform guidelines and improve patient outcomes.

Transient-Switch-Signal Suppressor

NASA Technical Reports Server (NTRS)

Bozeman, Richard J., Jr.

1995-01-01

Circuit delays transmission of switch-opening or switch-closing signal until after preset suppression time. Used to prevent transmission of undesired momentary switch signal. Basic mode of operation simple. Beginning of switch signal initiates timing sequence. If switch signal persists after preset suppression time, circuit transmits switch signal to external circuitry. If switch signal no longer present after suppression time, switch signal deemed transient, and circuit does not pass signal on to external circuitry, as though no transient switch signal. Suppression time preset at value large enough to allow for damping of underlying pressure wave or other mechanical transient.

Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding.

PubMed

Tenzer, S; Peters, B; Bulik, S; Schoor, O; Lemmel, C; Schatz, M M; Kloetzel, P-M; Rammensee, H-G; Schild, H; Holzhütter, H-G

2005-05-01

Epitopes presented by major histocompatibility complex (MHC) class I molecules are selected by a multi-step process. Here we present the first computational prediction of this process based on in vitro experiments characterizing proteasomal cleavage, transport by the transporter associated with antigen processing (TAP) and MHC class I binding. Our novel prediction method for proteasomal cleavages outperforms existing methods when tested on in vitro cleavage data. The analysis of our predictions for a new dataset consisting of 390 endogenously processed MHC class I ligands from cells with known proteasome composition shows that the immunological advantage of switching from constitutive to immunoproteasomes is mainly to suppress the creation of peptides in the cytosol that TAP cannot transport. Furthermore, we show that proteasomes are unlikely to generate MHC class I ligands with a C-terminal lysine residue, suggesting processing of these ligands by a different protease that may be tripeptidyl-peptidase II (TPPII).

A switch in disulfide linkage during minicollagen assembly in Hydra nematocysts.

PubMed

Engel, U; Pertz, O; Fauser, C; Engel, J; David, C N; Holstein, T W

2001-06-15

The smallest known collagens with only 14 Gly-X-Y repeats referred to as minicollagens are the main constituents of the capsule wall of nematocysts. These are explosive organelles found in Hydra, jellyfish, corals and other Cnidaria. Minicollagen-1 of Hydra recombinantly expressed in mammalian 293 cells contains disulfide bonds within its N- and C-terminal Cys-rich domains but no interchain cross-links. It is soluble and self-associates through non-covalent interactions to form 25-nm-long trimeric helical rod-like molecules. We have used a polyclonal antibody prepared against the recombinant protein to follow the maturation of minicollagens from soluble precursors present in the endoplasmic reticulum and post-Golgi vacuoles to the disulfide-linked insoluble assembly form of the wall. The switch from intra- to intermolecular disulfide bonds is associated with 'hardening' of the capsule wall and provides an explanation for its high tensile strength and elasticity. The process is comparable to disulfide reshuffling between the NC1 domains of collagen IV in mammalian basement membranes.

Endogenous Sensory Discrimination and Selection by a Fast Brain Switch for a High Transfer Rate Brain-Computer Interface.

PubMed

Xu, Ren; Jiang, Ning; Dosen, Strahinja; Lin, Chuang; Mrachacz-Kersting, Natalie; Dremstrup, Kim; Farina, Dario

2016-08-01

In this study, we present a novel multi-class brain-computer interface (BCI) for communication and control. In this system, the information processing is shared by the algorithm (computer) and the user (human). Specifically, an electro-tactile cycle was presented to the user, providing the choice (class) by delivering timely sensory input. The user discriminated these choices by his/her endogenous sensory ability and selected the desired choice with an intuitive motor task. This selection was detected by a fast brain switch based on real-time detection of movement-related cortical potentials from scalp EEG. We demonstrated the feasibility of such a system with a four-class BCI, yielding a true positive rate of  ∼ 80% and  ∼ 70%, and an information transfer rate of  ∼ 7 bits/min and  ∼ 5 bits/min, for the movement and imagination selection command, respectively. Furthermore, when the system was extended to eight classes, the throughput of the system was improved, demonstrating the capability of accommodating a large number of classes. Combining the endogenous sensory discrimination with the fast brain switch, the proposed system could be an effective, multi-class, gaze-independent BCI system for communication and control applications.

Stability analysis for uncertain switched neural networks with time-varying delay.

PubMed

Shen, Wenwen; Zeng, Zhigang; Wang, Leimin

2016-11-01

In this paper, stability for a class of uncertain switched neural networks with time-varying delay is investigated. By exploring the mode-dependent properties of each subsystem, all the subsystems are categorized into stable and unstable ones. Based on Lyapunov-like function method and average dwell time technique, some delay-dependent sufficient conditions are derived to guarantee the exponential stability of considered uncertain switched neural networks. Compared with general results, our proposed approach distinguishes the stable and unstable subsystems rather than viewing all subsystems as being stable, thus getting less conservative criteria. Finally, two numerical examples are provided to show the validity and the advantages of the obtained results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Low-Loss, High-Isolation Microwave Microelectromechanical Systems (MEMS) Switches Being Developed

NASA Technical Reports Server (NTRS)

Ponchak, George E.

2002-01-01

Switches, electrical components that either permit or prevent the flow of electricity, are the most important and widely used electrical devices in integrated circuits. In microwave systems, switches are required for switching between the transmitter and receiver; in communication systems, they are needed for phase shifters in phased-array antennas, for radar and communication systems, and for the new class of digital or software definable radios. Ideally, switches would be lossless devices that did not depend on the electrical signal's frequency or power, and they would not consume electrical power to change from OFF to ON or to maintain one of these two states. Reality is quite different, especially at microwave frequencies. Typical switches in microwave integrated circuits are pin diodes or gallium arsenide (GaAs) field-effect transistors that are nonlinear, with characteristics that depend on the power of the signal. In addition, they are frequency-dependent, lossy, and require electrical power to maintain a certain state. A new type of component has been developed that overcomes most of these technical difficulties. Microelectromechanical (MEMS) switches rely on mechanical movement as a response to an applied electrical force to either transmit or reflect electrical signal power. The NASA Glenn Research Center has been actively developing MEMS for microwave applications for over the last 5 years. Complete fabrication procedures have been developed so that the moving parts of the switch can be released with near 100-percent yield. Moreover, the switches fabricated at Glenn have demonstrated state-of-the-art performance. A typical MEMS switch is shown. The switch extends over the signal and ground lines of a finite ground coplanar waveguide, a commonly used microwave transmission line. In the state shown, the switch is in the UP state and all the microwave power traveling along the transmission line proceeds unimpeded. When a potential difference is applied

Serologic Diagnosis of Lyme Borreliosis by Using Enzyme-Linked Immunosorbent Assays with Recombinant Antigens

PubMed Central

Magnarelli, Louis A.; Ijdo, Jacob W.; Padula, Steven J.; Flavell, Richard A.; Fikrig, Erol

2000-01-01

Class-specific enzyme-linked immunosorbent assays (ELISAs) with purified recombinant antigens of Borrelia burgdorferi sensu stricto and Western blot analyses with whole cells of this spirochete were used to test human sera to determine which antigens were diagnostically important. In analyses for immunoglobulin M (IgM) antibodies, 14 (82%) of 17 serum samples from persons who had erythema migrans reacted positively by an ELISA with one or more recombinant antigens. There was frequent antibody reactivity to protein 41-G (p41-G), outer surface protein C (OspC), and OspF antigens. In an ELISA for IgG antibodies, 13 (87%) of 15 serum samples had antibodies to recombinant antigens; reactivity to p22, p39, p41-G, OspC, and OspF antigens was frequent. By both ELISAs, serum specimens positive for OspB, OspE, and p37 were uncommon. Analyses of sera obtained from persons who were suspected of having human granulocytic ehrlichiosis (HGE) but who lacked antibodies to ehrlichiae revealed IgM antibodies to all recombinant antigens of B. burgdorferi except OspB and IgG antibodies to all antigens except OspE. Immunoblotting of sera from the study group of individuals suspected of having HGE reaffirmed antibody reactivity to multiple antigens of B. burgdorferi. There was minor cross-reactivity when sera from healthy subjects or persons who had syphilis, oral infections, or rheumatoid arthritis were tested by ELISAs with p37, p41-G, OspB, OspC, OspE, and OspF antigens. Although the results of class-specific ELISAs with recombinant antigens were comparable to those recorded for assays with whole-cell antigen and for individuals with confirmed clinical diagnoses of Lyme borreliosis, immunoblotting is still advised as an adjunct procedure, particularly when there are low antibody titers by an ELISA. PMID:10790090

Pharmacy and medical costs associated with switching between venlafaxine and SSRI antidepressant therapy for the treatment of major depressive disorder.

PubMed

Khandker, Rezaul K; Kruzikas, Denise T; McLaughlin, Trent P

2008-06-01

While much has been published on utilization of antidepressants and associated resource use, surprisingly little information is available on the relationship between a change in antidepressant agent and health care utilization. Given that many patients will not respond to initial therapy (and therefore would be candidates for switching treatment) and the array of antidepressant medications on the market, information on the impact of switching would be beneficial to both providers and policymakers. To explore patterns of antidepressant drug use and depression-related and all-cause medical costs for patients who switched therapy between 2 drug classes, selective serotonin reuptake inhibitors (SSRIs) and the selective norepinephrine reuptake inhibitor (SNRI) venlafaxine. Using an administrative claims database of 36 million members from 61 health plans, this retrospective cohort analysis examined patients who had (1) a diagnosis of major depressive disorder (MDD, International Classification of Diseases, Ninth Revision, Clinical Modification [ICD-9-CM] code 296.2x for MDD single episode, 296.3x for MDD recurrent episode, 300.4 for dysthymic disorder, and 311 for depressive disorder not elsewhere classified) and (2) a newly prescribed antidepressant during the year 2002. Costs were defined as amounts paid by health plans for all inpatient, outpatient, physician and pharmacy services (i.e., allowed charges after subtraction of member cost-share). Depression-related costs were defined using (1) medical claims with primary diagnosis of depression and (2) pharmacy claims for antidepressants. Using an index date of the first antidepressant claim, 12 months of pre-index and postindex data were available for all eligible patients. Switching was defined as occurring between the SSRIs and venlafaxine (i.e., patients who switched within the SSRI drug class across different SSRIs were treated as non-switchers until they switched to venlafaxine), and there was no minimum or

Quantitative analysis of recombination between YFP and CFP genes of FRET biosensors introduced by lentiviral or retroviral gene transfer

PubMed Central

Komatsubara, Akira T.; Matsuda, Michiyuki; Aoki, Kazuhiro

2015-01-01

Biosensors based on the principle of Förster (or fluorescence) resonance energy transfer (FRET) have been developed to visualize spatio-temporal dynamics of signalling molecules in living cells. Many of them adopt a backbone of intramolecular FRET biosensor with a cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) as donor and acceptor, respectively. However, there remains the difficulty of establishing cells stably expressing FRET biosensors with a YFP and CFP pair by lentiviral or retroviral gene transfer, due to the high incidence of recombination between YFP and CFP genes. To address this, we examined the effects of codon-diversification of YFP on the recombination of FRET biosensors introduced by lentivirus or retrovirus. The YFP gene that was fully codon-optimized to E.coli evaded the recombination in lentiviral or retroviral gene transfer, but the partially codon-diversified YFP did not. Further, the length of spacer between YFP and CFP genes clearly affected recombination efficiency, suggesting that the intramolecular template switching occurred in the reverse-transcription process. The simple mathematical model reproduced the experimental data sufficiently, yielding a recombination rate of 0.002–0.005 per base. Together, these results show that the codon-diversified YFP is a useful tool for expressing FRET biosensors by lentiviral or retroviral gene transfer. PMID:26290434

THE SEARCH FOR CELESTIAL POSITRONIUM VIA THE RECOMBINATION SPECTRUM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ellis, S. C.; Bland-Hawthorn, J., E-mail: sce@physics.usyd.edu.a, E-mail: jbh@physics.usyd.edu.a

2009-12-10

Positronium is a short-lived atom consisting of a bound electron-positron pair. In the triplet state, when the spins of both particles are parallel, radiative recombination lines will be emitted prior to annihilation. The existence of celestial positronium is revealed through gamma-ray observations of its annihilation products. These observations, however, have intrinsically low angular resolution. In this paper, we examine the prospects for detecting the positronium recombination spectrum. Such observations have the potential to reveal discrete sources of e {sup +} for the first time and will allow the acuity of optical telescopes and instrumentation to be applied to observations ofmore » high-energy phenomena. We review the theory of the positronium recombination spectrum and provide formulae to calculate expected line strengths from the e {sup +} production rate and for different conditions in the interstellar medium. We estimate the positronium emission line strengths for several classes of Galactic and extragalactic sources. These are compared to current observational limits and to current and future sensitivities of optical and infrared instrumentation. We find that observations of the Psalpha line should soon be possible due to recent advances in NIR spectroscopy.« less

Switch-mediated activation and retargeting of CAR-T cells for B-cell malignancies

PubMed Central

Rodgers, David T.; Mazagova, Magdalena; Hampton, Eric N.; Cao, Yu; Ramadoss, Nitya S.; Hardy, Ian R.; Schulman, Andrew; Du, Juanjuan; Wang, Feng; Singer, Oded; Ma, Jennifer; Nunez, Vanessa; Shen, Jiayin; Woods, Ashley K.; Wright, Timothy M.; Schultz, Peter G.; Kim, Chan Hyuk; Young, Travis S.

2016-01-01

Chimeric antigen receptor T (CAR-T) cell therapy has produced impressive results in clinical trials for B-cell malignancies. However, safety concerns related to the inability to control CAR-T cells once infused into the patient remain a significant challenge. Here we report the engineering of recombinant antibody-based bifunctional switches that consist of a tumor antigen-specific Fab molecule engrafted with a peptide neo-epitope, which is bound exclusively by a peptide-specific switchable CAR-T cell (sCAR-T). The switch redirects the activity of the bio-orthogonal sCAR-T cells through the selective formation of immunological synapses, in which the sCAR-T cell, switch, and target cell interact in a structurally defined and temporally controlled manner. Optimized switches specific for CD19 controlled the activity, tissue-homing, cytokine release, and phenotype of sCAR-T cells in a dose-titratable manner in a Nalm-6 xenograft rodent model of B-cell leukemia. The sCAR–T-cell dosing regimen could be tuned to provide efficacy comparable to the corresponding conventional CART-19, but with lower cytokine levels, thereby offering a method of mitigating cytokine release syndrome in clinical translation. Furthermore, we demonstrate that this methodology is readily adaptable to targeting CD20 on cancer cells using the same sCAR-T cell, suggesting that this approach may be broadly applicable to heterogeneous and resistant tumor populations, as well as other liquid and solid tumor antigens. PMID:26759369

Mechanism of polarization switching in wurtzite-structured zinc oxide thin films

NASA Astrophysics Data System (ADS)

Konishi, Ayako; Ogawa, Takafumi; Fisher, Craig A. J.; Kuwabara, Akihide; Shimizu, Takao; Yasui, Shintaro; Itoh, Mitsuru; Moriwake, Hiroki

2016-09-01

The properties of a potentially new class of ferroelectric materials based on wurtzite-structured ZnO thin films are examined using the first-principles calculations. Theoretical P-E hysteresis loops were calculated using the fixed-D method for both unstrained and (biaxially) strained single crystals. Ferroelectric polarization switching in ZnO (S.G. P63mc) is shown to occur via an intermediate non-polar structure with centrosymmetric P63/mmc symmetry by displacement of cations relative to anions in the long-axis direction. The calculated coercive electric field (Ec) for polarization switching was estimated to be 7.2 MV/cm for defect-free monocrystalline ZnO. During switching, the short- and long-axis lattice parameters expand and contract, respectively. The large structural distortion required for switching may explain why ferroelectricity in this compound has not been reported experimentally for pure ZnO. Applying an epitaxial tensile strain parallel to the basal plane is shown to be effective in lowering Ec during polarization, with a 5% biaxial expansion resulting in a decrease of Ec to 3.5 MV/cm. Comparison with calculated values for conventional ferroelectric materials suggests that the ferroelectric polarization switching of wurtzite-structured ZnO may be achievable by preparing high-quality ZnO thin films with suitable strain levels and low defect concentrations.

Digital switched hydraulics

NASA Astrophysics Data System (ADS)

Pan, Min; Plummer, Andrew

2018-06-01

This paper reviews recent developments in digital switched hydraulics particularly the switched inertance hydraulic systems (SIHSs). The performance of SIHSs is presented in brief with a discussion of several possible configurations and control strategies. The soft switching technology and high-speed switching valve design techniques are discussed. Challenges and recommendations are given based on the current research achievements.

Enhancement of resistive switching properties in Al2O3 bilayer-based atomic switches: multilevel resistive switching.

PubMed

Vishwanath, Sujaya Kumar; Woo, Hyunsuk; Jeon, Sanghun

2018-06-08

Atomic switches are considered to be building blocks for future non-volatile data storage and internet of things. However, obtaining device structures capable of ultrahigh density data storage, high endurance, and long data retention, and more importantly, understanding the switching mechanisms are still a challenge for atomic switches. Here, we achieved improved resistive switching performance in a bilayer structure containing aluminum oxide, with an oxygen-deficient oxide as the top switching layer and stoichiometric oxide as the bottom switching layer, using atomic layer deposition. This bilayer device showed a high on/off ratio (10 5 ) with better endurance (∼2000 cycles) and longer data retention (10 4 s) than single-oxide layers. In addition, depending on the compliance current, the bilayer device could be operated in four different resistance states. Furthermore, the depth profiles of the hourglass-shaped conductive filament of the bilayer device was observed by conductive atomic force microscopy.

Enhancement of resistive switching properties in Al2O3 bilayer-based atomic switches: multilevel resistive switching

NASA Astrophysics Data System (ADS)

Vishwanath, Sujaya Kumar; Woo, Hyunsuk; Jeon, Sanghun

2018-06-01

Atomic switches are considered to be building blocks for future non-volatile data storage and internet of things. However, obtaining device structures capable of ultrahigh density data storage, high endurance, and long data retention, and more importantly, understanding the switching mechanisms are still a challenge for atomic switches. Here, we achieved improved resistive switching performance in a bilayer structure containing aluminum oxide, with an oxygen-deficient oxide as the top switching layer and stoichiometric oxide as the bottom switching layer, using atomic layer deposition. This bilayer device showed a high on/off ratio (105) with better endurance (∼2000 cycles) and longer data retention (104 s) than single-oxide layers. In addition, depending on the compliance current, the bilayer device could be operated in four different resistance states. Furthermore, the depth profiles of the hourglass-shaped conductive filament of the bilayer device was observed by conductive atomic force microscopy.

Adaptive Fuzzy Output Feedback Control for Switched Nonlinear Systems With Unmodeled Dynamics.

PubMed

Tong, Shaocheng; Li, Yongming

2017-02-01

This paper investigates a robust adaptive fuzzy control stabilization problem for a class of uncertain nonlinear systems with arbitrary switching signals that use an observer-based output feedback scheme. The considered switched nonlinear systems possess the unstructured uncertainties, unmodeled dynamics, and without requiring the states being available for measurement. A state observer which is independent of switching signals is designed to solve the problem of unmeasured states. Fuzzy logic systems are used to identify unknown lumped nonlinear functions so that the problem of unstructured uncertainties can be solved. By combining adaptive backstepping design principle and small-gain approach, a novel robust adaptive fuzzy output feedback stabilization control approach is developed. The stability of the closed-loop system is proved via the common Lyapunov function theory and small-gain theorem. Finally, the simulation results are given to demonstrate the validity and performance of the proposed control strategy.

Finite Ground Coplanar Waveguide Shunt MEMS Switches for Switched Line Phase Shifters

NASA Technical Reports Server (NTRS)

Ponchak, George E.; Simons, Rainee N.; Scardelletti, Maximillian; Varaljay, Nicholas C.

2000-01-01

Switches with low insertion loss and high isolation are required for switched line phase shifters and the transmit/receive switch at the front end of communication systems. A Finite Ground Coplanar (FGC) waveguide capacitive, shunt MEMS switch has been implemented on high resistivity Si. The switch has demonstrated an insertion loss of less than 0.3 dB and a return loss greater than 15 dB from 10 to 20, GHz. The switch design, fabrication, and characteristics are presented.

Reconstitution of the yeast RNA polymerase III transcription system with all recombinant factors.

PubMed

Ducrot, Cécile; Lefebvre, Olivier; Landrieux, Emilie; Guirouilh-Barbat, Josée; Sentenac, André; Acker, Joel

2006-04-28

Transcription factor TFIIIC is a multisubunit complex required for promoter recognition and transcriptional activation of class III genes. We describe here the reconstitution of complete recombinant yeast TFIIIC and the molecular characterization of its two DNA-binding domains, tauA and tauB, using the baculovirus expression system. The B block-binding module, rtauB, was reconstituted with rtau138, rtau91, and rtau60 subunits. rtau131, rtau95, and rtau55 formed also a stable complex, rtauA, that displayed nonspecific DNA binding activity. Recombinant rTFIIIC was functionally equivalent to purified yeast TFIIIC, suggesting that the six recombinant subunits are necessary and sufficient to reconstitute a transcriptionally active TFIIIC complex. The formation and the properties of rTFIIIC-DNA complexes were affected by dephosphorylation treatments. The combination of complete recombinant rTFIIIC and rTFIIIB directed a low level of basal transcription, much weaker than with the crude B'' fraction, suggesting the existence of auxiliary factors that could modulate the yeast RNA polymerase III transcription system.

Intentional preparation of auditory attention-switches: Explicit cueing and sequential switch-predictability.

PubMed

Seibold, Julia C; Nolden, Sophie; Oberem, Josefa; Fels, Janina; Koch, Iring

2018-06-01

In an auditory attention-switching paradigm, participants heard two simultaneously spoken number-words, each presented to one ear, and decided whether the target number was smaller or larger than 5 by pressing a left or right key. An instructional cue in each trial indicated which feature had to be used to identify the target number (e.g., female voice). Auditory attention-switch costs were found when this feature changed compared to when it repeated in two consecutive trials. Earlier studies employing this paradigm showed mixed results when they examined whether such cued auditory attention-switches can be prepared actively during the cue-stimulus interval. This study systematically assessed which preconditions are necessary for the advance preparation of auditory attention-switches. Three experiments were conducted that controlled for cue-repetition benefits, modality switches between cue and stimuli, as well as for predictability of the switch-sequence. Only in the third experiment, in which predictability for an attention-switch was maximal due to a pre-instructed switch-sequence and predictable stimulus onsets, active switch-specific preparation was found. These results suggest that the cognitive system can prepare auditory attention-switches, and this preparation seems to be triggered primarily by the memorised switching-sequence and valid expectations about the time of target onset.

Air-bridge and Vertical CNT Switches for High Performance Switching Applications

NASA Technical Reports Server (NTRS)

Kaul, Anupama B.; Wong, Eric W.; Epp, Larry; Bronikowski, Michael J.; Hunt, BBrian D.

2006-01-01

Carbon nanotubes are attractive for switching applications since electrostatically-actuated CNT switches have low actuation voltages and power requirements, while allowing GHz switching speeds that stem from the inherently high elastic modulus and low mass of the CNT.Our first NEM structure, the air-bridge switch, consists of suspended single-walled nanotubes (SWNTs) that lie above a sputtered Nb base electrode, where contact to the CNTs is made using evaporated Au/Ti. Electrical measurements of these air-bridge devices show well-defined ON and OFF states as a dc bias of a few volts is applied between the CNT and the Nb-base electrode. The CNT air-bridge switches were measured to have switching times down to a few nanoseconds. Our second NEM structure, the vertical CNT switch, consists of nanotubes grown perpendicular to the substrate. Vertical multi-walled nanotubes (MWNTs) are grown directly on a heavily doped Si substrate, from 200 - 300 nm wide, approximately 1 micrometer deep nano-pockets, with Nb metal electrodes to result in the formation of a vertical single-pole-double-throw switch architecture.

On the asymptotic stability of nonlinear mechanical switched systems

NASA Astrophysics Data System (ADS)

Platonov, A. V.

2018-05-01

Some classes of switched mechanical systems with dissipative and potential forces are considered. The case, where either dissipative or potential forces are essentially nonlinear, is studied. It is assumed that the zero equilibrium position of the system is asymptotically stable at least for one operating mode. We will look for sufficient conditions which guarantee the preservation of asymptotic stability of the equilibrium position under the switching of modes. The Lyapunov direct method is used. A Lyapunov function for considered system is constructed, which satisfies the differential inequality of special form for every operating mode. This inequality is nonlinear for the chosen mode with asymptotically stable equilibrium position, and it is linear for the rest modes. The correlations between the intervals of activity of the pointed mode and the intervals of activity of the rest modes are obtained which guarantee the required properties.

Recombinant aequorin and recombinant semi-synthetic aequorins. Cellular Ca2+ ion indicators.

PubMed Central

Shimomura, O; Inouye, S; Musicki, B; Kishi, Y

1990-01-01

Properties of a recombinant aequorin were investigated in comparison with those of natural aequorin. In chromatographic behaviour the recombinant aequorin did not match any of ten isoaequorins tested, although it was very similar to aequorin J. Its sensitivity to Ca2+ was found to be higher than that of any isoaequorin except aequorin D. The recombinant aequorin exhibited no toxicity when tested in various kinds of cells, even where samples of natural aequorin had been found to be toxic. Properties of four recombinant semi-synthetic aequorins (fch-, hcp-, e- and n-types), prepared from the recombinant apo-aequorin and synthetic analogues of coelenterazine, were approximately parallel with those of corresponding semi-synthetic aequorins prepared from natural apo-aequorin. Both recombinant e-aequorin and natural e-aequorin J luminesced with high values of the luminescence intensity ratio I400/I465, although the ratios were not pCa-dependent. The recombinant aequorin and recombinant semi-synthetic aequorins are highly suited for monitoring cellular Ca2+. PMID:2400391

Isolation and characterization of major histocompatibility complex class II B genes in cranes.

PubMed

Kohyama, Tetsuo I; Akiyama, Takuya; Nishida, Chizuko; Takami, Kazutoshi; Onuma, Manabu; Momose, Kunikazu; Masuda, Ryuichi

2015-11-01

In this study, we isolated and characterized the major histocompatibility complex (MHC) class II B genes in cranes. Genomic sequences spanning exons 1 to 4 were amplified and determined in 13 crane species and three other species closely related to cranes. In all, 55 unique sequences were identified, and at least two polymorphic MHC class II B loci were found in most species. An analysis of sequence polymorphisms showed the signature of positive selection and recombination. A phylogenetic reconstruction based on exon 2 sequences indicated that trans-species polymorphism has persisted for at least 10 million years, whereas phylogenetic analyses of the sequences flanking exon 2 revealed a pattern of concerted evolution. These results suggest that both balancing selection and recombination play important roles in the crane MHC evolution.

AID binds cooperatively with UNG and Msh2-Msh6 to Ig switch regions dependent upon the AID C terminus*

PubMed Central

Ranjit, Sanjay; Khair, Lyne; Linehan, Erin K.; Ucher, Anna J.; Chakrabarti, Mrinmay; Schrader, Carol E.; Stavnezer, Janet

2011-01-01

Activation-induced cytidine deaminase (AID) is induced in B cells during an immune response and is essential for both class switch recombination (CSR) and somatic hypermutation (SHM) of antibody genes. The C terminal 10 amino acids of AID are required for CSR but not for SHM, although their role in CSR is unknown. Using retroviral transduction into mouse splenic B cells, we show that the C terminus is not required for S region DSBs, and therefore functions downstream of DSBs. Using chromatin immunoprecipitation, we show that AID binds cooperatively with UNG and the mismatch repair proteins Msh2-Msh6 to Ig Sμ and Sγ3 regions, and this depends on the C terminus and the deaminase activity of AID. We also show that mismatch repair does not contribute to the efficiency of CSR in the absence of the AID C terminus. Although it has been demonstrated that both UNG and Msh2-Msh6 are important for introduction of S region DSBs, our data suggest that the ability of AID to recruit these proteins is important for DSB resolution, perhaps by directing the S region DSBs toward accurate and efficient CSR via non-homologous end joining. PMID:21804017

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.

Cooperative Adaptive Output Regulation for Second-Order Nonlinear Multiagent Systems With Jointly Connected Switching Networks.

PubMed

Liu, Wei; Huang, Jie

2018-03-01

This paper studies the cooperative global robust output regulation problem for a class of heterogeneous second-order nonlinear uncertain multiagent systems with jointly connected switching networks. The main contributions consist of the following three aspects. First, we generalize the result of the adaptive distributed observer from undirected jointly connected switching networks to directed jointly connected switching networks. Second, by performing a new coordinate and input transformation, we convert our problem into the cooperative global robust stabilization problem of a more complex augmented system via the distributed internal model principle. Third, we solve the stabilization problem by a distributed state feedback control law. Our result is illustrated by the leader-following consensus problem for a group of Van der Pol oscillators.

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.

HIV-1 evades virus-specific IgG2 and IgA class switching by targeting systemic and intestinal B cells via long-range intercellular conduits

PubMed Central

Xu, Weifeng; Santini, Paul A.; Sullivan, John S.; He, Bing; Shan, Meimei; Ball, Susan C.; Dyer, Wayne B.; Ketas, Thomas J.; Chadburn, Amy; Cohen-Gould, Leona; Knowles, Daniel M.; Chiu, April; Sanders, Rogier W.; Chen, Kang; Cerutti, Andrea

2009-01-01

Contact-dependent communication between immune cells generates protection, but also facilitates viral spread. We found that macrophages formed long-range actin-propelled conduits in response to negative factor (Nef), a human immunodeficiency virus type-1 (HIV-1) protein with immunosuppressive functions. Conduits attenuated immunoglobulin G2 (IgG2) and IgA class switching in systemic and intestinal lymphoid follicles by shuttling Nef from infected macrophages to B cells through a guanine exchange factor-dependent pathway involving the amino-terminal anchor, central core and carboxy-terminal flexible loop of Nef. By showing stronger virus-specific IgG2 and IgA responses in patients harboring Nef-deficient virions, our data suggest that HIV-1 exploits intercellular highways as a “Trojan horse” to deliver Nef to B cells and evade humoral immunity systemically and at mucosal sites of entry. PMID:19648924

Switching antipsychotic medications.

PubMed

Weiden, P J; Aquila, R; Dalheim, L; Standard, J M

1997-01-01

Compared with conventional antipsychotics, the so-called "atypical" antipsychotics promise improved side effect profiles and better control of the symptoms of schizophrenia. Therefore, most patients currently taking conventional antipsychotics could potentially benefit from a switch to an atypical antipsychotic. Often, the key issue in deciding whether to switch is the presence of countervailing factors that mitigate against the change. This paper discusses the indications and contraindications for switching antipsychotics, plus issues that require consideration before a switch is made. Also, the advantages and disadvantages of various switching techniques are discussed, with a particular focus on the newer antipsychotic olanzapine.

An acoustic switch.

PubMed

Vanhille, Christian; Campos-Pozuelo, Cleofé

2014-01-01

The benefits derived from the development of acoustic transistors which act as switches or amplifiers have been reported in the literature. Here we propose a model of acoustic switch. We theoretically demonstrate that the device works: the input signal is totally restored at the output when the switch is on whereas the output signal nulls when the switch is off. The switch, on or off, depends on a secondary acoustic field capable to manipulate the main acoustic field. The model relies on the attenuation effect of many oscillating bubbles on the main travelling wave in the liquid, as well as on the capacity of the secondary acoustic wave to move the bubbles. This model evidences the concept of acoustic switch (transistor) with 100% efficiency. Copyright © 2013 Elsevier B.V. All rights reserved.

Coaxial Switch

DTIC Science & Technology

2014-04-23

0005] RF coaxial switches are typically used in environments that are prone to mechanical shocks and vibrations . For example, in military...withstand mechanical shocks and vibrations and to maintain an RF connection throughout a shock or a vibration event. Attorney Docket No. 102139...3 of 16 [0006] It has been found that shocks and vibrations on prior art rotary-type coaxial switches may cause the shaft in the coaxial switch

High power solar array switching regulation

NASA Technical Reports Server (NTRS)

Decker, D. K.; Cassinelli, J.; Valgora, M.

1981-01-01

It is pointed out that spacecraft utilization projections for the 1980s and beyond show a trend toward extended lifetimes and larger electric power systems. The need for improved power management and energy transfer arising in connection with this trend has resulted in the conduction of a Solar Array Switching Power Management study. A description is presented of initial development work performed in the study, taking into account the characteristics for three mission classes. Attention is given to the manned LEO platform (250-kW average load), the unmanned GEO platform (50-kW average load), and an ion propulsion orbit transfer vehicle (50- to 250 kW load).

Hydrogen-peroxide-modified egg albumen for transparent and flexible resistive switching memory

NASA Astrophysics Data System (ADS)

Zhou, Guangdong; Yao, Yanqing; Lu, Zhisong; Yang, Xiude; Han, Juanjuan; Wang, Gang; Rao, Xi; Li, Ping; Liu, Qian; Song, Qunliang

2017-10-01

Egg albumen is modified by hydrogen peroxide with concentrations of 5%, 10%, 15% and 30% at room temperature. Compared with devices without modification, a memory cell of Ag/10% H2O2-egg albumen/indium tin oxide exhibits obviously enhanced resistive switching memory behavior with a resistance ratio of 104, self-healing switching endurance for 900 cycles and a prolonged retention time for a 104 s @ 200 mV reading voltage after being bent 103 times. The breakage of massive protein chains occurs followed by the recombination of new protein chain networks due to the oxidation of amidogen and the synthesis of disulfide during the hydrogen peroxide modifying egg albumen. Ions such as Fe3+, Na+, K+, which are surrounded by protein chains, are exposed to the outside of protein chains to generate a series of traps during the egg albumen degeneration process. According to the fitting results of the double logarithm I-V curves and the current-sensing atomic force microscopy (CS-AFM) images of the ON and OFF states, the charge transfer from one trap center to its neighboring trap center is responsible for the resistive switching memory phenomena. The results of our work indicate that hydrogen- peroxide-modified egg albumen could open up a new avenue of biomaterial application in nanoelectronic systems.

DNA Supercoiling and the Lrp Protein Determine the Directionality of fim Switch DNA Inversion in Escherichia coli K-12

PubMed Central

Kelly, Arlene; Conway, Colin; Ó Cróinín, Tadhg; Smith, Stephen G. J.; Dorman, Charles J.

2006-01-01

Site-specific recombinases of the integrase family usually require cofactors to impart directionality in the recombination reactions that they catalyze. The FimB integrase inverts the Escherichia coli fim switch (fimS) in the on-to-off and off-to-on directions with approximately equal efficiency. Inhibiting DNA gyrase with novobiocin caused inversion to become biased in the off-to-on direction. This directionality was not due to differential DNA topological distortion of fimS in the on and off phases by the activity of its resident PfimA promoter. Instead, the leucine-responsive regulatory (Lrp) protein was found to determine switching outcomes. Knocking out the lrp gene or abolishing Lrp binding sites 1 and 2 within fimS completely reversed the response of the switch to DNA relaxation. Inactivation of either Lrp site alone resulted in mild on-to-off bias, showing that they act together to influence the response of the switch to changes in DNA supercoiling. Thus, Lrp is not merely an architectural element organizing the fim invertasome, it collaborates with DNA supercoiling to determine the directionality of the DNA inversion event. PMID:16855224

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

Genome-wide recombination rate variation in a recombination map of cotton.

PubMed

Shen, Chao; Li, Ximei; Zhang, Ruiting; Lin, Zhongxu

2017-01-01

Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species' genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton.

Genome-wide recombination rate variation in a recombination map of cotton

PubMed Central

Shen, Chao; Li, Ximei; Zhang, Ruiting

2017-01-01

Recombination is crucial for genetic evolution, which not only provides new allele combinations but also influences the biological evolution and efficacy of natural selection. However, recombination variation is not well understood outside of the complex species’ genomes, and it is particularly unclear in Gossypium. Cotton is the most important natural fibre crop and the second largest oil-seed crop. Here, we found that the genetic and physical maps distances did not have a simple linear relationship. Recombination rates were unevenly distributed throughout the cotton genome, which showed marked changes along the chromosome lengths and recombination was completely suppressed in the centromeric regions. Recombination rates significantly varied between A-subgenome (At) (range = 1.60 to 3.26 centimorgan/megabase [cM/Mb]) and D-subgenome (Dt) (range = 2.17 to 4.97 cM/Mb), which explained why the genetic maps of At and Dt are similar but the physical map of Dt is only half that of At. The translocation regions between A02 and A03 and between A04 and A05, and the inversion regions on A10, D10, A07 and D07 indicated relatively high recombination rates in the distal regions of the chromosomes. Recombination rates were positively correlated with the densities of genes, markers and the distance from the centromere, and negatively correlated with transposable elements (TEs). The gene ontology (GO) categories showed that genes in high recombination regions may tend to response to environmental stimuli, and genes in low recombination regions are related to mitosis and meiosis, which suggested that they may provide the primary driving force in adaptive evolution and assure the stability of basic cell cycle in a rapidly changing environment. Global knowledge of recombination rates will facilitate genetics and breeding in cotton. PMID:29176878

Circulation of HIV-1 Multiple Complexity Recombinant Forms Among Female Sex Workers Recently Infected with HIV-1 in Thailand.

PubMed

Saeng-Aroon, Siriphan; Loket, Ruangchai; Plipat, Tanarak; Lumyai, Suttiwat; Chu, Pei-Yu; Sangkitporn, Somchai; Nakayama, Emi E; Takeda, Naokazu; Shioda, Tatsuo; Motomura, Kazushi

2016-07-01

The circulating subtype distribution of HIV-1 has not been well characterized in female sex worker (FSW) populations in Thailand. To understand the mechanisms and interrelationships of epidemics involving FSWs in Thailand, we performed a large molecular epidemiological study of FSWs aged 25 years with recently acquired HIV-1 infections. The samples were collected in 2005, 2007, 2009, and 2011 in 38 provinces, representing every region of Thailand. After gag (p24), pol (pro-RT), and env (C2/V3) were sequenced, comprehensive genome analysis was performed. Genetic subtypes were determined in 159 plasma samples. The percentage of circulating recombinant forms (CRFs) CRF01_AE (90.6%) predominated, while subtype B (1.3%), other CRFs (1.9%), and unique recombinant forms (URFs) (6.2%) were identified as minor populations. Interestingly, the unique recombinant nature of these HIV-1 strains was verified in 10 specimens, indicating the presence of new forms of HIV-1 intersubtypes G/A, C/B, AE/B/C, and AE/B with different recombination breakpoints. Subtype B has contributed to these new generations of unique CRF01/B recombinants, especially in the pol (RT) gene, in which the template switching of the RT genomes occurred during reverse transcription. These results imply that the several unique recombinant viruses circulating in Thailand were probably generated in the population or introduced from neighboring countries. Our study helps clarify the patterns of viral transmission and define transmission pathways in Thailand.

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

PubMed Central

Stukenbrock, Eva H.; Dutheil, Julien Y.

2018-01-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. PMID:29263029

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

PubMed

Stukenbrock, Eva H; Dutheil, Julien Y

2018-03-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

Recombination monitor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, S. Y.; Blaskiewicz, M.

This is a brief report on LEReC recombination monitor design considerations. The recombination produced Au 78+ ion rate is reviewed. Based on this two designs are discussed. One is to use the large dispersion lattice. It is shown that even with the large separation of the Au 78+ beam from the Au 79+ beam, the continued monitoring of the recombination is not possible. Accumulation of Au 78+ ions is needed, plus collimation of the Au79+ beam. In another design, it is shown that the recombination monitor can be built based on the proposed scheme with the nominal lattice. From machinemore » operation point of view, this design is preferable. Finally, possible studies and the alternative strategies with the basic goal of the monitor are discussed.« less

Modeling of driver's collision avoidance maneuver based on controller switching model.

PubMed

Kim, Jong-Hae; Hayakawa, Soichiro; Suzuki, Tatsuya; Hayashi, Koji; Okuma, Shigeru; Tsuchida, Nuio; Shimizu, Masayuki; Kido, Shigeyuki

2005-12-01

This paper presents a modeling strategy of human driving behavior based on the controller switching model focusing on the driver's collision avoidance maneuver. The driving data are collected by using the three-dimensional (3-D) driving simulator based on the CAVE Automatic Virtual Environment (CAVE), which provides stereoscopic immersive virtual environment. In our modeling, the control scenario of the human driver, that is, the mapping from the driver's sensory information to the operation of the driver such as acceleration, braking, and steering, is expressed by Piecewise Polynomial (PWP) model. Since the PWP model includes both continuous behaviors given by polynomials and discrete logical conditions, it can be regarded as a class of Hybrid Dynamical System (HDS). The identification problem for the PWP model is formulated as the Mixed Integer Linear Programming (MILP) by transforming the switching conditions into binary variables. From the obtained results, it is found that the driver appropriately switches the "control law" according to the sensory information. In addition, the driving characteristics of the beginner driver and the expert driver are compared and discussed. These results enable us to capture not only the physical meaning of the driving skill but the decision-making aspect (switching conditions) in the driver's collision avoidance maneuver as well.

Simulation of the Plasma Afterglow in the Discharge Gap of a Subnanosecond Switch Based on an Open Discharge in Helium

NASA Astrophysics Data System (ADS)

Alexandrov, A. L.; Schweigert, I. V.

2018-05-01

The phenomenon of subnanosecond electrical breakdown in a strong electric field observed in an open discharge in helium at pressures of 6-20 Torr can be used to create ultrafast plasma switches triggering into a conducting state for a time shorter than 1 ns. To evaluate the possible repetition rate of such a subnanosecond switch, it is interesting to study the decay dynamics of the plasma remaining in the discharge gap after ultrafast breakdown. In this paper, a kinetic model based on the particle-in-cell Monte Carlo collision method is used to study the dynamics of the plasma afterglow in the discharge gap of a subnanosecond switch operating with helium at a pressure of 6 Torr. The simulation results show that the radiative, collisional-radiative, and three-body collision recombination mechanisms significantly contribute to the afterglow decay only while the plasma density remains higher than 1012 cm-3; the main mechanism of the further plasma decay is diffusion of plasma particles onto the wall. Therefore, the effect of recombination in the plasma bulk is observed only during the first 10-20 μs of the afterglow. Over nearly the same time, plasma electrons become thermalized. The afterglow time can be substantially reduced by applying a positive voltage U c to the cathode. Since diffusive losses are limited by the ion mobility, the additional ion drift toward the wall significantly accelerates plasma decay. As U c increases from 0 to +500 V, the characteristic time of plasma decay is reduced from 35 to 10 μs.

Mechanism of polarization switching in wurtzite-structured zinc oxide thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konishi, Ayako; Ogawa, Takafumi; Fisher, Craig A. J.

2016-09-05

The properties of a potentially new class of ferroelectric materials based on wurtzite-structured ZnO thin films are examined using the first-principles calculations. Theoretical P-E hysteresis loops were calculated using the fixed-D method for both unstrained and (biaxially) strained single crystals. Ferroelectric polarization switching in ZnO (S.G. P6{sub 3}mc) is shown to occur via an intermediate non-polar structure with centrosymmetric P6{sub 3}/mmc symmetry by displacement of cations relative to anions in the long-axis direction. The calculated coercive electric field (E{sub c}) for polarization switching was estimated to be 7.2 MV/cm for defect-free monocrystalline ZnO. During switching, the short- and long-axis latticemore » parameters expand and contract, respectively. The large structural distortion required for switching may explain why ferroelectricity in this compound has not been reported experimentally for pure ZnO. Applying an epitaxial tensile strain parallel to the basal plane is shown to be effective in lowering E{sub c} during polarization, with a 5% biaxial expansion resulting in a decrease of E{sub c} to 3.5 MV/cm. Comparison with calculated values for conventional ferroelectric materials suggests that the ferroelectric polarization switching of wurtzite-structured ZnO may be achievable by preparing high-quality ZnO thin films with suitable strain levels and low defect concentrations.« less

Increased Heat Transport in Ultra-hot Jupiter Atmospheres through H2 Dissociation and Recombination

NASA Astrophysics Data System (ADS)

Bell, Taylor J.; Cowan, Nicolas B.

2018-04-01

A new class of exoplanets is beginning to emerge: planets with dayside atmospheres that resemble stellar atmospheres as most of their molecular constituents dissociate. The effects of the dissociation of these species will be varied and must be carefully accounted for. Here we take the first steps toward understanding the consequences of dissociation and recombination of molecular hydrogen (H2) on atmospheric heat recirculation. Using a simple energy balance model with eastward winds, we demonstrate that H2 dissociation/recombination can significantly increase the day–night heat transport on ultra-hot Jupiters (UHJs): gas giant exoplanets where significant H2 dissociation occurs. The atomic hydrogen from the highly irradiated daysides of UHJs will transport some of the energy deposited on the dayside toward the nightside of the planet where the H atoms recombine into H2; this mechanism bears similarities to latent heat. Given a fixed wind speed, this will act to increase the heat recirculation efficiency; alternatively, a measured heat recirculation efficiency will require slower wind speeds after accounting for H2 dissociation/recombination.

Miniature intermittent contact switch

NASA Technical Reports Server (NTRS)

Sword, A.

1972-01-01

Design of electric switch for providing intermittent contact is presented. Switch consists of flexible conductor surrounding, but separated from, fixed conductor. Flexing of outside conductor to contact fixed conductor completes circuit. Advantage is small size of switch compared to standard switches.

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.

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.

Electronic logic to enhance switch reliability in detecting openings and closures of redundant switches

DOEpatents

Cooper, James A.

1986-01-01

A logic circuit is used to enhance redundant switch reliability. Two or more switches are monitored for logical high or low output. The output for the logic circuit produces a redundant and failsafe representation of the switch outputs. When both switch outputs are high, the output is high. Similarly, when both switch outputs are low, the logic circuit's output is low. When the output states of the two switches do not agree, the circuit resolves the conflict by memorizing the last output state which both switches were simultaneously in and produces the logical complement of this output state. Thus, the logic circuit of the present invention allows the redundant switches to be treated as if they were in parallel when the switches are open and as if they were in series when the switches are closed. A failsafe system having maximum reliability is thereby produced.

Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes

PubMed Central

Norman, Paul J.; Abi-Rached, Laurent; Gendzekhadze, Ketevan; Hammond, John A.; Moesta, Achim K.; Sharma, Deepti; Graef, Thorsten; McQueen, Karina L.; Guethlein, Lisbeth A.; Carrington, Christine V.F.; Chandanayingyong, Dasdayanee; Chang, Yih-Hsin; Crespí, Catalina; Saruhan-Direskeneli, Güher; Hameed, Kamran; Kamkamidze, Giorgi; Koram, Kwadwo A.; Layrisse, Zulay; Matamoros, Nuria; Milà, Joan; Park, Myoung Hee; Pitchappan, Ramasamy M.; Ramdath, D. Dan; Shiau, Ming-Yuh; Stephens, Henry A.F.; Struik, Siske; Tyan, Dolly; Verity, David H.; Vaughan, Robert W.; Davis, Ronald W.; Fraser, Patricia A.; Riley, Eleanor M.; Ronaghi, Mostafa; Parham, Peter

2009-01-01

Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are a variable and rapidly evolving family of MHC Class I receptors. Studied here is KIR3DL1/S1, which encodes receptors for highly polymorphic human HLA-A and -B and comprises three ancient allelic lineages that have been preserved by balancing selection throughout human evolution. While the 3DS1 lineage of activating receptors has been conserved, the two 3DL1 lineages of inhibitory receptors were diversified through inter-lineage recombination with each other and with 3DS1. Prominent targets for recombination were D0-domain polymorphisms, which modulate enhancer function, and dimorphism at position 283 in the D2 domain, which influences inhibitory function. In African populations, unequal crossing over between the 3DL1 and 3DL2 genes produced a deleted KIR haplotype in which the telomeric “half” was reduced to a single fusion gene with functional properties distinct from its 3DL1 and 3DL2 parents. Conversely, in Eurasian populations, duplication of the KIR3DL1/S1 locus by unequal crossing over has enabled individuals to carry and express alleles of all three KIR3DL1/S1 lineages. These results demonstrate how meiotic recombination combines with an ancient, preserved diversity to create new KIR phenotypes upon which natural selection acts. A consequence of such recombination is to blur the distinction between alleles and loci in the rapidly evolving human KIR gene family. PMID:19411600

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)

Effective switching frequency multiplier inverter

DOEpatents

Su, Gui-Jia [Oak Ridge, TN; Peng, Fang Z [Okemos, MI

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.

Non-mechanical optical path switching and its application to dual beam spectroscopy including gas filter correlation radiometry

NASA Technical Reports Server (NTRS)

Sachse, Glen W. (Inventor); Wang, Liang-Guo (Inventor)

1992-01-01

A non-mechanical optical switch is developed for alternately switching a monochromatic or quasi-monochromatic light beam along two optical paths. A polarizer polarizes light into a single, e.g., vertical component which is then rapidly modulated into vertical and horizontal components by a polarization modulator. A polarization beam splitter then reflects one of these components along one path and transmits the other along the second path. In the specific application of gas filter correlation radiometry, one path is directed through a vacuum cell and one path is directed through a gas correlation cell containing a desired gas. Reflecting mirrors cause these two paths to intersect at a second polarization beam splitter which reflects one component and transmits the other to recombine them into a polarization modulated beam which can be detected by an appropriate single sensor.

Extended Minus-Strand DNA as Template for R-U5-Mediated Second-Strand Transfer in Recombinational Rescue of Primer Binding Site-Modified Retroviral Vectors

PubMed Central

Mikkelsen, Jacob Giehm; Lund, Anders H.; Dybkær, Karen; Duch, Mogens; Pedersen, Finn Skou

1998-01-01

We have previously demonstrated recombinational rescue of primer binding site (PBS)-impaired Akv murine leukemia virus-based vectors involving initial priming on endogenous viral sequences and template switching during cDNA synthesis to obtain PBS complementarity in second-strand transfer of reverse transcription (Mikkelsen et al., J. Virol. 70:1439–1447, 1996). By use of the same forced recombination system, we have now found recombinant proviruses of different structures, suggesting that PBS knockout vectors may be rescued through initial priming on endogenous virus RNA, read-through of the mutated PBS during minus-strand synthesis, and subsequent second-strand transfer mediated by the R-U5 complementarity of the plus strand and the extended minus-strand DNA acceptor template. Mechanisms for R-U5-mediated second-strand transfer and its possible role in retrovirus replication and evolution are discussed. PMID:9499117

Roundup Ready soybean gene concentrations in field soil aggregate size classes.

PubMed

Levy-Booth, David J; Gulden, Robert H; Campbell, Rachel G; Powell, Jeff R; Klironomos, John N; Pauls, K Peter; Swanton, Clarence J; Trevors, Jack T; Dunfield, Kari E

2009-02-01

Roundup Ready (RR) soybeans containing recombinant Agrobacterium spp. CP4 5-enol-pyruvyl-shikimate-3-phosphate synthase (cp4 epsps) genes tolerant to the herbicide glyphosate are extensively grown worldwide. The concentration of recombinant DNA from RR soybeans in soil aggregates was studied due to the possibility of genetic transformation of soil bacteria. This study used real-time PCR to examine the concentration of cp4 epsps in four field soil aggregate size classes (>2000 microm, 2000-500 microm, 500-250 microm and <250 microm). Aggregates over 2000 microm in diameter had significantly greater gene concentrations than those with diameters under 2000 microm. The >2000 mum fraction contained between 66.62% and 99.18% of total gene copies, although it only accounted for about 30.00% of the sampled soil. Aggregate formation may facilitate persistence of recombinant DNA.

Prominent mitochondrial DNA recombination intermediates in human heart muscle.

PubMed

Kajander, O A; Karhunen, P J; Holt, I J; Jacobs, H T

2001-11-01

Recombination intermediates containing four-way (Holliday) junctions are generated during DNA repair and replication in many systems, including yeast mitochondrial DNA (mtDNA). In contrast, convincing evidence for recombination in mammalian mtDNA is lacking. We have used two-dimensional agarose-gel electrophoresis to analyse non-linear forms of mtDNA in human heart muscle. Replication intermediates from both the coupled and strand-asynchronous mtDNA replication pathways were detected. An additional class of non-linear molecules, with the electrophoretic properties of four-way junctions, was also prominent. These molecules were insensitive to topoisomerase I or RNase H, but were diminished by branch migration or RuvC treatment. Junctional molecules were detected in all regions of the mitochondrial genome, were found in myocardial DNA from young and old adults, but were present at lower levels in skeletal muscle and placenta. We suggest that they could represent intermediates of mtDNA repair, given their prevalence in the oxyradical-rich environment of heart muscle mitochondria.

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.

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.

Diplexer switch

NASA Technical Reports Server (NTRS)

Grauling, C. H., Jr.; Parker, T. W.

1977-01-01

Switch achieves high isolation and continuous input/output matching by using resonant coupling structure of diplexer. Additionally, dc bias network used to control switch is decoupled from RF input and output lines. Voltage transients in external circuits are thus minimized.

Increased recombinant activated factor VII use and need for surgical reexploration following a switch from aprotinin to epsilon-aminocaproic acid in infant cardiac surgery.

PubMed

Scott, John P; Costigan, Daniel J; Hoffman, George M; Simpson, Pippa M; Dasgupta, Mahua; Punzalan, Rowena; Berens, Richard J; Tweddell, James S; Stuth, Eckehard A E

2014-05-01

To evaluate whether conversion from aprotinin to epsilon-aminocaproic acid (EACA) during infant cardiac surgery was associated with increased perioperative bleeding. Structured retrospective chart review. University-affiliated large congenital cardiac surgery program. Records from 145 infants (age < 1 yr) receiving aprotinin as antifibrinolytic therapy for cardiac surgery between 6/1/2006 and 12/31/2006 were compared with a cohort of infants receiving EACA for cardiac surgery between 6/1/2008 and 12/31/2008. Sixty-eight infants received aprotinin and 77 infants received EACA. Measured indicators of perioperative bleeding included transfusion volumes, recombinant activated clotting factor VIIa (rFVIIa) administration, need for reexploration, and perioperative chest tube output. EACA treated patients received significantly more rFVIIa for uncontrolled bleeding (19/77 [25%] vs 3/68 [4%]; P < 0.001) and required surgical reexploration more frequently (21/77 [27%] vs 7/68 [10%]; P = 0.01]. Median (25th-75th percentiles) intraoperative platelet transfusion requirements were also increased after the switch to EACA (28 mL [0-58 mL] vs 0 mL [0 mL - 34.5 mL]), but this difference did not reach statistical significance (P = 0.06). Bleeding in infant cardiac surgery increased following the change in antifibrinolytic therapy from aprotinin to EACA. Given the potential for major harm, especially thrombotic complications, from rFVIIa use, prospective studies examining the safety of postcardiopulmonary bypass rFVIIa administration in infants are necessary before the routine off-label use may be recommended. Copyright © 2014 Elsevier Inc. All rights reserved.

Task Uncertainty Can Account for Mixing and Switch Costs in Task-Switching

PubMed Central

Rennie, Jaime L.

2015-01-01

Cognitive control is required in situations that involve uncertainty or change, such as when resolving conflict, selecting responses and switching tasks. Recently, it has been suggested that cognitive control can be conceptualised as a mechanism which prioritises goal-relevant information to deal with uncertainty. This hypothesis has been supported using a paradigm that requires conflict resolution. In this study, we examine whether cognitive control during task switching is also consistent with this notion. We used information theory to quantify the level of uncertainty in different trial types during a cued task-switching paradigm. We test the hypothesis that differences in uncertainty between task repeat and task switch trials can account for typical behavioural effects in task-switching. Increasing uncertainty was associated with less efficient performance (i.e., slower and less accurate), particularly on switch trials and trials that afford little opportunity for advance preparation. Interestingly, both mixing and switch costs were associated with a common episodic control process. These results support the notion that cognitive control may be conceptualised as an information processor that serves to resolve uncertainty in the environment. PMID:26107646

Investigating a method for reducing residual switch costs in cued task switching.

PubMed

Schneider, Darryl W

2016-07-01

Residual switch costs in cued task switching are performance decrements that occur despite a long cue-target interval (CTI) to prepare for a task switch. Verbruggen, Liefooghe, Vandierendonck, and Demanet (Journal of Experimental Psychology: Learning, Memory, and Cognition, 33; 342-356, 2007) showed that briefly presenting the cue during the CTI and leaving it absent after target onset yielded smaller residual switch costs than those obtained when the cue was available for the full CTI and remained present after target onset. The potential effects of cue availability during the CTI (full or partial) and cue status after target onset (present or absent) on residual switch costs were investigated in the present study. In Experiments 1 and 2, cue status was manipulated while holding cue availability constant. In Experiments 3 and 4, cue status and cue availability were manipulated factorially. Residual switch costs were obtained, but they were not modulated consistently by cue status or cue availability across experiments. In Experiment 5, a direct replication of one of Verbruggen and colleagues' experiments yielded divergent results. Implications for understanding task switching are discussed.

Adaptive synchronized switch damping on an inductor: a self-tuning switching law

NASA Astrophysics Data System (ADS)

Kelley, Christopher R.; Kauffman, Jeffrey L.

2017-03-01

Synchronized switch damping (SSD) techniques exploit low-power switching between passive circuits connected to piezoelectric material to reduce structural vibration. In the classical implementation of SSD, the piezoelectric material remains in an open circuit for the majority of the vibration cycle and switches briefly to a shunt circuit at every displacement extremum. Recent research indicates that this switch timing is only optimal for excitation exactly at resonance and points to more general optimal switch criteria based on the phase of the displacement and the system parameters. This work proposes a self-tuning approach that implements the more general optimal switch timing for synchronized switch damping on an inductor (SSDI) without needing any knowledge of the system parameters. The law involves a gradient-based search optimization that is robust to noise and uncertainties in the system. Testing of a physical implementation confirms this law successfully adapts to the frequency and parameters of the system. Overall, the adaptive SSDI controller provides better off-resonance steady-state vibration reduction than classical SSDI while matching performance at resonance.

Controllability of multi-agent systems with periodically switching topologies and switching leaders

NASA Astrophysics Data System (ADS)

Tian, Lingling; Zhao, Bin; Wang, Long

2018-05-01

This paper considers controllability of multi-agent systems with periodically switching topologies and switching leaders. The concept of m-periodic controllability is proposed, and a criterion for m-periodic controllability is established. The effect of the duration of subsystems on controllability is analysed by utilising a property of analytic functions. In addition, the influence of switching periods on controllability is investigated, and an algorithm is proposed to search for the fewest periods to ensure controllability. A necessary condition for m-periodic controllability is obtained from the perspective of eigenvectors of the subsystems' Laplacian matrices. For a system with switching leaders, it is proved that switching-leader controllability is equivalent to multiple-leader controllability. Furthermore, both the switching order and the tenure of agents being leaders have no effect on the controllability. Some examples are provided to illustrate the theoretical results.

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.

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…

Analysis of continuous-time switching networks

NASA Astrophysics Data System (ADS)

Edwards, R.

2000-11-01

Models of a number of biological systems, including gene regulation and neural networks, can be formulated as switching networks, in which the interactions between the variables depend strongly on thresholds. An idealized class of such networks in which the switching takes the form of Heaviside step functions but variables still change continuously in time has been proposed as a useful simplification to gain analytic insight. These networks, called here Glass networks after their originator, are simple enough mathematically to allow significant analysis without restricting the range of dynamics found in analogous smooth systems. A number of results have been obtained before, particularly regarding existence and stability of periodic orbits in such networks, but important cases were not considered. Here we present a coherent method of analysis that summarizes previous work and fills in some of the gaps as well as including some new results. Furthermore, we apply this analysis to a number of examples, including surprising long and complex limit cycles involving sequences of hundreds of threshold transitions. Finally, we show how the above methods can be extended to investigate aperiodic behaviour in specific networks, though a complete analysis will have to await new results in matrix theory and symbolic dynamics.

Switch-connected HyperX network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Dong; Heidelberger, Philip

A network system includes a plurality of sub-network planes and global switches. The sub-network planes have a same network topology as each other. Each of the sub-network planes includes edge switches. Each of the edge switches has N ports. Each of the global switches is configured to connect a group of edge switches at a same location in the sub-network planes. In each of the sub-network planes, some of the N ports of each of the edge switches are connected to end nodes, and others of the N ports are connected to other edge switches in the same sub-network plane,more » other of the N ports are connected to at least one of the global switches.« less

Membrane Switches Check Seal Pressure

NASA Technical Reports Server (NTRS)

Hodgetts, P. J.; Stuckenberg, F. H.; Morrissey, E. T.

1984-01-01

Array of flexible membrane switches used to indicate closure of seal. Switch membrane responds to pressure exerted by rigid surface on compliant sealing medium and provides switch contacts monitored electronically. Membrane switches connected in series and placed under seal. When all switches are closed lamp or LED lights up, indicating requisite seal pressure has been realized at all switch positions. Principle used to ensure integrity of seals on refrigerator and oven doors, weatherstripping, hatches, spacecraft, airplanes, and submarines.

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.

Task-set switching under cue-based versus memory-based switching conditions in younger and older adults.

PubMed

Kray, Jutta

2006-08-11

Adult age differences in task switching and advance preparation were examined by comparing cue-based and memory-based switching conditions. Task switching was assessed by determining two types of costs that occur at the general (mixing costs) and specific (switching costs) level of switching. Advance preparation was investigated by varying the time interval until the next task (short, middle, very long). Results indicated that the implementation of task sets was different for cue-based switching with random task sequences and memory-based switching with predictable task sequences. Switching costs were strongly reduced under cue-based switching conditions, indicating that task-set cues facilitate the retrieval of the next task. Age differences were found for mixing costs and for switching costs only under cue-based conditions in which older adults showed smaller switching costs than younger adults. It is suggested that older adults adopt a less extreme bias between two tasks than younger adults in situations associated with uncertainty. For cue-based switching with random task sequences, older adults are less engaged in a complete reconfiguration of task sets because of the probability of a further task change. Furthermore, the reduction of switching costs was more pronounced for cue- than memory-based switching for short preparation intervals, whereas the reduction of switch costs was more pronounced for memory- than cue-based switching for longer preparation intervals at least for older adults. Together these findings suggest that the implementation of task sets is functionally different for the two types of task-switching conditions.

TLR4- and TRIF-dependent stimulation of B lymphocytes by peptide liposomes enables T cell-independent isotype switch in mice.

PubMed

Pihlgren, Maria; Silva, Alberto B; Madani, Rime; Giriens, Valérie; Waeckerle-Men, Ying; Fettelschoss, Antonia; Hickman, David T; López-Deber, María Pilar; Ndao, Dorin Mlaki; Vukicevic, Marija; Buccarello, Anna Lucia; Gafner, Valérie; Chuard, Nathalie; Reis, Pedro; Piorkowska, Kasia; Pfeifer, Andrea; Kündig, Thomas M; Muhs, Andreas; Johansen, Pål

2013-01-03

Immunoglobulin class switching from IgM to IgG in response to peptides is generally T cell-dependent and vaccination in T cell-deficient individuals is inefficient. We show that a vaccine consisting of a dense array of peptides on liposomes induced peptide-specific IgG responses totally independent of T-cell help. Independency was confirmed in mice lacking T cells and in mice deficient for MHC class II, CD40L, and CD28. The IgG titers were high, long-lived, and comparable with titers obtained in wild-type animals, and the antibody response was associated with germinal center formation, expression of activation-induced cytidine deaminase, and affinity maturation. The T cell-independent (TI) IgG response was strictly dependent on ligation of TLR4 receptors on B cells, and concomitant TLR4 and cognate B-cell receptor stimulation was required on a single-cell level. Surprisingly, the IgG class switch was mediated by TIR-domain-containing adapter inducing interferon-β (TRIF), but not by MyD88. This study demonstrates that peptides can induce TI isotype switching when antigen and TLR ligand are assembled and appropriately presented directly to B lymphocytes. A TI vaccine could enable efficient prophylactic and therapeutic vaccination of patients with T-cell deficiencies and find application in diseases where induction of T-cell responses contraindicates vaccination, for example, in Alzheimer disease.

THESEUS: A wavelength division multiplexed/microwave subcarrier multiplexed optical network, its ATM switch applications and device requirements

NASA Astrophysics Data System (ADS)

Xin, Wei

1997-10-01

A Terabit Hybrid Electro-optical /underline[Se]lf- routing Ultrafast Switch (THESEUS) has been proposed. It is a self-routing wavelength division multiplexed (WDM) / microwave subcarrier multiplexed (SCM) asynchronous transfer mode (ATM) switch for the multirate ATM networks. It has potential to be extended to a large ATM switch as 1000 x 1000 without internal blocking. Among the advantages of the hybrid implementation are flexibility in service upgrade, relaxed tolerances on optical filtering, protocol simplification and less processing overhead. For a small ATM switch, the subcarrier can be used as output buffers to solve output contention. A mathematical analysis was conducted to evaluate different buffer configurations. A testbed has been successfully constructed. Multirate binary data streams have been switched through the testbed and error free reception ([<]10-9 bit error rate) has been achieved. A simple, intuitive theoretical model has been developed to describe the heterodyne optical beat interference. A new concept of interference time and interference length has been introduced. An experimental confirmation has been conducted. The experimental results match the model very well. It shows that a large portion of optical bandwidth is wasted due to the beat interference. Based on the model, several improvement approaches have been proposed. The photo-generated carrier lifetime of silicon germanium has been measured using time-resolved reflectivity measurement. Via oxygen ion implantation, the carrier lifetime has been reduced to as short as 1 ps, corresponding to 1 THz of photodetector bandwidth. It has also been shown that copper dopants act as recombination centers in the silicon germanium.

Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes

PubMed Central

Dreissig, Steven; Fuchs, Jörg; Himmelbach, Axel; Mascher, Martin; Houben, Andreas

2017-01-01

Meiotic recombination is a fundamental mechanism to generate novel allelic combinations which can be harnessed by breeders to achieve crop improvement. The recombination landscape of many crop species, including the major crop barley, is characterized by a dearth of recombination in 65% of the genome. In addition, segregation distortion caused by selection on genetically linked loci is a frequent and undesirable phenomenon in double haploid populations which hampers genetic mapping and breeding. Here, we present an approach to directly investigate recombination at the DNA sequence level by combining flow-sorting of haploid pollen nuclei of barley with single-cell genome sequencing. We confirm the skewed distribution of recombination events toward distal chromosomal regions at megabase resolution and show that segregation distortion is almost absent if directly measured in pollen. Furthermore, we show a bimodal distribution of inter-crossover distances, which supports the existence of two classes of crossovers which are sensitive or less sensitive to physical interference. We conclude that single pollen nuclei sequencing is an approach capable of revealing recombination patterns in the absence of segregation distortion. PMID:29018459

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

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.

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.

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

Rapid protein production from stable CHO cell pools using plasmid vector and the cumate gene-switch.

PubMed

Poulain, Adeline; Perret, Sylvie; Malenfant, Félix; Mullick, Alaka; Massie, Bernard; Durocher, Yves

2017-08-10

To rapidly produce large amounts of recombinant proteins, the generation of stable Chinese Hamster Ovary (CHO) cell pools represents a useful alternative to large-scale transient gene expression (TGE). We have developed a cell line (CHO BRI/rcTA ) allowing the inducible expression of recombinant proteins, based on the cumate gene switch. After the identification of optimal plasmid DNA topology (supercoiled vs linearized plasmid) for PEIpro™ mediated transfection and of optimal conditions for methionine sulfoximine (MSX) selection, we were able to generate CHO BRI/rcTA pools producing high levels of recombinant proteins. Volumetric productivities of up to 900mg/L were reproducibly achieved for a Fc fusion protein and up to 350mg/L for an antibody after 14days post-induction in non-optimized fed-batch cultures. In addition, we show that CHO pool volumetric productivities are not affected by a freeze-thaw cycle or following maintenance in culture for over one month in the presence of MSX. Finally, we demonstrate that volumetric protein production with the CR5 cumate-inducible promoter is three- to four-fold higher than with the human CMV or hybrid EF1α-HTLV constitutive promoters. These results suggest that the cumate-inducible CHO BRI/rcTA stable pool platform is a powerful and robust system for the rapid production of gram amounts of recombinant proteins. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Diffusion controlled initial recombination

NASA Astrophysics Data System (ADS)

Christen, T.; Büttiker, M.

1998-08-01

This work addresses nucleation rates in systems with strong initial recombination. Initial (or ``geminate'') recombination is a process where a dissociated structure (anion, vortex, kink, etc.) recombines with its twin brother (cation, antivortex, antikink) generated in the same nucleation event. Initial recombination is important if there is an asymptotically vanishing interaction force instead of a generic saddle-type activation barrier. At low temperatures, initial recombination strongly dominates homogeneous recombination. In a first part, we discuss the effect in one-, two-, and three-dimensional diffusion controlled systems with spherical symmetry. Since there is no well-defined saddle, we introduce a threshold which is to some extent arbitrary but which is restricted by physically reasonable conditions. We show that the dependence of the nucleation rate on the specific choice of this threshold is strongest for one-dimensional systems and decreases in higher dimensions. We also discuss the influence of a weak driving force, and show that the transport current is directly determined by the imbalance of the activation rate in the direction of the field and the rate against this direction. In a second part, we apply the results to the overdamped sine-Gordon system at equilibrium. It turns out that diffusive initial recombination is the essential mechanism which governs the equilibrium kink nucleation rate. We emphasize analogies between the single particle problem with initial recombination and the multidimensional kink-antikink nucleation problem.

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.

KRAS G12C Drug Development: Discrimination between Switch II Pocket Configurations Using Hydrogen/Deuterium-Exchange Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Jia; Harrison, Rane A.; Li, Lianbo

KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders. We investigated the structural basismore » for differences in HDX MS using X-ray crystallography and discovered a new SIIP configuration in response to binding of a quinazoline chemotype. These results have implications for structure-guided drug design targeting the RAS SIIP.« less

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.

The Cosmology Large Angular Scale Surveyor (CLASS)

NASA Astrophysics Data System (ADS)

Cleary, Joseph

2018-01-01

The Cosmology Large Angular Scale Surveyor (CLASS) is an array of four telescopes designed to measure the polarization of the Cosmic Microwave Background. CLASS aims to detect the B-mode polarization from primordial gravitational waves predicted by cosmic inflation theory, as well as the imprint left by reionization upon the CMB E-mode polarization. This will be achieved through a combination of observing strategy and state-of-the-art instrumentation. CLASS is observing 70% of the sky to characterize the CMB at large angular scales, which will measure the entire CMB power spectrum from the reionization peak to the recombination peak. The four telescopes operate at frequencies of 38, 93, 145, and 217 GHz, in order to estimate Galactic synchrotron and dust foregrounds while avoiding atmospheric absorption. CLASS employs rapid polarization modulation to overcome atmospheric and instrumental noise. Polarization sensitive cryogenic detectors with low noise levels provide CLASS the sensitivity required to constrain the tensor-to-scalar ratio down to levels of r ~ 0.01 while also measuring the optical depth the reionization to sample-variance levels. These improved constraints on the optical depth to reionization are required to pin down the mass of neutrinos from complementary cosmological data. CLASS has completed a year of observations at 38 GHz and is in the process of deploying the rest of the telescope array. This poster provides an overview and update on the CLASS science, hardware and survey operations.

High-power microstrip switch

NASA Technical Reports Server (NTRS)

Choi, S. D.

1974-01-01

Switch, which uses only two p-i-n diodes on microstrip substrate, has been developed for application in spacecraft radio systems. Switch features improved power drain, weight, volume, magnetic cleanliness, and reliability, over currently-used circulator and electromechanical switches.

Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila

PubMed Central

Smukowski Heil, Caiti S.; Ellison, Chris; Dubin, Matthew; Noor, Mohamed A.F.

2015-01-01

Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human–chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms. PMID:26430062

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

Adaptive output-feedback control for switched stochastic uncertain nonlinear systems with time-varying delay.

PubMed

Song, Zhibao; Zhai, Junyong

2018-04-01

This paper addresses the problem of adaptive output-feedback control for a class of switched stochastic time-delay nonlinear systems with uncertain output function, where both the control coefficients and time-varying delay are unknown. The drift and diffusion terms are subject to unknown homogeneous growth condition. By virtue of adding a power integrator technique, an adaptive output-feedback controller is designed to render that the closed-loop system is bounded in probability, and the state of switched stochastic nonlinear system can be globally regulated to the origin almost surely. A numerical example is provided to demonstrate the validity of the proposed control method. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Research and development of a NYNEX switched multi-megabit data service prototype system

NASA Astrophysics Data System (ADS)

Maman, K. H.; Haines, Robert; Chatterjee, Samir

1991-02-01

Switched Multi-megabit Data Service (SMDS) is a proposed high-speed packet-switched service which will support broadband applications such as Local Area Network (LAN) interconnections across a metropolitan area and beyond. This service is designed to take advantage of evolving Metropolitan Area Network (MAN) standards and technology which will provide customers with 45-mbps and 1 . 5-mbps access to high-speed public data communications networks. This paper will briefly discuss SMDS and review its architecture including the Subscriber Network Interface (SNI) and the SMDS Interface Protocol (SIP). It will review the fundamental features of SMDS such as address screening addressing scheme and access classes. Then it will describe the SMDS prototype system developed in-house by NYNEX Science Technology.

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

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

Low-Crosstalk Composite Optical Crosspoint Switches

NASA Technical Reports Server (NTRS)

Pan, Jing-Jong; Liang, Frank

1993-01-01

Composite optical switch includes two elementary optical switches in tandem, plus optical absorbers. Like elementary optical switches, composite optical switches assembled into switch matrix. Performance enhanced by increasing number of elementary switches. Advantage of concept: crosstalk reduced to acceptably low level at moderate cost of doubling number of elementary switches rather than at greater cost of tightening manufacturing tolerances and exerting more-precise control over operating conditions.

Novel polarization diversity without switch duplication of a Si-wire PILOSS optical switch.

PubMed

Tanizawa, Ken; Suzuki, Keijiro; Ikeda, Kazuhiro; Namiki, Shu; Kawashima, Hitoshi

2016-04-04

We demonstrate the compact polarization diversity based on the bidirectional full-port use of a path-independent-insertion-loss (PILOSS) optical switch. A polarization-diversity 4 × 4 strictly non-blocking optical switch is developed using a single thermooptic PILOSS Si-wire switch and fiber-based polarization beam splitters (PBSs) and combiners (PBCs). We measure characteristics of the switch and confirm that the proposed configuration demonstrates the performance in the insertion loss, polarization-dependent loss (PDL), and differential group delay (DGD) comparable with that of a conventional polarization-diversity 4 × 4 PILOSS switch using double switch elements. On the other hand, higher crosstalk is observed. The crosstalk increase is associated with the backward crosstalk at a waveguide intersection based on a directional coupler. The effect of the backward crosstalk on the total crosstalk is estimated, and future prospects are discussed.

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.

Long-Range Regulation of V(D)J Recombination.

PubMed

Proudhon, Charlotte; Hao, Bingtao; Raviram, Ramya; Chaumeil, Julie; Skok, Jane A

2015-01-01

Given their essential role in adaptive immunity, antigen receptor loci have been the focus of analysis for many years and are among a handful of the most well-studied genes in the genome. Their investigation led initially to a detailed knowledge of linear structure and characterization of regulatory elements that confer control of their rearrangement and expression. However, advances in DNA FISH and imaging combined with new molecular approaches that interrogate chromosome conformation have led to a growing appreciation that linear structure is only one aspect of gene regulation and in more recent years, the focus has switched to analyzing the impact of locus conformation and nuclear organization on control of recombination. Despite decades of work and intense effort from numerous labs, we are still left with an incomplete picture of how the assembly of antigen receptor loci is regulated. This chapter summarizes our advances to date and points to areas that need further investigation. © 2015 Elsevier Inc. All rights reserved.

LONG RANGE REGULATION OF V(D)J RECOMBINATION

PubMed Central

Proudhon, Charlotte; Hao, Bingtao; Raviram, Ramya; Chaumeil, Julie; Skok, Jane A.

2015-01-01

Given their essential role in adaptive immunity, antigen receptor loci have been the focus of analysis for many years and are among a handful of the most well studied genes in the genome. Their investigation led initially to a detailed knowledge of linear structure and characterization of regulatory elements that confer control of their rearrangement and expression. However, advances in DNA FISH and imaging combined with new molecular approaches that interrogate chromosome conformation have led to a growing appreciation that linear structure is only one aspect of gene regulation and in more recent years the focus has switched to analyzing the impact of locus conformation and nuclear organization on control of recombination. Despite decades of work and intense effort from numerous labs we are still left with an incomplete picture of how antigen receptor loci are regulated. This chapter summarizes our advances to date and points to areas that need further investigation. PMID:26477367

Improved Electro-Optical Switches

NASA Technical Reports Server (NTRS)

Nelson, Bruce N.; Cooper, Ronald F.

1994-01-01

Improved single-pole, double-throw electro-optical switches operate in switching times less than microsecond developed for applications as optical communication systems and networks of optical sensors. Contain no moving parts. In comparison with some prior electro-optical switches, these are simpler and operate with smaller optical losses. Beam of light switched from one output path to other by applying, to electro-optical crystal, voltage causing polarization of beam of light to change from vertical to horizontal.

Organization of the channel-switching process in parallel computer systems based on a matrix optical switch

NASA Technical Reports Server (NTRS)

Golomidov, Y. V.; Li, S. K.; Popov, S. A.; Smolov, V. B.

1986-01-01

After a classification and analysis of electronic and optoelectronic switching devices, the design principles and structure of a matrix optical switch is described. The switching and pair-exclusion operations in this type of switch are examined, and a method for the optical switching of communication channels is elaborated. Finally, attention is given to the structural organization of a parallel computer system with a matrix optical switch.

Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila.

PubMed

Smukowski Heil, Caiti S; Ellison, Chris; Dubin, Matthew; Noor, Mohamed A F

2015-10-01

Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human-chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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…

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.

Non-latching relay switch assembly

DOEpatents

Duimstra, Frederick A.

1991-01-01

A non-latching relay switch assembly which includes a coil section and a switch or contact section. The coil section includes a permanent magnet and an electromagnet. The respective sections are arranged in separate locations or cavities in the assembly. The switch has a "normal" position and is selectively switched by an overriding electromagnetic assembly. The switch returns to the "normal" position when the overriding electromagnetic assembly is inactive.

A Josephson Junction based SPDT switch

NASA Astrophysics Data System (ADS)

Zhang, Helin; Earnest, Nathan; Lu, Yao; Ma, Ruichao; Chakram, Srivatsan; Schuster, David

RF microwave switches are useful tools in cryogenic experiments, allowing for multiple experiments to be connected to a single cryogenic measurement chain. However, these switches dissipate a substantial amount of heat, preventing fast switching. Josephson junction (JJ) are a promising avenue for realizing millikelvin microwave switching. We present a JJ based single-pole-double throw (SPDT) switch that has fast switching time, no heat dissipation, large on/off contrast, and works over a wide bandwidth. The switch can be used for real-time switching between experiments, routing single photons, or even generating entanglement. We will describe the design of the switch and present experimental characterization of its performance.

Detecting genetic introgression: high levels of intersubspecific recombination found in Xylella fastidiosa in Brazil.

PubMed

Nunney, Leonard; Yuan, Xiaoli; Bromley, Robin E; Stouthamer, Richard

2012-07-01

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.

Detecting Genetic Introgression: High Levels of Intersubspecific Recombination Found in Xylella fastidiosa in Brazil

PubMed Central

Yuan, Xiaoli; Bromley, Robin E.; Stouthamer, Richard

2012-01-01

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee. PMID:22544234

Optical burst switching for the next generation Optical Internet

NASA Astrophysics Data System (ADS)

Yoo, Myungsik

2000-11-01

In recent years, Internet Protocol (IP) over Wavelength Division Multiplexing (WDM) networks for the next generation Internet (or the so-called Optical Internet) have received enormous attention. There are two main drivers for an Optical Internet. One is the explosion of Internet traffic, which seems to keep growing exponentially. The other driver is the rapid advance in the WDM optical networking technology. In this study, key issues in the optical (WDM) layer will be investigated. As a novel switching paradigm for Optical Internet, Optical Burst Switching (OBS) is discussed. By leveraging the attractive properties of optical communications and at the same time, taking into account its limitations, OBS can combine the best of optical circuit-switching and packet/cell switching. The general concept of JET-based OBS protocol is described, including offset time and delayed reservation. In the next generation Optical Internet, one must address how to support Quality of Service (QoS) at the WDM layer since current IP provides only best effort services. The offset-time- based QoS scheme is proposed as a way of supporting QoS at the WDM layer. Unlike existing QoS schemes, offset- time-based QoS scheme does not mandate the use of buffer to differentiate services. For the bufferless WDM switch, the performance of offset- time-based QoS scheme is evaluated in term of blocking probability. In addition, the extra offset time required for class isolation is quantified and the theoretical bounds on blocking probability are analyzed. The offset-time-based scheme is applied to WDM switch with limited fiber delay line (FDL) buffer. We evaluate the effect of having a FDL buffer on the QoS performance of the offset-time-based scheme in terms of the loss probability and queuing delay of bursts. Finally, in order to dimension the network resources in Optical Internet backbone networks, the performance of the offset-time-based QoS scheme is evaluated for the multi-hop case. In

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.

Cutting Edge: Active TGF-β1 Released from GARP/TGF-β1 Complexes on the Surface of Stimulated Human B Lymphocytes Increases Class-Switch Recombination and Production of IgA.

PubMed

Dedobbeleer, Olivier; Stockis, Julie; van der Woning, Bas; Coulie, Pierre G; Lucas, Sophie

2017-07-15

Production of active TGF-β is regulated at a posttranslational level and implies release of the mature cytokine dimer from the inactive, latent TGF-β precursor. There are several cell-type specific mechanisms of TGF-β activation. We identified a new mechanism operating on the surface of human regulatory T cells and involving membrane protein GARP, which binds latent TGF-β1. The paracrine activity of regulatory T cell-derived TGF-β1 contributes to immunosuppression and can be inhibited with anti-GARP Abs. Whether other immune cell types use surface GARP to activate latent TGF-β1 was not known. We show in this study that stimulated, human B lymphocytes produce active TGF-β1 from surface GARP/latent TGF-β1 complexes with isotype switching to IgA production. Copyright © 2017 by The American Association of Immunologists, Inc.

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.

A new RT-PCR assay for the identification of the predominant recombination types in 2C and 3D genomic regions of vaccine-derived poliovirus strains.

PubMed

Pliaka, V; Dedepsidis, E; Kyriakopoulou, Z; Mpirli, K; Tsakogiannis, D; Pratti, A; Levidiotou-Stefanou, S; Markoulatos, P

2010-06-01

In the post-eradication era of wild polioviruses, the only remaining sources of poliovirus infection worldwide would be the vaccine-derived polioviruses (VDPVs). As the preponderance of countries certified to be polio-free has switched from OPV (oral poliovirus vaccine) to IPV (inactivated poliovirus vaccine), importation of recombinant evolved derivatives of vaccinal strains would have serious implication for public health. To test the robustness of the proposed RT-PCR screening analysis, eleven recombinant vaccine-derived polioviruses that were characterized previously by sequencing by our group, in addition to three recently identified recombinant environmental isolates were assayed. Although the most definitive characterization of VDPVs is by genomic sequencing, in this study we describe a new, inexpensive and broadly applicable RT-PCR assay for the identification of the predominant recombination types S3/Sx in 2C and S2/Sx in 3D genomic regions respectively of VDPVs, that can be readily implemented in laboratories lacking sequencing facilities as a first approach for the early detection of vaccine-derived poliovirus (VDPVs).

Characterisation of major histocompatibility complex class I transcripts in an Australian dragon lizard.

PubMed

Hacking, Jessica; Bertozzi, Terry; Moussalli, Adnan; Bradford, Tessa; Gardner, Michael

2018-07-01

Characterisation of squamate major histocompatibility complex (MHC) genes has lagged behind other taxonomic groups. MHC genes encode cell-surface glycoproteins that present self- and pathogen-derived peptides to T cells and play a critical role in pathogen recognition. Here we characterise MHC class I transcripts for an agamid lizard (Ctenophorus decresii) and investigate the evolution of MHC class I in Iguanian lizards. An iterative assembly strategy was used to identify six full-length C. decresii MHC class I transcripts, which were validated as likely to encode classical class I MHC molecules. Evidence for exon shuffling recombination was uncovered for C. decresii transcripts and Bayesian phylogenetic analysis of Iguanian MHC class I sequences revealed a pattern expected under a birth-and-death mode of evolution. This work provides a stepping stone towards further research on the agamid MHC class I region. Copyright © 2018 Elsevier Ltd. All rights reserved.

Patient acceptability and experiences of therapeutic switching of proton pump inhibitors within the National Preferred Drugs initiative in Ireland.

PubMed

O'Connor, G; O'Keeffe, D; Darker, C; O'Shea, B

2017-08-01

A 'Preferred Drugs' initiative was introduced into Ireland in 2013. This identified a single recommended drug to be prescribed to patients requiring treatment from a particular class of drugs. This study investigates how patients on established proton pump inhibitor (PPI) therapy experienced the therapeutic switching of their medication to the 'preferred drug', and the extent to which they regarded it as an acceptable practice. The experiences of 61 patients on established proton pump inhibitor (PPI) therapy were sought before and after their drug was switched to the 'preferred drug'. Eighty per cent of patients were happy to switch medications. When asked for their opinions on medications in general, 71% felt doctors should prescribe the least expensive medication, 84% agreed that all licensed medications were safe while 67% felt their GP changing medication for cost reasons was safe. After 8 weeks, 20% of patients had switched back to their old PPI. When asked how they felt about their medication change, 74% felt happy or pleased. The majority of patients in our study were satisfied to have their medication switched. However, prescribers should be mindful that 1 in 5 patients encountered problems as a result of the switching process.

Optical switch based on thermocapillarity

NASA Astrophysics Data System (ADS)

Sakata, Tomomi; Makihara, Mitsuhiro; Togo, Hiroyoshi; Shimokawa, Fusao; Kaneko, Kazumasa

2001-11-01

Space-division optical switches are essential for the protection, optical cross-connects (OXCs), and optical add/drop multiplexers (OADMs) needed in future fiber-optic communication networks. For applications in these areas, we proposed a thermocapillarity switch called oil-latching interfacial-tension variation effect (OLIVE) switch. An OLIVE switch is a micro-mechanical optical switch fabricated on planar lightwave circuits (PLC) using micro-electro-mechanical systems (MEMS) technology. It consists of a crossing waveguide that has a groove at each crossing point and a pair of microheaters. The groove is partially filled with the refractive-index-matching liquid, and optical signals are switched according to the liquid's position in the groove, i.e., whether it is passing straight through the groove or reflecting at the sidewall of the groove. The liquid is driven by thermocapillarity and latched by capillarity. Using the total internal reflection to switch the optical path, the OLIVE switch exhibits excellent optical characteristics, such as high transparency (insertion loss: < 2 dB), high extinction ratio (> 50 dB), and low crosstalk (< -50 dB). Moreover, since this switch has a simple structure and bi-stability, it has wide variety of applications in wavelength division multiplexing (WDM) networks.

Finite-time resilient decentralized control for interconnected impulsive switched systems with neutral delay.

PubMed

Ren, Hangli; Zong, Guangdeng; Hou, Linlin; Yang, Yi

2017-03-01

This paper is concerned with the problem of finite-time control for a class of interconnected impulsive switched systems with neutral delay in which the time-varying delay appears in both the state and the state derivative. The concepts of finite-time boundedness and finite-time stability are respectively extended to interconnected impulsive switched systems with neutral delay for the first time. By applying the average dwell time method, sufficient conditions are first derived to cope with the problem of finite-time boundedness and finite-time stability for interconnected impulsive switched systems with neutral delay. In addition, the purpose of finite-time resilient decentralized control is to construct a resilient decentralized state-feedback controller such that the closed-loop system is finite-time bounded and finite-time stable. All the conditions are formulated in terms of linear matrix inequalities to ensure finite-time boundedness and finite-time stability of the given system. Finally, an example is presented to illustrate the effectiveness of the proposed approach. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Plastic Transition to Switch Nonlinear Optical Properties Showing the Record High Contrast in a Single-Component Molecular Crystal.

PubMed

Sun, Zhihua; Chen, Tianliang; Liu, Xitao; Hong, Maochun; Luo, Junhua

2015-12-23

To switch bulk nonlinear optical (NLO) effects represents an exciting new branch of NLO material science, whereas it remains a great challenge to achieve high contrast for "on/off" of quadratic NLO effects in crystalline materials. Here, we report the supereminent NLO-switching behaviors of a single-component plastic crystal, 2-(hydroxymethyl)-2-nitro-1,3-propanediol (1), which shows a record high contrast of at least ∼150, exceeding all the known crystalline switches. Such a breakthrough is clearly elucidated from the slowing down of highly isotropic molecular motions during plastic-to-rigid transition. The deep understanding of its intrinsic plasticity and superior NLO property allows the construction of a feasible switching mechanism. As a unique class of substances with short-range disorder embedded in long-range ordered crystalline lattice, plastic crystals enable response to external stimuli and fulfill specific photoelectric functions, which open a newly conceptual avenue for the designing of new functional materials.

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.

Treatment switch guided by HIV-1 genotyping in Brazil.

PubMed

Tupinambás, Unaí; Ribeiro, Flávia Andrade; Aleixo, Agdemir; Greco, Dirceu

2006-04-01

We assessed the performance of HIV-1 genotyping tests in rescue therapy. Patients were divided into two groups: group 1 (genotyped), included those switching to new antiretroviral drugs based on HIV-1 genotyping data, and group 2 (standard of care -SOC), comprised those in rescue therapy who had not used this test. This was an open and non-randomized study, with 74 patients, followed up for a mean period of 12 months, from February 2002 to May 2003. The groups differed in the duration of antiretroviral use, experience with diverse drug classes (non-nucleoside reverse transcriptase inhibitors and protease inhibitors) and viral load <2.6 log10 copies/mL at any time during treatment. In 23 patients (group 1), the switch in antiretroviral (ARV) regimen was based on genotyping data; this test was not used for 51 patients (group 2). Two CD4 + lymphocyte counts and viral load counts were made for each patient during the study. Data from the pharmacy where patients received antiretroviral agents, medical charts, and direct interviews with patients to assess compliance to treatment, were analyzed. In the genotyped group, the average drop in viral load was 2.8 log10, compared with a 1.5 log10 difference in group 2; the difference was significant in the first assessment performed six months after switching (p=0.001). Considering the patients with viral load < 2.6 log10 (400 copies/mL) after switching, the patients in group 1 had a better performance in the first assessment (73.9% versus 31.1% in groups 1 and 2, respectively); this difference was significant (p=0.001). In multivariate analysis, the variables associated with a greater drop in viral load in the first assessment were the patients whose switching was based on genotyping (group 1), those with a past history of viral load < 2.6 log10 and correct use of antiretroviral agents. In conclusion, the genotyping test and adherence were found to be independent factors for success in the management of patients who failed

Apollo Ring Optical Switch

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Shark IgW C region diversification through RNA processing and isotype switching.

PubMed

Zhang, Cecilia; Du Pasquier, Louis; Hsu, Ellen

2013-09-15

Sharks and skates represent the earliest vertebrates with an adaptive immune system based on lymphocyte Ag receptors generated by V(D)J recombination. Shark B cells express two classical Igs, IgM and IgW, encoded by an early, alternative gene organization consisting of numerous autonomous miniloci, where the individual gene cluster carries a few rearranging gene segments and one C region, μ or ω. We have characterized eight distinct Ig miniloci encoding the nurse shark ω H chain. Each cluster consists of VH, D, and JH segments and six to eight C domain exons. Two interspersed secretory exons, in addition to the 3'-most C exon with tailpiece, provide the gene cluster with the ability to generate at least six secreted isoforms that differ as to polypeptide length and C domain combination. All clusters appear to be functional, as judged by the capability for rearrangement and absence of defects in the deduced amino acid sequence. We previously showed that IgW VDJ can perform isotype switching to μ C regions; in this study, we found that switching also occurs between ω clusters. Thus, C region diversification for any IgW VDJ can take place at the DNA level by switching to other ω or μ C regions, as well as by RNA processing to generate different C isoforms. The wide array of pathogens recognized by Abs requires different disposal pathways, and our findings demonstrate complex and unique pathways for C effector function diversity that evolved independently in cartilaginous fishes.

Electronic logic for enhanced switch reliability

DOEpatents

Cooper, J.A.

1984-01-20

A logic circuit is used to enhance redundant switch reliability. Two or more switches are monitored for logical high or low output. The output for the logic circuit produces a redundant and fail-safe representation of the switch outputs. When both switch outputs are high, the output is high. Similarly, when both switch outputs are low, the logic circuit's output is low. When the output states of the two switches do not agree, the circuit resolves the conflict by memorizing the last output state which both switches were simultaneously in and produces the logical complement of this output state. Thus, the logic circuit of the present invention allows the redundant switches to be treated as if they were in parallel when the switches are open and as if they were in series when the switches are closed. A failsafe system having maximum reliability is thereby produced.

Construction of large scale switch matrix by interconnecting integrated optical switch chips with EDFAs

NASA Astrophysics Data System (ADS)

Liao, Mingle; Wu, Baojian; Hou, Jianhong; Qiu, Kun

2018-03-01

Large scale optical switches are essential components in optical communication network. We aim to build up a large scale optical switch matrix by the interconnection of silicon-based optical switch chips using 3-stage CLOS structure, where EDFAs are needed to compensate for the insertion loss of the chips. The optical signal-to-noise ratio (OSNR) performance of the resulting large scale optical switch matrix is investigated for TE-mode light and the experimental results are in agreement with the theoretical analysis. We build up a 64 ×64 switch matrix by use of 16 ×16 optical switch chips and the OSNR and receiver sensibility can respectively be improved by 0.6 dB and 0.2 dB by optimizing the gain configuration of the EDFAs.

Prediction of recombinant protein overexpression in Escherichia coli using a machine learning based model (RPOLP).

PubMed

Habibi, Narjeskhatoon; Norouzi, Alireza; Mohd Hashim, Siti Z; Shamsir, Mohd Shahir; Samian, Razip

2015-11-01

Recombinant protein overexpression, an important biotechnological process, is ruled by complex biological rules which are mostly unknown, is in need of an intelligent algorithm so as to avoid resource-intensive lab-based trial and error experiments in order to determine the expression level of the recombinant protein. The purpose of this study is to propose a predictive model to estimate the level of recombinant protein overexpression for the first time in the literature using a machine learning approach based on the sequence, expression vector, and expression host. The expression host was confined to Escherichia coli which is the most popular bacterial host to overexpress recombinant proteins. To provide a handle to the problem, the overexpression level was categorized as low, medium and high. A set of features which were likely to affect the overexpression level was generated based on the known facts (e.g. gene length) and knowledge gathered from related literature. Then, a representative sub-set of features generated in the previous objective was determined using feature selection techniques. Finally a predictive model was developed using random forest classifier which was able to adequately classify the multi-class imbalanced small dataset constructed. The result showed that the predictive model provided a promising accuracy of 80% on average, in estimating the overexpression level of a recombinant protein. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bowl Inversion and Electronic Switching of Buckybowls on Gold.

PubMed

Fujii, Shintaro; Ziatdinov, Maxim; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kiguchi, Manabu

2016-09-21

Bowl-shaped π-conjugated compounds, or buckybowls, are a novel class of sp(2)-hybridized nanocarbon materials. In contrast to tubular carbon nanotubes and ball-shaped fullerenes, the buckybowls feature structural flexibility. Bowl-to-bowl structural inversion is one of the unique properties of the buckybowls in solutions. Bowl inversion on a surface modifies the metal-molecule interactions through bistable switching between bowl-up and bowl-down states on the surface, which makes surface-adsorbed buckybowls a relevant model system for elucidation of the mechano-electronic properties of nanocarbon materials. Here, we report a combination of scanning tunneling microscopy (STM) measurements and ab initio atomistic simulations to identify the adlayer structure of the sumanene buckybowl on Au(111) and reveal its unique bowl inversion behavior. We demonstrate that the bowl inversion can be induced by approaching the STM tip toward the molecule. By tuning the local metal-molecule interaction using the STM tip, the sumanene buckybowl exhibits structural bistability with a switching rate that is two orders of magnitude faster than that of the stochastic inversion process.

Co-evolution with chicken class I genes.

PubMed

Kaufman, Jim

2015-09-01

The concept of co-evolution (or co-adaptation) has a long history, but application at molecular levels (e.g., 'supergenes' in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I-like genes, only two classical class I genes, two CD1 genes and some non-classical Rfp-Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co-evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co-evolution with TAP and class I genes remains unclear. T-cell receptors, natural killer (NK) cell receptors, and CD8 co-receptor genes are found on non-MHC chromosomes, with some evidence for co-evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co-evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen-processing genes in the primordial MHC. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Asynchronous State Estimation for Discrete-Time Switched Complex Networks With Communication Constraints.

PubMed

Zhang, Dan; Wang, Qing-Guo; Srinivasan, Dipti; Li, Hongyi; Yu, Li

2018-05-01

This paper is concerned with the asynchronous state estimation for a class of discrete-time switched complex networks with communication constraints. An asynchronous estimator is designed to overcome the difficulty that each node cannot access to the topology/coupling information. Also, the event-based communication, signal quantization, and the random packet dropout problems are studied due to the limited communication resource. With the help of switched system theory and by resorting to some stochastic system analysis method, a sufficient condition is proposed to guarantee the exponential stability of estimation error system in the mean-square sense and a prescribed performance level is also ensured. The characterization of the desired estimator gains is derived in terms of the solution to a convex optimization problem. Finally, the effectiveness of the proposed design approach is demonstrated by a simulation example.

Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.

PubMed

Cowley, Lauren A; Petersen, Fernanda C; Junges, Roger; Jimson D Jimenez, Med; Morrison, Donald A; Hanage, William P

2018-06-01

Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important in the adaptation and evolution of this pathogen. While competent pneumococci are able to scavenge DNA added to laboratory cultures, large-scale transfers of multiple kb are rare under these conditions. We used whole genome sequencing (WGS) to map transfers in recombinants arising from contact of competent cells with non-competent 'target' cells, using strains with known genomes, distinguished by a total of ~16,000 SNPs. Experiments designed to explore the effect of environment on large scale recombination events used saturating purified donor DNA, short-term cell assemblages on Millipore filters, and mature biofilm mixed cultures. WGS of 22 recombinants for each environment mapped all SNPs that were identical between the recombinant and the donor but not the recipient. The mean recombination event size was found to be significantly larger in cell-to-cell contact cultures (4051 bp in filter assemblage and 3938 bp in biofilm co-culture versus 1815 bp with saturating DNA). Up to 5.8% of the genome was transferred, through 20 recombination events, to a single recipient, with the largest single event incorporating 29,971 bp. We also found that some recombination events are clustered, that these clusters are more likely to occur in cell-to-cell contact environments, and that they cause significantly increased linkage of genes as far apart as 60,000 bp. We conclude that pneumococcal evolution through homologous recombination is more likely to occur on a larger scale in environments that permit cell-to-cell contact.

Switching Phenomena

NASA Astrophysics Data System (ADS)

Stanley, H. E.; Buldyrev, S. V.; Franzese, G.; Havlin, S.; Mallamace, F.; Mazza, M. G.; Kumar, P.; Plerou, V.; Preis, T.; Stokely, K.; Xu, L.

One challenge of biology, medicine, and economics is that the systems treated by these serious scientific disciplines can suddenly "switch" from one behavior to another, even though they possess no perfect metronome in time. As if by magic, out of nothing but randomness one finds remarkably fine-tuned processes in time. The past century has, philosophically, been concerned with placing aside the human tendency to see the universe as a fine-tuned machine. Here we will address the challenge of uncovering how, through randomness (albeit, as we shall see, strongly correlated randomness), one can arrive at some of the many temporal patterns in physics, economics, and medicine and even begin to characterize the switching phenomena that enable a system to pass from one state to another. We discuss some applications of correlated randomness to understanding switching phenomena in various fields. Specifically, we present evidence from experiments and from computer simulations supporting the hypothesis that water's anomalies are related to a switching point (which is not unlike the "tipping point" immortalized by Malcolm Gladwell), and that the bubbles in economic phenomena that occur on all scales are not "outliers" (another Gladwell immortalization).

The Cosmology Large Angular Scale Surveyor (CLASS)

NASA Technical Reports Server (NTRS)

Harrington, Kathleen; Marriange, Tobias; Aamir, Ali; Appel, John W.; Bennett, Charles L.; Boone, Fletcher; Brewer, Michael; Chan, Manwei; Chuss, David T.; Colazo, Felipe;

Working memory costs of task switching.

PubMed

Liefooghe, Baptist; Barrouillet, Pierre; Vandierendonck, André; Camos, Valérie

2008-05-01

Although many accounts of task switching emphasize the importance of working memory as a substantial source of the switch cost, there is a lack of evidence demonstrating that task switching actually places additional demands on working memory. The present study addressed this issue by implementing task switching in continuous complex span tasks with strictly controlled time parameters. A series of 4 experiments demonstrate that recall performance decreased as a function of the number of task switches and that the concurrent load of item maintenance had no influence on task switching. These results indicate that task switching induces a cost on working memory functioning. Implications for theories of task switching, working memory, and resource sharing are addressed.

First principles investigation of the unipolar resistive switching mechanism in an interfacial phase change memory based on a GeTe/Sb2Te3 superlattice

NASA Astrophysics Data System (ADS)

Shirakawa, Hiroki; Araidai, Masaaki; Shiraishi, Kenji

2018-04-01

The interfacial phase change memory (iPCM) based on a GeTe/Sb2Te3 superlattice is one of the candidates for future storage class memories. However, the atomic structures of the high and low resistance states (HRS/LRS) remain unclear and the resistive switching mechanism is still under debate. Clarifying the switching mechanism is essential for developing further high-reliability and low-power-consumption iPCM. We propose, on the basis of the results of first-principles molecular dynamics simulations, a mechanism for resistive switching, and describe the atomic structures of the high and low resistance states of iPCM for unipolar switching. Our simulations indicated that switching from HRS to LRS occurs with Joule heating only, while that from LRS to HRS occurs with both hole injection and Joule heating.

Optical switching using IP protocol

NASA Astrophysics Data System (ADS)

Utreras, Andres J.; Gusqui, Luis; Reyes, Andres; Mena, Ricardo I.; Licenko, Gennady L.; Amirgaliyev, Yedilkhan; Komada, Paweł; Luganskaya, Saule; Kashaganova, Gulzhan

2017-08-01

To understand and evaluate the Optical Layer, and how it will affect the IP protocols over WDM (Switching), the present analyse is proposed. Optical communications have attractive proprieties, but also have some disadvantages, so the challenge is to combine the best of both branches. In this paper, general concepts for different options of switching are reviewed as: optical burst switching (OBS) and automatically switching optical network (ASON). Specific details such as their architectures are also discussed. In addition, the relevant characteristics of each variation for switching are reviewed.

Complementary resistive switching in BaTiO3/NiO bilayer with opposite switching polarities

NASA Astrophysics Data System (ADS)

Li, Shuo; Wei, Xianhua; Lei, Yao; Yuan, Xincai; Zeng, Huizhong

2016-12-01

Resistive switching behaviors have been investigated in the Au/BaTiO3/NiO/Pt structure by stacking the two elements with different switching types. The conducting atomic force microscope measurements on BaTiO3 thin films and NiO thin films suggest that with the same active resistive switching region, the switching polarities in the two semiconductors are opposite to each other. It is in agreement with the bipolar hysteresis I-V curves with opposite switching polarities for single-layer devices. The bilayer devices show complementary resistive switching (CRS) without electroforming and unipolar resistive switching (URS) after electroforming. The coexistence of CRS and URS is mainly ascribed to the co-effect of electric field and Joule heating mechanisms, indicating that changeable of resistance in this device is dominated by the redistribution of oxygen vacancies in BaTiO3 and the formation, disruption, restoration of conducting filaments in NiO. CRS in bilayer with opposite switching polarities is effective to solve the sneak current without the introduction of any selector elements or an additional metal electrode.

Regulation of Meiotic Recombination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory p. Copenhaver

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 diversemore » 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

Hybrid switch for resonant power converters

DOEpatents

Lai, Jih-Sheng; Yu, Wensong

2014-09-09

A hybrid switch comprising two semiconductor switches connected in parallel but having different voltage drop characteristics as a function of current facilitates attainment of zero voltage switching and reduces conduction losses to complement reduction of switching losses achieved through zero voltage switching in power converters such as high-current inverters.

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.

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.

Switching from an oral dopamine receptor agonist to rotigotine transdermal patch: a review of clinical data with a focus on patient perspective.

PubMed

Chung, Sun Ju; Asgharnejad, Mahnaz; Bauer, Lars; Benitez, Arturo; Boroojerdi, Babak; Heidbrede, Tanja; Little, Allison; Kim, Han Joon

2017-07-01

Dopamine receptor agonists (DAs) are commonly used to treat Parkinson's disease (PD) and restless legs syndrome (RLS). In certain situations, switching from oral DAs to rotigotine transdermal patch may be beneficial for the patient (e.g., optimal symptom control/side effects/perioperative management, preference for once-daily/non-oral administration, RLS augmentation treatment). Areas covered: This narrative review summarizes available data on DA dose equivalency, dose conversions, switching schedules, safety, tolerability, efficacy and patient treatment preferences of switching from oral DAs to rotigotine (and vice versa) in patients with PD/RLS. The studies were identified in a PubMed search (up to 8 November 2016) using terms ('dopamine receptor agonist' OR 'rotigotine') AND 'switch'. Expert commentary: Randomized controlled studies often do not address the challenges clinicians face in practice, e.g., switching medications within the same class when dosing is not a one-to-one ratio. The authors describe three open-label studies in PD where oral DAs were successfully switched to rotigotine, and review three studies in RLS where oral DAs/levodopa were switched to rotigotine. Finally, the authors provide a suggested tool for switching from oral DAs to rotigotine, which includes dose conversion factors and switching schedules. The authors' view is that low-dose oral DAs (equivalent to ≤8 mg/24 h rotigotine) may be switched overnight.

Development of a Glycoprotein D-Expressing Dominant-Negative and Replication-Defective Herpes Simplex Virus 2 (HSV-2) Recombinant Viral Vaccine against HSV-2 Infection in Mice ▿

PubMed Central

Akhrameyeva, Natalie V.; Zhang, Pengwei; Sugiyama, Nao; Behar, Samuel M.; Yao, Feng

2011-01-01

Using the T-REx (Invitrogen, California) gene switch technology and a dominant-negative mutant polypeptide of herpes simplex virus 1 (HSV-1)-origin binding protein UL9, we previously constructed a glycoprotein D-expressing replication-defective and dominant-negative HSV-1 recombinant viral vaccine, CJ9-gD, for protection against HSV infection and disease. It was demonstrated that CJ9-gD is avirulent following intracerebral inoculation in mice, cannot establish detectable latent infection following different routes of infection, and offers highly effective protective immunity against primary HSV-1 and HSV-2 infection and disease in mouse and guinea pig models of HSV infections. Given these favorable safety and immunological profiles of CJ9-gD, aiming to maximize levels of HSV-2 glycoprotein D (gD2) expression, we have constructed an ICP0 null mutant-based dominant-negative and replication-defective HSV-2 recombinant, CJ2-gD2, that contains 2 copies of the gD2 gene driven by the tetracycline operator (tetO)-bearing HSV-1 major immediate-early ICP4 promoter. CJ2-gD2 expresses gD2 as efficiently as wild-type HSV-2 infection and can lead to a 150-fold reduction in wild-type HSV-2 viral replication in cells coinfected with CJ2-gD2 and wild-type HSV-2 at the same multiplicity of infection. CJ2-gD2 is avirulent following intracerebral injection and cannot establish a detectable latent infection following subcutaneous (s.c.) immunization. CJ2-gD2 is a more effective vaccine than HSV-1 CJ9-gD and a non-gD2-expressing dominant-negative and replication-defective HSV-2 recombinant in protection against wild-type HSV-2 genital disease. Using recall response, we showed that immunization with CJ2-gD2 elicited strong HSV-2-specific memory CD4+ and CD8+ T-cell responses. Collectively, given the demonstrated preclinical immunogenicity and its unique safety profiles, CJ2-gD2 represents a new class of HSV-2 replication-defective recombinant viral vaccines in protection against HSV-2

Recombinant modified vaccinia virus Ankara–simian immunodeficiency virus gag pol elicits cytotoxic T lymphocytes in rhesus monkeys detected by a major histocompatibility complex class I/peptide tetramer

PubMed Central

Seth, Aruna; Ourmanov, Ilnour; Kuroda, Marcelo J.; Schmitz, Jörn E.; Carroll, Miles W.; Wyatt, Linda S.; Moss, Bernard; Forman, Meryl A.; Hirsch, Vanessa M.; Letvin, Norman L.

1998-01-01

The utility of modified vaccinia virus Ankara (MVA) as a vector for eliciting AIDS virus-specific cytotoxic T lymphocytes (CTL) was explored in the simian immunodeficiency virus (SIV)/rhesus monkey model. After two intramuscular immunizations with recombinant MVA-SIVSM gag pol, the monkeys developed a Gag epitope-specific CTL response readily detected in peripheral blood lymphocytes by using a functional killing assay. Moreover, those immunizations also elicited a population of CD8+ T lymphocytes in the peripheral blood that bound a specific major histocompatibility complex class I/peptide tetramer. These Gag epitope-specific CD8+ T lymphocytes also were demonstrated by using both functional and tetramer-binding assays in lymph nodes of the immunized monkeys. These observations suggest that MVA may prove a useful vector for an HIV-1 vaccine. They also suggest that tetramer staining may be a useful technology for monitoring CTL generation in vaccine trials in nonhuman primates and in humans. PMID:9707609

A Ferredoxin Disulfide Reductase Delivers Electrons to the Methanosarcina barkeri Class III Ribonucleotide Reductase

DOE PAGES

Wei, Yifeng; Li, Bin; Prakash, Divya; ...

2015-11-04

Two subtypes of class III anaerobic ribonucleotide reductases (RNRs) studied so far couple the reduction of ribonucleotides to the oxidation of formate, or the oxidation of NADPH via thioredoxin and thioredoxin reductase. Certain methanogenic archaea contain a phylogenetically distinct third subtype of class III RNR, with distinct active-site residues. Here we report the cloning and recombinant expression of the Methanosarcina barkeri class III RNR and show that the electrons required for ribonucleotide reduction can be delivered by a [4Fe-4S] protein ferredoxin disulfide reductase, and a conserved thioredoxin-like protein NrdH present in the RNR operon. The diversity of class III RNRsmore » reflects the diversity of electron carriers used in anaerobic metabolism« less

N-terminal processing of affinity-tagged recombinant proteins purified by IMAC procedures.

PubMed

Mooney, Jane T; Fredericks, Dale P; Christensen, Thorkild; Bruun Schiødt, Christine; Hearn, Milton T W

2015-07-01

The ability of a new class of metal binding tags to facilitate the purification of recombinant proteins, exemplified by the tagged glutathione S-transferase and human growth hormone, from Escherichia coli fermentation broths and lysates has been further investigated. These histidine-containing tags exhibit high affinity for borderline metal ions chelated to the immobilised ligand, 1,4,7-triazacyclononane (tacn). The use of this tag-tacn immobilised metal ion affinity chromatography (IMAC) system engenders high selectivity with regard to host cell protein removal and permits facile tag removal from the E. coli-expressed recombinant protein. In particular, these tags were specifically designed to enable their efficient removal by the dipeptidyl aminopeptidase 1 (DAP-1), thus capturing the advantages of high substrate specificity and rates of cleavage. MALDI-TOF MS analysis of the cleaved products from the DAP-1 digestion of the recombinant N-terminally tagged proteins confirmed the complete removal of the tag within 4-12 h under mild experimental conditions. Overall, this study demonstrates that the use of tags specifically designed to target tacn-based IMAC resins offers a comprehensive and flexible approach for the purification of E. coli-expressed recombinant proteins, where complete removal of the tag is an essential prerequisite for subsequent application of the purified native proteins in studies aimed at delineating the molecular and cellular basis of specific biological processes. Copyright © 2015 John Wiley & Sons, Ltd.

Age-related differences in BOLD modulation to cognitive control costs in a multitasking paradigm: Global switch, local switch, and compatibility-switch costs.

PubMed

Nashiro, Kaoru; Qin, Shuo; O'Connell, Margaret A; Basak, Chandramallika

2018-05-15

It is well documented that older adults recruit additional brain regions compared to those recruited by younger adults while performing a wide variety of cognitive tasks. However, it is unclear how such age-related over-recruitment interacts with different types of cognitive control, and whether this over-recruitment is compensatory. To test this, we used a multitasking paradigm, which allowed us to examine age-related over-activation associated with three types of cognitive costs (i.e., global switch, local switch, compatibility-switch costs). We found age-related impairments in global switch cost (GSC), evidenced by slower response times for maintaining and coordinating two tasks vs. performing only one task. However, no age-related declines were observed in either local switch cost (LSC), a cognitive cost associated with switching between the two tasks while maintaining two task loads, or compatibility-switch cost (CSC), a cognitive cost associated with incompatible vs. compatible stimulus-response mappings across the two tasks. The fMRI analyses allowed for identification of distinct cognitive cost-sensitive brain regions associated with GSC and LSC. In fronto-parietal GSC and LSC regions, older adults' increased activations were associated with poorer performance (greater costs), whereas a reverse relationship was observed in younger adults. Older adults also recruited additional fronto-parietal brain regions outside the cognitive cost-sensitive areas, which was associated with poorer performance or no behavioral benefits. Our results suggest that older adults exhibit a combination of inefficient activation within cognitive cost-sensitive regions, specifically the GSC and LSC regions, and non-compensatory over-recruitment in age-sensitive regions. Age-related declines in global switching, compared to local switching, was observed earlier in old age at both neural and behavioral levels. Copyright © 2018 Elsevier Inc. All rights reserved.

BRN2, a POUerful driver of melanoma phenotype switching and metastasis.

PubMed

Fane, Mitchell E; Chhabra, Yash; Smith, Aaron G; Sturm, Richard A

2018-05-21

The POU domain family of transcription factors play a central role in embryogenesis and are highly expressed in neural crest cells and the developing brain. BRN2 is a class III POU domain protein that is a key mediator of neuroendocrine and melanocytic development and differentiation. While BRN2 is a central regulator in numerous developmental programs, it has also emerged as a major player in the biology of tumourigenesis. In melanoma, BRN2 has been implicated as one of the master regulators of the acquisition of invasive behavior within the phenotype-switching model of progression. As a mediator of melanoma cell phenotype-switching it co-ordinates the transition to a de-differentiated, slow cycling and highly motile cell type. Its inverse expression relationship with MITF is believed to mediate tumour progression and metastasis within this model. Recent evidence has now outlined a potential epigenetic switching mechanism in melanoma cells driven by BRN2 expression that induces melanoma cell invasion. We summarise the role of BRN2 in tumour cell dissemination and metastasis in melanoma, while also examining it as a potential metastatic regulator in other tumour models. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Tutorial: Integrated-photonic switching structures

NASA Astrophysics Data System (ADS)

Soref, Richard

2018-02-01

Recent developments in waveguided 2 × 2 and N × M photonic switches are reviewed, including both broadband and narrowband resonant devices for the Si, InP, and AlN platforms. Practical actuation of switches by electro-optical and thermo-optical techniques is discussed. Present datacom-and-computing applications are reviewed, and potential applications are proposed for chip-scale photonic and optoelectronic integrated switching networks. Potential is found in the reconfigurable, programmable "mesh" switches that enable a promising group of applications in new areas beyond those in data centers and cloud servers. Many important matrix switches use gated semiconductor optical amplifiers. The family of broadband, directional-coupler 2 × 2 switches featuring two or three side-coupled waveguides deserves future experimentation, including devices that employ phase-change materials. The newer 2 × 2 resonant switches include standing-wave resonators, different from the micro-ring traveling-wave resonators. The resonant devices comprise nanobeam interferometers, complex-Bragg interferometers, and asymmetric contra-directional couplers. Although the fast, resonant devices offer ultralow switching energy, ˜1 fJ/bit, they have limitations. They require several trade-offs when deployed, but they do have practical application.

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.

Markov-switching multifractal models as another class of random-energy-like models in one-dimensional space

NASA Astrophysics Data System (ADS)

Saakian, David B.

2012-03-01

We map the Markov-switching multifractal model (MSM) onto the random energy model (REM). The MSM is, like the REM, an exactly solvable model in one-dimensional space with nontrivial correlation functions. According to our results, four different statistical physics phases are possible in random walks with multifractal behavior. We also introduce the continuous branching version of the model, calculate the moments, and prove multiscaling behavior. Different phases have different multiscaling properties.

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.

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.

Exploring the Potential of Smartphones and Tablets for Performance Support in Food Chemistry Laboratory Classes

NASA Astrophysics Data System (ADS)

van der Kolk, Koos; Hartog, Rob; Beldman, Gerrit; Gruppen, Harry

2013-12-01

Increasingly, mobile applications appear on the market that can support students in chemistry laboratory classes. In a multiple app-supported laboratory, each of these applications covers one use-case. In practice, this leads to situations in which information is scattered over different screens and written materials. Such a multiple app-supported laboratory will become awkward with the growth of the number of applications and use cases. In particular, using and switching between applications is likely to induce extraneous cognitive load that can easily be avoided. The manuscript describes the design of a prototype smartphone web app (LabBuddy) designed to support students in food chemistry laboratory classes. The manuscript describes a case study ( n = 26) of the use of a LabBuddy prototype in such a laboratory class. Based on the evaluation of this case study, design requirements for LabBuddy were articulated. LabBuddy should work on HTML5 capable devices, independent of screen size, by having a responsive layout. In addition, LabBuddy should enable a student using LabBuddy to switch between devices without much effort. Finally, LabBuddy should offer an integrated representation of information.

In vivo production of recombinant proteins using occluded recombinant AcMNPV-derived baculovirus vectors.

PubMed

Guijarro-Pardo, Eva; Gómez-Sebastián, Silvia; Escribano, José M

2017-12-01

Trichoplusia ni insect larvae infected with vectors derived from the Autographa californica multiple nucleopolyhedrovirus (AcMNPV), are an excellent alternative to insect cells cultured in conventional bioreactors to produce recombinant proteins because productivity and cost-efficiency reasons. However, there is still a lot of work to do to reduce the manual procedures commonly required in this production platform that limit its scalability. To increase the scalability of this platform technology, a current bottleneck to be circumvented in the future is the need of injection for the inoculation of larvae with polyhedrin negative baculovirus vectors (Polh-) because of the lack of oral infectivity of these viruses, which are commonly used for production in insect cell cultures. In this work we have developed a straightforward alternative to obtain orally infective vectors derived from AcMNPV and expressing recombinant proteins that can be administered to the insect larvae (Trichoplusia ni) by feeding, formulated in the insect diet. The approach developed was based on the use of a recombinant polyhedrin protein expressed by a recombinant vector (Polh+), able to co-occlude any recombinant Polh- baculovirus vector expressing a recombinant protein. A second alternative was developed by the generation of a dual vector co-expressing the recombinant polyhedrin protein and the foreign gene of interest to obtain the occluded viruses. Additionally, by the incorporation of a reporter gene into the helper Polh+ vector, it was possible the follow-up visualization of the co-occluded viruses infection in insect larvae and will help to homogenize infection conditions. By using these methodologies, the production of recombinant proteins in per os infected larvae, without manual infection procedures, was very similar in yield to that obtained by manual injection of recombinant Polh- AcMNPV-based vectors expressing the same proteins. However, further analyses will be required for a

K-Band Latching Switches

NASA Technical Reports Server (NTRS)

Piotrowski, W. S.; Raue, J. E.

1984-01-01

Design, development, and tests are described for two single-pole-double-throw latching waveguide ferrite switches: a K-band switch in WR-42 waveguide and a Ka-band switch in WR-28 waveguide. Both switches have structurally simple junctions, mechanically interlocked without the use of bonding materials; they are impervious to the effects of thermal, shock, and vibration stresses. Ferrite material for the Ka-band switch with a proper combination of magnetic and dielectric properties was available and resulted in excellent low loss, wideband performance. The high power handling requirement of the K-band switch limited the choice of ferrite to nickel-zinc compositions with adequate magnetic properties, but with too low relative dielectric constant. The relative dielectric constant determines the junction dimensions for given frequency responses. In this case the too low value unavoidably leads to a larger than optimum junction volume, increasing the insertion loss and restricting the operating bandwidth. Efforts to overcome the materials-related difficulties through the design of a composite junction with increased effective dielectric properties efforts to modify the relative dielectric constant of nickel-zinc ferrite are examined.

Optically triggered high voltage switch network and method for switching a high voltage

DOEpatents

El-Sharkawi, Mohamed A.; Andexler, George; Silberkleit, Lee I.

1993-01-19

An optically triggered solid state switch and method for switching a high voltage electrical current. A plurality of solid state switches (350) are connected in series for controlling electrical current flow between a compensation capacitor (112) and ground in a reactive power compensator (50, 50') that monitors the voltage and current flowing through each of three distribution lines (52a, 52b and 52c), which are supplying three-phase power to one or more inductive loads. An optical transmitter (100) controlled by the reactive power compensation system produces light pulses that are conveyed over optical fibers (102) to a switch driver (110') that includes a plurality of series connected optical triger circuits (288). Each of the optical trigger circuits controls a pair of the solid state switches and includes a plurality of series connected resistors (294, 326, 330, and 334) that equalize or balance the potential across the plurality of trigger circuits. The trigger circuits are connected to one of the distribution lines through a trigger capacitor (340). In each switch driver, the light signals activate a phototransistor (300) so that an electrical current flows from one of the energy reservoir capacitors through a pulse transformer (306) in the trigger circuit, producing gate signals that turn on the pair of serially connected solid state switches (350).

Software Defined Networking (SDN) controlled all optical switching networks with multi-dimensional switching architecture

NASA Astrophysics Data System (ADS)

Zhao, Yongli; Ji, Yuefeng; Zhang, Jie; Li, Hui; Xiong, Qianjin; Qiu, Shaofeng

2014-08-01

Ultrahigh throughout capacity requirement is challenging the current optical switching nodes with the fast development of data center networks. Pbit/s level all optical switching networks need to be deployed soon, which will cause the high complexity of node architecture. How to control the future network and node equipment together will become a new problem. An enhanced Software Defined Networking (eSDN) control architecture is proposed in the paper, which consists of Provider NOX (P-NOX) and Node NOX (N-NOX). With the cooperation of P-NOX and N-NOX, the flexible control of the entire network can be achieved. All optical switching network testbed has been experimentally demonstrated with efficient control of enhanced Software Defined Networking (eSDN). Pbit/s level all optical switching nodes in the testbed are implemented based on multi-dimensional switching architecture, i.e. multi-level and multi-planar. Due to the space and cost limitation, each optical switching node is only equipped with four input line boxes and four output line boxes respectively. Experimental results are given to verify the performance of our proposed control and switching architecture.

Optically Driven Q-Switches For Lasers

NASA Technical Reports Server (NTRS)

Hemmati, Hamid

1994-01-01

Optically driven Q-switches for pulsed lasers proposed, taking place of acousto-optical, magneto-optical, and electro-optical switches. Optical switching beams of proposed Q-switching most likely generated in pulsed diode lasers or light-emitting diodes, outputs of which are amplitude-modulated easily by direct modulation of relatively small input currents. Energy efficiencies exceed those of electrically driven Q-switches.

A Repeated Trajectory Class Model for Intensive Longitudinal Categorical Outcome

PubMed Central

Lin, Haiqun; Han, Ling; Peduzzi, Peter N.; Murphy, Terrence E.; Gill, Thomas M.; Allore, Heather G.

2014-01-01

This paper presents a novel repeated latent class model for a longitudinal response that is frequently measured as in our prospective study of older adults with monthly data on activities of daily living (ADL) for more than ten years. The proposed method is especially useful when the longitudinal response is measured much more frequently than other relevant covariates. The repeated trajectory classes represent distinct temporal patterns of the longitudinal response wherein an individual’s membership in the trajectory classes may renew or change over time. Within a trajectory class, the longitudinal response is modeled by a class-specific generalized linear mixed model. Effectively, an individual may remain in a trajectory class or switch to another as the class membership predictors are updated periodically over time. The identification of a common set of trajectory classes allows changes among the temporal patterns to be distinguished from local fluctuations in the response. An informative event such as death is jointly modeled by class-specific probability of the event through shared random effects. We do not impose the conditional independence assumption given the classes. The method is illustrated by analyzing the change over time in ADL trajectory class among 754 older adults with 70500 person-months of follow-up in the Precipitating Events Project. We also investigate the impact of jointly modeling the class-specific probability of the event on the parameter estimates in a simulation study. The primary contribution of our paper is the periodic updating of trajectory classes for a longitudinal categorical response without assuming conditional independence. PMID:24519416

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.

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

Non-coding RNA generated following lariat-debranching mediates targeting of AID to DNA

PubMed Central

Zheng, Simin; Vuong, Bao Q.; Vaidyanathan, Bharat; Lin, Jia-Yu; Huang, Feng-Ting; Chaudhuri, Jayanta

2015-01-01

SUMMARY Transcription through immunoglobulin switch (S) regions is essential for class switch recombination (CSR) but no molecular function of the transcripts has been described. Likewise, recruitment of activation-induced cytidine deaminase (AID) to S regions is critical for CSR; however, the underlying mechanism has not been fully elucidated. Here, we demonstrate that intronic switch RNA acts in trans to target AID to S region DNA. AID binds directly to switch RNA through G-quadruplexes formed by the RNA molecules. Disruption of this interaction by mutation of a key residue in the putative RNA-binding domain of AID impairs recruitment of AID to S region DNA, thereby abolishing CSR. Additionally, inhibition of RNA lariat processing leads to loss of AID localization to S regions and compromises CSR; both defects can be rescued by exogenous expression of switch transcripts in a sequence-specific manner. These studies uncover an RNA-mediated mechanism of targeting AID to DNA. PMID:25957684

Chimeric switch receptor: switching for improved adoptive T-cell therapy against cancers.

PubMed

Tay, Johan Ck; Zha, Shijun; Wang, Shu

2017-12-01

Adoptive T-lymphocyte transfer-based immunotherapy for cancers has seen huge leaps with both CARs and engineered TCRs. Despite this, issues relating to safety and efficacy persist. To address this, chimeric switch receptors have been created to reverse the outcomes of their original signaling pathways in order to confer immune cells with the ability to overcome the immunosuppressive tumor microenvironment and to allow them to have greater in vivo persistence. Activating switch receptors exploit the inhibitory molecules expressed by cancer cells to further stimulate the tumor antigen-specific T lymphocytes. On the other hand, inhibitory switch receptors inhibit the effects of tumor-reactive T lymphocytes on unintended targets. This paper reviews the switch receptors reported thus far, and lists out potential improvements and future works.

Electro-optic Q-switch

NASA Technical Reports Server (NTRS)

Zou, Yingyin (Inventor); Chen, Qiushui (Inventor); Zhang, Run (Inventor); Jiang, Hua (Inventor)

2006-01-01

An electro-optic Q-switch for generating sequence of laser pulses was disclosed. The Q-switch comprises a quadratic electro-optic material and is connected with an electronic unit generating a radio frequency wave with positive and negative pulses alternatively. The Q-switch is controlled by the radio frequency wave in such a way that laser pulse is generated when the radio frequency wave changes its polarity.

Adaptive Neural Tracking Control for Switched High-Order Stochastic Nonlinear Systems.

PubMed

Zhao, Xudong; Wang, Xinyong; Zong, Guangdeng; Zheng, Xiaolong

2017-10-01

This paper deals with adaptive neural tracking control design for a class of switched high-order stochastic nonlinear systems with unknown uncertainties and arbitrary deterministic switching. The considered issues are: 1) completely unknown uncertainties; 2) stochastic disturbances; and 3) high-order nonstrict-feedback system structure. The considered mathematical models can represent many practical systems in the actual engineering. By adopting the approximation ability of neural networks, common stochastic Lyapunov function method together with adding an improved power integrator technique, an adaptive state feedback controller with multiple adaptive laws is systematically designed for the systems. Subsequently, a controller with only two adaptive laws is proposed to solve the problem of over parameterization. Under the designed controllers, all the signals in the closed-loop system are bounded-input bounded-output stable in probability, and the system output can almost surely track the target trajectory within a specified bounded error. Finally, simulation results are presented to show the effectiveness of the proposed approaches.

Investigation of resistance switching in SiO x RRAM cells using a 3D multi-scale kinetic Monte Carlo simulator

NASA Astrophysics Data System (ADS)

Sadi, Toufik; Mehonic, Adnan; Montesi, Luca; Buckwell, Mark; Kenyon, Anthony; Asenov, Asen

2018-02-01

We employ an advanced three-dimensional (3D) electro-thermal simulator to explore the physics and potential of oxide-based resistive random-access memory (RRAM) cells. The physical simulation model has been developed recently, and couples a kinetic Monte Carlo study of electron and ionic transport to the self-heating phenomenon while accounting carefully for the physics of vacancy generation and recombination, and trapping mechanisms. The simulation framework successfully captures resistance switching, including the electroforming, set and reset processes, by modeling the dynamics of conductive filaments in the 3D space. This work focuses on the promising yet less studied RRAM structures based on silicon-rich silica (SiO x ) RRAMs. We explain the intrinsic nature of resistance switching of the SiO x layer, analyze the effect of self-heating on device performance, highlight the role of the initial vacancy distributions acting as precursors for switching, and also stress the importance of using 3D physics-based models to capture accurately the switching processes. The simulation work is backed by experimental studies. The simulator is useful for improving our understanding of the little-known physics of SiO x resistive memory devices, as well as other oxide-based RRAM systems (e.g. transition metal oxide RRAMs), offering design and optimization capabilities with regard to the reliability and variability of memory cells.

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.

Gain and Efficiency of a Superconducting Microwave Compressor with a Switching Cavity in an Interference Switch

NASA Astrophysics Data System (ADS)

Artemenko, S. N.; Samoylenko, G. M.

2016-11-01

We study the processes of radiation output from a microwave storage cavity through a superconducting interference switch, which is based on a H-junction with a superconducting switching cavity connected to the side branch of the junction for various ways of controlling the parameters of the switching cavity. It is shown that efficient control over radiation output in such a switch can be achieved by varying the resonance frequency or Q-factor of the switching cavity, as well as by varying these parameters simultaneously. It is found that in the case of controlling the resonance frequency of the switching cavity, there exists an optimal interval of the frequency variation, within which the total efficiency and extraction efficiency are maximum. When the Q-factor of the switching cavity changes, the dependence of the total efficiency and extraction efficiency on the Q-factor has the monotonic character. The mixed regime of radiation output control is also studied. The envelopes of the output compressor pulses are plotted on the basis of recurrent relationships between the amplitudes of the waves in the system for three regimes of switch operation. It is shown that pulses with an almost rectangular shape of the envelope can be formed in the regime of controlling the switching cavity by varying the Q-factor. An example of possible realization of the switching cavity is considered.

Delayed avalanche breakdown of high-voltage silicon diodes: Various structures exhibit different picosecond-range switching behavior

NASA Astrophysics Data System (ADS)

Brylevskiy, Viktor; Smirnova, Irina; Gutkin, Andrej; Brunkov, Pavel; Rodin, Pavel; Grekhov, Igor

2017-11-01

We present a comparative study of silicon high-voltage diodes exhibiting the effect of delayed superfast impact-ionization breakdown. The effect manifests itself in a sustainable picosecond-range transient from the blocking to the conducting state and occurs when a steep voltage ramp is applied to the p+-n-n+ diode in the reverse direction. Nine groups of diodes with graded and abrupt pn-junctions have been specially fabricated for this study by different techniques from different Si substrates. Additionally, in two groups of these structures, the lifetime of nonequilibrium carriers was intentionally reduced by electron irradiation. All diodes have identical geometrical parameters and similar stationary breakdown voltages. Our experimental setup allows measuring both device voltage and current during the kilovolt switching with time resolution better than 50 ps. Although all devices are capable of forming a front with kilovolt amplitude and 100 ps risetime in the in-series load, the structures with graded pn-junctions have anomalously large residual voltage. The Deep Level Transient Spectroscopy study of all diode structures has been performed in order to evaluate the effect of deep centers on device performance. It was found that the presence of deep-level electron traps negatively correlates with parameters of superfast switching, whereas a large concentration of recombination centers created by electron irradiation has virtually no influence on switching characteristics.

Quantum dot single-photon switches of resonant tunneling current for discriminating-photon-number detection.

PubMed

Weng, Qianchun; An, Zhenghua; Zhang, Bo; Chen, Pingping; Chen, Xiaoshuang; Zhu, Ziqiang; Lu, Wei

2015-03-23

Low-noise single-photon detectors that can resolve photon numbers are used to monitor the operation of quantum gates in linear-optical quantum computation. Exactly 0, 1 or 2 photons registered in a detector should be distinguished especially in long-distance quantum communication and quantum computation. Here we demonstrate a photon-number-resolving detector based on quantum dot coupled resonant tunneling diodes (QD-cRTD). Individual quantum-dots (QDs) coupled closely with adjacent quantum well (QW) of resonant tunneling diode operate as photon-gated switches- which turn on (off) the RTD tunneling current when they trap photon-generated holes (recombine with injected electrons). Proposed electron-injecting operation fills electrons into coupled QDs which turn "photon-switches" to "OFF" state and make the detector ready for multiple-photons detection. With proper decision regions defined, 1-photon and 2-photon states are resolved in 4.2 K with excellent propabilities of accuracy of 90% and 98% respectively. Further, by identifying step-like photon responses, the photon-number-resolving capability is sustained to 77 K, making the detector a promising candidate for advanced quantum information applications where photon-number-states should be accurately distinguished.

The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End Joining Pathway

PubMed Central

Lieber, Michael R.

2011-01-01

Double-strand DNA breaks are common events in eukaryotic cells, and there are two major pathways for repairing them: homologous recombination and nonhomologous DNA end joining (NHEJ). The diverse causes of DSBs result in a diverse chemistry of DNA ends that must be repaired. Across NHEJ evolution, the enzymes of the NHEJ pathway exhibit a remarkable degree of structural tolerance in the range of DNA end substrate configurations upon which they can act. In vertebrate cells, the nuclease, polymerases and ligase of NHEJ are the most mechanistically flexible and multifunctional enzymes in each of their classes. Unlike repair pathways for more defined lesions, NHEJ repair enzymes act iteratively, act in any order, and can function independently of one another at each of the two DNA ends being joined. NHEJ is critical not only for the repair of pathologic DSBs as in chromosomal translocations, but also for the repair of physiologic DSBs created during V(D)J recombination and class switch recombination. Therefore, patients lacking normal NHEJ are not only sensitive to ionizing radiation, but also severely immunodeficient. PMID:20192759

Submicrosecond Power-Switching Test Circuit

NASA Technical Reports Server (NTRS)

Folk, Eric N.

2006-01-01

A circuit that changes an electrical load in a switching time shorter than 0.3 microsecond has been devised. This circuit can be used in testing the regulation characteristics of power-supply circuits . especially switching power-converter circuits that are supposed to be able to provide acceptably high degrees of regulation in response to rapid load transients. The combination of this power-switching circuit and a known passive constant load could be an attractive alternative to a typical commercially available load-bank circuit that can be made to operate in nominal constant-voltage, constant-current, and constant-resistance modes. The switching provided by a typical commercial load-bank circuit in the constant-resistance mode is not fast enough for testing of regulation in response to load transients. Moreover, some test engineers do not trust the test results obtained when using commercial load-bank circuits because the dynamic responses of those circuits are, variously, partly unknown and/or excessively complex. In contrast, the combination of this circuit and a passive constant load offers both rapid switching and known (or at least better known) load dynamics. The power-switching circuit (see figure) includes a signal-input section, a wide-hysteresis Schmitt trigger that prevents false triggering in the event of switch-contact bounce, a dual-bipolar-transistor power stage that drives the gate of a metal oxide semiconductor field-effect transistor (MOSFET), and the MOSFET, which is the output device that performs the switching of the load. The MOSFET in the specific version of the circuit shown in the figure is rated to stand off a potential of 100 V in the "off" state and to pass a current of 20 A in the "on" state. The switching time of this circuit (the characteristic time of rise or fall of the potential at the drain of the MOSFET) is .300 ns. The circuit can accept any of three control inputs . which one depending on the test that one seeks to perform: a