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Sample records for cp motif affects

  1. CpG oligodeoxynucleotides containing GACGTT motifs enhance the immune responses elicited by a goose parvovirus vaccine in ducks.

    Science.gov (United States)

    Lee, Jai-Wei; Lin, Yu-Ming; Yen, Ting-Ying; Yang, Wen-Jen; Chu, Chun-Yen

    2010-11-23

    Recombinant parvovirus VP2 (rVP2) was formulated with different types of adjuvant, including aluminum adjuvant and CpG oligodeoxynucleotides (ODNs), and the immunological responses after vaccination in ducks were examined. In comparison with the control group, production of rVP2-specific antibodies, expression of cytokines in peripheral blood mononuclear cells (PBMC) stimulated by rVP2, and percentage of CD4(+)/CD8(+) cells in PBMC were significantly increased in ducks immunized with rVP2 formulated with CpG ODNs containing 3 copies of GACGTT motif. CpG ODNs with GACGTT motifs might be used to improve the efficacy of vaccines for ducks. Copyright © 2010 Elsevier Ltd. All rights reserved.

  2. Activity of the rat osteocalcin basal promoter in osteoblastic cells is dependent upon homeodomain and CP1 binding motifs.

    Science.gov (United States)

    Towler, D A; Bennett, C D; Rodan, G A

    1994-05-01

    A detailed analysis of the transcriptional machinery responsible for osteoblast-specific gene expression should provide tools useful for understanding osteoblast commitment and differentiation. We have defined three cis-elements important for basal activity of the rat osteocalcin (OC) promoter, located at about -200 to -180, -170 to -138, and -121 to -64 relative to the transcription initiation site. A motif (TCTGATTGTGT) present in the region between -200 and -170 that binds a multisubunit CP1/NFY/CBF-like CAAT factor complex contributes significantly to high level basal activity and presumably functions as the CAAT box for the rat OC promoter. We show that the region -121 to 32 is sufficient to confer osteoblastic cell type specificity in transient transfection assays of cultured cell lines using luciferase as a reporter. The basal promoter is active in rodent osteoblastic cell lines, but not in rodent fibroblastic or muscle cell lines. Although the rat OC box (-100 to -74) contains a CAAT motif, we could not detect CP1-like CAAT factor binding to this region. In fact, we demonstrate that a Msx-1 (Hox 7.1) homeodomain binding motif (ACTAATTG; bottom strand) in the 3'-end of the rat OC box is necessary for high level activity of the rat OC basal promoter in osteoblastic cells. A nuclear factor that recognizes this motif appears to be present in osteoblastic ROS 17/2.8 cells, which produce OC, but not in fibroblastic ROS 25/1 cells, which fail to express OC. This ROS 17/2.8 nuclear factor also recognizes the A/T-rich DNA cognates of the homeodomain-containing POU family of transcription factors. Taken together, these data suggest that a ubiquitous CP1-like CAAT factor and a cell type-restricted homeodomain containing (Msx or POU family) transcription factor interact with the proximal rat OC promoter to direct appropriate basal OC transcription in osteoblastic cells.

  3. Improvement of the Immunogenicity of Porcine Circovirus Type 2 DNA Vaccine by Recombinant ORF2 Gene and CpG Motifs.

    Science.gov (United States)

    Li, Jun; Shi, Jian-Li; Wu, Xiao-Yan; Fu, Fang; Yu, Jiang; Yuan, Xiao-Yuan; Peng, Zhe; Cong, Xiao-Yan; Xu, Shao-Jian; Sun, Wen-Bo; Cheng, Kai-Hui; Du, Yi-Jun; Wu, Jia-Qiang; Wang, Jin-Bao; Huang, Bao-Hua

    2015-06-01

    Nowadays, adjuvant is still important for boosting immunity and improving resistance in animals. In order to boost the immunity of porcine circovirus type 2 (PCV2) DNA vaccine, CpG motifs were inserted. In this study, the dose-effect was studied, and the immunity of PCV2 DNA vaccines by recombinant open reading frame 2 (ORF2) gene and CpG motifs was evaluated. Three-week-old Changbai piglets were inoculated intramuscularly with 200 μg, 400 μg, and 800 μg DNA vaccines containing 14 and 18 CpG motifs, respectively. Average gain and rectum temperature were recorded everyday during the experiments. Blood was collected from the piglets after vaccination to detect the changes of specific antibodies, interleukin-2, and immune cells every week. Tissues were collected for histopathology and polymerase chain reaction. The results indicated that compared to those of the control piglets, all concentrations of two DNA vaccines could induce PCV2-specific antibodies. A cellular immunity test showed that PCV2-specific lymphocytes proliferated the number of TH, TC, and CD3+ positive T-cells raised in the blood of DNA vaccine immune groups. There was no distinct pathological damage and viremia occurring in pigs that were inoculated with DNA vaccines, but there was some minor pathological damage in the control group. The results demonstrated that CpG motifs as an adjuvant could boost the humoral and cellular immunity of pigs to PCV2, especially in terms of cellular immunity. Comparing two DNA vaccines that were constructed, the one containing 18 CpG motifs was more effective. This is the first report that CpG motifs as an adjuvant insert to the PCV2 DNA vaccine could boost immunity.

  4. Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

    Directory of Open Access Journals (Sweden)

    Adam G Marsh

    Full Text Available Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera and an anemone (Nematostella vectensis. Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to

  5. Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

    Science.gov (United States)

    Marsh, Adam G; Hoadley, Kenneth D; Warner, Mark E

    2016-01-01

    Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in

  6. Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production

    International Nuclear Information System (INIS)

    Wang, Tingting; Chen, Man; Liu, Lian; Cheng, Huaiyan; Yan, You-E; Feng, Ying-Hong; Wang, Hui

    2011-01-01

    Steroidogenic acute regulatory protein (StAR) mediates the rate-limiting step in the synthesis of steroid hormones, essential to fetal development. We have reported that the StAR expression in fetal adrenal is inhibited in a rat model of nicotine-induced intrauterine growth retardation (IUGR). Here using primary human fetal adrenal cortex (pHFAC) cells and a human fetal adrenal cell line NCI-H295A, we show that nicotine inhibits StAR expression and cortisol production in a dose- and time-dependent manner, and prolongs the inhibitory effect on cells proliferating over 5 passages after termination of nicotine treatment. Methylation detection within the StAR promoter region uncovers a single site CpG methylation at nt -377 that is sensitive to nicotine treatment. Nicotine-induced alterations in frequency of this point methylation correlates well with the levels of StAR expression, suggesting an important role of the single site in regulating StAR expression. Further studies using bioinformatics analysis and siRNA approach reveal that the single CpG site is part of the Pax6 binding motif (CGCCTGA) in the StAR promoter. The luciferase activity assays validate that Pax6 increases StAR gene expression by binding to the glucagon G3-like motif (CGCCTGA) and methylation of this site blocks Pax6 binding and thus suppresses StAR expression. These data identify a nicotine-sensitive CpG site at the Pax6 binding motif in the StAR promoter that may play a central role in regulating StAR expression. The results suggest an epigenetic mechanism that may explain how nicotine contributes to onset of adult diseases or disorders such as metabolic syndrome via fetal programming. -- Highlights: ► Nicotine-induced StAR inhibition in two human adrenal cell models. ► Nicotine-induced single CpG site methylation in StAR promoter. ► Persistent StAR inhibition and single CpG methylation after nicotine termination. ► Single CpG methylation located at Pax6 binding motif regulates St

  7. Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Tingting [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Chen, Man; Liu, Lian [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Cheng, Huaiyan [Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Yan, You-E [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Feng, Ying-Hong, E-mail: yhfeng@usuhs.edu [Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Wang, Hui, E-mail: wanghui19@whu.edu.cn [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Research Center of Food and Drug Evaluation, Wuhan University, Wuhan 430071 (China)

    2011-12-15

    Steroidogenic acute regulatory protein (StAR) mediates the rate-limiting step in the synthesis of steroid hormones, essential to fetal development. We have reported that the StAR expression in fetal adrenal is inhibited in a rat model of nicotine-induced intrauterine growth retardation (IUGR). Here using primary human fetal adrenal cortex (pHFAC) cells and a human fetal adrenal cell line NCI-H295A, we show that nicotine inhibits StAR expression and cortisol production in a dose- and time-dependent manner, and prolongs the inhibitory effect on cells proliferating over 5 passages after termination of nicotine treatment. Methylation detection within the StAR promoter region uncovers a single site CpG methylation at nt -377 that is sensitive to nicotine treatment. Nicotine-induced alterations in frequency of this point methylation correlates well with the levels of StAR expression, suggesting an important role of the single site in regulating StAR expression. Further studies using bioinformatics analysis and siRNA approach reveal that the single CpG site is part of the Pax6 binding motif (CGCCTGA) in the StAR promoter. The luciferase activity assays validate that Pax6 increases StAR gene expression by binding to the glucagon G3-like motif (CGCCTGA) and methylation of this site blocks Pax6 binding and thus suppresses StAR expression. These data identify a nicotine-sensitive CpG site at the Pax6 binding motif in the StAR promoter that may play a central role in regulating StAR expression. The results suggest an epigenetic mechanism that may explain how nicotine contributes to onset of adult diseases or disorders such as metabolic syndrome via fetal programming. -- Highlights: Black-Right-Pointing-Pointer Nicotine-induced StAR inhibition in two human adrenal cell models. Black-Right-Pointing-Pointer Nicotine-induced single CpG site methylation in StAR promoter. Black-Right-Pointing-Pointer Persistent StAR inhibition and single CpG methylation after nicotine termination

  8. MeCP2 Rett mutations affect large scale chromatin organization

    DEFF Research Database (Denmark)

    Gupta, Noopur Agarwal; Becker, Annette; Jost, K Laurence

    2011-01-01

    Rett syndrome is a neurological, X chromosomal-linked disorder associated with mutations in the MECP2 gene. MeCP2 protein has been proposed to play a role in transcriptional regulation as well as in chromatin architecture. Since MeCP2 mutant cells exhibit surprisingly mild changes in gene...... expression, we have now explored the possibility that Rett mutations may affect the ability of MeCP2 to bind and organize chromatin. We found that all but one of the 21 missense MeCP2 mutants analyzed accumulated at heterochromatin and about half of them were significantly affected. Furthermore, two......-thirds of all mutants showed a significantly decreased ability to cluster heterochromatin. Three mutants containing different proline substitutions (P101H, P101R and P152R) were severely affected only in heterochromatin clustering and located far away from the DNA interface in the MeCP2 methyl-binding domain...

  9. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

  10. Local therapy with CpG motifs in a murine model of allergic airway inflammation in IFN-beta knock-out mice

    DEFF Research Database (Denmark)

    Matheu, Victor; Treschow, Alexandra; Teige, Ingrid

    2005-01-01

    BACKGROUND: CpG oligodeoxynucleotides (CpG-ODN) are capable of inducing high amounts of type I IFNs with many immunomodulatory properties. Furthermore, type-I IFNs have been proposed to play a key role in mediating effects of CpG-ODN. The precise role of IFN-beta in the immunomodulatory effects o...

  11. Antibody classes & subclasses induced by mucosal immunization of mice with Streptococcus pyogenes M6 protein & oligodeoxynucleotides containing CpG motifs.

    Science.gov (United States)

    Teloni, R; von Hunolstein, C; Mariotti, S; Donati, S; Orefici, G; Nisini, R

    2004-05-01

    Type-specific antibodies against M protein are critical for human protection as they enhance phagocytosis and are protective. An ideal vaccine for the protection against Streptococcus pyogenes would warrant mucosal immunity, but mucosally administered M-protein has been shown to be poorly immunogenic in animals. We used a recombinant M type 6 protein to immunize mice in the presence of synthetic oligodeoxynucleotides containing CpG motifs (immunostimulatory sequences: ISS) or cholera toxin (CT) to explore its possible usage in a mucosal vaccine. Mice were immunized by intranasal (in) or intradermal (id) administration with four doses at weekly intervals of M6-protein (10 microg/mouse) with or without adjuvant (ISS, 10 microg/mouse or CT, 0,5 microg/mouse). M6 specific antibodies were measured by enzyme linked immunosorbent assay using class and subclass specific monoclonal antibodies. The use of ISS induced an impressive anti M-protein serum IgG response but when id administered was not detectable in the absence of adjuvant. When used in, M-protein in the presence of both ISS and CT induced anti M-protein IgA in the bronchoalveolar lavage, as well as specific IgG in the serum. IgG were able to react with serotype M6 strains of S. pyogenes. The level of antibodies obtained by immunizing mice in with M-protein and CT was higher in comparison to M-protein and ISS. The analysis of anti-M protein specific IgG subclasses showed high levels of IgG1, IgG2a and IgG2b, and low levels of IgG3 when ISS were used as adjuvant. Thus, in the presence of ISS, the ratio IgG2a/IgG1 and (IgG2a+IgG3)/IgG1 >1 indicated a type 1-like response obtained both in mucosally or systemically vaccinated mice. Our study offers a reproducible model of anti-M protein vaccination that could be applied to test new antigenic formulations to induce an anti-group A Streptococcus (GAS) vaccination suitable for protection against the different diseases caused by this bacterium.

  12. MeCP2 Affects Skeletal Muscle Growth and Morphology through Non Cell-Autonomous Mechanisms.

    Directory of Open Access Journals (Sweden)

    Valentina Conti

    Full Text Available Rett syndrome (RTT is an autism spectrum disorder mainly caused by mutations in the X-linked MECP2 gene and affecting roughly 1 out of 10.000 born girls. Symptoms range in severity and include stereotypical movement, lack of spoken language, seizures, ataxia and severe intellectual disability. Notably, muscle tone is generally abnormal in RTT girls and women and the Mecp2-null mouse model constitutively reflects this disease feature. We hypothesized that MeCP2 in muscle might physiologically contribute to its development and/or homeostasis, and conversely its defects in RTT might alter the tissue integrity or function. We show here that a disorganized architecture, with hypotrophic fibres and tissue fibrosis, characterizes skeletal muscles retrieved from Mecp2-null mice. Alterations of the IGF-1/Akt/mTOR pathway accompany the muscle phenotype. A conditional mouse model selectively depleted of Mecp2 in skeletal muscles is characterized by healthy muscles that are morphologically and molecularly indistinguishable from those of wild-type mice raising the possibility that hypotonia in RTT is mainly, if not exclusively, mediated by non-cell autonomous effects. Our results suggest that defects in paracrine/endocrine signaling and, in particular, in the GH/IGF axis appear as the major cause of the observed muscular defects. Remarkably, this is the first study describing the selective deletion of Mecp2 outside the brain. Similar future studies will permit to unambiguously define the direct impact of MeCP2 on tissue dysfunctions.

  13. Factors Affecting the Binding of a Recombinant Heavy Metal-Binding Domain (CXXC motif Protein to Heavy Metals

    Directory of Open Access Journals (Sweden)

    Kamala Boonyodying

    2012-06-01

    Full Text Available A number of heavy metal-binding proteins have been used to study bioremediation. CXXC motif, a metal binding domain containing Cys-X-X-Cys motif, has been identified in various organisms. These proteins are capable of binding various types of heavy metals. In this study, heavy metal binding domain (CXXC motif recombinant protein encoded from mcsA gene of S. aureus were cloned and overexpressed in Escherichia coli. The factors involved in the metal-binding activity were determined in order to analyze the potential of recombinant protein for bioremediation. A recombinant protein can be bound to Cd2+, Co2+, Cu2+ and Zn2+. The thermal stability of a recombinant protein was tested, and the results showed that the metal binding activity to Cu2+ and Zn2+ still exist after treating the protein at 85ºC for 30 min. The temperature and pH that affected the metal binding activity was tested and the results showed that recombinant protein was still bound to Cu2+ at 65ºC, whereas a pH of 3-7 did not affect the metal binding E. coli harboring a pRset with a heavy metal-binding domain CXXC motif increased the resistance of heavy metals against CuCl2 and CdCl2. This study shows that metal binding domain (CXXC motif recombinant protein can be effectively bound to various types of heavy metals and may be used as a potential tool for studying bioremediation.

  14. Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli.

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    Cristóbal Almendros

    Full Text Available Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR and CRISPR associated (cas genes conform the CRISPR-Cas systems of various bacteria and archaea and produce degradation of invading nucleic acids containing sequences (protospacers that are complementary to repeat intervening spacers. It has been demonstrated that the base sequence identity of a protospacer with the cognate spacer and the presence of a protospacer adjacent motif (PAM influence CRISPR-mediated interference efficiency. By using an original transformation assay with plasmids targeted by a resident spacer here we show that natural CRISPR-mediated immunity against invading DNA occurs in wild type Escherichia coli. Unexpectedly, the strongest activity is observed with protospacer adjoining nucleotides (interference motifs that differ from the PAM both in sequence and location. Hence, our results document for the first time native CRISPR activity in E. coli and demonstrate that positions next to the PAM in invading DNA influence their recognition and degradation by these prokaryotic immune systems.

  15. Two C3H Type Zinc Finger Protein Genes, CpCZF1 and CpCZF2, from Chimonanthus praecox Affect Stamen Development in Arabidopsis

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    Huamin Liu

    2017-08-01

    Full Text Available Wintersweet (Chimonanthus praecox is a popular garden plant because of its flowering time, sweet fragrance, and ornamental value. However, research into the molecular mechanism that regulates flower development in wintersweet is still limited. In this study, we sought to investigate the molecular characteristics, expression patterns, and potential functions of two C3H-type zinc finger (CZF protein genes, CpCZF1 and CpCZF2, which were isolated from the wintersweet flowers based on the flower developmental transcriptome database. CpCZF1 and CpCZF2 were more highly expressed in flower organs than in vegetative tissues, and during the flower development, their expression profiles were associated with flower primordial differentiation, especially that of petal and stamen primordial differentiation. Overexpression of either CpCZF1 or CpCZF2 caused alterations on stamens in transgenic Arabidopsis. The expression levels of the stamen identity-related genes, such as AGAMOUS (AG, PISTILLATA (PI, SEPALLATA1 (SEP1, SEPALLATA2 (SEP2, SEPALLATA3 (SEP3, APETALA1 (AP1, APETALA2 (AP2, and boundary gene RABBIT EAR (RBE were significantly up-regulated in CpCZF1 overexpression lines. Additionally, the transcripts of AG, PI, APETALA3 SEP1-3, AP1, and RBE were markedly increased in CpCZF2 overexpressed plant inflorescences. Moreover, CpCZF1 and CpCZF2 could interact with each other by using yeast two-hybrid and bimolecular fluorescence complementation assays. Our results suggest that CpCZF1 and CpCZF2 may be involved in the regulation of stamen development and cause the formation of abnormal flowers in transgenic Arabidopsis plants.

  16. Mutations altering the gammaretrovirus endoproteolytic motif affect glycosylation of the envelope glycoprotein and early events of the virus life cycle

    Energy Technology Data Exchange (ETDEWEB)

    Argaw, Takele; Wilson, Carolyn A., E-mail: carolyn.wilson@fda.hhs.gov

    2015-01-15

    Previously, we found that mutation of glutamine to proline in the endoproteolytic cleavage signal of the PERV-C envelope (RQKK to RPKK) resulted in non-infectious vectors. Here, we show that RPKK results in a non-infectious vector when placed in not only a PERV envelope, but also the envelope of a related gammaretrovirus, FeLV-B. The amino acid substitutions do not prevent envelope precursor cleavage, viral core and genome assembly, or receptor binding. Rather, the mutations result in the formation of hyperglycosylated glycoprotein and a reduction in the reverse transcribed minus strand synthesis and undetectable 2-LTR circular DNA in cells exposed to vectors with these mutated envelopes. Our findings suggest novel functions associated with the cleavage signal sequence that may affect trafficking through the glycosylation machinery of the cell. Further, the glycosylation status of the envelope appears to impact post-binding events of the viral life cycle, either membrane fusion, internalization, or reverse transcription. - Highlights: • Env cleavage signal impacts infectivity of gammaretroviruses. • Non-infectious mutants have hyper-glycosylated envelope that bind target cells. • Non-infectious mutants have defects in the formation of the double-stranded DNA. • Env cleavage motif has functions beyond cleavage of the env precursor.

  17. CP violation

    CERN Document Server

    1989-01-01

    Contents: CP Phenomenology: Introduction to CP Violation (C Jarlskog); CP-Violation in the K 0 -K 0 -System (K Kleinknecht); The Quark Mixing Matrix, Charm Decays and B Decays (S Stone); The Question of CP Noninvariance - As Seen through the Eyes of Neutral Beauty (I I Bigi et al.); In Search of CP Noninvariance in Heavy Quark Systems (L-L Chau); CP Violation at High Energy e + e - Colliders (J Bernabéu & M B Gavela); CP Violation in the Standard Model with Four Families (A Datta & E A Paschos); CP Effects When Neutrinos are their Own Antiparticles (B Kayser); On Spontaneous CP Violation Trigg

  18. CP violation

    CERN Multimedia

    CERN. Geneva

    1999-01-01

    In the first two lectures, CP violation in the K system is pedagogically reviewed: its manifestations in the neutral K meson systems, in rare K meson decays and in decays of charged K mesons, and results from classical and current experiments, are discussed. In the third lecture, CP Violation in the B system and the forthcoming experimental tests will be discussed.

  19. CP violation

    Indian Academy of Sciences (India)

    We have just entered a period during which we expect considerable progress toward understanding CP violation. Here we review what we have learnt so far, and what is to be expected in the near future. To do this we cover the foundation of CP violation at a level which can be understood by physicists who are not working ...

  20. CP violation

    International Nuclear Information System (INIS)

    Gronau, M.

    1995-01-01

    We review the present status of the Standard Model of CP violation, which is based on a complex phase in the Cabibbo-Kobayashi-Maskawa (CKM) matrix. So far CP violation has been observed only in K 0 -K 0 mixing, consistent with a sizable phase. The implications of future CP nonconserving measusrements in K and B decays are discussed within the model. Direct CP violation in K→2π may be observed in the near future, however this would not be a powerful test of the model. B decays provide a wide variety of CP asymmetry measurements, which can serve as precise tests of the Standard Model in cases where the asymmetry is cleanly related to phases of CKM matrix elements. Some of the most promising cases are discussed. ((orig.))

  1. Statistical analysis of the influence of lancing on the secondary corrosion affecting SG tube ends in the CP0 series of PWRs

    International Nuclear Information System (INIS)

    Souchois, T.

    1995-05-01

    The main method of tube sheet cleaning during unit outages is high pressure lancing. A new tool called CECIL has been in use for this purpose since 1991 on the CP0 series of PWRs. This paper presents a statistical analysis of inspection data providing a basis for determining whether the type of lancing tool used has a 'statistically' significant effect, on the one hand, on the progression of the secondary corrosion affecting the CP0 type PWR SG tube ends and, on the other hand, on the appearance of corrosion on sound tubes after one operating cycle. The study results showed the CECIL cleaning method to be more efficient in tat larger amounts of accumulated deposits were removed and the risks of early corrosion were 14 times lower, with slower degradation in the course of subsequent cycles. (author). 2 refs., 8 figs., 19 tabs

  2. CP violation

    International Nuclear Information System (INIS)

    Gilman, F.J.

    1989-12-01

    Predictions for CP violation in the three generation Standard Model are reviewed based on what is known about the Cabibbo-Kobayashi-Maskawa matrix. Application to the K and B meson systems are emphasized. 43 refs., 13 figs

  3. CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

    DEFF Research Database (Denmark)

    Hobolth, Asger; Nielsen, Rasmus; Wang, Ying

    2006-01-01

    We develop codon-based models for simultaneously inferring the mutational effects of CpG and CpNpG methylation in coding regions. In a data set of 369 tomato genes, we show that there is very little effect of CpNpG methylation but a strong effect of CpG methylation affecting almost all genes. We...... further show that the CpNpG and CpG effects are largely uncorrelated. Our results suggest different roles of CpG and CpNpG methylation, with CpNpG methylation possibly playing a specialized role in defense against transposons and RNA viruses....

  4. CP violation

    International Nuclear Information System (INIS)

    Quinn, H.

    1995-12-01

    In this talk the author briefly reviews the cosmological importance of CP violation and the status of calculations of baryogenisis in the context of the Standard Model. The author then turns to a discussion of Standard Model Predictions for CP violation in B decays, stressing the importance of multiple measurements to overconstrain the model parameters and thus search for indications of beyond-Standard-Model physics

  5. Conserved retinoblastoma protein-binding motif in human cytomegalovirus UL97 kinase minimally impacts viral replication but affects susceptibility to maribavir

    Directory of Open Access Journals (Sweden)

    Chou Sunwen

    2009-01-01

    Full Text Available Abstract The UL97 kinase has been shown to phosphorylate and inactivate the retinoblastoma protein (Rb and has three consensus Rb-binding motifs that might contribute to this activity. Recombinant viruses containing mutations in the Rb-binding motifs generally replicated well in human foreskin fibroblasts with only a slight delay in replication kinetics. Their susceptibility to the specific UL97 kinase inhibitor, maribavir, was also examined. Mutation of the amino terminal motif, which is involved in the inactivation of Rb, also renders the virus hypersensitive to the drug and suggests that the motif may play a role in its mechanism of action.

  6. Immune response in domestic ducks following intradermal delivery of inactivated vaccine against H5N1 highly pathogenic avian influenza virus adjuvanted with oligodeoxynucleotides containing CpG motifs.

    Science.gov (United States)

    Yuk, Seong-Su; Lee, Dong-Hun; Park, Jae-Keun; To, Eredene-Ochir; Kwon, Jung-Hoon; Noh, Jin-Yong; Gomis, Susantha; Song, Chang-Seon

    2015-08-01

    Ducks are a natural reservoir for H5N1 highly pathogenic avian influenza (HPAI) viruses, which produces a range of clinical outcomes from asymptomatic infections to severe disease with mortality. Vaccination against HPAI is one of the few methods available for controlling avian influenza virus (AIV) infection in domestic ducks; therefore, it is necessary to improve vaccine efficacy against HPAI in domestic ducks. However, few studies have focused on enhancing the immune response by testing alternative administration routes and adjuvants. While attempting to maximize the efficacy of a vaccine, it is important to select an appropriate vaccine delivery route and adjuvant to elicit an enhanced immune response. Although several studies have indicated that the vaccination of ducks against HPAI viruses has offered protection against lethal virus challenge, the immunogenicity of the vaccine still requires improvement. In this study, we characterized the immune response following a novel vaccination strategy against H5N1 HPAI virus in domestic ducks. Our novel intradermal delivery system and the application of the cytosine-phosphodiester-guanine (CpG) oligodeoxynucleotide (ODN) adjuvant allowed us to obtain information regarding the sustained vaccine immunity. Compared with the intramuscular route of vaccination, the intradermal route resulted in higher antibody titer as well as lower antibody deviation following secondary vaccination. In addition, the use of a CpG-ODN adjuvant had a dose-sparing effect on antibody titer. Furthermore, when a high dose of antigen was used, the CpG-ODN-adjuvanted vaccine maintained a high mean antibody titer. This data demonstrates that intradermal immunization combined with administration of CpG-ODN as an adjuvant may be a promising strategy for improving vaccine efficacy in domestic ducks. © 2015 Poultry Science Association Inc.

  7. An EAR-motif-containing ERF transcription factor affects herbivore-induced signaling, defense and resistance in rice.

    Science.gov (United States)

    Lu, Jing; Ju, Hongping; Zhou, Guoxin; Zhu, Chuanshu; Erb, Matthias; Wang, Xiaopeng; Wang, Peng; Lou, Yonggen

    2011-11-01

    Ethylene responsive factors (ERFs) are a large family of plant-specific transcription factors that are involved in the regulation of plant development and stress responses. However, little to nothing is known about their role in herbivore-induced defense. We discovered a nucleus-localized ERF gene in rice (Oryza sativa), OsERF3, that was rapidly up-regulated in response to feeding by the rice striped stem borer (SSB) Chilo suppressalis. Antisense and over-expression of OsERF3 revealed that it positively affects transcript levels of two mitogen-activated protein kinases (MAPKs) and two WRKY genes as well as concentrations of jasmonate (JA), salicylate (SA) and the activity of trypsin protease inhibitors (TrypPIs). OsERF3 was also found to mediate the resistance of rice to SSB. On the other hand, OsERF3 was slightly suppressed by the rice brown planthopper (BPH) Nilaparvata lugens (Stål) and increased susceptibility to this piercing sucking insect, possibly by suppressing H(2)O(2) biosynthesis. We propose that OsERF3 affects early components of herbivore-induced defense responses by suppressing MAPK repressors and modulating JA, SA, ethylene and H(2)O(2) pathways as well as plant resistance. Our results also illustrate that OsERF3 acts as a central switch that gears the plant's metabolism towards an appropriate response to chewing or piercing/sucking insects. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  8. CP Violation

    International Nuclear Information System (INIS)

    Aleksan, R.

    1993-06-01

    The violation of the CP symmetry is a phenomenon, the origin of which is not yet well established and deserves a particular attention since it may be a fundamental property of Nature with very important consequences for the evolution of the universe. We propose in these lectures to have an overview of this phenomenon as we understand it so far. To this end, and after introducing the discrete space-time symmetries, we discuss the observation of the violation of the CP symmetry in the neutral kaon decays. We then derive the general formalism for any neutral system made of a particle and its antiparticle and discuss how CP violation is introduced. We show how this phenomenon is generated in the Standard Model of the electroweak interactions and what are the predictions that can be made. In particular we shall concentrate on the expected effects in the decays of mesons involving the b quark. We review the various possibilities for observing these effects, calculate their magnitudes and show how the consistency of the theory can be tested. Finally, we outline the experimental prospects for studying CP non conservation at an asymmetric B Factory to either verify the Standard Model mechanism or provide evidence for new physics. (author)

  9. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  10. CP violation with an unbroken CP transformation

    Energy Technology Data Exchange (ETDEWEB)

    Ratz, Michael [Department of Physics and Astronomy, University of California,Irvine, California 92697-4575 (United States); Trautner, Andreas [Bethe Center for Theoretical Physics und Physikalisches Institut der Universität Bonn,Nussallee 12, 53115 Bonn (Germany)

    2017-02-21

    A CP conserving SU(3) gauge theory is spontaneously broken to T{sub 7} by the vacuum expectation value (VEV) of a 15-plet. Even though the SU(3)-CP transformation is not broken by the VEV, the theory exhibits physical CP violation in the broken phase. This is because the SU(3)-CP transformation corresponds to the unique order-two outer automorphism of T{sub 7}, which is not a physical CP transformation for the T{sub 7} states, and there is no other possible CP transformation. We explicitly demonstrate that CP is violated by calculating a CP odd decay asymmetry in the broken phase. This scenario provides us with a natural protection for topological vacuum terms, ensuring that θ G{sub μν}G̃{sup μν} is absent even though CP is violated for the physical states of the model.

  11. CompariMotif: quick and easy comparisons of sequence motifs.

    Science.gov (United States)

    Edwards, Richard J; Davey, Norman E; Shields, Denis C

    2008-05-15

    CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

  12. Structural and Electrochemical Consequences of [Cp*] Ligand Protonation.

    Science.gov (United States)

    Peng, Yun; Ramos-Garcés, Mario V; Lionetti, Davide; Blakemore, James D

    2017-09-05

    There are few examples of the isolation of analogous metal complexes bearing [η 5 -Cp*] and [η 4 -Cp*H] (Cp* = pentamethylcyclopentadienyl) complexes within the same metal/ligand framework, despite the relevance of such structures to catalytic applications. Recently, protonation of Cp*Rh(bpy) (bpy = 2,2'-bipyridyl) has been shown to yield a complex bearing the uncommon [η 4 -Cp*H] ligand, rather than generating a [Rh III -H] complex. We now report the purification and isolation of this protonated species, as well as characterization of analogous complexes of 1,10-phenanthroline (phen). Specifically, reaction of Cp*Rh(bpy) or Cp*Rh(phen) with 1 equiv of Et 3 NH + Br - affords rhodium compounds bearing endo-η 4 -pentamethylcyclopentadiene (η 4 -Cp*H) as a ligand. NMR spectroscopy and single-crystal X-ray diffraction studies confirm protonation of the Cp* ligand, rather than formation of metal hydride complexes. Analysis of new structural data and electronic spectra suggests that phen is significantly reduced in Cp*Rh(phen), similar to the case of Cp*Rh(bpy). Backbonding interactions with olefinic motifs are activated by formation of [η 4 -Cp*H]; protonation of [Cp*] stabilizes the low-valent metal center and results in loss of reduced character on the diimine ligands. In accord with these changes in electronic structure, electrochemical studies reveal a distinct manifold of redox processes that are accessible in the [Cp*H] complexes in comparison with their [Cp*] analogues; these processes suggest new applications in catalysis for the complexes bearing endo-η 4 -Cp*H.

  13. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity

    NARCIS (Netherlands)

    Witteveen, Josefine S.; Willemsen, Marjolein H.; Dombroski, Thais C. D.; van Bakel, Nick H. M.; Nillesen, Willy M.; van Hulten, Josephus A.; Jansen, Eric J. R.; Verkaik, Dave; Veenstra-Knol, Hermine E.; van Ravenswaaij-Arts, Conny M. A.; Wassink-Ruiter, Jolien S. Klein; Vincent, Marie; David, Albert; Le Caignec, Cedric; Schieving, Jolanda; Gilissen, Christian; Foulds, Nicola; Rump, Patrick; Strom, Tim; Cremer, Kirsten; Zink, Alexander M.; Engels, Hartmut; de Munnik, Sonja A.; Visser, Jasper E.; Brunner, Han G.; Martens, Gerard J. M.; Pfundt, Rolph; Kleefstra, Tjitske; Kolk, Sharon M.

    Numerous genes are associated with neurodevelopmental disorders such as intellectual disability and autism spectrum disorder ( ASD), but their dysfunction is often poorly characterized. Here we identified dominant mutations in the gene encoding the transcriptional repressor and MeCP2 interactor

  14. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity

    NARCIS (Netherlands)

    Witteveen, J.S.; Willemsen, M.H.; Dombroski, T.C.; Bakel, N.H. van; Nillesen, W.M.; Hulten, J.A. van; Jansen, E.J.; Verkaik, D.; Veenstra-Knol, H.E.; Ravenswaaij-Arts, C.M.A. van; Wassink-Ruiter, J.S.; Vincent, M.; David, A.; Le Caignec, C.; Schieving, J.; Gilissen, C.; Foulds, N.; Rump, P.; Strom, T.; Cremer, K.; Zink, A.M.; Engels, H.; Munnik, S.A. de; Visser, J.E.; Brunner, H.G.; Martens, G.J.; Pfundt, R.P.; Kleefstra, T.; Kolk, S.M.

    2016-01-01

    Numerous genes are associated with neurodevelopmental disorders such as intellectual disability and autism spectrum disorder (ASD), but their dysfunction is often poorly characterized. Here we identified dominant mutations in the gene encoding the transcriptional repressor and MeCP2 interactor

  15. PISMA: A Visual Representation of Motif Distribution in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Rogelio Alcántara-Silva

    2017-03-01

    Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

  16. Giant CP stars

    International Nuclear Information System (INIS)

    Loden, L.O.; Sundman, A.

    1989-01-01

    This study is part of an investigation of the possibility of using chemically peculiar (CP) stars to map local galactic structure. Correct luminosities of these stars are therefore crucial. CP stars are generally regarded as main-sequence or near-main-sequence objects. However, some CP stars have been classified as giants. A selection of stars, classified in literature as CP giants, are compared to normal stars in the same effective temperature interval and to ordinary 'non giant' CP stars. There is no clear confirmation of a higher luminosity for 'CP giants', than for CP stars in general. In addition, CP characteristics seem to be individual properties not repeated in a component star or other cluster members. (author). 50 refs., 5 tabs., 3 figs

  17. An Inhibitory Motif on the 5’UTR of Several Rotavirus Genome Segments Affects Protein Expression and Reverse Genetics Strategies

    Science.gov (United States)

    Papa, Guido; Eichwald, Catherine; Burrone, Oscar R.

    2016-01-01

    Rotavirus genome consists of eleven segments of dsRNA, each encoding one single protein. Viral mRNAs contain an open reading frame (ORF) flanked by relatively short untranslated regions (UTRs), whose role in the viral cycle remains elusive. Here we investigated the role of 5’UTRs in T7 polymerase-driven cDNAs expression in uninfected cells. The 5’UTRs of eight genome segments (gs3, gs5-6, gs7-11) of the simian SA11 strain showed a strong inhibitory effect on the expression of viral proteins. Decreased protein expression was due to both compromised transcription and translation and was independent of the ORF and the 3’UTR sequences. Analysis of several mutants of the 21-nucleotide long 5’UTR of gs 11 defined an inhibitory motif (IM) represented by its primary sequence rather than its secondary structure. IM was mapped to the 5’ terminal 6-nucleotide long pyrimidine-rich tract 5’-GGY(U/A)UY-3’. The 5’ terminal position within the mRNA was shown to be essentially required, as inhibitory activity was lost when IM was moved to an internal position. We identified two mutations (insertion of a G upstream the 5’UTR and the U to A mutation of the fifth nucleotide of IM) that render IM non-functional and increase the transcription and translation rate to levels that could considerably improve the efficiency of virus helper-free reverse genetics strategies. PMID:27846320

  18. CP Violation course

    CERN Multimedia

    CERN. Geneva HR-RFA

    2006-01-01

    The lecture introduces the concepts and phenomena of matter-antimatter symmetry violation, so-called "CP" violation. The lecture is organized in four courses, the first being devoted to a historical overview and an introduction into fundamental discrete symmetries. The second course introduces the most compelling CP-violating phenomena, and presents the first experimental discovery of CP violation in the neutral kaon system. The third course discusses how CP violation is beautifully incorporated into the Standard Model of particle interactions, and how modern B-meson "factories" provide precise tests of this picture. Finally, the fourth and last course introduces CP violation and the genesis of our matter world.

  19. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2008-01-01

    . Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...

  20. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2010-09-01

    Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

  1. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

  2. CP violation in B decay

    OpenAIRE

    Yamamoto, Hitoshi

    2001-01-01

    We review the physics of CP violation in B decays. After introducing the CKM matrix and how it causes CP violation, we cover three types of CP violation that can occur in B decays: CP violation in mixing, CP violation by mixing-decay interference, and CP violation in decay.

  3. Environmental stress affects DNA methylation of a CpG rich promoter region of serotonin transporter gene in a nurse cohort.

    Directory of Open Access Journals (Sweden)

    Jukka S Alasaari

    Full Text Available Shift-working nurses are exposed to a stressful work environment, which puts them at an increased risk for burnout and depression. We explored the effect of environmental stress on serotonin transporter gene (SLC6A4 promoter methylation among nurses from high and low work stress environments.Using bisulfite sequencing, we investigated the methylation status of five CpG residues of a CpG-rich region in the promoter of SLC6A4 by comparing female shift working nurses from a high work stress environment (n = 24 to low work stress environment (n = 25. We also analyzed the association of 5-HTTLPR polymorphism at 5' end of SLC6A4. Work stress was assessed by the Karasek's Model and possible signs of burnout or depression were measured by the Maslach Burnout Index General Survey and Beck Depression Index. Methylation levels were assessed by bisulfite sequencing of DNA extracted from peripheral blood leucocytes. Restriction enzyme treatment followed by standard PCR was used to identify 5-HTTLPR genotypes.We found that nurses in the high stress environment had significantly lower promoter methylation levels at all five CpG residues compared to nurses in the low stress environment (p<0.01. There was no significant interaction of 5-HTTLPR genotype and work stress with methylation (p = 0.58. In unadjusted (bivariate analysis, burnout was not significantly associated to methylation levels. However, when mutually adjusted for both, burnout and work stress were significant contributors (p = 0.038 and p<0.0001 respectively to methylation levels.Our findings show that environmental stress is concurrent with decreased methylation of the SLC6A4 promoter. This may lead to increased transcriptional activity of the gene, increased reuptake of serotonin from synaptic clefts, and termination of the activity of serotonin. This could present a possible coping mechanism for environmental stress in humans that could eventually increase risk for disturbed functional

  4. Phenomenology of CP violation

    International Nuclear Information System (INIS)

    Ecker, G.

    1987-01-01

    A short survey of the theoretical status of CP violation is presented. The Standart Model is confronted with the present experimental situation. Possible future tests of our notions of CP violation are discussed, concentrating on rare K decays. Other promising reactions such as B decays are briefly reviewed. Among alternative models of CP violation, multi-Higgs extensions of the Standart Model, left-right symmetric gauge theories and minimal SUSY models are discussed. Finally, the relevance of generalized CP invariance is emphasized. 64 refs., 7 figs. (Author)

  5. Leptonic CP violation theory

    DEFF Research Database (Denmark)

    Hagedorn, C.

    2017-01-01

    I summarize the status of theoretical predictions for the yet to be measured leptonic CP phases, the Dirac phase δ and the two Majorana phases α and β. I discuss different approaches based on: (a) a flavor symmetry without and with corrections, (b) different types of sum rules and (c) flavor and CP...... symmetries. I show their predictive power with examples. In addition, I present scenarios in which low and high energy CP phases are connected so that predictions for the CP phases α, β and δ become correlated to the sign of the baryon asymmetry YB of the Universe that is generated via leptogenesis....

  6. Is CP violation maximal

    International Nuclear Information System (INIS)

    Gronau, M.

    1984-01-01

    Two ambiguities are noted in the definition of the concept of maximal CP violation. The phase convention ambiguity is overcome by introducing a CP violating phase in the quark mixing matrix U which is invariant under rephasing transformations. The second ambiguity, related to the parametrization of U, is resolved by finding a single empirically viable definition of maximal CP violation when assuming that U does not single out one generation. Considerable improvement in the calculation of nonleptonic weak amplitudes is required to test the conjecture of maximal CP violation. 21 references

  7. Motif enrichment tool.

    Science.gov (United States)

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides.

    Science.gov (United States)

    Chowdhury, Kaushik; Kumar, Suresh; Sharma, Tanu; Sharma, Ankit; Bhagat, Meenakshi; Kamai, Asangla; Ford, Bridget M; Asthana, Shailendra; Mandal, Chandi C

    2018-01-10

    Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing

  9. CpG Oligodeoxynucleotides as a Future Vaccine for Allergic Diseases

    Directory of Open Access Journals (Sweden)

    Kunio Sano

    2005-01-01

    Full Text Available An astounding feature of the DNA sequences termed CpG motifs is the induction of immune and inflammatory responses in a senseless manner. CpG motifs exist abundantly in microbes and evoke innate immunity that constitutes the first line of defense against microbial infections in vertebrates. CpG motifs that essentially work in an antigen-nonspecific fashion, however, turn into novel immunomodulators that can manipulate acquired immunity in an antigen-specific manner if oligodeoxynucleotides containing CpG motifs (CpG ODNs are directly conjugated to the antigen. CpG ODNs with potent polyclonal Th1-inducing ability show promise for application in immunotherapy whereby neutralization of dominant allergy-prone Th2 cells is achieved by inducing allergen-specific Th1 cells. The underlying mechanisms include an unexpected enhancement of dendritic cell function as a linker between innate and acquired immunity. In the foreseeable future the mainstream therapeutic role of corticosteroids in anti-inflammatory therapy for allergic diseases could possibly be replaced by immunotherapy using CpG ODN-conjugated antigens.

  10. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity.

    Science.gov (United States)

    Witteveen, Josefine S; Willemsen, Marjolein H; Dombroski, Thaís C D; van Bakel, Nick H M; Nillesen, Willy M; van Hulten, Josephus A; Jansen, Eric J R; Verkaik, Dave; Veenstra-Knol, Hermine E; van Ravenswaaij-Arts, Conny M A; Wassink-Ruiter, Jolien S Klein; Vincent, Marie; David, Albert; Le Caignec, Cedric; Schieving, Jolanda; Gilissen, Christian; Foulds, Nicola; Rump, Patrick; Strom, Tim; Cremer, Kirsten; Zink, Alexander M; Engels, Hartmut; de Munnik, Sonja A; Visser, Jasper E; Brunner, Han G; Martens, Gerard J M; Pfundt, Rolph; Kleefstra, Tjitske; Kolk, Sharon M

    2016-08-01

    Numerous genes are associated with neurodevelopmental disorders such as intellectual disability and autism spectrum disorder (ASD), but their dysfunction is often poorly characterized. Here we identified dominant mutations in the gene encoding the transcriptional repressor and MeCP2 interactor switch-insensitive 3 family member A (SIN3A; chromosome 15q24.2) in individuals who, in addition to mild intellectual disability and ASD, share striking features, including facial dysmorphisms, microcephaly and short stature. This phenotype is highly related to that of individuals with atypical 15q24 microdeletions, linking SIN3A to this microdeletion syndrome. Brain magnetic resonance imaging showed subtle abnormalities, including corpus callosum hypoplasia and ventriculomegaly. Intriguingly, in vivo functional knockdown of Sin3a led to reduced cortical neurogenesis, altered neuronal identity and aberrant corticocortical projections in the developing mouse brain. Together, our data establish that haploinsufficiency of SIN3A is associated with mild syndromic intellectual disability and that SIN3A can be considered to be a key transcriptional regulator of cortical brain development.

  11. CP violation and modular symmetries

    OpenAIRE

    Dent, Thomas

    2001-01-01

    We reconsider the origin of CP violation in fundamental theory. Existing string models of spontaneous CP violation make ambiguous predictions, due to the arbitrariness of CP transformation and the apparent non-invariance of the results under duality. We find an unambiguous modular CP invariance condition, applicable to predictive models of spontaneous CP violation, which circumvents these problems; it strongly constrains CP violation by heterotic string moduli. The dilaton is also evaluated a...

  12. Intratracheal synthetic CpG oligodeoxynucleotide causes acute lung injury with systemic inflammatory response

    Directory of Open Access Journals (Sweden)

    Hasegawa Naoki

    2009-09-01

    Full Text Available Abstract Bacterial genome is characterized by frequent unmethylated cytosine-phosphate-guanine (CpG motifs. Deleterious effects can occur when synthetic oligodeoxynucleotides (ODN with unmethylated CpG dinucleotides (CpG-ODN are administered in a systemic fashion. We aimed to evaluate the effect of intratracheal CpG-ODN on lung inflammation and systemic inflammatory response. C57BL/6J mice received intratracheal administration of CpG-ODN (0.01, 0.1, 1.0, 10, or 100 μM or control ODN without CpG motif. Bronchoalveolar lavage (BAL fluid was obtained 3 or 6 h or 1, 2, 7, or 14 days after the instillation and subjected to a differential cell count and cytokine measurement. Lung permeability was evaluated as the BAL fluid-to-plasma ratio of the concentration of human serum albumin that was injected 1 h before euthanasia. Nuclear factor (NF-κB DNA binding activity was also evaluated in lung homogenates. Intratracheal administration of 10 μM or higher concentration of CpG-ODN induced significant inflammatory cell accumulation into the airspace. The peak accumulation of neutrophils and lymphocytes occurred 1 and 2 days after the CpG-ODN administration, respectively. Lung permeability was increased 1 day after the 10 μM CpG-ODN challenge. CpG-ODN also induced nuclear translocation of NF-κB and upregulation of various inflammatory cytokines in BAL fluid and plasma. Histopathology of the lungs and liver revealed acute lung injury and liver damage with necrosis, respectively. Control ODN without CpG motif did not induce any inflammatory change. Since intratracheal CpG-ODN induced acute lung injury as well as systemic inflammatory response, therapeutic strategies to neutralize bacterial DNA that is released after administration of bactericidal agents should be considered.

  13. CP violation and modular symmetries

    International Nuclear Information System (INIS)

    Dent, Thomas

    2001-01-01

    We reconsider the origin of CP violation in fundamental theory. Existing string models of spontaneous CP violation make ambiguous predictions, due to the arbitrariness of CP transformation and the apparent noninvariance of the results under duality. We find a modular CP invariance condition, applicable to any predictive model of spontaneous CP violation, which circumvents these problems; it strongly constrains CP violation by heterotic string moduli. The dilaton is also evaluated as a source of CP violation, but is likely experimentally excluded. We consider the prospects for explaining CP violation in strongly coupled strings and brane worlds

  14. Dietary fish protein hydrolysates containing bioactive motifs affect serum and adipose tissue fatty acid compositions, serum lipids, postprandial glucose regulation and growth in obese Zucker fa/fa rats.

    Science.gov (United States)

    Drotningsvik, Aslaug; Mjøs, Svein A; Pampanin, Daniela M; Slizyte, Rasa; Carvajal, Ana; Remman, Tore; Høgøy, Ingmar; Gudbrandsen, Oddrun A

    2016-10-01

    The world's fisheries and aquaculture industries produce vast amounts of protein-containing by-products that can be enzymatically hydrolysed to smaller peptides and possibly be used as additives to functional foods and nutraceuticals targeted for patients with obesity-related metabolic disorders. To investigate the effects of fish protein hydrolysates on markers of metabolic disorders, obese Zucker fa/fa rats consumed diets with 75 % of protein from casein/whey (CAS) and 25 % from herring (HER) or salmon (SAL) protein hydrolysate from rest raw material, or 100 % protein from CAS for 4 weeks. The fatty acid compositions were similar in the experimental diets, and none of them contained any long-chain n-3 PUFA. Ratios of lysine:arginine and methionine:glycine were lower in HER and SAL diets when compared with CAS, and taurine was detected only in fish protein hydrolysate diets. Motifs with reported hypocholesterolemic or antidiabetic activities were identified in both fish protein hydrolysates. Rats fed HER diet had lower serum HDL-cholesterol and LDL-cholesterol, and higher serum TAG, MUFA and n-3:n-6 PUFA ratio compared with CAS-fed rats. SAL rats gained more weight and had better postprandial glucose regulation compared with CAS rats. Serum lipids and fatty acids were only marginally affected by SAL, but adipose tissue contained less total SFA and more total n-3 PUFA when compared with CAS. To conclude, diets containing hydrolysed rest raw material from herring or salmon proteins may affect growth, lipid metabolism, postprandial glucose regulation and fatty acid composition in serum and adipose tissue in obese Zucker rats.

  15. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  16. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  17. CP violation in gauge theories

    International Nuclear Information System (INIS)

    Escobar, C.O.

    Some aspects of CP violation in gauge theories are reviewed. The topics covered include a discussion of the Kobayashi-Maskawa six-quarks model, models of soft- CP violation (extended Higgs sector), the strong CP problem and finally some speculations relating CP violation and magnetic charges in non-abelian gauge theories. (Author) [pt

  18. CP violation in atoms

    International Nuclear Information System (INIS)

    Barr, S.M.

    1992-01-01

    Electric dipole moments of large atoms are an excellent tool to search for CP violation beyond the Standard Model. These tell us about the electron EDM but also about CP-violating electron-nucleon dimension-6 operators that arise from Higgs-exchange. Rapid strides are being made in searches for atomic EDMs. Limits on the electron EDM approaching the values which would be expected from Higgs-exchange mediated CP violation have been achieved. It is pointed out that in this same kind of model if tan β is large the effects in atoms of the dimension-6 e - n operators may outweigh the effect of the electron EDM. (author) 21 refs

  19. Highlights of CP 2000

    CERN Document Server

    Ellis, John R.

    2001-01-01

    Various developing topics in CP violation are reviewed. There are many theoretical reasons to hope that the CKM paradigm may be incomplete. It is surely too soon to be claiming new physics in \\epsilon^\\prime/\\epsilon or in D^0-\\bar D^0 mixing, but rare K decays offer interesting places to search for new physics. It is probably also premature to see a clash between global CKM fits and current estimates of sin \\beta and \\gamma, where much more precise data will soon be available. There are interesting possibilities to look for CP violation in neutrino oscillations and in Higgs physics. Rapid progress can be expected now that CP violation is moving to the top of the particle physics agenda.

  20. Topics in CP violation

    International Nuclear Information System (INIS)

    Quinn, H.R.

    1993-02-01

    Given the varied backgrounds of the members of this audience this talk will be a grab bag of topics related to the general theme of CP Violation. I do not have time to dwell in detail on any of them. First, for the astronomers and astrophysicists among you, I want to begin by reviewing the experimental status of evidence for CP violation in particle processes. There is only one system where this has been observed, and that is in the decays of neutral K mesons

  1. Topics in CP violation

    Science.gov (United States)

    Quinn, H. R.

    1993-02-01

    Given the varied backgrounds of the members of this audience this talk will be a grab bag of topics related to the general theme of CP Violation. I do not have time to dwell in detail on any of them. First, for the astronomers and astrophysicists among you, I want to begin by reviewing the experimental status of evidence for CP violation in particle processes. There is only one system where this has been observed, and that is in the decays of neutral K mesons.

  2. Translational Control of Host Gene Expression by a Cys-Motif Protein Encoded in a Bracovirus.

    Directory of Open Access Journals (Sweden)

    Eunseong Kim

    Full Text Available Translational control is a strategy that various viruses use to manipulate their hosts to suppress acute antiviral response. Polydnaviruses, a group of insect double-stranded DNA viruses symbiotic to some endoparasitoid wasps, are divided into two genera: ichnovirus (IV and bracovirus (BV. In IV, some Cys-motif genes are known as host translation-inhibitory factors (HTIF. The genome of endoparasitoid wasp Cotesia plutellae contains a Cys-motif gene (Cp-TSP13 homologous to an HTIF known as teratocyte-secretory protein 14 (TSP14 of Microplitis croceipes. Cp-TSP13 consists of 129 amino acid residues with a predicted molecular weight of 13.987 kDa and pI value of 7.928. Genomic DNA region encoding its open reading frame has three introns. Cp-TSP13 possesses six conserved cysteine residues as other Cys-motif genes functioning as HTIF. Cp-TSP13 was expressed in Plutella xylostella larvae parasitized by C. plutellae. C. plutellae bracovirus (CpBV was purified and injected into non-parasitized P. xylostella that expressed Cp-TSP13. Cp-TSP13 was cloned into a eukaryotic expression vector and used to infect Sf9 cells to transiently express Cp-TSP13. The synthesized Cp-TSP13 protein was detected in culture broth. An overlaying experiment showed that the purified Cp-TSP13 entered hemocytes. It was localized in the cytosol. Recombinant Cp-TSP13 significantly inhibited protein synthesis of secretory proteins when it was added to in vitro cultured fat body. In addition, the recombinant Cp-TSP13 directly inhibited the translation of fat body mRNAs in in vitro translation assay using rabbit reticulocyte lysate. Moreover, the recombinant Cp-TSP13 significantly suppressed cellular immune responses by inhibiting hemocyte-spreading behavior. It also exhibited significant insecticidal activities by both injection and feeding routes. These results indicate that Cp-TSP13 is a viral HTIF.

  3. Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics.

    Science.gov (United States)

    Panopoulos, Athanasia D; Smith, Erin N; Arias, Angelo D; Shepard, Peter J; Hishida, Yuriko; Modesto, Veronica; Diffenderfer, Kenneth E; Conner, Clay; Biggs, William; Sandoval, Efren; D'Antonio-Chronowska, Agnieszka; Berggren, W Travis; Izpisua Belmonte, Juan Carlos; Frazer, Kelly A

    2017-04-06

    Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming. Published by Elsevier Inc.

  4. Response of porcine peripheral blood mononuclear cells to CpG-containing oligodeoxynucleotide

    DEFF Research Database (Denmark)

    Kamstrup, Søren; Verthelyi, D.; Klinman, D.M.

    2001-01-01

    Exposure to bacterial DNA generates a "danger signal" that stimulates cellular elements of the mammalian immune system to proliferate and/or secrete cytokines. Stimulation is critically dependent on hexameric motifs that contain an unmethylated CpG dinucleotide: these are commonly found in bacter......Exposure to bacterial DNA generates a "danger signal" that stimulates cellular elements of the mammalian immune system to proliferate and/or secrete cytokines. Stimulation is critically dependent on hexameric motifs that contain an unmethylated CpG dinucleotide: these are commonly found...... in bacterial but not vertebrate DNA. Different motifs are optimally stimulatory in different species. This work examines whether oligodeoxynucleotides (ODNs) containing CpG motifs stimulate peripheral blood mononuclear cells from pigs. Results show that pigs respond to CpG ODN by proliferating and secreting IL......-6, IL-12 and TNF-alpha. By screening a large panel (>100) of ODNs, the palindromic hexamer 'ATCGAT' was identified as being optimally active in all animals examined (N = 10). These findings are the first to establish the immunostimulatory activity of CpG ODN in pigs, and suggest that the therapeutic...

  5. Beautiful CP violation

    International Nuclear Information System (INIS)

    Dunietz, I.

    1997-01-01

    CP violation is observed to date only in K 0 decays and is parameterizable by a single quantity ε. Because it is one of the least understood phenomena in the Standard Model and holds a clue to baryogenesis, it must be investigated further. Highly specialized searches in K 0 decays are possible. Effects in B decays are much larger. In addition to the traditional B d → J/ψK S , π + π - asymmetries, CP violation could be searched for in already existing inclusive B data samples. The rapid B s --anti B s oscillations cancel in untagged B s data samples, which therefore allow feasibility studies for the observation of CP violation and the extraction of CKM elements with present vertex detectors. The favored method for the extraction of the CKM angle γ is shown to be unfeasible and a solution is presented involving striking direct CP violation in charged B decays. Novel methods for determining the B s mixing parameter Δm are described without the traditional requirement of flavor-specific final states

  6. MotifMark: Finding regulatory motifs in DNA sequences.

    Science.gov (United States)

    Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

    2017-07-01

    The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

  7. CP violation in ATLAS

    International Nuclear Information System (INIS)

    Saavedra, A.F.

    1995-01-01

    Full text: In the standard model CP violation is generated by a non trivial complex phase in the CKM matrix. The Standard Model does not predict the elements of the CKM matrix, they need to be experimentally measured. This will show if all the CP violation phenomena can be accounted by the complex phase or there are other contributing mechanisms which lie beyond the scope of Standard Model. It is of interest to overconstraint the so called unitary triangle by measuring each angle (α, β and γ) from the CP asymmetry that occurs in different decay modes. During the initial low luminosity period of the LHC a large effort will be concentrated in studying B physics, especially CP violation in the B 0 - B-bar 0 system, with the ATLAS detector. The features of the detector which are important for CP studies are: sharp trigger from the muon spectrometer (muons will be identify down to p T ≅ 5GeV, be able to distinguish electrons from hadrons (down to p T ≅ 1 GeV) with the Straw Tracker and Transition detector and high resolution of tracks, secondary vertices with the Semiconductor Tracker (resolution of 10-90 μm. For some decays modes ATLAS is expected to obtain larger sample of events than the B-factories that are being proposed. It has been calculated that the systematic error σ sin (2 α) = 0.06 and σ sin ( 2 β) = 0.027 which is comparable with other future experiments

  8. Biophysical characterization of the basic cluster in the transcription repression domain of human MeCP2 with AT-rich DNA.

    Science.gov (United States)

    Mushtaq, Ameeq Ul; Lee, Yejin; Hwang, Eunha; Bang, Jeong Kyu; Hong, Eunmi; Byun, Youngjoo; Song, Ji-Joon; Jeon, Young Ho

    2018-01-01

    MeCP2 is a chromatin associated protein which is highly expressed in brain and relevant with Rett syndrome (RTT). There are AT-hook motifs in MeCP2 which can bind with AT-rich DNA, suggesting a role in chromatin binding. Here, we report the identification and characterization of another AT-rich DNA binding motif (residues 295 to 313) from the C-terminal transcription repression domain of MeCP2 by nuclear magnetic resonance (NMR) and isothermal calorimetry (ITC). This motif shows a micromolar affinity to AT-rich DNA, and it binds to the minor groove of DNA like AT-hook motifs. Together with the previous studies, our results provide an insight into a critical role of this motif in chromatin structure and function. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. CP violation in K decays

    International Nuclear Information System (INIS)

    Gilman, F.J.

    1989-05-01

    Recent theoretical and experimental progress on the manifestation of CP violation in K decays, and toward understanding whether CP violation originates in a phase, or phases, in the weak mixing matrix of quarks is reviewed. 23 refs., 10 figs

  10. CP violation in B decays

    International Nuclear Information System (INIS)

    Kayser, B.

    1990-01-01

    The study of CP-violating effects in B decays will be a good test of whether CP violation is caused by the known weak interaction. If this is its origin, then large, cleanly-predicted CP-violating effects are expected in certain neutral B decays to hadronic CP eigenstates. The phenomenology of CP violation in the B system is reviewed, and the genesis of these large effects is explained. In this it is shown that large, cleanly-predicted effects are also expected in some decays to states which are not CP eigenstates. The combined study of the latter decays and those to CP eigenstates may make it possible to obtain a statistically-significant CP-violating signal with fewer B mesons that would otherwise be required

  11. CpG oligodeoxynucleotide induces apoptosis and cell cycle arrest in A20 lymphoma cells via TLR9-mediated pathways.

    Science.gov (United States)

    Qi, Xu-Feng; Zheng, Li; Kim, Cheol-Su; Lee, Kyu-Jae; Kim, Dong-Heui; Cai, Dong-Qing; Qin, Jun-Wen; Yu, Yan-Hong; Wu, Zheng; Kim, Soo-Ki

    2013-07-01

    Recent studies have suggested that the anti-cancer activity of CpG-oligodeoxynucleotides (CpG-ODNs) is owing to their immunomodulatory effects in tumor-bearing host. The purpose of this study is to investigate the directly cytotoxic activity of KSK-CpG, a novel CpG-ODN with an alternative CpG motif, against A20 and EL4 lymphoma cells in comparison with previously used murine CpG motif (1826-CpG). To evaluate the potential cytotoxic effects of KSK-CpG on lymphoma cells, cell viability assay, confocal microscopy, flow cytometry, DNA fragmentation, Western blotting, and reverse transcription-polymerase chain reaction (RT-PCR) analysis were used. We found that KSK-CpG induced direct cytotoxicity in A20 lymphoma cells, but not in EL4 lymphoma cells, at least in part via TLR9-mediated pathways. Apoptotic cell death was demonstrated to play an important role in CpG-ODNs-induced cytotoxicity. In addition, both mitochondrial membrane potential decrease and G1-phase arrest were involved in KSK-CpG-induced apoptosis in A20 cells. The activities of apoptotic molecules such as caspase-3, PARP, and Bax were increased, but the activation of p27 Kip1 and ERK were decreased in KSK-CpG-treated A20 cells. Furthermore, autocrine IFN-γ partially contributed to apoptotic cell death in KSK-CpG-treated A20 cells. Collectively, our findings suggest that KSK-CpG induces apoptotic cell death in A20 lymphoma cells at least in part by inducing G1-phase arrest and autocrine IFN-γ via increasing TLR9 expression, without the need for immune system of tumor-bearing host. This new understanding supports the development of TLR9-targeted therapy with CpG-ODN as a direct therapeutic agent for treating B lymphoma. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Status in CP violation

    International Nuclear Information System (INIS)

    Fayard, L.

    1989-11-01

    Twenty-five years after the discovery of CP violation in the neutral Kaon system, we still dont know exactly the origin and the components of that weak non invariance. The two more precise experiments give slightly different answers concerning the direct way of CP violation NA 31 gives ε prime/ε incompatible with the Superweak Model (for which ε prime=0) and in agreement with Standard Model predictions compatible with both. Again, one needs new and precise results in order to conclude about ε prime. E731 and NA31 are actually working on their new data samples. Longer term ideas are also being discussed, looking for new experiments able to give ε prime/ε with a precision. Concerning CPT invariance the situation seems to be more clear

  13. LHCb CP violation

    CERN Document Server

    Vesterinen, Mika

    2016-01-01

    The study of $CP$ violation in the beauty hadron sector is a promising approach to search for the effects of physics beyond the Standard Model. Several recent measurements in this area from the LHCb experiment are reported in these proceedings. These are based on the Run-I dataset of 3~fb$^{-1}$ of data collected at proton-proton centre of mass energies of 7 and 8~TeV.

  14. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L

    1998-01-01

    Many integral membrane proteins contain leucine-based motifs within their cytoplasmic domains that mediate internalization and intracellular sorting. Two types of leucine-based motifs have been identified. One type is dependent on phosphorylation, whereas the other type, which includes an acidic...... amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane...... and the phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic...

  15. Does transgenic Cry1Ac + CpTI cotton pollen affect hypopharyngeal gland development and midgut proteolytic enzyme activity in the honey bee Apis mellifera L. (Hymenoptera, Apidae)?

    Science.gov (United States)

    Han, Peng; Niu, Chang-Ying; Biondi, Antonio; Desneux, Nicolas

    2012-11-01

    The transgenic Cry1Ac (Bt toxin) + CpTI (Cowpea Trypsin Inhibitor) cotton cultivar CCRI41 is increasingly used in China and potential side effects on the honey bee Apis mellifera L. have been documented recently. Two studies have assessed potential lethal and sublethal effects in young bees fed with CCRI41 cotton pollen but no effect was observed on learning capacities, although lower feeding activity in exposed honey bees was noted (antifeedant effect). The present study aimed at providing further insights into potential side effects of CCRI41 cotton on honey bees. Emerging honey bees were exposed to different pollen diets using no-choice feeding protocols (chronic exposure) in controlled laboratory conditions and we aimed at documenting potential mechanisms underneath the CCRI41 antifeedant effect previously reported. Activity of midgut proteolytic enzyme of young adult honey bees fed on CCRI41 cotton pollen were not significantly affected, i.e. previously observed antifeedant effect was not linked to disturbed activity of the proteolytic enzymes in bees' midgut. Hypopharyngeal gland development was assessed by quantifying total extractable proteins from the glands. Results suggested that CCRI41 cotton pollen carries no risk to hypopharyngeal gland development of young adult honey bees. In the two bioassays, honey bees exposed to 1 % soybean trypsin inhibitor were used as positive controls for both midgut proteolytic enzymes and hypopharyngeal gland proteins quantification, and bees exposed to 48 ppb (part per billion) (i.e. 48 ng g(-1)) imidacloprid were used as controls for exposure to a sublethal concentration of toxic product. The results show that the previously reported antifeedant effect of CCRI41 cotton pollen on honey bees is not linked to effects on their midgut proteolytic enzymes or on the development of their hypopharyngeal glands. The results of the study are discussed in the framework of risk assessment of transgenic crops on honey bees.

  16. Silencing of the CaCP Gene Delays Salt- and Osmotic-Induced Leaf Senescence in Capsicum annuum L.

    Directory of Open Access Journals (Sweden)

    Huai-Juan Xiao

    2014-05-01

    Full Text Available Cysteine proteinases have been known to participate in developmental processes and in response to stress in plants. Our present research reported that a novel CP gene, CaCP, was involved in leaf senescence in pepper (Capsicum annuum L.. The full-length CaCP cDNA is comprised of 1316 bp, contains 1044 nucleotides in open reading frame (ORF, and encodes a 347 amino acid protein. The deduced protein belongs to the papain-like cysteine proteases (CPs superfamily, containing a highly conserved ERFNIN motif, a GCNGG motif and a conserved catalytic triad. This protein localized to the vacuole of plant cells. Real-time quantitative PCR analysis revealed that the expression level of CaCP gene was dramatically higher in leaves and flowers than that in roots, stems and fruits. Moreover, CaCP transcripts were induced upon during leaf senescence. CaCP expression was upregulated by plant hormones, especially salicylic acid. CaCP was also significantly induced by abiotic and biotic stress treatments, including high salinity, mannitol and Phytophthora capsici. Loss of function of CaCP using the virus-induced gene-silencing technique in pepper plants led to enhanced tolerance to salt- and osmotic-induced stress. Taken together, these results suggest that CaCP is a senescence-associated gene, which is involved in developmental senescence and regulates salt- and osmotic-induced leaf senescence in pepper.

  17. Silencing of the CaCP Gene Delays Salt- and Osmotic-Induced Leaf Senescence in Capsicum annuum L.

    Science.gov (United States)

    Xiao, Huai-Juan; Yin, Yan-Xu; Chai, Wei-Guo; Gong, Zhen-Hui

    2014-01-01

    Cysteine proteinases have been known to participate in developmental processes and in response to stress in plants. Our present research reported that a novel CP gene, CaCP, was involved in leaf senescence in pepper (Capsicum annuum L.). The full-length CaCP cDNA is comprised of 1316 bp, contains 1044 nucleotides in open reading frame (ORF), and encodes a 347 amino acid protein. The deduced protein belongs to the papain-like cysteine proteases (CPs) superfamily, containing a highly conserved ERFNIN motif, a GCNGG motif and a conserved catalytic triad. This protein localized to the vacuole of plant cells. Real-time quantitative PCR analysis revealed that the expression level of CaCP gene was dramatically higher in leaves and flowers than that in roots, stems and fruits. Moreover, CaCP transcripts were induced upon during leaf senescence. CaCP expression was upregulated by plant hormones, especially salicylic acid. CaCP was also significantly induced by abiotic and biotic stress treatments, including high salinity, mannitol and Phytophthora capsici. Loss of function of CaCP using the virus-induced gene-silencing technique in pepper plants led to enhanced tolerance to salt- and osmotic-induced stress. Taken together, these results suggest that CaCP is a senescence-associated gene, which is involved in developmental senescence and regulates salt- and osmotic-induced leaf senescence in pepper. PMID:24823878

  18. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  19. CP violating scalar Dark Matter

    Science.gov (United States)

    Cordero-Cid, A.; Hernández-Sánchez, J.; Keus, V.; King, S. F.; Moretti, S.; Rojas, D.; Sokołowska, D.

    2016-12-01

    We study an extension of the Standard Model (SM) in which two copies of the SM scalar SU(2) doublet which do not acquire a Vacuum Expectation Value (VEV), and hence are inert, are added to the scalar sector. We allow for CP-violation in the inert sector, where the lightest inert state is protected from decaying to SM particles through the conservation of a Z 2 symmetry. The lightest neutral particle from the inert sector, which has a mixed CP-charge due to CP-violation, is hence a Dark Matter (DM) candidate. We discuss the new regions of DM relic density opened up by CP-violation, and compare our results to the CP-conserving limit and the Inert Doublet Model (IDM). We constrain the parameter space of the CP-violating model using recent results from the Large Hadron Collider (LHC) and DM direct and indirect detection experiments.

  20. Present status of CP violation

    International Nuclear Information System (INIS)

    Ng, J.N.

    1989-06-01

    A review of the status of CP violation in kaons is given. Status of our knowledge of quark mixing angles in the standard six quark model is presented. The role Β d o - Βd o transition plays in this study is examined. A comparison of the estimates of CP violation effects from models beyond the standard one is given. Other experiments that have the capability of testing different CP violation models are also discussed. (Author) 35 refs., 6 figs., tab

  1. Mutations in the alpha-helical region of the amino terminus of the Maize rayado fino virus capsid protein and CP:RNA ratios affect virus-like particle encapsidation of RNAs.

    Science.gov (United States)

    Natilla, Angela; Murphy, Charles; Hammond, Rosemarie W

    2015-01-22

    Viral-based nanoplatforms rely on balancing the delicate array of virus properties to optimally achieve encapsidation of foreign materials with various potential objectives. We investigated the use of Maize rayado fino virus (MRFV)-virus-like particles (VLPs) as a multifunctional nanoplatform and their potential application as protein cages. MRFV-VLPs are composed of two serologically related, carboxy co-terminal coat proteins (CP1 and CP2) which are capable of self-assembling in Nicotiana benthamiana plants into 30nm particles with T=3 symmetry. The N-terminus of CP1 was targeted for genetic modification to exploit the driving forces for VLP assembly, packaging and retention of RNA in vivo and in vitro. The N-terminus of MRFV-CP1 contains a peptide sequence of 37 amino acids which has been predicted to have an alpha-helical structure, is rich in hydrophobic amino acids, facilitates CP-RNA interactions, and is not required for self-assembly. Amino acid substitutions were introduced in the 37 amino acid N-terminus by site-directed mutagenesis and the mutant VLPs produced in plants by a Potato virus X (PVX)-based vector were tested for particle stability and RNA encapsidation. All mutant CPs resulted in production of VLPs which encapsidated non-viral RNAs, including PVX genomic and subgenomic (sg) RNAs, 18S rRNA and cellular and viral mRNAs. In addition, MRFV-VLPs encapsidated GFP mRNA when was expressed in plant cells from the pGD vector. These results suggest that RNA packaging in MRFV-VLPs is predominantly driven by electrostatic interactions between the N-terminal 37 amino acid extension of CP1 and RNA, and that the overall species concentration of RNA in the cellular pool may determine the abundance and species of the RNAs packaged into the VLPs. Furthermore, RNA encapsidation is not required for VLPs stability, VLPs formed from MRFV-CP1 were stable at temperatures up to 70°C, and can be disassembled into CP monomers, which can then reassemble in vitro into

  2. Cosmological CP Violation

    CERN Document Server

    Tomaschitz, R

    1994-01-01

    Spinor fields are studied in infinite, topologically multiply connected Robertson-Walker cosmologies. Unitary spinor representations for the discrete covering groups of the spacelike slices are constructed. The spectral resolution of Dirac's equation is given in terms of horospherical elementary waves, on which the treatment of spin and energy is based in these cosmologies. The meaning of the energy and the particle-antiparticle concept is explained in the context of this varying cosmic background. Discrete symmetries, in particular inversions of the multiply connected spacelike slices, are studied. The violation of the unitarity of the parity operator, due to self-interference of P-reflected wave packets, is discussed. The violation of the CP and CPT invariance - already on the level of the free Dirac equation on this cosmological background - is pointed out.

  3. Leptogenesis and residual CP symmetry

    International Nuclear Information System (INIS)

    Chen, Peng; Ding, Gui-Jun; King, Stephen F.

    2016-01-01

    We discuss flavour dependent leptogenesis in the framework of lepton flavour models based on discrete flavour and CP symmetries applied to the type-I seesaw model. Working in the flavour basis, we analyse the case of two general residual CP symmetries in the neutrino sector, which corresponds to all possible semi-direct models based on a preserved Z 2 in the neutrino sector, together with a CP symmetry, which constrains the PMNS matrix up to a single free parameter which may be fixed by the reactor angle. We systematically study and classify this case for all possible residual CP symmetries, and show that the R-matrix is tightly constrained up to a single free parameter, with only certain forms being consistent with successful leptogenesis, leading to possible connections between leptogenesis and PMNS parameters. The formalism is completely general in the sense that the two residual CP symmetries could result from any high energy discrete flavour theory which respects any CP symmetry. As a simple example, we apply the formalism to a high energy S 4 flavour symmetry with a generalized CP symmetry, broken to two residual CP symmetries in the neutrino sector, recovering familiar results for PMNS predictions, together with new results for flavour dependent leptogenesis.

  4. Flavour physics and CP violation

    Indian Academy of Sciences (India)

    It is well known that the study of flavour physics and CP violation is very important to critically test the Standard Model and to look for possible signature of new physics beyond it. The observation of CP violation in kaon system in 1964 has ignited a lot of experimental and theoretical efforts to understand its origin and to look ...

  5. Revisiting and re-engineering the classical zinc finger peptide: consensus peptide-1 (CP-1).

    Science.gov (United States)

    Besold, Angelique N; Widger, Leland R; Namuswe, Frances; Michalek, Jamie L; Michel, Sarah L J; Goldberg, David P

    2016-04-01

    Zinc plays key structural and catalytic roles in biology. Structural zinc sites are often referred to as zinc finger (ZF) sites, and the classical ZF contains a Cys2His2 motif that is involved in coordinating Zn(II). An optimized Cys2His2 ZF, named consensus peptide 1 (CP-1), was identified more than 20 years ago using a limited set of sequenced proteins. We have reexamined the CP-1 sequence, using our current, much larger database of sequenced proteins that have been identified from high-throughput sequencing methods, and found the sequence to be largely unchanged. The CCHH ligand set of CP-1 was then altered to a CAHH motif to impart hydrolytic activity. This ligand set mimics the His2Cys ligand set of peptide deformylase (PDF), a hydrolytically active M(II)-centered (M = Zn or Fe) protein. The resultant peptide [CP-1(CAHH)] was evaluated for its ability to coordinate Zn(II) and Co(II) ions, adopt secondary structure, and promote hydrolysis. CP-1(CAHH) was found to coordinate Co(II) and Zn(II) and a pentacoordinate geometry for Co(II)-CP-1(CAHH) was implicated from UV-vis data. This suggests a His2Cys(H2O)2 environment at the metal center. The Zn(II)-bound CP-1(CAHH) was shown to adopt partial secondary structure by 1-D (1)H NMR spectroscopy. Both Zn(II)-CP-1(CAHH) and Co(II)-CP-1(CAHH) show good hydrolytic activity toward the test substrate 4-nitrophenyl acetate, exhibiting faster rates than most active synthetic Zn(II) complexes.

  6. Testing New Indirect CP Violation

    International Nuclear Information System (INIS)

    Grossman, Yuval; Nir, Yosef; Perez, Gilad

    2009-01-01

    If new CP violating physics contributes to neutral meson mixing, but its contribution to CP violation in decay amplitudes is negligible, then there is a model independent relation between four (generally independent) observables related to the mixing: the mass splitting (x), the width splitting (y), the CP violation in mixing (1-|q/p|), and the CP violation in the interference of decays with and without mixing (φ). For the four neutral meson systems, this relation can be written in a simple approximate form: ytanφ≅x(1-|q/p|). In the K system, all four observables have been measured and obey the relation to excellent accuracy. For the B s and D systems, new predictions are provided. The success or failure of these relations will probe the physics that is responsible for the CP violation.

  7. CP-violation and instantons

    International Nuclear Information System (INIS)

    Han, C.G.

    1980-01-01

    Effects of Yang-Mills instantons on CP-violating strong interactions are studied. Using simplified models of CP-noninvariant weak interactions, we calculate the induced strong CP-violation. Even in the simple examples studied, the CP-violating phase of a vacuum-to-vacuum transition amplitude differs in general from the phase of the determinant of the quark mass matrix multiplied by the topological charge of the background Yang-Mills field. Then several CP-violating phenomena such as eta → 2π decay and neutron electric dipole moment induced by instantons are studied. The result of our explicit calculation of eta → 2π decay strength verifies the current algebraic method used by Crewther et al. We also present a calculation of the instanton contribution, in the dilute gas approximation for instanton gas, to the electric dipole moment of a free quark without using 't Hooft's effective Lagrangian

  8. A CpG oligonucleotide can protect mice from a low aerosol challenge dose of Burkholderia mallei.

    Science.gov (United States)

    Waag, David M; McCluskie, Michael J; Zhang, Ningli; Krieg, Arthur M

    2006-03-01

    Treatment with an oligodeoxynucleotide (ODN) containing CPG motifs (CpG ODN 7909) was found to protect BALB/c mice from lung infection or death after aerosol challenge with Burkholderia mallei. Protection was associated with enhanced levels of gamma interferon (IFN-gamma)-inducible protein 10, interleukin-12 (IL-12), IFN-gamma, and IL-6. Preexposure therapy with CpG ODNs may protect victims of a biological attack from glanders.

  9. Affect

    NARCIS (Netherlands)

    Cetinic, M.; Diamanti, J.; Szeman, I.; Blacker, S.; Sully, J.

    2017-01-01

    This chapter historicizes four divergent but historically contemporaneous genres of affect theory – romantic, realist, speculative, and materialist. While critics credited with the turn to affect in the 1990s wrote largely in the wake of poststructuralism from the perspective of gender and queer

  10. Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation.

    LENUS (Irish Health Repository)

    Murphy, Derek M

    2009-01-01

    BACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified\\/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the

  11. Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember

    Directory of Open Access Journals (Sweden)

    Irfa'ina Rohana Salma

    2015-06-01

    Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik  baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi;  (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources

  12. CP-Recursion in Danish

    DEFF Research Database (Denmark)

    Nyvad, Anne Mette; Christensen, Ken Ramshøj; Vikner, Sten

    2017-01-01

    Based on data from extraction, embedded V2, and complementizer stacking, this paper proposes a cP/CP-analysis of CP-recursion in Danish. Because extraction can be shown to be possible from relative clauses, wh-islands, and adverbial clauses, and given that long extraction is successive......-cyclic, an extra specifier position has to be available as an escape hatch. Consequently, such extractions require a CP-recursion analysis, as has been argued for embedded V2 and for complementizer stacking. Given that CP-recursion in embedded V2 clauses does not allow extraction, whereas other types of CP......-recursion do, we suggest that embedded V2 is fundamentally different, in that main clause V2 and embedded V2 involve a CP (“big CP”), whereas all other clausal projections above IP are instances of cP (“little cP”). The topmost “little” c° has an occurrence feature that enables extraction but bars spell...

  13. Is CP a gauge symmetry?

    International Nuclear Information System (INIS)

    Choi, K.; Kaplan, D.B.; Nelson, A.E.

    1993-01-01

    Conventional solutions to the strong CP problem all require the existence of global symmetries. However, quantum gravity may destroy global symmetries, making it hard to understand why the electric dipole moment of the neutron (EDMN) is so small. We suggest here that CP is actually a discrete gauge symmetry, and is therefore not violated by quantum gravity. We show that four-dimensional CP can arise as a discrete gauge symmetry in theories with dimensional compactification, if the original number of Minkowski dimensions equals 8k+1, 8k+2 or 8k+3, and if there are certain restrictions on the gauge group; these conditions are met by superstrings. CP may then be broken spontaneously below 10 9 GeV, explaining the observed CP violation in the kaon system without inducing a large EDMN. We discuss the phenomenology of such models, as well as the peculiar properties of cosmic 'SP strings' which could be produced at the compactification scale. Such strings have the curious property that a particle carried around the string is turned into its CP conjugate. A single CP string renders four-dimensional space-time nonorientable. (orig.)

  14. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  15. Flavour Physics and CP Violation

    CERN Document Server

    Fleischer, Robert

    2006-01-01

    The starting point of these lectures is an introduction to the weak interactions of quarks and the Standard-Model description of CP violation, where the central role is played by the Cabibbo-Kobayashi-Maskawa matrix and the corresponding unitarity triangles. Since the B-meson system will govern the stage of (quark) flavour physics and CP violation in this decade, it will be our main focus. We shall classify B-meson decays, introduce the theoretical tools to deal with them, investigate the requirements for non-vanishing CP-violating asymmetries, and discuss the main strategies to explore CP violation and the preferred avenues for physics beyond the Standard Model to enter. This formalism is then applied to discuss the status of important B-factory benchmark modes, where we focus on puzzling patterns in the data that may indicate new-physics effects, as well as the prospects for B-decay studies at the LHC.

  16. Flavour physics and CP violation

    Indian Academy of Sciences (India)

    status and prospectives of the flavour physics associated with the strange, charm and .... might reveal something completely unexpected. Standard Model weak ..... Thus, in order to have an observable CP violation effect in the SM, the mixing.

  17. Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeffrey L.; Francino, M. Pilar

    2007-05-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

  18. BayesMotif: de novo protein sorting motif discovery from impure datasets.

    Science.gov (United States)

    Hu, Jianjun; Zhang, Fan

    2010-01-18

    Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

  19. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed....

  20. New physics effects on CP violation in B decays

    International Nuclear Information System (INIS)

    Nir, Y.

    1993-01-01

    The author reviews new physics effects on CP violation in B decays. In chapter 2 he introduces the formalism, and discusses the Standard Model picture of CP violation in B decays, with special emphasis on the cleanliness of the predictions. Chapter 3 gives a general discussion of new physics effects: he points out the ingredients in the analysis that are sensitive to new physics and deduces the type of new physics that is most likely to modify the Standard Model predictions. Explicit examples are given in chapter 4: a model with Z-mediated flavor changing neutral currents demonstrates in which ways the new physics will manifest itself in CP asymmetries in B decays; a supersymmetric model with open-quotes quark-squark alignmentclose quotes mechanism shows that supersymmetry may affect CP asymmetries in B decays, even though the minimal supersymmetric Standard Model does not; multi-scalar models may affect the asymmetries even in the absence of new CP violating phases; schemes for quark mass matrices will be crucially tested by the CP asymmetries. In chapter 5 he explains how, if deviations from the Standard Model predictions are measured, one will be able to learn detailed features of the New Physics that is responsible for that

  1. CP violation and supersymmetry-breaking in superstring models

    International Nuclear Information System (INIS)

    Dent, T.E.

    2000-09-01

    In this thesis I discuss aspects of the phenomenology of heterotic string, theory, using low-energy effective supergravity models. I investigate the origin of CP violation, the implications for low-energy physics of the modular invariance of the theory, supersymmetry-breaking via gaugino condensation in a hidden sector, and the interplay between these topics. I review the theory of CP violation and the problem of CP violation in supersymmetry phenomenology. In a scenario where the origin of CP violation lies in the compactification of the extra dimensions of string theory, I present simple models which include a duality symmetry acting on the compactification modulus and on observable fields. I show how the structure of the theory affects CP-violating observables, and discuss the effect of such a symmetry on low-energy physics in general. I present a detailed investigation of supersymmetry-breaking by gaugino condensation in supergravity, in particular as applied to the stabilisation of string moduli. For hidden sectors with or without matter I calculate corrections to the usual formulae for the scalar potential and soft supersymmetry-breaking terms. I discuss the phenomenological implications of these corrections and show that they may affect the value of the compactification modulus. and consequently the prospects for predictions of CP violation in string models. (author)

  2. CpG-DNA enhancement the immune elicited as adjuvant of foot- and- mouth disease vaccine

    Directory of Open Access Journals (Sweden)

    Morshedi, A.

    2010-01-01

    Full Text Available In the present study the effect of the locally produced genetic adjuvant of ginea pig specific CpG-motif-containing oligodeoxynucleotide (CpG-ODN in an inactivated FMD virus vaccine was evaluated. Boosting the ginea pigs with FMD vaccine along with CpG-ODN adjuvant produced relatively higher ratio (5-fold of FMDV-specific IgG2a / IgG1 than those vaccinated in the absence of CpG-ODN. The neutralizing antibody (NA titer induced by FMD vaccine along with CpG-ODN adjuvant was significantly higher (8-fold than NA titer induced by the classical FMD vaccine in Alum adjuvant. The titer of NA and virus clearance from serum was consistently and significantly higher in animals primed with FMD vaccine and boosted by CpG-ODN than the classical FMD vaccine. The results of this study showed the potential of CpG-ODN as a genetic adjuvant to FMD vaccine in the development of Th1 responses.

  3. Measuring $CP$ violation with $\\Delta A_{CP}$ at LHCb

    CERN Document Server

    Pearce, Alex

    2014-01-01

    The control of systematic uncertainties is a key component of many analyses performed at the Large Hadron Collider, and will only become more important as more data are taken during Run II. Many of the CP measurements performed using the LHCb detector have statistical precisions below the per cent level, and so particular care must be taken in this area. One technique for dealing with the various production and detection asymmetries which can mask the physics asymmetry of interest, and increase the measurement’s systematic uncertainty, is $\\Delta A_{CP}$ . The application of $\\Delta A_{CP}$ in three separate LHCb analyses of $D^{0}$ and $\\Lambda_{b}^{0}$ decays will be discussed, along with prospects for applying the technique to $\\Lambda_{c}^{+}$ decays.

  4. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

    Science.gov (United States)

    Tran, Ngoc Tam L; Huang, Chun-Hsi

    2014-02-20

    ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.

  5. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  6. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

    Directory of Open Access Journals (Sweden)

    Keightley Peter D

    2008-09-01

    Full Text Available Abstract Background Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related. Results Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misassigned as CpG. Paradoxically, this bias is most severe between closely related species, because a minimum of two substitutions are required to misassign a true ancestral CpG site as non-CpG whereas only a single substitution is required to misassign a true ancestral non-CpG site as CpG in a two branch tree. We also show that CpG misassignment bias differentially affects fourfold degenerate and noncoding sites due to differences in base composition such that fourfold degenerate sites can appear to be evolving more slowly than noncoding sites. We demonstrate that the effects predicted by our simulations occur in a real evolutionary setting by comparing substitution rates estimated from human-chimp coding and intronic sequence using CpG/non-CpG assignment with estimates derived from a method that is largely free from bias. Conclusion Our study demonstrates that a common method of assigning sites into CpG and non CpG classes in pairwise alignments is seriously biased and recommends against the adoption of ad hoc methods of ancestral state assignment.

  7. Finding CP-violating Higgses

    OpenAIRE

    Kalinowski, Jan

    1999-01-01

    In a general two-Higgs-doublet model with CP violation in the Higgs sector, the three neutral physical Higgs bosons have no definite CP properties. A new sum rule relating Yukawa and Higgs-Z couplings implies that a neutral Higgs boson cannot escape detection at an e^+e^- collider if it is kinematically accessible in Z+Higgs, $b\\bar b+$Higgs and $t\\bar t+$Higgs production, irrespective of the mixing angles and the masses of the other neutral Higgs bosons. The implications of the sum rules for...

  8. On the strong CP problem

    Energy Technology Data Exchange (ETDEWEB)

    Dowrick, N.J. (Dept. of Physics, Oxford (United Kingdom)); McDougall, N.A. (National Lab. for High Energy Physics, Tsukuba, Ibaraki (Japan))

    1992-07-09

    We show that two well-known solutions to the strong CP problem, the axion and a massless quark, may be understood in terms of the mechanism recently proposed by Samuel where long-range interactions between topological charges may be responsible for the removal of CP violation. We explain how the axion and a QCD meson (identified as the {eta}' if all quarks are massless) suppress fluctuations in global topological charge by almost identical dynamical although the masses, couplings and relevant length scales are very different. Furthermore, we elucidate the precise origin of the {eta}' mass. (orig.).

  9. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  10. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

  11. MotifNet: a web-server for network motif analysis.

    Science.gov (United States)

    Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

    2017-06-15

    Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  12. CP violation in B decays

    International Nuclear Information System (INIS)

    Quinn, H.R.

    1994-02-01

    She reviews how one can test the Standard Model predictions for CP violation. This test requires sufficient independent measurements to overconstrain the model parameters and thus be sensitive to possible beyond Standard Model contributions. She addresses the challenges for theory as well as for experiment to achieve such a test

  13. CP Violation and B Physics

    International Nuclear Information System (INIS)

    Quinn, Helen R

    2001-01-01

    These lectures provide a basic overview of topics related to the study of CP Violation in B decays. In the first lecture, I review the basics of discrete symmetries in field theories, the quantum mechanics of neutral but flavor-non-trivial mesons, and the classification of three types of CP violation [1]. The actual second lecture which I gave will be separately published as it is my Dirac award lecture and is focused on the separate topic of strong CP Violation. In Lecture 2 here, I cover the Standard Model predictions for neutral B decays, and in particular discuss some channels of interest for CP Violation studies. Lecture 3 reviews the various tools and techniques used to deal with the hadronic physics effects. In Lecture 4, I briefly review the present and planned experiments that can study B decays. I cannot teach all the details of this subject in this short course, so my approach is instead to try to give students a grasp of the relevant concepts and an overview of the available tools. The level of these lectures is introductory. I will provide some references to more detailed treatments and current literature, but this is not a review article so I do not attempt to give complete references to all related literature. By now there are some excellent textbooks that cover this subject in great detail [1]. I refer students to these for more details and for more complete references to the original literature

  14. B physics and CP violation

    International Nuclear Information System (INIS)

    Quinn, H.

    2002-01-01

    These lectures provide a basic overview of topics related to the study of CP Violation in B decays. In the first lecture, I review the basics of discrete symmetries in field theories, the quantum mechanics of neutral but flavor-non-trivial mesons, and the classification of three types of CP violation. The actual second lecture which I gave will be separately published as it is my Dirac award lecture and is focussed on the separate topic of strong CP Violation. In Lecture 2 here, I cover the Standard Model predictions for neutral B decays, and in particular discuss some channels of interest for CP Violation studies. Lecture 3 reviews the various tools and techniques used to deal with the hadronic physics effects. In Lecture 4, I briefly review the present and planned experiments that can study B decays. I cannot teach all the details of this subject in this short course, so my approach is instead to try to give students a grasp of the relevant concepts and an overview of the available tools. The level of these lectures is introductory. I will provide some references to more detailed treatments and current literature, but this is not a review article so I do not attempt to give complete references to all related literature. By now there are some excellent textbooks that cover this subject in great detail. I refer students to these for more details and for more complete references to the original literature. (author)

  15. Flavour Physics and CP Violation

    CERN Document Server

    Fleischer, Robert

    2005-01-01

    The starting point of these lectures is an introduction to the weak interactions of quarks and the Standard-Model description of CP violation, where the key element is the Cabibbo--Kobayashi--Maskawa matrix and the corresponding unitarity triangles. Since the B-meson system will govern the stage of (quark) flavour physics and CP violation in this decade, it will be -- after a brief look at the kaon system -- our main focus. We shall classify B-meson decays, introduce the theoretical tools to deal with them, explore the requirements for non-vanishing CP-violating asymmetries, and discuss B^0_q--B^0_q_bar mixing (q={d,s}). We will then turn to B-factory benchmark modes, discuss the physics potential of B^0_s mesons, which is particularly promising for B-decay experiments at hadron colliders, and emphasize the importance of studies of rare decays, which are absent at the tree level in the Standard Model, complement nicely the studies of CP violation, and provide interesting probes for new physics.

  16. CP violation in neutral B decays to non-CP-eigenstates

    International Nuclear Information System (INIS)

    Kayser, B.

    1992-01-01

    If CP violation comes from complex phases in the quark mixing matrix, then neutral B decays to CP eigenstates will exhibit large, cleanly-predicted CP-violating effects. The authors show that the same is true of neutral B decays to several types of ''near-CP-eigenstates.'' By experimentally studying the latter decays as well as those to the CP eigenstates, one will be able to obtain more definitive information on CP violation from a given number of B mesons

  17. Discriminative Motif Discovery via Simulated Evolution and Random Under-Sampling

    OpenAIRE

    Song, Tao; Gu, Hong

    2014-01-01

    Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the sta...

  18. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    Science.gov (United States)

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  19. Polycomb-like proteins link the PRC2 complex to CpG islands

    Energy Technology Data Exchange (ETDEWEB)

    Li, Haojie; Liefke, Robert; Jiang, Junyi; Kurland, Jesse Vigoda; Tian, Wei; Deng, Pujuan; Zhang, Weidi; He, Qian; Patel, Dinshaw J.; Bulyk, Martha L.; Shi, Yang; Wang, Zhanxin

    2017-09-06

    The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression1,2 and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as PHF1, MTF2 and PHF19, are PRC2-associated factors that form sub-complexes with PRC2 core components3, and have been proposed to modulate the enzymatic activity of PRC2 or the recruitment of PRC2 to specific genomic loci4,5,6,7,8,9,10,11,12,13. Mammalian PRC2-binding sites are enriched in CG content, which correlates with CpG islands that display a low level of DNA methylation14. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. Here we solve the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We show that the extended homologous regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a completely different manner from the canonical winged-helix DNA recognition motif. We also show that the PCL extended homologous domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic stem cells. Our research provides the first, to our knowledge, direct evidence to demonstrate that PCL proteins are crucial for PRC2 recruitment to CpG islands, and further clarifies the roles of these proteins in transcriptional regulation in vivo.

  20. Hunting Motifs in Situla Art

    Directory of Open Access Journals (Sweden)

    Andrej Preložnik

    2013-07-01

    Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th  and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and

  1. Precise predictions for CP asymmetries in B decays

    Energy Technology Data Exchange (ETDEWEB)

    Nierste, Ulrich; Frings, Philipp [Institut fuer Theoretische Teilchenphysik, KIT, Karlsruhe (Germany)

    2016-07-01

    The extraction of fundamental CP phases from B{sub d} or B{sub s} decays to charmonium is affected by penguin contributions. We show how these contributions can be calculated with dynamical QCD-based methods and present our predictions for a variety of decay modes and briefly discuss branching ratios in B→ DD decays.

  2. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  3. Deciphering functional glycosaminoglycan motifs in development.

    Science.gov (United States)

    Townley, Robert A; Bülow, Hannes E

    2018-03-23

    Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Bayesian centroid estimation for motif discovery.

    Science.gov (United States)

    Carvalho, Luis

    2013-01-01

    Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  5. Bayesian centroid estimation for motif discovery.

    Directory of Open Access Journals (Sweden)

    Luis Carvalho

    Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  6. Flavour physics and CP violation

    CERN Document Server

    Nir, Y.

    2015-05-22

    We explain the many reasons for the interest in flavor physics. We describe flavor physics and the related CP violation within the Standard Model, and explain how the B-factories proved that the Kobayashi-Maskawa mechanism dominates the CP violation that is observed in meson decays. We explain the implications of flavor physics for new physics, with emphasis on the “new physics flavor puzzle”, and present the idea of minimal flavor violation as a possible solution. We explain why the values flavor parameters of the Standard Model are puzzling, present the Froggatt-Nielsen mechanism as a possible solution, and describe how measurements of neutrino parameters are interpreted in the context of this puzzle. We show that the recently discovered Higgs-like boson may provide new opportunities for making progress on the various flavor puzzles.

  7. Constraints on the CP-Violating MSSM

    CERN Document Server

    Arbey, A; Godbole, R M; Mahmoudi, F

    2016-01-01

    We discuss the prospects for observing CP violation in the MSSM with six CP-violating phases, using a geometric approach to maximise CP-violating observables subject to the experimental upper bounds on electric dipole moments. We consider constraints from Higgs physics, flavour physics, the dark matter relic density and spin-independent scattering cross section with matter.

  8. CP violation without elementary scalar fields

    International Nuclear Information System (INIS)

    Eichten, E.; Lane, K.; Preskill, J.

    1980-04-01

    Dynamically broken gauge theories of electroweak interactions provide a natural mechanism for generating CP violation. Even if all vacuum angles are unobservable, strong CP violation is not automatically avoided. In the absence of strong CP violation, the neutron electric dipole moment is expected to be of order 10 -24 e cm

  9. CP-violations in B decays

    Indian Academy of Sciences (India)

    Recent results on CP-violation measurements in decays from energy asymmetric -factory experiments are reported. Thanks to large accumulated data samples, CP-violations in decays in mixing-decay interference and direct CP-violation are now firmly established. The measurements of three angles of the unitarity ...

  10. ANNIVERSARY: 25 years without CP

    International Nuclear Information System (INIS)

    Riordan, Michael

    1989-01-01

    In 1964 a small group of Princeton University physicists led by Jim Cronin and Val Fitch performed a landmark experiment at Brookhaven. Using a double-arm spectrometer, they showed that long-lived neutral kaons occasionally decayed into a pair of pions - violating the hitherto sacrosanct CP symmetry of combined mirror reflection and particle-antiparticle switching. From May 21-26 scientists gathered at the Chateau de Blois, southwest of Paris, to celebrate the 25th anniversary of this achievement

  11. ANNIVERSARY: 25 years without CP

    Energy Technology Data Exchange (ETDEWEB)

    Riordan, Michael

    1989-07-15

    In 1964 a small group of Princeton University physicists led by Jim Cronin and Val Fitch performed a landmark experiment at Brookhaven. Using a double-arm spectrometer, they showed that long-lived neutral kaons occasionally decayed into a pair of pions - violating the hitherto sacrosanct CP symmetry of combined mirror reflection and particle-antiparticle switching. From May 21-26 scientists gathered at the Chateau de Blois, southwest of Paris, to celebrate the 25th anniversary of this achievement.

  12. New look at CP violation

    International Nuclear Information System (INIS)

    Iqbal, M.J.; Miller, G.A.

    1990-01-01

    The CP-violating (CPV) kaonic matrix elements ε', ImA 0 , and ImA 2 are used to compute CPV observables in baryonic systems. The numerical results for the electric dipole moment and the difference between Λ and bar Λ decay parameters are similar to other approaches that use quark operators. Relations between the neutron electric dipole moment, CPV pion-nucleon coupling constants, and Λ-decay parameters are derived

  13. Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

    OpenAIRE

    Zabet, NR; Catoni, Marco; Prischi, F; Paszkowski, Jerzy Waclaw

    2017-01-01

    Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylas...

  14. Quark mixing and CP violation

    International Nuclear Information System (INIS)

    Paschos, E.A.

    1992-01-01

    These lectures present a pedagogical introduction to the topics quark mixing and CP violation. They explain how the mixing matrix comes about and reviews the values of constraints for its elements. The second chapter reviews the CP transformation properties of amplitudes and defines the quantities which are measured in the experiments. Then it reviews the theory of CP violation in the standard model. In addition to the phase and the angles introduced through the flavor matrix, numerical predictions also depend (a) on hadronic matrix elements of weak current operators and (b) the short distance expansion of effective Hamiltonians computed by methods of Quantum Chromodynamics (QCD). I also review these topics and present predictions for (ε'/ε) which are shown to be consistent with the experiments. Last but not least, the article is divided into sections which are as self-contained as possible. The article assumes a general knowledge of the electroweak theory. For guidance, the interested reader will find a table of contents at the end of the text. (author). 29 refs, 5 figs, 1 tab

  15. CP violation experiment at Fermilab

    International Nuclear Information System (INIS)

    Hsiung, Yee B.

    1990-07-01

    The E731 experiment at Fermilab has searched for ''direct'' CP violation in K 0 → ππ, which is parametrized by var-epsilon '/var-epsilon. For the first time, in 20% of the data set, all four modes of the K L,S → π + π - (π 0 π 0 ) were collected simultaneously, providing a great check on the systematic uncertainty. The result is Re(var-epsilon '/var-epsilon) = -0.0004 ± 0.0014 (stat) ± 0.0006(syst), which provides no evidence for ''direct'' CP violation. The CPT symmetry has also been tested by measuring the phase difference Δφ = φ 00 - φ ± between the two CP violating parameters η 00 and η ± . We fine Δφ = -0.3 degrees ± 2.4 degree(stat) ± 1.2 degree(syst). Using this together with the world average φ ± , we fine that the phase of the K 0 -bar K 0 mixing parameter var-epsilon is 44.5 degree ± 1.5 degree. Both of these results agree well with the predictions of CPT symmetry. 17 refs., 10 figs

  16. Some ideas for learning CP-theories

    OpenAIRE

    Fierens, Daan

    2008-01-01

    Causal Probabilistic logic (CP-logic) is a language for describing complex probabilistic processes. In this talk we consider the problem of learning CP-theories from data. We briefly discuss three possible approaches. First, we review the existing algorithm by Meert et al. Second, we show how simple CP-theories can be learned by using the learning algorithm for Logical Bayesian Networks and converting the result into a CP-theory. Third, we argue that for learning more complex CP-theories, an ...

  17. B decays and models for CP violation

    International Nuclear Information System (INIS)

    He, X.

    1996-01-01

    The decay modes B to ππ, ψK S , K - D, πK, and ηK are promising channels to study the unitarity triangle of the CP-violating Cabibbo-Kobayashi-Maskawa (CKM) matrix. In this paper I study the consequences of these measurements in the Weinberg model. I show that using the same set of measurements, the following different mechanisms for CP violation can be distinguished: (1) CP is violated in the CKM sector only; (2) CP is violated spontaneously in the Higgs sector only; and (3) CP is violated in both the CKM and Higgs sectors. copyright 1996 The American Physical Society

  18. ROMANIAN TRADITIONAL MOTIF ELEMENT OF MODERNITY IN CLOTHING

    Directory of Open Access Journals (Sweden)

    ŞUTEU Marius Darius

    2017-05-01

    Full Text Available In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the T-shirt for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the University of Oradea and traditional motif was selected from a collection comprising a number of Romanian traditional motifs from different parts of the country and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. The embroidery was done using BERNINA Embroidery Software Designer Plus Software. This software allows you to export the model to any domestic or industrial embroidery machine regardless of brand. Finally we observed the resistance of the printed and embroided model to various: elasticity, resistance to abrasion and a sensory analysis on the preservation of color. After testing we noticed the imprint resistance applied to the fabric, resulting in a quality that makes possible to keep the Romanian traditional motif from generation to generation.

  19. V2 and cP/CP

    DEFF Research Database (Denmark)

    Vikner, Sten; Christensen, Ken Ramshøj; Nyvad, Anne Mette

    2017-01-01

    As in Nyvad et al. (2017), we will explore a particular derivation of (embedded) V2, in terms of a cP/CP-distinction, which may be seen as a version of the CP-recursion analysis (de Haan & Weerman 1986; Vikner 1995 and many others). e idea is that because embedded V2 clauses do not allow extraction......, whereas other types of CP-recursion clauses do (Christensen et al. 2013a; 2013b; Christensen & Nyvad 2014), CP-recursion in embedded V2 is assumed to be fundamentally di erent from other kinds of CP-recursion, in that main clause V2 and embedded V2 involve a CP (“big CP”), whereas other clausal...... projections above IP are instances of cP (“little cP”)....

  20. CP invariance: a point of view

    International Nuclear Information System (INIS)

    Mohan, Gyan

    1983-01-01

    That the longlived component L of K 0 has both CP = +1 and CP = -1 modes of decay is often cited as evidence of violation of CP invariance. The careful ones find the compelling evidence to be the non-dilution of the regeneration interference pattern when the incident K 0 beam is mixed even substantially with anti-K 0 . However the two phenomena comprehensively imply that L has a CP = +1 component Lsub(+) and CP = -1 component Lsub(-) and that the longlived component of both K 0 and anti-K 0 are one and the same L. This does not demand abandoning CP invariance. It does imply that anti-K 0 is not the CP conjugate of K 0 . (author)

  1. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

  2. Circadian cycle-dependent MeCP2 and brain chromatin changes.

    Directory of Open Access Journals (Sweden)

    Alexia Martínez de Paz

    Full Text Available Methyl CpG binding protein 2 (MeCP2 is a chromosomal protein of the brain, very abundant especially in neurons, where it plays an important role in the regulation of gene expression. Hence it has the potential to be affected by the mammalian circadian cycle. We performed expression analyses of mice brain frontal cortices obtained at different time points and we found that the levels of MeCP2 are altered circadianly, affecting overall organization of brain chromatin and resulting in a circadian-dependent regulation of well-stablished MeCP2 target genes. Furthermore, this data suggests that alterations of MeCP2 can be responsible for the sleeping disorders arising from pathological stages, such as in autism and Rett syndrome.

  3. Completing the Heterocubane Family [Cp*AlE]4 (E = O, S, Se, and Te) by Selective Oxygenation and Sulfuration of [Cp*Al]4: Density Functional Theory Calculations of [Cp*AlE]4 and Reactivity of [Cp*AlO]4 toward Hydrolysis.

    Science.gov (United States)

    Stelzer, Adrian C; Hrobárik, Peter; Braun, Thomas; Kaupp, Martin; Braun-Cula, Beatrice

    2016-05-16

    The subvalent aluminum compound [Cp*Al]4 (1) reacts with dioxygen, N2O, or sulfur to yield the heterocubane complexes [Cp*AlX]4 [X = O (2) and S (3)]. Treatment of [Cp*AlO]4 (2) with (tBuO)3SiOH gave [(tBuO)3SiOAlO]4 (6) and Cp*H. The structures and spectroscopic data of the Al clusters are supported by density functional theory (DFT) calculations, which also demonstrate the importance of noncovalent interactions (NCI) in oligomeric Al(I) complexes as well as in [Cp*AlS]4 and the heavier homologues of Se and Te. The computed (27)Al NMR shifts indicate a deshielding at the Al centers with increasing electronegativity of the chalcogen atom as well as significant spin-orbit shielding effects within the heavier heterocubane [Al4E4] cores. Further hydrolysis of 6 with an additional amount of silanol in the presence of water resulted in the formation of [Al4(OH)6(OH2)2(OSiOtBu3)6] (7), which shows a structural motif found in boehmite and diaspore.

  4. Flavor Physics & CP Violation 2015

    Science.gov (United States)

    "Flavor Physics & CP violation 2015" (FPCP 2015) was held in Nagoya, Japan, at Nagoya University, from May 25 to May 29 2015. This is the 13th meeting of the series of annual conferences started in Philadelphia, PA, USA in 2002. The aim of the conference is to review developments in flavor physics and CP violation, in both theory and experiment, exploiting the potential to study new physics at the LHC and future facilities. The topics include CP violation, rare decays, CKM elements with heavy quark decays, flavor phenomena in charged leptons and neutrinos, and also interplay between flavor and LHC high Pt physics. The FPCP2015 conference had more than 140 participants, including researchers from abroad and many young researchers (postdocs and students). The conference consisted of plenary talks and poster presentations. The plenary talks include 2 overview talks, 48 review talks, and 2 talks for outlook in theories and experiments, given by world leading researchers. There was also a special lecture by Prof. Makoto Kobayashi, one of the Nobel laureates in 2008. The poster session had 41 contributions. Many young researchers presented their works. These proceedings contain written documents for these plenary and poster presentations. The full scientific program and presentation materials can be found at http://fpcp2015.hepl.phys.nagoya-u.ac.jp/. We would like to thank the International Advisory Committee for their invaluable assistance in coordinating the scientific program and in helping to identifying many speakers. Thanks are also due to the Local Organizing Committee for tireless efforts for smooth running of the conference and very enjoyable social activities. We also thank the financial supports provided by Japanese Scociety for the Promotion of Science (JSPS) unfer the Grant-in-Aid for Scientific Research (S) "Probing New Physics with Tau-Lepton" (No. 26220706), by Nagoya University under the Program for Promoting the Enhancement of Research Universities, and

  5. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  6. Analisis Unsur Matematika pada Motif Sulam Usus

    Directory of Open Access Journals (Sweden)

    Fredi Ganda Putra

    2017-12-01

    Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the

  7. Experience on CP1 turbines

    International Nuclear Information System (INIS)

    Moinaud, C.

    1984-01-01

    Analysis of the experience acquired on the behaviour of the turbine itself, excluding alternators, superheaters... of the nuclear power plants of the French program contract CP1 (Fessenhein prototype): method of anomaly process (assumption, scenarios, calculations and hierarchy of the assumptions), study of the accidents on the shutdown valves and control valves (HP admission devices), on the LP admission devices, on the HP module (leakage at the parting line, bolt and screw accidents), on the LP module (diaphragm, diapragm support erosion, rotor anomaly, blade anomaly with rupture of the wire bracing), behaviour of the shafting and of the pillars (radial and axial floating) and at last global behaviour of the group [fr

  8. Para-psychobiotic Lactobacillus gasseri CP2305 ameliorates stress-related symptoms and sleep quality.

    Science.gov (United States)

    Nishida, K; Sawada, D; Kawai, T; Kuwano, Y; Fujiwara, S; Rokutan, K

    2017-12-01

    To confirm the stress-relieving effects of heat-inactivated, enteric-colonizing Lactobacillus gasseri CP2305 (paraprobiotic CP2305) in medical students taking a cadaver dissection course. Healthy students (21 males and 11 females) took paraprobiotic CP2305 daily for 5 weeks during a cadaver dissection course. The General Health Questionnaire and the Pittsburgh Sleep Quality Index were employed to assess stress-related somatic symptoms and sleep quality respectively. The aggravation of stress-associated somatic symptoms was observed in female students (P = 0·029). Sleep quality was improved in the paraprobiotic CP2305 group (P = 0·038), particularly in men (P = 0·004). Among men, paraprobiotic CP2305 shortened sleep latency (P = 0·035) and increased sleep duration (P = 0·048). Diarrhoea-like symptoms were also effectively controlled with CP2305 (P = 0·005) in men. Thus, we observed sex-related differences in the effects of paraprobiotic CP2305. In addition, CP2305 affected the growth of faecal Bacteroides vulgatus and Dorea longicatena, which are involved in intestinal inflammation. CP2305 is a potential paraprobiotic that regulates stress responses, and its beneficial effects may depend on specific cell component(s). This study characterizes the effects of a stress-relieving para-psychobiotic in humans. © 2017 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

  9. CpG oligodeoxynucleotides are potent enhancers of radio- and chemoresponses of murine tumors

    International Nuclear Information System (INIS)

    Mason, Kathryn A.; Neal, Robert; Hunter, Nancy; Ariga, Hisanori; Ang, Kian; Milas, Luka

    2006-01-01

    Background and purpose: Synthetic oligodeoxynucleotides (ODNs) containing unmethylated cytosine-guanine (CpG) motifs bind to Toll-like receptor 9 (TLR9) and stimulate both innate and adaptive immune reactions and possess anti-tumor activity. We recently reported that CpG ODN 1826 strongly enhances radioresponse of both immunogenic [Milas L, Mason K, Ariga H, et al. CpG oligodeoxynucleotide enhances tumor response to radiation. Cancer Res 2004;64:5074-7] and non-immunogenic [Mason KA, Ariga H, Neal R, et al. Targeting toll-like receptor-9 with CpG oligodeoxynucleotides enhances tumor response to fractionated radiotherapy. Clin Cancer Res 2005;11:361-9] murine tumors. Using two immunogenic murine tumors, a fibrosarcoma (FSa) and a mammary carcinoma (MCa-K), the present study explored whether CpG ODN 1826 also improves the response of murine tumors to the chemotherapeutic agent docetaxel (DOC). Materials and methods: CpG ODN 1826 (100 μg) was given sc three times: when leg tumors were 6 mm, when they grew to 8 mm and again 1 week later. DOC (33 mg/kg iv) and local tumor radiation (10 Gy) were given when tumors were 8 mm. Effects of the treatments were assayed by tumor growth delay, defined as days for tumors to grow from 8 to 12 mm in diameter. Results: Treatment with CpG ODN 1826 resulted in strongly enhanced response of FSa tumors to radiation and MCa-K tumors to the chemotherapeutic agent DOC. Enhancement of tumor treatment response was demonstrated by a strong prolongation in the primary tumor treatment endpoint, tumor growth delay. Coincidentally, this treatment also resulted in a higher rate of tumor cure than that observed after tumor radiotherapy or chemotherapy alone. When all three agents were combined the effect was comparable to that of the combination of CpG ODN 1826 with radiation in the case of FSa or of the combination of CpG ODN 1826 with DOC in the case of MCa-K. Conclusion: Overall results show that CpG ODN 1826 can markedly improve tumor response

  10. A Built-In CpG Adjuvant in RSV F Protein DNA Vaccine Drives a Th1 Polarized and Enhanced Protective Immune Response

    Directory of Open Access Journals (Sweden)

    Yao Ma

    2018-01-01

    Full Text Available Human respiratory syncytial virus (RSV is the most significant cause of acute lower respiratory infection in children. However, there is no licensed vaccine available. Here, we investigated the effect of five or 20 copies of C-Class of CpG ODN (CpG-C motif incorporated into a plasmid DNA vaccine encoding RSV fusion (F glycoprotein on the vaccine-induced immune response. The addition of CpG-C motif enhanced serum binding and virus-neutralizing antibody responses in BALB/c mice immunized with the DNA vaccines. Moreover, mice vaccinated with CpG-modified vaccines, especially with the higher 20 copies, resulted in an enhanced shift toward a Th1-biased antibody and T-cell response, a decrease in pulmonary pathology and virus replication, and a decrease in weight loss after RSV challenge. This study suggests that CpG-C motif, cloned into the backbone of DNA vaccine encoding RSV F glycoprotein, functions as a built-in adjuvant capable of improving the efficacy of DNA vaccine against RSV infection.

  11. Armadillo motifs involved in vesicular transport.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

  12. DNA mutation motifs in the genes associated with inherited diseases.

    Directory of Open Access Journals (Sweden)

    Michal Růžička

    Full Text Available Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which reflects particular population where an effect of a common ancestor plays a role. To detect coldspots/hotspots unaffected by population bias, we analysed the presence of germline mutations obtained from HGMD database in the 5-nucleotide segments repeatedly occurring in genes associated with common inherited disorders, in particular, the PAH, LDLR, CFTR, F8, and F9 genes. Statistically significant sequences (mutational motifs rarely associated with mutations (coldspots and frequently associated with mutations (hotspots exhibited characteristic sequence patterns, e.g. coldspots contained purine tract while hotspots showed alternating purine-pyrimidine bases, often with the presence of CpG dinucleotide. Using molecular dynamics simulations and free energy calculations, we analysed the global bending properties of two selected coldspots and two hotspots with a G/T mismatch. We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutSα protein is noticeably bent.

  13. Direct AUC optimization of regulatory motifs.

    Science.gov (United States)

    Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

    2017-07-15

    The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  14. Phosphoinositide 3-kinaseγ controls the intracellular localization of CpG to limit DNA-PKcs-dependent IL-10 production in macrophages.

    Directory of Open Access Journals (Sweden)

    Kaoru Hazeki

    Full Text Available Synthetic oligodeoxynucleotides containing unmethylated CpG motifs (CpG stimulate innate immune responses. Phosphoinositide 3-kinase (PI3K has been implicated in CpG-induced immune activation; however, its precise role has not yet been clarified. CpG-induced production of IL-10 was dramatically increased in macrophages deficient in PI3Kγ (p110γ(-/-. By contrast, LPS-induced production of IL-10 was unchanged in the cells. CpG-induced, but not LPS-induced, IL-10 production was almost completely abolished in SCID mice having mutations in DNA-dependent protein kinase catalytic subunit (DNA-PKcs. Furthermore, wortmannin, an inhibitor of DNA-PKcs, completely inhibited CpG-induced IL-10 production, both in wild type and p110γ(-/- cells. Microscopic analyses revealed that CpG preferentially localized with DNA-PKcs in p110γ(-/- cells than in wild type cells. In addition, CpG was preferentially co-localized with the acidic lysosomal marker, LysoTracker, in p110γ(-/- cells, and with an early endosome marker, EEA1, in wild type cells. Over-expression of p110γ in Cos7 cells resulted in decreased acidification of CpG containing endosome. A similar effect was reproduced using kinase-dead mutants, but not with a ras-binding site mutant, of p110γ. Thus, it is likely that p110γ, in a manner independent of its kinase activity, inhibits the acidification of CpG-containing endosomes. It is considered that increased acidification of CpG-containing endosomes in p110γ(-/- cells enforces endosomal escape of CpG, which results in increased association of CpG with DNA-PKcs to up-regulate IL-10 production in macrophages.

  15. Discriminative motif discovery via simulated evolution and random under-sampling.

    Directory of Open Access Journals (Sweden)

    Tao Song

    Full Text Available Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  16. Discriminative motif discovery via simulated evolution and random under-sampling.

    Science.gov (United States)

    Song, Tao; Gu, Hong

    2014-01-01

    Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  17. B decays and models for CP violation

    International Nuclear Information System (INIS)

    He, Xiao Gang

    1995-12-01

    The decay modes B to π π,υK S , K - D, πK and ηK are promising channels to study the unitarity triangle of the CP violating Cabibbo-Kobayashi-Maskawa (CKM) matrix. The consequences of these measurements in the Weinberg model are discussed. It is shown that measurements of CP violation in B decay can be used to distinguish Standard Model from Weinberg model and that the following different mechanisms for CP violation can be distinguished: 1) CP is violated in the CKM sector only; 2) CP is violated spontaneously in the Higgs sector only; and 3) CP is violated in both the CKM and Higgs sectors. 27 refs., 4 figs

  18. Exploring CP Violation in the MSSM

    CERN Document Server

    Arbey, A.; Godbole, R.M.; Mahmoudi, F.

    2015-01-01

    We explore the prospects for observing CP violation in the minimal supersymmetric extension of the Standard Model (MSSM) with six CP-violating parameters, three gaugino mass phases and three phases in trilinear soft supersymmetry-breaking parameters, using the CPsuperH code combined with a geometric approach to maximize CP-violating observables subject to the experimental upper bounds on electric dipole moments. We also implement CP-conserving constraints from Higgs physics, flavour physics and the upper limits on the cosmological dark matter density and spin-independent scattering. We study possible values of observables within the constrained MSSM (CMSSM), the non-universal Higgs model (NUHM), the CPX scenario and a variant of the phenomenological MSSM (pMSSM). We find values of the CP-violating asymmetry A_CP in b -> s gamma decay that may be as large as 3%, so future measurements of A_CP may provide independent information about CP violation in the MSSM. We find that CP-violating MSSM contributions to the...

  19. Superweak-like models of CP violation

    International Nuclear Information System (INIS)

    Lavoura, L.

    1992-01-01

    I put forward a two-Higgs-doublet model in which CP violation is mediated only by the neutral Higgs bosons, via the mechanism of scalar-pseudoscalar mixing. In this model there is no CP violation in the exchange of either W bosons or of charged Higgs bosons. The model is therefore an approximate realization of the superweak theory of CP violation. It has only two basic CP-violating quantities. I point out that other models of this kind, but with more than two Higgs doublets, may also be built

  20. Alanine substitutions in the GXXXG motif alter C99 cleavage by γ-secretase but not its dimerization.

    Science.gov (United States)

    Higashide, Hidekazu; Ishihara, Seiko; Nobuhara, Mika; Ihara, Yasuo; Funamoto, Satoru

    2017-03-01

    The amyloid β (Aβ) protein is a major component of senile plaques, one of the neuropathological hallmarks of Alzheimer's disease. Amyloidogenic processing of amyloid precursor protein (APP) by β- and γ-secretases leads to production of Aβ. APP contains tandem triple repeats of the GXXXG motif in its extracellular juxtamembrane and transmembrane regions. It is reported that the GXXXG motif is related to protein-protein interactions, but it remains controversial whether the GXXXG motif in APP is involved in substrate dimerization and whether dimerization affects γ-secretase-dependent cleavage. Therefore, the relationship between the GXXXG motifs, substrate dimerization, and γ-secretase-dependent cleavage sites remains unclear. Here, we applied blue native poly acrylamide gel electrophoresis to examine the effect of alanine substitutions within the GXXXG motifs of APP carboxyl terminal fragment (C99) on its dimerization and Aβ production. Surprisingly, alanine substitutions in the motif failed to alter C99 dimerization in detergent soluble state. Cell-based and solubilized γ-secretase assays demonstrated that increasing alanine substitutions in the motif tended to decrease long Aβ species such as Aβ42 and Aβ43 and to increase in short Aβ species concomitantly. Our data suggest that the GXXXG motif is crucial for Aβ production, but not for C99 dimerization. © 2016 International Society for Neurochemistry.

  1. Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

    Directory of Open Access Journals (Sweden)

    Guo Hao

    2011-05-01

    Full Text Available Abstract Background High-throughput screens have revealed large-scale protein interaction networks defining most cellular functions. How the proteins were added to the protein interaction network during its growth is a basic and important issue. Network motifs represent the simplest building blocks of cellular machines and are of biological significance. Results Here we study the evolution of protein interaction networks from the perspective of network motifs. We find that in current protein interaction networks, proteins of the same age class tend to form motifs and such co-origins of motif constituents are affected by their topologies and biological functions. Further, we find that the proteins within motifs whose constituents are of the same age class tend to be densely interconnected, co-evolve and share the same biological functions, and these motifs tend to be within protein complexes. Conclusions Our findings provide novel evidence for the hypothesis of the additions of clustered interacting nodes and point out network motifs, especially the motifs with the dense topology and specific function may play important roles during this process. Our results suggest functional constraints may be the underlying driving force for such additions of clustered interacting nodes.

  2. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  3. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  4. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  5. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  6. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  7. LHCb : Measuring $CP$ violation with $\\Delta A_{CP}$ at LHCb

    CERN Multimedia

    Pearce, A

    2014-01-01

    Measurements are presented of direct $CP$ violation in $D^{0}$ meson decays in LHCb, using the $\\Delta A_{CP}$ technique, and a proposal is outlined to make similar measurements in the decays of the charmed baryon $\\Lambda_{c}^{+}$. The motivations for use of the $\\Delta A_{CP}$ method are discussed, along with the current results and future prospects.

  8. CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

    Science.gov (United States)

    Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

    2014-12-01

    Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

  9. Registration of 'CP 09-2392' Sugarcane

    Science.gov (United States)

    CP 09-2392’ (Reg. No.____; PI _____) sugarcane, a complex hybrid of Saccharum spp, was developed through cooperative research conducted by the USDA-ARS, the University of Florida, and the Florida Sugar Cane League, Inc., and was released to growers in June 2016. ‘CP 09-2392’ was selected from a cro...

  10. Spontaneous CP violation on the lattice

    CERN Document Server

    Laine, Mikko

    2000-01-01

    At finite temperatures around the electroweak phase transition, the thermodynamics of the MSSM can be described by a three-dimensional two Higgs doublet effective theory. This effective theory has a phase where CP is spontaneously violated. We study spontaneous CP violation with non-perturbative lattice simulations, and analyse whether one could end up in this phase for any physical MSSM parameter values.

  11. The comparison of antioxidative and hepatoprotective activities of Codonopsis pilosula polysaccharide (CP) and sulfated CP.

    Science.gov (United States)

    Liu, Cui; Chen, Jin; Li, Entao; Fan, Qiang; Wang, Deyun; Li, Peng; Li, Xiuping; Chen, Xingying; Qiu, Shulei; Gao, Zhenzhen; Li, Hongquan; Hu, Yuanliang

    2015-02-01

    Codonopsis pilosula polysaccharide (CP) was extracted, purified and modified by chlorosulfonic acid-pyridine method to obtain a sulfated CP (sCP). Their antioxidative activities in vitro were compared through the free radical-scavenging test. The results demonstrated that the scavenging capabilities of sCP were significantly stronger than those of CP. In vivo test, the mice hepatic injury model was prepared by BCG/LPS method, then administrated respectively with sCP and CP at three dosages, the biochemical indexes in serum, antioxidative indexes in liver homogenate and histopathological change in liver of the mice were compared. The results showed that in high (200mg/kg) and middle (150mg/kg) dosages of sCP groups, the contents of ALT, AST and TNF-α in serum and MDA in liver homogenate were significantly lower than those in the model group and numerically lower than those in the CP groups, the activities of SOD and GSH-Px in liver homogenate were significantly higher than those in the model group and numerically higher than those in the CP groups. In the model group there were obvious pathological changes in the liver, while in the sCP groups were near normal. These results indicate that sCP and CP possess antioxidative activity in vitro and in vivo, the activity of sCP is stronger than that of CP and sulfation modification can enhance the antioxidative and hepatoprotective activities of Codonopsis pilosula polysaccharide. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. CP nonconservation in dynamically broken gauge theories

    International Nuclear Information System (INIS)

    Lane, K.

    1981-01-01

    The recent proposal of Eichten, Lane, and Preskill for CP nonconservation in electroweak gauge theories with dynamical symmetry breaking is reviewed. Through the alignment of the vacuum with the explicit chiral symmetry breaking Hamiltonian, these theories provide a natural way to understand the dynamical origin of CP nonconservation. Special attention is paid to the problem of strong CP violation. Even through all vacuum angles are zero, this problem is not automatically avoided. In the absence of strong CP violation, the neutron electric dipole moment is expected to be 10 -24 -10 -26 e-cm. A new class of models is proposed in which both strong CP violation and large /ΔS/ = 2 effects may be avoided. In these models, /ΔC/ = 2 processes such as D/sup o/ D/sup -o/ mixing may be large enough to observe

  13. CP violation and the top quark

    International Nuclear Information System (INIS)

    Atwood, D.

    1994-02-01

    We consider signals of CP violation in semi-leptonic decay of the top quark. We show that the transverse polarization asymmetries of the τ-lepton in the decay t → brv is extremely sensitive CP violation. As an illustration we consider CP phases arising from the charged Higgs exchange in the Weinberg three Higgs doublet model. Qualitatively, the polarization asymmetries are enhanced over rate or energy asymmetries by a factor of O(m t /m r ) ∼ 100 with a corresponding increase in sensitivity to CP violating parameters. We also examine τ polarization in b decays via b → cvr and find that may also be very effective in constraining CP violating effects such as those that arise from an extended Higgs sector

  14. Theory prospective on leptonic CP violation

    International Nuclear Information System (INIS)

    Petcov, S.T.

    2016-01-01

    The phenomenology of 3-neutrino mixing, the current status of our knowledge about the 3-neutrino mixing parameters, including the absolute neutrino mass scale, and of the Dirac and Majorana CP violation in the lepton sector are reviewed. The problems of CP violation in neutrino oscillations and of determining the nature – Dirac or Majorana – of massive neutrinos are discussed. The seesaw mechanism of neutrino mass generation and the related leptogenesis scenario of generation of the baryon asymmetry of the Universe are considered. The results showing that the CP violation necessary for the generation of the baryon asymmetry of the Universe in leptogenesis can be due exclusively to the Dirac and/or Majorana CP-violating phase(s) in the neutrino mixing matrix U are briefly reviewed. The discrete symmetry approach to understanding the observed pattern of neutrino mixing and the related predictions for the leptonic Dirac CP violation are also reviewed.

  15. Deviation from bimaximal mixing and leptonic CP phases in S4 family symmetry and generalized CP

    International Nuclear Information System (INIS)

    Li, Cai-Chang; Ding, Gui-Jun

    2015-01-01

    The lepton flavor mixing matrix having one row or one column in common with the bimaximal mixing up to permutations is still compatible with the present neutrino oscillation data. We provide a thorough exploration of generating such a mixing matrix from S 4 family symmetry and generalized CP symmetry H CP . Supposing that S 4 ⋊H CP is broken down to Z 2 ST 2 SU ×H CP ν in the neutrino sector and Z 4 TST 2 U ⋊H CP l in the charged lepton sector, one column of the PMNS matrix would be of the form (1/2,1/√2,1/2) T up to permutations, both Dirac CP phase and Majorana CP phases are trivial to accommodate the observed lepton mixing angles. The phenomenological implications of the remnant symmetry K 4 (TST 2 ,T 2 U) ×H CP ν in the neutrino sector and Z 2 SU ×H CP l in the charged lepton sector are studied. One row of PMNS matrix is determined to be (1/2,1/2,−i/√2), and all the three leptonic CP phases can only be trivial to fit the measured values of the mixing angles. Two models based on S 4 family symmetry and generalized CP are constructed to implement these model independent predictions enforced by remnant symmetry. The correct mass hierarchy among the charged leptons is achieved. The vacuum alignment and higher order corrections are discussed.

  16. CP violations in the Universe

    Science.gov (United States)

    Auriemma, Giulio

    2003-12-01

    The origin of the asymmetry between matter and antimatter that is evident in our part of the Universe is one of the open questions in cosmology, because the CPT symmetry between matter and antimatter seems to be absolutely conserved at microscopic level. We repeat here the classical proofs which exclude the viability of a Universe baryon symmetric on the average, or the observed asymmetry as an initial conditions. The current understanding is that the asymmetry should have been dynamically generated before nucleosynthesis, by B, C, and CP violating processes, acting out of thermodynamical equilibrium, as suggested by Sakharov in the 70's. The physical realizations of these conditions would be possible, in principle, also in the framework of the Standard Model of elementary particles, but the present limits on the mass of the higgs particle exclude this possibility. Finally we present the model of baryogenesis through leptogenesis, which is allowed by a minimal extension of the Standard Model, which has the appeal of being testable in future long-baseline neutrino oscillation experiments.

  17. The structure of completely positive matrices according to their CP-rank and CP-plus-rank

    NARCIS (Netherlands)

    Dickinson, Peter James Clair; Bomze, Immanuel M.; Still, Georg J.

    2015-01-01

    We study the topological properties of the cp-rank operator $\\mathrm{cp}(A)$ and the related cp-plus-rank operator $\\mathrm{cp}^+(A)$ (which is introduced in this paper) in the set $\\mathcal{S}^n$ of symmetric $n\\times n$-matrices. For the set of completely positive matrices, $\\mathcal{CP}^n$, we

  18. SCFβ-TrCP ubiquitin ligase-mediated processing of NF-κB p105 requires phosphorylation of its C-terminus by IκB kinase

    Science.gov (United States)

    Orian, Amir; Gonen, Hedva; Bercovich, Beatrice; Fajerman, Ifat; Eytan, Esther; Israël, Alain; Mercurio, Frank; Iwai, Kazuhiro; Schwartz, Alan L.; Ciechanover, Aaron

    2000-01-01

    Processing of the p105 precursor to form the active subunit p50 of the NF-κB transcription factor is a unique case in which the ubiquitin system is involved in limited processing rather than in complete destruction of the target substrate. A glycine-rich region along with a downstream acidic domain have been demonstrated to be essential for processing. Here we demonstrate that following IκB kinase (IκK)-mediated phosphorylation, the C-terminal domain of p105 (residues 918–934) serves as a recognition motif for the SCFβ-TrCP ubiquitin ligase. Expression of IκKβ dramatically increases processing of wild-type p105, but not of p105-Δ918–934. Dominant-negative β-TrCP inhibits IκK-dependent processing. Furthermore, the ligase and wild-type p105 but not p105-Δ918–934 associate physically following phosphorylation. In vitro, SCFβ-TrCP specifically conjugates and promotes processing of phosphorylated p105. Importantly, the TrCP recognition motif in p105 is different from that described for IκBs, β-catenin and human immunodeficiency virus type 1 Vpu. Since p105-Δ918–934 is also conjugated and processed, it appears that p105 can be recognized under different physiological conditions by two different ligases, targeting two distinct recognition motifs. PMID:10835356

  19. Annotating RNA motifs in sequences and alignments.

    Science.gov (United States)

    Gardner, Paul P; Eldai, Hisham

    2015-01-01

    RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  1. Reducing the CP content in broiler feeds: impact on animal performance, meat quality and nitrogen utilization.

    Science.gov (United States)

    Belloir, P; Méda, B; Lambert, W; Corrent, E; Juin, H; Lessire, M; Tesseraud, S

    2017-11-01

    Reducing the dietary CP content is an efficient way to limit nitrogen excretion in broilers but, as reported in the literature, it often reduces performance, probably because of an inadequate provision in amino acids (AA). The aim of this study was to investigate the effect of decreasing the CP content in the diet on animal performance, meat quality and nitrogen utilization in growing-finishing broilers using an optimized dietary AA profile based on the ideal protein concept. Two experiments (1 and 2) were performed using 1-day-old PM3 Ross male broilers (1520 and 912 for experiments 1 and 2, respectively) using the minimum AA:Lys ratios proposed by Mack et al. with modifications for Thr and Arg. The digestible Thr (dThr): dLys ratio was increased from 63% to 68% and the dArg:dLys ratio was decreased from 112% to 108%. In experiment 1, the reduction of dietary CP from 19% to 15% (five treatments) did not alter feed intake or BW, but the feed conversion ratio was increased for the 16% and 15% CP diets (+2.4% and +3.6%, respectively), while in experiment 2 (three treatments: 19%, 17.5% and 16% CP) there was no effect of dietary CP on performance. In both experiments, dietary CP content did not affect breast meat yield. However, abdominal fat content (expressed as a percentage of BW) was increased by the decrease in CP content (up to +0.5 and +0.2 percentage point, in experiments 1 and 2, respectively). In experiment 2, meat quality traits responded to dietary CP content with a higher ultimate pH and lower lightness and drip loss values for the low CP diets. Nitrogen retention efficiency increased when reducing CP content in both experiments (+3.5 points/CP percentage point). The main consequence of this higher efficiency was a decrease in nitrogen excretion (-2.5 g N/kg BW gain) and volatilization (expressed as a percentage of excretion: -5 points/CP percentage point). In conclusion, this study demonstrates that with an adapted AA profile, it is possible to reduce

  2. Strong CP, flavor, and twisted split fermions

    International Nuclear Information System (INIS)

    Harnik, Roni; Perez, Gilad; Schwartz, Matthew D.; Shirman, Yuri

    2005-01-01

    We present a natural solution to the strong CP problem in the context of split fermions. By assuming CP is spontaneously broken in the bulk, a weak CKM phase is created in the standard model due to a twisting in flavor space of the bulk fermion wavefunctions. But the strong CP phase remains zero, being essentially protected by parity in the bulk and CP on the branes. As always in models of spontaneous CP breaking, radiative corrections to theta bar from the standard model are tiny, but even higher dimension operators are not that dangerous. The twisting phenomenon was recently shown to be generic, and not to interfere with the way that split fermions naturally weaves small numbers into the standard model. It follows that out approach to strong CP is compatible with flavor, and we sketch a comprehensive model. We also look at deconstructed version of this setup which provides a viable 4D model of spontaneous CP breaking which is not in the Nelson-Barr class. (author)

  3. Romanian traditional motif - element of modernity in clothing

    Science.gov (United States)

    Doble, L.; Stan, O.; Suteu, M. D.; Albu, A.; Bohm, G.; Tsatsarou-Michalaki, A.; Gialinou, E.

    2017-10-01

    In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the jacket respectively, with a straight cut for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the Ethnographic Museum of Transylvania from Cluj Napoca where more traditional motifs were selected specific to Transylvania etnographic region and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. In the patterns design phase Gemini CAD software was used and for the modeling and model development Optitex software was used. The part for garnishing the model was performed using Embrodery machine software reproducing the stylized motif identically. In order to obtain a significantly improved aesthetic look and an added artistic value the pattern chosen for the jacket was done using a combination of modern textile technologies. This has allowed the realization of a particular texture on the surface of the designed product, demonstrating that traditional patterns can be reintepreted in modern clothing

  4. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  5. Exploring CP violation in the MSSM.

    Science.gov (United States)

    Arbey, Alexandre; Ellis, John; Godbole, Rohini M; Mahmoudi, Farvah

    We explore the prospects for observing CP violation in the minimal supersymmetric extension of the Standard Model (MSSM) with six CP-violating parameters, three gaugino mass phases and three phases in trilinear soft supersymmetry-breaking parameters, using the CPsuperH code combined with a geometric approach to maximise CP-violating observables subject to the experimental upper bounds on electric dipole moments. We also implement CP-conserving constraints from Higgs physics, flavour physics and the upper limits on the cosmological dark matter density and spin-independent scattering. We study possible values of observables within the constrained MSSM (CMSSM), the non-universal Higgs model (NUHM), the CPX scenario and a variant of the phenomenological MSSM (pMSSM). We find values of the CP-violating asymmetry [Formula: see text] in [Formula: see text] decay that may be as large as 3 %, so future measurements of [Formula: see text] may provide independent information about CP violation in the MSSM. We find that CP-violating MSSM contributions to the [Formula: see text] meson mass mixing term [Formula: see text] are in general below the present upper limit, which is dominated by theoretical uncertainties. If these could be reduced, [Formula: see text] could also provide an interesting and complementary constraint on the six CP-violating MSSM phases, enabling them all to be determined experimentally, in principle. We also find that CP violation in the [Formula: see text] and [Formula: see text] couplings can be quite large, and so may offer interesting prospects for future [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] colliders.

  6. CP -symmetry of order 4 and its consequences

    International Nuclear Information System (INIS)

    Ivanov, Igor P.

    2017-01-01

    Extended Higgs sectors offer rich opportunities for various forms of CP -violation. Here, we describe a new form of CP-conservation and discuss its consequences. We give a concrete example of a three-Higgs-doublet model dubbed CP4-3HDM with a CP -symmetry of order 4 and no other other accidental symmetries. If the vacuum conserves this symmetry, the model is CP -conserving with pairwise mass-degenerate extra neutral Higgs bosons. These fields cannot be classified as CP -even or CP -odd but they can be combined into complex physical fields which are CP -half-odd, that is, they pick up the i factor upon CP transformation. These CP -half-odd scalars can be Yukawa-coupled to the fermion bilinears in a CP -conserving way. We discuss fundamental and phenomenological features of the model, and stress a peculiar clash between the CP -symmetry and any convention for the particle-antiparticle assignment. (paper)

  7. Disease modeling using embryonic stem cells: MeCP2 regulates nuclear size and RNA synthesis in neurons

    NARCIS (Netherlands)

    S. Yazdani (Saami); R. Deogracias (Rubén); J.A. Guy (Jacqueline); R.A. Poot (Raymond); A. Bird (Adrian); Y.A. Barde

    2012-01-01

    textabstractMutations in the gene encoding the methyl-CpG-binding protein MECP2 are the major cause of Rett syndrome, an autism spectrum disorder mainly affecting young females. MeCP2 is an abundant chromatin-associated protein, but how and when its absence begins to alter brain function is still

  8. Through the Portal: Viking Motifs Incorporated in the Romanesque Style in Telemark, Norway

    Directory of Open Access Journals (Sweden)

    Kristine Ødeby

    2013-09-01

    Full Text Available This paper presents the results of an analysis of motifs identified on six carved wooden Romanesque portal panels from the Norwegian county of Telemark. The findings suggest that animal motifs in the Late Viking style survived long into the Late Medieval period and were reused on these medieval portals. Stylistically, late expressions of Viking animal art do not differ a great deal from those of the subsequent Romanesque style. However, their symbolical differences are considered to be significant. The motifs themselves, and the issue of whether the Romanesque style adopted motifs from pre-Christian art, have attracted less attention. The motif portraying Sigurd slaying the dragon is considered in depth. It will be suggested that Sigurd, serving as a mediator between the old and the new beliefs when he appeared in late Viking contexts, was given a new role when portrayed in Christian art. Metaphor and liminality are a central part of this paper, and the theories of Alfred Gell and Margrete Andås suggest that the portal itself affects those who pass through it, and that the iconography is meaningful from a liminal perspective.

  9. The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity.

    Science.gov (United States)

    Johnson, Rachel M; Rath, Arianna; Deber, Charles M

    2006-12-01

    Although the intrinsic low solubility of membrane proteins presents challenges to their high-resolution structure determination, insight into the amino acid sequence features and forces that stabilize their folds has been provided through study of sequence-dependent helix-helix interactions between single transmembrane (TM) helices. While the stability of helix-helix partnerships mediated by the Gly-xxx-Gly (GG4) motif is known to be generally modulated by distal interfacial residues, it has not been established whether the position of this motif, with respect to the ends of a given TM segment, affects dimer affinity. Here we examine the relationship between motif position and affinity in the homodimers of 2 single-spanning membrane protein TM sequences: glycophorin A (GpA) and bacteriophage M13 coat protein (MCP). Using the TOXCAT assay for dimer affinity on a series of GpA and MCP TM segments that have been modified with either 4 Leu residues at each end or with 8 Leu residues at the N-terminal end, we show that in each protein, centrally located GG4 motifs are capable of stronger helix-helix interactions than those proximal to TM helix ends, even when surrounding interfacial residues are maintained. The relative importance of GG4 motifs in stabilizing helix-helix interactions therefore must be considered not only in its specific residue context but also in terms of the location of the interactive surface relative to the N and C termini of alpha-helical TM segments.

  10. Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

    Science.gov (United States)

    Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

    2003-08-15

    DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

  11. DXD Motif-Dependent and -Independent Effects of the Chlamydia trachomatis Cytotoxin CT166

    Directory of Open Access Journals (Sweden)

    Miriam Bothe

    2015-02-01

    Full Text Available The Gram-negative, intracellular bacterium Chlamydia trachomatis causes acute and chronic urogenital tract infection, potentially leading to infertility and ectopic pregnancy. The only partially characterized cytotoxin CT166 of serovar D exhibits a DXD motif, which is important for the enzymatic activity of many bacterial and mammalian type A glycosyltransferases, leading to the hypothesis that CT166 possess glycosyltransferase activity. CT166-expressing HeLa cells exhibit actin reorganization, including cell rounding, which has been attributed to the inhibition of the Rho-GTPases Rac/Cdc42. Exploiting the glycosylation-sensitive Ras(27H5 antibody, we here show that CT166 induces an epitope change in Ras, resulting in inhibited ERK and PI3K signaling and delayed cell cycle progression. Consistent with the hypothesis that these effects strictly depend on the DXD motif, CT166 with the mutated DXD motif causes neither Ras-ERK inhibition nor delayed cell cycle progression. In contrast, CT166 with the mutated DXD motif is still capable of inhibiting cell migration, suggesting that CT166 with the mutated DXD motif cannot be regarded as inactive in any case. Taken together, CT166 affects various fundamental cellular processes, strongly suggesting its importance for the intracellular survival of chlamydia.

  12. Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

    Science.gov (United States)

    Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

    2009-03-01

    Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

  13. CP violation in the baryon sector

    CERN Document Server

    Smith, Eluned Anne

    2017-01-01

    The study of CP violation in the baryon sector is still a relatively new field and offers the possibility to make many CP measurements which could complement those performed in the meson sector. This is especially true of late given the large number of baryons currently being produced at the LHC. Such measurements could help further over-constrain the CKM unitary triangle, as well as furthering our understand of baryongenesis. These proceedings will give an overview of the current state of the search for CP violation in the baryon sector.

  14. CP violation in CMS expected performance

    CERN Document Server

    Stefanescu, J

    1999-01-01

    The CMS experiment can contribute significantly to the measurement of the CP violation asymmetries. A recent evaluation of the expected precision on the CP violation parameter sin 2 beta in the channel B /sub d//sup 0/ to J/ psi $9 K/sub s//sup 0/ has been performed using a simulation of the CMS tracker including full pattern recognition. CMS has also studied the possibility to observe CP violation in the decay channel B/sub s//sup 0/ to J/ psi phi . The $9 results of these studies are reviewed. (7 refs).

  15. CP Violation in Single Top Quark Production

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Weigang [Michigan State Univ., East Lansing, MI (United States)

    2012-01-01

    We present a search for CP violation in single top quark production with the DØ experiment at the Tevatron proton-antiproton collider. CP violation in the top electroweak interaction results in different single top quark production cross sections for top and antitop quarks. We perform the search in the single top quark final state using 5.4 fb-1 of data, in the s-channel, t-channel, and for both combined. At this time, we do not see an observable CP asymmetry.

  16. Baryogenesis and standard model CP violation

    International Nuclear Information System (INIS)

    Huet, P.

    1994-08-01

    The standard model possesses a natural source of CP violation contained in the phase of the CKM matrix. Whether the latter participated to the making of the matter-antimatter asymmetry of the observable universe is a fundamental question which has been addressed only recently. The generation of a CP observable occurs through interference of quantum paths along which a sequence of flavor mixings and chirality flips take place. The coherence of this phenomenon in the primeval plasma is limited by the fast quark-gluon interactions. At the electroweak era, this phenomenon of decoherence forbids a successful baryogenesis based on the sole CP violation of the CKM matrix

  17. The seesaw path to leptonic CP violation

    Energy Technology Data Exchange (ETDEWEB)

    Caputo, A.; Hernandez, P. [Universidad de Valencia and CSIC, Edificio Institutos Investigacion, Instituto de Fisica Corpuscular, Paterna (Spain); CERN, Theoretical Physics Department, Geneva (Switzerland); Kekic, M.; Salvado, J. [Universidad de Valencia and CSIC, Edificio Institutos Investigacion, Instituto de Fisica Corpuscular, Paterna (Spain); Lopez-Pavon, J. [CERN, Theoretical Physics Department, Geneva (Switzerland)

    2017-04-15

    Future experiments such as SHiP and high-intensity e{sup +}e{sup -} colliders will have a superb sensitivity to heavy Majorana neutrinos with masses below M{sub Z}. We show that the measurement of the mixing to electrons and muons of one such state could establish the existence of CP violating phases in the neutrino mixing matrix, in the context of low-scale seesaw models. We quantify in the minimal model the CP reach of these future experiments, and demonstrate that CP violating phases in the mixing matrix could be established at 5σ CL in a very significant fraction of parameter space. (orig.)

  18. The seesaw path to leptonic CP violation

    CERN Document Server

    Caputo, A.; Kekic, M.; López-Pavón, J.; Salvado, J.

    2017-04-24

    Future experiments such as SHiP and high-intensity $e^+ e^-$ colliders will have a superb sensitivity to heavy Majorana neutrinos with masses below $M_Z$. We show that the measurement of the mixing to electrons and muons of one such state could imply the discovery of leptonic CP violation in the context of seesaw models. We quantify in the minimal model the CP discovery potential of these future experiments, and demonstrate that a 5$\\sigma$ CL discovery of leptonic CP violation would be possible in a very significant fraction of parameter space.

  19. Flavor physics and CP violation

    Science.gov (United States)

    Chang, Paoti; Chen, Kai-Feng; Hou, Wei-Shu

    2017-11-01

    We currently live in the age of the CKM paradigm. The 3 × 3 matrix that links (d , s , b) quarks to (u , c , t) in the charged current weak interaction, being complex and nominally with 18 parameters, can be accounted for by just 3 rotation angles and one CP violating (CPV) phase, with unitarity and the CKM phases triumphantly tested at the B factories. But the CKM picture is unsatisfactory and has too many parameters. The main aim of Flavor Physics and CP violation (FPCP) studies is the pursuit to uncover New Physics beyond the Standard Model (SM). Two highlights of LHC Run 1 period are the CPV phase ϕs of Bs mixing and Bs →μ+μ- decay, which were found to be again consistent with SM, though the saga is yet unfinished. We also saw the emergence of the P5‧ angular variable anomaly in B0 →K∗0μ+μ- decay and R K (∗) anomaly in B →K (∗)μ+μ- to B →K (∗)e+e- rate ratios, and the BaBar anomaly in B →D (∗) τν decays, which suggest possible New Physics in these flavor processes, pointing to extra Z‧, charged Higgs, or leptoquarks. Charmless hadronic, semileptonic, purely leptonic and radiative B decays continue to offer various further windows on New Physics. Away from B physics, the rare K → πνν decays and ε‧ / ε in the kaon sector, μ → e transitions, muon g - 2 and electric dipole moments of the neutron and electron, τ → μγ , μμμ , eee, and a few charm physics probes, offer broadband frontier windows on New Physics. Lastly, flavor changing neutral transitions involving the top quark t and the 125 GeV Higgs boson h, such as t → ch and h → μτ, offer a new window into FPCP, while a new Z‧ related or inspired by the P5‧ anomaly, could show up in analogous top quark processes, perhaps even link with low energy phenomena such as muon g - 2 or rare kaon processes. In particular, we advocate the potential new SM, the two Higgs doublet model without discrete symmetries to control flavor violation, as SM2. As we are

  20. The effect of TLR9 agonist CpG oligodeoxynucleotides on the intestinal immune response of cobia (Rachycentron canadum).

    Science.gov (United States)

    Byadgi, Omkar; Puteri, Dinda; Lee, Jai-Wei; Chang, Tsung-Chou; Lee, Yan-Horn; Chu, Chun-Yen; Cheng, Ta-Chih

    2014-01-01

    Cytosine-guanine oligodeoxynucleotide (CpG ODN) motifs of bacterial DNA are recognized through toll-like receptor 9 (TLR9) and are potent activators of innate immunity. However, the interaction between TLR9 and CpG ODN in aquatic species has not been well characterized. Hence, cobia TLR9 isoform B (RCTLR9B) was cloned and its expression and induction in intestine were investigated. RCTLR9B cDNA consists of 3113bp encoding 1009 amino acids containing three regions, leucine rich repeats, transmembrane domain, and toll/interleukin-1 receptor (TIR) domain. Intraperitoneal injection of CpG ODN 2395 upregulated RCTLR9 A and B and MyD88 and also induced the expressions of Mx, chemokine CC, and interleukin IL-1 β . Cobia intraperitoneally injected with CpG ODN 1668 and 2395 had increased survival rates after challenge with Photobacterium damselae subsp. piscicida. In addition, formulation of CpG ODN with formalin-killed bacteria (FKB) and aluminum hydroxide gel significantly increased expressions of RCTLR9 A (50 folds) and B (30 folds) isoforms at 10 dpi (CpG ODN 1668) and MyD88 (21 folds) at 6 dpv (CpG ODN 2395). Subsequently, IL-1 β increased at 6 dpv in 1668 group. No histopathological damage and inflammatory responses were observed in the injected cobia. Altogether, these results facilitate CpG ODNs as an adjuvant to increase bacterial disease resistance and efficacy of vaccines in cobia.

  1. The Effect of TLR9 Agonist CpG Oligodeoxynucleotides on the Intestinal Immune Response of Cobia (Rachycentron canadum

    Directory of Open Access Journals (Sweden)

    Omkar Byadgi

    2014-01-01

    Full Text Available Cytosine-guanine oligodeoxynucleotide (CpG ODN motifs of bacterial DNA are recognized through toll-like receptor 9 (TLR9 and are potent activators of innate immunity. However, the interaction between TLR9 and CpG ODN in aquatic species has not been well characterized. Hence, cobia TLR9 isoform B (RCTLR9B was cloned and its expression and induction in intestine were investigated. RCTLR9B cDNA consists of 3113bp encoding 1009 amino acids containing three regions, leucine rich repeats, transmembrane domain, and toll/interleukin-1 receptor (TIR domain. Intraperitoneal injection of CpG ODN 2395 upregulated RCTLR9 A and B and MyD88 and also induced the expressions of Mx, chemokine CC, and interleukin IL-1β. Cobia intraperitoneally injected with CpG ODN 1668 and 2395 had increased survival rates after challenge with Photobacterium damselae subsp. piscicida. In addition, formulation of CpG ODN with formalin-killed bacteria (FKB and aluminum hydroxide gel significantly increased expressions of RCTLR9 A (50 folds and B (30 folds isoforms at 10 dpi (CpG ODN 1668 and MyD88 (21 folds at 6 dpv (CpG ODN 2395. Subsequently, IL-1β increased at 6 dpv in 1668 group. No histopathological damage and inflammatory responses were observed in the injected cobia. Altogether, these results facilitate CpG ODNs as an adjuvant to increase bacterial disease resistance and efficacy of vaccines in cobia.

  2. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  3. A CACGTG motif of the Antirrhinum majus chalcone synthase promoter is recognized by an evolutionarily conserved nuclear protein

    International Nuclear Information System (INIS)

    Staiger, D.; Kaulen, H.; Schell, J.

    1989-01-01

    In the chalcone synthase gene of Antirrhinum majus (snapdragon), 150 base pairs of the 5' flanking region contain cis-acting signals for UV light-induced expression. A nuclear factor, designated CG-1, specifically recognizes a hexameric motif with internal dyad symmetry, CACGTG, located within this light-responsive sequence. Binding of CG-1 is influenced by C-methylation of the CpG dinucleotide in the recognition sequence. CG-1 is a factor found in a variety of dicotyledonous plant species including Nicotiana tabacum, A. majus, Petunia hybrida, Arabidopsis thaliana, and Glycine max. CACGTG motifs contained within trans-acting factor recognition sites in various other plant promoters can interact with CG-1. In addition, the binding site of the human adenovirus major late transcription factor USF can compete for CG-1 binding to the chalcone synthase promoter. This suggests an evolutionary conservation of trans-acting factor recognition sites involved in divergent mechanisms of gene control. (author)

  4. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    Directory of Open Access Journals (Sweden)

    Masiswo Masiswo

    2016-04-01

    Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa

  5. Identity and functions of CxxC-derived motifs.

    Science.gov (United States)

    Fomenko, Dmitri E; Gladyshev, Vadim N

    2003-09-30

    Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

  6. Aspects of soft and spontaneous CP violation

    International Nuclear Information System (INIS)

    Frampton, P.H.; Harada, M.

    1999-01-01

    We study four different models for CP violation: the standard Kobayashi-Maskawa (KM) model, the aspon model of spontaneous breaking, and two models of soft breaking. In all except the standard model, the strong CP problem is addressed and solved. Testable predictions for the area of the unitarity triangle and for (ε ' /ε) K are emphasized. The issue of CP violation may well become the first place where the standard model of particle theory is shown definitively to be deficient. There are two reasons for expecting this to happen: (1) the strong CP problem is still not understood in the unadorned standard model and (2) the KM mechanism, although unquestionably present, may not provide the full explanation of ε K and (ε ' /ε) K . copyright 1999 The American Physical Society

  7. CP violation in B and D decays

    International Nuclear Information System (INIS)

    Bigi, I.I.

    1986-06-01

    Non-leptonic B decays offer the best opportunity to discover the violation of CP invariance outside the neutral K system. Employing the Standard Model one predicts - with reasonable confidence - CP asymmetries of up to 205 (or even more in some cases). The branching ratios for the individual exclusive modes of interest are not expected to exceed the 10 -3 level in most cases; the identification of such decays poses non-trivial problems. It is shown that by summing intelligently over appropriate classes of decays one can greatly enhance statistics without jeopardizing the signal. Data that contain 10 6 produced B mesons would allow meaningful searches for CP violation. It is noted that ''New Physics'' could lead to CP asymmetries in D 0 decays of order 1%. Due to higher branching ratios one can search for such effects in samples of 10 6 produced D mesons. 7 refs

  8. Instantons, CP-violation and axions

    Energy Technology Data Exchange (ETDEWEB)

    Choudhury, S. R.

    1980-07-01

    Some specific aspects of the developments in pseudoparticle solutions of Gauge theories are discussed. The general features of the Lagrangian are described. The concepts of instantons, confinement, O-vacua and CP nonconservation are explained.

  9. CP violation in b-hadrons

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00341004

    2016-01-01

    Latest LHCb measurements of $CP$ violation in b-hadrons are presented based on $pp$ collision data collected in 2011 and 2012 at centre-of-mass energies of $\\sqrt{s}=7$ $\\rm TeV$ and $8\\ \\rm TeV$ respectively. The total integrated luminosity collected is 3.0 fb$^{-1}$. Results include recent measurements of $CP$ violation in $B_d$ and $B_s$ mixing, along with those of quantifying the effects of $b\\to c\\bar{c} s$ loop pollution. Standard Model $CP$ violation tests in loop transitions are discussed with results consistent with expectations. New decays of b-baryons are presented and preliminary studies of $CP$ violation are performed.

  10. A definition of maximal CP-violation

    International Nuclear Information System (INIS)

    Roos, M.

    1985-01-01

    The unitary matrix of quark flavour mixing is parametrized in a general way, permitting a mathematically natural definition of maximal CP violation. Present data turn out to violate this definition by 2-3 standard deviations. (orig.)

  11. First evidence for direct CP violation

    International Nuclear Information System (INIS)

    Schaffer, A.C.

    1988-06-01

    The double ratio R of the relative decay rates of the short-and long-lived neutral kaons into two charged and two neutral pions was measured to be 0.980 ± 0.004 ± 0.005. The deviation of R from unity implies CP violation in the transition of the CP-odd K 2 into two pions with ε , / ε = (3.3 ± 1.1) X 10 -3

  12. Status of the CP-PACS Project

    International Nuclear Information System (INIS)

    Ukawa, A.

    1995-01-01

    The CP-PACS Project, which started in April 1992, is a five-year plan to develop a massively parallel computer for carrying out research in computational physics with primary emphasis on lattice QCD. This article describes the architectural design of the CP-PACS computer, the entire computing system including the front end and mass storage, and results of benchmarks for the expected performance for lattice QCD applications. ((orig.))

  13. Toimintaterapeuttinen nukkekoti CP-vammaisille lapsille

    OpenAIRE

    Ruotsalainen, Ulla; Tokola, Eveliina

    2009-01-01

    Toiminnallisen opinnäytetyön tarkoitus oli suunnitella ja rakentaa toimintaterapeuttinen nukkekoti CP-vammaisille lapsille. Työn toimeksiantajana oli toimintaterapeutti Päivi Raitanen Terapiapajalta. Työn tavoitteena oli toteuttaa mukana kuljetettava ja lapsen pyörätuolin pöytälevylle sopiva nukkekoti, jolla leikkiminen tukee CP-vammaisen lapsen toimintaterapiaa. Yleisimpiä tavoitteita ovat muun muuassa hienomotoristen taitojen, leikkitaitojen, syy-seuraussuhteiden ja visuaalisen hahmott...

  14. Heavy quarks and CP: Moriond 1985

    International Nuclear Information System (INIS)

    Bjorken, J.D.

    1985-03-01

    The presentations at the Fifth Moriond Workshop on Heavy Quarks, Flavor Mixing, and CP Violation (La Plagne, France, January 13-19, 1985) are summarized. The following topics are reviewed. What's New (beyond the top, top quarks, bottom quarks, charm quarks, strange quarks, and others); why is all this being done (strong interactions and hadron structure, and electroweak properties); and what next (facilities and can one see CP violation in the B-anti B system). 64 refs., 10 figs

  15. Penguins and cp violation in β decays

    International Nuclear Information System (INIS)

    He, X.C.

    1996-11-01

    The measurement of the ε-parameter in the K 0 - K-bar 0 meson system is the only direct evidence for CP violation in the laboratory. The Standard Model (SM) of three generations with the source for CP violation arising from the phases in the Cabibbo-Kobayashi-Maskawa (CKM) matrix is consistent with the experiment. An unique feature of this model is that the CKM matrix is a 3 x 3 unitary matrix. (author)

  16. Neutrino mass textures with maximal CP violation

    International Nuclear Information System (INIS)

    Aizawa, Ichiro; Kitabayashi, Teruyuki; Yasue, Masaki

    2005-01-01

    We show three types of neutrino mass textures, which give maximal CP violation as well as maximal atmospheric neutrino mixing. These textures are described by six real mass parameters: one specified by two complex flavor neutrino masses and two constrained ones and the others specified by three complex flavor neutrino masses. In each texture, we calculate mixing angles and masses, which are consistent with observed data, as well as Majorana CP phases

  17. Proinflammatory Stimulation of Toll-Like Receptor 9 with High Dose CpG ODN 1826 Impairs Endothelial Regeneration and Promotes Atherosclerosis in Mice.

    Directory of Open Access Journals (Sweden)

    Alexander O Krogmann

    Full Text Available Toll-like receptors (TLR of the innate immune system have been closely linked with the development of atherosclerotic lesions. TLR9 is activated by unmethylated CpG motifs within ssDNA, but also by CpG motifs in nucleic acids released during vascular apoptosis and necrosis. The role of TLR9 in vascular disease remains controversial and we sought to investigate the effects of a proinflammatory TLR9 stimulation in mice.TLR9-stimulation with high dose CpG ODN at concentrations between 6.25 nM to 30 nM induced a significant proinflammatory cytokine response in mice. This was associated with impaired reendothelialization upon acute denudation of the carotid and increased numbers of circulating endothelial microparticles, as a marker for amplified endothelial damage. Chronic TLR9 agonism in apolipoprotein E-deficient (ApoE-/- mice fed a cholesterol-rich diet increased aortic production of reactive oxygen species, the number of circulating endothelial microparticles, circulating sca-1/flk-1 positive cells, and most importantly augmented atherosclerotic plaque formation when compared to vehicle treated animals. Importantly, high concentrations of CpG ODN are required for these proatherogenic effects.Systemic stimulation of TLR9 with high dose CpG ODN impaired reendothelialization upon acute vascular injury and increased atherosclerotic plaque development in ApoE-/- mice. Further studies are necessary to fully decipher the contradictory finding of TLR9 agonism in vascular biology.

  18. CP and CP-PGN protect mice against MRSA infection by inducing M1 macrophages.

    Science.gov (United States)

    Zhang, Yang; Li, Xiang-Xiang; Ma, Yuan; Xu, Jie; Zhao, Li-Na; Qian, Xue-Feng; Zhang, Xian-Feng; Shi, Jin-Fang; Han, Qing-Zhen

    2017-12-04

    Corynebacterium pyruviciproducens (C. pyruviciproducens, CP), as a newly discovered immunomodulator, has been confirmed to have a stronger immunoregulation than Propionibacterium acnes (P. acnes) of the traditional immune adjuvant, by previous experiments with model antigen ovalbumin and sheep red blood cells. Here, it was designed to assess its ability to resist methicillin-resistant Staphylococcus aureus (MRSA), since MRSA as a vital gram positive pathogen is characterized by high morbidity and mortality. In this report, it was indicated that C. pyruviciproducens and its peptidoglycan (CP-PGN) could help to be against bloodstream infection of MRSA with raised survival rate, decreased bacteria load and alleviated systemic inflammation, and these effects of CP-PGN were more pronounced. However, the whole CP was inclined to prevent localized abdominal infection of MRSA from progressing to a systemic infection. And they showed the potential as a therapeutic drug alone or combined with vancomycin. The diversity of capacity of activating macrophages induced by CP and CP-PGN may result in distinct resistance to MRSA in different infection models. Furthermore, both CP and CP-PGN induced M1 macrophages. In conclusion, CP and its PGN could act as promising immune agents to treat and prevent MRSA infection.

  19. UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO

    Directory of Open Access Journals (Sweden)

    Irfa ina Rohana Salma

    2016-12-01

    Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo

  20. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  1. Revisiting Lynam's notion of the "fledgling psychopath": are HIA-CP children truly psychopathic-like?

    Directory of Open Access Journals (Sweden)

    Michonski Jared D

    2010-09-01

    Full Text Available Abstract Background In his developmental model of emerging psychopathy, Lynam proposed that the "fledgling psychopath" is most likely to be located within a subgroup of children elevated in both hyperactivity/inattention/impulsivity (HIA and conduct problems (CP. This approach has garnered some empirical support. However, the extent to which Lynam's model captures children who resemble psychopathy with regard to the core affective and interpersonal features remains unclear. Methods In the present study, we investigated this issue within a large community sample of youth (N = 617. Four groups (non-HIA-CP, HIA-only, CP-only, and HIA-CP, defined on the basis of teacher reports of the Strengths and Difficulties Questionnaire (SDQ, were compared with respect to parent-reported psychopathic-like traits and subjective emotional reactivity in response to unpleasant, emotionally-laden pictures from the International Affective Pictures System (IAPS. Results Results did not support Lynam's model. HIA-CP children did not appear most psychopathic-like on dimensions of callous-unemotional and narcissistic personality, nor did they report reduced emotional reactivity to the IAPS relative to the other children. Post-hoc regression analyses revealed a significant moderation such that elevated HIA weakened the association between CP and emotional underarousal. Conclusions Implications of these findings with regard to the development of psychopathy are discussed.

  2. On the Universality of CP Violation in Delta F = 1 Processes

    CERN Document Server

    Gedalia, Oram; Ligeti, Zoltan; Perez, Gilad

    2012-01-01

    We show that new physics that breaks the left-handed SU(3)_Q quark flavor symmetry induces contributions to CP violation in Delta F = 1 processes which are approximately universal, in that they are not affected by flavor rotations between the up and the down mass bases. Therefore, such flavor violation cannot be aligned, and is constrained by the strongest bound from either the up or the down sectors. We use this result to show that the bound from eps'/eps prohibits an SU(3)_Q breaking explanation of the recent LHCb evidence for CP violation in D meson decays. Another consequence of this universality is that supersymmetric alignment models with a moderate mediation scale are consistent with the data, and are harder to probe via CP violating observables. With current constraints, therefore, squarks need not be degenerate. However, future improvements in the measurement of CP violation in D-Dbar mixing will start to probe alignment models.

  3. Effects of probiotics, probiotic DNA and the CpG oligodeoxynucleotides on ovalbumin-sensitized Brown-Norway rats via TLR9/NF-κB pathway.

    Science.gov (United States)

    Zhong, Yan; Huang, Juan; Tang, Wenjing; Chen, Bing; Cai, Wei

    2012-10-01

    The aim of the study was to investigate the effect of living probiotics, probiotic DNA and the synthetic oligodeoxynucleotides containing CpG motifs (CpG-ODN) on both immune response and intestinal barrier function in ovalbumin-sensitized rat and the underlying mechanisms. Brown-Norway rats were orally sensitized with ovalbumin, and living probiotics, probiotic DNA extraction, synthetic CpG-ODN or non-CpG ODN control was administered. In the living probiotics, probiotic DNA and CpG-ODN groups, the allergic response was significantly inhibited, the Th1/Th2 cytokine balance was shifted away from Th2 side, the percentage of CD4(+) CD25(+high) Treg cells was increased, and the intestinal barrier function was improved. The levels of toll-like receptor (TLR) 9 mRNA and nuclear factor (NF)-κB activity, as well as the IκB-α phosphorylation (p-IκB-α) was significantly increased in these three intervention groups compared with the OVA-positive group, whereas no such effects were found in the non-CpG ODN control group. These data show that the probiotic genomic DNA and the synthetic CpG-ODN was comparable with living probiotics in preventing food allergic response by immune modulation and intestinal barrier function enhancement, and the activation of TLR9/NF-κB signal pathway might be involved in this process. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  4. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

    Science.gov (United States)

    Hernández-Sánchez, Itzell E.; Maruri-López, Israel; Ferrando, Alejandro; Carbonell, Juan; Graether, Steffen P.; Jiménez-Bremont, Juan F.

    2015-01-01

    The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA) proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC) approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine-rich motif is proposed as a targeting element for OpsDHN1 nuclear localization. PMID:26442018

  5. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

    Directory of Open Access Journals (Sweden)

    Itzell Euridice Hernández-Sánchez

    2015-09-01

    Full Text Available The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine rich motif is proposed as a targeting element for OpsDHN1 nuclear localization.

  6. Evidence for leptonic CP phase from NOνA, T2K and ICAL: A chronological progression

    International Nuclear Information System (INIS)

    Ghosh, Monojit; Ghoshal, Pomita; Goswami, Srubabati; Raut, Sushant K.

    2014-01-01

    We study the synergy between the long-baseline (LBL) experiments NOνA and T2K and the atmospheric neutrino experiment ICAL@INO for obtaining the first hint of CP violation in the lepton sector. We also discuss how precisely the leptonic CP phase (δ CP ) can be measured by these experiments. The CP sensitivity is first described at the level of oscillation probabilities, discussing its dependence on the parameters – θ 13 , mass hierarchy and θ 23 . In particular, we discuss how the precise knowledge or lack thereof of these parameters can affect the CP sensitivity of LBL experiments. We follow a staged approach and analyze the δ CP sensitivity that can be achieved at different points of time over the next 15 years from these LBL experiments alone and/or in conjunction with ICAL@INO. We find that the CP sensitivity of NOνA/T2K is enhanced due to the synergies between the different channels and between the two experiments. On the other hand the lack of knowledge of hierarchy and octant makes the CP sensitivity poorer for some parameter ranges. Addition of ICAL data to T2K and NOνA can exclude these spurious wrong-hierarchy and/or wrong-octant solutions and cause a significant increase in the range of δ CP values for which a hint of CP violation can be achieved. In fact in parameter regions unfavourable for NOνA/T2K, we may get the first evidence of CP violation by adding the ICAL data to these. Similarly the precision with which δ CP can be measured also improves with inclusion of ICAL data

  7. Synthesis and oxidation of CpIrIII compounds: functionalization of a Cp methyl group.

    Science.gov (United States)

    Park-Gehrke, Lisa S; Freudenthal, John; Kaminsky, Werner; Dipasquale, Antonio G; Mayer, James M

    2009-03-21

    [CpIrCl(2)](2) () and new CpIr(III)(L-L)X complexes (L-L = N-O or C-N chelating ligands; X = Cl, I, Me) have been prepared and their reactivity with two-electron chemical oxidants explored. Reaction of with PhI(OAc)(2) in wet solvents yields a new chloro-bridged dimer in which each of the Cp ligands has been singly acetoxylated to form [Cp(OAc)Ir(III)Cl(2)](2) () (Cp(OAc) = eta(5)-C(5)Me(4)CH(2)OAc). Complex and related carboxy- and alkoxy-functionalized Cp(OR) complexes can also be prepared from plus (PhIO)(n) and ROH. [Cp(OAc)Ir(III)Cl(2)](2) () and the methoxy analogue [Cp(OMe)Ir(III)Cl(2)](2) () have been structurally characterized. Treatment of [CpIrCl(2)](2) () with 2-phenylpyridine yields CpIr(III)(ppy)Cl () (ppy = cyclometallated 2-phenylpyridyl) which is readily converted to its iodide and methyl analogues CpIr(III)(ppy)I and CpIr(III)(ppy)Me (). CpIr(III) complexes were also prepared with N-O chelating ligands derived from anthranilic acid (2-aminobenzoic acid) and alpha-aminoisobutyric acid (H(2)NCMe(2)COOH), ligands chosen to be relatively oxidation resistant. These complexes and were reacted with potential two-electron oxidants including PhI(OAc)(2), hexachlorocyclohexadienone (C(6)Cl(6)O), N-fluoro-2,4,6-trimethylpyridinium (Me(3)pyF(+)), [Me(3)O]BF(4) and MeOTf (OTf = triflate, CF(3)SO(3)). Iridium(V) complexes were not observed or implicated in these reactions, despite the similarity of the potential products to known CpIr(V) species. The carbon electrophiles [Me(3)O]BF(4) and MeOTf appear to react preferentially at the N-O ligands, to give methyl esters in some cases. Overall, the results indicate that Cp is not inert under oxidizing conditions and is therefore not a good supporting ligand for oxidizing organometallic complexes.

  8. Structural motifs of pre-nucleation clusters.

    Science.gov (United States)

    Zhang, Y; Türkmen, I R; Wassermann, B; Erko, A; Rühl, E

    2013-10-07

    Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15-30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre-nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions.

  9. POWRS: position-sensitive motif discovery.

    Directory of Open Access Journals (Sweden)

    Ian W Davis

    Full Text Available Transcription factors and the short, often degenerate DNA sequences they recognize are central regulators of gene expression, but their regulatory code is challenging to dissect experimentally. Thus, computational approaches have long been used to identify putative regulatory elements from the patterns in promoter sequences. Here we present a new algorithm "POWRS" (POsition-sensitive WoRd Set for identifying regulatory sequence motifs, specifically developed to address two common shortcomings of existing algorithms. First, POWRS uses the position-specific enrichment of regulatory elements near transcription start sites to significantly increase sensitivity, while providing new information about the preferred localization of those elements. Second, POWRS forgoes position weight matrices for a discrete motif representation that appears more resistant to over-generalization. We apply this algorithm to discover sequences related to constitutive, high-level gene expression in the model plant Arabidopsis thaliana, and then experimentally validate the importance of those elements by systematically mutating two endogenous promoters and measuring the effect on gene expression levels. This provides a foundation for future efforts to rationally engineer gene expression in plants, a problem of great importance in developing biotech crop varieties.BSD-licensed Python code at http://grassrootsbio.com/papers/powrs/.

  10. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Science.gov (United States)

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  11. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Graziele Pereira Oliveira

    2017-01-01

    Full Text Available For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV, raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’ that could be evolved gradually by nucleotides’ gain and loss and point mutations.

  12. CP and other gauge symmetries in string theory

    International Nuclear Information System (INIS)

    Dine, M.; Leigh, R.G.; MacIntire, D.A.

    1992-01-01

    We argue that CP is a gauge symmetry in string theory. As a consequence, CP cannot be explicitly broken either perturbatively or nonperturbatively; there can be no nonperturbative CP-violating parameters. String theory is thus an example of a theory where all θ angles arise due to spontaneous CP violation, and are in principle calculable

  13. Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

    Directory of Open Access Journals (Sweden)

    Rudi - Nababan

    2012-04-01

    Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

  14. Did the CP audits promote the enterprises' CP? A case study in Beijing.

    Science.gov (United States)

    Yu, Gang; Huang, Jun; Chen, Qing

    2002-03-09

    Seven enterprises that have had recent Cleaner Production (CP) audits in Beijing were interviewed to identify whether these enterprises implemented the audit recommendations. If enterprises did implement the recommendations, their reasons and the results were analyzed. Finally, some suggestions on how to promote enterprise-wide CP were given.

  15. Flavor and CP invariant composite Higgs models

    International Nuclear Information System (INIS)

    Redi, Michele; Weiler, Andreas

    2011-09-01

    The flavor protection in composite Higgs models with partial compositeness is known to be insufficient. We explore the possibility to alleviate the tension with CP odd observables by assuming that flavor or CP are symmetries of the composite sector, broken by the coupling to Standard Model fields. One realization is that the composite sector has a flavor symmetry SU(3) or SU(3) U x SU(3) D which allows us to realize Minimal Flavor Violation. We show how to avoid the previously problematic tension between a flavor symmetric composite sector and electro-weak precision tests. Some of the light quarks are substantially or even fully composite with striking signals at the LHC. We discuss the constraints from recent dijet mass measurements and give an outlook on the discovery potential. We also present a different protection mechanism where we separate the generation of flavor hierarchies and the origin of CP violation. This can eliminate or safely reduce unwanted CP violating effects, realizing effectively ''Minimal CP Violation'' and is compatible with a dynamical generation of flavor at low scales. (orig.)

  16. Flavor and CP invariant composite Higgs models

    Energy Technology Data Exchange (ETDEWEB)

    Redi, Michele [CERN - European Organization for Nuclear Research, Geneva (Switzerland). Theory Div.; INFN, Firenze (Italy); Weiler, Andreas [CERN - European Organization for Nuclear Research, Geneva (Switzerland). Theory Div.; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2011-09-15

    The flavor protection in composite Higgs models with partial compositeness is known to be insufficient. We explore the possibility to alleviate the tension with CP odd observables by assuming that flavor or CP are symmetries of the composite sector, broken by the coupling to Standard Model fields. One realization is that the composite sector has a flavor symmetry SU(3) or SU(3){sub U} x SU(3){sub D} which allows us to realize Minimal Flavor Violation. We show how to avoid the previously problematic tension between a flavor symmetric composite sector and electro-weak precision tests. Some of the light quarks are substantially or even fully composite with striking signals at the LHC. We discuss the constraints from recent dijet mass measurements and give an outlook on the discovery potential. We also present a different protection mechanism where we separate the generation of flavor hierarchies and the origin of CP violation. This can eliminate or safely reduce unwanted CP violating effects, realizing effectively ''Minimal CP Violation'' and is compatible with a dynamical generation of flavor at low scales. (orig.)

  17. CpG plus radiotherapy: a review of preclinical works leading to clinical trial

    International Nuclear Information System (INIS)

    Mason, Kathy A.; Hunter, Nancy R.

    2012-01-01

    Studies performed three decades ago in our laboratory supported the hypothesis that radiation efficacy may be augmented by bacterial extracts that stimulate non-specific systemic antitumor immune responses. Application to the clinic was halted by unacceptable side effects and toxicities resulting from exposure to whole bacterial pathogens. Later scientific advances demonstrated that DNA isolated from bacteria was immunostimulatory and could be reproduced with synthetic oligodeoxynucleotides (ODNs), thus fueling the transition from bugs to drugs. Unmethylated CpG motifs within bacterial DNA induce activation of Toll-like receptor 9 and subsequently activate antigen-specific cellular immune responses. CpG ODNs have demonstrated favorable toxicity profiles in phase I clinical trials. We showed that this potent immunoadjuvant can be used in combination with radiation therapy to enhance local and systemic responses of several murine tumors. Studies demonstrated that enhanced tumor response is mediated in part by the host immune system. Antitumor efficacy was diminished in immunocompromised mice. Animals cured by combination of radiation and CpG ODN were resistant to subsequent tumor rechallenge. This body of work contributes to our understanding of the dynamic interplay between tumor irradiation and the host immune system and may facilitate translation to clinical trials.

  18. CpG plus radiotherapy: a review of preclinical works leading to clinical trial

    Energy Technology Data Exchange (ETDEWEB)

    Mason, Kathy A.; Hunter, Nancy R., E-mail: kmason@mdanderson.org [Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX (United States)

    2012-08-14

    Studies performed three decades ago in our laboratory supported the hypothesis that radiation efficacy may be augmented by bacterial extracts that stimulate non-specific systemic antitumor immune responses. Application to the clinic was halted by unacceptable side effects and toxicities resulting from exposure to whole bacterial pathogens. Later scientific advances demonstrated that DNA isolated from bacteria was immunostimulatory and could be reproduced with synthetic oligodeoxynucleotides (ODNs), thus fueling the transition from bugs to drugs. Unmethylated CpG motifs within bacterial DNA induce activation of Toll-like receptor 9 and subsequently activate antigen-specific cellular immune responses. CpG ODNs have demonstrated favorable toxicity profiles in phase I clinical trials. We showed that this potent immunoadjuvant can be used in combination with radiation therapy to enhance local and systemic responses of several murine tumors. Studies demonstrated that enhanced tumor response is mediated in part by the host immune system. Antitumor efficacy was diminished in immunocompromised mice. Animals cured by combination of radiation and CpG ODN were resistant to subsequent tumor rechallenge. This body of work contributes to our understanding of the dynamic interplay between tumor irradiation and the host immune system and may facilitate translation to clinical trials.

  19. CP-even and CP-odd transverse polarization of the electron in muon decay

    International Nuclear Information System (INIS)

    Kuznetsov, A.

    1981-01-01

    A model of the weak interaction which contains intermediate vector bosons of the most general form and which admits CP violation in muon decay is used to calculate the CP-even and CP-odd transverse polarization of the μ-decay electrons with inclusion of radiative corrections. It is shown that these corrections are important only at the beginning of the spectrum, and their contribution reduces the observed effects of the transverse polarization. The transverse polarization grows appreciably at electron energies close to the maximum energy and at small emission angles. It is expedient to search for the CP-even and CP-odd transverse polarization of the electrons at energies E/sub e/ = 0.975E/sup max//sub e/ and emission angles theta = 25--35 0

  20. CP-even and CP-odd transverse polarization of the electron in the muon decay

    International Nuclear Information System (INIS)

    Kuznetsov, A.V.

    1981-01-01

    In the most general weak interaction model with intermediate vector bosons, allowing CP breaking in the muon decay, CP- even and CP-odd transverse polarization of the μ-decay electrons is calculated taking into account the radiative corrections. It is shown that such corrections are essential only at the beginning of the spectrum reducing the observed transverse polarization effects. When the electron energy is close to its maximum and the emission angles are small, the transverse polarization considerably grows. Search for CP-even and CP-odd transverse polarization of the electrons should be carried out at energies Esub(e) approximately equal to O.975 Esub(e)sup(max) and emission angles THETA approximately equal to 25+35 deg [ru

  1. Lectures on Flavor Physics and CP Violation

    CERN Document Server

    Grinstein, Benjamín

    2016-12-20

    These lectures on flavor physics are an introduction to the subject. First lec- ture: We discuss the meaning of flavor and the importance of flavor physics in restricting extensions of the Standard Model (SM) of Electroweak interactions. We explain the origin of the KM matrix and how its elements are determined. We discuss FCNC and the GIM mechanism, followed by how a principle of Minimal Flavor Violation leads to SM extensions that are safe as far as FCNC are concerned even if the new physics comes in at low, TeVish scales. This is illustrated by the example of B radiative decays ( b → sγ ). Second lecture: We then turn our attention to CP-violation. We start by presenting neutral meson mixing. Then we consider various CP-asymmetries, culminating in the theoretically clean interference between mixing and decay into CP eigenstates.

  2. CP asymmetries in semiinclusive B0 decays

    Energy Technology Data Exchange (ETDEWEB)

    Dunietz, Isard

    1999-02-01

    It was recently pointed out that inclusive B^0(t) decays could show CP violation. The totally inclusive asymmetry is expected to be tiny [O(10^{-3})] because of large cancellations among the asymmetries in the charmless, single charm and double charm final states. Enriching particular final state configurations could significantly increase the CP-asymmetry and observability. Such studies can extract fundamental CKM (Cabibbo-Kobayashi-Maskawa) parameters, and (perhaps) even Delta m(B_s). A superb vertex detector could see CP violation with 10^5 (10^6) flavor-tagged B_s (B_d) mesons within the CKM model. Because the effects could be significantly larger due to new physics, they should be searched for in existing or soon available data samples.

  3. On the measurement of leptonic CP violation

    International Nuclear Information System (INIS)

    Burguet Castell, J.; Gavela, M.B.; Gomez Cadenas, J.J.; Hernandez, P.; Mena, O.

    2001-01-01

    We show that the simultaneous determination of the leptonic CP-odd phase δ and the angle θ 13 from the subleading transitions ν e →ν μ and ν-bar e →ν-bar μ results generically, at fixed neutrino energy and baseline, in two degenerate solutions. In light of this, we refine a previous analysis of the sensitivity to leptonic CP violation at a neutrino factory, in the LMA-MSW scenario, by exploring the full range of δ and θ 13 . Furthermore, we take into account the expected uncertainties on the solar and atmospheric oscillation parameters and in the average Earth matter density along the neutrino path. An intermediate baseline of O(3000) km is still the best option to tackle CP violation, although a combination of two baselines turns out to be very important in resolving degeneracies

  4. The CpG island searcher: a new WWW resource.

    Science.gov (United States)

    Takai, Daiya; Jones, Peter A

    2003-01-01

    Clusters of CpG dinucleotides in GC rich regions of the genome called "CpG islands" frequently occur in the 5' ends of genes. Methylation of CpG islands plays a role in transcriptional silencing in higher organisms in certain situations. We have established a CpG-island-extraction algorithm, which we previously developed [Takai and Jones, 2002], on a web site which has a simple user interface to identify CpG islands from submitted sequences of up to 50kb. The web site determines the locations of CpG islands using parameters (lower limit of %GC, ObsCpG/ExpCpG, length) set by the user, to display the value of parameters on each CpG island, and provides a graphical map of CpG dinucleotide distribution and borders of CpG islands. A command-line version of the CpG islands searcher has also been developed for larger sequences. The CpG Island Searcher was applied to the latest sequence and mapping information of human chromosomes 20, 21 and 22, and a total of 2345 CpG islands were extracted and 534 (23%) of them contained first coding exons and 650 (28%) contained other exons. The CpG Island Searcher is available on the World Wide Web at http://www.cpgislands.com or http://www.uscnorris.com/cpgislands/cpg.cgi.

  5. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  6. Rekayasa Pengembangan Desain Motif Batik Khas Melayu

    Directory of Open Access Journals (Sweden)

    Eustasia Sri Murwati

    2016-04-01

    Full Text Available ABSTRAKPengembangan desain batik melalui rancang bangun perekayasaan desain menurut ragam hias Melayu meliputi pengembangan motif dan proses, termasuk pemilihan komposisi warna. Proses yang sering dilakukan yaitu proses celup, penghilangan lilin dan celup warna tumpangan atau proses colet, celup, penghilangan lilin atau celup kemudian penghilangan lilin yang disebut Batik Kelengan. Setiap pulau di Indonesia mempunyai ciri khas budaya dan kesenian yang dikenal dengan corak/ragam hias khas daerah, juga ornamen yang diminati oleh masyarakat dari daerah tersebut atau dari daerah lain. Kondisi demikian mendorong pertumbuhan industri kerajinan yang memanfaatkan unsur–unsur seni. Adapun motif yang diperoleh adalah: Ayam Berlaga, Bungo Matahari, Kuntum Bersanding, Lancang Kuning, Encong Kerinci, Durian Pecah, Bungo Bintang, Bungo Pauh Kecil, Riang-riang, Bungo Nagaro. Pengembangan desain tersebut dipilih 3 produk terbaik yang dinilai oleh 5 penilai yang ahli di bidang desain batik, yaitu motif Durian Pecah, Ayam Berlaga, dan Bungo Matahari. Rancang bangun diversifikasi desain dengan memanfaatkan unsur–unsur seni dan ketrampilan etnis Melayu yaitu pemilihan ragam hias dan motif batik Melayu untuk diterapkan ke bahan sandang dengan komposisi warna yang menarik, sehingga produk memenuhi selera konsumen. Memperbaiki keberagaman batik dengan meningkatkan desain produk antara lain menuangkan ragam hias Melayu ke dalam proses batik yang menggunakan berbagai macam warna sehingga komposisi warna memadai. Diperoleh hasil produk batik dengan ragam hias Melayu yang berkualitas dan komposisi warna yang sesuai dengan karakter ragam hias Melayu. Rancang bangun desain produk untuk mendapatkan formulasi desain serta kelayakan prosesnya dengan penekanan pada teknologi akrab lingkungan dilaksanakan dengan alternatif pendekatan yaitu penciptaan desain bentuk baru.Kata kunci: desain, batik, rancang bangun, ragam hias, MelayuABSTRACTDevelopment of batik design through

  7. Transnationalism as a motif in family stories.

    Science.gov (United States)

    Stone, Elizabeth; Gomez, Erica; Hotzoglou, Despina; Lipnitsky, Jane Y

    2005-12-01

    Family stories have long been recognized as a vehicle for assessing components of a family's emotional and social life, including the degree to which an immigrant family has been willing to assimilate. Transnationalism, defined as living in one or more cultures and maintaining connections to both, is now increasingly common. A qualitative study of family stories in the family of those who appear completely "American" suggests that an affiliation with one's home country is nevertheless detectable in the stories via motifs such as (1) positively connotated home remedies, (2) continuing denigration of home country "enemies," (3) extensive knowledge of the home country history and politics, (4) praise of endogamy and negative assessment of exogamy, (5) superiority of home country to America, and (6) beauty of home country. Furthermore, an awareness of which model--assimilationist or transnational--governs a family's experience may help clarify a clinician's understanding of a family's strengths, vulnerabilities, and mode of framing their cultural experiences.

  8. A possible explanation of the CP puzzle

    International Nuclear Information System (INIS)

    Takhtamyshev, Georgij

    1996-03-01

    The problem of mirror-reflection symmetry (MRS) and time-reversal symmetry (TRS) in our world is discussed. The opinion is expressed, that well-known experiments on parity violation and CP-violation can be treated as signals of some new, yet unknown, level of matter. An hypothesis, which can be used as a base for some future model or theory is formulated. In the framework of this hypothesis, experiments will demonstrate parity violation or CP-violation do not contradict MRS or TRS conservation. (author). 14 refs

  9. CP violation in rare K decays

    International Nuclear Information System (INIS)

    Ecker, G.

    1990-01-01

    The investigation of rare K decays calls for a unified treatment of short- and long-distance aspects as provided by chiral perturbation theory. For the standard model with three generations, the theoretical predictions for signals of CP violation in those decays are reviewed. With direct CP violation as the main target, special emphasis is given to the charge asymmetries in charged K decays and to the especially rare decays K L → π 0 ll-bar. Time dependent rate asymmetries in K 0 decays and the longitudinal muon polarization in K L → μ + μ - are also discussed. 50 refs., 3 figs., 1 tab. (Author)

  10. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.

    2008-01-01

    set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...

  11. Dysregulation of C-X-C motif ligand 10 during aging and association with cognitive performance.

    Science.gov (United States)

    Bradburn, Steven; McPhee, Jamie; Bagley, Liam; Carroll, Michael; Slevin, Mark; Al-Shanti, Nasser; Barnouin, Yoann; Hogrel, Jean-Yves; Pääsuke, Mati; Gapeyeva, Helena; Maier, Andrea; Sipilä, Sarianna; Narici, Marco; Robinson, Andrew; Mann, David; Payton, Antony; Pendleton, Neil; Butler-Browne, Gillian; Murgatroyd, Chris

    2018-03-01

    Chronic low-grade inflammation during aging (inflammaging) is associated with cognitive decline and neurodegeneration; however, the mechanisms underlying inflammaging are unclear. We studied a population (n = 361) of healthy young and old adults from the MyoAge cohort. Peripheral levels of C-X-C motif chemokine ligand 10 (CXCL10) was found to be higher in older adults, compared with young, and negatively associated with working memory performance. This coincided with an age-related reduction in blood DNA methylation at specific CpGs within the CXCL10 gene promoter. In vitro analysis supported the role of DNA methylation in regulating CXCL10 transcription. A polymorphism (rs56061981) that altered methylation at one of these CpG sites further associated with working memory performance in 2 independent aging cohorts. Studying prefrontal cortex samples, we found higher CXCL10 protein levels in those with Alzheimer's disease, compared with aged controls. These findings support the association of peripheral inflammation, as demonstrated by CXCL10, in aging and cognitive decline. We reveal age-related epigenetic and genetic factors which contribute to the dysregulation of CXCL10. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  13. DNA motif alignment by evolving a population of Markov chains.

    Science.gov (United States)

    Bi, Chengpeng

    2009-01-30

    Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

  14. Immunomodulatory Effects of CP-25 on Splenic T Cells of Rats with Adjuvant Arthritis.

    Science.gov (United States)

    Wang, Yang; Han, Chen-Chen; Cui, Dongqian; Luo, Ting-Ting; Li, Yifan; Zhang, Yuwen; Ma, Yang; Wei, Wei

    2018-06-01

    Rheumatoid arthritis (RA) is an autoimmune disease in which T cells play an important role. Paeoniflorin-6-oxy-benzenesulfonate (CP-25) shows a strong anti-inflammatory and immunomodulatory effect in the joint of adjuvant arthritis (AA) rats, but the role of the spleen function is still unclear. The aim of this study was to research how CP-25 regulated spleen function of AA rats. Male Sprague-Dawley rats were administered with CP-25 (50 mg/kg) orally from day 17 to 29 after immunization. The spleen histopathological changes were analyzed by hematoxylin-eosin staining. G protein-coupled receptor kinases (GRKs) and prostaglandin receptor subtypes (EPs) were screened by Western blot and immunohistochemistry. The co-expression of GRK2 and EP2 as well as GRK2 and EP4 was measured by immunofluorescence and co-immunoprecipitation. The expression of GRK2 and EP4 in splenic T cells was further detected by immunofluorescence. CP-25 was found to relieve the secondary paw swelling, attenuate histopathologic changes, and downregulate GRK2, EP2 and EP4 expression in AA rats. Additionally, CP-25 not only downregulated the co-expression of GRK2 and EP4 but also downregulated GRK2, EP4 expression in splenic T cells of AA rats. From these results, we can infer that CP-25 play an anti-inflammatory and immune function by affecting the function of the splenic T cells.

  15. Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

    Science.gov (United States)

    Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

    2017-11-01

    Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  16. Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

    Directory of Open Access Journals (Sweden)

    Nils E. R. Zimmermann

    2017-11-01

    Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  17. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  18. The identification of functional motifs in temporal gene expression analysis

    Directory of Open Access Journals (Sweden)

    Michael G. Surette

    2005-01-01

    Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

  19. RNA recognition motif (RRM)-containing proteins in Bombyx mori

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...

  20. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

    2013-01-01

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...

  1. Fingerprint motifs of phytases | Fan | African Journal of Biotechnology

    African Journals Online (AJOL)

    Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.

  2. Regulatory effect of paraprobiotic Lactobacillus gasseri CP2305 on gut environment and function

    Directory of Open Access Journals (Sweden)

    Tomonori Sugawara

    2016-03-01

    activity was elevated in the CP2305 group (p=0.0401 and p=0.011, respectively. Conclusions: The continuous ingestion of heat-treated CP2305 cells clearly affected intestinal functionality. This is the first report of sterilized Lactobacillus cells having a significant impact on the environment and functions of the intestinal tract. The observed effects might be due, at least in part, to the brain–gut interaction.

  3. Expression of Toll-like receptor 9 and response to bacterial CpG oligodeoxynucleotides in human intestinal epithelium

    DEFF Research Database (Denmark)

    Pedersen, G; Andresen, Lars; Matthiessen, M W

    2005-01-01

    Recognition of repeat CpG motifs, which are common in bacterial, but not in mammalian, DNA, through Toll-like receptor (TLR)9 is an integral part of the innate immune system. As the role of TLR9 in the human gut is unknown, we determined the spectrum of TLR9 expression in normal and inflamed colo...... in vitro despite spontaneous TLR9 gene expression. This suggests that the human epithelium is able to avoid inappropriate immune responses to luminal bacterial products through modulation of the TLR9 pathway....

  4. Newly identified CpG ODNs, M5-30 and M6-395, stimulate mouse immune cells to secrete TNF-alpha and enhance Th1-mediated immunity.

    Science.gov (United States)

    Choi, Sun-Shim; Chung, Eunkyung; Jung, Yu-Jin

    2010-08-01

    Bacterial CpG motifs are known to induce both innate and adaptive immunity in infected hosts via toll-like receptor 9 (TLR9). Because small oligonucleotides (ODNs) mimicking bacterial CpG motifs are easily synthesized, they have found use as immunomodulatory agents in a number of disease models. We have developed a novel bioinformatics approach to identify effective CpG ODN sequences and evaluate their function as TLR9 ligands in a murine system. Among the CpG ODNs we identified, M5-30 and M6-395 showed significant ability to stimulate TNF-alpha and IFN-gamma production in a mouse macrophage cell line and mouse splenocytes, respectively. We also found that these CpG ODNs activated cells through the canonical NF-kappa B signaling pathway. Moreover, both CpG ODNs were able to induce Th1-mediated immunity in Mycobacterium tuberculosis (Mtb)-infected mice. Our results demonstrate that M5-30 and M6-395 function as TLR9-specific ligands, making them useful in the study of TLR9 functionality and signaling in mice.

  5. Natural strong CP conservation in flipped physics

    Energy Technology Data Exchange (ETDEWEB)

    Frampton, P.H. (Institute of Field Physics, Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC (USA)); Kephart, T.W. (Department of Physics and Astronomy, Vanderbilt University, Nashville, TN (USA))

    1990-08-13

    A natural axion-free solution of the strong {ital CP} problem {ital at} {ital tree} {ital level} is noted within an E(6) grand unified theory. Using this as a springboard, it is shown that several flipped SU(5) theories which occur in superstring phenomenology contain within them a mechanism which enforces {bar {theta}}=0 at high accuracy.

  6. CP and B Physics: Progress and prospects

    International Nuclear Information System (INIS)

    Bjorken, J.D.

    1997-06-01

    This summary of the 2nd International Conference on B Physics and CP Violation (Honolulu, 24--27 March, 1997) contains, in addition to what is implied in the title, some extended remarks on the limitations of theory as well as speculations regarding nonperturbative enhancement of decay modes of the class b → s+ charmless hadrons

  7. CP violating phenomena and theoretical results

    International Nuclear Information System (INIS)

    Grimus, W.

    1987-01-01

    An introduction to CP violating phenomena is given and the standard model and its most popular low energy extensions in this context are reviewed. The discussion comprises the minimal supersymmetric extension of the standard model, left-right symmetry, the standard model with more than one Higgs doublet and gauged horizontal symmetries. (Author)

  8. Discrete symmetries, strong CP problem and gravity

    International Nuclear Information System (INIS)

    Senjanovic, G.

    1993-05-01

    Spontaneous breaking of parity or time reversal invariance offers a solution to the strong CP problem, the stability of which under quantum gravitational effects provides an upper limit on the scale of symmetry breaking. Even more important, these Planck scale effects may provide a simple and natural way out of the resulting domain wall problem. (author). 22 refs

  9. Sigma decomposition: the CP-odd Lagrangian

    Energy Technology Data Exchange (ETDEWEB)

    Hierro, I.M. [Dipartimento di Fisica “G. Galilei”, Università di Padova and INFN, Sezione di Padova,Via Marzolo 8, I-35131 Padua (Italy); Merlo, L. [Instituto de Física Teórica, IFT-UAM/CSIC, Universidad Autónoma de Madrid,Cantoblanco, 28049, Madrid (Spain); Rigolin, S. [Dipartimento di Fisica “G. Galilei”, Università di Padova and INFN, Sezione di Padova,Via Marzolo 8, I-35131 Padua (Italy)

    2016-04-04

    In Alonso et al., http://dx.doi.org/10.1007/JHEP12(2014)034, the CP-even sector of the effective chiral Lagrangian for a generic composite Higgs model with a symmetric coset has been constructed, up to four momenta. In this paper, the CP-odd couplings are studied within the same context. If only the Standard Model bosonic sources of custodial symmetry breaking are considered, then at most six independent operators form a basis. One of them is the weak-θ term linked to non-perturbative sources of CP violation, while the others describe CP-odd perturbative couplings between the Standard Model gauge bosons and an Higgs-like scalar belonging to the Goldstone boson sector. The procedure is then applied to three distinct exemplifying frameworks: the original SU(5)/SO(5) Georgi-Kaplan model, the minimal custodial-preserving SO(5)/SO(4) model and the minimal SU(3)/(SU(2)×U(1)) model, which intrinsically breaks custodial symmetry. Moreover, the projection of the high-energy electroweak effective theory to the low-energy chiral effective Lagrangian for a dynamical Higgs is performed, uncovering strong relations between the operator coefficients and pinpointing the differences with the elementary Higgs scenario.

  10. Masses, flavor mix and CP violation

    International Nuclear Information System (INIS)

    Chaussard, L.

    2004-06-01

    The author describes the relationships between masses, mixing of flavors and CP violation. This document is divided into 4 chapters: 1) fermions' masses, 2) mixing of flavors and CP violation, 3) beauty physics and 4) neutrino physics. In chapter 1 an attempt is made to explain what is behind the concepts of lepton mass and quark mass. As for neutrinos, the only neutral fermion, Dirac's and Majorana's views are exposed as well as their consequences. Fermion flavors are mixed in the process of mass generation and this mix is responsible for the breaking of CP and T symmetries. In chapter 2 the author shows how the analysis of particle oscillations from neutral mesons (K 0 , D 0 , B d 0 and B s 0 ) and from neutrinos can shed light on CP violation. Chapter 3 is dedicated to the contribution of beauty physics to the determination of the unitary triangle, through the oscillations of beauty mesons. In chapter 4 the author reviews the experimental results obtained recently concerning neutrino mass and neutrino oscillations and draws some perspectives on future neutrino experiments. (A.C.)

  11. CP violation in exclusive B decays

    International Nuclear Information System (INIS)

    Numata, Ken

    1991-01-01

    We review some decay modes of B 0 or B-bar 0 , with which we measure CP violation or phases of Cabibbo-Kobayashi-Maskawa (CKM) matrix elements. For simplicity, we restrict the topics to the cases of B d 0 -B d -bar 0 system. (author)

  12. CP violation in B decays and supersymmetry

    International Nuclear Information System (INIS)

    Barbieri, R.; Strumia, A.

    1997-01-01

    CP violation in hadronic B decays is studied in a definite and well-motivated framework of flavour physics and supersymmetry. Possible deviations from the standard model both in mixing and in decay amplitudes are discussed. An attempt is made to describe an experimental strategy for looking at these deviations and for measuring the relevant parameters. (orig.)

  13. [Review of experiments measuring CP nonconservation

    International Nuclear Information System (INIS)

    Gollin, G.D.

    1985-08-01

    Recent experiments setting limits on the magnitude of the ratio of two CP nonconservation parameters epsilon'/epsilon are discussed. Gauge theory calculations suggest that epsilon'/epsilon > .005, somewhat at odds with the results epsilon'/epsilon = -.0046 +- .0058 from a Chicago-Saclay measurement and epsilon'/epsilon = .0017 +- .0082 from a Yale-BNL experiment. 9 refs., 5 figs., 2 tabs

  14. A standard form for generalized CP transformations

    International Nuclear Information System (INIS)

    Ecker, G.; Grimus, W.; Neufeld, H.

    1987-01-01

    The investigation of general CP transformations leads to transformations of the form U → W T UW with unitary matrices U, W. It is shown that a basis for weak eigenstates can always be chosen such that W T UW has a certain real standard form. (Author)

  15. CP violation in $b$ hadrons at LHCb

    CERN Document Server

    Hicheur, Adlene

    2017-01-01

    The most recent results on $CP$ violation in b hadrons obtained by the LHCb Collaboration with Run I and years 2015-2016 of Run II are reviewed. The different types of violation are covered by the studies presented in this paper.

  16. Identification of sequence motifs significantly associated with antisense activity

    Directory of Open Access Journals (Sweden)

    Peek Andrew S

    2007-06-01

    Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

  17. Generation and characterization of rat and mouse monoclonal antibodies specific for MeCP2 and their use in X-inactivation studies.

    Directory of Open Access Journals (Sweden)

    K Laurence Jost

    Full Text Available Methyl CpG binding protein 2 (MeCP2 binds DNA, and has a preference for methylated CpGs and, hence, in cells, it accumulates in heterochromatin. Even though it is expressed ubiquitously MeCP2 is particularly important during neuronal maturation. This is underscored by the fact that in Rett syndrome, a neurological disease, 80% of patients carry a mutation in the MECP2 gene. Since the MECP2 gene lies on the X chromosome and is subjected to X chromosome inactivation, affected patients are usually chimeric for wild type and mutant MeCP2. Here, we present the generation and characterization of the first rat monoclonal MeCP2 specific antibodies as well as mouse monoclonal antibodies and a rabbit polyclonal antibody. We demonstrate that our antibodies are suitable for immunoblotting, (chromatin immunoprecipitation and immunofluorescence of endogenous and ectopically expressed MeCP2. Epitope mapping revealed that most of the MeCP2 monoclonal antibodies recognize the C-terminal domain and one the N-terminal domain of MeCP2. Using slot blot analysis, we determined a high sensitivity of all antibodies, detecting amounts as low as 1 ng of MeCP2 protein. Moreover, the antibodies recognize MeCP2 from different species, including human, mouse, rat and pig. Lastly, we have validated their use by analyzing and quantifying X chromosome inactivation skewing using brain tissue of MeCP2 heterozygous null female mice. The new MeCP2 specific monoclonal antibodies described here perform well in a large variety of immunological applications making them a very valuable set of tools for studies of MeCP2 pathophysiology in situ and in vitro.

  18. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  19. Measurement of CP-Violating Asymmetries in B0 Decays to CP Eigenstates

    Energy Technology Data Exchange (ETDEWEB)

    MacFarlane, David B

    2001-02-26

    We present measurements of time-dependent CP-violating asymmetries in neutral B decays to several CP eigenstates. The measurement uses a data sample of 23 million {Upsilon}(4S) {yields} B{bar B} decays collected by the BABAR detector at the PEP-II asymmetric B Factory at SLAC. In this sample, we find events where one neutral B meson is fully reconstructed in a CP eigenstate containing charmonium and the flavor of the other neutral B meson is determined from its decay products. The amplitude of the CP-violating asymmetry, which in the Standard Model is proportional to sin2{beta}, is derived from the decay time distributions in such events. The result is sin2{beta} = 0.34 {+-} 0.20 (stat) {+-} 0.05 (syst).

  20. Measurement of CP-violating asymmetries in B0 decays to CP eigenstates.

    Science.gov (United States)

    Aubert, B; Boutigny, D; De Bonis, I; Gaillard, J M; Jeremie, A; Karyotakis, Y; Lees, J P; Robbe, P; Tisserand, V; Palano, A; Chen, G P; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Reinertsen, P L; Stugu, B; Abbott, B; Abrams, G S; Borgland, A W; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Clark, A R; Dardin, S; Day, C; Dow, S F; Elioff, T; Fan, Q; Gaponenko, I; Gill, M S; Goozen, F R; Gowdy, S J; Gritsan, A; Groysman, Y; Jacobsen, R G; Jared, R C; Kadel, R W; Kadyk, J; Karcher, A; Kerth, L T; Kipnis, I; Kluth, S; Kolomensky, Y G; Kral, J F; Lafever, R; LeClerc, C; Levi, M E; Lewis, S A; Lionberger, C; Liu, T; Long, M; Lynch, G; Marino, M; Marks, K; Meyer, A B; Mokhtarani, A; Momayezi, M; Nyman, M; Oddone, P J; Ohnemus, J; Oshatz, D; Patton, S; Perazzo, A; Peters, C; Pope, W; Pripstein, M; Quarrie, D R; Rasson, J E; Roe, N A; Romosan, A; Ronan, M T; Shelkov, V G; Stone, R; Telnov, A V; von der Lippe, H; Weber, T; Wenzel, W A; Zisman, M S; Bright-Thomas, P G; Harrison, T J; Hawkes, C M; Kirk, A; Knowles, D J; O'Neale, S W; Watson, A T; Watson, N K; Deppermann, T; Koch, H; Krug, J; Kunze, M; Lewandowski, B; Peters, K; Schmuecker, H; Steinke, M; Andress, J C; Barlow, N R; Bhimji, W; Chevalier, N; Clark, P J; Cottingham, W N; De Groot, N; Dyce, N; Foster, B; Mass, A; McFall, J D; Wallom, D; Wilson, F F; Abe, K; Hearty, C; Mattison, T S; McKenna, J A; Thiessen, D; Camanzi, B; Jolly, S; McKemey, A K; Tinslay, J; Blinov, V E; Bukin, A D; Bukin, D A; Buzykaev, A R; Dubrovin, M S; Golubev, V B; Ivanchenko, V N; Kolachev, G M; Korol, A A; Kravchenko, E A; Onuchin, A P; Salnikov, A A; Serednyakov, S I; Skovpen, Y I; Telnov, V I; Yushkov, A N; Lankford, A J; Mandelkern, M; McMahon, S; Stoker, D P; Ahsan, A; Buchanan, C; Chun, S; MacFarlane, D B; Prell, S; Rahatlou, S; Raven, G; Sharma, V; Burke, S; Campagnari, C; Dahmes, B; Hale, D; Hart, P A; Kuznetsova, N; Kyre, S; Levy, S L; Long, O; Lu, A; Richman, J D; Verkerke, W; Witherell, M; Yellin, S; Beringer, J; Dorfan, D E; Eisner, A M; Frey, A; Grillo, A A; Grothe, M; Heusch, C A; Johnson, R P; Kroeger, W; Lockman, W S; Pulliam, T; Sadrozinski, H; Schalk, T; Schmitz, R E; Schumm, B A; Seiden, A; Spencer, E N; Turri, M; Walkowiak, W; Williams, D C; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hanson, J E; Hitlin, D G; Metzler, S; Oyang, J; Porter, F C; Ryd, A; Samuel, A; Weaver, M; Yang, S; Zhu, R Y; Devmal, S; Geld, T L; Jayatilleke, S; Jayatilleke, S M; Mancinelli, G; Meadows, B T; Sokoloff, M D; Bloom, P; Fahey, S; Ford, W T; Gaede, F; van Hoek, W C; Johnson, D R; Michael, A K; Nauenberg, U; Olivas, A; Park, H; Rankin, P; Roy, J; Sen, S; Smith, J G; Wagner, D L; Blouw, J; Harton, J L; Krishnamurthy, M; Soffer, A; Toki, W H; Warner, D W; Wilson, R J; Zhang, J; Brandt, T; Brose, J; Colberg, T; Dahlinger, G; Dickopp, M; Dubitzky, R S; Eckstein, P; Futterschneider, H; Krause, R; Maly, E; Müller-Pfefferkorn, R; Otto, S; Schubert, K R; Schwierz, R; Spaan, B; Wilden, L; Behr, L; Bernard, D; Bonneaud, G R; Brochard, F; Cohen-Tanugi, J; Ferrag, S; Fouque, G; Gastaldi, F; Matricon, P; Mora de Freitas, P; Renard, C; Roussot, E; T'Jampens, S; Thiebaux, C; Vasileiadis, G; Verderi, M; Anjomshoaa, A; Bernet, R; Di Lodovico, F; Khan, A; Muheim, F; Playfer, S; Swain, J E; Falbo, M; Bozzi, C; Dittongo, S; Folegani, M; Piemontese, L; Treadwell, E; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Falciai, D; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Xie, Y; Zallo, A; Bagnasco, S; Buzzo, A; Contri, R; Crosetti, G; Lo Vetere, M; Macri, M; Monge, M R; Pallavicini, M; Passaggio, S; Pastore, F C; Patrignani, C; Pia, M G; Robutti, E; Santroni, A; Morii, M; Bartoldus, R; Dignan, T; Hamilton, R; Mallik, U; Cochran, J; Crawley, H B; Fischer, P A; Lamsa, J; McKay, R; Meyer, W T; Rosenberg, E I; Albert, J N; Beigbeder, C; Benkebil, M; Breton, D; Cizeron, R; Du, S; Grosdidier, G; Hast, C; Höcker, A; LePeltier, V; Lutz, A M; Plaszczynski, S; Schune, M H; Trincaz-Duvoid, S; Truong, K; Valassi, A; Wormser, G; Bionta, R M; Brigljević, V; Brooks, A; Fackler, O; Fujino, D; Lange, D J; Mugge, M; O'Connor, T G; Pedrotti, B; Shi, X; van Bibber, K; Wenaus, T J; Wright, D M; Wuest, C R; Yamamoto, B; Carroll, M; Fry, J R; Gabathuler, E; Gamet, R; George, M; Kay, M; Payne, D J; Sloane, R J; Touramanis, C; Aspinwall, M L; Bowerman, D A; Dauncey, P D; Egede, U; Eschrich, I; Gunawardane, N J; Martin, R; Nash, J A; Price, D R; Sanders, P; Smith, D; Azzopardi, D E; Back, J J; Dixon, P; Harrison, P F; Newman-Coburn, D; Potter, R J; Shorthouse, H W; Strother, P; Vidal, P B; Williams, M I; Cowan, G; George, S; Green, M G; Kurup, A; Marker, C E; McGrath, P; McMahon, T R; Salvatore, F; Scott, I; Vaitsas, G; Brown, D; Davis, C L; Ford, K; Li, Y; Pavlovich, J; Allison, J; Barlow, R J; Boyd, J T; Fullwood, J; Jackson, F; Lafferty, G D; Savvas, N; Simopoulos, E T; Thompson, R J; Weatherall, J H; Bard, R; Farbin, A; Jawahery, A; Lillard, V; Olsen, J; Roberts, D A; Schieck, J R; Blaylock, G; Dallapiccola, C; Flood, K T; Hertzbach, S S; Kofler, R; Lin, C S; Staengle, H; Willocq, S; Wittlin, J; Brau, B; Cowan, R; Sciolla, G; Taylor, F; Yamamoto, R K; Britton, D I; Milek, M; Patel, P M; Trischuk, J; Lanni, F; Palombo, F; Bauer, J M; Booke, M; Cremaldi, L; Eschenberg, V; Kroeger, R; Reep, M; Reidy, J; Sanders, D A; Summers, D J; Beaulieu, M; Martin, J P; Nief, J Y; Seitz, R; Taras, P; Zacek, V; Nicholson, H; Sutton, C S; Cavallo, N; Cartaro, C; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Paolucci, P; Piccolo, D; Sciacca, C; LoSecco, J M; Alsmiller, J R; Gabriel, T A; Handler, T; Heck, J; Brau, J E; Frey, R; Iwasaki, M; Sinev, N B; Strom, D; Borsato, E; Colecchia, F; Dal Corso, F; Galeazzi, F; Margoni, M; Marzolla, M; Michelon, G; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Torassa, E; Voci, C; Bailly, P; Benayoun, M; Briand, H; Chauveau, J; David, P; De La Vaissière, C; Del Buono, L; Genat, J F; Hamon, O; Le Diberder, F; Lebbolo, H; Leruste, P; Lory, J; Martin, L; Roos, L; Stark, J; Versillé, S; Zhang, B; Manfredi, P F; Ratti, L; Re, V; Speziali, V; Frank, E D; Gladney, L; Guo, Q H; Panetta, J H; Angelini, C; Batignani, G; Bettarini, S; Bondioli, M; Bosi, F; Carpinelli, M; Forti, F; Giorgi, M A; Lusiani, A; Martinez-Vidal, F; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Sandrelli, F; Simi, G; Triggiani, G; Walsh, J; Hairre, M; Judd, D; Paick, K; Turnbull, L; Wagoner, D E; Albert, J; Bula, C; Fernholz, R; Lu, C; McDonald, K T; Miftakov, V; Sands, B; Schaffner, S F; Smith, A J; Tumanov, A; Varnes, E W; Bronzini, F; Buccheri, A; Bulfon, C; Cavoto, G; del Re, D; Faccini, R; Ferrarotto, F; Ferroni, F; Fratini, K; Lamanna, E; Leonardi, E; Mazzoni, M A; Morganti, S; Piredda, G; Safai Tehrani, F; Serra, M; Voena, C; Waldi, R; Jacques, P F; Kalelkar, M; Plano, R J; Adye, T; Claxton, B; Franek, B; Galagedera, S; Geddes, N I; Gopal, G P; Lidbury, J; Xella, S M; Aleksan, R; Besson, P; Bourgeois, P; De Domenico, G; Emery, S; Gaidot, A; Ganzhur, S F; Gosset, L; Hamel de Monchenault, G; Kozanecki, W; Langer, M; London, G W; Mayer, B; Serfass, B; Vasseur, G; Yeche, C; Zito, M; Copty, N; Purohit, M V; Singh, H; Yumiceva, F X; Adam, I; Anthony, P L; Aston, D; Baird, K; Bartelt, J; Becla, J; Bell, R; Bloom, E; Boeheim, C T; Boyarski, A M; Boyce, R F; Bulos, F; Burgess, W; Byers, B; Calderini, G; Claus, R; Convery, M R; Coombes, R; Cottrell, L; Coupal, D P; Coward, D H; Craddock, W W; DeStaebler, H; Dorfan, J; Doser, M; Dunwoodie, W; Ecklund, S; Fieguth, T H; Field, R C; Freytag, D R; Glanzman, T; Godfrey, G L; Grosso, P; Haller, G; Hanushevsky, A; Harris, J; Hasan, A; Hewett, J L; Himel, T; Huffer, M E; Innes, W R; Jessop, C P; Kawahara, H; Keller, L; Kelsey, M H; Kim, P; Klaisner, L A; Kocian, M L; Krebs, H J; Kunz, P F; Langenegger, U; Langeveld, W; Leith, D W; Louie, S K; Luitz, S; Luth, V; Lynch, H L; MacDonald, J; Manzin, G; Mariske, H; McCulloch, M; McShurley, D; Menke, S; Messner, R; Metcalfe, S; Moffeit, K C; Mount, R; Muller, D R; Nelson, D; Nordby, M; O'Grady, C P; O'Neill, F G; Oxoby, G; Pavel, T; Perl, J; Petrak, S; Putallaz, G; Quinn, H; Raines, P E; Ratcliff, B N; Reif, R; Robertson, S H; Rochester, L S; Roodman, A; Russell, J J; Sapozhnikov, L; Saxton, O H; Schietinger, T; Schindler, R H; Schwiening, J; Seeman, J T; Serbo, V V; Skarpass, K; Snyder, A; Soha, A; Spanier, S M; Stahl, A; Stelzer, J; Su, D; Sullivan, M K; Talby, M; Tanaka, H A; Va'vra, J; Wagner, S R; Weinstein, A J; White, J L; Wienands, U; Wisniewski, W J; Young, C C; Zioulas, G; Burchat, P R; Cheng, C H; Kirkby, D; Meyer, T I; Roat, C; De Silva, A; Henderson, R; Berridge, S; Bugg, W; Cohn, H; Hart, E; Weidemann, A W; Benninger, T; Izen, J M; Kitayama, I; Lou, X C; Turcotte, M; Bianchi, F; Bona, M; Di Girolamo, B; Gamba, D; Smol, A; Zanin, D; Bosisio, L; Della Ricca, G; Lanceri, L; Pompili, A; Poropat, P; Vuagnin, G; Panvini, R S; Brown, C M; Kowalewski, R; Roney, J M; Band, H R; Charles, E; Dasu, S; Elmer, P; Hu, H; Johnson, J R; Nielsen, J; Orejudos, W; Pan, Y; Prepost, R; Scott, I J; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Zobernig, H; Kordich, T M; Moore, T B; Neal, H

    2001-03-19

    We present measurements of time-dependent CP-violating asymmetries in neutral B decays to several CP eigenstates. The measurement uses a data sample of 23x10(6) Upsilon(4S)-->BbarB decays collected by the BABAR detector at the PEP-II asymmetric B Factory at SLAC. In this sample, we find events in which one neutral B meson is fully reconstructed in a CP eigenstate containing charmonium and the flavor of the other neutral B meson is determined from its decay products. The amplitude of the CP-violating asymmetry, which in the standard model is proportional to sin2beta, is derived from the decay time distributions in such events. The result is sin2beta = 0.34+/-0.20 (stat)+/-0.05 (syst).

  1. Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration.

    Directory of Open Access Journals (Sweden)

    Sergio eTofanelli

    2014-11-01

    Full Text Available Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA and the non-recombining portion of the Y chromosome (NRY to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their classical 6 STR marker format or in the extended 12 STR format, as well as four founder mtDNA lineages (HVS-I segments accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same haplotype signatures. Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes.

  2. A search for CP violation in hyperon decays by the hyper-CP experiment at Fermilab

    International Nuclear Information System (INIS)

    Holmstrom, T.

    2002-01-01

    The Hyper-CP collaboration is performing a precision search for CP violation in hyperon decays, these decays are sensitive to sources of CP violation to which neutral kaon decays are not. The measured CP observable is proportional to the difference between the product of the Ξ and Λ decay α parameters and that of the CP-conjugate decays. About 2.5 billion fully-reconstructed Ξ - → Λπ - → pπ - π - and Ξ-bar + → Λ-barπ + → p-barπ + π + decays were taken in 2 fixed-target runs at Fermilab, allowing a statistical sensitivity of about 2.10 -4 in the CP asymmetry. These 2 runs gave us the largest sample of Ξ and Ω ever collected. An initial study has been done on a fraction of the data and we have obtained: A ΞΛ equals (-7±12(statistical)±6.2(systematic))*10 -4 . Other preliminary results are also presented in this series of slides

  3. Motif statistics and spike correlations in neuronal networks

    International Nuclear Information System (INIS)

    Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir

    2013-01-01

    Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)

  4. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  5. RNA motif search with data-driven element ordering.

    Science.gov (United States)

    Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

    2016-05-18

    In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

  6. Triadic motifs in the dependence networks of virtual societies.

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-10

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  7. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  8. Higgs pair production in the MSSM with explicit CP violation

    International Nuclear Information System (INIS)

    Demir, D.A.

    1999-07-01

    In the minimal supersymmetric standard model with explicit CP violation, associated production of the lightest Higgs boson with heavier ones is analyzed. Due to explicit CP violation, the Higgs bosons are no longer CP eigenstates so that both of the heavy Higgs bosons contribute to the process. While the radiative corrections in the Higgs sector turn out to be quite important, the vertex radiative corrections remain small as in the CP conserving theory. (author)

  9. Testing CP in K/sub μ/3 decays

    International Nuclear Information System (INIS)

    Leurer, M.

    1989-01-01

    K factories will open the way for high-precision CP tests in K/sub μ/ 3 decays. The standard model does not predict CP breaking in this process. We consider here the effects of nonstandard interactions mediated by vector and scalar particles and by leptoquarks. We show that, for the only experimentally measurable quantity, vector particles alone never induce CP violation, and give a general expression for the CP breaking induced by scalars and leptoquarks

  10. Soft CP violation in K-meson systems

    International Nuclear Information System (INIS)

    Montero, J.C.; Nishi, C.C.; Pleitez, V.; Ravinez, O.; Rodriguez, M.C.

    2006-01-01

    We consider a model with soft CP violation which accommodates the CP violation in the neutral kaons even if we assume that the Cabibbo-Kobayashi-Maskawa mixing matrix is real and the sources of CP violation are three complex vacuum expectation values and a trilinear coupling in the scalar potential. We show that for some reasonable values of the masses and other parameters the model allows us to explain all the observed CP violation processes in the K 0 -K 0 system

  11. The CP 1 type separators-superheaters

    International Nuclear Information System (INIS)

    Palacio, G.

    1984-01-01

    Analysis of the functionnement of the separators superheaters in the first French 900 MW PWR units (Fessenhein 1-2 and Bugey 2-3-4-5) and in the program CP 1 units: localization of the separators superheaters, design, tests and choice of the materials, description of the separators superheaters (shells, separators, superheater bundles, internal lagging, purging tank and condensate stank, steam line equipments); study of the various operation modes (nominals, transients, malfunctions, conservation during shutdowns) and the in service behaviour of the components; study of the modifications on the CP 1 equipments and their behaviour; description of the measures, tests and on site controls (controls during planned shutdowns and controls during service) [fr

  12. A CP violetion model of cosmological origin

    International Nuclear Information System (INIS)

    Truppel, W.L.

    1987-01-01

    It's presented a model of spontaneous violation of the CP symmetry whose mechanism of symmetry breaking is of cosmological nature. The main feature is the conformal coupling of the field of a λφ 4 theory with a background gravitational field. We show that, for the open Friedmann model of the universe, the reason of the critical temperaTure for the symmetry restoration to the equilibrium temperature of the universe rrmains constant, so that either the symmetry breaking never happened or, if happened, it can't be reverted by means of thermal effects. Upon coupling the boson to a fermion, this symmetry breaking id related to the CP non-conservation in two distinct ways: violating the P and T symmetries, and violating the C and T symmetries. (author) [pt

  13. Origin of CP-violation through quark mass matrix

    International Nuclear Information System (INIS)

    Kang, K.

    1990-01-01

    After a brief review of the CP violation models, we trace the origin of CP-phases from the phases of a class of quark mass matrices compatible with the calculability condition. The case of three generations corresponding to the standard milliweak CP model is discussed explicitly for the generic case of Fritzsch-type mass matrices. (orig.)

  14. James Cronin, CP Violation, and the Pierre Auger Observatory

    Science.gov (United States)

    dropdown arrow Site Map A-Z Index Menu Synopsis James Cronin, CP Violation and the Pierre Auger Observatory matter over antimatter."1 "The experiment uncovered the CP [charge-parity] violation, or a with Additional Information Additional information about James Cronin and the charge-parity (CP

  15. Val L. Fitch, the CP Violation, and Antimatter

    Science.gov (United States)

    dropdown arrow Site Map A-Z Index Menu Synopsis Val L. Fitch, the CP Violation, and Antimatter Resources ) 'to verify a fundamental tenet of physics, known as CP [charge-parity] symmetry, by showing that two into two pi mesons. Cronin and Fitch had found an example of CP violation. The discovery's

  16. Neutrinos as a probe of CP-violation and leptogenesis

    Indian Academy of Sciences (India)

    Establishing CP-violation in the lepton sector is one of the most challenging future tasks in neutrino physics. The lepton mixing matrix contains one Dirac phase and, if neutrinos are Majorana particles, two additional CP-violating phases. I will review the main theoretical aspects of CP-violation in the lepton sector. Then, I will ...

  17. Light Higgs boson in THDM with explicit CP violation

    International Nuclear Information System (INIS)

    Akhmetzyanova, Eh.N.; Dolgopolov, M.V.; Smirnov, I.A.; Dubinin, M.N.

    2005-01-01

    The effective Lagrangian of the two-doublet Higgs sector with complex parameters is considered in the case of Minimal Supersymmetric Model with explicit CP violation. Light Higgs boson decay widths are calculated for the scenario with maximal mixing of CP even and CP odd states [ru

  18. A new look at CP violation

    International Nuclear Information System (INIS)

    Iqbal, M.J.; Miller, G.A.

    1989-12-01

    The CP violating (CPV) kaonic matrix elements ε', ImA 0 , and ImA 2 , are used to compute CPV observables in baryonic systems. The numerical results for the electric dipole moment and the difference between Λ and Λ - decay parameters are similar to other approaches that use quark operators. Relations between the neutron electric dipole moment, CPV pion-nucleon coupling constants, and Λ decay parameters are derived

  19. NODAL interpreter for CP/M

    International Nuclear Information System (INIS)

    Oide, Katsunobu.

    1982-11-01

    A NODAL interpreter which works under CP/M operating system is made for microcomputers. This interpreter language named NODAL-80 has a similar structure to the NODAL of SPS, but its commands, variables, and expressions are modified to increase the flexibility of programming. NODAL-80 also uses a simple intermediate code to make the execution speed fast without imposing any restriction on the dynamic feature of NODAL language. (author)

  20. Status of CP violation in hyperon decays

    International Nuclear Information System (INIS)

    He, X.G.; Steger, H.; Valencia, G.

    1991-01-01

    We update the estimate of CP violating observables in hyperon decays. We consider the effect of a heavy top quark, as well as recent bounds on the CKM angles. We present an estimate of the uncertainties associated with the evaluation of the hadronic matrix elements by comparing different models. We find that A(Λ - 0 ) is likely to occur at the 10 -5 level within the standard model, although it could reach 10 -4 . (orig.)

  1. CP violating mixings of toponium states

    International Nuclear Information System (INIS)

    Loew, U.

    1988-01-01

    In the present thesis the possibility of an admixture χ of the 2 1 P 1 toponium state which has the CP quantum number -1 to the 2 3 S 1 toponium state with CP quantum number +1 is discussed. The value of χ was estimated in 3 different models of the electroweak interaction. In the standard model the lowest contribution to χ is of 6th order in the weak coupling g or of 4th order in g and of 2nd order in the strong coupling g S . The Feynman diagrams which contribute to χ contain 2 loops. According to a crude estimate of these diagrams it is expected that they yield a contribution smaller than 10 -10 . In the model with extended Higgs sector - for a top-quark mass of 45 GeV - a value of 7x10 -4 resulted for χ. For a top-quark mass of 100 GeV it is expected that χ is even of the order of magnitude of 10 -2 . The large contributions originate from CP violating coupling neutral Higgs particles. In the right-left symmetric model two contributions to χ were calculated. The first one results from the exchange of the right- and left-handed W bosons. For a mass m R =500 GeV this contribution lies at χ ≅ 10 -14 . The second contribution is again based on the exchange of two neutral CP violating coupling Higgs particles. It lies in the order of magnitude at 10 -8 . Possibilities were indicated to find the estimated admixture χ in an experiment. A correlation in the 3-gluon decay of toponium and the decay of toponium into exclusive decays was discussed. (orig./HSI) [de

  2. CP-violation and electric dipole moments

    Energy Technology Data Exchange (ETDEWEB)

    Le Dall, Matthias; Ritz, Adam, E-mail: aritz@uvic.ca [University of Victoria, Department of Physics and Astronomy (Canada)

    2013-03-15

    Searches for intrinsic electric dipole moments of nucleons, atoms and molecules are precision flavour-diagonal probes of new -odd physics. We review and summarise the effective field theory analysis of the observable EDMs in terms of a general set of CP-odd operators at 1 GeV, and the ensuing model-independent constraints on new physics. We also discuss the implications for supersymmetric models, in light of the mass limits emerging from the LHC.

  3. Implication of b → sγ for CP violation in charged scalar exchange

    International Nuclear Information System (INIS)

    Grossman, Y.; Nir, Y.

    1993-06-01

    In model of three or more scalar doublets, new CP violating phases appear in charged scalar exchange. These phases affect CP asymmetries in natural B decay, even is Natural Flavor Conservation holds. The recent upper bound on the decay b → sγ constraints the effect to be at most of order a few percent. Modifications of constraints on CKM parameters open an interesting new region in the sin 2α - sin 2 β plane even in the absence of new phases. (authors)

  4. CP asymmetries in Strange Baryon Decays

    Science.gov (United States)

    Bigi, I. I.; Kang, Xian-Wei; Li, Hai-Bo

    2018-01-01

    While indirect and direct CP violation (CPV) has been established in the decays of strange and beauty mesons, no CPV has yet been found for baryons. There are different paths to finding CP asymmetry in the decays of strange baryons; they are all highly non-trivial. The HyperCP Collaboration has probed CPV in the decays of single Ξ and Λ [1]. We discuss future lessons from {{{e}}}+{{{e}}}- collisions at BESIII/BEPCII: probing decays of pairs of strange baryons, namely Λ, Σ and Ξ. Realistic goals are to learn about non-perturbative QCD. One can hope to find CPV in the decays of strange baryons; one can also dream of finding the impact of New Dynamics. We point out that an important new era will start with the BESIII/BEPCII data accumulated by the end of 2018. This also supports new ideas to trigger {{J}}/{{\\psi }}\\to \\bar{{{Λ }}}{{Λ }} at the LHCb collaboration. Supported by National Science Foundation (PHY-1520966), National Natural Science Foundation of China (11335009, 11125525), Joint Large-Scale Scientific Facility Funds of the NSFC and CAS (U1532257), the National Key Basic Research Program of China (2015CB856700), Key Research Program of Frontier Sciences, CAS, (QYZDJ-SSW-SLH003), XWK’s work is also supported by MOST (Taiwan) (104-2112-M-001-022)

  5. On the Nature of CP Pup

    Science.gov (United States)

    Mason, E.; Orio, M.; Mukai, K.; Bianchini, A.; deMartino, D.; diMille, F.; Williams, R. E.

    2013-01-01

    We present new X-ray and optical spectra of the old nova CP Pup (nova Pup 1942) obtained with Chandra and the CTIO 4m telescope. The X-ray spectrum reveals a multi-temperature optically thin plasma reaching a maximum temperature of 36+19 keV 16 absorbed by local complex neutral material. The time resolved optical spectroscopy confirms the presence of the 1.47 hr period, with cycle-to-cycle amplitude changes, as well as of an additional long term modulation which is suggestive either of a longer pe- riod or of non-Keplerian velocities in the emission line regions. These new observational facts add further support to CP Pup as a magnetic cataclysmic variable (mCV). We compare the mCV and the non-mCV scenarios and while we cannot conclude whether CP Pup is a long period system, all observational evidences point at an intermediate polar (IP) type CV.

  6. CP Violation in Heavy MSSM Higgs Scenarios

    CERN Document Server

    Carena, M; Lee, J S; Pilaftsis, A; Wagner, C E M

    2016-01-01

    We introduce and explore new heavy Higgs scenarios in the Minimal Supersymmetric Standard Model (MSSM) with explicit CP violation, which have important phenomenological implications that may be testable at the LHC. For soft supersymmetry-breaking scales M_S above a few TeV and a charged Higgs boson mass M_H+ above a few hundred GeV, new physics effects including those from explicit CP violation decouple from the light Higgs boson sector. However, such effects can significantly alter the phenomenology of the heavy Higgs bosons while still being consistent with constraints from low-energy observables, for instance electric dipole moments. To consider scenarios with a charged Higgs boson much heavier than the Standard Model (SM) particles but much lighter than the supersymmetric particles, we revisit previous calculations of the MSSM Higgs sector. We compute the Higgs boson masses in the presence of CP violating phases, implementing improved matching and renormalization group (RG) effects, as well as two-loop RG...

  7. Quaternionic potentials and CP-violation

    International Nuclear Information System (INIS)

    Nishi, Celso Chikahiro

    2000-01-01

    Full text follows: In the formulation of Quantum Mechanics by using a non-commutative ring of quaternions, we attempt to solve the Schroedinger equation with quaternionic potentials. Decay processes can easily be modeled by including complex imaginary potentials. Although, it could be explained as a transition between states under action of a perturbation. Purely imaginary quaternionic potentials can be used to describe CP-violation effects. The neutral kaon system, K 0 - K-bar 0 or K L - K S , represents an example of CP-violation phenomenon. The inclusion of quaternionic potentials imply a reformulation of the whole quantum theory. The use of a quaternionic algebra in discussing the Schroedinger equation leads to the lost of time reversal invariance (T), closely connected to CP violation by the well-known CPT theorem. In particular, we study the Schroedinger equation in presence of a quaternionic potential barrier given in terms of V, real potential acting in the region of width a, and jW, purely quaternionic potential acting in the region of width b. Different cases, |W|/V and b/a, are discussed in view of possible deviations of standard Quantum Mechanics. The complex linear Schroedinger equation is solved for stationary states. The explicit solution contains complex and quaternionic transmission/reflection coefficients. A wave packet treatment needs to make a more realistic and physical description. We briefly discuss possible interpretations and remaining questions. (author)

  8. An essential GT motif in the lamin A promoter mediates activation by CREB-binding protein

    International Nuclear Information System (INIS)

    Janaki Ramaiah, M.; Parnaik, Veena K.

    2006-01-01

    Lamin A is an important component of nuclear architecture in mammalian cells. Mutations in the human lamin A gene lead to highly degenerative disorders that affect specific tissues. In studies directed towards understanding the mode of regulation of the lamin A promoter, we have identified an essential GT motif at -55 position by reporter gene assays and mutational analysis. Binding of this sequence to Sp transcription factors has been observed in electrophoretic mobility shift assays and by chromatin immunoprecipitation studies. Further functional analysis by co-expression of recombinant proteins and ChIP assays has shown an important regulatory role for CREB-binding protein in promoter activation, which is mediated by the GT motif

  9. Requirement for asparagine in the aquaporin NPA sequence signature motifs for cation exclusion

    DEFF Research Database (Denmark)

    Wree, Dorothea; Wu, Binghua; Zeuthen, Thomas

    2011-01-01

    Two highly conserved NPA motifs are a hallmark of the aquaporin (AQP) family. The NPA triplets form N-terminal helix capping structures with the Asn side chains located in the centre of the water or solute-conducting channel, and are considered to play an important role in AQP selectivity. Although...... interchangeable at both NPA sites without affecting protein expression or water, glycerol and methylamine permeability. However, other mutations in the NPA region led to reduced permeability (S186C and S186D), to nonfunctional channels (N64D), or even to lack of protein expression (S186A and S186T). Using...... electrophysiology, we found that an analogous mammalian AQP1 N76S mutant excluded protons and potassium ions, but leaked sodium ions, providing an argument for the overwhelming prevalence of Asn over other amino acids. We conclude that, at the first position in the NPA motifs, only Asn provides efficient helix cap...

  10. Targeting functional motifs of a protein family

    Science.gov (United States)

    Bhadola, Pradeep; Deo, Nivedita

    2016-10-01

    The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

  11. ROMANIAN FOLKLORE MOTIFS IN FASHION DESIGN

    Directory of Open Access Journals (Sweden)

    MOCENCO Alexandra

    2014-05-01

    Full Text Available The traditional Romanian costume such as the entire popular art (architecture, woodcarvins, pottery etc. was born and lasted in our country since ancient times. Closely related to human existence, the traditional costume reflected over the years as reflected nowadays, the mentality and artistic conception of the people. Today the traditional Romanian costume became an inspiration source to the wholesale fashion production industry designers, both Romanian and international. Although the contemporary designers are working in accordance with a vision, using a wide area of styles, methods and current technology, they usually return to traditional techniques and ethnic folklore motifs, which converts and resize them, integrating them in their contemporary space. Adrian Oianu is a very appreciated Romanian designer who launched two collections inspired by his native’s country traditional costumes: “Suflecata pan’ la brau” (“Turned up ‘til the belt” and “Bucurie” (“Joy”. Dorin Negrau had as inspiration for his “Lost” collection the traditional costume from the Bihor region. Yves Saint Laurent had a collection inspired by the Romanian traditional flax blouses called “La blouse roumaine”. The paper presents the traditional Romanian values throw fashion collections. The research activity will create innovative concepts to support the garment industry in order to develop their own brand and to bring the design activities in Romania at an international level. The research was conducted during the initial stage of a project, financed through national founds, consisting in a documentary study on ethnographic characteristics of the popular costume from different regions of the country.

  12. CP violation in charmless two-body B decays at LHCb

    CERN Multimedia

    CERN. Geneva

    2013-01-01

    The study of CP violation in charmless charged two-body decays of neutral B mesons provides a test of the Cabibbo-Kobayashi-Maskawa picture of the Standard Model, and is a sensitive probe to contributions of processes beyond it. Using a data sample of proton-proton collisions, corresponding to an integrated luminosity of 1.0 fb-1, collected with the LHCb detector at a centre-of-mass energy of 7 TeV, CP violation has been observed for the first time in the B0_s to K-pi+ decay with a significance of more than 5 sigma. Furthermore, first measurements of direct and mixing-induced CP-violating asymmetries in the B0_s to K+K- decay have been performed, opening new avenues to the determination of the unitarity triangle angle gamma using decays affected by penguin processes.

  13. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-09-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  14. Methods and statistics for combining motif match scores.

    Science.gov (United States)

    Bailey, T L; Gribskov, M

    1998-01-01

    Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

  15. DNA regulatory motif selection based on support vector machine ...

    African Journals Online (AJOL)

    ... machine (SVM) and its application in microarray experiment of Kashin-Beck disease. ... speed and amount of the corresponding mRNA in gene replication process. ... and revealed that some motifs may be related to the immune reactions.

  16. On the determination of CP-even and CP-odd components of a mixed CP Higgs boson at e+e- linear colliders

    International Nuclear Information System (INIS)

    Dova, Maria Teresa; Ferrari, Sergio

    2005-01-01

    We present a method to investigate the CP quantum numbers of the Higgs boson in the process e + e - ->Zφ at a future e + e - linear collider (LC), where φ, a generic Higgs boson, is a mixture of CP-even and CP-odd states. The procedure consists of a comparison of the data with predictions obtained from Monte Carlo simulations corresponding to the productions of scalar and pseudoscalar Higgs and the interference term which constitutes a distinctive signal of CP violation. We present estimates of the sensitivity of the method from Monte Carlo studies using hypothetical data samples with a full LC detector simulation taking into account the background signals

  17. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  18. Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2014-10-01

    Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

  19. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  20. Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

    Science.gov (United States)

    Roy, Indranil; Aluru, Srinivas

    2016-01-01

    Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

  1. An experimental test of a fundamental food web motif.

    Science.gov (United States)

    Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

    2010-06-07

    Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

  2. CP violation outside the standard model phenomenology for pedestrians

    International Nuclear Information System (INIS)

    Lipkin, H.J.

    1993-01-01

    So far the only experimental evidence for CP violation is the 1964 discovery of K L →2π where the two mass eigenstates produced by neutral meson mixing both decay into the same CP eigenstate. This result is described by two parameters ε and ε'. Today ε ∼ its 1964 value, ε' data are still inconclusive and there is no new evidence for CP violation. One might expect to observe similar phenomena in other systems and also direct CP violation as charge asymmetries between decays of charge conjugate hadrons H ± → f ± . Why is it so hard to find CP violation? How can B Physics help? Does CP lead beyond the standard model? The author presents a pedestrian symmetry approach which exhibits the difficulties and future possibilities of these two types of CP-violation experiments, neutral meson mixing and direct charge asymmetry: what may work, what doesn't work and why

  3. CP asymmetries in the supersymmetric trilepton signal at the LHC

    International Nuclear Information System (INIS)

    Bornhauser, S.; Drees, M.; Dreiner, H.; Eboli, O.J.P.; Kim, J.S.; Kittel, O.

    2012-01-01

    In the CP-violating Minimal Supersymmetric Standard Model, we study the production of a neutralino-chargino pair at the LHC. For their decays into three leptons, we analyze CP asymmetries which are sensitive to the CP phases of the neutralino and chargino sector. We present analytical formulas for the entire production and decay process, and identify the CP-violating contributions in the spin correlation terms. This allows us to define the optimal CP asymmetries. We present a detailed numerical analysis of the cross sections, branching ratios, and the CP observables. For light neutralinos, charginos, and squarks, the asymmetries can reach several 10%. We estimate the discovery potential for the LHC to observe CP violation in the trilepton channel. (orig.)

  4. Analysis list: Cp190 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Cp190 Cell line,Embryo,Larvae + dm3 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/...target/Cp190.1.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/target/Cp190.5.tsv http://dbarchive.bioscience...dbc.jp/kyushu-u/dm3/target/Cp190.10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/colo/Cp190.Cell_l...ine.tsv,http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/colo/Cp190.Embryo.tsv,http://dbarchive.bioscience...dbc.jp/kyushu-u/dm3/colo/Cp190.Larvae.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/

  5. Physiologic TLR9-CpG-DNA interaction is essential for the homeostasis of the intestinal immune system.

    Science.gov (United States)

    Hofmann, Claudia; Dunger, Nadja; Doser, Kristina; Lippert, Elisabeth; Siller, Sebastian; Edinger, Matthias; Falk, Werner; Obermeier, Florian

    2014-01-01

    Cytosine-guanosine dinucleotide (CpG) motifs are immunostimulatory components of bacterial DNA and activators of innate immunity through Toll-like receptor 9 (TLR9). Administration of CpG oligodeoxynucleotides before the onset of experimental colitis prevents intestinal inflammation by enforcement of regulatory mechanisms. It was investigated whether physiologic CpG/TLR9 interactions are critical for the homeostasis of the intestinal immune system. Mesenteric lymph node cell and lamina propria mononuclear cell (LPMC) populations from BALB/c wild-type (wt) or TLR9 mice were assessed by flow cytometry and proteome profiling. Cytokine secretion was determined and nuclear extracts were analyzed for nuclear factor kappa B (NF-κB) and cAMP response-element binding protein activity. To assess the colitogenic potential of intestinal T cells, CD4-enriched cells from LPMC of wt or TLR9 donor mice were injected intraperitoneally in recipient CB-17 SCID mice. TLR9 deficiency was accompanied by slight changes in cellular composition and phosphorylation of signaling proteins of mesenteric lymph node cell and LPMC. LPMC from TLR9 mice displayed an increased proinflammatory phenotype compared with wt LPMC. NF-κB activity in cells from TLR9 mice was enhanced, whereas cAMP response-element binding activity was reduced compared with wt. Transfer of lamina propria CD4-enriched T cells from TLR9 mice induced severe colitis, whereas wt lamina propria CD4-enriched T cells displayed an attenuated phenotype. Lack of physiologic CpG/TLR9 interaction impairs the function of the intestinal immune system indicated by enhanced proinflammatory properties. Thus, physiologic CpG/TLR interaction is essential for homeostasis of the intestinal immune system as it is required for the induction of counterregulating anti-inflammatory mechanisms.

  6. A CP violating mixing matrix compatible with neutral flavour conservation and spontaneous CP violation

    International Nuclear Information System (INIS)

    Ecker, G.; Grimus, W.; Neufeld, H.

    1987-01-01

    A specific ansatz for the Yukawa couplings of a four-generation SU(2) L x U(I) model with two Higgs doublets is discussed which leads to neutral flavour conservation, spontaneous CP violation and to a genuinely complex mixing matrix. W exchange conserves CP in the limit m t' = m t only. The decay rate for t → b is reduced by a factor two compared to the Standard Model with three generations. The phenomenological implications for K 0 -K-bar 0 and B 0 -B-bar 0 are investigated. (Author)

  7. Radiative violation of CP-symmetry

    International Nuclear Information System (INIS)

    Galvan Herrera, J.B.

    1990-01-01

    The left-right quiral symmetry is not conserved by the Standard model. A subgroup of the standard gauge group (SU(2) L ) breaks this symmetry in a explicit way. Moreover, the standard model, if there are theree or more matter generations, violates the CP discrete symmetry. This prediction has been experimentally demonstrated correct in the Kaon anti Kaon system. In this work some possible explanations to the CP violation parameter magnitude are researched. We have studied the variation of the Kobayashi-Maskawa matrix with the energy scale. To realize this work we have developed a general method to calculate the renormalization group equations of the Kobayashi-Maskawa matrix parameters. From these equations we could also calculate the renormalization group equation of the J parameter that characterizes the CP violation. This calculus has been applied in a concrete example: a typical supersymmetric model from superstring theories. This model can be seen like a natural extension of the supersymmetric standard model. This kind of models have a gauge group bigger that the standard one more particles and new terms of the Lagrangian. We have verified that such model provides us of a correct low energy fenomenology and, moreover other results, some particle spectrums have been developed. In the elaboration of this model some conditions, that the model has to respected to be compatible with the actual fenomenology, have been studied. The most interesting results of this thesis are the develop of a general method to calculate the renormalization group equations of the Kobayashi-Maskawa matrix parameters and the develop of a new mechanism of the radiative violation. This mechanism is related with the new terms of the Lagrangian. (Author)

  8. The HyperCP data acquisition system

    International Nuclear Information System (INIS)

    Kaplan, D.M.

    1997-06-01

    For the HyperCP experiment at Fermilab, we have assembled a data acquisition system that records on up to 45 Exabyte 8505 tape drives in parallel at up to 17 MB/s. During the beam spill, data are acquired from the front-end digitization systems at ∼ 60 MB/s via five parallel data paths. The front-end systems achieve typical readout deadtime of ∼ 1 micros per event, allowing operation at 75-kHz trigger rate with approx-lt 30% deadtime. Event building and tapewriting are handled by 15 Motorola MVME167 processors in 5 VME crates

  9. Gravitational leptogenesis, C, CP and strong equivalence

    International Nuclear Information System (INIS)

    McDonald, Jamie I.; Shore, Graham M.

    2015-01-01

    The origin of matter-antimatter asymmetry is one of the most important outstanding problems at the interface of particle physics and cosmology. Gravitational leptogenesis (baryogenesis) provides a possible mechanism through explicit couplings of spacetime curvature to appropriate lepton (or baryon) currents. In this paper, the idea that these strong equivalence principle violating interactions could be generated automatically through quantum loop effects in curved spacetime is explored, focusing on the realisation of the discrete symmetries C, CP and CPT which must be broken to induce matter-antimatter asymmetry. The related issue of quantum corrections to the dispersion relation for neutrino propagation in curved spacetime is considered within a fully covariant framework.

  10. The CKM matrix and CP violation

    International Nuclear Information System (INIS)

    Nir, Y.

    1991-10-01

    The CKM picture of the quark sector is reviewed. We explain how the phenomena of quark mixing, CP violation and the absence of flavor changing neutral currents arise in the Standard Model. We describe the determination of the CKM elements from direct measurements, from unitarity and from indirect measurements. We discuss the motivation for schemes of quark mass matrices and analyze the Fritzsch scheme as an example. Finally, we list the experimental and theoretical improvements expected in the future in the determination of the CKM matrix. 86 refs., 6 figs

  11. CP violating decays in leptogenesis scenarios

    International Nuclear Information System (INIS)

    Covi, L.; Roulet, E.; Vissani, F.

    1996-05-01

    We compute the CP violation in the decays of heavy electroweak singlet neutrinos, arising from both the one-loop vertex corrections and the wave function mixing. We extend the computation to the supersymmetric version of the model and discuss the implications for the generation of a lepton number asymmetry by the out of equilibrium decay of the heavy (s)neutrinos in the early Universe, to be reprocessed later in the observed baryon excess by anomalous electroweak processes. (author). 14 refs, 2 figs

  12. Gravitational leptogenesis, C, CP and strong equivalence

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, Jamie I.; Shore, Graham M. [Department of Physics, Swansea University,Swansea, SA2 8PP (United Kingdom)

    2015-02-12

    The origin of matter-antimatter asymmetry is one of the most important outstanding problems at the interface of particle physics and cosmology. Gravitational leptogenesis (baryogenesis) provides a possible mechanism through explicit couplings of spacetime curvature to appropriate lepton (or baryon) currents. In this paper, the idea that these strong equivalence principle violating interactions could be generated automatically through quantum loop effects in curved spacetime is explored, focusing on the realisation of the discrete symmetries C, CP and CPT which must be broken to induce matter-antimatter asymmetry. The related issue of quantum corrections to the dispersion relation for neutrino propagation in curved spacetime is considered within a fully covariant framework.

  13. Stanniocalcin 1 binds hemin through a partially conserved heme regulatory motif

    International Nuclear Information System (INIS)

    Westberg, Johan A.; Jiang, Ji; Andersson, Leif C.

    2011-01-01

    Highlights: → Stanniocalcin 1 (STC1) binds heme through novel heme binding motif. → Central iron atom of heme and cysteine-114 of STC1 are essential for binding. → STC1 binds Fe 2+ and Fe 3+ heme. → STC1 peptide prevents oxidative decay of heme. -- Abstract: Hemin (iron protoporphyrin IX) is a necessary component of many proteins, functioning either as a cofactor or an intracellular messenger. Hemoproteins have diverse functions, such as transportation of gases, gas detection, chemical catalysis and electron transfer. Stanniocalcin 1 (STC1) is a protein involved in respiratory responses of the cell but whose mechanism of action is still undetermined. We examined the ability of STC1 to bind hemin in both its reduced and oxidized states and located Cys 114 as the axial ligand of the central iron atom of hemin. The amino acid sequence differs from the established (Cys-Pro) heme regulatory motif (HRM) and therefore presents a novel heme binding motif (Cys-Ser). A STC1 peptide containing the heme binding sequence was able to inhibit both spontaneous and H 2 O 2 induced decay of hemin. Binding of hemin does not affect the mitochondrial localization of STC1.

  14. Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons.

    Science.gov (United States)

    Diaz de Arce, Alexander J; Noderer, William L; Wang, Clifford L

    2018-01-25

    The initiation of mRNA translation from start codons other than AUG was previously believed to be rare and of relatively low impact. More recently, evidence has suggested that as much as half of all translation initiation utilizes non-AUG start codons, codons that deviate from AUG by a single base. Furthermore, non-AUG start codons have been shown to be involved in regulation of expression and disease etiology. Yet the ability to gauge expression based on the sequence of a translation initiation site (start codon and its flanking bases) has been limited. Here we have performed a comprehensive analysis of translation initiation sites that utilize non-AUG start codons. By combining genetic-reporter, cell-sorting, and high-throughput sequencing technologies, we have analyzed the expression associated with all possible variants of the -4 to +4 positions of non-AUG translation initiation site motifs. This complete motif analysis revealed that 1) with the right sequence context, certain non-AUG start codons can generate expression comparable to that of AUG start codons, 2) sequence context affects each non-AUG start codon differently, and 3) initiation at non-AUG start codons is highly sensitive to changes in the flanking sequences. Complete motif analysis has the potential to be a key tool for experimental and diagnostic genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Stanniocalcin 1 binds hemin through a partially conserved heme regulatory motif

    Energy Technology Data Exchange (ETDEWEB)

    Westberg, Johan A., E-mail: johan.westberg@helsinki.fi [Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, P.O. Box 21, Haartmaninkatu 3, FI-00014 Helsinki (Finland); Jiang, Ji, E-mail: ji.jiang@helsinki.fi [Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, P.O. Box 21, Haartmaninkatu 3, FI-00014 Helsinki (Finland); Andersson, Leif C., E-mail: leif.andersson@helsinki.fi [Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, P.O. Box 21, Haartmaninkatu 3, FI-00014 Helsinki (Finland)

    2011-06-03

    Highlights: {yields} Stanniocalcin 1 (STC1) binds heme through novel heme binding motif. {yields} Central iron atom of heme and cysteine-114 of STC1 are essential for binding. {yields} STC1 binds Fe{sup 2+} and Fe{sup 3+} heme. {yields} STC1 peptide prevents oxidative decay of heme. -- Abstract: Hemin (iron protoporphyrin IX) is a necessary component of many proteins, functioning either as a cofactor or an intracellular messenger. Hemoproteins have diverse functions, such as transportation of gases, gas detection, chemical catalysis and electron transfer. Stanniocalcin 1 (STC1) is a protein involved in respiratory responses of the cell but whose mechanism of action is still undetermined. We examined the ability of STC1 to bind hemin in both its reduced and oxidized states and located Cys{sup 114} as the axial ligand of the central iron atom of hemin. The amino acid sequence differs from the established (Cys-Pro) heme regulatory motif (HRM) and therefore presents a novel heme binding motif (Cys-Ser). A STC1 peptide containing the heme binding sequence was able to inhibit both spontaneous and H{sub 2}O{sub 2} induced decay of hemin. Binding of hemin does not affect the mitochondrial localization of STC1.

  16. Double-hydrophobic elastin-like polypeptides with added functional motifs: Self-assembly and cytocompatibility.

    Science.gov (United States)

    Le, Duc H T; Tsutsui, Yoko; Sugawara-Narutaki, Ayae; Yukawa, Hiroshi; Baba, Yoshinobu; Ohtsuki, Chikara

    2017-09-01

    We have recently developed a novel double-hydrophobic elastin-like triblock polypeptide called GPG, designed after the uneven distribution of two different hydrophobic domains found in elastin, an extracellular matrix protein providing elasticity and resilience to tissues. Upon temperature trigger, GPG undergoes a sequential self-assembling process to form flexible beaded nanofibers with high homogeneity and excellent dispersibility in water. Given that GPG might be a potential elastin-mimetic material, we sought to explore the biological activities of this block polypeptide. Besides GPG, several functionalized derivatives were also constructed by fusing functional motifs such as KAAK or KAAKGRGDS at the C-terminal of GPG. Although the added motifs affected the kinetics of fiber formation and β-sheet contents, all three GPGs assembled into beaded nanofibers at the physiological temperature. The resulting GPG nanofibers preserved their beaded structures in cell culture medium; therefore, they were coated on polystyrene substrates to study their cytocompatibility toward mouse embryonic fibroblasts, NIH-3T3. Among the three polypeptides, GPG having the cell-binding motif GRGDS derived from fibronectin showed excellent cell adhesion and cell proliferation properties compared to other conventional materials, suggesting its promising applications as extracellular matrices for mammalian cells. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2475-2484, 2017. © 2017 Wiley Periodicals, Inc.

  17. Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae.

    Science.gov (United States)

    Moon, Jaewoong; Liu, Z Lewis

    2015-04-01

    The aldehyde reductase gene ARI1 is a recently characterized member of an intermediate subfamily within the short-chain dehydrogenase/reductase (SDR) superfamily that clarified mechanisms of in situ detoxification of 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde by Saccharomyces cerevisiae. Uncharacterized open reading frames (ORFs) are common among tolerant candidate genes identified for lignocellulose-to-advanced biofuels conversion. This study presents partially purified proteins of two ORFs, YDR541C and YGL039W, and direct enzyme assay evidence against aldehyde-inhibitory compounds commonly encountered during lignocellulosic biomass fermentation processes. Each of the partially purified proteins encoded by these ORFs showed a molecular mass of approximately 38 kDa, similar to Ari1p, a protein encoded by aldehyde reductase gene. Both proteins demonstrated strong aldehyde reduction activities toward 14 aldehyde substrates, with high levels of reduction activity for Ydr541cp toward both aromatic and aliphatic aldehydes. While Ydr541cp was observed to have a significantly higher specific enzyme activity at 20 U/mg using co-factor NADPH, Ygl039wp displayed a NADH preference at 25 U/mg in reduction of butylaldehyde. Amino acid sequence analysis identified a characteristic catalytic triad, Ser, Tyr and Lys; a conserved catalytic motif of Tyr-X-X-X-Lys; and a cofactor-binding sequence motif, Gly-X-X-Gly-X-X-Ala, near the N-terminus that are shared by Ydr541cp, Ygl039wp, Yol151wp/GRE2 and Ari1p. Findings of aldehyde reductase genes contribute to the yeast gene annotation and aids development of the next-generation biocatalyst for advanced biofuels production. Copyright © 2015 John Wiley & Sons, Ltd.

  18. A novel fibronectin binding motif in MSCRAMMs targets F3 modules.

    Directory of Open Access Journals (Sweden)

    Sabitha Prabhakaran

    Full Text Available BBK32 is a surface expressed lipoprotein and fibronectin (Fn-binding microbial surface component recognizing adhesive matrix molecule (MSCRAMM of Borrelia burgdorferi, the causative agent of Lyme disease. Previous studies from our group showed that BBK32 is a virulence factor in experimental Lyme disease and located the Fn-binding region to residues 21-205 of the lipoprotein.Studies aimed at identifying interacting sites between BBK32 and Fn revealed an interaction between the MSCRAMM and the Fn F3 modules. Further analysis of this interaction showed that BBK32 can cause the aggregation of human plasma Fn in a similar concentration-dependent manner to that of anastellin, the superfibronectin (sFn inducing agent. The resulting Fn aggregates are conformationally distinct from plasma Fn as indicated by a change in available thermolysin cleavage sites. Recombinant BBK32 and anastellin affect the structure of Fn matrices formed by cultured fibroblasts and inhibit endothelial cell proliferation similarly. Within BBK32, we have located the sFn-forming activity to a region between residues 160 and 175 which contains two sequence motifs that are also found in anastellin. Synthetic peptides mimicking these motifs induce Fn aggregation, whereas a peptide with a scrambled sequence motif was inactive, suggesting that these motifs represent the sFn-inducing sequence.We conclude that BBK32 induces the formation of Fn aggregates that are indistinguishable from those formed by anastellin. The results of this study provide evidence for how bacteria can target host proteins to manipulate host cell activities.

  19. Verification of the MOTIF code version 3.0

    International Nuclear Information System (INIS)

    Chan, T.; Guvanasen, V.; Nakka, B.W.; Reid, J.A.K.; Scheier, N.W.; Stanchell, F.W.

    1996-12-01

    As part of the Canadian Nuclear Fuel Waste Management Program (CNFWMP), AECL has developed a three-dimensional finite-element code, MOTIF (Model Of Transport In Fractured/ porous media), for detailed modelling of groundwater flow, heat transport and solute transport in a fractured rock mass. The code solves the transient and steady-state equations of groundwater flow, solute (including one-species radionuclide) transport, and heat transport in variably saturated fractured/porous media. The initial development was completed in 1985 (Guvanasen 1985) and version 3.0 was completed in 1986. This version is documented in detail in Guvanasen and Chan (in preparation). This report describes a series of fourteen verification cases which has been used to test the numerical solution techniques and coding of MOTIF, as well as demonstrate some of the MOTIF analysis capabilities. For each case the MOTIF solution has been compared with a corresponding analytical or independently developed alternate numerical solution. Several of the verification cases were included in Level 1 of the International Hydrologic Code Intercomparison Project (HYDROCOIN). The MOTIF results for these cases were also described in the HYDROCOIN Secretariat's compilation and comparison of results submitted by the various project teams (Swedish Nuclear Power Inspectorate 1988). It is evident from the graphical comparisons presented that the MOTIF solutions for the fourteen verification cases are generally in excellent agreement with known analytical or numerical solutions obtained from independent sources. This series of verification studies has established the ability of the MOTIF finite-element code to accurately model the groundwater flow and solute and heat transport phenomena for which it is intended. (author). 20 refs., 14 tabs., 32 figs

  20. Mechanisms of zero-lag synchronization in cortical motifs.

    Directory of Open Access Journals (Sweden)

    Leonardo L Gollo

    2014-04-01

    Full Text Available Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying"--a mechanism that relies on a specific network motif--has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair--a "resonance pair"--plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying from those that do not (such as the common driving triad. Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain.

  1. Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

    Directory of Open Access Journals (Sweden)

    O. V. Galzitskaya

    2015-01-01

    Full Text Available How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern and third (the two amino acids occur randomly groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62 is higher than between fungi and plants (0.54. Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

  2. Bc meson weak decays and CP violation

    International Nuclear Information System (INIS)

    Liu, J.; Chao, K.

    1997-01-01

    The form factors for B c transitions are calculated with a relativistic constituent quark model based on the Bethe-Salpeter formalism. The rates for some semileptonic and nonleptonic B c weak decays and CP-violating asymmetries for two-body hardonic B c decays are estimated as well. The calculated widths are compared with those predicted in other quark models of mesons. For the most promising signatures for the discovery of B c : B c →ψlν→(l '+ l '- )lν and B c →ψπ→(l '+ l '- )π (with l ' =e or μ), the combined branching ratios are, respectively, estimated to be 1.06x10 -3 and 4.8a 1 2 x10 -5 for τ B c =0.5 ps and as large as 2.56x10 -3 and 1.15a 1 2 x10 -4 for τ B c =1.2 ps. There are large CP-violating effects in some B c decay modes, and the rates for some of these (e.g., B c →ψD * ,η c D, and η c D * , etc.) are large too. copyright 1997 The American Physical Society

  3. Higgs pair production at NLO QCD for CP-violating Higgs sectors

    Science.gov (United States)

    Gröber, R.; Mühlleitner, M.; Spira, M.

    2017-12-01

    Higgs pair production through gluon fusion is an important process at the LHC to test the dynamics underlying electroweak symmetry breaking. Higgs sectors beyond the Standard Model (SM) can substantially modify this cross section through novel couplings not present in the SM or the on-shell production of new heavy Higgs bosons that subsequently decay into Higgs pairs. CP violation in the Higgs sector is important for the explanation of the observed matter-antimatter asymmetry through electroweak baryogenesis. In this work we compute the next-to-leading order (NLO) QCD corrections in the heavy top quark limit, including the effects of CP violation in the Higgs sector. We choose the effective theory (EFT) approach, which provides a rather model-independent way to explore New Physics (NP) effects by adding dimension-6 operators, both CP-conserving and CP-violating ones, to the SM Lagrangian. Furthermore, we perform the computation within a specific UV-complete model and choose as benchmark model the general 2-Higgs-Doublet Model with CP violation, the C2HDM. Depending on the dimension-6 coefficients, the relative NLO QCD corrections are affected by several per cent through the new CP-violating operators. This is also the case for SM-like Higgs pair production in the C2HDM, while the relative QCD corrections in the production of heavier C2HDM Higgs boson pairs deviate more strongly from the SM case. The absolute cross sections both in the EFT and the C2HDM can be modified by more than an order of magnitude. In particular, in the C2HDM the resonant production of Higgs pairs can by far exceed the SM cross section.

  4. Apoptotic Activity of MeCP2 Is Enhanced by C-Terminal Truncating Mutations.

    Directory of Open Access Journals (Sweden)

    Alison A Williams

    Full Text Available Methyl-CpG binding protein 2 (MeCP2 is a widely abundant, multifunctional protein most highly expressed in post-mitotic neurons. Mutations causing Rett syndrome and related neurodevelopmental disorders have been identified along the entire MECP2 locus, but symptoms vary depending on mutation type and location. C-terminal mutations are prevalent, but little is known about the function of the MeCP2 C-terminus. We employ the genetic efficiency of Drosophila to provide evidence that expression of p.Arg294* (more commonly identified as R294X, a human MECP2 E2 mutant allele causing truncation of the C-terminal domains, promotes apoptosis of identified neurons in vivo. We confirm this novel finding in HEK293T cells and then use Drosophila to map the region critical for neuronal apoptosis to a small sequence at the end of the C-terminal domain. In vitro studies in mammalian systems previously indicated a role of the MeCP2 E2 isoform in apoptosis, which is facilitated by phosphorylation at serine 80 (S80 and decreased by interactions with the forkhead protein FoxG1. We confirm the roles of S80 phosphorylation and forkhead domain transcription factors in affecting MeCP2-induced apoptosis in Drosophila in vivo, thus indicating mechanistic conservation between flies and mammalian cells. Our findings are consistent with a model in which C- and N-terminal interactions are required for healthy function of MeCP2.

  5. Higgs pair production at NLO QCD for CP-violating Higgs sectors

    Directory of Open Access Journals (Sweden)

    R. Gröber

    2017-12-01

    Full Text Available Higgs pair production through gluon fusion is an important process at the LHC to test the dynamics underlying electroweak symmetry breaking. Higgs sectors beyond the Standard Model (SM can substantially modify this cross section through novel couplings not present in the SM or the on-shell production of new heavy Higgs bosons that subsequently decay into Higgs pairs. CP violation in the Higgs sector is important for the explanation of the observed matter-antimatter asymmetry through electroweak baryogenesis. In this work we compute the next-to-leading order (NLO QCD corrections in the heavy top quark limit, including the effects of CP violation in the Higgs sector. We choose the effective theory (EFT approach, which provides a rather model-independent way to explore New Physics (NP effects by adding dimension-6 operators, both CP-conserving and CP-violating ones, to the SM Lagrangian. Furthermore, we perform the computation within a specific UV-complete model and choose as benchmark model the general 2-Higgs-Doublet Model with CP violation, the C2HDM. Depending on the dimension-6 coefficients, the relative NLO QCD corrections are affected by several per cent through the new CP-violating operators. This is also the case for SM-like Higgs pair production in the C2HDM, while the relative QCD corrections in the production of heavier C2HDM Higgs boson pairs deviate more strongly from the SM case. The absolute cross sections both in the EFT and the C2HDM can be modified by more than an order of magnitude. In particular, in the C2HDM the resonant production of Higgs pairs can by far exceed the SM cross section.

  6. Molecular characterization of a CpTRIM35-like protein and its splice variants from whitespotted bamboo shark (Chiloscyllium plagiosum)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xinshang, E-mail: sanmaosound@163.com; Zhao, Heng, E-mail: hengzhao2000@gmail.com; Chen, Yeyu, E-mail: cyyleaf@126.com; Luo, Huiying, E-mail: luohuiying@caas.cn; Yao, Bin, E-mail: binyao@caas.cn

    2014-10-24

    Highlights: • A TRIM gene and three splice variants were firstly cloned from elasmobranch fish. • The genes were constitutively expressed with high levels in spleen and kidney. • The gene products were distributed in cytoplasm alone or cytoplasm and nucleus. • As E3 ubiquitin ligases, the proteins differed in immune responses to challenges. - Abstract: The tripartite motif (TRIM) proteins play important roles in a broad range of biological processes, including apoptosis, cell proliferation and innate immunity response. In this study, a TRIM gene and its three splice variants were cloned from an elasmobranch fish—whitespotted bamboo shark (Chiloscyllium plagiosum Bennett). Phylogenetic analysis indicated that the gene was closely related to TRIM35 homologs, thus termed CpTRIM35-like. Deduced CpTRIM35 has a RBCC-PRY/SPRY structure typical of TRIM proteins, and its splice variants (CpTRIM35-1–3) have different truncations at the C-terminus. The gene products were constitutively expressed in adult sharks with the highest levels in spleen and kidney. The different subcellular locations, upregulation upon LPS and poly I:C stimulation, and significant E3 ubiquitin ligase activities suggested their different roles in immune responses as an E3 ubiquitin ligase. This is the first TRIM protein ever characterized in elasmobranch fish.

  7. Molecular characterization of a CpTRIM35-like protein and its splice variants from whitespotted bamboo shark (Chiloscyllium plagiosum)

    International Nuclear Information System (INIS)

    Zhang, Xinshang; Zhao, Heng; Chen, Yeyu; Luo, Huiying; Yao, Bin

    2014-01-01

    Highlights: • A TRIM gene and three splice variants were firstly cloned from elasmobranch fish. • The genes were constitutively expressed with high levels in spleen and kidney. • The gene products were distributed in cytoplasm alone or cytoplasm and nucleus. • As E3 ubiquitin ligases, the proteins differed in immune responses to challenges. - Abstract: The tripartite motif (TRIM) proteins play important roles in a broad range of biological processes, including apoptosis, cell proliferation and innate immunity response. In this study, a TRIM gene and its three splice variants were cloned from an elasmobranch fish—whitespotted bamboo shark (Chiloscyllium plagiosum Bennett). Phylogenetic analysis indicated that the gene was closely related to TRIM35 homologs, thus termed CpTRIM35-like. Deduced CpTRIM35 has a RBCC-PRY/SPRY structure typical of TRIM proteins, and its splice variants (CpTRIM35-1–3) have different truncations at the C-terminus. The gene products were constitutively expressed in adult sharks with the highest levels in spleen and kidney. The different subcellular locations, upregulation upon LPS and poly I:C stimulation, and significant E3 ubiquitin ligase activities suggested their different roles in immune responses as an E3 ubiquitin ligase. This is the first TRIM protein ever characterized in elasmobranch fish

  8. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  9. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  10. Is CP violation observable in long baseline neutrino oscillation experiments?

    International Nuclear Information System (INIS)

    Tanimoto, M.

    1997-01-01

    We have studied CP violation originating from the phase of the neutrino-mixing matrix in the long baseline neutrino oscillation experiments. The direct measurement of CP violation is the difference of the transition probabilities between CP-conjugate channels. In those experiments, the CP-violating effect is not suppressed if the highest neutrino mass scale is taken to be 1 endash 5 eV, which is appropriate for the cosmological hot dark matter. Assuming the hierarchy for the neutrino masses, the upper bounds of CP violation have been calculated for three cases, in which mixings are constrained by the recent short baseline ones. The calculated upper bounds are larger than 10 -2 , which will be observable in the long baseline accelerator experiments. The matter effect, which is not CP invariant, has been also estimated in those experiments. copyright 1997 The American Physical Society

  11. SU(4) x U(1) gauge theory. II. CP nonconservation

    International Nuclear Information System (INIS)

    Deshpande, N.G.; Hwa, R.C.; Mannheim, P.D.

    1979-01-01

    We exploit the higher symmetry inherent in an SU(4) x U(1) gauge theory to construct a spontaneously broken theory of CP nonconservation. Higgs multiplets in the adjoint representation of SU(4) contain both even and odd CP fields; thus, requiring the simultaneous nonvanishing of the vacuum expectation values of these fields leads to CP noninvariance of the vacuum. We find that all the CP-nonconserving effects are mediated in our theory by the superheavy gauge bosons of the broken SU(4) x U(1) symmetry. In fact, the very existence of CP violation sets an upper limit on the masses of these bosons. In our model the dominant CP effect lies in the neutral kaon system and is found to arise through a direct (ΔS = 2) K 1 -K 2 transition. The model has all the features of a superweak theory, with a neutron electric dipole moment substantially smaller than 10 -24 e cm

  12. CP violation in the K and B systems

    International Nuclear Information System (INIS)

    Kayser, B.

    1997-01-01

    Although CP violation was discovered more than thirty years ago, its origin is still unknown. In these lectures, we describe the CP-violation effects which have been seen in K decays, and explain how CP violation can be caused by the Standard Model weak interaction. The hypothesis that this interaction is indeed the origin of CP violation will be incisively tested by future experiments on B and K decays. We explain what quantities these experiments will try to determine, and how they will be able to determine them in a theoretically clean way. To clarify the physics of the K system, we give a phase-convention-free description of CP violation in this system. We conclude by briefly exploring whether electric dipole moments actually violate CP even if CPT invariance is not assumed. (author)

  13. Invariant approach to CP in unbroken Δ(27

    Directory of Open Access Journals (Sweden)

    Gustavo C. Branco

    2015-10-01

    Full Text Available The invariant approach is a powerful method for studying CP violation for specific Lagrangians. The method is particularly useful for dealing with discrete family symmetries. We focus on the CP properties of unbroken Δ(27 invariant Lagrangians with Yukawa-like terms, which proves to be a rich framework, with distinct aspects of CP, making it an ideal group to investigate with the invariant approach. We classify Lagrangians depending on the number of fields transforming as irreducible triplet representations of Δ(27. For each case, we construct CP-odd weak basis invariants and use them to discuss the respective CP properties. We find that CP violation is sensitive to the number and type of Δ(27 representations.

  14. CP violation in the K and B systems

    International Nuclear Information System (INIS)

    Kayser, B.

    1996-11-01

    Although CP violation was discovered more than thirty years ago, its origin is still unknown. In these lectures, we describe the CP- violating effects which have been seen in K decays, and explain how CP violation can be caused by the Standard Model weak interaction. The hypothesis that this interaction is indeed the origin of CP violation will be incisively tested by future experiments on B and K decays. We explain what quantities these experiments will try to determine, and how they will be able to determine them in a theoretically clean way. To clarify the physics of the K system, we give a phase-convention-free description of CP violation in this system. We conclude by briefly exploring whether electric dipole moments actually violate CP even if CPT invariance is not assumed

  15. CP violation in the lepton sector and implications for leptogenesis

    DEFF Research Database (Denmark)

    Hagedorn, C.; Mohapatra, R. N.; Molinaro, E.

    2018-01-01

    We review the current status of the data on neutrino masses and lepton mixing and the prospects for measuring the CP-violating phases in the lepton sector. The possible connection between low energy CP violation encoded in the Dirac and Majorana phases of the Pontecorvo-Maki-Nakagawa-Sakata mixing...... matrix and successful leptogenesis is emphasized in the context of seesaw extensions of the Standard Model with a flavor symmetry Gf (and CP symmetry)....

  16. Benchmark test of CP-PACS for lattice QCD

    International Nuclear Information System (INIS)

    Yoshie, Tomoteru

    1996-01-01

    The CP-PACS is a massively parallel computer dedicated for calculations in computational physics and will be in operation in the spring of 1996 at Center for Computational Physics, University of Tsukuba. In this paper, we describe the architecture of the CP-PACS and report the results of the estimate of the performance of the CP-PACS for typical lattice QCD calculations. (author)

  17. Discrete ambiguities in CP-violating asymmetries in B decays

    International Nuclear Information System (INIS)

    London, David

    1998-01-01

    The CP-angles α, β and γ can be extracted from CP-violating asymmetries in the B system, but only up to discrete ambiguities. These discrete ambiguities make it difficult to determine with certainty whether or not new physics is present. I show that, if the condition α+β+γ=π is imposed, there remains a twofold ambiguity in the CP-angle set (α,β,γ), and I discuss ways to cleanly resolve this final discrete ambiguity

  18. A brief introduction to the strong CP problem

    International Nuclear Information System (INIS)

    Wu, Dan-di; Melbourne Univ., Parkville

    1991-09-01

    The present status of the strong CP problem is briefly reviewed in a heuristic way. A crisis in EDMN calculation is explained. The equation of vacuum alignment obtained by the author and collaborators last year put a constraint on strong CP parameters. Thus the strong CP will be forced to vanish in one of the three scenarios characterized by axion, zero quark mass, and vanishing quark condensate. 12 refs

  19. Phenomenology of CP violation from the Kobayashi-Maskawa model

    International Nuclear Information System (INIS)

    Wang, L.L.C.

    1980-01-01

    The CP violation consequences of the K-M model, which Kobayashi, Maskawa introduced in 1977 for the purpose of incorporating CP violation via the complexity in the mixing matrix of the quarks are discussed. Much of the talk is a review of current work on the subject. Some new results on the CP violation effects in exclusive and inclusive decays of bottom, charm and strange particles are also given

  20. Rephasing-invariant CP violating parameters with Majorana neutrinos

    International Nuclear Information System (INIS)

    Nieves, Jose F.; Pal, Palash B.

    2001-06-01

    We analyze the dependence of the squared amplitudes on the rephasing-invariant CP-violating parameters of the lepton sector, involving Majorana neutrinos, for various lepton- conserving and lepton-violating processes. We analyze the conditions under which the CP-violating effects in such processes vanish, in terms of the minimal set of rephasing invariants, giving special attention to the dependence on the extra CP-violating parameters that are due to the Majorana nature of the neutrinos. (author)

  1. MeCP2 regulates ethanol sensitivity and intake.

    Science.gov (United States)

    Repunte-Canonigo, Vez; Chen, Jihuan; Lefebvre, Celine; Kawamura, Tomoya; Kreifeldt, Max; Basson, Oan; Roberts, Amanda J; Sanna, Pietro Paolo

    2014-09-01

    We have investigated the expression of chromatin-regulating genes in the prefrontal cortex and in the shell subdivision of the nucleus accumbens during protracted withdrawal in mice with increased ethanol drinking after chronic intermittent ethanol (CIE) vapor exposure and in mice with a history of non-dependent drinking. We observed that the methyl-CpG binding protein 2 (MeCP2) was one of the few chromatin-regulating genes to be differentially regulated by a history of dependence. As MeCP2 has the potential of acting as a broad gene regulator, we investigated sensitivity to ethanol and ethanol drinking in MeCP2(308/) (Y) mice, which harbor a truncated MeCP2 allele but have a milder phenotype than MeCP2 null mice. We observed that MeCP2(308/) (Y) mice were more sensitive to ethanol's stimulatory and sedative effects than wild-type (WT) mice, drank less ethanol in a limited access 2 bottle choice paradigm and did not show increased drinking after induction of dependence with exposure to CIE vapors. Alcohol metabolism did not differ in MeCP2(308/) (Y) and WT mice. Additionally, MeCP2(308/) (Y) mice did not differ from WT mice in ethanol preference in a 24-hour paradigm nor in their intake of graded solutions of saccharin or quinine, suggesting that the MeCP2(308/) (Y) mutation did not alter taste function. Lastly, using the Gene Set Enrichment Analysis algorithm, we found a significant overlap in the genes regulated by alcohol and by MeCP2. Together, these results suggest that MeCP2 contributes to the regulation of ethanol sensitivity and drinking. © 2013 The Authors, Addiction Biology © 2013 Society for the Study of Addiction.

  2. How pathogens use linear motifs to perturb host cell networks

    KAUST Repository

    Via, Allegra; Uyar, Bora; Brun, Christine; Zanzoni, Andreas

    2015-01-01

    Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.

  3. Measurements of direct CP violation in charm decays at LHCb

    CERN Document Server

    INSPIRE-00257861

    2013-01-01

    Two searches for direct CP violation in D 0 ! h h + (where h = K or ) are presented using data corresponding to an integrated luminosity of 1.0 fb 1 collected in 2011 by LHCb in pp collisions at a centre-of-mass energy of 7 TeV. One analysis uses D 0 mesons produced via a D resonance and the other analysis uses D 0 mesons originating from semileptonic b - decays. In the rst case the avour is tagged by the charge of the accompanying pion and in the latter by the muon charge. The dierence of the CP -violating asymmetries ( A CP = A CP ( K K + ) A CP ( + )) in the two decay channels is measured to be A CP (muon tagged) = (0 : 49 0 : 30 (stat) 0 : 14 (syst))% ; A CP (pion tagged) = ( 0 : 35 0 : 15 (stat) 0 : 10 (syst))% ; A CP (LHCb) = ( 0 : 15 0 : 16)% : These results do not conrm evidence for CP violation in the charm sector

  4. Evidence for non-CpG methylation in mammals

    DEFF Research Database (Denmark)

    Yan, Jie; Zierath, Juleen R; Barres, Romain

    2011-01-01

    In mammals, the existence of cytosine methylation on non-CpG sequences is controversial. Here, we adapted a LuminoMetric-based Assay (LUMA) to determine global non-CpG methylation levels in rodent and human tissues. We observed that......In mammals, the existence of cytosine methylation on non-CpG sequences is controversial. Here, we adapted a LuminoMetric-based Assay (LUMA) to determine global non-CpG methylation levels in rodent and human tissues. We observed that...

  5. CP violation conditions in N-Higgs-doublet potentials

    International Nuclear Information System (INIS)

    Nishi, C. C.

    2006-01-01

    Conditions for CP violation in the scalar potential sector of general N-Higgs-doublet models are analyzed from a group theoretical perspective. For the simplest two-Higgs-doublet model potential, a minimum set of conditions for explicit and spontaneous CP violation is presented. The conditions can be given a clear geometrical interpretation in terms of quantities in the adjoint representation of the basis transformation group for the two doublets. Such conditions depend on CP-odd pseudoscalar invariants. When the potential is CP invariant, the explicit procedure to reach the real CP-basis and the explicit CP transformation can also be obtained. The procedure to find the real basis and the conditions for CP violation are then extended to general N-Higgs-doublet model potentials. The analysis becomes more involved and only a formal procedure to reach the real basis is found. Necessary conditions for CP invariance can still be formulated in terms of group invariants: the CP-odd generalized pseudoscalars. The problem can be completely solved for three Higgs-doublets

  6. CP violation in KL → π0e+e-

    International Nuclear Information System (INIS)

    Littenberg, L.S.

    1989-01-01

    It's been appreciated for many years that the decays K L → π 0 ell bar ell are CP violating to lowest order in the Standard Model, and that the component of direct CP violation in these decays is likely to be comparable to that of the CP violation due to state mixing (ε). This is to be contrasted with the case of K 0 → ππ wherein the latter contribution is predicted to be hundreds of times larger than the former. This paper investigates this CP violation further. 19 refs., 2 figs

  7. Frequency Constrained ShiftCP Modeling of Neuroimaging Data

    DEFF Research Database (Denmark)

    Mørup, Morten; Hansen, Lars Kai; Madsen, Kristoffer H.

    2011-01-01

    The shift invariant multi-linear model based on the CandeComp/PARAFAC (CP) model denoted ShiftCP has proven useful for the modeling of latency changes in trial based neuroimaging data[17]. In order to facilitate component interpretation we presently extend the shiftCP model such that the extracted...... components can be constrained to pertain to predefined frequency ranges such as alpha, beta and gamma activity. To infer the number of components in the model we propose to apply automatic relevance determination by imposing priors that define the range of variation of each component of the shiftCP model...

  8. Investigation of Inclusive CP Asymmetries in B$^{0}$ Decays

    CERN Document Server

    Barate, R; Ghez, P; Goy, C; Lees, J P; Merle, E; Minard, M N; Pietrzyk, B; Bravo, S; Casado, M P; Chmeissani, M; Crespo, J M; Fernández, E; Fernández-Bosman, M; Garrido, L; Graugès-Pous, E; Martínez, M; Merino, G; Miquel, R; Mir, L M; Pacheco, A; Ruiz, H; Colaleo, A; Creanza, D; De Palma, M; Iaselli, Giuseppe; Maggi, G; Maggi, M; Nuzzo, S; Ranieri, A; Raso, G; Ruggieri, F; Selvaggi, G; Silvestris, L; Tempesta, P; Tricomi, A; Zito, G; Huang, X; Lin, J; Ouyang, Q; Wang, T; Xie, Y; Xu, R; Xue, S; Zhang, J; Zhang, L; Zhao, W; Abbaneo, D; Boix, G; Buchmüller, O L; Cattaneo, M; Cerutti, F; Dissertori, G; Drevermann, H; Forty, Roger W; Frank, M; Greening, T C; Hansen, J B; Harvey, J; Janot, P; Jost, B; Lehraus, Ivan; Mato, P; Minten, Adolf G; Moutoussi, A; Ranjard, F; Rolandi, Luigi; Schlatter, W D; Schmitt, M; Schneider, O; Spagnolo, P; Tejessy, W; Teubert, F; Tournefier, E; Wright, A E; Ajaltouni, Ziad J; Badaud, F; Chazelle, G; Deschamps, O; Falvard, A; Gay, P; Guicheney, C; Henrard, P; Jousset, J; Michel, B; Monteil, S; Montret, J C; Pallin, D; Perret, P; Podlyski, F; Hansen, J D; Hansen, J R; Hansen, P H; Nilsson, B S; Petersen, B; Wäänänen, A; Daskalakis, G; Kyriakis, A; Markou, C; Simopoulou, Errietta; Vayaki, Anna; Blondel, A; Bonneaud, G R; Brient, J C; Rougé, A; Rumpf, M; Swynghedauw, M; Verderi, M; Videau, H L; Focardi, E; Parrini, G; Zachariadou, K; Antonelli, A; Antonelli, M; Bencivenni, G; Bologna, G; Bossi, F; Campana, P; Capon, G; Chiarella, V; Laurelli, P; Mannocchi, G; Murtas, F; Murtas, G P; Passalacqua, L; Pepé-Altarelli, M; Halley, A W; Lynch, J G; Negus, P; O'Shea, V; Raine, C; Teixeira-Dias, P; Thompson, A S; Cavanaugh, R J; Dhamotharan, S; Geweniger, C; Hanke, P; Hansper, G; Hepp, V; Kluge, E E; Putzer, A; Sommer, J; Tittel, K; Werner, S; Wunsch, M; Beuselinck, R; Binnie, David M; Cameron, W; Dornan, Peter J; Girone, M; Marinelli, N; Sedgbeer, J K; Thompson, J C; Thomson, E; Ghete, V M; Girtler, P; Kneringer, E; Kuhn, D; Rudolph, G; Bowdery, C K; Buck, P G; Finch, A J; Foster, F; Hughes, G; Jones, R W L; Robertson, N A; Giehl, I; Jakobs, K; Kleinknecht, K; Quast, G; Renk, B; Rohne, E; Sander, H G; Wachsmuth, H W; Zeitnitz, C; Bonissent, A; Carr, J; Coyle, P; Leroy, O; Payre, P; Rousseau, D; Talby, M; Aleppo, M; Ragusa, F; Dietl, H; Ganis, G; Heister, A; Hüttmann, K; Lütjens, G; Mannert, C; Männer, W; Moser, H G; Schael, S; Settles, Ronald; Stenzel, H; Wiedenmann, W; Wolf, G; Azzurri, P; Boucrot, J; Callot, O; Chen, S; Cordier, A; Davier, M; Duflot, L; Grivaz, J F; Heusse, P; Jacholkowska, A; Le Diberder, F R; Lefrançois, J; Lutz, A M; Schune, M H; Veillet, J J; Videau, I; Yuan, C; Zerwas, D; Bagliesi, G; Boccali, T; Calderini, G; Ciulli, V; Foà, L; Giassi, A; Ligabue, F; Messineo, A; Palla, Fabrizio; Rizzo, G; Sanguinetti, G; Sciabà, A; Sguazzoni, G; Tenchini, Roberto; Venturi, A; Verdini, P G; Blair, G A; Cowan, G D; Green, M G; Medcalf, T; Strong, J A; Von Wimmersperg-Töller, J H; Clifft, R W; Edgecock, T R; Norton, P R; Tomalin, I R; Bloch-Devaux, B; Colas, P; Emery, S; Kozanecki, Witold; Lançon, E; Lemaire, M C; Locci, E; Pérez, P; Rander, J; Renardy, J F; Roussarie, A; Schuller, J P; Schwindling, J; Trabelsi, A; Vallage, B; Black, S N; Dann, J H; Johnson, R P; Kim, H Y; Konstantinidis, N P; Litke, A M; McNeil, M A; Taylor, G; Booth, C N; Cartwright, S L; Combley, F; Lehto, M H; Thompson, L F; Affholderbach, K; Böhrer, A; Brandt, S; Grupen, Claus; Misiejuk, A; Prange, G; Sieler, U; Giannini, G; Gobbo, B; Rothberg, J E; Wasserbaech, S R; Armstrong, S R; Cranmer, K; Elmer, P; Ferguson, D P S; Gao, Y; González, S; Hayes, O J; Hu, H; Jin, S; Kile, J; McNamara, P A; Nielsen, J; Orejudos, W; Pan, Y B; Saadi, Y; Scott, I J; Walsh, J; Wu Sau Lan; Wu, X; Zobernig, G

    2001-01-01

    A search for CP violating effects in the mixing of neutral B mesons is performed using a sample of 4.1 million hadronic Z decays collected with the ALEPH detector from 1991 to 1995. By studying time-dependent asymmetries in flavour-tagged samples of semileptonic and fully inclusive b-hadron decays, two measurements of the semileptonic asymmetry a_cp are extracted. No evidence for CP violation is observed, and the combined value a_cp = -0.013 +- 0.026 is obtained.

  9. CpG island mapping by epigenome prediction.

    Directory of Open Access Journals (Sweden)

    Christoph Bock

    2007-06-01

    Full Text Available CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1 reliance on arbitrary threshold parameters that bear little biological justification, (2 failure to account for widespread heterogeneity among CpG islands, and (3 apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of "CpG island strength" that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted "bona fide" CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to

  10. CpG island mapping by epigenome prediction.

    Science.gov (United States)

    Bock, Christoph; Walter, Jörn; Paulsen, Martina; Lengauer, Thomas

    2007-06-01

    CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by simple DNA sequence criteria, which allowed for genome-wide annotation of CpG islands in the absence of large-scale epigenetic datasets. Although widely used, the current CpG island criteria incur significant disadvantages: (1) reliance on arbitrary threshold parameters that bear little biological justification, (2) failure to account for widespread heterogeneity among CpG islands, and (3) apparent lack of specificity when applied to the human genome. This study is driven by the idea that a quantitative score of "CpG island strength" that incorporates epigenetic and functional aspects can help resolve these issues. We construct an epigenome prediction pipeline that links the DNA sequence of CpG islands to their epigenetic states, including DNA methylation, histone modifications, and chromatin accessibility. By training support vector machines on epigenetic data for CpG islands on human Chromosomes 21 and 22, we identify informative DNA attributes that correlate with open versus compact chromatin structures. These DNA attributes are used to predict the epigenetic states of all CpG islands genome-wide. Combining predictions for multiple epigenetic features, we estimate the inherent CpG island strength for each CpG island in the human genome, i.e., its inherent tendency to exhibit an open and transcriptionally competent chromatin structure. We extensively validate our results on independent datasets, showing that the CpG island strength predictions are applicable and informative across different tissues and cell types, and we derive improved maps of predicted "bona fide" CpG islands. The mapping of CpG islands by epigenome prediction is conceptually superior to identifying CpG islands by widely used sequence criteria since it links CpG island detection to their characteristic

  11. Search for CP violation in baryon decays at LHCb

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The phenomenon of CP violation has been observed in the K- and B-meson systems, but not yet with any baryonic particle. We report on searches for CP violation in baryon decays at LHCb using Run I data. We find evidence for CP violation in Lambda0b -> p pi- pi+ pi- decays with a statistical significance corresponding to 3.3 standard deviations, including systematic uncertainties. This represents the first evidence of CP violation in the baryon sector. An overview of other recent results of baryon decays will be presented, along with some highlights of the charmless B-decay programme.

  12. CP violation in τ → ντ + 3π

    International Nuclear Information System (INIS)

    Tsai, Y.S.

    1998-01-01

    In the Standard Model no CP violation can occur in decay processes involving leptons either as a parent or a daughter because these processes involve one W exchange and thus, even if the CP violating complex coupling exists in these decays, its effect will not show up when the amplitude is squared. The author needs two diagrams to interfere with each other to see the CP violating effects. Here, he discusses ways to find CP violation in the decay of τ ± → ν τ + 3π from unpolarized as well as polarized τ ±

  13. A model for the origin and mechanisms of CP violation

    International Nuclear Information System (INIS)

    Wu, Y.

    1995-01-01

    In this talk I will show that the two-Higgs doublet model with vacuum CP violation and approximate global U(1) family symmetries may provide one of the simplest and attractive models for understanding the origin and mechanisms of CP violation. It is shown that the mechanism of spontaneous symmetry breaking provides not only a mechanism for generating masses of the bosons and fermions, but also a mechanism for creating CP-phases of the bosons and fermions, so that CP violation occurs, after spontaneous symmetry breaking, in all possible ways from a single CP phase of the vacuum and is generally classified into four types of CP-violating mechanism. A new type of CP-violating mechanism in the charged Higgs boson interactions of the fermions is emphasized and can provide a consistent description for both established and reported CP-, P-, and T-violating phenomena. Of particular importance is the new source of CP violation for charged Higgs boson interactions that lead to the value of ε'/ε as large as 10 -3 independent of the CKM phase. copyright 1995 American Institute of Physics

  14. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

    Science.gov (United States)

    Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

    2008-02-15

    KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

  15. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    Ahmad A. Malik

    2017-05-01

    Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

  16. Single isospin decay amplitude and CP violation

    Energy Technology Data Exchange (ETDEWEB)

    Deshpande, N.G. [Oregon Univ., Eugene, OR (United States). Inst. of Theoretical Science; He, Xiaogang [Melbourne Univ., Parkville, VIC (Australia). School of Physics; Pakvasa, S. [Hawaii Univ., Honolulu, HI (United States). Dept. of Physics and Astronomy

    1996-06-01

    While for K meson or hyperon decays, the partial rate asymmetries are always zero if the final states are single isospin states, in B decays the situation is dramatically different and partial rate asymmetries can be non-zero if the final states are single isospin states. Partial rate asymmetries were calculated for several B decays with single isospin amplitude in the finale states using factorization approximation. It was found that more intermediate on-shell states with different Cabbibbo-Kobayashi-Maskawa factors are allowed in B decay and CP violating partial rate asymmetries need not to be zero even if the final state contains only a single isospin state. 17 refs., 4 figs.

  17. 60 years controlled nuclear fission: CP-1

    International Nuclear Information System (INIS)

    Anon.

    2002-01-01

    On December 2, 1942, the Chicago Pile 1 (CP-1) went critical for the first time. In this way, the scientists and engineers involved in the project under the leadership of Enrico Fermi succeeded in demonstrating that a self-sustaining nuclear reaction with nuclear fission processes was technically feasible. Only four years after the discovery and proof of nuclear fission by Otto Hahn, Fritz Strassmann, and Lise Meitner, the experiment consisting of graphite blocks as the moderator and uranium dioxide pellets as the fuel, as well as instrumentation and control devices, had been set up in the former squash court of the field and track stadium of the University of Chicago. Precisely at 3.36 a.m. Chicago time, after control rods had been withdrawn, the instruments showed the chain reaction by the neutron flux they indicated. An important cornerstone in the use of nuclear power had thus been laid. (orig.)

  18. Experimental hint for gravitational CP violation

    Energy Technology Data Exchange (ETDEWEB)

    Gharibyan, Vahagn [Deutsches Elektronen-Synchrotron, Hamburg (Germany). MDI Group

    2016-01-15

    An equality of particle and antiparticle gravitational interactions holds in general relativity and is supported by indirect observations. Gravity dependence on rotation or spin direction is experimentally constrained only at low energies. Here a method based on high energy Compton scattering is developed to measure the gravitational interaction of accelerated charged particles. Within that formalism the Compton spectra measured at HERA rule out the positron's anti-gravity and hint for a gravitational CP violation around 13 GeV energies, at a maximal level of 1.3±0.2% for the charge and 0.68±0.09% for the space parity. A stronger gravitational coupling to left helicity electrons relative to right helicity positrons is detected.

  19. Experimental hint for gravitational CP violation

    International Nuclear Information System (INIS)

    Gharibyan, Vahagn

    2016-01-01

    An equality of particle and antiparticle gravitational interactions holds in general relativity and is supported by indirect observations. Gravity dependence on rotation or spin direction is experimentally constrained only at low energies. Here a method based on high energy Compton scattering is developed to measure the gravitational interaction of accelerated charged particles. Within that formalism the Compton spectra measured at HERA rule out the positron's anti-gravity and hint for a gravitational CP violation around 13 GeV energies, at a maximal level of 1.3±0.2% for the charge and 0.68±0.09% for the space parity. A stronger gravitational coupling to left helicity electrons relative to right helicity positrons is detected.

  20. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

  1. Restoration of CpG Methylation in The Egf Promoter Region during Rat Liver Regeneration

    Science.gov (United States)

    Deming, Li; Ziwei, Li; Xueqiang, Guo; Cunshuan, Xu

    2015-01-01

    Epidermal growth factor (EGF) is an important factor for healing after tissue damage in diverse experimental models. It plays an important role in liver regeneration (LR). The objective of this experiment is to investigate the methylation variation of 10 CpG sites in the Egf promoter region and their relevance to Egf expression during rat liver regenera- tion. As a follow up of our previous study, rat liver tissue was collected after rat 2/3 partial hepatectomy (PH) during the re-organization phase (from days 14 to days 28). Liver DNA was extracted and modified by sodium bisulfate. The methylation status of 10 CpG sites in Egf promoter region was determined using bisulfite sequencing polymerase chain reaction (PCR), as BSP method. The results showed that 3 (sites 3, 4 and 9) out of 10 CpG sites have strikingly methylation changes during the re-organization phase compared to the regeneration phase (from 2 hours to 168 hours, P=0.002, 0.048 and 0.018, respectively). Our results showed that methylation modification of CpGs in the Egf promoter region could be restored to the status before PH operation and changes of methylation didn’t affect Egf mRNA expression during the re-organization phase. PMID:26464832

  2. Search for neutral Higgs bosons in CP-conserving and CP-violating MSSM scenarios

    CERN Document Server

    Abbiendi, G.; Akesson, P.F.; Alexander, G.; Allison, John; Amaral, P.; Anagnostou, G.; Anderson, K.J.; Asai, S.; Axen, D.; Azuelos, G.; Bailey, I.; Barberio, E.; Barillari, T.; Barlow, R.J.; Batley, R.J.; Bechtle, P.; Behnke, T.; Bell, Kenneth Watson; Bell, P.J.; Bella, G.; Bellerive, A.; Benelli, G.; Bethke, S.; Biebel, O.; Boeriu, O.; Bock, P.; Boutemeur, M.; Braibant, S.; Brigliadori, L.; Brown, Robert M.; Buesser, K.; Burckhart, H.J.; Campana, S.; Carnegie, R.K.; Carter, A.A.; Carter, J.R.; Chang, C.Y.; Charlton, D.G.; Ciocca, C.; Csilling, A.; Cuffiani, M.; Dado, S.; De Roeck, A.; De Wolf, E.A.; Desch, K.; Dienes, B.; Donkers, M.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Duerdoth, I.P.; Etzion, E.; Fabbri, F.; Feld, L.; Ferrari, P.; Fiedler, F.; Fleck, I.; Ford, M.; Frey, A.; Gagnon, P.; Gary, John William; Gaycken, G.; Geich-Gimbel, C.; Giacomelli, G.; Giacomelli, P.; Giunta, Marina; Goldberg, J.; Gross, E.; Grunhaus, J.; Gruwe, M.; Gunther, P.O.; Gupta, A.; Hajdu, C.; Hamann, M.; Hanson, G.G.; Harel, A.; Hauschild, M.; Hawkes, C.M.; Hawkings, R.; Hemingway, R.J.; Herten, G.; Heuer, R.D.; Hill, J.C.; Hoffman, Kara Dion; Horvath, D.; Igo-Kemenes, P.; Ishii, K.; Jeremie, H.; Jovanovic, P.; Junk, T.R.; Kanaya, N.; Kanzaki, J.; Karlen, D.; Kawagoe, K.; Kawamoto, T.; Keeler, R.K.; Kellogg, R.G.; Kennedy, B.W.; Kluth, S.; Kobayashi, T.; Kobel, M.; Komamiya, S.; Kramer, T.; Krieger, P.; von Krogh, J.; Kruger, K.; Kuhl, T.; Kupper, M.; Lafferty, G.D.; Landsman, H.; Lanske, D.; Layter, J.G.; Lellouch, D.; Lettso, J.; Levinson, L.; Lillich, J.; Lloyd, S.L.; Loebinger, F.K.; Lu, J.; Ludwig, A.; Ludwig, J.; Mader, W.; Marcellini, S.; Martin, A.J.; Masetti, G.; Mashimo, T.; Mattig, Peter; McKenna, J.; McPherson, R.A.; Meijers, F.; Menges, W.; Merritt, F.S.; Mes, H.; Meyer, Niels T.; Michelini, A.; Mihara, S.; Mikenberg, G.; Miller, D.J.; Moed, S.; Mohr, W.; Mori, T.; Mutter, A.; Nagai, K.; Nakamura, I.; Nanjo, H.; Neal, H.A.; Nisius, R.; O'Neale, S.W.; Oh, A.; Oreglia, M.J.; Orito, S.; Pahl, C.; Pasztor, G.; Pater, J.R.; Pilcher, J.E.; Pinfold, J.; Plane, David E.; Poli, B.; Pooth, O.; Przybycien, M.; Quadt, A.; Rabbertz, K.; Rembser, C.; Renkel, P.; Roney, J.M.; Rozen, Y.; Runge, K.; Sachs, K.; Saeki, T.; Sarkisyan, E.K.G.; Schaile, A.D.; Schaile, O.; Scharff-Hansen, P.; Schieck, J.; Schorner-Sadenius, T.; Schroder, Matthias; Schumacher, M.; Scott, W.G.; Seuster, R.; Shears, T.G.; Shen, B.C.; Sherwood, P.; Skuja, A.; Smith, A.M.; Sobie, R.; Soldner-Rembold, S.; Spano, F.; Stahl, A.; Strom, David M.; Strohmer, R.; Tarem, S.; Tasevsky, M.; Teuscher, R.; Thomson, M.A.; Torrence, E.; Toya, D.; Tran, P.; Trigger, I.; Trocsanyi, Z.; Tsur, E.; Turner-Watson, M.F.; Ueda, I.; Ujvari, B.; Vollmer, C.F.; Vannerem, P.; Vertesi, R.; Verzocchi, M.; Voss, H.; Vossebeld, J.; Ward, C.P.; Ward, D.R.; Watkins, P.M.; Watson, A.T.; Watson, N.K.; Wells, P.S.; Wengler, T.; Wermes, N.; Wilson, G.W.; Wilson, J.A.; Wolf, G.; Wyatt, T.R.; Yamashita, S.; Zer-Zion, D.; Zivkovic, Lidija

    2004-01-01

    This report summarizes the final results from the OPAL collaboration on searches for neutral Higgs bosons predicted by the Minimal Supersymmetric Standard Model (MSSM). CP-conserving and for the first time at LEP CP-violating scenarios are studied. New scenarios are also included, which aim to set the stage for Higgs searches at future colliders. The results are based on the data collected with the OPAL detector at e+e- centre-of-mass energies up to 209 GeV. The data are consistent with the prediction of the Standard Model with no Higgs boson produced. Model-independent limits are derived for the cross-section of a number of events topologies motivated by prediction of the MSSM. Limits on Higgs boson masses and other MSSM parameters are obtained for a number of representative MSSM benchmark scenarios. For example, in the CP-conserving scenario mh-max where the MSSM parameters are adjusted to predict the largest range of values for mh at each tan beta, and for a top quark mass of 174.3 GeV, the domain 0.784.5 ...

  3. Synthesis and reactivity of dimolybdathiaborane cluster [(Cp Mo ...

    Indian Academy of Sciences (India)

    Cluster 2 has a bicapped octahedral geometry with the {Fe(CO)3} fragment occupying one of the ... thesis and characterization of [(Cp. ∗ ... Infrared spectra were obtained on a Nicolet 6700 FT-. IR spectrometer. Microanalyses for C, H, and N were performed on .... tains signals attributable to the one type of Cp. ∗ ligand.

  4. Solution of the strong CP problem by color exchange

    International Nuclear Information System (INIS)

    Barr, S.M.; Zee, A.

    1985-08-01

    We present a new way to solve the strong CP problem in models with a spontaneously broken CP invariance. It is simpler than existing non-Peccei-Quinn approaches. It predicts the existence of light (i.e. weak scale) colored Higgs bosons which could be seen in colliders. 25 refs., 3 figs

  5. Proceedings of the Workshop on CP Violation at KAON Factory

    International Nuclear Information System (INIS)

    Ng, J.N.

    1989-07-01

    These proceedings contain the written version of eight talks delivered at the Workshop on CP Violation at KAON Factory. The articles contain reviews on the exploration of CP violation effects associated with the s-quark. Discussion on the use of intense kaon fluxes, which will be available at the proposed KAON Factory, are included

  6. Isospin analysis of CP asymmetries in B decays

    International Nuclear Information System (INIS)

    Gronau, M.; London, D.

    1990-09-01

    There is some theoretical uncertainty in the predictions for CP violating hadronic asymmetries in neutral B decays to CP eigenstates due to the existence of penguin diagrams. Using isospin relatins, we show that it is possible to remove this uncertainty for the decays B d 0 → ππ, up to a 4-fold ambiguity. (orig.)

  7. A mini review on CP-violating minimal supersymmetric Standard

    Indian Academy of Sciences (India)

    We discuss the present status of the Higgs sector of the CP-violating minimal supersymmetric Standard Model (CPVMSSM). In the Standard Model (SM) of particle physics, the only source of CP violation is the complex phase in the Cabibbo–Kobayashi–Maskawa (CKM) matrix. By now we all know that this singlephase is ...

  8. Difficulty for Weinberg model of CP nonconservation through Higgs exchange

    International Nuclear Information System (INIS)

    Deshpande, N.G.

    1981-01-01

    We evaluate the CP violation parameter element of'/element of in the Weinberg model of CP nonconservation. When gluon exchange effects are included, we find element of'/element of approx. -.045, which is in conflict with the experimental measurement element of'/element of = -.003 +- .015

  9. On the determination of the CP of the Higgs boson

    Energy Technology Data Exchange (ETDEWEB)

    Skjold, A.

    1995-12-31

    While the Higgs particle of the Standard Models is a Cp-even scalar particle, extended models may contain Higgs particles that are odd under CP, and also models invoking Higgs-like particles which are not eigenstates of CP may be considered. In the context of Higgs production via the Bjorken process and Higgs decay to tour fermions distributions that are sensitive to the CP parity are discussed. The author also discuss observables which may demonstrate presence of CP violation and identify a phase shift {delta} which is a measure of the strength of CP violation in the Higgs-vector-vector coupling, and which can be measured directly in the relevant distribution. In the case of Higgs production via the Bjorken process at a future e{sup +}e{sup -}collider, Monte Carlo data on the expected efficiency is presented, and it is concluded that it is relatively easy to determine whether the produced particle is even or odd under CP. However, observation of any CP violation would require a very large amount of data. It is argued that the analogous prospects at LEP2 or at a future hadron collider like the LHC seem to be less promising. 63 refs.

  10. On the determination of the CP of the Higgs boson

    International Nuclear Information System (INIS)

    Skjold, A.

    1995-01-01

    While the Higgs particle of the Standard Models is a Cp-even scalar particle, extended models may contain Higgs particles that are odd under CP, and also models invoking Higgs-like particles which are not eigenstates of CP may be considered. In the context of Higgs production via the Bjorken process and Higgs decay to tour fermions distributions that are sensitive to the CP parity are discussed. The author also discuss observables which may demonstrate presence of CP violation and identify a phase shift δ which is a measure of the strength of CP violation in the Higgs-vector-vector coupling, and which can be measured directly in the relevant distribution. In the case of Higgs production via the Bjorken process at a future e + e - collider, Monte Carlo data on the expected efficiency is presented, and it is concluded that it is relatively easy to determine whether the produced particle is even or odd under CP. However, observation of any CP violation would require a very large amount of data. It is argued that the analogous prospects at LEP2 or at a future hadron collider like the LHC seem to be less promising. 63 refs

  11. Why does CP violation matter to the universe?

    CERN Document Server

    Ellis, Jonathan Richard

    1999-01-01

    The seemingly obscure phenomenon of CP violation is increasingly being viewed as the key to a deeper understanding of both the behaviour of elementary particles and the big bang origin of the universe. Here, John Ellis of CERN explains how far and how deep the implications of CP violation extend. (0 refs).

  12. On the determination of the CP of the Higgs boson

    Energy Technology Data Exchange (ETDEWEB)

    Skjold, A

    1996-12-31

    While the Higgs particle of the Standard Models is a Cp-even scalar particle, extended models may contain Higgs particles that are odd under CP, and also models invoking Higgs-like particles which are not eigenstates of CP may be considered. In the context of Higgs production via the Bjorken process and Higgs decay to tour fermions distributions that are sensitive to the CP parity are discussed. The author also discuss observables which may demonstrate presence of CP violation and identify a phase shift {delta} which is a measure of the strength of CP violation in the Higgs-vector-vector coupling, and which can be measured directly in the relevant distribution. In the case of Higgs production via the Bjorken process at a future e{sup +}e{sup -}collider, Monte Carlo data on the expected efficiency is presented, and it is concluded that it is relatively easy to determine whether the produced particle is even or odd under CP. However, observation of any CP violation would require a very large amount of data. It is argued that the analogous prospects at LEP2 or at a future hadron collider like the LHC seem to be less promising. 63 refs.

  13. CP violation searches in the charm sector at LHCb

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    LHCb has collected the world's largest sample of charmed hadrons, thus enabling measurements of direct and indirect CP violation parameters of D^0 mesons to be made with unprecedented precision. The difference in CP asymmetries between the singly Cabibbo-suppressed (SCS) D^0 -> K+K- and D^0 -> pi+pi- decays (Delta A_CP) has emerged as a powerful observable to search for direct CPV in the charm sector. By taking the difference between the two modes, most of the asymmetries induced by the detector or coming from the production mechanism are cancelled. The measurement of Delta A_CP done at LHCb is the most precise measurement of a time-integrated CP asymmetry in the charm sector from a single experiment, with a precision reaching the sub-permille level. Two independent measurements of Delta A_CP based on complementary data sets will be presented. Related 2-body searches and searches for direct CP violation in multi-body decays of the D^0 mesons will be discussed. Indirect CP violation in charm is measured throug...

  14. SSTRAP: A computational model for genomic motif discovery ...

    African Journals Online (AJOL)

    Computational methods can potentially provide high-quality prediction of biological molecules such as DNA binding sites and Transcription factors and therefore reduce the time needed for experimental verification and challenges associated with experimental methods. These biological molecules or motifs have significant ...

  15. Identification of a Baeyer-Villiger monooxygenase sequence motif

    NARCIS (Netherlands)

    Fraaije, MW; Kamerbeek, NM; van Berkel, WJH; Janssen, DB; Kamerbeek, Nanne M.; Berkel, Willem J.H. van

    2002-01-01

    Baeyer-Villiger monooxygenases (BVMOs) form a distinct class of flavoproteins that catalyze the insertion of an oxygen atom in a C-C bond using dioxygen and NAD(P)H. Using newly characterized BVMO sequences, we have uncovered a BVMO-identifying sequence motif: FXGXXXRXXXW(P/D). Studies with

  16. Linear motif atlas for phosphorylation-dependent signaling

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Jensen, LJ; Diella, F

    2008-01-01

    bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling...

  17. [Cover motifs of the Tidsskrift. A 14-year cavalcade].

    Science.gov (United States)

    Nylenna, M

    1998-12-10

    In 1985 the Journal of the Norwegian Medical Association changed its cover policy, moving the table of contents inside the Journal and introducing cover illustrations. This article provides an analysis of all cover illustrations published over this 14-year period, 420 covers in all. There is a great variation in cover motifs and designs and a development towards more general motifs. The initial emphasis on historical and medical aspects is now less pronounced, while the use of works of art and nature motifs has increased, and the cover now more often has a direct bearing on the specific contents of the issue. Professor of medical history Oivind Larsen has photographed two thirds of the covers and contributed 95% of the inside essay-style reflections on the cover motif. Over the years, he has expanded the role of the historian of medicine disseminating knowledge to include that of the raconteur with a personal tone of voice. The Journal's covers are now one of its most characteristic features, emblematic of the Journal's ambition of standing for quality and timelessness vis-à-vis the news media, and of its aim of bridging the gap between medicine and the humanities.

  18. Perspektif Psikologi Humanistik Abraham Maslow dalam Meninjau Motif Pelaku Pembunuhan

    OpenAIRE

    Nurwatie, Azrina; Fauzia, Rahmi; Akbar, Sukma Noor

    2014-01-01

    Fokus penelitian ini diarahkan pada motif pelaku pembunuhan dengan meninjaunya melalui perspektif psikologi humanistik Abraham Maslow. Subyek dalam penelitian ini berjumlah dua orang narapidana yang berada di Lapas Kelas IIA Anak Martapura dengan kasus pembunuhan. Metode penelitian yang digunakan dalam penelitian ini adalah metode penelitian kualitatif. Teknik pengumpulan data melalui wawancara, observasi, dokumentasi,dan pemeriksaan psikologis (tes grafis). Berdasarkan hasil analisis data da...

  19. Motifs in triadic random graphs based on Steiner triple systems

    Science.gov (United States)

    Winkler, Marco; Reichardt, Jörg

    2013-08-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade, the overabundance of certain subnetwork patterns, i.e., the so-called motifs, has attracted much attention. It has been hypothesized that these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information, is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graph models (ERGMs) to define models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obstacle, we use Steiner triple systems (STSs). These are partitions of sets of nodes into pair-disjoint triads, which thus can be specified independently. Combining the concepts of ERGMs and STSs, we suggest generative models capable of generating ensembles of networks with nontrivial triadic Z-score profiles. Further, we discover inevitable correlations between the abundance of triad patterns, which occur solely for statistical reasons and need to be taken into account when discussing the functional implications of motif statistics. Moreover, we calculate the degree distributions of our triadic random graphs analytically.

  20. Genetic analysis of beta1 integrin "activation motifs" in mice

    DEFF Research Database (Denmark)

    Czuchra, Aleksandra; Meyer, Hannelore; Legate, Kyle R

    2006-01-01

    -null phenotype in vivo. Surprisingly, neither the substitution of the tyrosines with phenylalanine nor the aspartic acid with alanine resulted in an obvious defect. These data suggest that the NPXY motifs of the beta1 integrin tail are essential for beta1 integrin function, whereas tyrosine phosphorylation...

  1. Insights into the motif preference of APOBEC3 enzymes.

    Directory of Open Access Journals (Sweden)

    Diako Ebrahimi

    Full Text Available We used a multivariate data analysis approach to identify motifs associated with HIV hypermutation by different APOBEC3 enzymes. The analysis showed that APOBEC3G targets G mainly within GG, TG, TGG, GGG, TGGG and also GGGT. The G nucleotides flanked by a C at the 3' end (in +1 and +2 positions were indicated as disfavoured targets by APOBEC3G. The G nucleotides within GGGG were found to be targeted at a frequency much less than what is expected. We found that the infrequent G-to-A mutation within GGGG is not limited to the inaccessibility, to APOBEC3, of poly Gs in the central and 3'polypurine tracts (PPTs which remain double stranded during the HIV reverse transcription. GGGG motifs outside the PPTs were also disfavoured. The motifs GGAG and GAGG were also found to be disfavoured targets for APOBEC3. The motif-dependent mutation of G within the HIV genome by members of the APOBEC3 family other than APOBEC3G was limited to GA→AA changes. The results did not show evidence of other types of context dependent G-to-A changes in the HIV genome.

  2. $CP$ violation in the B system at LHCb

    CERN Document Server

    AUTHOR|(CDS)2067431

    2014-01-01

    A selection of recent LHCb results on $CP$ violation in the $B$ system is presented. These include direct $CP$ violation measurements in $B^0 \\to \\phi K^*(892)^0$, $B_{(s)}^0 \\to K^\\pm\\pi^\\pm$, $B^\\pm \\to K^\\pm \\pi^+\\pi^-$, $B^\\pm \\to K^\\pm K^+K^-$ and $B^\\pm \\to \\phi K^\\pm$ decays; time-dependent $CP$ violation measurements in $B_s^0 \\to K^+K^-$ and $B^0 \\to \\pi^+\\pi^-$ decays; determination of the flavour-specific $CP$-violating asymmetry $a_{sl}^s$ in $B_s^0$ decays; and study of the mixing-induced $CP$ violation in $B_s^0 \\to J/\\psi K^+K^-$ and $B_s^0 \\to J/\\psi \\pi^+\\pi^-$ decays.

  3. The possibility of leptonic CP-violation measurement with JUNO

    Science.gov (United States)

    Smirnov, M. V.; Hu, Zh. J.; Li, S. J.; Ling, J. J.

    2018-06-01

    The existence of CP-violation in the leptonic sector is one of the most important issues for modern science. Neutrino physics is a key to the solution of this problem. JUNO (under construction) is the near future of neutrino physics. However CP-violation is not a priority for the current scientific program. We estimate the capability of δCP measurement, assuming a combination of the JUNO detector and a superconductive cyclotron as the antineutrino source. This method of measuring CP-violation is an alternative to conventional beam experiments. A significance level of 3σ can be reached for 22% of the δCP range. The accuracy of measurement lies between 8o and 22o. It is shown that the dominant influence on the result is the uncertainty in the mixing angle Θ23.

  4. Neutrino mixing and lepton CP-phase in neutrino oscillations

    International Nuclear Information System (INIS)

    Ryzhikh, D.A.; Ter-Martirosyan, K.A.

    2001-01-01

    One studied oscillations of the Dirac neutrinos belonging to three generations in vacuum with regard to the effect of the lepton CP-breaking phase on them in the matrix of lepton mixing (analogue of the quark CP-phase). In the general form one obtained formulae for probabilities of transition of neutrino of one kind to another at oscillations depending on three angles of mixing and on CP-phase. It was pointed that when measuring oscillation average probabilities of transition of neutrino of one kind to another one might in principle, restore the value of lepton CP-phase. Manifestation of CP-phase in the form of deviation of the values of probabilities of direct neutrino transition from reverse one is the effect practically escaping observation [ru

  5. Testing non-standard CP violation in neutrino propagation

    International Nuclear Information System (INIS)

    Winter, Walter

    2009-01-01

    Non-standard physics which can be described by effective four fermion interactions may be an additional source of CP violation in the neutrino propagation. We discuss the detectability of such a CP violation at a neutrino factory. We assume the current baseline setup of the international design study of a neutrino factory (IDS-NF) for the simulation. We find that the CP violation from certain non-standard interactions is, in principle, detectable significantly below their current bounds - even if there is no CP violation in the standard oscillation framework. Therefore, a new physics effect might be mis-interpreted as the canonical Dirac CP violation, and a possibly even more exciting effect might be missed

  6. Implications of maximal Jarlskog invariant and maximal CP violation

    International Nuclear Information System (INIS)

    Rodriguez-Jauregui, E.; Universidad Nacional Autonoma de Mexico

    2001-04-01

    We argue here why CP violating phase Φ in the quark mixing matrix is maximal, that is, Φ=90 . In the Standard Model CP violation is related to the Jarlskog invariant J, which can be obtained from non commuting Hermitian mass matrices. In this article we derive the conditions to have Hermitian mass matrices which give maximal Jarlskog invariant J and maximal CP violating phase Φ. We find that all squared moduli of the quark mixing elements have a singular point when the CP violation phase Φ takes the value Φ=90 . This special feature of the Jarlskog invariant J and the quark mixing matrix is a clear and precise indication that CP violating Phase Φ is maximal in order to let nature treat democratically all of the quark mixing matrix moduli. (orig.)

  7. Four-dimensional CP2 model on a lattice

    International Nuclear Information System (INIS)

    Bitar, K.M.; Raja, R.

    1983-01-01

    We investigate the phenomenon of dynamical generation of gauge interactions from CP/sup N/-1 models in four dimensions. We do this for the CP 2 model on a lattice. The phase diagram of a model that interpolates between CP 2 and U(1) gauge theory on a lattice is first mapped out. The potential between static charges in various regions of this diagram is also measured. Contrary to hopes based on the large-N behavior of similar models in two dimensions and on our phase diagram, we find that the potentials generated by CP 2 do not bear any resemblance to those of U(1). They are rather similar to the Higgs phase of an Abelian gauge theory in both phases displayed by CP 2

  8. On the energy crisis in noncommutative CP(1) model

    International Nuclear Information System (INIS)

    Sourrouille, Lucas

    2010-01-01

    We study the CP(1) system in (2+1)-dimensional noncommutative space with and without Chern-Simons term. Using the Seiberg-Witten map we convert the noncommutative CP(1) system to an action written in terms of the commutative fields. We find that this system presents the same infinite size instanton solution as the commutative Chern-Simons-CP(1) model without a potential term. Based on this result we argue that the BPS equations are compatible with the full variational equations of motion, rejecting the hypothesis of an 'energy crisis'. In addition we examine the noncommutative CP(1) system with a Chern-Simons interaction. In this case we find that when the theory is transformed by the Seiberg-Witten map it also presents the same instanton solution as the commutative Chern-Simons-CP(1) model.

  9. Addressing the strong CP problem with quark mass ratios

    Energy Technology Data Exchange (ETDEWEB)

    Diaz-Cruz, J.L.; Saldana-Salazar, U.J. [Benemerita Univ. Autonoma de Puebla (Mexico). Facultad de Ciencias Fisico-Matematicas; Hollik, W.G. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2016-05-15

    The strong CP problem is one of many puzzles in the theoretical description of elementary particles physics that still lacks an explanation. Solutions to that problem usually comprise new symmetries or fields or both. The main problem seems to be how to achieve small CP in the strong interactions despite large CP violation in weak interactions. Observation of CP violation is exclusively through the Higgs-Yukawa interactions. In this letter, we show that with minimal assumptions on the structure of mass (Yukawa) matrices the strong CP problem does not exist in the Standard Model and no extension to solve this is needed. However, to solve the flavor puzzle, models based on minimal SU(3) flavor groups leading to the proposed flavor matrices are favored.

  10. Addressing the strong CP problem with quark mass ratios

    International Nuclear Information System (INIS)

    Diaz-Cruz, J.L.; Saldana-Salazar, U.J.

    2016-05-01

    The strong CP problem is one of many puzzles in the theoretical description of elementary particles physics that still lacks an explanation. Solutions to that problem usually comprise new symmetries or fields or both. The main problem seems to be how to achieve small CP in the strong interactions despite large CP violation in weak interactions. Observation of CP violation is exclusively through the Higgs-Yukawa interactions. In this letter, we show that with minimal assumptions on the structure of mass (Yukawa) matrices the strong CP problem does not exist in the Standard Model and no extension to solve this is needed. However, to solve the flavor puzzle, models based on minimal SU(3) flavor groups leading to the proposed flavor matrices are favored.

  11. CP violation in the lepton sector with Majorana neutrinos

    International Nuclear Information System (INIS)

    Aguila, F. del

    1995-01-01

    We study CP violation in the lepton sector in extended models with right-handed neutrinos, without and with left-right symmetry, and with arbitrary mass terms. We find the conditions which must be satisfied by the neutrino and charged lepton mass matrices for CP conservation. These constraints, which are independent of the choice of weak basis, are proven to be also sufficient in simple cases. This invariant formulation makes apparent the necessary requirements for CP violation, as well as the size of CP violating effects. As an example, we show that CP violation can be much larger in left-right symmetric models than in models with only additional right-handed neutrinos, i.e., without right-handed currents. (orig.)

  12. Strong-Weak CP Hierarchy from Non-Renormalization Theorems

    Energy Technology Data Exchange (ETDEWEB)

    Hiller, Gudrun

    2002-01-28

    We point out that the hierarchy between the measured values of the CKM phase and the strong CP phase has a natural origin in supersymmetry with spontaneous CP violation and low energy supersymmetry breaking. The underlying reason is simple and elegant: in supersymmetry the strong CP phase is protected by an exact non-renormalization theorem while the CKM phase is not. We present explicit examples of models which exploit this fact and discuss corrections to the non-renormalization theorem in the presence of supersymmetry breaking. This framework for solving the strong CP problem has generic predictions for the superpartner spectrum, for CP and flavor violation, and predicts a preferred range of values for electric dipole moments.

  13. Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

    Directory of Open Access Journals (Sweden)

    Perry Evans

    Full Text Available Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs. MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard docking motifs from two to one. The proposed patterns are shown to be consistent with in silico docking between ERK1 and the HIV matrix protein. The motif usage on HIV proteins is sufficiently different from human proteins in amino acid sequence similarity to allow for HIV specific targeting using small-molecule drugs.

  14. Potato virus X TGBp1 induces plasmodesmata gating and moves between cells in several host species whereas CP moves only in N. benthamiana leaves

    International Nuclear Information System (INIS)

    Howard, Amanda R.; Heppler, Marty L.; Ju, Ho-Jong; Krishnamurthy, Konduru; Payton, Mark E.; Verchot-Lubicz, Jeanmarie

    2004-01-01

    Experiments were conducted to compare the plasmodesmal transport activities of Potato virus X (PVX) TGBp1 and coat protein (CP) in several plant species. Microinjection experiments indicated that TGBp1 gates plasmodesmata in Nicotiana tabacum leaves. These results support previous microinjection studies indicating that TGBp1 gates plasmodesmata in Nicotiana benthamiana and Nicotiana clevelandii leaves. To study protein movement, plasmids expressing the green fluorescent protein (GFP) gene fused to the PVX TGBp1 or CP genes were biolistically bombarded to leaves taken from four different PVX host species. GFP/TGBp1 moved between adjacent cells in N. tabacum, N. clevelandii, N. benthamiana, and Lycopersicon esculentum, whereas GFP/CP moved only in N. benthamiana leaves. Mutations m12 and m13 were introduced into the TGBp1 gene and both mutations eliminated TGBp1 ATPase active site motifs, inhibited PVX movement, reduced GFP/TGBp1 cell-to-cell movement in N. benthamiana leaves, and eliminated GFP/TGBp1 movement in N. tabacum, N. clevelandii, and L. esculentum leaves. GFP/TGBp1m13 formed aggregates in tobacco cells. The ability of GFP/CP and mutant GFP/TGBp1 fusion proteins to move in N. benthamiana and not in the other PVX host species suggests that N. benthamiana plants have a unique ability to promote protein intercellular movement

  15. Leptogenesis and low energy CP-violation in neutrino physics

    International Nuclear Information System (INIS)

    Pascoli, S.; Petcov, S.T.; Riotto, A.

    2007-01-01

    Taking into account the recent progress in the understanding of the lepton flavor effects in leptogenesis, we investigate in detail the possibility that the CP-violation necessary for the generation of the baryon asymmetry of the Universe is due exclusively to the Dirac and/or Majorana CP-violating phases in the PMNS neutrino mixing matrix U, and thus is directly related to the low energy CP-violation in the lepton sector (e.g., in neutrino oscillations, etc.). We first derive the conditions of CP-invariance of the neutrino Yukawa couplings λ in the see-saw Lagrangian, and of the complex orthogonal matrix R in the 'orthogonal' parametrization of λ. We show, e.g. that under certain conditions (i) real R and specific CP-conserving values of the Majorana and Dirac phases can imply CP-violation, and (ii) purely imaginary R does not necessarily imply breaking of CP-symmetry. We study in detail the case of hierarchical heavy Majorana neutrino mass spectrum, presenting results for three possible types of light neutrino mass spectrum: (i) normal hierarchical, (ii) inverted hierarchical, and (iii) quasi-degenerate. Results in the alternative case of quasi-degenerate in mass heavy Majorana neutrinos, are also derived. The minimal supersymmetric extension of the standard theory with right-handed Majorana neutrinos and see-saw mechanism of neutrino mass generation is discussed as well. We illustrate the possible correlations between the baryon asymmetry of the Universe and (i) the rephasing invariant J CP controlling the magnitude of CP-violation in neutrino oscillations, or (ii) the effective Majorana mass in neutrinoless double beta decay, in the cases when the only source of CP-violation is respectively the Dirac or the Majorana phases in the neutrino mixing matrix

  16. Measurements of the B0 bar B0 CP asymmetry

    International Nuclear Information System (INIS)

    Lueth, V.

    1993-01-01

    A figure of merit for a measurement of CP violation is the error on the intrinsic asymmetry A CP . The observed asymmetry A obs will always be smaller than A CP due to a number of effects that dilute the measurement. If one defines A obs =DA CP , where D represents the product of all dilution factors, then the error on A CP , δA CP is related to the number of produced B 0 or bar B 0 , N prod , needed to obtain a given error on δA CP by N prod =1/((δA CP ) 2 D 2 εBr). To determine the figure of merit for a particular decay mode one must determine the number of reconstructed events N obs and calculate the corresponding dilution factor D. N obs depends on the luminosity and production cross section, on the branching ratio of the B 0 or bar B 0 into the specific final state under study, Br, and on ε, the reconstruction efficiency for both the combination of the signal CP state and any tagging signal. The production rate N prod , the dilution factor D, and the efficiency ε, differ substantially in magnitude as a function of energy and detector layout. The detection efficiency and dilution factor can both be written as a product of several factors that can be estimated for a particular experiment. These factors depend critically on the decay mode under study, the tagging method, the detector configuration, and more generally on the production process, backgrounds, and detector performance. Furthermore, the present knowledge of these quantities varies largely, as well as ones ability to ultimately measure the dilution factor which relates the experimentally observed asymmetry to the true CP asymmetry

  17. Arsenic-Rich Polyarsenides Stabilized by Cp*Fe Fragments.

    Science.gov (United States)

    Schmidt, Monika; Konieczny, David; Peresypkina, Eugenia V; Virovets, Alexander V; Balázs, Gabor; Bodensteiner, Michael; Riedlberger, Felix; Krauss, Hannes; Scheer, Manfred

    2017-06-12

    The redox chemistry of [Cp*Fe(η 5 -As 5 )] (1, Cp*=η 5 -C 5 Me 5 ) has been investigated by cyclic voltammetry, revealing a redox behavior similar to that of its lighter congener [Cp*Fe(η 5 -P 5 )]. However, the subsequent chemical reduction of 1 by KH led to the formation of a mixture of novel As n scaffolds with n up to 18 that are stabilized only by [Cp*Fe] fragments. These include the arsenic-poor triple-decker complex [K(dme) 2 ][{Cp*Fe(μ,η 2:2 -As 2 )} 2 ] (2) and the arsenic-rich complexes [K(dme) 3 ] 2 [(Cp*Fe) 2 (μ,η 4:4 -As 10 )] (3), [K(dme) 2 ] 2 [(Cp*Fe) 2 (μ,η 2:2:2:2 -As 14 )] (4), and [K(dme) 3 ] 2 [(Cp*Fe) 4 (μ 4 ,η 4:3:3:2:2:1:1 -As 18 )] (5). Compound 4 and the polyarsenide complex 5 are the largest anionic As n ligand complexes reported thus far. Complexes 2-5 were characterized by single-crystal X-ray diffraction, 1 H NMR spectroscopy, EPR spectroscopy (2), and mass spectrometry. Furthermore, DFT calculations showed that the intermediate [Cp*Fe(η 5 -As 5 )] - , which is presumably formed first, undergoes fast dimerization to the dianion [(Cp*Fe) 2 (μ,η 4:4 -As 10 )] 2- . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Analysis of alkaptonuria (AKU) mutations and polymorphisms reveals that the CCC sequence motif is a mutational hot spot in the homogentisate 1,2 dioxygenase gene (HGO).

    Science.gov (United States)

    Beltrán-Valero de Bernabé, D; Jimenez, F J; Aquaron, R; Rodríguez de Córdoba, S

    1999-01-01

    We recently showed that alkaptonuria (AKU) is caused by loss-of-function mutations in the homogentisate 1,2 dioxygenase gene (HGO). Herein we describe haplotype and mutational analyses of HGO in seven new AKU pedigrees. These analyses identified two novel single-nucleotide polymorphisms (INV4+31A-->G and INV11+18A-->G) and six novel AKU mutations (INV1-1G-->A, W60G, Y62C, A122D, P230T, and D291E), which further illustrates the remarkable allelic heterogeneity found in AKU. Reexamination of all 29 mutations and polymorphisms thus far described in HGO shows that these nucleotide changes are not randomly distributed; the CCC sequence motif and its inverted complement, GGG, are preferentially mutated. These analyses also demonstrated that the nucleotide substitutions in HGO do not involve CpG dinucleotides, which illustrates important differences between HGO and other genes for the occurrence of mutation at specific short-sequence motifs. Because the CCC sequence motifs comprise a significant proportion (34.5%) of all mutated bases that have been observed in HGO, we conclude that the CCC triplet is a mutational hot spot in HGO. PMID:10205262

  19. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells

    KAUST Repository

    Takahashi, Yuta; Wu, Jun; Suzuki, Keiichiro; Martinez-Redondo, Paloma; Li, Mo; Liao, Hsin-Kai; Wu, Min-Zu; Herná ndez-Bení tez, Reyna; Hishida, Tomoaki; Shokhirev, Maxim Nikolaievich; Esteban, Concepcion Rodriguez; Sancho-Martinez, Ignacio; Belmonte, Juan Carlos Izpisua

    2017-01-01

    that insertion of CpG-free DNA into targeted CGIs induces de novo methylation of the entire CGI in human pluripotent stem cells (PSCs). The methylation status is stably maintained even after CpG-free DNA removal, extensive passaging, and differentiation

  20. First CP violation results from BABAR

    International Nuclear Information System (INIS)

    Hitlin, D.G.

    2001-01-01

    We present a preliminary measurement of time-dependent Cp-violating asymmetries in B 0 → J/ψK 0 S and B 0 → ψ(2S)K 0 S decays recorded by the BABAR. detector at the PEP-2 asymmetric B Factory at SLAC. The data sample consists of 9.0 fb -1 collected at the γ(4S) resonance and 0.8 fb -1 off-resonance. One of the neutral B mesons, produced in pairs at the γ(4S), is fully reconstructed. The flavor of the other neutral B meson is tagged at the time of its decay, mainly with the charge of identified leptons and kaons. The time difference between the decays is determined by measuring the distance between the decay vertices. Wrong-tag probabilities and the time resolution function are measured with samples of fully-reconstructed semileptonic and hadronic neutral B final states. The value of the asymmetry amplitude, sin 2β, is determined from a maximum likelihood fit to the time distribution of 120 tagged B 0 → J/ψK 0 S and B 0 → ψ(2S)K 0 S candidates: sin 2β=0.12±O.37(stat)±0.09(syst). (author)

  1. A rare male patient with classic Rett syndrome caused by MeCP2_e1 mutation.

    Science.gov (United States)

    Tokaji, Narumi; Ito, Hiromichi; Kohmoto, Tomohiro; Naruto, Takuya; Takahashi, Rizu; Goji, Aya; Mori, Tatsuo; Toda, Yoshihiro; Saito, Masako; Tange, Shoichiro; Masuda, Kiyoshi; Kagami, Shoji; Imoto, Issei

    2018-03-01

    Rett syndrome (RTT) is a severe neurodevelopmental disorder typically affecting females. It is mainly caused by loss-of-function mutations that affect the coding sequence of exon 3 or 4 of methyl-CpG-binding protein 2 (MECP2). Severe neonatal encephalopathy resulting in death before the age of 2 years is the most common phenotype observed in males affected by a pathogenic MECP2 variant. Mutations in MECP2 exon 1 affecting the MeCP2_e1 isoform are relatively rare causes of RTT in females, and only one case of a male patient with MECP2-related severe neonatal encephalopathy caused by a mutation in MECP2 exon 1 has been reported. This is the first reported case of a male with classic RTT caused by a 5-bp duplication in the open-reading frame of MECP2 exon 1 (NM_001110792.1:c.23_27dup) that introduced a premature stop codon [p.(Ser10Argfs*36)] in the MeCP2_e1 isoform, which has been reported in one female patient with classic RTT. Therefore, both males and females displaying at least some type of MeCP2_e1 mutation may exhibit the classic RTT phenotype. © 2018 Wiley Periodicals, Inc.

  2. Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

    Science.gov (United States)

    Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

    2015-06-01

    Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

    KAUST Repository

    Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian; Huser, Raphaë l; Ali, Amal J.; Merzaban, Jasmeen; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T.

    2018-01-01

    and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter

  4. Entamoeba histolytica EhCP112 Dislocates and Degrades Claudin-1 and Claudin-2 at Tight Junctions of the Intestinal Epithelium

    Directory of Open Access Journals (Sweden)

    Patricia Cuellar

    2017-08-01

    Full Text Available During intestinal invasion, Entamoeba histolytica opens tight junctions (TJs reflected by transepithelial electrical resistance (TEER dropping. To explore the molecular mechanisms underlying this, we studied in vitro and in vivo the damage produced by the recombinant E. histolytica cysteine protease (rEhCP112 on TJ functions and proteins. rEhCP112 reduced TEER in Caco-2 cells in a dose- and time-dependent manner; and EhCP112-overexpressing trophozoites provoked major epithelial injury compared to control trophozoites. rEhCP112 penetrated through the intercellular space, and consequently the ion flux increased and the TJs fence function was disturbed. However, macromolecular flux was not altered. Functional in vitro assays revealed specific association of rEhCP112 with claudin-1 and claudin-2, that are both involved in regulating ion flux and fence function. Of note, rEhCP112 did not interact with occludin that is responsible for regulating macromolecular flux. Moreover, rEhCP112 degraded and delocalized claudin-1, thus affecting interepithelial adhesion. Concomitantly, expression of the leaky claudin-2 at TJ, first increased and then it was degraded. In vivo, rEhCP112 increased intestinal epithelial permeability in the mouse colon, likely due to apical erosion and claudin-1 and claudin-2 degradation. In conclusion, we provide evidence that EhCP112 causes epithelial dysfunction by specifically altering claudins at TJ. Thus, EhCP112 could be a potential target for therapeutic approaches against amoebiasis.

  5. MeCP2-Related Diseases and Animal Models

    Directory of Open Access Journals (Sweden)

    Chinelo D. Ezeonwuka

    2014-01-01

    Full Text Available The role of epigenetics in human disease has become an area of increased research interest. Collaborative efforts from scientists and clinicians have led to a better understanding of the molecular mechanisms by which epigenetic regulation is involved in the pathogenesis of many human diseases. Several neurological and non-neurological disorders are associated with mutations in genes that encode for epigenetic factors. One of the most studied proteins that impacts human disease and is associated with deregulation of epigenetic processes is Methyl CpG binding protein 2 (MeCP2. MeCP2 is an epigenetic regulator that modulates gene expression by translating epigenetic DNA methylation marks into appropriate cellular responses. In order to highlight the importance of epigenetics to development and disease, we will discuss how MeCP2 emerges as a key epigenetic player in human neurodevelopmental, neurological, and non-neurological disorders. We will review our current knowledge on MeCP2-related diseases, including Rett Syndrome, Angelman Syndrome, Fetal Alcohol Spectrum Disorder, Hirschsprung disease, and Cancer. Additionally, we will briefly discuss about the existing MeCP2 animal models that have been generated for a better understanding of how MeCP2 impacts certain human diseases.

  6. Scalar mesons and kaons in φ radiative decay and their implications for studies of CP violation at DAφNE

    International Nuclear Information System (INIS)

    Brown, N.; Close, F.E.

    1991-12-01

    We had become interested in the possibility that radiative decays of the φ meson might be so prominent that they would undermine the primary aim of the φ factory, namely the study of (CP) charge-parity violation. As a result of previous work we can now be confident that the CP programme will not be significantly affected by this possibility. At the same time, the DAφNE facility will create opportunities for studying φ radiative processes, in particular the production of the enigmatic scalar resonances, in their own right. (author)

  7. CP violation as a probe of flavor origin in supersymmetry

    International Nuclear Information System (INIS)

    Demir, D.A.; Masiero, A.; Vives, O.

    1999-11-01

    We address the question of the relation between supersymmetry breaking and the origin of flavor in the context of CP violating phenomena. We prove that, in the absence of the Cabibbo-Kobayashi-Maskawa phase, a general Minimal Supersymmetric Standard Model with all possible phases in the soft-breaking terms, but no new flavor structure beyond the usual Yukawa matrices, can never give a sizeable contribution to ε K , ε'/ε or hadronic B 0 CP asymmetries. Observation of supersymmetric contributions to CP asymmetries in B decays would hint at a non-flavor blind mechanism of supersymmetry breaking. (author)

  8. CP nonconservation in decays of W and Z bosons

    International Nuclear Information System (INIS)

    Hou, W.; Deshpande, N.G.; Eilam, G.; Soni, A.

    1986-01-01

    The possibility of CP asymmetries in decays of W and Z bosons is examined. The asymmetries studied are the differences in the branching ratios of charge-conjugate modes such as W + →tb-bar vs W - →t-barb or Z→b-bars vs Z→bs-bar. In the standard model, with three generations, such effects are found to be vanishingly small. With four generations, flavor-changing transitions such as Z→bs-bar or b'b-bar may be observable, but the prospects for observing CP asymmetries appear discouraging. We also discuss the situation in some other models of CP nonconservation

  9. Constructing co-Higgs bundles on CP^2

    OpenAIRE

    Rayan, Steven

    2013-01-01

    On a complex manifold, a co-Higgs bundle is a holomorphic vector bundle with an endomorphism twisted by the tangent bundle. The notion of generalized holomorphic bundle in Hitchin's generalized geometry coincides with that of co-Higgs bundle when the generalized complex manifold is ordinary complex. Schwarzenberger's rank-2 vector bundle on the projective plane, constructed from a line bundle on the double cover CP^1 \\times CP^1 \\to CP^2, is naturally a co-Higgs bundle, with the twisted endom...

  10. Towards a dynamical solution of the strong CP problem

    International Nuclear Information System (INIS)

    Schierholz, G.

    1994-01-01

    One may argue that QCD solves the strong CP problem by itself. To test this idea, a lattice simulation suggests itself. In view of the difficulty of such a calculation we have, as a first step, investigated the problem in the CP 3 model. The CP 3 model is in many respects similar to QCD. In this talk I present some first results of our calculation. Among other things it is shown that the model has a first order deconfining phase transition in θ and that the critical value of θ decreases towards zero as β is taken to infinity. This suggests that θ is tuned to zero in the continuum limit. ((orig.))

  11. arXiv Flavour Physics and CP Violation

    CERN Document Server

    Kamenik, J.F.

    2016-01-01

    These notes represent a summary of three lectures on flavour and CP violation, given at the CERNs European School of High Energy Physics in 2014. They cover flavour physics within the standard model, phenomenology of CP violation in meson mixing and decays, as well as constraints of flavour observableson physics beyond the standard model. In preparing the lectures (and consequently this summary) I drew heavily from several existing excellent and exhaustive sets of lecture notes and reviews on flavour physics and CP violation [1]. The reader is encouraged to consult those as well as the original literature for a more detailed study.

  12. CP violation in K- and B-meson decays

    CERN Multimedia

    2000-01-01

    These lectures will describe CP violation in K- and B-meson decays and will include the following topics:i) Grand view of the field including CKM matrix and the unitarily triangle ii) General aspects of the theoretical framework iii) Fundamentals of particle-antiparticle mixing iv) Fundamentals of CP violation v) Standard analysis of the unitarily triangle vi) The ratio e'/e including most recent developments vii) CP Violation in rare K- decays viii) Violation in B-Decays (asymmetries and other strategies) ix) A brief look beyond the Standard Model

  13. Methods for detection of methyl-CpG dinucleotides

    Science.gov (United States)

    Dunn, John J.

    2012-09-11

    The invention provides methods for enriching methyl-CpG sequences from a DNA sample. The method makes use of conversion of cytosine residues to uracil under conditions in which methyl-cytosine residues are preserved. Additional methods of the invention enable to preservation of the context of me-CpG dinucleotides. The invention also provides a recombinant, full length and substantially pure McrA protein (rMcrA) for binding and isolation of DNA fragments containing the sequence 5'-C.sup.MeCpGG-3'. Methods for making and using the rMcrA protein, and derivatives thereof are provided.

  14. First Search for {ital CP} Violation in Tau Lepton Decay

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, S.; Kubota, Y.; Lee, S.J.; ONeill, J.J.; Poling, R.; Riehle, T.; Smith, A. [University of Minnesota, Minneapolis, Minnesota 55455 (United States); Alam, M.S.; Athar, S.B.; Ling, Z.; Mahmood, A.H.; Timm, S.; Wappler, F. [State University of New York at Albany, Albany, New York 12222 (United States); Anastassov, A.; Duboscq, J.E.; Fujino, D.; Gan, K.K.; Hart, T.; Honscheid, K.; Kagan, H.; Kass, R.; Lee, J.; Schwarthoff, H.; Spencer, M.B.; Sung, M.; Undrus, A.; Wolf, A.; Zoeller, M.M. [The Ohio State University, Columbus, Ohio 43210 (United States); Richichi, S.J.; Severini, H.; Skubic, P. [University of Oklahoma, Norman, Oklahoma 73019 (United States); Bishai, M.; Fast, J.; Hinson, J.W.; Menson, N.; Miller, D.H.; Shibata, E.I.; Shipsey, I.P.; Yurko, M. [Purdue University, West Lafayette, Indiana 47907 (United States); Glenn, S.; Kwon, Y.; Lyon, A.L.; Roberts, S.; Thorndike, E.H. [University of Rochester, Rochester, New York 14627 (United States); Jessop, C.P.; Lingel, K.; Marsiske, H.; Perl, M.L.; Savinov, V.; Ugolini, D.; Zhou, X. [Stanford Linear Accelerator Center, Stanford University, Stanford, California 94309 (United States); Coan, T.E.; Fadeyev, V.; Korolkov, I.; Maravin, Y.; Narsky, I.; Shelkov, V.; Staeck, J.; Stroynowski, R.; Volobouev, I.; Ye, J. [Southern Methodist University, Dallas, Texas 75275 (United States); Artuso, M.; Azfar, F.; Efimov, A.; Goldberg, M.; He, D.; Kopp, S.; Moneti, G.C.; Mountain, R.; Schuh, S.; Skwarnicki, T.; Stone, S.; Viehhauser, G.; Wang, J.C.; Xing, X. [Syracuse University, Syracuse, New York 13244 (United States); Bartelt, J.; Csorna, S.E.; Jain, V.; McLean, K.W.; Marka, S. [Vanderbilt University, Nashville, Tennessee 37235 (United States); Godang, R.; Kinoshita, K.; Lai, I.C.; Pomianowski, P.; Schrenk, S. [Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 (United States); Bonvicini, G.; Cinabro, D.; Greene, R.; Perera, L.P.; Zhou, G.J. [Wayne State Univ., (United States)

    1998-11-01

    We have performed the first search for CP violation in tau lepton decay. CP violation in lepton decay does not occur in the minimal standard model but can occur in extensions such as the multi-Higgs doublet model. It appears as a characteristic difference between the {tau}{sup {minus}} and {tau}{sup +} decay angular distributions for the semileptonic decay modes such as {tau}{sup {minus}}{r_arrow}K{sup 0}{pi}{sup {minus}}{nu} . We define an observable asymmetry to exploit this and find no evidence for any CP violation. {copyright} {ital 1998} {ital The American Physical Society }

  15. Up sector of minimal flavor violation: top quark properties and direct D meson CP violation

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Yang; Berger, Joshua; Hewett, JoAnne L.; Li, Ye

    2013-07-01

    Minimal Flavor Violation in the up-type quark sector leads to particularly interesting phenomenology due to the interplay of flavor physics in the charm sector and collider physics from flavor changing processes in the top sector. We study the most general operators that can affect top quark properties and D meson decays in this scenario, concentrating on two CP violating operators for detailed studies. The consequences of these effective operators on charm and top flavor changing processes are generically small, but can be enhanced if there exists a light flavor mediator that is a Standard Model gauge singlet scalar and transforms under the flavor symmetry group. This flavor mediator can satisfy the current experimental bounds with a mass as low as tens of GeV and explain observed D-meson direct CP violation. Additionally, the model predicts a non-trivial branching fraction for a top quark decay that would mimic a dijet resonance.

  16. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-01

    LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  17. DMINDA: an integrated web server for DNA motif identification and analyses.

    Science.gov (United States)

    Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

    2014-07-01

    DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  19. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

    Science.gov (United States)

    Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

    2018-04-01

    The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

  20. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2011-06-20

    One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  1. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode

  2. Core signalling motif displaying multistability through multi-state enzymes

    DEFF Research Database (Denmark)

    Feng, Song; Saez Cornellana, Meritxell; Wiuf, Carsten Henrik

    2016-01-01

    Bistability, and more generally multistability, is a key system dynamics feature enabling decision-making and memory in cells. Deciphering the molecular determinants of multistability is thus crucial for a better understanding of cellular pathways and their (re)engineering in synthetic biology....... Here, we show that a key motif found predominantly in eukaryotic signalling systems, namely a futile signalling cycle, can display bistability when featuring a two-state kinase. We provide necessary and sufficient mathematical conditions on the kinetic parameters of this motif that guarantee...... the existence of multiple steady states. These conditions foster the intuition that bistability arises as a consequence of competition between the two states of the kinase. Extending from this result, we find that increasing the number of kinase states linearly translates into an increase in the number...

  3. Factoring local sequence composition in motif significance analysis.

    Science.gov (United States)

    Ng, Patrick; Keich, Uri

    2008-01-01

    We recently introduced a biologically realistic and reliable significance analysis of the output of a popular class of motif finders. In this paper we further improve our significance analysis by incorporating local base composition information. Relying on realistic biological data simulation, as well as on FDR analysis applied to real data, we show that our method is significantly better than the increasingly popular practice of using the normal approximation to estimate the significance of a finder's output. Finally we turn to leveraging our reliable significance analysis to improve the actual motif finding task. Specifically, endowing a variant of the Gibbs Sampler with our improved significance analysis we demonstrate that de novo finders can perform better than has been perceived. Significantly, our new variant outperforms all the finders reviewed in a recently published comprehensive analysis of the Harbison genome-wide binding location data. Interestingly, many of these finders incorporate additional information such as nucleosome positioning and the significance of binding data.

  4. Neoanalysis, Orality, and Intertextuality: An Examination of Homeric Motif Transference

    Directory of Open Access Journals (Sweden)

    Jonathan Burgess

    2006-03-01

    Full Text Available In Homeric studies scholars have speculated on the influence of (non-surviving preHomeric material on the Iliad. This article expands this line of argument from an oralist perspective, with reference to modern intertextual theory. It concludes that preHomeric and nonHomeric motifs from oral traditions were transferred into the epic poem, creating an intertextually allusive poetics that would have been recognizable to an early Greek audience informed of mythological traditions.

  5. Motif Subscriber Menonton Channel YouTube Raditya Dika

    OpenAIRE

    Mellyaningsih, Adinda

    2016-01-01

    Penelitian ini dilakukan untuk mengetahui motif para subscriber dalam menonton channelYouTube Raditya Dika. Raditya Dika merupakan YouTuber Indonesia dengan jumlah subscriber terbanyak dan merupakan orang pertama di Indonesia yang mendapatkan penghargaan Certifies Award oleh YouTube. Peneliti menggunakan teori Uses and Gratification dengan empat indikator, yaitu hiburan dan relaksasi, hubungan antar pribadi, mencari informasi, dan persahabatan. Metode dalam penelitian ini adalah online survei...

  6. Perception Enhancement using Visual Attributes in Sequence Motif Visualization

    OpenAIRE

    Oon, Yin; Lee, Nung; Kok, Wei

    2016-01-01

    Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principl...

  7. Exon silencing by UAGG motifs in response to neuronal excitation.

    Directory of Open Access Journals (Sweden)

    Ping An

    2007-02-01

    Full Text Available Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay with a tight neuron-specific readout. In this system, exon silencing in response to neuronal excitation was mediated by multiple UAGG-type silencing motifs, and transfer of the motifs to a constitutive exon conferred a similar responsiveness by gain of function. Biochemical analysis of protein binding to UAGG motifs in extracts prepared from treated and mock-treated cortical cultures showed an increase in nuclear hnRNP A1-RNA binding activity in parallel with excitation. Evidence for the role of the NMDA receptor and calcium signaling in the induced splicing response was shown by the use of specific antagonists, as well as cell-permeable inhibitors of signaling pathways. Finally, a wider role for exon-skipping responsiveness is shown to involve additional exons with UAGG-related silencing motifs, and transcripts involved in synaptic functions. These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation.

  8. Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

    Science.gov (United States)

    Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

    2004-01-05

    The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

  9. Efficient sequential and parallel algorithms for planted motif search.

    Science.gov (United States)

    Nicolae, Marius; Rajasekaran, Sanguthevar

    2014-01-31

    Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We want to find all sequences of length l that appear in each of the input sequences with at most d mismatches. The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging. Despite ample research in the area, a considerable performance gap exists because many state of the art algorithms have large runtimes even for moderately challenging instances. This paper presents a fast exact parallel PMS algorithm called PMS8. PMS8 is the first algorithm to solve the challenging (l,d) instances (25,10) and (26,11). PMS8 is also efficient on instances with larger l and d such as (50,21). We include a comparison of PMS8 with several state of the art algorithms on multiple problem instances. This paper also presents necessary and sufficient conditions for 3 l-mers to have a common d-neighbor. The program is freely available at http://engr.uconn.edu/~man09004/PMS8/. We present PMS8, an efficient exact algorithm for Planted Motif Search. PMS8 introduces novel ideas for generating common neighborhoods. We have also implemented a parallel version for this algorithm. PMS8 can solve instances not solved by any previous algorithms.

  10. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    OpenAIRE

    Masiswo Masiswo; Vivin Atika

    2016-01-01

    ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pa...

  11. GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences.

    Science.gov (United States)

    Yu, Ning; Guo, Xuan; Zelikovsky, Alexander; Pan, Yi

    2017-05-24

    As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+C content is ≥ 50%, (b) the ratio of the observed CpG content and the expected CpG content is ≥ 0.6, and (c) the general length of CGI is greater than 200 nucleotides. Most existing computational methods for the prediction of CpG island are programmed on these rules. However, many experimentally verified CpG islands deviate from these artificial criteria. Experiments indicate that in many cases %G+C is human genome. We analyze the energy distribution over genomic primary structure for each CpG site and adopt the parameters from statistics of Human genome. The evaluation results show that the new model can predict CpG islands efficiently by balancing both sensitivity and specificity over known human CGI data sets. Compared with other models, GaussianCpG can achieve better performance in CGI detection. Our Gaussian model aims to simplify the complex interaction between nucleotides. The model is computed not by the linear statistical method but by the Gaussian energy distribution and accumulation. The parameters of Gaussian function are not arbitrarily designated but deliberately chosen by optimizing the biological statistics. By using the pseudopotential analysis on CpG islands, the novel model is validated on both the real and artificial data sets.

  12. Insertion of tetracysteine motifs into dopamine transporter extracellular domains.

    Directory of Open Access Journals (Sweden)

    Deanna M Navaroli

    Full Text Available The neuronal dopamine transporter (DAT is a major determinant of extracellular dopamine (DA levels and is the primary target for a variety of addictive and therapeutic psychoactive drugs. DAT is acutely regulated by protein kinase C (PKC activation and amphetamine exposure, both of which modulate DAT surface expression by endocytic trafficking. In order to use live imaging approaches to study DAT endocytosis, methods are needed to exclusively label the DAT surface pool. The use of membrane impermeant, sulfonated biarsenic dyes holds potential as one such approach, and requires introduction of an extracellular tetracysteine motif (tetraCys; CCPGCC to facilitate dye binding. In the current study, we took advantage of intrinsic proline-glycine (Pro-Gly dipeptides encoded in predicted DAT extracellular domains to introduce tetraCys motifs into DAT extracellular loops 2, 3, and 4. [(3H]DA uptake studies, surface biotinylation and fluorescence microscopy in PC12 cells indicate that tetraCys insertion into the DAT second extracellular loop results in a functional transporter that maintains PKC-mediated downregulation. Introduction of tetraCys into extracellular loops 3 and 4 yielded DATs with severely compromised function that failed to mature and traffic to the cell surface. This is the first demonstration of successful introduction of a tetracysteine motif into a DAT extracellular domain, and may hold promise for use of biarsenic dyes in live DAT imaging studies.

  13. Codon based co-occurrence network motifs in human mitochondria

    Directory of Open Access Journals (Sweden)

    Pramod Shinde

    2017-10-01

    Full Text Available The nucleotide polymorphism in human mitochondrial genome (mtDNA tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, we constructed genome-wide nucleotide co-occurrence networks using a massive data consisting of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns between codon and non-codon positions. It was interesting to report a different evolution of Asian genomes than those of the rest which is divulged by network motifs. We found evidence that mtDNA undergoes substantial amounts of adaptive evolution, a finding which was supported by a number of previous studies. The dominance of higher order motifs indicated the importance of long-range nucleotide co-occurrence in genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analyses manifested that codon position co-evolution is very well conserved across human sub-populations and independently maintained within human sub-populations implying the selective role of evolutionary processes on codon position co-evolution. Ergo, this study provided a framework to investigate cooperative genomic interactions which are critical in underlying complex mitochondrial evolution.

  14. Organofluorine chemistry: synthesis and conformation of vicinal fluoromethylene motifs.

    Science.gov (United States)

    O'Hagan, David

    2012-04-20

    The C-F bond is the most polar bond in organic chemistry, and thus the bond has a relatively large dipole moment with a significant -ve charge density on the fluorine atom and correspondingly a +ve charge density on carbon. The electrostatic nature of the bond renders it the strongest one in organic chemistry. However, the fluorine atom itself is nonpolarizable, and thus, despite the charge localization on fluorine, it is a poor hydrogen-bonding acceptor. These properties of the C-F bond make it attractive in the design of nonviscous but polar organic compounds, with a polarity limited to influencing the intramolecular nature of the molecule and less so intermolecular interactions with the immediate environment. In this Perspective, the synthesis of aliphatic chains carrying multivicinal fluoromethylene motifs is described. It emerges that the dipoles of adjacent C-F bonds orientate relative to each other, and thus, individual diastereoisomers display different backbone carbon chain conformations. These conformational preferences recognize the influence of the well-known gauche effect associated with 1,2-difluoroethane but extend to considering 1,3-fluorine-fluorine dipolar repulsions. The synthesis of carbon chains carrying two, three, four, five, and six vicinal fluoromethylene motifs is described, with an emphasis on our own research contributions. These motifs obey almost predictable conformational behavior, and they emerge as candidates for inclusion in the design of performance organic molecules. © 2012 American Chemical Society

  15. iFORM: Incorporating Find Occurrence of Regulatory Motifs.

    Science.gov (United States)

    Ren, Chao; Chen, Hebing; Yang, Bite; Liu, Feng; Ouyang, Zhangyi; Bo, Xiaochen; Shu, Wenjie

    2016-01-01

    Accurately identifying the binding sites of transcription factors (TFs) is crucial to understanding the mechanisms of transcriptional regulation and human disease. We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use and efficient tool for scanning DNA sequences with TF motifs described as position weight matrices (PWMs). Both performance assessment with a receiver operating characteristic (ROC) curve and a correlation-based approach demonstrated that iFORM achieves higher accuracy and sensitivity by integrating five classical motif discovery programs using Fisher's combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and the tool has demonstrated its utility in further elucidating individual roles of functional elements. Both the source and binary codes for iFORM can be freely accessed at https://github.com/wenjiegroup/iFORM. The identified TF binding sites across human cell and tissue types using iFORM have been deposited in the Gene Expression Omnibus under the accession ID GSE53962.

  16. THE MOTIF OF THE PRODIGAL SON IN IVAN TURGENEV'S NOVELS

    Directory of Open Access Journals (Sweden)

    Valentina Ivanovna Gabdullina

    2013-11-01

    Full Text Available The author questions the perception of Ivan Turgenev as a “non- Christian writer” and studies the problem of the prodigal son motif functioning in a series of his novels. In his novels, Turgenev pictured different phases of the archetypal story, originating from the Gospel parable of the prodigal son. In the novel Rudin he depicted the phase of spiritual wanderings of the hero who had lost touch with his native land — Russia. In his next novels (Home of the Gentry, Fathers and Sons and Smoke, after leading his hero in circles and sending him back to his paternal home, Turgenev reconstructs the model of human behavior, represented in the parable, thereby recognizing the immutability of the idea formalized in the Gospel. The motif of the return to Russian land gets its completion in Turgenev's last novel Virgin Soil, in which the author paradoxically connects the Westernist idea with the Gospel imperative. Solomin, the son of a deacon, sent by his wise father out to Europe “to get education”, studies in England, masters the European knowledge and returns back “to his native land” to establish his own business in inland Russia. Thus, a series of Turgenev's novels, in which he portrayed different phases of social life, are interlinked with the motif of the prodigal son, who is represented by novels' main characters.

  17. The city as a motif in Slovene youth literature

    Directory of Open Access Journals (Sweden)

    Milena Mileva Blažić

    2003-01-01

    Full Text Available The article presents the city as motif of Slovenian youth literature in four different periods, beginning in the first period of original Slovenian youth literature in the second half of the 19th century, second period in the first half of the 20th century, third period in the second half of the 20th century and after 1950, when significant books were produced in the field of short modern stories, emphasising on picture books and realistic narrative prose, and the fourth period after 1990. A discernable shift can be observed in the thirties of the 20th century, during the times of socialist realism. The most significant change occurred after 1960, when massive migration from rural to urban environments caused by industrialisation began. The motif of urban environment especially marked modern realistic narrative, coined problematic narrative after 1990, with its focus on issues of growing up in such environments. The city as motif or theme doesn’t appear only in realistic narrative, but since the early 20th century also in fantastic narrative, thus it dichotomically presents the image of real world in Slovenian youth realistic narrative.

  18. TOPDOM: database of conservatively located domains and motifs in proteins.

    Science.gov (United States)

    Varga, Julia; Dobson, László; Tusnády, Gábor E

    2016-09-01

    The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  19. Allexiviruses may have acquired inserted sequences between the CP and CRP genes to change the translation reinitiation strategy of CRP.

    Science.gov (United States)

    Yoshida, Naoto; Shimura, Hanako; Masuta, Chikara

    2018-06-01

    Allexiviruses are economically important garlic viruses that are involved in garlic mosaic diseases. In this study, we characterized the allexivirus cysteine-rich protein (CRP) gene located just downstream of the coat protein (CP) gene in the viral genome. We determined the nucleotide sequences of the CP and CRP genes from numerous allexivirus isolates and performed a phylogenetic analysis. According to the resulting phylogenetic tree, we found that allexiviruses were clearly divided into two major groups (group I and group II) based on the sequences of the CP and CRP genes. In addition, the allexiviruses in group II had distinct sequences just before the CRP gene, while group I isolates did not. The inserted sequence between the CP and CRP genes was partially complementary to garlic 18S rRNA. Using a potato virus X vector, we showed that the CRPs affected viral accumulation and symptom induction in Nicotiana benthamiana, suggesting that the allexivirus CRP is a pathogenicity determinant. We assume that the inserted sequences before the CRP gene may have been generated during viral evolution to alter the termination-reinitiation mechanism for coupled translation of CP and CRP.

  20. Dynamical symmetry breaking: Exotic quarks and the strong CP problem

    International Nuclear Information System (INIS)

    Furlong, R.C.

    1988-10-01

    Decuplet quarks (quens) transforming as 10's under SU(3)/sub C/ are shown to be superior to sextet quarks (quixes) in their ability to resolve the Strong CP problem, resulting in composite invisible axions (CIAs). 8 refs

  1. Measurement of CP violation at a Neutrino Factory

    CERN Document Server

    Gómez-Cadenas, J J

    2001-01-01

    The prospects of measuring CP violation in the leptonic sector using the intense neutrino beams arising from muon decay in the straight sections of a muon accumulator ring (the so-called neutrino factory) are discussed.

  2. LHC experimental sensitivity to CP violating gtt couplings

    CERN Document Server

    Sjölin, J

    2003-01-01

    The level of CP violation in pp to tt+X induced by the standard model is known to be below the experimental sensitivity by many orders of magnitude. However, in some effective theories, it is plausible that new CP violating physics could reveal itself as additional non- renormalizable terms in the Lagrangian. Since these should respect the symmetries of the low-energy gauge interaction, violate CP and generate the correct event topology, the set of allowed terms is highly restricted. This analysis gives an estimate of the expected experimental sensitivity to the lowest order effective CP violating gtt interaction term beyond the standard model using simulated data from the ATLAS detector at the LHC. (36 refs).

  3. Introduction to heavy meson decays and CP asymmetries

    International Nuclear Information System (INIS)

    Ligeti, Zoltan

    2003-01-01

    These lectures are intended to provide an introduction to heavy meson decays and CP violation. The first lecture contains a brief review of the standard model and how the CKM matrix and CP violation arise, mixing and CP violation in neutral meson systems, and explanation of the cleanliness of the sin 2β measurement. The second lecture deals with the heavy quark limit, some applications of heavy quark symmetry and the operator product expansion for exclusive and inclusive semileptonic B decays. The third lecture concerns with theoretically clean CP violation measurements that may become possible in the future, and some developments toward a better understanding of nonleptonic B decays. The conclusions include a subjective best buy list for the near future

  4. CP-violating profile of the electroweak bubble wall

    Energy Technology Data Exchange (ETDEWEB)

    Funakubo, Koichi [Saga Univ. (Japan). Dept. of Physics; Kakuto, Akira; Otsuki, Shoichiro; Takenaga, Kazunori; Toyoda, Fumihiko

    1995-11-01

    In any scenario of the electroweak baryogenesis, the profile of the CP violating bubble wall, created at the first-order phase transition, plays an essential role. We attempt to determine it by solving the equations of motion for the scalars in the two-Higgs-doublet model at the transition temperature. According to the parameters in the potential, we found three solutions. Two of them smoothly connect the CP-violating broken phase and the symmetric phase, while the other connects CP-conserving vacua but violates CP in the intermediate region. We also estimate the chiral charge flux, which will be turned into the baryon density in the symmetric phase by the sphaleron process. (author).

  5. 50 years of CP violation — What have we learned?

    Energy Technology Data Exchange (ETDEWEB)

    McKellar, Bruce H. J. [Centre of Excellence for Particle Physics at the Terrascale School of Physics, University of Melbourne, Australia 3010 (Australia)

    2015-04-24

    Early after the discovery of CP violation, the explanation of how the Standard Model of particle physics could allow CP violation was quickly given, but it took many years for the original observation to be unequivocally explained on that basis. It was also proposed that this observation opened up the possibility that we could now explain the fact that the universe is made of matter. Remarkably, 50 years later we have no evidence in particle physics that there is any CP violation except that of the Kobayashi Maskawa mechanism of the standard model. Yet we fail completely to explain the baryon asymmetry of the Universe through that mechanism. After reviewing the main points in the history I describe the present experimental attempts to find CP violation beyond the standard model, and explain the theoretical attempts to explain the matter in the Universe.

  6. CP violation in multibody decays of beauty baryons

    Energy Technology Data Exchange (ETDEWEB)

    Durieux, Gauthier

    2016-08-15

    Beauty baryons are being observed in large numbers in the LHCb detector. The rich kinematic distributions of their multibody decays are therefore becoming accessible and provide us with new opportunities to search for CP violation. We analyse the angular distributions of some three- and four-body decays of spin-1/2 baryons using the Jacob-Wick helicity formalism. The asymmetries that provide access to small differences of CP-odd phases between decay amplitudes of identical CP-even phases are notably discussed. The understanding gained on processes featuring specific resonant intermediate states allows us to establish which asymmetries are relevant for what purpose. It is for instance shown that some CP-odd angular asymmetries measured by the LHCb collaboration in the Λ{sub b}→Λφ→pπ K{sup +}K{sup -} decay are expected to vanish identically.

  7. Flavour Physics and CP Violation : Expecting the LHC

    CERN Document Server

    Fleischer, Robert

    2008-01-01

    The starting point of these lectures is an introduction to the weak interactions of quarks and the Standard-Model description of CP violation, where the central role is played by the Cabibbo-Kobayashi-Maskawa matrix and the corresponding unitarity triangles. Since the B-meson system governs the stage of (quark) flavour physics and CP violation, it is our main focus: we shall classify B-meson decays, introduce the theoretical tools to deal with them, investigate the requirements for non-vanishing CP-violating asymmetries, and discuss the main strategies to explore CP violation and the preferred avenues for physics beyond the Standard Model to enter. This formalism allows us then to discuss important benchmark modes, where we will also address the question of how much space for new-physics effects in the B studies at the LHC is left by the recent experimental results from the B factories and the Tevatron.

  8. CP violating observables in e$^{-}$e$^{+}$ --> W$^{-}$W$^{+}$

    CERN Document Server

    Chang, D; Phillips, I

    1993-01-01

    We consider various integrated lepton charge-energy asymmetries and azimuthal asymmetries as tests of CP violation in the process $e^-e^+ \\to W^-W^+$. These asymmetries are sensitive to different linear combinations of the CP violating form factors in the three gauge boson $W^-W^+$ production vertex, and can distinguish dispersive and absorptive parts of the form factors. It makes use of purely hadronic and purely leptonic modes of $W$'s decays as well as the mixed modes. The techniques of using the kinematics of jets or missing momentum to construct CP--odd observables are also employed. These CP violating observables are illustrated in the generalized Left-Right Model and the Charged Higgs Model.

  9. CP violation in the B and D systems at LHCb

    CERN Document Server

    Romero Vidal, A

    2014-01-01

    The large samples of mesons containing a $b$ or a $c$ quark collected by the LHCb experiment in 2011 and 2012, corresponding to an integrated luminosity of 3 fb$^{-1}$, provide an unprecedent framework to perform high precision measurements of CP violation. A comparison of measurements of CP violating observables with the Standard Model predictions can reveal contributions from physics beyond the Standard Model. Studies of $B$ and $D$ meson decays at LHCb are presented in this document.

  10. Quark flavor mixing, CP violation, and all that

    International Nuclear Information System (INIS)

    Gilman, F.J.

    1988-04-01

    We review the present state of knowledge of the mixing of quark flavors under weak interactions and the associated explanation of CP violation inherent in the single nontrivial phase present in the three-generation mixing matrix. In this context we present the phenomenological basis for the increasing possibility that large CP violation asymmetries can be experimentally observed in the B meson system. 39 refs., 11 figs.,

  11. New results on Bs mixing and CP violation from LHCb

    CERN Multimedia

    CERN. Geneva

    2013-01-01

    Oscillation effects in the Bs meson system provide a window on physics beyond the Standard Model. The latest results from LHCb on the mass and width differences between the two physical eigenstates, and the CP violating phase measured in the Bs -> J/psi phi decay channel are presented. In addition, results of a first study of the CP violating phase in the penguin-dominated Bs -> phiphi decays are shown.

  12. 14th Conference on Flavor Physics and CP Violation

    CERN Document Server

    2016-01-01

    The 2016 edition of the Conference on Flavor Physics and CP Violation will be held at on the campus of the California Institute of Technology on 6-9 June. The FPCP conference series was founded in 2002 through the merger of the Heavy Flavor (HF) and B Physics and CP Violation (BPCP) conference series. A list of previous FPCP venues can be found here.

  13. [Stress-corrosion test of TIG welded CP-Ti].

    Science.gov (United States)

    Li, H; Wang, Y; Zhou, Z; Meng, X; Liang, Q; Zhang, X; Zhao, Y

    2000-12-01

    In this study TIG (Tungsten Inert Gas) welded CP-Ti were subjected to stress-corrosion test under 261 MPa in artificial saliva of 37 degrees C for 3 months. No significant difference was noted on mechanical test (P > 0.05). No color-changed and no micro-crack on the sample's surface yet. These results indicate that TIG welded CP-Ti offers excellent resistance to stress corrosion.

  14. Dynamical CP violation of the generalized Yang-Mills model

    International Nuclear Information System (INIS)

    Wang Dianfu; Chang Xiaojing; Sun Xiaoyu

    2011-01-01

    Starting from the generalized Yang-Mills model which contains, besides the vector part V μ , also a scalar part S and a pseudoscalar part P . It is shown, in terms of the Nambu-Jona-Lasinio (NJL) mechanism, that CP violation can be realized dynamically. The combination of the generalized Yang-Mills model and the NJL mechanism provides a new way to explain CP violation. (authors)

  15. Search for CP violation in D0 decay

    International Nuclear Information System (INIS)

    Bartelt, J.; Csorna, S.E.; Egyed, Z.; Jain, V.; Gibaut, D.; Kinoshita, K.; Pomianowski, P.; Barish, B.; Chadha, M.; Chan, S.; Cowen, D.F.; Eigen, G.; Miller, J.S.; O'Grady, C.; Urheim, J.; Weinstein, A.J.; Wuerthwein, F.; Asner, D.M.; Athanas, M.; Bliss, D.W.; Brower, W.S.; Masek, G.; Paar, H.P.; Gronberg, J.; Korte, C.M.; Kutschke, R.; Menary, S.; Morrison, R.J.; Nakanishi, S.; Nelson, H.N.; Nelson, T.K.; Qiao, C.; Richman, J.D.; Roberts, D.; Ryd, A.; Tajima, H.; Witherell, M.S.; Balest, R.; Cho, K.; Ford, W.T.; Lohner, M.; Park, H.; Rankin, P.; Smith, J.G.; Alexander, J.P.; Bebek, C.; Berger, B.E.; Berkelman, K.; Bloom, K.; Browder, T.E.; Cassel, D.G.; Cho, H.A.; Coffman, D.M.; Crowcroft, D.S.; Dickson, M.; Drell, P.S.; Dumas, D.J.; Ehrlich, R.; Elia, R.; Gaidarev, P.; Garcia-Sciveres, M.; Gittelman, B.; Gray, S.W.; Hartill, D.L.; Heltsley, B.K.; Henderson, S.; Jones, C.D.; Jones, S.L.; Kandaswamy, J.; Katayama, N.; Kim, P.C.; Kreinick, D.L.; Lee, T.; Liu, Y.; Ludwig, G.S.; Masui, J.; Mevissen, J.; Mistry, N.B.; Ng, C.R.; Nordberg, E.; Patterson, J.R.; Peterson, D.; Riley, D.; Soffer, A.; Avery, P.; Freyberger, A.; Lingel, K.; Rodriguez, J.; Yang, S.; Yelton, J.; Brandenburg, G.; Cinabro, D.; Liu, T.; Saulnier, M.; Wilson, R.; Yamamoto, H.; Bergfeld, T.; Eisenstein, B.I.; Ernst, J.

    1995-01-01

    Using 2.7 fb -1 of data taken with the CLEO II detector, we have searched for CP violation in the charm system. We looked for asymmetries in the number of decays of D 0 's and bar D 0 's to the CP eigenstates K + K - , K S 0 φ, and K S 0 π 0 . Confidence intervals (90%) on these asymmetries were found to be -0.020 KK KS 0 φ KS 0 π 0 <0.031, respectively

  16. A Chiang-type lagrangian in CP^2

    Science.gov (United States)

    Cannas da Silva, Ana

    2018-03-01

    We analyse a monotone lagrangian in CP^2 that is hamiltonian isotopic to the standard lagrangian RP^2, yet exhibits a distinguishing behaviour under reduction by one of the toric circle actions, namely it intersects transversally the reduction level set and it projects one-to-one onto a great circle in CP^1. This lagrangian thus provides an example of embedded composition fitting work of Wehrheim-Woodward and Weinstein.

  17. A violation of CP symmetry in B meson decays

    International Nuclear Information System (INIS)

    Karyotakis, Y.; Monchenault, G.H. de

    2002-01-01

    This article reviews the issue of CP-violation and reports the most recent results about the observation of large CP asymmetries in the decay of neutral B-mesons. Some of the CP asymmetries in the neutral B-meson decay are expected to be large. CP-violation always involves quantum mechanical interference. This occurs for instance when there are 2 paths for a particle to decay into a given final state. The interference between the mixing-induced amplitude (B 0 → B-bar 0 → f) and the decay amplitude (B 0 → f) to a CP eigenstate f leads to a time dependent CP asymmetry that can be interpreted in terms of the angles of the unitary triangle (sin(2β)). The experimental challenge comes from the fact that B decays to some CP eigenstates have very small branching ratios and low efficiencies for complete reconstruction of the final state. It is therefore necessary to produce a very large number of B-mesons to perform a CP-measurement. To make the measurement possible, a new type of e + e - collider, called asymmetric B-factory has been designed. 2 asymmetric B-factories are operating in the world: PEP2 (Stanford, Usa) fitted with the Babar detector and KEK-B (Japan) which hosts Belle detector. The measurements given by Babar and Belle are in good agreement and can be combined. The average value is sin(2β) = 0.78 ± 0.08 and this value is in excellent agreement with the standard model predictions based on available experimental data. (A.C.)

  18. The N-terminal leucine-zipper motif in PTRF/cavin-1 is essential and sufficient for its caveolae-association

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Zhuang [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Laboratory of System Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Zou, Xinle [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Wang, Hongzhong; Lei, Jigang; Wu, Yuan [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Laboratory of System Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Liao, Kan, E-mail: kliao@sibs.ac.cn [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Laboratory of System Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China)

    2015-01-16

    Highlight: • The N-terminal leucine-zipper motif in PTRF/cavin-1 determines caveolar association. • Different cellular localization of PTRF/cavin-1 influences its serine 389 and 391 phosphorylation state. • PTRF/cavin-1 regulates cell motility via its caveolar association. - Abstract: PTRF/cavin-1 is a protein of two lives. Its reported functions in ribosomal RNA synthesis and in caveolae formation happen in two different cellular locations: nucleus vs. plasma membrane. Here, we identified that the N-terminal leucine-zipper motif in PTRF/cavin-1 was essential for the protein to be associated with caveolae in plasma membrane. It could counteract the effect of nuclear localization sequence in the molecule (AA 235–251). Deletion of this leucine-zipper motif from PTRF/cavin-1 caused the mutant to be exclusively localized in nuclei. The fusion of this leucine-zipper motif with histone 2A, which is a nuclear protein, could induce the fusion protein to be exported from nucleus. Cell migration was greatly inhibited in PTRF/cavin-1{sup −/−} mouse embryonic fibroblasts (MEFs). The inhibited cell motility could only be rescued by exogenous cavin-1 but not the leucine-zipper motif deleted cavin-1 mutant. Plasma membrane dynamics is an important factor in cell motility control. Our results suggested that the membrane dynamics in cell migration is affected by caveolae associated PTRF/cavin-1.

  19. The N-terminal leucine-zipper motif in PTRF/cavin-1 is essential and sufficient for its caveolae-association

    International Nuclear Information System (INIS)

    Wei, Zhuang; Zou, Xinle; Wang, Hongzhong; Lei, Jigang; Wu, Yuan; Liao, Kan

    2015-01-01

    Highlight: • The N-terminal leucine-zipper motif in PTRF/cavin-1 determines caveolar association. • Different cellular localization of PTRF/cavin-1 influences its serine 389 and 391 phosphorylation state. • PTRF/cavin-1 regulates cell motility via its caveolar association. - Abstract: PTRF/cavin-1 is a protein of two lives. Its reported functions in ribosomal RNA synthesis and in caveolae formation happen in two different cellular locations: nucleus vs. plasma membrane. Here, we identified that the N-terminal leucine-zipper motif in PTRF/cavin-1 was essential for the protein to be associated with caveolae in plasma membrane. It could counteract the effect of nuclear localization sequence in the molecule (AA 235–251). Deletion of this leucine-zipper motif from PTRF/cavin-1 caused the mutant to be exclusively localized in nuclei. The fusion of this leucine-zipper motif with histone 2A, which is a nuclear protein, could induce the fusion protein to be exported from nucleus. Cell migration was greatly inhibited in PTRF/cavin-1 −/− mouse embryonic fibroblasts (MEFs). The inhibited cell motility could only be rescued by exogenous cavin-1 but not the leucine-zipper motif deleted cavin-1 mutant. Plasma membrane dynamics is an important factor in cell motility control. Our results suggested that the membrane dynamics in cell migration is affected by caveolae associated PTRF/cavin-1

  20. Report of the CP-violation working group

    International Nuclear Information System (INIS)

    Hoffman, C.M.

    1982-01-01

    The CP-Violation Working Group met twice during the workshop. A nice summary of our present knowledge of CP-violation was presented in the talk by Prof. James W. Cronin. In the final paragraph of his talk, Prof. Cronin argues that higher precision experiments studying CP-violation at LAMPF II will be extremely important no matter what additional knowledge we acquire in the time before LAMPF II is constructed. The crucial issue at present is to uncover the underlying mechanism responsible for CP-violation. The Working Group heard several talks aimed at reviewing the theoretical status of CP-violation and the directions that future experimental efforts might take. These talks included: Kaon Experiments at KEK, T. Yamazaki, University of Tokyo; Mechanisms for CP Violation, P. Herczeg, Los Alamos; and The Experimental Status of eta 00 Experiments, J.W. Cronin, Univ. of Chicago. There were also extended discussions on which experiments appear to be the most important and how to best perform these measurements. A summary of these discussions is given

  1. A bottom-up approach to the strong CP problem

    Science.gov (United States)

    Diaz-Cruz, J. L.; Hollik, W. G.; Saldana-Salazar, U. J.

    2018-05-01

    The strong CP problem is one of many puzzles in the theoretical description of elementary particle physics that still lacks an explanation. While top-down solutions to that problem usually comprise new symmetries or fields or both, we want to present a rather bottom-up perspective. The main problem seems to be how to achieve small CP violation in the strong interactions despite the large CP violation in weak interactions. In this paper, we show that with minimal assumptions on the structure of mass (Yukawa) matrices, they do not contribute to the strong CP problem and thus we can provide a pathway to a solution of the strong CP problem within the structures of the Standard Model and no extension at the electroweak scale is needed. However, to address the flavor puzzle, models based on minimal SU(3) flavor groups leading to the proposed flavor matrices are favored. Though we refrain from an explicit UV completion of the Standard Model, we provide a simple requirement for such models not to show a strong CP problem by construction.

  2. CP-violation and Todd effects at lep-II

    International Nuclear Information System (INIS)

    Bilal, A.; Masso, E.; Rujula, A. de

    1991-01-01

    LEP-II will be a tool study CP-violation in processes involving vector bosons, and will test in particular the CP properties of the coupling of photons and Z's to W-pairs. While it is difficult to observe truly CP-odd effects, it is easy to measure T-odd ones. The latter can originate from CP-violation, or from radiative corrections involving the absorptive part of the scattering amplitude. T-odd effects are interesting in themselves, in that they accurately test the standard model and are sensitive to its unmeasured ingredients, such as the WW→WW scattering amplitude of the masses of the top quark and the elementary scalar. The prediction of the standard T-odd effects is a necessary stepping stone in the search for an honest-to-goodness violation of CP in the pure gauge sector. We thoroughly analyse the T-odd observables in the e + e - →W + W - process within the standard model, as well as the extra effects to be expected if the γW + W - and/or ZW + W - vertices were to violate CP in a non-standard fashion. (orig.)

  3. A Cp-theory problem book compactness in function spaces

    CERN Document Server

    Tkachuk, Vladimir V

    2015-01-01

    This third volume in Vladimir Tkachuk's series on Cp-theory problems applies all modern methods of Cp-theory to study compactness-like properties in function spaces and introduces the reader to the theory of compact spaces widely used in Functional Analysis. The text is designed to bring a dedicated reader from basic topological principles to the frontiers of modern research covering a wide variety of topics in Cp-theory and general topology at the professional level.  The first volume, Topological and Function Spaces © 2011, provided an introduction from scratch to Cp-theory and general topology, preparing the reader for a professional understanding of Cp-theory in the last section of its main text. The second volume, Special Features of Function Spaces © 2014, continued from the first, giving reasonably complete coverage of Cp-theory, systematically introducing each of the major topics and providing 500 carefully selected problems and exercises with complete solutions. This third volume is self-contained...

  4. Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

    Science.gov (United States)

    Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

    2018-03-01

    Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

  5. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells

    KAUST Repository

    Takahashi, Yuta

    2017-05-05

    CpG islands (CGIs) are primarily promoter-associated genomic regions and are mostly unmethylated within highly methylated mammalian genomes. The mechanisms by which CGIs are protected from de novo methylation remain elusive. Here we show that insertion of CpG-free DNA into targeted CGIs induces de novo methylation of the entire CGI in human pluripotent stem cells (PSCs). The methylation status is stably maintained even after CpG-free DNA removal, extensive passaging, and differentiation. By targeting the DNA mismatch repair gene MLH1 CGI, we could generate a PSC model of a cancer-related epimutation. Furthermore, we successfully corrected aberrant imprinting in induced PSCs derived from an Angelman syndrome patient. Our results provide insights into how CpG-free DNA induces de novo CGI methylation and broaden the application of targeted epigenome editing for a better understanding of human development and disease.

  6. Measurement of the direct $CP$-violating parameter $A_{CP}$ in the decay $D^+ \\to K^-\\pi^+\\pi^+$

    CERN Document Server

    Abazov, Victor Mukhamedovich; Acharya, Bannanje Sripath; Adams, Mark Raymond; Adams, Todd; Agnew, James P; Alexeev, Guennadi D; Alkhazov, Georgiy D; Alton, Andrew K; Askew, Andrew Warren; Atkins, Scott; Augsten, Kamil; Avila, Carlos A; Badaud, Frederique; Bagby, Linda F; Baldin, Boris; Bandurin, Dmitry V; Banerjee, Sunanda; Barberis, Emanuela; Baringer, Philip S; Bartlett, JFrederick; Bassler, Ursula Rita; Bazterra, Victor; Bean, Alice L; Begalli, Marcia; Bellantoni, Leo; Beri, Suman B; Bernardi, Gregorio; Bernhard, Ralf Patrick; Bertram, Iain A; Besancon, Marc; Beuselinck, Raymond; Bhat, Pushpalatha C; Bhatia, Sudeep; Bhatnagar, Vipin; Blazey, Gerald Charles; Blessing, Susan K; Bloom, Kenneth A; Boehnlein, Amber S; Boline, Daniel Dooley; Boos, Edward E; Borissov, Guennadi; Borysova, Maryna; Brandt, Andrew; Brandt, Oleg; Brock, Raymond L; Bross, Alan D; Brown, Duncan Paul; Bu, Xue-Bing; Buehler, Marc; Buescher, Volker; Bunichev, Viacheslav Yevgenyevich; Burdin, Sergey; Buszello, Claus Peter; Camacho-Perez, Enrique; Casey, Brendan Cameron Kieran; Castilla-Valdez, Heriberto; Caughron, Seth Aaron; Chakrabarti, Subhendu; Chan, Kwok Ming Leo; Chandra, Avdhesh; Chapon, Emilien; Chen, Guo; Cho, Sung-Woong; Choi, Suyong; Choudhary, Brajesh C; Cihangir, Selcuk; Claes, Daniel R; Clutter, Justace Randall; Cooke, Michael P; Cooper, William Edward; Corcoran, Marjorie D; Couderc, Fabrice; Cousinou, Marie-Claude; Cutts, David; Das, Amitabha; Davies, Gavin John; de Jong, Sijbrand Jan; De La Cruz-Burelo, Eduard; Deliot, Frederic; Demina, Regina; Denisov, Dmitri S; Denisov, Sergei P; Desai, Satish Vijay; Deterre, Cecile; DeVaughan, Kayle Otis; Diehl, HThomas; Diesburg, Michael; Ding, Pengfei; Dominguez, DAaron M; Dubey, Abhinav Kumar; Dudko, Lev V; Duperrin, Arnaud; Dutt, Suneel; Eads, Michael T; Edmunds, Daniel L; Ellison, John A; Elvira, VDaniel; Enari, Yuji; Evans, Harold G; Evdokimov, Valeri N; Faure, Alexandre; Feng, Lei; Ferbel, Thomas; Fiedler, Frank; Filthaut, Frank; Fisher, Wade Cameron; Fisk, HEugene; Fortner, Michael R; Fox, Harald; Fuess, Stuart C; Garbincius, Peter H; Garcia-Bellido, Aran; Garcia-Gonzalez, Jose Andres; Gavrilov, Vladimir B; Geng, Weigang; Gerber, Cecilia Elena; Gershtein, Yuri S; Ginther, George E; Gogota, Olga; Golovanov, Georgy Anatolievich; Grannis, Paul D; Greder, Sebastien; Greenlee, Herbert B; Grenier, Gerald Jean; Gris, Phillipe Luc; Grivaz, Jean-Francois; Grohsjean, Alexander; Gruenendahl, Stefan; Gruenewald, Martin Werner; Guillemin, Thibault; Gutierrez, Gaston R; Gutierrez, Phillip; Haley, Joseph Glenn Biddle; Han, Liang; Harder, Kristian; Harel, Amnon; Hauptman, John Michael; Hays, Jonathan M; Head, Tim; Hebbeker, Thomas; Hedin, David R; Hegab, Hatim; Heinson, Ann; Heintz, Ulrich; Hensel, Carsten; Heredia-De La Cruz, Ivan; Herner, Kenneth Richard; Hesketh, Gavin G; Hildreth, Michael D; Hirosky, Robert James; Hoang, Trang; Hobbs, John D; Hoeneisen, Bruce; Hogan, Julie; Hohlfeld, Mark; Holzbauer, Jenny Lyn; Howley, Ian James; Hubacek, Zdenek; Hynek, Vlastislav; Iashvili, Ia; Ilchenko, Yuriy; Illingworth, Robert A; Ito, Albert S; Jabeen, Shabnam; Jaffre, Michel J; Jayasinghe, Ayesh; Jeong, Min-Soo; Jesik, Richard L; Jiang, Peng; Johns, Kenneth Arthur; Johnson, Emily; Johnson, Marvin E; Jonckheere, Alan M; Jonsson, Per Martin; Joshi, Jyoti; Jung, Andreas Werner; Juste, Aurelio; Kajfasz, Eric; Karmanov, Dmitriy Y; Katsanos, Ioannis; Kaur, Manbir; Kehoe, Robert Leo Patrick; Kermiche, Smain; Khalatyan, Norayr; Khanov, Alexander; Kharchilava, Avto; Kharzheev, Yuri N; Kiselevich, Ivan Lvovich; Kohli, Jatinder M; Kozelov, Alexander V; Kraus, James Alexander; Kumar, Ashish; Kupco, Alexander; Kurca, Tibor; Kuzmin, Valentin Alexandrovich; Lammers, Sabine Wedam; Lebrun, Patrice; Lee, Hyeon-Seung; Lee, Seh-Wook; Lee, William M; Lei, Xiaowen; Lellouch, Jeremie; Li, Dikai; Li, Hengne; Li, Liang; Li, Qi-Zhong; Lim, Jeong Ku; Lincoln, Donald W; Linnemann, James Thomas; Lipaev, Vladimir V; Lipton, Ronald J; Liu, Huanzhao; Liu, Yanwen; Lobodenko, Alexandre; Lokajicek, Milos; Lopes de Sa, Rafael; Luna-Garcia, Rene; Lyon, Adam Leonard; Maciel, Arthur KA; Madar, Romain; Magana-Villalba, Ricardo; Malik, Sudhir; Malyshev, Vladimir L; Mansour, Jason; Martinez-Ortega, Jorge; McCarthy, Robert L; Mcgivern, Carrie Lynne; Meijer, Melvin M; Melnitchouk, Alexander S; Menezes, Diego D; Mercadante, Pedro Galli; Merkin, Mikhail M; Meyer, Arnd; Meyer, Jorg Manfred; Miconi, Florian; Mondal, Naba K; Mulhearn, Michael James; Nagy, Elemer; Narain, Meenakshi; Nayyar, Ruchika; Neal, Homer A; Negret, Juan Pablo; Neustroev, Petr V; Nguyen, Huong Thi; Nunnemann, Thomas P; Hernandez Orduna, Jose de Jesus; Osman, Nicolas Ahmed; Osta, Jyotsna; Pal, Arnab; Parashar, Neeti; Parihar, Vivek; Park, Sung Keun; Partridge, Richard A; Parua, Nirmalya; Patwa, Abid; Penning, Bjoern; Perfilov, Maxim Anatolyevich; Peters, Reinhild Yvonne Fatima; Petridis, Konstantinos; Petrillo, Gianluca; Petroff, Pierre; Pleier, Marc-Andre; Podstavkov, Vladimir M; Popov, Alexey V; Prewitt, Michelle; Price, Darren; Prokopenko, Nikolay N; Qian, Jianming; Quadt, Arnulf; Quinn, Breese; Ratoff, Peter N; Razumov, Ivan A; Ripp-Baudot, Isabelle; Rizatdinova, Flera; Rominsky, Mandy Kathleen; Ross, Anthony; Royon, Christophe; Rubinov, Paul Michael; Ruchti, Randal C; Sajot, Gerard; Sanchez-Hernandez, Alberto; Sanders, Michiel P; Santos, Angelo Souza; Savage, David G; Savitskyi, Mykola; Sawyer, HLee; Scanlon, Timothy P; Schamberger, RDean; Scheglov, Yury A; Schellman, Heidi M; Schwanenberger, Christian; Schwienhorst, Reinhard H; Sekaric, Jadranka; Severini, Horst; Shabalina, Elizaveta K; Shary, Viacheslav V; Shaw, Savanna; Shchukin, Andrey A; Simak, Vladislav J; Skubic, Patrick Louis; Slattery, Paul F; Smirnov, Dmitri V; Snow, Gregory R; Snow, Joel Mark; Snyder, Scott Stuart; Soldner-Rembold, Stefan; Sonnenschein, Lars; Soustruznik, Karel; Stark, Jan; Stoyanova, Dina A; Strauss, Michael G; Suter, Louise; Svoisky, Peter V; Titov, Maxim; Tokmenin, Valeriy V; Tsai, Yun-Tse; Tsybychev, Dmitri; Tuchming, Boris; Tully, Christopher George T; Uvarov, Lev; Uvarov, Sergey L; Uzunyan, Sergey A; Van Kooten, Richard J; van Leeuwen, Willem M; Varelas, Nikos; Varnes, Erich W; Vasilyev, Igor A; Verkheev, Alexander Yurievich; Vertogradov, Leonid S; Verzocchi, Marco; Vesterinen, Mika; Vilanova, Didier; Vokac, Petr; Wahl, Horst D; Wang, Michael HLS; Warchol, Jadwiga; Watts, Gordon Thomas; Wayne, Mitchell R; Weichert, Jonas; Welty-Rieger, Leah Christine; Williams, Mark Richard James; Wilson, Graham Wallace; Wobisch, Markus; Wood, Darien Robert; Wyatt, Terence R; Xie, Yunhe; Yamada, Ryuji; Yang, Siqi; Yasuda, Takahiro; Yatsunenko, Yuriy A; Ye, Wanyu; Ye, Zhenyu; Yin, Hang; Yip, Kin; Youn, Sungwoo; Yu, Jiaming; Zennamo, Joseph; Zhao, Tianqi Gilbert; Zhou, Bing; Zhu, Junjie; Zielinski, Marek; Zieminska, Daria; Zivkovic, Lidija

    2014-12-11

    We measure the direct CP-violating parameter A_CP for the decay of the charged charm meson, D+ -> K-pi+pi+ (and charge conjugate), using the full 10.4 fb-1 sample of ppbar collisions at sqrt(s) = 1.96 TeV collected by the D0 detector at the Fermilab Tevatron collider. We extract the raw reconstructed charge asymmetry by fitting the invariant mass distributions for the sum and difference of charge-specific samples. This quantity is then corrected for detector-related asymmetries using data-driven methods and for possible physics asymmetries (from B -> D processes) using input from Monte Carlo simulation. We measure A_CP = [-0.16 +- 0.15 (stat.) +- 0.09 (syst.)]%, which is consistent with zero, as expected from the standard model prediction of CP conservation, and is the most precise measurement of this quantity to date

  7. CP trajectory diagram--a tool for a pictorial representation of CP and matter effects in neutrino oscillations

    International Nuclear Information System (INIS)

    Minakata, Hisakazu; Nunokawa, Hiroshi

    2003-01-01

    We introduce a 'CP trajectory diagram in bi-probability space' as a powerful tool for a pictorial representation of the genuine CP and the matter effects in neutrino oscillations. The existence of correlated ambiguity in the determination of CP-violating phase δ and the sign of Δm 13 2 is uncovered. The principles of tuning the beam energy for a given baseline distance are proposed to resolve the ambiguity and to maximize the CP-odd effect. We finally point out, quite contrary to what is usually believed, that the ambiguity may be resolved with ∼50% chance in the super-JHF experiment despite its relatively short baseline of 300 km

  8. A CpG-containing oligodeoxynucleotide as an efficient adjuvant counterbalancing the Th1/Th2 immune response in diphtheria-tetanus-pertussis vaccine.

    Science.gov (United States)

    Sugai, Toshiyuki; Mori, Masaaki; Nakazawa, Masatoshi; Ichino, Motohide; Naruto, Takuya; Kobayashi, Naoki; Kobayashi, Yoshinori; Minami, Mutsuhiko; Yokota, Shumpei

    2005-11-16

    Adjuvants in vaccines are immune stimulants that play an important role in the induction of effective and appropriate immune responses to vaccine component(s). Diphtheria-tetanus-pertussis (DPT) vaccine contains not only aluminum hydrate (alum) to enhance the immune response to the vaccine ingredients, but also, both for that purpose and as a principal ingredient, pertussis toxin (PT). However, both adjuvants strongly promote T helper (Th) 2 type immune responses. Th1 and Th2 type immune responses are counterbalanced in vivo, and a Th2-prone immune response is not effective against intracellular infections but promotes IgE production, which is related to allergic disease. In this study, we used the CpG motif contained in oligodeoxynucleotide (CpG-ODN), which has an adjuvant effect and also induces the Th1 response, as an adjuvant to this vaccine, and we investigated its adjuvanticity and its potential to modulate immune responses to DPT vaccine. Administration of DPT vaccine with CpG-ODN (DPT-alum/ODN) to mice significantly reduced the total IgE levels and increased the anti-PT specific IgG2a titer in serum, in comparison with ordinary DPT vaccine (DPT-alum). Moreover, we investigated the antibody response to orally administrated ovalbumin (OVA) after vaccine administration. In the DPT-alum/ODN-administered group, the OVA specific IgE production in serum greatly decreased in comparison with that in the DPT-alum-administered group. These data indicate that CpG-ODN was not useful only as an efficient vaccine adjuvant but also shifted the immune responses substantially toward Th1 and modulated the Th1/Th2 immune response in DPT vaccine. These data suggested new applications of CpG-ODN as adjuvants in DPT vaccine.

  9. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

    Directory of Open Access Journals (Sweden)

    Launey Thomas

    2011-06-01

    Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  10. B-CLL cells acquire APC- and CTL-like phenotypic characteristics after stimulation with CpG ODN and IL-21

    Science.gov (United States)

    Hagn, Magdalena; Blackwell, Sue E.; Beyer, Thamara; Ebel, Verena; Fabricius, Dorit; Lindner, Stefanie; Stilgenbauer, Stefan; Simmet, Thomas; Tam, Constantine; Neeson, Paul; Trapani, Joseph A.; Schrezenmeier, Hubert; Weiner, George J.

    2014-01-01

    CpG oligodeoxynucleotides (CpG) and IL-21 are two promising agents for the treatment of B-cell chronic lymphocytic leukemia (B-CLL). Recently, we reported that the combination of CpG and IL-21 (CpG/IL-21) can induce granzyme B (GrB)-dependent apoptosis in B-CLL cells. Here, we demonstrate that treatment of B-CLL cells with CpG and IL-21 results in the development of antigen-presenting cell (APC)-like cells with cytotoxic features. These properties eventually give rise to B-CLL cell apoptosis, independently of their cytogenetic phenotype, whereas normal B-cell survival is not negatively affected by CpG/IL-21. APC- and CTL-typical molecules found to be up-regulated in CpG/IL-21-stimulated B-CLL cells include GrB, perforin, T-bet, monokine-induced by IFN-γ and IFN-γ-inducible protein 10 (IP-10), as well as molecules important for cell adhesion, antigen cross-presentation and costimulation. Also induced are molecules involved in GrB induction, trafficking and processing, whereas the GrB inhibitor Serpin B9 [formerly proteinase inhibitor-9 (PI-9)] is down-modulated by CpG/IL-21. In conclusion, CpG/IL-21-stimulated B-CLL cells acquire features that are reminiscent of killer dendritic cells, and which result in enhanced immunogenicity, cytotoxicity and apoptosis. Our results provide novel insights into the aberrant immune state of B-CLL cells and may establish a basis for the development of an innovative cellular vaccination approach in B-CLL. PMID:24497611

  11. CP determination and tests for CP or P violation by the V1V2 decay mode

    International Nuclear Information System (INIS)

    Nelson, C.A.

    1984-01-01

    A decay mode such as phiphi, UPSILONUPSILON, K/sup asterisk+/K/sup asterisk-/, or D/sup asterisk+/D/sup asterisk-/ can be used to distinguish between a neutral spin-0 technipion and a neutral spin-0 Higgs particle. By this generalization of phiphi parity test, the CP eigenvalue γ/sub C/P can be determined for an X particle of any spin J which decays CP invariantly into VV, or VV-bar, where each vector meson either decays into two spin-0 bosons, or is ω. The absence in a VV, or VV-bar, decay channel of sin2phi and sinphi terms in the azimuthal distribution is due to CP invariance and/or P invariance. For a V 1 V 2 decay channel without a V 1 bold-arrow-left-rightV 2 exchange property, and in a mode like K/sup asterisk+/K /sup asterisk0/, such terms would imply that P is violated. For a V 1 V 2 mode such as phiω where each vector meson is its own antiparticle, such terms would imply that both P and CP are violated; when CP invariance holds, the γ/sub C/P(-)/sup J/ eigenvalue of X can be determined provided certain amplitudes do not accidentally vanish

  12. CP-25 Attenuates the Activation of CD4+ T Cells Stimulated with Immunoglobulin D in Human.

    Science.gov (United States)

    Wu, Yu-Jing; Chen, Heng-Shi; Chen, Wen-Sheng; Dong, Jin; Dong, Xiao-Jie; Dai, Xing; Huang, Qiong; Wei, Wei

    2018-01-01

    Researchers have shown that the level of immunoglobulin D (IgD) is often elevated in patients with autoimmune diseases. The possible roles of IgD on the function of human T cell activation are still unclear. Paeoniflorin-6'- O -benzene sulfonate (code: CP-25), the chemistry structural modifications of paeoniflorin, was a novel drug of anti-inflammation and immunomodulation. The aims of this study were to determine if human CD4 + T cells could be activated by IgD via the IgD receptor (IgDR)-Lck pathway and whether the novel compound CP-25 could affect the activation of T cells by regulating Lck. Human CD4 + T cells were purified from peripheral blood mononuclear cells using microbeads. T cell viability and proliferation were detected by Cell Counting Kit-8 and CFSE Cell Proliferation Kit. Cytokines secreted by T cells were assessed with the Quantibody Human Inflammation Array. The binding affinity and expression of IgDR on T cells were detected by flow cytometry, and protein expression of IgDR, Lck, and P-Lck were analyzed by western blot. IgD was shown to bind to IgDR on CD4 + T cells in a concentration-dependent manner and stimulate the activation and proliferation of these cells by enhancing phosphorylation of the activating tyrosine residue of Lck (Tyr 394 ). CP-25 inhibited the IgD-stimulated activation and proliferation of CD4 + T cells, as well as the production of inflammatory cytokines; it was thus suggested that this process might be related to the downregulation of Lck (Tyr 394 ) phosphorylation. These results demonstrate that IgD amplifies the activation of CD4 + T cells, which could be mediated by Lck phosphorylation. Further, CP-25, via its ability to modulate Lck, is a novel potential therapeutic agent for the treatment of human autoimmune diseases.

  13. Deviations in upper limb function of the less-affected side in congenital hemiparesis

    NARCIS (Netherlands)

    Steenbergen, B.; Meulenbroek, R.G.J.

    2006-01-01

    In the present study we examined upper-limb function of the less-affected side in young adolescents with congenital hemiparesis (cerebral palsy: CP). Five participants with hemiparetic CP and five control participants performed a cyclical reach-and-grasp task with the less-affected hand towards

  14. Study of inclusive CP-asymmetries in B0 decays

    International Nuclear Information System (INIS)

    Huettmann, K.

    2000-01-01

    The object of the present thesis is the search for CP-violating effects in the mixing of neutral B mesons. For this the time-dependent CP asymmetry in the decay of completely inclusively reconstructed B 0 mesons was studied. The basis of the analysis were about 4.1 millions hadronic Z decays, which were token up in the years 1991-1995 with the ALEPH detector at the e + e - storage ring LEP at CERN. From the data b hadron decays were inclusively reconstructed by means of a search for secondary decay vertices. By a fit to the decay-time spectra od identified B 0 and anti B 0 decays the following value of the semileptonic asymmetry in the B d 0 - anti B d 0 system could be determined: a CP =0.016±0.034(stat.)±0.009(syst.). This value can be alternatively interpreted as a measurement of the CP-violating parameter Re ε B : Re εB/(1+ vertical stroke ε B vertical stroke 2 )=0.004±0.009(stat.)±0.002(syst.). Furthermore a combination of the results of this analysis with a further ALEPH measurement was performed. The value of a CP determined from this, which was obtained under regardment of the statistical correlation of both measurements as well as correlated systematic uncertainties, is: a CP =-0.013±0.026. The present result is compatible with the standard model prediction and yields no significant hint to CP violation in the B d 0 - anti B 0 d mixing. (orig.) [de

  15. Tuning structural motifs and alloying of bulk immiscible Mo-Cu bimetallic nanoparticles by gas-phase synthesis

    Science.gov (United States)

    Krishnan, Gopi; Verheijen, Marcel A.; Ten Brink, Gert H.; Palasantzas, George; Kooi, Bart J.

    2013-05-01

    Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape.Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still

  16. Sequence-based classification using discriminatory motif feature selection.

    Directory of Open Access Journals (Sweden)

    Hao Xiong

    Full Text Available Most existing methods for sequence-based classification use exhaustive feature generation, employing, for example, all k-mer patterns. The motivation behind such (enumerative approaches is to minimize the potential for overlooking important features. However, there are shortcomings to this strategy. First, practical constraints limit the scope of exhaustive feature generation to patterns of length ≤ k, such that potentially important, longer (> k predictors are not considered. Second, features so generated exhibit strong dependencies, which can complicate understanding of derived classification rules. Third, and most importantly, numerous irrelevant features are created. These concerns can compromise prediction and interpretation. While remedies have been proposed, they tend to be problem-specific and not broadly applicable. Here, we develop a generally applicable methodology, and an attendant software pipeline, that is predicated on discriminatory motif finding. In addition to the traditional training and validation partitions, our framework entails a third level of data partitioning, a discovery partition. A discriminatory motif finder is used on sequences and associated class labels in the discovery partition to yield a (small set of features. These features are then used as inputs to a classifier in the training partition. Finally, performance assessment occurs on the validation partition. Important attributes of our approach are its modularity (any discriminatory motif finder and any classifier can be deployed and its universality (all data, including sequences that are unaligned and/or of unequal length, can be accommodated. We illustrate our approach on two nucleosome occupancy datasets and a protein solubility dataset, previously analyzed using enumerative feature generation. Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is

  17. 77 FR 37098 - Proposed Collection; Comment Request for Form 8038-CP

    Science.gov (United States)

    2012-06-20

    ... 8038-CP AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice and request for comments... Form 8038-CP, Return for Credit Payments to Issuers of Qualified Bonds. DATES: Written comments should... Issuers of Qualified Bonds. OMB Number: 1545-2142. Form Number: Form 8038-CP. Abstract: Form 8038-CP...

  18. Characterization of the GXXXG motif in the first transmembrane segment of Japanese encephalitis virus precursor membrane (prM protein

    Directory of Open Access Journals (Sweden)

    Wu Suh-Chin

    2010-05-01

    Full Text Available Abstract The interaction between prM and E proteins in flavivirus-infected cells is a major driving force for the assembly of flavivirus particles. We used site-directed mutagenesis to study the potential role of the transmembrane domains of the prM proteins of Japanese encephalitis virus (JEV in prM-E heterodimerization as well as subviral particle formation. Alanine insertion scanning mutagenesis within the GXXXG motif in the first transmembrane segment of JEV prM protein affected the prM-E heterodimerization; its specificity was confirmed by replacing the two glycines of the GXXXG motif with alanine, leucine and valine. The GXXXG motif was found to be conserved in the JEV serocomplex viruses but not other flavivirus groups. These mutants with alanine inserted in the two prM transmembrane segments all impaired subviral particle formation in cell cultures. The prM transmembrane domains of JEV may play importation roles in prM-E heterodimerization and viral particle assembly.

  19. Indonesian Traditional Toys and the Development of Batik Motifs

    Directory of Open Access Journals (Sweden)

    Bagus Indrayana

    2016-06-01

    Full Text Available There is a wide array of traditional toys in Indonesia. In the past, traditional toys played an important role for skill and creativity development of children. Today, the position of traditional toys in the society is displaced by toys from large-scale manufacturers. Given the critical role of traditional toys for children’s motoric and social development, there is a need to develop media that can be used to promote these traditional products and strengthen their position in the public. We propose to use Batik as a way to effectively disseminate and promote traditional toys to the general public. Apart from this, using traditional toys to create new Batik motifs can have an economic value for the producers of Batik, promote Indonesian products and enrich the Indonesian Batik. This study aims to explore the variety of traditional toys, mainly from Klaten and Magelang, in the Central Java province of Indonesia, and use them as the basis for the development of Batik motif creation. This study used Trilogi Keseimbangan (or Harmony Trilogy aesthetic theory analytical approach that explains the creation of craft consists of the following phases: exploration, design, and materialization. The creation method in this study adopts Tiga Tahap Enam Langkah (Three Phases, Six Steps method offered in the theory. The finding in the field found that the traditional toys material used in Klaten and Magelang, mostly made from waste wood, plywood, and zinc. The manufacturing process is done manually by two or three craftsmen using a simple technology. The traditional toys are designed by the artisans mostly, although there may be designs from the clients. In addition, we also found that the traditional toys have never been used as a Batik motif. The traditional toys Batik motif presented in this work is researcher’s design. For the purposes of this study, we first research the variety of traditional toys available in the market today in Indonesia. We look

  20. Dimensionality of social networks using motifs and eigenvalues.

    Directory of Open Access Journals (Sweden)

    Anthony Bonato

    Full Text Available We consider the dimensionality of social networks, and develop experiments aimed at predicting that dimension. We find that a social network model with nodes and links sampled from an m-dimensional metric space with power-law distributed influence regions best fits samples from real-world networks when m scales logarithmically with the number of nodes of the network. This supports a logarithmic dimension hypothesis, and we provide evidence with two different social networks, Facebook and LinkedIn. Further, we employ two different methods for confirming the hypothesis: the first uses the distribution of motif counts, and the second exploits the eigenvalue distribution.