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Sample records for pst gene pairs

  1. INHERITANCE OF RESISTANCE TO PStV IN TRANSGENIC PEANUTS CONTAINING cp PStV GENE

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    Dwi Hapsoro, Hajrial Aswidinnoor, Rusmilah Suseno, Jumanto, dan Sudarsono .

    2011-11-01

    Full Text Available Inheritance of Resistance to PStV in Transgenic Peanuts Containing cp PStV Gene. We have obtained transgenic peanut lines containing coat protein gene of PStV. To get maximal use of the transgenic character in a breeding program, it is necessary that the transgene is also stably inherited and expressed.  This experiment was conducted from June 2002 – January 2005 at Plant Molecular Biology Laboratory, Bogor Agricultural University, and Queensland Agricultural Biotechnology Center, The University of Queensland, Australia. The research aimed (1 to test whether PStV cp transgene was functional in progenies derived from crosses between transgenic peaanut plants containing PStV cp gene and non-transgenic ones and (2 to determine pattern of inheritance of resistance to PStV as a result of PStV  cp gene action. Several crosses were made between trangenic peanut cv.Gajah resistant to PStV (T4 generation and non-transgenic peanut line WS susceptible to PStV. The F1 and F2 populations were mechanically inoculated with PStV two weeks after planting. The experiment showed that all plants in the F1 population were less susceptible to PStV, suggesting that the transgene was partially dominant.  Phenotipic segregation in F2 population was not Mendelian with the appearance of quick and slow recovery plants and the number of resistant plants being more than expected. However, the proportion of transgenic and non-transgenic plants followed 3:1 ratio, which was Mendelian.

  2. Parallel Evolution and Horizontal Gene Transfer of the pst Operon in Firmicutes from Oligotrophic Environments

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    Alejandra Moreno-Letelier

    2011-01-01

    Full Text Available The high affinity phosphate transport system (pst is crucial for phosphate uptake in oligotrophic environments. Cuatro Cienegas Basin (CCB has extremely low P levels and its endemic Bacillus are closely related to oligotrophic marine Firmicutes. Thus, we expected the pst operon of CCB to share the same evolutionary history and protein similarity to marine Firmicutes. Orthologs of the pst operon were searched in 55 genomes of Firmicutes and 13 outgroups. Phylogenetic reconstructions were performed for the pst operon and 14 concatenated housekeeping genes using maximum likelihood methods. Conserved domains and 3D structures of the phosphate-binding protein (PstS were also analyzed. The pst operon of Firmicutes shows two highly divergent clades with no correlation to the type of habitat nor a phylogenetic congruence, suggesting horizontal gene transfer. Despite sequence divergence, the PstS protein had a similar 3D structure, which could be due to parallel evolution after horizontal gene transfer events.

  3. [Cloning and expression of a class II chitin synthase gene PstChs II from the rust fungus Puccinia striiformis].

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    Liang, Xiaofei; Liu, Bo; Zhu, Lin; Zhang, Xiaoyu; Wang, Xiaojie; Huang, Lili; Kang, Zhensheng

    2009-12-01

    To clone the chitin synthase gene PstChs II from Puccinia striiformis and to analyze its expression pattern. We isolated the cDNA and genomic DNA of PstChs II via RT-PCR and PCR,analyzed the sequences with different bioinformatic tools, characterized the gene expression pattern via real-time PCR. The coding region of PstChs II (Genbank accession no: GQ329851), interrupted by 15 introns, corresponded to a 2727 bp open reading frame encoding 908 amino acids. PstChs II showed a highest 94% similarity to PgtChs II from Puccinia graminis. PstChs II had 7 transmembrance regions and several conserved chitin synthase domains and motifs such as "QXRRW", "GXGPL" and "DXD". PstChs II belonged to the class II sub-family and had a closer phylogenetic relationship to its homologs from basidiomycetes than those from ascomycetes. PstChs II expression level increased by 10-fold at the urediospore germination stage. PstChs II might be involved in the cell wall synthesis during the germ tube elongation process. The cloning and expression analysis of PstChs II served as a good foundation for further analyzing the role of this gene in the pathogenesis process.

  4. Polimorfismo no gene GH1-PstI associado a características corporais de linhagens de tilápia-do-nilo Polymorphism in the GH1-PstI gene associated to corporal characteristics in Nile tilapia strains

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    Danielly Veloso Blanck

    2009-06-01

    Full Text Available O objetivo deste trabalho foi determinar a associação de polimorfismos no gene do hormônio crescimento GH1 às características corporais, em linhagens de tilápia-do-nilo (Oreochromis niloticus. Foram coletados fragmentos da nadadeira caudal de exemplares das linhagens, aos cinco meses de idade, para as análises de "polymerase chain reaction-restriction fragment lenght polymorphism" (PCR-RFLP. Foram realizadas as seguintes mensurações: comprimento total, comprimento padrão, altura, largura e comprimento da cabeça. Realizou-se a amplificação de um fragmento com 652 pb do gene GH1, com subsequente restrição com a enzima PstI. Para a análise de associação do marcador molecular com as características quantitativas, utilizou-se o procedimento GLM do SAS. O polimorfismo descrito para o íntron 1, do gene GH1 da tilápia-do-nilo, apresentou correlação significativa com o comprimento total, comprimento padrão, altura e largura corporal. Foi verificado que o genótipo PstI+/- está associado ao melhor crescimento, independentemente da linhagem. A associação verificada pode ter ocorrido em razão do efeito direto da regulação do próprio gene GH.The objective of this study was to determine the association polymorphisms in growth hormone gene GH1 with the corporal characteristics in Nile tilapia (Oreochromis niloticus strains. Fragments of the caudal fin were collected from 5-month old fishes for analysis by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP. The following measurements were accomplished: total length, standard length, height, width, and head length. A fragment with 652 bp of the GH1 gene was amplified with subsequent restriction with the enzyme PstI. For the analysis of the association of the molecular marker with the quantitative traits the SAS GLM procedure was used. The polymorphism described for the intron 1 of the GH1 gene of Nile tilapia had significant correlation with total length

  5. The polymorphism of CYP2E1 Rsa I/Pst I gene and susceptibility to respiratory system cancer: a systematic review and meta-analysis of 34 studies.

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    Xu, Li; Yang, Mingyuan; Zhao, Tiejun; Jin, Hai; Xu, Zhiyun; Li, Ming; Chen, Hezhong

    2014-12-01

    The purpose of this articles is to determine whether the cytochrome P450 2E1 (CYP2E1) Rsa I/Pst I gene polymorphism is correlated with respiratory system cancers. Respiratory system cancers included lung cancer, laryngeal cancer, nasopharyngeal cancer, and cancers of other respiratory organs, which are the most common malignant tumors worldwide; the significant relationship between CYP2E1 Rsa I/Pst I gene polymorphism and some respiratory system cancer have been reported, but results of some other studies are controversial. The pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to assess the association. PubMed, EMBASE, Cochrane Library Databases, China National Knowledge Infrastructure, and Wanfang Database (up to July 20, 2014) were searched for all case-control studies those mainly studied the relationship between CYP2E1 Rsa I/Pst I gene polymorphism and the susceptibility of respiratory system cancer. A total of 332 articles were collected, among which 34 studies that involved 7028 cases and 9822 controls fulfilled the inclusion criteria after being assessed by 2 reviewers. When stratified by cancer site, the C2/C2 polymorphism could increase the risk of nasopharyngeal cancer under the homozygote model (C2C2 vs C1C1: OR = 1.85, 95% CI = 1.20-2.85, P = 0.005) and recessive model (C2C2 vs C1C2/C1C1: OR = 1.89, 95% CI = 1.23-2.89, P = 0.003). Protection effect was found in lung cancer in heterozygote model (C1C2 vs C1C1: OR = 0.82, 95% CI = 0.74-0.91, P Rsa I/Pst I gene polymorphism may reduce the risk of respiratory system cancer. Furthermore, significant association was also found in Asian populations.

  6. Expression of myriapod pair rule gene orthologs

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    Janssen Ralf

    2011-02-01

    Full Text Available Abstract Background Segmentation is a hallmark of the arthropods; most knowledge about the molecular basis of arthropod segmentation comes from work on the fly Drosophila melanogaster. In this species a hierarchic cascade of segmentation genes subdivides the blastoderm stepwise into single segment wide regions. However, segmentation in the fly is a derived feature since all segments form virtually simultaneously. Conversely, in the vast majority of arthropods the posterior segments form one at a time from a posterior pre-segmental zone. The pair rule genes (PRGs comprise an important level of the Drosophila segmentation gene cascade and are indeed the first genes that are expressed in typical transverse stripes in the early embryo. Information on expression and function of PRGs outside the insects, however, is scarce. Results Here we present the expression of the pair rule gene orthologs in the pill millipede Glomeris marginata (Myriapoda: Diplopoda. We find evidence that these genes are involved in segmentation and that components of the hierarchic interaction of the gene network as found in insects may be conserved. We further provide evidence that segments are formed in a single-segment periodicity rather than in pairs of two like in another myriapod, the centipede Strigamia maritima. Finally we show that decoupling of dorsal and ventral segmentation in Glomeris appears already at the level of the PRGs. Conclusions Although the pair rule gene network is partially conserved among insects and myriapods, some aspects of PRG interaction are, as suggested by expression pattern analysis, convergent, even within the Myriapoda. Conserved expression patterns of PRGs in insects and myriapods, however, may represent ancestral features involved in segmenting the arthropod ancestor.

  7. Evolution of closely linked gene pairs in vertebrate genomes

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    Franck, E.; Hulsen, T.; Huynen, M.A.; Jong, de W.W.; Lunsen, N.H.; Madsen, O.

    2008-01-01

    The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of

  8. Evolution of closely linked gene pairs in vertebrate genomes.

    NARCIS (Netherlands)

    Franck, E.; Hulsen, T.; Huynen, M.A.; Jong, W.W.W. de; Lubsen, N.H.; Madsen, O.

    2008-01-01

    The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of

  9. Role of Phosphate Transport System Component PstB1 in Phosphate Internalization by Nostoc punctiforme.

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    Hudek, L; Premachandra, D; Webster, W A J; Bräu, L

    2016-11-01

    of active uptake systems. The Pst phosphate transport system is one such system, responsible for the internalization of phosphate when cells are in phosphate-limited environments. Our investigations reveal the presence of multiple Pst phosphate uptake systems that exist across three distinct operons in Nostoc punctiforme and functionally characterize the role of the gene product PstB1 as being crucial for the maintenance of phosphate accumulation. We demonstrate that the genes pstB2, pstB3, and pstB4 show alterations in expression to compensate for the deletion of pstB1 The overall outcomes of this work provide insights as to the complex transport mechanisms that exist in cyanobacteria like N. punctiforme, allowing them to thrive in low-phosphate environments. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  10. Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant.

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    Crépin, Sébastien; Lamarche, Martin G; Garneau, Philippe; Séguin, Julie; Proulx, Julie; Dozois, Charles M; Harel, Josée

    2008-11-28

    Avian pathogenic E. coli (APEC) are associated with extraintestinal diseases in poultry. The pstSCAB-phoU operon belongs to the Pho regulon and encodes the phosphate specific transport (Pst) system. A functional Pst system is required for full virulence in APEC and other bacteria and contributes to resistance of APEC to serum, to cationic antimicrobial peptides and acid shock. The global mechanisms contributing to the attenuation and decreased resistance of the APEC pst mutant to environmental stresses have not been investigated at the transcriptional level. To determine the global effect of a pst mutation on gene expression, we compared the transcriptomes of APEC strain chi7122 and its isogenic pst mutant (K3) grown in phosphate-rich medium. Overall, 470 genes were differentially expressed by at least 1.5-fold. Interestingly, the pst mutant not only induced systems involved in phosphate acquisition and metabolism, despite phosphate availability, but also modulated stress response mechanisms. Indeed, transcriptional changes in genes associated with the general stress responses, including the oxidative stress response were among the major differences observed. Accordingly, the K3 strain was less resistant to reactive oxygen species (ROS) than the wild-type strain. In addition, the pst mutant demonstrated reduced expression of genes involved in lipopolysaccharide modifications and coding for cell surface components such as type 1 and F9 fimbriae. Phenotypic tests also established that the pst mutant was impaired in its capacity to produce type 1 fimbriae, as demonstrated by western blotting and agglutination of yeast cells, when compared to wild-type APEC strain chi7122. Overall, our data elucidated the effects of a pst mutation on the transcriptional response, and further support the role of the Pho regulon as part of a complex network contributing to phosphate homeostasis, adaptive stress responses, and E. coli virulence.

  11. Pst Pst (1896-1898. Een erotisch weekblad tussen naturalisme en utopie

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    Janna Coomans

    2012-12-01

    Full Text Available Amsterdam-based Pst Pst (1896-1898 was more than an erotic magazine. It not only tried to excite and provoke its audience with drawings of naked ladies and obscene jests, it also contained elements of two important literary trends: utopianism and naturalism. On the one hand, it was naturalistic in its attempt to uncover morals and sexual practices that were concealed in public discourse. The magazine ridiculed the double standard of Dutch society through jokes and prints about prostitution. On the other hand, it described the manifestations, mainly the nightlife, of the urban bohemian subculture to which it was - both geographically and mentally - connected. Pst Pst tried to dissociate itself from social conventions by creating a small world of its own. It announced mysterious erotic events, placed extravagant fake advertisements and depicted prostitutes as insatiable, merry young girls. Obviously, Pst Pst was not the only publication engaged in the production of erotica, but in this period it was the only erotic magazine, with corresponding characteristics such as a connection with a specific audience and an engagement with current affairs.

  12. Modeling gene regulation from paired expression and chromatin accessibility data.

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    Duren, Zhana; Chen, Xi; Jiang, Rui; Wang, Yong; Wong, Wing Hung

    2017-06-20

    The rapid increase of genome-wide datasets on gene expression, chromatin states, and transcription factor (TF) binding locations offers an exciting opportunity to interpret the information encoded in genomes and epigenomes. This task can be challenging as it requires joint modeling of context-specific activation of cis-regulatory elements (REs) and the effects on transcription of associated regulatory factors. To meet this challenge, we propose a statistical approach based on paired expression and chromatin accessibility (PECA) data across diverse cellular contexts. In our approach, we model (i) the localization to REs of chromatin regulators (CRs) based on their interaction with sequence-specific TFs, (ii) the activation of REs due to CRs that are localized to them, and (iii) the effect of TFs bound to activated REs on the transcription of target genes (TGs). The transcriptional regulatory network inferred by PECA provides a detailed view of how trans- and cis-regulatory elements work together to affect gene expression in a context-specific manner. We illustrate the feasibility of this approach by analyzing paired expression and accessibility data from the mouse Encyclopedia of DNA Elements (ENCODE) and explore various applications of the resulting model.

  13. Dopamine genes and pathological gambling in discordant sib-pairs.

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    da Silva Lobo, Daniela Sabbatini; Vallada, Homero P; Knight, Joanne; Martins, Silvia S; Tavares, Hermano; Gentil, Valentim; Kennedy, James L

    2007-12-01

    Pathological gambling (PG) is an impulse control disorder that has been considered as a behavioral addiction. Recent studies have suggested the involvement of the dopaminergic system in addictions and impulse control disorders and associations of dopamine receptor genes (DRD1, DRD2, and DRD4) and PG have been reported. In the present study, 140 sib-pairs discordant for the diagnosis of PG (70 males and 70 females on each group) were recruited through the Gambling Outpatient Unit at the Institute of Psychiatry, University of Sao Paulo and were assessed by trained psychiatrists. A family-based association design was chosen to prevent population stratification. All subjects were genotyped for dopamine receptor genes (DRD1 -800 T/C, DRD2 TaqIA RFLP, DRD3 Ser9Gly, DRD4 48bp exon III VNTR, DRD5 (CA) repeat) and the dopamine transporter gene (SCL6A3 40 bp VNTR). Our results suggest the association of PG with DRD1 -800 T/C allele T (P = .03).

  14. The relation between the PST1 restriction fragment length ...

    African Journals Online (AJOL)

    in patients with coronary heart disease. In both cases the association is with the P2 allele (the allele not containing the PST1 cutting site). Prolonged exercise is known to increase steady-state plasma apo-AI concentrations. We investigated the effect of adaptation to endurance exercise on the association of the PST1 marker ...

  15. Expression of pair rule gene orthologs in the blastoderm of a myriapod: evidence for pair rule-like mechanisms?

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    Janssen Ralf

    2012-05-01

    Full Text Available Abstract Background A hallmark of Drosophila segmentation is the stepwise subdivision of the body into smaller and smaller units, and finally into the segments. This is achieved by the function of the well-understood segmentation gene cascade. The first molecular sign of a segmented body appears with the action of the pair rule genes, which are expressed as transversal stripes in alternating segments. Drosophila development, however, is derived, and in most other arthropods only the anterior body is patterned (almost simultaneously from a pre-existing field of cells; posterior segments are added sequentially from a posterior segment addition zone. A long-standing question is to what extent segmentation mechanisms known from Drosophila may be conserved in short-germ arthropods. Despite the derived developmental modes, it appears more likely that conserved mechanisms can be found in anterior patterning. Results Expression analysis of pair rule gene orthologs in the blastoderm of the pill millipede Glomeris marginata (Myriapoda: Diplopoda suggests that these genes are generally involved in segmenting the anterior embryo. We find that the Glomeris pairberry-1 ( pby-1 gene is expressed in a pair rule pattern that is also found in insects and a chelicerate, the mite Tetraynchus urticae. Other Glomeris pair rule gene orthologs are expressed in double segment wide domains in the blastoderm, which at subsequent stages split into two stripes in adjacent segments. Conclusions The expression patterns of the millipede pair rule gene orthologs resemble pair rule patterning in Drosophila and other insects, and thus represent evidence for the presence of an ancestral pair rule-like mechanism in myriapods. We discuss the possibilities that blastoderm patterning may be conserved in long-germ and short-germ arthropods, and that a posterior double segmental mechanism may be present in short-germ arthropods.

  16. Expression of pair rule gene orthologs in the blastoderm of a myriapod: evidence for pair rule-like mechanisms?

    Science.gov (United States)

    2012-01-01

    Background A hallmark of Drosophila segmentation is the stepwise subdivision of the body into smaller and smaller units, and finally into the segments. This is achieved by the function of the well-understood segmentation gene cascade. The first molecular sign of a segmented body appears with the action of the pair rule genes, which are expressed as transversal stripes in alternating segments. Drosophila development, however, is derived, and in most other arthropods only the anterior body is patterned (almost) simultaneously from a pre-existing field of cells; posterior segments are added sequentially from a posterior segment addition zone. A long-standing question is to what extent segmentation mechanisms known from Drosophila may be conserved in short-germ arthropods. Despite the derived developmental modes, it appears more likely that conserved mechanisms can be found in anterior patterning. Results Expression analysis of pair rule gene orthologs in the blastoderm of the pill millipede Glomeris marginata (Myriapoda: Diplopoda) suggests that these genes are generally involved in segmenting the anterior embryo. We find that the Glomeris pairberry-1 ( pby-1) gene is expressed in a pair rule pattern that is also found in insects and a chelicerate, the mite Tetraynchus urticae. Other Glomeris pair rule gene orthologs are expressed in double segment wide domains in the blastoderm, which at subsequent stages split into two stripes in adjacent segments. Conclusions The expression patterns of the millipede pair rule gene orthologs resemble pair rule patterning in Drosophila and other insects, and thus represent evidence for the presence of an ancestral pair rule-like mechanism in myriapods. We discuss the possibilities that blastoderm patterning may be conserved in long-germ and short-germ arthropods, and that a posterior double segmental mechanism may be present in short-germ arthropods. PMID:22595029

  17. Sublingual immunization with the phosphate-binding-protein (PstS) reduces oral colonization by Streptococcus mutans.

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    Ferreira, E L; Batista, M T; Cavalcante, R C M; Pegos, V R; Passos, H M; Silva, D A; Balan, A; Ferreira, L C S; Ferreira, R C C

    2016-10-01

    Bacterial ATP-binding cassette (ABC) transporters play a crucial role in the physiology and pathogenicity of different bacterial species. Components of ABC transporters have also been tested as target antigens for the development of vaccines against different bacterial species, such as those belonging to the Streptococcus genus. Streptococcus mutans is the etiological agent of dental caries, and previous studies have demonstrated that deletion of the gene encoding PstS, the substrate-binding component of the phosphate uptake system (Pst), reduced the adherence of the bacteria to abiotic surfaces. In the current study, we generated a recombinant form of the S. mutans PstS protein (rPstS) with preserved structural features, and we evaluated the induction of antibody responses in mice after sublingual mucosal immunization with a formulation containing the recombinant protein and an adjuvant derived from the heat-labile toxin from enterotoxigenic Escherichia coli strains. Mice immunized with rPstS exhibited systemic and secreted antibody responses, measured by the number of immunoglobulin A-secreting cells in draining lymph nodes. Serum antibodies raised in mice immunized with rPstS interfered with the adhesion of bacteria to the oral cavity of naive mice challenged with S. mutans. Similarly, mice actively immunized with rPstS were partially protected from oral colonization after challenge with the S. mutans NG8 strain. Therefore, our results indicate that S. mutans PstS is a potential target antigen capable of inducing specific and protective antibody responses after sublingual administration. Overall, these observations raise interesting perspectives for the development of vaccines to prevent dental caries. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. The Vibrio cholerae Pst2 phosphate transport system is upregulated in biofilms and contributes to biofilm-induced hyperinfectivity.

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    Mudrak, Benjamin; Tamayo, Rita

    2012-05-01

    Vibrio cholerae is the causative agent of the deadly diarrheal disease cholera. As part of its life cycle, V. cholerae persists in marine environments, where it forms surface-attached communities commonly described as biofilms. Evidence indicates that these biofilms constitute the infectious form of the pathogen during outbreaks. Previous work has shown that biofilm-derived V. cholerae cells, even when fully dispersed from the biofilm matrix, are vastly more infectious than planktonic (free-living) cells. Here, we sought to identify factors that contribute to biofilm-induced hyperinfectivity in V. cholerae, and we present evidence for one aspect of the molecular basis of this phenotype. We identified proteins upregulated during growth in biofilms and determined their contributions to the hyperinfectivity phenotype. We found that PstS2, the periplasmic component of the Pst2 phosphate uptake system, was enriched in biofilms. Another gene in the pst2 locus was transcriptionally upregulated in biofilms. Using the infant mouse model, we found that mutation of two pst2 components resulted in impaired colonization. Importantly, deletion of the Pst2 inner membrane complex caused a greater colonization defect after growth in a biofilm compared to shaking culture. Based on these data, we propose that V. cholerae cells in biofilms upregulate the Pst2 system and therefore gain an advantage upon entry into the host. Further characterization of factors contributing to biofilm-induced hyperinfectivity in V. cholerae will improve our understanding of the transmission of the bacteria from natural aquatic habitats to the human host.

  19. Human phenol sulfotransferases hP-PST and hM-PST activate propane 2-nitronate to a genotoxicant.

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    Kreis, P; Brandner, S; Coughtrie, M W; Pabel, U; Meinl, W; Glatt, H; Andrae, U

    2000-02-01

    The industrial solvent 2-nitropropane (2-NP) is a genotoxic hepatocarcinogen in rats. The genotoxicity of the compound in rats has been attributed to sulfotransferase-mediated formation of DNA-reactive nitrenium ions from the anionic form of 2-NP, propane 2-nitronate (P2N). Whether human sulfotransferases are capable of activating P2N is unknown. In the present study we have addressed this question by investigating the genotoxicity of P2N in various V79-derived cell lines engineered for expression of individual forms of human sulfotransferases, the phenol-sulfating and the monoamine-sulfating phenol sulfotransferases (hP-PST and hM-PST) and the human hydroxysteroid sulfotransferase (hHST). Genotoxicity was assessed by measuring the induction of DNA repair synthesis and by analyzing the formation of DNA modifications. P2N induced repair synthesis in V79-hP-PST and V79-hM-PST cells, whereas induction of repair synthesis in V79-hHST cells was negligible. P2N also resulted in the formation of 8-aminodeoxyguanosine and increased the level of 8-oxodeoxyguanosine in V79-hP-PST cells, but not in the parental V79-MZ cells, which do not show any sulfotransferase activity. Acetone oxime, the tautomeric form of the first reduction product of 2-NP, 2-nitrosopropane, was inactive in all cell lines. The results show that the human phenol sulfotransferases P-PST and M-PST are capable of metabolically activating P2N (P-PST > M-PST) and that the underlying mechanism is apparently identical to that resulting in the activation of P2N in rat liver, where 2-NP causes carcinomas. These results support the notion that 2-NP should be regarded as a potential human carcinogen.

  20. Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium.

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    Catherine Cheng

    Full Text Available The phosphate-specific transport operon, pstSCAB-phoU, of Gram-negative bacteria is an essential part of the Pho regulon. Its key roles are to encode a high-affinity inorganic phosphate transport system and to prevent activation of PhoB in phosphate-rich environments. In general, mutations in pstSCAB-phoU lead to the constitutive expression of the Pho regulon. Previously, we constructed a pstCA deletion mutant of Citrobacter rodentium and found it to be attenuated for virulence in mice, its natural host. This attenuation was dependent on PhoB or PhoB-regulated gene(s because a phoB mutation restored virulence for mice to the pstCA mutant. To investigate how downstream genes may contribute to the virulence of C. rodentium, we used microarray analysis to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA mutant when grown in phosphate-rich medium. Overall 323 genes of the pstCA mutant were differentially expressed by at least 1.5-fold compared to the wild-type C. rodentium. Of these 145 were up-regulated and 178 were down-regulated. Differentially expressed genes included some involved in phosphate homoeostasis, cellular metabolism and protein metabolism. A large number of genes involved in stress responses and of unknown function were also differentially expressed, as were some virulence-associated genes. Up-regulated virulence-associated genes in the pstCA mutant included that for DegP, a serine protease, which appeared to be directly regulated by PhoB. Down-regulated genes included those for the production of the urease, flagella, NleG8 (a type III-secreted protein and the tad focus (which encodes type IVb pili in Yersinia enterocolitica. Infection studies using C57/BL6 mice showed that DegP and NleG8 play a role in bacterial virulence. Overall, our study provides evidence that Pho is a global regulator of gene expression in C. rodentium and indicates the presence of at least two previously unrecognized

  1. Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs.

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    Tian, Feng-Xia; Zang, Jian-Lei; Wang, Tan; Xie, Yu-Li; Zhang, Jin; Hu, Jian-Jun

    2015-01-01

    Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.

  2. Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs.

    Directory of Open Access Journals (Sweden)

    Feng-Xia Tian

    Full Text Available Aldehyde dehydrogenases (ALDHs constitute a superfamily of NAD(P+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.

  3. Homologue Pairing in Flies and Mammals: Gene Regulation When Two Are Involved

    Directory of Open Access Journals (Sweden)

    Manasi S. Apte

    2012-01-01

    Full Text Available Chromosome pairing is usually discussed in the context of meiosis. Association of homologues in germ cells enables chromosome segregation and is necessary for fertility. A few organisms, such as flies, also pair their entire genomes in somatic cells. Most others, including mammals, display little homologue pairing outside of the germline. Experimental evidence from both flies and mammals suggests that communication between homologues contributes to normal genome regulation. This paper will contrast the role of pairing in transmitting information between homologues in flies and mammals. In mammals, somatic homologue pairing is tightly regulated, occurring at specific loci and in a developmentally regulated fashion. Inappropriate pairing, or loss of normal pairing, is associated with gene misregulation in some disease states. While homologue pairing in flies is capable of influencing gene expression, the significance of this for normal expression remains unknown. The sex chromosomes pose a particularly interesting situation, as females are able to pair X chromosomes, but males cannot. The contribution of homologue pairing to the biology of the X chromosome will also be discussed.

  4. Altered Regulation of the Diguanylate Cyclase YaiC Reduces Production of Type 1 Fimbriae in a Pst Mutant of Uropathogenic Escherichia coli CFT073.

    Science.gov (United States)

    Crépin, Sébastien; Porcheron, Gaëlle; Houle, Sébastien; Harel, Josée; Dozois, Charles M

    2017-12-15

    The pst gene cluster encodes the phosphate-specific transport (Pst) system. Inactivation of the Pst system constitutively activates the two-component regulatory system PhoBR and attenuates the virulence of pathogenic bacteria. In uropathogenic Escherichia coli strain CFT073, attenuation by inactivation of pst is predominantly attributed to the decreased expression of type 1 fimbriae. However, the molecular mechanisms connecting the Pst system and type 1 fimbriae are unknown. To address this, a transposon library was constructed in the pst mutant, and clones were tested for a regain in type 1 fimbrial production. Among them, the diguanylate cyclase encoded by yaiC ( adrA in Salmonella ) was identified to connect the Pst system and type 1 fimbrial expression. In the pst mutant, the decreased expression of type 1 fimbriae is connected by the induction of yaiC This is predominantly due to altered expression of the FimBE-like recombinase genes ipuA and ipbA , affecting at the same time the inversion of the fim promoter switch ( fimS ). In the pst mutant, inactivation of yaiC restored fim -dependent adhesion to bladder cells and virulence. Interestingly, the expression of yaiC was activated by PhoB, since transcription of yaiC was linked to the PhoB-dependent phoA-psiF operon. As YaiC is involved in cyclic di-GMP (c-di-GMP) biosynthesis, an increased accumulation of c-di-GMP was observed in the pst mutant. Hence, the results suggest that one mechanism by which deletion of the Pst system reduces the expression of type 1 fimbriae is through PhoBR-mediated activation of yaiC , which in turn increases the accumulation of c-di-GMP, represses the fim operon, and, consequently, attenuates virulence in the mouse urinary tract infection model. IMPORTANCE Urinary tract infections (UTIs) are common bacterial infections in humans. They are mainly caused by uropathogenic Escherichia coli (UPEC). We previously showed that interference with phosphate homeostasis decreases the

  5. Text generation from Taiwanese Sign Language using a PST-based language model for augmentative communication.

    Science.gov (United States)

    Wu, Chung-Hsien; Chiu, Yu-Hsien; Guo, Chi-Shiang

    2004-12-01

    This paper proposes a novel approach to the generation of Chinese sentences from ill-formed Taiwanese Sign Language (TSL) for people with hearing impairments. First, a sign icon-based virtual keyboard is constructed to provide a visualized interface to retrieve sign icons from a sign database. A proposed language model (LM), based on a predictive sentence template (PST) tree, integrates a statistical variable n-gram LM and linguistic constraints to deal with the translation problem from ill-formed sign sequences to grammatical written sentences. The PST tree trained by a corpus collected from the deaf schools was used to model the correspondence between signed and written Chinese. In addition, a set of phrase formation rules, based on trigger pair category, was derived for sentence pattern expansion. These approaches improved the efficiency of text generation and the accuracy of word prediction and, therefore, improved the input rate. For the assessment of practical communication aids, a reading-comprehension training program with ten profoundly deaf students was undertaken in a deaf school in Tainan, Taiwan. Evaluation results show that the literacy aptitude test and subjective satisfactory level are significantly improved.

  6. Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.).

    Science.gov (United States)

    Ho-Huu, Joan; Ronfort, Joëlle; De Mita, Stéphane; Bataillon, Thomas; Hochu, Isabelle; Weber, Audrey; Chantret, Nathalie

    2012-10-01

    Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selective pressures acting on gene copies immediately after the duplication event. The ratio of non-synonymous to synonymous substitution rates in protein-coding sequences provides a means to investigate selective pressures based on genic sequences. Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication. We studied three pairs of genes that are known to be involved in an interaction with symbiotic bacteria and were recently duplicated in the history of the Medicago genus (Fabaceae). We sequenced two pairs of polygalacturonase genes (Pg11-Pg3 and Pg11a-Pg11c) and one pair of auxine transporter-like genes (Lax2-Lax4) in 17 species belonging to the Medicago genus, and sought for molecular signatures of differentiation between copies. Selective histories revealed by these three signatures of molecular differentiation were found to be markedly different between each pair of paralogs. We found sites under positive selection in the Pg11 paralogs while Pg3 has mainly evolved under purifying selection. The most recent paralogs examined Pg11a and Pg11c, are both undergoing positive selection and might be acquiring new functions. Lax2 and Lax4 paralogs are both under strong purifying selection, but still underwent a temporary relaxation of purifying selection immediately after duplication. This study illustrates the variety of selective pressures undergone by duplicated genes and the effect of age of the duplication. We found that relaxation of selective constraints immediately after duplication might promote adaptive divergence.

  7. A proteomic analysis of penicillin resistance in Streptococcus pneumoniae reveals a novel role for PstS, a subunit of the phosphate ABC transporter.

    Science.gov (United States)

    Soualhine, Hafid; Brochu, Vicky; Ménard, François; Papadopoulou, Barbara; Weiss, Karl; Bergeron, Michel G; Légaré, Danielle; Drummelsmith, Jolyne; Ouellette, Marc

    2005-12-01

    Resistance to penicillin is widespread in the Gram-positive bacterium Streptococcus pneumoniae, and while several mutations are known to be implicated in resistance other mechanisms are likely to occur. We used a proteomic screen of two independent mutants in which resistance was selected in vitro. We found a number of differentially expressed proteins including PstS, a subunit of the phosphate ABC transporter of S. pneumoniae. This protein was increased in both mutants, a phenotype correlated to increased RNA expression of the entire phosphate ABC transporter operon. Inactivation of the pstS gene led to increased susceptibility to penicillin in the wild-type strain. To further link the expression of the ABC phosphate transporter with penicillin resistance, we looked at pstS mRNA levels in 12 independent clinical isolates sensitive and resistant to penicillin and found an excellent correlation between resistance and increased expression of pstS. Inactivation of pstS in one of the clinical isolates significantly reduced penicillin resistance. Global approaches are ideally suited for the discovery of novel factors in the biology of resistance.

  8. Promoter-sharing by different genes in human genome – CPNE1 and RBM12 gene pair as an example

    Directory of Open Access Journals (Sweden)

    Yiu Siu-Ming

    2008-10-01

    Full Text Available Abstract Background Regulation of gene expression plays important role in cellular functions. Co-regulation of different genes may indicate functional connection or even physical interaction between gene products. Thus analysis on genomic structures that may affect gene expression regulation could shed light on the functions of genes. Results In a whole genome analysis of alternative splicing events, we found that two distinct genes, copine I (CPNE1 and RNA binding motif protein 12 (RBM12, share the most 5' exons and therefore the promoter region in human. Further analysis identified many gene pairs in human genome that share the same promoters and 5' exons but have totally different coding sequences. Analysis of genomic and expressed sequences, either cDNAs or expressed sequence tags (ESTs for CPNE1 and RBM12, confirmed the conservation of this phenomenon during evolutionary courses. The co-expression of the two genes initiated from the same promoter is confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR in different tissues in both human and mouse. High degrees of sequence conservation among multiple species in the 5'UTR region common to CPNE1 and RBM12 were also identified. Conclusion Promoter and 5'UTR sharing between CPNE1 and RBM12 is observed in human, mouse and zebrafish. Conservation of this genomic structure in evolutionary courses indicates potential functional interaction between the two genes. More than 20 other gene pairs in human genome were found to have the similar genomic structure in a genome-wide analysis, and it may represent a unique pattern of genomic arrangement that may affect expression regulation of the corresponding genes.

  9. Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome sequencing.

    Science.gov (United States)

    Hu, Lijuan; Lin, Zhirui; Wu, Yanheng; Dong, Juqin; Zhao, Bo; Cheng, Yanbing; Huang, Peiyu; Xu, Lihua; Xia, Tianliang; Xiong, Dan; Wang, Hongbo; Li, Manzhi; Guo, Ling; Kieff, Elliott; Zeng, Yixin; Zhong, Qian; Zeng, Musheng

    2016-03-01

    The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through realtime PCR.We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.

  10. TABASCO: A single molecule, base-pair resolved gene expression simulator

    Directory of Open Access Journals (Sweden)

    Endy Drew

    2007-12-01

    Full Text Available Abstract Background Experimental studies of gene expression have identified some of the individual molecular components and elementary reactions that comprise and control cellular behavior. Given our current understanding of gene expression, and the goals of biotechnology research, both scientists and engineers would benefit from detailed simulators that can explicitly compute genome-wide expression levels as a function of individual molecular events, including the activities and interactions of molecules on DNA at single base pair resolution. However, for practical reasons including computational tractability, available simulators have not been able to represent genome-scale models of gene expression at this level of detail. Results Here we develop a simulator, TABASCO http://openwetware.org/wiki/TABASCO, which enables the precise representation of individual molecules and events in gene expression for genome-scale systems. We use a single molecule computational engine to track individual molecules interacting with and along nucleic acid polymers at single base resolution. Tabasco uses logical rules to automatically update and delimit the set of species and reactions that comprise a system during simulation, thereby avoiding the need for a priori specification of all possible combinations of molecules and reaction events. We confirm that single molecule, base-pair resolved simulation using TABASCO (Tabasco can accurately compute gene expression dynamics and, moving beyond previous simulators, provide for the direct representation of intermolecular events such as polymerase collisions and promoter occlusion. We demonstrate the computational capacity of Tabasco by simulating the entirety of gene expression during bacteriophage T7 infection; for reference, the 39,937 base pair T7 genome encodes 56 genes that are transcribed by two types of RNA polymerases active across 22 promoters. Conclusion Tabasco enables genome-scale simulation of

  11. Expression of polysialyltransferases (STX and PST) in adult rat olfactory bulb after an olfactory associative discrimination task.

    Science.gov (United States)

    Mione, J; Manrique, C; Duhoo, Y; Roman, F S; Guiraudie-Capraz, G

    2016-04-01

    Neuronal plasticity and neurogenesis occur in the adult hippocampus and in other brain structures such as the olfactory bulb and often involve the neural cell adhesion molecule NCAM. During an olfactory associative discrimination learning task, NCAM polysialylation triggers neuronal plasticity in the adult hippocampus. The PST enzyme likely modulates this polysialylation, but not STX, a second sialyltransferase. How the two polysialyltransferases are involved in the adult olfactory bulb remains unknown. We addressed this question by investigating the effect of olfactory associative learning on plasticity and neurogenesis. After a hippocampo-dependent olfactory associative task learning, we measured the expression of both PST and STX polysialyltransferases in the olfactory bulbs of adult rats using quantitative PCR. In parallel, immunohistochemistry was used to evaluate both NCAM polysialylation level and newly-born cells, with or without learning. After learning, no changes were observed neither in the expression level of PST and NCAM polysialylation, nor in STX gene expression level and newly-born cells number in the olfactory bulb. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Identification of fusion genes in breast cancer by paired-end RNA-sequencing.

    Science.gov (United States)

    Edgren, Henrik; Murumagi, Astrid; Kangaspeska, Sara; Nicorici, Daniel; Hongisto, Vesa; Kleivi, Kristine; Rye, Inga H; Nyberg, Sandra; Wolf, Maija; Borresen-Dale, Anne-Lise; Kallioniemi, Olli

    2011-01-01

    Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including the discovery of expressed fusion genes resulting from underlying genomic rearrangements. We applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival. In summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells.

  13. Low X/Y divergence in four pairs of papaya sex-linked genes.

    Science.gov (United States)

    Yu, Qingyi; Hou, Shaobin; Feltus, F Alex; Jones, Meghan R; Murray, Jan E; Veatch, Olivia; Lemke, Cornelia; Saw, Jimmy H; Moore, Richard C; Thimmapuram, Jyothi; Liu, Lei; Moore, Paul H; Alam, Maqsudul; Jiang, Jiming; Paterson, Andrew H; Ming, Ray

    2008-01-01

    Sex chromosomes in flowering plants, in contrast to those in animals, evolved relatively recently and only a few are heteromorphic. The homomorphic sex chromosomes of papaya show features of incipient sex chromosome evolution. We investigated the features of paired X- and Y-specific bacterial artificial chromosomes (BACs), and estimated the time of divergence in four pairs of sex-linked genes. We report the results of a comparative analysis of long contiguous genomic DNA sequences between the X and hermaphrodite Y (Y(h)) chromosomes. Numerous chromosomal rearrangements were detected in the male-specific region of the Y chromosome (MSY), including inversions, deletions, insertions, duplications and translocations, showing the dynamic evolutionary process on the MSY after recombination ceased. DNA sequence expansion was documented in the two regions of the MSY, demonstrating that the cytologically homomorphic sex chromosomes are heteromorphic at the molecular level. Analysis of sequence divergence between four X and Y(h) gene pairs resulted in a estimated age of divergence of between 0.5 and 2.2 million years, supporting a recent origin of the papaya sex chromosomes. Our findings indicate that sex chromosomes did not evolve at the family level in Caricaceae, and reinforce the theory that sex chromosomes evolve at the species level in some lineages.

  14. Chapter 3: The influence of porcine somatatropin (pST) on ...

    African Journals Online (AJOL)

    SStC Botha

    initial weight of 27.2 ± 2 kg were used to investigate the effect of porcine somatotropin (pST) administered for six weeks prior to slaughter ... bone, % fat or % lean meat, but a significant increase in percentage skin was found. Keywords: FCR, P2 back fat, pST, porcine somatotropin, pork, tissue yield. # Corresponding author.

  15. Linkage of the VNTR/insulin-gene and type I diabetes mellitus: Increased gene sharing in affected sibling pairs

    Energy Technology Data Exchange (ETDEWEB)

    Owerbach, D.; Gabbay, K.H. (Baylor College of Medicine, Houston, TX (United States))

    1994-05-01

    Ninety-six multiplex type I diabetic families were typed at the 5' flanking region of the insulin gene by using a PCR assay that better resolves the VNTR into multiple alleles. Affected sibling pairs shared 2, 1, and 0 VNTR alleles - identical by descent - at a frequency of .47, .45, and .08, respectively, a ratio that deviated from the expected 1:2:1 ratio (P<.001). These results confirm linkage of the chromosome 11p15.5 region with type I diabetes mellitus susceptibility. 20 refs., 2 tabs.

  16. Immune dysregulation and tumor-associated gene changes in recurrent respiratory papillomatosis: a paired microarray analysis.

    Science.gov (United States)

    DeVoti, James A; Rosenthal, David W; Wu, Rong; Abramson, Allan L; Steinberg, Bettie M; Bonagura, Vincent R

    2008-01-01

    Recurrent respiratory papillomas (RRP) are benign airway tumors, caused primarily by human papillomaviruses (HPV) types 6 and 11. The disease is characterized by multiple recurrences after surgical removal, with limited effective therapy. To identify novel targets for future therapy, we established transcriptional profiles for actively growing papillomas compared with autologous, clinically normal, laryngeal epithelia (adjacent tissue). Total ribonucleic acid (RNA) from 12 papillomas and 12 adjacent tissues were analyzed by microarray, and the matched sets of tissues compared by paired t test, to identify differentially expressed genes in papilloma tissues while minimizing variations intrinsic to individual patients. Quantitative polymerase chain reaction (PCR) was used to confirm the relative expression levels for a subset of genes. Within the 109 differentially expressed transcripts whose expression varied at least three-fold were two large groups of genes with related functions. The first group consisted of 18 genes related to host defense, including both innate and adaptive immunity. The second group contained 37 genes that likely contribute to growth of papillomas as benign tumors, since the altered pattern of expression also had been reported previously in many cancers. Our results support our previous studies that document a systemic T(H)2-like adaptive immune response in RRP, and suggest that there is a role for altered innate immunity in RRP as well. We propose that HPV 6 and 11 infection establishes a tumorigenic microenvironment characterized by alteration of both innate inflammatory signals and adaptive immune responses that prevent effective T(H)1-like response, in conjunction with altered expression of numerous genes that regulate cellular growth and differentiation.

  17. CIPDSS-PST: CIPDSS portfolio slection tool documentation and user's guide.

    Energy Technology Data Exchange (ETDEWEB)

    VanKuiken, J. C.; Jusko, M. J.; Samsa, M. E.; Decision and Information Sciences

    2008-06-27

    The Critical Infrastructure Protection Decision Support System--Portfolio Support Tool (CIPDSS-PST) provides a versatile and powerful tool for selecting, optimizing, and analyzing portfolios. The software introduces a compact interface that facilitates problem definition, constraint specification, and portfolio analysis. The tool also provides a simple screen design for comparing user-preferred choices with optimized selections. CIPDSS-PST uses a portable, efficient, mixed-integer optimization engine (lp{_}solve) to derive the optimal mix of projects that satisfies the constraints and maximizes the total portfolio utility. The CIPDSS-PST software can be readily applied to other nonportfolio, resource-constrained optimization problems.

  18. Frequent attenders in general practice: problem solving treatment (PST) provided by nurses

    NARCIS (Netherlands)

    Schreuder, B.; van Oppen, P.C.; van Marwijk, H.W.J.; Smit, J.H.; Stalman, W.A.B.

    2005-01-01

    Background: There is a need for assistance from primary care mental health workers in general practice in the Netherlands. General practitioners (GPs) experience an overload of frequent attenders suffering from psychological problems. Problem Solving Treatment (PST) is a brief psychological

  19. Integrated miRNA-risk gene-pathway pair network analysis provides prognostic biomarkers for gastric cancer

    Directory of Open Access Journals (Sweden)

    Cai H

    2016-05-01

    Full Text Available Hui Cai,1 Jiping Xu,2 Yifang Han,3 Zhengmao Lu,1 Ting Han,1 Yibo Ding,4 Liye Ma1 1Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai, 2Department of Medical Administration, Changhai Hospital, Second Military Medical University, Shanghai, 3Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 4Department of Epidemiology, Changhai Hospital, Second Military Medical University, Shanghai, People’s Republic of China Purpose: This study aimed to identify molecular prognostic biomarkers for gastric cancer. Methods: mRNA and miRNA expression profiles of eligible gastric cancer and control samples were downloaded from Gene Expression Omnibus to screen the differentially expressed genes (DEGs and differentially expressed miRNAs (DEmiRs, using MetaDE and limma packages, respectively. Target genes of the DEmiRs were also collected from both predictive and experimentally validated target databases of miRNAs. The overlapping genes between selected targets and DEGs were identified as risk genes, followed by functional enrichment analysis. Human pathways and their corresponding genes were downloaded from the Kyoto Encyclopedia of Genes and Genomes (KEGG database for the expression analysis of each pathway in gastric cancer samples. Next, co-pathway pairs were selected according to the Pearson correlation coefficients. Finally, the co-pathway pairs, miRNA–target pairs, and risk gene–pathway pairs were merged into a complex interaction network, the most important nodes (miRNAs/target genes/co-pathway pairs of which were selected by calculating their degrees.Results: Totally, 1,260 DEGs and 144 DEmiRs were identified. There were 336 risk genes found in the 9,572 miRNA–target pairs. Judging from the pathway expression files, 45 co-pathway pairs were screened out. There were 1,389 interactive pairs and 480 nodes in the integrated network. Among all nodes in the network, focal

  20. Mutation analysis of paired box 6 gene in inherited aniridia in northern China.

    Science.gov (United States)

    Chen, Peng; Zang, Xinjie; Sun, Dapeng; Wang, Ye; Wang, Yao; Zhao, Xiaowen; Zhang, Mohan; Xie, Lixin

    2013-01-01

    Aniridia is phenotypically and genetically heterogeneous. This study is to summarize the phenotypes and identify the underlying genetic cause of the paired box 6 (PAX6) gene responsible for aniridia in two three-generation Chinese families in northern China. A detailed family history and clinical data were collected from patients during an ophthalmologic examination. All exons and flanking intronic sequences of the PAX6 gene were amplified with PCR and screened for mutation with direct DNA sequencing. Haplotyping was used to confirm the mutation sequence. Real-time PCR was used to determine the PAX6 messenger ribonucleic acid(mRNA) level in patients with aniridia and in unaffected family members. The probands and other patients in the two families were affected with aniridia accompanied with or without congenital cataract. A heterozygous PAX6 mutation in exon 5 (c.112delC, p.Arg38GlyfsX16) was identified in FAMILY-1, which was predicted to generate a frameshift and created a premature termination codon. A heterozygous PAX6 mutation in exon 7 (c.362C>T, p.Ser121Leu) was identified in FAMILY-2. Each mutation cosegregated with the affected individuals in the family and did not exist in unaffected family members and 200 unrelated normal controls. The PAX6 messenger ribonucleic acid level was about 50% lower in patients with aniridia than in unaffected family members in FAMILY-1. The deletion mutation (c.112delC) in the PAX6 gene was first identified in a Chinese family with aniridia, congenital progressive cataract, developmental delay, or the absence of ulna. The mutation (c.362C>T, p.Ser121Leu) in the PAX6 gene was first identified in a patient with aniridia with congenital ptosis. We summarized the variable phenotypes among the patients, which expanded the phenotypic spectrum of aniridia in a different ethnic background.

  1. Using Self-Guided Treatment Software (ePST to Teach Clinicians How to Deliver Problem-Solving Treatment for Depression

    Directory of Open Access Journals (Sweden)

    James A. Cartreine

    2012-01-01

    Full Text Available Problem-solving treatment (PST offers a promising approach to the depression care; however, few PST training opportunities exist. A computer-guided, interactive media program has been developed to deliver PST electronically (ePST, directly to patients. The program is a six-session, weekly intervention modeled on an evidence-based PST protocol. Users are guided through each session by a clinician who is presented via hundreds of branching audio and video clips. Because expert clinician behaviors are modeled in the program, not only does the ePST program have the potential to deliver PST to patients but it may also serve as a training tool to teach clinicians how to deliver PST. Thirteen social workers and trainees used ePST self-instructionally and subsequently attended a day-long workshop on PST. Participants’ PST knowledge level increased significantly from baseline to post-ePST (P=.001 and did not increase significantly further after attending the subsequent workshop. Additionally, attending the workshop did not significantly increase the participants' skill at performing PST beyond the use of the ePST program. Using the ePST program appears to train novices to a sufficient level of competence to begin practicing PST under supervision. This self-instructional training method could enable PST for depression to be widely disseminated, although follow-up supervision is still required.

  2. Using Self-Guided Treatment Software (ePST) to Teach Clinicians How to Deliver Problem-Solving Treatment for Depression.

    Science.gov (United States)

    Cartreine, James A; Chang, Trina E; Seville, Janette L; Sandoval, Luis; Moore, John B; Xu, Shuai; Hegel, Mark T

    2012-01-01

    Problem-solving treatment (PST) offers a promising approach to the depression care; however, few PST training opportunities exist. A computer-guided, interactive media program has been developed to deliver PST electronically (ePST), directly to patients. The program is a six-session, weekly intervention modeled on an evidence-based PST protocol. Users are guided through each session by a clinician who is presented via hundreds of branching audio and video clips. Because expert clinician behaviors are modeled in the program, not only does the ePST program have the potential to deliver PST to patients but it may also serve as a training tool to teach clinicians how to deliver PST. Thirteen social workers and trainees used ePST self-instructionally and subsequently attended a day-long workshop on PST. Participants' PST knowledge level increased significantly from baseline to post-ePST (P = .001) and did not increase significantly further after attending the subsequent workshop. Additionally, attending the workshop did not significantly increase the participants' skill at performing PST beyond the use of the ePST program. Using the ePST program appears to train novices to a sufficient level of competence to begin practicing PST under supervision. This self-instructional training method could enable PST for depression to be widely disseminated, although follow-up supervision is still required.

  3. Analyzing State Sequences with Probabilistic Suffix Trees: The PST R Package

    Directory of Open Access Journals (Sweden)

    Alexis Gabadinho

    2016-08-01

    Full Text Available This article presents the PST R package for categorical sequence analysis with probabilistic suffix trees (PSTs, i.e., structures that store variable-length Markov chains (VLMCs. VLMCs allow to model high-order dependencies in categorical sequences with parsimonious models based on simple estimation procedures. The package is specifically adapted to the field of social sciences, as it allows for VLMC models to be learned from sets of individual sequences possibly containing missing values; in addition, the package is extended to account for case weights. This article describes how a VLMC model is learned from one or more categorical sequences and stored in a PST. The PST can then be used for sequence prediction, i.e., to assign a probability to whole observed or artificial sequences. This feature supports data mining applications such as the extraction of typical patterns and outliers. This article also introduces original visualization tools for both the model and the outcomes of sequence prediction. Other features such as functions for pattern mining and artificial sequence generation are described as well. The PST package also allows for the computation of probabilistic divergence between two models and the fitting of segmented VLMCs, where sub-models fitted to distinct strata of the learning sample are stored in a single PST.

  4. Gene expression profiling of lymphoblasts from autistic and nonaffected sib pairs: altered pathways in neuronal development and steroid biosynthesis.

    Directory of Open Access Journals (Sweden)

    Valerie W Hu

    2009-06-01

    Full Text Available Despite the identification of numerous autism susceptibility genes, the pathobiology of autism remains unknown. The present "case-control" study takes a global approach to understanding the molecular basis of autism spectrum disorders based upon large-scale gene expression profiling. DNA microarray analyses were conducted on lymphoblastoid cell lines from over 20 sib pairs in which one sibling had a diagnosis of autism and the other was not affected in order to identify biochemical and signaling pathways which are differentially regulated in cells from autistic and nonautistic siblings. Bioinformatics and gene ontological analyses of the data implicate genes which are involved in nervous system development, inflammation, and cytoskeletal organization, in addition to genes which may be relevant to gastrointestinal or other physiological symptoms often associated with autism. Moreover, the data further suggests that these processes may be modulated by cholesterol/steroid metabolism, especially at the level of androgenic hormones. Elevation of male hormones, in turn, has been suggested as a possible factor influencing susceptibility to autism, which affects approximately 4 times as many males as females. Preliminary metabolic profiling of steroid hormones in lymphoblastoid cell lines from several pairs of siblings reveals higher levels of testosterone in the autistic sibling, which is consistent with the increased expression of two genes involved in the steroidogenesis pathway. Global gene expression profiling of cultured cells from ASD probands thus serves as a window to underlying metabolic and signaling deficits that may be relevant to the pathobiology of autism.

  5. Filaggrin gene loss-of-function mutations explain discordance of atopic dermatitis within dizygotic twin pairs

    DEFF Research Database (Denmark)

    Thomsen, S. F.; Elmose, C.; Szecsi, P. B.

    2016-01-01

    no significant differences in risk for asthma by FLG mutation status in individuals with and without AD, respectively (P-value for interaction, 0.595). In 11 dizygotic twin pairs discordant for FLG mutation status, risk for AD was higher in the twin carrying the FLG mutation (five of 11 [45.5%] twins had...... for the presence and persistence of AD and explain the discordance of AD within dizygotic twin pairs. © 2016 The International Society of Dermatology...

  6. Authoring Effective Embedded Tutors: An Overview of the Extensible Problem Specific Tutor (xPST) System

    Science.gov (United States)

    Gilbert, Stephen B.; Blessing, Stephen B.; Guo, Enruo

    2015-01-01

    The Extensible Problem Specific Tutor (xPST) allows authors who are not cognitive scientists and not programmers to quickly create an intelligent tutoring system that provides instruction akin to a model-tracing tutor. Furthermore, this instruction is overlaid on existing software, so that the learner's interface does not have to be made from…

  7. The effect of porcine somatotropin (pST) and gender on production ...

    African Journals Online (AJOL)

    Eighteen F1 crossbred (commercial-type terminal crosses) pigs (boars, barrows and gilts) with an initial weight of 27.2 ± 2 kg were used to investigate the effect of porcine somatotropin (pST) administered for six weeks prior to slaughter on production parameters and tissue yield in the South African scenario. Pigs were ...

  8. Chapter 3: The influence of porcine somatatropin (pST) on ...

    African Journals Online (AJOL)

    SStC Botha

    Abstract. Eighteen F1 crossbred (commercial-type terminal crosses) pigs (boars, barrows and gilts) with an initial weight of 27.2 ± 2 kg were used to investigate the effect of porcine somatotropin (pST) administered for six weeks prior to slaughter on production parameters and tissue yield in the South African scenario. Pigs.

  9. DNA methylation and gene expression patterns in adipose tissue differ significantly within young adult monozygotic BMI-discordant twin pairs.

    Science.gov (United States)

    Pietiläinen, K H; Ismail, K; Järvinen, E; Heinonen, S; Tummers, M; Bollepalli, S; Lyle, R; Muniandy, M; Moilanen, E; Hakkarainen, A; Lundbom, J; Lundbom, N; Rissanen, A; Kaprio, J; Ollikainen, M

    2016-04-01

    Little is known about epigenetic alterations associated with subcutaneous adipose tissue (SAT) in obesity. Our aim was to study genome-wide DNA methylation and gene expression differences in SAT in monozygotic (MZ) twin pairs who are discordant for body mass index (BMI). This design completely matches lean and obese groups for genetic background, age, gender and shared environment. 14We analyzed DNA methylome and gene expression from SAT, together with body composition (magnetic resonance imaging/spectroscopy) and glucose tolerance test, lipids and C-reactive protein from 26 rare BMI-discordant (intrapair difference in BMI ⩾3 kg m(-2)) MZ twin pairs identified from 10 birth cohorts of young adult Finnish twins. We found 17 novel obesity-associated genes that were differentially methylated across the genome between heavy and lean co-twins. Nine of them were also differentially expressed. Pathway analyses indicated that dysregulation of SAT in obesity includes a paradoxical downregulation of lipo/adipogenesis and upregulation of inflammation and extracellular matrix remodeling. Furthermore, CpG sites whose methylation correlated with metabolically harmful fat depots (intra-abdominal and liver fat) also correlated with measures of insulin resistance, dyslipidemia and low-grade inflammation, thus suggesting that epigenetic alterations in SAT are associated with the development of unhealthy obesity. This is the first study in BMI-discordant MZ twin pairs reporting genome-wide DNA methylation and expression profiles in SAT. We found a number of novel genes and pathways whose methylation and expression patterns differ within the twin pairs, suggesting that the pathological adaptation of SAT to obesity is, at least in part, epigenetically regulated.

  10. Comparison between Hybridoma and Fab/phage Anti-RhD: Their V Gene Usage and Pairings

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    W. S. Perera

    2000-01-01

    Full Text Available Our 11 anti-RhD's in conjunction with 37 previously published RhD antibodies, produced by hybridoma technology were analysed for germline gene usage and restriction in VH and VL pairings. The 17 VH germline genes used by the hybridoma anti-RhD IgG were derived from 4 VH families (VH1, VH2, VH3 and VH4. Eighteen kappa chains were restricted to only 5 germline genes from only 2 Vκ families (Vκ1 and κ3. However, the 13 lambda chains were not as restricted, using 10 Vλ germline genes from 4 families (Vλ1, Vλ2, Vλ3 and Vλ8. Fifty six unique Fab/phage anti-RhD were also analysed. In all cases the Fab/phage VH germline genes were derived from the VH3 family (41/41. The 29 kappa chains were restricted to 4 germline genes primarily from Vκ1 (97% germline genes from 5 families (Vλ1, Vλ2, Vλ3, Vλ4 and Vλ7. The VH germline genes of the Fab/phage were restricted to 4 of the 17 used by the hybridoma anti-RhD IgG (DP46, DP49, DP50 and DP77. Ninety percent of the Fab/phage were restricted to 1 of the 5 Vκ germline genes used by the IgG (DPK9. However, the repertoire of the Vλ germline genes used in these two systems is different, with analysis showing greater diversity in Vλ gene usage with 8 unique germline genes used by 76% Fab/phage compared to 4 unique genes used by 46% hybriboma anti-RhD.

  11. Functional PstI/RsaI polymorphism in CYP2E1 is associated with the development, progression and poor outcome of gastric cancer.

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    Jin Feng

    Full Text Available BACKGROUND: Cytochrome P450 2E1 (CYP2E1, an ethanol-inducible enzyme, has been shown to metabolically activate various carcinogens, which is critical for the development and progression of cancers. It has demonstrated that CYP2E1 polymorphisms alter the transcriptional activity of the gene. However, studies on the association between CYP2E1 polymorphisms (PstI/RsaI or DraI and gastric cancer have reported conflicting results. Thus, the aim of the present study was to investigate whether CYP2E1 polymorphisms is associated with the development and progression of gastric cancer and its prognosis in Chinese patients. METHODS: A case-control study was conducted in which CYP2E1 PstI/RsaI and DraI polymorphisms were analyzed in 510 Chinese patients with gastric cancer and 510 age- and sex- matched healthy controls by PCR-RFLP. Odds ratios were estimated by multivariate logistic regression, and the lifetime was calculated by Kaplan-Meier survival curves. In addition, a meta-analysis was also conducted to verify the findings. RESULTS: For CYP2E1 PstI/RsaI polymorphism, C2C2 homozygotes (OR = 2.15; CI: 1.18-3.94 and C2 carriers (OR = 1.48; CI: 1.13-1.96 were associated with an increased risk of gastric cancer when compared with C1C1 homozygotes. Both C1C2 and C2C2 genotypes were associated with advanced stage, but not the grade of gastric cancer. Moreover, C2C2 genotype was identified as an independent marker of poor overall survival for gastric cancer. However, there was not any significant association between CYP2E1 DraI polymorphism and the risk of gastric cancer. In the meta-analysis, pooled data from 13 studies confirmed that the CYP2E1 PstI/RsaI polymorphism was associated with a significantly increased risk of gastric cancer. CONCLUSION: CYP2E1 PstI/RsaI polymorphism is associated with increased risk of development, progression and poor prognosis of gastric cancer in Chinese patients. Pooled data from 13 studies, mainly in Asian countries, are in

  12. rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.

    Science.gov (United States)

    Guo, Liyuan; Wang, Jing

    2017-11-11

    Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Biphasic Hoxd gene expression in shark paired fins reveals an ancient origin of the distal limb domain.

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    Renata Freitas

    Full Text Available The evolutionary transition of fins to limbs involved development of a new suite of distal skeletal structures, the digits. During tetrapod limb development, genes at the 5' end of the HoxD cluster are expressed in two spatiotemporally distinct phases. In the first phase, Hoxd9-13 are activated sequentially and form nested domains along the anteroposterior axis of the limb. This initial phase patterns the limb from its proximal limit to the middle of the forearm. Later in development, a second wave of transcription results in 5' HoxD gene expression along the distal end of the limb bud, which regulates formation of digits. Studies of zebrafish fins showed that the second phase of Hox expression does not occur, leading to the idea that the origin of digits was driven by addition of the distal Hox expression domain in the earliest tetrapods. Here we test this hypothesis by investigating Hoxd gene expression during paired fin development in the shark Scyliorhinus canicula, a member of the most basal lineage of jawed vertebrates. We report that at early stages, 5'Hoxd genes are expressed in anteroposteriorly nested patterns, consistent with the initial wave of Hoxd transcription in teleost and tetrapod paired appendages. Unexpectedly, a second phase of expression occurs at later stages of shark fin development, in which Hoxd12 and Hoxd13 are re-expressed along the distal margin of the fin buds. This second phase is similar to that observed in tetrapod limbs. The results indicate that a second, distal phase of Hoxd gene expression is not uniquely associated with tetrapod digit development, but is more likely a plesiomorphic condition present the common ancestor of chondrichthyans and osteichthyans. We propose that a temporal extension, rather than de novo activation, of Hoxd expression in the distal part of the fin may have led to the evolution of digits.

  14. dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes

    Science.gov (United States)

    Korenjak, Michael; Kwon, Eunjeong; Morris, Robert T.; Anderssen, Endre; Amzallag, Arnaud; Ramaswamy, Sridhar; Dyson, Nicholas J.

    2014-01-01

    dREAM complexes represent the predominant form of E2F/RBF repressor complexes in Drosophila. dREAM associates with thousands of sites in the fly genome but its mechanism of action is unknown. To understand the genomic context in which dREAM acts we examined the distribution and localization of Drosophila E2F and dREAM proteins. Here we report a striking and unexpected overlap between dE2F2/dREAM sites and binding sites for the insulator-binding proteins CP190 and Beaf-32. Genetic assays show that these components functionally co-operate and chromatin immunoprecipitation experiments on mutant animals demonstrate that dE2F2 is important for association of CP190 with chromatin. dE2F2/dREAM binding sites are enriched at divergently transcribed genes, and the majority of genes upregulated by dE2F2 depletion represent the repressed half of a differentially expressed, divergently transcribed pair of genes. Analysis of mutant animals confirms that dREAM and CP190 are similarly required for transcriptional integrity at these gene pairs and suggest that dREAM functions in concert with CP190 to establish boundaries between repressed/activated genes. Consistent with the idea that dREAM co-operates with insulator-binding proteins, genomic regions bound by dREAM possess enhancer-blocking activity that depends on multiple dREAM components. These findings suggest that dREAM functions in the organization of transcriptional domains. PMID:25053843

  15. A low-temperature-responsive element involved in the regulation of the Arabidopsis thaliana At1g71850/At1g71860 divergent gene pair.

    Science.gov (United States)

    Liu, Shijuan; Chen, Huiqing; Li, Xiulan; Zhang, Wei

    2016-08-01

    The bidirectional promoter of the Arabidopsis thaliana gene pair At1g71850/At1g71860 harbors low-temperature-responsive elements, which participate in anti-correlated transcription regulation of the driving genes in response to environmental low temperature. A divergent gene pair is defined as two adjacent genes organized head to head in opposite orientation, sharing a common promoter region. Divergent gene pairs are mainly coexpressed, but some display opposite regulation. The mechanistic basis of such anti-correlated regulation is not well understood. Here, the regulation of the Arabidopsis thaliana gene pair At1g71850/At1g71860 was investigated. Semi-quantitative RT-PCR and Genevestigator analyses showed that while one of the pair was upregulated by exposure to low temperature, the same treatment downregulated the other. Promoter::GUS fusion transgenes were used to show that this behavior was driven by a bidirectional promoter, which harbored an as-1 motif, associated with the low-temperature response; mutation of this sequence produced a significant decrease in cold-responsive expression. With regard to the as-1 motif in the native orientation repressing the promoter's low-temperature responsiveness, the same as-1 motif introduced in the reverse direction showed a slight enhancement in the promoter's responsiveness to low-temperature exposure, indicating that the orientation of the motif was important for the promoter's activity. These findings provide new insights into the complex transcriptional regulation of bidirectional gene pairs as well as plant stress response.

  16. POSSIBLE RELATED FUNCTIONS OF THE NON-HOMOLOGOUS CO-REGULATED GENE PAIR PDCD10 AND SERPINI1

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    Concetta Scimone

    2017-04-01

    Full Text Available Gene expression in mammalians is a very finely controlled mechanism, and bidirectional promoters can be considered one of the most compelling examples of the accuracy of genic expression coordination. As recently reported, a bidirectional promoter regulates the expression of the PDCD10(whose mutations cause familial Cerebral Cavernous Malformations (CCMs and SERPINI1 gene pair, even though they are non-homologous genes. The aim of this study was to identify any potential common roles of these two coregulated genes. An in-silico approach was used to identify functional correlations, using the BioGraph, IPA® and Cytoscape tools and the KEGG pathway database. The results obtained show that PDCD10 and SERPINI1 may co-regulate some cellular processes, particularly those related to focal adhesion maintenance. All common pathways identified for PDCD10 and SERPINI1 are closely associated with the pathogenic characteristics of CCMs; we thus hypothesize that genes involved in these networks may contribute to the development of CCMs.

  17. The AVR2-SIX5 gene pair is required to activate I-2-mediated immunity in tomato.

    Science.gov (United States)

    Ma, Lisong; Houterman, Petra M; Gawehns, Fleur; Cao, Lingxue; Sillo, Fabiano; Richter, Hanna; Clavijo-Ortiz, Myriam J; Schmidt, Sarah M; Boeren, Sjef; Vervoort, Jacques; Cornelissen, Ben J C; Rep, Martijn; Takken, Frank L W

    2015-10-01

    Plant-invading microbes betray their presence to a plant by exposure of antigenic molecules such as small, secreted proteins called 'effectors'. In Fusarium oxysporum f. sp. lycopersici (Fol) we identified a pair of effector gene candidates, AVR2-SIX5, whose expression is controlled by a shared promoter. The pathogenicity of AVR2 and SIX5 Fol knockouts was assessed on susceptible and resistant tomato (Solanum lycopersicum) plants carrying I-2. The I-2 NB-LRR protein confers resistance to Fol races carrying AVR2. Like Avr2, Six5 was found to be required for full virulence on susceptible plants. Unexpectedly, each knockout could breach I-2-mediated disease resistance. So whereas Avr2 is sufficient to induce I-2-mediated cell death, Avr2 and Six5 are both required for resistance. Avr2 and Six5 interact in yeast two-hybrid assays as well as in planta. Six5 and Avr2 accumulate in xylem sap of plants infected with the reciprocal knockouts, showing that lack of I-2 activation is not due to a lack of Avr2 accumulation in the SIX5 mutant. The effector repertoire of a pathogen determines its host specificity and its ability to manipulate plant immunity. Our findings challenge an oversimplified interpretation of the gene-for-gene model by showing requirement of two fungal genes for immunity conferred by one resistance gene. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  18. De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L..

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    Nan Fu

    Full Text Available BACKGROUND: Celery is an increasing popular vegetable species, but limited transcriptome and genomic data hinder the research to it. In addition, a lack of celery molecular markers limits the process of molecular genetic breeding. High-throughput transcriptome sequencing is an efficient method to generate a large transcriptome sequence dataset for gene discovery, molecular marker development and marker-assisted selection breeding. PRINCIPAL FINDINGS: Celery transcriptomes from four tissues were sequenced using Illumina paired-end sequencing technology. De novo assembling was performed to generate a collection of 42,280 unigenes (average length of 502.6 bp that represent the first transcriptome of the species. 78.43% and 48.93% of the unigenes had significant similarity with proteins in the National Center for Biotechnology Information (NCBI non-redundant protein database (Nr and Swiss-Prot database respectively, and 10,473 (24.77% unigenes were assigned to Clusters of Orthologous Groups (COG. 21,126 (49.97% unigenes harboring Interpro domains were annotated, in which 15,409 (36.45% were assigned to Gene Ontology(GO categories. Additionally, 7,478 unigenes were mapped onto 228 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG. Large numbers of simple sequence repeats (SSRs were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions. CONCLUSIONS: This study demonstrates the feasibility of generating a large scale of sequence information by Illumina paired-end sequencing and efficient assembling. Our results provide a valuable resource for celery research. The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

  19. The role of autophagy in chloroplast degradation and chlorophagy in immune defenses during Pst DC3000 (AvrRps4 infection.

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    Junjian Dong

    Full Text Available BACKGROUND: Chlorosis of leaf tissue normally observed during pathogen infection may result from the degradation of chloroplasts. There is a growing evidence to suggest that the chloroplast plays a significant role during pathogen infection. Although most degradation of the organelles and cellular structures in plants is mediated by autophagy, its role in chloroplast catabolism during pathogen infection is largely unknown. RESULTS: In this study, we investigated the function of autophagy in chloroplast degradation during avirulent Pst DC3000 (AvrRps4 infection. We examined the expression of defensive marker genes and suppression of bacterial growth using the electrolyte leakage assay in normal light (N and low light (L growing environments of wild-type and atg5-1 plants during pathogen treatment. Stroma-targeted GFP proteins (CT-GFP were observed with LysoTracker Red (LTR staining of autophagosome-like structures in the vacuole. The results showed that Arabidopsis expressed a significant number of small GFP-labeled bodies when infected with avirulent Pst DC3000 (AvrRps4. While barely detectable, there were small GFP-labeled bodies in plants with the CT-GFP expressing atg5-1 mutation. The results showed that chloroplast degradation depends on autophagy and this may play an important role in inhibiting pathogen growth. CONCLUSION: Autophagy plays a role in chloroplast degradation in Arabidopsis during avirulent Pst DC3000 (AvrRps4 infection. Autophagy dependent chloroplast degradation may be the primary source of reactive oxygen species (ROS as well as the pathogen-response signaling molecules that induce the defense response.

  20. CYP2E1 Rsa Ι/Pst Ι polymorphism and lung cancer susceptibility: a meta-analysis involving 10,947 subjects.

    Science.gov (United States)

    Shen, Ze-Tian; Wu, Xin-Hu; Li, Bing; Shen, Jun-shu; Wang, Zhen; Li, Jing; Zhu, Xi-Xu

    2015-09-01

    Many studies have examined the association between the CYP2E1 Rsa Ι/Pst Ι (rs3813867) polymorphism gene polymorphisms and lung cancer risk in various populations, but their results have been inconsistent. The PubMed and CNKI database was searched for case-control studies published up to October 2013. Data were extracted and pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated. In this meta-analysis, we assessed 23 published studies involving comprising 4727 lung cancer cases and 6220 controls of the association between CYP2E1 Rsa Ι/Pst Ι polymorphism and lung cancer risk. For the homozygote c2/c2 and c2 allele carriers (c1/c2 + c2/c2), the pooled ORs for all studies were 0.73(95% CI = 0.62-0.84; P = 0.005 for heterogeneity) and 0.84 (95% CI = 0.77-0.92; P = 0.001 for heterogeneity) when compared with the homozygous wild-type genotype (c1/c1). In the stratified analysis by ethnicity, the same significantly risks were found among Asians and mixed population for both the c2 allele carriers and homozygote c2/c2. However, no significant associations were found in Caucasian population all genetic models. This updated meta-analysis suggests that CYP2E1 Rsa Ι/Pst Ι c2 allele is a decreased risk factor for the developing lung cancer among Asians and mixed population. © 2015 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  1. Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites

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    Pierce Levi CT

    2009-01-01

    Full Text Available Abstract Background Gene rearrangements such as chromosomal translocations have been shown to contribute to cancer development. Human chromosomal fragile sites are regions of the genome especially prone to breakage, and have been implicated in various chromosome abnormalities found in cancer. However, there has been no comprehensive and quantitative examination of the location of fragile sites in relation to all chromosomal aberrations. Results Using up-to-date databases containing all cancer-specific recurrent translocations, we have examined 444 unique pairs of genes involved in these translocations to determine the correlation of translocation breakpoints and fragile sites in the gene pairs. We found that over half (52% of translocation breakpoints in at least one gene of these gene pairs are mapped to fragile sites. Among these, we examined the DNA sequences within and flanking three randomly selected pairs of translocation-prone genes, and found that they exhibit characteristic features of fragile DNA, with frequent AT-rich flexibility islands and the potential of forming highly stable secondary structures. Conclusion Our study is the first to examine gene pairs involved in all recurrent chromosomal translocations observed in tumor cells, and to correlate the location of more than half of breakpoints to positions of known fragile sites. These results provide strong evidence to support a causative role for fragile sites in the generation of cancer-specific chromosomal rearrangements.

  2. Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs

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    Martin Alexander Fischer

    2016-08-01

    Full Text Available The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community

  3. Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns

    Science.gov (United States)

    Grinchuk, Oleg V.; Jenjaroenpun, Piroon; Orlov, Yuriy L.; Zhou, Jiangtao; Kuznetsov, Vladimir A.

    2010-01-01

    Cis-antisense gene pairs (CASGPs) can transcribe mRNAs from an opposite strand of a given locus. To classify and understand diverse CASGP phenomena in the human we compiled a genome-wide catalog of CASGPs and integrated these sequences with microarray, SAGE and miRNA data. Using the concept of overlapping regions and clustering of SA transcripts by chromosome coordinates, we identified up to 9000 overlapping antisense loci. Four thousand three hundred and seventy-four of these CASGPs form 1759 complex gene architectures. We found that ∼35% (6347/18160) of RefSeq genes are overlapped with the antisense transcripts. About 30% of Affymetrix U133 microarray initial sequences map transcripts of ∼35% CASGPs and reveal mostly concordant expression in CASGPs. We found strong significant overrepresentation of human miRNA genes in loci of CASGPs. We developed a data-driven model of cross-talk between co-expressed CASGPs and DICER1-mediated miRNA pathway in normal spermatogenesis and in severe teratozoospermia. Specifically, we revealed complex SA structural–functional gene module composing the protein-coding genes, WDR6, DALRD3, NDUFAF3 and ncRNA precursors, mir-425 and mir-191, which could provide downregulation of ncRNA pathway via direct targeting DICER1 and basonuclin 2 transcripts by mir-425 and mir-191 in normal spermatogenesis, but this mechanism is switched off in severe teratozoospermia. The database is available from http://globalisland.bii.a-star.edu.sg/∼jiangtao/sas/index3.php?link =about PMID:19906709

  4. Inheritance of Resistance to Pstv in Transgenic Peanuts Containing Cp Pstv Gene

    OpenAIRE

    Dwi Hapsoro, Hajrial Aswidinnoor, Rusmilah Suseno, Jumanto, and Sudarsono

    2008-01-01

    Inheritance of Resistance to PStV in Transgenic Peanuts Containing cp PStV Gene. We have obtained transgenic peanut lines containing coat protein gene of PStV. To get maximal use of the transgenic character in a breeding program, it is necessary that the transgene is also stably inherited and expressed.  This experiment was conducted from June 2002 – January 2005 at Plant Molecular Biology Laboratory, Bogor Agricultural University, and Queensland Agricultural Biotechnology Center, The Univers...

  5. Correlation of global and gene-specific DNA methylation in maternal-infant pairs.

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    Molly L Kile

    2010-10-01

    Full Text Available The inheritance of DNA methylation patterns is a popular theory to explain the influence of parental genetic and environmental factors on the phenotype of their offspring but few studies have examined this relationship in humans. Using 120 paired maternal-umbilical cord blood samples randomly selected from a prospective birth cohort in Bangladesh, we quantified DNA methylation by pyrosequencing seven CpG positions in the promoter region of p16, four CpG positions in the promoter region of p53, LINE-1 and Alu. Positive correlations were observed between maternal and umbilical cord blood at p16, LINE-1, and Alu but not p53. Multiple linear regression models observed a significant association between maternal and umbilical cord blood at LINE-1 and Alu (LINE-1: β = 0.63, p<0.0001; Alu: β = 0.28, p = 0.009. After adjusting for multiple comparisons, maternal methylation of p16 at position 4 significantly predicted methylation at the same position in umbilical cord blood (β = 0.43, p = <0.0001. These models explained 48%, 5% and 16% of the observed variability in umbilical cord %5mC for LINE-1, Alu and p16 at position 4, respectively. These results suggest that DNA methylation in maternal blood was correlated with her offspring at LINE-1, Alu, and p16 but not p53. Additional studies are needed to confirm whether these observed associations were due to the inheritance of epigenetic events or the shared environment between mother and fetus. Future studies should also use a multi-generational family-based design that would quantify both maternal and paternal contributions to DNA methylation in offspring across more than one generation.

  6. 19-base pair deletion polymorphism of the dihydrofolate reductase (DHFR gene: maternal risk of Down syndrome and folate metabolism

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    Cristiani Cortez Mendes

    Full Text Available CONTEXT AND OBJECTIVE: Polymorphisms in genes involved in folate metabolism may modulate the maternal risk of Down syndrome (DS. This study evaluated the influence of a 19-base pair (bp deletion polymorphism in intron-1 of the dihydrofolate reductase (DHFR gene on the maternal risk of DS, and investigated the association between this polymorphism and variations in the concentrations of serum folate and plasma homocysteine (Hcy and plasma methylmalonic acid (MMA. DESIGN AND SETTING: Analytical cross-sectional study carried out at Faculdade de Medicina de São José do Rio Preto (Famerp. METHODS: 105 mothers of individuals with free trisomy of chromosome 21, and 184 control mothers were evaluated. Molecular analysis on the polymorphism was performed using the polymerase chain reaction (PCR through differences in the sizes of fragments. Folate was quantified by means of chemiluminescence, and Hcy and MMA by means of liquid chromatography and sequential mass spectrometry. RESULTS: There was no difference between the groups in relation to allele and genotype frequencies (P = 0.44; P = 0.69, respectively. The folate, Hcy and MMA concentrations did not differ significantly between the groups, in relation to genotypes (P > 0.05. CONCLUSIONS: The 19-bp deletion polymorphism of DHFR gene was not a maternal risk factor for DS and was not related to variations in the concentrations of serum folate and plasma Hcy and MMA in the study population.

  7. Core-corona PSt/P(BA-AA) composite particles by two-stage emulsion polymerization

    Science.gov (United States)

    Xie, Delong; Ren, Xiaolin; Zhang, Xinya; Liao, Shijun

    2016-03-01

    Raspberry-shaped composite particles with polystyrene (PSt) as core and poly(n-butyl acrylate-co-acrylic acid) (P(BA-AA)) as corona were synthesized via emulsion polymerization. The random copolymer, P(BA-AA), was pre-prepared and used as a polymeric surfactant, its emulsifying properties adjusted by changing the mass ratio of BA and AA. The morphology of the resulting core-corona composite particles, P(St/P(BA-AA)), could be regulated and controlled by varying the concentrations of P(BA-AA) or the mass ratio of BA:AA in P(BA-AA). The experimental results indicate that 3.0-6.0 wt% of P(BA-AA) is required to obtain stable composite emulsions, and P(BA-AA) with a mass ratio of BA:AA = 1:2 is able to generate distinct core-corona structures. A mechanism of composite particle formation is proposed based on the high affinity between the PSt core and the hydrophobic segments of P(BA-A). The regular morphology of the colloidal film is expected to facilitate potential application of core-corona particles in the field of light scattering. Furthermore, the diversity of core-corona particles can be expanded by replacing P(BA-AA) corona particles with other amphiphilic particles.

  8. TMPRSS2-ERG Gene Fusion Causing ERG Overexpression Precedes Chromosome Copy Number Changes in Prostate Carcinomas, Paired HGPIN Lesions

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    Nuno Cerveira

    2006-10-01

    Full Text Available TMPRSS2-ETS gene fusions have been found recurrently in prostate carcinomas, but not in the presumed precursor lesion, high-grade prostatic intraepithelial neoplasia (HGPIN. However, HGPIN lesions may share chromosomal changes with prostate cancer. To determine the relative order of genetic events in prostate carcinogenesis, we have analyzed 34 prostate carcinomas, 19 paired HGPIN lesions, 14 benign prostate hyperplasias, 11 morphologically normal prostatic tissues for TMPRSS2-ERG, TMPRSS2-ETV1 rearrangements, genomic imbalances. TMPRSS2 exon 1 was fused in-frame with ERG exon 4 in 17 of 34 (50% prostate carcinomas, in 4 of 19 (21% HGPIN lesions, but in none of controls. The findings were further validated by sequencing analysis, by the real-time polymerase chain reaction quantification of TMPRSS2-ERG fusion transcript, the ERG exons 5/6:exons 1/2 expression ratio. Chromosome copy number changes were detected by comparative genomic hybridization in 42% of clinically confined carcinomas, in none of the 16 HGPIN lesions analyzed. We demonstrate for the first time that the TMPRSS2-ERG fusion gene can be detected in a proportion of HGPIN lesions, that this molecular rearrangement is an early event that may precede chromosome-level alterations in prostate carcinogenesis.

  9. Power of non-parametric linkage analysis in mapping genes contributing to human longevity in long-lived sib-pairs

    DEFF Research Database (Denmark)

    Tan, Qihua; Zhao, J H; Iachine, I

    2004-01-01

    This report investigates the power issue in applying the non-parametric linkage analysis of affected sib-pairs (ASP) [Kruglyak and Lander, 1995: Am J Hum Genet 57:439-454] to localize genes that contribute to human longevity using long-lived sib-pairs. Data were simulated by introducing a recentl...... in case of a dominant effect. Although the power issue may depend heavily on the true genetic nature in maintaining survival, our study suggests that results from small-scale sib-pair investigations should be referred with caution, given the complexity of human longevity....

  10. Multiple Versions of the a Mating Type Locus of Coprinus Cinereus Are Generated by Three Paralogous Pairs of Multiallelic Homeobox Genes

    Science.gov (United States)

    Pardo, E. H.; O'Shea, S. F.; Casselton, L. A.

    1996-01-01

    The A mating type locus of Coprinus cinereus determines mating compatibility by regulating essential steps in sexual development. Each A locus contains several genes separated into two functionally independent complexes termed Aα and Aβ, and the multiple alleles of these genes generate an estimated 160 A mating specificities. The genes encode two classes of homeodomain-containing proteins designated HD1 and HD2. In this report we describe two newly cloned loci, A2 and A5, and compare them with A42, A43 and A6 that we have described previously. An Aβ-null locus, retaining just a single active HD1 gene from the α-complex, was generated by mutation. Using this as a transformation host, gene combinations that promote A-regulated development were identified. We demonstrate that each A locus contains members of three paralogous pairs of HD1 and HD2 genes. Different allelic versions of gene pairs are compatible but paralogous genes are incompatible. The genes present in four uncloned A loci were deduced using Southern analyses and transformations with available cloned genes. The combined analysis of nine A factors identifies sufficient A gene alleles to generate at least 72 A mating specificities. PMID:8878675

  11. Analysis of the effects of application of PST and SC on the performance of the UCPTE system in the Balkans

    Energy Technology Data Exchange (ETDEWEB)

    Papazoglou, T.M. [Technological Educational Inst., Iraklio (Greece); Popovic, D.P.; Mijailovic, S. [Nikola Tesla Inst., Belgrade (Yugoslavia)

    1995-11-01

    Comparison is made of the effectiveness on the steady state load flow control of the Phase Shifter and the Series Compensation. Attention is focused on the ability to reduce unscheduled loop flows and redirect power flows in the system. The Balkan section of UCPTE system resulting after the parallel synchronous interconnection of Bulgaria is used as test system with loading conditions corresponding to the 1995 peak load. The superior properties of PST on power flow control are shown. The positive effects of PST in maintaining a high level of steady state security while realizing relatively large multilateral power exchange programs are demonstrated. A comparison of the power flow control efficiencies and an economic estimate are made for PST and SC. 10 refs, 1 fig, 4 tabs

  12. Design of the PST: A Diagnostic for 1-D Imaging of Fast Z-Pinch Power Emissions

    Energy Technology Data Exchange (ETDEWEB)

    ROCHAU,GREGORY A.; DERZON,MARK S.; CHANDLER,GORDON A.; LAZIER,STEVEN EARL

    2000-08-03

    Fast Z-pinch technology developed on the Z machine at Sandia National Laboratories can produce up to 230 TW of thermal x-ray power for applications in inertial confinement fusion (ICF) and weapons physics experiments. During implosion, these Z-pinches develop Rayleigh-Taylor (R-T) instabilities which are very difficult to diagnose and which functionally diminish the overall pinch quality. The Power-Space-Time (PST) instrument is a newly configured diagnostic for measuring the pinch power as a function of both space and time in a Z-pinch. Placing the diagnostic at 90 degrees from the Z-pinch axis, the PST provides a new capability in collecting experimental data on R-T characteristics for making meaningful comparisons to magneto-hydrodynamic computer models. This paper is a summary of the PST diagnostic design. By slit-imaging the Z-pinch x-ray emissions onto a linear scintillator/fiber-optic array coupled to a streak camera system, the PST can achieve {approximately}100 {micro}m spatial resolution and {approximately}1.3 ns time resolution. Calculations indicate that a 20 {micro}m thick scintillating detection element filtered by 1,000 {angstrom} of Al is theoretically linear in response to Plankian x-ray distributions corresponding to plasma temperatures from 40 eV to 150 eV, By calibrating this detection element to x-ray energies up to 5,000 eV, the PST can provide pinch power as a function of height and time in a Z-pinch for temperatures ranging from {approximately}40 eV to {approximately}400 eV. With these system pm-meters, the PST can provide data for an experimental determination of the R-T mode number, amplitude, and growth rate during the late-time pinch implosion.

  13. Use of diplotypes – matched haplotype pairs from homologous chromosomes – in gene-disease association studies

    Science.gov (United States)

    ZUO, Lingjun; WANG, Kesheng; LUO, Xingguang

    2014-01-01

    Summary Alleles, genotypes and haplotypes (combinations of alleles) have been widely used in gene-disease association studies. More recently, association studies using diplotypes (haplotype pairs on homologous chromosomes) have become increasingly common. This article reviews the rationale of the four types of association analyses and discusses the situations in which diplotype-based analyses are more powerful than the other types of association analyses. Haplotype-based association analyses are more powerful than allele-based association analyses, and diplotype-based association analyses are more powerful than genotype-based analyses. In circumstances where there are no interaction effects between markers and where the criteria for Hardy-Weinberg Equilibrium (HWE) are met, the larger sample size and smaller degrees of freedom of allele-based and haplotype-based association analyses make them more powerful than genotype-based and diplotype-based association analyses, respectively. However, under certain circumstances diplotype-based analyses are more powerful than haplotype-based analysis. PMID:25114493

  14. Human liver estrone (E1), Estradiol (E2) and dehydroepiandrosterone (DHEA) sulfotransferases (STs): Comparison with thermostable (TS) and thermolabile (TL) phenol sulfotransferase (PST) activities

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, J.S.; Watson, R.W.G.; Weinshilboum, R.M. (Mayo Clinic/Mayo Foundation, Rochester, MN (United States))

    1991-03-11

    Sulfation plays an important role in the metabolism of E1, E2 and DHEA in humans. The relationship between the enzymes that catalyze the sulfation of E1, E2 and DHEA and TS and TL PST is unclear. The authors compared thermal stability, sensitivity to inhibition by 2,6-dichloro-4-nitrophenol (DCNP) and individual variation in the regulation of these steroid ST activities with those of TS PST and TL PST in the human liver. E2 ST and TS PST had very similar thermal stabilities. The thermal inactivation profile of E1 ST suggested that this activity might be related to both DHEA ST and TS PST. DCNP inhibition studies also showed similar profiles for E2 ST and TS PST, with a small resistant component for E2 ST. A multiphasic profile for DCNP inhibition of E1 ST activity was found. Finally, studies performed with human liver sample showed significant correlations between E2 ST and TS PST, E1 ST and DHEA ST, E2 St and E1 ST, and, to a lesser degree, between E1 ST and TS PST and E2 ST and DHEA ST. TL PST was not correlated significantly with any of the other activities. These results suggest that the sulfation of E2 in human liver is catalyzed predominantly by TS PST, although DHEA ST may also play a role. Their results also suggest that the sulfation of E1 is catalyzed by DHEA ST and by TS PST, although other ST(s) could also be involved.

  15. A prospective comparison of ER, PR, Ki67 and gene expression in paired sequential core biopsies of primary, untreated breast cancer.

    Science.gov (United States)

    Hadad, Sirwan M; Jordan, Lee B; Roy, Pankaj G; Purdie, Colin A; Iwamoto, Takayuki; Pusztai, Lajos; Moulder-Thompson, Stacy L; Thompson, Alastair M

    2016-09-22

    Sequential biopsy of breast cancer is used to assess biomarker effects and drug efficacy. The preoperative "window of opportunity" setting is advantageous to test biomarker changes in response to therapeutic agents in previously untreated primary cancers. This study tested the consistency over time of paired, sequential biomarker measurements on primary, operable breast cancer in the absence of drug therapy. Immunohistochemistry was performed for ER, PR and Ki67 on paired preoperative/operative tumor samples taken from untreated patients within 2 weeks of each other. Microarray analysis on mRNA extracted from formalin fixed paraffin embedded cores was performed using Affymetrix based arrays on paired core biopsies analysed using Ingenuity Pathway Analysis (IPA) and Gene Set Analysis (GSA). In 41 core/resection pairs, the recognised trend to lower ER, PR and Ki67 score on resected material was confirmed. Concordance for ER, PR and Ki67 without changing biomarker status (e.g. ER+ to ER-) was 90, 74 and 80 % respectively. However, in 23 paired core samples (diagnostic core v on table core), Ki67 using a cut off of 13.25 % was concordant in 22/23 (96 %) and differences in ER and PR immunohistochemistry by Allred or Quickscore between the pairs did not impact hormone receptor status. IPA and GSA demonstrated substantial gene expression changes between paired cores at the mRNA level, including reduced expression of ER pathway analysis on the second core, despite the absence of drug intervention. Sequential core biopsies of primary breast cancer (but not core versus resection) was consistent and is appropriate to assess the effects of drug therapy in vivo on ER, PR and Ki67 using immunohistochemistry. Conversely, studies utilising mRNA expression may require non-treatment controls to distinguish therapeutic from biopsy differences.

  16. Towards a clinical practice guide in pharmacogenomics testing for functional polymorphisms of drug-metabolising enzymes. Gene/drug pairs and barriers perceived in Spain.

    Directory of Open Access Journals (Sweden)

    José A G Agúndez

    2012-11-01

    Full Text Available The development of clinical practice recommendations or guidelines for the clinical use of biomarkers is an issue of great importance with regard to adverse drug reactions. The potential of pharmacogenomic biomarkers has been extensively investigated in recent years. However, several barriers to implementing the use of pharmacogenomics testing exist. We conducted a survey among members of the Spanish Societies of Pharmacology and Clinical Pharmacology to obtain information about the perception of such barriers and to compare the perceptions of participants about the relative importance of major gene/drug pairs.Of 11 potential barriers, the highest importance was attributed to lack of institutional support for pharmacogenomics testing, and to the issues related to the lack of guidelines. Of the proposed gene/drug pairs the highest importance was assigned to HLA-B/abacavir, UGT1A1/irinotecan and CYP2D6/tamoxifen. In this perspective article we compare the relative importance of 29 gene/drug pairs in the Spanish study with that of the same pairs in the American Society for Clinical Pharmacology & Therapeutics study, and we provide suggestions and areas of focus to develop a guide for clinical practice in pharmacogenomics testing.

  17. Role of an ER stress response element in regulating the bidirectional promoter of the mouse CRELD2 - ALG12 gene pair

    Directory of Open Access Journals (Sweden)

    Hirata Yoko

    2010-11-01

    Full Text Available Abstract Background Recently, we identified cysteine-rich with EGF-like domains 2 (CRELD2 as a novel endoplasmic reticulum (ER stress-inducible gene and characterized its transcriptional regulation by ATF6 under ER stress conditions. Interestingly, the CRELD2 and asparagine-linked glycosylation 12 homolog (ALG12 genes are arranged as a bidirectional (head-to-head gene pair and are separated by less than 400 bp. In this study, we characterized the transcriptional regulation of the mouse CRELD2 and ALG12 genes that is mediated by a common bidirectional promoter. Results This short intergenic region contains an ER stress response element (ERSE sequence and is well conserved among the human, rat and mouse genomes. Microarray analysis revealed that CRELD2 and ALG12 mRNAs were induced in Neuro2a cells by treatment with thapsigargin (Tg, an ER stress inducer, in a time-dependent manner. Other ER stress inducers, tunicamycin and brefeldin A, also increased the expression of these two mRNAs in Neuro2a cells. We then tested for the possible involvement of the ERSE motif and other regulatory sites of the intergenic region in the transcriptional regulation of the mouse CRELD2 and ALG12 genes by using variants of the bidirectional reporter construct. With regards to the promoter activities of the CRELD2-ALG12 gene pair, the entire intergenic region hardly responded to Tg, whereas the CRELD2 promoter constructs of the proximal region containing the ERSE motif showed a marked responsiveness to Tg. The same ERSE motif of ALG12 gene in the opposite direction was less responsive to Tg. The direction and the distance of this motif from each transcriptional start site, however, has no impact on the responsiveness of either gene to Tg treatment. Additionally, we found three putative sequences in the intergenic region that antagonize the ERSE-mediated transcriptional activation. Conclusions These results show that the mouse CRELD2 and ALG12 genes are arranged as a

  18. A four base pair deletion 5' to the A gamma T gene is associated not only with decreased expression of the A gamma T-globin gene, but also of the G gamma-globin gene in cis.

    Science.gov (United States)

    Coleman, M B; Adams, J G; Steinberg, M H; Winter, W P

    1994-12-01

    A four base pair deletion 5' to A gamma T-globin gene at positions -222 to -225 has been reported to reduce the expression of this gene. To evaluate the prevalence and effect of this deletion, PCR-based methods were employed. The deletion had a gene frequency of 0.06 in a sample of African-American individuals with sickle cell trait, 0.18 in adult African-Americans with normal Hb AA, and 0.36 in caucasians. Seventy cord blood samples from African-American newborns with Hb AA were evaluated by both HPLC and PCR. The frequency of the A gamma T allele was 0.13. The A gamma T-globin chain was always present in a lower proportion than the A gamma I allele (70% of A gamma I), but the percentage of A gamma-globin was the same whether or not A gamma T was present. The total percentage of Hb F, however, was significantly lower in the group with the A gamma T allele (77.1% vs. 87.4%, P < 0.01). These results indicate that the four base pair deletion is not only associated with reduced expression of the A gamma T allele, but also of the G gamma allele in cis, further suggesting a possible role of this region in the modulation of the expression of the linked gamma-globin genes.

  19. PhoU Allows Rapid Adaptation to High Phosphate Concentrations by Modulating PstSCAB Transport Rate in Sinorhizobium meliloti.

    Science.gov (United States)

    diCenzo, George C; Sharthiya, Harsh; Nanda, Anish; Zamani, Maryam; Finan, Turlough M

    2017-09-15

    Maintenance of cellular phosphate homeostasis is essential for cellular life. The PhoU protein has emerged as a key regulator of this process in bacteria, and it is suggested to modulate phosphate import by PstSCAB and control activation of the phosphate limitation response by the PhoR-PhoB two-component system. However, a proper understanding of PhoU has remained elusive due to numerous complications of mutating phoU, including loss of viability and the genetic instability of the mutants. Here, we developed two sets of strains of Sinorhizobium meliloti that overcame these limitations and allowed a more detailed and comprehensive analysis of the biological and molecular activities of PhoU. The data showed that phoU cannot be deleted in the presence of phosphate unless PstSCAB is inactivated also. However, phoU deletions were readily recovered in phosphate-free media, and characterization of these mutants revealed that addition of phosphate to the environment resulted in toxic levels of PstSCAB-mediated phosphate accumulation. Phosphate uptake experiments indicated that PhoU significantly decreased the PstSCAB transport rate specifically in phosphate-replete cells but not in phosphate-starved cells and that PhoU could rapidly respond to elevated environmental phosphate concentrations and decrease the PstSCAB transport rate. Site-directed mutagenesis results suggested that the ability of PhoU to respond to phosphate levels was independent of the conformation of the PstSCAB transporter. Additionally, PhoU-PhoU and PhoU-PhoR interactions were detected using a bacterial two-hybrid screen. We propose that PhoU modulates PstSCAB and PhoR-PhoB in response to local, internal fluctuations in phosphate concentrations resulting from PstSCAB-mediated phosphate import.IMPORTANCE Correct maintenance of cellular phosphate homeostasis is critical in all kingdoms of life and in bacteria involves the PhoU protein. This work provides novel insights into the role of the Sinorhizobium

  20. Immunodominant PstS1 antigen of mycobacterium tuberculosis is a potent biological response modifier for the treatment of bladder cancer

    Directory of Open Access Journals (Sweden)

    Böhle Andreas

    2004-11-01

    Full Text Available Abstract Background Bacillus Calmette Guérin (BCG-immunotherapy has a well-documented and successful clinical history in the treatment of bladder cancer. However, regularly observed side effects, a certain degree of nonresponders and restriction to superficial cancers remain a major obstacle. Therefore, alternative treatment strategies are intensively being explored. We report a novel approach of using a well defined immunostimulatory component of Mycobacterium tuberculosis for the treatment of bladder cancer. The phosphate transport protein PstS1 which represents the phosphate binding component of a mycobacterial phosphate uptake system is known to be a potent immunostimulatory antigen of M. tuberculosis. This preclinical study was designed to test the potential of recombinant PstS1 to serve as a non-viable and defined immunotherapeutic agent for intravesical bladder cancer therapy. Methods Mononuclear cells (PBMCs were isolated from human peripheral blood and stimulated with PstS1 for seven days. The activation of PBMCs was determined by chromium release assay, IFN-γ ELISA and measurement of lymphocyte proliferation. The potential of PstS1 to activate monocyte-derived human dendritic cells (DC was determined by flow cytometric analysis of the marker molecules CD83 and CD86 as well as the release of the cytokines TNF-α and IL-12. Survival of presensitized and intravesically treated, tumor-bearing mice was analyzed by Kaplan-Meier curve and log rank test. Local and systemic immune response in PstS1-immunotherapy was investigated by anti-PstS1-specific ELISA, splenocyte proliferation assay and immunohistochemistry. Results Our in vitro experiments showed that PstS1 is able to stimulate cytotoxicity, IFN-γ release and proliferation of PBMCs. Further investigations showed the potential of PstS1 to activate monocyte-derived human dendritic cells (DC. In vivo studies in an orthotopic murine bladder cancer model demonstrated the therapeutic

  1. New Invertebrate Vectors for PST, Spirolides and Okadaic Acid in the North Atlantic

    Directory of Open Access Journals (Sweden)

    Luis M. Botana

    2013-06-01

    Full Text Available The prevalence of poisoning events due to harmful algal blooms (HABs has declined during the last two decades through monitoring programs and legislation, implemented mainly for bivalves. However, new toxin vectors and emergent toxins pose a challenge to public health. Several locations on the Portuguese coast were surveyed between 2009 and 2010 for three distinct biotoxin groups [saxitoxin (PST, spirolide (SPX and okadaic acid (OA], in 14 benthic species of mollusks and echinoderms. Our main goals were to detect new vectors and unravel the seasonal and geographical patterns of these toxins. PSTs were analyzed by the Lawrence method, SPXs by LC-MS/MS, and OA by LC-MS/MS and UPLC-MS/MS. We report 16 new vectors for these toxins in the North Atlantic. There were differences in toxin contents among species, but no significant geographical or seasonal patterns were found. Our results suggest that legislation should be adjusted to extend the monitoring of marine toxins to a wider range of species besides edible bivalves.

  2. Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq

    OpenAIRE

    Dawei eZhang; qi epan; cheng ecui; chen etan; xianhong ege; yujiao eshao; zaiyun eli

    2015-01-01

    Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. olerac...

  3. Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis.

    Directory of Open Access Journals (Sweden)

    Xinan Yang

    Full Text Available Identification and characterization of crucial gene target(s that will allow focused therapeutics development remains a challenge. We have interrogated the putative therapeutic targets associated with the transcription factor Grainy head-like 2 (GRHL2, a critical epithelial regulatory factor. We demonstrate the possibility to define the molecular functions of critical genes in terms of their personalized expression profiles, allowing appropriate functional conclusions to be derived. A novel methodology, relative expression analysis with gene-set pairs (RXA-GSP, is designed to explore the potential clinical utility of cancer-biology discovery. Observing that Grhl2-overexpression leads to increased metastatic potential in vitro, we established a model assuming Grhl2-induced or -inhibited genes confer poor or favorable prognosis respectively for cancer metastasis. Training on public gene expression profiles of 995 breast cancer patients, this method prioritized one gene-set pair (GRHL2, CDH2, FN1, CITED2, MKI67 versus CTNNB1 and CTNNA3 from all 2717 possible gene-set pairs (GSPs. The identified GSP significantly dichotomized 295 independent patients for metastasis-free survival (log-rank tested p = 0.002; severe empirical p = 0.035. It also showed evidence of clinical prognostication in another independent 388 patients collected from three studies (log-rank tested p = 3.3e-6. This GSP is independent of most traditional prognostic indicators, and is only significantly associated with the histological grade of breast cancer (p = 0.0017, a GRHL2-associated clinical character (p = 6.8e-6, Spearman correlation, suggesting that this GSP is reflective of GRHL2-mediated events. Furthermore, a literature review indicates the therapeutic potential of the identified genes. This research demonstrates a novel strategy to integrate both biological experiments and clinical gene expression profiles for extracting and elucidating the genomic

  4. Structure, biochemical and kinetic properties of recombinant Pst2p from Saccharomyces cerevisiae, a FMN-dependent NAD(P)H:quinone oxidoreductase.

    Science.gov (United States)

    Koch, Karin; Hromic, Altijana; Sorokina, Marija; Strandback, Emilia; Reisinger, Manuel; Gruber, Karl; Macheroux, Peter

    2017-08-01

    The genome of the yeast Saccharomyces cerevisiae encodes four flavodoxin-like proteins, namely Lot6p, Pst2p, Rfs1p and Ycp4p. Thus far only Lot6p was characterized in detail demonstrating that the enzyme possesses NAD(P)H:quinone oxidoreductase activity. In the present study, we heterologously expressed PST2 in Escherichia coli and purified the produced protein to conduct a detailed biochemical and structural characterization. Determination of the three-dimensional structure by X-ray crystallography revealed that Pst2p adopts the flavodoxin-like fold and forms tetramers independent of cofactor binding. The lack of electron density for FMN indicated weak binding, which was confirmed by further biochemical analysis yielding a dissociation constant of 20±1μM. The redox potential of FMN bound to Pst2p was determined to -89±3mV and is thus 119mV more positive than that of free FMN indicating that reduced FMN binds ca. five orders of magnitude tighter to Pst2p than oxidized FMN. Due to this rather positive redox potential Pst2p is unable to reduce free FMN or azo dyes as reported for other members of the flavodoxin-like protein family. On the other hand, Pst2p efficiently catalyzes the NAD(P)H dependent two-electron reduction of natural and artificial quinones. The kinetic mechanism follows a ping-pong bi-bi reaction scheme. In vivo experiments with a PST2 knock out and overexpressing strain demonstrated that Pst2p enables yeast cells to cope with quinone-induced damage suggesting a role of the enzyme in managing oxidative stress. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  5. Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq.

    Science.gov (United States)

    Zhang, Dawei; Pan, Qi; Cui, Cheng; Tan, Chen; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2015-01-01

    Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC) were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids.

  6. Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq

    Directory of Open Access Journals (Sweden)

    Dawei eZhang

    2015-11-01

    Full Text Available Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids.

  7. CYP2E1 Rsa I/Pst I polymorphism contributes to oral cancer susceptibility: a meta-analysis.

    Science.gov (United States)

    Niu, Yuming; Hu, Yuanyuan; Wu, Mingyue; Jiang, Fei; Shen, Ming; Tang, Chunbo; Chen, Ning

    2012-01-01

    Previous data on association between CYP2E1 Rsa I/Pst I polymorphism and oral cancer risk were controversial. To investigate the association between CYP2E1 Rsa I/Pst I polymorphism and oral cancer risk. We performed a meta-analysis to assess the relationship between oral cancer and genotype with English language until June 2010. Twelve published case-control studies of 1259 patients with oral cancer and 2262 controls were acquired. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association in codominant and dominant models. Overall, the pooled ORs indicated a significant association between CYP2E1 Rsa I/Pst I polymorphism and oral cancer risk (for c1/c2 vs. c1/c1: OR=1.30, 95% CI=1.04-1.62, Pheterogeneity=0.57; for (c1/c2+c2/c2) vs. c1/c1: OR=1.32, 95% CI=1.07-1.64, Pheterogeneity=0.57, respectively). In subgroup analysis by race, the same significant risks were found among Asian (for c1/c2 vs. c1/c1: OR=1.41, 95% CI=1.05-1.91, Pheterogeneity=0.92; for (c1/c2+c2/c2) vs. c1/c1: OR=1.43, 95% CI=1.08-1.88, Pheterogeneity=0.97, respectively). In conclusion, this meta-analysis demonstrates that CYP2E1 Rsa I/Pst I c2 allele may be a biomarker for oral cancer, especially among Asian populations.

  8. PsT1: A Low-Cost Optical Simulator for Psychomotor Skills Training in Neuroendoscopy.

    Science.gov (United States)

    Espinoza, Daniel Lorias; González Carranza, Vicente; Chico-Ponce de León, Fernando; Martinez, Arturo Minor

    2015-06-01

    Well-developed psychomotor skills are important for competence in minimally invasive surgery. Neuroendoscopy is no exception, and adaptation to different visual perspectives and careful handling of the surgical instruments are mandatory. Few training systems, however, focus on developing psychomotor skills for neuroendoscopy. Here, we introduce a new training system called PsT1 that provides visual feedback via the use of simple optics that emulate the endoscope at 0° and 30°. Time and error metrics are generated automatically with integrated software to ensure objective assessment. Neuroendoscopic optics were emulated with a low-cost, commercially available universal serial bus 2.0 camera and a light-emitting diode light source. Visual feedback of 30° was obtained by displacing the optical axis of the universal serial bus camera by 30°, and metrics (time, precision, and errors) were generated automatically by the software. Three evaluation modules were developed (spatial adaptation, depth adaptation, and dissection), and 35 expert and nonexpert neurosurgeons performed an initial evaluation of the system. A total of 81% and 90% of surgeons agreed that the visuals were satisfactory and movement and control were accurately replicated, respectively. The advantages and disadvantages of the system were compared. Here, we present a novel, low-cost, and easy-to-implement training system for developing basic neuroendoscopic psychomotor skills. The use of objective metrics, surgical instruments, and emulation of the neuroendoscope at 0° and 30° are competitive advantages of the current system. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Obesity induced by a pair-fed high fat sucrose diet: methylation and expression pattern of genes related to energy homeostasis

    Directory of Open Access Journals (Sweden)

    Campión Javier

    2010-06-01

    Full Text Available Abstract Background The expression of some genes controlling energy homeostasis could be regulated by epigenetic mechanisms that may play a role in body weight regulation. Thus, it is known that various nutritional factors affect DNA methylation. In order to assess whether the macronutrient composition of the diet could be related to the epigenetic regulation of gene expression and with obesity development, we investigated the effects on methylation and expression patterns of two pair-fed isocaloric diets in rats: control (rich in starch and HFS (rich in fat and sucrose. Results The pair-fed HFS diet induced higher weight gain and adiposity as compared to the controls as well as liver triglyceride accumulation and oxidative stress. Feeding the HFS diet impaired glucose tolerance and serum triglycerides and cholesterol. Liver glucokinase expression, a key glycolytic gene, remained unaltered, as well as the mRNA values of fatty acid synthase and NADH dehydrogenase (ubiquinone 1 beta subcomplex, 6 (NDUFB6 in liver and visceral adipocytes, which regulate lipogenesis and mitochondrial oxidative metabolism, respectively. Liver expression of hydroxyacyl-coenzyme A dehydrogenase (HADHB, a key gene of β-oxidation pathway, was higher in the HFS-fed animals. However, the methylation status of CpG islands in HADHB and glucokinase genes remained unchanged after feeding the HFS diet. Conclusions These results confirm that the distribution and type of macronutrients (starch vs. sucrose, and percent of fat influence obesity onset and the associated metabolic complications. HFS diets produce obesity independently of total energy intake, although apparently no epigenetic (DNA methylation changes accompanied the modifications observed in gene expression.

  10. Antitumor and Immunopotentiating Activity of Polysaccharide PST001 Isolated from the Seed Kernel of Tamarindus indica: An In Vivo Study in Mice

    Directory of Open Access Journals (Sweden)

    S. R. Aravind

    2012-01-01

    Full Text Available Antitumor activity of polysaccharide PST001 isolated from the seed kernel of Tamarindus indica was evaluated using different cancer cell lines. Human cancer cell lines A549, KB, and MCF-7 and murine cancer cell lines DLA and EAC were treated with PST001 and cell growth inhibition was assessed by MTT assay. In vivo studies were carried out for toxicity, tumor reduction and immunomodulation. The respective IC50 of PST001 in A549, KB, and DLA was at 80.72, 190.99, and 91.14 μg/mL. Significant tumor reduction was obtained in both DLA and EAC tumors on treatment with PST001 which was more prominent when PST001 was administered with CTX/5-fluorouracil. Increase in total WBC, CD4+ T-cell population, and bone marrow cellularity suggested strong immunomodulatory activity for this compound. No significant abnormality was observed in toxicity studies. Thus the results of the present study suggest that PST001 has immunomodulatory and tumor inhibitory activities and has the potential to be developed as an anticancer agent and immunomodulator either as a sole agent or as an adjuvant to other chemotherapeutic drugs.

  11. Gene Expression Profiles in Paired Gingival Biopsies from Periodontitis-Affected and Healthy Tissues Revealed by Massively Parallel Sequencing

    Science.gov (United States)

    Båge, Tove; Lagervall, Maria; Jansson, Leif; Lundeberg, Joakim; Yucel-Lindberg, Tülay

    2012-01-01

    Periodontitis is a chronic inflammatory disease affecting the soft tissue and bone that surrounds the teeth. Despite extensive research, distinctive genes responsible for the disease have not been identified. The objective of this study was to elucidate transcriptome changes in periodontitis, by investigating gene expression profiles in gingival tissue obtained from periodontitis-affected and healthy gingiva from the same patient, using RNA-sequencing. Gingival biopsies were obtained from a disease-affected and a healthy site from each of 10 individuals diagnosed with periodontitis. Enrichment analysis performed among uniquely expressed genes for the periodontitis-affected and healthy tissues revealed several regulated pathways indicative of inflammation for the periodontitis-affected condition. Hierarchical clustering of the sequenced biopsies demonstrated clustering according to the degree of inflammation, as observed histologically in the biopsies, rather than clustering at the individual level. Among the top 50 upregulated genes in periodontitis-affected tissues, we investigated two genes which have not previously been demonstrated to be involved in periodontitis. These included interferon regulatory factor 4 and chemokine (C-C motif) ligand 18, which were also expressed at the protein level in gingival biopsies from patients with periodontitis. In conclusion, this study provides a first step towards a quantitative comprehensive insight into the transcriptome changes in periodontitis. We demonstrate for the first time site-specific local variation in gene expression profiles of periodontitis-affected and healthy tissues obtained from patients with periodontitis, using RNA-seq. Further, we have identified novel genes expressed in periodontitis tissues, which may constitute potential therapeutic targets for future treatment strategies of periodontitis. PMID:23029519

  12. Enhanced genome editing tools for multi-gene deletion knock-out approaches using paired CRISPR sgRNAs in CHO cells

    DEFF Research Database (Denmark)

    Schmieder, Valerie; Bydlinski, Nina; Strasser, Richard

    2017-01-01

    Since the establishment of clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9, powerful strategies for engineering of CHO cell lines have emerged. Nevertheless, there is still room to expand the scope of the CRISPR tool box for further applications to improve CHO cell factories....... Here, we demonstrate activity of the alternative CRISPR endonuclease Cpf1 in CHO-K1 for the first time and that it can be used in parallel to CRISPR/Cas9 without any interference. Both, Cas9 and Cpf1, can be effectively used for multi-gene engineering with a strategy based on paired single guide RNAs...... of application of CRISPR for novel gene editing approaches in CHO cells and also enable the efficient realization of a genome-wide deletion library....

  13. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

    OpenAIRE

    Mahadevan Padmanabhan; Seto Donald

    2010-01-01

    Abstract Background The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling. Findings GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the v...

  14. Genetic variants and effects on milk traits of the caprine paired-like homeodomain transcription factor 2 (PITX2) gene in dairy goats.

    Science.gov (United States)

    Zhao, Haiyu; Wu, Xianfeng; Cai, Hanfang; Pan, Chuanying; Lei, Chuzhao; Chen, Hong; Lan, Xianyong

    2013-12-15

    The paired-like homeodomain transcription factor 2 (PITX2) gene plays a critical role in cell proliferation, differentiation, hematopoiesis and organogenesis. This gene regulates several genes' expressions in the Wnt/beta-catenin and POU1F1 pathways, thereby probably affecting milk performance. The goal of this study was to characterize the genetic variants of the PITX2 gene and test their associations with milk traits in dairy goats. Herein, four novel single nucleotide polymorphisms (SNPs), AC_000163:g.18117T>C, g.18161C>G, g.18322C>A and g.18353T>C, within the caprine PITX2 gene, were found in two famous Chinese dairy goat breeds. These SNPs mapping at Cys28Arg, Pro42Pro, IVS1+79C>A and IVS1+110T>C, were genotyped by the MvaI, SmaI, MspI and RsaI aCRS-RFLP or PCR-RFLP methods, respectively. Accordingly, two main haplotypes (CGCT and CGCC) were identified among the specimens. Association testing revealed that the SmaI and RsaI polymorphisms were significantly associated with the milk fat content, milk lactose content and milk density (PPITX2 gene had the significant effects on milk traits. Hence, the RsaI and SmaI loci could be regarded as two DNA markers for selecting superior milk performance in dairy goats. These preliminary findings not only would extend the spectrum of genetic variation of the goat PITX2 gene, but also would contribute to implementing marker-assisted selection (MAS) in breeding and genetics in dairy goats. © 2013.

  15. Computer-aided codon-pairs deoptimization of the major envelope GP5 gene attenuates porcine reproductive and respiratory syndrome virus.

    Science.gov (United States)

    Ni, Yan-Yan; Zhao, Zhao; Opriessnig, Tanja; Subramaniam, Sakthivel; Zhou, Lei; Cao, Dianjun; Cao, Qian; Yang, Hanchun; Meng, Xiang-Jin

    2014-02-01

    Synthetic attenuated virus engineering (SAVE) is an emerging technology that enables rapid attenuation of viruses. In this study, by using SAVE we demonstrated rapid attenuation of an arterivirus, porcine reproductive and respiratory syndrome virus (PRRSV). The major envelope GP5 gene of PRRSV was codon-pair deoptimized aided by a computer algorithm. The codon-pair deoptimized virus, designated as SAVE5 with a deoptimized GP5 gene, was successfully rescued in vitro. The SAVE5 virus replicated at a lower level in vitro with a significant decrease of GP5 protein expression compared to the wild-type PRRSV VR2385 virus. Pigs experimentally infected with the SAVE5 virus had significantly lower viremia level up to 14 days post-infection as well as significantly reduced gross and histological lung lesions when compared to wild-type PRRSV VR2385 virus-infected pigs, indicating the attenuation of the SAVE5 virus. This study proved the feasibility of rapidly attenuating PRRSV by SAVE. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs.

    Science.gov (United States)

    Girelli Zubani, Giulia; Zivojnovic, Marija; De Smet, Annie; Albagli-Curiel, Olivier; Huetz, François; Weill, Jean-Claude; Reynaud, Claude-Agnès; Storck, Sébastien

    2017-04-03

    During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung-/-Pms2-/- mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases. © 2017 Girelli Zubani et al.

  17. Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3 gene.

    Directory of Open Access Journals (Sweden)

    Doreen Becker

    Full Text Available Microphthalmia in sheep is an autosomal recessive inherited congenital anomaly found within the Texel breed. It is characterized by extremely small or absent eyes and affected lambs are absolutely blind. For the first time, we use a genome-wide ovine SNP array for positional cloning of a Mendelian trait in sheep. Genotyping 23 cases and 23 controls using Illumina's OvineSNP50 BeadChip allowed us to localize the causative mutation for microphthalmia to a 2.4 Mb interval on sheep chromosome 22 by association and homozygosity mapping. The PITX3 gene is located within this interval and encodes a homeodomain-containing transcription factor involved in vertebrate lens formation. An abnormal development of the lens vesicle was shown to be the primary event in ovine microphthalmia. Therefore, we considered PITX3 a positional and functional candidate gene. An ovine BAC clone was sequenced, and after full-length cDNA cloning the PITX3 gene was annotated. Here we show that the ovine microphthalmia phenotype is perfectly associated with a missense mutation (c.338G>C, p.R113P in the evolutionary conserved homeodomain of PITX3. Selection against this candidate causative mutation can now be used to eliminate microphthalmia from Texel sheep in production systems. Furthermore, the identification of a naturally occurring PITX3 mutation offers the opportunity to use the Texel as a genetically characterized large animal model for human microphthalmia.

  18. [Delta⁰-thalassemia by insertion of 27 base pairs in δ-globin gene with decreased hemoglobin A₂ levels].

    Science.gov (United States)

    González Borrachero, Maria Luisa; de la Fuente-Gonzalo, Félix; González, Fernando Ataúlfo; Nieto, Jorge M; Villegas, Ana; Ropero, Paloma

    2015-04-08

    We describe a novel delta-thalassemia mutation causing decreased hemoglobin (Hb) A2 levels associated with Hb Watts, variant Hb resulting from a trinucleotide deletion in Spain. Hb variant analysis was performed by cation-exchange high performance liquid chromatography (HPLC) and capillary zone electrophoresis. Polymerase chain reaction and DNA sequence analyses were used to identify mutations in the δ- and α-globin genes. Abnormal Hb was observed on capillary zone electrophoresis in Z6 and by cation-exchange HPLC a slower peak than HbA was observed at an retention time of 4.19min. This variant Hb is called Hb Watts [α2 74(EF3)Asp->0 or α2 75(EF4)Asp->0; HBA2:c.226_228delGAC]. The decreased HbA2 percentage owes to an insertion of 27nt between nt 83 and 84 of IVS-I of the δ-globin gene. When analyzing a chromatogram, the possibility of the existence of delta-thalassemia or an HbA2 variant should be considered, apart from alfa-, beta-thalassemia and structural haemoglobinopathies. To this end, each of the peaks and their percentages should be considered to allow for correct interpretation and to avoid misdiagnosis as much as possible. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

  19. Novel single base-pair deletion in exon 1 of XK gene leading to McLeod syndrome with chorea, muscle wasting, peripheral neuropathy, acanthocytosis and haemolysis.

    Science.gov (United States)

    Wiethoff, Sarah; Xiromerisiou, Georgia; Bettencourt, Conceição; Kioumi, Anna; Tsiptsios, Iakovos; Tychalas, Athanasios; Evaggelia, Markousi; George, Kaltsounis; Makris, Vasileios; Hardy, John; Houlden, Henry

    2014-04-15

    We present a 70-year-old male patient of Greek origin with choreatic movements of the tongue and face, lower limb muscle weakness, peripheral neuropathy, elevated creatinephosphokinase (CPK), acanthocytosis and haemolysis in the absence of Kell RBC antigens with an additional Factor IX-deficiency. Genetic testing for mutations in the three exons of the XK gene revealed a previously unreported hemizygous single base-pair frameshift deletion at exon 1 (c.229delC, p.Leu80fs). In conclusion, we hereby describe a rare phenotype of a patient with McLeod syndrome which was discovered coincidentally during routine blood group testing and consecutively genetically confirmed. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Light and auxin responsive cytochrome P450s from Withania somnifera Dunal: cloning, expression and molecular modelling of two pairs of homologue genes with differential regulation.

    Science.gov (United States)

    Srivastava, Sudhakar; Sangwan, Rajender Singh; Tripathi, Sandhya; Mishra, Bhawana; Narnoliya, L K; Misra, L N; Sangwan, Neelam S

    2015-11-01

    Cytochrome P450s (CYPs) catalyse a wide variety of oxygenation/hydroxylation reactions that facilitate diverse metabolic functions in plants. Specific CYP families are essential for the biosynthesis of species-specialized metabolites. Therefore, we investigated the role of different CYPs related to secondary metabolism in Withania somnifera, a medicinally important plant of the Indian subcontinent. In this study, complete complementary DNAs (cDNAs) of four different CYP genes were isolated and christened as WSCYP93Id, WSCYP93Sm, WSCYP734B and WSCYP734R. These cDNAs encoded polypeptides comprising of 498, 496, 522 and 550 amino acid residues with their deduced molecular mass of 56.7, 56.9, 59.4 and 62.2 kDa, respectively. Phylogenetic study and molecular modelling analysis of the four cloned WSCYPs revealed their categorization into two CYP families (CYP83B1 and CYP734A1) belonging to CYP71 and CYP72 clans, respectively. BLASTp searches showed similarity of 75 and 56 %, respectively, between the two CYP members of CYP83B1 and CYP734A1 with major variances exhibited in their N-terminal regions. The two pairs of homologues exhibited differential expression profiles in the leaf tissues of selected chemotypes of W. somnifera as well as in response to treatments such as methyl jasmonate, wounding, light and auxin. Light and auxin regulated two pairs of WSCYP homologues in a developing seedling in an interesting differential manner. Their lesser resemblance and homology with other CYP sequences suggested these genes to be more specialized and distinct ones. The results on chemotype-specific expression patterns of the four genes strongly suggested their key/specialized involvement of the CYPs in the biosynthesis of chemotype-specific metabolites, though their further biochemical characterization would reveal the specificity in more detail. It is revealed that WSCYP93Id and WSCYP93Sm may be broadly involved in the oxygenation reactions in the plant and, thereby, control

  1. Pharmacological profile of the novel inotropic agent (E,Z)-3-((2-aminoethoxy)imino)androstane-6,17-dione hydrochloride (PST2744).

    Science.gov (United States)

    Micheletti, R; Mattera, G G; Rocchetti, M; Schiavone, A; Loi, M F; Zaza, A; Gagnol, R J P; De Munari, S; Melloni, P; Carminati, P; Bianchi, G; Ferrari, P

    2002-11-01

    The novel Na(+)/K(+)-ATPase inhibitor (E,Z)-3-((2-aminoethoxy)imino)androstane-6,17-dione hydrochloride (PST2744) was characterized for its inotropic and toxic properties. Inhibition potency on dog kidney Na(+)/K(+)-ATPase was comparable (0.43 microM) to that of digoxin (0.45 microM). PST2744 concentration-dependently increased force of contraction in guinea pig atria and twitch amplitude in isolated guinea pig myocytes; in the latter, aftercontractions developed significantly less than with digoxin. Intravenous infusion of 0.2 mg/kg/min PST2744 in anesthetized guinea pigs exerted an immediate and long-lasting inotropic effect (ED(80) of 1.89 +/- 0.37 mg/kg) without causing lethal arrhythmias up to a cumulative dose of 18 mg/kg. Conversely, an equieffective infusion of digoxin (0.016 mg/kg/min; ED(80) of 0.32 mg/kg) caused lethal arrhythmias at a cumulative dose of 0.81 mg/kg. At a higher rate (0.4 mg/kg/min), PST2744 induced lethal arrhythmias, with a lethal dose/ED(80) ratio significantly greater than digoxin (20.2 +/- 6.3 versus 3.23 +/- 0.55, p digoxin (18.3 +/- 4.5, p digoxin. In conscious dogs with a healed myocardial infarction, PST2744 significantly increased resting values of +dP/dt(max), left ventricular pressure, and SPB, and increased +dP/dt(max) throughout treadmill exercise while reverting the increase in left ventricular end diastolic pressure seen in control animals. Digoxin significantly decreased basal heart rate, while not affecting the hemodynamic response to exercise. Thus, PST2744 represents a new class of Na(+)/K(+)-ATPase inhibitors endowed with inotropic activity comparable with that of digitalis but having greater safety.

  2. Rapid genotyping assays for the 4-base pair deletion of canine MDR1/ABCB1 gene and low frequency of the mutant allele in Border Collie dogs.

    Science.gov (United States)

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2012-01-01

    P-glycoprotein, encoded by the MDR1 or ABCB1 gene, is an integral component of the blood-brain barrier as an efflux pump for xenobiotics crucial in limiting drug uptake into the central nervous system. Dogs homozygous for a 4-base pair deletion of the canine MDR1 gene show altered expression or function of P-glycoprotein, resulting in neurotoxicosis after administration of the substrate drugs. In the present study, the usefulness of microchip electrophoresis for genotyping assays detecting this deletion mutation was evaluated. Mutagenically separated polymerase chain reaction (MS-PCR) and real-time PCR assays were newly developed and evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies dogs in Japan to determine the allele frequency in this breed. Microchip electrophoresis showed advantages in detection sensitivity and time saving over other modes of electrophoresis. The MS-PCR assay clearly discriminated all genotypes. Real-time PCR assay was most suitable for a large-scale survey due to its high throughput and rapidity. The genotyping survey demonstrated that the carrier and mutant allele frequencies were 0.49% and 0.25%, respectively, suggesting that the mutant allele frequency in Border Collies is markedly low compared to that in the susceptible dog breeds such as rough and smooth Collies.

  3. CYP2E1PstI/RsaI polymorphism and interaction with tobacco, alcohol and GSTs in gastric cancer susceptibility: A meta-analysis of the literature.

    NARCIS (Netherlands)

    S. Boccia (Stefania); S. de Lauretis (Angelo); F. Gianfagna (Francesco); C.M. van Duijn (Cornelia); G. Ricciardi (Gualtiero)

    2007-01-01

    textabstractStudies investigating the association between cytochrome P450 2E1 (CYP2E1) 5'-flanking region (PstI/RsaI) polymorphism and gastric cancer risk report conflicting results. The rationale for this meta-analysis was to determine whether CYP2E1*2 (c2) variant allele of CYP2E1 increases

  4. Conserved regulation of p53 network dosage by microRNA-125b occurs through evolving miRNA-target gene pairs.

    Directory of Open Access Journals (Sweden)

    Minh T N Le

    2011-09-01

    Full Text Available MicroRNAs regulate networks of genes to orchestrate cellular functions. MiR-125b, the vertebrate homologue of the Caenorhabditis elegans microRNA lin-4, has been implicated in the regulation of neural and hematopoietic stem cell homeostasis, analogous to how lin-4 regulates stem cells in C. elegans. Depending on the cell context, miR-125b has been proposed to regulate both apoptosis and proliferation. Because the p53 network is a central regulator of both apoptosis and proliferation, the dual roles of miR-125b raise the question of what genes in the p53 network might be regulated by miR-125b. By using a gain- and loss-of-function screen for miR-125b targets in humans, mice, and zebrafish and by validating these targets with the luciferase assay and a novel miRNA pull-down assay, we demonstrate that miR-125b directly represses 20 novel targets in the p53 network. These targets include both apoptosis regulators like Bak1, Igfbp3, Itch, Puma, Prkra, Tp53inp1, Tp53, Zac1, and also cell-cycle regulators like cyclin C, Cdc25c, Cdkn2c, Edn1, Ppp1ca, Sel1l, in the p53 network. We found that, although each miRNA-target pair was seldom conserved, miR-125b regulation of the p53 pathway is conserved at the network level. Our results lead us to propose that miR-125b buffers and fine-tunes p53 network activity by regulating the dose of both proliferative and apoptotic regulators, with implications for tissue stem cell homeostasis and oncogenesis.

  5. Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH-III Shows SERAT3;2 Promoter is Nested Within the IDH-III Promoter.

    Science.gov (United States)

    Raipuria, Ritesh Kumar; Kumar, Vajinder; Guruprasad, Kadur Narayan; Bhat, Shripad Ramachandra

    2017-07-01

    Intergenic regions of divergent gene pairs show bidirectional promoter activity but whether regulatory sequences for gene expression in opposite directions are shared is not established. In this study, promoters of divergently arranged gene pair At4g35640-At4g35650 (SERAT3;2-IDH-III) of Arabidopsis thaliana were analyzed to identify overlapping regulatory regions. Both genes showed the highest expression in flower buds and flowers. 5' RACE experiments extended the intergenic region from 161 bp shown in TAIR annotation to 512 bp. GUS analysis of transgenic A. thaliana plants carrying the 691 bp fragment (512 bp intergenic region plus 5' UTR of both the genes) linked to uidA gene revealed that SERAT3;2 promoter drives gene expression in the tapetum, whereas IDH-III promoter functions specifically in microspores/pollen. Serial 5' deletion of the 691 bp fragment showed SERAT3;2 promoter extends up to -355 position, whereas IDH-III promoter encompasses the 512 bp intergenic region. In transgenics, uidA transcript levels were lower than native SERAT3;2 and IDH-III transcripts indicating presence of additional cis regulatory elements beyond the 691 bp fragment. The present study demonstrated for the first time occurrence of a nested promoter in plants and identified a novel bidirectional promoter capable of driving gene expression in tapetum and microspores/pollen.

  6. Aligned magnetic field effects on water based metallic nanoparticles over a stretching sheet with PST and thermal radiation effects

    Science.gov (United States)

    Rashid, Irfan; Ul Haq, Rizwan; Al-Mdallal, Qasem M.

    2017-05-01

    This study deals the simultaneous effects of inclined magnetic field and prescribed surface temperature (PST) on boundary layer flow of nanofluid over a stretching sheet. In order to make this mechanism more feasible, we have further considered the velocity slip and thermal radiation effects. Moreover, this perusal is made to consider the two kinds of nanofluid namely: Cu -water and A l2O3-water. Inclined magnetic field is utilized to accompanying an aligned angle that varies from 0 to π / 2 . The exact solutions are acquired from the transformed non-dimensional momentum and energy equations in the form of confluent hypergeometric function. Lorentz forces and aligned magnetic field depicts the significant effects on nanofluid. We found that, due to the increase in the aligned angle provides the enhancement in local skin friction coefficient and a reduction in the local Nusselt number. The combined impacts of inclined magnetic field with other emerging parameters such as velocity slip, thermal radiation and nanoparticles volume fraction on velocity, temperature, local Nusselt number and skin friction coefficient are examined. Flow behavior of nanofluid is also determined via stream lines pattern.

  7. Cloning and expression in Escherichia coli of genes involved in the lysine pathway of Brevibacterium lactofermentum.

    Science.gov (United States)

    Márquez, G; Sousa, J M; Sánchez, F

    1985-01-01

    The Brevibacterium lactofermentum genes which complement Escherichia coli lysA and asd-1 mutants were identified, respectively, as a 1.9-kilobase PstI-ClaI fragment and a 2.5-kilobase PstI fragment by cloning into pBR325. Southern blot transfers show hybridization to chromosomal fragments of identical size. The putative B. lactofermentum asd and lysA products are 44 and 48 kilodaltons, respectively. Images PMID:2864331

  8. Intercepción de partículas suspendidas totales (PST por cinco especies de árboles urbanos en el Valle de Aburrá

    Directory of Open Access Journals (Sweden)

    Byron Duran Rivera

    2009-01-01

    Full Text Available Durante los meses de mayo a julio de 2005, se evaluó la capacidad de retención de Partículas Suspendidas Totales (PST en cinco especies arbóreas plantadas en el Valle de Aburrá, mediante la cuantificación de la cantidad de sólidos presentes en el follaje de las especies. Adicionalmente se analizaron características foliares que pudieran influir en la retención de PST. La información obtenida fue extrapolada a la vegetación mantenida por el Metro de Medellín. Se encontró que Syzygium malaccense y Lagerstroemia speciosa, son mas eficientes en cuanto a la intercepción de PST, estimándose que 1379 individuos pertenecientes a las cinco especies evaluadas y establecidas en el perímetro del Metro de Medellín, interceptan 658 Kg/año. Esta investigación buscó generar información que ayude en la toma de decisión de especies a plantar en sitios poluidos, con el fin de maximizar la intercepción de este contaminante.

  9. Genetic polymorphism of five genes associated with growth traits in ...

    African Journals Online (AJOL)

    While IGF-1gene revealed three fragments after digestion with Haelll with genotype AA, AB and BB and the frequencies of allele A varied from 0.432 to 0.731. Furthermore, PCR-RFLP of POUIF1 gene showed two fragments after digestion by Pst1 endonuclease with genotype TT and CC and the frequencies of allele T ...

  10. Expression of the pair-rule gene homologs runt, Pax3/7, even-skipped-1 and even-skipped-2 during larval and juvenile development of the polychaete annelid Capitella teleta does not support a role in segmentation

    Directory of Open Access Journals (Sweden)

    Seaver Elaine C

    2012-04-01

    Full Text Available Abstract Background Annelids and arthropods each possess a segmented body. Whether this similarity represents an evolutionary convergence or inheritance from a common segmented ancestor is the subject of ongoing investigation. Methods To investigate whether annelids and arthropods share molecular components that control segmentation, we isolated orthologs of the Drosophila melanogaster pair-rule genes, runt, paired (Pax3/7 and eve, from the polychaete annelid Capitella teleta and used whole mount in situ hybridization to characterize their expression patterns. Results When segments first appear, expression of the single C. teleta runt ortholog is only detected in the brain. Later, Ct-runt is expressed in the ventral nerve cord, foregut and hindgut. Analysis of Pax genes in the C. teleta genome reveals the presence of a single Pax3/7 ortholog. Ct-Pax3/7 is initially detected in the mid-body prior to segmentation, but is restricted to two longitudinal bands in the ventral ectoderm. Each of the two C. teleta eve orthologs has a unique and complex expression pattern, although there is partial overlap in several tissues. Prior to and during segment formation, Ct-eve1 and Ct-eve2 are both expressed in the bilaterial pair of mesoteloblasts, while Ct-eve1 is expressed in the descendant mesodermal band cells. At later stages, Ct-eve2 is expressed in the central and peripheral nervous system, and in mesoderm along the dorsal midline. In late stage larvae and adults, Ct-eve1 and Ct-eve2 are expressed in the posterior growth zone. Conclusions C. teleta eve, Pax3/7 and runt homologs all have distinct expression patterns and share expression domains with homologs from other bilaterians. None of the pair-rule orthologs examined in C. teleta exhibit segmental or pair-rule stripes of expression in the ectoderm or mesoderm, consistent with an independent origin of segmentation between annelids and arthropods.

  11. Upregulation of the Nr2f1-A830082K12Rik gene pair in murine neural crest cells results in a complex phenotype reminiscent of Waardenburg syndrome type 4.

    Science.gov (United States)

    Bergeron, Karl-F; Nguyen, Chloé M A; Cardinal, Tatiana; Charrier, Baptiste; Silversides, David W; Pilon, Nicolas

    2016-11-01

    Waardenburg syndrome is a neurocristopathy characterized by a combination of skin and hair depigmentation, and inner ear defects. In the type 4 form, these defects show comorbidity with Hirschsprung disease, a disorder marked by an absence of neural ganglia in the distal colon, triggering functional intestinal obstruction. Here, we report that the Spot mouse line - obtained through an insertional mutagenesis screen for genes involved in neural crest cell (NCC) development - is a model for Waardenburg syndrome type 4. We found that the Spot insertional mutation causes overexpression of an overlapping gene pair composed of the transcription-factor-encoding Nr2f1 and the antisense long non-coding RNA A830082K12Rik in NCCs through a mechanism involving relief of repression of these genes. Consistent with the previously described role of Nr2f1 in promoting gliogenesis in the central nervous system, we further found that NCC-derived progenitors of the enteric nervous system fail to fully colonize Spot embryonic guts owing to their premature differentiation in glial cells. Taken together, our data thus identify silencer elements of the Nr2f1-A830082K12Rik gene pair as new candidate loci for Waardenburg syndrome type 4. © 2016. Published by The Company of Biologists Ltd.

  12. Upregulation of the Nr2f1-A830082K12Rik gene pair in murine neural crest cells results in a complex phenotype reminiscent of Waardenburg syndrome type 4

    Directory of Open Access Journals (Sweden)

    Karl-F. Bergeron

    2016-11-01

    Full Text Available Waardenburg syndrome is a neurocristopathy characterized by a combination of skin and hair depigmentation, and inner ear defects. In the type 4 form, these defects show comorbidity with Hirschsprung disease, a disorder marked by an absence of neural ganglia in the distal colon, triggering functional intestinal obstruction. Here, we report that the Spot mouse line – obtained through an insertional mutagenesis screen for genes involved in neural crest cell (NCC development – is a model for Waardenburg syndrome type 4. We found that the Spot insertional mutation causes overexpression of an overlapping gene pair composed of the transcription-factor-encoding Nr2f1 and the antisense long non-coding RNA A830082K12Rik in NCCs through a mechanism involving relief of repression of these genes. Consistent with the previously described role of Nr2f1 in promoting gliogenesis in the central nervous system, we further found that NCC-derived progenitors of the enteric nervous system fail to fully colonize Spot embryonic guts owing to their premature differentiation in glial cells. Taken together, our data thus identify silencer elements of the Nr2f1-A830082K12Rik gene pair as new candidate loci for Waardenburg syndrome type 4.

  13. Identification of expressed genes during compatible interaction between stripe rust (Puccinia striiformis and wheat using a cDNA library

    Directory of Open Access Journals (Sweden)

    Huang Lili

    2009-12-01

    Full Text Available Abstract Background Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst, is one of the most destructive diseases of wheat worldwide. To establish compatibility with the host, Pst forms special infection structures to invade the plant with minimal damage to host cells. Although compatible interaction between wheat and Pst has been studied using various approaches, research on molecular mechanisms of the interaction is limited. The aim of this study was to develop an EST database of wheat infected by Pst in order to determine transcription profiles of genes involved in compatible wheat-Pst interaction. Results Total RNA, extracted from susceptible infected wheat leaves harvested at 3, 5 and 8 days post inoculation (dpi, was used to create a cDNA library, from which 5,793 ESTs with high quality were obtained and clustered into 583 contigs and 2,160 singletons to give a set of 2,743 unisequences (GenBank accessions: GR302385 to GR305127. The BLASTx program was used to search for homologous genes of the unisequences in the GenBank non-redundant protein database. Of the 2,743 unisequences, 52.8% (the largest category were highly homologous to plant genes; 16.3% to fungal genes and 30% of no-hit. The functional classification of all ESTs was established based on the database entry giving the best E-value using the Bevan's classification categories. About 50% of the ESTs were significantly homologous to genes encoding proteins with known functions; 20% were similar to genes encoding proteins with unknown functions and 30% did not have significant homology to any sequence in the database. The quantitative real-time PCR (qRT-PCR analysis determined the transcription profiles and their involvement in the wheat-Pst interaction for seven of the gene. Conclusion The cDNA library is useful for identifying the functional genes involved in the wheat-Pst compatible interaction, and established a new database for studying Pst pathogenesis genes

  14. Estudo do papel do sistema de captação de fosfato inorgânico (Pst) na fisiologia e patogênese de Streptococcus mutans.

    OpenAIRE

    Daniela Eleuterio da Luz

    2011-01-01

    O fosfato inorgânico é um composto essencial por estar relacionado com diversos processos metabólicos e biossíntese de moléculas relevantes à sobrevivência celular. Em bactéria são conhecidos dois tipos principais de transportadores específicos de fosfato inorgânico, o sistema Pit, de baixa afinidade, e o sistema Pst de alta afinidade, um ABC transportador, ativado sob carência de fosfato extracelular. A interação deste sistema com a fisiologia e patogênese de Streptococcus mutans, o principa...

  15. Pairing dynamics and the origin of species

    OpenAIRE

    Puebla, Oscar; Bermingham, Eldredge; Guichard, Frédéric

    2011-01-01

    Whether sexual selection alone can drive the evolution of assortative mating in the presence of gene flow is a long-standing question in evolutionary biology. Here, we report a role for pairing dynamics of individuals when mate choice is mutual, which is sufficient for the evolution of assortative mating by sexual selection alone in the presence of gene flow. Through behavioural observation, individual-based simulation and population genetic analysis, we evaluate the pairing dynamics of coral...

  16. Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs

    Directory of Open Access Journals (Sweden)

    Nakai Kenta

    2008-04-01

    Full Text Available Abstract Background Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial. Results We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation. Conclusion Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.

  17. Determining the Advantages, Costs, and Trade-Offs of a Novel Sodium Channel Mutation in the Copepod Acartia hudsonica to Paralytic Shellfish Toxins (PST)

    Science.gov (United States)

    Finiguerra, Michael; Avery, David E.; Dam, Hans G.

    2015-01-01

    The marine copepod Acartia hudsonica was shown to be adapted to dinoflagellate prey, Alexandrium fundyense, which produce paralytic shellfish toxins (PST). Adaptation to PSTs in other organisms is caused by a mutation in the sodium channel. Recently, a mutation in the sodium channel in A. hudsonica was found. In this study, we rigorously tested for advantages, costs, and trade-offs associated with the mutant isoform of A. hudsonica under toxic and non-toxic conditions. We combined fitness with wild-type: mutant isoform ratio measurements on the same individual copepod to test our hypotheses. All A. hudsonica copepods express both the wild-type and mutant sodium channel isoforms, but in different proportions; some individuals express predominantly mutant (PMI) or wild-type isoforms (PWI), while most individuals express relatively equal amounts of each (EI). There was no consistent pattern of improved performance as a function of toxin dose for egg production rate (EPR), ingestion rate (I), and gross growth efficiency (GGE) for individuals in the PMI group relative to individuals in the PWI expression group. Neither was there any evidence to indicate a fitness benefit to the mutant isoform at intermediate toxin doses. No clear advantage under toxic conditions was associated with the mutation. Using a mixed-diet approach, there was also no observed relationship between individual wild-type: mutant isoform ratios and among expression groups, on both toxic and non-toxic diets, for eggs produced over three days. Lastly, expression of the mutant isoform did not mitigate the negative effects of the toxin. That is, the reductions in EPR from a toxic to non-toxic diet for copepods were independent of expression groups. Overall, the results did not support our hypotheses; the mutant sodium channel isoform does not appear to be related to adaptation to PST in A. hudsonica. Other potential mechanisms responsible for the adaptation are discussed. PMID:26075900

  18. Determining the Advantages, Costs, and Trade-Offs of a Novel Sodium Channel Mutation in the Copepod Acartia hudsonica to Paralytic Shellfish Toxins (PST.

    Directory of Open Access Journals (Sweden)

    Michael Finiguerra

    Full Text Available The marine copepod Acartia hudsonica was shown to be adapted to dinoflagellate prey, Alexandrium fundyense, which produce paralytic shellfish toxins (PST. Adaptation to PSTs in other organisms is caused by a mutation in the sodium channel. Recently, a mutation in the sodium channel in A. hudsonica was found. In this study, we rigorously tested for advantages, costs, and trade-offs associated with the mutant isoform of A. hudsonica under toxic and non-toxic conditions. We combined fitness with wild-type: mutant isoform ratio measurements on the same individual copepod to test our hypotheses. All A. hudsonica copepods express both the wild-type and mutant sodium channel isoforms, but in different proportions; some individuals express predominantly mutant (PMI or wild-type isoforms (PWI, while most individuals express relatively equal amounts of each (EI. There was no consistent pattern of improved performance as a function of toxin dose for egg production rate (EPR, ingestion rate (I, and gross growth efficiency (GGE for individuals in the PMI group relative to individuals in the PWI expression group. Neither was there any evidence to indicate a fitness benefit to the mutant isoform at intermediate toxin doses. No clear advantage under toxic conditions was associated with the mutation. Using a mixed-diet approach, there was also no observed relationship between individual wild-type: mutant isoform ratios and among expression groups, on both toxic and non-toxic diets, for eggs produced over three days. Lastly, expression of the mutant isoform did not mitigate the negative effects of the toxin. That is, the reductions in EPR from a toxic to non-toxic diet for copepods were independent of expression groups. Overall, the results did not support our hypotheses; the mutant sodium channel isoform does not appear to be related to adaptation to PST in A. hudsonica. Other potential mechanisms responsible for the adaptation are discussed.

  19. Homozygosity for a single base-pair mutation in the oocyte-specific GDF9 gene results in sterility in Thoka sheep

    DEFF Research Database (Denmark)

    Nicel, Linda; Bishop, Stephen; Pong-Wong, Richardo

    2009-01-01

    ovulation rate, although in some cases homozygous ewes are infertile. In the present study we present a detailed characterisation of a novel mutation in growth differentiation factor 9 (GDF9), found in Icelandic Thoka sheep. This mutation is a single base change (A1279C) resulting in a non...... and infertility in homozygotes. Analysis of homozygote ovarian morphology and a number of genes normally activated in growing follicles showed that GDF9 was not involved in oocyte activation, but in subsequent development of the follicle. This study highlights the importance of oocyte factors in regulating...

  20. Matched-pair classification

    Energy Technology Data Exchange (ETDEWEB)

    Theiler, James P [Los Alamos National Laboratory

    2009-01-01

    Following an analogous distinction in statistical hypothesis testing, we investigate variants of machine learning where the training set comes in matched pairs. We demonstrate that even conventional classifiers can exhibit improved performance when the input data has a matched-pair structure. Online algorithms, in particular, converge quicker when the data is presented in pairs. In some scenarios (such as the weak signal detection problem), matched pairs can be generated from independent samples, with the effect not only doubling the nominal size of the training set, but of providing the structure that leads to better learning. A family of 'dipole' algorithms is introduced that explicitly takes advantage of matched-pair structure in the input data and leads to further performance gains. Finally, we illustrate the application of matched-pair learning to chemical plume detection in hyperspectral imagery.

  1. Oxylipin biosynthesis genes positively regulate programmed cell death during compatible infections with the synergistic pair potato virus X-potato virus Y and Tomato spotted wilt virus.

    Science.gov (United States)

    García-Marcos, Alberto; Pacheco, Remedios; Manzano, Aranzazu; Aguilar, Emmanuel; Tenllado, Francisco

    2013-05-01

    One of the most severe symptoms caused by compatible plant-virus interactions is systemic necrosis, which shares common attributes with the hypersensitive response to incompatible pathogens. Although several studies have identified viral symptom determinants responsible for systemic necrosis, mechanistic models of how they contribute to necrosis in infected plants remain scarce. Here, we examined the involvement of different branches of the oxylipin biosynthesis pathway in the systemic necrosis response caused either by the synergistic interaction of Potato virus X with Potato virus Y (PVX-PVY) or by Tomato spotted wilt virus (TSWV) in Nicotiana benthamiana. Silencing either 9-lipoxygenase (LOX), 13-LOX, or α-dioxygenase-1 (α-DOX-1) attenuated the programmed cell death (PCD)-associated symptoms caused by infection with either PVX-PVY or TSWV. In contrast, silencing of the jasmonic acid perception gene, COI1 (Coronatine insensitive 1), expedited cell death during infection with compatible viruses. This correlated with an enhanced expression of oxylipin biosynthesis genes and dioxygenase activity in PVX-PVY-infected plants. Moreover, the Arabidopsis thaliana double lox1 α-dox-1 mutant became less susceptible to TSWV infection. We conclude that oxylipin metabolism is a critical component that positively regulates the process of PCD during compatible plant-virus interactions but does not play a role in restraining virus accumulation in planta.

  2. Expression of interferon regulatory factor 6, muscle segment homeobox 1, paired box gene 9, homeo box B3, and related to tyrosine kinases in human cleft-affected tissue

    Directory of Open Access Journals (Sweden)

    Benita Krivicka-Uzkurele

    2016-01-01

    Full Text Available Background and Aim: Recent studies demonstrate direct roles of different genes during formation of secondary palate, but there are no still data about local expression and distribution of gene products in cleft palate affected human tissue. Thus, the aim of our study was to investigate cleft disordered cartilage and bone for detection of local expression of key regulators of palatogenesis and its correlations. Materials and Methods: The study involved 16 patients with unilateral cleft lip and palate. Tissue samples were proceeded for detection of interferon regulatory factor 6 (IRF6, muscle segment homeobox 1 (MSX1, paired box gene 9 (PAX9, homeo box B3 (HOXB3, and related to tyrosine kinases with biotin-streptavidin immunohistochemistry. Distribution of immunoreactive structures was detected semiquantitatively. Statistical analysis included the Mann-Whitney test and Pearson′s correlation test. Results: Statistically significant differences were found between expression of IGFR6, MSX1, and HOXB3 in the cartilage and bone. We also detected statistically significant correlation between the expressions of PAX9 and MSX1 in the bone tissue. Conclusions: Cleft lip and palate disordered cartilage is characterized by more pronounced expression of IRF6, MSX1, and PAX9. Expression of HOXB3 is more characteristic for cleft lip and palate affected bone. Considered as a whole, our results suggest that the cleft lip and palate affected cartilage seems more plastic in tissue remodeling what can probably result in qualitative postoperative tissue reconstruction.

  3. Two single-base-pair substitutions causing desensitization to tryptophan feedback inhibition of anthranilate synthase and enhanced expression of tryptophan genes of Brevibacterium lactofermentum.

    Science.gov (United States)

    Matsui, K; Miwa, K; Sano, K

    1987-01-01

    A 5-fluorotryptophan-resistant mutant, termed 1041, was isolated from Brevibacterium lactofermentum AJ12036. The anthranilate synthase of 1041 was insensitive to feedback inhibition by tryptophan, and the specific activities of the anthranilate synthase and anthranilate phosphoribosyltransferase of 1041 were 29- and 23-fold higher than those in parental strain AJ12036, respectively. A single-base change (adenine to cytosine) that resulted in a Ser-to-Arg substitution was found in the trpE structural gene of 1041. This substitution was identified as the cause of the desensitization to feedback inhibition by tryptophan of anthranilate synthase in 1041. Another substitution (guanine to adenine) was found at a position in which a mutation would destabilize the rho-independent terminator structure within the putative attenuator. The enhanced synthesis of tryptophan enzymes in 1041 could be caused by this substitution in the attenuator. PMID:3667535

  4. The information contained in multiple sibling pairs.

    Science.gov (United States)

    Hodge, S E

    1984-01-01

    In a sibship of size s, s(s-1)/2 sib pairs can be formed, but these pairs are statistically dependent when s greater than 2. This study examines how much independent information is obtained when all possible pairs are used to evaluate the sharing of genes identical by descent. A logarithmic measure of information, sigma pilog2pi [Shannon, 1948], is used. The basic unit of information is the binomial "bit," or the amount of information in the toss of a fair coin. It is shown that a single independent sib pair contains 1.5 bits. The complete sibship contains a total of 2s-3+(1/2)s-1 bits, or (2s-3+(1/2)s-1)/1.5 pair-equivalents of information. The information is reduced if all sib genotypes do not occur with equal probability.

  5. Quantity of the dinoflagellate sxtA4 gene and cell density correlates with paralytic shellfish toxin production in Alexandrium ostenfeldii blooms.

    Science.gov (United States)

    Savela, Henna; Harju, Kirsi; Spoof, Lisa; Lindehoff, Elin; Meriluoto, Jussi; Vehniäinen, Markus; Kremp, Anke

    2016-02-01

    Many marine dinoflagellates, including several species of the genus Alexandrium, Gymnodinium catenatum, and Pyrodinium bahamense are known for their capability to produce paralytic shellfish toxins (PST), which can cause severe, most often food-related poisoning. The recent discovery of the first PST biosynthesis genes has laid the foundation for the development of molecular detection methods for monitoring and study of PST-producing dinoflagellates. In this study, a probe-based qPCR method for the detection and quantification of the sxtA4 gene present in Alexandrium spp. and Gymnodinium catenatum was designed. The focus was on Alexandrium ostenfeldii, a species which recurrently forms dense toxic blooms in areas within the Baltic Sea. A consistent, positive correlation between the presence of sxtA4 and PST biosynthesis was observed, and the species was found to maintain PST production with an average of 6 genomic copies of sxtA4. In August 2014, A. ostenfeldii populations were studied for cell densities, PST production, as well as sxtA4 and species-specific LSU copy numbers in Föglö, Åland, Finland, where an exceptionally dense bloom, consisting of 6.3×106cellsL-1, was observed. Cell concentrations, and copy numbers of both of the target genes were positively correlated with total STX, GTX2, and GTX3 concentrations in the environment, the cell density predicting toxin concentrations with the best accuracy (Spearman's ρ=0.93, p<0.01). The results indicated that all A. ostenfeldii cells in the blooms harbored the genetic capability of PST production, making the detection of sxtA4 a good indicator of toxicity. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Selection and validation of candidate reference genes for quantitative real-time PCR studies in the shrimp Penaeus vannamei under viral infection.

    Science.gov (United States)

    Valenzuela-Castillo, Adán; Mendoza-Cano, Fernando; Enríquez-Espinosa, Tania; Grijalva-Chon, José Manuel; Sánchez-Paz, Arturo

    2017-06-01

    The decapod Penstyldensovirus 1 (PstDV-1) represents one of the most serious threats for penaeid shrimp farming. Studies aimed at defining relevant molecular effects of this virus over its host are imperative in the attempt to increase our understanding of its pathogenesis. Unfortunately, few studies have focused on the definition of the expression profile of reference genes in shrimp challenged with a pathogen. As a result, there are no studies on the selection of reference genes for the normalization of target gene expression changes yielding reliable data of the effects following PstDV-1 infection in shrimp. Therefore, the aim of the present study was to evaluate and validate the appropriateness of four candidate reference genes (ef1-α, gapdh, rpl8 and β-tubulin) for their use as reference genes to normalize qPCR data in gene expression studies of PstDV-1-shrimp interactions. By analyzing the expression profile of those genes, gapdh was validated as a suitable reference gene to normalize expression data gathered from a PstDV1-challenge, while ef1-α, β-tubulin, and rpl8 were identified as unstably expressed during the infectious process. The suitability of gapdh as a common reference gene in studies of host gene response to viral infections is underlined. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. De-novo assembly and characterization of Chlorella minutissima UTEX2341 transcriptome by paired-end sequencing and the identification of genes related to the biosynthesis of lipids for biodiesel.

    Science.gov (United States)

    Yu, Mingjia; Yang, Shanjun; Lin, Xiangzhi

    2016-02-01

    Chlorella minutissima is considered to be one of the promising feedstocks for biofuels in the future. In this study, the transcriptome from the oil-rich strain UTEX2341 of C. minutissima was generated based on Illumina paired-end sequencing. Through de-novo assembly, a total of 14,905 isogenes were obtained and compacted into 6216 unigenes. A total of 80% of the unigenes were assigned with GO terms and were further subdivided into 55 sub-categories. KEGG analysis demonstrated that 37.2% of the unigenes could be accessed and mapped into 278 pathways. Interestingly, the genes that encoded key enzymes that are involved in the biosynthesis, elongation, and metabolism of fatty acids were identified, including malonyl-CoA-ACP transacylase, 3-ketoacyl-ACP synthase, 3-ketoacyl-ACP reductase, and others. Moreover, the genes that are involved in triacylglycerol (TAG) biosynthesis and metabolism were also observed. Therefore, the transcriptome analysis of C. minutissima UTEX2341 not only supplies comprehensive insight into the molecular pathway that is involved in the biosynthesis of biofuel precursors but also provides substantial valuable genomic resources to accelerate the further development and utilization of biofuels. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Pairing in spherical nanograins

    Energy Technology Data Exchange (ETDEWEB)

    Kuzmenko, N.K., E-mail: kuzmenko@NK9433.spb.ed [V.G. Khlopin Radium Institute, 2-nd Murinsky avenue 28, 194021 St.-Petersburg (Russian Federation); Mikhajlov, V.M. [Institute of Physics, St.-Petersburg State University, Ul' yanovskaya 3, 198904 Petergof (Russian Federation)

    2010-02-01

    Conditions are ascertained when the pairing and other thermodynamic properties of spherical nanograins with numbers of delocalized electrons N<10{sup 5} can be investigated by using the Single Shell Model (SSM) that gives the eigenvalues of the pairing Hamiltonian for a solitary shell. In the frame of SSM the exact canonical and grand canonical descriptions are employed first to analyze the absence of the abrupt superconducting-normal phase transition in finite systems in which an increase of the pairing and BCS critical temperature can be observed and secondly to study such new phenomena as the temperature re-entrance of the pairing in postcritical magnetic fields and also low temperature oscillations of the magnetic susceptibility and electronic heat capacity in an increasing uniform magnetic field.

  9. A three base pair gene variation within the distal 5'-flanking region of the interleukin-10 (IL-10) gene is related to the in vitro IL-10 production capacity of lipopolysaccharide-stimulated peripheral blood mononuclear cells.

    NARCIS (Netherlands)

    Rieth, H.; Mormann, M.; Luty, J.F.; Assohou-Luty, C.A.; Roupelieva, M.; Kremsner, P.G.; Kube, D.

    2004-01-01

    Interleukin-10 (IL-10) is an important multifunctional immunmodulator. There is evidence that IL-10 secretion is associated with certain genetic elements of the proximal IL-10 gene 5'-flanking region. The allelic and genotypic comparison of IL-10 expression by lipopolysaccharide (LPS)- stimulated

  10. Junctionless Cooper pair transistor

    Energy Technology Data Exchange (ETDEWEB)

    Arutyunov, K. Yu., E-mail: konstantin.yu.arutyunov@jyu.fi [National Research University Higher School of Economics , Moscow Institute of Electronics and Mathematics, 101000 Moscow (Russian Federation); P.L. Kapitza Institute for Physical Problems RAS , Moscow 119334 (Russian Federation); Lehtinen, J.S. [VTT Technical Research Centre of Finland Ltd., Centre for Metrology MIKES, P.O. Box 1000, FI-02044 VTT (Finland)

    2017-02-15

    Highlights: • Junctionless Cooper pair box. • Quantum phase slips. • Coulomb blockade and gate modulation of the Coulomb gap. - Abstract: Quantum phase slip (QPS) is the topological singularity of the complex order parameter of a quasi-one-dimensional superconductor: momentary zeroing of the modulus and simultaneous 'slip' of the phase by ±2π. The QPS event(s) are the dynamic equivalent of tunneling through a conventional Josephson junction containing static in space and time weak link(s). Here we demonstrate the operation of a superconducting single electron transistor (Cooper pair transistor) without any tunnel junctions. Instead a pair of thin superconducting titanium wires in QPS regime was used. The current–voltage characteristics demonstrate the clear Coulomb blockade with magnitude of the Coulomb gap modulated by the gate potential. The Coulomb blockade disappears above the critical temperature, and at low temperatures can be suppressed by strong magnetic field.

  11. Maternal homozygocity for a 14 base pair insertion in exon 8 of the HLA-G gene and carriage of HLA class II alleles restricting HY immunity predispose to unexplained secondary recurrent miscarriage and low birth weight in children born to these patients

    DEFF Research Database (Denmark)

    Christiansen, Ole B; Kolte, Astrid M; Dahl, Mette

    2012-01-01

    Homozygous carriage of a 14 base pair (bp) insertion in exon 8 of the HLA-G gene may be associated with low levels of soluble HLA-G and recurrent miscarriage (RM). We investigated the G14bp insertion(ins)/deletion(del) polymorphism in 339 women with unexplained RM and 125 control women. In all...

  12. Au pair trajectories

    DEFF Research Database (Denmark)

    Dalgas, Karina Märcher

    2015-01-01

    Since 2000, thousands of young Filipino migrants have come to Denmark as au pairs. Officially, they are there to “broaden their cultural horizons” by living temporarily with a Danish host family, but they also conduct domestic labor in exchange for food and money, which allows them to send...

  13. Paired fuzzy sets

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco de los Ríos, Camilo; Gómez, Daniel

    2015-01-01

    In this paper we want to stress the relevance of paired fuzzy sets, as already proposed in previous works of the authors, as a family of fuzzy sets that offers a unifying view for different models based upon the opposition of two fuzzy sets, simply allowing the existence of different types of neu...

  14. Aspectual Pairing in Polish

    NARCIS (Netherlands)

    Młynarczyk, A.K.

    2004-01-01

    The received view on Slavic aspect is that it is intrinsically complex, and that there is little hope of discerning any substantial regularity. We argue that this view is mistaken. We argue that the vast majority of Polish verbs really do come in aspectual pairs and that far from being a mysterious

  15. Excited cooper pairs

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Arrietea, M. G.; Solis, M. A.; De Llano, M. [Universidad Nacional Autonoma de Mexico, Mexico, D.F (Mexico)

    2001-02-01

    Excited cooper pairs formed in a many-fermion system are those with nonzero total center-of mass momentum (CMM). They are normally neglected in the standard Bardeen-Cooper-Schrieffer (BCS) theory of superconductivity for being too few compared with zero CMM pairs. However, a Bose-Einstein condensation picture requires both zero and nonzero CMM pairs. Assuming a BCS model interaction between fermions we determine the populations for all CMM values of Cooper pairs by actually calculating the number of nonzero-CMM pairs relative to that of zero-CMM ones in both 2D and 3D. Although this ratio decreases rapidly with CMM, the number of Cooper pairs for any specific CMM less than the maximum (or breakup of the pair) momentum turns out to be typically larger than about 95% of those with zero-CMM at zero temperature T. Even at T {approx}100 K this fraction en 2D is still as large as about 70% for typical quasi-2D cuprate superconductor parameters. [Spanish] Los pares de cooper excitados formados en un sistema de muchos electrones, son aquellos con momentos de centro de masa (CMM) diferente de cero. Normalmente estos no son tomados en cuenta en la teoria estandar de la superconductividad de Bardeen-Cooper-Schrieffer (BCS) al suponer que su numero es muy pequeno comparados con los pares de centro de masa igual a cero. Sin embargo, un esquema de condensacion Bose-Einstein requiere de ambos pares, con CMM cero y diferente de cero. Asumiendo una interaccion modelo BCS entre los fermiones, determinamos la poblacion de pares cooper con cada uno de todos los posibles valores del CMM calculando el numero de pares con momentos de centro de masa diferente de cero relativo a los pares de CMM igual a cero, en 2D y 3D. Aunque esta razon decrece rapidamente con el CMM, el numero de pares de cooper para cualquier CMM especifico menor que el momento maximo (o rompimiento de par) es tipicamente mas grande que el 95% de aquellos con CMM cero. Aun a T {approx}100 K esta fraccion en 2D es

  16. Two distinct Ras genes from Puccinia striiformis exhibit differential roles in rust pathogenicity and cell death.

    Science.gov (United States)

    Cheng, Yulin; Wang, Wumei; Yao, Juanni; Huang, Lili; Voegele, Ralf T; Wang, Xiaojie; Kang, Zhensheng

    2016-11-01

    Ras genes have been shown to regulate a variety of cellular processes in higher eukaryotes. However, much less is known about their function(s) in fungi, especially plant pathogenic fungi. Here, we report the identification and functional analysis of Ras genes from Puccinia striiformis f. sp. tritici (Pst), an important fungal pathogen in wheat production worldwide. Pst contains two Ras genes, PsRas1 and PsRas2, which share 48.6% similarity at the protein level and fall into two different phylogenetic clades. Both PsRas1 and PsRas2 have conserved protein sequences among different Pst isolates, but exhibit different transcript profiles during Pst infection. Silencing of PsRas1 or PsRas2 indicates that PsRas2 but not PsRas1 contributes significantly to rust pathogenicity. However, overexpression of PsRas1, but not PsRas2, promotes cell death in yeast and plants. Further studies show that all conserved domains of Ras GTPases in PsRas1 are needed to induce this cell death. In plants, PsRas1-triggered cell death shows similar characteristics as plant hypersensitive response. Our findings suggest that PsRas1 and PsRas2 take over different functions in rust pathogenicity and cell death, thus facilitating the understanding of cell death, pathogenic mechanisms of plant pathogenic fungi and the search for novel pathogen control strategies. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. PHYLOGENETIC RELATIONSHIPS AMONGST 10 Durio SPECIES BASED ON PCR-RFLP ANALYSIS OF TWO CHLOROPLAST GENES

    Directory of Open Access Journals (Sweden)

    Panca J. Santoso

    2013-07-01

    Full Text Available Twenty seven species of Durio have been identified in Sabah and Sarawak, Malaysia, but their relationships have not been studied. This study was conducted to analyse phylogenetic relationships amongst 10 Durio species in Malaysia using PCR-RFLP on two chloroplast DNA genes, i.e. ndhC-trnV and rbcL. DNAs were extracted from young leaves of 11 accessions from 10 Durio species collected from the Tenom Agriculture Research Station, Sabah, and University Agriculture Park, Universiti Putra Malaysia. Two pairs of oligonucleotide primers, N1-N2 and rbcL1-rbcL2, were used to flank the target regions ndhC-trnV and rbcL. Eight restriction enzymes, HindIII, BsuRI, PstI, TaqI, MspI, SmaI, BshNI, and EcoR130I, were used to digest the amplicons. Based on the results of PCR-RFLP on ndhC-trnV gene, the 10 Durio species were grouped into five distinct clusters, and the accessions generally showed high variations. However, based on the results of PCR-RFLP on the rbcL gene, the species were grouped into three distinct clusters, and generally showed low variations. This means that ndhC-trnV gene is more reliable for phylogenetic analysis in lower taxonomic level of Durio species or for diversity analysis, while rbcL gene is reliable marker for phylogenetic analysis at higher taxonomic level. PCR-RFLP on the ndhC-trnV and rbcL genes could therefore be considered as useful markers to phylogenetic analysis amongst Durio species. These finding might be used for further molecular marker assisted in Durio breeding program.

  18. SxtA and sxtG Gene Expression and Toxin Production in the Mediterranean Alexandrium minutum (Dinophyceae

    Directory of Open Access Journals (Sweden)

    Federico Perini

    2014-10-01

    Full Text Available The dinoflagellate Alexandrium minutum is known for the production of potent neurotoxins affecting the health of human seafood consumers via paralytic shellfish poisoning (PSP. The aim of this study was to investigate the relationship between the toxin content and the expression level of the genes involved in paralytic shellfish toxin (PST production. The algal cultures were grown both in standard f/2 medium and in phosphorus/nitrogen limitation. In our study, LC-HRMS analyses of PST profile and content in different Mediterranean A. minutum strains confirmed that this species was able to synthesize mainly the saxitoxin analogues Gonyautoxin-1 (GTX1 and Gonyautoxin-4 (GTX4. The average cellular toxin content varied among different strains, and between growth phases, highlighting a decreasing trend from exponential to stationary phase in all culture conditions tested. The absolute quantities of intracellular sxtA1 and sxtG mRNA were not correlated with the amount of intracellular toxins in the analysed A. minutum suggesting that the production of toxins may be regulated by post-transcriptional mechanisms and/or by the concerted actions of alternative genes belonging to the PST biosynthesis gene cluster. Therefore, it is likely that the sxtA1 and sxtG gene expression could not reflect the PST accumulation in the Mediterranean A. minutum populations under the examined standard and nutrient limiting conditions.

  19. MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences.

    Science.gov (United States)

    Wong, Ka-Chun

    2017-10-01

    In higher eukaryotes, protein-DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter-enhancer pairs) systematically. To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences. In particular, two expectation maximization algorithms are derived for efficient model training with linear computational complexity. Under diverse scenarios, MotifHyades is demonstrated faster and more accurate than the existing ad hoc computational pipeline. In addition, MotifHyades is applied to discover thousands of DNA motif pairs with higher gold standard motif matching ratio, higher DNase accessibility and higher evolutionary conservation than the previous ones in the human K562 cell line. Lastly, it has been run on five other human cell lines (i.e. GM12878, HeLa-S3, HUVEC, IMR90, and NHEK), revealing another thousands of novel DNA motif pairs which are characterized across a broad spectrum of genomic features on long-range promoter-enhancer pairs. The matrix-algebra-optimized versions of MotifHyades and the discovered DNA motif pairs can be found in http://bioinfo.cs.cityu.edu.hk/MotifHyades. kc.w@cityu.edu.hk. Supplementary data are available at Bioinformatics online.

  20. Au pairs on Facebook

    DEFF Research Database (Denmark)

    Dalgas, Karina Märcher

    2016-01-01

    Ethnographers are increasingly making use of Facebook to acquire access and general acquaintance with their field of study. However, little has been written on how Facebook is used methodologically in research that does not have social media sites as the main focus of interest. This article argues...... that engagement with Facebook as a methodological tool can be useful in research among migrants in highly politicised fields. Pointing to a discursive construction of Filipina au pairs as victims of labour exploitation, the article shows how fieldwork on Facebook enables the exploration of the ways in which...... and on Facebook....

  1. Hypoalphalipoproteinaemia and polymorphisms associated with reduced expression of the apolipoprotein A-I gene and resolution of disputed paternity in a large English family.

    Science.gov (United States)

    Matsakis, M; Wile, D B; Humphries, S E; Winder, A F

    1993-01-01

    A Pst-I RFLP polymorphism adjacent to the 3' end of the apolipoprotein A-I gene is reported to associate with hypoalphalipoproteinaemia with dominant inheritance in families identified through accelerated coronary heart disease. This association was not apparent in a large English family identified through voluntary health screening, and with no evident premature coronary disease. Any association could, however, be masked by sex, or by further undetermined variation affecting Pst-I restriction sites. Analysis of this and other polymorphisms present also led to resolution both of disputed paternity and of a long-standing family feud.

  2. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  3. Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.

    Directory of Open Access Journals (Sweden)

    Dario Cantu

    Full Text Available BACKGROUND: The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130. METHODOLOGY/PRINCIPAL FINDINGS: We obtained nearly 80 million high quality paired-end reads (>50x coverage that were assembled into 29,178 contigs (64.8 Mb, which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase. CONCLUSIONS/SIGNIFICANCE: The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for

  4. Multi-pair states in electron–positron pair creation

    Directory of Open Access Journals (Sweden)

    Anton Wöllert

    2016-09-01

    Full Text Available Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron–positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron–positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron–positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron–positron pairs.

  5. Cooper pairs in atomic nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Pittel, S. [Bartol Research Institute and Department of Physics and Astronomy, University of Delaware, Newark, 19716 Delaware (United States); Dussel, G. G. [Departamento de Fisica J.J. Giambiagi, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Dukelsky, J.; Sarriguren, P. [Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid (Spain)

    2008-12-15

    We describe recent efforts to study Cooper pairs in atomic nuclei. We consider a self-consistent Hartree Fock mean field for the even Sm isotopes and compare results based on three treatments of pairing correlations: a BCS treatment, a number-projected BCS treatment and an exact treatment using the Richardson Ansatz. Significant differences are seen in the pairing correlation energies. Furthermore, because it does not average over the properties of the fermion pairs, the Richardson solution permits a more meaningful definition of the Cooper wave function and of the fraction of pairs that are collective. Our results confirm that only a few pairs near the Fermi surface in realistic atomic nuclei are collective. (Author)

  6. A change in temperature modulates defence to yellow (stripe) rust in wheat line UC1041 independently of resistance gene Yr36.

    Science.gov (United States)

    Bryant, Ruth R M; McGrann, Graham R D; Mitchell, Alice R; Schoonbeek, Henk-Jan; Boyd, Lesley A; Uauy, Cristobal; Dorling, Steve; Ridout, Christopher J

    2014-01-08

    Rust diseases are of major importance in wheat production worldwide. With the constant evolution of new rust strains and their adaptation to higher temperatures, consistent and durable disease resistance is a key challenge. Environmental conditions affect resistance gene performance, but the basis for this is poorly understood. Here we show that a change in day temperature affects wheat resistance to Puccinia striiformis f. sp tritici (Pst), the causal agent of yellow (or stripe) rust. Using adult plants of near-isogenic lines UC1041 +/- Yr36, there was no significant difference between Pst percentage uredia coverage in plants grown at day temperatures of 18°C or 25°C in adult UC1041 + Yr36 plants. However, when plants were transferred to the lower day temperature at the time of Pst inoculation, infection increased up to two fold. Interestingly, this response was independent of Yr36, which has previously been reported as a temperature-responsive resistance gene as Pst development in adult UC1041 -Yr36 plants was similarly affected by the plants experiencing a temperature reduction. In addition, UC1041 -Yr36 plants grown at the lower temperature then transferred to the higher temperature were effectively resistant and a temperature change in either direction was shown to affect Pst development up to 8 days prior to inoculation. Results for seedlings were similar, but more variable compared to adult plants. Enhanced resistance to Pst was observed in seedlings of UC1041 and the cultivar Shamrock when transferred to the higher temperature. Resistance was not affected in seedlings of cultivar Solstice by a temperature change in either direction. Yr36 is effective at 18°C, refining the lower range of temperature at which resistance against Pst is conferred compared to previous studies. Results reveal previously uncharacterised defence temperature sensitivity in the UC1041 background which is caused by a change in temperature and independently of Yr36. This novel

  7. Lone pairs: an electrostatic viewpoint.

    Science.gov (United States)

    Kumar, Anmol; Gadre, Shridhar R; Mohan, Neetha; Suresh, Cherumuttathu H

    2014-01-16

    A clear-cut definition of lone pairs has been offered in terms of characteristics of minima in molecular electrostatic potential (MESP). The largest eigenvalue and corresponding eigenvector of the Hessian at the minima are shown to distinguish lone pair regions from the other types of electron localization (such as π bonds). A comparative study of lone pairs as depicted by various other scalar fields such as the Laplacian of electron density and electron localization function is made. Further, an attempt has been made to generalize the definition of lone pairs to the case of cations.

  8. Genotypic association analysis using discordant-relative-pairs.

    Science.gov (United States)

    Yan, T; Yang, Y-N; Cheng, X; DeAngelis, M M; Hoh, J; Zhang, H

    2009-01-01

    In practice, family-based design has been widely used in disease-gene association analysis. The major advantage of such design is that it is not subject to spurious association due to population structure such as population stratification (PS) and admixture. A disadvantage is that parental genotypes are hard to obtain if the disease is late onset for which a discordant-relative-pair design is useful. Designs of such kind include full-sib-pair, half-sib-pair, first-cousin-pair, and so on. The closer the relatedness of the pair, the less possible that they are subject to population stratification. On the other hand, the association test using close relative-pairs may be less powerful due to over-matching. Trade-off between these two factors (population structure and over-matching) is the major concern of this study. Some tests, namely McNemar's test, matched Cochran-Armitage trend tests (CATTs), matched maximum efficient robust test (MERT), and Bhapkar's test, are used for testing disease-gene association based on relative-pair designs. These tests are shown to be valid in the presence of PS but not admixture. Numerical studies show that the McNemar's test, additive CATT, MERT, and Bhapkar's test are robust in power, but none of them is uniformly more powerful than the others. In most simulations, the power of any of the tests increases as the pair is more distant. The proposed methods are applied to two real examples.

  9. Estimating meiotic chromosome pairing and recombination parameters in telocentric trisomics.

    Science.gov (United States)

    Sybenga, J; Verhaar, H; Botje, D G A

    2007-11-01

    Telocentric trisomics (telotrisomics; one arm of a metacentric chromosome present in addition to two complete genomes) are used in theoretical studies of pairing affinities and chiasma formation in competitive situations and applied in genome analysis, gene localization, gene transfer, and breakage of close linkages. These applications require knowledge of the recombination characteristics of telotrisomics. Appropriate cytological and molecular markers and favorable chromosome morphology are not always available or applicable for quantitative analyses. We developed new mathematical models for extracting the maximum information from simple metaphase I observations. Two types of telotrisomics of the short arm of chromosome 1R of rye (Secale cereale), including several genotypes, were used as test material. In simple telotrisomics, pairing between morphologically identical complete chromosomes was more frequent than pairing between the telocentric and either of the normal chromosomes. In the telocentric substitution, morphologically identical telocentrics paired less frequently with each other than either one with the normal chromosome. Pairing partner switch was significant. Interaction between the two arms was variable. Variation within plants was considerable. Telotrisomics without markers are suitable for analyzing pairing preferences, for gene localization and gene transfer, and for breaking tight linkages, but less so for genome analysis.

  10. Stereo Pair: Patagonia, Argentina

    Science.gov (United States)

    2000-01-01

    This view of northern Patagonia, near El Cain, Argentina shows complexly eroded volcanic terrain, with basalt mesas, sinkholes, landslide debris, playas, and relatively few integrated drainage channels. Surrounding this site (but also extending far to the east) is a broad plateau capped by basalt, the Meseta de Somuncura. Here, near the western edge of the plateau, erosion has broken through the basalt cap in a variety of ways. On the mesas, water-filled sinkholes (lower left) are most likely the result of the collapse of old lava tubes. Along the edges of the mesas (several locations) the basalt seems to be sliding away from the plateau in a series of slices. Water erosion by overland flow is also evident, particularly in canyons where vegetation blankets the drainage channels (green patterns, bottom of image). However, overland water flow does not extend very far at any location. This entire site drains to local playas, some of which are seen here (blue). While the water can reach the playas and then evaporate, what becomes of the eroded rock debris? Wind might excavate some of the finer eroded debris, but the fate of much of the missing bedrock remains mysterious.This cross-eyed stereoscopic image pair was generated using topographic data from the Shuttle Radar Topography Mission, combined with an enhanced Landsat 7 satellite color image. The topography data are used to create two differing perspectives of a single image, one perspective for each eye. In doing so, each point in the image is shifted slightly, depending on its elevation. When stereoscopically merged, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions.Landsat satellites have provided visible light and infrared images of the Earth continuously since 1972. SRTM topographic data match the 30-meter (99-foot) spatial resolution of most Landsat images and provide a valuable complement for studying the historic and growing Landsat data archive. The Landsat 7

  11. Instability of vortex pair leapfrogging

    DEFF Research Database (Denmark)

    Tophøj, Laust; Aref, Hassan

    2013-01-01

    Leapfrogging is a periodic solution of the four-vortex problem with two positive and two negative point vortices all of the same absolute circulation arranged as co-axial vortex pairs. The set of co-axial motions can be parameterized by the ratio 0 vortex pair sizes at the time when one...... pair passes through the other. Leapfrogging occurs for α > σ2, where is the silver ratio. The motion is known in full analytical detail since the 1877 thesis of Gröbli and a well known 1894 paper by Love. Acheson ["Instability of vortex leapfrogging," Eur. J. Phys.21, 269-273 (2000...... pairs fly off to infinity, and a "walkabout" mode, where the vortices depart from leapfrogging but still remain within a finite distance of one another. We show numerically that this transition is more gradual, a result that we relate to earlier investigations of chaotic scattering of vortex pairs [L...

  12. CHROMOSOME BANDING IN CRUSTACEA. I. KARYOTYPE, Ag-NORs, C BANDING AND TREATMENT WITH EcoRI, PstI and KpnI RESTRICTION ENDONUCLEASES IN Artemia franciscana

    Directory of Open Access Journals (Sweden)

    Ingrid Vilar Accioly

    2014-08-01

    Full Text Available Características cariotípicas do microcrustáceo Artemia franciscana Kellog, 1906, introduzida nas salinas do litoral nordeste do Brasil, na década de 70, foram investigadas através de coloração convencional, bandamento C, endonucleases de restrição (EcoRI, PstI e KpnI e Ag-NORs. O cariótipo consiste de 42 cromossomos, onde se individualiza sobre alguns pares a presença de constrições secundárias. Grandes blocos heterocromáticos encontram-se distribuídos nas porções teloméricas da maioria dos cromossomos. A digestão com PstI e KpnI revelou um padrão similar ao obtido pelo bandamento C. Preparações tratadas com EcoRI apresentam digestão das regiões heterocromáticas indicando a presença de sítios de restrição nestas regiões. Ag-NORs múltiplas estão associadas a blocos heterocromáticos. Os dados apresentados representam passo inicial para identificação de possíveis modificações ocorridas após o isolamento geográfico desta amostra, assim como no entendimento das modificações evolutivas ocorridas no cariótipo deste grupo. Palavras-chave: bandamento cromossômico, camarão de água salgada, citogenética de crustáceos. DOI: http://dx.doi.org/10.18561/2179-5746/biotaamazonia.v4n2p15-19

  13. High Specificity of a Quantitative PCR Assay Targeting a Saxitoxin Gene for Monitoring Toxic Algae Associated with Paralytic Shellfish Toxins in the Yellow Sea.

    Science.gov (United States)

    Gao, Yan; Yu, Ren-Cheng; Murray, Shauna A; Chen, Jian-Hua; Kang, Zhen-Jun; Zhang, Qing-Chun; Kong, Fan-Zhou; Zhou, Ming-Jiang

    2015-10-01

    The identification of core genes involved in the biosynthesis of saxitoxin (STX) offers a great opportunity to detect toxic algae associated with paralytic shellfish toxins (PST). In the Yellow Sea (YS) in China, both toxic and nontoxic Alexandrium species are present, which makes it a difficult issue to specifically monitor PST-producing toxic algae. In this study, a quantitative PCR (qPCR) assay targeting sxtA4, a domain in the sxt gene cluster that encodes a unique enzyme involved in STX biosynthesis, was applied to analyze samples collected from the YS in spring of 2012. The abundance of two toxic species within the Alexandrium tamarense species complex, i.e., A. fundyense and A. pacificum, was also determined with TaqMan-based qPCR assays, and PSTs in net-concentrated phytoplankton samples were analyzed with high-performance liquid chromatography coupled with a fluorescence detector. It was found that the distribution of the sxtA4 gene in the YS was consistent with the toxic algae and PSTs, and the quantitation results of sxtA4 correlated well with the abundance of the two toxic species (r=0.857). These results suggested that the two toxic species were major PST producers during the sampling season and that sxtA-based qPCR is a promising method to detect toxic algae associated with PSTs in the YS. The correlation between PST levels and sxtA-based qPCR results, however, was less significant (r=0.552), implying that sxtA-based qPCR is not accurate enough to reflect the toxicity of PST-producing toxic algae. The combination of an sxtA-based qPCR assay and chemical means might be a promising method for monitoring toxic algal blooms. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. Photonic Counterparts of Cooper Pairs

    Science.gov (United States)

    Saraiva, André; Júnior, Filomeno S. de Aguiar; de Melo e Souza, Reinaldo; Pena, Arthur Patrocínio; Monken, Carlos H.; Santos, Marcelo F.; Koiller, Belita; Jorio, Ado

    2017-11-01

    The microscopic theory of superconductivity raised the disruptive idea that electrons couple through the elusive exchange of virtual phonons, overcoming the strong Coulomb repulsion to form Cooper pairs. Light is also known to interact with atomic vibrations, as, for example, in the Raman effect. We show that photon pairs exchange virtual vibrations in transparent media, leading to an effective photon-photon interaction identical to that for electrons in the BCS theory of superconductivity, in spite of the fact that photons are bosons. In this scenario, photons may exchange energy without matching a quantum of vibration of the medium. As a result, pair correlations for photons scattered away from the Raman resonances are expected to be enhanced. An experimental demonstration of this effect is provided here by time-correlated Raman measurements in different media. The experimental data confirm our theoretical interpretation of a photonic Cooper pairing, without the need for any fitting parameters.

  15. Exact solution for generalized pairing

    OpenAIRE

    Pan, Feng; Draayer, J. P.

    1997-01-01

    An infinite dimensional algebra, which is useful for deriving exact solutions of the generalized pairing problem, is introduced. A formalism for diagonalizing the corresponding Hamiltonian is also proposed. The theory is illustrated with some numerical examples.

  16. Precision Targeted Mutagenesis via Cas9 Paired Nickases in Rice.

    Science.gov (United States)

    Mikami, Masafumi; Toki, Seiichi; Endo, Masaki

    2016-05-01

    Recent reports of CRISPR- (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) mediated heritable mutagenesis in plants highlight the need for accuracy of the mutagenesis directed by this system. Off-target mutations are an important issue when considering functional gene analysis, as well as the molecular breeding of crop plants with large genome size, i.e. with many duplicated genes, and where the whole-genome sequence is still lacking. In mammals, off-target mutations can be suppressed by using Cas9 paired nickases together with paired guide RNAs (gRNAs). However, the performance of Cas9 paired nickases has not yet been fully assessed in plants. Here, we analyzed on- and off-target mutation frequency in rice calli and regenerated plants using Cas9 nuclease or Cas9 nickase with paired gRNAs. When Cas9 paired nickases were used, off-target mutations were fully suppressed in rice calli and regenerated plants. However, on-target mutation frequency also decreased compared with that induced by the Cas9 paired nucleases system. Since the gRNA sequence determines specific binding of Cas9 protein-gRNA ribonucleoproteins at the targeted sequence, the on-target mutation frequency of Cas9 paired nickases depends on the design of paired gRNAs. Our results suggest that a combination of gRNAs that can induce mutations at high efficiency with Cas9 nuclease should be used together with Cas9 nickase. Furthermore, we confirmed that a combination of gRNAs containing a one nucleotide (1 nt) mismatch toward the target sequence could not induce mutations when expressed with Cas9 nickase. Our results clearly show the effectiveness of Cas9 paired nickases in delivering on-target specific mutations. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

  17. Organometallic frustrated Lewis pair chemistry.

    Science.gov (United States)

    Erker, Gerhard

    2011-08-07

    Frustrated Lewis pairs are playing an increasingly important role in organometallic chemistry. Examples are presented and discussed where organometallic systems themselves serve as the Lewis base or Lewis acid components in frustrated Lewis pair chemistry, mostly through their attached functional groups. Activation of dihydrogen takes place easily in many of these systems. This may lead to the generation of novel catalyst systems but also in many cases to the occurrence of specific reactions at the periphery of the organometallic frameworks. Increasingly, FLP reactions are used to carry out functional group conversions in organometallic systems under mild reaction conditions. The limits of typical FLP reactivity are explored with selected organometallic examples, a discussion that points toward new developments, such as the discovery of facile new 1,1-carboboration reactions. Learning more and more about the broad spectrum of frustrated Lewis pair chemistry helps us to find novel reactions and applications.

  18. Characterisation of the paralytic shellfish toxin biosynthesis gene clusters in Anabaena circinalis AWQC131C and Aphanizomenon sp. NH-5

    Directory of Open Access Journals (Sweden)

    Neilan Brett A

    2009-03-01

    Full Text Available Abstract Background Saxitoxin and its analogues collectively known as the paralytic shellfish toxins (PSTs are neurotoxic alkaloids and are the cause of the syndrome named paralytic shellfish poisoning. PSTs are produced by a unique biosynthetic pathway, which involves reactions that are rare in microbial metabolic pathways. Nevertheless, distantly related organisms such as dinoflagellates and cyanobacteria appear to produce these toxins using the same pathway. Hypothesised explanations for such an unusual phylogenetic distribution of this shared uncommon metabolic pathway, include a polyphyletic origin, an involvement of symbiotic bacteria, and horizontal gene transfer. Results We describe the identification, annotation and bioinformatic characterisation of the putative paralytic shellfish toxin biosynthesis clusters in an Australian isolate of Anabaena circinalis and an American isolate of Aphanizomenon sp., both members of the Nostocales. These putative PST gene clusters span approximately 28 kb and contain genes coding for the biosynthesis and export of the toxin. A putative insertion/excision site in the Australian Anabaena circinalis AWQC131C was identified, and the organization and evolution of the gene clusters are discussed. A biosynthetic pathway leading to the formation of saxitoxin and its analogues in these organisms is proposed. Conclusion The PST biosynthesis gene cluster presents a mosaic structure, whereby genes have apparently transposed in segments of varying size, resulting in different gene arrangements in all three sxt clusters sequenced so far. The gene cluster organizational structure and sequence similarity seems to reflect the phylogeny of the producer organisms, indicating that the gene clusters have an ancient origin, or that their lateral transfer was also an ancient event. The knowledge we gain from the characterisation of the PST biosynthesis gene clusters, including the identity and sequence of the genes involved

  19. Atomic pair-state interferometer

    DEFF Research Database (Denmark)

    Nipper, J.; Balewski, Jonathan B.; Krupp, Alexander T.

    2012-01-01

    We present experiments measuring an interaction-induced phase shift of Rydberg atoms at Stark-tuned Förster resonances. The phase shift features a dispersive shape around the resonance, showing that the interaction strength and sign can be tuned coherently. We use a pair-state interferometer...

  20. Pairs of dual periodic frames

    DEFF Research Database (Denmark)

    Christensen, Ole; Goh, Say Song

    2012-01-01

    is needed. The purpose of the present paper is to provide constructions of dual pairs of frames in the setting of the Hilbert space of periodic functions L2(0,2π). The frames constructed are given explicitly as trigonometric polynomials, which allows for an efficient calculation of the coefficients...

  1. Electron pair creation by photons

    NARCIS (Netherlands)

    Holtwijk, Theodoor

    1960-01-01

    In our experiment on the creation of electron pairs a 5 MeV betatron was used as radiation source and a cloud chamber (with magnetic field) was used as detection instrument. The experimental arrangement is described in section 2.1. The cloud chamber was of the overcompression type so that the

  2. Instantons in lepton pair production

    NARCIS (Netherlands)

    Brandenburg, A.; Ringwald, A.; Utermann, A.

    2006-01-01

    We consider QCD instanton-induced contributions to lepton pair production in hadron-hadron collisions. We relate these contributions to those known from deep inelastic scattering and demonstrate that they can be calculated reliably for sufficiently large momentum transfer. We observe that the

  3. Conjugal Pairing in Escherichia Coli

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 8. Conjugal Pairing in Escherichia Coli. Joshua Lederberg. Classics Volume 13 Issue 8 August 2008 pp 793-794. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/013/08/0793-0794 ...

  4. Pairing Linguistic and Music Intelligences

    Science.gov (United States)

    DiEdwardo, MaryAnn Pasda

    2005-01-01

    This article describes how music in the language classroom setting can be a catalyst for developing reading, writing, and understanding skills. Studies suggest that pairing music and linguistic intelligences in the college classroom improves students' grades and abilities to compose theses statements for research papers in courses that emphasize…

  5. Pairing gaps in nucleonic superfluids

    Energy Technology Data Exchange (ETDEWEB)

    Chen, J.M.C. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States)); Clark, J.W. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States)); Dave, R.D. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States)); Khodel, V.V. (McDonnell Center for the Space Sciences and Dept. of Physics, Washington Univ., St. Louis, MO (United States))

    1993-04-05

    Singlet S-wave nucleonic superfluids are studied within a microscopic many-body theory that incorporates explicit spatial correlations due to strong short-range repulsive forces as well as the momentum-space pairing correlations of BCS theory. The theory is formulated within the method of correlated basis functions (CBF). Within this scheme, there results a nonlinear problem for the superfluid energy gap that is identical in form to the gap problem of conventional BCS theory. However, the input single-particle energies and pairing matrix elements are dressed by the short-range spatial correlations and accordingly incorporate an important class of medium corrections. The effective pairing force of the theory is finite even if the bare two-nucleon potential contains an infinitely hard core; both the pairing matrix elements and single-particle energies are to be constructed from normal-state CBF matrix elements and may be evaluated by cluster-expansion techniques. The theory is explicated and applied at a variational level that is equivalent to the leading order of a CBF superstate perturbation theory. New results are presented for the [sup 1]S[sub 0] pairing gap [Delta][sub kF] in pure neutron matter at densities relevant to the inner crust of a neutron star, based on a simplified version of the Reid soft-core interaction and spin-dependent spatial correlations optimized in the correlated normal state. Careful considering is given to the treatment of the gap equation at large intermediate-state momenta. The variational gap function evaluated at the Fermi surface, [Delta][sub F], is found to be larger than predicted in earlier work. Estimates of the suppression of the gap due to polarization processes (and other particle-particle and hole-irreducible medium effects of higher order within CBF superstate perturbation theory) yield values of [Delta][sub kF].

  6. Evolutionary Transitions of MicroRNA-Target Pairs

    KAUST Repository

    Nozawa, Masafumi

    2016-04-27

    How newly generated microRNA (miRNA) genes are integrated into gene regulatory networks during evolution is fundamental in understanding the molecular and evolutionary bases of robustness and plasticity in gene regulation. A recent model proposed that after the birth of a miRNA, the miRNA is generally integrated into the network by decreasing the number of target genes during evolution. However, this decreasing model remains to be carefully examined by considering in vivo conditions. In this study, we therefore compared the number of target genes among miRNAs with different ages, combining experiments with bioinformatics predictions. First, we focused on three Drosophila miRNAs with different ages. As a result, we found that an older miRNA has a greater number of target genes than a younger miRNA, suggesting the increasing number of targets for each miRNA during evolution (increasing model). To further confirm our results, we also predicted all target genes for all miRNAs in D. melanogaster, considering co-expression of miRNAs and mRNAs in vivo. The results obtained also do not support the decreasing model but are reasonably consistent with the increasing model of miRNA-target pairs. Furthermore, our large-scale analyses of currently available experimental data of miRNA-target pairs also showed a weak but the same trend in humans. These results indicate that the current decreasing model of miRNA-target pairs should be reconsidered and the increasing model may be more appropriate to explain the evolutionary transitions of miRNA-target pairs in many organisms.

  7. Paired box mutations in familial and sporadic aniridia predicts truncated aniridia proteins

    Energy Technology Data Exchange (ETDEWEB)

    Martha, A.; Saunders, G.F. (Univ. of Texas M.D. Anderson Cancer Center, Houston, TX (United States)); Mintz-Hittner, H. (Baylor College of Medicine, Houston, TX (United States)); Lyons, L.A. (Univ. of Pittsburgh, PA (United States))

    1994-05-01

    Aniridia, an autosomal dominant ocular disorder characterized by iris hypoplasia, results from mutations in the PAX6 gene, which encodes paired box and homeobox motifs. In this report the authors describe five new mutations in the paired box region of the human PAX6 gene that are associated with aniridia. The paired box mutations detected were in both familial (three) and sporadic (two cases) cases. All five mutations predict truncated PAX6 proteins. This study indicates that early premature translational termination mutations in the PAX6 gene result in haploinsufficiency and generate the aniridia phenotype. 32 refs., 6 figs., 2 tabs.

  8. Asymmetric Ion-Pairing Catalysis

    Science.gov (United States)

    Brak, Katrien

    2014-01-01

    Charged intermediates and reagents are ubiquitous in organic transformations. The interaction of these ionic species with chiral neutral, anionic, or cationic small molecules has emerged as a powerful strategy for catalytic, enantioselective synthesis. This review describes developments in the burgeoning field of asymmetric ion-pairing catalysis with an emphasis on the insights that have been gleaned into the structural and mechanistic features that contribute to high asymmetric induction. PMID:23192886

  9. The ion pairs and superconducting bosons

    OpenAIRE

    Minasyan, V. N.

    2008-01-01

    First, it is shown that the creation of the spinless ion pairs in the lattice, which are hold by the binding with neighbor ion pairs together regarded as covalent. These ion pairs are created by the repulsive potential interaction of two ions which is bound as linear oscillator. The repulsive S-wave scattering between ion pairs and electrons is transformed to the attractive effective interaction between electrons which leads to a creation of electron pairs by a binding energy depending on the...

  10. Charge Aspects of Composite Pair Superconductivity

    Science.gov (United States)

    Flint, Rebecca

    2014-03-01

    Conventional Cooper pairs form from well-defined electronic quasiparticles, making the internal structure of the pair irrelevant. However, in the 115 family of superconductors, the heavy electrons are forming as they pair and the internal pair structure becomes as important as the pairing mechanism. Conventional spin fluctuation mediated pairing cannot capture the direct transition from incoherent local moments to heavy fermion superconductivity, but the formation of composite pairs favored by the two channel Kondo effect can. These composite pairs are local d-wave pairs formed by two conduction electrons in orthogonal Kondo channels screening the same local moment. Composite pairing shares the same symmetries as magnetically mediated pairing, however, only composite pairing necessarily involves a redistribution of charge within the unit cell originating from the internal pair structure, both as a monopole (valence change) and a quadrupole effect. This redistribution will onset sharply at the superconducting transition temperature. A smoking gun test for composite pairing is therefore a sharp signature at Tc - for example, a cusp in the Mossbauer isomer shift in NpPd5Al2 or in the NQR shift in (Ce,Pu)CoIn5.

  11. Germline progenitors escape the widespread phenomenon of homolog pairing during Drosophila development.

    Directory of Open Access Journals (Sweden)

    Eric F Joyce

    Full Text Available Homolog pairing, which plays a critical role in meiosis, poses a potential risk if it occurs in inappropriate tissues or between nonallelic sites, as it can lead to changes in gene expression, chromosome entanglements, and loss-of-heterozygosity due to mitotic recombination. This is particularly true in Drosophila, which supports organismal-wide pairing throughout development. Discovered over a century ago, such extensive pairing has led to the perception that germline pairing in the adult gonad is an extension of the pairing established during embryogenesis and, therefore, differs from the mechanism utilized in most species to initiate pairing specifically in the germline. Here, we show that, contrary to long-standing assumptions, Drosophila meiotic pairing in the gonad is not an extension of pairing established during embryogenesis. Instead, we find that homologous chromosomes are unpaired in primordial germ cells from the moment the germline can be distinguished from the soma in the embryo and remain unpaired even in the germline stem cells of the adult gonad. We further establish that pairing originates immediately after the stem cell stage. This pairing occurs well before the initiation of meiosis and, strikingly, continues through the several mitotic divisions preceding meiosis. These discoveries indicate that the spatial organization of the Drosophila genome differs between the germline and the soma from the earliest moments of development and thus argue that homolog pairing in the germline is an active process as versus a passive continuation of pairing established during embryogenesis.

  12. Squark pair production at NLO

    Energy Technology Data Exchange (ETDEWEB)

    Kraemer, Michael; Pellen, Mathieu [RWTH Aachen University, Institut fuer Theoretische Teilchenphysik und Kosmologie (Germany); Hangst, Christian; Muehlleitner, Margarete [KIT, Institut fuer Theoretische Physik (Germany); Popenda, Eva; Spira, Michael [PSI, Theory Group LTP (Switzerland)

    2013-07-01

    A lot of effort is and will be put in the search for supersymmetric particles at the LHC. For the interpretation of the experimental data precise theoretical predictions are crucial. The work presented in the talk contributes to this effort by providing NLO corrections to the pair production of squarks of the first two generations in a flexible partonic Monte Carlo program. In contrast to previous works no assumptions regarding the squark masses have been made and the different subchannels have been treated independently. The Monte Carlo framework allows investigating the impact of the supersymmetric QCD corrections at NLO on arbitrary distributions.

  13. Lost Chevalier Pairs - A Followup

    Science.gov (United States)

    2012-01-01

    correct, but the true 19 position angle was 180° minus the Chevalier value. The initial conclusion was that Chevalier had made a trigonometry error... trigonometry /plate errors, there was an additional 10’ error in Chevalier’s declination, due to an error in applying the y offset. Berk6 was unable to find...a match. After correcting for the plate center and trigonometry /plate errors, this pair was found to match 19498+2324 = J 496AB, as noted by Berko

  14. Coisotropic Submanifolds and Dual Pairs

    Science.gov (United States)

    Cattaneo, Alberto S.

    2014-03-01

    The Poisson sigma model is a widely studied two-dimensional topological field theory. This note shows that boundary conditions for the Poisson sigma model are related to coisotropic submanifolds (a result announced in [math.QA/0309180]) and that the corresponding reduced phase space is a (possibly singular) dual pair between the reduced spaces of the given two coisotropic submanifolds. In addition the generalization to a more general tensor field is considered and it is shown that the theory produces Lagrangian evolution relations if and only if the tensor field is Poisson.

  15. Endocrine factors of pair bonding.

    Science.gov (United States)

    Stárka, L

    2007-01-01

    Throughout literature--fiction and poetry, fine arts and music--falling in love and enjoying romantic love plays a central role. While several psychosocial conceptions of pair attachment consider the participation of hormones, human endocrinology has dealt with this theme only marginally. According to some authors in addictology, falling in love shows some signs of hormonal response to stressors with changes in dopamine and serotonin signalling and neurotrophin (transforming growth factor b) concentration. Endorphins, oxytocin and vasopressin may play a role during the later phases of love. However, proof of hormonal events associated with love in humans has, until recently, been lacking.

  16. An entropy-based improved k-top scoring pairs (TSP) method for ...

    African Journals Online (AJOL)

    DR. NJ TONUKARI

    2012-06-05

    Jun 5, 2012 ... Engineering of the Ministry of Education, Changdhun 130012, People's Republic of China. 2Supercomputing Center ... disjoint top scoring pairs of genes as decision rules rather than only the highest pair and both ..... including C4.5 decision trees (DT), Naive Bayes (NB), k-nearest neighbor (k-NN), support ...

  17. DJ Pairing during VDJ Recombination Shows Positional Biases That Vary among Individuals with Differing IGHD Locus Immunogenotypes.

    Science.gov (United States)

    Kidd, Marie J; Jackson, Katherine J L; Boyd, Scott D; Collins, Andrew M

    2016-02-01

    Human IgH diversity is influenced by biases in the pairing of IGHD and IGHJ genes, but these biases have not been described in detail. We used high-throughput sequencing of VDJ rearrangements to explore DJ pairing biases in 29 individuals. It was possible to infer three contrasting IGHD-IGHJ haplotypes in nine of these individuals, and two of these haplotypes include deletion polymorphisms involving multiple contiguous IGHD genes. Therefore, we were able to explore how the underlying genetic makeup of the H chain locus influences the formation of particular DJ pairs. Analysis of nonproductive rearrangements demonstrates that 3' IGHD genes tend to pair preferentially with 5' IGHJ genes, whereas 5' IGHD genes pair preferentially with 3' IGHJ genes; the relationship between IGHD gene pairing frequencies and IGHD gene position is a near linear one for each IGHJ gene. However, striking differences are seen in individuals who carry deletion polymorphisms in the D locus. The absence of different blocks of IGHD genes leads to increases in the utilization frequencies of just a handful of genes, and these genes have no clear positional relationships to the deleted genes. This suggests that pairing frequencies may be influenced by additional complex positional relationships that perhaps arise from chromatin structure. In contrast to IGHD gene usage, IGHJ gene usage is unaffected by the IGHD gene-deletion polymorphisms. Such an outcome would be expected if the recombinase complex associates with an IGHJ gene before associating with an IGHD gene partner. Copyright © 2016 by The American Association of Immunologists, Inc.

  18. DJ pairing during VDJ recombination shows positional biases that vary between individuals with differing IGHD locus immunogenotypes

    Science.gov (United States)

    Kidd, Marie J.; Jackson, Katherine J. L.; Boyd, Scott D.; Collins, Andrew M.

    2015-01-01

    Human immunoglobulin heavy chain diversity is influenced by biases in the pairing of IGHD and IGHJ genes, but these biases have not been described in detail. We have used high throughput sequencing of VDJ rearrangements to explore DJ pairing biases in twenty-nine individuals. It was possible to infer three contrasting IGHD-IGHJ haplotypes in nine of these individuals, and two of these haplotypes include deletion polymorphisms involving multiple contiguous IGHD genes. We were therefore able to explore how the underlying genetic makeup of the heavy chain locus influences the formation of particular DJ pairs. Analysis of non-productive rearrangements demonstrates that 3′ IGHD genes tend to pair preferentially with 5′ IGHJ genes, while 5′ IGHD genes pair preferentially with 3′ IGHJ genes, and the relationship between IGHD gene pairing frequencies and IGHD gene position is a near linear one for each IGHJ gene. Striking differences are seen, however, in individuals who carry deletion polymorphisms in the D locus. The absence of different blocks of IGHD genes lead to increases in the utilization frequencies of just a handful of genes, and these genes have no clear positional relationships to the deleted genes. This suggests that pairing frequencies may be influenced by additional complex positional relationships that arise perhaps from chromatin structure. In contrast to IGHD gene usage, IGHJ gene usage is unaffected by the IGHD gene deletion polymorphisms. Such an outcome would be expected if the recombinase complex associates first with an IGHJ gene, before associating with an IGHD gene partner. PMID:26700767

  19. Regulation of ecmF gene expression and genetic hierarchy among STATa, CudA, and MybC on several prestalk A-specific gene expressions in Dictyostelium.

    Science.gov (United States)

    Saga, Yukika; Inamura, Tomoka; Shimada, Nao; Kawata, Takefumi

    2016-05-01

    STATa, a Dictyostelium homologue of metazoan signal transducer and activator of transcription, is important for the organizer function in the tip region of the migrating Dictyostelium slug. We previously showed that ecmF gene expression depends on STATa in prestalk A (pstA) cells, where STATa is activated. Deletion and site-directed mutagenesis analysis of the ecmF/lacZ fusion gene in wild-type and STATa null strains identified an imperfect inverted repeat sequence, ACAAATANTATTTGT, as a STATa-responsive element. An upstream sequence element was required for efficient expression in the rear region of pstA zone; an element downstream of the inverted repeat was necessary for sufficient prestalk expression during culmination. Band shift analyses using purified STATa protein detected no sequence-specific binding to those ecmF elements. The only verified upregulated target gene of STATa is cudA gene; CudA directly activates expL7 gene expression in prestalk cells. However, ecmF gene expression was almost unaffected in a cudA null mutant. Several previously reported putative STATa target genes were also expressed in cudA null mutant but were downregulated in STATa null mutant. Moreover, mybC, which encodes another transcription factor, belonged to this category, and ecmF expression was downregulated in a mybC null mutant. These findings demonstrate the existence of a genetic hierarchy for pstA-specific genes, which can be classified into two distinct STATa downstream pathways, CudA dependent and independent. The ecmF expression is indirectly upregulated by STATa in a CudA-independent activation manner but dependent on MybC, whose expression is positively regulated by STATa. © 2016 Japanese Society of Developmental Biologists.

  20. Cloning and characterization of a wheat beta-1,3-glucanase gene induced by the stripe rust pathogen Puccinia striiformis f. sp. tritici.

    Science.gov (United States)

    Liu, Bo; Xue, Xiaodan; Cui, Suping; Zhang, Xiaoyu; Han, Qingmei; Zhu, Lin; Liang, Xiaofei; Wang, Xiaojie; Huang, Lili; Chen, Xianming; Kang, Zhensheng

    2010-02-01

    b-1,3-Glucanases are a group of pathogenesis related proteins that have been reported to be involved in plant defense against pathogens in many other plant pathogen systems. However, it was not clear if these genes play similar role in wheat (Triticum aestivum L.) against Puccinia striiformis f. sp. tritici (Pst), the stripe rust pathogen. To investigate the role of b-1,3-glucanase (EC3.2.1.39) in the resistance response of wheat (cv. Suwon11) to stripe rust, a wheat b-1,3-glucanase gene induced by Pst, designated as TaGlu, was cloned and characterized.TaGlu was predicted to encode a basic protein of 334 amino acids. Quantitative real-time PCR analyses revealed that the transcription of TaGlu was induced during both compatible and incompatible interactions with Pst, but the transcription level was much higher in the incompatible interaction than that in the compatible interaction. TaGlu also showed noticeable induction of gene expression in young green leaf tissues treated with salicylic acid, methyl jasmonate or ethylene. Immunogold labeling assays showed that the enzyme were localized mainly in the host cell wall and over the extra haustorial matrix, and the labeling densities were found significantly higher in the incompatible interaction than those in the compatible interaction.

  1. Virus-induced Gene Silencing-based Functional Analyses Revealed the Involvement of Several Putative Trehalose-6-Phosphate Synthase/Phosphatase Genes in Disease Resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in Tomato

    Directory of Open Access Journals (Sweden)

    Huijuan Zhang

    2016-08-01

    Full Text Available Trehalose and its metabolism have been demonstrated to play important roles in control of plant growth, development and stress responses. However, direct genetic evidence supporting the functions of trehalose and its metabolism in defense response against pathogens is lacking. In the present study, genome-wide characterization of putative trehalose-related genes identified 11 SlTPSs for trehalose-6-phosphate synthase, 8 SlTPPs for trehalose-6-phosphate phosphatase and one SlTRE1 for trehalase in tomato genome. Nine SlTPSs, 4 SlTPPs and SlTRE1 were selected for functional analyses to explore their involvement in tomato disease resistance. Some selected SlTPSs, SlTPPs and SlTRE1 responded with distinct expression induction patterns to Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst DC3000 as well as to defense signaling hormones (e.g. salicylic acid, jasmonic acid and a precursor of ethylene. Virus-induced gene silencing-mediated silencing of SlTPS3, SlTPS4 or SlTPS7 led to deregulation of ROS accumulation and attenuated the expression of defense-related genes upon pathogen infection and thus deteriorated the resistance against B. cinerea or Pst DC3000. By contrast, silencing of SlTPS5 or SlTPP2 led to an increased expression of the defense-related genes upon pathogen infection and conferred an increased resistance against Pst DC3000. Silencing of SlTPS3, SlTPS4, SlTPS5, SlTPS7 or SlTPP2 affected trehalose level in tomato plants with or without infection of B. cinerea or Pst DC3000. These results demonstrate that SlTPS3, SlTPS4, SlTPS5, SlTPS7 and SlTPP2 play roles in resistance against B. cinerea and Pst DC3000, implying the importance of trehalose and tis metabolism in regulation of defense response against pathogens in tomato.

  2. Pollutant Source Tracking (PST) Technical Guidance

    Science.gov (United States)

    2011-12-01

    certain animals (livestock, wild life, and humans) tend to have normal flora that are resistant to certain types of antibiotics (Wiggins et al., 2003d...pallial sinus) in Bugula neritina (bryozoan invertebrate that resembles moss ) larvae. Close-up view of a FISH hybridization of a larva with Eub338 (a

  3. Turuhoone Tallinnas Mere pst. 10. / Kalle Vellevoog

    Index Scriptorium Estoniae

    Vellevoog, Kalle, 1963-

    1998-01-01

    Turuhoone on ümberehitus kahest 20. sajandi algaastatel püstitatud historitsistlikus laadis tellis- ja paekivihoonest. Turuhoone uus peasissepääs koos keskse trepisõlmega on paigutatud kahe olemasolnud hoone vahelisse koridori. Vaheehitiuse küljel on robustsest võrgust punutud sein. Tellija: AS Talrand. Peaprojekteerija: AS Restauraatorprojekt. Arhitektid Kalle Vellevoog, Velle Kadalipp. Sisekujundus: lisaks arhitektidele Maria Kruus. Ehituse peatöövõtt: AS Kolle. Projekt 1997, valmis 1998.

  4. Pair distribution function computed tomography.

    Science.gov (United States)

    Jacques, Simon D M; Di Michiel, Marco; Kimber, Simon A J; Yang, Xiaohao; Cernik, Robert J; Beale, Andrew M; Billinge, Simon J L

    2013-01-01

    An emerging theme of modern composites and devices is the coupling of nanostructural properties of materials with their targeted arrangement at the microscale. Of the imaging techniques developed that provide insight into such designer materials and devices, those based on diffraction are particularly useful. However, to date, these have been heavily restrictive, providing information only on materials that exhibit high crystallographic ordering. Here we describe a method that uses a combination of X-ray atomic pair distribution function analysis and computed tomography to overcome this limitation. It allows the structure of nanocrystalline and amorphous materials to be identified, quantified and mapped. We demonstrate the method with a phantom object and subsequently apply it to resolving, in situ, the physicochemical states of a heterogeneous catalyst system. The method may have potential impact across a range of disciplines from materials science, biomaterials, geology, environmental science, palaeontology and cultural heritage to health.

  5. Universalities of Triplet Pairing in Neutron Matter

    OpenAIRE

    Khodel, V. A.; Khodel, V. V.; Clark, J. W.

    1998-01-01

    The fundamental structure of the full set of solutions of the BCS $^3 P_2$ pairing problem in neutron matter is established. The relations between different spin-angle components in these solutions are shown to be practically independent of density, temperature, and the specific form of the pairing interaction. The spectrum of pairing energies is found to be highly degenerate.

  6. Long-range RNA pairings contribute to mutually exclusive splicing

    Science.gov (United States)

    Yue, Yuan; Yang, Yun; Dai, Lanzhi; Cao, Guozheng; Chen, Ran; Hong, Weiling; Liu, Baoping; Shi, Yang; Meng, Yijun; Shi, Feng; Xiao, Mu; Jin, Yongfeng

    2016-01-01

    Mutually exclusive splicing is an important means of increasing the protein repertoire, by which the Down's syndrome cell adhesion molecule (Dscam) gene potentially generates 38,016 different isoforms in Drosophila melanogaster. However, the regulatory mechanisms remain obscure due to the complexity of the Dscam exon cluster. Here, we reveal a molecular model for the regulation of the mutually exclusive splicing of the serpent pre-mRNA based on competition between upstream and downstream RNA pairings. Such dual RNA pairings confer fine tuning of the inclusion of alternative exons. Moreover, we demonstrate that the splicing outcome of alternative exons is mediated in relative pairing strength-correlated mode. Combined comparative genomics analysis and experimental evidence revealed similar bidirectional structural architectures in exon clusters 4 and 9 of the Dscam gene. Our findings provide a novel mechanistic framework for the regulation of mutually exclusive splicing and may offer potentially applicable insights into long-range RNA–RNA interactions in gene regulatory networks. PMID:26554032

  7. Long-range RNA pairings contribute to mutually exclusive splicing.

    Science.gov (United States)

    Yue, Yuan; Yang, Yun; Dai, Lanzhi; Cao, Guozheng; Chen, Ran; Hong, Weiling; Liu, Baoping; Shi, Yang; Meng, Yijun; Shi, Feng; Xiao, Mu; Jin, Yongfeng

    2016-01-01

    Mutually exclusive splicing is an important means of increasing the protein repertoire, by which the Down's syndrome cell adhesion molecule (Dscam) gene potentially generates 38,016 different isoforms in Drosophila melanogaster. However, the regulatory mechanisms remain obscure due to the complexity of the Dscam exon cluster. Here, we reveal a molecular model for the regulation of the mutually exclusive splicing of the serpent pre-mRNA based on competition between upstream and downstream RNA pairings. Such dual RNA pairings confer fine tuning of the inclusion of alternative exons. Moreover, we demonstrate that the splicing outcome of alternative exons is mediated in relative pairing strength-correlated mode. Combined comparative genomics analysis and experimental evidence revealed similar bidirectional structural architectures in exon clusters 4 and 9 of the Dscam gene. Our findings provide a novel mechanistic framework for the regulation of mutually exclusive splicing and may offer potentially applicable insights into long-range RNA-RNA interactions in gene regulatory networks. © 2015 Yue et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. DNA polymorphism analysis of candidate genes for type 2 diabetes mellitus in a Mexican ethnic group.

    Science.gov (United States)

    Flores-Martínez, S E; Islas-Andrade, S; Machorro-Lazo, M V; Revilla, M C; Juárez, R E; Mújica-López, K I; Morán-Moguel, M C; López-Cardona, M G; Sánchez-Corona, J

    2004-01-01

    Type 2 diabetes mellitus is a complex metabolic disorder resulting from the action and interaction of many genetic and environmental factors. It has been reported that polymorphisms in genes involved in the metabolism of glucose are associated with the susceptibility to develop type 2 diabetes mellitus. Although the risk of developing type 2 diabetes mellitus increases with age, as well as with obesity and hypertension, its prevalence and incidence are different among geographical regions and ethnic groups. In Mexico, a higher prevalence and incidence has been described in the south of the country, and differences between urban and rural communities have been observed. We studied 73 individuals from Santiago Jamiltepec, a small indigenous community from Oaxaca State, Mexico. This population has shown a high prevalence of type 2 diabetes mellitus, and the aim of this study was to analyze the relationship between the Pst I (insulin gene), Nsi I (insulin receptor gene) and Gly972Arg (insulin receptor substrate 1 gene) polymorphisms and type 2 diabetes mellitus, obesity and hypertension in this population. Clinical evaluation consisted of BMI and blood pressure measurements, and biochemical assays consisted of determination of fasting plasma insulin and glucose levels. PCR and restriction enzyme digestion analysis were applied to genomic DNA to identify the three polymorphisms. From statistical analysis carried out here, individually, the Pst I, Nsi I and Gly972Arg polymorphisms were not associated with the type 2 diabetes, obese or hypertensive phenotypes in this population. Nevertheless, there was an association between the Nsi I and Pst I polymorphisms and increased serum insulin levels.

  9. Report on Pairing-based Cryptography.

    Science.gov (United States)

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.

  10. Use of PCR-RFLP (Polymerase Chain Reaction - Restricted Fragment Length Polymorphism in the gene of the enzyme Stearoyl-CoA-Desaturase in Bubalus bubalis

    Directory of Open Access Journals (Sweden)

    H. Tonhati

    2010-02-01

    Full Text Available The milk is an important food because it contents Conjugated Linoleic Acids (CLA. These fatty acids are synthesized in mammary gland under action of the enzyme Stearoyl CoA-Desaturase (SCD and have showed some positive effects in human disease prevention and treatments. A variation of CLA in milk fat exists and can be partially explained by the different levels of expression of SCD. The aim was to study part of the encoding regions of SCD´s gene using PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism. Genomic DNA was extracted from lactating Murrah females. After this, PCR reactions were made by using primers Z43D1 that encloses exon I, II and intron I. The fragments amplified are composed by 938 pb. Then, RFLP techniques were applied in the fragments using the restriction enzymes Pst I and Sma I. The enzyme Pst I has generated fragments of 788pb and 150bp and the Sma I has generated fragments of 693pb and 245pb. All the animals showed the same migration standard for both enzymes, characterizing a genetic monomorphism for this region of SCD gene. The analysis determined that there aren’t genetic differences between these animals in the studied regions by using Pst I and Sma I enzymes.

  11. Two novel mutations in the glycine-rich region of human PAX6 gene: Implications for an association of cataracts and anosmia with aniridia

    Energy Technology Data Exchange (ETDEWEB)

    Martha, A.; Ferrel, R.E.; Hittner, H.M.; Saunders, G.F. [Univ. of Texas M.D. Anderson Cancer Center, Houston, TX (United States)

    1994-09-01

    Aniridia (iris hyplasia) is a autosomal dominant congenital disorder of the eye. Mutations in the human aniridia (PAX6) gene have now been identified in many patients from various ethnic groups. In the present study we describe new mutations in this gene. Out of four mutations found, three were novel mutations; the fourth one is identical to the previously reported mutations (C{yields}T transition at nt 240). The three novel mutations analyzed were in the glycine-rich region (two) and in the proline/serine/threonine-rich (PST) region (one). Previously no mutations were reported for the glycine-rich region in humans. One of the mutations found in this region is associated with cataracts in an aniridia family. The other splice mutation found in the PST domain is associated with anosmia (lack of sensation to smell) in a sporadic aniridia case. Two of the mutations presented here, one in the glycine-rich region and the other in the PST domain, were not detected by SSCR. These mutations could be detected by using MDE gel and heteroduplex information. All mutations found in the present study are similar in that 32 of 33 PAX6 mutations result in protein truncation and haploinsufficiency.

  12. A restriction fragment length polymorphism results in a nonconservative amino acid substitution encoded within the first exon of the human lysyl oxidase gene

    Energy Technology Data Exchange (ETDEWEB)

    Csiszar, K.; Mariani, T.J.; Gosin, J.S.; Deak, S.B.; Boyd, C.D. [Robert Wood Johnson Medical School, New Brunswick, NJ (United States)

    1993-05-01

    A cDNA covering most of the coding sequence for human lysyl oxidase was used to screen, by Southern blot analysis, genomic DNA from circulating lymphocytes obtained from unrelated, apparently normal individuals. A heritable restriction fragment length polymorphism (RFLP) within a PstI restriction site was detected in 36% of individuals screened (a total of 72 chromosomes were analyzed). The major allele was represented as a 1.7-kb PstI restriction fragment. The minor allele was detected as 1.4 and 0.3kb restriction fragments. Lambda phage-DNA recombinants were isolated from a human lung fibroblast genomic DNA library using the human lysyl oxidase cDNA clone. DNA sequence analysis of several selected phage recombinants revealed that 83% of the coding sequence of lysyl oxidase was localized in four separate exons. Analysis of the coding sequence within exon 1, the most 5{prime} exon within the lysyl oxidase gene, revealed that the PstI RFLP was due to a G {r_arrow} A transition resulting in a nonconservative arginine to glutamine substitution proximal to a propeptide cleavage domain encoded by exon 1 of the lysyl oxidase gene. 33 refs., 5 figs., 1 tab.

  13. Ordered pairing in liquid metallic hydrogen

    Science.gov (United States)

    Carlsson, A. E.; Ashcroft, N. W.

    1983-01-01

    We study two possible types of pairing involving the protons of a proposed low-temperature liquid phase metallic hydrogen. Electron-proton pairing, which can result in an insulating phase, is investigated by using an approximate solution of an Eliashberg-type equation for the anomalous self-energy. A very low estimate of the transition temperature is obtained by including proton correlations in the effective interaction. For proton-proton pairing, we derive a new proton pair potential based on the Abrikosov wave function. This potential includes the electron-proton interaction to all orders and has a much larger well depth than is obtained with linear screening methods. This suggests the possibility of either a superfluid paired phase analogous to that in He-3, or alternatively a phase with true molecular pairing.

  14. An Entropic Approach for Pair Trading

    Directory of Open Access Journals (Sweden)

    Daisuke Yoshikawa

    2017-06-01

    Full Text Available In this paper, we derive the optimal boundary for pair trading. This boundary defines the points of entry into or exit from the market for a given stock pair. However, if the assumed model contains uncertainty, the resulting boundary could result in large losses. To avoid this, we develop a more robust strategy by accounting for the model uncertainty. To incorporate the model uncertainty, we use the relative entropy as a penalty function in the expected profit from pair trading.

  15. Dual origin of pairing in nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Idini, A. [University of Jyvaskyla, Department of Physics (Finland); Potel, G. [Michigan State University, National Superconducting Cyclotron Laboratory (United States); Barranco, F. [Escuela Superior de Ingenieros, Universidad de Sevilla, Departamento de Fìsica Aplicada III (Spain); Vigezzi, E., E-mail: enrico.vigezzi@mi.infn.it [INFN Sezione di Milano (Italy); Broglia, R. A. [Università di Milano, Dipartimento di Fisica (Italy)

    2016-11-15

    The pairing correlations of the nucleus {sup 120}Sn are calculated by solving the Nambu–Gor’kov equations, including medium polarization effects resulting from the interweaving of quasiparticles, spin and density vibrations, taking into account, within the framework of nuclear field theory (NFT), processes leading to self-energy and vertex corrections and to the induced pairing interaction. From these results one can not only demonstrate the inevitability of the dual origin of pairing in nuclei, but also extract information which can be used at profit to quantitatively disentangle the contributions to the pairing gap Δ arising from the bare and from the induced pairing interaction. The first is the strong {sup 1}S{sub 0} short-range NN potential resulting from meson exchange between nucleons moving in time reversal states within an energy range of hundreds of MeV from the Fermi energy. The second results from the exchange of vibrational modes between nucleons moving within few MeV from the Fermi energy. Short- (v{sub p}{sup bare}) and long-range (v{sub p}{sup ind}) pairing interactions contribute essentially equally to nuclear Cooper pair stability. That is to the breaking of gauge invariance in open-shell superfluid nuclei and thus to the order parameter, namely to the ground state expectation value of the pair creation operator. In other words, to the emergent property of generalized rigidity in gauge space, and associated rotational bands and Cooper pair tunneling between members of these bands.

  16. Space-Efficient Re-Pair Compression

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Prezza, Nicola

    2017-01-01

    Re-Pair [5] is an effective grammar-based compression scheme achieving strong compression rates in practice. Let n, σ, and d be the text length, alphabet size, and dictionary size of the final grammar, respectively. In their original paper, the authors show how to compute the Re-Pair grammar...

  17. Exploring Pair Programming Benefits for MIS Majors

    Science.gov (United States)

    Dongo, Tendai; Reed, April H.; O'Hara, Margaret

    2016-01-01

    Pair programming is a collaborative programming practice that places participants in dyads, working in tandem at one computer to complete programming assignments. Pair programming studies with Computer Science (CS) and Software Engineering (SE) majors have identified benefits such as technical productivity, program/design quality, academic…

  18. Enzymatic incorporation of a third nucleobase pair

    National Research Council Canada - National Science Library

    Yang, Zunyi; Sismour, A. Michael; Sheng, Pinpin; Puskar, Nyssa L; Benner, Steven A

    2007-01-01

    DNA polymerases are identified that copy a non-standard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC pairs. 6-Amino-5-nitro-3-(1′-β-d-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ...

  19. Drift wave in pair-ion plasma

    Indian Academy of Sciences (India)

    ion plasma are discussed. It is shown that the temperature and/or mass difference of both species could produce drift wave in a pair-ion plasma. The results are discussed in the context of the fullerene pair-ion plasma experiment.

  20. How to Analyze Paired Comparison Data

    Science.gov (United States)

    2011-05-01

    How to Analyze Paired Comparison Data Kristi Tsukida and Maya R. Gupta Department of Electrical Engineering University of Washington Seattle, WA...REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE How to Analyze Paired Comparison Data 5a. CONTRACT NUMBER 5b. GRANT

  1. Electron pairing in nonlinear nanoelectromechanical systems

    Science.gov (United States)

    Droth, Matthias; Szechenyi, Gabor; Palyi, Andras

    Despite the success of BCS-theory, the underlying mechanism for electron-pairing remains elusive for many superconducting materials. For SrTiO3, it has been shown that electron-pairing outside the superconducting regime can be explained with an effectively negative charging energy U graphene resonator.

  2. Drift wave in pair-ion plasma

    Indian Academy of Sciences (India)

    Xz; 52.27.Cm; 52.35.Kt. 1. Introduction. There has been an accrued interest in pair-ion plasmas, motivated by a recent experiment. [1] on particles with equal charge-to-mass ratio. Pair plasmas are also found in astro- physical environments [2].

  3. Kinetic energy driven pairing in cuprate superconductors

    NARCIS (Netherlands)

    Maier, TA; Jarrell, M; Macridin, A; Slezak, C

    2004-01-01

    Pairing occurs in conventional superconductors through a reduction of the electronic potential energy accompanied by an increase in kinetic energy. In the underdoped cuprates, optical experiments show that pairing is driven by a reduction of the electronic kinetic energy. Using the dynamical cluster

  4. An AvaII polymorphism in the haptoglobin. alpha. gene (HPA)

    Energy Technology Data Exchange (ETDEWEB)

    Bashir, A.; Powell, J. (Charing Cross Hospital, London (England)); Dawson, S.; Vincent, J.; Humphries, S.; Henney, A. (Charing Cross Sunley Research Centre, London (England))

    1989-06-26

    A 480bp cDNA clone in pEMBL9 was excised by PstI, with BamHI digestion representing the haptoglobin {alpha}{sup 2} chain. A constant band is seen at 3.2kb with polymorphic bands at 2.7 and 4.4 Kb. This represents a length polymorphism, not a site polymorphism. It is reflecting the same gene duplication seen in the HindIII polymorphism at this locus. The allele frequency was determined in 76 unrelated individuals. Mendelian inheritance was demonstrated in two extended families.

  5. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes.

    Directory of Open Access Journals (Sweden)

    Marcela Dávila López

    Full Text Available The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional

  6. Weird Stellar Pair Puzzles Scientists

    Science.gov (United States)

    2008-05-01

    Astronomers have discovered a speedy spinning pulsar in an elongated orbit around an apparent Sun-like star, a combination never seen before, and one that has them puzzled about how the strange system developed. Orbital Comparison Comparing Orbits of Pulsar and Its Companion to our Solar System. CREDIT: Bill Saxton, NRAO/AUI/NSF Click on image for full caption information and available graphics. "Our ideas about how the fastest-spinning pulsars are produced do not predict either the kind of orbit or the type of companion star this one has," said David Champion of the Australia Telescope National Facility. "We have to come up with some new scenarios to explain this weird pair," he added. Astronomers first detected the pulsar, called J1903+0327, as part of a long-term survey using the National Science Foundation's Arecibo radio telescope in Puerto Rico. They made the discovery in 2006 doing data analysis at McGill University, where Champion worked at the time. They followed up the discovery with detailed studies using the Arecibo telescope, the NSF's Robert C. Byrd Green Bank Telescope (GBT) in West Virginia, the Westerbork radio telescope in the Netherlands, and the Gemini North optical telescope in Hawaii. The pulsar, a city-sized superdense stellar corpse left over after a massive star exploded as a supernova, is spinning on its axis 465 times every second. Nearly 21,000 light-years from Earth, it is in a highly-elongated orbit that takes it around its companion star once every 95 days. An infrared image made with the Gemini North telescope in Hawaii shows a Sun-like star at the pulsar's position. If this is an orbital companion to the pulsar, it is unlike any companions of other rapidly rotating pulsars. The pulsar, a neutron star, also is unusually massive for its type. "This combination of properties is unprecedented. Not only does it require us to figure out how this system was produced, but the large mass may help us understand how matter behaves at extremely

  7. A Curious Pair of Galaxies

    Science.gov (United States)

    2009-03-01

    The ESO Very Large Telescope has taken the best image ever of a strange and chaotic duo of interwoven galaxies. The images also contain some surprises -- interlopers both far and near. ESO PR Photo 11a/09 A Curious Pair of Galaxies ESO PR Video 11a/09 Arp 261 zoom in ESO PR Video 11b/09 Pan over Arp 261 Sometimes objects in the sky that appear strange, or different from normal, have a story to tell and prove scientifically very rewarding. This was the idea behind Halton Arp's catalogue of Peculiar Galaxies that appeared in the 1960s. One of the oddballs listed there is Arp 261, which has now been imaged in more detail than ever before using the FORS2 instrument on ESO's Very Large Telescope. The image proves to contain several surprises. Arp 261 lies about 70 million light-years distant in the constellation of Libra, the Scales. Its chaotic and very unusual structure is created by the interaction of two galaxies that are engaged in a slow motion, but highly disruptive close encounter. Although individual stars are very unlikely to collide in such an event, the huge clouds of gas and dust certainly do crash into each other at high speed, leading to the formation of bright new clusters of very hot stars that are clearly seen in the picture. The paths of the existing stars in the galaxies are also dramatically disrupted, creating the faint swirls extending to the upper left and lower right of the image. Both interacting galaxies were probably dwarfs not unlike the Magellanic Clouds orbiting our own galaxy. The images used to create this picture were not actually taken to study the interacting galaxies at all, but to investigate the properties of the inconspicuous object just to the right of the brightest part of Arp 261 and close to the centre of the image. This is an unusual exploding star, called SN 1995N, that is thought to be the result of the final collapse of a massive star at the end of its life, a so-called core collapse supernova. SN 1995N is unusual because

  8. String pair production in non homogeneous backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Bolognesi, S. [Department of Physics “E. Fermi” University of Pisa, and INFN - Sezione di Pisa,Largo Pontecorvo, 3, Ed. C, 56127 Pisa (Italy); Rabinovici, E. [Racah Institute of Physics, The Hebrew University of Jerusalem,91904 Jerusalem (Israel); Tallarita, G. [Departamento de Ciencias, Facultad de Artes Liberales,Universidad Adolfo Ibáñez, Santiago 7941169 (Chile)

    2016-04-28

    We consider string pair production in non homogeneous electric backgrounds. We study several particular configurations which can be addressed with the Euclidean world-sheet instanton technique, the analogue of the world-line instanton for particles. In the first case the string is suspended between two D-branes in flat space-time, in the second case the string lives in AdS and terminates on one D-brane (this realizes the holographic Schwinger effect). In some regions of parameter space the result is well approximated by the known analytical formulas, either the particle pair production in non-homogeneous background or the string pair production in homogeneous background. In other cases we see effects which are intrinsically stringy and related to the non-homogeneity of the background. The pair production is enhanced already for particles in time dependent electric field backgrounds. The string nature enhances this even further. For spacial varying electrical background fields the string pair production is less suppressed than the rate of particle pair production. We discuss in some detail how the critical field is affected by the non-homogeneity, for both time and space dependent electric field backgrouds. We also comment on what could be an interesting new prediction for the small field limit. The third case we consider is pair production in holographic confining backgrounds with homogeneous and non-homogeneous fields.

  9. Exploring Pair Programming Benefits for MIS Majors

    Directory of Open Access Journals (Sweden)

    April H. Reed

    2016-12-01

    Full Text Available Pair programming is a collaborative programming practice that places participants in dyads, working in tandem at one computer to complete programming assignments. Pair programming studies with Computer Science (CS and Software Engineering (SE majors have identified benefits such as technical productivity, program/design quality, academic performance, and increased satisfaction for their participants. In this paper, pair programming is studied with Management Information Systems (MIS majors, who (unlike CS and SE majors taking several programming courses typically take only one programming course and often struggle to develop advanced programming skills within that single course. The researchers conducted two pair programming experiments in an introductory software development course for MIS majors over three semesters to determine if pair programming could enhance learning for MIS students. The program results, researchers’ direct observations, and participants’ responses to a survey questionnaire were analyzed after each experiment. The results indicate that pair programming appears to be beneficial to MIS students’ technical productivity and program design quality, specifically the ability to create programs using high-level concepts. Additionally, results confirmed increased student satisfaction and reduced frustration, as the pairs worked collaboratively to produce a program while actively communicating and enjoying the process.

  10. Geometrical ambiguity of pair statistics: point configurations.

    Science.gov (United States)

    Jiao, Y; Stillinger, F H; Torquato, S

    2010-01-01

    Point configurations have been widely used as model systems in condensed-matter physics, materials science, and biology. Statistical descriptors, such as the n -body distribution function g(n), are usually employed to characterize point configurations, among which the most extensively used is the pair distribution function g(2). An intriguing inverse problem of practical importance that has been receiving considerable attention is the degree to which a point configuration can be reconstructed from the pair distribution function of a target configuration. Although it is known that the pair-distance information contained in g(2) is, in general, insufficient to uniquely determine a point configuration, this concept does not seem to be widely appreciated and general claims of uniqueness of the reconstructions using pair information have been made based on numerical studies. In this paper, we present the idea of the distance space called the D space. The pair distances of a specific point configuration are then represented by a single point in the D space. We derive the conditions on the pair distances that can be associated with a point configuration, which are equivalent to the realizability conditions of the pair distribution function g(2). Moreover, we derive the conditions on the pair distances that can be assembled into distinct configurations, i.e., with structural degeneracy. These conditions define a bounded region in the D space. By explicitly constructing a variety of degenerate point configurations using the D space, we show that pair information is indeed insufficient to uniquely determine the configuration in general. We also discuss several important problems in statistical physics based on the D space, including the reconstruction of atomic structures from experimentally obtained g(2) and a recently proposed "decorrelation" principle. The degenerate configurations have relevance to open questions involving the famous traveling salesman problem.

  11. Filipino au pairs on the move

    DEFF Research Database (Denmark)

    Dalgas, Karina Märcher

    2016-01-01

    interdependence, whilst they continuously form their trajectories in relation to opportunities and restraints posed along the way by their local and transnational social relations. The article argues that examinations of migration trajectories benefit from broadening the research out in both time and space......Most Filipina au pairs in Denmark send remittances back home, and for many, au pairing forms part of longer-term migration trajectories. This article explores how Filipina au pairs try to carve out a future for themselves abroad. It shows that they navigate within tight webs of financial...

  12. Becoming independent through au pair migration

    DEFF Research Database (Denmark)

    Dalgas, Karina Märcher

    2015-01-01

    . This article argues that, despite this critique, au pairing does play an important formative role for young Filipinas because it opens up for experiences abroad that enable them to be recognised as independent adults in Philippine society. Rather than autonomy, however, au pairs define their independence...... in terms of their capacity to assume responsibility for others, thereby achieving a position of social respect. Based on ethnographic fieldwork in Denmark and the Philippines, this article explores how young Filipinas use the social, economic, and cultural resources they gain from their au pair stay abroad...

  13. Pairing symmetries in cuprates: A Gorkov formalism

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Angsula, E-mail: angsula@ufam.edu.br [Departamento de Fisica, UFAM, Av. Rodrigo Octavio 3000, Japiim, 69077-000 Manaus, AM (Brazil); Pimentel, B.M. [Instituto de Fisica Teorica, Sao Paulo State University, P.O. Box 70532-2, 01156-970 Sao Paulo, SP (Brazil)

    2012-10-01

    Inspite of the direct evidence for Cooper pairing in the cuprates as in conventional superconductors, the pairing symmetry in the cuprate superconductors is still considered to be a controversial and a highly debatable topic. The microscopic equations appropriate for these new materials, essentially the yttrium based compounds, are discussed following Gorkov's formalism for the conventional superconductors. Various types of symmetry of the pairing parameter are considered. In this study we consider the anisotropic nature of the gap parameter to write the mean-field equations of the cuprates. We observe that the symmetry of the potential is fundamental in deciding the nature of the anisotropy in the gap parameter.

  14. English for au pairs the au pair's guide to learning English

    CERN Document Server

    Curtis, Lucy

    2014-01-01

    English for Au Pairs has interlinked stories about a group of au pairs new to England. Marta, an 18-year-old from Poland arrives in the UK to work as an au pair. Throughout her year-long stay she has many different experiences - some bad, some good - but with the support of her host family she finds new friends and improves her English. English for Au Pairs offers insight into the joys and difficulties of being an au pair while at the same time reinforcing English language learning through grammar explanations and exercises.

  15. Amplification of Cooper pair splitting current in a graphene-based Cooper pair beam splitter geometry

    Science.gov (United States)

    Islam, SK Firoz; Saha, Arijit

    2017-09-01

    Motivated by the recent experiments [Scientific Reports 6, 23051 (2016), 10.1038/srep23051; Phys. Rev. Lett. 114, 096602 (2015), 10.1103/PhysRevLett.114.096602], we theoretically investigate Cooper pair splitting current in a graphene-based Cooper pair beam splitter geometry. By considering the graphene-based superconductor as an entangler device, instead of normal [two-dimensional (2D)] BCS superconductor, we show that the Cooper pair splitting current mediated by the crossed Andreev process is amplified compared to its normal superconductor counterpart. This amplification is attributed to the strong suppression of the local normal Andreev reflection process (arising from the Cooper pair splitting) from the graphene-based superconductor to lead via the same quantum dot, in comparison to the usual 2D superconductor. Due to the vanishing density of states at the Dirac point of undoped graphene, a doped graphene-based superconductor is considered here and it is observed that Cooper pair splitting current is very insensitive to the doping level in comparison to the usual 2D superconductor. The transport process of nonlocal spin-entangled electrons also depends on the type of pairing, i.e., whether the electron-hole pairing is onsite, intersublattice or the combination of both. The intersublattice pairing of graphene causes the maximum nonlocal Cooper pair splitting current, whereas the presence of both pairings reduces the Cooper pair splitting current.

  16. Comparison of the locations of homologous fowlpox and vaccinia virus genes reveals major genome reorganization.

    Science.gov (United States)

    Mockett, B; Binns, M M; Boursnell, M E; Skinner, M A

    1992-10-01

    We have derived a restriction enzyme map for the fowlpox virus FP9 strain. Sites for BamHI, PvuII, PstI and NcoI have been mapped mainly by Southern blotting. The size of the genome derived from the restriction maps (254 kb) corresponds to the figure of 260 +/- 8 kb determined from analysis of genomic DNA by pulsed-field electrophoresis. The map can be compared with a previously published map for a different strain of fowlpox virus using the PstI digest which is common to both studies. Some 65 kb of fowlpox virus sequence, in 11 blocks, as well as individual M13 clones have been aligned with the map. Where those blocks correspond with blocks of homologous genes in vaccinia virus, it is possible to compare the genomic locations for those genes in the two viruses. This comparison reveals that, whereas there are blocks of sequence within which genes exist in the same relative position in the two viruses, the genomic location of those sequence blocks differs widely between the two viruses.

  17. Somatic pairing of chromosome 19 in renal oncocytoma is associated with deregulated EGLN2-mediated [corrected] oxygen-sensing response.

    Directory of Open Access Journals (Sweden)

    Julie M Koeman

    2008-09-01

    Full Text Available Chromosomal abnormalities, such as structural and numerical abnormalities, are a common occurrence in cancer. The close association of homologous chromosomes during interphase, a phenomenon termed somatic chromosome pairing, has been observed in cancerous cells, but the functional consequences of somatic pairing have not been established. Gene expression profiling studies revealed that somatic pairing of chromosome 19 is a recurrent chromosomal abnormality in renal oncocytoma, a neoplasia of the adult kidney. Somatic pairing was associated with significant disruption of gene expression within the paired regions and resulted in the deregulation of the prolyl-hydroxylase EGLN2 [corrected] a key protein that regulates the oxygen-dependent degradation of hypoxia-inducible factor (HIF. Overexpression of EGLN2 [corrected] in renal oncocytoma increased ubiquitin-mediated destruction of HIF and concomitantly suppressed the expression of several HIF-target genes, including the pro-death BNIP3L gene. The transcriptional changes that are associated with somatic pairing of chromosome 19 mimic the transcriptional changes that occur following DNA amplification. Therefore, in addition to numerical and structural chromosomal abnormalities, alterations in chromosomal spatial dynamics should be considered as genomic events that are associated with tumorigenesis. The identification of EGLN2 as a significantly deregulated gene that maps within the paired chromosome region directly implicates defects in the oxygen-sensing network to the biology of renal oncocytoma.

  18. Introducing a model of pairing based on base pair specific interactions between identical DNA sequences

    Science.gov (United States)

    (O’ Lee, Dominic J.

    2018-02-01

    At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.

  19. Eramu Tallinnas : Lootuse pst. 78 = Private home, Lootuse puiestee : Lootuse pst. 78, Tallinn / Epp Lankots

    Index Scriptorium Estoniae

    Lankots, Epp, 1976-

    2005-01-01

    Kahepereelamu mõlemad korterid ulatuvad läbi kahe tasapinna, nende vahele jääb saunast, panipaigast ning tehnilistest ruumidest koosnev plokk. Arhitektid: Tõnu Laigu, Tõnu Laanemäe. Sisearhitekt: Taevo Gans. Ill.: 2 värv. välis- ja 2 sisevaadet

  20. Correlated electron pairs in metal clusters

    Science.gov (United States)

    Iachello, F.; Lipparini, E.; Ventura, A.

    We show that the experimental data on ionization energies and photoabsorption cross sections of alkali metal clusters are consistent with a model of clusters in terms of a system of interacting electron pairs with L=0 and L=2.

  1. Four square mile survey pair count instructions

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This standard operating procedure (SOP) provides guidance for conducting bird pair count measurements on wetlands for the HAPETs Four-Square-Mile survey. This set of...

  2. Pairing properties of realistic effective interactions

    Directory of Open Access Journals (Sweden)

    Gargano A.

    2016-01-01

    Full Text Available We investigate the pairing properties of an effective shell-model interaction defined within a model space outside 132Sn and derived by means of perturbation theory from the CD-Bonn free nucleon-nucleon potential. It turns out that the neutron pairing component of the effective interaction is significantly weaker than the proton one, which accounts for the large pairing gap difference observed in the two-valence identical particle nuclei 134Sn and 134Te. The role of the contribution arising from one particle-one hole excitations in determining the pairing force is discussed and its microscopic structure is also analyzed in terms of the multipole decomposition.

  3. Microfluidic Control of Cell Pairing and Fusion

    Science.gov (United States)

    Skelley, Alison M.; Kirak, Oktay; Suh, Heikyung; Jaenisch, Rudolf; Voldman, Joel

    2011-01-01

    Cell fusion has been used for many different purposes, including generation of hybridomas and reprogramming of somatic cells. The fusion step represents the key event in initiation of these procedures. Standard fusion techniques, however, provide poor and random cell contact, leading to low yields. We present here a microfluidic device to trap and properly pair thousands of cells. Using this device we were able to pair different cell types, including fibroblasts, mouse embryonic stem cells (mESCs), and myeloma cells, achieving pairing efficiencies up to 70%. The device is compatible with both chemical and electrical fusion protocols. We observed that electrical fusion was more efficient than chemical fusion, with membrane reorganization efficiencies of up to 89%. We achieved greater than 50% properly paired and fused cells over the entire device, 5× greater than a commercial electrofusion chamber, and were able to observe reprogramming in hybrids between mESCs and mouse embryonic fibroblasts. PMID:19122668

  4. Temporal Multimode Storage of Entangled Photon Pairs.

    Science.gov (United States)

    Tiranov, Alexey; Strassmann, Peter C; Lavoie, Jonathan; Brunner, Nicolas; Huber, Marcus; Verma, Varun B; Nam, Sae Woo; Mirin, Richard P; Lita, Adriana E; Marsili, Francesco; Afzelius, Mikael; Bussières, Félix; Gisin, Nicolas

    2016-12-09

    Multiplexed quantum memories capable of storing and processing entangled photons are essential for the development of quantum networks. In this context, we demonstrate and certify the simultaneous storage and retrieval of two entangled photons inside a solid-state quantum memory and measure a temporal multimode capacity of ten modes. This is achieved by producing two polarization-entangled pairs from parametric down-conversion and mapping one photon of each pair onto a rare-earth-ion-doped (REID) crystal using the atomic frequency comb (AFC) protocol. We develop a concept of indirect entanglement witnesses, which can be used as Schmidt number witnesses, and we use it to experimentally certify the presence of more than one entangled pair retrieved from the quantum memory. Our work puts forward REID-AFC as a platform compatible with temporal multiplexing of several entangled photon pairs along with a new entanglement certification method, useful for the characterization of multiplexed quantum memories.

  5. Z-related pairs in microtonal systems

    NARCIS (Netherlands)

    Althuis, T.A.; Gobel, F.

    2000-01-01

    Various infinite families of Z-related pairs in microtonal systems are presented. Soderberg's dual inversion is compared to a more special transformation, the one-pitch shift. The material is illustrated by several examples.

  6. Quantum delocalization in photon-pair generation

    Science.gov (United States)

    Forbes, Kayn A.; Ford, Jack S.; Jones, Garth A.; Andrews, David L.

    2017-08-01

    The generation of correlated photon pairs is a key to the production of entangled quantum states, which have a variety of applications within the area of quantum information. In spontaneous parametric down-conversion—the primary method of generating correlated photon pairs—the associated photon annihilation and creation events are generally thought of as being colocated: The correlated pair of photons is localized with regards to the pump photon and its positional origin. A detailed quantum electrodynamical analysis highlights a mechanism exhibiting the possibility of a delocalized origin for paired output photons: The spatial extent of the region from which the pair is generated can be much larger than previously thought. The theory of both localized and nonlocalized degenerate down-conversion is presented, followed by a quantitative analysis using discrete-volume computational methods. The results may have significant implications for quantum information and imaging applications, and the design of nonlinear optical metamaterials.

  7. 22 CFR 62.31 - Au pairs.

    Science.gov (United States)

    2010-04-01

    ....31 Au pairs. (a) Introduction. This section governs Department of State-designated exchange visitor... requirements set forth at § 62.10 sponsors shall: (1) Inform all host families of the philosophy, rules, and...

  8. Alloy solution hardening with solute pairs

    Science.gov (United States)

    Mitchell, John W.

    1976-08-24

    Solution hardened alloys are formed by using at least two solutes which form associated solute pairs in the solvent metal lattice. Copper containing equal atomic percentages of aluminum and palladium is an example.

  9. Degenerated differential pair with controllable transconductance

    NARCIS (Netherlands)

    Mensink, Clemens; Mensink, Clemens H.J.; Nauta, Bram

    1998-01-01

    A differential pair with input transistors and provided with a variable degeneration resistor. The degeneration resistor comprises a series arrangement of two branches of coupled resistors which are shunted in mutually corresponding points by respective control transistors whose gates are

  10. a Norm Pairing in Formal Modules

    Science.gov (United States)

    Vostokov, S. V.

    1980-02-01

    A pairing of the multiplicative group of a local field (a finite extension of the field of p-adic numbers Qp) with the group of points of a Lubin-Tate formal group is defined explicitly. The values of the pairing are roots of an isogeny of the formal group. The main properties of this pairing are established: bilinearity, invariance under the choice of a local uniformizing element, and independence of the method of expanding elements into series with respect to this uniformizing element. These properties of the pairing are used to prove that it agrees with the generalized Hilbert norm residue symbol when the field over whose ring of integers the formal group is defined is totally ramified over Qp. This yields an explicit expression for the generalized Hilbert symbol on the group of points of the formal group. Bibliography: 12 titles.

  11. Marcus Theory of Ion-Pairing

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.; Schenter, Gregory K.

    2017-08-08

    We present a theory for ion pair dissociation and association, motivated by the concepts of the Marcus theory of electron transfer. Despite the extensive research on ion-pairing in many chemical and biological processes, much can be learned from the exploration of collective reaction coordinates. To this end, we explore two reaction coordinates, ion pair distance and coordination number. The study of the correlation between these reaction coordinates provides a new insight into the mechanism and kinetics of ion pair dissociation and association in water. The potential of mean force on these 2D-surfaces computed from molecular dynamics simulations of different monovalent ion pairs reveal a Marcus-like mechanism for ion-pairing: Water molecules rearrange forming an activated coordination state prior to ion pair dissociation or association, followed by relaxation of the coordination state due to further water rearrangement. Like Marcus theory, we find the existence of an inverted region where the transition rates are slower with increasing exergonicity. This study provides a new perspective for the future investigations of ion-pairing and transport. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). The research was performed using PNNL Institutional Computing. PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.

  12. Development of artificial nucleic acid that recognizes a CG base pair in triplex DNA formation.

    Science.gov (United States)

    Hari, Yoshiyuki

    2013-01-01

    An oligonucleotide that can form a triplex with double-stranded DNA is called a triplex-forming oligonucleotide (TFO). TFOs have gained considerable attention because of their potential as gene targeting tools. However, triplex DNA formation involves inherent problems for practical use. The most important problem is that natural nucleotides in TFO do not have sufficient affinity and base pair-selectivity to pyrimidine-purine base pair, like a CG or TA base pair, within dsDNA. This suggests that dsDNA region including a CG or TA base pair cannot be targeted. Therefore, artificial nucleotides, especially with non-natural nucleobases, capable of direct recognition of a CG or TA base pair via hydrogen bond formation have been developed; however, nucleotides with better selectivity and stronger affinity are necessary for implementing this dsDNA-targeting technology using TFOs. Under such a background, we considered that facile and efficient synthesis of various nucleobase derivatives in TFOs would be useful for finding an ideal nucleobase for recognition of a CG or TA base pair because detailed and rational exploration of nucleobase structures is facilitated. Recently, to develop a nucleobase recognizing a CG base pair, we have used post-elongation modification, i.e., modification after oligonucleotide synthesis, for the facile synthesis of nucleobase derivatives. This review mainly summarizes our recent findings on the development of artificial nucleobases and nucleotides for recognition of a CG base pair in triplexes formed between dsDNA and TFOs.

  13. Neurobiology of pair bonding in fishes; convergence of neural mechanisms across distant vertebrate lineages

    KAUST Repository

    Nowicki, Jessica

    2017-11-14

    Pair bonding has independently evolved numerous times among vertebrates. The governing neural mechanisms of pair bonding have only been studied in depth in the mammalian model species, the prairie vole, Microtus ochrogaster. In this species, oxytocin (OT), arginine vasopressin (AVP), dopamine (DA), and opioid (OP) systems play key roles in signaling in the formation and maintenance of pair bonding by targeting specific social and reward-mediating brain regions. By contrast, the neural basis of pair bonding is poorly studied in other vertebrates, and especially those of early origins, limiting our understanding of the evolutionary history of pair bonding regulatory mechanisms. We compared receptor gene expression between pair bonded and solitary individuals across eight socio-functional brain regions. We found that in females, ITR and V1aR receptor expression varied in the lateral septum-like region (the Vv/Vl), while in both sexes D1R, D2R, and MOR expression varied within the mesolimbic reward system, including a striatum-like region (the Vc); mirroring sites of action in M. ochrogaster. This study provides novel insights into the neurobiology of teleost pair bonding. It also reveals high convergence in the neurochemical mechanisms governing pair bonding across actinopterygians and sarcopterygians, by repeatedly co-opting and similarly assembling deep neurochemical and neuroanatomical homologies that originated in ancestral osteithes.

  14. The grammar of approximating number pairs.

    Science.gov (United States)

    Eriksson, Kimmo; Bailey, Drew H; Geary, David C

    2010-04-01

    In the present article, we studied approximating pairs of numbers (a, b) that were used to estimate quantity in a single phrase ("two, three years ago"). Pollmann and Jansen (1996) found that only a few of the many possible pairs are actually used, suggesting an interaction between the ways in which people estimate quantity and their use of quantitative phrases in colloquial speech. They proposed a set of rules that describe which approximating pairs are used in Dutch phrases. We revisited this issue in an analysis of Swedish and American language corpora and in a series of three experiments in which Swedish and American adults rated the acceptability of various approximating pairs and created approximating pairs of their own in response to various estimation tasks. We found evidence for Pollmann and Jansen's rules in both Swedish and English phrases, but we also identified additional rules and substantial individual and cross-language variation. We will discuss implications for the origin of this loose "grammar" of approximating pairs.

  15. Formation of asteroid pairs by rotational fission.

    Science.gov (United States)

    Pravec, P; Vokrouhlický, D; Polishook, D; Scheeres, D J; Harris, A W; Galád, A; Vaduvescu, O; Pozo, F; Barr, A; Longa, P; Vachier, F; Colas, F; Pray, D P; Pollock, J; Reichart, D; Ivarsen, K; Haislip, J; Lacluyze, A; Kusnirák, P; Henych, T; Marchis, F; Macomber, B; Jacobson, S A; Krugly, Yu N; Sergeev, A V; Leroy, A

    2010-08-26

    Pairs of asteroids sharing similar heliocentric orbits, but not bound together, were found recently. Backward integrations of their orbits indicated that they separated gently with low relative velocities, but did not provide additional insight into their formation mechanism. A previously hypothesized rotational fission process may explain their formation-critical predictions are that the mass ratios are less than about 0.2 and, as the mass ratio approaches this upper limit, the spin period of the larger body becomes long. Here we report photometric observations of a sample of asteroid pairs, revealing that the primaries of pairs with mass ratios much less than 0.2 rotate rapidly, near their critical fission frequency. As the mass ratio approaches 0.2, the primary period grows long. This occurs as the total energy of the system approaches zero, requiring the asteroid pair to extract an increasing fraction of energy from the primary's spin in order to escape. We do not find asteroid pairs with mass ratios larger than 0.2. Rotationally fissioned systems beyond this limit have insufficient energy to disrupt. We conclude that asteroid pairs are formed by the rotational fission of a parent asteroid into a proto-binary system, which subsequently disrupts under its own internal system dynamics soon after formation.

  16. Photon pair production in astrophysical transrelativistic plasmas

    Science.gov (United States)

    Stoeger, W. R.

    1977-01-01

    Photon pair-production processes in marginally relativistic (transrelativistic) accretion plasmas are investigated in both Planckian and non-Planckian cases. Pair production in a plasma with an equilibrium (Planck) spectrum is reviewed, and pair-concentration calculations are performed for three general non-Planckian situations most relevant to black-hole accretion scenarios: steady-state transrelativistic plasmas of relatively high density characterized by a pure bremsstrahlung spectrum, a comptonized bremsstrahlung spectrum, and an unsaturated Compton scattering spectrum. The results obtained indicate that for transrelativistic temperatures (600 million to 6 billion K) photon pair production is not generally a dominant process for a plasma with a pure bremsstrahlung spectrum, but becomes dominant for plasmas where comptonization is important. It is also shown that photon pair-creation processes in a transrelativistic bremsstrahlung-radiating plasma that is more than marginally optically thick to Compton scattering significantly alter the plasma's spectrum by forcing it to become black-body before it reaches relativistic temperatures. Pair production and instabilities in unsteady-state plasmas are briefly considered

  17. Modelling prokaryote gene content

    Directory of Open Access Journals (Sweden)

    Edward Susko

    2006-01-01

    Full Text Available The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time to blocks models (allowing gain and loss of multiple genes within a family. We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea and Bacillus subtilis (gram positive bacteria. Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common. For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model.

  18. [Studies of mtDNA of Ustilago maydis. I. Cloning and gene mapping].

    Science.gov (United States)

    Feng, G H; Cheng, W; Lu, S Y

    1991-01-01

    This paper covers the following studies of mtDNA of Ustilago maydis. (1) By inserting the Bam HI and Pst I fragments of the mtDNA into the corresponding sites of pBR322, we cloned a unique sequence of 49.6 kb, accounting for 89.3% of the mitochondrial genome (60.7 kb). (2) With heterogenous genes from plants or fungi as probes, we identified seven genes, and mapped them onto the restriction map of the mt DNA. The genes were arranged in such an order: -UmCOB-UmOXII-S-rR NA-UmOXIII-L-rRNA-UmATPase6-UmOXI-. (3) We tried to express the three cloned genes, UmOXII, UmOXIII, and Um-ATPase 6, in E. coli maxcel expression system, but no specific protein was observed.

  19. A review of the correlation of tergites, sternites, and leg pairs in diplopods

    Science.gov (United States)

    Janssen, Ralf; Prpic, Nikola-Michael; Damen, Wim GM

    2006-01-01

    In some arthropods there is a discrepancy in the number of dorsal tergites compared to the number of ventral sternites and leg pairs. The posterior tergites of the Diplopoda (millipedes) each cover two sternites and two pairs of legs. This segment arrangement is called diplosegmentation. The molecular nature of diplosegmentation is still unknown. There are even conflicting theories on the way the tergites and sternites/leg pairs should be correlated to each other. The different theories are based either on embryological analyses or on studies of the adult morphology and turned out to be not compatible with each other. We have previously used the expression patterns of segmentation genes in the pill millipede Glomeris marginata (Myriapoda: Diplopoda) to study millipede segmentation. Here we review the existing models on the alignment of tergites and leg pairs in millipedes with special emphasis on the implications the gene expression data have on the debate of tergite and leg pair assignment in millipedes. The remarkable outcome of the gene expression analysis was that (1) there is no coupling of dorsal and ventral segmentation and, importantly, that (2) the boundaries delimiting the tergites do neither correlate to the embryonic boundaries of the dorsal embryonic segments nor to the boundaries of the ventral embryonic segments. Using these new insights, we critically reinvestigated the correlation of tergites, sternites, and leg pairs in millipedes. Our model, which takes into account that the tergite boundaries are different from the dorsal embryonic segment boundaries, provides a solution of the problem of tergite to sternite/leg pair correlation in basal milipedes with non-fused exoskeletal elements and also has implications for derived species with exoskeletal rings. Moreover, lack of coupling of dorsal and ventral segmentation may also explain the discrepancy in numbers of dorsal tergites and ventral leg pairs seen in some other arthropods. PMID:16451739

  20. A review of the correlation of tergites, sternites, and leg pairs in diplopods

    Directory of Open Access Journals (Sweden)

    Damen Wim GM

    2006-02-01

    Full Text Available Abstract In some arthropods there is a discrepancy in the number of dorsal tergites compared to the number of ventral sternites and leg pairs. The posterior tergites of the Diplopoda (millipedes each cover two sternites and two pairs of legs. This segment arrangement is called diplosegmentation. The molecular nature of diplosegmentation is still unknown. There are even conflicting theories on the way the tergites and sternites/leg pairs should be correlated to each other. The different theories are based either on embryological analyses or on studies of the adult morphology and turned out to be not compatible with each other. We have previously used the expression patterns of segmentation genes in the pill millipede Glomeris marginata (Myriapoda: Diplopoda to study millipede segmentation. Here we review the existing models on the alignment of tergites and leg pairs in millipedes with special emphasis on the implications the gene expression data have on the debate of tergite and leg pair assignment in millipedes. The remarkable outcome of the gene expression analysis was that (1 there is no coupling of dorsal and ventral segmentation and, importantly, that (2 the boundaries delimiting the tergites do neither correlate to the embryonic boundaries of the dorsal embryonic segments nor to the boundaries of the ventral embryonic segments. Using these new insights, we critically reinvestigated the correlation of tergites, sternites, and leg pairs in millipedes. Our model, which takes into account that the tergite boundaries are different from the dorsal embryonic segment boundaries, provides a solution of the problem of tergite to sternite/leg pair correlation in basal milipedes with non-fused exoskeletal elements and also has implications for derived species with exoskeletal rings. Moreover, lack of coupling of dorsal and ventral segmentation may also explain the discrepancy in numbers of dorsal tergites and ventral leg pairs seen in some other

  1. Generalized pairing strategies-a bridge from pairing strategies to colorings

    Directory of Open Access Journals (Sweden)

    Győrffy Lajos

    2016-12-01

    Full Text Available In this paper we define a bridge between pairings and colorings of the hypergraphs by introducing a generalization of pairs called t-cakes for t ∈ ℕ, t ≥ 2. For t = 2 the 2-cakes are the same as the well-known pairs of system of distinct representatives, that can be turned to pairing strategies in Maker-Breaker hypergraph games, see Hales and Jewett [12]. The two-colorings are the other extremity of t-cakes, in which the whole ground set of the hypergraph is one big cake that we divide into two parts (color classes. Starting from the pairings (2-cake placement and two-colorings we define the generalized t-cake placements where we pair p elements by q elements (p, q ∈ ℕ, 1 ≤ p, q < t, p + q = t.

  2. Screening for resistance against Pseudomonas syringae in rice-FOX Arabidopsis lines identified a putative receptor-like cytoplasmic kinase gene that confers resistance to major bacterial and fungal pathogens in Arabidopsis and rice.

    Science.gov (United States)

    Dubouzet, Joseph G; Maeda, Satoru; Sugano, Shoji; Ohtake, Miki; Hayashi, Nagao; Ichikawa, Takanari; Kondou, Youichi; Kuroda, Hirofumi; Horii, Yoko; Matsui, Minami; Oda, Kenji; Hirochika, Hirohiko; Takatsuji, Hiroshi; Mori, Masaki

    2011-05-01

    Approximately 20,000 of the rice-FOX Arabidopsis transgenic lines, which overexpress 13,000 rice full-length cDNAs at random in Arabidopsis, were screened for bacterial disease resistance by dip inoculation with Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). The identities of the overexpressed genes were determined in 72 lines that showed consistent resistance after three independent screens. Pst DC3000 resistance was verified for 19 genes by characterizing other independent Arabidopsis lines for the same genes in the original rice-FOX hunting population or obtained by reintroducing the genes into ecotype Columbia by floral dip transformation. Thirteen lines of these 72 selections were also resistant to the fungal pathogen Colletotrichum higginsianum. Eight genes that conferred resistance to Pst DC3000 in Arabidopsis have been introduced into rice for overexpression, and transformants were evaluated for resistance to the rice bacterial pathogen, Xanthomonas oryzae pv. oryzae. One of the transgenic rice lines was highly resistant to Xanthomonas oryzae pv. oryzae. Interestingly, this line also showed remarkably high resistance to Magnaporthe grisea, the fungal pathogen causing rice blast, which is the most devastating rice disease in many countries. The causal rice gene, encoding a putative receptor-like cytoplasmic kinase, was therefore designated as BROAD-SPECTRUM RESISTANCE 1. Our results demonstrate the utility of the rice-FOX Arabidopsis lines as a tool for the identification of genes involved in plant defence and suggest the presence of a defence mechanism common between monocots and dicots. © 2010 The Authors. Plant Biotechnology Journal © 2010 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

  3. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  4. The inverse problem for Schwinger pair production

    Directory of Open Access Journals (Sweden)

    F. Hebenstreit

    2016-02-01

    Full Text Available The production of electron–positron pairs in time-dependent electric fields (Schwinger mechanism depends non-linearly on the applied field profile. Accordingly, the resulting momentum spectrum is extremely sensitive to small variations of the field parameters. Owing to this non-linear dependence it is so far unpredictable how to choose a field configuration such that a predetermined momentum distribution is generated. We show that quantum kinetic theory along with optimal control theory can be used to approximately solve this inverse problem for Schwinger pair production. We exemplify this by studying the superposition of a small number of harmonic components resulting in predetermined signatures in the asymptotic momentum spectrum. In the long run, our results could facilitate the observation of this yet unobserved pair production mechanism in quantum electrodynamics by providing suggestions for tailored field configurations.

  5. Asymmetric pair distribution functions in catalysts

    DEFF Research Database (Denmark)

    Clausen, B. S.; Nørskov, Jens Kehlet

    2000-01-01

    of asymmetric pair distribution functions for nano-sized particles and how they influence the structural parameters obtained from the standard data analysis. An alternative method, which takes into account deviations from the Gaussian pair distribution function typically used in the analysis of EXAFS spectra......, will be described. The method is based on an analysis of the pair distribution functions derived from molecular dynamics simulations of small metal particles and its reliability is demonstrated by comparing structural parameters obtained from independent X-ray diffraction experiments.......The structural parameters, i.e., coordination numbers, bond distances and disorder obtained from the analysis of EXAFS spectra may sometimes be significantly influenced by errors introduced due to the inadequacy of the analysis method applied. Especially in the case of heterogeneous catalysts...

  6. Pair condensation in massless scalar electrodynamics

    Science.gov (United States)

    Hey, Anthony J. G.; Mandula, Jeffrey E.

    1982-05-01

    Motivated by the instabilities of the vacuum to bound-state pair production at large coupling in both abelian and non-abelian gauge theories, we examine the stability of the vacuum of a constrained version of massless scalar electrodynamics to the formation of a scalar pair condensate. The trial states are constructed by analogy with the BCS ground state of super-conductivity and are such that the vacuum expectation value of the scalar field vanishes. Analysis of the minimization equation for the energy density indicates that there are two phases as a function of the coupling constant. Under the constraint that the vacuum expectation value of the scalar field be zero, we find what, for small coupling, the perturbative vacuum minimizes the energy, while for large coupling a condensate of particle-antiparticle pairs is energetically favored. After discussing the relation of our results to the phase structure of unconstrained scalar electrodynamics, we speculate on possible implications for QCD.

  7. Pair condensation in massless scalar electrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hey, A.J.G. (Southampton Univ. (UK). Dept. of Physics); Mandula, J.E. (Washington Univ., St. Louis, MO (USA). Dept. of Physics)

    1982-05-03

    Motivated by the instabilities of the vacuum to bound-state pair production at large coupling in both abelian and non-abelian gauge theories, we examine the stability of the vacuum of a constrained version of massless scalar electrodynamics to the formation of a scalar pair condensate. The trial states are constructed by analogy with the BCS ground state of super-conductivity and are such that the vacuum expectation value of the scalar field vanishes. Analysis of the minimization equation for the energy density indicates that there are two phases as a function of the coupling constant. Under the constraint that the vacuum expectation value of the scalar field be zero, we find that, for small coupling, the perturbative vacuum minimizes the energy, while for large coupling a condensate of particle-antiparticle pairs is energetically favored. After discussing the relation of our results to the phase structure of unconstrained scalar electrodynamics, we speculate on possible implications for QCD.

  8. Narrowband photon pair source for quantum networks.

    Science.gov (United States)

    Monteiro, F; Martin, A; Sanguinetti, B; Zbinden, H; Thew, R T

    2014-02-24

    We demonstrate a compact photon pair source based on a periodically poled lithium niobate nonlinear crystal in a short cavity. This approach provides efficient, low-loss, mode selection that is compatible with standard telecommunication networks. Photons with a coherence time of 8.6 ns (116 MHz) are produced and their purity is demonstrated. A source brightness of 134 pairs (s. mW. MHz)(-1) is reported. The cavity parameters are chosen such that the photon pair modes emitted can be matched to telecom ultra dense wavelength division multiplexing (U-DWDM) channel spacings. The high level of purity and compatibility with standard telecom networks is of great importance for complex quantum communication networks.

  9. Cooper-pair splitter: towards an efficient source of spin-entangled EPR pairs

    Science.gov (United States)

    Schonenberger, Christian

    2011-03-01

    In quantum mechanics the properties of two and more particles can be entangled. In basic science pairs of entangled particles, so called Einstein-Podolsky-Rosen (EPR) pairs, play a special role as toy objects for fundamental studies. They provide such things as ``spooky interaction at distance,'' but they also enable secure encoding and teleportation and are thus important for applications in quantum information technology. Whereas EPR pairs of photons can be generated by parametric down conversion (PDC) in a crystal, a similar source for EPR pairs of electrons does not exists yet. In several theory papers, it has been suggested to use a superconductor for this purpose. The superconducting ground state is formed by a condensate of Cooper-pairs which are electron pairs in a spin-singlet state. Since there are many Cooper pairs in a metallic superconductor like Al, the main tasks are to extract Cooper pairs one by one and to split them into different arms. A controlled and efficient splitting is possible if one makes use of Coulomb interaction. This has recently be demonstrated by two groups [2-4] using hybrid quantum-dot devices with both superconducting and normal metal contacts. In the present talk, I will discuss the Cooper-pair splitter results from the Basel-Budapest-Copenhagen team and compare with the other experiments. As an outlook we discuss approaches that aim at entanglement detection. The Cooper pair splitter holds great promises because very large splitting efficiencies approaching 100% and large pair current rates appear feasible. This work has been done by L. Hofstetter, S. Csonka, A. Geresdi, M. Aagesen, J. Nygard and C. Schönenberger

  10. Influence of shell structure on multipole pairing

    Directory of Open Access Journals (Sweden)

    K. Mühlhans

    1983-01-01

    Full Text Available Using the surface delta interaction as the generating two-body force, we investigate the interdependence between the composition of the multipole pair field and the multipole moments of the relevant single-particle states. A decrease of the quadrupole pair field is found in going from light to heavy rare earth nuclei. The inclusion of higher multipole moments shifts an existing backbend to higher frequency but when the force parameters are readjusted to reproduce the experimental odd-even mass difference the shift is strongly reduced.

  11. Optimal generation of pulsed entangled photon pairs

    Science.gov (United States)

    Hodelin, Juan F.; Khoury, George; Bouwmeester, Dirk

    2006-07-01

    We experimentally investigate a double-pass parametric down-conversion scheme for producing pulsed, polarization-entangled photon pairs with high visibility. The amplitudes for creating photon pairs on each pass interfere to compensate for distinguishing characteristics that normally degrade two-photon visibility. The result is a high-flux source of polarization-entangled photon pulses that does not require spectral filtering. We observe quantum interference visibility of over 95% without the use of spectral filters for 200fs pulses, and up to 98.1% with 5nm bandwidth filters.

  12. Cotunneling in pairs of coupled flux qubits

    Science.gov (United States)

    Lanting, T.; Harris, R.; Johansson, J.; Amin, M. H. S.; Berkley, A. J.; Gildert, S.; Johnson, M. W.; Bunyk, P.; Tolkacheva, E.; Ladizinsky, E.; Ladizinsky, N.; Oh, T.; Perminov, I.; Chapple, E. M.; Enderud, C.; Rich, C.; Wilson, B.; Thom, M. C.; Uchaikin, S.; Rose, G.

    2010-08-01

    We report measurements of macroscopic resonant tunneling between the two lowest energy states of a pair of magnetically coupled rf-superconducting quantum interference device flux qubits. This technique provides both a direct means of measuring the energy gap of the two-qubit system and a method for probing of the environment coupled to the pair of qubits. Measurements of the tunneling rate as a function of qubit flux bias show a Gaussian line shape that is well matched to theoretical predictions. Moreover, the peak widths indicate that each qubit is coupled to a local environment whose fluctuations are uncorrelated with that of the other qubit.

  13. Comment on ``Pairing interaction and Galilei invariance''

    Science.gov (United States)

    Arias, J. M.; Gallardo, M.; Gómez-Camacho, J.

    1999-05-01

    A recent article by Dussel, Sofia, and Tonina studies the relation between Galilei invariance and dipole energy weighted sum rule (EWSR). The authors find that the pairing interaction, which is neither Galilei nor Lorentz invariant, produces big changes in the EWSR and in effective masses of the nucleons. They argue that these effects of the pairing force could be realistic. In this Comment we stress the validity of Galilei invariance to a very good approximation in this context of low-energy nuclear physics and show that the effective masses and the observed change in the EWSR for the electric dipole operator relative to its classical value are compatible with this symmetry.

  14. Discovering implicit entity relation with the gene-citation-gene network.

    Directory of Open Access Journals (Sweden)

    Min Song

    Full Text Available In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner.

  15. Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status.

    Directory of Open Access Journals (Sweden)

    Christel Krueger

    Full Text Available Although somatic homologous pairing is common in Drosophila it is not generally observed in mammalian cells. However, a number of regions have recently been shown to come into close proximity with their homologous allele, and it has been proposed that pairing might be involved in the establishment or maintenance of monoallelic expression. Here, we investigate the pairing properties of various imprinted and non-imprinted regions in mouse tissues and ES cells. We find by allele-specific 4C-Seq and DNA FISH that the Kcnq1 imprinted region displays frequent pairing but that this is not dependent on monoallelic expression. We demonstrate that pairing involves larger chromosomal regions and that the two chromosome territories come close together. Frequent pairing is not associated with imprinted status or DNA repair, but is influenced by chromosomal location and transcription. We propose that homologous pairing is not exclusive to specialised regions or specific functional events, and speculate that it provides the cell with the opportunity of trans-allelic effects on gene regulation.

  16. Na Cl-ion pair association in water-DMSO mixtures: Effect of ion pair ...

    Indian Academy of Sciences (India)

    The physical picturethat emerges is that there is a strong contact ion pair (CIP) and strong to moderate solvent separated ion pair(SSIP) in these solutions. Analysis of local ion clusters shows that ions are dominantly solvated by watermolecules. The 12-6-1 potential model predicts running coordination numbers closest to ...

  17. Na Cl ion pair association in water-DMSO mixtures: Effect of ion pair ...

    Indian Academy of Sciences (India)

    ion pair in water–dimethyl sulfoxide (DMSO) mixtures for three DMSO mole fractions have been computed using constrained Molecular Dynamics (MD) simulations and confirmed by dynamical trajectories and residence times of the ion pair at various inter-ionic separations. The three ion-ion direct potentials used are 12-6-1 ...

  18. Neutrino Pair Cerenkov Radiation for Tachyonic Neutrinos

    Directory of Open Access Journals (Sweden)

    Ulrich D. Jentschura

    2017-01-01

    Full Text Available The emission of a charged light lepton pair by a superluminal neutrino has been identified as a major factor in the energy loss of highly energetic neutrinos. The observation of PeV neutrinos by IceCube implies their stability against lepton pair Cerenkov radiation. Under the assumption of a Lorentz-violating dispersion relation for highly energetic superluminal neutrinos, one may thus constrain the Lorentz-violating parameters. A kinematically different situation arises when one assumes a Lorentz-covariant, space-like dispersion relation for hypothetical tachyonic neutrinos, as an alternative to Lorentz-violating theories. We here discuss a hitherto neglected decay process, where a highly energetic tachyonic neutrino may emit other (space-like, tachyonic neutrino pairs. We find that the space-like dispersion relation implies the absence of a q2 threshold for the production of a tachyonic neutrino-antineutrino pair, thus leading to the dominant additional energy loss mechanism for an oncoming tachyonic neutrino in the medium-energy domain. Surprisingly, the small absolute values of the decay rate and energy loss rate in the tachyonic model imply that these models, in contrast to the Lorentz-violating theories, are not pressured by the cosmic PeV neutrinos registered by the IceCube collaboration.

  19. Pair Negotiation When Developing English Speaking Tasks

    Science.gov (United States)

    Bohórquez Suárez, Ingrid Liliana; Gómez Sará, Mary Mily; Medina Mosquera, Sindy Lorena

    2011-01-01

    This study analyzes what characterizes the negotiations of seventh graders at a public school in Bogotá when working in pairs to develop speaking tasks in EFL classes. The inquiry is a descriptive case study that follows the qualitative paradigm. As a result of analyzing the data, we obtained four consecutive steps that characterize students'…

  20. Neutrino signal from pair-instability supernovae

    Science.gov (United States)

    Wright, Warren P.; Gilmer, Matthew S.; Fröhlich, Carla; Kneller, James P.

    2017-11-01

    A very massive star with a carbon-oxygen core in the range of 64M ⊙evolution at the extreme of stellar masses. Much will be sought within the electromagnetic radiation we detect from such a supernova but we should not forget that the neutrinos from a pair-instability supernova contain unique signatures of the event that unambiguously identify this type of explosion. We calculate the expected neutrino flux at Earth from two, one-dimensional pair-instability supernova simulations which bracket the mass range of stars which explode by this mechanism taking into account the full time and energy dependence of the neutrino emission and the flavor evolution through the outer layers of the star. We calculate the neutrino signals in five different detectors chosen to represent present or near future designs. We find the more massive progenitors explode as pair-instability supernova which can easily be detected in multiple different neutrino detectors at the "standard" supernova distance of 10 kpc producing several events in DUNE, JUNO, and Super-Kamiokande, while the lightest progenitors produce only a handful of events (if any) in the same detectors. The proposed Hyper-Kamiokande detector would detect neutrinos from a large pair-instability supernova as far as ˜50 kpc allowing it to reach the Megallanic Clouds and the several very high mass stars known to exist there.

  1. Frustrated Lewis pairs: Design and reactivity

    Indian Academy of Sciences (India)

    Abstract. The interaction of a Lewis acid with a Lewis base results in the formation of a Lewis acid–base adduct. Understanding Lewis acids and bases is central to conceptualizing chemical interactions and constitutes a major portion of metal–ligand chemistry. Sterically encumbered/constrained Lewis pairs cannot form ...

  2. Array-Based Discovery of Aptamer Pairs

    Science.gov (United States)

    2014-12-11

    aptamer pairs that bind to human angiopoeitin-2 (Ang2), an important protein mediator of angiogenesis for colon , prostate and breast cancers.22,23 To...Sullenger, B. A. RNA 2009, 15, 2105−2111. (28) Zhou, G.; Huang, X.; Qu, Y. Biochem. Eng. J. 2010, 52, 117−122. (29) Drolet, D. W.; Moon -McDermott, L

  3. The mother of all pair potentials

    DEFF Research Database (Denmark)

    Dyre, J. C.; Bacher, Andreas Kvist

    2014-01-01

    This paper presents a computer simulation study of the exponentially repulsive pair potential system. The simulations show that the system has strong virial potential energy correlations in a large part of its thermodynamic phase diagram. Consequences of this are briefly discussed; these include ...

  4. Computing Hypercrossed Complex Pairings in Digital Images

    Directory of Open Access Journals (Sweden)

    Simge Öztunç

    2013-01-01

    Full Text Available We consider an additive group structure in digital images and introduce the commutator in digital images. Then we calculate the hypercrossed complex pairings which generates a normal subgroup in dimension 2 and in dimension 3 by using 8-adjacency and 26-adjacency.

  5. Frustrated Lewis pairs: Design and reactivity

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 2. Frustrated Lewis pairs: Design and reactivity. Sanjoy Mukherjee Pakkirisamy Thilagar. Volume 127 Issue 2 ... main group as well as transition metal chemistry. The design strategies adopted for FLP systems and their unique reactivity are discussed here.

  6. Pairs of paths and critical points

    Directory of Open Access Journals (Sweden)

    Florin Caragiu

    2001-01-01

    Full Text Available Two sufficient conditions are presented, in terms of the values taken by a holomorphic function f(z on a pair of smooth paths intersecting at a point z0 in its domain, implying that f′(z0=0.

  7. Evacuation dynamics of asymmetrically coupled pedestrian pairs

    CERN Document Server

    Müller, Frank

    2016-01-01

    We propose and analyze extended floor field cellular automaton models for evacuation dynamics of inhomogeneous pedestrian pairs which are coupled by asymmetric group interactions. Such pairs consist of a leader, who mainly determines the couple's motion and a follower, who has a defined tendency to follow the leader. Examples for such pairs are mother and child or two siblings of different age. We examine the system properties and compare them to the case of a homogeneous crowd. We find a strong impact on evacuation times for the regime of strong pair coupling due to the occurrence of a clogging phenomenon. In addition we obtain a non-trivial dependence of evacuation times on the followers' coupling to the static floor field, which carries the information of the shortest way to the exit location. In particular we find that systems with fully passive followers, who are solely coupled to their leaders, show lower evacuation times than homogeneous systems where all pedestrians have an equal tendency to move towa...

  8. Protein Subcellular Relocalization of Duplicated Genes in Arabidopsis

    Science.gov (United States)

    Liu, Shao-Lun; Pan, An Qi; Adams, Keith L.

    2014-01-01

    Gene duplications during eukaroytic evolution, by successive rounds of polyploidy and by smaller scale duplications, have provided an enormous reservoir of new genes for the evolution of new functions. Preservation of many duplicated genes can be ascribed to changes in sequences, expression patterns, and functions. Protein subcellular relocalization (protein targeting to a new location within the cell) is another way that duplicated genes can diverge. We studied subcellular relocalization of gene pairs duplicated during the evolution of the Brassicaceae including gene pairs from the alpha whole genome duplication that occurred at the base of the family. We analyzed experimental localization data from green fluorescent protein experiments for 128 duplicate pairs in Arabidopsis thaliana, revealing 19 pairs with subcellular relocalization. Many more of the duplicate pairs with relocalization than with the same localization showed an accelerated rate of amino acid sequence evolution in one duplicate, and one gene showed evidence for positive selection. We studied six duplicate gene pairs in more detail. We used gene family analysis with several pairs to infer which gene shows relocalization. We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products. We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen. This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized. PMID:25193306

  9. Asynchronous replication and autosome-pair non-equivalence in human embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Devkanya Dutta

    Full Text Available A number of mammalian genes exhibit the unusual properties of random monoallelic expression and random asynchronous replication. Such exceptional genes include genes subject to X inactivation and autosomal genes including odorant receptors, immunoglobulins, interleukins, pheromone receptors, and p120 catenin. In differentiated cells, random asynchronous replication of interspersed autosomal genes is coordinated at the whole chromosome level, indicative of chromosome-pair non-equivalence. Here we have investigated the replication pattern of the random asynchronously replicating genes in undifferentiated human embryonic stem cells, using fluorescence in situ hybridization based assay. We show that allele-specific replication of X-linked genes and random monoallelic autosomal genes occur in human embryonic stem cells. The direction of replication is coordinated at the whole chromosome level and can cross the centromere, indicating the existence of autosome-pair non-equivalence in human embryonic stem cells. These results suggest that epigenetic mechanism(s that randomly distinguish between two parental alleles are emerging in the cells of the inner cell mass, the source of human embryonic stem cells.

  10. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  11. Spontaneous deletion in the FMR-1 gene in a patient with fragile X syndrome and cherubism

    Energy Technology Data Exchange (ETDEWEB)

    Popovich, B.W.; Anoe, K.S.; Johnson, D.B. [Oregon Health Sciences Univ., Portland, OR (United States)] [and others

    1994-09-01

    Fragile X mental retardation results from the transcriptional inactivation of the FMR-1 gene and is commonly caused by the expansion of an unstable CGG trinucleotide repeat located in the first exon of the FMR-1 gene. We describe here a two generation fragile X family in which expansion of the CGG repeat may have resulted in a deletion of a least portion of the FMR-1 gene. One member of this family, AB, carries an apparent deletion of the FMR-1 gene and presents with mental retardation and also cherubism, a feature not usually associated with fragile X syndrome. Cherubism is a condition characterized by a swelling of the lower face and is caused by giant cell lesions of the mandible and maxilla, and often the anterior ends of the ribs. The size of the CGG repeat region in this family was determined by Southern analysis of BglII, EcoRI, and PstI digested genomic DNA, isolated from peripheral blood lymphocytes, using a 558 bp PstI-Xhol fragment specific for the 5{prime}-end of the FMR-1 gene. SB and TB, the mother and maternal half-brother of AB, respectively, were both found to carry an expanded FMR-1 allele with greater than 200 CGG repeats. Negligible hybridization was observed in the DNA of AB. In addition, no amplification was observed when the polymerase chain reaction (PCR) was performed using primers flanking the CGG repeat region. These results are consistent with a deletion of at least the 5{prime} portion of the FMR-1 gene in the majority of peripheral blood lymphocytes. Further work is underway using FMR-1 cDNA probes and additional PCR primers to determine the nature of the molecular lesion in AB`s DNA and determine the relationship of this lesion to his cherubism.

  12. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  13. Differential regulation of polyphosphate genes in Pseudomonas aeruginosa.

    Science.gov (United States)

    Munévar, Nicolás Federico Villamil; de Almeida, Luiz Gustavo; Spira, Beny

    2017-02-01

    Phosphate homeostasis is tightly regulated in bacteria. Phosphate scarcity is overcome by inducing the expression of genes associated with the scavenging of phosphate and phosphate-containing molecules, while phosphate surplus is stored in the form of polyphosphate (polyP). Regulation of the genes involved in polyP metabolism was investigated. Knockout of the most distal gene of the pstSCAB-phoU operon that encodes a Pi-transport system results in large accumulation of polyphosphate (polyP). Here, we show that the phoU mutation differentially affects the transcription of ppk and ppx, that respectively, encode a polyP kinase and a polyP exopolyphosphatase, by increasing the former and reducing the latter, further contributing the accumulation of polyP. We also show that ppk forms an operon with the upstream gene hemB and that neither ppk nor ppx positively respond to Pi starvation. Furthermore, a putative PHO-box sequence in ppx regulatory region did not show a strong affinity for the PHO response regulator PhoB, while the promoter of hemB does not carry a PHO-box sequence. Altogether, the data indicate that the main genes involved in polyP metabolism, ppk and ppx, are differentially regulated in the absence of phoU, but neither gene belongs to the PHO regulon.

  14. Pairing success of Kirtland's warblers in marginal vs. suitable habitat

    Science.gov (United States)

    John R. Probst; Jack P. Hayes

    1987-01-01

    We compared pairing success of male Kirtland's Warblers (Dendroica kirtlandii) in different habitats to test the hypothesis that a lower proportion of males in marginal habitat are mated. Fewer than 60% of the males in marginal habitat were paired, but 95% of the males in suitable habitat were paired. We estimated the overall pairing success of...

  15. Water-Mediated Ion Pairing: Occurrence and Relevance

    DEFF Research Database (Denmark)

    van der Vegt, Nico F.A.; Haldrup, Kristoffer; Roke, Sylvie

    2016-01-01

    salt solutions and their interfaces, the measured and calculated structure and dynamics reveal the presence of a distinct concentration of contact ion pairs (CIPs), solvent shared ion pairs (SIPs), and solvent-separated ion pairs (2SIPs). We discuss the importance of specific ion-pairing interactions...

  16. A search for resonant Z pair production

    Energy Technology Data Exchange (ETDEWEB)

    Boveia, Antonio [Univ. of California, Santa Barbara, CA (United States)

    2008-12-01

    I describe a search for anomalous production of Z pairs through a new massive resonance X in 2.5-2.9 fb-1 of p$\\bar{p}$ collisions at √s = 1.96 TeV using the CDFII Detector at the Fermilab Tevatron. I reconstruct Z pairs through their decays to electrons, muons, and quarks. To achieve perhaps the most efficient lepton reconstruction ever used at CDF, I apply a thorough understanding of the detector and new reconstruction software heavily revised for this purpose. In particular, I have designed and employ new general-purpose algorithms for tracking at large η in order to increase muon acceptance. Upon analyzing the unblinded signal samples, I observe no X → ZZ candidates and set upper limits on the production cross section using a Kaluza-Klein graviton-like acceptance.

  17. Pair creation constrains superluminal neutrino propagation.

    Science.gov (United States)

    Cohen, Andrew G; Glashow, Sheldon L

    2011-10-28

    The OPERA collaboration claims that muon neutrinos with a mean energy of 17.5 GeV travel 730 km from CERN to the Gran Sasso at a speed exceeding that of light by about 7.5 km/s or 25 ppm. However, we show that superluminal neutrinos may lose energy rapidly via the bremsstrahlung of electron-positron pairs (ν → ν + e- + e+). For the claimed superluminal velocity and at the stated mean energy, we find that most of the neutrinos would have suffered several pair emissions en route, causing the beam to be depleted of higher energy neutrinos. This presents a significant challenge to the superluminal interpretation of the OPERA data. Furthermore, we appeal to Super-Kamiokande and IceCube data to establish strong new limits on the superluminal propagation of high-energy neutrinos.

  18. Digital processing of stereoscopic image pairs.

    Science.gov (United States)

    Levine, M. D.

    1973-01-01

    The problem under consideration is concerned with scene analysis during robot navigation on the surface of Mars. In this mode, the world model of the robot must be continuously updated to include sightings of new obstacles and scientific samples. In order to describe the content of a particular scene, it is first necessary to segment it into known objects. One technique for accomplishing this segmentation is by analyzing the pair of images produced by the stereoscopic cameras mounted on the robot. A heuristic method is presented for determining the range for each point in the two-dimensional scene under consideration. The method is conceptually based on a comparison of corresponding points in the left and right images of the stereo pair. However, various heuristics which are adaptive in nature are used to make the algorithm both efficient and accurate. Examples are given of the use of this so-called range picture for the purpose of scene segmentation.

  19. Chiral Spin Pairing in Helical Magnets

    Science.gov (United States)

    Onoda, Shigeki; Nagaosa, Naoto

    2007-07-01

    A concept of chiral spin pairing is introduced to describe a vector-chiral liquid-crystal order in frustrated spin systems. It is found that the chiral spin pairing is induced by the coupling to phonons through the Dzyaloshinskii-Moriya interaction and the four-spin exchange interaction of the Coulomb origin under the edge-sharing network of magnetic and ligand ions. This produces two successive second-order phase transitions upon cooling: an O(2) chiral spin nematic, i.e., spin cholesteric, order appears with an either parity, and then the O(2) symmetry is broken to yield a helical magnetic order. Possible candidate materials are also discussed as new multiferroic systems.

  20. Dual Resolution Images from Paired Fingerprint Cards

    Science.gov (United States)

    NIST Dual Resolution Images from Paired Fingerprint Cards (Web, free access)   NIST Special Database 30 is being distributed for use in development and testing of fingerprint compression and fingerprint matching systems. The database allows the user to develop and evaluate data compression algorithms for fingerprint images scanned at both 19.7 ppmm (500 dpi) and 39.4 ppmm (1000 dpi). The data consist of 36 ten-print paired cards with both the rolled and plain images scanned at 19.7 and 39.4 pixels per mm. A newer version of the compression/decompression software on the CDROM can be found at the website http://www.nist.gov/itl/iad/ig/nigos.cfm as part of the NBIS package.

  1. Transmission properties of cryogenic twisted pair filters

    Energy Technology Data Exchange (ETDEWEB)

    Song, Woon; Rehman, Mushtaq; Chong, Yonuk [Korea Research Institute of Standards and Science, Daejeon (Korea, Republic of); Ryu, Sangwan [Chonnam National University, Gwangju (Korea, Republic of)

    2010-12-15

    We fabricated a cryogenic low pass filter that consists of twisted pairs of manganin wires wrapped in copper tape and measured its transmission characteristics at frequencies up to 18 GHz. The dependence of the microwave transmission characteristics on the filter length was studied, which showed that a filter of length 1.0 m had a 70-dB attenuation at 1 GHz. We also studied the dependence of common- and differential-mode transmission on the number of twists per unit length and found that the number of twists per unit length affects differential-mode transmission but not common-mode transmission. Because the shielded twisted pair filter is more compact than a conventional copper powder filter, it can solve the space and thermal load issues when many cables are required for precision electronic transport experiments at low temperatures.

  2. Construction of Sziklai Pair using Mixed Components

    Science.gov (United States)

    Singh, Ramendra; Tripathi, Ankit; Anand, Vartika

    2017-08-01

    To design Sziklai pair topology for small-signal amplifier circuit with RC coupled voltage divider bias, both BJT and JFET are used. Such a design amplifier circuit can be tuned in the frequency range of 108Hz-620 KHz. The circuit proposed in this paper can amplify audio range signal excursions swinging in the range of 0.1-12mV at 1KHz. Features like high voltage gain, current gain greater than unity, wider bandwidth and considerably low harmonic distortion makes this amplifier superior than earlier announced small-signal Sziklai pair amplifier. Various applications for this proposed amplifier is in Radio/TV receivers, low frequency power sources and other audible range communication applications

  3. Modulation effect in multiphoton pair production

    Directory of Open Access Journals (Sweden)

    Ibrahim Sitiwaldi

    2017-05-01

    Full Text Available We investigate the electron–positron pair production process in an oscillating field with modulated amplitude in the quantum kinetic formalism. By comparing the number density in the oscillating field with and without modulation, we find that the pair production rate can be enhanced by several orders when the photon energy just reaches the threshold with the help of shifted frequency due to modulation. We also detect the same effect in a pulse train with subcycle structure. We demonstrate that the frequency threshold can be lowered by the frequency of the pulse train due to the modulation effect. We also find that the momentum distribution for a N-pulse train can reach N2 times the single pulse at the maximum value and the number density as a function of pulse number follows the power law with index 1.6 when the modulation effect is maximized.

  4. Projecting Fermion Pair Condensates into Molecular Condensates

    OpenAIRE

    Diener, Roberto B.; Ho, Tin-Lun

    2004-01-01

    We offer strong evidence that the recent observations by M. Greiner, C. Regal, and D. Jin and by MIT group are signatures of a fermion superfluid in the strongly interacting regime made up of large fermion pairs. Our conclusions are based on calculations using crossover theory for different potentials including those with the characteristics of two-channel models. Our results demonstrate clearly universality near resonance. The $T_{c}$ predicted by crossover theory is a perfect match with the...

  5. On the pairing effects in triaxial nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Oudih, M. R. [Laboratoire de Physique Théorique, Faculté de Physique,USTHB BP 32, El Alia, 16111 Bab Ezzouar, Algiers (Algeria); Fellah, M.; Allal, N. H. [Centre de Recherche Nucléaire d' Alger, 2 Bd. Frantz Fanon, BP. 399 Alger-Gare, Algiers, Algeria and Laboratoire de Physique Théorique, Faculté de Physique,USTHB BP 32, El Alia, 16111 Bab Ezzouar, Algiers (Algeria)

    2014-03-05

    Triaxial deformation effect on the pairing correlations is studied in the framework of the Skyrme Hartree-Fock-Bogoliubov theory. Quantities such as binding energy, gap parameter and particle-number fluctuation are considered in neutron-rich Mo isotopes. The results are compared with those of axially symmetric calculation and with available experimental data. The role played by the particle-number projection is outlined.

  6. Pair production and ionizing radiation from superconductors

    OpenAIRE

    Hirsch, J. E.

    2005-01-01

    We show that an alternative theory of superconductivity recently proposed (theory of hole superconductivity) leads to the surprising consequence that real electron-positron pair production will occur for superconductors larger than a critical size. High frequency radiation with frequencies up to $0.511MeV/\\hbar$ is predicted to be emitted from superconductors out of equilibrium. Attention to the possibility of harmful consequences is called for.

  7. DNA-Directed Base Pair Opening

    Directory of Open Access Journals (Sweden)

    Youri Timsit

    2012-10-01

    Full Text Available Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Current models propose that negative supercoiling destabilizes the double helix and promotes the spontaneous, sequence-dependent DNA melting. The present review examines an alternative view and reveals how DNA compaction may trigger the sequence dependent opening of the base pairs. This analysis shows that in DNA crystals, tight DNA-DNA interactions destabilize the double helices at various degrees, from the alteration of the base-stacking to the opening of the base-pairs. The electrostatic repulsion generated by the DNA close approach of the negatively charged sugar phosphate backbones may therefore provide a potential source of the energy required for DNA melting. These observations suggest a new molecular mechanism for the initial steps of strand separation in which the coupling of the DNA tertiary and secondary interactions both actively triggers the base pair opening and stabilizes the intermediate states during the melting pathway.

  8. Galactic Pairs in the Early Universe

    Science.gov (United States)

    Kohler, Susanna

    2018-02-01

    In the spirit of Valentines Day, today well be exploring apparent pairs of galaxies in the distant, early universe. How can we tell whether these duos are actually paired galaxies, as opposed to disguised singles?Real Pair, or Trick of the Light?In the schematic timeline of the universe, the epoch of reionization is when the first galaxies and quasars began to form and evolve. [NASA]The statistics of merging galaxies throughout the universe reveal not only direct information about how galaxies interact, but also cosmological information about the structure of the universe. While weve observed many merging galaxy pairs at low redshift, however, its much more challenging to identify these duos in the early universe.A merging pair of galaxies at high redshift appears to us as a pair of unresolved blobs that lie close to each other in the sky. But spotting such a set of objects doesnt necessarily mean were looking at a merger! There are three possible scenarios to explain an observed apparent duo:Its a pair of galaxies in a stage of merger.Its a projection coincidence; the two galaxies arent truly near each other.Its a single galaxy being gravitationally lensed by a foreground object. This strong lensing produces the appearance of multiple galaxies.Hubble photometry of one of the three galaxy groups identified at z 8, with the galaxies in the image labeled with their corresponding approximate photometric redshifts. [Adapted from Chaikin et al. 2018]Hunting for Distant DuosIn a recent study led by Evgenii Chaikin (Peter the Great St. Petersburg Polytechnic University, Russia), a team of scientists has explored the Hubble Ultra Deep Field in search ofhigh-redshift galaxies merging during the epoch of reionization, when the first galaxies formed and evolved.Using an approach called the dropout technique, which leverages the visibility of the galaxies in different wavelength filters, Chaikin and collaborators obtain approximate redshifts for an initial sample of 7

  9. Pairing in the presence of a pseudogap

    Science.gov (United States)

    Scalapino, Douglas; Maier, Thomas; Staar, Peter; Mishra, Vivek

    After 30 years, the quest to experimentally identify the mechanism responsible for pairing in the high Tc superconductors continues. Here we discuss an approach in which angle resolved photoemission (ARPES)data for BSCCO 2212(Tc=89K) is used to extract the single particle spectral weight A(k,w). This spectral weight is then used to calculate the BCS kernel and estimate the RPA spin-fluctuation d-wave pairing strength. Previously A(k,w) results at T=140K, extrapolated to lower temperatures, found that the BSCCO pseudo gap suppressed the logarithmic singularity of the BCS kernel and the spin-fluctuation interaction was too weak to produce superconductivity [V.Mishra et al.,Nat.Phys.10,357]. Here using results for A(k,w) at T=40K for this same system, we find that while the BCS kernel is suppressed, there is a significant increase in the d-wave pairing strength for the spin-fluctuation interaction when the temperature drops from T=140K and 40K. These results are shown to be consistent with DCA calculations for a 2D Hubbard model of a BSCCO like system which has a pseudo gap. We conclude that in spite of the suppression of the usual BCS logarithmic instability by the pseudo gap, the increase in strength of the spin-fluctuation interaction is sufficient to lead to superconductivity. Center for Nanophase Materials Sciences, Oak Ridge National Laboratory.

  10. Exclusive production of W pairs in CMS

    Directory of Open Access Journals (Sweden)

    Silveira Da

    2014-04-01

    Full Text Available We report the results on the search for exclusive production of W pairs in the LHC with data collected by the Compact Muon Solenoid detector in proton-proton collisions at √s = 7 TeV. The analysis comprises the two-photon production of a W pairs, pp → pW+ W− p → p νe± νµ∓ p. Two events are observed in data for pT(ℓ > 4 GeV, |η(ℓ| 20 GeV, in agreement with the standard model prediction of 2.2 ± 0.4 signal events with 0.84 ± 0.15 background events. Moreover, a study of the tail of the lepton pair transverse momentum distribution is performed to search for an evidence of anomalous quartic gauge couplings in the γγ → W+ W− vertex. As no events are observed in data, it results in a model-independent upper limits for the anomalous W quartic gauge couplings aW0,C/Λ2, which are of the order of 10−4.

  11. Persistent ion pairing in aqueous hydrochloric acid.

    Science.gov (United States)

    Baer, Marcel D; Fulton, John L; Balasubramanian, Mahalingam; Schenter, Gregory K; Mundy, Christopher J

    2014-07-03

    For strong acids, like hydrochloric acid, the complete dissociation into an excess proton and conjugated base as well as the formation of independent solvated charged fragments is assumed. The existence of chloride-hydronium (Cl(-)···H3O(+)) contact ion pairs even in moderate concentration hydrochloric acid (2.5 m) demonstrates that the counterions do not behave merely as spectators. Through comparison of recent extended X-ray absorption fine structure (EXAFS) measurements to state-of-the-art density functional theory (DFT) simulations, we are able to obtain a unique view into the molecular structure of medium-to-high concentrated electrolytes. Here we report that the Cl(-)···H3O(+) contact ion pair structure persists throughout the entire concentration range studied and that these structures differ significantly from moieties studied in microsolvated hydrochloric acid gas phase clusters. Characterizing distinct populations of these ion pairs gives rise to a novel molecular level description of how to view the reaction network for acid dissociation and how it relates to our picture of acid-base equilibria.

  12. Pairing in half-filled Landau level

    Science.gov (United States)

    Wang, Zhiqiang; Mandal, Ipsita; Chung, Suk Bum; Chakravarty, Sudip

    2015-03-01

    Pairing of composite fermions in half-filled Landau level state is reexamined by solving the BCS gap equation with full frequency dependent current-current interactions. Our results show that there can be a continuous transition from the Halperin-Lee-Read state to a chiral odd angular momentum Cooper pair state for short-range contact interaction. This is at odds with the previously established conclusion of first order pairing transition, in which the low frequency effective interaction was assumed for the entire frequency range. We find that even if the low frequency effective interaction is repulsive, it is compensated by the high frequency regime, which is attractive. We construct the phase diagrams and show that l = 1 angular momentum channel is quite different from higher angular momentum channel l >= 3 . Remarkably, the full frequency dependent analysis applied to the bilayer Hall system with a total filling fraction ν =1/2 +1/2 is quantitatively changed from the previously established results but not qualitatively. This work was supported by US NSF under the Grant DMR-1004520, the funds from the David S. Saxon Presidential Chair at UCLA(37952), and by the Institute for Basic Science in Korea through the Young Scientist grant (5199-2014003).

  13. Differing von Hippel Lindau genotype in paired primary and metastatic tumors in patients with clear cell renal cell carcinoma

    Directory of Open Access Journals (Sweden)

    Susan A.J. Vaziri

    2012-05-01

    Full Text Available In sporadic clear cell renal cell carcinoma (CCRCC, the von Hippel Lindau (VHL gene is inactivated by mutation or methylation in the majority of primary (P tumors. Due to differing effects of wild-type (WT and mutant (MT VHL gene on downstream signaling pathways regulating angiogenesis, VHL gene status could impact clinical outcome. In CCRCC, comparative genomic hybridization (CGH analysis studies have reported genetic differences between paired P and metastatic (M tumors. We thus sequenced the VHL gene in paired tumor specimens from 10 patients to determine a possible clonal relationship between the P tumor and M lesion(s in patients with CCRCC. Using paraffin embedded specimens, genomic DNA from microdissected samples (>80% tumor of paired P tumor and M lesions from all 10 patients, as well as in normal tissue from 6 of these cases, was analyzed. The DNA was used for PCR-based amplification of each of the 3 exons of the VHL gene. Sequences derived from amplified samples were compared to the wild-type VHL gene sequence (GeneBank Accession No. AF010238. Methylation status of the VHL gene was determined using VHL methylation-specific PCR primers after DNA bisulfite modification. In 4/10 (40% patients the VHL gene status differed between the P tumor and the M lesion. As expected, when the VHL gene was mutated in both the P tumor and M lesion, the mutation was identical. Further, while the VHL genotype differed between the primary tumor in different kidneys or multiple metastatic lesions in the same patient, the VHL germline genotype in the normal adjacent tissue was always wild-type irrespective of the VHL gene status in the P tumor. These results demonstrate for the first time that the VHL gene status can be different between paired primary and metastatic tissue in patients with CCRCC.

  14. Detecting nonlocal Cooper pair entanglement by optical Bell inequality violation

    OpenAIRE

    Nigg, Simon E.; Tiwari, Rakesh P.; Walter, Stefan; Schmidt, Thomas L.

    2014-01-01

    Based on the Bardeen Cooper Schrieffer (BCS) theory of superconductivity, the coherent splitting of Cooper pairs from a superconductor to two spatially separated quantum dots has been predicted to generate nonlocal pairs of entangled electrons. In order to test this hypothesis, we propose a scheme to transfer the spin state of a split Cooper pair onto the polarization state of a pair of optical photons. We show that the produced photon pairs can be used to violate a Bell inequality, unambiguo...

  15. Substituent effects on the pairing and polymerase recognition of simple unnatural base pairs

    Science.gov (United States)

    Hwang, Gil Tae; Romesberg, Floyd E.

    2006-01-01

    As part of an effort to develop stable and replicable unnatural base pairs, we have evaluated a large number of unnatural nucleotides with predominantly hydrophobic nucleobases. Despite its limited aromatic surface area, a nucleobase analog scaffold that has emerged as being especially promising is the simple phenyl ring. Modifications of this scaffold with methyl and fluoro groups have been shown to impact base pair stability and polymerase recognition, suggesting that nucleobase shape, hydrophobicity and electrostatics are important. To further explore the impact of heteroatom substitution within this nucleobase scaffold, we report the synthesis, stability and polymerase recognition of nucleoside analogs bearing single bromo- or cyano-derivatized phenyl rings. Both modifications are found to generally stabilize base pair formation to a greater extent than methyl or fluoro substitution. Moreover, polymerase recognition of the unnatural base pairs is found to be very sensitive to both the position and nature of the heteroatom substituent. The results help identify the determinants of base pair stability and efficient replication and should contribute to the effort to develop stable and replicable unnatural base pairs. PMID:16617144

  16. Extra-pair paternity as the result of reproductive transactions between paired mates.

    Science.gov (United States)

    Shellman-Reeve, J S; Reeve, H K

    2000-12-22

    Transactional ('optimal skew' or concessions') models of social evolution emphasize that dominant members of society can be favoured for donating parcels of reproduction to same-sexed subordinates in return for cooperation by the latter. We developed a mathematically similar model in which extra-pair paternity in broods receiving biparental care is viewed as emerging from a reproductive transaction between the paired mates. The model quantitatively predicted the maximum paternity that a male mate can demand before its female mate is favoured to break the pair bond and caring solitarily for a brood sired entirely by a neighbouring male. The model predicts that extra-pair paternity results when the neighbouring male is of sufficiently higher quality than the male mate. In such cases, the exact amount of extra-pair paternity will vary directly with the difference in quality between the two males and inversely with the value (fitness impact) of the male mate's parental care. Importantly, the transactional model provided a unified explanation for experimental and observational evidence that extra-pair paternity rises with decreasing quality of the male mate, increasing genetic variability among breeding males, increasing breeding density, increasing availability of food and decreasing involvement of the male mate in parental care.

  17. NFAT5 genes are part of the osmotic regulatory system in Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Lorgen, Marlene; Jorgensen, Even H; Jordan, William C; Martin, Samuel A M; Hazlerigg, David G

    2017-02-01

    The anadromous Atlantic salmon utilizes both fresh and salt water (FW and SW) habitats during its life cycle. The parr-smolt transformation (PST) is an important developmental transition from a FW adapted juvenile parr to a SW adapted smolt. Physiological changes in osmoregulatory tissues, particularly the gill, are key in maintaining effective ion regulation during PST. Changes are initiated prior to SW exposure (preparative phase), and are completed when smolts enter the sea (activational phase) where osmotic stress may directly stimulate changes in gene expression. In this paper we identify 4 nuclear factor of activated T cells (NFAT5, an osmotic stress transcription factor) paralogues in Atlantic salmon, which showed strong homology in characterized functional domains with those identified in other vertebrates. Two of the identified paralogues (NFAT5b1 and NFAT5b2) showed increased expression following transfer from FW to SW. This effect was largest in parr that were maintained under short day photoperiod, and showed the highest increases in chloride ion levels in response to SW exposure. The results of this study suggest that NFAT5 is involved in the osmotic stress response of Atlantic salmon. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  18. Meiotic chromosome pairing is promoted by telomere-led chromosome movements independent of bouquet formation.

    Directory of Open Access Journals (Sweden)

    Chih-Ying Lee

    Full Text Available Chromosome pairing in meiotic prophase is a prerequisite for the high fidelity of chromosome segregation that haploidizes the genome prior to gamete formation. In the budding yeast Saccharomyces cerevisiae, as in most multicellular eukaryotes, homologous pairing at the cytological level reflects the contemporaneous search for homology at the molecular level, where DNA double-strand broken ends find and interact with templates for repair on homologous chromosomes. Synapsis (synaptonemal complex formation stabilizes pairing and supports DNA repair. The bouquet stage, where telomeres have formed a transient single cluster early in meiotic prophase, and telomere-promoted rapid meiotic prophase chromosome movements (RPMs are prominent temporal correlates of pairing and synapsis. The bouquet has long been thought to contribute to the kinetics of pairing, but the individual roles of bouquet and RPMs are difficult to assess because of common dependencies. For example, in budding yeast RPMs and bouquet both require the broadly conserved SUN protein Mps3 as well as Ndj1 and Csm4, which link telomeres to the cytoskeleton through the intact nuclear envelope. We find that mutants in these genes provide a graded series of RPM activity: wild-type>mps3-dCC>mps3-dAR>ndj1Δ>mps3-dNT = csm4Δ. Pairing rates are directly correlated with RPM activity even though only wild-type forms a bouquet, suggesting that RPMs promote homologous pairing directly while the bouquet plays at most a minor role in Saccharomyces cerevisiae. A new collision trap assay demonstrates that RPMs generate homologous and heterologous chromosome collisions in or before the earliest stages of prophase, suggesting that RPMs contribute to pairing by stirring the nuclear contents to aid the recombination-mediated homology search.

  19. Gene therapy in periodontics

    Science.gov (United States)

    Chatterjee, Anirban; Singh, Nidhi; Saluja, Mini

    2013-01-01

    GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person's genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is ‘the use of genes as medicine’. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone. PMID:23869119

  20. Top quark pair production at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Baernreuther, Peter

    2012-06-28

    One of the most interesting and manifold processes in the Standard Model of elementary particle physics is the top quark pair production. It enabled the discovery of the top quark at the Tevatron in 1995 and the determination of many of its properties. By means of a precise measurement and calculation of the cross section of top quark pair production it is possible to extract the top quark mass. Improvements in the gluon parton distribution functions (important for the Higgs boson production) or improvements in the prediction of the Higgs mass are also closely linked with the top quark pair production. Furthermore, the production process plays an important role in the discovery of new physics. On the one hand the top quark pair decays form the largest part of the background in many BSM models, on the other hand BSM physics can be detected directly in the decay process by investigating the charge symmetry or the invariant mass spectrum. At the LHC it will be possible for the first time to produce a large amount of top quarks; thereby the statistical errors of the observables will be strongly reduced. The enormous increase in the production rate has two reasons. On the one hand, the acceleration energy of the LHC (14 TeV and 7 TeV) is significantly greater than that of the Tevatron (1.96 Tev). This leads to an increase of the cross section by a factor of 100 ({proportional_to}7.3 pb at the Tevatron to {proportional_to}800 pb at 14 TeV LHC). On the other hand, the luminosity of the LHC outperforms the Tevatron by a factor of 10-100. The reduced experimental errors for the observables demand an improvement of the theoretical error. The experimental accuracy of the LHC and the great relevance of the process led to an intensive activity of different research groups in order to improve the calculation of the cross section of top quark pair production. This work presents for the first time a complete numerical result for the full NNLO correction for the top quark pair

  1. Topological edge states of bound photon pairs

    Science.gov (United States)

    Gorlach, Maxim A.; Poddubny, Alexander N.

    2017-05-01

    We predict the existence of interaction-driven edge states of bound two-photon quasiparticles in a dimer periodic array of nonlinear optical cavities. The energy spectrum of photon pairs is dramatically richer than in the noninteracting case or in a simple lattice, featuring collapse and revival of multiple edge and bulk modes as well as edge states in continuum. We link the edge-state existence to the two-photon quantum walk graph connectivity. Our results offer a route to control quantum entanglement and provide insights into the physics of many-body topological states.

  2. Z Boson Pair-Production at LEP

    CERN Document Server

    Achard, P; Aguilar-Benítez, M; Alcaraz, J; Alemanni, G; Allaby, James V; Aloisio, A; Alviggi, M G; Anderhub, H; Andreev, V P; Anselmo, F; Arefev, A; Azemoon, T; Aziz, T; Bagnaia, P; Bajo, A; Baksay, G; Baksay, L; Baldew, S V; Banerjee, S; Banerjee, Sw; Barczyk, A; Barillère, R; Bartalini, P; Basile, M; Batalova, N; Battiston, R; Bay, A; Becattini, F; Becker, U; Behner, F; Bellucci, L; Berbeco, R; Berdugo, J; Berges, P; Bertucci, B; Betev, B L; Biasini, M; Biglietti, M; Biland, A; Blaising, J J; Blyth, S C; Bobbink, Gerjan J; Böhm, A; Boldizsar, L; Borgia, B; Bottai, S; Bourilkov, D; Bourquin, Maurice; Braccini, S; Branson, J G; Brochu, F; Burger, J D; Burger, W J; Cai, X D; Capell, M; Cara Romeo, G; Carlino, G; Cartacci, A M; Casaus, J; Cavallari, F; Cavallo, N; Cecchi, C; Cerrada, M; Chamizo-Llatas, M; Chang, Y H; Chemarin, M; Chen, A; Chen, G; Chen, G M; Chen, H F; Chen, H S; Chiefari, G; Cifarelli, Luisa; Cindolo, F; Clare, I; Clare, R; Coignet, G; Colino, N; Costantini, S; de la Cruz, B; Cucciarelli, S; van Dalen, J A; De Asmundis, R; Déglon, P L; Debreczeni, J; Degré, A; Dehmelt, K; Deiters, K; Della Volpe, D; Delmeire, E; Denes, P; De Notaristefani, F; De Salvo, A; Diemoz, M; Dierckxsens, M; Dionisi, C; Dittmar, M; Doria, A; Dova, M T; Duchesneau, D; Duda, M; Echenard, B; Eline, A; El-Hage, A; El-Mamouni, H; Engler, A; Eppling, F J; Extermann, P; Falagán, M A; Falciano, S; Favara, A; Fay, J; Fedin, O; Felcini, M; Ferguson, T; Fesefeldt, H S; Fiandrini, E; Field, J H; Filthaut, Frank; Fisher, P H; Fisher, W; Fisk, I; Forconi, G; Freudenreich, Klaus; Furetta, C; Galaktionov, Yu; Ganguli, S N; García-Abia, P; Gataullin, M; Gentile, S; Giagu, S; Gong, Z F; Grenier, G; Grimm, O; Grünewald, M W; Guida, M; van Gulik, R; Gupta, V K; Gurtu, A; Gutay, L J; Haas, D; Hatzifotiadou, D; Hebbeker, T; Hervé, A; Hirschfelder, J; Hofer, H; Hohlmann, M; Holzner, G; Hou, S R; Hu, Y; Jin, B N; Jones, L W; de Jong, P; Josa-Mutuberria, I; Käfer, D; Kaur, M; Kienzle-Focacci, M N; Kim, J K; Kirkby, Jasper; Kittel, E W; Klimentov, A; König, A C; Kopal, M; Koutsenko, V F; Kräber, M H; Krämer, R W; Krüger, A; Kunin, A; Ladrón de Guevara, P; Laktineh, I; Landi, G; Lebeau, M; Lebedev, A; Lebrun, P; Lecomte, P; Lecoq, P; Le Coultre, P; Le Goff, J M; Leiste, R; Levtchenko, M; Levchenko, P M; Li, C; Likhoded, S; Lin, C H; Lin, W T; Linde, Frank L; Lista, L; Liu, Z A; Lohmann, W; Longo, E; Lü, Y S; Luci, C; Luminari, L; Lustermann, W; Ma Wen Gan; Malgeri, L; Malinin, A; Maña, C; Mans, J; Martin, J P; Marzano, F; Mazumdar, K; McNeil, R R; Mele, S; Merola, L; Meschini, M; Metzger, W J; Mihul, A; Milcent, H; Mirabelli, G; Mnich, J; Mohanty, G B; Muanza, G S; Muijs, A J M; Musicar, B; Musy, M; Nagy, S; Natale, S; Napolitano, M; Nessi-Tedaldi, F; Newman, H; Nisati, A; Novák, T; Nowak, H; Ofierzynski, R A; Organtini, G; Pal, I; Palomares, C; Paolucci, P; Paramatti, R; Passaleva, G; Patricelli, S; Paul, T; Pauluzzi, M; Paus, C; Pauss, Felicitas; Pedace, M; Pensotti, S; Perret-Gallix, D; Petersen, B; Piccolo, D; Pierella, F; Pioppi, M; Piroué, P A; Pistolesi, E; Plyaskin, V; Pohl, M; Pozhidaev, V; Pothier, J; Prokofev, D; Prokofiev, D O; Quartieri, J; Rahal-Callot, G; Rahaman, M A; Raics, P; Raja, N; Ramelli, R; Rancoita, P G; Ranieri, R; Raspereza, A V; Razis, P A; Ren, D; Rescigno, M; Reucroft, S; Riemann, S; Riles, K; Roe, B P; Romero, L; Rosca, A; Rosier-Lees, S; Roth, S; Rosenbleck, C; Roux, B; Rubio, J A; Ruggiero, G; Rykaczewski, H; Sakharov, A; Saremi, S; Sarkar, S; Salicio, J; Sánchez, E; Schäfer, C; Shchegelskii, V; Schopper, Herwig Franz; Schotanus, D J; Sciacca, C; Servoli, L; Shevchenko, S; Shivarov, N; Shoutko, V; Shumilov, E; Shvorob, A V; Son, D; Souga, C; Spillantini, P; Steuer, M; Stickland, D P; Stoyanov, B; Strässner, A; Sudhakar, K; Sultanov, G G; Sun, L Z; Sushkov, S; Suter, H; Swain, J D; Szillási, Z; Tang, X W; Tarjan, P; Tauscher, Ludwig; Taylor, L; Tellili, B; Teyssier, D; Timmermans, C; Ting, Samuel C C; Ting, S M; Tonwar, S C; Tóth, J; Tully, C; Tung, K L; Ulbricht, J; Valente, E; Van de Walle, R T; Vásquez, R; Veszpremi, V; Vesztergombi, G; Vetlitskii, I; Vicinanza, D; Viertel, Gert M; Villa, S; Vivargent, M; Vlachos, S; Vodopyanov, I; Vogel, H; Vogt, H; Vorobev, I; Vorobyov, A A; Wadhwa, M; Wang, Q; Wang, X L; Wang, Z M; Weber, M; Wienemann, P; Wilkens, H; Wynhoff, S; Xia, L; Xu, Z Z; Yamamoto, J; Yang, B Z; Yang, C G; Yang, H J; Yang, M; Yeh, S C; Zalite, A; Zalite, Yu; Zhang, Z P; Zhao, J; Zhu, G Y; Zhu, R Y; Zhuang, H L; Zichichi, A; Zimmermann, B; Zöller, M

    2003-01-01

    Events stemming from the pair-production of Z bosons in e^+e^- collisions are studied using 217.4 pb^-1 of data collected with the L3 detector at centre-of-mass energies from 200 GeV up to 209 GeV. The special case of events with b quarks is also investigated. Combining these events with those collected at lower centre-of-mass energies, the Standard Model predictions for the production mechanism are verified. In addition, limits are set on anomalous couplings of neutral gauge bosons and on effects of extra space dimensions.

  3. Pair Negotiation When Developing English Speaking Tasks

    Directory of Open Access Journals (Sweden)

    Ingrid Liliana Bohórquez Suárez

    2011-12-01

    Full Text Available This study analyzes what characterizes the negotiations of seventh graders at a public school in Bogotá when working in pairs to develop speaking tasks in EFL classes. The inquiry is a descriptive case study that follows the qualitative paradigm. As a result of analyzing the data, we obtained four consecutive steps that characterize students’ negotiations: Establishing a connection with a partner to work with, proposing practical alternatives, refusing mates’ propositions, and making practical decisions. Moreover, we found that the constant performance of the process of negotiation provokes students to construct a sociolinguistic identity that allows agreements to emerge.

  4. Paired structures and bipolar knowledge representation

    DEFF Research Database (Denmark)

    Montero, Javier; Bustince, Humberto; Franco, Camilo

    In this strictly positional paper we propose a general approach to bipolar knowledge representation, where the meaning of concepts can be modelled by examining their decomposition into opposite and neutral categories. In particular, it is the semantic relationship between the opposite categories...... and at the same time the type of neutrality rising in between opposites. Based on this first level of bipolar knowledge representation, paired structures in fact offer the means to characterize a specific bipolar valuation scale depending on the meaning of the concept that has to be verified. In this sense...

  5. Mated Fingerprint Card Pairs 2 (MFCP2)

    Science.gov (United States)

    NIST Mated Fingerprint Card Pairs 2 (MFCP2) (Web, free access)   NIST Special Database 14 is being distributed for use in development and testing of automated fingerprint classification and matching systems on a set of images which approximate a natural horizontal distribution of the National Crime Information Center (NCIC) fingerprint classes. A newer version of the compression/decompression software on the CDROM can be found at the website http://www.nist.gov/itl/iad/ig/nigos.cfm as part of the NBIS package.

  6. Formation Time of a Fermion Pair Condensate

    OpenAIRE

    Zwierlein, M. W.; Schunck, C. H.; Stan, C. A.; Raupach, S. M. F.; Ketterle, W.

    2004-01-01

    The formation time of a condensate of fermionic atom pairs close to a Feshbach resonance was studied. This was done using a phase-shift method in which the delayed response of the many-body system to a modulation of the interaction strength was recorded. The observable was the fraction of condensed molecules in the cloud after a rapid magnetic field ramp across the Feshbach resonance. The measured response time was slow compared to the rapid ramp, which provides final proof that the molecular...

  7. A Guide to Fluorescent Protein FRET Pairs.

    Science.gov (United States)

    Bajar, Bryce T; Wang, Emily S; Zhang, Shu; Lin, Michael Z; Chu, Jun

    2016-09-14

    Förster or fluorescence resonance energy transfer (FRET) technology and genetically encoded FRET biosensors provide a powerful tool for visualizing signaling molecules in live cells with high spatiotemporal resolution. Fluorescent proteins (FPs) are most commonly used as both donor and acceptor fluorophores in FRET biosensors, especially since FPs are genetically encodable and live-cell compatible. In this review, we will provide an overview of methods to measure FRET changes in biological contexts, discuss the palette of FP FRET pairs developed and their relative strengths and weaknesses, and note important factors to consider when using FPs for FRET studies.

  8. A biometric signcryption scheme without bilinear pairing

    Science.gov (United States)

    Wang, Mingwen; Ren, Zhiyuan; Cai, Jun; Zheng, Wentao

    2013-03-01

    How to apply the entropy in biometrics into the encryption and remote authentication schemes to simplify the management of keys is a hot research area. Utilizing Dodis's fuzzy extractor method and Liu's original signcryption scheme, a biometric identity based signcryption scheme is proposed in this paper. The proposed scheme is more efficient than most of the previous proposed biometric signcryption schemes for that it does not need bilinear pairing computation and modular exponentiation computation which is time consuming largely. The analysis results show that under the CDH and DL hard problem assumption, the proposed scheme has the features of confidentiality and unforgeability simultaneously.

  9. Nuclear orbital and spin scissors with pairing

    Directory of Open Access Journals (Sweden)

    Balbutsev Evgeny

    2016-01-01

    Full Text Available Nuclear scissors modes are considered in the frame of the Wigner function moments method generalized to take into account spin degrees of freedom and pair correlations simultaneously. A new source of nuclear magnetism, connected with counter-rotation of spins up and down around the symmetry axis (hidden angular momenta, is discovered. Its inclusion into the theory allows one to improve substantially the agreement with experimental data in the description of energies and transition probabilities of scissors modes in rare earth nuclei.

  10. [Kidney paired donation. Combination with extracorporeal desensitization].

    Science.gov (United States)

    Bond, G; Böhmig, G A

    2014-09-01

    Live kidney donation represents the gold standard for renal replacement therapy. Due to ABO and HLA incompatibility between donor and recipient pairs, one third of possible transplantations cannot be performed. Kidney exchange programs in combination with extracorporeal desensitization have been introduced to enable successful kidney transplantation in such circumstances. This review discusses the current indications, methods, ethical problems and results within such programs. Relevant Medline articles were analyzed and personal experiences of the authors are included in this article. Kidney exchange programs in combination with extracorporeal desensitization enable successful transplantation for most patients. The best combinations of existing strategies have to be defined and newly arisen ethical questions have to be answered.

  11. Detecting nonlocal Cooper pair entanglement by optical Bell inequality violation

    Science.gov (United States)

    Nigg, Simon E.; Tiwari, Rakesh P.; Walter, Stefan; Schmidt, Thomas L.

    2015-03-01

    Based on the Bardeen-Cooper-Schrieffer theory of superconductivity, the coherent splitting of Cooper pairs from a superconductor to two spatially separated quantum dots has been predicted to generate nonlocal pairs of entangled electrons. In order to test this hypothesis, we propose a scheme to transfer the spin state of a split Cooper pair onto the polarization state of a pair of optical photons. We show that the photon pairs produced can be used to violate a Bell inequality, unambiguously demonstrating the entanglement of the split Cooper pairs.

  12. Pair Production Constraints on Superluminal Neutrinos Revisited

    Energy Technology Data Exchange (ETDEWEB)

    Brodsky, Stanley J.; /SLAC; Gardner, Susan; /Kentucky U.

    2012-02-16

    We revisit the pair creation constraint on superluminal neutrinos considered by Cohen and Glashow in order to clarify which types of superluminal models are constrained. We show that a model in which the superluminal neutrino is effectively light-like can evade the Cohen-Glashow constraint. In summary, any model for which the CG pair production process operates is excluded because such timelike neutrinos would not be detected by OPERA or other experiments. However, a superluminal neutrino which is effectively lightlike with fixed p{sup 2} can evade the Cohen-Glashow constraint because of energy-momentum conservation. The coincidence involved in explaining the SN1987A constraint certainly makes such a picture improbable - but it is still intrinsically possible. The lightlike model is appealing in that it does not violate Lorentz symmetry in particle interactions, although one would expect Hughes-Drever tests to turn up a violation eventually. Other evasions of the CG constraints are also possible; perhaps, e.g., the neutrino takes a 'short cut' through extra dimensions or suffers anomalous acceleration in matter. Irrespective of the OPERA result, Lorentz-violating interactions remain possible, and ongoing experimental investigation of such possibilities should continue.

  13. Generalized quantum interference of correlated photon pairs.

    Science.gov (United States)

    Kim, Heonoh; Lee, Sang Min; Moon, Han Seb

    2015-05-07

    Superposition and indistinguishablility between probability amplitudes have played an essential role in observing quantum interference effects of correlated photons. The Hong-Ou-Mandel interference and interferences of the path-entangled photon number state are of special interest in the field of quantum information technologies. However, a fully generalized two-photon quantum interferometric scheme accounting for the Hong-Ou-Mandel scheme and path-entangled photon number states has not yet been proposed. Here we report the experimental demonstrations of the generalized two-photon interferometry with both the interferometric properties of the Hong-Ou-Mandel effect and the fully unfolded version of the path-entangled photon number state using photon-pair sources, which are independently generated by spontaneous parametric down-conversion. Our experimental scheme explains two-photon interference fringes revealing single- and two-photon coherence properties in a single interferometer setup. Using the proposed interferometric measurement, it is possible to directly estimate the joint spectral intensity of a photon pair source.

  14. ``Schooling'' of wing pairs in flapping flight

    Science.gov (United States)

    Ramananarivo, Sophie; Zhang, Jun; Ristroph, Leif; AML, Courant Collaboration; Physics NYU Collaboration

    2015-11-01

    The experimental setup implements two independent flapping wings swimming in tandem. Both are driven with the same prescribed vertical heaving motion, but the horizontal motion is free, which means that the swimmers can take up any relative position and forward speed. Experiments show however clearly coordinated motions, where the pair of wings `crystallize' into specific stable arrangements. The follower wing locks into the path of the leader, adopting its speed, and with a separation distance that takes on one of several discrete values. By systematically varying the kinematics and wing size, we show that the set of stable spacings is dictated by the wavelength of the periodic wake structure. The forces maintaining the pair cohesion are characterized by applying an external force to the follower to perturb it away from the `stable wells'. These results show that hydrodynamics alone is sufficient to induce cohesive and coordinated collective locomotion through a fluid, and we discuss the hypothesis that fish schools and bird flocks also represent stable modes of motion.

  15. Optimisation of a quantum pair space thruster

    Directory of Open Access Journals (Sweden)

    Valeriu DRAGAN

    2012-06-01

    Full Text Available The paper addresses the problem of propulsion for long term space missions. Traditionally a space propulsion unit has a propellant mass which is ejected trough a nozzle to generate thrust; this is also the case with inert gases energized by an on-board power unit. Unconventional methods for propulsion include high energy LASERs that rely on the momentum of photons to generate thrust. Anti-matter has also been proposed for energy storage. Although the momentum of ejected gas is significantly higher, the LASER propulsion offers the perspective of unlimited operational time – provided there is a power source. The paper will propose the use of the quantum pair formation for generating a working mass, this is different than conventional anti-matter thrusters since the material particles generated are used as propellant not as energy storage.Two methods will be compared: LASER and positron-electron, quantum pair formation. The latter will be shown to offer better momentum above certain energy levels.For the demonstrations an analytical solution is obtained and provided in the form of various coefficients. The implications are, for now, theoretical however the practicality of an optimized thruster using such particles is not to be neglected for long term space missions.

  16. Generalized quantum interference of correlated photon pairs

    Science.gov (United States)

    Kim, Heonoh; Lee, Sang Min; Moon, Han Seb

    2015-01-01

    Superposition and indistinguishablility between probability amplitudes have played an essential role in observing quantum interference effects of correlated photons. The Hong-Ou-Mandel interference and interferences of the path-entangled photon number state are of special interest in the field of quantum information technologies. However, a fully generalized two-photon quantum interferometric scheme accounting for the Hong-Ou-Mandel scheme and path-entangled photon number states has not yet been proposed. Here we report the experimental demonstrations of the generalized two-photon interferometry with both the interferometric properties of the Hong-Ou-Mandel effect and the fully unfolded version of the path-entangled photon number state using photon-pair sources, which are independently generated by spontaneous parametric down-conversion. Our experimental scheme explains two-photon interference fringes revealing single- and two-photon coherence properties in a single interferometer setup. Using the proposed interferometric measurement, it is possible to directly estimate the joint spectral intensity of a photon pair source. PMID:25951143

  17. The leptoquark hunter's guide: pair production

    Science.gov (United States)

    Diaz, Bastian; Schmaltz, Martin; Zhong, Yi-Ming

    2017-10-01

    Leptoquarks occur in many new physics scenarios and could be the next big discovery at the LHC. The purpose of this paper is to point out that a model-independent search strategy covering all possible leptoquarks is possible and has not yet been fully exploited. To be systematic we organize the possible leptoquark final states according to a leptoquark matrix with entries corresponding to nine experimentally distinguishable leptoquark decays: any of {light-jet, b-jet, top} with any of {neutrino, e/ μ, τ}. The 9 possibilities can be explored in a largely model-independent fashion with pair-production of leptoquarks at the LHC. We review the status of experimental searches for the 9 components of the leptoquark matrix, pointing out which 3 have not been adequately covered. We plead that experimenters publish bounds on leptoquark cross sections as functions of mass for as wide a range of leptoquark masses as possible. Such bounds are essential for reliable recasts to general leptoquark models. To demonstrate the utility of the leptoquark matrix approach we collect and summarize searches with the same final states as leptoquark pair production and use them to derive bounds on a complete set of Minimal Leptoquark models which span all possible flavor and gauge representations for scalar and vector leptoquarks.

  18. [Cloning and transcriptional profiling of a cell division cycle gene PsCdc2 from stripe rust fungus during incompatible and compatible interaction between wheat and Puccinia striiformis f. sp. tritici].

    Science.gov (United States)

    Dai, Xiwei; Guo, Jun; Chen, Yueying; Duan, Yinghui; Xia, Ning; Wei, Guorong; Huang, Lili; Kang, Zhensheng

    2010-02-01

    We cloned a cell division cycle PsCdc2 from Puccinia striiformis f. sp. tritici (Pst) and analyze its expression profile. Using PCR and RT-PCR methods, we isolated the cDNA and genomic DNA sequences of PsCdc2. We analyzed the amino acid sequence of PsCdc2 using bioinformatic softwares. In addition, Real time RT-PCR was used to analyze the gene expression pattern of PsCdc2 at different time points after wheat inoculated. A 2279 bp DNA sequence of PsCdc2 was cloned and comprised of 11 extrons and 10 introns. The cDNA sequence of PsCdc2 included a complete 885 bp open reading frame and encoded a putative protein composed of 294 amino acids, with a molecular weight of 33.14 KDa and a pI of 6.26. PsCdc2 contained two conserved kinase domains and a transmembrane domain. Phylogenetic analysis indicated that PsCdc2 showed high similarity with Cdc2 from Puccinia graminis (73.1%), Cryptococcus neoformans (72.4%) and Ustilago maydis (70.4%), respectively. Real time RT-PCR analysis showed that in compatible interaction between Pst and wheat, PsCdc2 was up-regulated at early stage of infection. The maximum induction occurred at 12 hpi, at which transcripts were 1.62 fold over that in urediniospore. From 24 to 268 hpi, the accumulation of transcripts decreased steadily. The minimum accumulation occurred at 96 h, at which transcripts were only 0.07 fold of that in uredinisopore. During incompatible interaction between Pst and wheat, PsCdc2 was down-regulated and its accumulation was lower than that in urediniospore. The maximum induction occurred at 12 h, at which transcripts were 0.34 fold of that in urediniospore. The minimum accumulation occurred at 96 h, whose transcript was only 0.02 fold of that in urediniospore. PsCdc2 might be involved in primary hyphal growth and haustorium formation during early infection by regulating cell cycle of Pst. The present study would be helpful for understanding the essence of cell cycle control and provided basis for new chemical control of

  19. Postulation of rust resistance genes in Nordic spring wheat genotypes and identification of widely effective sources of resistance against the Australian rust flora.

    Science.gov (United States)

    Randhawa, Mandeep; Bansal, Urmil; Lillemo, Morten; Miah, Hanif; Bariana, Harbans

    2016-11-01

    Wild relatives, landraces and cultivars from different geographical regions have been demonstrated as the sources of genetic variation for resistance to rust diseases. This study involved assessment of diversity for resistance to three rust diseases among a set of Nordic spring wheat cultivars. These cultivars were tested at the seedling stage against several pathotypes of three rust pathogens in the greenhouse. All stage stem rust resistance genes Sr7b, Sr8a, Sr12, Sr15, Sr17, Sr23 and Sr30, and leaf rust resistance genes Lr1, Lr3a, Lr13, Lr14a, Lr16 and Lr20 were postulated either singly or in different combinations among these cultivars. A high proportion of cultivars were identified to carry linked rust resistance genes Sr15 and Lr20. Although 51 cultivars showed variation against Puccinia striiformis f. sp. tritici (Pst) pathotypes used in this study, results were not clearly contrasting to enable postulation of stripe rust resistance genes in these genotypes. Stripe rust resistance gene Yr27 was postulated in four cultivars and Yr1 was present in cultivar Zebra. Cultivar Tjalve produced low stripe rust response against all Pst pathotypes indicating the presence either of a widely effective resistance gene or combination of genes with compensating pathogenic specificities. Several cultivars carried moderate to high level of APR to leaf rust and stripe rust. Seedling stem rust susceptible cultivar Aston exhibited moderately resistant to moderately susceptible response, whereas other cultivars belonging to this class were rated moderately susceptible or higher. Molecular markers linked with APR genes Yr48, Lr34/Yr18/Sr57, Lr68 and Sr2 detected the presence of these genes in some genotypes.

  20. Quantifying inbreeding avoidance through extra-pair reproduction.

    Science.gov (United States)

    Reid, Jane M; Arcese, Peter; Keller, Lukas F; Germain, Ryan R; Duthie, A Bradley; Losdat, Sylvain; Wolak, Matthew E; Nietlisbach, Pirmin

    2015-01-01

    Extra-pair reproduction is widely hypothesized to allow females to avoid inbreeding with related socially paired males. Consequently, numerous field studies have tested the key predictions that extra-pair offspring are less inbred than females' alternative within-pair offspring, and that the probability of extra-pair reproduction increases with a female's relatedness to her socially paired male. However, such studies rarely measure inbreeding or relatedness sufficiently precisely to detect subtle effects, or consider biases stemming from failure to observe inbred offspring that die during early development. Analyses of multigenerational song sparrow (Melospiza melodia) pedigree data showed that most females had opportunity to increase or decrease the coefficient of inbreeding of their offspring through extra-pair reproduction with neighboring males. In practice, observed extra-pair offspring had lower inbreeding coefficients than females' within-pair offspring on average, while the probability of extra-pair reproduction increased substantially with the coefficient of kinship between a female and her socially paired male. However, simulations showed that such effects could simply reflect bias stemming from inbreeding depression in early offspring survival. The null hypothesis that extra-pair reproduction is random with respect to kinship therefore cannot be definitively rejected in song sparrows, and existing general evidence that females avoid inbreeding through extra-pair reproduction requires reevaluation given such biases. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  1. Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma.

    Science.gov (United States)

    Russo, Mariano; Broach, James; Sheldon, Kathryn; Houser, Kenneth R; Liu, Dajiang J; Kesterson, Joshua; Phaeton, Rebecca; Hossler, Carrie; Hempel, Nadine; Baker, Maria; Newell, Jordan M; Zaino, Richard; Warrick, Joshua I

    2017-09-01

    Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar to those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next-generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma. In evaluating all samples, EIN/AH and carcinoma did not differ in mutational burden, CNA burden, or specific genes mutated (all P>.1). All paired EIN/AH and carcinoma samples shared at least one identical somatic mutation, frequently in PI(3)K pathway members. Large CNAs (>10 genes in length) were identified in 83% of cases; paired EIN/AH and carcinoma samples shared at least one identical CNA in these cases. Mismatch repair protein expression matched in all paired EIN/AH and carcinoma samples. All paired EIN/AH and carcinoma samples had identical The Cancer Genome Atlas subtype, with 3 classified as "copy number low endometrioid" and 3 classified as "microsatellite instability hypermutated." Although paired EIN/AH and carcinoma samples were clonal, private mutations (ie, present in only one sample) were identified in EIN/AH and carcinoma in all cases, frequently in established cancer-driving genes. These findings indicate that EIN/AH gives rise to endometrioid adenocarcinoma by a complex process of subclone evolution, not a linear accumulation of molecular events. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. When mothers make sons sexy: maternal effects contribute to the increased sexual attractiveness of extra-pair offspring.

    Science.gov (United States)

    Tschirren, Barbara; Postma, Erik; Rutstein, Alison N; Griffith, Simon C

    2012-03-22

    Quality differences between offspring sired by the social and by an extra-pair partner are usually assumed to have a genetic basis, reflecting genetic benefits of female extra-pair mate choice. In the zebra finch (Taeniopygia guttata), we identified a colour ornament that is under sexual selection and appears to have a heritable basis. Hence, by engaging in extra-pair copulations with highly ornamented males, females could, in theory, obtain genes for increased offspring attractiveness. Indeed, sons sired by extra-pair partners had larger ornaments, seemingly supporting the genetic benefit hypothesis. Yet, when comparing ornament size of the social and extra-pair partners, there was no difference. Hence, the observed differences most likely had an environmental basis, mediated, for example, via differential maternal investment of resources into the eggs fertilized by extra-pair and social partners. Such maternal effects may (at least partly) be mediated by egg size, which we found to be associated with mean ornament expression in sons. Our results are consistent with the idea that maternal effects can shape sexual selection by altering the genotype-phenotype relationship for ornamentation. They also caution against automatically attributing greater offspring attractiveness or viability to an extra-pair mate's superior genetic quality, as without controlling for differential maternal investment we may significantly overestimate the role of genetic benefits in the evolution of extra-pair mating behaviour.

  3. [Gene analysis of Chinese barley dwarf germplasm resources. I. Inheritance and allelism test of the dwarf genes] [In Process Citation

    Science.gov (United States)

    Zhang

    1999-01-01

    The plant height inheritance of 24 Chinese barley dwarf germplasms and the allelic relationships between the dwarf genes in them and the known dwarf genes uz, sdw, br and denso were studied. It was found that most Chinese barley dwarfs were controlled by 1 pair, a few by 2 pairs of recessive genes, only one by 1 pair recessive and 1 pair incomplete dominant genes. Allele frequence at the known dwarf gene uz locus was very high in Chinese barley dwarfs. Most monogenic and 2 digenic barley dwarfs had allelic relationships with uz. A monogenic barley dwarf 11012.2 from India and a digenic dwarf Yan 66 were found allelic to the known dwarf gene sdw. But no dwarfs had allelic relationship with the known dwarf genes br and denso. Monogenic dwarf mutants 91G318, 91D27 and 93-597 carried 1 pair of new recessive dwarf genes respectively. Digenic dwarf mutant 1974E possessed 1 pair of new incomplete dominant dwarf genes. Besides, 4 pairs of new recessive dwarf genes were indentified in 6 Tibetan barley dwarfs.

  4. Evidence for homosexuality gene

    Energy Technology Data Exchange (ETDEWEB)

    Pool, R.

    1993-07-16

    A genetic analysis of 40 pairs of homosexual brothers has uncovered a region on the X chromosome that appears to contain a gene or genes for homosexuality. When analyzing the pedigrees of homosexual males, the researcheres found evidence that the trait has a higher likelihood of being passed through maternal genes. This led them to search the X chromosome for genes predisposing to homosexuality. The researchers examined the X chromosomes of pairs of homosexual brothers for regions of DNA that most or all had in common. Of the 40 sets of brothers, 33 shared a set of five markers in the q28 region of the long arm of the X chromosome. The linkage has a LOD score of 4.0, which translates into a 99.5% certainty that there is a gene or genes in this area that predispose males to homosexuality. The chief researcher warns, however, that this one site cannot explain all instances of homosexuality, since there were some cases where the trait seemed to be passed paternally. And even among those brothers where there was no evidence that the trait was passed paternally, seven sets of brothers did not share the Xq28 markers. It seems likely that homosexuality arises from a variety of causes.

  5. How Likely are Wide Pairs to be Physically Connected?

    Science.gov (United States)

    Bryant, T.

    2017-04-01

    There are numerous binary pairs that are not in the Washington Double Star Catalog (WDS)1 that appear to be physical binaries. We show in this study that such pairs are often optical using Monte Carlo simulations of the sky.

  6. Photon pair generation and manipulation in an integrated silicon chip

    NARCIS (Netherlands)

    Bonneau, D.; Silverstone, J.W.; Hadfield, R.H.; Zwiller, V.; Ohira, K.; Suzuki, N.; Yoshida, H.; Iizuka, N.; Ezaki, M.; Rarity, J.G.; O'Brien, J.L.; Thompson, M.G.

    2013-01-01

    Quantum photonics is a promising technology for implementing quantum information tasks. We demonstrate integration of multiple photon pair sources together with a circuit enabling creation and manipulation of photon pairs in a monolithic silicon-on-insulator chip.

  7. Development of Primer Pairs from Molecular Typing of Rabies Virus Variants Present in Mexico

    Directory of Open Access Journals (Sweden)

    Fernando Bastida-González

    2016-01-01

    Full Text Available Nucleoprotein (N gene from rabies virus (RABV is a useful sequence target for variant studies. Several specific RABV variants have been characterized in different mammalian hosts such as skunk, dog, and bats by using anti-nucleocapsid monoclonal antibodies (MAbs via indirect fluorescent antibody (IFA test, a technique not available in many laboratories in Mexico. In the present study, a total of 158 sequences of N gene from RABV were used to design eight pairs of primers (four external and four internal primers, for typing four different RABV variants (dog, skunk, vampire bat, and nonhematophagous bat which are most common in Mexico. The results indicate that the primer and the typing variant from the brain samples, submitted to nested and/or real-time PCR, are in agreement in all four singleplex reactions, and the designed primer pairs are an alternative for use in specific variant RABV typing.

  8. Synaptonemal complex extension from clustered telomeres mediates full-length chromosome pairing in Schmidtea mediterranea.

    Science.gov (United States)

    Xiang, Youbin; Miller, Danny E; Ross, Eric J; Sánchez Alvarado, Alejandro; Hawley, R Scott

    2014-12-02

    In the 1920s, József Gelei proposed that chromosome pairing in flatworms resulted from the formation of a telomere bouquet followed by the extension of synapsis from telomeres at the base of the bouquet, thus facilitating homolog pairing in a processive manner. A modern interpretation of Gelei's model postulates that the synaptonemal complex (SC) is nucleated close to the telomeres and then extends progressively along the full length of chromosome arms. We used the easily visible meiotic chromosomes, a well-characterized genome, and RNAi in the sexual biotype of the planarian Schmidtea mediterranea to test that hypothesis. By identifying and characterizing S. mediterranea homologs of genes encoding synaptonemal complex protein 1 (SYCP1), the topoisomerase-like protein SPO11, and RAD51, a key player in homologous recombination, we confirmed that SC formation begins near the telomeres and progresses along chromosome arms during zygotene. Although distal regions pair at the time of bouquet formation, pairing of a unique interstitial locus is not observed until the formation of full-length SC at pachytene. Moreover, neither full extension of the SC nor homologous pairing is dependent on the formation of double-strand breaks. These findings validate Gelei's speculation that full-length pairing of homologous chromosomes is mediated by the extension of the SC formed near the telomeres. S. mediterranea thus becomes the first organism described (to our knowledge) that forms a canonical telomere bouquet but does not require double-strand breaks for synapsis between homologous chromosomes. However, the initiation of SC formation at the base of the telomere bouquet, which then is followed by full-length homologous pairing in planarian spermatocytes, is not observed in other species and may not be conserved.

  9. Semiquantum secure direct communication using EPR pairs

    Science.gov (United States)

    Zhang, Ming-Hui; Li, Hui-Fang; Xia, Zhao-Qiang; Feng, Xiao-Yi; Peng, Jin-Ye

    2017-05-01

    Quantum secure direct communication can transmit a secret message directly through quantum channels without first generating a shared secret key. In the most of the existing protocols, quantum secure direct communication is possible only when both communicating participants have quantum capabilities. So what happens if either party of two participants just has classical capabilities? In this paper, we propose a semiquantum secure direct communication protocol with Einstein-Podolsky-Rosen photon pairs in which the classical sender Bob transmits a secret message to quantum Alice directly. After checking the security of quantum channels, Bob encodes his secret message on Alice's code sequence. Then, quantum Alice extracts Bob's secret message by measuring her home qubits and the received code qubits, respectively. In addition, we demonstrate the security of the proposed protocol against some individual eavesdropping attacks. The efficiency analysis shows that our protocol can provide higher efficiency.

  10. The stratospheric arrival pair in infrasound propagation.

    Science.gov (United States)

    Waxler, Roger; Evers, Läslo G; Assink, Jelle; Blom, Phillip

    2015-04-01

    The ideal case of a deep and well-formed stratospheric duct for long range infrasound propagation in the absence of tropospheric ducting is considered. A canonical form, that of a pair of arrivals, for ground returns of impulsive signals in a stratospheric duct is determined. The canonical form is derived from the geometrical acoustics approximation, and is validated and extended through full wave modeling. The full caustic structure of the field of ray paths is found and used to determine phase relations between the contributions to the wavetrain from different propagation paths. Finally, comparison with data collected from the 2005 fuel gas depot explosion in Buncefield, England is made. The correspondence between the theoretical results and the observations is shown to be quite good.

  11. Reconstruction of Low-Mass Electron Pairs

    CERN Document Server

    The ATLAS Collaboration

    2009-01-01

    This note discusses the reconstruction of J/y and ¡ decays to electron pairs based on ATLAS Monte Carlo simulated signal and background samples. The possible trigger strategies are described, one geared to select two low-energy electromagnetic objects in direct production, the second one taking advantage of the possible presence of a muon in the final state in b¯b production followed by the decay of one b-quark to J/y +X. The low-energy electrons are reconstructed using a dedicated algorithm seeded by a track reconstructed in the inner detector and identified combining information from the inner detector and the electromagnetic calorimeter. The performance of this algorithm is presented and the potential of using such events for early LHC data studies is investigated.

  12. Two-neutron pairing enhancement factors

    Energy Technology Data Exchange (ETDEWEB)

    Liu, X.T.; Cline, D.; Czosnyka, T.; Guidry, M.W.; Han, X.L.; Kavka, A.E.; Kernan, W.J.; Kincaid, R.W.; Sorensen, S.P.; Vogt, E.G.; Wu, C.Y. (Department of Physics, University of Tennessee, Knoxville, Tennessee 37996 ( O) Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830 Holifield Heavy Ion Research Facility, Joint Institute for Heavy Ion Research, Oak Ridge, Tennessee 37831 Nuclear Structure Research Laboratory, University of Rochester, Rochester, New York, 14627)

    1991-01-01

    The Spin Spectrometer was used to separate Dy ground-band and two-quasiparticle populations in one- and two-neutron transfer reactions with Sn and Ni projectiles. Transfer probabilities {ital P}{sub 1{ital n},2{ital n}} and two-neutron enhancement factors {ital F}=={ital P}{sub 2{ital n}}/{ital P}{sub 1{ital n}}{sup 2} were determined as a function of scattering angle. For the two-quasiparticle bands {ital F}{congruent}7--20, but for the ground band {ital F}{congruent}30--500, indicating large pairing effects in two-particle transfer to the ground band. The data also indicate larger enhancement factors in Sn than in Ni collisions.

  13. An advanced KB mirror pair for microfocusing

    CERN Document Server

    Ferme, J J

    2001-01-01

    A new range of micro-focusing mirrors based on KB pairs has been developed by SESO for Beamline Nanospectroscopy at the Elettra Storage Ring in Trieste, Italy. Both the focusing and the aspheric shape are adjustable with stepper motors. The goal of the beamline is to have a high photon density spot with a variable size in the experimental chamber over the whole soft X-ray range. The estimated dimension of the final spot should be smaller than 4 mu m sup 2 FWHM, with a photon density of the order of 10 sup 1 sup 3 photons/s mu m sup 2; this may be achieved only by accepting an angular divergence on these mirrors of between 5 and 10 mrad. This condition can be fulfilled only with elliptical (or plane elliptical) mirrors with very limited residual slope errors (below 1 mu rad RMS) that are able to correct even small focal distance errors.

  14. A pair spectrometer for nuclear astrophysics experiments

    Energy Technology Data Exchange (ETDEWEB)

    Guerro, L.; Saltarelli, A.; Tabassam, U. [University of Camerino, Division of Physics, School of Science and Technology, Camerino (Italy); INFN, Sezione di Perugia, Perugia (Italy); Di Leva, A. [INFN, Napoli (Italy); University of Naples ' ' Federico II' ' , Physics Department, Naples (Italy); Gialanella, L.; De Cesare, N.; D' Onofrio, A.; Terrasi, F. [Second University of Naples, Department of Mathematics and Physics, Caserta (Italy); INFN, Napoli (Italy); Schuermann, D.; Romoli, M. [INFN, Napoli (Italy); Busso, M. [INFN, Sezione di Perugia, Perugia (Italy); University of Perugia, Department of Physics, Perugia (Italy)

    2014-11-15

    Non-radiative transitions in nuclear capture reactions between light nuclei play a relevant role in stellar nuclear astrophysics, where nuclear processes occur at typical energies from tens to hundreds of keV. At higher energies, instead, the E0 contributions may be shadowed by more intense transitions. The experimental study of E0 transitions requires a specific detection setup, able to uniquely identify events where an electron-positron pair is produced. A compact ΔE-E charged-particle spectrometer based on two silicon detectors has been designed to be installed in the jet gas target chamber of the recoil mass separator ERNA (European Recoil separator for Nuclear Astrophysics) at the CIRCE laboratory of Caserta, Italy. The detector design, its performances and the first foreseen applications are described. (orig.)

  15. Ultracompact quantum splitter of degenerate photon pairs

    CERN Document Server

    He, Jiakun; Casas-Bedoya, Alvaro; Zhang, Yanbing; Xiong, Chunle; Eggleton, Benjamin J

    2015-01-01

    Integrated sources of indistinguishable photons have attracted a lot of attention because of their applications in quantum communication and optical quantum computing. Here, we demonstrate an ultra-compact quantum splitter for degenerate single photons based on a monolithic chip incorporating Sagnac loop and a micro-ring resonator with a footprint of 0.011 mm2, generating and deterministically splitting indistinguishable photon pairs using time-reversed Hong-Ou-Mandel interference. The ring resonator provides enhanced photon generation rate, and the Sagnac loop ensures the photons travel through equal path lengths and interfere with the correct phase to enable the reversed HOM effect to take place. In the experiment, we observed a HOM dip visibility of 94.5 +- 3.3 %, indicating the photons generated by the degenerate single photon source are in a suitable state for further integration with other components for quantum applications, such as controlled-NOT gates.

  16. Visualizing lone pairs in compounds containing heavier congeners ...

    Indian Academy of Sciences (India)

    Unknown

    and Powell1, to be refined later by Gillespie and Nyholm2, is the stuff of high school chemistry. The sequence of decreasing repulsion, lone pair–lone pair > lone pair–bond pair > bond pair–bond pair, is a familiar thumb rule that permits thousands of school and college students to hazard the geometry of molecules such as ...

  17. Extensions of Bessel sequences to dual pairs of frames

    DEFF Research Database (Denmark)

    Christensen, Ole; Kim, Hong Oh; Kim, Rae Young

    2013-01-01

    Tight frames in Hilbert spaces have been studied intensively for the past years. In this paper we demonstrate that it often is an advantage to use pairs of dual frames rather than tight frames. We show that in any separable Hilbert space, any pairs of Bessel sequences can be extended to a pair...

  18. Using Pair Programming to Teach CAD Based Engineering Graphics

    Science.gov (United States)

    Leland, Robert P.

    2010-01-01

    Pair programming was introduced into a course in engineering graphics that emphasizes solid modeling using SolidWorks. In pair programming, two students work at a single computer, and periodically trade off roles as driver (hands on the keyboard and mouse) and navigator (discuss strategy and design issues). Pair programming was used in a design…

  19. Internal pair decay of giant resonances in hot Pb-200

    NARCIS (Netherlands)

    Schadmand, S; Varma, R; Banerjee, S.R.; Back, BB; Hofman, DJ; Montoya, CP; Paul, P

    1996-01-01

    Electron-positron pairs emitted during the de-excitation of hot Pb-200 from the reaction 95 MeV F-19 + Ta-181 were detected with the Stony Brook pair detector. The internal pair decay from the giant dipole resonance (GDR) built on excited states in a heavy nucleus is cleanly observed for the first

  20. Au pair på ulige vilkår

    DEFF Research Database (Denmark)

    Christiansen, Connie Carøe

    2008-01-01

    Antallet af au pairs i Danmark fra Fillipinerne er steget markant i de seneste år. Mens danske myndigheder betragter au pair-ordningen som kulturudveksling blandt unge mennesker, ser fillipinske au pairs derimod den som en mulighed for at tjene penge så de kan forsørge deres egen familie i Fillip...

  1. Pair Taping: Increasing Motivation and Achievement with a Fluency Practice.

    Science.gov (United States)

    Schneider, Peter H.

    2001-01-01

    Japanese university students had the choice of pair taping--a fluency practice in which learners record themselves speaking freely in pairs--for an equivalent amount of time as their once a week English class. Results from self reports showed that learners who chose pair taping (73) over remaining in class (n=28) reported increases in ease of…

  2. minimal pairs of polytopes and their number of vertices

    African Journals Online (AJOL)

    Preferred Customer

    Using this operation we give a new algorithm to reduce and find a minimal pair of polytopes from the given class of the ... statement does not hold true in general for higher dimensional spaces. Key words/phrases: Pairs of compact ..... rem gives us the necessary and sufficient condition for a pair of polytopes in the plane to ...

  3. Keratoconus in 18 pairs of twins.

    Science.gov (United States)

    Tuft, Stephen J; Hassan, Hala; George, Sonia; Frazer, David G; Willoughby, Colin E; Liskova, Petra

    2012-09-01

    To describe the concordance of keratoconus in 18 sets of twins. Thirteen monozygotic (MZ) and five dizygotic (DZ) pairs of twins were identified during an investigation of familial keratoconus. We used 16 forensic microsatellite markers to confirm the zygosity of same sex twins. Patients and available relatives were examined for signs of keratoconus using corneal topography. For each pair of twins, the severity of keratoconus in each eye was graded according to the steepest keratometry value and the average difference in score between the MZ and DZ twins compared. All of the MZ twins and four of the five DZ twins were concordant for keratoconus but with differences in age of onset and severity of disease. The subjective age of onset of keratoconus tended to be earlier in the MZ twins (16.4 years, SD 4.66) than in the DZ twins (20.3 years, SD 7.55) (p=0.086). Additional relatives with keratoconus were identified in two (16%) of the families with MZ twins and in three (60%) of the families of DZ twins. The mean difference in severity scores was 1.4 (SD 1.73) for the MZ twins and 3.0 (SD 1.00) for the DZ twins (p=0.035). This data provide evidence that the severity of keratoconus is more concordant in MZ than in DZ twins. The results support the currently accepted hypothesis of an important genetic contribution towards the pathogenesis of keratoconus, but suggest that there is also an environmental effect on the expression of disease. © 2012 The Authors. Acta Ophthalmologica © 2012 Acta Ophthalmologica Scandinavica Foundation.

  4. PAIR'14 / PAIR'15 STUDENT CONFERENCES ON PLANNING IN ARTIFICIAL INTELLIGENCE AND ROBOTICS

    Directory of Open Access Journals (Sweden)

    Editorial Foreword

    2015-12-01

    Full Text Available Dear Readerthe original idea of the student conference on “Planning in Artificial Intelligence and Robotics” (PAIR is to join young researchers from particular laboratories in Czech Republic, where planning problems are investigated from artificial intelligence (AI or robotics points of view. The first year of PAIR has been organized at the Dept. of Computer Science, Faculty Electrical Engineering, Czech Technical University in 2014.At PAIR 2014, laboratories from Prague and Brno were presented. In particular, students and researchers from Charles University, Czech Technical University in Prague, Brno University of Technology, and Central European Institute of Technology participated at the event. Beside an introduction of the particular research groups and their topics, students presented contributions on their current research results. Ten papers were presented on topics ranging from domain–independent planning, trajectory planning to applications for unmanned aerial and legged robots. This first event provides us an initial experience with the community of young researchers in Czech Republic that are working planning in robotic or AI. Based on the success of PAIR 2014, we decided to continue with our effort to establish a suitable fora for students that are geographically very close, but usually do not meet, because of participation on different Robotics and AI events.The second student conference on Planning in Artificial Intelligence and Robotics (PAIR 2015 successfully continues the tradition of the first year of the conference organized in Prague. This year, the conference was collocated with 10th anniversary of RoboTour contest in Písek. This format enable us to extend the impact of the PAIR conference and improve the visibility of the growing student community. The conference reached a good amount of interesting papers focused on image processing for mobile robots, swarm control, driving simulation, robot control, or domain

  5. Demographic mechanisms of inbreeding adjustment through extra-pair reproduction.

    Science.gov (United States)

    Reid, Jane M; Duthie, A Bradley; Wolak, Matthew E; Arcese, Peter

    2015-07-01

    One hypothesis explaining extra-pair reproduction is that socially monogamous females mate with extra-pair males to adjust the coefficient of inbreeding (f) of extra-pair offspring (EPO) relative to that of within-pair offspring (WPO) they would produce with their socially paired male. Such adjustment of offspring f requires non-random extra-pair reproduction with respect to relatedness, which is in turn often assumed to require some mechanism of explicit pre-copulatory or post-copulatory kin discrimination. We propose three demographic processes that could potentially cause mean f to differ between individual females' EPO and WPO given random extra-pair reproduction with available males without necessarily requiring explicit kin discrimination. Specifically, such a difference could arise if social pairings formed non-randomly with respect to relatedness or persisted non-randomly with respect to relatedness, or if the distribution of relatedness between females and their sets of potential mates changed during the period through which social pairings persisted. We used comprehensive pedigree and pairing data from free-living song sparrows (Melospiza melodia) to quantify these three processes and hence investigate how individual females could adjust mean offspring f through instantaneously random extra-pair reproduction. Female song sparrows tended to form social pairings with unrelated or distantly related males slightly less frequently than expected given random pairing within the defined set of available males. Furthermore, social pairings between more closely related mates tended to be more likely to persist across years than social pairings between less closely related mates. However, these effects were small and the mean relatedness between females and their sets of potential extra-pair males did not change substantially across the years through which social pairings persisted. Our framework and analyses illustrate how demographic and social structuring within

  6. Synergistic drug combinations from electronic health records and gene expression.

    Science.gov (United States)

    Low, Yen S; Daugherty, Aaron C; Schroeder, Elizabeth A; Chen, William; Seto, Tina; Weber, Susan; Lim, Michael; Hastie, Trevor; Mathur, Maya; Desai, Manisha; Farrington, Carl; Radin, Andrew A; Sirota, Marina; Kenkare, Pragati; Thompson, Caroline A; Yu, Peter P; Gomez, Scarlett L; Sledge, George W; Kurian, Allison W; Shah, Nigam H

    2017-05-01

    Using electronic health records (EHRs) and biomolecular data, we sought to discover drug pairs with synergistic repurposing potential. EHRs provide real-world treatment and outcome patterns, while complementary biomolecular data, including disease-specific gene expression and drug-protein interactions, provide mechanistic understanding. We applied Group Lasso INTERaction NETwork (glinternet), an overlap group lasso penalty on a logistic regression model, with pairwise interactions to identify variables and interacting drug pairs associated with reduced 5-year mortality using EHRs of 9945 breast cancer patients. We identified differentially expressed genes from 14 case-control human breast cancer gene expression datasets and integrated them with drug-protein networks. Drugs in the network were scored according to their association with breast cancer individually or in pairs. Lastly, we determined whether synergistic drug pairs found in the EHRs were enriched among synergistic drug pairs from gene-expression data using a method similar to gene set enrichment analysis. From EHRs, we discovered 3 drug-class pairs associated with lower mortality: anti-inflammatories and hormone antagonists, anti-inflammatories and lipid modifiers, and lipid modifiers and obstructive airway drugs. The first 2 pairs were also enriched among pairs discovered using gene expression data and are supported by molecular interactions in drug-protein networks and preclinical and epidemiologic evidence. This is a proof-of-concept study demonstrating that a combination of complementary data sources, such as EHRs and gene expression, can corroborate discoveries and provide mechanistic insight into drug synergism for repurposing.

  7. A robust identity-by-descent procedure using affected sib pairs: multipoint mapping for complex diseases.

    Science.gov (United States)

    Liang, K Y; Chiu, Y F; Beaty, T H

    2001-01-01

    Multipoint linkage analysis is a powerful tool to localize susceptibility genes for complex diseases. However, the conventional lod score method relies critically on the correct specification of mode of inheritance for accurate estimation of gene position. On the other hand, allele-sharing methods, as currently practiced, are designed to test the null hypothesis of no linkage rather than estimate the location of the susceptibility gene(s). In this paper, we propose an identity-by-descent (IBD)-based procedure to estimate the location of an unobserved susceptibility gene within a chromosomal region framed by multiple markers. Here we deal with the practical situation where some of the markers might not be fully informative. Rather the IBD statistic at an arbitrary within the region is imputed using the multipoint marker information. The method is robust in that no assumption about the genetic mechanism is required other than that the region contains no more than one susceptibility gene. In particular, this approach builds upon a simple representation for the expected IBD at any arbitrary locus within the region using data from affected sib pairs. With this representation, one can carry out a parametric inference procedure to locate an unobserved susceptibility gene. In addition, here we derive a sample size formula for the number of affected sib pairs needed to detect linkage with multiple markers. Throughout, the proposed method is illustrated through simulated data. We have implemented this method including exploratory and formal model-fitting procedures to locate susceptibility genes, plus sample size and power calculations in a program, GENEFINDER, which will be made available shortly. Copyright 2000 S. Karger AG, Basel.

  8. Transcriptional regulation and spatial interactions of head-to-head genes.

    Science.gov (United States)

    Chen, Yunqin; Li, Yixue; Wei, Jia; Li, Yuan-Yuan

    2014-06-24

    In eukaryotic genomes, about 10% of genes are arranged in a head-to-head (H2H) orientation, and the distance between the transcription start sites of each gene pair is closer than 1 kb. Two genes in an H2H pair are prone to co-express and co-function. There have been many studies on bidirectional promoters. However, the mechanism by which H2H genes are regulated at the transcriptional level still needs further clarification, especially with regard to the co-regulation of H2H pairs. In this study, we first used the Hi-C data of chromatin linkages to identify spatially interacting H2H pairs, and then integrated ChIP-seq data to compare H2H gene pairs with and without evidence of spatial interactions in terms of their binding transcription factors (TFs). Using ChIP-seq and DNase-seq data, histones and DNase associated with H2H pairs were identified. Furthermore, we looked into the connections between H2H genes in a human co-expression network. We found that i) Similar to the behaviour of two genes within an H2H pair (intra-H2H pair), a gene pair involving two distinct H2H pairs (inter-H2H pair) which interact with each other spatially, share common transcription factors (TFs); ii) TFs of intra- and inter-H2H pairs are distributed differently. Factors such as HEY1, GABP, Sin3Ak-20, POL2, E2F6, and c-MYC are essential for the bidirectional transcription of intra-H2H pairs; while factors like CTCF, BDP1, GATA2, RAD21, and POL3 play important roles in coherently regulating inter-H2H pairs; iii) H2H gene blocks are enriched with hypersensitive DNase and modified histones, which participate in active transcriptions; and iv) H2H genes tend to be highly connected compared with non-H2H genes in the human co-expression network. Our findings shed new light on the mechanism of the transcriptional regulation of H2H genes through their linear and spatial interactions. For intra-H2H gene pairs, transcription factors regulate their transcriptions through bidirectional promoters

  9. An efficiently extended class of unnatural base pairs.

    Science.gov (United States)

    Leconte, Aaron M; Matsuda, Shigeo; Romesberg, Floyd E

    2006-05-31

    A third DNA base pair, which is synthesized efficiently and selectively, would have wide ranging applications from synthetic organisms to nucleic acids biotechnology. Hydrophobic unnatural nucleobases offer a promising route to such a pair, but are often limited by inefficient extension, defined as synthesis immediately following the unnatural pair. Here, we describe a simple screen which enables the characterization of large numbers of previously uncharacterized hetero base pairs. From this screen, we identified a class of unnatural base pairs which are extended more efficiently than any unnatural base pair reported to date. Screening, when complemented by further kinetic analysis, can improve the understanding of the determinants of efficient extension as well as identify viable hetero base pairs.

  10. Les livres pairs d’Alfred Jarry

    Directory of Open Access Journals (Sweden)

    Julien Schuh

    2008-10-01

    Full Text Available Dans les Gestes et opinions du Dr Faustroll, pataphysicien, Alfred Jarry décrit une bibliothèque idéale, composée de 27 ouvrages qu’il nomme mystérieusement des « livres pairs ». Dans cette liste, on trouve aussi bien des œuvres canoniques du symbolisme (Mallarmé, Verlaine, Poe traduit par Baudelaire, des titres des amis de Jarry et des piliers des revues de l’époque (Rachilde, Gustave Kahn, Léon Bloy, que des ouvrages que l’on assimile davantage aux lectures enfantines (un conte de Marceline Desbordes-Valmore, les Mille et une Nuits, le théâtre de Florian ou des textes hors-catégorie (l’œuvre de Rabelais, l’évangile de Luc, les Chants de Maldoror. Beaucoup de critiques se sont interrogés sur la notion de « parité », sur l’égalité supposée entre ces ouvrages n’appartenant pas aux mêmes catégories littéraires. Mais l’intérêt de cette liste n’est pas de fournir un classement, ou d’affirmer l’équivalence de toutes les formes textuelles, comme on l’analyse souvent, en faisant de Jarry un chantre du nihilisme qui chercherait à pervertir les hiérarchies littéraires pour montrer la vacuité du sens. Au contraire, en faisant débuter le Faustroll par une liste d’ouvrages, Jarry met en place les conditions de réception de son texte, dans une posture très littéraire. L’espace délimité par la liste des auteurs pairs fonctionne comme un portrait spirituel de Jarry-littérateur, et livre le contexte selon lequel son discours doit être reçu. La bibliothèque du Dr Faustroll fixe les références que le lecteur pourra voir convoquer dans le texte, et circonscrit l’espace littéraire dans lequel peut fonctionner cet ouvrage.

  11. PairWise Neighbours database: overlaps and spacers among prokaryote genomes

    Directory of Open Access Journals (Sweden)

    Garcia-Vallvé Santiago

    2009-06-01

    Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

  12. Heterologous microsatellite primer pairs informative for the whole genus Arachis

    Directory of Open Access Journals (Sweden)

    Andrea Akemi Hoshino

    2006-01-01

    Full Text Available The genus Arachis currently comprises 69 described species, some of which have potential and real value as human and animal foods. These Arachis species have been collected and maintained in germplasm banks to provide material that can be used as sources of genes in breeding programs and for the selection of new cultivars. One of the principal objectives of germplasm conservation is the evaluation of genetic variability, which is best conducted using molecular markers. We investigated the use of heterologous primers to amplify microsatellite loci that could be used to evaluate genetic variability in Arachis germplasm. Fifteen microsatellite primer pairs were tested in 76 accessions of 34 species from the nine Arachis sections. The data indicated that heterologous primers were very useful in Arachis since they had high transferability among the species (91% and allowed the amplification of very polymorphic putative loci, which allowed both the characterization of most accessions and to make inferences about the mating systems of some species analyzed. Our data also revealed that the germplasm analyzed showed high variability, even when represented by few accessions.

  13. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    DEFF Research Database (Denmark)

    van Beest, M; Dooijes, D; van De Wetering, M

    2000-01-01

    , 12, and 10 base pairs, respectively. Footprinting with a deletion mutant of Ste11 reveals a novel interaction between the 3' base pairs of the extended DNA motif and amino acids C-terminal to the HMG domain. The sequence-specific interaction of Ste11 with these 3' base pairs contributes significantly......Sequence-specific high mobility group (HMG) box factors bind and bend DNA via interactions in the minor groove. Three-dimensional NMR analyses have provided the structural basis for this interaction. The cognate HMG domain DNA motif is generally believed to span 6-8 bases. However, alignment...... of promoter elements controlled by the yeast genes ste11 and Rox1 has indicated strict conservation of a larger DNA motif. By site selection, we identify a highly specific 12-base pair motif for Ste11, AGAACAAAGAAA. Similarly, we show that Tcf1, MatMc, and Sox4 bind unique, highly specific DNA motifs of 12...

  14. Fermion pairing in Bose-Fermi mixtures

    Science.gov (United States)

    Matera, F.

    2003-10-01

    An effective interaction between fermions in a Bose-Fermi mixture is derived. It is induced by density fluctuations of the bosonic background. The contributions from states containing both one and two virtual phonons are taken into account self-consistently. The time dependence of the effective interaction has been removed by assuming that the velocity of the fermions at the Fermi surface is much larger than the sound velocity in the Bose gas. This assumption is more appropriate for the actual experimental situations than the usual approximation of neglecting retardation effects. The effective interaction turns out to be attractive and, as a consequence, can give rise to a superconducting phase in the Fermi component of the mixture. The fermions are considered in only one magnetic state, so that pairing can be effective only in odd-l channels. It has been found that the onset of the superconducting phase can occur at temperatures (>100 nK) of the same order of magnitude as the Fermi temperature (˜300 nK), and the energy gap in the excitation spectrum is a small fraction (˜1%) of the Fermi energy.

  15. Spin- and Pair-Density-Wave Glasses

    Science.gov (United States)

    Mross, David F.; Senthil, T.

    2015-07-01

    Spontaneous breaking of translational symmetry, known as density-wave order, is common in nature. However, such states are strongly sensitive to impurities or other forms of frozen disorder leading to fascinating glassy phenomena. We analyze impurity effects on a particularly ubiquitous form of broken translation symmetry in solids: a spin-density wave (SDW) with spatially modulated magnetic order. Related phenomena occur in pair-density-wave (PDW) superconductors where the superconducting order is spatially modulated. For weak disorder, we find that the SDW or PDW order can generically give way to a SDW or PDW glass—new phases of matter with a number of striking properties, which we introduce and characterize here. In particular, they exhibit an interesting combination of conventional (symmetry-breaking) and spin-glass (Edwards-Anderson) order. This is reflected in the dynamic response of such a system, which—as expected for a glass—is extremely slow in certain variables, but, surprisingly, is fast in others. Our results apply to all uniaxial metallic SDW systems where the ordering vector is incommensurate with the crystalline lattice. In addition, the possibility of a PDW glass has important consequences for some recent theoretical and experimental work on La2 -xBaxCu2O4 .

  16. Transgenic Arabidopsis Gene Expression System

    Science.gov (United States)

    Ferl, Robert; Paul, Anna-Lisa

    2009-01-01

    The Transgenic Arabidopsis Gene Expression System (TAGES) investigation is one in a pair of investigations that use the Advanced Biological Research System (ABRS) facility. TAGES uses Arabidopsis thaliana, thale cress, with sensor promoter-reporter gene constructs that render the plants as biomonitors (an organism used to determine the quality of the surrounding environment) of their environment using real-time nondestructive Green Fluorescent Protein (GFP) imagery and traditional postflight analyses.

  17. Adaptive value of same-sex pairing in Laysan albatross.

    Science.gov (United States)

    Young, Lindsay C; VanderWerf, Eric A

    2014-01-22

    Same-sex pairing is widespread among animals but is difficult to explain in an evolutionary context because it does not result in reproduction, and thus same-sex behaviour often is viewed as maladaptive. Here, we compare survival, fecundity and transition probabilities of female Laysan albatross in different pair types, and we show how female-female pairing could be an adaptive alternative mating strategy, albeit one that resulted in lower fitness than male-female pairing. Females in same-sex pairs produced 80% fewer chicks, had lower survival and skipped breeding more often than those in male-female pairs. Females in same-sex pairs that raised a chick sometimes acquired a male mate in the following year, but females in failed same-sex pairs never did, suggesting that males exert sexual selection by assessing female quality and relegating low-quality females into same-sex pairs. Sexual selection by males in a monomorphic, non-ornamented species is rare and suggests that reconsideration is needed of the circumstances in which alternative reproductive behaviour evolves. Given the lack of males and obligate biparental care in this species, this research demonstrates how same-sex pairing was better than not breeding and highlights how it could be an adaptive strategy under certain demographic conditions.

  18. Observing Pair-Work Task in an English Speaking Class

    Directory of Open Access Journals (Sweden)

    Diana Achmad

    2014-01-01

    Full Text Available This paper reports on students’ pair-work interactions to develop their speaking skills in an ELT classroom which consisted of international learners. A number of 16 learners of intermediate proficiency with IELTS score band 5.5 were observed. The teacher had paired those he considered among them to be the more competent ones (hereafter, stronger with the less competent ones (hereafter, weaker; therefore, eight pairs were observed during the lesson. The task given to the students was to express ‘Agree and Disagree’ in the context of giving opinions related to social life. Based on the observations, the task was successfully implemented by six pairs; thus, the two others faced some problems. From the first pair, it was seen that the stronger student had intimated the weaker one into speaking during the task. The other pair, who was both of the same native, did not converse in English as expected and mostly used their native language to speak with one another presumably due to respect from the stronger student towards the weaker one. In situations like this, when pair-work becomes unproductive, rotating pairs is recommended to strengthen information sharing and assigning roles to avoid a student from taking over the activity from his or her pair. In conclusion, pairing international learners with mixed speaking proficiency by teachers must be conducted as effectively as possible by initially identifying their ability and learning culture to profoundly expand the students’ language resources.

  19. Identification of a two base pair deletion in five unrelated families with adrenoleukodystrophy: a possible hot spot for mutations

    NARCIS (Netherlands)

    Kemp, S.; Ligtenberg, M. J.; van Geel, B. M.; Barth, P. G.; Wolterman, R. A.; Schoute, F.; Sarde, C. O.; Mandel, J. L.; van Oost, B. A.; Bolhuis, P. A.

    1994-01-01

    The gene for X-linked adrenoleukodystrophy (ALD) was recently identified. Intragenic deletions of several kilobases were found in about 7% of patients. Point mutations, expected to be very heterogeneous, were identified so far in only two patients. We report the identification of a two base pair

  20. Molecular design of the C alpha beta interface favors specific pairing of introduced TCR alpha beta in human T cells

    NARCIS (Netherlands)

    Voss, Ralf-Holger; Willemsen, Ralph A.; Kuball, Juergen; Grabowski, Margarete; Engel, Renate; Intan, Ratna S.; Guillaume, Philippe; Romero, Pedro; Huber, Christoph; Theobald, Matthias

    2008-01-01

    A promising approach to adoptive transfer therapy of tumors is to reprogram autologous T lymphocytes by TCR gene transfer of defined Ag specificity. An obstacle, however, is the undesired pairing of introduced TCR alpha- and TCR beta-chains with the endogenous TCR chains. These events vary depending

  1. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies.

    Science.gov (United States)

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie

    2012-12-18

    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  2. Pulsar Pair Cascades in Magnetic Fields with Offset Polar Caps

    Science.gov (United States)

    Harding, Alice K.; Muslimov, Alex G.

    2012-01-01

    Neutron star magnetic fields may have polar caps (PC) that are offset from the dipole axis, through field-line sweepback near the light cylinder or non-symmetric currents within the star. The effects of such offsets on electron-positron pair cascades are investigated, using simple models of dipole magnetic fields with small distortions that shift the PCs by different amounts or directions. Using a Monte Carlo pair cascade simulation, we explore the changes in the pair spectrum, multiplicity and energy flux across the PC, as well as the trends in pair flux and pair energy flux with spin-down luminosity, L(sub sd). We also give an estimate of the distribution of heating flux from returning positrons on the PC for different offsets. We find that even modest offsets can produce significant increases in pair multiplicity, especially for pulsars that are near or beyond the pair death lines for centered PCs, primarily because of higher accelerating fields. Pair spectra cover several decades in energy, with the spectral range of millisecond pulsars (MSPs) two orders of magnitude higher than for normal pulsars, and PC offsets allow significant extension of all spectra to lower pair energies. We find that the total PC pair luminosity L(sub pair) is proportional to L(sub sd), with L(sub pair) approximates 10(exp -3) L(sub sd) for normal pulsars and L(sub pair) approximates 10(exp -2) L(sub sd) for MSPs. Remarkably, the total PC heating luminosity for even large offsets increases by less than a factor of two, even though the PC area increases by much larger factors, because most of the heating occurs near the magnetic axis.

  3. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue.

    Science.gov (United States)

    Geybels, Milan S; Zhao, Shanshan; Wong, Chao-Jen; Bibikova, Marina; Klotzle, Brandy; Wu, Michael; Ostrander, Elaine A; Fan, Jian-Bing; Feng, Ziding; Stanford, Janet L

    2015-12-01

    Aberrant DNA methylation may promote prostate carcinogenesis. We investigated epigenome-wide DNA methylation profiles in prostate cancer (PCa) compared to adjacent benign tissue to identify differentially methylated CpG sites. The study included paired PCa and adjacent benign tissue samples from 20 radical prostatectomy patients. Epigenetic profiling was done using the Infinium HumanMethylation450 BeadChip. Linear models that accounted for the paired study design and False Discovery Rate Q-values were used to evaluate differential CpG methylation. mRNA expression levels of the genes with the most differentially methylated CpG sites were analyzed. In total, 2,040 differentially methylated CpG sites were identified in PCa versus adjacent benign tissue (Q-value < 0.001), the majority of which were hypermethylated (n = 1,946; 95%). DNA methylation profiles accurately distinguished between PCa and benign tissue samples. Twenty-seven top-ranked hypermethylated CpGs had a mean methylation difference of at least 40% between tissue types, which included 25 CpGs in 17 genes. Furthermore, for 10 genes over 50% of promoter region CpGs were hypermethylated in PCa versus benign tissue. The top-ranked differentially methylated genes included three genes that were associated with both promoter hypermethylation and reduced gene expression: SCGB3A1, HIF3A, and AOX1. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. This study of PCa versus adjacent benign tissue showed many differentially methylated CpGs and regions in and outside gene promoter regions, which may potentially be used for the development of future epigenetic-based diagnostic tests or as therapeutic targets. © 2015 Wiley Periodicals, Inc.

  4. Codon usage and amino acid usage influence genes expression level.

    Science.gov (United States)

    Paul, Prosenjit; Malakar, Arup Kumar; Chakraborty, Supriyo

    2018-02-01

    Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

  5. PLANNING IN ARTIFICIAL INTELLIGENCE AND ROBOTICS (PAIR

    Directory of Open Access Journals (Sweden)

    Editorial, Foreword

    2016-11-01

    Full Text Available September 18th, 2016Deggendorf, Germanyhttp://robotics.fel.cvut.cz/pair16/Organized by: Artificial Intelligence Center Department of Computer Science Faculty of Electrical Engineering Czech Technical University in PragueTechnicka 2, Prague 6, 166 27, Czech RepublicGuest editors:Jan Faigl (Artificial Intelligence Center, Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in PragueJiří Vokřínek (Artificial Intelligence Center, Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in PragueScientific comittee:D. Belter (Poznań University of Technology, PolandW. Dorner (Technische Hochschule Deggendorf, GermanyJ. Faigl (Czech Technical University in PragueT. Krajník (University of Lincoln, United KingdomA. Komenda (Czech Technical University in PragueG. Kupris (Technische Hochschule Deggendorf, GermanyM. Rollo (Czech Technical University in PragueM. Saska (Czech Technical University in PragueJ. Vokřínek (Czech Technical University in PragueV. Vonásek (Czech Technical University in PragueK. Walas (Poznań University of Technology, Poland Foreword:The third year of the student conference on “Planning in Artificial Intelligence and Robotics” (PAIR continues in joining young researchers and students interested in robotics and artificial intelligence. In 2016, we follow the schema of the last year as a joint event with the RoboTour competition in Deggendorf, Germany. Thanks to the great collaboration with Gerald Kupris and Wolfgang Donner from Technische Hochschule Deggendorf and support from Czech Technical University under project No. SVK 26/16/F3 and Bayerisches Staatsministerium der Finanzen, für Landesentwicklung und Heimat, we have been able to provide accommodations and travel support to participants and an invited speaker. Fourteen papers have accepted and listed in the conference program. The papers have been authored by students from Central Europe

  6. Stereo Pair, Salt Lake City, Utah

    Science.gov (United States)

    2002-01-01

    The 2002 Winter Olympics are hosted by Salt Lake City at several venues within the city, in nearby cities, and within the adjacent Wasatch Mountains. This image pair provides a stereoscopic map view of north central Utah that includes all of these Olympic sites. In the south, next to Utah Lake, Provo hosts the ice hockey competition. In the north, northeast of the Great Salt Lake, Ogden hosts curling and the nearby Snowbasin ski area hosts the downhill events. In between, southeast of the Great Salt Lake, Salt Lake City hosts the Olympic Village and the various skating events. Further east, across the Wasatch Mountains, the Park City ski resort hosts the bobsled, ski jumping, and snowboarding events. The Winter Olympics are always hosted in mountainous terrain. This view shows the dramatic landscape that makes the Salt Lake City region a world-class center for winter sports.This stereoscopic image was generated by draping a Landsat satellite image over a Shuttle Radar Topography Mission digital elevation model. Two differing perspectives were then calculated, one for each eye. They can be seen in 3-D by viewing the left image with the right eye and the right image with the left eye (cross-eyed viewing or by downloading and printing the image pair and viewing them with a stereoscope. When stereoscopically merged, the result is a vertically exaggerated view of Earth's surface in its full three dimensions.Landsat has been providing visible and infrared views of the Earth since 1972. SRTM elevation data matches the 30-meter (98-foot) resolution of most Landsat images and will substantially help in analyzing the large and growing Landsat image archive, managed by the U.S. Geological Survey (USGS).Elevation data used in this image was acquired by the Shuttle Radar Topography Mission (SRTM) aboard the Space Shuttle Endeavour, launched on Feb. 11, 2000. SRTM used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR

  7. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing.

    Science.gov (United States)

    Li, Sanshu; Breaker, Ronald R

    2013-03-01

    Thiamin pyrophosphate (TPP) riboswitches are found in organisms from all three domains of life. Examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic TPP riboswitches are predicted to regulate gene expression by modulating RNA splicing. Given the widespread distribution of eukaryotic TPP riboswitches and the diversity of their locations in precursor messenger RNAs (pre-mRNAs), we sought to examine the mechanism of alternative splicing regulation by a fungal TPP riboswitch from Neurospora crassa, which is mostly located in a large intron separating protein-coding exons. Our data reveal that this riboswitch uses a long-distance (∼530-nt separation) base-pairing interaction to regulate alternative splicing. Specifically, a portion of the TPP-binding aptamer can form a base-paired structure with a conserved sequence element (α) located near a 5' splice site, which greatly increases use of this 5' splice site and promotes gene expression. Comparative sequence analyses indicate that many fungal species carry a TPP riboswitch with similar intron architecture, and therefore the homologous genes in these fungi are likely to use the same mechanism. Our findings expand the scope of genetic control mechanisms relying on long-range RNA interactions to include riboswitches.

  8. An mre11 mutant of Coprinus cinereus has defects in meiotic chromosome pairing, condensation and synapsis.

    Science.gov (United States)

    Gerecke, E E; Zolan, M E

    2000-01-01

    The rad11 gene of the basidiomycete Coprinus cinereus is required for the completion of meiosis and for survival after gamma irradiation. We have cloned the rad11 gene and shown that it is a homolog of MRE11, a gene required for meiosis and DNA repair in numerous organisms. The expression of C. cinereus mre11 is induced during prophase I of meiosis and following gamma irradiation. The gene encodes a predicted polypeptide of 731 amino acids, and the mre11-1 (rad11-1) mutation is a single base pair change that results in a stop codon after amino acid 315. The mre11-1 mutant shows enhanced sensitivity to ionizing radiation, but no enhanced sensitivity to UV radiation. It shows a delay in fruitbody formation and a reduction in the number of mushrooms formed per dikaryon. The mre11-1 mutant also has several meiotic defects. Pachytene chromatin condensation is disrupted, and although some meiotic cells appear to achieve metaphase I condensation, no further meiotic progression is observed. The mre11-1 mutant also fails to undergo proper chromosome synapsis; neither axial elements nor mature synaptonemal complexes are complete. Finally, meiotic homolog pairing is reduced in the mre11-1 mutant. Thus, in C. cinereus, Mre11 is required for meiotic DNA metabolism. PMID:10757758

  9. Probing photospheric magnetic fields with new spectral line pairs

    Science.gov (United States)

    Smitha, H. N.; Solanki, S. K.

    2017-12-01

    Context. The magnetic line ratio (MLR) method has been extensively used in the measurement of photospheric magnetic field strength. It was devised for the neutral iron line pair at 5247.1 Å and 5250.2 Å (5250 Å pair). Other line pairs as well-suited as this pair have not been reported in the literature. Aims: The aim of the present work is to identify new line pairs useful for the MLR technique and to test their reliability. Methods: We used a three-dimensional magnetohydrodynamic 3D MHD simulation representing the quiet Sun atmosphere to synthesize the Stokes profiles. Then, we applied the MLR technique to the Stokes V profiles to recover the fields in the MHD cube both at original resolution and after degrading with a point spread function. In both these cases, we aim to empirically represent the field strengths returned by the MLR method in terms of the field strengths in the MHD cube. Results: We have identified two new line pairs that are very well adapted to be used for MLR measurements. The first pair is in the visible, Fe I 6820-6842 Å, whose intensity profiles have previously been used to measure stellar magnetic fields, and the other pair is in the infrared (IR), Fe I 15 534-15 542 Å. The lines in these pairs reproduce the magnetic fields in the MHD cube rather well and, in fact, somewhat better than the original 5250 Å pair. Conclusions: The newly identified line pairs complement the old pairs. The lines in the new IR pair, because of their higher Zeeman sensitivity, are ideal for the measurement of weak fields. The new visible pair works best above 300 G. The new IR pair, due to its large Stokes V signal samples more fields in the MHD cube than the old IR pair at 1.56 μm, even in the presence of noise, and hence likely also on the real Sun. Owing to their low formation heights (100-200 km above τ5000 = 1), both the new line pairs are well suited for probing magnetic fields in the lower photosphere.

  10. Paired Straight Hearth Furnace - Transformational Ironmaking Process

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Wei-Kao [McMaster Univ., Hamilton, ON (Canada); Debski, Paul [Andritz Metals Inc.,Canonsburg, PA (United States)

    2014-11-19

    The U. S. steel industry has reduced its energy intensity per ton of steel shipped by 33% since 1990. However, further significant gains in energy efficiency will require the development of new, transformational iron and steelmaking processes. The Paired Straight Hearth Furnace (PSH) process is an emerging alternative high productivity, direct reduced iron (DRI) technology that may achieve very low fuel rates and has the potential to replace blast furnace ironmaking. The PSH furnace can operate independently or may be coupled with other melting technologies to produce liquid hot metal that is both similar to blast furnace iron and suitable as a feedstock for basic oxygen steelmaking furnaces. The PSH process uses non-metallurgical coal as a reductant to convert iron oxides such as iron ore and steelmaking by-product oxides to DRI pellets. In this process, a multi-layer, nominally 120mm tall bed of composite “green balls” made from oxide, coal and binder is built up and contained within a moving refractory hearth. The pellet bed absorbs radiant heat energy during exposure to the high temperature interior refractory surfaces of the PSH while generating a strongly reducing gas atmosphere in the bed that yields a highly metalized DRI product. The PSH concept has been well tested in static hearth experiments. A moving bed design is being developed. The process developers believe that if successful, the PSH process has the potential to replace blast furnaces and coke ovens at a fraction of the operating and capital cost while using about 30% less energy relative to current blast furnace technology. DRI output could also feed electric arc furnaces (EAFs) by displacing a portion of the scrap charge.

  11. Genome-Wide Analysis and Evolution of the Pto-Like Protein Kinase (PLPK) Gene Family in Pepper.

    Science.gov (United States)

    Venkatesh, Jelli; Jahn, Molly; Kang, Byoung-Cheorl

    2016-01-01

    The tomato Pto gene, which encodes a serine/threonine kinase (STK) domain-containing protein, confers resistance to bacterial speck disease caused by Pseudomonas syringae pv. tomato (Pst). In this study, in vivo recognition assays using PVX constructs showed that AvrPto was specifically recognized in the pepper genotypes. This AvrPto recognition caused a nonhost hypersensitive response (HR) and localization of the PVX::AvrPto fusion protein to inoculated pepper leaf tissues, which indicates the presence of a similar Pto recognition mechanism in pepper as in tomato. However, genome-wide analysis in pepper revealed no Pto clade corresponding to that in tomato, suggesting an alternative system for Pto recognition in pepper. Nevertheless, 25 Pto-like protein kinases (PLPKs) with a highly conserved STK domain have been identified in the pepper genome. For the majority of the amino acid sites in the STK domain of Ptos and PLPKs, nonsynonymous (dN) to synonymous (dS) nucleotide substitution ratios (ω) were less than one, suggesting that purifying selection played a predominant role in the evolutionary process. However, some amino acid sites were found to be subjected to episodic positive selection in the course of evolution of Pto homologs, and, thus, different evolutionary processes might have shaped the Pto gene family in plants. Based on RNA-seq data, PLPK genes and other Pto pathway genes, such as Prf, Pti1, Pti5, and Pti6 were expressed in all tested pepper genotypes. Therefore, the nonhost HR against Pst in pepper may be due to the recognition of the AvrPto effector by a PLPK homolog, and subsequent action of downstream components of the Pto signaling pathway. However, the possibility remains that the recognition of AvrPto in pepper plants may involve activities of other receptor like kinases (RLKs). The identification of the PLPKs in this study will serve as a foundation for further efforts to understand the roles of PLPKs in nonhost resistance.

  12. Analysis of food pairing in regional cuisines of India

    CERN Document Server

    Jain, Anupam; Bagler, Ganesh

    2015-01-01

    Any national cuisine is a sum total of its variety of regional cuisines, which are the cultural and historical identifiers of their respective regions. India is home to a number of regional cuisines that showcase its culinary diversity. Here, we study recipes from eight different regional cuisines of India spanning various geographies and climates. We investigate the phenomenon of food pairing which examines compatibility of two ingredients in a recipe in terms of their shared flavor compounds. Food pairing was enumerated at the level of cuisine, recipes as well as ingredient pairs by quantifying flavor sharing between pairs of ingredients. Our results indicate that each regional cuisine follows negative food pairing pattern; more the extent of flavor sharing between two ingredients, lesser their co-occurrence in that cuisine. We find that frequency of ingredient usage is central in rendering the characteristic food pairing in each of these cuisines. Spice and dairy emerged as the most significant ingredient ...

  13. Enhanced scanning agility using a double pair of Risley prisms.

    Science.gov (United States)

    Roy, Gilles; Cao, Xiaoying; Bernier, Robert; Roy, Simon

    2015-12-01

    Scanners with one pair of Risley prisms are robust and precise and they can be operated continuously. In this paper, we present a new scanner based on the use of two pairs of Risley prisms. The concept was driven by the need to add flexibility to Risley prism scanners used for lidar 3D mapping applications, while maintaining compactness and robustness. The first pair covers a FOV narrower than the second pair. The second pair is used to position the first Risley pair scan pattern anywhere within its own, larger, FOV. Doing so, it becomes possible, without additional scanner components, to increase the sampling point density at a specific location, to increase the sampling uniformity of the scanned area, and, while in motion, to maintain the sampling of a specific area of interest.

  14. Watching the coherent birth of polaron pairs in conjugated polymers

    OpenAIRE

    De Sio, Antonietta; Troiani, Filippo; Maiuri, Margherita; Réhault, Julien; Sommer, Ephraim; Lim, James; Huelga, Susana F.; Plenio, Martin B.; Rozzi, Carlo Andrea; Cerullo, Giulio; Molinari, Elisa; Lienau, Christoph

    2016-01-01

    Organic semiconductors have the remarkable property that their optical excitation not only generates charge-neutral electron-hole pairs (excitons) but also charge-separated polaron pairs with high yield. The microscopic mechanisms underlying this charge separation have been debated for many years. Here we use ultrafast two-dimensional electronic spectroscopy to study the dynamics of polaron pair formation in a prototypical polymer thin film on a sub-20-fs time scale. We observe multi-period p...

  15. Chromosome pairing affinity and quadrivalent formation in polyploids: do segmental allopolyploids exist?

    Science.gov (United States)

    Sybenga, J

    1996-12-01

    When polyploid hybrids with closely related genomes are propagated by selfing or sib-breeding, the meiotic behaviour will turn into essentially autopolyploid behaviour as soon as the affinity between the genomes is sufficient to permit occasional homoeologous pairing. An allopolyploid will only be formed when the initial differentiation is sufficient to completely prevent homoeologous pairing (in some cases enhanced by specific genes), or when segregational dysgenesis prevents transmission of recombined chromosomes. A new polyploid hybrid may be considered a segmental allopolyploid and may show reduced multivalent formation as a result of preferential pairing between the least differentiated genomes. An established polyploid is either an autopolyploid or an allopolyploid. In exceptional cases it is thinkable that a stable segmental allopolyploid arises, in which some sets of chromosomes are well differentiated and behave as in an allopolyploid, whereas other sets are not well differentiated and behave as in an autopolyploid. No clear cases have been found in the literature so far. Key words : chromosome, pairing affinity, quadrivalent frequency, segmental allopolyploidy.

  16. ssDNA Pairing Accuracy Increases When Abasic Sites Divide Nucleotides into Small Groups.

    Directory of Open Access Journals (Sweden)

    Alexandra Peacock-Villada

    Full Text Available Accurate sequence dependent pairing of single-stranded DNA (ssDNA molecules plays an important role in gene chips, DNA origami, and polymerase chain reactions. In many assays accurate pairing depends on mismatched sequences melting at lower temperatures than matched sequences; however, for sequences longer than ~10 nucleotides, single mismatches and correct matches have melting temperature differences of less than 3°C. We demonstrate that appropriately grouping of 35 bases in ssDNA using abasic sites increases the difference between the melting temperature of correct bases and the melting temperature of mismatched base pairings. Importantly, in the presence of appropriately spaced abasic sites mismatches near one end of a long dsDNA destabilize the annealing at the other end much more effectively than in systems without the abasic sites, suggesting that the dsDNA melts more uniformly in the presence of appropriately spaced abasic sites. In sum, the presence of appropriately spaced abasic sites allows temperature to more accurately discriminate correct base pairings from incorrect ones.

  17. (DAD1) gene fragment of Chinese kale

    African Journals Online (AJOL)

    To clone the defective in anther dehiscence1 (DAD1) gene fragment of Chinese kale, about 700 bp product was obtained by PCR amplification using Chinese kale genomic DNA as the template and a pair of specific primers designed according to the conserved sequence of DAD1 genes of Arabidopsis thaliana and ...

  18. Genomics study of the exposure effect of Gymnodinium catenatum, a paralyzing toxin producer, on Crassostrea gigas' defense system and detoxification genes.

    Directory of Open Access Journals (Sweden)

    Norma García-Lagunas

    Full Text Available BACKGROUND: Crassostrea gigas accumulates paralytic shellfish toxins (PST associated with red tide species as Gymnodinium catenatum. Previous studies demonstrated bivalves show variable feeding responses to toxic algae at physiological level; recently, only one study has reported biochemical changes in the transcript level of the genes involved in C. gigas stress response. PRINCIPAL FINDINGS: We found that 24 h feeding on toxic dinoflagellate cells (acute exposure induced a significant decrease in clearance rate and expression level changes of the genes involved in antioxidant defense (copper/zinc superoxide dismutase, Cu/Zn-SOD, cell detoxification (glutathione S-transferase, GST and cytochrome P450, CPY450, intermediate immune response activation (lipopolysaccharide and beta glucan binding protein, LGBP, and stress responses (glutamine synthetase, GS in Pacific oysters compared to the effects with the non-toxic microalga Isochrysis galbana. A sub-chronic exposure feeding on toxic dinoflagellate cells for seven and fourteen days (30×10³ cells mL⁻¹ showed higher gene expression levels. A significant increase was observed in Cu/Zn-SOD, GST, and LGBP at day 7 and a major increase in GS and CPY450 at day 14. We also observed that oysters fed only with G. catenatum (3×10³ cells mL⁻¹ produced a significant increase on the transcription level than in a mixed diet (3×10³ cells mL⁻¹ of G. catenatum+0.75×10⁶ cells mL⁻¹ I. galbana in all the analyzed genes. CONCLUSIONS: Our results provide gene expression data of PST producer dinoflagellate G. catenatum toxic effects on C. gigas, a commercially important bivalve. Over expressed genes indicate the activation of a potent protective mechanism, whose response depends on both cell concentration and exposure time against these toxic microalgae. Given the importance of dinoflagellate blooms in coastal environments, these results provide a more comprehensive overview of how oysters respond to

  19. Conditional targeting of Ispd using paired Cas9 nickase and a single DNA template in mice

    Directory of Open Access Journals (Sweden)

    Angus Yiu-fai Lee

    2014-01-01

    Full Text Available CRISPR/Cas9 technology is a highly promising genome editing tool in the mouse, potentially overcoming the costs and time required for more traditional gene targeting methods in embryonic stem (ES cells. Recently, compared to the wildtype nuclease, paired Cas9 nickase (Cas9n combined with single guide RNA (sgRNA molecules has been found to enhance the specificity of genome editing while reducing off-target effects. Paired Cas9n has been shown to be as efficient as Cas9 for generating insertion and deletion (indel mutations by non-homologous end joining and targeted deletion in the genome. However, an efficient and reliable approach to the insertion of loxP sites flanking critical exon(s to create a conditional allele of a target gene remains an elusive goal. In this study, we microinjected Cas9n RNA with sgRNAs together with a single DNA template encoding two loxP sites flanking (floxing exon 2 of the isoprenoid synthase containing domain (Ispd into the pronucleus and cytoplasm of C57BL/6NCr one-cell stage zygotes. After surgical transfer, one F0 mouse expressing a conditional allele was produced (at a frequency of ∼8% of live pups born. The floxed allele was transmitted through the germline to F1 progeny, and could be successfully recombined using Cre recombinase. This study indicates that conditional targeting can be accomplished effectively using paired Cas9n and a single DNA template.

  20. [Prevalence of occult hepatitis B virus infection and its phylogenetic features among mother-teenager pairs].

    Science.gov (United States)

    Dong, Xiao-lian; Yao, Qing-qing; Wang, Xue-cai; Xu, Hai-tao; Wang, Xiao-li; Chen, Sheng-yu; Tang, Zhi-feng; Zheng, Ying-Jie

    2013-03-01

    Prevalence of occult hepatitis B virus (HBV) infection (OBI) was investigated in a paired mother-teenager population and HBV S gene variation including overt and occult HBV, was determined. A follow-up study based on an initial survey of 135 mother-teenager pairs was carried out through collection of questionnaires and blood samples HBsAg were detected by ELISA method, viral load by PCR amplification and HBV S gene by phylogenetic analysis. 102 pairs of subjects were followed-up. Blood samples from 94 mothers and 101 children were collected. OBI prevalence in mothers was 10.0% (6/60), significantly higher than 2.0% (2/101) in teenagers. Medians of viral load were 399.9 IU/ml and 247.6 IU/ml in overt and occult HBV strains, but without significant difference. 1 occult HBV strain belonged to genotype B with serotype adw while the other 7 were genotype C with serotype adr. 15 of the overt HBV strains belonged to genotype B with serotype adw and the other 8 were genotype C with serotype adr. Proportions of genotype-C strains were significantly higher in occult HBV strains than in overt HBV strains. OBI was seen in teenage-mother population.

  1. BPS: a database of RNA base-pair structures.

    Science.gov (United States)

    Xin, Yurong; Olson, Wilma K

    2009-01-01

    The BPS (http://bps.rutgers.edu) is a database of RNA base-pair structures, higher-order base interactions and isosteric pairs (base pairs with similar shape). The main functions of the BPS are to find and annotate the structural and chemical features of the Watson-Crick and non-Watson-Crick (noncanonical) base pairs in high-resolution RNA structures, and to provide a user-friendly interface to browse and search for the base pairs. The current database contains 91,265 bp and 3386 higher-order base interactions from 426 RNA crystal structures and 61,819 bp that fall into one of 17 different isosteric classes. The base-pair data can be accessed by searches of base-pair patterns, structure identifiers (IDs) and structural types. The BPS also includes an Atlas with representative images of the various base pairs, higher-order base interactions and isosteric pairs and links to statistical information about these groups of structures.

  2. Butterflyfishes as a System for Investigating Pair Bonding

    KAUST Repository

    Nowicki, Jessica

    2017-11-14

    For many animals, affiliative relationships such as pair bonds form the foundation of society, and are highly adaptive. Animal systems amenable for comparatively studying pair bonding are important for identifying underlying biological mechanisms, but mostly exist in mammals. Better establishing fish systems will enable comparison of pair bonding mechanisms across taxonomically distant lineages that may reveal general underlying principles. We examined the utility of wild butterflyfishes (f: Chaetodontidae; g: Chaetodon) for comparatively studying pair bonding. Stochastic character mapping inferred that within the family, pairing is ancestral, with at least seven independent transitions to group formation and seven transition to solitary behavior from the late Miocene to recent. In six sympatric and wide-spread species representing a clade with one ancestrally reconstructed transition from paired to solitary grouping, we then verified social systems at Lizard Island, Australia. In situ observations confirmed that Chaetodon baronessa, C. lunulatus, and C. vagabundus are predominantly pair bonding, whereas C. rainfordi, C. plebeius, and C. trifascialis are predominantly solitary. Even in the predominantly pair bonding species, C. lunulatus, a proportion of adults (15 %) are solitary. Importantly, inter- and intra-specific differences in social systems do not co-vary with other previously established attributes (geographic occurrence, parental care, diet, or territoriality). Hence, the proposed butterflyfish populations are promising for comparative analyses of pair bonding and its mechanistic underpinnings. Avenues for further developing the system are proposed, including determining whether the utility of these species applies across their geographic disruptions.

  3. Considerations on Velocities and Accelerations in Higher Pairs Mechanisms

    Directory of Open Access Journals (Sweden)

    Florina-Carmen Ciornei

    2015-12-01

    Full Text Available The paper proposes a method for finding the velocities and accelerations in the pairs from a mechanism with higher pairs in the case when the curvature radii of the curves achieving the higher pair are finite. There are obtained the characteristic equations of the motion in the higher pair for the case that one of the curves has zero curvature radius, condition characteristic to the knife edge follower. The relations are required to justify the difference between the particular cases of knife edge follower and flat face follower. The methodology is exemplified through an actual example.

  4. Mated Fingerprint Card Pairs (Volumes 1-5)

    Science.gov (United States)

    NIST Mated Fingerprint Card Pairs (Volumes 1-5) (Web, free access)   The NIST database of mated fingerprint card pairs (Special Database 9) consists of multiple volumes. Currently five volumes have been released. Each volume will be a 3-disk set with each CD-ROM containing 90 mated card pairs of segmented 8-bit gray scale fingerprint images (900 fingerprint image pairs per CD-ROM). A newer version of the compression/decompression software on the CDROM can be found at the website http://www.nist.gov/itl/iad/ig/nigos.cfm as part of the NBIS package.

  5. Communication: Improved pair approximations in local coupled-cluster methods

    Energy Technology Data Exchange (ETDEWEB)

    Schwilk, Max; Werner, Hans-Joachim [Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany); Usvyat, Denis [Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstrasse 31, D-93040 Regensburg (Germany)

    2015-03-28

    In local coupled cluster treatments the electron pairs can be classified according to the magnitude of their energy contributions or distances into strong, close, weak, and distant pairs. Different approximations are introduced for the latter three classes. In this communication, an improved simplified treatment of close and weak pairs is proposed, which is based on long-range cancellations of individually slowly decaying contributions in the amplitude equations. Benchmark calculations for correlation, reaction, and activation energies demonstrate that these approximations work extremely well, while pair approximations based on local second-order Møller-Plesset theory can lead to errors that are 1-2 orders of magnitude larger.

  6. The dynamics of galaxy pairs in a cosmological setting

    Science.gov (United States)

    Moreno, Jorge; Bluck, Asa F. L.; Ellison, Sara L.; Patton, David R.; Torrey, Paul; Moster, Benjamin P.

    2013-12-01

    We use the Millennium Simulation, and an abundance matching framework, to investigate the dynamical behaviour of galaxy pairs embedded in a cosmological context. Our main galaxy-pair sample, selected to have separations r ≤ 250 h-1 kpc, consists of over 1.3 million pairs at redshift z = 0, with stellar masses greater than 1010 M⊙, probing mass ratios down to 1:1000. We use dark matter halo membership and energy to classify our galaxy pairs. In terms of halo membership, central-satellite pairs tend to be in isolation (in relation to external more massive galaxies), are energetically bound to each other and are also weakly bound to a neighbouring massive galaxy. Satellite-satellite pairs, instead, inhabit regions in close proximity to a more massive galaxy, are energetically unbound and are often bound to that neighbour. We find that 60 per cent of our paired galaxies are bound to both their companion and to a third external object. Moreover, only 9 per cent of our pairs resemble the kind of systems described by idealized binary merger simulations in complete isolation. In sum, we demonstrate the importance of properly connecting galaxy pairs to the rest of the Universe.

  7. Behavioral correlates of extra-pair copulation in Indri indri.

    Science.gov (United States)

    Bonadonna, Giovanna; Torti, Valeria; Randrianarison, Rose Marie; Martinet, Nicole; Gamba, Marco; Giacoma, Cristina

    2014-01-01

    Active pursuit of extra-pair mating has been reported for Indri indri, the socially monogamous largest living lemur. This study, conducted in a mountain rainforest in eastern Madagascar, presents the first evidence for extra-pair mating of indri and discusses the alternative mating strategy and alteration of the social, territorial, spatial, and vocal behavior of the adult female of a group of wild indris. Further studies may investigate whether extra-pair copulation is an attempt to breed with a partner of superior quality and thus lead to extra-pair paternity. If so, it could potentially play a role in maintaining genetic variability within a population.

  8. Cooper-pair injection into quantum spin Hall insulators.

    Science.gov (United States)

    Sato, Koji; Loss, Daniel; Tserkovnyak, Yaroslav

    2010-11-26

    We theoretically study tunneling of Cooper pairs from a superconductor spanning a two-dimensional topological insulator strip into its helical edge states. The coherent low-energy electron-pair tunneling sets off positive current cross correlations along the edges, which reflect an interplay of two quantum-entanglement processes. Most importantly, superconducting spin pairing dictates a Cooper pair partitioning into the helical edge liquids, which transport electrons in opposite directions for opposite spin orientations. At the same time, Luttinger-liquid correlations fractionalize electrons injected at a given edge into counterpropagating charge pulses carrying definite fractions of the elementary electron charge.

  9. Excluded volume effect enhances the homology pairing of model chromosomes

    Science.gov (United States)

    Takamiya, Kazunori; Yamamoto, Keisuke; Isami, Shuhei; Nishimori, Hiraku; Awazu, Akinori

    To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We consider a simple model consist- ing of pairs of homologous polymers with the same structures that are confined in a cylindrical container, which represents the local parts of chromosomes contained in an elongated nucleus of S. pombe. Brownian dynamics simulations of this model showed that the excluded volume effects among non-homological chromosomes and the transitional dynamics of nuclear shape serve to enhance the pairing of homologous chromosomes.

  10. Newly identified paired box 6 mutation of variant familial aniridia: Congenital iris ectropion with foveal hypoplasia

    Directory of Open Access Journals (Sweden)

    Woo Jin Kim

    2017-01-01

    Full Text Available Congenital aniridia is a kind of eye disease characterized by complete or partial hypoplasia of the iris and is associated with other ocular anomalies including corneal opacity, glaucoma, and foveal hypoplasia. Heterozygous mutation of paired box 6 (PAX6 gene was identified in most cases of aniridia, with iatrogenic mutations accounting for about two-third of the cases and chromosomal rearrangements accounting for the other one-third. We report rare cases of variant aniridia, congenital iris ectropion associated with foveal hypoplasia in both a woman and her son with a mutation of PAX6 gene. To our knowledge, deletion c. 936delC in exon 8 of PAX6 gene has not been reported until now.

  11. Newly identified paired box 6 mutation of variant familial aniridia: Congenital iris ectropion with foveal hypoplasia.

    Science.gov (United States)

    Kim, Woo Jin; Kim, Jong Ha; Cho, Nam Chun

    2017-01-01

    Congenital aniridia is a kind of eye disease characterized by complete or partial hypoplasia of the iris and is associated with other ocular anomalies including corneal opacity, glaucoma, and foveal hypoplasia. Heterozygous mutation of paired box 6 (PAX6) gene was identified in most cases of aniridia, with iatrogenic mutations accounting for about two-third of the cases and chromosomal rearrangements accounting for the other one-third. We report rare cases of variant aniridia, congenital iris ectropion associated with foveal hypoplasia in both a woman and her son with a mutation of PAX6 gene. To our knowledge, deletion c. 936delC in exon 8 of PAX6 gene has not been reported until now.

  12. Derivative chromosome 1 and GLUT1 deficiency syndrome in a sibling pair

    Directory of Open Access Journals (Sweden)

    Akarsu Nurten

    2010-05-01

    Full Text Available Abstract Background Genomic imbalances constitute a major cause of congenital and developmental abnormalities. GLUT1 deficiency syndrome is caused by various de novo mutations in the facilitated human glucose transporter 1 gene (1p34.2 and patients with this syndrome have been diagnosed with hypoglycorrhachia, mental and developmental delay, microcephaly and seizures. Furthermore, 1q terminal deletions have been submitted in the recent reports and the absence of corpus callosum has been related to the deletion between C1orf100 and C1orf121 in 1q44. Results This study reports on a sibling pair with developmental delay, mental retardation, microcephaly, hypotonia, epilepsy, facial dysmorphism, ataxia and impaired speech. Chromosome analysis revealed a derivative chromosome 1 in both patients. FISH and MCB analysis showed two interstitial deletions at 1p34.2 and 1q44. SNP array and array-CGH analysis also determined the sizes of deletions detailed. The deleted region on 1p34.2 encompasses 33 genes, among which is GLUT1 gene (SLC2A1. However, the deleted region on 1q44 includes 59 genes and distal-proximal breakpoints were located in the ZNF672 gene and SMYD3 gene, respectively. Conclusion Haploinsufficiency of GLUT1 leads to GLUT1 deficiency syndrome, consistent with the phenotype in patients of this study. Conversely, in the deleted region on 1q44, none of the genes are related to findings in these patients. Additionally, the results confirm previous reports on that corpus callosal development may depend on the critical gene(s lying in 1q44 proximal to the SMYD3 gene.

  13. Gene Therapy

    Science.gov (United States)

    Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

  14. Sequence and functional conservation of the intergenic region between the head-to-head genes encoding the small heat shock proteins alphaB-crystallin and HspB2 in the mammalian lineage.

    NARCIS (Netherlands)

    Doerwald, L.; Rheede, T. van; Dirks, R.P.H.; Madsen, O.; Rexwinkel, R.; Genesen, S.T. van; Martens, G.J.M.; Jong, W.W.W. de; Lubsen, N.H.

    2004-01-01

    An unexpected feature of the large mammalian genome is the frequent occurrence of closely linked head-to-head gene pairs. Close apposition of such gene pairs has been suggested to be due to sharing of regulatory elements. We show here that the head-to-head gene pair encoding two small heat shock

  15. Peace Corps Gabon PST Technical Language: Math/Education.

    Science.gov (United States)

    Peace Corps, Washington, DC.

    A set of instructional materials on technical French for mathematics instruction is designed for Peace Corps volunteers teaching math in Gabon. The materials consist of six lessons on the use of French to teach and express mathematical concepts and procedures, and information about the Gabonese educational system, in English. The French lessons…

  16. Kaubamaja Lemon : Estonia pst. 1/3, Tallinn / Piret Lindpere

    Index Scriptorium Estoniae

    Lindpere, Piret, 1963-

    2003-01-01

    1953. a. projekteeritud ja 1958. a. valminud Eesti Energia peahoone (arhitektid P. Tarvas, U. Tölpus) ümberehitus Lemoni kaubamajaks (arhitekt Martin Aunin). 3.-5. korrusel paiknevad büroopinnad. Fassaadi täienduseks on projekteeritud mettallkonstruktsioonil punktkinnitusega eenduv klaasvitriin. 4 välis- ja 3 sisevaadet

  17. Kaubamaja "Lemon" - Arco Ärikeskus : Estonia pst. 1, Tallinn

    Index Scriptorium Estoniae

    2002-01-01

    1958. a. valminud hoone rekonstrueerimine. Projekteerija: EA Reng. Arhitekt Martin Aunin. Ehituskonstruktsioonid: Riho Märtson. Insenertehnilised osad: Karmo Pajo, Maarika Kurvits, Eha Treial. Valgusinstallatsioon: Meeli Kõiva. Kaupluste mööbel, kohtvalgustus: Priit Põldme, Ants Tolli, Ruth-Helene Kaasik, Hugo Mitt, Mart Vesker, Tarmo Piirmets. Projekt 2001, valmis 2002. I korruse põhiplaan, 4 vaadet

  18. Hoiupanga peahoone. Tallinn, Rävala pst. 5

    Index Scriptorium Estoniae

    1998-01-01

    Projekteerimise ajaloost: 1985. a. Tallinna Moemaja arhitektuurikonkurss ja 1988. a. RPIs "Eesti Tööstusprojekt" valmis ENSV Kergetööstuse Ministeeriumi Teaduslik-Tehnilise Keskuse ja Tallinna Moemaja I ehitusjärgu projekt (R. Kurvitz, U. Muru); !991. a. AS Astlanda ärikeskuse tellimusel krundi hoonestamiseks eskiisprojekt (J. Okas, M. Lõoke) ning alternatiivprojekt (T. Altosaar). Kvartali hoonestuskava: Arhitektuuribüroo Kalle Rõõmus. Projekteerijad: SRV OY, arhitekt Kari Mökkälä, Arhitektuuribüroo Kalle Rõõmus, arhitekt Kullervo Kliimand. Sisekujundus: ARS Interjöörprojekt, autorid Karolin Kõll, Eero Jürgenson, Martin Pärn. Projektijuht: SRV Teräsbetooni Oy. Ehituse peatöövõtt: Eesti Ehitus. Konstruktiivne osa: E - Inseneribüroo. Projekt 1995-97, valmis 1997. Täismonteeritav karkasssüsteemis 7-korruseline büroohoone

  19. Personality traits of pair members predict pair compatibility and reproductive success in a socially monogamous parrot breeding in captivity.

    Science.gov (United States)

    Fox, Rebecca A; Millam, James R

    2014-01-01

    While pair behavioral compatibility seems to be a determinant of reproductive success in at least some species of monogamous birds, the specific factors underlying among-pair variation in behavioral compatibility remain poorly understood. However, recent research on the relationship between personality traits and reproductive success in several species of socially monogamous birds suggests that the fit between mates' personality traits might play a role in determining behavioral compatibility. To test this hypothesis, we used ten pairs formed by free choice from a captive population of cockatiels (Nymphicus hollandicus) to investigate whether personality ratings could be used to predict pair compatibility and reproductive success in pairs breeding for the first time. We found that pairs that ultimately hatched eggs paired disassortatively for agreeableness (an aggregate measure of social style which measures birds' tendency to be aggressive vs. gentle, submissive, and tolerant of others' behavior), and, as predicted, showed lower intrapair aggression and better coordination during incubation. Conversely, unsuccessful pairs paired assortatively for agreeableness, showed higher levels of intrapair aggression, and showed poorer coordination during incubation. Our results suggest that personality measurements may provide a useful adjunct to other information currently used in selecting mates for birds breeding in captivity. © 2014 Wiley Periodicals, Inc.

  20. Differentially Methylated DNA Regions in Monozygotic Twin Pairs Discordant for Rheumatoid Arthritis

    DEFF Research Database (Denmark)

    Svendsen, Anders J; Gervin, Kristina; Lyle, Robert

    2016-01-01

    OBJECTIVES: In an explorative epigenome-wide association study (EWAS) to search for gene independent, differentially methylated DNA positions and regions (DMRs) associated with rheumatoid arthritis (RA) by studying monozygotic (MZ) twin pairs discordant for RA. METHODS: Genomic DNA was isolated...... from whole blood samples from 28 MZ twin pairs discordant for RA. DNA methylation was measured using the HumanMethylation450 BeadChips. Smoking, anti-cyclic citrullinated peptide antibodies, and immunosuppressive treatment were included as covariates. Pathway analysis was performed using GREAT. RESULTS......: We identified several differentially methylated regions associated with RA, which may represent environmental effects or consequences of the disease and plausible biological pathways pertinent to the pathogenesis of RA....

  1. HIM-8 binds to the X chromosome pairing center and mediateschromosome-specific meiotic synapsis

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, Carolyn M.; Wong, Chihunt; Bhalla, Needhi; Carlton,Peter M.; Weiser, Pinky; Meneely, Philip M.; Dernburg, Abby F.

    2005-06-05

    The him-8 gene is essential for proper meiotic segregationof the X chromosomes in C. elegans. Herewe show that loss of him-8function causes profound X-chromosome-specific defects in homolog pairingand synapsis.him-8 encodes a C2H2 zinc finger protein that is expressedduring meiosis andconcentrates at a site on the X chromosome known as themeiotic Pairing Center (PC). A role for HIM-8 in PC function is supportedby genetic interactions between PC lesions and him-8 mutations.HIM-8-bound chromosome sites associate with the nuclear envelope (NE)throughout meiotic prophase. Surprisingly, a point mutation in him-8 thatretains both chromosome binding and NE localization fails to stabilizepairing or promote synapsis. These observations indicate thatstabilization of homolog pairing is an active process in which thetethering of chromosome sites to the NE may be necessary but is notsufficient.

  2. AT Base Pair Anions vs. (9-methyl-A)(1-methyl-T) Base Pair Anions

    Energy Technology Data Exchange (ETDEWEB)

    Radisic, Dunja; Bowen, Kit H.; Dabkowska, Iwona; Storoniak, Piotr; Rak, Janusz; Gutowski, Maciej S.

    2005-05-04

    The anionic base pairs of adenine and thymine, (AT)-, and 9-methyladenine and 1-methylthymine, (MAMT)-, have been investigated both theoretically and experimentally in a complementary, synergistic study. Calculations on (AT)- found that it had undergone a barrier-free proton transfer (BFPT) similar to that seen in other dimer anion systems and that its structural configuration that was neither Watson-Crick (WC) nor Hoogsteen (HS). The vertical detachment energy (VDE) of (AT)- was determined by anion photoelectron spectroscopy and found to be in agreement with the VDE value predicted by theory for the BFPT mechanism. An AT pair in DNA is structurally immobilized into the WC configuration, in part, by being bonded to the sugars of the double helix. This circumstance was mimicked by methylating the sites on both A and T where these sugars would have been tied, viz., 9-methyladenine and 1-methylthymine. Calculations found no BFPT in (MAMT)- and a resulting (MAMT)- configuration that wa s either HS or WC, with the configurations differing in stability by ca. 2 kcal/mol. The photoelectron spectrum of (MAMT)- occurred at a completely different electron binding energy than had (AT)-. Moreover, the VDE value of (MAMT)- was in agreement with that predicted by theory. The configuration of (MAMT)- and its lack of electron-induced proton transfer are inter-related. While there may be other pathways for electron-induced damage, BFPT in the WC/HS configurations of (AT)- is not feasible.

  3. Stereo Pair: Basalt Cliffs, Patagonia, Argentina

    Science.gov (United States)

    2000-01-01

    Basalt cliffs along the northwest edge of the Meseta de Somuncura plateau near Sierra Colorada, Argentina show an unusual and striking pattern of erosion. Stereoscopic observation helps to clarify the landform changing processes active here. Many of the cliffs appear to be rock staircases that have the same color as the plateau's basaltic cap rock. Are these the edges of lower layers in the basalt or are they a train of slivers that are breaking off from, then sliding downslope and away from, the cap rock. They appear to be the latter. Close inspection shows that each stair step is too laterally irregular to be a continuous sheet of bedrock like the cap rock. Also, the steps are not flat but instead are little ridges, as one might expect from broken, tilted, and sliding slices of the cap rock. Stream erosion has cut some gullies into the cliffs and green vegetation shows that water springs from and flows down some channels, but landsliding is clearly a major agent of erosion here.This cross-eyed stereoscopic image pair was generated using topographic data from the Shuttle Radar Topography Mission, combined with an enhanced Landsat 7satellite color image. The topography data are used to create two differing perspectives of a single image, one perspective for each eye. In doing so, each point in the image is shifted slightly, depending on its elevation. When stereoscopically merged, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions.Landsat satellites have provided visible light and infrared images of the Earth continuously since 1972. SRTM topographic data match the 30-meter (99-foot) spatial resolution of most Landsat images and provide a valuable complement for studying the historic and growing Landsat data archive. The Landsat 7 Thematic Mapper image used here was provided to the SRTM project by the United States Geological Survey, Earth Resources Observation Systems (EROS) Data Center,Sioux Falls, South Dakota

  4. Stereo Pair: Inverted Topography, Patagonia, Argentina

    Science.gov (United States)

    2000-01-01

    The Meseta de Somuncura is a broad plateau capped by basalt. Near its western edge is evidence of multiple volcanic events and a complex erosion history. Most notable are the long, narrow-, and winding lava flows that run across most of the right side of the image. These formed from low-viscosity lava that flowed down gullies over fairly flat terrain. Later, erosion of the landscape continued and the solidified flows were more resistant than the older surrounding rocks. Consequently, the flows became the ridges we see here. This natural process of converting gullies to ridges is called topographic inversion. See image PIA02755 (upper left corner) for a good example of topographic inversion in its earlier stages.Other features seen here include numerous and varied closed depressions. The regional drainage is not well integrated, and drainage ends up in salty lakes (blue if shallow, black if deep). Wind streaks indicate that winds blow toward the east (right) and blow salt grains off the lakebeds when dry. The bowtie pattern in the upper left has resulted from differing grazing practices among fenced fields.This cross-eyed stereoscopic image pair was generated using topographic data from the Shuttle Radar Topography Mission, combined with an enhanced Landsat 7satellite color image. The topography data are used to create two differing perspectives of a single image, one perspective for each eye. In doing so, each point in the image is shifted slightly, depending on its elevation. When stereoscopically merged, the result is a vertically exaggerated view of the Earth's surface in its full three dimensions.Landsat satellites have provided visible light and infrared images of the Earth continuously since 1972. SRTM topographic data match the 30-meter (99-foot) spatial resolution of most Landsat images and provide a valuable complement for studying the historic and growing Landsat data archive. The Landsat 7 Thematic Mapper image used here was provided to the SRTM project

  5. SRTM Stereo Pair: Northwest of Bhuj, India

    Science.gov (United States)

    2001-01-01

    On January 26, 2001, the Kachchh region in western India suffered the most deadly earthquake in India's history. Shortly thereafter, geologists traversed the region looking for ground surface disruptions, such as fault breaks, that could provide clues to the tectonic processes here. Shuttle Radar Topography Mission (SRTM) scientists provided stereoscopic images to the geologists, similar to this 3-D view of the terrain northwest of the city of Bhuj. The geologists reported back that the images were essential in optimizing their field activities. Tectonic landforms are created by ground displacements that are repetitious over geologic time, so these landforms are good places to look for co-seismic faulting and warping. The stereoscopic images showed the geologists where the structures are located and their overall pattern, which could not be seen while standing on anyone hill or in any one gully. In general, the field studies found that surface disruptions by the recent earthquake were minimal and that the major landforms are quite old and probably not directly related to ongoing tectonic processes.Features of interest in the view shown here include the largest hill (upper left-center), which is a dome or anticline, upwardly convex layered rocks. Also visible are a possible volcanic plug (lower left-center) and an incised meandering stream (center). Agriculture in this arid region is concentrated on the alluvial fan of the major stream (green pattern, upper right).This stereoscopic image was generated by draping a Landsat satellite image (taken just two weeks after the earthquake) over a preliminary SRTM elevation model. Two differing perspectives were then calculated, one for each eye. They can be seen in 3-D by viewing the left image with the right eye and the right image with the left eye (cross-eyed viewing or by downloading and printing the image pair and viewing them with a stereoscope. When stereoscopically merged, the result is a vertically exaggerated view

  6. AGT, Burge pairs and minimal models

    Energy Technology Data Exchange (ETDEWEB)

    Bershtein, M. [Landau Institute for Theoretical Physics,Chernogolovka (Russian Federation); Institute for Information Transmission Problems,Moscow (Russian Federation); National Research University Higher School of Economics, International Laboratory of Representation Theory and Mathematical Physics, Independent University of Moscow, Moscow (Russian Federation); Foda, O. [Mathematics and Statistics, University of Melbourne,Parkville, VIC 3010 (Australia)

    2014-06-30

    We consider the AGT correspondence in the context of the conformal field theory M{sup p,p{sup ′}}⊗M{sup H}, where M{sup p,p{sup ′}} is the minimal model based on the Virasoro algebra V{sup p,p{sup ′}} labeled by two co-prime integers {p,p"′}, 1pairs {Y_1"ι,Y_2"ι} that satisfy Y{sub 2,σ}{sup ι,⊺}−Y{sub 1,σ+r{sub ι−1}{sup ι,⊺}}≥1−s{sub ι}, and Y{sub 1,σ}{sup ι,⊺}−Y{sub 2,σ+p−r{sub ι−1}{sup ι,⊺}}≥1−p{sup ′}+s{sub ι}, where Y{sub i,σ}{sup ι,⊺} is the σ-column of Y{sub i}{sup ι}, i∈{1,2}, we obtain a well-defined expression that we identify with B{sub n}{sup p,p{sup ′,H}}. We check the correctness of this expression for 1. Any 1-point B{sub 1}{sup p,p{sup ′,H}} on the torus, when the operator insertion is the identity, and 2. The 6-point B{sub 3}{sup 3,4,H} on the sphere that involves six Ising magnetic operators.

  7. Silver(I)-Mediated Hoogsteen-Type Base Pairs

    NARCIS (Netherlands)

    Megger, D.A.; Fonseca Guerra, C.; Bickelhaupt, F.M.; Müller, J.

    2011-01-01

    Metal-mediated Hoogsteen-type base pairs are useful for the construction of DNA duplexes containing contiguous stretches of metal ions along the helical axis. To fine-tune the stability of such base pairs and the selectivity toward different metal ions, the availability of a selection of artificial

  8. Visualizing lone pairs in compounds containing heavier congeners ...

    Indian Academy of Sciences (India)

    Visualizing lone pairs in compounds containing heavier congeners of the carbon and nitrogen group elements. Ram Seshadri. Volume ... Keywords. Main group elements; lone pairs; stereochemistry; ferroelectricity. ... Seshadri1. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India ...

  9. Optimization of unnatural base pair packing for polymerase recognition.

    Science.gov (United States)

    Matsuda, Shigeo; Henry, Allison A; Romesberg, Floyd E

    2006-05-17

    As part of an effort to expand the genetic alphabet, we have been examining the ability of predominately hydrophobic nucleobase analogues to pair in duplex DNA and during polymerase-mediated replication. We previously reported the synthesis and thermal stability of unnatural base pairs formed between nucleotides bearing simple methyl-substituted phenyl ring nucleobase analogues. Several of these pairs are virtually as stable and selective as natural base pairs in the same sequence context. Here, we report the characterization of polymerase-mediated replication of the same unnatural base pairs. We find that every facet of replication, including correct and incorrect base pair synthesis, as well as continued primer extension beyond the unnatural base pair, is sensitive to the specific methyl substitution pattern of the nucleobase analogue. The results demonstrate that neither hydrogen bonding nor large aromatic surface area is required for polymerase recognition, and that interstrand interactions between small aromatic rings may be optimized for replication. Combined with our previous results, these studies suggest that appropriately derivatized phenyl nucleobase analogues represent a promising approach toward developing a third base pair and expanding the genetic alphabet.

  10. Learning preferences from paired opposite-based semantics

    DEFF Research Database (Denmark)

    Franco de los Ríos, Camilo; Rodríguez, J. Tinguaro; Montero, Javier

    2017-01-01

    on the character of opposition, the compound meaning of preference emerges from the fuzzy reinforcement of paired opposite concepts, searching for significant evidence for affirming dominance among the decision objects. Here we propose a general model for the paired decomposition of preference, examining its...... characteristic semantics under a binary and fuzzy logical frame, and identifying solutions with different values of significance for preference learning....

  11. Pair of Heavy-Exotic-Quarks at LHC

    CERN Document Server

    Cieza-Montalvo, J E

    2002-01-01

    We study the production and signatures of heavy exotic quarks pairs at LHC in the framework of the vector singlet model (VSM), vector doublet model (VDM) and fermion-mirror-fermion (FMF) model. The pair production cross sections for the electroweak and strong sector are computed.

  12. Photometric characteristics of paired E and S0 galaxies

    Science.gov (United States)

    Demin, V. V.

    1984-12-01

    The properties of type EE and ES double galaxies are studied, using Tomov's UBV photoelectric photometry. Paired early-type galaxies have different color/absolute-magnitude diagrams from those belonging to groups. Since the (U-V)t0 colors of paired E, S0 galaxies are wholly uncorrelated with their absolute magnitude M(v), pair members evolve differently from group and cluster members. The same conclusion is drawn from comparison of the integrated photometric properties of the E, S0 galaxies in EE and in ES pairs: their color dispersion is greater than for group and cluster members, while the Holmberg color match and the M(v) correlation between pair components depend on morphological type, dynamical and kinematic behavior, and whether interaction is present. Thus the evolution of paired galaxies is controlled less by their intrinsic properties than by external factors. Star-formation bursts may alternate in the two pair components, accompanying active mass-exchange processes, but the evolution of the pairs in the sample studied will not be significantly affected by dynamical friction.

  13. Physicochemical studies on ion-pair amphiphiles: Solution and ...

    Indian Academy of Sciences (India)

    Administrator

    cation potentials in the field of membrane mimick- ing systems, drug delivery, nanoparticle synthesis, etc. 4–10 ... The phase diagrams consist- ing of a micellar solution phase, and a liquid crystal- line phase (at higher ... madzu, Japan) using a matched pair of quartz cells of path length 1cm. The ion-pairs produced appre-.

  14. Theory of pairing symmetry in the vortex states

    NARCIS (Netherlands)

    Yokoyama, Takehito; Ichioka, Yukio; Yanaka, Yukio; Golubov, Alexandre Avraamovitch

    2010-01-01

    We investigate pairing symmetry in an Abrikosov vortex and vortex lattice. It is shown that the Cooper pair wave function at the center of an Abrikosov vortex with vorticity m has a different parity with respect to frequency from that in the bulk if m is an odd number, while it has the same parity

  15. Pairing Books for Learning: The Union of Informational and Fiction

    Science.gov (United States)

    Baer, Allison L.

    2012-01-01

    This article aims to present an annotated bibliography of paired books--one fiction and one informational--about multiple topics in history and social studies that, when read together, can help support students' learning through experiencing the topic from multiple perspectives and voices. It begins with a brief rationale for pairing fiction and…

  16. Search for pair production of new particles in ATLAS

    CERN Document Server

    Berlendis, Simon; The ATLAS collaboration

    2017-01-01

    With the advent of 13 TeV collisions and the start of Run 2 of the LHC, the potential to directly observe new particles produced in pairs has been greatly increased. This presentation will discuss a recent search from the ATLAS collaboration searching for pair production of new particles using the Run 2 dataset.

  17. Observing Pair-Work Task in an English Speaking Class

    Science.gov (United States)

    Achmad, Diana; Yusuf, Yunisrina Qismullah

    2014-01-01

    This paper reports on students' pair-work interactions to develop their speaking skills in an ELT classroom which consisted of international learners. A number of 16 learners of intermediate proficiency with IELTS score band 5.5 were observed. The teacher had paired those he considered among them to be the more competent ones (hereafter, stronger)…

  18. Base pairing in RNA structures: A computational analysis of ...

    Indian Academy of Sciences (India)

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal ...

  19. Solving the Airline Crew Pairing Problem using Subsequence Generation

    DEFF Research Database (Denmark)

    Rasmussen, Matias Sevel; Lusby, Richard Martin; Ryan, David M.

    Good and fast solutions to the airline crew pairing problem are highly interesting for the airline industry, as crew costs are the biggest expenditure after fuel for an airline. The crew pairing problem is typically modelled as a set partitioning problem and solved by column generation. However...

  20. Subsequence Generation for the Airline Crew Pairing Problem

    DEFF Research Database (Denmark)

    Rasmussen, Matias Sevel; Lusby, Richard Martin; Ryan, David

    Good and fast solutions to the airline crew pairing problem are highly interesting for the airline industry, as crew costs are the biggest expenditure after fuel for an airline. The crew pairing problem is typically modelled as a set partitioning problem and solved by column generation. However...

  1. Solving the Airline Crew Pairing Problem using Subsequence Generation

    DEFF Research Database (Denmark)

    Rasmussen, Matias Sevel; Ryan, David M.; Lusby, Richard Martin

    2010-01-01

    Good and fast solutions to the airline crew pairing problem are highly interesting for the airline industry, as crew costs are the biggest expenditure after fuel for an airline. The crew pairing problem is typically modelled as a set partitioning problem and solved by column generation. However...

  2. Solving the Airline Crew Pairing Problem using Subsequence Generation

    DEFF Research Database (Denmark)

    Rasmussen, Matias Sevel; Ryan, David; Lusby, Richard Martin

    2009-01-01

    Good and fast solutions to the airline crew pairing problem are highly interesting for the airline industry, as crew costs are the biggest expenditure after fuel for an airline. The crew pairing problem is typically modelled as a set partitioning problem and solved by column generation. However...

  3. Vibrating and shaking soliton pairs in dissipative systems

    Energy Technology Data Exchange (ETDEWEB)

    Akhmediev, N. [Optical Sciences Group, Research School of Physical Sciences and Engineering, the Australian National University, Canberra ACT 0200 (Australia); Soto-Crespo, J.M. [Instituto de Optica, C.S.I.C., Serrano 121, 28006 Madrid (Spain)]. E-mail: iodsc09@io.cfmac.csic.es; Grelu, Ph. [Laboratoire de Physique de l' Universite de Bourgogne, UMR CNRS 5027, Faculte des Sciences Mirande, Avenue Savary BP 47870, 21078 Dijon Cedex (France)

    2007-05-07

    We show that two-soliton solutions in nonlinear dissipative systems can exist in various forms. As with single solitons, they can be stationary, periodic or chaotic. In particular, we find new types of vibrating and shaking soliton pairs. Each type of pair is stable in the sense that the bound state exists in the same form indefinitely.

  4. Pairs, sets and sequences in first order theories

    NARCIS (Netherlands)

    Visser, A.

    In this paper we study the idea of theories with containers, like sets, pairs, sequences. We provide a modest framework to study such theories. We prove two concrete results. First, we show that first order theories of finite signature that have functional non-surjective ordered pairing

  5. Gender pairing and bargaining—Beware the same sex!

    NARCIS (Netherlands)

    Sutter, M.; Bosman, R.; Kocher, M.G.; van Winden, F.

    2009-01-01

    We study the influence of gender and gender pairing on economic decision making in an experimental two-person bargaining game where the other party’s gender is known to both actors. We find that (1) gender per se has no significant effect on behavior, whereas (2) gender pairing systematically

  6. Machine learning for multi-view eye-pair detection

    NARCIS (Netherlands)

    Karaaba, Mahir Faik; Schomaker, Lambert; Wiering, Marco

    While face and eye detection is well known research topics in the field of object detection, eye-pair detection has not been much researched. Finding the location and size of an eye-pair in an image containing a face can enable a face recognition application to extract features from a face

  7. Antivortices due to competing orbital and paramagnetic pair ...

    Indian Academy of Sciences (India)

    states with co-existing vortices and antivortices exist in a small interval close to θ = 0. The results are compared with recent predictions of antivortices in mesoscopic samples. Keywords. Superconductivity; antivortices; paramagnetic pair-breaking; orbital pair- breaking. PACS Nos 74.20.-z; 74.78.-w; 74.90.+n. 1. Introduction.

  8. Teaching Valence Shell Electron Pair Repulsion (VSEPR) Theory

    Science.gov (United States)

    Talbot, Christopher; Neo, Choo Tong

    2013-01-01

    This "Science Note" looks at the way that the shapes of simple molecules can be explained in terms of the number of electron pairs in the valence shell of the central atom. This theory is formally known as valence shell electron pair repulsion (VSEPR) theory. The article explains the preferred shape of chlorine trifluoride (ClF3),…

  9. Distribution and polymorphism of the flagellin genes from isolates of Campylobacter coli and Campylobacter jejuni.

    Science.gov (United States)

    Alm, R A; Guerry, P; Trust, T J

    1993-01-01

    The complex flagellar filaments of the LIO8 serogroup member Campylobacter coli VC167 are composed of two highly related subunit proteins encoded by the flaA and flaB genes which share 92% identity. Using oligonucleotide primers based on the known DNA sequence of both the flaA and flaB genes from C. coli VC167 in the polymerase chain reaction, we have shown conservation of both fla genes among isolates within the LIO8 heat-labile serogroup by digestion of the amplified product with PstI and EcoRI restriction endonucleases. Amplification and subsequent restriction analysis of the flaA flagellin gene from Campylobacter isolates belonging to 13 different LIO serogroups further identified 10 unique polymorphic groups. Within most of the serogroups examined, isolates appeared to contain flaA genes with conserved primary structures. Only in serogroups LIO11 and LIO29 did independent isolates possess flagellin genes with different primary structures. Furthermore, by employing primers specific for the flaB gene of C. coli VC167, all serogroups examined contained a second fla gene corresponding to flaB. In all serogroups except the LIO5 and LIO6 isolates which were identical to each other, the polymorphic pattern of this flaB gene was identical to that of the corresponding flaA gene. These data indicate that the presence of a second highly homologous flagellin gene is widespread throughout Campylobacter isolates and that in most instances, the primary structure of the two fla genes is conserved within isolates belonging to the same heat-labile LIO serogroup. This may represent the presence of clonal evolutionary groups in Campylobacter spp. Images PMID:8098328

  10. Spectroscopy of asteroid pairs - new observations support previous conclusions

    Science.gov (United States)

    Polishook, David; Oszkiewicz, Dagmara Anna; None Kwiatkowski, Tomasz

    2015-08-01

    Asteroid pairs were split due to fast rotation of a strengthless body. Study them can reveal fundamental principles in asteroid interiors and evolution. We continue our spectroscopic survey of asteroid pairs in the near-IR range (IRTF) and work on completing the spectral coverage in the visible wavelength (SALT, NOT).Our new observations support our previous conclusions (Polishook et al. 2014):1. Primary and secondary members have very similar reflectance spectra supporting the claim that every pair originated from a single progenitor. We measured 2 more pairs that present the same taxonomy (4905-7813, 15107-291188). This increases to 22 the number of asteroid pairs with spectral similarities and supports the claim of a single progenitor for each pair to a significance of over 5 sigma.2. Rotational fission is not a function of the asteroid composition rather the asteroid’s structure. We present new reflectance spectra of S- and C-complex pairs that differ in their composition.3. Some asteroid pairs present spectral parameters that imply a fresh, non-weathered surface. This includes spectral slope, and a deep and wide absorption band at 1 micron. Among these, the asteroid 8306 can now be re-classified as a Q-type asteroid, a common class in the near-Earth environment, but rare in the main belt. 8306 is the 4th Q-type discovered within asteroid pairs (all locate in the main belt).4. A secondary member of an asteroid pair composed of ordinary chondrite (S-complex) might present a reflectance spectrum with lower spectral slope compared to its primary member. This is seen in the new measured reflectance spectrum of secondary 291188). This result supports the theory of Jacobson & Scheeres (2011) of continuous disintegration of the secondaries while still in the vicinity of their primaries.5. With time, the fresh surface becomes weathered. Dynamical calculations limit the disintegration time of the progenitor of the pair 4905-7813 to 1.65 millions years ago, what makes

  11. An Intelligent Model for Pairs Trading Using Genetic Algorithms.

    Science.gov (United States)

    Huang, Chien-Feng; Hsu, Chi-Jen; Chen, Chi-Chung; Chang, Bao Rong; Li, Chen-An

    2015-01-01

    Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice.

  12. An Intelligent Model for Pairs Trading Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Chien-Feng Huang

    2015-01-01

    Full Text Available Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA. Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice.

  13. Pulsar Pair Cascades in a Distorted Magnetic Dipole Field

    Science.gov (United States)

    Harding, Alice K.; Muslimov, Alex G.

    2010-01-01

    We investigate the effect of a distorted neutron star dipole magnetic field on pulsar pair cascade multiplicity and pair death lines. Using a simple model for a distorted dipole field that produces an offset polar cap (PC), we derive the accelerating electric field above the PC in space-charge-limited flow. We find that even a modest azimuthally asymmetric distortion can significantly increase the accelerating electric field on one side of the PC and, combined with a smaller field line radius of curvature, leads to larger pair multiplicity. The death line for producing pairs by curvature radiation moves downward in the P-P-dot diagram, allowing high pair multiplicities in a larger percentage of the radio pulsar population. These results could have important implications for the radio pulsar population, high energy pulsed emission, and the pulsar contribution to cosmic ray positrons.

  14. Overdensity of galaxies in the environment of quasar pairs

    Science.gov (United States)

    Sandrinelli, A.; Falomo, R.; Treves, A.; Scarpa, R.; Uslenghi, M.

    2018-03-01

    We report on a study of the galaxy environments of low redshift physical quasars pairs. We selected 20 pairs having projected separation Digital Sky Survey images, we evaluated the galaxy overdensity around these quasars in pairs and then compare it with that of a sample of isolated quasars with same redshift and luminosity. It is found that on average there is a systematic larger overdensity of galaxies around quasars in pairs with respect to that of isolated quasars. This may represent a significant link between nuclear activity and galaxy environment. However, at odds with that, the closest quasar pairs seem to inhabit poorer environments. Implications of present results and perspectives for future work are briefly discussed.

  15. Purification of an unpolarized spin ensemble into entangled singlet pairs.

    Science.gov (United States)

    Greiner, Johannes N; Dasari, Durga Bhaktavatsala Rao; Wrachtrup, Jörg

    2017-04-03

    Dynamical polarization of nuclear spin ensembles is of central importance for magnetic resonance studies, precision sensing and for applications in quantum information theory. Here we propose a scheme to generate long-lived singlet pairs in an unpolarized nuclear spin ensemble which is dipolar coupled to the electron spins of a Nitrogen Vacancy center in diamond. The quantum mechanical back-action induced by frequent spin-selective readout of the NV centers allows the nuclear spins to pair up into maximally entangled singlet pairs. Counterintuitively, the robustness of the pair formation to dephasing noise improves with increasing size of the spin ensemble. We also show how the paired nuclear spin state allows for enhanced sensing capabilities of NV centers in diamond.

  16. Preferential pairing estimates from multivalent frequencies in tetraploids.

    Science.gov (United States)

    Sybenga, J

    1994-12-01

    Mathematical models are presented for estimating preferential pairing and chiasma parameters in amphidiploids and autotetraploids on the basis of diakinesis or metaphase I configuration frequencies and are compared with other approaches of estimating affinity. With a preferential pairing factor p, estimated from quadrivalent and trivalent frequencies, and estimated chiasmate association factors for the two arms in quadrivalents (a(qu) and b(qu) for arms A and B, respectively) and in bivalents (a(bi) and b(bi)) a perfect fit between observed and predicted configuration frequencies can often be obtained in amphidiploids of several plant species, including Solanaceae and Gramineae. Since several proven autotetraploids give very similar apparent preferential pairing estimates, the biological significance of such parameters as preferential pairing and affinity factors is considered limited. The same is true for pairing parameters estimated by optimizing fit of configuration frequencies expected on the basis of theoretical models to observed data.

  17. Effects of Worked Examples, Example-Problem Pairs, and Problem-Example Pairs Compared to Problem Solving

    NARCIS (Netherlands)

    Van Gog, Tamara; Kester, Liesbeth; Paas, Fred

    2010-01-01

    Van Gog, T., Kester, L., & Paas, F. (2010, August). Effects of worked examples, example-problem pairs, and problem-example pairs compared to problem solving. Paper presented at the Biannual EARLI SIG meeting of Instructional design and Learning and instruction with computers, Ulm, Germany.

  18. The Number of Genes Controlling Resistance in Beans to Common ...

    African Journals Online (AJOL)

    At V3, two to many genes were found to control resistance with segregation ratios that were significantly (P≤0.05) different from that of three gene pairs. In some crosses transgressive segregation was observed. By application of appropriate variances to the equation provided by Stanisfield's formula, the number of genes in ...

  19. Expression profiles of genes involved in tanshinone biosynthesis of ...

    Indian Academy of Sciences (India)

    Expression profiles of genes involved in tanshinone biosynthesis of two. Salvia miltiorrhiza genotypes with different tanshinone contents. Zhenqiao Song, Jianhua Wang and Xingfeng Li. J. Genet. 95, 433–439. Table 1. S. miltiorrhiza genes and primer pairs used for qRT-PCR. Gene. GenBank accession. Primer name.

  20. Detecting Highways of Horizontal Gene Transfer

    Science.gov (United States)

    Bansal, Mukul S.; Gogarten, J. Peter; Shamir, Ron

    In a horizontal gene transfer (HGT) event a gene is transferred between two species that do not share an ancestor-descendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species, our method requires O(n 4) time, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method.

  1. The Effects of Learning from Word Pairs on Word Knowledge

    Directory of Open Access Journals (Sweden)

    Shamsudin Sarimah

    2015-01-01

    Full Text Available Vocabulary plays an essential role in language learning. The lack of vocabulary might cause incompetency to language users. It is therefore very important for language instructors to find suitable ways of teaching vocabulary since learning vocabulary consists of learning various aspects of word knowledge. These aspects include orthography, meaning and form, collocation, association and grammatical functions. There are various methods that could be used in gaining aspects of word knowledge. The purpose of this study is to investigate to what extent are aspects of word knowledge gained by learning from word pairs. 120 secondary school students were divided into four groups of thirty students. The first group was given a set of Malay Translation, the second, English Translation, the third, Malay Definition and the fourth, English Definition word pair to learn followed by word knowledge tests. The results show that all word pairs promote large gains in learning aspects of word knowledge. The scores between the groups were also compared and it was found that the mean score of the Malay Definition word pair group is the highest, followed by the Malay Translation word pair group, the English Translation word pair group, and English Definition word pair group.

  2. PAR-TERRA directs homologous sex chromosome pairing.

    Science.gov (United States)

    Chu, Hsueh-Ping; Froberg, John E; Kesner, Barry; Oh, Hyun Jung; Ji, Fei; Sadreyev, Ruslan; Pinter, Stefan F; Lee, Jeannie T

    2017-08-01

    In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including to the PAR and Xic. During X-chromosome pairing, PAR-TERRA anchors the Xic to the PAR, creating a 'tetrad' of pairwise homologous interactions (Xic-Xic, PAR-PAR, and Xic-PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We propose a 'constrained diffusion model' in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.

  3. The coevolution of long-term pair bonds and cooperation.

    Science.gov (United States)

    Song, Z; Feldman, M W

    2013-05-01

    The evolution of social traits may not only depend on but also change the social structure of the population. In particular, the evolution of pairwise cooperation, such as biparental care, depends on the pair-matching distribution of the population, and the latter often emerges as a collective outcome of individual pair-bonding traits, which are also under selection. Here, we develop an analytical model and individual-based simulations to study the coevolution of long-term pair bonds and cooperation in parental care, where partners play a Snowdrift game in each breeding season. We illustrate that long-term pair bonds may coevolve with cooperation when bonding cost is below a threshold. As long-term pair bonds lead to assortative interactions through pair-matching dynamics, they may promote the prevalence of cooperation. In addition to the pay-off matrix of a single game, the evolutionarily stable equilibrium also depends on bonding cost and accidental divorce rate, and it is determined by a form of balancing selection because the benefit from pair-bond maintenance diminishes as the frequency of cooperators increases. Our findings highlight the importance of ecological factors affecting social bonding cost and stability in understanding the coevolution of social behaviour and social structures, which may lead to the diversity of biological social systems. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  4. Genes2FANs: connecting genes through functional association networks

    Directory of Open Access Journals (Sweden)

    Dannenfelser Ruth

    2012-07-01

    Full Text Available Abstract Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs, researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our

  5. Gene Profiling of Cottontail Rabbit Papillomavirus-Induced Carcinomas Identifies Upregulated Genes Directly Involved in Stroma Invasion as Shown by Small Interfering RNA-Mediated Gene Silencing

    OpenAIRE

    Huber, Evamaria; Vlasny, Daniela; Jeckel, Sonja; Stubenrauch, Frank; Iftner, Thomas

    2004-01-01

    To investigate changes in cellular gene expression associated with malignant progression, we identified differentially expressed genes in a cottontail rabbit papillomavirus (CRPV) squamous carcinoma model employing New Zealand White rabbits. The technique of suppression subtractive cDNA hybridization was applied to pairs of mRNA isolates from CRPV-induced benign papillomas and carcinomas, with each pair derived from the same individual rabbit. The differential expression of 23 subtracted cDNA...

  6. A nucleon-pair and boson coexistent description of nuclei

    Science.gov (United States)

    Dai, Lianrong; Pan, Feng; Draayer, J. P.

    2017-07-01

    We study a mixture of s-bosons and like-nucleon pairs with the standard pairing interaction outside an inert core. Competition between the nucleon-pairs and s-bosons is investigated in this scenario. The robustness of the BCS-BEC coexistence and crossover phenomena are examined through an analysis of pf-shell nuclei with realistic single-particle energies, in which two configurations with Pauli blocking of nucleon-pair orbits due to the formation of the s-bosons is taken into account. When the nucleon-pair orbits are considered to be independent of the s-bosons, the BCS-BEC crossover becomes smooth, with the number of the s-bosons noticeably more than that of the nucleon-pairs near the half-shell point, a feature that is demonstrated in the pf-shell for several values of the standard pairing interaction strength. As a further test of the robustness of the BCS-BEC coexistence and crossover phenomena in nuclei, results are given for values of even-even 102-130Sn with 100Sn taken as a core and valence neutron pairs confined within the 1d 5/2, 0g 7/2, 1d 3/2, 2s 1/2, 1h 11/2 orbits in the nucleon-pair orbit and the s-boson independent approximation. The results indicate that the B(E2) values are reproduced well. Supported by National Natural Science Foundation of China (11375080, 11675071), the U.S. National Science Foundation (OCI-0904874 and ACI-1516338), U. S. Department of Energy (DE-SC0005248), the Southeastern Universities Research Association, the China-U. S. Theory Institute for Physics with Exotic Nuclei (CUSTIPEN) (DE-SC0009971), and the LSU-LNNU joint research program (9961) is acknowledged

  7. Analysis of Food Pairing in Regional Cuisines of India.

    Directory of Open Access Journals (Sweden)

    Anupam Jain

    Full Text Available Any national cuisine is a sum total of its variety of regional cuisines, which are the cultural and historical identifiers of their respective regions. India is home to a number of regional cuisines that showcase its culinary diversity. Here, we study recipes from eight different regional cuisines of India spanning various geographies and climates. We investigate the phenomenon of food pairing which examines compatibility of two ingredients in a recipe in terms of their shared flavor compounds. Food pairing was enumerated at the level of cuisine, recipes as well as ingredient pairs by quantifying flavor sharing between pairs of ingredients. Our results indicate that each regional cuisine follows negative food pairing pattern; more the extent of flavor sharing between two ingredients, lesser their co-occurrence in that cuisine. We find that frequency of ingredient usage is central in rendering the characteristic food pairing in each of these cuisines. Spice and dairy emerged as the most significant ingredient classes responsible for the biased pattern of food pairing. Interestingly while individual spices contribute to negative food pairing, dairy products on the other hand tend to deviate food pairing towards positive side. Our data analytical study highlighting statistical properties of the regional cuisines, brings out their culinary fingerprints that could be used to design algorithms for generating novel recipes and recipe recommender systems. It forms a basis for exploring possible causal connection between diet and health as well as prospection of therapeutic molecules from food ingredients. Our study also provides insights as to how big data can change the way we look at food.

  8. Analysis of Food Pairing in Regional Cuisines of India.

    Science.gov (United States)

    Jain, Anupam; N K, Rakhi; Bagler, Ganesh

    2015-01-01

    Any national cuisine is a sum total of its variety of regional cuisines, which are the cultural and historical identifiers of their respective regions. India is home to a number of regional cuisines that showcase its culinary diversity. Here, we study recipes from eight different regional cuisines of India spanning various geographies and climates. We investigate the phenomenon of food pairing which examines compatibility of two ingredients in a recipe in terms of their shared flavor compounds. Food pairing was enumerated at the level of cuisine, recipes as well as ingredient pairs by quantifying flavor sharing between pairs of ingredients. Our results indicate that each regional cuisine follows negative food pairing pattern; more the extent of flavor sharing between two ingredients, lesser their co-occurrence in that cuisine. We find that frequency of ingredient usage is central in rendering the characteristic food pairing in each of these cuisines. Spice and dairy emerged as the most significant ingredient classes responsible for the biased pattern of food pairing. Interestingly while individual spices contribute to negative food pairing, dairy products on the other hand tend to deviate food pairing towards positive side. Our data analytical study highlighting statistical properties of the regional cuisines, brings out their culinary fingerprints that could be used to design algorithms for generating novel recipes and recipe recommender systems. It forms a basis for exploring possible causal connection between diet and health as well as prospection of therapeutic molecules from food ingredients. Our study also provides insights as to how big data can change the way we look at food.

  9. Amperean Pairing and the Pseudogap Phase of Cuprate Superconductors

    Science.gov (United States)

    Lee, Patrick A.

    2014-07-01

    The enigmatic pseudogap phase in underdoped cuprate high-Tc superconductors has long been recognized as a central puzzle of the Tc problem. Recent data show that the pseudogap is likely a distinct phase, characterized by a medium range and quasistatic charge ordering. However, the origin of the ordering wave vector and the mechanism of the charge order is unknown. At the same time, earlier data show that precursive superconducting fluctuations are also associated with this phase. We propose that the pseudogap phase is a novel pairing state where electrons on the same side of the Fermi surface are paired, in strong contrast with conventional Bardeen-Cooper-Schrieffer theory which pairs electrons on opposite sides of the Fermi surface. In this state the Cooper pair carries a net momentum and belongs to a general class called pair density wave. The microscopic pairing mechanism comes from a gauge theory formulation of the resonating valence bond (RVB) picture, where spinons traveling in the same direction feel an attractive force in analogy with Ampere's effects in electromagnetism. We call this Amperean pairing. Charge order automatically appears as a subsidiary order parameter even when long-range pair order is destroyed by phase fluctuations. Our theory gives a prediction of the ordering wave vector which is in good agreement with experiment. Furthermore, the quasiparticle spectrum from our model explains many of the unusual features reported in photoemission experiments. The Fermi arc, the unusual way the tip of the arc terminates, and the relation of the spanning vector of the arc tips to the charge ordering wave vector also come out naturally. Finally, we propose an experiment that can directly test the notion of Amperean pairing.

  10. Analysis of Food Pairing in Regional Cuisines of India

    Science.gov (United States)

    Bagler, Ganesh

    2015-01-01

    Any national cuisine is a sum total of its variety of regional cuisines, which are the cultural and historical identifiers of their respective regions. India is home to a number of regional cuisines that showcase its culinary diversity. Here, we study recipes from eight different regional cuisines of India spanning various geographies and climates. We investigate the phenomenon of food pairing which examines compatibility of two ingredients in a recipe in terms of their shared flavor compounds. Food pairing was enumerated at the level of cuisine, recipes as well as ingredient pairs by quantifying flavor sharing between pairs of ingredients. Our results indicate that each regional cuisine follows negative food pairing pattern; more the extent of flavor sharing between two ingredients, lesser their co-occurrence in that cuisine. We find that frequency of ingredient usage is central in rendering the characteristic food pairing in each of these cuisines. Spice and dairy emerged as the most significant ingredient classes responsible for the biased pattern of food pairing. Interestingly while individual spices contribute to negative food pairing, dairy products on the other hand tend to deviate food pairing towards positive side. Our data analytical study highlighting statistical properties of the regional cuisines, brings out their culinary fingerprints that could be used to design algorithms for generating novel recipes and recipe recommender systems. It forms a basis for exploring possible causal connection between diet and health as well as prospection of therapeutic molecules from food ingredients. Our study also provides insights as to how big data can change the way we look at food. PMID:26430895

  11. Amperean Pairing and the Pseudogap Phase of Cuprate Superconductors

    Directory of Open Access Journals (Sweden)

    Patrick A. Lee

    2014-07-01

    Full Text Available The enigmatic pseudogap phase in underdoped cuprate high-T_{c} superconductors has long been recognized as a central puzzle of the T_{c} problem. Recent data show that the pseudogap is likely a distinct phase, characterized by a medium range and quasistatic charge ordering. However, the origin of the ordering wave vector and the mechanism of the charge order is unknown. At the same time, earlier data show that precursive superconducting fluctuations are also associated with this phase. We propose that the pseudogap phase is a novel pairing state where electrons on the same side of the Fermi surface are paired, in strong contrast with conventional Bardeen-Cooper-Schrieffer theory which pairs electrons on opposite sides of the Fermi surface. In this state the Cooper pair carries a net momentum and belongs to a general class called pair density wave. The microscopic pairing mechanism comes from a gauge theory formulation of the resonating valence bond (RVB picture, where spinons traveling in the same direction feel an attractive force in analogy with Ampere’s effects in electromagnetism. We call this Amperean pairing. Charge order automatically appears as a subsidiary order parameter even when long-range pair order is destroyed by phase fluctuations. Our theory gives a prediction of the ordering wave vector which is in good agreement with experiment. Furthermore, the quasiparticle spectrum from our model explains many of the unusual features reported in photoemission experiments. The Fermi arc, the unusual way the tip of the arc terminates, and the relation of the spanning vector of the arc tips to the charge ordering wave vector also come out naturally. Finally, we propose an experiment that can directly test the notion of Amperean pairing.

  12. MC1R variants predisposing to concomitant primary cutaneous melanoma in a monozygotic twin pair

    Directory of Open Access Journals (Sweden)

    Pellegrini Cristina

    2012-09-01

    Full Text Available Abstract Background Concomitant primary cutaneous melanoma in monozygotic twins has been reported in only two pairs but in neither of them genetic analysis was performed. Two high-penetrance susceptibility genes, CDKN2A and CDK4 and one low-penetrance gene, MC1R, are well-defined genetic risk factors for melanoma. MITF has been recently identified as a novel intermediate risk melanoma-predisposing gene. Case presentation We describe the extraordinary occurrence of a primary cutaneous invasive melanoma in two 44-year-old identical, female twins, on the same body site within 30 days of each other and report for the first time the genetic analysis of melanoma susceptibility genes in both twins. Data on characteristics of the twins were collected through a standardized questionnaire and skin examination. Exons 1α, 1β, 2 and 3 of CDKN2A, exon 2 of CDK4, the entire open reading frame of MC1R and the recently described MITF c.952 G > A (p.Glu318Lys variant were investigated by direct sequencing. Sequencing analysis of the high-penetrance susceptibility genes showed no changes in CDKN2A and in exon 2 of the CDK4 gene. Both patients were heterozygous for the same CDKN2A UTR c.*29C > G variant. Interestingly, the same two heterozygous variants of the MC1R were identified in both twins: the c.451C > T (p.Arg151Cys and the c.456C > A (p.Tyr152* variants. Neither patient showed the c.952 G > A (p.Glu318Lys substitution in the MITF gene. Conclusions Identification of two high-risk MC1R variants in our identical twins in the absence of CDKN2A and CDK4 mutations highlights the contribution of low penetrance genes, such as MC1R, in melanoma susceptibility.

  13. MC1R variants predisposing to concomitant primary cutaneous melanoma in a monozygotic twin pair.

    Science.gov (United States)

    Pellegrini, Cristina; Fargnoli, Maria Concetta; Suppa, Mariano; Peris, Ketty

    2012-09-14

    Concomitant primary cutaneous melanoma in monozygotic twins has been reported in only two pairs but in neither of them genetic analysis was performed. Two high-penetrance susceptibility genes, CDKN2A and CDK4 and one low-penetrance gene, MC1R, are well-defined genetic risk factors for melanoma. MITF has been recently identified as a novel intermediate risk melanoma-predisposing gene. We describe the extraordinary occurrence of a primary cutaneous invasive melanoma in two 44-year-old identical, female twins, on the same body site within 30 days of each other and report for the first time the genetic analysis of melanoma susceptibility genes in both twins. Data on characteristics of the twins were collected through a standardized questionnaire and skin examination. Exons 1α, 1β, 2 and 3 of CDKN2A, exon 2 of CDK4, the entire open reading frame of MC1R and the recently described MITF c.952 G > A (p.Glu318Lys) variant were investigated by direct sequencing. Sequencing analysis of the high-penetrance susceptibility genes showed no changes in CDKN2A and in exon 2 of the CDK4 gene. Both patients were heterozygous for the same CDKN2A UTR c.*29C > G variant. Interestingly, the same two heterozygous variants of the MC1R were identified in both twins: the c.451C > T (p.Arg151Cys) and the c.456C > A (p.Tyr152*) variants. Neither patient showed the c.952 G > A (p.Glu318Lys) substitution in the MITF gene. Identification of two high-risk MC1R variants in our identical twins in the absence of CDKN2A and CDK4 mutations highlights the contribution of low penetrance genes, such as MC1R, in melanoma susceptibility.

  14. Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes.

    Science.gov (United States)

    Taylor, Louis J; Strebel, Klaus

    2017-01-07

    Gene knockouts are a common tool used to study gene function in various organisms. However, designing gene knockouts is complicated in viruses, which frequently contain sequences that code for multiple overlapping genes. Designing mutants that can be traced by the creation of new or elimination of existing restriction sites further compounds the difficulty in experimental design of knockouts of overlapping genes. While software is available to rapidly identify restriction sites in a given nucleotide sequence, no existing software addresses experimental design of mutations involving multiple overlapping amino acid sequences in generating gene knockouts. Pyviko performed well on a test set of over 240,000 gene pairs collected from viral genomes deposited in the National Center for Biotechnology Information Nucleotide database, identifying a point mutation which added a premature stop codon within the first 20 codons of the target gene in 93.2% of all tested gene-overprinted gene pairs. This shows that Pyviko can be used successfully in a wide variety of contexts to facilitate the molecular cloning and study of viral overprinted genes. Pyviko is an extensible and intuitive Python tool for designing knockouts of overlapping genes. Freely available as both a Python package and a web-based interface ( http://louiejtaylor.github.io/pyViKO/ ), Pyviko simplifies the experimental design of gene knockouts in complex viruses with overlapping genes.

  15. Hybrid TLC-pair meter for the Sphinx Project

    Science.gov (United States)

    Wada, T.; Yamamoto, I.; Takahashi, N.; Misaki, A.

    1985-01-01

    The chief aims in THE SPHINX PROJECT are research of super lepton physics and new detector experiments. At the second phase of THE SPHINX PROJECT, a hybrid TLC-PAIR METER was designed for measuring high energy neutrino sources (E upsilon * TeV), searching high energy muon sources (E mu TeV) and measuring muon group (E mu 1 TeV). The principle of PAIR METER has been already proposed. In this TLC-PAIR METER, electromagnetic shower induced by cosmic ray muons are detected using TL (Thermoluminescence) sheets with position counters.

  16. Neutron-proton pairing correlations in odd mass systems

    Energy Technology Data Exchange (ETDEWEB)

    Fellah, M., E-mail: mfellah@usthb.dz; Allal, N. H. [Laboratoire de Physique Théorique, Faculté de Physique, USTHB BP32, El-Alia, 16111 Bab-Ezzouar, ALGER-ALGERIA (Algeria); Centre de Recherche Nucléaire d’Alger (CRNA)- COMENA BP399 Alger-Gare, ALGER- ALGERIA (Algeria); Oudih, M. R. [Laboratoire de Physique Théorique, Faculté de Physique, USTHB BP32, El-Alia, 16111 Bab-Ezzouar, ALGER-ALGERIA (Algeria)

    2015-03-30

    An expression of the ground-state which describes odd mass systems within the BCS approach in the isovector neutron-proton pairing case is proposed using the blocked level technique. The gap equations as well as the energy expression are then derived. It is shown that they exactly generalize the expressions obtained in the pairing between like-particles case. The various gap parameters and the energy are then numerically studied as a function of the pairing-strength within the schematic one-level model.

  17. Breathing solitary-pulse pairs in a linearly coupled system

    CERN Document Server

    Dana, Brenda; Bahabad, Alon

    2014-01-01

    It is shown that pairs of solitary pulses (SPs) in a linearly-coupled system with opposite group-velocity dispersions form robust breathing bound states. The system can be realized by temporal-modulation coupling of SPs with different carrier frequencies propagating in the same medium, or by coupling of SPs in a dual-core waveguide. Broad SP pairs are produced in a virtually exact form by means of the variational approximation. Strong nonlinearity tends to destroy the periodic evolution of the SP pairs.

  18. Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

    Science.gov (United States)

    Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

    2011-01-01

    We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

  19. Paired-pulse behavior of visually evoked potentials recorded in human visual cortex using patterned paired-pulse stimulation.

    Science.gov (United States)

    Höffken, Oliver; Grehl, Torsten; Dinse, Hubert R; Tegenthoff, Martin; Bach, Michael

    2008-07-01

    Paired-pulse stimulation techniques are used as common tools to investigate cortical excitability and cortical plastic changes. Similar to investigations in the somatosensory and motor system here we applied a new paired-pulse paradigm to study the paired-pulse behavior of visually evoked potentials (VEPs) in 25 healthy subjects. VEPs were recorded and the responses to the first and the second P100 peak were analyzed at different SOAs [stimulus onset asynchrony (SOA) = interstimulus interval (ISI) + pulse duration (13 ms)]. Two measures describe the paired pulse interaction: the "amplitude ratio", the ratio of the second to the first amplitude, and the "latency shift", the difference of the inter-peak interval between the P100 peaks and the respective SOA. To separate alterations in the amplitude of the second VEP response due to changes in paired-pulse inhibition from those originating from superposition of the two waveforms, particularly at short SOAs, we created a waveform template from recordings made at SOAs of 1 s, where interaction can be assumed to be negligible. Superposed traces of VEP recordings were then created by adding two templates at delays corresponding to the SOAs used. The original recordings were then digitally subtracted from the traces obtained by superposition. Analysis of the subtracted traces revealed evidence that at short SOAs the second VEP response is substantially suppressed, a finding comparable to the paired-pulse inhibition described for motor and somatosensory cortex following paired-pulse stimulation. However, paired-pulse inhibition seen in V1 varied considerably from subject to subject, both in respect to amplitude, and to time of maximal inhibition. We found paired-pulse inhibition ranging from 12 to 76% (mean 34%) at SOAs between 80 (shortest discriminable SOA) and 320 ms (mean 128 ms). At intermediate SOAs between 80 and 720 ms (mean 215 ms) the amplitude ratios were between 94 and 145% (mean 116%) indicative of slight

  20. Genome Filtering Using Methylation- Sensitive Restriction Enzymes with Six Base Pair Recognition Sites

    Directory of Open Access Journals (Sweden)

    John P. Fellers

    2008-11-01

    Full Text Available The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl-sensitive restriction enzymes, with six base pair recognition sites, were evaluated on genomic DNA of the bread wheat ‘Chinese Spring’ as a different approach to enrich for genes. I, I, I, and II were used to digest wheat genomic DNA and fragments ranging from 400 bp to 2.0 kb were cloned and unidirectionally sequenced. All four enzymes provided some level of enrichment for gene space; however, II and I reduced the number of clones with repeat elements to just 16.2 and 19.1%, respectively. II and I were also effective in enrichment in corn and tobacco. Corn libraries made with II and I had 58.7 and 71.2%, respectively, of the clones with significant expressed sequence tag (EST alignments, while tobacco libraries made with the same enzymes had 51.7 and 65.3%, respectively. With the development of ultra-throughput sequencing technologies, this technique provides an opportunity to rapidly and efficiently obtain sequencing from gene-rich regions.

  1. Paired structures and other opposite-based models

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco, Camilo; Gómez, Daniel

    2015-01-01

    , that we will assume dependent on a specific negation, previously determined. In this way we can define a paired fuzzy set as a couple of opposite valuation fuzzy sets. Then we shall explore what kind of new valuation fuzzy sets can be generated from the semantic tension between those two poles, leading...... to a more complex valuation structure that still keeps the essence of being paired. In this way several neutral fuzzy sets can appear, in particular indeterminacy, ambivalence and conflict. Two consequences are then presented: on one hand, we will show how Atanassov´s Intuitionistic Fuzzy Sets can be viewed...... as a particular paired structure when the classical fuzzy negation is considered; on the other hand, the relationship of this model with bipolarity is reconsidered from our paired view....

  2. Tunable microwave properties of rhomboid shaped nanomagnet pairs

    Science.gov (United States)

    Tian, Chang; Adeyeye, Adekunle Olusola

    2017-12-01

    The magnetization dynamics of a multilayer rhomboid shaped nanomagnet pair is investigated using micro-focused Brillouin light scattering spectroscopy. The multilayer structure consists of two permalloy layers separated by a nonmagnetic Cr spacer layer. As compared with a single-layer rhomboid shaped nanomagnet pair with two distinct magnetic ground states (ferromagnetic and antiferromagnetic), the multilayer nanomagnetic pair displays multiple magnetic ground states upon different initialization fields due to the presence of both in-plane and out-of-plane dipolar coupling. The dynamic response as a function of initialization field has been systematically investigated. Distinct microwave absorption behavior and resonance frequency shift are observed when the nanomagnet pair is switched into different magnetic ground states. Micromagnetic simulations validate our experimental observations.

  3. Using Single Colors and Color Pairs to Communicate Basic Tastes

    Directory of Open Access Journals (Sweden)

    Andy T. Woods

    2016-07-01

    Full Text Available Recently, it has been demonstrated that people associate each of the basic tastes (e.g., sweet, sour, bitter, and salty with specific colors (e.g., red, green, black, and white. In the present study, we investigated whether pairs of colors (both associated with a particular taste or taste word would give rise to stronger associations relative to pairs of colors that were associated with different tastes. We replicate the findings of previous studies highlighting the existence of a robust crossmodal correspondence between individual colors and basic tastes. However, while there was evidence that pairs of colors could indeed communicate taste information more consistently than single colors, our participants took more than twice as long to match the color pairs with tastes than the single colors. Possible reasons for these results are discussed.

  4. Wind power wetland survey and duck pair count instructions

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Initial Survey Instructions for wind power wetland survey and duck pair count instructions for Kulm Wetland Management District. This survey has two surveying...

  5. Complexation of Nitrous Oxide by Frustrated Lewis Pairs

    NARCIS (Netherlands)

    Otten, Edwin; Neu, Rebecca C.; Stephan, Douglas W.

    2009-01-01

    Frustrated Lewis pairs comprised of a basic yet sterically encumbered phosphine with boron Lewis acids bind nitrous oxide to give intact PNNOB linkages. The synthesis, structure, and bonding of these species are described.

  6. Kondo physics in double quantum dot based Cooper pair splitters

    Science.gov (United States)

    Wrześniewski, Kacper; Weymann, Ireneusz

    2017-11-01

    The Andreev transport properties of double quantum dot based Cooper pair splitters with one superconducting and two normal leads are studied theoretically in the Kondo regime. The influence of the superconducting pairing correlations on the local density of states, Andreev transmission coefficient, and Cooper pair splitting efficiency is thoroughly analyzed. It is shown that finite superconducting pairing potential quickly suppresses the SU(2 ) Kondo effect, which can however reemerge for relatively large values of coupling to superconductor. In the SU(4 ) Kondo regime, a crossover from the SU(4 ) to the SU(2 ) Kondo state is found as the coupling to superconductor is enhanced. The analysis is performed by means of the density-matrix numerical renormalization group method.

  7. Strongly exchange-coupled triplet pairs in an organic semiconductor

    Science.gov (United States)

    Weiss, Leah R.; Bayliss, Sam L.; Kraffert, Felix; Thorley, Karl J.; Anthony, John E.; Bittl, Robert; Friend, Richard H.; Rao, Akshay; Greenham, Neil C.; Behrends, Jan

    2017-02-01

    From biological complexes to devices based on organic semiconductors, spin interactions play a key role in the function of molecular systems. For instance, triplet-pair reactions impact operation of organic light-emitting diodes as well as photovoltaic devices. Conventional models for triplet pairs assume they interact only weakly. Here, using electron spin resonance, we observe long-lived, strongly interacting triplet pairs in an organic semiconductor, generated via singlet fission. Using coherent spin manipulation of these two-triplet states, we identify exchange-coupled (spin-2) quintet complexes coexisting with weakly coupled (spin-1) triplets. We measure strongly coupled pairs with a lifetime approaching 3 μs and a spin coherence time approaching 1 μs, at 10 K. Our results pave the way for the utilization of high-spin systems in organic semiconductors.

  8. Pairing and Short-Range Correlations in Nuclear Systems

    Science.gov (United States)

    Rios, A.; Polls, A.; Dickhoff, W. H.

    2017-12-01

    The structure and density dependence of the pairing gap in infinite matter is relevant for astrophysical phenomena and provides a starting point for the discussion of pairing properties in nuclear structure. Short-range correlations can significantly deplete the available single-particle strength around the Fermi surface and thus provide a reduction mechanism of the pairing gap. Here, we study this effect in the singlet and triplet channels of both neutron matter and symmetric nuclear matter. Our calculations use phase-shift equivalent interactions and chiral two-body and three-body interactions as a starting point. We find an unambiguous reduction of the gap in all channels with very small dependence on the NN force in the singlet neutron matter and the triplet nuclear matter channel. In the latter channel, SRC alone provide a 50% reduction of the pairing gap.

  9. Pairs Trading to the Commodities Futures Market Using Cointegration Method

    Directory of Open Access Journals (Sweden)

    Cüneyt Ungever

    2015-10-01

    Full Text Available This paper investigates pairs trading strategy by using the cointegration method among the 10 most popular agricultural future markets. It is found that only in 2 pairs shows trading signal. The pairs trading strategy is performed in two stages that are the formation period and the trading period with daily futures data from 2004 to 2015. After the formation period was constructed, it is assumed that the cointegration error continues to hold the trading period same as it does for the formation period. The pairs trading strategy is created by the long position cotton and the short position coffee and also long position cotton and short position the livecattle. It is found that the profitability of this strategy worked well in both formation period and trading period.

  10. Decision Making in Kidney Paired Donation Programs with Altruistic Donors.

    Science.gov (United States)

    Li, Yijiang; Song, Peter X-K; Leichtman, Alan B; Rees, Michael A; Kalbfleisch, John D

    2014-01-01

    In recent years, kidney paired donation (KPD) has been extended to include living non-directed or altruistic donors, in which an altruistic donor donates to the candidate of an incompatible donor-candidate pair with the understanding that the donor in that pair will further donate to the candidate of a second pair, and so on; such a process continues and thus forms an altruistic donor-initiated chain. In this paper, we propose a novel strategy to sequentially allocate the altruistic donor (or bridge donor) so as to maximize the expected utility; analogous to the way a computer plays chess, the idea is to evaluate different allocations for each altruistic donor (or bridge donor) by looking several moves ahead in a derived look-ahead search tree. Simulation studies are provided to illustrate and evaluate our proposed method.

  11. Decision Making in Kidney Paired Donation Programs with Altruistic Donors*

    Science.gov (United States)

    Li, Yijiang; Song, Peter X.-K.; Leichtman, Alan B.; Rees, Michael A.; Kalbfleisch, John D.

    2014-01-01

    In recent years, kidney paired donation (KPD) has been extended to include living non-directed or altruistic donors, in which an altruistic donor donates to the candidate of an incompatible donor-candidate pair with the understanding that the donor in that pair will further donate to the candidate of a second pair, and so on; such a process continues and thus forms an altruistic donor-initiated chain. In this paper, we propose a novel strategy to sequentially allocate the altruistic donor (or bridge donor) so as to maximize the expected utility; analogous to the way a computer plays chess, the idea is to evaluate different allocations for each altruistic donor (or bridge donor) by looking several moves ahead in a derived look-ahead search tree. Simulation studies are provided to illustrate and evaluate our proposed method. PMID:25309603

  12. Pairing mechanism in the ferromagnetic superconductor UCoGe.

    Science.gov (United States)

    Wu, Beilun; Bastien, Gaël; Taupin, Mathieu; Paulsen, Carley; Howald, Ludovic; Aoki, Dai; Brison, Jean-Pascal

    2017-02-23

    Superconductivity is a unique manifestation of quantum mechanics on a macroscopic scale, and one of the rare examples of many-body phenomena that can be explained by predictive, quantitative theories. The superconducting ground state is described as a condensate of Cooper pairs, and a major challenge has been to understand which mechanisms could lead to a bound state between two electrons, despite the large Coulomb repulsion. An even bigger challenge is to identify experimentally this pairing mechanism, notably in unconventional superconductors dominated by strong electronic correlations, like in high-Tc cuprates, iron pnictides or heavy-fermion compounds. Here we show that in the ferromagnetic superconductor UCoGe, the field dependence of the pairing strength influences dramatically its macroscopic properties like the superconducting upper critical field, in a way that can be quantitatively understood. This provides a simple demonstration of the dominant role of ferromagnetic spin fluctuations in the pairing mechanism.

  13. LePaProGen—lepton pair production generator

    Science.gov (United States)

    Dydyshka, Ya. V.; Yermolchyk, V. L.; Suarez, J. H.; Shumeiko, N. M.

    2017-09-01

    A Monte Carlo generator "LePaProGen" for simulation of lepton pair production at hadron colliders is presented. Higher order electroweak radiative effects are implemented. A new algorithm for selection of the optimal phase space parameterization is applied.

  14. Brain Activation during Memory Encoding in Type 2 Diabetes Mellitus: A Discordant Twin Pair Study.

    Science.gov (United States)

    Wood, Amanda G; Chen, Jian; Moran, Christopher; Phan, Thanh; Beare, Richard; Cooper, Kimberley; Litras, Stacey; Srikanth, Velandai

    2016-01-01

    Type 2 diabetes mellitus increases the risk of dementia and neuronal dysfunction may occur years before perceptible cognitive decline. We aimed to study the impact of type 2 diabetes on brain activation during memory encoding in middle-aged people, controlling for age, sex, genes, and early-shared environment. Twenty-two twin pairs discordant for type 2 diabetes mellitus (mean age 60.9 years) without neurological disease were recruited from the Australian Twin Registry (ATR) and underwent functional magnetic resonance imaging (fMRI) during a memory encoding task, cognitive tests, and structural MRI. Type 2 diabetes was associated with significantly reduced activation in left hemisphere temporoparietal regions including angular gyrus, supramarginal gyrus, and middle temporal gyrus and significantly increased activation in bilateral posteriorly distributed regions. These findings were present in the absence of within-pair differences in standard cognitive test scores, brain volumes, or vascular lesion load. Differences in activation were more pronounced among monozygotic (MZ) pairs, with MZ individuals with diabetes also displaying greater frontal activation. These results provide evidence for preclinical memory-related neuronal dysfunction in type 2 diabetes. They support the search for modifiable later-life environmental factors or epigenetic mechanisms linking type 2 diabetes and cognitive decline.

  15. The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs

    DEFF Research Database (Denmark)

    Keibler, Evan; Arumugam, Manimozhiyan; Brent, Michael R

    2007-01-01

    MOTIVATION: Hidden Markov models (HMMs) and generalized HMMs been successfully applied to many problems, but the standard Viterbi algorithm for computing the most probable interpretation of an input sequence (known as decoding) requires memory proportional to the length of the sequence, which can......, our pair HMM based cDNA-to-genome aligner. AVAILABILITY: The TWINSCAN/N-SCAN/PAIRAGON open source software package is available from http://genes.cse.wustl.edu....... be prohibitive. Existing approaches to reducing memory usage either sacrifice optimality or trade increased running time for reduced memory. RESULTS: We developed two novel decoding algorithms, Treeterbi and Parallel Treeterbi, and implemented them in the TWINSCAN/N-SCAN gene-prediction system. The worst case...

  16. Major groove derivatization of an unnatural base pair.

    Science.gov (United States)

    Seo, Young Jun; Romesberg, Floyd E

    2009-09-21

    An unnatural base pair that is replicated and transcribed with good efficiency would lay the foundation for the long term goal of creating a semisynthetic organism, but also would have immediate in vitro applications, such as the enzymatic synthesis of site-specifically modified DNA and/or RNA. One of the most promising of the unnatural base pairs that we have identified is formed between d5SICS and dMMO2. The ortho substituents of these nucleotides are included to facilitate unnatural base pair extension, presumably by forming a hydrogen-bond with the polymerase, but the synthesis of the unnatural base pair still requires optimization. Recently, we have shown that meta and/or para substituents within the dMMO2 scaffold can facilitate unnatural base pair synthesis, although the mechanism remains unclear. To explore this issue, we synthesized and evaluated several dMMO2 derivatives with meta-chlorine, -bromine, -iodine, -methyl, or -propinyl substituents. Complete characterization of unnatural base pair and mispair synthesis and extension reveal that the modifications have large effects only on the efficiency of unnatural base pair synthesis and that the effects likely result from a combination of changes in steric interactions, polarity, and polarizability. The results also suggest that functionalized versions of the propinyl moiety of d5PrM should serve as suitable linkers to site-specifically incorporate other chemical functionalities into DNA. Similar modifications of d5SICS should allow labeling of DNA with two different functionalities, and the previously demonstrated efficient transcription of the unnatural base pair suggests that derivatives might similarly enable site-specific labeling of RNA.

  17. Predicting Currency Pair Trends using the Fractal Market Hypothesis

    OpenAIRE

    Blackledge, Jonathan; Murphy, Kieran

    2011-01-01

    This paper reports on the results of a research and development pro- gramme concerned with the analysis of currency pair exchange time series for Forex trading in an intensive applications and services environment. In particular, we present some of the preliminary results obtained for Forex trading using MetaTrader 4 with a new set of trend indicators deigned using a mathematical model that is based on the Fractal Market Hypothesis. This includes examples of various currency pair exchange rat...

  18. Flavor network and the principles of food pairing

    Science.gov (United States)

    Ahn, Yong-Yeol; Ahnert, Sebastian; Bagrow, James; Barabasi, Albert-Laszlo

    2011-03-01

    We construct and investigate a flavor network capturing the chemical similarity between the culinary ingredients. We found that Western cuisines have a statistically significant tendency to use ingredient pairs that share many flavor compounds, in line with the food pairing hypothesis used by some chefs and molecular gastronmists. By contrast, East Asian cuisine tend to avoid compound sharing ingredients. We identify key ingredients in each cuisine that help us to explore the differences and similarities between regional cuisines.

  19. Training IBM Watson using Automatically Generated Question-Answer Pairs

    OpenAIRE

    Lee, Jangho; Kim, Gyuwan; Yoo, Jaeyoon; Jung, Changwoo; Kim, Minseok; Yoon, Sungroh

    2016-01-01

    IBM Watson is a cognitive computing system capable of question answering in natural languages. It is believed that IBM Watson can understand large corpora and answer relevant questions more effectively than any other question-answering system currently available. To unleash the full power of Watson, however, we need to train its instance with a large number of well-prepared question-answer pairs. Obviously, manually generating such pairs in a large quantity is prohibitively time consuming and...

  20. Semirelativistic N-boson systems bound by attractive pair potentials

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Richard L [Department of Mathematics and Statistics, Concordia University, 1455 de Maisonneuve Boulevard West, Montreal, Quebec, H3G 1M8 (Canada); Lucha, Wolfgang [Institute for High Energy Physics, Austrian Academy of Sciences, Nikolsdorfergasse 18, A-1050 Vienna (Austria)], E-mail: rhall@mathstat.concordia.ca, E-mail: wolfgang.lucha@oeaw.ac.at

    2009-10-02

    We establish bounds on the energy of a system of N identical bosons bound by attractive pair potentials and obeying the semirelativistic Salpeter equation. The lower bound is provided by a 'reduction', with the aid of Jacobi relative coordinates, to a suitably scaled one-body Klein-Gordon problem. Complementary upper energy bounds are provided by means of a Gaussian trial function. Detailed results are presented for the exponential pair potential V(r) = -vexp(-r/a)

  1. Pairing effects in low density domain of nuclear matter

    OpenAIRE

    Isayev, A. A.; Bastrukov, S. I.; Yang, J.

    2004-01-01

    Using equations, governing np pairing correlations in S=1, T=0 pairing channel (PRC 63 (2001) 021304(R)), it is shown that at low densities equations for the energy gap in the spectrum of quasiparticles and chemical potentials of protons and neutrons allow solutions with negative chemical potential. This corresponds to appearance of Bose--Einstein condensate (BEC) of deuterons in low density region of nuclear matter.

  2. Model of pair aggregation on the Bethe lattice

    DEFF Research Database (Denmark)

    Baillet, M.V.-P.; Pacheco, A.F.; Gómez, J.B.

    1997-01-01

    We extend a recent model of aggregation of pairs of particles, analyzing the case in which the supporting framework is a Bethe lattice. The model exhibits a critical behavior of the percolation theory type.......We extend a recent model of aggregation of pairs of particles, analyzing the case in which the supporting framework is a Bethe lattice. The model exhibits a critical behavior of the percolation theory type....

  3. Galaxy pairs as a probe for mergers at z ~ 2

    DEFF Research Database (Denmark)

    Man, A.W.S.; Zirm, Andrew Wasmuth; Toft, Sune

    2011-01-01

    In this work I investigate the redshift evolution of pair fraction of a sample of 196 massive galaxies from z = 0 to 3, selected from the COSMOS field. We find that on average a massive galaxy undergoes ~ 1.1 \\pm 0.5 major merger since z = 3. I will review the current limitations of using the pair...... fraction as a probe for quantifying the impact of mergers on galaxy evolution. This work is based on the paper Man et al. (2011)....

  4. Numerical studies of pair creation in counterpropagating laser fields

    Energy Technology Data Exchange (ETDEWEB)

    Ruf, Matthias

    2009-05-27

    Pair creation from vacuum induced by electromagnetic fields is probably one of the most intriguing phenomena in physics. If the fields are sufficiently strong, the QED vacuum become unstable. Due to the remarkable progress in laser technology during recent years an experimental investigation of pair creation by pure laser light is coming into reach. The focus of this thesis is on pair creation in counterpropagating laser beams. The pair creation probability is calculated employing the numerically obtained solutions of the Dirac equation. This numerical ansatz has the capability of calculating the momentum distribution of the created pairs in a single propagation, for pure time dependent field configurations. Furthermore, it allows to take the magnetic component of the laser fields into account, which is usually neglected. The latter strongly affects the creation process at high laser frequency. The involved numerical calculations are rather time consuming, therefore the second project of this thesis was to develop a highly efficient code for solving relativistic quantum mechanical problems. This is accomplished by adopting the split-operator method to the Klein-Gordon equation. Here the possibility arises to use parallel computing. However the corresponding spin-statistics becomes crucial in the case of pair creation, demonstrated in several examples. (orig.)

  5. Modulation of pairing symmetry with bond disorder in unconventional superconductors

    Science.gov (United States)

    Kang, Yao-Tai; Tsai, Wei-Feng; Yao, Dao-Xin

    2017-04-01

    We study a two-orbital t -J1-J2 model, originally developed to describe iron-based superconductors at low energies, in the presence of bond disorder (via next-nearest-neighbor J2-bond dilution). By using the Bogoliubov-de Gennes approach, we self-consistently calculate the local pairing amplitudes and the corresponding density of states, which demonstrate a change of dominant pairing symmetry from s± wave to d wave when increasing disorder strength as long as J1≲J2 . Moreover, the combined pairing interaction and strong bond disorder lead to the formation of s±-wave "islands" with length scale of the superconducting coherence length embedded in a d -wave "sea." This picture is further complemented by the disorder-averaged pair-pair correlation functions, distinct from the case with potential disorder, where the "sea" is insulating. Due to this inevitable formation of spatial inhomogeneity, the superconducting Tc determined by the superfluid density ρs(T ) obviously deviates from the value predicted by the conventional Abrikosov-Gorkov theory, where the pairing amplitudes are viewed as uniformly suppressed as the disorder increases.

  6. Pair-instability supernovae in the local universe

    Energy Technology Data Exchange (ETDEWEB)

    Whalen, Daniel J. [Zentrum für Astronomie, Institut für Theoretische Astrophysik, Universität Heidelberg, Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany); Smidt, Joseph [CCS-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Heger, Alexander [Monash Centre for Astrophysics, Monash University, Victoria 3800 (Australia); Hirschi, Raphael [Astrophysics Group, EPSAM, University of Keele, Lennard-Jones Labs, Keele ST5 5BG (United Kingdom); Yusof, Norhasliza [Department of Physics, University of Malaysia, 50603 Kuala Lampur (Malaysia); Even, Wesley; Fryer, Chris L. [T-2, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Stiavelli, Massimo [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Chen, Ke-Jung [Department of Astronomy and Astrophysics, UCSC, Santa Cruz, CA 95064 (United States); Joggerst, Candace C. [XTD-3, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2014-12-10

    The discovery of 150-300 M {sub ☉} stars in the Local Group and pair-instability supernova candidates at low redshifts has excited interest in this exotic explosion mechanism. Realistic light curves for pair-instability supernovae at near-solar metallicities are key to identifying and properly interpreting these events as more are found. We have modeled pair-instability supernovae of 150-500 M {sub ☉} Z ∼ 0.1-0.4 Z {sub ☉} stars. These stars lose up to 80% of their mass to strong line-driven winds and explode as bare He cores. We find that their light curves and spectra are quite different from those of Population III pair-instability explosions, which therefore cannot be used as templates for low-redshift events. Although non-zero metallicity pair-instability supernovae are generally dimmer than their Population III counterparts, in some cases they will be bright enough to be detected at the earliest epochs at which they can occur, the formation of the first galaxies at z ∼ 10-15. Others can masquerade as dim, short duration supernovae that are only visible in the local universe and that under the right conditions could be hidden in a wide variety of supernova classes. We also report for the first time that some pair-instability explosions can create black holes with masses of ∼100 M {sub ☉}.

  7. Successful same-sex pairing in Laysan albatross.

    Science.gov (United States)

    Young, Lindsay C; Zaun, Brenda J; Vanderwerf, Eric A

    2008-08-23

    Unrelated same-sex individuals pairing together and cooperating to raise offspring over many years is a rare occurrence in the animal kingdom. Cooperative breeding, in which animals help raise offspring that are not their own, is often attributed to kin selection when individuals are related, or altruism when individuals are unrelated. Here we document long-term pairing of unrelated female Laysan albatross (Phoebastria immutabilis) and show how cooperation may have arisen as a result of a skewed sex ratio in this species. Thirty-one per cent of Laysan albatross pairs on Oahu were female-female, and the overall sex ratio was 59% females as a result of female-biased immigration. Female-female pairs fledged fewer offspring than male-female pairs, but this was a better alternative than not breeding. In most female-female pairs that raised a chick in more than 1 year, at least one offspring was genetically related to each female, indicating that both females had opportunities to reproduce. These results demonstrate how changes in the sex ratio of a population can shift the social structure and cause cooperative behaviour to arise in a monogamous species, and they also underscore the importance of genetically sexing monomorphic species.

  8. a Study of Pairing Interaction in a Separable Form

    Science.gov (United States)

    Tian, Yuan; Ma, Zhongyu; Ring, P.

    2008-04-01

    The pairing force of Gogny in the 1S0 channel has been applied with great success in many applications in finite nuclei. It is of finite range and therefore rather complicated. Based on this force, we propose a new rather simple pairing interaction, which has basically the same properties as the Gogny force. It is separable in momentum space, translational invariant and, as the Gogny force of finite range. Using techniques of Talmi and Moshinsky, we show, that it can be represented as a sum of separable terms in oscillator space, which converges quickly. Because of its separability it is very easy to handle. It is fully determined by the Gogny force. It is used for the calculation of pairing properties of finite nuclei in the Relativistic Hartree Bogoliubov (RHB) approach. It is found that this new force can well depict the pairing properties on almost the same footing as the original pairing interaction not only in nuclear matter, but also in finite nuclei. This simple force can be easily applied in the calculation of deformed nuclei, and the investigation of pairing properties in nuclei close to the drip lines as well as for further investigations going beyond mean field.

  9. Extra-Pair Mating and Evolution of Cooperative Neighbourhoods

    Science.gov (United States)

    Eliassen, Sigrunn; Jørgensen, Christian

    2014-01-01

    A striking but unexplained pattern in biology is the promiscuous mating behaviour in socially monogamous species. Although females commonly solicit extra-pair copulations, the adaptive reason has remained elusive. We use evolutionary modelling of breeding ecology to show that females benefit because extra-pair paternity incentivizes males to shift focus from a single brood towards the entire neighbourhood, as they are likely to have offspring there. Male-male cooperation towards public goods and dear enemy effects of reduced territorial aggression evolve from selfish interests, and lead to safer and more productive neighbourhoods. The mechanism provides adaptive explanations for the common empirical observations that females engage in extra-pair copulations, that neighbours dominate as extra-pair sires, and that extra-pair mating correlates with predation mortality and breeding density. The models predict cooperative behaviours at breeding sites where males cooperate more towards public goods than females. Where maternity certainty makes females care for offspring at home, paternity uncertainty and a potential for offspring in several broods make males invest in communal benefits and public goods. The models further predict that benefits of extra-pair mating affect whole nests or neighbourhoods, and that cuckolding males are often cuckolded themselves. Derived from ecological mechanisms, these new perspectives point towards the evolution of sociality in birds, with relevance also for mammals and primates including humans. PMID:24987839

  10. Extra-pair mating and evolution of cooperative neighbourhoods.

    Directory of Open Access Journals (Sweden)

    Sigrunn Eliassen

    Full Text Available A striking but unexplained pattern in biology is the promiscuous mating behaviour in socially monogamous species. Although females commonly solicit extra-pair copulations, the adaptive reason has remained elusive. We use evolutionary modelling of breeding ecology to show that females benefit because extra-pair paternity incentivizes males to shift focus from a single brood towards the entire neighbourhood, as they are likely to have offspring there. Male-male cooperation towards public goods and dear enemy effects of reduced territorial aggression evolve from selfish interests, and lead to safer and more productive neighbourhoods. The mechanism provides adaptive explanations for the common empirical observations that females engage in extra-pair copulations, that neighbours dominate as extra-pair sires, and that extra-pair mating correlates with predation mortality and breeding density. The models predict cooperative behaviours at breeding sites where males cooperate more towards public goods than females. Where maternity certainty makes females care for offspring at home, paternity uncertainty and a potential for offspring in several broods make males invest in communal benefits and public goods. The models further predict that benefits of extra-pair mating affect whole nests or neighbourhoods, and that cuckolding males are often cuckolded themselves. Derived from ecological mechanisms, these new perspectives point towards the evolution of sociality in birds, with relevance also for mammals and primates including humans.

  11. On magnon mediated Cooper pair formation in ferromagnetic superconductors

    Directory of Open Access Journals (Sweden)

    Rakesh Kar

    2014-08-01

    Full Text Available Identification of pairing mechanism leading to ferromagnetic superconductivity is one of the most challenging issues in condensed matter physics. Although different models have been proposed to explain this phenomenon, a quantitative understanding about this pairing is yet to be achieved. Using the localized-itinerant model, we find that in ferromagnetic superconducting materials both triplet pairing and singlet pairing of electrons are possible through magnon exchange depending upon whether the Debye cut off frequency of magnons is greater or lesser than the Hund's coupling (J multiplied by average spin (S per site. Taking into account the repulsive interaction due to the existence of paramagnons, we also find an expression for effective interaction potential between a pair of electrons with opposite spins. We apply the developed formalism in case of UGe2 and URhGe. The condition of singlet pairing is found to be fulfilled in these cases, as was previously envisaged by Suhl [Suhl, Phys. Rev. Lett. 87, 167007 (2001]. We compute the critical temperatures of URhGe at ambient pressure and of UGe2 under different pressures for the first time through BCS equation. Thus, this work outlines a very simple way to evaluate critical temperature in case of a superconducting system. A close match with the available experimental results strongly supports our theoretical treatment.

  12. gene structure, gene expression

    Indian Academy of Sciences (India)

    Primer 5.0 software. To adjust for RNA quality and diffe- rences in cDNA concentration, we amplified actin as an internal control with the following primers: PtActin-F (5′-TG. AAGGAGAAACTTGCGTAT-3′) and PtActin-R (5′-GCA. CAATGTTACCGTACAGAT-3′). These genes were ampli- fied from first-strand cDNA using ...

  13. Whole-Genome Analysis of Gene Conversion Events

    Science.gov (United States)

    Hsu, Chih-Hao; Zhang, Yu; Hardison, Ross; Miller, Webb

    Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify orthologs and to transfer functional annotation between genomes. Here we examine 1,112,202 paralogous pairs of human genomic intervals, and detect conversion events in about 13.5% of them. Properties of the putative gene conversions are analyzed, such as the lengths of the paralogous pairs and the spacing between their sources and targets. Our approach is illustrated using conversion events in the beta-globin gene cluster.

  14. Analysis of copy number variants in 11 pairs of monozygotic twins with neurofibromatosis type 1.

    Science.gov (United States)

    Sites, Emily R; Smolarek, Teresa A; Martin, Lisa J; Viskochil, David H; Stevenson, David A; Ullrich, Nicole J; Messiaen, Ludwine M; Schorry, Elizabeth K

    2017-03-01

    Phenotypic variability among individuals with neurofibromatosis type 1 (NF1) has long been a challenge for clinicians and an enigma for researchers. Members of the same family and even identical twins with NF1 often demonstrate variable disease expression. Many mechanisms for this variability have been proposed. We have performed an exploratory study of copy number variants (CNVs) as a possible source of phenotypic variability in NF1. We enrolled 11 pairs of monozygotic (MZ) twins with NF1 and their parents, catalogued their clinical characteristics, and utilized a single nucleotide polymorphism (SNP) microarray to identify CNVs in blood and saliva. The 11 twin pairs showed high concordance for presence and number of café-au-lait spots, cutaneous neurofibromas, IQ, and ADHD. They were more likely to be discordant for optic pathway glioma, plexiform neurofibromas, skeletal manifestations, and malignancy. Microarray analysis identified a total of 81 CNVs meeting our conservative criteria, 37 of which overlap known genes. Of interest, three CNVs were previously unreported. Microarray analysis failed to ascertain any CNV differences within twin pairs, between twins and parents, or between tissues in any one individual. Results of this small pilot study did not demonstrate any de novo CNV events in our MZ twin pairs, nor were de novo CNVs overrepresented in these individuals with NF1. A much larger sample size would be needed to form any conclusions about the role of CNVs in NF1 variable expressivity. Alternative explanations for discordant phenotypes include epigenetic changes, smaller genetic alterations, or environmental factors. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  15. AtMND1 is required for homologous pairing during meiosis in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohan PA

    2006-07-01

    Full Text Available Abstract Background Pairing of homologous chromosomes at meiosis is an important requirement for recombination and balanced chromosome segregation among the products of meiotic division. Recombination is initiated by double strand breaks (DSBs made by Spo11 followed by interaction of DSB sites with a homologous chromosome. This interaction requires the strand exchange proteins Rad51 and Dmc1 that bind to single stranded regions created by resection of ends at the site of DSBs and promote interactions with uncut DNA on the homologous partner. Recombination is also considered to be dependent on factors that stabilize interactions between homologous chromosomes. In budding yeast Hop2 and Mnd1 act as a complex to promote homologous pairing and recombination in conjunction with Rad51 and Dmc1. Results We have analyzed the function of the Arabidopsis orthologue of the budding yeast MND1 gene (AtMND1. Loss of AtMND1 did not affect normal vegetative development but caused fragmentation and missegregation of chromosomes in male and female meiosis, formation of inviable gametes, and sterility. Analysis of the Atmnd1 Atspo11-1 double mutant indicated that chromosome fragmentation in Atmnd1 was suppressed by loss of Atspo11-1. Fluorescence in situ hybridization (FISH analysis showed that homologous pairing failed to occur and homologues remained apart throughout meiosis. AtMND1 showed strong expression in meiocytes as revealed by RNA in situs. Conclusion We conclude that AtMND1 is required for homologous pairing and is likely to play a role in the repair of DNA double strand breaks during meiosis in Arabidopsis, thus showing conservation of function with that of MND1 during meiosis in yeast.

  16. Does base-pairing strength play a role in microRNA repression?

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    Carmel, Ido; Shomron, Noam; Heifetz, Yael

    2012-11-01

    MicroRNAs (miRNAs) are short, single-stranded RNAs that silence gene expression by either degrading mRNA or repressing translation. Each miRNA regulates a specific set of mRNA "targets" by binding to complementary sequences in their 3' untranslated region. In this study, we examined the importance of the base-pairing strength of the miRNA-target duplex to repression. We hypothesized that if base-pairing strength affects the functionality of miRNA repression, organisms with higher body temperature or that live at higher temperatures will have miRNAs with higher G/C content so that the miRNA-target complex will remain stable. In the nine model organisms examined, we found a significant correlation between the average G/C content of miRNAs and physiological temperature, supporting our hypothesis. Next, for each organism examined, we compared the average G/C content of miRNAs that are conserved among distant organisms and that of miRNAs that are evolutionarily recent. We found that the average G/C content of ancient miRNAs is lower than recent miRNAs in homeotherms, whereas the trend was inversed in poikilotherms, suggesting that G/C content is associated with temperature, thus further supporting our hypothesis. In the organisms examined, the average G/C content of miRNA "seed" sequences was higher than that of mature miRNAs, which was higher than pre-miRNA loops, suggesting an association between the degree of functionality of the sequence and its average G/C content. Our analyses show a possible association between the base-pairing strength of miRNA-targets and the temperature of an organism, suggesting that base-pairing strength plays a role in repression by miRNAs.

  17. Caudal regulates the spatiotemporal dynamics of pair-rule waves in Tribolium.

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    Ezzat El-Sherif

    2014-10-01

    Full Text Available In the short-germ beetle Tribolium castaneum, waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes, partitioning the anterior-posterior axis into segments. Similar waves in vertebrates are assumed to arise due to the modulation of a molecular clock by a posterior-to-anterior frequency gradient. However, neither a molecular candidate nor a functional role has been identified to date for such a frequency gradient, either in vertebrates or elsewhere. Here we provide evidence that the posterior gradient of Tc-caudal expression regulates the oscillation frequency of pair-rule gene expression in Tribolium. We show this by analyzing the spatiotemporal dynamics of Tc-even-skipped expression in strong and mild knockdown of Tc-caudal, and by correlating the extension, level and slope of the Tc-caudal expression gradient to the spatiotemporal dynamics of Tc-even-skipped expression in wild type as well as in different RNAi knockdowns of Tc-caudal regulators. Further, we show that besides its absolute importance for stripe generation in the static phase of the Tribolium blastoderm, a frequency gradient might serve as a buffer against noise during axis elongation phase in Tribolium as well as vertebrates. Our results highlight the role of frequency gradients in pattern formation.

  18. Mutation Pattern of Paired Immunoglobulin Heavy and Light Variable Domains in Chronic Lymphocytic Leukemia B Cells

    KAUST Repository

    Ghiotto, Fabio

    2011-01-01

    B-cell chronic lymphocytic leukemia (CLL) patients display leukemic clones bearing either germline or somatically mutated immunoglobulin heavy variable (IGHV ) genes. Most information on CLL immunoglobulins (Igs), such as the definition of stereotyped B-cell receptors (BCRs), was derived from germline unmutated Igs. In particular, detailed studies on the distribution and nature of mutations in paired heavy- and light-chain domains of CLL clones bearing mutated Igs are lacking. To address the somatic hyper-mutation dynamics of CLL Igs, we analyzed the mutation pattern of paired IGHV-diversity-joining (IGHV-D-J ) and immunoglobulin kappa/lambda variable-joining (IGK/LV-J ) rearrangements of 193 leukemic clones that displayed ≥ 2% mutations in at least one of the two immunoglobulin variable (IGV ) genes (IGHV and/or IGK/LV ). The relationship between the mutation frequency in IGHV and IGK/LV complementarity determining regions (CDRs) and framework regions (FRs) was evaluated by correlation analysis. Replacement (R) mutation frequency within IGK/LV chain CDRs correlated significantly with mutation frequency of paired IGHV CDRs in λ but not κ isotype CLL clones. CDRs of IGKV-J rearrangements displayed a lower percentage of R mutations than IGHVs. The frequency/pattern of mutations in kappa CLL Igs differed also from that in κ-expressing normal B cells described in the literature. Instead, the mutation frequency within the FRs of IGHV and either IGKV or IGLV was correlated. Notably, the amount of diversity introduced by replaced amino acids was comparable between IGHVs and IGKVs. The data indicate a different mutation pattern between κ and λ isotype CLL clones and suggest an antigenic selection that, in κ samples, operates against CDR variation.

  19. Cytoplasmic and Genomic Effects on Meiotic Pairing in Brassica Hybrids and Allotetraploids from Pair Crosses of Three Cultivated Diploids

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    Cui, Cheng; Ge, Xianhong; Gautam, Mayank; Kang, Lei; Li, Zaiyun

    2012-01-01

    Interspecific hybridization and allopolyploidization contribute to the origin of many important crops. Synthetic Brassica is a widely used model for the study of genetic recombination and “fixed heterosis” in allopolyploids. To investigate the effects of the cytoplasm and genome combinations on meiotic recombination, we produced digenomic diploid and triploid hybrids and trigenomic triploid hybrids from the reciprocal crosses of three Brassica diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC). The chromosomes in the resultant hybrids were doubled to obtain three allotetraploids (B. juncea, AA.BB; B. napus, AA.CC; B. carinata, BB.CC). Intra- and intergenomic chromosome pairings in these hybrids were quantified using genomic in situ hybridization and BAC-FISH. The level of intra- and intergenomic pairings varied significantly, depending on the genome combinations and the cytoplasmic background and/or their interaction. The extent of intragenomic pairing was less than that of intergenomic pairing within each genome. The extent of pairing variations within the B genome was less than that within the A and C genomes, each of which had a similar extent of pairing. Synthetic allotetraploids exhibited nondiploidized meiotic behavior, and their chromosomal instabilities were correlated with the relationship of the genomes and cytoplasmic background. Our results highlight the specific roles of the cytoplasm and genome to the chromosomal behaviors of hybrids and allopolyploids. PMID:22505621

  20. Olfactory interference during inhibitory backward pairing in honey bees.

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    Matthieu Dacher

    Full Text Available Restrained worker honey bees are a valuable model for studying the behavioral and neural bases of olfactory plasticity. The proboscis extension response (PER; the proboscis is the mouthpart of honey bees is released in response to sucrose stimulation. If sucrose stimulation is preceded one or a few times by an odor (forward pairing, the bee will form a memory for this association, and subsequent presentations of the odor alone are sufficient to elicit the PER. However, backward pairing between the two stimuli (sucrose, then odor has not been studied to any great extent in bees, although the vertebrate literature indicates that it elicits a form of inhibitory plasticity.If hungry bees are fed with sucrose, they will release a long lasting PER; however, this PER can be interrupted if an odor is presented 15 seconds (but not 7 or 30 seconds after the sucrose (backward pairing. We refer to this previously unreported process as olfactory interference. Bees receiving this 15 second backward pairing show reduced performance after a subsequent single forward pairing (excitatory conditioning trial. Analysis of the results supported a relationship between olfactory interference and a form of backward pairing-induced inhibitory learning/memory. Injecting the drug cimetidine into the deutocerebrum impaired olfactory interference.Olfactory interference depends on the associative link between odor and PER, rather than between odor and sucrose. Furthermore, pairing an odor with sucrose can lead either to association of this odor to PER or to the inhibition of PER by this odor. Olfactory interference may provide insight into processes that gate how excitatory and inhibitory memories for odor-PER associations are formed.