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Sample records for terminal repeat retroelements

  1. The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species

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    Rangwala Sanjida H

    2010-03-01

    Full Text Available Abstract Background Sadhu elements are non-autonomous retroposons first recognized in Arabidopsis thaliana. There is a wide degree of divergence among different elements, suggesting that these sequences are ancient in origin. Here we report the results of several lines of investigation into the genomic organization and evolutionary history of this element family. Results We present a classification scheme for Sadhu elements in A. thaliana, describing derivative elements related to the full-length elements we reported previously. We characterized Sadhu5 elements in a set of A. thaliana strains in order to trace the history of radiation in this subfamily. Sequences surrounding the target sites of different Sadhu insertions are consistent with mobilization by LINE retroelements. Finally, we identified Sadhu elements grouping into distinct subfamilies in two related species, Arabidopsis arenosa and Arabidopsis lyrata. Conclusions Our analyses suggest that the Sadhu retroelement family has undergone target primed reverse transcription-driven retrotransposition during the divergence of different A. thaliana strains. In addition, Sadhu elements can be found at moderate copy number in three distinct Arabidopsis species, indicating that the evolutionary history of these sequences can be traced back at least several millions of years.

  2. LTR retroelements in the genome of Daphnia pulex.

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    Rho, Mina; Schaack, Sarah; Gao, Xiang; Kim, Sun; Lynch, Michael; Tang, Haixu

    2010-07-09

    Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex. We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95), BEL/Pao (66) and DIRS (19) retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals) and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed. Given the importance of LTR retroelements activity in the

  3. LTR retroelements in the genome of Daphnia pulex

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    Kim Sun

    2010-07-01

    Full Text Available Abstract Background Long terminal repeat (LTR retroelements represent a successful group of transposable elements (TEs that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex. Results We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95, BEL/Pao (66 and DIRS (19 retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed. Conclusions

  4. Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria.

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    Feng Jiang

    Full Text Available BACKGROUND: Retroelements can successfully colonize eukaryotic genome through RNA-mediated transposition, and are considered to be some of the major mediators of genome size. The migratory locust Locusta migratoria is an insect with a large genome size, and its genome is probably subject to the proliferation of retroelements. An analysis of deep-sequencing transcriptome data will elucidate the structure, diversity and expression characteristics of retroelements. RESULTS: We performed a de novo assembly from deep sequencing RNA-seq data and identified 105 retroelements in the locust transcriptome. Phylogenetic analysis of reverse transcriptase sequences revealed 1 copia, 1 BEL, 8 gypsy and 23 non-long terminal repeat (LTR retroelements in the locust transcriptome. A novel approach was developed to identify full-length LTR retroelements. A total of 5 full-length LTR retroelements and 2 full-length non-LTR retroelements that contained complete structures for retrotransposition were identified. Structural analysis indicated that all these retroelements may have been activated or deprived of retrotransposition activities very recently. Expression profiling analysis revealed that the retroelements exhibited a unique expression pattern at the egg stage and showed differential expression profiles between the solitarious and gregarious phases at the fifth instar and adult stage. CONCLUSION: We hereby present the first de novo transcriptome analysis of retroelements in a species whose genome is not available. This work contributes to a comprehensive understanding of the landscape of retroelements in the locust transcriptome. More importantly, the results reveal that non-LTR retroelements are abundant and diverse in the locust transcriptome.

  5. LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types.

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    Rodriguez, Fernando; Kenefick, Aubrey W; Arkhipova, Irina R

    2017-04-11

    Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highlydiversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotiferspecific and encode a dUTPase domain. However only one lineage contains a canonical envlike fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3'-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements.

  6. Adeno-associated virus inverted terminal repeats stimulate gene editing.

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    Hirsch, M L

    2015-02-01

    Advancements in genome editing have relied on technologies to specifically damage DNA which, in turn, stimulates DNA repair including homologous recombination (HR). As off-target concerns complicate the therapeutic translation of site-specific DNA endonucleases, an alternative strategy to stimulate gene editing based on fragile DNA was investigated. To do this, an episomal gene-editing reporter was generated by a disruptive insertion of the adeno-associated virus (AAV) inverted terminal repeat (ITR) into the egfp gene. Compared with a non-structured DNA control sequence, the ITR induced DNA damage as evidenced by increased gamma-H2AX and Mre11 foci formation. As local DNA damage stimulates HR, ITR-mediated gene editing was investigated using DNA oligonucleotides as repair substrates. The AAV ITR stimulated gene editing >1000-fold in a replication-independent manner and was not biased by the polarity of the repair oligonucleotide. Analysis of additional human DNA sequences demonstrated stimulation of gene editing to varying degrees. In particular, inverted yet not direct, Alu repeats induced gene editing, suggesting a role for DNA structure in the repair event. Collectively, the results demonstrate that inverted DNA repeats stimulate gene editing via double-strand break repair in an episomal context and allude to efficient gene editing of the human chromosome using fragile DNA sequences.

  7. Tdd-4, a DNA transposon of Dictyostelium that encodes proteins similar to LTR retroelement integrases.

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    Wells, D J

    1999-06-01

    Tdd-4 is the first DNA transposon to be isolated from Dictyostelium discoideum. This element was isolated by insertion into a target plasmid. Two classes of elements were identified which include a 3.8 kb version and a 3.4 kb deleted version. Sequence analysis reveals that the 145 bp inverted terminal repeats contain the 5'-TGellipsisCA-3' conserved terminal dinucleotides found in prokaryotic transposons and integrated LTR retroelement DNA sequences. Tdd-4 open reading frames are assembled by removal of six introns. Introns 1-5 conform to the GT-AG rule, whereas intron 6 appears to be an AT-AA intron. Also, intron 6 undergoes an alternative 5' splicing reaction. The alternatively spliced region encodes 15 tandem SPXX repeats that are proposed to function as a DNA binding motif. By analogy to other transposons that encode two proteins from the same gene, the full-length Tdd-4 protein is the putative transposase and the truncated Tdd-4 protein is the putative transposition inhibitor. Protein database searches demonstrate Tdd-4 encoded proteins are unique for a DNA element by containing similarities to retroviral/retrotransposon integrases. The putative Tdd-4 transposase contains the same structural relationship as integrases by possessing an N-terminal HHCC motif, a central DDE motif and a C-terminal DNA-binding domain composed of the SPXX motif.

  8. Do women with a repeat termination of pregnancy prefer a medical or a surgical regimen?

    DEFF Research Database (Denmark)

    Worm Frandsen, Maja; Rørbye, Christina; Nilas, Lisbeth

    2014-01-01

    We compared the risk of a repeat termination and the method of termination in women with a prior medical or surgical termination, or both, in a cohort study of women with a pregnancy termination at gestational age ≤63 days in 1999-2001. Within 5 years, 24% (330/1379) had a repeat abortion......, and repeat terminations were more frequent in the surgical [27% (159/588)] than the medical group [22% (171/791)] (p medical in 49% (83/171) of women with an earlier medical termination, compared with 13% (21/159) (p ... surgical termination. In 125 women who had experienced both procedures, 37% (46/125) of the next terminations were performed medically and 63% (79/125) surgically (p surgical termination....

  9. Adeno-associated virus inverted terminal repeats stimulate gene editing

    OpenAIRE

    Hirsch, ML

    2014-01-01

    Advancements in genome editing have relied on technologies to specifically damage DNA which, in turn, stimulates DNA repair including homologous recombination (HR). As off-target concerns complicate the therapeutic translation of site-specific DNA endonucleases, an alternative strategy to stimulate gene editing based on fragile DNA was investigated. To do this, an episomal gene-editing reporter was generated by a disruptive insertion of the adeno-associated virus (AAV) inverted terminal repea...

  10. Heat-shock induction of the human immunodeficiency virus long terminal repeat

    NARCIS (Netherlands)

    Geelen, J. L.; Minnaar, R. P.; Boom, R.; van der Noordaa, J.; Goudsmit, J.

    1988-01-01

    Rat cell lines were established in which the bacterial chloramphenicol acetyltransferase (CAT) gene under control of the human immunodeficiency virus (HIV) long terminal repeat (LTR) was stably integrated. The cell lines showed a repressed phenotype for CAT expression, but could be induced for it by

  11. [Repeated requests for termination of pregnancy. Some socio-cultural and psychological aspects].

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    Mattauer, B; Peyrot, D; Aussiloux, M T

    1984-04-01

    Characteristics of 170 women seeking abortions who had had no previous pregnancy terminations and 63 who had 1 or more previous terminations were compared. 49 women aged 20-43 had had 1 previous abortion, 9 aged 21-38 had had 2, 3 aged 29-33 had had 3, 1 aged 37 had had 4, and 1 aged 37 had had 5 previous abortions. 5 women, of whom 4 had had previous terminations, did not undergo abortions after completing the interviews. Among women seeking repeat abortions, 39.21% had psychological motivations, 36.04% had family motivations, and 26.9% had social motivations. Family motivations included difficulties with existing children and instability of the couple, while social motivations included preference for other activities, single marital status, and immaturity of the mother. Among sociocultural factors associated with repeated abortions, death and divorce were uncommon, unlike the situation in 1st abortions. Familial and social factors associated with repeat abortions were, in declining order of frequency, abandonment, difficult schooling, geographic or social instability, and conjugal conflicts. Religious practice was associated with a reduced risk of repeat abortion. Among psychological factors associated with repeat abortion, passivity, dependence, and immaturity were associated with a doubled risk, as were sadomasochistic or depressive personality and previous psychiatric treatment. Failure to use contraception, associated with ambivalence in relation to desire for children or moral aversion to the use of contraception, were other factors. Women with defective parental images had 3 times the risk of repeat abortion. Previous difficulties of pregnancy or delivery were associated with a higher risk of repeat abortion.

  12. Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

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    Cervera, Amelia; De la Peña, Marcos

    2014-01-01

    Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes. PMID:25135949

  13. Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens.

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    Choulet, Frédéric; Gallois, Alexandre; Aigle, Bertrand; Mangenot, Sophie; Gerbaud, Claude; Truong, Chantal; Francou, François-Xavier; Borges, Frédéric; Fourrier, Céline; Guérineau, Michel; Decaris, Bernard; Barbe, Valérie; Pernodet, Jean-Luc; Leblond, Pierre

    2006-09-01

    The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.

  14. Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes

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    Gladyshev, Eugene A.; Arkhipova, Irina R.

    2007-01-01

    The evolutionary origin of telomerases, enzymes that maintain the ends of linear chromosomes in most eukaryotes, is a subject of debate. Penelope-like elements (PLEs) are a recently described class of eukaryotic retroelements characterized by a GIY-YIG endonuclease domain and by a reverse transcriptase domain with similarity to telomerases and group II introns. Here we report that a subset of PLEs found in bdelloid rotifers, basidiomycete fungi, stramenopiles, and plants, representing four different eukaryotic kingdoms, lack the endonuclease domain and are located at telomeres. The 5′ truncated ends of these elements are telomere-oriented and typically capped by species-specific telomeric repeats. Most of them also carry several shorter stretches of telomeric repeats at or near their 3′ ends, which could facilitate utilization of the telomeric G-rich 3′ overhangs to prime reverse transcription. Many of these telomere-associated PLEs occupy a basal phylogenetic position close to the point of divergence from the telomerase-PLE common ancestor and may descend from the missing link between early eukaryotic retroelements and present-day telomerases. PMID:17483479

  15. Expression of Drosophila virilis retroelements and role of small RNAs in their intrastrain transposition.

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    Nikolay V Rozhkov

    Full Text Available Transposition of two retroelements (Ulysses and Penelope mobilized in the course of hybrid dysgenesis in Drosophila virilis has been investigated by in situ hybridization on polytene chromosomes in two D. virilis strains of different cytotypes routinely used to get dysgenic progeny. The analysis has been repeatedly performed over the last two decades, and has revealed transpositions of Penelope in one of the strains, while, in the other strain, the LTR-containing element Ulysses was found to be transpositionally active. The gypsy retroelement, which has been previously shown to be transpositionally inactive in D. virilis strains, was also included in the analysis. Whole mount is situ hybridization with the ovaries revealed different subcellular distribution of the transposable elements transcripts in the strains studied. Ulysses transpositions occur only in the strain where antisense piRNAs homologous to this TE are virtually absent and the ping-pong amplification loop apparently does not take place. On the other hand small RNAs homologous to Penelope found in the other strain, belong predominantly to the siRNA category (21nt, and consist of sense and antisense species observed in approximately equal proportion. The number of Penelope copies in the latter strain has significantly increased during the last decades, probably because Penelope-derived siRNAs are not maternally inherited, while the low level of Penelope-piRNAs, which are faithfully transmitted from mother to the embryo, is not sufficient to silence this element completely. Therefore, we speculate that intrastrain transposition of the three retroelements studied is controlled predominantly at the post-transcriptional level.

  16. Expression of Drosophila virilis Retroelements and Role of Small RNAs in Their Intrastrain Transposition

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    Rozhkov, Nikolay V.; Zelentsova, Elena S.; Shostak, Natalia G.; Evgen'ev, Michael B.

    2011-01-01

    Transposition of two retroelements (Ulysses and Penelope) mobilized in the course of hybrid dysgenesis in Drosophila virilis has been investigated by in situ hybridization on polytene chromosomes in two D. virilis strains of different cytotypes routinely used to get dysgenic progeny. The analysis has been repeatedly performed over the last two decades, and has revealed transpositions of Penelope in one of the strains, while, in the other strain, the LTR-containing element Ulysses was found to be transpositionally active. The gypsy retroelement, which has been previously shown to be transpositionally inactive in D. virilis strains, was also included in the analysis. Whole mount is situ hybridization with the ovaries revealed different subcellular distribution of the transposable elements transcripts in the strains studied. Ulysses transpositions occur only in the strain where antisense piRNAs homologous to this TE are virtually absent and the ping-pong amplification loop apparently does not take place. On the other hand small RNAs homologous to Penelope found in the other strain, belong predominantly to the siRNA category (21nt), and consist of sense and antisense species observed in approximately equal proportion. The number of Penelope copies in the latter strain has significantly increased during the last decades, probably because Penelope-derived siRNAs are not maternally inherited, while the low level of Penelope-piRNAs, which are faithfully transmitted from mother to the embryo, is not sufficient to silence this element completely. Therefore, we speculate that intrastrain transposition of the three retroelements studied is controlled predominantly at the post-transcriptional level. PMID:21779346

  17. A mouse mammary tumor virus-like long terminal repeat superantigen in human breast cancer.

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    Wang, Yue; Jiang, Jian-Dong; Xu, Dongping; Li, Yan; Qu, Chunfeng; Holland, James F; Pogo, Beatriz G-T

    2004-06-15

    We previously reported a 660-bp mouse mammary tumor virus (MMTV)-like env gene sequence in approximately 38% of human breast cancer DNA, but not in normal breasts or other tumors. This MMTV-like env gene sequence was expressed in 66% of the env gene-positive human breast cancers. An entire proviral structure was identified in human breast cancer DNA with high homology to MMTV and low homology to known human endogenous retrovirus. MMTV-like long terminal repeat (LTR) sequences were also detected in 41.5% of human breast cancers. They contain hormone-responsive elements, TEF-1 family elements, and the open reading frame for the superantigen (SAg). We have now amplified and sequenced MMTV-like sag sequences from 10 human breast cancers, and we found that they are highly homologous to those of MMTV. However, deletions and insertions at the COOH-terminal of sag were observed. The immune function of the human MMTV-like LTR SAg was also investigated. The sag gene was cloned and expressed in a human B-cell line (Ramos). T-cell proliferation and cytokine releasing assays were performed after cocultivation of T cells with irradiated Ramos SAg-expressing cells. The results indicate that expression of the human SAg stimulates T-cell activation in vitro, as the mouse SAg does. Because the T-cell responses in vitro are considered similar to those in vivo, these results suggest that the human LTR SAg might also play a role in human breast carcinogenesis.

  18. Reverse Transcription in the Saccharomyces cerevisiae Long-Terminal Repeat Retrotransposon Ty3

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    Jason W. Rausch

    2017-03-01

    Full Text Available Converting the single-stranded retroviral RNA into integration-competent double-stranded DNA is achieved through a multi-step process mediated by the virus-coded reverse transcriptase (RT. With the exception that it is restricted to an intracellular life cycle, replication of the Saccharomyces cerevisiae long terminal repeat (LTR-retrotransposon Ty3 genome is guided by equivalent events that, while generally similar, show many unique and subtle differences relative to the retroviral counterparts. Until only recently, our knowledge of RT structure and function was guided by a vast body of literature on the human immunodeficiency virus (HIV enzyme. Although the recently-solved structure of Ty3 RT in the presence of an RNA/DNA hybrid adds little in terms of novelty to the mechanistic basis underlying DNA polymerase and ribonuclease H activity, it highlights quite remarkable topological differences between retroviral and LTR-retrotransposon RTs. The theme of overall similarity but distinct differences extends to the priming mechanisms used by Ty3 RT to initiate (− and (+ strand DNA synthesis. The unique structural organization of the retrotransposon enzyme and interaction with its nucleic acid substrates, with emphasis on polypurine tract (PPT-primed initiation of (+ strand synthesis, is the subject of this review.

  19. Kinetics of HIV-1 long terminal repeat trans-activation. Use of intragenic ribozyme to assess rate-limiting steps

    NARCIS (Netherlands)

    Jeang, K. T.; Berkhout, B.

    1992-01-01

    We have examined, using self-cleaving ribozymes, the intracellular trans-activation kinetics of the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) by viral protein Tat. Experiments were designed to effect a competition (during RNA chain elongation) between cleavage of a

  20. Roles of the amino terminal region and repeat region of the Plasmodium berghei circumsporozoite protein in parasite infectivity.

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    Cassandra Aldrich

    Full Text Available The circumsporozoite protein (CSP plays a key role in malaria sporozoite infection of both mosquito salivary glands and the vertebrate host. The conserved Regions I and II have been well studied but little is known about the immunogenic central repeat region and the N-terminal region of the protein. Rodent malaria Plasmodium berghei parasites, in which the endogenous CS gene has been replaced with the avian Plasmodium gallinaceum CS (PgCS sequence, develop normally in the A. stephensi mosquito midgut but the sporozoites are not infectious. We therefore generated P. berghei transgenic parasites carrying the PgCS gene, in which the repeat region was replaced with the homologous region of P. berghei CS (PbCS. A further line, in which both the N-terminal region and repeat region were replaced with the homologous regions of PbCS, was also generated. Introduction of the PbCS repeat region alone, into the PgCS gene, did not rescue sporozoite species-specific infectivity. However, the introduction of both the PbCS repeat region and the N-terminal region into the PgCS gene completely rescued infectivity, in both the mosquito vector and the mammalian host. Immunofluorescence experiments and western blot analysis revealed correct localization and proteolytic processing of CSP in the chimeric parasites. The results demonstrate, in vivo, that the repeat region of P. berghei CSP, alone, is unable to mediate sporozoite infectivity in either the mosquito or the mammalian host, but suggest an important role for the N-terminal region in sporozoite host cell invasion.

  1. Repeated cycles of chilling and warming effectively terminate prolonged larval diapause in the chestnut weevil, Curculio sikkimensis.

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    Higaki, Morio

    2006-05-01

    Curculio sikkimensis (Coleoptera: Curculionidae) requires one or more years to complete its life cycle, owing to prolonged larval diapause. To compare the effects of temperature cycles and total periods of chilling on the termination of prolonged diapause, larvae were subjected to different chilling (5 degrees C) and warming (20 degrees C) cycles ranging from 30 to 720 days, and all cycles were repeated until the sum of chilling and warming periods reached 720 days. The prolonged diapause of C. sikkimensis was more effectively terminated by repeated cycles of chilling and warming than by prolonging the continuous chilling period. However, extremely short temperature cycles were not highly effective in enhancing diapause termination, even when such cycles were repeated many times. To examine the role of warming periods on diapause termination, diapause larvae were subjected to a sequence of chilling (120 days at 5 degrees C) and warming (240 days at 20 degrees C) with a warming period (0-120 days at 20 degrees C) inserted in the chilling period. Diapause larvae that were not reactivated in the first chilling period required exposure to a certain period of warming before they were able to complete diapause development in the subsequent chilling. Thus, C. sikkimensis appears to spread its reactivation times over several years in response to seasonal temperature cycles.

  2. Ligand-Binding Properties of the Carboxyl-Terminal Repeat Domain of Streptococcus mutans Glucan-Binding Protein A

    OpenAIRE

    Haas, Wolfgang; Banas, Jeffrey A.

    2000-01-01

    Streptococcus mutans glucan-binding protein A (GbpA) has sequence similarity in its carboxyl-terminal domain with glucosyltransferases (GTFs), the enzymes responsible for catalyzing the synthesis of the glucans to which GbpA and GTFs can bind and which promote S. mutans attachment to and accumulation on the tooth surface. It was predicted that this C-terminal region, comprised of what have been termed YG repeats, represents the GbpA glucan-binding domain (GBD). In an effort to test this hypot...

  3. Comparison of the carboxy-terminal DP-repeat region in the co-chaperones Hop and Hip.

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    Nelson, Gregory M; Huffman, Holly; Smith, David F

    2003-01-01

    Functional steroid receptor complexes are assembled and maintained by an ordered pathway of interactions involving multiple components of the cellular chaperone machinery. Two of these components, Hop and Hip, serve as co-chaperones to the major heat shock proteins (Hsps), Hsp70 and Hsp90, and participate in intermediate stages of receptor assembly. In an effort to better understand the functions of Hop and Hip in the assembly process, we focused on a region of similarity located near the C-terminus of each co-chaperone. Contained within this region is a repeated sequence motif we have termed the DP repeat. Earlier mutagenesis studies implicated the DP repeat of either Hop or Hip in Hsp70 binding and in normal assembly of the co-chaperones with progesterone receptor (PR) complexes. We report here that the DP repeat lies within a protease-resistant domain that extends to or is near the C-terminus of both co-chaperones. Point mutations in the DP repeats render the C-terminal regions hypersensitive to proteolysis. In addition, a Hop DP mutant displays altered proteolytic digestion patterns, which suggest that the DP-repeat region influences the folding of other Hop domains. Although the respective DP regions of Hop and Hip share sequence and structural similarities, they are not functionally interchangeable. Moreover, a double-point mutation within the second DP-repeat unit of Hop that converts this to the sequence found in Hip disrupts Hop function; however, the corresponding mutation in Hip does not alter its function. We conclude that the DP repeats are important structural elements within a C-terminal domain, which is important for Hop and Hip function.

  4. Young age and termination of pregnancy during the second trimester are risk factors for repeat second-trimester abortion.

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    Mentula, Maarit J; Niinimäki, Maarit; Suhonen, Satu; Hemminki, Elina; Gissler, Mika; Heikinheimo, Oskari

    2010-08-01

    The objective of the study was to characterize women undergoing a termination of pregnancy (TOP) during the second trimester and to evaluate the risk factors and timing of repeat TOP. This nationwide retrospective cohort study investigated 41,750 women who underwent TOP during the first (n = 39,850) or second (n = 1900) trimester in Finland in 2000-2005. The follow-up time was until repeat TOP or until Dec. 31, 2006. TOP during the second trimester increases the risk of repeat TOP (hazard ratio [HR], 1.4; 95% confidence interval [CI], 1.3-1.6), repeat second-trimester TOP (HR, 3.8; 95% CI, 2.9-5.1), and repeat TOP after 16 weeks of gestation (HR, 5.0; 95% CI, 3.3-7.7). The other risk factor for these is young age (HR, 7.0, 95% CI, 5.3-9.3; and HR, 12.5; 95% CI, 3.1-50.4 for age factors for repeat second-trimester TOP. Special focus on these women might be effective in decreasing repeat abortions. Copyright (c) 2010 Mosby, Inc. All rights reserved.

  5. A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells

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    Koziol, Uriel; Radio, Santiago; Smircich, Pablo; Zarowiecki, Magdalena; Fernández, Cecilia; Brehm, Klaus

    2015-01-01

    Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes. PMID:26133390

  6. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

    Science.gov (United States)

    Llorens, Carlos; Muñoz-Pomer, Alfonso; Bernad, Lucia; Botella, Hector; Moya, Andrés

    2009-01-01

    Background Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. Results We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. Conclusion The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network

  7. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees.

    Science.gov (United States)

    Llorens, Carlos; Muñoz-Pomer, Alfonso; Bernad, Lucia; Botella, Hector; Moya, Andrés

    2009-11-02

    Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as network-represented combinations, are power

  8. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Bernad Lucia

    2009-11-01

    Full Text Available Abstract Background Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. Results We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. Conclusion The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as

  9. Ligand-binding properties of the carboxyl-terminal repeat domain of Streptococcus mutans glucan-binding protein A.

    Science.gov (United States)

    Haas, W; Banas, J A

    2000-02-01

    Streptococcus mutans glucan-binding protein A (GbpA) has sequence similarity in its carboxyl-terminal domain with glucosyltransferases (GTFs), the enzymes responsible for catalyzing the synthesis of the glucans to which GbpA and GTFs can bind and which promote S. mutans attachment to and accumulation on the tooth surface. It was predicted that this C-terminal region, comprised of what have been termed YG repeats, represents the GbpA glucan-binding domain (GBD). In an effort to test this hypothesis and to quantitate the ligand-binding specificities of the GbpA GBD, several fusion proteins were generated and tested by affinity electrophoresis or by precipitation of protein-ligand complexes, allowing the determination of binding constants. It was determined that the 16 YG repeats in GbpA comprise its GBD and that GbpA has a greater affinity for dextran (a water-soluble form of glucan) than for mutan (a water-insoluble form of glucan). Placement of the GBD at the carboxyl terminus was necessary for maximum glucan binding, and deletion of as few as two YG repeats from either end of the GBD reduced the affinity for dextran by over 10-fold. Interestingly, the binding constant of GbpA for dextran was 34-fold higher than that calculated for the GBDs of two S. mutans GTFs, one of which catalyzes the synthesis of water-soluble glucan and the other of which catalyzes the synthesis of water-insoluble glucan.

  10. Footprint of APOBEC3 on the genome of human retroelements.

    Science.gov (United States)

    Anwar, Firoz; Davenport, Miles P; Ebrahimi, Diako

    2013-07-01

    Almost half of the human genome is composed of transposable elements. The genomic structures and life cycles of some of these elements suggest they are a result of waves of retroviral infection and transposition over millions of years. The reduction of retrotransposition activity in primates compared to that in nonprimates, such as mice, has been attributed to the positive selection of several antiretroviral factors, such as apolipoprotein B mRNA editing enzymes. Among these, APOBEC3G is known to mutate G to A within the context of GG in the genome of endogenous as well as several exogenous retroelements (the underlining marks the G that is mutated). On the other hand, APOBEC3F and to a lesser extent other APOBEC3 members induce G-to-A changes within the nucleotide GA. It is known that these enzymes can induce deleterious mutations in the genome of retroviral sequences, but the evolution and/or inactivation of retroelements as a result of mutation by these proteins is not clear. Here, we analyze the mutation signatures of these proteins on large populations of long interspersed nuclear element (LINE), short interspersed nuclear element (SINE), and endogenous retrovirus (ERV) families in the human genome to infer possible evolutionary pressure and/or hypermutation events. Sequence context dependency of mutation by APOBEC3 allows investigation of the changes in the genome of retroelements by inspecting the depletion of G and enrichment of A within the APOBEC3 target and product motifs, respectively. Analysis of approximately 22,000 LINE-1 (L1), 24,000 SINE Alu, and 3,000 ERV sequences showed a footprint of GG→AG mutation by APOBEC3G and GA→AA mutation by other members of the APOBEC3 family (e.g., APOBEC3F) on the genome of ERV-K and ERV-1 elements but not on those of ERV-L, LINE, or SINE.

  11. Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes?

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2008-01-01

    ). This is expected if genes are subject to selection against transcriptional interference. We do not find microRNAs to be associated with genomic regions devoid of either SINEs or LINEs. We further observe an increased relative activity of genes overlapping LINE-free regions during early embryogenesis, where...... regions being intolerant to insertions of retroelements. The inadvertent transcriptional activity of retroelements may affect neighbouring genes, which in turn could be detrimental to an organism. We speculate that such retroelement transcription, or transcriptional interference, is a contributing factor...... in generating and maintaining retroelement-free regions in the human genome. METHODOLOGY/PRINCIPAL FINDINGS: Based on the known transcriptional properties of retroelements, we expect long interspersed elements (LINEs) to be able to display a high degree of transcriptional interference. In contrast, we expect...

  12. Functional angucycline-like antibiotic gene cluster in the terminal inverted repeats of the Streptomyces ambofaciens linear chromosome.

    Science.gov (United States)

    Pang, Xiuhua; Aigle, Bertrand; Girardet, Jean-Michel; Mangenot, Sophie; Pernodet, Jean-Luc; Decaris, Bernard; Leblond, Pierre

    2004-02-01

    Streptomyces ambofaciens has an 8-Mb linear chromosome ending in 200-kb terminal inverted repeats. Analysis of the F6 cosmid overlapping the terminal inverted repeats revealed a locus similar to type II polyketide synthase (PKS) gene clusters. Sequence analysis identified 26 open reading frames, including genes encoding the beta-ketoacyl synthase (KS), chain length factor (CLF), and acyl carrier protein (ACP) that make up the minimal PKS. These KS, CLF, and ACP subunits are highly homologous to minimal PKS subunits involved in the biosynthesis of angucycline antibiotics. The genes encoding the KS and ACP subunits are transcribed constitutively but show a remarkable increase in expression after entering transition phase. Five genes, including those encoding the minimal PKS, were replaced by resistance markers to generate single and double mutants (replacement in one and both terminal inverted repeats). Double mutants were unable to produce either diffusible orange pigment or antibacterial activity against Bacillus subtilis. Single mutants showed an intermediate phenotype, suggesting that each copy of the cluster was functional. Transformation of double mutants with a conjugative and integrative form of F6 partially restored both phenotypes. The pigmented and antibacterial compounds were shown to be two distinct molecules produced from the same biosynthetic pathway. High-pressure liquid chromatography analysis of culture extracts from wild-type and double mutants revealed a peak with an associated bioactivity that was absent from the mutants. Two additional genes encoding KS and CLF were present in the cluster. However, disruption of the second KS gene had no effect on either pigment or antibiotic production.

  13. Mapping of a major osteomagenic determinant of murine leukemia virus RFB-14 to non-long terminal repeat sequences

    DEFF Research Database (Denmark)

    Østergaard, Mette; Pedersen, Lene; Schmidt, Jörg

    1997-01-01

    the pathogenic potential of recombinant viruses between RFB-14 and the nonosteomagenic, highly leukemogenic SL3-3 MuLV. The recombinants were constructed so as to reveal whether a major determinant of osteomagenicity maps to sequences within or outside the long terminal repeats (LTR). Our data show that a major...... determinant of the osteoma-inducing potential of RFB-14 MuLV maps to the non-LTR region of the genome. Furthermore, we demonstrate that a strong determinant of leukemogenicity is harbored by the non-LTR region of SL3-3 MuLV....

  14. [Effect of tandem repeats adjacent to 3'-terminal of FLO1 on the flocculation function of Saccharomyces cerevisiae].

    Science.gov (United States)

    Yue, Feng; Du, Zhaoli; Guo, Xuena; He, Xiuping; Zhang, Borun

    2013-12-04

    Many tandem repeats exist in FLO1 gene of Saccharomyces cerevisiae, which might have great regulatory effect on the conformation and function of flocculation protein (flocculin). In this study, we analyzed the effect of 3'-terminal tandem repeats B, C and D complete deletion on the function of flocculin. We constructed the derived gene FLO1 bcd with complete deletion of tandem repeats B, C and D of FLO1 by fusion PCR. We then constructed plasmid pYCF1 bcd by insertion of FLO1 bcd into YCp50, and transformed such plasmid, pYCF1 and YCp50 into S. cerevisiae YS58 separately to generate recombinant strains YSF1 bcd, YSF1 and YSP50. We compared the flocculation ability and characteristics of these strains. Compared to YSF1, YSF1 bcd displayed only a slight reduction (4%) in flocculation ability in optimal flocculation buffer (50 mmol/L NaAC, pH 4.5). Moreover, the dependence of flocculation on Ca2+, sensitivity to metal ions and ethanol, and the specificity to different sugars showed no obvious difference between strains YSF1 and YSF1 bcd. However, strain YSF1 bcd displayed much higher flocculation levels than strain YSF1 under conditions with extreme pH, high temperature, or high concentration of mannose. Combined deletion of tandem repeats B, C and D adjacent to the 3'-terminal of FLO1 increases the conformation stability of flocculin in response to changes of pH, temperature or concentration of mannose in environment, but does not influence the other characteristics of flocculation.

  15. Distribution of a Ty3/gypsy-like retroelement on the A and B-chromosomes of Cestrum strigilatum Ruiz & Pav. and Cestrum intermedium Sendtn. (Solanaceae

    Directory of Open Access Journals (Sweden)

    Jéferson Nunes Fregonezi

    2007-01-01

    Full Text Available Retroelements are a diversified fraction of eukaryotic genomes, with the Ty1/copia and Ty3/gypsy groups being very common in a large number of plant genomes. We isolated an internal segment of the Ty3/gypsy retroelement of Cestrum strigilatum (Solanaceae using PCR amplification with degenerate primers for a conserved region of reverse transcriptase. The isolated segment (pCs12 was sequenced and showed similarity with Ty3/gypsy retroelements of monocotyledons and dicotyledons. This segment was used as probe in chromosomes of C. strigilatum and Cestrum intermedium. Diffuse hybridization signals were observed along the chromosomes and more accentuated terminal signals in some chromosome pairs, always associated with nucleolus organizer regions (NORs. The physical relationship between the hybridization sites of pCs12 and pTa71 ribosomal probes was assessed after sequential fluorescence in situ hybridization (FISH. Hybridization signals were also detected in the B chromosomes of these species, indicating an entail among the chromosomes of A complement and B-chromosomes.

  16. New modules for the repeated internal and N-terminal epitope tagging of genes in Saccharomyces cerevisiae.

    Science.gov (United States)

    Gauss, Robert; Trautwein, Mark; Sommer, Thomas; Spang, Anne

    2005-01-15

    Epitope tagging is a powerful method for the rapid analysis of protein function. In Saccharomyces cerevisiae epitope tags are introduced easily into chromosomal loci by homologous recombination using a simple PCR-based strategy. Although quite a number of tools exist for C-terminal tagging as well as N-terminal tagging of proteins expressed by heterologous promoters, there are only very limited possibilities to tag proteins at the N-terminus and retain the endogenous expression level. Furthermore, no PCR-templates for internal tagging have been reported. Here we describe new modules that are suitable for both the repeated N-terminal and internal tagging of proteins, leaving their endogenous promoters intact. The tags include 6xHA, 9xMyc, yEGFP, TEV-GST-6xHIS, ProtA, TEV-ProtA and TEV-ProtA-7xHIS in conjunction with different heterologous selection markers. Copyright 2004 John Wiley & Sons, Ltd.

  17. Terminal Bacteroid Differentiation Is Associated With Variable Morphological Changes in Legume Species Belonging to the Inverted Repeat-Lacking Clade.

    Science.gov (United States)

    Montiel, Jesús; Szűcs, Attila; Boboescu, Iulian Z; Gherman, Vasile D; Kondorosi, Éva; Kereszt, Attila

    2016-03-01

    Medicago and closely related legume species from the inverted repeat-lacking clade (IRLC) impose terminal differentiation onto their bacterial endosymbionts, manifested in genome endoreduplication, cell enlargement, and loss of cell-division capacity. Nodule-specific cysteine-rich (NCR) secreted host peptides are plant effectors of this process. As bacteroids in other IRLC legumes, such as Cicer arietinum and Glycyrrhiza lepidota, were reported not to display features of terminal differentiation, we investigated the fate of bacteroids in species from these genera as well as in four other species representing distinct genera of the phylogenetic tree for this clade. Bacteroids in all tested legumes proved to be larger in size and DNA content than cultured cells; however, the degree of cell elongation was rather variable in the different species. In addition, the reproductive ability of the bacteroids isolated from these legumes was remarkably reduced. In all IRLC species with available sequence data, the existence of NCR genes was found. These results indicate that IRLC legumes provoke terminal differentiation of their endosymbionts with different morphotypes, probably with the help of NCR peptides.

  18. Foamy Virus Vector Carries a Strong Insulator in Its Long Terminal Repeat Which Reduces Its Genotoxic Potential.

    Science.gov (United States)

    Goodman, Michael Aaron; Arumugam, Paritha; Pillis, Devin Marie; Loberg, Anastacia; Nasimuzzaman, Mohammed; Lynn, Danielle; van der Loo, Johannes Christiaan Maria; Dexheimer, Phillip Joseph; Keddache, Mehdi; Bauer, Thomas Roy; Hickstein, Dennis Durand; Russell, David William; Malik, Punam

    2018-01-01

    Strong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in "enhancerless" self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for nongenic integrations than gammaretroviruses/lentiviruses and preferential integration near transcriptional start sites, like gammaretroviruses. We found that strong viral enhancers/promoters placed in foamy viral vectors caused extremely low immortalization of primary mouse hematopoietic stem/progenitor cells compared to analogous gammaretrovirus/lentivirus vectors carrying the same enhancers/promoters, an effect not explained solely by foamy virus' modest insertional site preference for nongenic regions compared to gammaretrovirus/lentivirus vectors. Using CRISPR/Cas9-mediated targeted insertion of analogous proviral sequences into the LMO2 gene and then measuring LMO2 expression, we demonstrate a sequence-specific effect of foamy virus, independent of insertional bias, contributing to reduced genotoxicity. We show that this effect is mediated by a 36-bp insulator located in the foamy virus long terminal repeat (LTR) that has high-affinity binding to the CCCTC-binding factor. Using our LMO2 activation assay, LMO2 expression was significantly increased when this insulator was removed from foamy virus and significantly reduced when the insulator was inserted into the lentiviral LTR. Our results elucidate a mechanism underlying the low genotoxicity of foamy virus, identify a novel insulator, and support the use of foamy virus as a vector for gene therapy, especially when strong enhancers/promoters are required.IMPORTANCE Understanding the genotoxic potential of viral vectors is important in designing safe and efficacious vectors for gene

  19. Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3

    Directory of Open Access Journals (Sweden)

    Katarzyna Pachulska-Wieczorek

    2016-07-01

    Full Text Available Long-terminal repeat (LTR retrotransposons are transposable genetic elements that replicate intracellularly, and can be considered progenitors of retroviruses. Ty1 and Ty3 are the most extensively characterized LTR retrotransposons whose RNA genomes provide the template for both protein translation and genomic RNA that is packaged into virus-like particles (VLPs and reverse transcribed. Genomic RNAs are not divided into separate pools of translated and packaged RNAs, therefore their trafficking and packaging into VLPs requires an equilibrium between competing events. In this review, we focus on Ty1 and Ty3 genomic RNA trafficking and packaging as essential steps of retrotransposon propagation. We summarize the existing knowledge on genomic RNA sequences and structures essential to these processes, the role of Gag proteins in repression of genomic RNA translation, delivery to VLP assembly sites, and encapsidation.

  20. Identification of multiple binding sites for the THAP domain of the Galileo transposase in the long terminal inverted-repeats.

    Science.gov (United States)

    Marzo, Mar; Liu, Danxu; Ruiz, Alfredo; Chalmers, Ronald

    2013-08-01

    Galileo is a DNA transposon responsible for the generation of several chromosomal inversions in Drosophila. In contrast to other members of the P-element superfamily, it has unusually long terminal inverted-repeats (TIRs) that resemble those of Foldback elements. To investigate the function of the long TIRs we derived consensus and ancestral sequences for the Galileo transposase in three species of Drosophilids. Following gene synthesis, we expressed and purified their constituent THAP domains and tested their binding activity towards the respective Galileo TIRs. DNase I footprinting located the most proximal DNA binding site about 70 bp from the transposon end. Using this sequence we identified further binding sites in the tandem repeats that are found within the long TIRs. This suggests that the synaptic complex between Galileo ends may be a complicated structure containing higher-order multimers of the transposase. We also attempted to reconstitute Galileo transposition in Drosophila embryos but no events were detected. Thus, although the limited numbers of Galileo copies in each genome were sufficient to provide functional consensus sequences for the THAP domains, they do not specify a fully active transposase. Since the THAP recognition sequence is short, and will occur many times in a large genome, it seems likely that the multiple binding sites within the long, internally repetitive, TIRs of Galileo and other Foldback-like elements may provide the transposase with its binding specificity. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  1. Retroelement demethylation associated with abnormal placentation in Mus musculus x Mus caroli hybrids.

    Science.gov (United States)

    Brown, Judith D; Piccuillo, Vanessa; O'Neill, Rachel J

    2012-03-01

    The proper functioning of the placenta requires specific patterns of methylation and the appropriate regulation of retroelements, some of which have been co-opted by the genome for placental-specific gene expression. Our inquiry was initiated to determine the causes of the placental defects observed in crosses between two species of mouse, Mus musculus and Mus caroli. M. musculus × M. caroli fetuses are rarely carried to term, possibly as a result of genomic incompatibility in the placenta. Taking into account that placental dysplasia is observed in Peromyscus and other Mus hybrids, and that endogenous retroviruses are expressed in the placental transcriptome, we hypothesized that these placental defects could result, in part, from failure of the genome defense mechanism, DNA methylation, to regulate the expression of retroelements. Hybrid M. musculus × M. caroli embryos were produced by artificial insemination, and dysplastic placentas were subjected to microarray and methylation screens. Aberrant overexpression of an X-linked Mus retroelement in these hybrid placentas is consistent with local demethylation of this retroelement, concomitant with genome instability, disruption of gene regulatory pathways, and dysgenesis. We propose that the placenta is a specific site of control that is disrupted by demethylation and retroelement activation in interspecific hybridization that occur as a result of species incompatibility of methylation machinery. To our knowledge, the present data provide the first report of retroelement activation linked to decreased methylation in a eutherian hybrid system.

  2. Off-target effects of sulforaphane include the derepression of long terminal repeats through histone acetylation events.

    Science.gov (United States)

    Baier, Scott R; Zbasnik, Richard; Schlegel, Vicki; Zempleni, Janos

    2014-06-01

    Sulforaphane is a naturally occurring isothiocyanate in cruciferous vegetables. Sulforaphane inhibits histone deacetylases, leading to the transcriptional activation of genes including tumor suppressor genes. The compound has attracted considerable attention in the chemoprevention of prostate cancer. Here we tested the hypothesis that sulforaphane is not specific for tumor suppressor genes but also activates loci such as long terminal repeats (LTRs), which might impair genome stability. Studies were conducted using chemically pure sulforaphane in primary human IMR-90 fibroblasts and in broccoli sprout feeding studies in healthy adults. Sulforaphane (2.0 μM) caused an increase in LTR transcriptional activity in cultured cells. Consumption of broccoli sprouts (34, 68 or 102 g) by human volunteers caused a dose dependent elevation in LTR mRNA in circulating leukocytes, peaking at more than a 10-fold increase. This increase in transcript levels was associated with an increase in histone H3 K9 acetylation marks in LTR 15 in peripheral blood mononuclear cells from subjects consuming sprouts. Collectively, this study suggests that sulforaphane has off-target effects that warrant further investigation when recommending high levels of sulforaphane intake, despite its promising activities in chemoprevention. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Rescue of avian adeno-associated virus from a recombinant plasmid containing deletions in the viral inverted terminal repeats.

    Science.gov (United States)

    Wang, Jianye; Zhu, Liqian; Zhu, Jun; Zhang, Xinjun; Tao, Jie; Duan, Qiangde; Zhu, Guoqiang

    2012-01-01

    We have previously reported the complete genome sequence of avian adeno-associated virus (AAAV) strain YZ-1, isolated from healthy chickens in China. In this study, we describe the successful rescue of infectious virions from a recombinant plasmid containing the genome of YZ-1 with deletions in the viral inverted terminal repeats (ITRs). The complete genome of YZ-1 was cloned into a bacterial plasmid by a modified "A-T" cloning method. Six recombinant plasmids were selected for further experiments. Sequence analysis indicated that the six clones shared identical internal sequences except for the various deletions within ITRs at either end of the cloned genome. The recombinant plasmid pYZ525, harboring a YZ-1 genome with a 96-nt deletion at the 5' end, was used to transfect CEL or HEK293 cells in the presence of the CELO virus or a helper plasmid, and rescued virions were obtained by both of the methods despite the presence of the deletions. Here, for the first time, we provide evidence that a certain number of nt deletions in the ITRs are not lethal for the rescue of viable AAAV from recombinant plasmids. This study provides insight into the unique biology of AAAV and the mechanism of viral replication.

  4. Female Choice Reveals Terminal Investment in Male Mealworm Beetles, Tenebrio molitor, after a Repeated Activation of the Immune System

    Science.gov (United States)

    Krams, I; Daukšte, J; Kivleniece, I; Krama, T; Rantala, MJ; Ramey, G; Šauša, L

    2011-01-01

    Increasing evidence suggests that secondary sexual traits reflect immunocompetence of males in many animal species. This study experimentally investigated whether a parasite-like immunological challenge via a nylon implant affects sexual attractiveness of males in Tenebrio molitor L. (Coleoptera: Tenebrionidae) Although a single immunological challenge significantly reduced sexual attractiveness and locomotor activity of males, it had no adverse effect on their survival. A second immune challenge of the same males increased their attractiveness. However, it was found that the repeated challenge significantly reduced locomotor activity of males and caused higher mortality. This result indicates terminal investment on sexual signaling, which is supposedly based on a trade-off between pheromone production and energy expenditures needed for such activities as recovery of immune system and locomotor activity. When the third implantation was carried out in the same group of males, melanization of nylon implants was found to be lower in more attractive than in less attractive males. This suggests that males that became sexually attractive after the second immune challenge did not invest in recovery of their immune system. PMID:21864151

  5. Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome.

    Science.gov (United States)

    De Nicola, Beatrice; Lech, Christopher J; Heddi, Brahim; Regmi, Sagar; Frasson, Ilaria; Perrone, Rosalba; Richter, Sara N; Phan, Anh Tuân

    2016-07-27

    The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma.

    Science.gov (United States)

    Lamprecht, Björn; Walter, Korden; Kreher, Stephan; Kumar, Raman; Hummel, Michael; Lenze, Dido; Köchert, Karl; Bouhlel, Mohamed Amine; Richter, Julia; Soler, Eric; Stadhouders, Ralph; Jöhrens, Korinna; Wurster, Kathrin D; Callen, David F; Harte, Michael F; Giefing, Maciej; Barlow, Rachael; Stein, Harald; Anagnostopoulos, Ioannis; Janz, Martin; Cockerill, Peter N; Siebert, Reiner; Dörken, Bernd; Bonifer, Constanze; Mathas, Stephan

    2010-05-01

    Mammalian genomes contain many repetitive elements, including long terminal repeats (LTRs), which have long been suspected to have a role in tumorigenesis. Here we present evidence that aberrant LTR activation contributes to lineage-inappropriate gene expression in transformed human cells and that such gene expression is central for tumor cell survival. We show that B cell-derived Hodgkin's lymphoma cells depend on the activity of the non-B, myeloid-specific proto-oncogene colony-stimulating factor 1 receptor (CSF1R). In these cells, CSF1R transcription initiates at an aberrantly activated endogenous LTR of the MaLR family (THE1B). Derepression of the THE1 subfamily of MaLR LTRs is widespread in the genome of Hodgkin's lymphoma cells and is associated with impaired epigenetic control due to loss of expression of the corepressor CBFA2T3. Furthermore, we detect LTR-driven CSF1R transcripts in anaplastic large cell lymphoma, in which CSF1R is known to be expressed aberrantly. We conclude that LTR derepression is involved in the pathogenesis of human lymphomas, a finding that might have diagnostic, prognostic and therapeutic implications.

  7. Reverse transcriptase domain sequences from tree peony (Paeonia suffruticosa) long terminal repeat retrotransposons: sequence characterization and phylogenetic analysis.

    Science.gov (United States)

    Guo, Da-Long; Hou, Xiao-Gai; Jia, Tian

    2014-05-04

    Tree peony is an important horticultural plant worldwide of great ornamental and medicinal value. Long terminal repeat retrotransposons (LTR-retrotransposons) are the major components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their sequence characteristics, genetic distribution and transcriptional activity; however, no information about them is available in tree peony. Ty1-copia-like reverse transcriptase sequences were amplified from tree peony genomic DNA by polymerase chain reaction (PCR) with degenerate oligonucleotide primers corresponding to highly conserved domains of the Ty1-copia-like retrotransposons in this study. PCR fragments of roughly 270 bp were isolated and cloned, and 33 sequences were obtained. According to alignment and phylogenetic analysis, all sequences were divided into six families. The observed difference in the degree of nucleotide sequence similarity is an indication for high level of sequence heterogeneity among these clones. Most of these sequences have a frame shift, a stop codon, or both. Dot-blot analysis revealed distribution of these sequences in all the studied tree peony species. However, different hybridization signals were detected among them, which is in agreement with previous systematics studies. Reverse transcriptase PCR (RT-PCR) indicated that Ty1-copia retrotransposons in tree peony were transcriptionally inactive. The results provide basic genetic and evolutionary information of tree peony genome, and will provide valuable information for the further utilization of retrotransposons in tree peony.

  8. Retroelements versus APOBEC3 family members: No great escape from the magnificent seven

    Directory of Open Access Journals (Sweden)

    Juan F Arias

    2012-08-01

    Full Text Available Retroelements comprise a large and successful family of transposable genetic elements that, through intensive infiltration, have shaped the genomes of humans and other mammals over millions of years. In fact, retrotransposons now account for approximately 45% of the human genome. Based on their genomic mobility, some retroelements are known to be the cause of genetic diseases, not only in germ and embryonic stem cells but also in somatic cells, posing a threat to genomic stability throughout all cellular populations. In response, mammals have developed intrinsic immunity mechanisms that provide resistance against the threat of the deleterious effects of retrotransposition. Among these, seven members of the APOBEC3 (A3 family of cytidine deaminases serve as highly active, intrinsic, antiretroviral host factors. Certain A3 proteins effectively counteract infections of retroviruses such as HIV-1, as well as those of other virus families, while also blocking the transposition of retroelements. Based on their preferential expression in the germ cells, in which retrotransposons may be active, it is likely that A3 proteins were acquired through mammalian evolution primarily to inhibit retrotransposition and thereby maintain genomic stability in these cells. This review summarizes the recent advances in our understanding of the interplay between the retroelements currently active in the human genome and the anti-retroelement A3 proteins.

  9. Mechanisms of LTR-Retroelement Transposition: Lessons from Drosophila melanogaster.

    Science.gov (United States)

    Nefedova, Lidia; Kim, Alexander

    2017-04-16

    Long terminal repeat (LTR) retrotransposons occupy a special place among all mobile genetic element families. The structure of LTR retrotransposons that have three open reading frames is identical to DNA forms of retroviruses that are integrated into the host genome. Several lines of evidence suggest that LTR retrotransposons share a common ancestry with retroviruses and thus are highly relevant to understanding mechanisms of transposition. Drosophila melanogaster is an exceptionally convenient model for studying the mechanisms of retrotransposon movement because many such elements in its genome are transpositionally active. Moreover, two LTRretrotransposons of D. melanogaster, gypsy and ZAM, have been found to have infectious properties and have been classified as errantiviruses. Despite numerous studies focusing on retroviral integration process, there is still no clear understanding of integration specificity in a target site. Most LTR retrotransposons non-specifically integrate into a target site. Site-specificity of integration at vertebrate retroviruses is rather relative. At the same time, sequence-specific integration is the exclusive property of errantiviruses and their derivatives with two open reading frames. The possible basis for the errantivirus integration specificity is discussed in the present review.

  10. Activation of the Long Terminal Repeat of Human Endogenous Retrovirus K by Melanoma-Specific Transcription Factor MITF-M

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    Iyoko Katoh

    2011-11-01

    Full Text Available The human and Old World primate genomes possess conserved endogenous retrovirus sequences that have been implicated in evolution, reproduction, and carcinogenesis. Human endogenous retrovirus (HERV-K with 5′LTR-gag-pro-pol-env-rec/np9-3′LTR sequences represents the newest retrovirus family that integrated into the human genome 1 to 5 million years ago. Although a high-level expression of HERV-K in melanomas, breast cancers, and terato-carcinomas has been demonstrated, the mechanism of the lineage-specific activation of the long terminal repeat (LTR remains obscure. We studied chromosomal HERV-K expression in MeWo melanoma cells in comparison with the basal expression in human embryonic kidney 293 (HEK293 cells. Cloned LTR of HERV-K (HML-2.HOM was also characterized by mutation and transactivation experiments. We detected multiple transcriptional initiator (Inr sites in the LTR by rapid amplification of complementary DNA ends (5′ RACE. HEK293 and MeWo showed different Inr usage. The most potent Inr was associated with a TATA box and three binding motifs of microphthalmia-associated transcription factor (MITF. Both chromosomal HERV-K expression and the cloned LTR function were strongly activated in HEK293 by transfection with MITF-M, a melanocyte/melanoma–specific isoform of MITF. Coexpression of MITF and the HERV-K core antigen was detected in retinal pigmented epithelium by an immunofluorescence analysis. Although malignant melanoma lines MeWo, G361, and SK-MEL-28 showed enhanced HERV-K transcription compared with normal melanocytes, the level of MITF-M messenger RNA persisted from normal to transformed melanocytes. Thus, MITF-M may be a prerequisite for the pigmented cell lineage–specific function of HERV-K LTR, leading to the high-level expression in malignant melanomas.

  11. Long Terminal Repeat Circular DNA as Markers of Active Viral Replication of Human T Lymphotropic Virus-1 in Vivo

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    James M Fox

    2016-03-01

    Full Text Available Clonal expansion of human T-lymphotropic virus type-1 (HTLV-1 infected cells in vivo is well documented. Unlike human immunodeficiency virus type 1 (HIV-1, HTLV-1 plasma RNA is sparse. The contribution of the “mitotic” spread of HTLV-1 compared with infectious spread of the virus to HTLV-1 viral burden in established infection is uncertain. Since extrachromosomal long terminal repeat (LTR DNA circles are indicators of viral replication in HIV-1 carriers with undetectable plasma HIV RNA, we hypothesised that HTLV-1 LTR circles could indicate reverse transcriptase (RT usage and infectious activity. 1LTR and 2LTR DNA circles were measured in HTLV-1 cell lines and peripheral blood mononuclear cells (PBMC of asymptomatic carriers (ACs and patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP or adult T cell leukaemia/lymphoma (ATLL. 1LTR DNA circles were detected in 14/20 patients at a mean of 1.38/100 PBMC but did not differentiate disease status nor correlate with HTLV-1 DNA copies. 2LTR DNA circles were detected in 30/31 patients and at higher concentrations in patients with HTLV-1-associated diseases, independent of HTLV-1 DNA load. In an incident case the 2LTR DNA circle concentration increased 2.1 fold at the onset of HAM/TSP compared to baseline. Detectable and fluctuating levels of HTLV-1 DNA circles in patients indicate viral RT usage and virus replication. Our results indicate HTLV-1 viral replication capacity is maintained in chronic infection and may be associated with disease onset.

  12. A new family of retroviral long terminal repeat elements in the human genome identified by their homologies to an element 5{prime} to the spider monkey haptoglobin gene

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, L.M.; Maeda, N. [Univ. of North Carolina, Chapel Hill, NC (United States)

    1995-06-10

    A new family of retroviral long terminal repeats that we name Spm-LTR has been identified as a result of DNA sequence comparisons between the entire Gen-Bank databank and an element, SPHP, located 5{prime} to the haptoglobin gene of spider monkeys. The 18 human Spm-LTR sequences so identified fall into three subtypes. There is no sequence similarity between Spm-LTR elements and any endogenous retroviral LTR sequences previously reported except for general features that define LTRs. However, a previously described repeated sequence (MER-4) forms a portion of the Spm-LTR sequence. 13 refs., 1 fig., 1 tab.

  13. Terminal Bacteroid Differentiation Is Associated With Variable Morphological Changes in Legume Species Belonging to the Inverted Repeat-Lacking Clade

    National Research Council Canada - National Science Library

    Montiel, Jesús; Szűcs, Attila; Boboescu, Iulian Z; Gherman, Vasile D; Kondorosi, Éva; Kereszt, Attila

    2016-01-01

    .... As bacteroids in other IRLC legumes, such as Cicer arietinum and Glycyrrhiza lepidota, were reported not to display features of terminal differentiation, we investigated the fate of bacteroids...

  14. The terminal immunoglobulin-like repeats of LigA and LigB of Leptospira enhance their binding to gelatin binding domain of fibronectin and host cells.

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    Yi-Pin Lin

    Full Text Available Leptospira spp. are pathogenic spirochetes that cause the zoonotic disease leptospirosis. Leptospiral immunoglobulin (Ig-like protein B (LigB contributes to the binding of Leptospira to extracellular matrix proteins such as fibronectin, fibrinogen, laminin, elastin, tropoelastin and collagen. A high-affinity Fn-binding region of LigB has been localized to LigBCen2, which contains the partial 11th and full 12th Ig-like repeats (LigBCen2R and 47 amino acids of the non-repeat region (LigBCen2NR of LigB. In this study, the gelatin binding domain of fibronectin was shown to interact with LigBCen2R (K(D = 1.91+/-0.40 microM. Not only LigBCen2R but also other Ig-like domains of Lig proteins including LigAVar7'-8, LigAVar10, LigAVar11, LigAVar12, LigAVar13, LigBCen7'-8, and LigBCen9 bind to GBD. Interestingly, a large gain in affinity was achieved through an avidity effect, with the terminal domains, 13th (LigA or 12th (LigB Ig-like repeat of Lig protein (LigAVar7'-13 and LigBCen7'-12 enhancing binding affinity approximately 51 and 28 fold, respectively, compared to recombinant proteins without this terminal repeat. In addition, the inhibited effect on MDCKs cells can also be promoted by Lig proteins with terminal domains, but these two domains are not required for gelatin binding domain binding and cell adhesion. Interestingly, Lig proteins with the terminal domains could form compact structures with a round shape mediated by multidomain interaction. This is the first report about the interaction of gelatin binding domain of Fn and Lig proteins and provides an example of Lig-gelatin binding domain binding mediating bacterial-host interaction.

  15. Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.

    Science.gov (United States)

    Paz, Rosalía Cristina; Kozaczek, Melisa Eliana; Rosli, Hernán Guillermo; Andino, Natalia Pilar; Sanchez-Puerta, Maria Virginia

    2017-10-01

    Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.

  16. Solution structure of the Arabidopsis thaliana telomeric repeat-binding protein DNA binding domain: a new fold with an additional C-terminal helix.

    Science.gov (United States)

    Sue, Shih-Che; Hsiao, Hsin-Hao; Chung, Ben C-P; Cheng, Ying-Hsien; Hsueh, Kuang-Lung; Chen, Chung Mong; Ho, Chia Hsing; Huang, Tai-Huang

    2006-02-10

    The double-stranded telomeric repeat-binding protein (TRP) AtTRP1 is isolated from Arabidopsis thaliana. Using gel retardation assays, we defined the C-terminal 97 amino acid residues, Gln464 to Val560 (AtTRP1(464-560)), as the minimal structured telomeric repeat-binding domain. This region contains a typical Myb DNA-binding motif and a C-terminal extension of 40 amino acid residues. The monomeric AtTRP1(464-560) binds to a 13-mer DNA duplex containing a single repeat of an A.thaliana telomeric DNA sequence (GGTTTAG) in a 1:1 complex, with a K(D) approximately 10(-6)-10(-7) M. Nuclear magnetic resonance (NMR) examination revealed that the solution structure of AtTRP1(464-560) is a novel four-helix tetrahedron rather than the three-helix bundle structure found in typical Myb motifs and other TRPs. Binding of the 13-mer DNA duplex to AtTRP1(464-560) induced significant chemical shift perturbations of protein amide resonances, which suggests that helix 3 (H3) and the flexible loop connecting H3 and H4 are essential for telomeric DNA sequence recognition. Furthermore, similar to that in hTRF1, the N-terminal arm likely contributes to or stabilizes DNA binding. Sequence comparisons suggested that the four-helix structure and the involvement of the loop residues in DNA binding may be features unique to plant TRPs.

  17. The conserved residue Arg46 in the N-terminal heptad repeat domain of HIV-1 gp41 is critical for viral fusion and entry.

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    Xiaoyi Wang

    Full Text Available During the process of HIV-1 fusion with the target cell, the N-terminal heptad repeat (NHR of gp41 interacts with the C-terminal heptad repeat (CHR to form fusogenic six-helix bundle (6-HB core. We previously identified a crucial residue for 6-HB formation and virus entry--Lys63 (K63 in the C-terminal region of NHR (aa 54-70, which forms a hydrophobic cavity. It can form an important salt bridge with Asp121 (D121 in gp41 CHR. Here, we found another important conserved residue for virus fusion and entry, Arg46 (R46, in the N-terminal region of NHR (aa 35-53, which forms a hydrogen bond with a polar residue, Asn43 (N43, in NHR, as a part of the hydrogen-bond network. R46 can also form a salt bridge with a negatively charged residue, Glu137 (E137, in gp41 CHR. Substitution of R46 with the hydrophobic residue Ala (R46A or the negatively charged residue Glu (R46E resulted in disruption of the hydrogen bond network, breakage of the salt bridge and reduction of 6-HB's stability, leading to impairment of viral fusion and decreased inhibition of N36, an NHR peptide. Similarly, CHR peptide C34 with substitution of E137 for Ala (E137A or Arg (E137R also exhibited reduced inhibitory activity against HIV-1 infection and HIV-1-mediated cell-to-cell fusion. These results suggest that the positively charged residue R46 and its hydrogen bond network, together with the salt bridge between R46 and E137, are important for viral fusion and entry and may therefore serve as a target for designing novel HIV fusion/entry inhibitors.

  18. Oncogenic LINE-1 Retroelements Sustain Prostate Tumor Cells and Promote Metastatic Progression

    Science.gov (United States)

    2015-10-01

    The goal of this hypothesis development project is ( 1 ) to determine if ectopic expression of LINE- 1 elements in prostate cancer contribute to its...Furthermore, we have subcloned a LINE- 1 Open reading frame sequence and will determine the effect of its expression in non-tumorigenic prostate cells...Finally, we have cloned the PIWIL- 1 gene, known as a repressor of LINE- 1 retroelement sequences in the testis, and have it under the control of a

  19. The cooperative activity between the carboxyl-terminal TSP1 repeats and the CUB domains of ADAMTS13 is crucial for recognition of von Willebrand factor under flow.

    Science.gov (United States)

    Zhang, Ping; Pan, Weilan; Rux, Ann H; Sachais, Bruce S; Zheng, X Long

    2007-09-15

    ADAMTS13 cleaves von Willebrand factor (VWF) between Tyr(1605) and Met(1606) residues at the central A2 subunit. The amino-terminus of ADAMTS13 protease appears to be sufficient to bind and cleave VWF under static and denatured condition. However, the role of the carboxyl-terminus of ADAMTS13 in substrate recognition remains controversial. Present study demonstrates that ADAMTS13 cleaves VWF in a rotation speed- and protease concentration-dependent manner on a mini vortexer. Removal of the CUB domains (delCUB) or truncation after the spacer domain (MDTCS) significantly impairs its ability to cleave VWF under the same condition. ADAMTS13 and delCUB (but not MDTCS) bind VWF under flow with dissociation constants (K(D)) of about 50 nM and about 274 nM, respectively. The isolated CUB domains are neither sufficient to bind VWF detectably nor capable of inhibiting proteolytic cleavage of VWF by ADAMTS13 under flow. Addition of the TSP1 5-8 (T5-8CUB) or TSP1 2-8 repeats (T2-8CUB) to the CUB domains restores the binding affinity toward VWF and the inhibitory effect on cleavage of VWF by ADAMTS13 under flow. These data demonstrate directly and quantitatively that the cooperative activity between the middle carboxyl-terminal TSP1 repeats and the distal carboxyl-terminal CUB domains may be crucial for recognition and cleavage of VWF under flow.

  20. Retrotransposon expression and incorporation of cloned human and mouse retroelements in human spermatozoa.

    Science.gov (United States)

    Lazaros, Leandros; Kitsou, Chrysoula; Kostoulas, Charilaos; Bellou, Sofia; Hatzi, Elissavet; Ladias, Paris; Stefos, Theodoros; Markoula, Sofia; Galani, Vasiliki; Vartholomatos, Georgios; Tzavaras, Theodore; Georgiou, Ioannis

    2017-03-01

    To investigate the expression of long interspersed element (LINE) 1, human endogenous retrovirus (HERV) K10, and short interspersed element-VNTR-Alu element (SVA) retrotransposons in ejaculated human spermatozoa by means of reverse-transcription (RT) polymerase chain reaction (PCR) analysis as well as the potential incorporation of cloned human and mouse active retroelements in human sperm cell genome. Laboratory study. University research laboratories and academic hospital. Normozoospermic and oligozoospermic white men. RT-PCR analysis was performed to confirm the retrotransposon expression in human spermatozoa. Exogenous retroelements were tagged with a plasmid containing a green fluorescence (EGFP) retrotransposition cassette, and the de novo retrotransposition events were tested with the use of PCR, fluorescence-activated cell sorting analysis, and confocal microscopy. Retroelement expression in human spermatozoa, incorporation of cloned human and mouse active retroelements in human sperm genome, and de novo retrotransposition events in human spermatozoa. RT-PCR products of expressed human LINE-1, HERV-K10, and SVA retrotransposons were observed in ejaculated human sperm samples. The incubation of human spermatozoa with either retrotransposition-active human LINE-1 and HERV-K10 or mouse reverse transcriptase-deficient VL30 retrotransposons tagged with an EGFP-based retrotransposition cassette led to EGFP-positive spermatozo; 16.67% of the samples were positive for retrotransposition. The respective retrotransposition frequencies for the LINE-1, HERV-K10, and VL30 retrotransposons in the positive samples were 0.34 ± 0.13%, 0.37 ± 0.17%, and 0.30 ± 0.14% per sample of 10,000 spermatozoa. Our results show that: 1) LINE-1, HERV-K10, and SVA retrotransposons are transcriptionally expressed in human spermatozoa; 2) cloned active retroelements of human and mammalian origin can be incorporated in human sperm genome; 3) active reverse transcriptases exist in human

  1. Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila

    Directory of Open Access Journals (Sweden)

    Carareto Claudia MA

    2009-12-01

    Full Text Available Abstract Background The Zaprionus genus shares evolutionary features with the melanogaster subgroup, such as space and time of origin. Although little information about the transposable element content in the Zaprionus genus had been accumulated, some of their elements appear to be more closely related with those of the melanogaster subgroup, indicating that these two groups of species were involved in horizontal transfer events during their evolution. Among these elements, the Gypsy and the Micropia retroelements were chosen for screening in seven species of the two Zaprionus subgenera, Anaprionus and Zaprionus. Results Screening allowed the identification of diverse Gypsy and Micropia retroelements only in species of the Zaprionus subgenus, showing that they are transcriptionally active in the sampled species. The sequences of each retroelement were closely related to those of the melanogaster species subgroup, and the most parsimonious hypothesis would be that 15 horizontal transfer events shaped their evolution. The Gypsy retroelement of the melanogaster subgroup probably invaded the Zaprionus genomes about 11 MYA. In contrast, the Micropia retroelement may have been introduced into the Zaprionus subgenus and the melanogaster subgroup from an unknown donor more recently (~3 MYA. Conclusion Gypsy and Micropia of Zaprionus and melanogaster species share similar evolutionary patterns. The sharing of evolutionary, ecological and ethological features probably allowed these species to pass through a permissive period of transposable element invasion, explaining the proposed waves of horizontal transfers.

  2. Mapping of functional regions of murine retrovirus long terminal repeat enhancers: Enhancer domains interact and are not independent in their contributions to enhancer activity

    Energy Technology Data Exchange (ETDEWEB)

    Hollon, T.; Yoshimura, F.K. (Univ. of Washington, Seattle (USA))

    1989-08-01

    The authors have used deletion and recombinant long terminal repeat (LTR) mutants to examine enhancer activity differences between LTRs of the nonpathogenic Akv and the thymus lymphomagenic MCF13 murine retroviruses. Deletion mutant analysis revealed that major control regions for MCF13 and Akv LTR enhancer activity were similar but not identical. For both LTRs, major control regions were distinctly different in a murine T-cell and a fibroblast cell line. Recombinant enhancer analysis showed that LTRs could be divided into three regions capable of altering the level of enhancer activity through cooperative or antagonistic interaction. The contribution of each region to enhancer activity was dependent on its context with respect to the other regions. LTR enhancer function in different cell types appears to be the result of the interaction of enhancer modular elements.

  3. DR1769, a protein with N-terminal beta propeller repeats and a low-complexity hydrophilic tail, plays a role in desiccation tolerance of Deinococcus radiodurans.

    Science.gov (United States)

    Rajpurohit, Yogendra S; Misra, Hari S

    2013-09-01

    The Deinococcus radiodurans genome encodes five putative quinoproteins. Among these, the Δdr2518 and Δdr1769 mutants became sensitive to gamma radiation. DR2518 with beta propeller repeats in the C-terminal domain was characterized as a radiation-responsive serine/threonine protein kinase in this bacterium. DR1769 contains beta propeller repeats at the N terminus, while its C-terminal domain is a proline-rich disordered structure and constitutes a low-complexity hydrophilic region with aliphatic-proline dipeptide motifs. The Δdr1769 mutant showed nearly a 3-log cycle sensitivity to desiccation at 5% humidity compared to that of the wild type. Interestingly, the gamma radiation and mitomycin C (MMC) resistance in mutant cells also dropped by ∼1-log cycle at 10 kGy and ∼1.5-fold, respectively, compared to those in wild-type cells. But there was no effect of UV (254 nm) exposure up to 800 J · m(-2). These cells showed defective DNA double-strand break repair, and the average size of the nucleoid in desiccated wild-type and Δdr1769 cells was reduced by approximately 2-fold compared to that of respective controls. However, the nucleoid in wild-type cells returned to a size almost similar to that of the untreated control, which did not happen in mutant cells, at least up to 24 h postdesiccation. These results suggest that DR1769 plays an important role in desiccation and radiation resistance of D. radiodurans, possibly by protecting genome integrity under extreme conditions.

  4. Group-sequential analysis may allow for early trial termination: illustration by an intra-observer repeatability study.

    Science.gov (United States)

    Gerke, Oke; Vilstrup, Mie H; Halekoh, Ulrich; Hildebrandt, Malene Grubbe; Høilund-Carlsen, Poul Flemming

    2017-09-26

    Group-sequential testing is widely used in pivotal therapeutic, but rarely in diagnostic research, although it may save studies, time, and costs. The purpose of this paper was to demonstrate a group-sequential analysis strategy in an intra-observer study on quantitative FDG-PET/CT measurements, illuminating the possibility of early trial termination which implicates significant potential time and resource savings. Primary lesion maximum standardised uptake value (SUVmax) was determined twice from preoperative FDG-PET/CTs in 45 ovarian cancer patients. Differences in SUVmax were assumed to be normally distributed, and sequential one-sided hypothesis tests on the population standard deviation of the differences against a hypothesised value of 1.5 were performed, employing an alpha spending function. The fixed-sample analysis (N = 45) was compared with the group-sequential analysis strategies comprising one (at N = 23), two (at N = 15, 30), or three interim analyses (at N = 11, 23, 34), respectively, which were defined post hoc. When performing interim analyses with one third and two thirds of patients, sufficient agreement could be concluded after the first interim analysis and the final analysis. Other partitions did not suggest early stopping after adjustment for multiple testing due to one influential outlier and our small sample size. Group-sequential testing may enable early stopping of a trial, allowing for potential time and resource savings. The testing strategy must, though, be defined at the planning stage, and sample sizes must be reasonably large at interim analysis to ensure robustness against single outliers. Group-sequential testing may have a place in accuracy and agreement studies.

  5. Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1

    Directory of Open Access Journals (Sweden)

    Yoshitake Kazutoshi

    2010-04-01

    Full Text Available Abstract Background The ends of chromosomes, termed telomeres consist of repetitive DNA. The telomeric sequences shorten with cell division and, when telomeres are critically abbreviated, cells stop proliferating. However, in cancer cells, by the expression of telomerase which elongates telomeres, the cells can continue proliferating. Many approaches for telomere shortening have been pursued in the past, but to our knowledge, cutting telomeres in vivo has not so far been demonstrated. In addition, there is lack of information on the cellular effects of telomere shortening in human cells. Results Here, we created novel chimeric endonucleases to cut telomeres by fusing the endonuclease domain (TRAS1EN of the silkworm's telomere specific non-long terminal repeat retrotransposon TRAS1 to the human telomere-binding protein, TRF1. An in vitro assay demonstrated that the TRAS1EN-TRF1 chimeric endonucleases (T-EN and EN-T cut the human (TTAGGGn repeats specifically. The concentration of TRAS1EN-TRF1 chimeric endonucleases necessary for the cleavage of (TTAGGGn repeats was about 40-fold lower than that of TRAS1EN alone. When TRAS1EN-TRF1 endonucleases were introduced into human U2OS cancer cells using adenovirus vectors, the enzymes localized at telomeres of nuclei, cleaved and shortened the telomeric DNA by double-strand breaks. When human U2OS and HFL-1 fibroblast cells were infected with EN-T recombinant adenovirus, their cellular proliferation was suppressed for about 2 weeks after infection. In contrast, the TRAS1EN mutant (H258A chimeric endonuclease fused with TRF1 (ENmut-T did not show the suppression effect. The EN-T recombinant adenovirus induced telomere shortening in U2OS cells, activated the p53-dependent pathway and caused the senescence associated cellular responses, while the ENmut-T construct did not show such effects. Conclusions A novel TRAS1EN-TRF1 chimeric endonuclease (EN-T cuts the human telomeric repeats (TTAGGGn specifically in

  6. Distinct repeat motifs at the C-terminal region of CagA of Helicobacter pylori strains isolated from diseased patients and asymptomatic individuals in West Bengal, India

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    Chattopadhyay Santanu

    2012-05-01

    Full Text Available Abstract Background Infection with Helicobacter pylori strains that express CagA is associated with gastritis, peptic ulcer disease, and gastric adenocarcinoma. The biological function of CagA depends on tyrosine phosphorylation by a cellular kinase. The phosphate acceptor tyrosine moiety is present within the EPIYA motif at the C-terminal region of the protein. This region is highly polymorphic due to variations in the number of EPIYA motifs and the polymorphism found in spacer regions among EPIYA motifs. The aim of this study was to analyze the polymorphism at the C-terminal end of CagA and to evaluate its association with the clinical status of the host in West Bengal, India. Results Seventy-seven H. pylori strains isolated from patients with various clinical statuses were used to characterize the C-ternimal polymorphic region of CagA. Our analysis showed that there is no correlation between the previously described CagA types and various disease outcomes in Indian context. Further analyses of different CagA structures revealed that the repeat units in the spacer sequences within the EPIYA motifs are actually more discrete than the previously proposed models of CagA variants. Conclusion Our analyses suggest that EPIYA motifs as well as the spacer sequence units are present as distinct insertions and deletions, which possibly have arisen from extensive recombination events. Moreover, we have identified several new CagA types, which could not be typed by the existing systems and therefore, we have proposed a new typing system. We hypothesize that a cagA gene encoding higher number EPIYA motifs may perhaps have arisen from cagA genes that encode lesser EPIYA motifs by acquisition of DNA segments through recombination events.

  7. Induction of endogenous retroelements as a potential mechanism for mouse-specific drug-induced carcinogenicity.

    Directory of Open Access Journals (Sweden)

    Timothy M Coskran

    Full Text Available A number of chemical compounds have been shown to induce liver tumors in mice but not in other species. While several mechanisms for this species-specific tumorigenicity have been proposed, no definitive mechanism has been established. We examined the effects of the nongenotoxic rodent hepatic carcinogen, WY-14,643, in male mice from a high liver tumor susceptible strain (C3H/HeJ, and from a low tumor susceptible strain (C57BL/6. WY-14,643, a PPARα activator induced widespread increases in the expression of some endogenous retroelements, namely members of LTR and LINE elements in both strains. The expression of a number of known retroviral defense genes was also elevated. We also demonstrated that basal immune-mediated viral defense was elevated in C57BL/6 mice (the resistant strain and that WY-14,643 further activated those immuno-defense processes. We propose that the previously reported >100X activity of retroelements in mice drives mouse-specific tumorigenicity. We also propose that C57BL/6's competent immune to retroviral activation allows it to remove cells before the activation of these elements can result in significant chromosomal insertions and mutation. Finally, we showed that WY-14,643 treatment induced gene signatures of DNA recombination in the sensitive C3H/HeJ strain.

  8. Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements

    Science.gov (United States)

    Pyatkov, Konstantin I.; Arkhipova, Irina R.; Malkova, Natalia V.; Finnegan, David J.; Evgen'ev, Michael B.

    2004-01-01

    Penelope-like elements are a class of retroelement that have now been identified in >50 species belonging to at least 10 animal phyla. The Penelope element isolated from Drosophila virilis is the only transpositionally active representative of this class isolated so far. The single ORF of Penelope and its relatives contains regions homologous to a reverse transcriptase of atypical structure and to the GIY-YIG, or Uri, an endonuclease (EN) domain not previously found in retroelements. We have expressed the single ORF of Penelope in a baculovirus expression system and have shown that it encodes a polyprotein with reverse transcriptase activity that requires divalent cations (Mn2+ and Mg2+). We have also expressed and purified the EN domain in Escherichia coli and have demonstrated that it has EN activity in vitro. Mutations in the conserved residues of the EN catalytic module abolish its nicking activity, whereas the DNA-binding properties of the mutant proteins remain unaffected. Only one strand of the target sequence is cleaved, and there is a certain degree of cleavage specificity. We propose that the Penelope EN cleaves the target DNA during transposition, generating a primer for reverse transcription. Our results show that an active Uri EN has been adopted by a retrotransposon. PMID:15465912

  9. Penelope retroelements from Drosophila virilis are active after transformation of Drosophila melanogaster

    Science.gov (United States)

    Pyatkov, Konstantin I.; Shostak, Natalia G.; Zelentsova, Elena S.; Lyozin, George T.; Melekhin, Michael I.; Finnegan, David J.; Kidwell, Margaret G.; Evgen'ev, Michael B.

    2002-01-01

    The Penelope family of retroelements was first described in species of the Drosophila virilis group. Intact elements encode a reverse transcriptase and an endonuclease of the UvrC type, which may play a role in Penelope integration. Penelope is a key element in the induction of D. virilis hybrid dysgenesis, which involves the mobilization of several unrelated families of transposable elements. We here report the successful introduction of Penelope into the germ line of Drosophila melanogaster by P element-mediated transformation with three different constructs. Penelope is actively transcribed in the D. melanogaster genome only in lines transformed with a construct containing a full-length Penelope clone. The transcript is identical to that detected in D. virilis dysgenic hybrids. Most newly transposed Penelope elements have a very complex organization. Significant proliferation of Penelope copy number occurred in some lines during the 24-month period after transformation. The absence of copy number increase with two other constructs suggests that the 5′ and/or 3′ UTRs of Penelope are required for successful transposition in D. melanogaster. No insect retroelement has previously been reported to be actively transcribed and to increase in copy number after interspecific transformation. PMID:12451171

  10. Penelope-like elements--a new class of retroelements: distribution, function and possible evolutionary significance.

    Science.gov (United States)

    Evgen'ev, M B; Arkhipova, I R

    2005-01-01

    Here we describe a new class of retroelements termed PLE (Penelope-like elements). The only transpositionally active representative of this lineage found so far has been isolated from Drosophila virilis. This element, Penelope, is responsible for the hybrid dysgenesis syndrome in this species, characterized by simultaneous mobilization of several unrelated TE families in the progeny of dysgenic crosses. Several lines of evidence favor the hypothesis of recent Penelope invasion into D. virilis. Moreover, when D. virilisPenelope was introduced by P element-mediated transformation into the genome of D. melanogaster, it underwent extensive amplification in the new host and induced several traits of the dysgenesis syndrome, including gonadal atrophy and numerous mutations. The single ORF encoded by PLE consists of two principal domains: reverse transcriptase (RT) and endonuclease (EN), which is similar to GIY-YIG intron-encoded endonucleases. With the appearance of a large number of PLEs in genome databases from diverse eukaryotes, including amoebae, fungi, cnidarians, rotifers, flatworms, roundworms, fish, amphibia, and reptilia, it becomes possible to resolve their phylogenetic relationships with other RT groups with a greater degree of confidence. On the basis of their peculiar structural features, distinct phylogenetic placement, and structure of transcripts, we conclude that PLE constitute a novel class of eukaryotic retroelements, different from non-LTR and LTR retrotransposons.

  11. Synthesis, Binding and Antiviral Properties of Potent Core-Extended Naphthalene Diimides Targeting the HIV-1 Long Terminal Repeat Promoter G-Quadruplexes.

    Science.gov (United States)

    Perrone, Rosalba; Doria, Filippo; Butovskaya, Elena; Frasson, Ilaria; Botti, Silvia; Scalabrin, Matteo; Lago, Sara; Grande, Vincenzo; Nadai, Matteo; Freccero, Mauro; Richter, Sara N

    2015-12-24

    We have previously reported that stabilization of the G-quadruplex structures in the HIV-1 long terminal repeat (LTR) promoter suppresses viral transcription. Here we sought to develop new G-quadruplex ligands to be exploited as antiviral compounds by enhancing binding toward the viral G-quadruplex structures. We synthesized naphthalene diimide derivatives with a lateral expansion of the aromatic core. The new compounds were able to bind/stabilize the G-quadruplex to a high extent, and some of them displayed clear-cut selectivity toward the viral G-quadruplexes with respect to the human telomeric G-quadruplexes. This feature translated into low nanomolar anti-HIV-1 activity toward two viral strains and encouraging selectivity indexes. The selectivity depended on specific recognition of LTR loop residues; the mechanism of action was ascribed to inhibition of LTR promoter activity in cells. This is the first example of G-quadruplex ligands that show increased selectivity toward the viral G-quadruplexes and display remarkable antiviral activity.

  12. Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools.

    Science.gov (United States)

    Coates, Brad S; Abel, Craig A; Perera, Omaththage P

    2017-04-01

    The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50 = 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.

  13. Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.

    Science.gov (United States)

    Hayes, Michael L; Giang, Karolyn; Berhane, Beniam; Mulligan, R Michael

    2013-12-20

    Many transcripts expressed from plant organelle genomes are modified by C-to-U RNA editing. Nuclear encoded pentatricopeptide repeat (PPR) proteins are required as RNA binding specificity determinants in the RNA editing mechanism. Bioinformatic analysis has shown that most of the Arabidopsis PPR proteins necessary for RNA editing events include a C-terminal portion that shares structural characteristics with a superfamily of deaminases. The DYW deaminase domain includes a highly conserved zinc binding motif that shares characteristics with cytidine deaminases. The Arabidopsis PPR genes, ELI1 and DOT4, both have DYW deaminase domains and are required for single RNA editing events in chloroplasts. The ELI1 DYW deaminase domain was expressed as a recombinant protein in Escherichia coli and was shown to bind two zinc atoms per polypeptide. Thus, the DYW deaminase domain binds a zinc metal ion, as expected for a cytidine deaminase, and is potentially the catalytic component of an editing complex. Genetic complementation experiments demonstrate that large portions of the DYW deaminase domain of ELI1 may be eliminated, but the truncated genes retain the ability to restore editing site conversion in a mutant plant. These results suggest that the catalytic activity can be supplied in trans by uncharacterized protein(s) of the editosome.

  14. C-Terminal Repeats of Clostridium difficile Toxin A Induce Production of Chemokine and Adhesion Molecules in Endothelial Cells and Promote Migration of Leukocytes▿

    Science.gov (United States)

    Yeh, Chiou-Yueh; Lin, Chun-Nan; Chang, Chuan-Fa; Lin, Chun-Hung; Lien, Huei-Ting; Chen, Jen-Yang; Chia, Jean-San

    2008-01-01

    The C-terminal repeating sequences of Clostridium difficile toxin A (designated ARU) are homologous to the carbohydrate-binding domain of streptococcal glucosyltransferases (GTFs) that were recently identified as potent modulins. To test the hypothesis that ARU might exert a similar biological activity on endothelial cells, recombinant ARU (rARU), which was noncytotoxic to cell cultures, was analyzed using human umbilical vein endothelial cells. The rARU could bind directly to endothelial cells in a serum- and calcium-dependent manner and induce the production of interleukin-6 (IL-6), IL-8, and monocyte chemoattractant protein 1 in a dose-dependent manner. An oligosaccharide binding assay indicated that rARU, but not GTFC, binds preferentially to Lewis antigens and 3′HSO3-containing oligosaccharides. Binding of rARU to human endothelial or intestinal cells correlated directly with the expression of Lewis Y antigen. Bound rARU directly activated mitogen-activated protein kinases and the NF-κB signaling pathway in endothelial cells to release biologically active chemokines and adhesion molecules that promoted migration in a transwell assay and the adherence of polymorphonuclear and mononuclear cells to the endothelial cells. These results suggest that ARU may bind to multiple carbohydrate motifs to exert its biological activity on human endothelial cells. PMID:18160482

  15. Selective ligand recognition by a diversity-generating retroelement variable protein.

    Directory of Open Access Journals (Sweden)

    Jason L Miller

    2008-06-01

    Full Text Available Diversity-generating retroelements (DGRs recognize novel ligands through massive protein sequence variation, a property shared uniquely with the adaptive immune response. Little is known about how recognition is achieved by DGR variable proteins. Here, we present the structure of the Bordetella bacteriophage DGR variable protein major tropism determinant (Mtd bound to the receptor pertactin, revealing remarkable adaptability in the static binding sites of Mtd. Despite large dissimilarities in ligand binding mode, principles underlying selective recognition were strikingly conserved between Mtd and immunoreceptors. Central to this was the differential amplification of binding strengths by avidity (i.e., multivalency, which not only relaxed the demand for optimal complementarity between Mtd and pertactin but also enhanced distinctions among binding events to provide selectivity. A quantitatively similar balance between complementarity and avidity was observed for Bordetella bacteriophage DGR as occurs in the immune system, suggesting that variable repertoires operate under a narrow set of conditions to recognize novel ligands.

  16. Usefulness of repeated N-terminal pro-B-type natriuretic peptide measurements as incremental predictor for long-term cardiovascular outcome after vascular surgery.

    Science.gov (United States)

    Goei, Dustin; van Kuijk, Jan-Peter; Flu, Willem-Jan; Hoeks, Sanne E; Chonchol, Michel; Verhagen, Hence J M; Bax, Jeroen J; Poldermans, Don

    2011-02-15

    Plasma N-terminal pro-B-type natriuretic peptide (NT-pro-BNP) levels improve preoperative cardiac risk stratification in vascular surgery patients. However, single preoperative measurements of NT-pro-BNP cannot take into account the hemodynamic stress caused by anesthesia and surgery. Therefore, the aim of the present study was to assess the incremental predictive value of changes in NT-pro-BNP during the perioperative period for long-term cardiac mortality. Detailed cardiac histories, rest left ventricular echocardiography, and NT-pro-BNP levels were obtained in 144 patients before vascular surgery and before discharge. The study end point was the occurrence of cardiovascular death during a median follow-up period of 13 months (interquartile range 5 to 20). Preoperatively, the median NT-pro-BNP level in the study population was 314 pg/ml (interquartile range 136 to 1,351), which increased to a median level of 1,505 pg/ml (interquartile range 404 to 6,453) before discharge. During the follow-up period, 29 patients (20%) died, 27 (93%) from cardiovascular causes. The median difference in NT-pro-BNP in the survivors was 665 pg/ml, compared to 5,336 pg/ml in the patients who died (p = 0.01). Multivariate Cox regression analyses, adjusted for cardiac history and cardiovascular risk factors (age, angina pectoris, myocardial infarction, stroke, diabetes mellitus, renal dysfunction, body mass index, type of surgery and the left ventricular ejection fraction), demonstrated that the difference in NT-pro-BNP level between pre- and postoperative measurement was the strongest independent predictor of cardiac outcome (hazard ratio 3.06, 95% confidence interval 1.36 to 6.91). In conclusion, the change in NT-pro-BNP, indicated by repeated measurements before surgery and before discharge is the strongest predictor of cardiac outcomes in patients who undergo vascular surgery. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Bipartite Topology of Treponema pallidum Repeat Proteins C/D and I: OUTER MEMBRANE INSERTION, TRIMERIZATION, AND PORIN FUNCTION REQUIRE A C-TERMINAL β-BARREL DOMAIN.

    Science.gov (United States)

    Anand, Arvind; LeDoyt, Morgan; Karanian, Carson; Luthra, Amit; Koszelak-Rosenblum, Mary; Malkowski, Michael G; Puthenveetil, Robbins; Vinogradova, Olga; Radolf, Justin D

    2015-05-08

    We previously identified Treponema pallidum repeat proteins TprC/D, TprF, and TprI as candidate outer membrane proteins (OMPs) and subsequently demonstrated that TprC is not only a rare OMP but also forms trimers and has porin activity. We also reported that TprC contains N- and C-terminal domains (TprC(N) and TprC(C)) orthologous to regions in the major outer sheath protein (MOSP(N) and MOSP(C)) of Treponema denticola and that TprC(C) is solely responsible for β-barrel formation, trimerization, and porin function by the full-length protein. Herein, we show that TprI also possesses bipartite architecture, trimeric structure, and porin function and that the MOSP(C)-like domains of native TprC and TprI are surface-exposed in T. pallidum, whereas their MOSP(N)-like domains are tethered within the periplasm. TprF, which does not contain a MOSP(C)-like domain, lacks amphiphilicity and porin activity, adopts an extended inflexible structure, and, in T. pallidum, is tightly bound to the protoplasmic cylinder. By thermal denaturation, the MOSP(N) and MOSP(C)-like domains of TprC and TprI are highly thermostable, endowing the full-length proteins with impressive conformational stability. When expressed in Escherichia coli with PelB signal sequences, TprC and TprI localize to the outer membrane, adopting bipartite topologies, whereas TprF is periplasmic. We propose that the MOSP(N)-like domains enhance the structural integrity of the cell envelope by anchoring the β-barrels within the periplasm. In addition to being bona fide T. pallidum rare outer membrane proteins, TprC/D and TprI represent a new class of dual function, bipartite bacterial OMP. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Transcriptional and Bioinformatic Analysis Provide a Relationship between Host Response Changes to Marek’s Disease Viruses Infection and an Integrated Long Terminal Repeat

    Directory of Open Access Journals (Sweden)

    Ning eCui

    2016-04-01

    Full Text Available GX0101, Marek’s disease virus (MDV strain with a long terminal repeat (LTR insert of reticuloendotheliosis virus (REV, was isolated from CVI988/Rispens vaccinated birds showing tumors. We have constructed a LTR deleted strain GX0101∆LTR in our previous study. To compare the host responses to GX0101 and GX0101∆LTR, chicken embryo fibroblasts (CEF cells were infected with two MDV strains and a gene-chip containing chicken genome was employed to examine gene transcription changes in host cells in the present study. Of the 42 368 chicken transcripts on the chip, there were 2199 genes that differentially expressed in CEF infected with GX0101 compared to GX0101∆LTR significantly. Differentially expressed genes were distributed to 25 possible gene networks according to their intermolecular connections and were annotated to 56 pathways. The insertion of REV LTR showed the greatest influence on cancer formation and metastasis, followed with immune changes, atherosclerosis and nervous system disorders in MDV-infected CEF cells. Based on these bio functions, GX0101 infection was predicated with a greater growth and survival inhibition but lower oncogenicity in chickens than GX0101∆LTR, at least in the acute phase of infection. In summary, the insertion of REV LTR altered the expression of host genes in response to MDV infection, possibly resulting in novel phenotypic properties in chickens. Our study has provided the evidence of retroviral insertional changes of host responses to herpesvirus infection for the first time, which will promote to elucidation of the possible relationship between the LTR insertion and the observed phenotypes.

  19. Lipid-associated membrane proteins of Mycoplasma fermentans and M. penetrans activate human immunodeficiency virus long-terminal repeats through Toll-like receptors.

    Science.gov (United States)

    Shimizu, Takashi; Kida, Yutaka; Kuwano, Koichi

    2004-09-01

    Mycoplasmas are known to enhance human immunodeficiency virus (HIV) replication, and mycoplasma-derived lipid extracts have been reported to activate nuclear factor-kappaB (NF-kappaB) through Toll-like receptors (TLRs). In this study, we examined the involvement of TLRs in the activation of HIV long-terminal repeats (LTR) by mycoplasma and their active components responsible for the TLR activation. Lipid-associated membrane proteins (LAMPs) from two species of mycoplasma (Mycoplasma fermentans and M. penetrans) that are associated with acquired immune-deficiency syndrome (AIDS), were found to activate HIV LTRs in a human monocytic cell line, THP-1. NF-kappaB deletion from the LTR resulted in inhibition of the activation. The LTR activation by M. fermentans LAMPs was inhibited by a dominant negative (DN) construct of TLR1 and TLR6, whereas HIV LTR activation by M. penetrans LAMPs was inhibited by DN TLR1, but not by DN TLR6. These results indicate that the activation of HIV LTRs by M. fermentans and M. penetrans LAMPs is dependent on NF-kappaB, and that the activation of HIV LTR by M. fermentans LAMPs is mediated through TLR1, TLR2 and TLR6. In contrast, the LTR activation by M. penetrans LAMPs is carried out through TLR1 and TLR2, but not TLR6. Subsequently, the active component of M. penetrans and M. fermentans LAMPs was purified by reverse-phase high-performance liquid chromatography (HPLC). Interestingly, the purified lipoprotein of M. penetrans LAMPs (LPMp) was able to activate NF-kappaB through TLR1 and TLR2. On the other hand, the activation of NF-kappaB by purified lipoprotein of M. fermentans LAMPs (LPMf) was mediated through TLR2 and TLR6, but not TLR1.

  20. Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retrotransposon EhLINE1.

    Science.gov (United States)

    Yadav, Vijay Pal; Mandal, Prabhat Kumar; Rao, Desirazu N; Bhattacharya, Sudha

    2009-12-01

    The genome of the human pathogen Entamoeba histolytica, a primitive protist, contains non-long terminal repeat retrotransposable elements called EhLINEs. These encode reverse transcriptase and endonuclease required for retrotransposition. The endonuclease shows sequence similarity with bacterial restriction endonucleases. Here we report the salient enzymatic features of one such endonuclease. The kinetics of an EhLINE1-encoded endonuclease catalyzed reaction, determined under steady-state and single-turnover conditions, revealed a significant burst phase followed by a slower steady-state phase, indicating that release of product could be the slower step in this reaction. For circular supercoiled DNA the K(m) was 2.6 x 10(-8) M and the k(cat) was 1.6 x 10(-2) sec(-1). For linear E. histolytica DNA substrate the K(m) and k(cat) values were 1.3 x 10(-8) M and 2.2 x 10(-4) sec(-1) respectively. Single-turnover reaction kinetics suggested a noncooperative mode of hydrolysis. The enzyme behaved as a monomer. While Mg(2+) was required for activity, 60% activity was seen with Mn(2+) and none with other divalent metal ions. Substitution of PDX(12-14)D (a metal-binding motif) with PAX(12-14)D caused local conformational change in the protein tertiary structure, which could contribute to reduced enzyme activity in the mutated protein. The protein underwent conformational change upon the addition of DNA, which is consistent with the known behavior of restriction endonucleases. The similarities with bacterial restriction endonucleases suggest that the EhLINE1-encoded endonuclease was possibly acquired from bacteria through horizontal gene transfer. The loss of strict sequence specificity for nicking may have been subsequently selected to facilitate spread of the retrotransposon to intergenic regions of the E. histolytica genome.

  1. N-Terminal Pro-B-Type Natriuretic Peptide-Guided Therapy in Chronic Heart Failure Reduces Repeated Hospitalizations-Results From TIME-CHF.

    Science.gov (United States)

    Davarzani, Nasser; Sanders-van Wijk, Sandra; Karel, Joël; Maeder, Micha T; Leibundgut, Gregor; Gutmann, Marc; Pfisterer, Matthias E; Rickenbacher, Peter; Peeters, Ralf; Brunner-la Rocca, Hans-Peter

    2017-05-01

    Although heart failure (HF) patients are known to experience repeated hospitalizations, most studies evaluated only time to first event. N-Terminal B-type natriuretic peptide (NT-proBNP)-guided therapy has not convincingly been shown to improve HF-specific outcomes, and effects on recurrent all-cause hospitalization are uncertain. Therefore, we investigated the effect of NT-proBNP-guided therapy on recurrent events in HF with the use of a time-between-events approach in a hypothesis-generating analysis. The Trial of Intensified Versus Standard Medical Therapy in Elderly Patients With Congestive Heart Failure (TIME-CHF) randomized 499 HF patients, aged ≥60 years, left ventricular ejection fraction ≤45%, New York Heart Association functional class ≥I,I to NT-proBNP-guided versus symptom-guided therapy for 18 months, with further follow-up for 5.5 years. The effect of NT-proBNP-guided therapy on recurrent HF-related and all-cause hospitalizations and/or all-cause death was explored. One hundred four patients (49 NT-proBNP-guided, 55 symptom-guided) experienced 1 and 275 patients (133 NT-proBNP-guided, 142 symptom-guided) experienced ≥2 all-cause hospitalization events. Regarding HF hospitalization, 132 patients (57 NT-proBNP-guided, 75 symptom-guided) experienced 1 and 122 patients (57 NT-proBNP-guided, 65 symptom-guided) experienced ≥2 events. NT-proBNP-guided therapy was significant in preventing 2nd all-cause hospitalizations (hazard ratio [HR] 0.83; P = .01), in contrast to nonsignificant results in preventing 1st all-cause hospitalization events (HR 0.91; P = .35). This was not the case regarding HF hospitalization events (HR 0.85 [P = .14] vs HR 0.73 [P = .01]) The beneficial effect of NT-proBNP-guided therapy was seen only in patients aged <75 years, and not in those aged ≥75 years (interaction terms with P = .01 and P = .03 for all-cause hospitalization and HF hospitalization events, respectively). NT-proBNP-guided therapy

  2. Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes

    Science.gov (United States)

    Levy, Orr; Knisbacher, Binyamin A.; Levanon, Erez Y.; Havlin, Shlomo

    2017-01-01

    Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements. We develop a computational framework based on network theory that tracks the path of RE proliferation throughout evolution. We analyze SVA (SINE-VNTR-Alu), the youngest RE family in human genomes, to understand RE dynamics across hominids. Integrating comparative genomics and network tools enables us to track the course of SVA proliferation, identify yet unknown active communities, and detect tentative “master REs” that played key roles in SVA propagation, providing strong support for the fundamental “master gene” model of RE proliferation. The method is generic and thus can be applied to REs of any of the thousands of available genomes to identify active RE communities and master REs that were pivotal in the evolution of their host genomes. PMID:29043294

  3. A new retroelement constituted by a natural alternatively spliced RNA of murine replication-competent retroviruses.

    Science.gov (United States)

    Houzet, Laurent; Battini, Jean Luc; Bernard, Eric; Thibert, Valerie; Mougel, Marylène

    2003-09-15

    Replication of simple retroviruses depends on the recruitment of a single large primary transcript toward splicing, transport/packaging and translation regulations. In this respect, we studied the novel SD' 4.4 kb RNA of murine leukemia retroviruses (MLV) which results from alternative splicing of the primary transcript. We showed that SD' RNA was required for optimal replication since expression of a pre-spliced SD' RNA trans-complemented the impaired infectivity of a SD'-defective mutant. We monitored the fate of this novel transcript throughout early and late events of the viral life cycle. SD' RNA was specifically incorporated into virions demonstrating that the unspliced RNA was not the unique viral RNA present in virions. Furthermore, SD' RNA was reverse transcribed and its DNA copy integrated into the host genome, thus constituting a new splice donor-associated retroelement (SDARE) in infected cells. Finally, we showed that SD' mRNA encoded a 50 kDa polyprotein, and to a lower extent an additional 60 kDa polyprotein, which harbored Gag and integrase domains.

  4. Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes

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    Jan Attig

    2017-12-01

    Full Text Available In addition to evolutionarily-accrued sequence mutation or deletion, endogenous retroelements (EREs in eukaryotic genomes are subject to epigenetic silencing, preventing or reducing their transcription, particularly in the germplasm. Nevertheless, transcriptional activation of EREs, including endogenous retroviruses (ERVs and long interspersed nuclear elements (LINEs, is observed in somatic cells, variably upon cellular differentiation and frequently upon cellular transformation. ERE transcription is modulated during physiological and pathological immune cell activation, as well as in immune cell cancers. However, our understanding of the potential consequences of such modulation remains incomplete, partly due to the relative scarcity of information regarding genome-wide ERE transcriptional patterns in immune cells. Here, we describe a methodology that allows probing RNA-sequencing (RNA-seq data for genome-wide expression of EREs in murine and human cells. Our analysis of B cells reveals that their transcriptional response during immune activation is dominated by induction of gene transcription, and that EREs respond to a much lesser extent. The transcriptional activity of the majority of EREs is either unaffected or reduced by B cell activation both in mice and humans, albeit LINEs appear considerably more responsive in the latter host. Nevertheless, a small number of highly distinct ERVs are strongly and consistently induced during B cell activation. Importantly, this pattern contrasts starkly with B cell transformation, which exhibits widespread induction of EREs, including ERVs that minimally overlap with those responsive to immune stimulation. The distinctive patterns of ERE induction suggest different underlying mechanisms and will help separate physiological from pathological expression.

  5. Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae.

    Science.gov (United States)

    Khan, Hameed; Kozera, Catherine; Curtis, Bruce A; Bussey, Jillian Tarrant; Theophilou, Stan; Bowman, Sharen; Archibald, John M

    2007-02-01

    The cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endosymbiont. The endosymbiont nuclear genome, or nucleomorph, of the cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of approximately 1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the cryptomonad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fosmid clone libraries from two distantly related cryptomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corresponding to approximately 150 and approximately 235 kb of sequence, respectively. Very few of the random end sequences determined in this study show similarity to known genes in other eukaryotes, underscoring the considerable evolutionary distance between the cryptomonads and other eukaryotes whose nuclear genomes have been completely sequenced. Using a combination of fosmid clone end-sequencing, Southern hybridizations, and PCR, we demonstrate that Ty3-gypsy long-terminal repeat (LTR) retrotransposons and tandem repeat sequences are a prominent feature of the nuclear genomes of both organisms. The complete sequence of a 30.9-kb genomic fragment from R. salina was found to contain a full-length Ty3-gypsy element with near-identical LTRs and a chromodomain, a protein module suggested to mediate the site-specific integration of the retrotransposon. The discovery of chromodomain-containing retroelements in cryptomonads further expands the known distribution of the so-called chromoviruses across the tree of eukaryotes.

  6. Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF

    Directory of Open Access Journals (Sweden)

    Schillinger Thomas

    2012-08-01

    Full Text Available Abstract Background Diversity Generating Retroelements (DGRs are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. They achieve hypermutation through replacement of the variable region with a strongly mutated cDNA copy generated by the element-encoded reverse transcriptase. In contrast to “selfish” retroelements such as group II introns and retrotransposons, DGRs impart an advantage to their host by increasing its adaptive potential. DGRs were discovered in a bacteriophage, but since then additional examples have been identified in some bacterial genomes. Results Here we present the program DiGReF that allowed us to comprehensively screen available databases for DGRs. We identified 155 DGRs which are found in all major classes of bacteria, though exhibiting sporadic distribution across species. Phylogenetic analysis and sequence comparison showed that DGRs move between genomes by associating with various mobile elements such as phages, transposons and plasmids. The DGR cassettes exhibit high flexibility in the arrangement of their components and easily acquire additional paralogous target genes. Surprisingly, the genomic data alone provide new insights into the molecular mechanism of DGRs. Most notably, our data suggest that the template RNA is transcribed separately from the rest of the element. Conclusions DiGReF is a valuable tool to detect DGRs in genome data. Its output allows comprehensive analysis of various aspects of DGR biology, thus deepening our understanding of the role DGRs play in prokaryotic genome plasticity, from the global down to the molecular level.

  7. The Ma Gene for Complete-Spectrum Resistance to Meloidogyne Species in Prunus Is a TNL with a Huge Repeated C-Terminal Post-LRR Region1[C][W

    Science.gov (United States)

    Claverie, Michel; Dirlewanger, Elisabeth; Bosselut, Nathalie; Van Ghelder, Cyril; Voisin, Roger; Kleinhentz, Marc; Lafargue, Bernard; Abad, Pierre; Rosso, Marie-Noëlle; Chalhoub, Boulos; Esmenjaud, Daniel

    2011-01-01

    Root-knot nematode (RKN) Meloidogyne species are major polyphagous pests of most crops worldwide, and cultivars with durable resistance are urgently needed because of nematicide bans. The Ma gene from the Myrobalan plum (Prunus cerasifera) confers complete-spectrum, heat-stable, and high-level resistance to RKN, which is remarkable in comparison with the Mi-1 gene from tomato (Solanum lycopersicum), the sole RKN resistance gene cloned. We report here the positional cloning and the functional validation of the Ma locus present at the heterozygous state in the P.2175 accession. High-resolution mapping totaling over 3,000 segregants reduced the Ma locus interval to a 32-kb cluster of three Toll/Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat (LRR) genes (TNL1–TNL3), including a pseudogene (TNL2) and a truncated gene (TNL3). The sole complete gene in this interval (TNL1) was validated as Ma, as it conferred the same complete-spectrum and high-level resistance (as in P.2175) using its genomic sequence and native promoter region in Agrobacterium rhizogenes-transformed hairy roots and composite plants. The full-length cDNA (2,048 amino acids) of Ma is the longest of all Resistance genes cloned to date. Its TNL structure is completed by a huge post-LRR (PL) sequence (1,088 amino acids) comprising five repeated carboxyl-terminal PL exons with two conserved motifs. The amino-terminal region (213 amino acids) of the LRR exon is conserved between alleles and contrasts with the high interallelic polymorphisms of its distal region (111 amino acids) and of PL domains. The Ma gene highlights the importance of these uncharacterized PL domains, which may be involved in pathogen recognition through the decoy hypothesis or in nuclear signaling. PMID:21482634

  8. A substrate specificity-determining unit of three Lin12-Notch repeat modules is formed in trans within the pappalysin-1 dimer and requires a sequence stretch C-terminal to the third module

    DEFF Research Database (Denmark)

    Weyer, Kathrin; Boldt, Henning Bünsow; Poulsen, Christine Bruun

    2007-01-01

    Members of the pappalysin family of metzincin metalloproteinases, pregnancy-associated plasma protein-A (PAPP-A, pappalysin-1) and PAPP-A2 (pappalysin-2), regulate the bioavailability of insulin-like growth factors (IGFs) by specific proteolytic inactivation of IGF-binding proteins (IGFBPs). PAPP-A...... cleaves IGFBP-4 and IGFBP-5, whereas PAPP-A2 cleaves only IGFBP-5. The pappalysins contain three Lin12-Notch repeat (LNR1-3) modules, previously considered unique to the Notch receptor family in which they function to regulate receptor cleavage. In contrast to the Notch receptor where three LNR modules...... are tandemly arranged, LNR3 is separated by more than 1000 residues from LNR1-2 in the pappalysin sequence. Each of the three LNR modules of PAPP-A is required for proteolysis of IGFBP-4, but not IGFBP-5. However, we here find that a C-terminal truncated variant of PAPP-A, which lacks LNR3 and therefore...

  9. Conservation of the C-type lectin fold for massive sequence variation in a Treponema diversity-generating retroelement

    Energy Technology Data Exchange (ETDEWEB)

    Le Coq, Johanne; Ghosh, Partho (UCSD)

    2012-06-19

    Anticipatory ligand binding through massive protein sequence variation is rare in biological systems, having been observed only in the vertebrate adaptive immune response and in a phage diversity-generating retroelement (DGR). Earlier work has demonstrated that the prototypical DGR variable protein, major tropism determinant (Mtd), meets the demands of anticipatory ligand binding by novel means through the C-type lectin (CLec) fold. However, because of the low sequence identity among DGR variable proteins, it has remained unclear whether the CLec fold is a general solution for DGRs. We have addressed this problem by determining the structure of a second DGR variable protein, TvpA, from the pathogenic oral spirochete Treponema denticola. Despite its weak sequence identity to Mtd ({approx}16%), TvpA was found to also have a CLec fold, with predicted variable residues exposed in a ligand-binding site. However, this site in TvpA was markedly more variable than the one in Mtd, reflecting the unprecedented approximate 10{sup 20} potential variability of TvpA. In addition, similarity between TvpA and Mtd with formylglycine-generating enzymes was detected. These results provide strong evidence for the conservation of the formylglycine-generating enzyme-type CLec fold among DGRs as a means of accommodating massive sequence variation.

  10. Deep Sequencing Analysis of Human T Cell Lymphotropic Virus Type 1 Long Terminal Repeat 5' Region from Patients with Tropical Spastic Paraparesis/Human T Cell Lymphotropic Virus Type 1-Associated Myelopathy and Asymptomatic Carriers.

    Science.gov (United States)

    Rego, Filipe Ferreira de Almeida; de Oliveira, Tulio; Giovanetti, Marta; Galvão-Castro, Bernardo; Gonçalves, Marilda de Souza; Alcantara, Luiz Carlos

    2016-03-01

    The aim of this study was to analyze patients by deep sequencing the human T cell lymphotropic virus type 1 (HTLV-1) long terminal repeat (LTR) region in order to determine if minor and/or major mutations in this promoter region might be associated with tropical spastic paraparesis (TSP)/human T cell lymphotropic virus type 1-associated myelopathy (HAM) outcome or proviral load or HTLV-1 expression. This study is a cross-sectional analyze of 29 HTLV-1-infected patients with TSP/HAM or asymptomatic carriers. Proviral DNA from those subjects was submitted to a nested PCR for the HTLV-1 LTR5' region. The HTLV-1 LTR5' purified products were submitted to deep sequencing using the Ion Torrent sequencing technology (Life Technologies, Carlsbad, CA). We found that samples with low proviral load showed more detected minor mutations than the samples with high proviral load. Mutations in 136 positions were found over the 520-bp analyzed fragment of HTLV-1 LTR5' with at least 1% frequency. Eleven mutations were present in the previously determined major transcription factor binding sites (TFBS) and in more than one patient, indicating that there might be a differential HTLV-1 expression comparing individuals or in comparing different cells from the same individual. Three mutations were statistically significant using the Fisher nonparametric test between the groups but were not present in previously determined TFBS (G126C/T, G306C, and C479T). Those mutations that were not present in previously determined TFBS were statistically significant in this study and were most frequent in patients with low proviral load or in asymptomatic carriers. Although those mutations were not present in previously determined TFBS, one of those mutations (G306C/A) was present in an Sp-1 binding site determined by in silico analysis, and its presence abrogated the site for Sp-1 binding and created a new possible ATF binding site.

  11. Identification of a retroelement from the resurrection plant Boea hygrometrica that confers osmotic and alkaline tolerance in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Yan Zhao

    Full Text Available Functional genomic elements, including transposable elements, small RNAs and non-coding RNAs, are involved in regulation of gene expression in response to plant stress. To identify genomic elements that regulate dehydration and alkaline tolerance in Boea hygrometrica, a resurrection plant that inhabits drought and alkaline Karst areas, a genomic DNA library from B. hygrometrica was constructed and subsequently transformed into Arabidopsis using binary bacterial artificial chromosome (BIBAC vectors. Transgenic lines were screened under osmotic and alkaline conditions, leading to the identification of Clone L1-4 that conferred osmotic and alkaline tolerance. Sequence analyses revealed that L1-4 contained a 49-kb retroelement fragment from B. hygrometrica, of which only a truncated sequence was present in L1-4 transgenic Arabidopsis plants. Additional subcloning revealed that activity resided in a 2-kb sequence, designated Osmotic and Alkaline Resistance 1 (OAR1. In addition, transgenic Arabidopsis lines carrying an OAR1-homologue also showed similar stress tolerance phenotypes. Physiological and molecular analyses demonstrated that OAR1-transgenic plants exhibited improved photochemical efficiency and membrane integrity and biomarker gene expression under both osmotic and alkaline stresses. Short transcripts that originated from OAR1 were increased under stress conditions in both B. hygrometrica and Arabidopsis carrying OAR1. The relative copy number of OAR1 was stable in transgenic Arabidopsis under stress but increased in B. hygrometrica. Taken together, our results indicated a potential role of OAR1 element in plant tolerance to osmotic and alkaline stresses, and verified the feasibility of the BIBAC transformation technique to identify functional genomic elements from physiological model species.

  12. Susceptibility of various parental lines of commercial white leghorn layers to infection with a naturally occurring recombinant avian leukosis virus containing subgroup B envelope and subgroup J long terminal repeat.

    Science.gov (United States)

    Mays, Jody K; Pandiri, Arun R; Fadly, Aly M

    2006-09-01

    Chickens from seven different parental lines of commercial White Leghorn layer flocks from three independent breeders were inoculated with a naturally occurring avian leukosis virus (ALV) containing an ALV-B envelope and an ALV-J long terminal repeat (LTR) termed ALV-B/J. Additional groups of chickens from the same seven parental lines were inoculated with ALV-B. Chickens were tested for ALV viremia and antibody at 0, 4, 8, 16, and 32 wk postinfection. Chickens from all parental lines studied were susceptible to infection with ALV-B with 40%-100% of inoculated chickens positive for ALV at hatch following embryo infection. Similarly, infection of egg layer flocks with the ALV-B/J recombinant virus at 8 days of embryonation induced tolerance to ALV with 86%-100% of the chickens viremic, 40%-75% of the chickens shedding virus, and only 2/125 (2%) of the chickens producing serum-neutralizing antibodies against homologous ALV-B/J recombinant virus at 32 wk postinfection. In contrast, when infected with the ALV-B/J recombinant virus at hatch, 33%-82% of the chickens were viremic, 28%-47% shed virus, and 0%-56% produced serum-neutralizing antibodies against homologous ALV-B/J recombinant virus at 32 wk postinfection. Infection with the ALV-B/J recombinant virus at embryonation and at hatch induced predominately lymphoid leukosis (LL), along with other common ALV neoplasms, including erythroblastosis, osteopetrosis, nephroblastomas, and rhabdosarcomas. No incidence of myeloid leukosis (ML) was observed in any of the commercial White Leghorn egg layer flocks infected with ALV-B/J in the present study. Data suggest that the parental line of commercial layers may influence development of ALV-B/J-induced viremia and antibody, but not tumor type. Differences in type of tumors noted in the present study and those noted in the field case where the ALV-B/J was first isolated may be attributed to differences in the genetics of the commercial layer flock in which ML was first

  13. DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.

    Directory of Open Access Journals (Sweden)

    Janet M Young

    2013-11-01

    Full Text Available The human double-homeodomain retrogene DUX4 is expressed in the testis and epigenetically repressed in somatic tissues. Facioscapulohumeral muscular dystrophy (FSHD is caused by mutations that decrease the epigenetic repression of DUX4 in somatic tissues and result in mis-expression of this transcription factor in skeletal muscle. DUX4 binds sites in the human genome that contain a double-homeobox sequence motif, including sites in unique regions of the genome as well as many sites in repetitive elements. Using ChIP-seq and RNA-seq on myoblasts transduced with DUX4 we show that DUX4 binds and activates transcription of mammalian apparent LTR-retrotransposons (MaLRs, endogenous retrovirus (ERVL and ERVK elements, and pericentromeric satellite HSATII sequences. Some DUX4-activated MaLR and ERV elements create novel promoters for genes, long non-coding RNAs, and antisense transcripts. Many of these novel transcripts are expressed in FSHD muscle cells but not control cells, and thus might contribute to FSHD pathology. For example, HEY1, a repressor of myogenesis, is activated by DUX4 through a MaLR promoter. DUX4-bound motifs, including those in repetitive elements, show evolutionary conservation and some repeat-initiated transcripts are expressed in healthy testis, the normal expression site of DUX4, but more rarely in other somatic tissues. Testis expression patterns are known to have evolved rapidly in mammals, but the mechanisms behind this rapid change have not yet been identified: our results suggest that mobilization of MaLR and ERV elements during mammalian evolution altered germline gene expression patterns through transcriptional activation by DUX4. Our findings demonstrate a role for DUX4 and repetitive elements in mammalian germline evolution and in FSHD muscular dystrophy.

  14. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

    Directory of Open Access Journals (Sweden)

    Green Eric D

    2009-07-01

    Full Text Available Abstract Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB, are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN, euchromatic regions (EU, and an evolutionary breakpoint (EB that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s and endogenous retroviruses (ERVs and a depletion of short interspersed nucleotide elements (SINEs shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33, known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the

  15. Terminating supervision.

    Science.gov (United States)

    Levendosky, Alytia A; Hopwood, Christopher J

    2017-03-01

    The focus of this paper is on the termination of clinical supervision. Although clinical supervision is considered the backbone of most mental health training programs, it gets relatively little theoretical or empirical attention. The termination of supervision has received even less attention. In this paper, we describe an approach to terminating supervision in our treatment team, which integrates intensive assessment with a relational perspective in a clinical science training program (Levendosky & Hopwood, 2016). We describe our established conceptual framework, review empirical evidence, and provide verbatim examples from final supervision meetings on our team to elaborate the importance of conceptualizing individual differences across trainees and parallels between supervision and psychotherapy dynamics. We conclude by emphasizing the need for research on supervision in general and supervision termination in particular. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  16. Terminal Ballistics

    CERN Document Server

    Rosenberg, Zvi

    2012-01-01

    This book covers the important issues of terminal ballistics in a comprehensive way combining experimental data, numerical simulations and analytical modeling. The first chapter reviews the experimental equipment which are used for ballistic tests and the diagnostics for material characterization under impulsive loading conditions. The second chapter covers essential features of the codes which are used for terminal ballistics such as the Euler vs. Lagrange schemes and meshing techniques, as well as the most popular material models. The third chapter, devoted to the penetration mechanics of rigid penetrators, brings the update of modeling in this field. The fourth chapter deals with plate perforation and the fifth chapter deals with the penetration mechanics of shaped charge jets and eroding long rods. The last two chapters discuss several techniques for the disruption and defeating of the main threats in armor design. Throughout the book the authors demonstrate the advantages of numerical simulations in unde...

  17. The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.

    Science.gov (United States)

    Jordà, Mireia; Díez-Villanueva, Anna; Mallona, Izaskun; Martín, Berta; Lois, Sergi; Barrera, Víctor; Esteller, Manel; Vavouri, Tanya; Peinado, Miguel A

    2017-01-01

    Cancer cells exhibit multiple epigenetic changes with prominent local DNA hypermethylation and widespread hypomethylation affecting large chromosomal domains. Epigenome studies often disregard the study of repeat elements owing to technical complexity and their undefined role in genome regulation. We have developed NSUMA (Next-generation Sequencing of UnMethylated Alu), a cost-effective approach allowing the unambiguous interrogation of DNA methylation in more than 130,000 individual Alu elements, the most abundant retrotransposon in the human genome. DNA methylation profiles of Alu repeats have been analyzed in colon cancers and normal tissues using NSUMA and whole-genome bisulfite sequencing. Normal cells show a low proportion of unmethylated Alu (1%-4%) that may increase up to 10-fold in cancer cells. In normal cells, unmethylated Alu elements tend to locate in the vicinity of functionally rich regions and display epigenetic features consistent with a direct impact on genome regulation. In cancer cells, Alu repeats are more resistant to hypomethylation than other retroelements. Genome segmentation based on high/low rates of Alu hypomethylation allows the identification of genomic compartments with differential genetic, epigenetic, and transcriptomic features. Alu hypomethylated regions show low transcriptional activity, late DNA replication, and its extent is associated with higher chromosomal instability. Our analysis demonstrates that Alu retroelements contribute to define the epigenetic landscape of normal and cancer cells and provides a unique resource on the epigenetic dynamics of a principal, but largely unexplored, component of the primate genome. © 2017 Jordà et al.; Published by Cold Spring Harbor Laboratory Press.

  18. Terminal ballistics

    CERN Document Server

    Rosenberg, Zvi

    2016-01-01

    This book comprehensively discusses essential aspects of terminal ballistics, combining experimental data, numerical simulations and analytical modeling. Employing a unique approach to numerical simulations as a measure of sensitivity for the major physical parameters, the new edition also includes the following features: new figures to better illustrate the problems discussed; improved explanations for the equation of state of a solid and for the cavity expansion process; new data concerning the Kolsky bar test; and a discussion of analytical modeling for the hole diameter in a thin metallic plate impacted by a shaped charge jet. The section on thick concrete targets penetrated by rigid projectiles has now been expanded to include the latest findings, and two new sections have been added: one on a novel approach to the perforation of thin concrete slabs, and one on testing the failure of thin metallic plates using a hydrodynamic ram.

  19. Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila.

    Directory of Open Access Journals (Sweden)

    Miriam Merenciano

    2016-08-01

    Full Text Available Promoters are structurally and functionally diverse gene regulatory regions. The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters. Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contribute to promote diversity. In this work, we analyzed in detail one of the transposable element insertions, named FBti0019985, that has been co-opted to drive expression of CG18446, a candidate stress response gene. We analyzed strains from different natural populations and we found that besides FBti0019985, there are another eight independent transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed the sequence of the nine roo insertions and we investigated whether the different insertions were functionally equivalent by performing 5'-RACE, gene expression, and cold-stress survival experiments. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.

  20. Intermodal freight terminals : terminal business planning

    NARCIS (Netherlands)

    Nijkamp, Peter; Wiegmans, Bart W.

    2000-01-01

    The main purpose of this paper is to provide a framework for existing- and newly proposedinter-modal freight terminals in their business planning process. This framework is importantfor constructing- and improving the central terminal service portfolio of handling (loading,discharging, and

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  1. kbff Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  2. kprc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  3. kmdt Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  4. kals Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  5. kgrb Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  6. khdn Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  7. kgso Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  8. khlg Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  9. kjan Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  10. kbce Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  11. ktys Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  12. kcha Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  13. kdug Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  14. Terminated Multifamily Mortgages Database

    Data.gov (United States)

    Department of Housing and Urban Development — This Excel 2010 file includes all terminated HUD Multifamily insured mortgages. It includes the Holder and Servicer at the time the mortgage was terminated. The data...

  15. kpub Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  16. ksrq Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  17. kaeg Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  18. pata Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  19. klgu Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  20. pamc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  1. kmsl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  2. kbrl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  3. ksfb Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  4. kpsc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  5. kely Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  6. ksyr Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  7. katw Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  8. kama Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  9. kpae Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  10. kmli Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  11. kokc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  12. kjst Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  13. kgup Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  14. padl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  15. klit Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  16. kalb Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  17. kact Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  18. kink Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  19. kshv Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  20. pajn Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  1. kpna Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  2. ktph Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  3. ksux Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  4. kcon Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  5. khio Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  6. konp Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  7. kpnc Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  8. kmlu Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  9. kgsp Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  10. kgpt Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  11. kflo Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  12. keri Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  13. kcid Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  14. ksaf Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  15. kcvg Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  16. ptya Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  17. katl Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  18. kmth Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  19. Intermodal freight terminals : terminal business planning

    OpenAIRE

    Nijkamp, Peter; Bart W Wiegmans

    2000-01-01

    The main purpose of this paper is to provide a framework for existing- and newly proposedinter-modal freight terminals in their business planning process. This framework is importantfor constructing- and improving the central terminal service portfolio of handling (loading,discharging, and transhipping) and storage of containerised cargo. Supportive activities (e.g. administration, customs) are taken into account as well.In particular, its aim is to investigate whether business planning offer...

  20. 29 CFR 4043.24 - Termination or partial termination.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Termination or partial termination. 4043.24 Section 4043.24....24 Termination or partial termination. (a) Reportable event. A reportable event occurs when the Secretary of the Treasury determines that there has been a termination or partial termination of a plan...

  1. CONTAINER TERMINALS IN EUROPE

    Directory of Open Access Journals (Sweden)

    Bart W. WIEGMANS

    2001-01-01

    Full Text Available This paper aims to address the linkage between logistics (in particular, the management of marketing channel flows and transport markets, while also the interaction between these two markets and intermodal container terminals is analysed. The marketing channel theory is used to describe all relevant actors and flows that run through marketing channels, starting with customer needs and ending with customer satisfaction. Porter's theory of competitive advantages is used to review competitive forces in both markets. Finally, a competitor analysis is performed for the logistics and transport market. These theories are applied so as to be able to determine the competitive position of intermodal container terminals with a view to the management of marketing channel flows and the physical transport of freight flows. Hence, the central question of this paper is: Which markets are served by intermodal container terminals and with whom are they competing? At present, neither the maritime container terminals nor the continental container terminals appear to have a significant influence in the logistics service market; they concentrate mainly on the physical movement of containers (transshipment. Furthermore, maritime container terminals and continental container terminals are not dominant players in the transport service market. Our conclusion is that continental terminals are predominantly competing with unimodal road transport, with neighbouring continental terminals and with barge transport companies.

  2. Organizational Relationship Termination Competence

    DEFF Research Database (Denmark)

    Ritter, Thomas; Geersbro, Jens

    2011-01-01

    that a firm's percentage of unwanted customers decreases significantly as acceptance of termination increases, if the firm's definition of unwanted customers is well understood, and if a firm has clear termination routines. In addition, general focus on profitability and external constraints on relationship...

  3. Honesty through repeated interactions.

    Science.gov (United States)

    Rich, Patricia; Zollman, Kevin J S

    2016-04-21

    In the study of signaling, it is well known that the cost of deception is an essential element for stable honest signaling in nature. In this paper, we show how costs for deception can arise endogenously from repeated interactions between individuals. Utilizing the Sir Philip Sidney game as an illustrative case, we show that repeated interactions can sustain honesty with no observable signal costs, even when deception cannot be directly observed. We provide a number of potential experimental tests for this theory which distinguish it from the available alternatives. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. One repeat of the cell wall binding domain is sufficient for anchoring the Lactobacillus acidophilus surface layer protein

    NARCIS (Netherlands)

    Smit, E.; Pouwels, P.H.

    2002-01-01

    The N-terminal repeat (SAC1) of the S-protein of Lactobacillus acidophilus bound efficiently and specifically to cell wall fragments (CWFs) when fused to green fluorescent protein, whereas the C-terminal repeat (SAC2) did not. Treatment of CWFs with hydrofluoric acid, but not phenol, prevented

  5. Repeated Infections in Children

    Science.gov (United States)

    ... he/she have ear tubes?What are the dangers of my child’s repeated infections?Should my child ... affect you or your baby through your breast milk.December 2017December 2017familydoctor.org editorial staffHip Problems in ...

  6. Comsat's TDMA traffic terminal

    Science.gov (United States)

    Benjamin, M. C.; Bogaert, W. M.

    1985-06-01

    Comsat has installed two traffic terminals in the Etam earth-station and is currently installing a third in the new Roaring Creek earth-station to access the Intelsat TDMA network. This paper describes the Comsat TDMA traffic terminal equipment from the supergroup interface to the antenna. Comsat's 1: N redundancy approach for terrestrial interface equipment and DSI unit back-up is described as well as electrical path length, amplitude and group delay equalization techniques, special on-line RF monitoring and failure reporting facilities and the operation and maintenance center which can operate and perform diagnostic testing on up to four traffic terminals from a central location.

  7. Terminated Multifamily Mortgages Database

    Data.gov (United States)

    Department of Housing and Urban Development — This dataset includes all terminated HUD Multifamily mortgages except those from the Hospital Mortgage Insurance Program. It includes the Holder and Servicer at the...

  8. Allowing repeat winners

    OpenAIRE

    Marco D. Huesch; Richard Brady

    2010-01-01

    Unbiased lotteries seem the least unfair and simplest procedures to allocate scarce indivisible resources to those with equal claims. But, when lotteries are repeated, it is not immediately obvious whether prior winners should be included or excluded. As in design questions surrounding single-shot lotteries, considerations of self-interest and distributive social preferences may interact. We investigate preferences for allowing participation of earlier winners in sequential lotteries. We foun...

  9. Antecedents of Customer Relationship Termination

    DEFF Research Database (Denmark)

    Geersbro, Jens; Ritter, Thomas

    relationships as a managerial task. This paper contributes by (1) developing a conceptualization of relationship termination competence and (2) analyzing its antecedents. The empirical results identify termination acceptance, definition non-customers, organizational relationship termination routines...

  10. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  11. Role of the origin of transfer in termination of strand transfer during bacterial conjugation.

    Science.gov (United States)

    Bhattacharjee, M; Rao, X M; Meyer, R J

    1992-10-01

    Conjugal transfer of the broad-host-range plasmid R1162 is initiated and terminated at the nic site within the 38-bp origin of transfer (oriT). Termination involves ligation of the transferred single strand by the plasmid-encoded MobA protein. Several different assays were used to identify the oriT DNA required for termination. For plasmids containing two oriTs, with transfer initiated at one and terminated at the other, the inverted repeat within oriT is important for termination. Deletion of the outer arm reduces the termination frequency; those terminations that do occur probably depend upon nicking at this oriT prior to transfer. The locations of second-site suppressor mutations indicate that base pairing between the arms of the inverted repeat is important for termination. In vitro, the inverted repeat is not required for specific cleavage of single-stranded DNA at nic, but competition experiments indicate that oriTs with the inverted repeat are preferentially cleaved. We propose that the function of the oriT inverted repeat is to trap the plasmid-encoded MobA protein at the end of a round of strand transfer, thus ensuring that the protein is available for the ligation step.

  12. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-01-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  13. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-12-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation (MLI) has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five Glenn Research Center (GRC) provided coupons with 25 layers was shown to be +/- 8.4% whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0%. A second group of 10 coupons has been fabricated by Yetispace and tested by Florida State University, the repeatability between coupons has been shown to be +/- 15-25%. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  14. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-08-01

    The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques for duct leakage using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards. The three duct leak measurement methods assessed in this report are the two duct pressurization methods that are commonly used by many practitioners and the DeltaQ technique. These are methods B, C and A, respectively of the ASTM E1554 standard. Although it would be useful to evaluate other duct leak test methods, this study focused on those test methods that are commonly used and are required in various test standards, such as BPI (2010), RESNET (2014), ASHRAE 62.2 (2013), California Title 24 (CEC 2012), DOE Weatherization and many other energy efficiency programs.

  15. Coal terminal guide 1999

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-08-01

    IBJ`s third edition of its annual guide to the world`s multi-user coal terminals includes comprehensive details of terminals in 44 countries. The guide sets out information for rapid and easy reference comprising contact, full address and communication details as well as berth dimensions and constraints, loading equipment and daily loading rate, annual loading capacity, daily discharge rate, annual discharge capacity, annual throughput capacity, storage facilities, stockyard capacity and equipment, processing facilities and so on. All information has been compiled from specific questionnaires and is presented alphabetically in country order.

  16. Windows Terminal Servers Orchestration

    Science.gov (United States)

    Bukowiec, Sebastian; Gaspar, Ricardo; Smith, Tim

    2017-10-01

    Windows Terminal Servers provide application gateways for various parts of the CERN accelerator complex, used by hundreds of CERN users every day. The combination of new tools such as Puppet, HAProxy and Microsoft System Center suite enable automation of provisioning workflows to provide a terminal server infrastructure that can scale up and down in an automated manner. The orchestration does not only reduce the time and effort necessary to deploy new instances, but also facilitates operations such as patching, analysis and recreation of compromised nodes as well as catering for workload peaks.

  17. EXTREME AND TERMINAL STATES

    Directory of Open Access Journals (Sweden)

    P.F. Litvitsky

    2010-01-01

    Full Text Available Author brings modern conception of extreme and terminal states, their types, likenesses and differences, etiology, key common chains of pathogenesis, principles and methods of their treatment. Pathophysiological data on one of extreme states — collapse — is described in details. Next publications will present the data on shock and coma.Key words: extreme and terminal states, vicious circle of pathogenesis, extreme regulation, principles of treatment.(Voprosy sovremennoi pediatrii — Current Pediatrics. – 2010;9(3:74-80

  18. Electrical termination techniques

    Science.gov (United States)

    Oakey, W. E.; Schleicher, R. R.

    1976-01-01

    A technical review of high reliability electrical terminations for electronic equipment was made. Seven techniques were selected from this review for further investigation, experimental work, and preliminary testing. From the preliminary test results, four techniques were selected for final testing and evaluation. These four were: (1) induction soldering, (2) wire wrap, (3) percussive arc welding, and (4) resistance welding. Of these four, induction soldering was selected as the best technique in terms of minimizing operator errors, controlling temperature and time, minimizing joint contamination, and ultimately producing a reliable, uniform, and reusable electrical termination.

  19. Terminal oxidases of cyanobacteria.

    Science.gov (United States)

    Hart, S E; Schlarb-Ridley, B G; Bendall, D S; Howe, C J

    2005-08-01

    The respiratory chain of cyanobacteria appears to be branched rather than linear; furthermore, respiratory and photosynthetic electron-transfer chains co-exist in the thylakoid membrane and even share components. This review will focus on the three types of terminal respiratory oxidases identified so far on a genetic level in cyanobacteria: aa3-type cytochrome c oxidase, cytochrome bd-quinol oxidase and the alternative respiratory terminal oxidase. We summarize here their genetic, biochemical and biophysical characterization to date and discuss their interactions with electron donors as well as their physiological roles.

  20. Repeat Customer Success in Extension

    Science.gov (United States)

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  1. ORIGINAL ARTICLES Impact of the Choice on Termination of ...

    African Journals Online (AJOL)

    The impact of the Choice on Termination of Pregnancy Act of. 1996 on maternal deaths has not yet been clearly defined. The. 1994 national incomplete abortion survey reported 3 deaths in 803 cases.' A repeat national survey using very similar methodology (a multicentre, prospective, descriptive study) in. 2000 reported 1 ...

  2. Repeated judgment sampling: Boundaries

    Directory of Open Access Journals (Sweden)

    Johannes Muller-Trede

    2011-06-01

    Full Text Available This paper investigates the boundaries of the recent result that eliciting more than one estimate from the same person and averaging these can lead to accuracy gains in judgment tasks. It first examines its generality, analysing whether the kind of question being asked has an effect on the size of potential gains. Experimental results show that the question type matters. Previous results reporting potential accuracy gains are reproduced for year-estimation questions, and extended to questions about percentage shares. On the other hand, no gains are found for general numerical questions. The second part of the paper tests repeated judgment sampling's practical applicability by asking judges to provide a third and final answer on the basis of their first two estimates. In an experiment, the majority of judges do not consistently average their first two answers. As a result, they do not realise the potential accuracy gains from averaging.

  3. Allowing repeat winners

    Directory of Open Access Journals (Sweden)

    Marco D. Huesch

    2010-08-01

    Full Text Available Unbiased lotteries seem the least unfair and simplest procedures to allocate scarce indivisible resources to those with equal claims. But, when lotteries are repeated, it is not immediately obvious whether prior winners should be included or excluded. As in design questions surrounding single-shot lotteries, considerations of self-interest and distributive social preferences may interact. We investigate preferences for allowing participation of earlier winners in sequential lotteries. We found a strong preference for exclusion, both in settings where subjects were involved, and those where they were not. Subjects who answered questions about both settings did not differ in their tendency to prefer exclusion. Stated rationales significantly predicted choice but did not predict switching of choices between the two settings.

  4. Settings for Terminal Care.

    Science.gov (United States)

    Corless, Inge B.

    1988-01-01

    Examines topics related to delivery of terminal care services: ability of various hospice programs to survive financially, contributions of various models of hospice care, impact of Medicare legislation on hospice movement, demonstration of unique hospice intervention, integration of spiritual care into hospice, and role of hospice in care of…

  5. Termination of protein synthesis.

    Science.gov (United States)

    Tuite, M F; Stansfield, I

    1994-05-01

    One of three mRNA codons--UAA, UAG and UGA--is used to signal to the elongating ribosome that translation should be terminated at this point. Upon the arrival of the stop codon at the ribosomal acceptor(A)-site, a protein release factor (RF) binds to the ribosome resulting in the peptidyl transferase centre of the ribosome switching to a hydrolytic function to remove the completed polypeptide chain from the peptidyl-tRNA bound at the adjacent ribosomal peptidyl(P)-site. In this review recent advances in our understanding of the mechanism of termination in the bacterium Escherichia coli will be summarised, paying particular attention to the roles of 16S ribosomal RNA and the release factors RF-1, RF-2 and RF-3 in stop codon recognition. Our understanding of the translation termination process in eukaryotes is much more rudimentary with the identity of the single eukaryotic release factor (eRF) still remaining elusive. Finally, several examples of how the termination mechanism can be subverted either to expand the genetic code (e.g. selenocysteine insertion at UGA codons) or to regulate the expression of mammalian retroviral or plant viral genomes will be discussed.

  6. Making Wireless Terminals Simpler

    DEFF Research Database (Denmark)

    Christensen, Søren Skovgaard; Popovski, Petar; De Carvalho, Elisabeth

    2005-01-01

    The exponential growth of user demands and the limitations of 3G systems have brought researchers and industry to propose solutions for the next generation. Among the requirements are higher bit rates and cheaper deployment. In this paper we focus on a terminal complexity problem related to channel...

  7. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes

    DEFF Research Database (Denmark)

    Peng, Xu; Brügger, Kim; Shen, Biao

    2003-01-01

    that are identical in sequence to one of the repeat variants in the S. solfataricus chromosome. Repeats from the pNOB8 cluster were amplified and tested for protein binding with cell extracts from S. solfataricus. A 17.5-kDa SRSR-binding protein was purified from the cell extracts and sequenced. The protein is N...... terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also...... with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure...

  8. Ice age terminations.

    Science.gov (United States)

    Cheng, Hai; Edwards, R Lawrence; Broecker, Wallace S; Denton, George H; Kong, Xinggong; Wang, Yongjin; Zhang, Rong; Wang, Xianfeng

    2009-10-09

    230Th-dated oxygen isotope records of stalagmites from Sanbao Cave, China, characterize Asian Monsoon (AM) precipitation through the ends of the third- and fourthmost recent ice ages. As a result, AM records for the past four glacial terminations can now be precisely correlated with those from ice cores and marine sediments, establishing the timing and sequence of major events. In all four cases, observations are consistent with a classic Northern Hemisphere summer insolation intensity trigger for an initial retreat of northern ice sheets. Meltwater and icebergs entering the North Atlantic alter oceanic and atmospheric circulation and associated fluxes of heat and carbon, causing increases in atmospheric CO2 and Antarctic temperatures that drive the termination in the Southern Hemisphere. Increasing CO2 and summer insolation drive recession of northern ice sheets, with probable positive feedbacks between sea level and CO2.

  9. Equilibrium and Termination

    Directory of Open Access Journals (Sweden)

    Nicolas Oury

    2010-06-01

    Full Text Available We present a reduction of the termination problem for a Turing machine (in the simplified form of the Post correspondence problem to the problem of determining whether a continuous-time Markov chain presented as a set of Kappa graph-rewriting rules has an equilibrium. It follows that the problem of whether a computable CTMC is dissipative (ie does not have an equilibrium is undecidable.

  10. Coal terminal project report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2004-03-01

    Malaysia is building the necessary infrastructure to cope with an increasing demand for electricity. Its restructured energy policy has led to construction of the 2,100 MW Manjung coal-fired power plant in the state of Perak, for which coal has to be imported via the new Lekiv Bulk Terminal (LBT) adjacent to the plant. Contracts for the LBC and the TNBJ coal stockyard were awarded to the Koch Consortium. The article describes equipment for handling and storing coal. 4 photos.

  11. Terminal Satisfiability in GSTE

    OpenAIRE

    Yongsheng Xu; Guowu Yang; Zhengwei Chang; Desheng Zheng; Wensheng Guo

    2014-01-01

    Generalized symbolic trajectory evaluation (GSTE) is an extension of symbolic trajectory evaluation (STE) and a method of model checking. GSTE specifications are given as assertion graphs. There are four efficient methods to verify whether a circuit model obeys an assertion graph in GSTE, Model Checking Strong Satisfiability (SMC), Model Checking Normal Satisfiability (NMC), Model Checking Fair Satisfiability (FMC), and Model Checking Terminal Satisfiability (TMC). SMC, NMC, and FMC have been...

  12. Why prevention of repeat abortion is so challenging: psychosocial characteristics of women at risk.

    Science.gov (United States)

    Leeners, Brigitte; Bieli, Simone; Huang, Dorothy; Tschudin, Sibil

    2017-02-01

    Abortion rates have declined in recent decades; however, the rate of repeat abortion remains high. In order to identify keys to making efficient interventions against repeat abortion, our objectives were: to assess the percentage of repeat abortions in women opting for termination of pregnancy over a period of 1 year; to identify the risk factors for repeat abortion; and to assess the characteristics of women who opted for a further pregnancy termination despite having received standard post-abortion care. A retrospective cross-sectional survey was carried out among 362 women who underwent pregnancy termination during a 1-year period. Women with and without repeat abortion were compared with regard to age, nationality, marital status, parity and use of contraception. In a subsample of 160 women who were available for follow-up over 4 years, those who underwent a further pregnancy termination during the observation period were also analysed qualitatively. The rate of repeat abortion was 30.1% in the survey population. Age and immigrant status were identified as risk factors. The use of long-acting reversible contraception (LARC) was significantly higher after repeat abortion than after a first termination of pregnancy. Among women with repeat abortion in the follow-up group, those with psychological problems tended to discontinue contraception and those with partnership conflicts were prone to using unreliable contraceptive methods. Aside from promoting LARC methods, strategies to reduce repeat abortion should consider the psychosocial risk factors and characteristics of women at risk identified in this study. An interdisciplinary approach including social care and counselling would be the most appropriate means to enable this.

  13. 78 FR 72655 - Taking of Marine Mammals Incidental to Specified Activities; Bremerton Ferry Terminal Wingwall...

    Science.gov (United States)

    2013-12-03

    ... interpret important sounds. Repeated noise exposure that leads to TTS could cause PTS. Experiments on a..., animals being exposed for a prolonged period to repeated hammer strikes could receive more noise exposure... wingwall replacement work at the Bremerton Ferry Terminal, only vibratory pile driving would be used. Noise...

  14. Death Anxiety, Disclosure Behaviors, and Attitudes of Oncologists toward Terminal Care.

    Science.gov (United States)

    Cochrane, Joyce B.; And Others

    1991-01-01

    Examined relationships among death anxiety, disclosure behaviors, and attitudes toward terminal care of 99 oncologists. Found death anxiety scores lower for oncologists than typically reported for physicians. Short-term repeated exposure to dying patients resulted in comfort with dying patients whereas long-term repeated exposure resulted in…

  15. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  16. To Repeat or Not to Repeat a Course

    Science.gov (United States)

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…

  17. The Ethics of Terminal Care

    Science.gov (United States)

    Agich, George J.

    1978-01-01

    Need for a critical and analytical approach to ethics of terminal care is suggested by considering a series of unexamined questions regarding justification of terminal care. If terminal care is a moral and ethical enterprise, such considerations must be given a more prominent place in discussions of the hospice movement. (Author)

  18. Loss and terminal illness.

    Science.gov (United States)

    Benoliel, J Q

    1985-06-01

    The experience of terminal illness can best be viewed as a situation of multiple losses involving the dying person, family members and friends, and the health care providers engaged in offering services to them. It is a major transition during which the central participants must cope with the personal meanings of the forthcoming death as well as other losses brought about by the disease process, medical treatments, and the need to provide care for the dying person. How families adapt to the stresses and changes imposed by the experience of living with dying depends on their previous experiences with death, their established patterns of communication about serious matters, and their decision-making practices. Some individuals and families are at greater risk than others for developing maladaptive responses and behaviors during and after the experience of terminal illness. Risk factors to be considered in making hypotheses about the potential for maladaptive reactions include the strength of the attachment to the dying person, uncontrollable and distressing symptoms, and coping limitations associated with age and other factors contributing to increased vulnerability to the demands of continuous change. Working effectively with different kinds of families during the transition of terminal illness can best be accomplished within a conceptual framework built upon knowledge about people undergoing change. The concept of safe conduct can serve as an overall guide for the creation of nursing services designed to offer personalized care and accessibility of professional help at times of maximum need by the family. Assisting dying patients and their families toward the achievement of their personal goals is fundamental to the idea of safe conduct. The delivery of nursing care in terminal illness requires an orientation to assessment as an ongoing process that makes use of knowledge about disease processes, medical treatments, individual and group adaptations to loss, risk

  19. Nifty Nines and Repeating Decimals

    Science.gov (United States)

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  20. All-photonic quantum repeaters

    Science.gov (United States)

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  1. Prevalence of Repeat Pregnancy Including Pregnancy Outcome of Teenage Women

    Directory of Open Access Journals (Sweden)

    Pattarawalai Talungchit, M.D., Ph.D.

    2017-11-01

    Full Text Available Objective: To determine the prevalence and possible factors of repeat teenage pregnancy including their pregnancy outcomes compared to primi-gravida teenage pregnancy. Methods: 1,684 medical records of teenage pregnancy delivered or received termination of pregnancy at Siriraj hospital from July 2009 to June 2011 were reviewed. The characteristics and pregnancy outcomes of primi- and multi-gravida teenage pregnancies were studied and compared between groups. Results: The prevalence of repeat pregnancies among the study population was around 20% (338/1,684. Age of multi-gravida teenagers and their husbands were significantly higher than those of primi-gravida. Only 5% of primigravida and 25% of multi-gravida were documented as using contraception before getting pregnant (p < 0.001. Oral contraceptive was the most common method using in both groups. Multi-gravida teenagers were significantly diagnosed as anemia before delivery or termination of pregnancy (p = 0.03, although immediate pregnancy outcomes among the two groups were not significantly different. Before they were discharged from the hospital, less than half of them got immediate contraceptive methods especially long-acting reversible contraception. Conclusion: The prevalence of repeat pregnancy among teenagers at Siriraj Hospital was approximately 20%. Lack of proper contraception might be the factor related to repeat pregnancy. Although immediate pregnancy outcomes among primi-and multi-gravida teenagers were not significantly different, long term outcomes of both teenage mothers and their children were still limited.

  2. Ising Model Reprogramming of a Repeat Protein's Equilibrium Unfolding Pathway.

    Science.gov (United States)

    Millership, C; Phillips, J J; Main, E R G

    2016-05-08

    Repeat proteins are formed from units of 20-40 aa that stack together into quasi one-dimensional non-globular structures. This modular repetitive construction means that, unlike globular proteins, a repeat protein's equilibrium folding and thus thermodynamic stability can be analysed using linear Ising models. Typically, homozipper Ising models have been used. These treat the repeat protein as a series of identical interacting subunits (the repeated motifs) that couple together to form the folded protein. However, they cannot describe subunits of differing stabilities. Here we show that a more sophisticated heteropolymer Ising model can be constructed and fitted to two new helix deletion series of consensus tetratricopeptide repeat proteins (CTPRs). This analysis, showing an asymmetric spread of stability between helices within CTPR ensembles, coupled with the Ising model's predictive qualities was then used to guide reprogramming of the unfolding pathway of a variant CTPR protein. The designed behaviour was engineered by introducing destabilising mutations that increased the thermodynamic asymmetry within a CTPR ensemble. The asymmetry caused the terminal α-helix to thermodynamically uncouple from the rest of the protein and preferentially unfold. This produced a specific, highly populated stable intermediate with a putative dimerisation interface. As such it is the first step in designing repeat proteins with function regulated by a conformational switch. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Acetylene terminated matrix resins

    Science.gov (United States)

    Goldfarb, I. J.; Lee, Y. C.; Arnold, F. E.; Helminiak, T. E.

    1985-01-01

    The synthesis of resins with terminal acetylene groups has provided a promising technology to yield high performance structural materials. Because these resins cure through an addition reaction, no volatile by-products are produced during the processing. The cured products have high thermal stability and good properties retention after exposure to humidity. Resins with a wide variety of different chemical structures between the terminal acetylene groups are synthesized and their mechanical properties studied. The ability of the acetylene cured polymers to give good mechanical properties is demonstrated by the resins with quinoxaline structures. Processibility of these resins can be manipulated by varying the chain length between the acetylene groups or by blending in different amounts of reactive deluents. Processing conditions similar to the state-of-the-art epoxy can be attained by using backbone structures like ether-sulfone or bis-phenol-A. The wide range of mechanical properties and processing conditions attainable by this class of resins should allow them to be used in a wide variety of applications.

  4. Termination: A Case Study.

    Science.gov (United States)

    Friedberg, Ahron L

    2015-12-01

    In this article I posit and examine certain criteria and qualities for ending an analysis. The case study describes the end phase of a four-year psychoanalysis in which the patient's decision to move to another area forced the end of his analysis. We continued to explore and work through his core neurotic conflicts that included issues of competitive rivalry, dominance and submission, control, and anxiety about birth and death. A shift in the transference from me as a negative father to me as a supportive but competitive older brother was also examined in the context of ending treatment as well as other aspects of the transference. In addition, we analyzed the meaning of his ending treatment based on an extra-analytic circumstance. In discussing this phase of treatment, the definition and history of the term "termination" and its connotations are reviewed. Various criteria for completing an analysis are examined, and technical observations about this phase of treatment are investigated. It was found that while a significant shift in the transference occurred in this phase of the patient's analysis, conflicts related to the transference were not "resolved" in the classical sense. Terminating treatment was considered as a practical matter in which the patient's autonomy and sense of choice were respected and analyzed.

  5. 77 FR 38817 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2012-06-29

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... procedures for terminating Underwriting Authority of Direct Endorsement mortgagees. Termination of Direct...

  6. Resolution and termination

    Directory of Open Access Journals (Sweden)

    Adina FOLTIŞ

    2012-01-01

    Full Text Available The resolution, the termination and the reduction of labour conscription are regulated by articles 1549-1554 in the new Civil Code, which represents the common law in this matter. We appreciate that the new regulation does not conclusively clarify the issue related to whether the existence of liability in order to call upon the resolution is necessary or not, because the existence of this condition has been inferred under the previous regulation from the fact that the absence of liability shifts the inexecution issue on the domain of fortuitous impossibility of execution, situation in which the resolution of the contract is not in question, but that of the risk it implies.

  7. Analysis of repeated measures data

    CERN Document Server

    Islam, M Ataharul

    2017-01-01

    This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

  8. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S.K.

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  9. Mobile termination and mobile penetration

    OpenAIRE

    Hurkens, Sjaak; Jeon, Doh-Shin

    2009-01-01

    In this paper, we study how access pricing affects network competition when subscription demand is elastic and each network uses non-linear prices and can apply termination-based price discrimination. In the case of a fixed per minute termination charge, we find that a reduction of the termination charge below cost has two oppos- ing effects: it softens competition but helps to internalize network externalities. The former reduces mobile penetration while the latter boosts it. We find that fi...

  10. Is Lake Tahoe Terminal?

    Science.gov (United States)

    Coats, R. N.; Reuter, J.; Heyvaert, A.; Lewis, J.; Sahoo, G. B.; Schladow, G.; Thorne, J. H.

    2014-12-01

    ) the climatic water deficit will increase, especially at high elevations that will be most affected by the loss of snow, with likely consequences for existing vegetation and fire frequency. Hydrologically, Lake Tahoe is intermittently terminal; in a medical sense it is not yet terminal, but its condition—especially its valued clarity and deep blue color--is serious.

  11. Terminal Satisfiability in GSTE

    Directory of Open Access Journals (Sweden)

    Yongsheng Xu

    2014-01-01

    Full Text Available Generalized symbolic trajectory evaluation (GSTE is an extension of symbolic trajectory evaluation (STE and a method of model checking. GSTE specifications are given as assertion graphs. There are four efficient methods to verify whether a circuit model obeys an assertion graph in GSTE, Model Checking Strong Satisfiability (SMC, Model Checking Normal Satisfiability (NMC, Model Checking Fair Satisfiability (FMC, and Model Checking Terminal Satisfiability (TMC. SMC, NMC, and FMC have been proved and applied in industry, but TMC has not. This paper gives a six-tuple definition and presents a new algorithm for TMC. Based on these, we prove that our algorithm is sound and complete. It solves the SMC’s limitation (resulting in false negative without extending from finite specification to infinite specification. At last, a case of using TMC to verify a realistic hardware circuit round-robin arbiter is achieved. Avoiding verifying the undesired paths which are not related to the specifications, TMC makes it possible to reduce the computational complexity, and the experimental results suggest that the time cost by SMC is 3.14× with TMC in the case.

  12. Acetylene-Terminated Polyimide Siloxanes

    Science.gov (United States)

    St. Clair, Terry L.; Maudgal, Shubba

    1987-01-01

    Siloxane-containing addition polyimides yield toughened high-temperature adhesives and matrix resins. Addition polyimide made by reaction of aromatic tetracarboxylic acid dianhydride with aromatic diamine in presence of ethynyl-substituted aromatic monoamine. Acetylene-terminated siloxane imide cured by heating to yield acetylene-terminated polyimide siloxane.

  13. Selection of Air Terminal Device

    DEFF Research Database (Denmark)

    Nielsen, Peter V.

    This paper discusses the selection of the air terminal device for the experiments and numerical prediction in the International Energy Agency Annex 20 work: Air Flow Pattern within Buildings,......This paper discusses the selection of the air terminal device for the experiments and numerical prediction in the International Energy Agency Annex 20 work: Air Flow Pattern within Buildings,...

  14. Ports and Terminals : Planning and Functional Design

    NARCIS (Netherlands)

    Groenveld, R.; Velsink, H.

    1993-01-01

    1. Maritime transport, means and commodities 3. Principles of integrated port planning 4. Planning and design of a port's water areas 5. Port terminals - introduction 6. Conventional general cargo terminals 7. Container terminals 8. Oil & liquid gas terminals 9. Dry bulk cargo terminals 10. Fishery

  15. Efficiency of repeated network interactions

    NARCIS (Netherlands)

    Timmer, Judith B.; Mandjes, M.R.H.

    2009-01-01

    In this paper we consider a network with interactions by two users. Each of them repeatedly issues download requests on the network. These requests may be unsuccessful due to congestion or non-congestion related errors. A user decides when to cancel a request (that is, what his impatience threshold

  16. Terminal Antennas in ACE2

    Directory of Open Access Journals (Sweden)

    M. Martinez-Vazquez

    2008-06-01

    Full Text Available The ACE Network of Excellence was a European Commission funded Network of Excellence, which lasted from 2004 to 2007. One of the activities performed by this Network was in the frame of terminal antennas. In this activity, three aspects were covered in three projects: Small antenna technologies, small terminal antenna technologies and benchmarking of small terminal antennas measurement facilities. The overall aim was to identify the newest trends in antenna design and measurement for personal communications devices, and suggest novel solutions and design methodologies for various applications. The results of this work are presented in this paper.

  17. Pentapeptide Repeat Proteins and Cyanobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Buchko, Garry W.

    2009-10-16

    Cyanobacteria are unique in many ways and one unusual feature is the presence of a suite of proteins that contain at least one domain with a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. The function of such pentapeptide repeat proteins (PRPs) are still unknown, however, their prevalence in cyanobacteria suggests that they may play some role in the unique biological activities of cyanobacteria. As part of an inter-disciplinary Membrane Biology Grand Challenge at the Environmental Molecular Sciences Laboratory (Pacific Northwest National Laboratory) and Washington University in St. Louis, the genome of Cyanothece 51142 was sequenced and its molecular biology studied with relation to circadian rhythms. The genome of Cyanothece encodes for 35 proteins that contain at least one PRP domain. These proteins range in size from 105 (Cce_3102) to 930 (Cce_2929) kDa with the PRP domains ranging in predicted size from 12 (Cce_1545) to 62 (cce_3979) tandem pentapeptide repeats. Transcriptomic studies with 29 out of the 35 genes showed that at least three of the PRPs in Cyanothece 51142 (cce_0029, cce_3083, and cce_3272) oscillated with repeated periods of light and dark, further supporting a biological function for PRPs. Using X-ray diffraction crystallography, the structure for two pentapeptide repeat proteins from Cyanothece 51142 were determined, cce_1272 (aka Rfr32) and cce_4529 (aka Rfr23). Analysis of their molecular structures suggests that all PRP may share the same structural motif, a novel type of right-handed quadrilateral β-helix, or Rfr-fold, reminiscent of a square tower with four distinct faces. Each pentapeptide repeat occupies one face of the Rfr-fold with four consecutive pentapeptide repeats completing a coil that, in turn, stack upon each other to form “protein skyscrapers”. Details of the structural features of the Rfr-fold are reviewed here together with a discussion for the possible role of end

  18. 75 FR 61165 - Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2010-10-04

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... advised the extended procedures for ] terminating Underwriting Authority of Direct Endorsement mortgagees...

  19. 76 FR 38407 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2011-06-30

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... advised the extended procedures for ] terminating Underwriting Authority of Direct Endorsement mortgagees...

  20. 77 FR 5262 - Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2012-02-02

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... the extended procedures for terminating Underwriting Authority of Direct Endorsement (DE) mortgagees...

  1. 76 FR 53148 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2011-08-25

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... advised the extended procedures for terminating Underwriting Authority of Direct Endorsement mortgagees...

  2. Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription

    NARCIS (Netherlands)

    Berkhout, B.; Vastenhouw, N. L.; Klasens, B. I.; Huthoff, H.

    2001-01-01

    Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer is facilitated by terminal repeat (R) elements in the viral genome. This strand-transfer reaction depends on base pairing between the cDNA of the 5'R and the 3'R. There

  3. Mechanisms of DNA replication termination.

    Science.gov (United States)

    Dewar, James M; Walter, Johannes C

    2017-08-01

    Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.

  4. Flight Termination Systems Commonality Standard

    Science.gov (United States)

    2014-09-01

    EFI exploding foil initiator EFTR enhanced flight termination receiver EFTS enhanced flight termination system ELS equivalent level of safety EMC ...account shielding effectiveness of the vehicle. 3.3.13 Other Environments An FTS component shall satisfy all of its performance requirements and not...solid-state power transfer switches, and arm-and-enable circuits. 3.9.6 Circuit Isolation, Shielding , and Grounding The circuitry of an FTS

  5. A repeating fast radio burst

    Science.gov (United States)

    Spitler, L. G.; Scholz, P.; Hessels, J. W. T.; Bogdanov, S.; Brazier, A.; Camilo, F.; Chatterjee, S.; Cordes, J. M.; Crawford, F.; Deneva, J.; Ferdman, R. D.; Freire, P. C. C.; Kaspi, V. M.; Lazarus, P.; Lynch, R.; Madsen, E. C.; McLaughlin, M. A.; Patel, C.; Ransom, S. M.; Seymour, A.; Stairs, I. H.; Stappers, B. W.; van Leeuwen, J.; Zhu, W. W.

    2016-03-01

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star.

  6. Timeless links replication termination to mitotic kinase activation.

    Directory of Open Access Journals (Sweden)

    Jayaraju Dheekollu

    2011-05-01

    Full Text Available The mechanisms that coordinate the termination of DNA replication with progression through mitosis are not completely understood. The human Timeless protein (Tim associates with S phase replication checkpoint proteins Claspin and Tipin, and plays an important role in maintaining replication fork stability at physical barriers, like centromeres, telomeres and ribosomal DNA repeats, as well as at termination sites. We show here that human Tim can be isolated in a complex with mitotic entry kinases CDK1, Auroras A and B, and Polo-like kinase (Plk1. Plk1 bound Tim directly and colocalized with Tim at a subset of mitotic structures in M phase. Tim depletion caused multiple mitotic defects, including the loss of sister-chromatid cohesion, loss of mitotic spindle architecture, and a failure to exit mitosis. Tim depletion caused a delay in mitotic kinase activity in vivo and in vitro, as well as a reduction in global histone H3 S10 phosphorylation during G2/M phase. Tim was also required for the recruitment of Plk1 to centromeric DNA and formation of catenated DNA structures at human centromere alpha satellite repeats. Taken together, these findings suggest that Tim coordinates mitotic kinase activation with termination of DNA replication.

  7. NFAT5 regulates HIV-1 in primary monocytes via a highly conserved long terminal repeat site.

    Directory of Open Access Journals (Sweden)

    Shahin Ranjbar

    2006-12-01

    Full Text Available To replicate, HIV-1 capitalizes on endogenous cellular activation pathways resulting in recruitment of key host transcription factors to its viral enhancer. RNA interference has been a powerful tool for blocking key checkpoints in HIV-1 entry into cells. Here we apply RNA interference to HIV-1 transcription in primary macrophages, a major reservoir of the virus, and specifically target the transcription factor NFAT5 (nuclear factor of activated T cells 5, which is the most evolutionarily divergent NFAT protein. By molecularly cloning and sequencing isolates from multiple viral subtypes, and performing DNase I footprinting, electrophoretic mobility shift, and promoter mutagenesis transfection assays, we demonstrate that NFAT5 functionally interacts with a specific enhancer binding site conserved in HIV-1, HIV-2, and multiple simian immunodeficiency viruses. Using small interfering RNA to ablate expression of endogenous NFAT5 protein, we show that the replication of three major HIV-1 viral subtypes (B, C, and E is dependent upon NFAT5 in human primary differentiated macrophages. Our results define a novel host factor-viral enhancer interaction that reveals a new regulatory role for NFAT5 and defines a functional DNA motif conserved across HIV-1 subtypes and representative simian immunodeficiency viruses. Inhibition of the NFAT5-LTR interaction may thus present a novel therapeutic target to suppress HIV-1 replication and progression of AIDS.

  8. Chromatin condensation during terminal erythropoiesis.

    Science.gov (United States)

    Zhao, Baobing; Yang, Jing; Ji, Peng

    2016-09-02

    Mammalian terminal erythropoiesis involves gradual but dramatic chromatin condensation steps that are essential for cell differentiation. Chromatin and nuclear condensation is followed by a unique enucleation process, which is believed to liberate more spaces for hemoglobin enrichment and enable the generation of a physically flexible mature red blood cell. Although these processes have been known for decades, the mechanisms are still unclear. Our recent study reveals an unexpected nuclear opening formation during mouse terminal erythropoiesis that requires caspase-3 activity. Major histones, except H2AZ, are partially released from the opening, which is important for chromatin condensation. Block of the nuclear opening through caspase inhibitor or knockdown of caspase-3 inhibits chromatin condensation and enucleation. We also demonstrate that nuclear opening and histone release are cell cycle regulated. These studies reveal a novel mechanism for chromatin condensation in mammalia terminal erythropoiesis.

  9. SIRKULASI TERMINAL PENUMPANG KAPAL LAUT

    Directory of Open Access Journals (Sweden)

    Etsa Purnama Sari

    2014-01-01

    Full Text Available Wilayah Indonesia yang terdiri dari pulau dan perairan menjadikan angkutan laut menjadi salah satu sarana transportasi yang cukup efektif di negara ini. Daya angkut yang besar dan beragam serta biaya yang lebih murah dengan jarak jangkauan yang luas, membuat sarana ini banyak diminati oleh masyarakat sekaligus juga merupakan pendukung utama perkembangan kehidupan sosial budaya dan roda perekonomian. Untuk mendukung proses transportasi laut ini perlu sarana berupa pelabuhan. Pelabuhan dalam melakukan pelayanan terhadap kapal memiliki beberapa fasilitas pokok dan penunjang yang wajib dimiliki. Salah satunya adalah terminal penumpang kapal laut dengan berbagai kegiatan di dalamnya untuk kedatangan maupun keberangkatan. Masalah ketidaknyamanan dalam berkegiatan, jauhnya akses sirkulasi antara satu kegiatan dengan kegiatan kegiatan embarkasi dan debarkasi yang tidak teratur, pembagian jalur sirkulasi penumpang dan pengantar penumpang yang tidak jelas seringkali muncul akibat sirkulasi yang tidak direncanakan dengan baik pada terminal penumpang kapal laut. Bahkan tidak jarang dapat menimbulkan adanya calo tiket hingga adanya penumpang tanpa tiket yang dapat masuk ke dalam kapal hingga kapal berlayar. Perencanaan sebuah sirkulasi yang tepat pada terminal penumpang kapal laut memerlukan kajian terhadap unsur-unsur sirkulasi seperti pencapaian, pola sirkulasi, jalur sirkulasi, serta bentuk ruang sirkulasi. Kajian unsur-unsur ini selanjutnya diselidiki melalui penelusuran masalah dengan analisis deskriptif melalui penggambaran objek penelitian yang terdapat pada Terminal Penumpang Pelabuhan International Yokohama, Terminal Penumpang Pelabuhan Kobe dan Terminal Penumpang Pelabuhan Osanbashi Hall   As one of the largest archipelago country, sea transportation acts as one of the most effective means of transportation in Indonesia. Large and diverse carrying capacity, lower cost with wide range of distances, are factors which making sea

  10. Terminal Disease: A Biolaw Management

    Directory of Open Access Journals (Sweden)

    Francisco Rivas García

    2017-10-01

    Full Text Available There are numerous and varied pathologies that can lead to a state of terminal illness, provoking numerous bioethical dilemmas that are inherent and specific to each circumstance. The objective of the present work has been to provide a current and useful analysis that can help to understand the main bioethical problems, from the perspective of biolaw that must be solved in the inevitable path towards the end of life that any terminal illness implies. The methodology used included a study of bibliographic documentation in the main databases of interest in bioethics. It can be concluded that the biolaw is a very useful tool that helps health care professionals and relatives when it comes to the analysis and decision making regarding a terminal illness. Independently of medical practice based on protocols and scientific knowledge, it is necessary to ensure that not everything that can legally be carried out is accepted in the field of biolaw.

  11. Coordinated hybrid automatic repeat request

    KAUST Repository

    Makki, Behrooz

    2014-11-01

    We develop a coordinated hybrid automatic repeat request (HARQ) approach. With the proposed scheme, if a user message is correctly decoded in the first HARQ rounds, its spectrum is allocated to other users, to improve the network outage probability and the users\\' fairness. The results, which are obtained for single- and multiple-antenna setups, demonstrate the efficiency of the proposed approach in different conditions. For instance, with a maximum of M retransmissions and single transmit/receive antennas, the diversity gain of a user increases from M to (J+1)(M-1)+1 where J is the number of users helping that user.

  12. Improving repeatability by improving quality

    Energy Technology Data Exchange (ETDEWEB)

    Ronen, Shuki; Ackers, Mark; Schlumberger, Geco-Prakla; Brink, Mundy

    1998-12-31

    Time lapse (4-D) seismic is a promising tool for reservoir characterization and monitoring. The method is apparently simple: to acquire data repeatedly over the same reservoir, process and interpret the data sets, then changes between the data sets indicate changes in the reservoir. A problem with time lapse seismic data is that reservoirs are a relatively small part of the earth and important reservoir changes may cause very small differences to the time lapse data. The challenge is to acquire and process economical time lapse data such that reservoir changes can be detected above the noise of varying acquisition and environment. 7 refs., 9 figs.

  13. Sistem Pengelolaan Terminal Mangkang Kota Semarang

    OpenAIRE

    Sushernawan, Prasetya; Sulistyowati; Fitriyah

    2014-01-01

    This study, entitled "SYSTEM MANAGEMENT TERMINAL CITY MangkangSemarang". Terminal Mangkang a master terminal type A that is in the province of CentralJava is managed by Dishubkominfo. Terminal is a facility for public service units, as publicfacilities, the terminal should be able to provide services to the community as well as possible.So that they can be expected to contribute the maximum to PAD (the original income) withoutcompromising service to the community.Formulation of the problem in...

  14. Getting a Suitable Terminal Cost and Maximizing the Terminal Region for MPC

    Directory of Open Access Journals (Sweden)

    Wang Ya-feng

    2010-01-01

    Full Text Available The model predictive control (MPC subject to control and state constraint is studied. Given a terminal cost, a terminal region is obtained through iterative estimation by using support vector machine (SVM. It is proved that the obtained terminal region is the largest terminal region when the terminal cost is given. The relationships between terminal cost and terminal region and between terminal cost and total cost are discussed, respectively. Based on these relationships, a simple method to get a suitable terminal cost is proposed and it can be adjusted according to our need. Finally, some experiment results are presented.

  15. New offshore terminal for Ecuador

    Energy Technology Data Exchange (ETDEWEB)

    1979-04-15

    W. Halcrow and Partners will design and supervise construction of the second phase of Corporacion Estatal Petrolera Ecuatoriana's offshore tanker terminal for the export of refined products from its 65,000 bbl/day Esmeraldas refinery, which will be expanded to 130,000 bbl/day. Ewbank and Partners Ltd. will handle mechanical and electrical engineering of the terminal. Halcrow also designed and built the first stage of the terminal, which comprised a four-hose seabed manifold 4 km offshore in water depths of 16 m and which became operational in Nov. 1977 with capacity to handle tankers up to 20,000 dwt and with pipeline connection to the Esmeradas refinery. The seabed manifold will be replaced by a two-berth sea island terminal to handle tankers up to 50,000 dwt; a contract for this has been signed. Future plans call for a two-berth central loading platform, separate berthing and mooring dolphins, an accommodation platform, and auxiliary services. The main structure will be a steel-piled jacket design interconnected by steel access bridges. The additional works should be completed by the end of 1981.

  16. The impact of 'terminator' technology

    NARCIS (Netherlands)

    Visser, B.; Meer, van der I.J.M.; Louwaars, N.; Beekwilder, J.; Eaton, D.

    2001-01-01

    Genetic use-restriction technologies enable the developers of transgenic plants or animals to protect their variety or breed from unauthorized use in a biological way. The use of 'terminator technology' can have different impacts on farmers and breeders. If the technology is effective, it impacts on

  17. What Determines Joint Venture Termination?

    DEFF Research Database (Denmark)

    Nielsen, Bo Bernhard

    2012-01-01

    Joint venture (JV) research continues to flourish as researchers seek to advance our understanding of why so many JVs fail. Cui and Kumar (this issue) take a contingency approach to explain how and why business relatedness may provide new insights as to what determines JV termination...

  18. Combining norms to prove termination

    DEFF Research Database (Denmark)

    Genaim, S.; Codish, M.; Gallagher, John Patrick

    2002-01-01

    Automatic termination analysers typically measure the size of terms applying norms which are mappings from terms to the natural numbers. This paper illustrates howt o enable the use of size functions defined as tuples of these simpler norm functions. This approach enables us to simplify the problem...

  19. Isotopes, ice ages, and terminal Proterozoic earth history

    Science.gov (United States)

    Kaufman, Alan J.; Knoll, Andrew H.; Narbonne, Guy M.

    1997-01-01

    Detailed correlations of ancient glacial deposits, based on temporal records of carbon and strontium isotopes in seawater, indicate four (and perhaps five) discrete ice ages in the terminal Proterozoic Eon. The close and repeated stratigraphic relationship between C-isotopic excursions and glaciogenic rocks suggests that unusually high rates of organic carbon burial facilitated glaciation by reducing atmospheric greenhouse capacity. The emerging framework of time and environmental change contributes to the improved resolution of stratigraphic and evolutionary pattern in the early fossil record of animals. PMID:11038552

  20. Isotopes, ice ages, and terminal Proterozoic earth history.

    Science.gov (United States)

    Kaufman, A J; Knoll, A H; Narbonne, G M

    1997-06-24

    Detailed correlations of ancient glacial deposits, based on temporal records of carbon and strontium isotopes in seawater, indicate four (and perhaps five) discrete ice ages in the terminal Proterozoic Eon. The close and repeated stratigraphic relationship between C-isotopic excursions and glaciogenic rocks suggests that unusually high rates of organic carbon burial facilitated glaciation by reducing atmospheric greenhouse capacity. The emerging framework of time and environmental change contributes to the improved resolution of stratigraphic and evolutionary pattern in the early fossil record of animals.

  1. 26 CFR 1.411(d)-2 - Termination or partial termination; discontinuance of contributions.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 5 2010-04-01 2010-04-01 false Termination or partial termination... Bonus Plans, Etc. § 1.411(d)-2 Termination or partial termination; discontinuance of contributions. (a... such plan is not a qualified trust) unless the plan provides that— (i) Upon the termination or partial...

  2. Solid-state power converter repeatability analysis

    CERN Document Server

    Dal Gobbo, Anthony; Aguglia, Davide

    2015-01-01

    This paper presents a method for evaluating power converter repeatability. The focus is on solid-state switch mode power converter for which the most problematic non-repeatability sources are the jitter of the drivers and of the switches leading to output voltage pulses bad repeatability. Both driver and switch turn-on and turn-off delay dispersion have been measured. These measurements confirm that the delay is Gaussian distributed and that the repeatability prediction method is valid.

  3. Terminal decline in motor function.

    Science.gov (United States)

    Wilson, Robert S; Segawa, Eisuke; Buchman, Aron S; Boyle, Patricia A; Hizel, Loren P; Bennett, David A

    2012-12-01

    The study aim was to test the hypothesis that motor function undergoes accelerated decline proximate to death. As part of a longitudinal clinical-pathologic study, 124 older Roman Catholic nuns, priests, and monks completed at least 7 annual clinical evaluations, died, and underwent brain autopsy and uniform neuropathologic examination. Each evaluation included administration of 11 motor tests and 19 cognitive tests from which global measures of motor and cognitive function were derived. The global motor measure (baseline M = 0.82, SD = 0.21) declined a mean 0.024 unit per year (95% confidence interval [CI]: -0.032, -0.016) until a mean of 2.46 years (95% CI: -2.870, -2.108) before death when rate of decline increased nearly fivefold to -0.117 unit per year (95% CI: -0.140, -0.097). The global cognitive measure (baseline M = 0.07, SD = 0.45) declined a mean of 0.027-unit per year (95% CI: -0.041, -0.014) until a mean of 2.76 years (95% CI: -3.157, -2.372) before death when rate of decline increased more than 13-fold to -0.371 unit per year (95% CI: -0.443, -0.306). Onset of terminal motor decline was highly correlated with onset of terminal cognitive decline (r = .94, 95% CI: 0.81, 0.99), but rates of motor and cognitive change were not strongly correlated (preterminal r = .20, 95% CI: -0.05, 0.38; terminal r = .34, 95% CI: 0.03, 0.62). Higher level of plaques and tangles was associated with earlier onset of terminal decline in motor function, but no pathologic measures were associated with rate of preterminal or terminal motor decline. The results demonstrate that motor and cognitive functions both undergo a period of accelerated decline in the last few years of life. 2013 APA, all rights reserved

  4. Topological characteristics of helical repeat proteins

    NARCIS (Netherlands)

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  5. Repeated expansion in burn sequela.

    Science.gov (United States)

    Pitanguy, Ivo; Gontijo de Amorim, Natale Ferreira; Radwanski, Henrique N; Lintz, José Eduardo

    2002-08-01

    This paper presents a retrospective study of the use of 346 expanders in 132 patients operated at the Ivo Pitanguy Clinic, between the period of 1985 and 2000. The expanders were used in the treatment of burn sequela. In the majority of cases, more than one expander was used at the same time. In 42 patients, repeated tissue expansion was done. The re-expanded flaps demonstrated good distension and viability. With the increase in area at each new expansion, larger volume expanders were employed, achieving an adequate advancement of the flaps to remove the injured tissue. The great advantage of using tissue re-expansion in the burned patient is the reconstruction of extensive areas with the same color and texture of neighboring tissues, without the addition of new scars.

  6. Clothes Dryer Automatic Termination Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    TeGrotenhuis, Ward E.

    2014-10-01

    Volume 2: Improved Sensor and Control Designs Many residential clothes dryers on the market today provide automatic cycles that are intended to stop when the clothes are dry, as determined by the final remaining moisture content (RMC). However, testing of automatic termination cycles has shown that many dryers are susceptible to over-drying of loads, leading to excess energy consumption. In particular, tests performed using the DOE Test Procedure in Appendix D2 of 10 CFR 430 subpart B have shown that as much as 62% of the energy used in a cycle may be from over-drying. Volume 1 of this report shows an average of 20% excess energy from over-drying when running automatic cycles with various load compositions and dryer settings. Consequently, improving automatic termination sensors and algorithms has the potential for substantial energy savings in the U.S.

  7. ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

    NARCIS (Netherlands)

    Luo, H.; Lin, K.; David, A.; Nijveen, H.; Leunissen, J.A.M.

    2012-01-01

    ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85

  8. Complexity of Terminating Preference Elicitation

    OpenAIRE

    Walsh, Toby

    2009-01-01

    Complexity theory is a useful tool to study computational issues surrounding the elicitation of preferences, as well as the strategic manipulation of elections aggregating together preferences of multiple agents. We study here the complexity of determining when we can terminate eliciting preferences, and prove that the complexity depends on the elicitation strategy. We show, for instance, that it may be better from a computational perspective to elicit all preferences from one agent at a time...

  9. High Octane Fuel: Terminal Backgrounder

    Energy Technology Data Exchange (ETDEWEB)

    Moriarty, Kristi [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-02-11

    The Bioenergy Technologies Office of the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy sponsored a scoping study to assess the potential of ethanol-based high octane fuel (HOF) to reduce energy consumption and greenhouse gas emissions. When the HOF blend is made with 25%-40% ethanol by volume, this energy efficiency improvement is potentially sufficient to offset the reduced vehicle range often associated with the decreased volumetric energy density of ethanol. The purpose of this study is to assess the ability of the fuel supply chain to accommodate more ethanol at fuel terminals. Fuel terminals are midstream in the transportation fuel supply chain and serve to store and distribute fuels to end users. While there are no technical issues to storing more ethanol at fuel terminals, there are several factors that could impact the ability to deploy more ethanol. The most significant of these issues include the availability of land to add more infrastructure and accommodate more truck traffic for ethanol deliveries as well as a lengthy permitting process to erect more tanks.

  10. A 135-kilodalton surface antigen of Mycoplasma hominis PG21 contains multiple directly repeated sequences

    DEFF Research Database (Denmark)

    Ladefoged, Søren; Birkelund, Svend; Hauge, S

    1995-01-01

    A monoclonal antibody was used to characterize a 135-kDa surface-located membrane protein (Lmp1) generally present in Mycoplasma hominis strains. The monoclonal antibody, 552, was applied to identify the corresponding gene in an expression library of M. hominis PG21 DNA. The M. hominis PG21 lmp1......,000, was identified. Analysis of the deduced amino acid sequence predicted a hydrophilic protein with a basic pI (10.0). The N-terminal 24 amino acids were a typical leader sequence. Downstream from the first 726 nucleotides, six similar direct repeats of 471 nucleotides were found. In repeat 7, a single...

  11. Repeated Maxima of Sunspot Cycles

    Science.gov (United States)

    Krivodubskij, V.

    2015-12-01

    The explanation for the observed phenomenon of repeated maxima of sunspot cycles is proposed. Key roles in the proposed scenarioplay two tides of toroidal field from the lower base of the solar convection zone (SCZ) to the surface. Deep toroidal field is excited due to Ω-effectnear the bottom of the SCZ at the beginning of the cycle. Then this field is transported to the surface due to combined acting of magnetic buoyancy,magnetic ∇ρ-flow and turbulent diamagnetism in the equatorial domain. Over time the magnetic fragments can be seen as bipolar spots in themiddle latitudes in the "royal zone". This first wave of toroidal field, which is directed up, gives the main maximum activity spots. However, theunderlying toroidal field in the high-latitude polar domains at the beginning of the cycle is blocked by directed downward magnetic∇ρ-pumping and turbulent diamagnetism. Directed to the equator deep meridional flow replaces this field to the low latitudes (the equatorialdomain) during about 1 - 2 years. After that the turn of floating this "retarded" field to surface (second tide of toroidal field). Coming to the surfaceat low latitudes this second portion of toroidal field leads to second sunspot maximum.

  12. NMR assignments of the N-terminal domain of Nephila clavipes spidroin 1.

    Science.gov (United States)

    Parnham, Stuart; Gaines, William A; Duggan, Brendan M; Marcotte, William R; Hennig, Mirko

    2011-10-01

    The building blocks of spider dragline silk are two fibrous proteins secreted from the major ampullate gland named spidroins 1 and 2 (MaSp1, MaSp2). These proteins consist of a large central domain composed of approximately 100 tandem copies of a 35-40 amino acid repeat sequence. Non-repetitive N and C-terminal domains, of which the C-terminal domain has been implicated to transition from soluble and insoluble states during spinning, flank the repetitive core. The N-terminal domain until recently has been largely unknown due to difficulties in cloning and expression. Here, we report nearly complete assignment for all (1)H, (13)C, and (15)N resonances in the 14 kDa N-terminal domain of major ampullate spidroin 1 (MaSp1-N) of the golden orb-web spider Nephila clavipes.

  13. k36u Terminal Aerodrome Forecast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — TAF (terminal aerodrome forecast or terminal area forecast) is a format for reporting weather forecast information, particularly as it relates to aviation. TAFs are...

  14. THE FORMALIZATION PROCESS OF CARGO TERMINAL OPERATION

    Directory of Open Access Journals (Sweden)

    N. Yu. Shramenko

    2011-01-01

    Full Text Available The mathematical formalization of operation process for a terminal complex is proposed and a model taking into account characteristics of a freight terminal and all the possible states of a system is developed.

  15. Repeats and EST analysis for new organisms

    Directory of Open Access Journals (Sweden)

    Jonassen Inge

    2008-01-01

    Full Text Available Abstract Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask against known repeats from other species (i.e., model organisms. There are few studies that investigate the effectiveness of this approach, or attempt to evaluate the different methods for identifying and masking repeats. Results Using zebrafish and medaka as example organisms, we show that accurate repeat masking is an important factor for obtaining a high quality clustering. Furthermore, we show that masking with standard repeat libraries based on curated genomic information from other species has little or no positive effect on the quality of the resulting EST clustering. Library based repeat masking which often constitutes a computational bottleneck in the EST analysis pipeline can therefore be reduced to species specific repeat libraries, or perhaps eliminated entirely. In contrast, substantially improved results can be achived by applying a repeat library derived from a partial reference clustering (e.g., from mapping sequences against a partially sequenced genome. Conclusion Of the methods explored, we find that the best EST clustering is achieved after masking with repeat libraries that are species specific. In the absence of such libraries, library-less masking gives results superior to the current practice of using cross-species, genome-based libraries.

  16. Prevalence of repeat pregnancies and associated factors among teenagers in KwaZulu-Natal, South Africa.

    Science.gov (United States)

    Mphatswe, Wendy; Maise, Hopolang; Sebitloane, Motshedisi

    2016-05-01

    To determine the prevalence of repeat teenage pregnancy and the interval between first/most recent and repeat pregnancies, as well as to evaluate the sexual/reproductive health characteristics of teenagers with repeat pregnancies. A prospective observational study was undertaken at a hospital in KwaZulu-Natal, South Africa, between May and September 2013. Teenagers aged 13-19years who were pregnant, had recently delivered, or had terminated a pregnancy were enrolled. A questionnaire was used to obtain data. Among 341 participants, 281 (82.4%) were seen for a first pregnancy and 60 (17.6%) for a repeat pregnancy. The interval between first/most recent and repeat pregnancies was 24months or lower in 45 (75.0%) of repeat pregnancy participants. Only 58 (17.0%) participants had previously used contraception (54 [93.1%] of whom stopped within 12months) and 28 (8.2%) had used emergency contraception. More participants with repeat pregnancy than with first pregnancy had a positive HIV status (18 [30.0%] vs 26 [9.3%]; Pteenagers in South Africa is worrying. Focused interventions targeting teenagers following their first pregnancy need to be urgently implemented. Copyright © 2016 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

  17. Ankyrin Repeats Convey Force to Gate the NOMPC Mechanotransduction Channel.

    Science.gov (United States)

    Zhang, Wei; Cheng, Li E; Kittelmann, Maike; Li, Jiefu; Petkovic, Maja; Cheng, Tong; Jin, Peng; Guo, Zhenhao; Göpfert, Martin C; Jan, Lily Yeh; Jan, Yuh Nung

    2015-09-10

    How metazoan mechanotransduction channels sense mechanical stimuli is not well understood. The NOMPC channel in the transient receptor potential (TRP) family, a mechanotransduction channel for Drosophila touch sensation and hearing, contains 29 Ankyrin repeats (ARs) that associate with microtubules. These ARs have been postulated to act as a tether that conveys force to the channel. Here, we report that these N-terminal ARs form a cytoplasmic domain essential for NOMPC mechanogating in vitro, mechanosensitivity of touch receptor neurons in vivo, and touch-induced behaviors of Drosophila larvae. Duplicating the ARs elongates the filaments that tether NOMPC to microtubules in mechanosensory neurons. Moreover, microtubule association is required for NOMPC mechanogating. Importantly, transferring the NOMPC ARs to mechanoinsensitive voltage-gated potassium channels confers mechanosensitivity to the chimeric channels. These experiments strongly support a tether mechanism of mechanogating for the NOMPC channel, providing insights into the basis of mechanosensitivity of mechanotransduction channels. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Tandemly repeated tRNA pseudogenes in photobacterium.

    Science.gov (United States)

    Giroux, S; Cedergren, R

    1988-01-01

    A region distal to three tRNA genes in Photobacterium phosphoreum, a Gram-negative eubacterium, unexpectedly contains a high number of repeated DNA segments that are closely related to the adjacent tRNAPro gene. The 5' to 3' order of this cluster is tRNAPro-tRNAHis-tRNAPro followed by eight tRNAPro-like structures interspersed by rho-independent terminators. The two tRNAPro genes, which are identical, and the tRNAHis gene have 86% and 87% positional identity, respectively, to their counterparts in the argT operon of Escherichia coli. The facts that these tRNA-like structures are not transcribed, in contrast to the tRNA retropseudogenes of eukaryotes, and that these structures are clustered near their progenitor suggest they are an unusual class of tRNA pseudogenes that arose by tandem duplication. Images PMID:3194413

  19. 29 CFR 402.5 - Terminal reports.

    Science.gov (United States)

    2010-07-01

    ... organization at the time of its termination or loss of reporting identity and, together with a copy thereof... such termination or loss of reporting identity, as the case may be. (b) Labor organizations which... other form of termination of its existence as a labor organization, or which loses its identity as a...

  20. Kajian Kinerja Terminal Batu Ampar Kota Balikpapan

    Directory of Open Access Journals (Sweden)

    Randha Alief Chikita

    2018-01-01

    Full Text Available Batu Ampar Terminal Balikpapan is the only type A passenger terminal in Balikpapan City. The purpose of this study is to determine the operational performance of the terminal at this time and also to determine the level of service in the terminal. The results of this study indicate that for FIFO queue discipline analysis on AKDP and AKAP bus lines, it is known that ρ <1 means that there is currently no queue in the terminal. For the analysis of terminal facilities it is known that there are still some terminal facilities that are not yet available from the main facilities and supporting facilities, therefore the need for additional facilities in order to meet the standard of passenger terminal type A. In the next 15 years analysis for traffic intensity value is approaching 1 which means in the future will cause the queue in the terminal, so it is necessary for the improvement of terminal performance. For the service performance with IPA method there are 35 variables that there are 7 variables that enter in quadrant I. In the next step to do analysis to know the priority of handling by using QFD method. Keywords: Batu Ampar Terminal Balikpapan, IPA, terminal performance, QFD

  1. 42 CFR 460.54 - Termination procedures.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Termination procedures. 460.54 Section 460.54 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... ELDERLY (PACE) Sanctions, Enforcement Actions, and Termination § 460.54 Termination procedures. (a) Except...

  2. HERV-K and LINE-1 DNA methylation and reexpression in urothelial carcinoma

    Directory of Open Access Journals (Sweden)

    Ulrike eKreimer

    2013-09-01

    Full Text Available Changes in DNA methylation frequently accompany cancer development. One prominent change is an apparently genome-wide decrease in methylcytosine that is often ascribed to DNA hypomethylation at retroelements comprising nearly half the genome. DNA hypomethylation may allow reactivation of retroelements, enabling retrotransposition and causing gene expression disturbances favoring tumor development. However, neither the extent of hypomethylation nor of retroelement reactivation are precisely known. We therefore assessed DNA methylation and expression of three major classes of retroelements (LINE-1, HERV-K and AluY in human urinary bladder cancer tissues and cell lines by pyrosequencing and quantitative reverse transcription–polymerase chain reaction, respectively. We found substantial global LINE-1 DNA hypomethylation in bladder cancer going along with a shift towards full-length LINE-1 expression. Thus, pronounced differences in LINE-1 expression were observed, which may be promoted, among others, by LINE-1 hypomethylation. Significant DNA hypomethylation was found at the HERV-K_22q11.23 proviral long terminal repeat (LTR in bladder cancer tissues but without reactivation of its expression. DNA methylation of HERVK17, essentially absent from normal urothelial cells, was elevated in cell lines from invasive bladder cancers. Accordingly, the faint expression of HERVK17 in normal urothelial cells disappeared in such cancer cell lines. Of 16 additional HERV-Ks, expression of 7 could be detected in the bladder, albeit generally at low levels. Unlike in prostate cancers, none of these showed significant expression changes in bladder cancer. In contrast, expression of the AluYb8 but not of the AluYa5 family was significantly increased in bladder cancer tissues. Collectively, our findings demonstrate a remarkable specificity of changes in expression and DNA methylation of retroelements in bladder cancer with a significantly different pattern from that

  3. Strengthening concept learning by repeated testing

    Science.gov (United States)

    Wiklund-Hörnqvist, Carola; Jonsson, Bert; Nyberg, Lars

    2014-01-01

    The aim of this study was to examine whether repeated testing with feedback benefits learning compared to rereading of introductory psychology key-concepts in an educational context. The testing effect was examined immediately after practice, after 18 days, and at a five-week delay in a sample of undergraduate students (n = 83). The results revealed that repeated testing with feedback significantly enhanced learning compared to rereading at all delays, demonstrating that repeated retrieval enhances retention compared to repeated encoding in the short- and the long-term. In addition, the effect of repeated testing was beneficial for students irrespectively of working memory capacity. It is argued that teaching methods involving repeated retrieval are important to consider by the educational system. PMID:24313425

  4. 76 FR 22119 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2011-04-20

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval.... SUMMARY: This notice advises of the cause and effect of termination of Direct Endorsement (DE) Approval... Endorsement mortgagees. Termination of Direct Endorsement Approval: Approval of a DE mortgagee by HUD/FHA...

  5. Repeatability & Workability Evaluation of SIGMOD 2009

    KAUST Repository

    Manegold, Stefan

    2010-12-15

    SIGMOD 2008 was the first database conference that offered to test submitters\\' programs against their data to verify the repeatability of the experiments published [1]. Given the positive feedback concerning the SIGMOD 2008 repeatability initiative, SIGMOD 2009 modified and expanded the initiative with a workability assessment.

  6. UK 2009-2010 repeat station report

    Directory of Open Access Journals (Sweden)

    Thomas J.G. Shanahan

    2013-03-01

    Full Text Available The British Geological Survey is responsible for conducting the UK geomagnetic repeat station programme. Measurements made at the UK repeat station sites are used in conjunction with the three UK magnetic observatories: Hartland, Eskdalemuir and Lerwick, to produce a regional model of the local field each year. The UK network of repeat stations comprises 41 stations which are occupied at approximately 3-4 year intervals. Practices for conducting repeat station measurements continue to evolve as advances are made in survey instrumentation and as the usage of the data continues to change. Here, a summary of the 2009 and 2010 UK repeat station surveys is presented, highlighting the measurement process and techniques, density of network, reduction process and recent results.

  7. Effects of Friedreich's ataxia (GAA)n*(TTC)n repeats on RNA synthesis and stability.

    Science.gov (United States)

    Krasilnikova, Maria M; Kireeva, Maria L; Petrovic, Vladimir; Knijnikova, Nelli; Kashlev, Mikhail; Mirkin, Sergei M

    2007-01-01

    Expansions of (GAA)n repeats within the first intron of the frataxin gene reduce its expression, resulting in a hereditary neurodegenerative disorder, Friedreich's ataxia. While it is generally believed that expanded (GAA)n repeats block transcription elongation, fine mechanisms responsible for gene repression are not fully understood. To follow the effects of (GAA)n*(TTC)n repeats on gene expression, we have chosen E. coli as a convenient model system. (GAA)n*(TTC)n repeats were cloned into bacterial plasmids in both orientations relative to a promoter, and their effects on transcription and RNA stability were evaluated both in vitro and in vivo. Expanded (GAA)n repeats in the sense strand for transcription caused a significant decrease in the mRNA levels in vitro and in vivo. This decrease was likely due to the tardiness of the RNA polymerase within expanded (GAA)n runs but was not accompanied by the enzyme's dissociation and premature transcription termination. Unexpectedly, positioning of normal- and carrier-size (TTC)n repeats into the sense strand for transcription led to the appearance of RNA transcripts that were truncated within those repetitive runs in vivo. We have determined that these RNA truncations are consistent with cleavage of the full-sized mRNAs at (UUC)n runs by the E. coli degradosome.

  8. A Comparison of DWI Repeaters and Non-repeaters Who Attended a Level I Rehabilitation Program.

    Science.gov (United States)

    Landrum, James W.; Windham, Gerald O.

    1981-01-01

    Compares behavioral and demographic characteristics of drunk drivers with repeated arrests and drivers not having repeated arrests, after attending an alcohol education program. Previous public drunkeness and previous drunk driving arrests were strong predictors of repeat arrests and were judged useful in screening offenders for rehabilitation…

  9. N-terminal nesprin-2 variants regulate β-catenin signalling

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qiuping; Minaisah, Rose-Marie; Ferraro, Elisa; Li, Chen; Porter, Lauren J.; Zhou, Can; Gao, Fang; Zhang, Junyi; Rajgor, Dipen; Autore, Flavia; Shanahan, Catherine M.; Warren, Derek T., E-mail: derek.warren@kcl.ac.uk

    2016-07-15

    The spatial compartmentalisation of biochemical signalling pathways is essential for cell function. Nesprins are a multi-isomeric family of proteins that have emerged as signalling scaffolds, herein, we investigate the localisation and function of novel nesprin-2 N-terminal variants. We show that these nesprin-2 variants display cell specific distribution and reside in both the cytoplasm and nucleus. Immunofluorescence microscopy revealed that nesprin-2 N-terminal variants colocalised with β-catenin at cell-cell junctions in U2OS cells. Calcium switch assays demonstrated that nesprin-2 and β-catenin are lost from cell-cell junctions in low calcium conditions whereas emerin localisation at the NE remained unaltered, furthermore, an N-terminal fragment of nesprin-2 was sufficient for cell-cell junction localisation and interacted with β-catenin. Disruption of these N-terminal nesprin-2 variants, using siRNA depletion resulted in loss of β-catenin from cell-cell junctions, nuclear accumulation of active β-catenin and augmented β-catenin transcriptional activity. Importantly, we show that U2OS cells lack nesprin-2 giant, suggesting that the N-terminal nesprin-2 variants regulate β-catenin signalling independently of the NE. Together, these data identify N-terminal nesprin-2 variants as novel regulators of β-catenin signalling that tether β-catenin to cell-cell contacts to inhibit β-catenin transcriptional activity. - Highlights: • N-terminal nesprin-2 variants display cell specific expression patterns. • N-terminal spectrin repeats of nesprin-2 interact with β-catenin. • N-terminal nesprin-2 variants scaffold β-catenin at cell-cell junctions.. • Nesprin-2 variants play multiple roles in β-catenin signalling.

  10. Gambling with video lottery terminals.

    Science.gov (United States)

    Doiron, J P; Mazer, D B

    2001-09-01

    Semistructured interviews were conducted with 7 persons who had significant involvements with video lottery terminal (VLT) gambling, and themes associated with different phases of the gambling experience were identified. The preinvolvement phase was characterized by lack of meaningful relationships, problematic relationships, and feelings of loss. Early involvement reflected attempts to "fill the void" and the casual innocence of initial VLT playing. The deepening involvement phase indicated themes of the language of relationship, for example, focused engagement, emotional highs and lows, and the escape and competition offered by gambling. Ending involvement themes included the emotional difficulty of quitting and strategies used to break the habit. Implications of these results for models of addiction and for the treatment of gambling problems are explored.

  11. A neuroanatomical correlate of sensorimotor recovery in response to repeated vaginocervical stimulation in rats.

    Directory of Open Access Journals (Sweden)

    Barry R Komisaruk

    2012-04-01

    Full Text Available Gentle probing against the cervix via the vagina (VCS increases tail flick latency (TFL to radiant heat; greater force totally abolishes the tail flick response and other withdrawal responses. This effect occurs in spinal cord-transected rats and in intact rats. On the basis of our earlier finding that vaginocervical stimulation (VCS releases vasoactive intestinal peptide (VIP into the spinal cord, and others’ reports of neurotrophic effects of VIP in vitro, we hypothesized that repeated VCS would stimulate sprouting and sensorimotor function of terminals of genital nerve primary afferents in the sacral spinal cord. To test this hypothesis, in the present study, we denervated the genital tract only unilaterally, which significantly reduced the TFL-elevating effect of VCS. Then we applied repeated daily VCS for one week and compared the subsequent effectiveness of acute VCS in elevating TFL. The rats that received the repeated daily VCS showed a significantly greater elevation in TFL in response to acute VCS than control rats that did not receive the repeated stimulation. Then, to test whether daily repeated VCS stimulates sprouting of genital primary afferents in such unilaterally genital tract-denervated rats, we transected the contralateral remaining intact pelvic nerve, applied horseradish peroxidase (HRP to its proximal cut end for 1-2h, and 2-3d later counted HRP particles in its terminal zone (S1 in the spinal cord. There were significantly more HRP particles in the rats that received the daily repeated VCS than in the control rats. In the context of these findings, we conclude that vaginocervical stimulation in rats can produce a functional sensorimotor recovery via a neurotrophic effect on compromised primary afferents in the spinal cord. Based on our previous research, we speculate that a similar functional sprouting antinociceptive process could occur supraspinally, after spinal cord injury, via an alternative vaginocervical sensory

  12. Finding and Characterizing Repeats in Plant Genomes.

    Science.gov (United States)

    Nicolas, Jacques; Peterlongo, Pierre; Tempel, Sébastien

    2016-01-01

    Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of available software that can help biologists to look for these repeats and check some hypothetical models intended to characterize their structures. Since transposable elements are a major source of repeats in plants, many methods have been used or developed for this large class of sequences. They are representative of the range of tools available for other classes of repeats and we have provided a whole section on this topic as well as a selection of the main existing software. In order to better understand how they work and how repeats may be efficiently found in genomes, it is necessary to look at the technical issues involved in the large-scale search of these structures. Indeed, it may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of the search for repeats and more complex patterns. The second section introduces the key concepts that are useful for understanding the current state of the art in playing with words, applied to genomic sequences. This can be seen as the first stage of a very general approach called linguistic analysis that is interested in the analysis of natural or artificial texts. Words, the lexical level, correspond to simple repeated entities in texts or strings. In fact, biologists need to represent more complex entities where a repeat family is built on more abstract structures, including direct or inverted small repeats, motifs, composition constraints as well as ordering and distance constraints between these elementary blocks. In terms of linguistics, this corresponds to the syntactic level of a language. The last section introduces concepts and practical tools that can be used to reach this syntactic level in biological sequence analysis.

  13. A large-scale biomass bulk terminal

    OpenAIRE

    Wu, M.R.

    2012-01-01

    This research explores the possibility of a large-scale bulk terminal in West Europe dedicated to handle solid and liquid biomass materials. Various issues regarding the conceptual design of such a terminal have been investigated and demonstrated in this research: the potential biomass materials that will be the major international trade flows in the future, the characteristics of these potential biomass materials, the interaction between the material properties and terminal equipment, the pe...

  14. Dynamic optimization problems with bounded terminal conditions

    Science.gov (United States)

    Lee, A. Y.

    1987-01-01

    Bounded terminal conditions of nonlinear optimization problems are converted to equality terminal conditions via Valentine's device. In so doing, additional unknown parameters are introduced into the problem. The transformed problems can still be easily solved using the sequential gradient-restoration algorithm (SGRA) via a simple augmentation of the unknown parameter vector pi. Three example problems with bounded terminal conditions are solved to verify this technique.

  15. The child accident repeater: a review.

    Science.gov (United States)

    Jones, J G

    1980-04-01

    The child accident repeater is defined as one who has at least three accidents that come to medical attention within a year. The accident situation has features in common with those of the child who has a single accident through simple "bad luck", but other factors predispose him to repeated injury. In the child who has a susceptible personality, a tendency for accident repetition may be due to a breakdown in adjustment to a stressful environment. Prevention of repeat accidents should involve the usual measures considered appropriate for all children as well as an attempt to provide treatment of significant maladjustment and modification of a stressful environment.

  16. Childhood experiences and repeated suicidal behavior

    DEFF Research Database (Denmark)

    Krarup, Gertrud; Nielsen, Bent; Rask, P

    1991-01-01

    suicidal behavior. The results showed that three fourths of the patients attempted suicide more than once (62% nonfatal and 14% fatal outcome). The sex distribution was about the same among the first-evers as among the repeaters. Most repeaters were younger people in their twenties and thirties...... that the psychological climate of the home may be more important than the rupture of early home life. It is noteworthy that the group of repeaters, as against the first-evers, could be characterized by personality disorders and abuse, especially of alcohol: disorders known to be precipitated by a discordant childhood...

  17. Performance Evaluation and Modelling of Container Terminals

    Science.gov (United States)

    Venkatasubbaiah, K.; Rao, K. Narayana; Rao, M. Malleswara; Challa, Suresh

    2017-11-01

    The present paper evaluates and analyzes the performance of 28 container terminals of south East Asia through data envelopment analysis (DEA), principal component analysis (PCA) and hybrid method of DEA-PCA. DEA technique is utilized to identify efficient decision making unit (DMU)s and to rank DMUs in a peer appraisal mode. PCA is a multivariate statistical method to evaluate the performance of container terminals. In hybrid method, DEA is integrated with PCA to arrive the ranking of container terminals. Based on the composite ranking, performance modelling and optimization of container terminals is carried out through response surface methodology (RSM).

  18. CDC Vital Signs: Preventing Repeat Teen Births

    Science.gov (United States)

    ... text version SOURCE: Adapted from Trussell J in Contraceptive Technology, 2011, and FDA Office of Women’s Health ... about how to avoid repeat births with both male and female teens. http://www.cdc.gov/teenpregnancy/ ...

  19. DNA repair in the trinucleotide repeat disorders.

    Science.gov (United States)

    Jones, Lesley; Houlden, Henry; Tabrizi, Sarah J

    2017-01-01

    Inherited diseases caused by unstable repeated DNA sequences are rare, but together represent a substantial cause of morbidity. Trinucleotide repeat disorders are severe, usually life-shortening, neurological disorders caused by nucleotide expansions, and most have no disease-modifying treatments. Longer repeat expansions are associated with genetic anticipation (ie, earlier disease onset in successive generations), although the differences in age at onset are not entirely accounted for by repeat length. Such phenotypic variation within disorders implies the existence of additional modifying factors in pathways that can potentially be modulated to treat disease. A genome-wide association study detected genetic modifiers of age at onset in Huntington's disease. Similar findings were seen in the spinocerebellar ataxias, indicating an association between DNA damage-response and repair pathways and the age at onset of disease. These studies also suggest that a common genetic mechanism modulates age at onset across polyglutamine diseases and could extend to other repeat expansion disorders. Genetic defects in DNA repair underlie other neurodegenerative disorders (eg, ataxia-telangiectasia), and DNA double-strand breaks are crucial to the modulation of early gene expression, which provides a mechanistic link between DNA repair and neurodegeneration. Mismatch and base-excision repair are important in the somatic expansion of repeated sequences in mouse models of trinucleotide repeat disorders, and somatic expansion of the expanded CAG tract in HTT correlates with age at onset of Huntington's disease and other trinucleotide repeat disorders. WHERE NEXT?: To understand the common genetic architecture of trinucleotide repeat disorders and any further genetic susceptibilities in individual disorders, genetic analysis with increased numbers of variants and sample sizes is needed, followed by sequencing approaches to define the phenotype-modifying variants. The findings must

  20. Archaeal Nucleosome Positioning by CTG Repeats

    OpenAIRE

    Sandman, Kathleen; Reeve, John N.

    1999-01-01

    DNA shape recognition determines the preferred binding sites for sequence-independent DNA binding proteins, and here we document that archaeal histones assemble archaeal nucleosomes in vitro centered preferentially within (CTG)6 and (CTG)8 repeats, close to junctions with flanking mixed-sequence DNA. Archaeal nucleosomes were not positioned by (CTG)4-, (CTG)5-, or (CTG)3AA(CTG)3-containing DNA sequences. The features of CTG repeat-containing sequences that direct eucaryal nucleosome positioni...

  1. Blockwise Repeated Burst Error Correcting Linear Codes

    Directory of Open Access Journals (Sweden)

    B.K. Dass

    2010-12-01

    Full Text Available This paper presents a lower and an upper bound on the number of parity check digits required for a linear code that corrects a single sub-block containing errors which are in the form of 2-repeated bursts of length b or less. An illustration of such kind of codes has been provided. Further, the codes that correct m-repeated bursts of length b or less have also been studied.

  2. St. James marine terminal facility description

    Energy Technology Data Exchange (ETDEWEB)

    1993-10-01

    The US Department of Energy (DOE) currently owns and operates a marine terminal on the west bank of the Mississippi River at St. James, Louisiana. The St. James facility was constructed by the Department to provide marine services associated with the fill and drawdown of the Strategic Petroleum Reserve (SPR) crude oil storage facilities located at Bayou Choctaw and Weeks Island, Louisiana. Although strategic to the mission of the SPR in the event of a national emergency, the St. James terminal is situated such that it has a high potential to also serve the commercial industry`s needs for crude oil terminalling and storage. The St. James terminal is located approximately 45 miles west of New Orleans and 30 miles southeast of Baton Rouge, and approximately 160 miles upstream from the mouth of the Mississippi River. Construction of the St. James terminal was initiated in 1978 and was completed in 1980. Since then, the terminal has received and transferred over 125 million barrels of crude oil to the SPR sites for storage. For crude oil distribution, the St. James terminal was connected to the neighboring LOCAP terminal by a 0.1 mile 36-inch pipeline in 1981 and to the Capline terminal by a 0.5 mile 30-inch pipeline in 1988. The terminal also has a 30-inch pipeline connection to the Koch oil terminal which was used for initial fill purposes; however, this pipeline has been disconnected and is currently inactive. A complete description of the St. James terminal facilities, operational capabilities, operational certifications, and future Government requirements are presented in Sections 2, 3, 4, and 5 respectively.

  3. Non-terminal blood sampling techniques in Guinea pigs

    DEFF Research Database (Denmark)

    Birck, Malene Muusfeldt; Tveden-Nyborg, Pernille; Lindblad, Maiken Marie

    2014-01-01

    of guinea pigs are slightly different from other rodent models, hence modulation of sampling techniques to accommodate for species-specific differences, e.g., compared to mice and rats, are necessary to obtain sufficient and high quality samples. As both long and short term in vivo studies often require...... repeated blood sampling the choice of technique should be well considered in order to reduce stress and discomfort in the animals but also to ensure survival as well as compliance with requirements of sample size and accessibility. Venous blood samples can be obtained at a number of sites in guinea pigs e.......g., the saphenous and jugular veins, each technique containing both advantages and disadvantages(4,5). Here, we present four different blood sampling techniques for either conscious or anaesthetized guinea pigs. The procedures are all non-terminal procedures provided that sample volumes and number of samples do...

  4. Monitoring plant phenology using digital repeat photography.

    Science.gov (United States)

    Crimmins, Michael A; Crimmins, Theresa M

    2008-06-01

    Repeated observations of plant phenology have been shown to be important indicators of global change. However, capturing the exact date of key events requires daily observations during the growing season, making phenologic observations relatively labor intensive and costly to collect. One alternative to daily observations for capturing the dates of key phenologic events is repeat photography. In this study, we explored the utility of repeat digital photography for monitoring phenologic events in plants. We provide an illustration of this approach and its utility by placing observations made using repeat digital imagery in context with local meteorologic and edaphic variables. We found that repeat photography provides a reliable, consistent measurement of phenophase. In addition, digital photography offers advantages in that it can be mathematically manipulated to detect and enhance patterns; it can classify objects; and digital photographs can be archived for future analysis. In this study, an estimate of greenness and counts of individual flowers were extracted by way of mathematic algorithms from the photo time series. These metrics were interpreted using meteorologic measurements collected at the study site. We conclude that repeat photography, coupled with site-specific meteorologic measurements, could greatly enhance our understanding environmental triggers of phenologic events. In addition, the methods described could easily be adopted by citizen scientists and the general public as well as professionals in the field.

  5. Digital repeat analysis; setup and operation.

    Science.gov (United States)

    Nol, J; Isouard, G; Mirecki, J

    2006-06-01

    Since the emergence of digital imaging, there have been questions about the necessity of continuing reject analysis programs in imaging departments to evaluate performance and quality. As a marketing strategy, most suppliers of digital technology focus on the supremacy of the technology and its ability to reduce the number of repeats, resulting in less radiation doses given to patients and increased productivity in the department. On the other hand, quality assurance radiographers and radiologists believe that repeats are mainly related to positioning skills, and repeat analysis is the main tool to plan training needs to up-skill radiographers. A comparative study between conventional and digital imaging was undertaken to compare outcomes and evaluate the need for reject analysis. However, digital technology still being at its early development stages, setting a credible reject analysis program became the major task of the study. It took the department, with the help of the suppliers of the computed radiography reader and the picture archiving and communication system, over 2 years of software enhancement to build a reliable digital repeat analysis system. The results were supportive of both philosophies; the number of repeats as a result of exposure factors was reduced dramatically; however, the percentage of repeats as a result of positioning skills was slightly on the increase for the simple reason that some rejects in the conventional system qualifying for both exposure and positioning errors were classified as exposure error. The ability of digitally adjusting dark or light images reclassified some of those images as positioning errors.

  6. The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

    Directory of Open Access Journals (Sweden)

    Bhattacharyya Madan K

    2008-03-01

    Full Text Available Abstract Background A series of Rps (resistance to Pytophthora sojae genes have been protecting soybean from the root and stem rot disease caused by the Oomycete pathogen, Phytophthora sojae. Five Rps genes were mapped to the Rps1 locus located near the 28 cM map position on molecular linkage group N of the composite genetic soybean map. Among these five genes, Rps1-k was introgressed from the cultivar, Kingwa. Rps1-k has been providing stable and broad-spectrum Phytophthora resistance in the major soybean-producing regions of the United States. Rps1-k has been mapped and isolated. More than one functional Rps1-k gene was identified from the Rps1-k locus. The clustering feature at the Rps1-k locus might have facilitated the expansion of Rps1-k gene numbers and the generation of new recognition specificities. The Rps1-k region was sequenced to understand the possible evolutionary steps that shaped the generation of Phytophthora resistance genes in soybean. Results Here the analyses of sequences of three overlapping BAC clones containing the 184,111 bp Rps1-k region are reported. A shotgun sequencing strategy was applied in sequencing the BAC contig. Sequence analysis predicted a few full-length genes including two Rps1-k genes, Rps1-k-1 and Rps1-k-2. Previously reported Rps1-k-3 from this genomic region 1 was evolved through intramolecular recombination between Rps1-k-1 and Rps1-k-2 in Escherichia coli. The majority of the predicted genes are truncated and therefore most likely they are nonfunctional. A member of a highly abundant retroelement, SIRE1, was identified from the Rps1-k region. The Rps1-k region is primarily composed of repetitive sequences. Sixteen simple repeat and 63 tandem repeat sequences were identified from the locus. Conclusion These data indicate that the Rps1 locus is located in a gene-poor region. The abundance of repetitive sequences in the Rps1-k region suggested that the location of this locus is in or near a

  7. Proliferating cell nuclear antigen prevents trinucleotide repeat expansions by promoting repeat deletion and hairpin removal

    Science.gov (United States)

    Beaver, Jill M.; Lai, Yanhao; Rolle, Shantell J.; Liu, Yuan

    2017-01-01

    DNA base lesions and base excision repair (BER) within trinucleotide repeat (TNR) tracts modulate repeat instability through the coordination among the key BER enzymes DNA polymerase β, flap endonuclease 1 (FEN1) and DNA ligase I (LIG I). However, it remains unknown whether BER cofactors can also alter TNR stability. In this study, we discovered that proliferating cell nuclear antigen (PCNA), a cofactor of BER, promoted CAG repeat deletion and removal of a CAG repeat hairpin during BER in a duplex CAG repeat tract and CAG hairpin loop, respectively. We showed that PCNA stimulated LIG I activity on a nick across a small template loop during BER in a duplex (CAG)20 repeat tract promoting small repeat deletions. Surprisingly, we found that during BER in a hairpin loop, PCNA promoted reannealing of the upstream flap of a double-flap intermediate, thereby facilitating the formation of a downstream flap and stimulating FEN1 cleavage activity and hairpin removal. Our results indicate that PCNA plays a critical role in preventing CAG repeat expansions by modulating the structures of dynamic DNA via cooperation with BER enzymes. We provide the first evidence that PCNA prevents CAG repeat expansions during BER by promoting CAG repeat deletion and removal of a TNR hairpin. PMID:27793507

  8. 78 FR 5717 - Safety Zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal...

    Science.gov (United States)

    2013-01-28

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Military Ocean Terminal Concord Safety Zone, Suisun Bay, Military Ocean Terminal Concord, CA AGENCY: Coast Guard, DHS. ACTION: Interim rule and... Suisun Bay near Military Ocean Terminal Concord, CA in support of military onload and offload operations...

  9. Challenges encountered by women seeking termination of ...

    African Journals Online (AJOL)

    The purpose of the study was to identify possible challenges that prevented women from utilising termination of pregnancy services in the North West Province of South Africa. Fifty structured interviews were conducted with conveniently selected women who requested termination of pregnancy services but who could not ...

  10. A large-scale biomass bulk terminal

    NARCIS (Netherlands)

    Wu, M.R.

    2012-01-01

    This research explores the possibility of a large-scale bulk terminal in West Europe dedicated to handle solid and liquid biomass materials. Various issues regarding the conceptual design of such a terminal have been investigated and demonstrated in this research: the potential biomass materials

  11. [Terminal phase hydration, pain and delirium

    DEFF Research Database (Denmark)

    Heick, A.

    2009-01-01

    Hydration of the terminal patient may relieve confusion and complaints of "dry mouth". But it may worsen oedema of the brain, lungs, and extremities, worsen terminal rattling and cause a need for frequent changing of diapers. The decision of whether and how to treat a dying patient with fluids sh...

  12. 29 CFR 406.4 - Terminal report.

    Science.gov (United States)

    2010-07-01

    ... immediately prior to the time of the person's loss of reporting identity (or by the person himself if he is an individual), together with a statement of the effective date of termination or loss of reporting identity... year ending on the effective date of the termination or loss of identity. ...

  13. Functionalization of hydroxyl terminated polybutadiene with ...

    Indian Academy of Sciences (India)

    ... hydroxyl value and microstructure of the parent HTPB. The formation of hydrogen bonding between the terminal hydroxyl groups and the nitrogen atoms of triazine moiety is the driving force for the terminal attachment chemistry. The functionalized HTPB (HTPB–CBDT) shows a strong fluorescence emission at 385 nm.

  14. 30 CFR 755.15 - Termination.

    Science.gov (United States)

    2010-07-01

    ... Resources OFFICE OF SURFACE MINING RECLAMATION AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR INDIAN LANDS... by either party upon written notice to the other specifying the date upon which the agreement will be terminated. The date of termination shall be no less than 30 days from the date of the notice. ...

  15. Multidisciplinary care of the terminally ill patient.

    Science.gov (United States)

    O'Mahony, S; Coyle, N; Payne, R

    2000-04-01

    This article discusses sedation, the assessment and management of physical symptoms, and symptom-assessment scales for the terminally ill patient. The evaluation of the ability of the family or community to care for a terminally ill patient in pain also is discussed.

  16. Bargaining in Mergers and Termination Fees

    NARCIS (Netherlands)

    Weitzel, U.; Rosenkranz, S.

    We model takeovers as a bargaining process and explain termination fees for, both, the target and the acquirer, subject to parties’ bargaining power and outside options. In equilibrium, termination fees are offered by firms with outside options in exchange for a greater share of merger synergies.

  17. 9 CFR 3.65 - Terminal facilities.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Terminal facilities. 3.65 Section 3.65... WELFARE STANDARDS Specifications for the Humane Handling, Care, Treatment and Transportation of Rabbits Transportation Standards § 3.65 Terminal facilities. No person subject to the Animal Welfare regulations shall...

  18. 9 CFR 3.141 - Terminal facilities.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Terminal facilities. 3.141 Section 3... ANIMAL WELFARE STANDARDS Specifications for the Humane Handling, Care, Treatment, and Transportation of... Mammals Transportation Standards § 3.141 Terminal facilities. Carriers and intermediate handlers shall not...

  19. 9 CFR 3.40 - Terminal facilities.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Terminal facilities. 3.40 Section 3.40... WELFARE STANDARDS Specifications for the Humane Handling, Care, Treatment, and Transportation of Guinea Pigs and Hamsters Transportation Standards § 3.40 Terminal facilities. No person subject to the Animal...

  20. Diffuse transition state structure for the unfolding of a leucine-rich repeat protein.

    Science.gov (United States)

    Kelly, Sadie E; Meisl, Georg; Rowling, Pamela J E; McLaughlin, Stephen H; Knowles, Tuomas; Itzhaki, Laura S

    2014-04-14

    Tandem-repeat proteins, such as leucine-rich repeats, comprise arrays of small structural motifs that pack in a linear fashion to produce elongated architectures. They lack contacts between residues that are distant in primary sequence, a feature that distinguishes them from the complex topologies of globular proteins. Here we have investigated the unfolding pathway of the leucine-rich repeat domain of the mRNA export protein TAP (TAPLRR) using Φ-value analysis. Whereas most of the tandem-repeat proteins studied to date have been found to unfold via a polarised mechanism in which only a small, localised number of repeats are structured in the transition state, the unfolding mechanism of TAPLRR is more diffuse in nature. In the transition state for unfolding of TAPLRR, three of the four LRRs are highly structured and non-native interactions are formed within the N-terminal α-helical cap and the first LRR. Thus, the α-helical cap plays an important role in which non-native interactions are required to provide a scaffold for the LRRs to pack against in the folding reaction.

  1. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  2. Potential air toxics hot spots in truck terminals and cabs.

    Science.gov (United States)

    Smith, Thomas J; Davis, Mary E; Hart, Jaime E; Blicharz, Andrew; Laden, Francine; Garshick, Eric

    2012-12-01

    Hot spots are areas where concentrations of one or more air toxics--organic vapors or particulate matter (PM)--are expected to be elevated. The U.S. Environmental Protection Agency's (EPA*) screening values for air toxics were used in our definition of hot spots. According to the EPA, a screening value "is used to indicate a concentration of a chemical in the air to which a person could be continually exposed for a lifetime ... and which would be unlikely to result in a deleterious effect (either cancer or noncancer health effects)" (U.S. EPA 2006). Our characterization of volatile organic compounds (VOCs; namely 18 hydrocarbons, methyl tert-butyl ether [MTBE], acetone, and aldehydes) was added onto our ongoing National Cancer Institute-funded study of lung cancer and particulate pollutant concentrations (PM with an aerodynamic diameter parks; downwind areas affected by upwind and terminal sources; and the loading docks and mechanic shops within terminal as well as the interior of cabs of trucks being driven on city, suburban, and rural streets and on highways. In Phase 1 of our study, 15 truck terminals across the United States were each visited for five consecutive days. During these site visits, sorbent tubes were used to collect 12-hour integrated samples of hydrocarbons and aldehydes from upwind and downwind fence-line locations as well as inside truck cabs. Meteorologic data and extensive site information were collected with each sample. In Phase 2, repeat visits to six terminals were conducted to test the stability of concentrations across time and judge the representativeness of our previous measurements. During the repeat site visits, the sampling procedure was expanded to include real-time sampling for total hydrocarbon (HC) and PM2.5 at the terminal upwind and downwind sites and inside the truck cabs, two additional monitors in the yard for four-quadrant sampling to better characterize the influence of wind, and indoor sampling in the loading dock and

  3. Two-terminal video coding.

    Science.gov (United States)

    Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

    2009-03-01

    Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

  4. Risk factors for repeat abortion in Nepal.

    Science.gov (United States)

    Thapa, Shyam; Neupane, Shailes

    2013-01-01

    To examine the incidence of and risk factors for repeat abortion in Nepal. Data were analyzed from a survey of 1172 women who had surgical abortions between December 2009 and March 2010 in 2 clinics in Kathmandu, Nepal. Bivariate and multivariate logistic regressions were performed to estimate odds ratios for the risk factors. Among the respondents, 32.3% (95% confidence interval, 29.6-34.9) had repeat abortions. This incidence rose sharply with age and parity, and was higher among those with no intention of having a future child, those attaining primary or secondary level education, and those attending the non-governmental sector clinic. Women with repeat abortion were similar to those with 1 abortion in terms of contraceptive practice. Among women not using contraceptives at the time of the unintended pregnancy, the 3 most commonly cited reasons were ill health, non-compliance with the method intended for use, and dislike of the method. Women with repeat abortion showed a pattern of contraceptive acceptance immediately after the procedure similar to that of women who had 1 abortion. Repeat abortion is emerging as a major public health issue in Nepal, with implications for counseling and provision of abortion, and for family planning services. Copyright © 2012 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

  5. Participation of Private Investors in Container Terminal Operation: Influence of Global Terminal Operators

    Directory of Open Access Journals (Sweden)

    Heejung YEO

    2015-09-01

    Full Text Available Private container terminal operators have begun to participate in the port business in Asia since the late 1980s. Terminal operators decide whether to invest in terminal infrastructures, and the enhancement of the quality of service level. The paper analyses the influence of global terminal operators and the port ownership structure on the container terminal's efficiency. Two hundred and sixty container terminal data for China, Korea, and Japan were collected. The paper applies a negative binomial regression analysis. The paper finds that the port restructuring has contributed to productivity gains. It is found that the influence of GTO on the efficiency is evident and positively related to the port efficiency. The paper also finds that the country effect prevails over a terminal operator group effect.

  6. Concept Layout Model of Transportation Terminals

    Directory of Open Access Journals (Sweden)

    Li-ya Yao

    2012-01-01

    Full Text Available Transportation terminal is the key node in transport systems. Efficient terminals can improve operation of passenger transportation networks, adjust the layout of public transportation networks, provide a passenger guidance system, and regulate the development of commercial forms, as well as optimize the assembly and distribution of modern logistic modes, among others. This study aims to clarify the relationship between the function and the structure of transportation terminals and establish the function layout design. The mapping mechanism of demand, function, and structure was analyzed, and a quantitative relationship between function and structure was obtained from a design perspective. Passenger demand and terminal structure were decomposed into several demand units and structural elements following the principle of reverse engineering. The relationship maps between these two kinds of elements were then analyzed. Function-oriented concept layout model of transportation terminals was established using the previous method. Thus, a technique in planning and design of transportation structures was proposed. Meaningful results were obtained from the optimization of transportation terminal facilities, which guide the design of the functional layout of transportation terminals and improve the development of urban passenger transportation systems.

  7. Acetylene terminated aspartimides and resins therefrom

    Science.gov (United States)

    Hergenrother, Paul M. (Inventor); Connell, John W. (Inventor); Havens, Stephen J. (Inventor)

    1989-01-01

    Acetylene terminated aspartimides are prepared using two methods. In the first, an amino-substituted aromatic acetylene is reacted with an aromatic bismaleimide in a solvent of glacial acetic acid and/or m-cresol. In the second method, an aromatic diamine is reacted with an ethynyl containing maleimide, such an N-(3-ethynyl phenyl) maleimide, in a solvent of glacial acetic acid and/or m-cresol. In addition, acetylene terminated aspartimides are blended with various acetylene terminated oligomers and polymers to yield composite materials exhibiting improved mechanical properties.

  8. International Joint Venture Termination: An Empirical Investigation

    DEFF Research Database (Denmark)

    Nielsen, Ulrik B.; Rasmussen, Erik Stavnsager; Siersbæk, Nikolaj

    for the article stems from data from the project portfolio of a Danish Investment Fund for Developing Countries with a total of 773 investments. A number of hypotheses are established from the literature review and tested related to the empirical data. The result indicates that the most important factor...... the difference between intended termination and unintended termination has left a significant gap in the literature. The purpose of this article is to contribute to a better understanding of IJV exit literature by differentiating empirically between intended and unintended IJV termination. The empirical data...

  9. Graded junction termination extensions for electronic devices

    Science.gov (United States)

    Merrett, J. Neil (Inventor); Isaacs-Smith, Tamara (Inventor); Sheridan, David C. (Inventor); Williams, John R. (Inventor)

    2007-01-01

    A graded junction termination extension in a silicon carbide (SiC) semiconductor device and method of its fabrication using ion implementation techniques is provided for high power devices. The properties of silicon carbide (SiC) make this wide band gap semiconductor a promising material for high power devices. This potential is demonstrated in various devices such as p-n diodes, Schottky diodes, bipolar junction transistors, thyristors, etc. These devices require adequate and affordable termination techniques to reduce leakage current and increase breakdown voltage in order to maximize power handling capabilities. The graded junction termination extension disclosed is effective, self-aligned, and simplifies the implementation process.

  10. Operational Optimization in Port Container Terminals

    DEFF Research Database (Denmark)

    As a result of the significant increase in worldwide containerized transportation the development of efficient handling systems in marine terminals has become very important for port competitiveness. In order to optimize the productivity the total handling time for containers in the terminal must...... be minimized. An overview of the different operational problems in port container terminals is presented and an aggregated model and solution approach is shown. Next, there will be focused on the yard storage problem and a mathematical formulation and solution proposals will be presented....

  11. Duplication of the ureter with extravesical termination

    Energy Technology Data Exchange (ETDEWEB)

    Steidle, B.; Wolf, K.J.

    1984-02-01

    The renal segment supplying an ectopic ureter is nearly always dysplastic. Usually the ureters cross and the ectopic ureter terminates caudally in relation to the ureter from the normal portion of the kidney. Extravesical termination in women leads to urinary incontinence, since it frequently ends in the vagina or the labia. In men, the effects are much less noticeable. The ureters usually terminate in the urethra, the seminal vesicles, the ductus deferens or the epididymis. Duplication of a ureter or mega-ureter with dysplasia of the appropriate part of the kidney can be readily explained embryologically.

  12. Tyrolean termination tool: Techniques and features

    OpenAIRE

    Hirokawa, Nao; Middeldorp, Aart

    2007-01-01

    The Tyrolean Termination Tool (T_T for short) is a powerful tool for automatically proving termination of rewrite systems. It incorporates several new refinements of the dependency pair method that are easy to implement, increase the power of the method, result in simpler termination proofs, and make the method more efficient. T_T employs polynomial interpretations with negative coefficients, like x − 1 for a unary function symbol or x − y for a binary function symbol, which are useful for ex...

  13. [Confirmation of intention by signature regarding terminal care treatment in elderly people].

    Science.gov (United States)

    Sato, Takeshi; Sato, Kazunori; Sato, Akira

    2011-01-01

    In Japan, it is rare for patients to confirm their intentions regarding terminal care treatment in hospital by signature. To maintain respect for the autonomy of elderly patients, we encouraged confirmation by signature regarding terminal care treatment in elderly patients, after repeated discussions. The purpose of this study was to clarify the status of confirmation of intention by signature. The subjects were 98 patients who signed documents signaling their intention regarding terminal care (signature group), and 165 patients who did not sign such documents (non-signature group), all of whom died in our hospital between April 2009 and March 2010. We surveyed and examined their backgrounds and treatment experiences based on the clinical records. Furthermore, we gave a questionnaire survey to these patients. A total of 31 (35.2%) patients from the signature group and 58 (35.2%) patients from the non-signature group responded. In the signature group 32 (32.7%) patients judged to be in a terminal state were discharged alive. Those in the signature group had a significantly higher age, higher ratio of dementia, lower activity level in their daily life and were hospitalized with respiratory illnesses. In addition, the frequency of the informed consent discussions was greater than that of the non-signature group. A total of 90% of the signature group was able to accept the confirmation of their intention regarding terminal care by signature. In both groups, the doctors' explanations were understood, and the patients' wishes were successfully conveyed. In Japan, confirmation of intention regarding terminal care by signature can be effective and useful as one of the methods to determine intention regarding terminal care treatment in elderly patients.

  14. Oligomers Terminated By Maleimide And Acetylene

    Science.gov (United States)

    St. Clair, Terry L.; Pater, Ruth H.; Gerber, Margaret K.

    1994-01-01

    Oligomeric molecules terminated with maleimide and acetylene groups synthesized and thermally treated to form cross-linked polymers exhibiting high or undetectable glass-transition temperatures and high thermo-oxidative stabilities. Compounds used to make thermally stable, glassy polymers.

  15. 38 CFR 36.4322 - Loan termination.

    Science.gov (United States)

    2010-07-01

    ... require prior approval from VA. VA will maintain the loan termination time allowable timeframes on a Web... writing a shorter validity period, not less than 90 calendar days, for a liquidation appraisal or...

  16. Keerukas terminal valiti aasta betoonehitiseks / Aivo Vahemets

    Index Scriptorium Estoniae

    Vahemets, Aivo

    2002-01-01

    Aasta Betoonehitise nimetuse võitis Muuga kuivpuisteainete terminal, projekteerija Randväli&Karema AS. Eriauhind arhitektuurse osa eest - Birgitta klooster Pirital. Eriauhind tellijale - büroohoone Tallinnas Toompuiestee 33. Eriauhind ehitajale - konteinerterminal Muugal, projekteerija AS Merin

  17. Location of terminals in a communications network

    DEFF Research Database (Denmark)

    2015-01-01

    A method (400, 500) of identifying nodes in a communications network is disclosed, the nodes being for use in locating wireless terminals within the network based upon reports from the wireless terminals of transmissions received from the nodes. The method (400, 500) comprises prioritising......, a reference node. Also disclosed is a method (100, 200) for locating a plurality of wireless terminals in a communications network, the network comprising a plurality of network nodes at known locations, wherein the nodes emit wireless transmissions in an unsynchronised manner, such that a time difference...... exists between the emission time of corresponding transmissions from different nodes. The method comprises receiving reports from a plurality of wireless terminals of transmissions received from the network nodes (110, 210), selecting a subset of network nodes (120, 220) and identifying a plurality...

  18. 22 CFR 62.78 - Termination.

    Science.gov (United States)

    2010-04-01

    ... Relations DEPARTMENT OF STATE PUBLIC DIPLOMACY AND EXCHANGES EXCHANGE VISITOR PROGRAM Student and Exchange Visitor Information System (SEVIS) § 62.78 Termination. An exchange visitor who willfully or negligently... from the Exchange Visitor Program by the sponsor. ...

  19. Cholesterol: the debate should be terminated.

    Science.gov (United States)

    Nathan, David G

    2017-07-01

    Here, I offer personal perspectives on cholesterol homeostasis that reflect my belief that certain aspects of the debate have been overstated.-Nathan, D. G. Cholesterol: the debate should be terminated. © FASEB.

  20. Conflict Termination: Every Conflict Must End

    National Research Council Canada - National Science Library

    Garza, Mario

    1997-01-01

    .... The operational commander and his staff must understand the nature of conflict termination and the post-conflict activities so that they will be able to effectively translate the desired end state...

  1. Terminal Area Conflict Detection and Resolution Tool

    Science.gov (United States)

    Verma, Savita Arora

    2011-01-01

    This poster will describe analysis of a conflict detection and resolution tool for the terminal area called T-TSAFE. With altitude clearance information, the tool can reduce false alerts to as low as 2 per hour.

  2. The role of physiotherapy in terminal care

    National Research Council Canada - National Science Library

    Przewłocki Sławomir; Ronikier Aleksander

    2016-01-01

    Introduction: Terminal patients require proper care standards and professional team of doctors, physiotherapists, social workers, educators, psychologists and clergy directly involved in mitigating the suffering of a dying person...

  3. Multiemployer Pension Plan Terminations, Mergers, and Insolvencies

    Data.gov (United States)

    Pension Benefit Guaranty Corporation — A listing of multiemployer pension plan terminations, mergers, and insolvencies reported to the PBGC for the current fiscal year. This data set will be updated...

  4. Photometric Repeatability of Scanned Imagery: UVIS

    Science.gov (United States)

    Shanahan, Clare E.; McCullough, Peter; Baggett, Sylvia

    2017-08-01

    We provide the preliminary results of a study on the photometric repeatability of spatial scans of bright, isolated white dwarf stars with the UVIS channel of the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST). We analyze straight-line scans from the first pair of identical orbits of HST program 14878 to assess if sub 0.1% repeatability can be attained with WFC3/UVIS. This study is motivated by the desire to achieve better signal-to-noise in the UVIS contamination and stability monitor, in which observations of standard stars in staring mode have been taken from the installation of WFC3 in 2009 to the present to assess temporal photometric stability. Higher signal to noise in this program would greatly benefit the sensitivity to detect contamination, and to better characterize the observed small throughput drifts over time. We find excellent repeatability between identical visits of program 14878, with sub 0.1% repeatability achieved in most filters. These! results support the initiative to transition the staring mode UVIS contamination and photometric stability monitor from staring mode images to spatial scans.

  5. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Yomi

    2012-01-19

    Jan 19, 2012 ... repeats (EST-SSR) markers characterized by new bioinformatic criteria reveal high genetic similarity in sugarcane (Saccharum spp.) breeding lines. Kittipat Ukoskit1*, Penjun Thipmongkolcharoen1 and Prasert Chatwachirawong2. 1Department of Biotechnology, Faculty of Science and Technology, ...

  6. FRB 121102: A Starquake-induced Repeater?

    Science.gov (United States)

    Wang, Weiyang; Luo, Rui; Yue, Han; Chen, Xuelei; Lee, Kejia; Xu, Renxin

    2018-01-01

    Since its initial discovery, the fast radio burst (FRB) FRB 121102 has been found to be repeating with millisecond-duration pulses. Very recently, 14 new bursts were detected by the Green Bank Telescope during its continuous monitoring observations. In this paper, we show that the burst energy distribution has a power-law form which is very similar to the Gutenberg–Richter law of earthquakes. In addition, the distribution of burst waiting time can be described as a Poissonian or Gaussian distribution, which is consistent with earthquakes, while the aftershock sequence exhibits some local correlations. These findings suggest that the repeating FRB pulses may originate from the starquakes of a pulsar. Noting that the soft gamma-ray repeaters (SGRs) also exhibit such distributions, the FRB could be powered by some starquake mechanisms associated with the SGRs, including the crustal activity of a magnetar or solidification-induced stress of a newborn strangeon star. These conjectures could be tested with more repeating samples.

  7. Adaptation and complexity in repeated games

    DEFF Research Database (Denmark)

    Maenner, Eliot Alexander

    2008-01-01

    The paper presents a learning model for two-player infinitely repeated games. In an inference step players construct minimally complex inferences of strategies based on observed play, and in an adaptation step players choose minimally complex best responses to an inference. When players randomly...

  8. [Preventive maintenance of repeated ischemic insults].

    Science.gov (United States)

    Gavrilenko, A V; Kuklin, A V; Kravchenko, A A; Agafonov, I N

    2008-01-01

    In the review we offer analysis of the effectiveness of carotid endarterectomy in treatment of post-functional apoplexy or stroke patients. Published results of the researches specify possible efficiency of carotid endarterectomy in preventive maintenance against repeated apoplectic attack or strokes. Yet the criteria of usage and execution of the carotid endarterectomy are still to be discussed.

  9. Early repeated maternal separation induces alterations of ...

    Indian Academy of Sciences (India)

    The long-term effects of repeated maternal separation (MS) during early postnatal life on reelin expression in the hippocampus of developing rats were investigated in the present study. MS was carried out by separating Wistar rat pups singly from their mothers for 3 h a day during postnatal days (PND) 2–14. Reelin mRNA ...

  10. 47 CFR 22.1015 - Repeater operation.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Repeater operation. 22.1015 Section 22.1015 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES PUBLIC MOBILE SERVICES... the time. Table I-2—Maximum ERP (Watts) Distance from the 4.8 km (3 mi) limit 30 meters (100 feet) 61...

  11. Repeated events and total time on test

    DEFF Research Database (Denmark)

    Kvist, Kajsa; Andersen, Per Kragh; Angst, Jules

    2008-01-01

    We adopt the total time on test procedure to investigate monotone time trends in the intensity in a repeated event setting. The correct model is assumed to be a proportional hazards model, with a random effect to account for dependence within subjects. The method offers a simple routine for testi...... and a long-term Swiss clinical study on recurrence in affective disorder....

  12. On balanced minimal repeated measurements designs

    Directory of Open Access Journals (Sweden)

    Shakeel Ahmad Mir

    2014-10-01

    Full Text Available Repeated Measurements designs are concerned with scientific experiments in which each experimental unit is assigned more than once to a treatment either different or identical. This class of designs has the property that the unbiased estimators for elementary contrasts among direct and residual effects are obtainable. Afsarinejad (1983 provided a method of constructing balanced Minimal Repeated Measurements designs p < t , when t is an odd or prime power, one or more than one treatment may occur more than once in some sequences and  designs so constructed no longer remain uniform in periods. In this paper an attempt has been made to provide a new method to overcome this drawback. Specifically, two cases have been considered                RM[t,n=t(t-t/(p-1,p], λ2=1 for balanced minimal repeated measurements designs and  RM[t,n=2t(t-t/(p-1,p], λ2=2 for balanced  repeated measurements designs. In addition , a method has been provided for constructing              extra-balanced minimal designs for special case RM[t,n=t2/(p-1,p], λ2=1.

  13. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    Prakash

    2006-12-18

    Dec 18, 2006 ... Simple sequence repeats (SSRs) or microsatellites are the repetitive sequence motifs of 1–6 bp (Schlotterer 2000). They are scattered throughout the genomes of all the known organisms ranging from viruses to eukaryotes (Heller et al. 1982; Ellegren 2004). The origin, evolution and ubiquitous occurrence ...

  14. Preventing Repeat Teen Births PSA (:60)

    Centers for Disease Control (CDC) Podcasts

    2013-04-02

    This 60 second public service announcement is based on the April 2013 CDC Vital Signs report, which discusses repeat teen births and ways teens, parents and guardians, health care providers, and communities can help prevent them.  Created: 4/2/2013 by Centers for Disease Control and Prevention (CDC).   Date Released: 4/2/2013.

  15. Multivariate linear models and repeated measurements revisited

    DEFF Research Database (Denmark)

    Dalgaard, Peter

    2009-01-01

    Methods for generalized analysis of variance based on multivariate normal theory have been known for many years. In a repeated measurements context, it is most often of interest to consider transformed responses, typically within-subject contrasts or averages. Efficiency considerations leads to s...... method involving differences between orthogonal projections onto subspaces generated by within-subject models....

  16. Four Terminal Gallium Nitride MOSFETs

    Science.gov (United States)

    Veety, Matthew Thomas

    All reported gallium nitride (GaN) transistors to date have been three-terminal devices with source, drain, and gate electrodes. In the case of GaN MOSFETs, this leaves the bulk of the device at a floating potential which can impact device threshold voltage. In more traditional silicon-based MOSFET fabrication a bulk contact can be made on the back side of the silicon wafer. For GaN grown on sapphire substrates, however, this is not possible and an alternate, front-side bulk contact must be investigated. GaN is a III-V, wide band gap semiconductor that as promising material parameters for use in high frequency and high power applications. Possible applications are in the 1 to 10 GHz frequency band and power inverters for next generation grid solid state transformers and inverters. GaN has seen significant academic and commercial research for use in Heterojunction Field Effect Transistors (HFETs). These devices however are depletion-mode, meaning the device is considered "on" at zero gate bias. A MOSFET structure allows for enhancement mode operation, which is normally off. This mode is preferrable in high power applications as the device has lower off-state power consumption and is easier to implement in circuits. Proper surface passivation of seminconductor surface interface states is an important processing step for any device. Preliminary research on surface treatments using GaN wet etches and depletion-mode GaN devices utilizing this process are discussed. Devices pretreated with potassium pursulfate prior to gate dielectric deposition show significant device improvements. This process can be applied to any current GaN FET. Enhancement-mode GaN MOSFETs were fabricated on magnesium doped p-type Wurtzite gallium nitride grown by Metal Organic Chemical Vapor Deposition (MOCVD) on c-plane sapphire substrates. Devices utilized ion implant source and drain which was activated under NH3 overpressure in MOCVD. Also, devices were fabricated with a SiO2 gate dielectric

  17. An Axiomatization for the Terminal Cycle

    OpenAIRE

    Fokkink, W. J.

    1996-01-01

    Milner proposed an axiomatization for the Kleene star in basic process algebra, in the presence of deadlock and empty process, modulo bisimulation equivalence. In this paper, Milner's axioms are adapted to the terminal cycle xω, which executes x infinitely many times in a row, and it is shown that this axiomatization is complete for the terminal cycle in basic process algebra with deadlock and empty process modulo bisimulation.

  18. Termination of dependently typed rewrite rules

    OpenAIRE

    Jouannaud, Jean-Pierre; Li, Jian-Qi

    2015-01-01

    International audience; Our interest is in automated termination proofs of higher-order rewrite rules in presence of dependent types modulo a theory T on base types. We first describe an original transformation to a type discipline without type dependencies which preserves non-termination. Since the user must reason on expressions of the transformed language, we then introduce an extension of the computability path ordering CPO for comparing dependently typed expressions named DCPO. Using the...

  19. Size-change termination and transition invariants

    DEFF Research Database (Denmark)

    Heizmann, Matthias; Jones, Neil; Podelski, Andreas

    2010-01-01

    Two directions of recent work on program termination use the concepts of size-change termination resp. transition invariants. The difference in the setting has as consequence the inherent incomparability of the analysis and verification methods that result from this work. Yet, in order to facilit...... to facilitate the crossover of ideas and techniques in further developments, it seems interesting to identify which aspects in the respective formal foundation are related. This paper presents initial results in this direction....

  20. Transthoracic impedance does not decrease with rapidly repeated countershocks in a swine cardiac arrest model.

    Science.gov (United States)

    Niemann, James T; Garner, Daniel; Lewis, Roger J

    2003-01-01

    Successful defibrillation is dependent upon the delivery of adequate electrical current to the myocardium. One of the major determinant of current flow is transthoracic impedance. Prior work has suggested that impedance falls with repeated shocks during sinus rhythm. The purpose of this study was to evaluate changes in transthoracic impedance with repeated defibrillation shocks in an animal model of cardiac arrest due to ventricular fibrillation (VF). VF was electrically induced in anesthetized swine. After 5 min of untreated VF, monophasic or biphasic waveform defibrillation was attempted using a standard sequence of 'stacked shocks' (200, 300, then 360 J, if necessary) administered via adhesive electrodes. If one of the first three shocks failed to convert VF, conventional CPR was initiated and defibrillation (360 J) attempted 1 min later. Strength-duration curves for delivered voltage and current were measured during each shock and transthoracic impedance calculated. Animals requiring a minimum of four shocks were selected for study inclusion. Impedance data from sequential shocks were analyzed using mixed linear models to account for the repeated-measures design and the variability of the initial impedance of individual animals. Thirteen animals (monophasic waveform, n=7, biphasic waveform, n=6) required at least four shocks to terminate VF (range 4-6). Transthoracic impedance did not change from the first shock in the 13 animals (46+/-8 Omega) to the fourth shock (46+/-9 Omega). In animals receiving more than four shocks, transthoracic impedance likewise did not change significantly from the first to the last shock, which terminated VF. The lack of a significant change in impedance was also observed when animals were analyzed according to defibrillation waveform. Transthoracic impedance does not change significantly with repeated shocks in a VF cardiac arrest model. This is likely due to the lack of reactive skin and soft tissue hyperemia and edema observed in

  1. Inhibition of breast cancer cell proliferation in repeated and non-repeated treatment with zoledronic acid

    Directory of Open Access Journals (Sweden)

    Ibrahim Toni

    2012-11-01

    Full Text Available Abstract Background Zoledronic acid is used to treat bone metastases and has been shown to reduce skeletal-related events and exert antitumor activity. The present in vitro study investigates the mechanism of action of Zoledronic Acid on breast cancer cell lines with different hormonal and HER2 patterns. Furthermore, we investigated the efficacy of repeated versus non-repeated treatments. Methods The study was performed on 4 breast cancer cell lines (BRC-230, SkBr3, MCF-7 and MDA-MB-231. Non-repeated treatment (single exposure of 168 hrs’ duration with zoledronic acid was compared with repeated treatment (separate exposures, each of 48 hrs’ duration, for a total of 168 hrs at different dosages. A dose–response profile was generated using sulforhodamine B assay. Apoptosis was evaluated by TUNEL assay and biomolecular characteristics were analyzed by western blot. Results Zoledronic acid produced a dose-dependent inhibition of proliferation in all cell lines. Anti-proliferative activity was enhanced with the repeated treatment, proving to be statistically significant in the triple-negative lines. In these lines repeated treatment showed a cytocidal effect, with apoptotic cell death caused by caspase 3, 8 and 9 activation and decreased RAS and pMAPK expression. Apoptosis was not observed in estrogen receptor-positive line: p21 overexpression suggested a slowing down of cell cycle. A decrease in RAS and pMAPK expression was seen in HER2-overexpressing line after treatment. Conclusions The study suggests that zoledronic acid has an antitumor activity in breast cancer cell lines. Its mechanism of action involves the decrease of RAS and RHO, as in osteoclasts. Repeated treatment enhances antitumor activity compared to non-repeated treatment. Repeated treatment has a killing effect on triple-negative lines due to apoptosis activation. Further research is warranted especially in the treatment of triple-negative breast cancer.

  2. Identification of the ankyrin repeat proteins ANKRA and RFXANK as novel partners of class IIa histone deacetylases.

    Science.gov (United States)

    Wang, Audrey H; Grégoire, Serge; Zika, Eleni; Xiao, Lin; Li, Cathy S; Li, Hongwei; Wright, Kenneth L; Ting, Jenny P; Yang, Xiang-Jiao

    2005-08-12

    Eighteen human histone deacetylases (HDACs) have been identified, and according to their sequence similarity to yeast homologs, these enzymes are grouped into distinct classes. Within class II, HDAC4, HDAC5, HDAC7, and HDAC9 share similar domain organization both within the N-terminal extension and the C-terminal catalytic domain, thus forming a subclass known as class IIa. These HDACs function as signal-responsive transcriptional corepressors. To gain further insight into their function and regulation, we utilized an N-terminal fragment of HDAC4 as bait in yeast two-hybrid screens, which uncovered myocyte enhancer factor 2C, 14-3-3zeta, and ankyrin repeat family A protein (ANKRA). ANKRA is a poorly characterized protein with an ankyrin repeat domain similar to RFXANK, a subunit of the trimeric transcription factor RFX. Mutations on genes of the RFX subunits and the coactivator CIITA are responsible for the bare lymphocyte syndrome, an immunodeficiency disorder attributed to the lack of major histocompatibility complex class II (MHCII) antigens. Through its ankyrin repeat domain, RFXANK interacted with HDAC4. Two RFXANK-binding sites were found on HDAC4 with one located within residues 118-279 and another within residues 448-666. Interestingly, this deacetylase also interacted with CIITA. Consistent with the physical interaction with RFXANK and CIITA, HDAC4 and homologs repressed MHCII expression. These results identify ANKRA, RFXANK, and CIITA as novel targets of class IIa HDACs and suggest that these deacetylases play a role in regulating MHCII expression.

  3. Design of a "Mini" Nucleic Acid Probe for Cooperative Binding of an RNA-Repeated Transcript Associated with Myotonic Dystrophy Type 1.

    Science.gov (United States)

    Hsieh, Wei-Che; Bahal, Raman; Thadke, Shivaji A; Bhatt, Kirti; Sobczak, Krzysztof; Thornton, Charles; Ly, Danith H

    2018-01-19

    Toxic RNAs containing expanded trinucleotide repeats are the cause of many neuromuscular disorders, one being myotonic dystrophy type 1 (DM1). DM1 is triggered by CTG-repeat expansion in the 3'-untranslated region of the DMPK gene, resulting in a toxic gain of RNA function through sequestration of MBNL1 protein, among others. Herein, we report the development of a relatively short miniPEG-γ peptide nucleic acid probe, two triplet repeats in length, containing terminal pyrene moieties, that is capable of binding rCUG repeats in a sequence-specific and selective manner. The newly designed probe can discriminate the pathogenic rCUGexp from the wild-type transcript and disrupt the rCUGexp-MBNL1 complex. The work provides a proof of concept for the development of relatively short nucleic acid probes for targeting RNA-repeat expansions associated with DM1 and other related neuromuscular disorders.

  4. Incidence of Repeat Breeding Syndrome in Cattle from Four Local ...

    African Journals Online (AJOL)

    The study investigated the incidence of repeat breeding syndrome in cattle and determined the progesterone profile of repeat breeders in four Local Government Areas of Adamawa State, Nigeria. One hundred herds were sampled during the study and fifty-seven repeat breeders were identified. The proportions of repeat ...

  5. Antecedents and Consequences of Sales Representatives' Relationship Termination Competence

    DEFF Research Database (Denmark)

    Geersbro, Jens; Ritter, Thomas

    2013-01-01

    . The impact of the constructs "termination acceptance", "definition of non-customer", "termination routines" and "termination incentives" on termination competence are analyzed using PLS. Findings: A sales representative's termination competence is positively influenced by greater clarity and wider...... dissemination of the definition of a "non-customer", higher prevalence of termination routines, and increasing degrees of termination incentives. Acceptance of relationship termination at the firm level does not appear to have a significant impact on sales representatives' relationship termination competence......'s customer portfolio, managers must not only provide a clear definition of the types of customers the organization does not want to serve, but must also implement termination routines within the organization. Managers also need to establish incentives for sales representatives to terminate relationships...

  6. Repeated interactions in open quantum systems

    Energy Technology Data Exchange (ETDEWEB)

    Bruneau, Laurent, E-mail: laurent.bruneau@u-cergy.fr [Laboratoire AGM, Université de Cergy-Pontoise, Site Saint-Martin, BP 222, 95302 Cergy-Pontoise (France); Joye, Alain, E-mail: Alain.Joye@ujf-grenoble.fr [Institut Fourier, UMR 5582, CNRS-Université Grenoble I, BP 74, 38402 Saint-Martin d’Hères (France); Merkli, Marco, E-mail: merkli@mun.ca [Department of Mathematics and Statistics Memorial University of Newfoundland, St. John' s, NL Canada A1C 5S7 (Canada)

    2014-07-15

    Analyzing the dynamics of open quantum systems has a long history in mathematics and physics. Depending on the system at hand, basic physical phenomena that one would like to explain are, for example, convergence to equilibrium, the dynamics of quantum coherences (decoherence) and quantum correlations (entanglement), or the emergence of heat and particle fluxes in non-equilibrium situations. From the mathematical physics perspective, one of the main challenges is to derive the irreversible dynamics of the open system, starting from a unitary dynamics of the system and its environment. The repeated interactions systems considered in these notes are models of non-equilibrium quantum statistical mechanics. They are relevant in quantum optics, and more generally, serve as a relatively well treatable approximation of a more difficult quantum dynamics. In particular, the repeated interaction models allow to determine the large time (stationary) asymptotics of quantum systems out of equilibrium.

  7. Nonparametric additive regression for repeatedly measured data

    KAUST Repository

    Carroll, R. J.

    2009-05-20

    We develop an easily computed smooth backfitting algorithm for additive model fitting in repeated measures problems. Our methodology easily copes with various settings, such as when some covariates are the same over repeated response measurements. We allow for a working covariance matrix for the regression errors, showing that our method is most efficient when the correct covariance matrix is used. The component functions achieve the known asymptotic variance lower bound for the scalar argument case. Smooth backfitting also leads directly to design-independent biases in the local linear case. Simulations show our estimator has smaller variance than the usual kernel estimator. This is also illustrated by an example from nutritional epidemiology. © 2009 Biometrika Trust.

  8. Hypoglycaemic hemiplegia: a repeat SPECT study.

    Science.gov (United States)

    Shintani, S; Tsuruoka, S; Shiigai, T

    1993-01-01

    During a hypoglycaemic right hemiplegia induced by a deliberate overdose of oral hypoglycaemics, brain CT and angiography revealed no abnormalities. SPECTs made one day and six days later showed relative hypoperfusion in the left hemisphere. Repeat SPECT study suggested that the left hemisphere was more vulnerable than the right in the cerebral blood perfusion. This vulnerability might provoke the right hemiplegia in a critical condition, such as severe hypoglycaemia. Images PMID:8509788

  9. Repeated extraction of DNA from FTA cards

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Ferrero, Laura; Børsting, Claus

    2011-01-01

    Extraction of DNA using magnetic bead based techniques on automated DNA extraction instruments provides a fast, reliable and reproducible method for DNA extraction from various matrices. However, the yield of extracted DNA from FTA-cards is typically low. Here, we demonstrate that it is possible...... to repeatedly extract DNA from the processed FTA-disk. The method increases the yield from the nanogram range to the microgram range....

  10. 2D Metals by Repeated Size Reduction.

    Science.gov (United States)

    Liu, Hanwen; Tang, Hao; Fang, Minghao; Si, Wenjie; Zhang, Qinghua; Huang, Zhaohui; Gu, Lin; Pan, Wei; Yao, Jie; Nan, Cewen; Wu, Hui

    2016-10-01

    A general and convenient strategy for manufacturing freestanding metal nanolayers is developed on large scale. By the simple process of repeatedly folding and calendering stacked metal sheets followed by chemical etching, free-standing 2D metal (e.g., Ag, Au, Fe, Cu, and Ni) nanosheets are obtained with thicknesses as small as 1 nm and with sizes of the order of several micrometers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Repeatability and Workability Evaluation of SIGMOD 2011

    DEFF Research Database (Denmark)

    Bonnet, Philippe

    2011-01-01

    SIGMOD has offered, since 2008, to verify the experiments published in the papers accepted at the conference. This year, we have been in charge of reproducing the experiments provided by the authors (repeatability), and exploring changes to experiment parameters (workability). In this paper, we a...... find that most experiments are distributed as Linux packages accompanied by instructions on how to setup and run the experiments. We are still far from the vision of executable papers...

  12. Repeated Measurement of Divers’ Word Fluency.

    Science.gov (United States)

    1987-04-01

    side if necessary and identify by block number) WORD FLUENCY MEASUREMENT NEUROPSYCHOLOGY PSYCHOLOGY DIVING NAVSEA TASK NO. 86-54 SATURATION NEDU TEST...WORDS: <II Word Fluency--,, Neuropsychology’-" Diving Saturation Measurement Pyschology NAVSEA Task #86-54 NEDU Test Plan #86-10 v N. .,#7V REPEATED...function (Fillskov & Boll, -V 1981). One type of test with clinical significance reflects Word Fluency (Borkowski, Benton & Spreen, 1967; Lezak, 1983). Word

  13. Multiplexed Memory-Insensitive Quantum Repeaters

    OpenAIRE

    Collins, O. A.; Jenkins, S. D.; Kuzmich, A.; Kennedy, T. A. B.

    2006-01-01

    Long-distance quantum communication via distant pairs of entangled quantum bits (qubits) is the first step towards more secure message transmission and distributed quantum computing. To date, the most promising proposals require quantum repeaters to mitigate the exponential decrease in communication rate due to optical fiber losses. However, these are exquisitely sensitive to the lifetimes of their memory elements. We propose a multiplexing of quantum nodes that should enable the construction...

  14. Security of Quantum Repeater Network Operation

    Science.gov (United States)

    2016-10-03

    taxonomies for RFID tags, because both RFID tags and quantum links and nodes are sensitive to their local environment, and attacks at the physical level...vulnerable to being hacked . Thus, operation of the quantum repeater network is vulnerable to undetectable disruption of the network operation. This...Jogenfors, J., Elhassan, A. M., Ahrens, J., Bourennane, M., & Larsson, J. (2015). Hacking the Bell test using classical light in energy-time

  15. 25 CFR 11.1114 - Termination.

    Science.gov (United States)

    2010-04-01

    ... by the parents or guardian of the child. The petition shall state: (1) The name, birth date, and... abandoned; (ii) The minor has suffered physical injuries, willfully and repeatedly inflicted by his or her...

  16. Revisiting plus-strand DNA synthesis in retroviruses and long terminal repeat retrotransposons: dynamics of enzyme: substrate interactions.

    Science.gov (United States)

    Fabris, Daniele; Marino, John P; Le Grice, Stuart F J

    2009-12-01

    Although polypurine tract (PPT)-primed initiation of plus-strand DNA synthesis in retroviruses and LTR-containing retrotransposons can be accurately duplicated, the molecular details underlying this concerted series of events remain largely unknown. Importantly, the PPT 3' terminus must be accommodated by ribonuclease H (RNase H) and DNA polymerase catalytic centers situated at either terminus of the cognate reverse transcriptase (RT), and in the case of the HIV-1 enzyme, ∼70Å apart. Communication between RT and the RNA/DNA hybrid therefore appears necessary to promote these events. The crystal structure of the HIV-1 RT/PPT complex, while informative, positions the RNase H active site several bases pairs from the PPT/U3 junction, and thus provides limited information on cleavage specificity. To fill the gap between biochemical and crystallographic approaches, we review a multidisciplinary approach combining chemical probing, mass spectrometry, NMR spectroscopy and single molecule spectroscopy. Our studies also indicate that nonnucleoside RT inhibitors affect enzyme orientation, suggesting initiation of plus-strand DNA synthesis as a potential therapeutic target.

  17. Revisiting Plus-Strand DNA Synthesis in Retroviruses and Long Terminal Repeat Retrotransposons: Dynamics of Enzyme: Substrate Interactions

    Directory of Open Access Journals (Sweden)

    Stuart F. J. Le Grice

    2009-11-01

    Full Text Available Although polypurine tract (PPT-primed initiation of plus-strand DNA synthesis in retroviruses and LTR-containing retrotransposons can be accurately duplicated, the molecular details underlying this concerted series of events remain largely unknown. Importantly, the PPT 3’ terminus must be accommodated by ribonuclease H (RNase H and DNA polymerase catalytic centers situated at either terminus of the cognate reverse transcriptase (RT, and in the case of the HIV-1 enzyme, ~70Å apart. Communication between RT and the RNA/DNA hybrid therefore appears necessary to promote these events. The crystal structure of the HIV-1 RT/PPT complex, while informative, positions the RNase H active site several bases pairs from the PPT/U3 junction, and thus provides limited information on cleavage specificity. To fill the gap between biochemical and crystallographic approaches, we review a multidisciplinary approach combining chemical probing, mass spectrometry, NMR spectroscopy and single molecule spectroscopy. Our studies also indicate that nonnucleoside RT inhibitors affect enzyme orientation, suggesting initiation of plus-strand DNA synthesis as a potential therapeutic target.

  18. Multiplexing schemes for quantum repeater networks

    Science.gov (United States)

    Aparicio, Luciano; Van Meter, Rodney

    2011-08-01

    When built, quantum repeaters will allow the distribution of entangled quantum states across large distances, playing a vital part in many proposed quantum technologies. Enabling multiple users to connect through the same network will be key to their real-world deployment. Previous work on repeater technologies has focussed only on simple entanglment production, without considering the issues of resource scarcity and competition that necessarily arise in a network setting. In this paper we simulated a thirteen-node network with up to five flows sharing different parts of the network, measuring the total throughput and fairness for each case. Our results suggest that the Internet-like approach of statistical multiplexing use of a congested link gives the highest aggregate throughput. Time division multiplexing and buffer space multiplexing were slightly less effective, but all three schemes allow the sum of multiple flows to substantially exceed that of any one flow, improving over circuit switching by taking advantage of resources that are forced to remain idle in circuit switching. All three schemes proved to have excellent fairness. The high performance, fairness and simplicity of implementation support a recommendation of statistical multiplexing for shared quantum repeater networks.

  19. Gait termination in individuals with multiple sclerosis.

    Science.gov (United States)

    Roeing, Kathleen L; Wajda, Douglas A; Motl, Robert W; Sosnoff, Jacob J

    2015-09-01

    Despite the ubiquitous nature of gait impairment in multiple sclerosis (MS), there is limited information concerning the control of gait termination in individuals with MS. The purpose of this investigation was to examine planned gait termination in individuals with MS and healthy controls with and without cognitive distractors. Individuals with MS and age matched controls completed a series of gait termination tasks over a pressure sensitive walkway under non-distracting and cognitively distracting conditions. As expected the MS group had a lower velocity (89.9±33.3 cm/s) than controls (142.8±22.4 cm/s) and there was a significant reduction in velocity in both groups under the cognitive distracting conditions (MS: 73.9±30.7 cm/s; control: 120.0±25.9 cm/s). Although individuals with MS walked slower, there was no difference between groups in the rate a participant failed to stop at the target (i.e. failure rate). Overall failure rate had a 10-fold increase in the cognitively distracting condition across groups. Individuals with MS were more unstable during termination. Future research examining the neuromuscular mechanisms contributing to gait termination is warranted. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Terminal addition in a cellular world.

    Science.gov (United States)

    Torday, J S; Miller, William B

    2017-12-19

    Recent advances in our understanding of evolutionary development permit a reframed appraisal of Terminal Addition as a continuous historical process of cellular-environmental complementarity. Within this frame of reference, evolutionary terminal additions can be identified as environmental induction of episodic adjustments to cell-cell signaling patterns that yield the cellular-molecular pathways that lead to differing developmental forms. Phenotypes derive, thereby, through cellular mutualistic/competitive niche constructions in reciprocating responsiveness to environmental biophysical stresses and epigenetic impacts. In such terms, Terminal Addition flows according to a logic of cellular needs confronting environmental challenges over space-time. A reconciliation of evolutionary development and Terminal Addition can be achieved through a combined focus on cell-cell signaling, molecular phylogenies and a broader understanding of epigenetic phenomena among eukaryotic organisms. When understood in this manner, Terminal Addition has an important role in evolutionary development, and chronic disease might be considered as a form of 'reverse evolution' of the self-same processes. Copyright © 2017. Published by Elsevier Ltd.

  1. A Unified Model for Repeating and Non-repeating Fast Radio Bursts

    Energy Technology Data Exchange (ETDEWEB)

    Bagchi, Manjari, E-mail: manjari@imsc.res.in [The Institute of Mathematical Sciences (IMSc-HBNI), 4th Cross Road, CIT Campus, Taramani, Chennai 600113 (India)

    2017-04-01

    The model that fast radio bursts (FRBs) are caused by plunges of asteroids onto neutron stars can explain both repeating and non-repeating bursts. If a neutron star passes through an asteroid belt around another star, there would be a series of bursts caused by a series of asteroid impacts. Moreover, the neutron star would cross the same belt repetitively if it were in a binary with the star hosting the asteroid belt, leading to a repeated series of bursts. I explore the properties of neutron star binaries that could lead to the only known repeating FRB so far (FRB121102). In this model, the next two epochs of bursts are expected around 2017 February 27 and 2017 December 18. On the other hand, if the asteroid belt is located around the neutron star itself, then a chance fall of an asteroid from that belt onto the neutron star would lead to a non-repeating burst. Even a neutron star grazing an asteroid belt can lead to a non-repeating burst caused by just one asteroid plunge during the grazing. This is possible even when the neutron star is in a binary with the asteroid-hosting star, if the belt and the neutron star orbit are non-coplanar.

  2. Stalled DNA Replication Forks at the Endogenous GAA Repeats Drive Repeat Expansion in Friedreich's Ataxia Cells.

    Science.gov (United States)

    Gerhardt, Jeannine; Bhalla, Angela D; Butler, Jill Sergesketter; Puckett, James W; Dervan, Peter B; Rosenwaks, Zev; Napierala, Marek

    2016-08-02

    Friedreich's ataxia (FRDA) is caused by the expansion of GAA repeats located in the Frataxin (FXN) gene. The GAA repeats continue to expand in FRDA patients, aggravating symptoms and contributing to disease progression. The mechanism leading to repeat expansion and decreased FXN transcription remains unclear. Using single-molecule analysis of replicated DNA, we detected that expanded GAA repeats present a substantial obstacle for the replication machinery at the FXN locus in FRDA cells. Furthermore, aberrant origin activation and lack of a proper stress response to rescue the stalled forks in FRDA cells cause an increase in 3'-5' progressing forks, which could enhance repeat expansion and hinder FXN transcription by head-on collision with RNA polymerases. Treatment of FRDA cells with GAA-specific polyamides rescues DNA replication fork stalling and alleviates expansion of the GAA repeats, implicating DNA triplexes as a replication impediment and suggesting that fork stalling might be a therapeutic target for FRDA. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  3. Glider and Vision: two new families of miniature inverted-repeat transposable elements in Xenopus laevis genome.

    Science.gov (United States)

    Lepetit, D; Pasquet, S; Olive, M; Thézé, N; Thiébaud, P

    2000-01-01

    We have characterised from Xenopus laevis two new short interspersed repetitive elements, we have named Glider and Vision, that belong to the family of miniature inverted-repeat transposable elements (MITEs). Glider was first characterised in an intronic region of the alpha-tropomyosin (alpha-TM) gene and database search has revealed the presence of this element in 10 other Xenopus laevis genes. Glider elements are about 150 bp long and for some of them, their terminal inverted repeats are flanked by potential target-site duplications. Evidence for the mobility of Glider element has been provided by the presence/absence of one element at corresponding location in duplicated alpha-TM genes. Vision element has been identified in the promoter region of the cyclin dependant kinase 2 gene (cdk2) where it is boxed in a Glider element. Vision is 284bp long and is framed by 14-bp terminal inverted repeats that are flanked by 7-bp direct repeats. We have estimated that there are about 20,000 and 300 copies of Glider and Vision respectively scattered throughout the Xenopus laevis genome. Every MITEs elements but two described in our study are found either in 5' or in 3' regulatory regions of genes suggesting a potential role in gene regulation.

  4. Repeated buckling of composite shear panels

    Science.gov (United States)

    Singer, Josef; Weller, Tanchum

    1990-01-01

    Failures in service of aerospace structures and research at the Technion Aircraft Structures Laboratory have revealed that repeatedly buckled stiffened shear panels might be susceptible to premature fatigue failures. Extensive experimental and analytical studies have been performed at Technion on repeated buckling, far in excess of initial buckling, for both metal and composite shear panels with focus on the influence of the surrounding structure. The core of the experimental investigation consisted of repeated buckling and postbuckling tests on Wagner beams in a three-point loading system under realistic test conditions. The effects of varying sizes of stiffeners, of the magnitude of initial buckling loads, of the panel aspect ratio and of the cyclic shearing force, V sub cyc, were studied. The cyclic to critical shear buckling ratios, (V sub cyc/V sub cr) were on the high side, as needed for efficient panel design, yet all within possible flight envelopes. The experiments were supplemented by analytical and numerical analyses. For the metal shear panels the test and numerical results were synthesized into prediction formulas, which relate the life of the metal shear panels to two cyclic load parameters. The composite shear panels studied were hybrid beams with graphite/epoxy webs bonded to aluminum alloy frames. The test results demonstrated that composite panels were less fatigue sensitive than comparable metal ones, and that repeated buckling, even when causing extensive damage, did not reduce the residual strength by more than 20 percent. All the composite panels sustained the specified fatigue life of 250,000 cycles. The effect of local unstiffened holes on the durability of repeatedly buckled shear panels was studied for one series of the metal panels. Tests on 2024 T3 aluminum panels with relatively small unstiffened holes in the center of the panels demonstrated premature fatigue failure, compared to panels without holes. Preliminary tests on two graphite

  5. 76 FR 4364 - Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval

    Science.gov (United States)

    2011-01-25

    ... URBAN DEVELOPMENT Credit Watch Termination Initiative; Termination of Direct Endorsement (DE) Approval..., Department of Housing and Urban Development, 451 Seventh Street, SW., Room B133-P3214, Washington, DC 20410.... NTFN Inc 5301 Village Creek Oklahoma City.... 11/26/10 Denver. Dr., Ste B, Plano, TX 75093. Pine State...

  6. Effects of Repeated Ropinirole Treatment on Phencyclidine-Induced Hyperlocomotion, Prepulse Inhibition Deficits, and Social Avoidance in Rats.

    Science.gov (United States)

    Maple, Amanda M; Call, Tanessa; Kimmel, Phylicia C; Hammer, Ronald P

    2017-04-01

    Phencyclidine (PCP), a noncompetitive N-methyl d-aspartate (NMDA) receptor antagonist, provides the most complete pharmacologic model of schizophrenia in humans and animals. Acute PCP causes hyperlocomotion, disrupts prepulse inhibition (PPI), and increases social avoidance in rats. We have previously shown that repeated treatment with the dopamine (DA) D2-like receptor agonists, quinpirole or ropinirole, prevents agonist-induced PPI disruption. In the present study, we examined whether repeated ropinirole treatment similarly attenuates the effects of PCP in a more complete model of schizophrenia symptoms and examined the effect of repeated D2-like agonist treatment on locomotion, PPI, and social interaction after acute PCP challenge. The acute effect of PCP (3.0 or 6.0 mg/kg) on locomotor activity was examined to establish a minimum effective dose. Thereafter, the effect of PCP challenge (3.0 mg/kg) on locomotor activity, PPI, and social interaction was assessed in adult male rats before or 7-10 days after termination of repeated daily treatment with ropinirole (0.1 mg/kg) or saline vehicle (0.1 ml/kg) for 28 days. Repeated ropinirole treatment attenuates PCP-induced hyperlocomotion, PPI deficits, and social avoidance. These findings suggest that repeated ropinirole treatment might affect a final common pathway that is vulnerable to both PCP- and dopamine agonist-induced behavioral disruption, thereby providing an alternative approach to block the effects of PCP. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

  7. Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance.

    Science.gov (United States)

    Cervantes, Carla F; Markwick, Phineus R L; Sue, Shih-Che; McCammon, J Andrew; Dyson, H Jane; Komives, Elizabeth A

    2009-08-25

    Inhibition of nuclear factor kappaB (NF-kappaB) is mainly accomplished by IkappaB alpha, which consists of a signal response sequence at the N-terminus, a six-ankyrin repeat domain (ARD) that binds NF-kappaB, and a C-terminal PEST sequence. Previous studies with the ARD revealed that the fifth and sixth repeats are only partially folded in the absence of NF-kappaB. Here we report NMR studies of a truncated version of IkappaB alpha, containing only the first four ankyrin repeats, IkappaB alpha(67-206). This four-repeat segment is well-structured in the free state, enabling full resonance assignments to be made. H-D exchange, backbone dynamics, and residual dipolar coupling (RDC) experiments reveal regions of flexibility. In addition, regions consistent with the presence of micro- to millisecond motions occur periodically throughout the repeat structure. Comparison of the RDCs with the crystal structure gave only moderate agreement, but an ensemble of structures generated by accelerated molecular dynamics gave much better agreement with the measured RDCs. The regions showing flexibility correspond to those implicated in entropic compensation for the loss of flexibility in ankyrin repeats 5 and 6 upon binding to NF-kappaB. The regions showing micro- to millisecond motions in the free protein are the ends of the beta-hairpins that directly interact with NF-kappaB in the complex.

  8. Termination Criteria for Computerized Classification Testing

    Directory of Open Access Journals (Sweden)

    Nathan A. Thompson

    2011-02-01

    Full Text Available Computerized classification testing (CCT is an approach to designing tests with intelligent algorithms, similar to adaptive testing, but specifically designed for the purpose of classifying examinees into categories such as - pass- and - fail.- Like adaptive testing for point estimation of ability, the key component is the termination criterion, namely the algorithm that decides whether to classify the examinee and end the test or to continue and administer another item. This paper applies a newly suggested termination criterion, the generalized likelihood ratio (GLR, to CCT. It also explores the role of the indifference region in the specification of likelihood-ratio based termination criteria, comparing the GLR to the sequential probability ratio test. Results from simulation studies suggest that the GLR is always at least as efficient as existing methods.

  9. Three-Terminal Amorphous Silicon Solar Cells

    Directory of Open Access Journals (Sweden)

    Cheng-Hung Tai

    2011-01-01

    Full Text Available Many defects exist within amorphous silicon since it is not crystalline. This provides recombination centers, thus reducing the efficiency of a typical a-Si solar cell. A new structure is presented in this paper: a three-terminal a-Si solar cell. The new back-to-back p-i-n/n-i-p structure increased the average electric field in a solar cell. A typical a-Si p-i-n solar cell was also simulated for comparison using the same thickness and material parameters. The 0.28 μm-thick three-terminal a-Si solar cell achieved an efficiency of 11.4%, while the efficiency of a typical a-Si p-i-n solar cell was 9.0%. Furthermore, an efficiency of 11.7% was achieved by thickness optimization of the three-terminal solar cell.

  10. 22 CFR 42.83 - Termination of registration.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Termination of registration. 42.83 Section 42... IMMIGRATION AND NATIONALITY ACT, AS AMENDED Refusal, Revocation, and Termination of Registration § 42.83 Termination of registration. (a) Termination following failure of applicant to apply for visa. In accordance...

  11. 47 CFR 68.610 - Database of terminal equipment.

    Science.gov (United States)

    2010-10-01

    ... Attachments § 68.610 Database of terminal equipment. (a) The Administrative Council for Terminal Attachments... Administrative Council for Terminal Attachments shall ensure that the database is created and maintained in an... how the Administrative Council for Terminal Attachments will administer the database, the pertinent...

  12. Fuzzy containers allocation problem in maritime terminal

    Directory of Open Access Journals (Sweden)

    Seyed-Mohammad Seyed-Hosseini

    2009-09-01

    Full Text Available Normal.dotm 0 0 1 140 799 UPC 6 1 981 12.0 0 false 18 pt 18 pt 0 0 false false false /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:??; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Containers allocation in terminals has attracted lots of research works due to practical & theoretical importance in transportation literature. In this paper, we developed a fuzzy mathematical programming model for solving problem of allocating the containers in terminal area. The objective is minimizing the total distance traversed by the containers from the ship to the terminal area they are assigned. Fuzzy set concepts are used to treat imprecision regarding the distances between berth and terminals area, number of containers in an arrived ship and estimation of available area in each terminal at a port. We proposed two types of models for optimistic and pessimistic situations. The proposed models have been coded in LINGO8.0 solver and a numerical example has been solved for illustration purpose. The full analysis of the proposed models can cause an optimum allocation of containers of several ships to different terminals of berths in fuzzy environment.

  13. Nueva terminal del aeropuerto de Barcelona

    Directory of Open Access Journals (Sweden)

    Bofill, Ricardo

    1992-02-01

    Full Text Available The lack of integral and modernized design and the saturation of the Barcelona Airport made the remodelling of the old terminal building necessary. The old building elements conditioned the lineal solution in the remodelling. An elevated street forms the backbone of the building which, like the Ramblas in Barcelona, has shops, news stands, etc. Other new elements are the pre-boarding modules and the International terminal. The former have a glazed gallery in their perimeter: a transparent division which allows the separation of the arrival and departure flows. The new terminal rests on four large columns and has double glazing in the entire perimeter

    Ante la saturación y falta de diseño unitario y actualizado del Aeropuerto de Barcelona se aborda la remodelación del antiguo edificio terminal. La situación de los antiguos elementos de edificación, condiciona la solución lineal de la misma. Una calle elevada es la espina dorsal del edificio que al modo de las Ramblas de Barcelona ofrecen comercios, kioscos, etc. Los otros nuevos elementos de edificación son los módulos de preembarque y la terminal de Internacional. Los primeros tienen una galería acristalada en su perímetro: una división transparente que permite separar los flujos de llegadas y salidas. La nueva terminal, se apoya sobre cuatro grandes columnas, y está dotada de un doble acristalamiento en todo su perímetro.

  14. Rational suicide in the terminally ill.

    Science.gov (United States)

    Fontana, Joyce S

    2002-01-01

    To examine the current debate over the right to die specific to the rational suicide of terminally ill patients. Literature was reviewed for information concerning historical end-of-life practices and the past acceptance of suicide. Another review showed philosophical opinions and perspectives that spanned from ancient Greece and the Roman Empire to modern philosophical discourse. A case study of a terminally ill woman who chose suicide is presented to apply the history and philosophy to nursing care today. As more nursing care is delivered in patients' homes, nurses will face this situation with increasing frequency. A call is made for organizations to provide guidelines for nursing practice.

  15. Terminating a long-term clinical trial.

    Science.gov (United States)

    Klimt, C R

    1981-05-01

    Long-term clinical trials often include more than one active treatment group. These may be discontinued independently if found to be ineffective or possibly harmful. Certain subgroups of patients may be discovered, in the course of a clinical trial, who do not respond satisfactorily and are, therefore, excluded during the course of a trial. Yet another kind of termination comes when we have a therapeutic breakthrough or when hope has to be abandoned for demonstrating beneficial effects for one, several, or all treatments included in a trial. Examples from the authors' experience are presented, as are successful and unsuccessful techniques in managing terminations of various types.

  16. Enhancing data locality by using terminal propagation

    Energy Technology Data Exchange (ETDEWEB)

    Hendrickson, B.; Leland, R. [Sandia National Labs., Albuquerque, NM (United States); Van Driessche, R. [Katholieke Univ. Leuven (Belgium). Dept. Computer Sciences

    1995-12-31

    Terminal propagation is a method developed in the circuit placement community for adding constraints to graph partitioning problems. This paper adapts and expands this idea, and applies it to the problem of partitioning data structures among the processors of a parallel computer. We show how the constraints in terminal propagation can be used to encourage partitions in which messages are communicated only between architecturally near processors. We then show how these constraints can be handled in two important partitioning algorithms, spectral bisection and multilevel-KL. We compare the quality of partitions generated by these algorithms to each other and to Partitions generated by more familiar techniques.

  17. OPTIMAL GOODS STOWAGE IN AIR CARGO TERMINALS

    Directory of Open Access Journals (Sweden)

    Gennadiy Yun

    2011-03-01

    Full Text Available Abstract. Lack of system research done by domestic and foreign scientists in the field of optimal cargostraffic distribution problem in Air Cargo Terminal, proves necessity of investigation and optimization of thisprocess. Mathematical models and algorithms of optimal problem solving for air cargos distribution inwarehouses on the basis of established functional dependence between freight flow stowage in warehousesand transport vehicle loading (unloading processes are presented in the article.Keywords:algorithms, dimensions of air cargo terminal, effectiveness of loading-unloading processes,freight flow, models.

  18. Size-change termination and bound analysis

    DEFF Research Database (Denmark)

    Avery, James Emil

    2006-01-01

    Despite its simplicity, the size-change termination principle, presented by Lee, Jones and Ben-Amram in [LJB01], is surprisingly strong and is able to show termination for a large class of programs. A significant limitation for its use, however, is the fact that the SCT requires data types to be ...... implemented in a subject language independent shared library, libesct (available at http://esct.kvante.org), as well as for the ANSI C specializer C-Mix/ii, handling a subset of its internal language Core-C....

  19. Advancing land-terminating ice cliffs in Northwest Greenland

    Science.gov (United States)

    Prinz, Rainer; Abermann, Jakob; Steiner, Jakob

    2017-04-01

    Land-terminating ice cliffs are intriguing features that occur in various ice-covered regions around the world both in high and low latitudes. Over flat terrain land-terminating ice cliffs can only persist under a complex interplay between certain climatic and ice dynamic conditions with "cold" and "dry" being the common pillars for their occurrence. In North Greenland, dry calving ice cliffs are an abundant feature, however, to our knowledge, detailed investigations are limited to studies more than six decades ago in the Thule area. Rough estimates state that approximately 45% of the ice sheet in Northwest Greenland terminate as cliffs on land. The ice cliff position and its change with time is a combined signal of the ice flow and mass balance at the cliff. The ice flow is triggered by a mass imbalance upstream the ice cliff integrating a potentially long response time, basal sliding and ice deformation, whereas the mass balance of the ice cliff is determined by the sum of the energy fluxes at the cliff face and the calving flux. Studies during the 1950s and 1960s report counterintuitive results with a generally negative mass balance and a reduction of ice cliff height versus a net advance of the cliff. This intriguing evolvement warrants closer attention as it remained unstudied thereafter even though it is likely relevant for a large portion of cold and dry North Greenland. Thus, the purpose of this contribution is to build a relevant basis for future process studies by (i) determining the occurrence of ice cliffs in Northern Greenland, (ii) classifying them by obvious morphological distinctions such as height and steepness and (iii) give a first-order estimate on percentage of advancing vs retreating areas. Repeating the past study above using recent space-borne earth observation data (digital elevation models from 1985, 2007 and 2015) we mapped the evolution of the ice sheet margin. Results at the same cliff and at another independent location in Northwest

  20. Conformational change-induced repeat domain expansion regulates Rap phosphatase quorum-sensing signal receptors.

    Directory of Open Access Journals (Sweden)

    Vijay Parashar

    Full Text Available The large family of Gram-positive quorum-sensing receptors known as the RNPP proteins consists of receptors homologous to the Rap, NprR, PlcR, and PrgX proteins that are regulated by imported oligopeptide autoinducers. Rap proteins are phosphatases and transcriptional anti-activators, and NprR, PlcR, and PrgX proteins are DNA binding transcription factors. Despite their obvious importance, the mechanistic basis of oligopeptide receptor regulation is largely unknown. Here, we report the X-ray crystal structure of the Bacillus subtilis quorum-sensing receptor RapJ in complex with the centrally important oligopeptide autoinducer competence and sporulation factor (CSF, also termed PhrC, a member of the Phr family of quorum-sensing signals. Furthermore, we present the crystal structure of RapI. Comparison of the RapJ-PhrC, RapI, RapH-Spo0F, and RapF-ComA(C crystal structures reveals the mechanistic basis of Phr activity. More specifically, when complexed with target proteins, Rap proteins consist of a C-terminal tetratricopeptide repeat (TPR domain connected by a flexible helix-containing linker to an N-terminal 3-helix bundle. In the absence of a target protein or regulatory peptide, the Rap protein 3-helix bundle adopts different conformations. However, in the peptide-bound conformation, the Rap protein N-terminal 3-helix bundle and linker undergo a radical conformational change, form TPR-like folds, and merge with the existing C-terminal TPR domain. To our knowledge, this is the first example of conformational change-induced repeat domain expansion. Furthermore, upon Phr binding, the entire Rap protein is compressed along the TPR superhelical axis, generating new intramolecular contacts that lock the Rap protein in an inactive state. The fact that Rap proteins are conformationally flexible is surprising considering that it is accepted dogma that TPR proteins do not undergo large conformational changes. Repeat proteins are widely used as scaffolds

  1. Storage Allocation in Automated Container Terminals: the Upper Level

    OpenAIRE

    Mengjue Xia; Ning Zhao; Weijian Mi

    2016-01-01

    Nowadays automation is a trend of container terminals all over the world. Although not applied in current automated container terminals, storage allocation is indispensable in conventional container terminals, and promising for automated container terminals in future. This paper seeks into the storage allocation problem in automated container terminals and proposed a two level structure for the problem. A mixed integer programming model is built for the upper level, and a modified Particle Sw...

  2. 47 CFR 25.134 - Licensing provisions of Very Small Aperture Terminal (VSAT) and C-band Small Aperture Terminal...

    Science.gov (United States)

    2010-10-01

    ... Terminal (VSAT) and C-band Small Aperture Terminal (CSAT) networks. 25.134 Section 25.134 Telecommunication... Applications and Licenses Earth Stations § 25.134 Licensing provisions of Very Small Aperture Terminal (VSAT) and C-band Small Aperture Terminal (CSAT) networks. (a)(1) VSAT networks operating in the 12/14 GHz...

  3. Repeated-sprint ability and aerobic fitness.

    Science.gov (United States)

    Thébault, Nicolas; Léger, Luc A; Passelergue, Philippe

    2011-10-01

    The purpose of this study was to reinvestigate the relationship between aerobic fitness and fatigue indices of repeated-sprint ability (RSA), with special attention to methodological normalization. Soldiers were divided into low (n = 10) and high (n = 9) fitness groups according to a preset maximal aerobic speed (MAS) of 17 km·h(-1) (∼60 ml O2·kg(-1)·min) measured with the University of Montreal Track Test (UMTT). Subjects' assessment included the RSA test (3 sets of 5 40-m sprints with 1-minute rest between sprints and 1.5 minutes between sets), a 40-m sprint (criterion test used in the computation of fatigue indices for the RSA test), strength and power measurement of the lower limbs, and the 20-m shuttle run test (20-m SRT) and the UMTT, which are measures of maximal aerobic power. The highest correlation with the RSA fatigue indices was obtained with the 20-m SRT (r = 0.90, p = 0.0001, n = 19), a test with 180° direction changes and accelerations and decelerations. The lower correlation (r = 0.66, p tests better disclose the importance of aerobic fitness for RSA and that aerobic power is not the sole determinant of RSA. However, neither strength nor vertical jumping power was correlated to the RSA fatigue indices. Subjects with greater MAS were able to maintain almost constant level of speed throughout series of repeated sprints and achieved better recovery between series. A MAS of at least 17 km·h(-1) favors constant and high speed level during repeated sprints. From a practical point of view, a high aerobic fitness is a precious asset in counteracting fatigue in sports with numerous sprint repetitions.

  4. Identifying uniformly mutated segments within repeats.

    Science.gov (United States)

    Sahinalp, S Cenk; Eichler, Evan; Goldberg, Paul; Berenbrink, Petra; Friedetzky, Tom; Ergun, Funda

    2004-12-01

    Given a long string of characters from a constant size alphabet we present an algorithm to determine whether its characters have been generated by a single i.i.d. random source. More specifically, consider all possible n-coin models for generating a binary string S, where each bit of S is generated via an independent toss of one of the n coins in the model. The choice of which coin to toss is decided by a random walk on the set of coins where the probability of a coin change is much lower than the probability of using the same coin repeatedly. We present a procedure to evaluate the likelihood of a n-coin model for given S, subject a uniform prior distribution over the parameters of the model (that represent mutation rates and probabilities of copying events). In the absence of detailed prior knowledge of these parameters, the algorithm can be used to determine whether the a posteriori probability for n=1 is higher than for any other n>1. Our algorithm runs in time O(l4logl), where l is the length of S, through a dynamic programming approach which exploits the assumed convexity of the a posteriori probability for n. Our test can be used in the analysis of long alignments between pairs of genomic sequences in a number of ways. For example, functional regions in genome sequences exhibit much lower mutation rates than non-functional regions. Because our test provides means for determining variations in the mutation rate, it may be used to distinguish functional regions from non-functional ones. Another application is in determining whether two highly similar, thus evolutionarily related, genome segments are the result of a single copy event or of a complex series of copy events. This is particularly an issue in evolutionary studies of genome regions rich with repeat segments (especially tandemly repeated segments).

  5. Repeatability and Reproducibility of Virtual Subjective Refraction.

    Science.gov (United States)

    Perches, Sara; Collados, M Victoria; Ares, Jorge

    2016-10-01

    To establish the repeatability and reproducibility of a virtual refraction process using simulated retinal images. With simulation software, aberrated images corresponding with each step of the refraction process were calculated following the typical protocol of conventional subjective refraction. Fifty external examiners judged simulated retinal images until the best sphero-cylindrical refraction and the best visual acuity were achieved starting from the aberrometry data of three patients. Data analyses were performed to assess repeatability and reproducibility of the virtual refraction as a function of pupil size and aberrometric profile of different patients. SD values achieved in three components of refraction (M, J0, and J45) are lower than 0.25D in repeatability analysis. Regarding reproducibility, we found SD values lower than 0.25D in the most cases. When the results of virtual refraction with different pupil diameters (4 and 6 mm) were compared, the mean of differences (MoD) obtained were not clinically significant (less than 0.25D). Only one of the aberrometry profiles with high uncorrected astigmatism shows poor results for the M component in reproducibility and pupil size dependence analysis. In all cases, vision achieved was better than 0 logMAR. A comparison between the compensation obtained with virtual and conventional subjective refraction was made as an example of this application, showing good quality retinal images in both processes. The present study shows that virtual refraction has similar levels of precision as conventional subjective refraction. Moreover, virtual refraction has also shown that when high low order astigmatism is present, the refraction result is less precise and highly dependent on pupil size.

  6. Mechanical processes with repeated attenuated impacts

    CERN Document Server

    Nagaev, R F

    1999-01-01

    This book is devoted to considering in the general case - using typical concrete examples - the motion of machines and mechanisms of impact and vibro-impact action accompanied by a peculiar phenomenon called "impact collapse". This phenomenon is that after the initial collision, a sequence of repeated gradually quickening collisions of decreasing-to-zero intensity occurs, with the final establishment of protracted contact between the interacting bodies. The initiation conditions of the impact collapse are determined and calculation techniques for the quantitative characteristics of the corresp

  7. Costly renegotiation in repeated Bertand games

    DEFF Research Database (Denmark)

    Andersson, Ola; Wengström, Erik Roland

    2010-01-01

    This paper extends the concept of weak renegotiation-proof equilibrium (WRP) to allow for costly renegotiation and shows that even small renegotiation costs can have dramatic effects on the set of equilibria. More specifically, the paper analyzes the infinitely repeated Bertrand game. It is shown...... that for every level of renegotiation cost, there exists a discount factor such that any collusive profit can be supported as an equilibrium outcome. Hence, any arbitrary small renegotiation cost will suffice to facilitate collusive outcomes for sufficiently patient firms. This result stands in stark contrast...

  8. Repeat Sequence Proteins as Matrices for Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Drummy, L.; Koerner, H; Phillips, D; McAuliffe, J; Kumar, M; Farmer, B; Vaia, R; Naik, R

    2009-01-01

    Recombinant protein-inorganic nanocomposites comprised of exfoliated Na+ montmorillonite (MMT) in a recombinant protein matrix based on silk-like and elastin-like amino acid motifs (silk elastin-like protein (SELP)) were formed via a solution blending process. Charged residues along the protein backbone are shown to dominate long-range interactions, whereas the SELP repeat sequence leads to local protein/MMT compatibility. Up to a 50% increase in room temperature modulus and a comparable decrease in high temperature coefficient of thermal expansion occur for cast films containing 2-10 wt.% MMT.

  9. Adeno-Associated Virus (AAV) Type 5 Rep Protein Cleaves a Unique Terminal Resolution Site Compared with Other AAV Serotypes

    OpenAIRE

    Chiorini, John A.; Afione, Sandra; Kotin, Robert M

    1999-01-01

    Adeno-associated virus (AAV) replication depends on two viral components for replication: the AAV nonstructural proteins (Rep) in trans, and inverted terminal repeat (ITR) sequences in cis. AAV type 5 (AAV5) is a distinct virus compared to the other cloned AAV serotypes. Whereas the Rep proteins and ITRs of other serotypes are interchangeable and can be used to produce recombinant viral particles of a different serotype, AAV5 Rep proteins cannot cross-complement in the packaging of a genome w...

  10. Anxiety in Terminally Ill Cancer Patients

    Science.gov (United States)

    Kolva, Elissa; Rosenfeld, Barry; Pessin, Hayley; Breitbart, William; Brescia, Robert

    2011-01-01

    Context Anxiety in terminal cancer is linked to diminished quality of life, yet overall it is poorly understood with regard to prevalence and relationship to other aspects of psychological distress. Objectives This study examines anxiety in terminally ill cancer patients, including the prevalence of anxiety symptoms, the relationship between anxiety and depression, differences in anxiety between participants receiving inpatient palliative care and those receiving outpatient care, and characteristics that distinguish highly anxious from less anxious patients. Methods Participants were 194 patients with terminal cancer. Approximately half (n = 103) were receiving inpatient care in a palliative care facility and half (n = 91) were receiving outpatient care in a tertiary care cancer center. The Hospital Anxiety and Depression Scale was used to assess anxiety and depression, and was administered along with measures of hopelessness, desire for hastened death, and social support. Results Moderately elevated anxiety symptoms were found in 18.6% of participants (n = 36) and 12.4% (n = 24) had clinically significant anxiety symptoms. Level of anxiety did not differ between the two treatment settings. However, participants receiving palliative care reported significantly higher levels of depression and desire for hastened death. A multivariate prediction model indicated that belief in an afterlife, social support, and anxiolytic and antidepressant use were unique, significant predictors of anxiety. Conclusion Severity of anxiety symptoms did not differ between the study sites, suggesting that anxiety may differ from depression and desire for hastened death in the course that it takes over the duration of terminal cancer. PMID:21565460

  11. 29 CFR 405.4 - Terminal report.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 2 2010-07-01 2010-07-01 false Terminal report. 405.4 Section 405.4 Labor Regulations... of this part, who during its fiscal year loses its identity as a reporting employer through merger... of the employer's loss of reporting identity, together with a statement of the effective date of such...

  12. Termination Criteria in Evolutionary Algorithms: A Survey

    DEFF Research Database (Denmark)

    Ghoreishi, Newsha; Clausen, Anders; Jørgensen, Bo Nørregaard

    2017-01-01

    Over the last decades, evolutionary algorithms have been extensively used to solve multi-objective optimization problems. However, the number of required function evaluations is not determined by nature of these algorithms which is often seen as a drawback. Therefore, a robust and reliable termin...

  13. Kolmveerand miljardit maksev terminal avatud / Koit Brinkmann

    Index Scriptorium Estoniae

    Brinkmann, Koit

    2006-01-01

    21. juulil avati 750 miljonit krooni maksma läinud AS-i Trendgate nafta ja tumedate naftaproduktide ümberlaadimise terminal. Avamisel viibisid ka majandus- ja kommunikatsiooniminister Edgar Savisaar ja Vene transpordiminister Igor Levitin. Lisa: Trendigate'i neli aastat

  14. Optimizing yard operations in port container terminals

    DEFF Research Database (Denmark)

    Kallehauge, Louise Sibbesen

    2005-01-01

    This paper deals with the problem of positioning containers in a yard block of a port container terminal. The objective of the container positioning problem (CPP) is to minimise the total handling time in the block, i.e. the time required for storage and reshuffling of containers. One...

  15. 49 CFR 212.113 - Program termination.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Program termination. 212.113 Section 212.113 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION STATE SAFETY PARTICIPATION REGULATIONS State/Federal Roles § 212.113 Program...

  16. Terminal investment in multiple sexual signals

    DEFF Research Database (Denmark)

    Nielsen, Mattias Lange; Holman, Luke

    2012-01-01

    examples of such facultative terminal investment are known. 2. In the mealworm beetle, Tenebrio molitor, males"odours become more attractive to females following a life-threatening immune challenge. However, the pheromones involved are unknown, hindering further insight into the proximate mechanisms...

  17. 77 FR 21981 - Maher Terminal, LLC

    Science.gov (United States)

    2012-04-12

    ... unreasonable preference or advantage with respect to Maersk, APM, MSC, PNCT, NYCT, and Global, and other marine... considerations, restrictions on transfers and/or changes in ownership or control interests, lost business, forgone business, and additional obligations not required of * * * other marine terminals and other...

  18. Self-Terminating, Oxidative Radical Cyclizations

    Directory of Open Access Journals (Sweden)

    Uta Wille

    2004-05-01

    Full Text Available The recently discovered novel concept of self-terminating, oxidative radical cyclizations, through which alkynes can be converted into carbonyl compounds under very mild reaction conditions using O-centered inorganic and organic radicals as oxidants, is described

  19. An Axiomatization for the Terminal Cycle

    NARCIS (Netherlands)

    Fokkink, W.J.

    Milner proposed an axiomatization for the Kleene star in basic process algebra, in the presence of deadlock and empty process, modulo bisimulation equivalence. In this paper, Milner's axioms are adapted to the terminal cycle xω, which executes x infinitely many times in a row, and it is shown

  20. 24 CFR 247.4 - Termination notice.

    Science.gov (United States)

    2010-04-01

    ... in rent shall in all cases be governed by 24 CFR parts 245, 246 and other applicable HUD regulations... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Termination notice. 247.4 Section 247.4 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued...

  1. Splash of a waterdrop at terminal velocity.

    Science.gov (United States)

    Mutchler, C K; Hansen, L M

    1970-09-25

    High-speed movies of splash formation caused by waterdrop impact at terminal velocity in thin water layers show that splash size increases with drop size. For increasing water depth, splash size increases to a maximum at a depth of one-third drop diameter; splash size then decreases to a constant size for depths greater than three drop diameters.

  2. 45 CFR 74.61 - Termination.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Termination. 74.61 Section 74.61 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION UNIFORM ADMINISTRATIVE REQUIREMENTS FOR AWARDS AND SUBAWARDS TO INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, OTHER NONPROFIT ORGANIZATIONS, AND COMMERCIAL ORGANIZATIONS Post-Award...

  3. 76 FR 32316 - Gap in Termination Provisions

    Science.gov (United States)

    2011-06-06

    ... example, the Software and Information Industry Association (SIIA) stated that the better practice would be... Copyright Office 37 CFR Part 201 Gap in Termination Provisions AGENCY: Copyright Office, Library of Congress. ACTION: Final rule. SUMMARY: The Copyright Office is amending its regulations governing notices of...

  4. Towards the N-terminal acetylome

    DEFF Research Database (Denmark)

    Zhang, Xumin; Højrup, Peter

    2013-01-01

    Protein N-terminal acetylation (N(α)-acetylation) is observed widely from prokaryotes to eukaryotes. It gains increased importance in biological field, due to its multiple roles in many aspects of the protein life, such as assembly, stability, activity, and location. Today, mass spectrometry (MS...

  5. 24 CFR 84.61 - Termination.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Termination. 84.61 Section 84.61 Housing and Urban Development Office of the Secretary, Department of Housing and Urban Development UNIFORM ADMINISTRATIVE REQUIREMENTS FOR GRANTS AND AGREEMENTS WITH INSTITUTIONS OF HIGHER EDUCATION, HOSPITALS, AND OTHER...

  6. The Tiny Terminators-Mosquitoes and Diseases

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 6; Issue 5. The Tiny Terminators - Mosquitoes and Diseases. P K Sumodan. General Article Volume 6 Issue 5 May 2001 pp 48-55 ... Author Affiliations. P K Sumodan1. District Medical Office of Health Mananthavady, Wayanad Kerala 670 645, India.

  7. The terminal oxidases of Paracoccus denitrificans

    NARCIS (Netherlands)

    de Gier, J.-W.; Lübben, M; Reijnders, W N; Tipker, C A; Slotboom, D.J.; van Spanning, R J; Stouthamer, A.H.; van der Oost, J.

    Three distinct types of terminal oxidases participate in the aerobic respiratory pathways of Paracoccus denitrificans. Two alternative genes encoding subunit I of the aa3-type cytochrome c oxidase have been isolated before, namely ctaDI and ctaDII. Each of these genes can be expressed separately to

  8. The terminal oxidases of Paracoccus denitrificans

    NARCIS (Netherlands)

    Gier, Jan-Willem L. de; Lübben, Mathias; Reijnders, Willem N.M.; Tipker, Corinne A.; Slotboom, Dirk-Jan; Spanning, Rob J.M. van; Stouthamer, Adriaan H.; Oost, John van der

    1994-01-01

    Three distinct types of terminal oxidases participate in the aerobic respiratory pathways of Paracoccus denitrificans. Two alternative genes encoding subunit I of the aa3-type cytochrome c oxidase have been isolated before, namely ctaDI and ctaDII. Each of these genes can be expressed separately to

  9. ICU nurses' experiences in providing terminal care.

    Science.gov (United States)

    Espinosa, Laura; Young, Anne; Symes, Lene; Haile, Brenda; Walsh, Teresa

    2010-01-01

    At least 1 in 5 Americans die while using intensive care service-a number that is expected to increase as society ages. Many of these deaths involve withholding or withdrawing life-sustaining therapies. In these situations, the role of intensive care nurses shifts from providing aggressive care to end-of-life care. While hospice and palliative care nurses typically receive specialized support to cope with death and dying, intensive care nurses usually do not receive this support. Understanding the experiences of intensive care nurses in providing care at the end of life is an important first step to improving terminal care in the intensive care unit (ICU). This phenomenological research study explores the experiences of intensive care nurses who provide terminal care in the ICU. The sample consisted of 18 registered nurses delivering terminal care in an ICU that participated in individual interviews and focus groups. Colaizzi's steps for data analysis were used to identify themes within the context of nursing. Three major themes consisted of (1) barriers to optimal care, (2) internal conflict, and (3) coping. Providing terminal care creates significant personal and professional struggles among ICU nurses.

  10. Terminating DNA Tile Assembly with Nanostructured Caps.

    Science.gov (United States)

    Agrawal, Deepak K; Jiang, Ruoyu; Reinhart, Seth; Mohammed, Abdul M; Jorgenson, Tyler D; Schulman, Rebecca

    2017-10-24

    Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes. We find that nanostructures that present binding interfaces for all of the binding sites on a growing facet can bind selectively to growing ends and stop growth when these interfaces are presented on either a rigid or floppy scaffold. In contrast, nucleation of nanotubes requires the presentation of binding sites in an arrangement that matches the shape of the structure's facet. As a result, it is possible to build nanostructures that can terminate the growth of existing nanotubes but cannot nucleate a new structure. The resulting design principles for constructing structures that direct nucleation and termination of the growth of one-dimensional nanostructures can also serve as a starting point for programmatically directing two- and three-dimensional crystallization processes using nanostructure design.

  11. Heathrow Terminal 5 Excavation Archive (Data Paper

    Directory of Open Access Journals (Sweden)

    Framework Archaeology

    2014-06-01

    Full Text Available Framework Archaeology is a Joint Venture agreement between Oxford Archaeology (OA and Wessex Archaeology (WA to provide archaeological services to BAA (formerly British Airports Authority, now Heathrow Airport Holdings Ltd. Given the potential scale of some of BAA's projects, the joint venture enables Framework Archaeology to draw on the full resources of both OA and WA, including site staff, specialist managers, administrative support, and technical facilities. In 1993, BAA plc and Heathrow Airport Limited submitted a joint planning application to develop an additional passenger terminal complex (Terminal 5, together with the provision of aircraft aprons and taxiways, and include the realignment of rivers and landscaping. The resulting archaeological excavations were undertaken as three main phases of work. Excavations in 1996 by the Museum of London Archaeology Service of approximately 4 ha of sludge stockpile areas (site code POK96. Between 1999-2000 Framework Archaeology excavated approximately 21 ha in the Perry Oaks sludge works and adjacent areas (WPR98. Framework Archaeology also undertook excavations between 2002-2007 as part of the construction of Terminal 5 (PSH02, TEC05 covering a further 50 hectares. Importantly the aim of the Terminal 5 archaeological programme was to move beyond the description and recovery of archaeological remains and to arrive at an understanding of the history of human inhabitation and the practical ways in which people established their presence in the material, social and political conditions of their day.

  12. 77 FR 13322 - Termination of Dormant Proceedings

    Science.gov (United States)

    2012-03-06

    ... available for public inspection and copying via ECFS, and during regular business hours at the FCC Reference... (PDF) at: http://transition.fcc.gov/Daily_Releases/Daily_Business/2012/db0216/DA-12-220A1.doc . The spreadsheet associated with document DA 12-220 listing the proceedings proposed for termination for dormancy...

  13. New Families of LDPC Block Codes Formed by Terminating Irregular Protograph-Based LDPC Convolutional Codes

    CERN Document Server

    Mitchell, David G M; Costello, Daniel J

    2010-01-01

    In this paper, we present a method of constructing new families of LDPC block code ensembles formed by terminating irregular protograph-based LDPC convolutional codes. Using the accumulate-repeat-by-4-jagged-accumulate (AR4JA) protograph as an example, a density evolution analysis for the binary erasure channel shows that this flexible design technique gives rise to a large selection of LDPC block code ensembles with varying code rates and thresholds close to capacity. Further, by means of an asymptotic weight enumerator analysis, we show that all the ensembles in this family also have minimum distance that grows linearly with block length, i.e., they are asymptotically good.

  14. Comparative Analysis of the Proteins with Tandem Repeats from 8 Microsporidia and Characterization of a Novel Endospore Wall Protein Colocalizing with Polar Tube from Nosema bombycis.

    Science.gov (United States)

    Wang, Ying; Geng, Huixia; Dang, Xiaoqun; Xiang, Heng; Li, Tian; Pan, Guoqing; Zhou, Zeyang

    2017-09-01

    As a common feature of eukaryotic proteins, tandem amino acid repeat has been studied extensively in both animal and plant proteins. Here, a comparative analysis focusing on the proteins having tandem repeats was conducted in eight microsporidia, including four mammal-infecting microsporidia (Encephalitozoon cuniculi, Encephalitozoon intestinalis, Encephalitozoon hellem and Encephalitozoon bieneusi) and four insect-infecting microsporidia (Nosema apis, Nosema ceranae, Vavraia culicis and Nosema bombycis). We found that the proteins with tandem repeats were abundant in these species. The quantity of these proteins in insect-infecting microsporidia was larger than that of mammal-infecting microsporidia. Additionally, the hydrophilic residues were overrepresented in the tandem repeats of these eight microsporidian proteins and the amino acids residues in these tandem repeat sequences tend to be encoded by GC-rich codons. The tandem repeat position within proteins of insect-infecting microsporidia was randomly distributed, whereas the tandem repeats within proteins of mammal-infecting microsporidia rarely tend to be present in the N terminal regions, when compared with those present in the C terminal and middle regions. Finally, a hypothetical protein EOB14572 possessing four tandem repeats was successfully characterized as a novel endospore wall protein, which colocalized with polar tube of N. bombycis. Our study provided useful insight for the study of the proteins with tandem repeats in N. bombycis, but also further enriched the spore wall components of this obligate unicellular eukaryotic parasite. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

  15. Engineered bacterial hydrophobic oligopeptide repeats in a synthetic yeast prion, [REP-PSI+

    Directory of Open Access Journals (Sweden)

    Fátima eGasset-Rosa

    2015-04-01

    Full Text Available The yeast translation termination factor Sup35p, by aggregating as the [PSI+] prion, enables ribosomes to read-through stop codons, thus expanding the diversity of the Saccharomyces cerevisiae proteome. Yeast prions are functional amyloids that replicate by templating their conformation on native protein molecules, then assembling as large aggregates and fibers. Prions propagate epigenetically from mother to daughter cells by fragmentation of such assemblies. In the N-terminal prion-forming domain, Sup35p has glutamine/asparagine-rich oligopeptide repeats (OPRs, which enable propagation through chaperone-elicited shearing. We have engineered chimeras by replacing the polar OPRs in Sup35p by up to five repeats of a hydrophobic amyloidogenic sequence from the synthetic bacterial prionoid RepA-WH1. The resulting hybrid, [REP-PSI+], i was functional in a stop codon read-through assay in S. cerevisiae; ii generates weak phenotypic variants upon both its expression or transformation into [psi-] cells; iii these variants correlated with high molecular weight aggregates resistant to SDS during electrophoresis; and iv according to fluorescence microscopy, the fusion of the prion domains from the engineered chimeras to the reporter protein mCherry generated perivacuolar aggregate foci in yeast cells. All these are signatures of bona fide yeast prions. As assessed through biophysical approaches, the chimeras assembled as oligomers rather than as the fibers characteristic of [PSI+]. These results suggest that it is the balance between polar and hydrophobic residues in OPRs what determines prion conformational dynamics. In addition, our findings illustrate the feasibility of enabling new propagation traits in yeast prions by engineering OPRs with heterologous amyloidogenic sequence repeats.

  16. The Perpetual Repeater: an Educative Musical Experience.

    Directory of Open Access Journals (Sweden)

    Svetlana Skriagina

    2014-05-01

    Full Text Available To commemorate the 40th anniversary of the Music Undergraduate Program of the Universidad Pedagógica Nacional (National Pedagogic University, two musical events were planned: an original work written for choir, soloists and symphonic band, and an opera for children. As a result, the cantata ‘The Perpetual Repeater” has been created as an adaptation of a work named “50 Milions de Segons” (50 Millions of Seconds, staged by the CATANIA project of the Barcelona Servei Educatiu de L’Auditori. This work tells the story of those school teachers who, paradoxically enough repeat the same course year after year. After visiting L’Auditori of Barcelona to participate in the pedagogic musical work carried out with school children, we considered the possibility of developing an analogous project, in a similar sociocultural and educational environment, within our Music Undergraduate Program. So, this article deals with two fundamental moments which are essential to understand the educational work implemented with the ISPA students of sixth degree, as well as with a group of the program’s students: The Purpose, which describes in detail the planning of the musical work for children, and The Experience, in which the way the process of The Perpetual Repeater Cantatawas carried out is described.

  17. Aggregating quantum repeaters for the quantum internet

    Science.gov (United States)

    Azuma, Koji; Kato, Go

    2017-09-01

    The quantum internet holds promise for accomplishing quantum teleportation and unconditionally secure communication freely between arbitrary clients all over the globe, as well as the simulation of quantum many-body systems. For such a quantum internet protocol, a general fundamental upper bound on the obtainable entanglement or secret key has been derived [K. Azuma, A. Mizutani, and H.-K. Lo, Nat. Commun. 7, 13523 (2016), 10.1038/ncomms13523]. Here we consider its converse problem. In particular, we present a universal protocol constructible from any given quantum network, which is based on running quantum repeater schemes in parallel over the network. For arbitrary lossy optical channel networks, our protocol has no scaling gap with the upper bound, even based on existing quantum repeater schemes. In an asymptotic limit, our protocol works as an optimal entanglement or secret-key distribution over any quantum network composed of practical channels such as erasure channels, dephasing channels, bosonic quantum amplifier channels, and lossy optical channels.

  18. Extending Teach and Repeat to Pivoting Wheelchairs

    Directory of Open Access Journals (Sweden)

    Guillermo Del Castillo

    2003-02-01

    Full Text Available The paper extends the teach-and-repeat paradigm that has been successful for the control of holonomic robots to nonholonomic wheelchairs which may undergo pivoting action over the course of their taught movement. Due to the nonholonomic nature of the vehicle kinematics, estimation is required -- in the example given herein, based upon video detection of wall-mounted cues -- both in the teaching and the tracking events. In order to accommodate motion that approaches pivoting action as well as motion that approaches straight-line action, the estimation equations of the Extended Kalman Filter and the control equations are formulated using two different definitions of a nontemporal independent variable. The paper motivates the need for pivoting action in real-life settings by reporting extensively on the abilities and limitations of estimation-based teach-and-repeat action where pivoting and near-pivoting action is disallowed. Following formulation of the equations in the near-pivot mode, the paper reports upon experiments where taught trajectories which entail a seamless mix of near-straight and near-pivot action are tracked.

  19. Chromosome-specific DNA Repeat Probes

    Energy Technology Data Exchange (ETDEWEB)

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  20. Repeatable assessment protocol for electromagnetic trackers

    Science.gov (United States)

    Haidegger, Tamas; Sirokai, Beáta; Fenyvesi, Gábor; Kovács, Levente; Benyó, Balázs; Benyó, Zoltán

    2012-02-01

    In the past decades, many new trends appeared in interventional medicine. One of the most groundbreaking ones is Image-Guided Surgery (IGS). The main benefit of IGS procedures is the reduction of the patient's pain and collateral damage through improved accuracy and targeting. Electromagnetic Tracking (EMT) has been introduced to medical applications as an effective tool for navigation. However, magnetic fields can be severely distorted by ferromagnetic materials and electronic equipment, which is a major barrier towards their wider application. The focus of the study is to determine and compensate the inherent errors of the different types of EMTs, in order to improve their accuracy. Our aim is to develop a standardized, simple and repeatable assessment protocol; to determine tracking errors with sub-millimeter accuracy, hence increasing the measurement precision and reliability. For initial experiments, the NDI Aurora and the Ascension medSAFE systems were used in a standard laboratory environment. We aim to advance to the state-of-the art by describing and disseminating an easily reproducible calibration method, publishing the CAD files of the accuracy phantom and the source of the evaluation data. This should allow the wider spread of the technique, and eventually lead to the repeatable and comparable assessment of EMT systems.

  1. TERRA: telomeric repeat-containing RNA.

    Science.gov (United States)

    Luke, Brian; Lingner, Joachim

    2009-09-02

    Telomeres, the physical ends of eukaryotic chromosomes, consist of tandem arrays of short DNA repeats and a large set of specialized proteins. A recent analysis has identified telomeric repeat-containing RNA (TERRA), a large non-coding RNA in animals and fungi, which forms an integral component of telomeric heterochromatin. TERRA transcription occurs at most or all chromosome ends and it is regulated by RNA surveillance factors and in response to changes in telomere length. TERRA functions that are emerging suggest important roles in the regulation of telomerase and in orchestrating chromatin remodelling throughout development and cellular differentiation. The accumulation of TERRA at telomeres can also interfere with telomere replication, leading to a sudden loss of telomere tracts. Such a phenotype can be observed upon impairment of the RNA surveillance machinery or in cells from ICF (Immunodeficiency, Centromeric region instability, Facial anomalies) patients, in which TERRA is upregulated because of DNA methylation defects in the subtelomeric region. Thus, TERRA may mediate several crucial functions at the telomeres, a region of the genome that had been considered to be transcriptionally silent.

  2. Function and control of RNA polymerase II C-terminal domain phosphorylation in vertebrate transcription and RNA processing.

    Science.gov (United States)

    Hsin, Jing-Ping; Xiang, Kehui; Manley, James L

    2014-07-01

    The C-terminal domain of the RNA polymerase II largest subunit (the Rpb1 CTD) is composed of tandem heptad repeats of the consensus sequence Y(1)S(2)P(3)T(4)S(5)P(6)S(7). We reported previously that Thr 4 is phosphorylated and functions in histone mRNA 3'-end formation in chicken DT40 cells. Here, we have extended our studies on Thr 4 and to other CTD mutations by using these cells. We found that an Rpb1 derivative containing only the N-terminal half of the CTD, as well as a similar derivative containing all-consensus repeats (26r), conferred full viability, while the C-terminal half, with more-divergent repeats, did not, reflecting a strong and specific defect in snRNA 3'-end formation. Mutation in 26r of all Ser 2 (S2A) or Ser 5 (S5A) residues resulted in lethality, while Ser 7 (S7A) mutants were fully viable. While S2A and S5A cells displayed defects in transcription and RNA processing, S7A cells behaved identically to 26r cells in all respects. Finally, we found that Thr 4 was phosphorylated by cyclin-dependent kinase 9 in cells and dephosphorylated both in vitro and in vivo by the phosphatase Fcp1. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  3. Effect of Terminal Patient Care Training on the Nurses' Attitudes Toward Death in an Oncology Hospital in Turkey.

    Science.gov (United States)

    Göriş, Songül; Taşcı, Sultan; Özkan, Birgül; Ceyhan, Özlem; Kartın, Pınar Tekinsoy; Çeliksoy, Aliye; Elmalı, Ferhan; Eser, Bülent

    2017-03-01

    This is an experimental research aiming at identifying the effect of terminal patient care training on the nurses' attitudes toward death. The sample of this study (n = 41) involves 20 nurses in the training group and 21 nurses in the control group. Nurses were offered terminal patient care training and their attitudes toward death were assessed before and after the intervention. The Death Attitude Profile-Revised (DAP-R) subscale mean scores for fear of death (3.9-4.6, p  .05) in any of the five DAP-R subscales. In accordance with these findings, this study suggests that terminal patient care training should be implemented in the nursing curriculum more extensively and should be frequently repeated as part of the nurses' in-service education.

  4. Performance Comparisons of Improved Regular Repeat Accumulate (RA and Irregular Repeat Accumulate (IRA Turbo Decoding

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulkadhim Hamad

    2017-08-01

    Full Text Available In this paper, different techniques are used to improve the turbo decoding of regular repeat accumulate (RA and irregular repeat accumulate (IRA codes. The adaptive scaling of a-posteriori information produced by Soft-output Viterbi decoder (SOVA is proposed. The encoded pilots are another scheme that applied for short length RA codes. This work also suggests a simple and a fast method to generate a random interleaver having a free 4 cycle Tanner graph. Progressive edge growth algorithm (PEG is also studied and simulated to create the Tanner graphs which have a great girth.

  5. The terminal DNA structure of mammalian chromosomes.

    OpenAIRE

    McElligott, R; Wellinger, R J

    1997-01-01

    In virtually all eukaryotic organisms, telomeric DNA is composed of a variable number of short direct repeats. While the primary sequence of telomeric repeats has been determined for a great variety of species, the actual physical DNA structure at the ends of a bona fide metazoan chromosome with a centromere is unknown. It is shown here that an overhang of the strand forming the 3' ends of the chromosomes, the G-rich strand, is found at mammalian chromosome ends. Moreover, on at least some te...

  6. The absolute number of repeat operations for complex intra ...

    African Journals Online (AJOL)

    abdominal sepsis, questions about futility of treatment frequently arise. This study focuses specifically on patients who required two or more repeat laparotomies and describes the spectrum of disease necessitating multiple repeat laparotomies ...

  7. Intramolecular folding in human ILPR fragment with three C-rich repeats.

    Directory of Open Access Journals (Sweden)

    Soma Dhakal

    Full Text Available Enrichment of four tandem repeats of guanine (G rich and cytosine (C rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA, circular dichroism (CD, and ultraviolet (UV spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3, in the human insulin linked polymorphic region (ILPR. The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br(2 footprinting experiments on a mixture of the ILPR-I3 and a 5'-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures.

  8. Two new miniature inverted-repeat transposable elements in the genome of the clam Donax trunculus.

    Science.gov (United States)

    Šatović, Eva; Plohl, Miroslav

    2017-10-01

    Repetitive sequences are important components of eukaryotic genomes that drive their evolution. Among them are different types of mobile elements that share the ability to spread throughout the genome and form interspersed repeats. To broaden the generally scarce knowledge on bivalves at the genome level, in the clam Donax trunculus we described two new non-autonomous DNA transposons, miniature inverted-repeat transposable elements (MITEs), named DTC M1 and DTC M2. Like other MITEs, they are characterized by their small size, their A + T richness, and the presence of terminal inverted repeats (TIRs). DTC M1 and DTC M2 are 261 and 286 bp long, respectively, and in addition to TIRs, both of them contain a long imperfect palindrome sequence in their central parts. These elements are present in complete and truncated versions within the genome of the clam D. trunculus. The two new MITEs share only structural similarity, but lack any nucleotide sequence similarity to each other. In a search for related elements in databases, blast search revealed within the Crassostrea gigas genome a larger element sharing sequence similarity only to DTC M1 in its TIR sequences. The lack of sequence similarity with any previously published mobile elements indicates that DTC M1 and DTC M2 elements may be unique to D. trunculus.

  9. Triplet repeat DNA structures and human genetic disease: dynamic ...

    Indian Academy of Sciences (India)

    Unknown

    of triplet repeats (Pearson and Sinden 1998a; Sinden. 1999). Expansions or deletions can occur by simple. Table 1. Trinucleotide repeats in human genetic disease. Repeat length. Disease. Gene. Locus. Repeata. Normal. Pre- mutation. Disease. Protein/possible biological effect of expansion. Fragile X syndrome. FMR1.

  10. Novel expressed sequence tag- simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  11. Triplet repeat DNA structures and human genetic disease: dynamic ...

    Indian Academy of Sciences (India)

    Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. Richard R Sinden Vladimir N ... Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, ...

  12. Repeat Testing Effects on Credentialing Exams: Are Repeaters Misinformed or Uninformed?

    Science.gov (United States)

    Feinberg, Richard A.; Raymond, Mark R.; Haist, Steven A.

    2015-01-01

    To mitigate security concerns and unfair score gains, credentialing programs routinely administer new test material to examinees retesting after an initial failing attempt. Counterintuitively, a small but growing body of recent research suggests that repeating the identical form does not create an unfair advantage. This study builds upon and…

  13. Who Repeats Algebra, and How Does Initial Performance Relate to Improvement When the Course Is Repeated?

    Science.gov (United States)

    Fong, Anthony; Jaquet, Karina; Finkelstein, Neal

    2016-01-01

    The information provided in this report shows how students perform when they repeat algebra I and how the level of improvement varies depending on initial course performance and the academic measure (course grades or CST scores). This information can help inform decisions and policies regarding whether and under what circumstances students should…

  14. Germ-line CAG repeat instability causes extreme CAG repeat expansion with infantile-onset spinocerebellar ataxia type 2.

    Science.gov (United States)

    Vinther-Jensen, Tua; Ek, Jakob; Duno, Morten; Skovby, Flemming; Hjermind, Lena E; Nielsen, Jørgen E; Nielsen, Troels Tolstrup

    2013-06-01

    The spinocerebellar ataxias (SCA) are a genetically and clinically heterogeneous group of diseases, characterized by dominant inheritance, progressive cerebellar ataxia and diverse extracerebellar symptoms. A subgroup of the ataxias is caused by unstable CAG-repeat expansions in their respective genes leading to pathogenic expansions of polyglutamine stretches in the encoded proteins. In general, unstable CAG repeats have an uninterrupted CAG repeat, whereas stable CAG repeats are either short or interrupted by CAA codons, which - like CAG codons - code for glutamine. Here we report on an infantile SCA2 patient who, due to germ-line CAG repeat instability in her father, inherited an extremely expanded CAG repeat in the SCA2 locus. Surprisingly, the expanded allele of the father was an interrupted CAG repeat sequence. Furthermore, analyses of single spermatozoa showed a high frequency of paternal germ-line repeat sequence instability of the expanded SCA2 locus.

  15. Functionalization of hydroxyl terminated polybutadiene with ...

    Indian Academy of Sciences (India)

    Administrator

    gas transport properties (Chen et al 2000; Yang and Lin. 2001; Gupta et al ... gas. The solvent was removed at 50°C in rotary evapo- rator. The resulting product was washed thoroughly and repeatedly with methanol followed by hexane to remove traces of ... attached cyanuric chloride by replacing the chlorine from the CYC ...

  16. The hidden price of repeated traumatic exposure.

    Science.gov (United States)

    Levy-Gigi, Einat; Richter-Levin, Gal

    2014-07-01

    Neuroimaging studies have demonstrated reduced hippocampal volume in trauma-exposed individuals without posttraumatic stress disorder (PTSD). However, the implications of such a deficit in this non-clinical population are still unclear. Animal and human models of PTSD suggest that hippocampal deficit may result in impaired learning and use of associations between contextual information and aversive events. Previous study has shown that individuals with PTSD have a selective impairment in reversing the negative outcome of context-related information. The aim of this study was to test whether non-PTSD individuals who are repeatedly exposed to traumatic events display similar impairment. To that end, we compared the performance of active-duty firefighters who are frequently exposed to traumatic events as part of their occupational routine and civilian matched-controls with no history of trauma-exposure. We used a novel cue-context reversal paradigm, which separately evaluates reversal of negative and positive outcomes of cue and context-related information. As predicted, we found that while both trauma-exposed firefighters and unexposed matched-controls were able to acquire and retain stimulus-outcome associations, firefighters struggled to learn that a previously negative context is later associated with a positive outcome. This impairment did not correlate with levels of PTSD, anxiety or depressive symptoms. The results suggest that similar to individuals with PTSD, highly exposed individuals fail to associate traumatic outcomes with their appropriate context. This impairment may reflect a possible hidden price of repeated traumatic exposure, which is not necessarily associated with PTSD diagnosis, and may affect the way highly exposed individuals interpret and react to their environment.

  17. Duodenoscope reprocessing surveillance with adenosine triphosphate testing and terminal cultures: a clinical pilot study.

    Science.gov (United States)

    Visrodia, Kavel; Hanada, Yuri; Pennington, Kelly M; Tosh, Pritish K; Topazian, Mark D; Petersen, Bret T

    2017-07-01

    Recent reports of infectious outbreaks linked to duodenoscopes have led to proposals for duodenoscope surveillance culturing, which has inherent limitations. We aimed to assess the feasibility of real-time adenosine triphosphate (ATP) testing after manual cleaning and its ability to predict reprocessing adequacy, as determined by terminal duodenoscope cultures. Clinically used duodenoscopes underwent reprocessing per current guidelines. After manual cleaning, ATP samples were obtained from the elevator, within the proximal biopsy port, and by flushing of the biopsy channel. After high-level disinfection (HLD), aerobic cultures of the elevator and biopsy channel were obtained using sterile technique. Duodenoscopes with any ATP sample ≥200 relative light units underwent repeated cycles of cleaning, ATP testing, HLD, and terminal culturing. Twenty clinically used duodenoscopes were included; 18 underwent a second reprocessing cycle, and 6 underwent a third reprocessing cycle because of detection of high ATP. After the initial reprocessing cycle, 12 of 20 (60%) duodenoscopes had positive culture results, most commonly yielding gram-negative bacilli (GNB, n = 11 from 9 duodenoscopes), and catalase-positive gram-positive cocci (CP-GPC, n = 7 from 7 duodenoscopes), suggesting staphylococcal organisms. Ambient environmental controls also showed GNB and CP-GPC growth. The overall sensitivity and specificity of ATP testing compared with terminal cultures were 30% and 53%, respectively. ATP sampling appears to correlate poorly with terminal culture results and cannot be recommended as a surrogate for terminal cultures. The performance and interpretation of cultures remains complicated by the potential recovery of environmental contaminants. Copyright © 2017 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

  18. Repeat spine imaging in transferred emergency department patients.

    Science.gov (United States)

    Bible, Jesse E; Kadakia, Rishin J; Kay, Harrison F; Zhang, Chi E; Casimir, Geoffrey E; Devin, Clinton J

    2014-02-15

    Retrospective study. Assess frequency of repeat spine imaging in patients transferred with known spine injuries from outside hospital (OSH) to tertiary receiving institution (RI). Unnecessary repeat imaging after transfer has started to become a recognized problem with the obvious issues related to repeat imaging along with potential for iatrogenic injury with movement of patients with spine problems. Consecutive adult patients presenting to a single 1-level trauma center with spine injuries during a 51-month period were reviewed (n = 4500), resulting in 1427 patients transferred from OSH emergency department. All imaging and radiology reports from the OSH were reviewed, as well as studies performed at RI. A repeat was the same imaging modality used on the same spine region as OSH imaging. The overall rate of repeat spine imaging for both OSH imaging sent and not sent was 23%, and 6% if repeat spine imaging via traumagram (partial/full-body computed tomography [CT]) was excluded as a repeat. The overall rate of repeat CT was 29% (7% dedicated spine CT scans and 22% part of nondedicated spine CT scan).An observation of only those patients with OSH imaging that was sent and viewable revealed that 23% underwent repeat spine imaging with 23% undergoing repeat spine CT and 41% repeat magnetic resonance imaging.In those patients with sent and viewable OSH imaging, a lack of reconstructions prompted 14% of repeats, whereas inadequate visualization of injury site prompted 8%. In only 8% of the repeats did it change management or provide necessary surgical information. This study is the first to investigate the frequency of repeat spine imaging in transfers with known spine injuries and found a substantially high rate of repeat spine CT with minimal alteration in care. Potential solutions include only performing scans at the OSH necessary to establish a diagnosis requiring transfer and improving communication between OSH and RI physicians. 4.

  19. Terminal investment in multiple sexual signals

    DEFF Research Database (Denmark)

    Nielsen, Mattias Lange; Holman, Luke

    2012-01-01

    1. Trade-offs between current and future resource allocation can select for elevated reproductive effort in individuals facing mortality. Males are predicted to benefit from increasing investment in costly sexually selected signals after experiencing an acute life span reduction, although few...... examples of such facultative terminal investment are known. 2. In the mealworm beetle, Tenebrio molitor, males"odours become more attractive to females following a life-threatening immune challenge. However, the pheromones involved are unknown, hindering further insight into the proximate mechanisms...... and ultimate consequences of terminal investment. 3. Using chemical and behavioural analyses, we show that the cuticular hydrocarbons (CHCs) of T.molitor are sexually dimorphic and are used by females to locate and select males. Moreover, both male CHCs and glandular pheromones were affected by experimental...

  20. Vehicle drive module having improved terminal design

    Science.gov (United States)

    Beihoff, Bruce C.; Radosevich, Lawrence D.; Phillips, Mark G.; Kehl, Dennis L.; Kaishian, Steven C.; Kannenberg, Daniel G.

    2006-04-25

    A terminal structure for vehicle drive power electronics circuits reduces the need for a DC bus and thereby the incidence of parasitic inductance. The structure is secured to a support that may receive one or more power electronic circuits. The support may aid in removing heat from the circuits through fluid circulating through the support. The support may form a shield from both external EMI/RFI and from interference generated by operation of the power electronic circuits. Features may be provided to permit and enhance connection of the circuitry to external circuitry, such as by direct contact between the terminal assembly and AC and DC circuit components. Modular units may be assembled that may be coupled to electronic circuitry via plug-in arrangements or through interface with a backplane or similar mounting and interconnecting structures.

  1. Cure Chemistry of Phenylethynyl Terminated Oligomers

    Science.gov (United States)

    Wood, Karen H.; Orwoll, Robert A.; Young, Philip R.; Jensen, Brian J.; McNair, Harold M.

    1997-01-01

    The ability to process high performance polymers into quality, void-free composites has been significantly advanced using oligomers terminated with reactive groups which cure or crosslink at elevated temperature without the evolution of volatile byproducts. Several matrix resin systems of considerable interest to the aerospace community utilize phenylethynyl-terminated imide (PETI) technology to achieve this advantage. The present paper addresses the cure chemistry of PETI oligomers. The thermal cure of a low molecular weight model compound was studied using a variety of analytical techniques including differential scanning calorimetry, Fourier transform infrared spectroscopy, and liquid chromatography-mass spectroscopy. The studies indicate an extremely complex cure process. Many stable products were isolated and this paper reports current work on identification of those products. The intent of this research is to provide fundamental insight into the molecular structure of the cured PETI engineering materials so that performance and durability can be more fully assessed.

  2. [Spiritual care model for terminal cancer patients].

    Science.gov (United States)

    Cheng, Ju-Fen; Lin, Ya-Ching; Huang, Pai-Ho; Wei, Chih-Hsin; Sun, Jia-Ling

    2014-12-01

    Providing spiritual care to patients with advanced cancer may improve the quality of life of these patients and help them experience a good death. Cancer patients are eager for additional spiritual care and for a sense of peace at the end of their life. However, spirituality is an abstract concept. The literature on spiritual care focuses primarily on elaborations of spirituality theory. Thus, first-line medical care professionals lack clear guidelines for managing the spiritual needs of terminal cancer patients. The purposes of this article were to: 1) introduce a spiritual care model based on the concept of repair and recovery of relationships that addresses the relationship between the self and God, others, id, and objects and 2) set out a four-step strategy for this model that consists of understanding, empathizing, guiding, and growing. This article provides operational guidelines for the spiritual care of terminal cancer patients.

  3. IMPORTANCE-PERFORMANCE ANALYSIS TO ARJOSARI TERMINAL

    Directory of Open Access Journals (Sweden)

    SEDAYU Agung

    2014-12-01

    Full Text Available Public transport is one of the important solutions to solve transportation problems in Indonesia. At this present, the level of congestion and traffic accidents were very high. This was caused by increasing in using cars and motorcycles. This condition is not matched by public transport services that are decreasing in quantity and performance quality of the vehicles. Therefore with the issues it needs improve public transport services that are reliable and cheap. This study suggests efforts to improve public transport services based terminal user perceptions. This study location is Arjosari terminal. The method is Importance-Performance Analysis (IPA. The analysis results obtained service attributes include assurance, responsiveness, performance, aesthetics, easy, reliability, durability, frequency, comfort, and the availability of facilities. The results get priority to be repaired include security protection and safety, Aesthetics waiting room, no long in waiting time, provide information and complaint center, and the available of Goods repository.

  4. Acetylene-Terminated Aspartimides And Derived Resins

    Science.gov (United States)

    Hergenrother, Paul M.; Connell, John W.; Havens, Stephen J.

    1989-01-01

    New polymers and derived blends exhibit improved processability and properties. New toughened epoxies exhibit excellent properties, but use temperatures limited. Bismaleimide resins are some base materials formulated to develop materials having moderate use temperatures. Work conducted on use of acetylenic (ethynyl) group to cross-link and extend chains of oligomers and polymers to obtain materials to perform at higher temperatures. Extended to include acetylene-terminated aspartimides (ATA's).

  5. Una riflessione interdisciplinare sul termine cambiamento

    OpenAIRE

    Giuseppe Licari,

    2013-01-01

    Riassunto Il focus che presento propone una riflessione interdisciplinare sul campo semantico del termine cambiamento. Lo scopo è quello di cogliere, attraverso uno sguardo sulla complessità del reale, alcune delle situazioni e alcuni processi dove la parola cambiamento si va a collocare. Come sappiamo il cambiamento lo possiamo ritrovare sia nei processi evolutivi, come in quelli formativi, o in quelli epistemologici, si pensi ad esempio al cambio di paradigma più famoso nella conoscenza uma...

  6. Terminal hemimyelocystocele associated with Chiari II malformation

    Directory of Open Access Journals (Sweden)

    Umamaheswara Reddy V.

    2014-06-01

    Full Text Available Terminal myelocystocele (TMC results from failure of embryonic CSF to drain outside the neural tube creating CSF reservoir within a dorsal meningocele. Association of Chiari II malformation with diastematomyelia and myelocystocele is extremely rare. Myelocystoceles do not have neural tissue so they have good prognosis after treatment, however when associated with hydromelia and Chiari malformation they present with neurological deficits. We present details of a 2 year old female who presented to us with this rare anomaly.

  7. Autoregulation of Neuromuscular Transmission by Nerve Terminals.

    Science.gov (United States)

    1985-09-01

    chlorpromazine (CPZ) and trifluoperazine (TFP), with known anti-calmodulin activity’l induced a decrease in FC via indirect, but not direct muscle...release ACh synthesis by motor nerve terminals requires an adequate supply of its precusor, choline. We have found that diisopropyl1fluorophosphate (DFP...inhibits choline efflux from the isolated hemidiaphragm and futher suggest that, by limiting the availability of choline for ACh synthesis , DFP reduces the

  8. Living with a terminal illness: patients' priorities.

    Science.gov (United States)

    Carter, Helen; MacLeod, Rod; Brander, Penny; McPherson, Kath

    2004-03-01

    Our understanding of terminal illness and its consequences has been predominantly based on models derived from expert definition, rather than the patient's perspective. More recently, quality of life tools have been developed to enable patient choice in responses. However, an even broader approach may be needed to help identify goals for care for patients who are terminally ill. The aim of this paper is to report on an exploratory, qualitative study exploring what people living with terminal illness considered were the areas of priority in their lives. Ten people living with terminal cancer were interviewed. Analysis of the interviews incorporated principles of narrative analysis and grounded theory. Over 30 categories were identified and collated into five inter-related themes (personal/intrinsic factors, external/extrinsic factors, future issues, perceptions of normality and taking charge) encompassing the issues of importance to all participants. Each theme focused on 'life and living' in relation to life as it was or would be without illness. Practical issues of daily living and the opportunity to address philosophical issues around the meaning of life emerged as important areas. The central theme, 'taking charge', concerned with people's levels of life engagement, was integrally connected to all other themes. The findings suggest that the way in which health professionals manage patients' involvement in matters such as symptom relief can impact on existential areas of concern. Understanding patients' perspectives in relation to each theme may assist health professionals to develop management strategies appropriate to their needs. The findings challenge some aspects of traditional 'expert-defined' outcome measures. As this was an exploratory study, further work is needed to test and develop the model presented.

  9. Human U4/U6 snRNP recycling factor p110: Mutational analysis reveals the function of the tetratricopeptide repeat domain in recycling

    OpenAIRE

    Medenbach, J.; Schreiner, S.; Liu, S.; Luehrmann, R.; Bindereif, A

    2004-01-01

    After each spliceosome cycle, the U4 and U6 snRNAs are released separately and are recycled to the functional U4/U6 snRNP, requiring in the mammalian system the U6-specific RNA binding protein p110 (SART3). Its domain structure is made up of an extensive N-terminal domain with at least seven tetratricopeptide repeat (TPR) motifs, followed by two RNA recognition motifs (RRMs) and a highly conserved C-terminal sequence of 10 amino acids. Here we demonstrate under in vitro recycling conditions t...

  10. Orientations of terminal cladodes of Platyopuntias

    Energy Technology Data Exchange (ETDEWEB)

    Nobel, P.S.

    1982-01-01

    The orientations of terminal unshaded cladodes of 23 species of platyopuntias were observed in North America, South America, Australia, and Israel. When the seasonality of rainfall favored cladode development in the winter and the site was located above 27/sup 0/N, the cladodes tended to face north-south (five cases, P < .001 for each). In all other cases without topographical blockage of incoming radiation, the tendency was to face east-west. For example, terminal cladodes of Opuntia phaeacantha var. discata and O. stricta tended to face north-south in Israel but east-west in the United States (P > .001). Such dissimilar orientation patterns also occurred for cladodes of 0. chlorotica at two sites in the Sonoran Desert and for O. basilaris var. basilaris developing at different seasons at a single site. Contrary to previously published observations, cladodes of O. ficus-indica and O. compressa had a significant tendency to orient (P > .001). When topographical features affected the direction of prevailing photosynthetically active radiation (PAR), the preferred orientation of terminal cladodes was changed accordingly. The preferred direction always maximized the interception of PAR, which is often a limiting factor in the productivity of cacti, even in a putatively high radiation environment.

  11. Role of DNA Polymerases in Repeat-Mediated Genome Instability

    Directory of Open Access Journals (Sweden)

    Kartik A. Shah

    2012-11-01

    Full Text Available Expansions of simple DNA repeats cause numerous hereditary diseases in humans. We analyzed the role of DNA polymerases in the instability of Friedreich’s ataxia (GAAn repeats in a yeast experimental system. The elementary step of expansion corresponded to ∼160 bp in the wild-type strain, matching the size of Okazaki fragments in yeast. This step increased when DNA polymerase α was mutated, suggesting a link between the scale of expansions and Okazaki fragment size. Expandable repeats strongly elevated the rate of mutations at substantial distances around them, a phenomenon we call repeat-induced mutagenesis (RIM. Notably, defects in the replicative DNA polymerases δ and ∊ strongly increased rates for both repeat expansions and RIM. The increases in repeat-mediated instability observed in DNA polymerase δ mutants depended on translesion DNA polymerases. We conclude that repeat expansions and RIM are two sides of the same replicative mechanism.

  12. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.

    Directory of Open Access Journals (Sweden)

    R Gonzalo Parra

    2015-12-01

    Full Text Available Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins.

  13. Optimization of thrie beam terminal end shoe connection.

    Science.gov (United States)

    2017-04-01

    Terminal thrie end shoes connect nested thrie beams to parapets or other bridge rail structure to provide a robust connectivity between a transition section and a rigid railing section. When connecting terminal end shoe to thrie beam transitions, the...

  14. Fail-safe transcription termination: Because one is never enough.

    Science.gov (United States)

    Lemay, Jean-François; Bachand, François

    2015-01-01

    Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that involves the release of the nascent transcript and dissociation of RNAPII from the DNA template. As transcription termination is intimately linked to RNA 3' end processing, termination pathways have a key decisive influence on the fate of the transcribed RNA. Quite remarkably, when reaching the 3' end of genes, a substantial fraction of RNAPII fail to terminate transcription, requiring the contribution of alternative or "fail-safe" mechanisms of termination to release the polymerase. This point of view covers redundant mechanisms of transcription termination and how they relate to conventional termination models. In particular, we expand on recent findings that propose a reverse torpedo model of termination, in which the 3'5' exonucleolytic activity of the RNA exosome targets transcription events associated with paused and backtracked RNAPII.

  15. Safe use of mine winding ropes, volume 3: rope terminations.

    CSIR Research Space (South Africa)

    Borrello, M

    1996-04-01

    Full Text Available and evaluating a less labour intensive, less skill dependent termination with better efficiencies. The work carried out here investigated the applicability of resin and white metal cappings as rope terminations on South African mines....

  16. THE ANALYSIS OF TECHNICAL PROCESS OF TERMINAL SYSTEMS

    Directory of Open Access Journals (Sweden)

    N. Yu. Shramenko

    2010-10-01

    Full Text Available The analysis of technological processes of the terminal systems is conducted, features are exposed and the basic problems of modern technology are certain. Directions of improvement technology of functioning of the terminal systems are offered.

  17. Genome-wide analysis of repeat diversity across the family Musaceae.

    Directory of Open Access Journals (Sweden)

    Petr Novák

    Full Text Available BACKGROUND: The banana family (Musaceae includes genetically a diverse group of species and their diploid and polyploid hybrids that are widely cultivated in the tropics. In spite of their socio-economic importance, the knowledge of Musaceae genomes is basically limited to draft genome assemblies of two species, Musa acuminata and M. balbisiana. Here we aimed to complement this information by analyzing repetitive genome fractions of six species selected to represent various phylogenetic groups within the family. RESULTS: Low-pass sequencing of M. acuminata, M. ornata, M. textilis, M. beccarii, M. balbisiana, and Ensete gilletii genomes was performed using a 454/Roche platform. Sequence reads were subjected to analysis of their overall intra- and inter-specific similarities and, all major repeat families were quantified using graph-based clustering. Maximus/SIRE and Angela lineages of Ty1/copia long terminal repeat (LTR retrotransposons and the chromovirus lineage of Ty3/gypsy elements were found to make up most of highly repetitive DNA in all species (14-34.5% of the genome. However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA. These differences were most pronounced between species from different taxonomic sections of the Musaceae family, whereas pairs of closely related species (M. acuminata/M. ornata and M. beccarii/M. textilis shared similar populations of repetitive elements. CONCLUSIONS: This study provided the first insight into the composition and sequence variation of repetitive parts of Musaceae genomes. It allowed identification of repetitive sequences specific for a single species or a group of species that can be utilized as molecular markers in breeding programs and generated computational resources that will be instrumental in repeat masking and annotation in future genome assembly projects.

  18. Analysis of the operations of an intermodal barge terminal

    OpenAIRE

    Verdonck, L.; Caris, A.; Ramaekers, K.; Janssens, G.K.

    2012-01-01

    This paper studies the operations of intermodal barge terminals. The objective is to increase the terminal’s efficiency by supporting the operational planning of the terminal operator. For this purpose a review on general and process specific barge terminal planning problems, discussed in current scientific literature, is provided. This theoretical knowledge is verified in practice by means of a comparison with operational planning realities at Haven Genk, a Belgian trimodal terminal. Finally...

  19. Analysis of the operations of an intermodal barge terminal

    OpenAIRE

    Verdonck, Lotte; Caris, An; Ramaekers, Katrien; Janssens, Gerrit, K.

    2014-01-01

    This paper studies the operations of intermodal barge terminals. The objective is to increase the terminal’s efficiency by supporting the operational planning of the terminal operator. For this purpose, a review on general and process-specific barge terminal planning problems, discussed in current scientific literature, is provided. This theoretical knowledge is validated in practice by means of a comparison with operational planning realities at Haven Genk, a Belgian trimodal terminal. Final...

  20. 5 CFR 875.412 - When will my coverage terminate?

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false When will my coverage terminate? 875.412... REGULATIONS (CONTINUED) FEDERAL LONG TERM CARE INSURANCE PROGRAM Coverage § 875.412 When will my coverage terminate? Your coverage will terminate on the earliest of the following dates: (a) The date you specify to...