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Sample records for active cacta-like transposable

  1. Transcriptional activity of transposable elements in coelacanth.

    Science.gov (United States)

    Forconi, Mariko; Chalopin, Domitille; Barucca, Marco; Biscotti, Maria Assunta; De Moro, Gianluca; Galiana, Delphine; Gerdol, Marco; Pallavicini, Alberto; Canapa, Adriana; Olmo, Ettore; Volff, Jean-Nicolas

    2014-09-01

    The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity.

  2. Evolutionary active transposable elements in the genome of the coelacanth.

    Science.gov (United States)

    Chalopin, Domitille; Fan, Shaohua; Simakov, Oleg; Meyer, Axel; Schartl, Manfred; Volff, Jean-Nicolas

    2014-09-01

    The apparent morphological stasis in the lineage of the coelacanth, which has been called a "living fossil" by many, has been suggested to be causally related to a slow evolution of its genome, with strongly reduced activity of transposable elements (TEs). Analysis of the African coelacanth showed that at least 25% of its genome is constituted of transposable elements including retrotransposons, endogenous retroviruses and DNA transposons, with a strong predominance of non-Long Terminal Repeat (non-LTR) retrotransposons. The coelacanth genome has been shaped by four major general bursts of transposition during evolution, with major contributions of LINE1, LINE2, CR1, and Deu non-LTR retrotransposons. Many transposable elements are expressed in different tissues and might be active. The number of TE families in coelacanth, but also in lungfish, is lower than in teleost fish, but is higher than in chicken and human. This observation is in agreement with the hypothesis of a sequential elimination of many TE families in the sarcopterygian lineage during evolution. Taken together, our analysis indicates that the coelacanth contains more TE families than birds and mammals, and that these elements have been active during the evolution of the coelacanth lineage. Hence, at the level of transposable element activity, the coelacanth genome does not appear to evolve particularly slowly.

  3. Mammary Cancer and Activation of Transposable Elements

    Science.gov (United States)

    2012-09-01

    SV40Tag is transcriptionally activated during pregnancy and lactation , and the mice are predisposed to develop mammary cancer after 3 pregnancies...and lactations . Using this model, populations of marked cells can be collected for integrated analysis of gene expression, promoter usage, and DNA...completed over the first 6 months on the job . Training included mouse husbandry and colony management, mammary cell isolations in preparation for

  4. Mammary Cancer and Activation of Transposable Elements

    Science.gov (United States)

    2015-03-01

    derived adipo- cytes and ADS-derived induced pluripotent stem cells (ADS-iPSCs) (19) and primary mouse ES cells to isolated sperm and oocytes (20). We...Mesendoderm 2353 765 051 59 5 92% H9-IMR90 5875 7 669 782 605 58 91% oocyte - ES cell (mouse) 4727 1 204 883 334 25 93% sperm - ES cell (mouse) 4580 4 364 748...engineered mouse model in which a specific mammary cell population is fluorescently marked upon initial transcriptional activation of the SV40 large T

  5. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.

    Science.gov (United States)

    Naville, Magali; Chalopin, Domitille; Volff, Jean-Nicolas

    2014-01-01

    Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.

  6. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.

    Directory of Open Access Journals (Sweden)

    Magali Naville

    Full Text Available Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2% of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.

  7. A DNA fingerprint probe from Mycosphaerella graminicola identifies an active transposable element

    NARCIS (Netherlands)

    Goodwin, S.B.; Cavaletto, J.R.; Waalwijk, C.; Kema, G.H.J.

    2001-01-01

    DNA fingerprinting has been used extensively to characterize populations of Mycosphaerella graminicola, the Septoria tritici blotch pathogen of wheat. The highly polymorphic DNA fingerprints of Mycosphaerella graminicola were assumed to reflect the action of transposable elements. However, there was

  8. An active hAT transposable element causing bud mutation of carnation by insertion into the flavonoid 3'-hydroxylase gene.

    Science.gov (United States)

    Momose, Masaki; Nakayama, Masayoshi; Itoh, Yoshio; Umemoto, Naoyuki; Toguri, Toshihiro; Ozeki, Yoshihiro

    2013-04-01

    The molecular mechanisms underlying spontaneous bud mutations, which provide an important breeding tool in carnation, are poorly understood. Here we describe a new active hAT type transposable element, designated Tdic101, the movement of which caused a bud mutation in carnation that led to a change of flower color from purple to deep pink. The color change was attributed to Tdic101 insertion into the second intron of F3'H, the gene for flavonoid 3'-hydroxylase responsible for purple pigment production. Regions on the deep pink flowers of the mutant can revert to purple, a visible phenotype of, as we show, excision of the transposable element. Sequence analysis revealed that Tdic101 has the characteristics of an autonomous element encoding a transposase. A related, but non-autonomous element dTdic102 was found to move in the genome of the bud mutant as well. Its mobilization might be the result of transposase activities provided by other elements such as Tdic101. In carnation, therefore, the movement of transposable elements plays an important role in the emergence of a bud mutation.

  9. Transposable DNA elements and life history traits: II. Transposition of P DNA elements in somatic cells reduces fitness, mating activity, and locomotion of Drosophila melanogaster.

    Science.gov (United States)

    Woodruff, R C; Thompson, J N; Barker, J S; Huai, H

    1999-01-01

    Some transposable DNA elements in higher organisms are active in somatic cells, as well as in germinal cells. What effect does the movement of DNA elements in somatic cells have on life history traits? It has previously been reported that somatically active P and mariner elements in Drosophila induce genetic damage and significantly reduce lifespan. In this study, we report that the movement of P elements in somatic cells also significantly reduces fitness, mating activity, and locomotion of Drosophila melanogaster. If other elements cause similar changes in life history traits, it is doubtful if transposable DNA elements remain active for long in somatic cells in natural populations.

  10. Heavy-ion radiation induces both activation of multiple endogenous transposable elements and alterations in DNA methylation in rice

    Science.gov (United States)

    Zhang, Meng; Sun, Yeqing; Li, Xishan; Xiaolin, Cui; Li, Xiang

    2012-07-01

    Space radiation represents a complex environmental condition in which several interacting factors such as electron, neutron, proton, heavy-ion are involved, which may provoke stress responses and jeopardize genome integrity. Given the inherent property of epigenetic modifications to respond to intrinsic aswell as external perturbations, it is conceivable that epigenetic markers like DNA methylation and transposition may undergo alterations in response to space radiation. Cytosine DNA methylation plays important roles in maintaining genome stability and controlling gene expression. A predominant means for Transposable elements (TEs) to cause genetic instability is via their transpositional activation. To find the detailed molecular characterization of the nature of genomic changes induced by space radiation, the seeds of rice were exposed to 0.02, 0.2, 1, 2 and 20 Gy dose of ^{12}C heavy-ion radiation, respectively. We found that extensive alteration in both DNA methylation and gene expression occurred in rice plants after different dose of heavy-ion radiation. Here we shown that heavy-ion radiation has induced transposition of mPing and Tos17 in rice, which belong to distinct classes including the miniature inverted terminal repeat TEs (MITEs) and long-terminal repeat (LTR) retrotransposons, respectively. mPing and Tos17 mobility were found to correlate with cytosine methylation alteration detected by MSAP and genetic variation detected by AFLP. The result showed that at least in some cases transposition of TEs was associated with cytosine demethylation within the elements. Our results implicate that the heavy-ion radiation represents a potent mutagenic agent that can cause genomic instabilities by eliciting transposition of endogenous TEs in rice. Keywords: Heavy-ion radiation, DNA methylation, Transposable elements, mPing, Tos17

  11. Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex

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    Shrivastava Savita

    2008-12-01

    Full Text Available Abstract Background The Burkholderia cepacia complex (BCC is a versatile group of Gram negative organisms that can be found throughout the environment in sources such as soil, water, and plants. While BCC bacteria can be involved in beneficial interactions with plants, they are also considered opportunistic pathogens, specifically in patients with cystic fibrosis and chronic granulomatous disease. These organisms also exhibit resistance to many antibiotics, making conventional treatment often unsuccessful. KS10 was isolated as a prophage of B. cenocepacia K56-2, a clinically relevant strain of the BCC. Our objective was to sequence the genome of this phage and also determine if this prophage encoded any virulence determinants. Results KS10 is a 37,635 base pairs (bp transposable phage of the opportunistic pathogen Burkholderia cenocepacia. Genome sequence analysis and annotation of this phage reveals that KS10 shows the closest sequence homology to Mu and BcepMu. KS10 was found to be a prophage in three different strains of B. cenocepacia, including strains K56-2, J2315, and C5424, and seven tested clinical isolates of B. cenocepacia, but no other BCC species. A survey of 23 strains and 20 clinical isolates of the BCC revealed that KS10 is able to form plaques on lawns of B. ambifaria LMG 19467, B. cenocepacia PC184, and B. stabilis LMG 18870. Conclusion KS10 is a novel phage with a genomic organization that differs from most phages in that its capsid genes are not aligned into one module but rather separated by approximately 11 kb, giving evidence of one or more prior genetic rearrangements. There were no potential virulence factors identified in KS10, though many hypothetical proteins were identified with no known function.

  12. Characterization of transcriptional activation and inserted-into-gene preference of various transposable elements in the Brassica species.

    Science.gov (United States)

    Gao, Caihua; Xiao, Meili; Jiang, Lingyan; Li, Jiana; Yin, Jiaming; Ren, Xiaodong; Qian, Wei; Oscar, Ortegón; Fu, Donghui; Tang, Zhanglin

    2012-07-01

    Transposable elements (TEs) have attracted increasing attention because of their tremendous contributions to genome reorganization and gene variation through dramatic proliferation and excision via transposition. However, less known are the transcriptional activation of various TEs and the characteristics of TE insertion into genomes at the genome-wide level. In the present study, we focused on TE genes for transposition and gene disruption by insertion of TEs in expression sequences of Brassica, to investigate the transcriptional activation of TEs, the biased insertion of TEs into genes, and their salient characteristics. Long terminal repeat (LTR-retrotransposon) accounted for the majority of these active TE genes (70.8%), suggesting that transposition activation varied with TE type. 6.1% genes were interrupted by LTR-retrotransposons, which indicated their preference for insertion into genes. TEs were preferentially inserted into cellular component-specific genes acted as "binding" elements and involved in metabolic processes. TEs have a biased insertion into some host genes that were involved with important molecular functions and TE genes exhibited spatiotemporal expression. These results suggested that various types of transposons differentially contributed to gene variation and affected gene function.

  13. Transcriptional activation of transposable elements in mouse zygotes is independent of Tet3-mediated 5-methylcytosine oxidation

    Institute of Scientific and Technical Information of China (English)

    Azusa Inoue; Shogo Matoba; Yi Zhang

    2012-01-01

    The methylation state of the paternal genome is rapidly reprogrammed shortly after fertilization.Recent studies have revealed that loss of 5-methylcytosine(5mC)in zygotes correlates with appearance of 5-hydroxymethylcytosine (5hmC),5-formylcytosine(5fC),and 5-carboxylcytosine(5caC).This process is mediated by Tet3 and the 5mC oxidation products generated in zygotes are gradually lost during preimplantation development through a replicationdependent dilution process.Despite these findings,the biological significance of Tet3-mediated oxidation of 5mC to 5hmC/5fC/5caC in zygotes is unknown.DNA methylation plays an important role in silencing gene expression including the repression of transposable elements(TEs).Given that the activation of TEs during preimplantation development correlates with loss of DNA methylation,it is believed that paternal DNA demethylation may have an important role in TE activation.Here we examined this hypothesis and found that Tet3-mediated 5mC oxidation does not have a significant contribution to TE activation.We show that the expression of LINE-1(long interspersed nucleotide element 1)and ERVL(endogenous retroviruses class Ⅲ)are activated from both paternal and maternal genomes in zygotes.Inhibition of 5mC oxidation by siRNA-mediated depletion of Tet3 affected neither TE activation,nor global transcription in zygotes.Thus,our study provides the first evidence demonstrating that activation of both TEs and global transcription in zygotes are independent of Tet3-mediated 5mC oxidation.

  14. Trans-activation of an artificial dTam3 transposable element in transgenic tobacco plants

    NARCIS (Netherlands)

    Haring, Michel A.; Teeuwen-de Vroomen, Marianne J.; Nijkamp, H. John J.; Hille, Jacques

    1991-01-01

    In Antirrhinum majus only autonomous Tam3 transposons have been characterized. We investigated whether an artificial dTam3 element, with a deletion in the presumptive transposase coding region, can be trans-activated in tobacco by an activator Tam3 element, which was immobilized by the deletion of o

  15. Increased Variation in Adh Enzyme Activity in Drosophila Mutation-Accumulation Experiment Is Not Due to Transposable Elements at the Adh Structural Gene

    Science.gov (United States)

    Aquadro, C. F.; Tachida, H.; Langley, C. H.; Harada, K.; Mukai, T.

    1990-01-01

    We present here a molecular analysis of the region surrounding the structural gene encoding alcohol dehydrogenase (Adh) in 47 lines of Drosophila melanogaster that have each accumulated mutations for 300 generations. While these lines show a significant increase in variation of alcohol dehydrogenase enzyme activity compared to control lines, we found no restriction map variation in a 13-kb region including the complete Adh structural gene and roughly 5 kb of both 5' and 3' sequences. Thus, the rapid accumulation of ADH activity variation after 28,200 allele generations does not appear to have been due to the mobilization of transposable elements into or out of the Adh structural gene region. PMID:1963870

  16. Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus.

    Science.gov (United States)

    Chung, Daehwan; Farkas, Joel; Westpheling, Janet

    2013-05-01

    We show that a previously annotated hypothetical protein is the transposase of a new and active IS element, ISCahy1, widespread in Caldicellulosiruptor species. Transposition generated an 11-bp direct repeat at the insertion site in Caldicellulosiruptor hydrothermalis, suggesting a cut-and-paste mechanism. The discovery of an active insertion sequence in Caldicellulosiruptor species led to a survey of potential IS elements in the genome sequences of eight Caldicellulosiruptor species that identified several new elements, including one novel to this genus.

  17. Characteristics of transposable element exonization within human and mouse.

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    Noa Sela

    Full Text Available Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.

  18. [Transposition of the maize transposable element dSpm in transgenic sugar beets].

    Science.gov (United States)

    Kishchenko, E M; Komarnitskiĭ, I K; Kuchuk, N V

    2010-01-01

    Transgenic sugar beet plants carrying maize Spmn/dSpm transposable elements system have been constructed. Heterologous system of maize transposable elements Spm/dSpm was active in transgenic sugar beets that permits transposon-based gene tagging and obtaining of marker-free transgenic sugar beet.

  19. Transposable elements and genetic instabilities in crop plants

    Energy Technology Data Exchange (ETDEWEB)

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  20. Transposable Elements and Genetic Instabilities in Crop Plants

    Science.gov (United States)

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  1. Transposable elements and circular DNAs

    KAUST Repository

    Mourier, Tobias

    2016-09-26

    Circular DNAs are extra-chromosomal fragments that become circularized by genomic recombination events. We have recently shown that yeast LTR elements generate circular DNAs through recombination events between their flanking long terminal repeats (LTRs). Similarly, circular DNAs can be generated by recombination between LTRs residing at different genomic loci, in which case the circular DNA will contain the intervening sequence. In yeast, this can result in gene copy number variations when circles contain genes and origins of replication. Here, I speculate on the potential and implications of circular DNAs generated through recombination between human transposable elements.

  2. Transposable elements: The enemies within.

    Science.gov (United States)

    Scarfò, Irene; Pellegrino, Elisa; Mereu, Elisabetta; Inghirami, Giorgio; Piva, Roberto

    2016-10-01

    Understanding transformation mechanisms other than genetic aberrations has recently captured the attention of cancer researchers. To date, the role of transposable elements (TEs) in tumor development remains largely undefined. However, an increasing number of studies have reported that loss of epigenetic control causes TE reactivation and consequent oncogenic transcription. Here, we discuss principal examples of TEs-driven oncogenesis. Available data suggest that long terminal repeats and long interspersed nuclear elements play a pivotal role as alternative promoters. These findings provide definitive experimental evidence that repetitive elements are a powerful underestimated force toward oncogenesis and open the possibility to new therapeutic treatments.

  3. Quantum states with strong positive partial transpose

    Science.gov (United States)

    Chruściński, Dariusz; Jurkowski, Jacek; Kossakowski, Andrzej

    2008-02-01

    We construct a large class of bipartite M⊗N quantum states which defines a proper subset of states with positive partial transposes (PPTs). Any state from this class has PPT but the positivity of its partial transposition is recognized with respect to canonical factorization of the original density operator. We propose to call elements from this class states with strong positive partial transposes (SPPTs). We conjecture that all SPPT states are separable.

  4. On circulant states with positive partial transpose

    OpenAIRE

    Chruściński, Dariusz; Kossakowski, Andrzej

    2007-01-01

    We construct a large class of quantum "d x d" states which are positive under partial transposition (so called PPT states). The construction is based on certain direct sum decomposition of the total Hilbert space displaying characteristic circular structure - that is way we call them circulant states. It turns out that partial transposition maps any such decomposition into another one and hence both original density matrix and its partially transposed partner share similar cyclic properties. ...

  5. Computing partial transposes and related entanglement functions

    CERN Document Server

    Maziero, Jonas

    2016-01-01

    The partial transpose (PT) is an important function for entanglement testing and quantification and also for the study of geometrical aspects of the quantum state space. In this article, considering general bipartite and multipartite discrete systems, explicit formulas ready for the numerical implementation of the PT and of related entanglement functions are presented and the Fortran code produced for that purpose is described. What is more, we obtain an analytical expression for the Hilbert-Schmidt entanglement of two-qudit systems and for the associated closest separable state. In contrast to previous works on this matter, we only use the properties of the PT, not applying Lagrange multipliers.

  6. Circulant states with positive partial transpose

    Science.gov (United States)

    Chruściński, Dariusz; Kossakowski, Andrzej

    2007-09-01

    We construct a large class of quantum d⊗d states which are positive under partial transposition (so called PPT states). The construction is based on certain direct sum decomposition of the total Hilbert space displaying characteristic circular structure—that is why we call them circulant states. It turns out that partial transposition maps any such decomposition into another one and hence both original density matrix and its partially transposed partner share similar cyclic properties. This class contains many well-known examples of PPT states from the literature and gives rise to a huge family of completely new states.

  7. Transposed Paternò-Büchi Reaction.

    Science.gov (United States)

    Kumarasamy, Elango; Raghunathan, Ramya; Kandappa, Sunil Kumar; Sreenithya, A; Jockusch, Steffen; Sunoj, Raghavan B; Sivaguru, J

    2017-01-18

    A complementary strategy of utilizing ππ* excited state of alkene instead of nπ* excited state of the carbonyl chromophore in a "transposed Paternò-Büchi" reaction is evaluated with atropisomeric enamides as the model system. Based on photophysical investigations, the nature of excited states and the reactive pathway was deciphered leading to atropselective reaction. This new concept of switching of excited-state configuration should pave the way to control the stereochemical course of photoreaction due to the orbital approaches required for photochemical reactivity.

  8. Computing Partial Transposes and Related Entanglement Functions

    Science.gov (United States)

    Maziero, Jonas

    2016-10-01

    The partial transpose (PT) is an important function for entanglement testing and quantification and also for the study of geometrical aspects of the quantum state space. In this article, considering general bipartite and multipartite discrete systems, explicit formulas ready for the numerical implementation of the PT and of related entanglement functions are presented and the Fortran code produced for that purpose is described. What is more, we obtain an analytical expression for the Hilbert-Schmidt entanglement of two-qudit systems and for the associated closest separable state. In contrast to previous works on this matter, we only use the properties of the PT, not applying Lagrange multipliers.

  9. Transposed-Letter and Laterality Effects in Lexical Decision

    Science.gov (United States)

    Perea, Manuel; Fraga, Isabel

    2006-01-01

    Two divided visual field lexical decision experiments were conducted to examine the role of the cerebral hemispheres in transposed-letter similarity effects. In Experiment 1, we created two types of nonwords: nonadjacent transposed-letter nonwords ("TRADEGIA"; the base word was "TRAGEDIA," the Spanish for "TRAGEDY") and two-letter different…

  10. Transposable elements in TDP-43-mediated neurodegenerative disorders.

    Directory of Open Access Journals (Sweden)

    Wanhe Li

    Full Text Available Elevated expression of specific transposable elements (TEs has been observed in several neurodegenerative disorders. TEs also can be active during normal neurogenesis. By mining a series of deep sequencing datasets of protein-RNA interactions and of gene expression profiles, we uncovered extensive binding of TE transcripts to TDP-43, an RNA-binding protein central to amyotrophic lateral sclerosis (ALS and frontotemporal lobar degeneration (FTLD. Second, we find that association between TDP-43 and many of its TE targets is reduced in FTLD patients. Third, we discovered that a large fraction of the TEs to which TDP-43 binds become de-repressed in mouse TDP-43 disease models. We propose the hypothesis that TE mis-regulation contributes to TDP-43 related neurodegenerative diseases.

  11. Unwrapping ADMM: Efficient Distributed Computing via Transpose Reduction

    Science.gov (United States)

    2016-05-11

    Unwrapping ADMM: Efficient Distributed Computing via Transpose Reduction Thomas Goldstein Gavin Taylor Kawika Barabin Kent Sayre University of...of yk+1 is computed with either an analytical solution, or using a simple 1-dimensional lookup table of solutions. Thomas Goldstein, Gavin Taylor ... Taylor , Kawika Barabin, Kent Sayre On the other hand, transpose reduction removes the ma- trix D from the objective function and corresponds to (4

  12. Characterization of Transposable Elements in Laccaria bicolor

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Tuskan, Gerald A [ORNL; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

    2012-01-01

    Background: The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. Methodology/Principal Findings: TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copies elements distributed within 172 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs are ancient except some terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TEs expansion in L. bicolor; the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 500,000 years ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. Conclusions: This analysis represents an initial characterization of TEs in the L. bicolor genome, contributes to genome assembly and to a greater understanding of the role TEs played in genome organization and evolution, and provides a valuable resource for the ongoing Laccaria Pan-Genome project supported by the U.S.-DOE Joint Genome Institute.

  13. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements.

    Science.gov (United States)

    Staton, S Evan; Bakken, Bradley H; Blackman, Benjamin K; Chapman, Mark A; Kane, Nolan C; Tang, Shunxue; Ungerer, Mark C; Knapp, Steven J; Rieseberg, Loren H; Burke, John M

    2012-10-01

    Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.

  14. Parallel matrix transpose algorithms on distributed memory concurrent computers

    Energy Technology Data Exchange (ETDEWEB)

    Choi, J.; Walker, D.W. [Oak Ridge National Lab., TN (United States); Dongarra, J.J. [Oak Ridge National Lab., TN (United States)]|[Univ. of Tennessee, Knoxville, TN (United States). Dept. of Computer Science

    1993-10-01

    This paper describes parallel matrix transpose algorithms on distributed memory concurrent processors. It is assumed that the matrix is distributed over a P x Q processor template with a block scattered data distribution. P, Q, and the block size can be arbitrary, so the algorithms have wide applicability. The communication schemes of the algorithms are determined by the greatest common divisor (GCD) of P and Q. If P and Q are relatively prime, the matrix transpose algorithm involves complete exchange communication. If P and Q are not relatively prime, processors are divided into GCD groups and the communication operations are overlapped for different groups of processors. Processors transpose GCD wrapped diagonal blocks simultaneously, and the matrix can be transposed with LCM/GCD steps, where LCM is the least common multiple of P and Q. The algorithms make use of non-blocking, point-to-point communication between processors. The use of nonblocking communication allows a processor to overlap the messages that it sends to different processors, thereby avoiding unnecessary synchronization. Combined with the matrix multiplication routine, C = A{center_dot}B, the algorithms are used to compute parallel multiplications of transposed matrices, C = A{sup T}{center_dot}B{sup T}, in the PUMMA package. Details of the parallel implementation of the algorithms are given, and results are presented for runs on the Intel Touchstone Delta computer.

  15. Survey of transposable elements in sugarcane expressed sequence tags (ESTs

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    Rossi Magdalena

    2001-01-01

    Full Text Available The sugarcane expressed sequence tag (SUCEST project has produced a large number of cDNA sequences from several plant tissues submitted or not to different conditions of stress. In this paper we report the result of a search for transposable elements (TEs revealing a surprising amount of expressed TEs homologues. Of the 260,781 sequences grouped in 81,223 fragment assembly program (Phrap clusters, a total of 276 clones showed homology to previously reported TEs using a stringent cut-off value of e-50 or better. Homologous clones to Copia/Ty1 and Gypsy/Ty3 groups of long terminal repeat (LTR retrotransposons were found but no non-LTR retroelements were identified. All major transposon families were represented in sugarcane including Activator (Ac, Mutator (MuDR, Suppressor-mutator (En/Spm and Mariner. In order to compare the TE diversity in grasses genomes, we carried out a search for TEs described in sugarcane related species O.sativa, Z. mays and S. bicolor. We also present preliminary results showing the potential use of TEs insertion pattern polymorphism as molecular markers for cultivar identification.

  16. Epigenetic regulation of transposable element derived human gene promoters.

    Science.gov (United States)

    Huda, Ahsan; Bowen, Nathan J; Conley, Andrew B; Jordan, I King

    2011-04-01

    It was previously thought that epigenetic histone modifications of mammalian transposable elements (TEs) serve primarily to defend the genome against deleterious effects associated with their activity. However, we recently showed that, genome-wide, human TEs can also be epigenetically modified in a manner consistent with their ability to regulate host genes. Here, we explore the ability of TE sequences to epigenetically regulate individual human genes by focusing on the histone modifications of promoter sequences derived from TEs. We found 1520 human genes that initiate transcription from within TE-derived promoter sequences. We evaluated the distributions of eight histone modifications across these TE-promoters, within and between the GM12878 and K562 cell lines, and related their modification status with the cell-type specific expression patterns of the genes that they regulate. TE-derived promoters are significantly enriched for active histone modifications, and depleted for repressive modifications, relative to the genomic background. Active histone modifications of TE-promoters peak at transcription start sites and are positively correlated with increasing expression within cell lines. Furthermore, differential modification of TE-derived promoters between cell lines is significantly correlated with differential gene expression. LTR-retrotransposon derived promoters in particular play a prominent role in mediating cell-type specific gene regulation, and a number of these LTR-promoter genes are implicated in lineage-specific cellular functions. The regulation of human genes mediated by histone modifications targeted to TE-derived promoters is consistent with the ability of TEs to contribute to the epigenomic landscape in a way that provides functional utility to the host genome.

  17. Transposed-Letter Priming across Inflectional Morpheme Boundaries

    Science.gov (United States)

    Zargar, Ehsan Shafiee; Witzel, Naoko

    2017-01-01

    This study reports findings from two experiments testing whether a transposed-letter (TL) priming effect can be obtained when the transposition occurs across morphological boundaries. Previous studies have primarily tested derivationally complex words or compound words, but have not examined a more rule-based and productive morphological…

  18. Prediction of transposable element derived enhancers using chromatin modification profiles.

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    Ahsan Huda

    Full Text Available Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.

  19. Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

    Science.gov (United States)

    Kijima, T E; Innan, Hideki

    2013-11-01

    A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

  20. Transposable elements re-wire and fine-tune the transcriptome.

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    Michael Cowley

    Full Text Available What good are transposable elements (TEs? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs-particularly retrotransposons-contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.

  1. Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene

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    Shomron Noam

    2007-11-01

    Full Text Available Abstract Background Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of transposed elements in duplicated genes than in single-copy genes. Results Genome-wide analysis of exonization of transposed elements revealed a higher rate of exonization within duplicated genes relative to single-copy genes. The gene for TIF-IA, an RNA polymerase I transcription initiation factor, underwent a humanoid-specific triplication, all three copies of the gene are active transcriptionally, although only one copy retains the ability to generate the TIF-IA protein. Prior to TIF-IA triplication, an Alu element was inserted into the first intron. In one of the non-protein coding copies, this Alu is exonized. We identified a single point mutation leading to exonization in one of the gene duplicates. When this mutation was introduced into the TIF-IA coding copy, exonization was activated and the level of the protein-coding mRNA was reduced substantially. A very low level of exonization was detected in normal human cells. However, this exonization was abundant in most leukemia cell lines evaluated, although the genomic sequence is unchanged in these cancerous cells compared to normal cells. Conclusion The definition of the Alu element within the TIF-IA gene as an exon is restricted to certain types of cancers; the element is not exonized in normal human cells. These results further our understanding of the delicate interplay between gene duplication and alternative splicing and of the molecular evolutionary mechanisms leading to genetic innovations. This implies the existence of purifying selection against exonization in single copy genes, with duplicate genes free from such constrains.

  2. BLAT-based comparative analysis for transposable elements: BLATCAT.

    Science.gov (United States)

    Lee, Sangbum; Oh, Sumin; Kang, Keunsoo; Han, Kyudong

    2014-01-01

    The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes.

  3. BLAT-Based Comparative Analysis for Transposable Elements: BLATCAT

    Directory of Open Access Journals (Sweden)

    Sangbum Lee

    2014-01-01

    Full Text Available The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT based comparative analysis for transposable elements (BLATCAT program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes.

  4. Cooperation is fleeting in the world of transposable elements.

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    Andreas Wagner

    2006-12-01

    Full Text Available Composite transposons are key vehicles for the worldwide spreading of genes that allow bacteria to survive toxic compounds. Composite transposons consist of two smaller transposable elements called insertion sequences (ISs, which flank the genes that permit such survival. Each IS in a composite transposon can either transpose alone, selfishly, or it can transpose cooperatively, jointly with the other IS. Cooperative transposition can enhance an IS's chance of survival, but it also carries the risk of transposon destruction. I use game theory to show that the conditions under which cooperative transposition is an evolutionarily stable strategy (ESS are not biologically realistic. I then analyze the distribution of thousands of ISs in more than 200 bacterial genomes to test the following prediction of the game-theoretical model: if cooperative transposition was an ESS, then the closely spaced ISs that characterize composite transposons should be more abundant in genomes than expected by chance. The data show that this is not the case. Cooperativity can only be maintained in a transitional, far-from-equilibrium state shortly after a selection pressure first arises. This is the case in the spreading of antibiotic resistance, where we are witnessing a fleeting moment in evolution, a moment in which cooperation among selfish DNA molecules has provided a means of survival. Because such cooperation does not pay in the long run, the vehicles of such survival will eventually disappear again. My analysis demonstrates that game theory can help explain behavioral strategies even for mobile DNA.

  5. Population and clinical genetics of human transposable elements in the (post) genomic era

    Science.gov (United States)

    Rishishwar, Lavanya; Wang, Lu; Clayton, Evan A.; Mariño-Ramírez, Leonardo; McDonald, John F.; Jordan, I. King

    2017-01-01

    ABSTRACT Recent technological developments—in genomics, bioinformatics and high-throughput experimental techniques—are providing opportunities to study ongoing human transposable element (TE) activity at an unprecedented level of detail. It is now possible to characterize genome-wide collections of TE insertion sites for multiple human individuals, within and between populations, and for a variety of tissue types. Comparison of TE insertion site profiles between individuals captures the germline activity of TEs and reveals insertion site variants that segregate as polymorphisms among human populations, whereas comparison among tissue types ascertains somatic TE activity that generates cellular heterogeneity. In this review, we provide an overview of these new technologies and explore their implications for population and clinical genetic studies of human TEs. We cover both recent published results on human TE insertion activity as well as the prospects for future TE studies related to human evolution and health.

  6. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

    Science.gov (United States)

    Castanera, Raúl; López-Varas, Leticia; Borgognone, Alessandra; LaButti, Kurt; Lapidus, Alla; Schmutz, Jeremy; Grimwood, Jane; Pisabarro, Antonio G.; Grigoriev, Igor V.; Ramírez, Lucía

    2016-01-01

    Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation. PMID:27294409

  7. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.

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    Raúl Castanera

    2016-06-01

    Full Text Available Transposable elements (TEs are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.

  8. A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes.

    Science.gov (United States)

    Gupta, Smriti; Gallavotti, Andrea; Stryker, Gabrielle A; Schmidt, Robert J; Lal, Shailesh K

    2005-01-01

    We recently described a maize mutant caused by an insertion of a Helitron type transposable element (Lal, S.K., Giroux, M.J., Brendel, V., Vallejos, E. and Hannah, L.C., 2003, Plant Cell, 15: 381-391). Here we describe another Helitron insertion in the barren stalk1 gene of maize. The termini of a 6525 bp insertion in the proximal promoter region of the mutant reference allele of maize barren stalk1 gene (ba1-ref) shares striking similarity to the Helitron insertion we reported in the Shrunken-2 gene. This insertion is embedded with pseudogenes that differ from the pseudogenes discovered in the mutant Shrunken-2 insertion. Using the common terminal ends of the mutant insertions as a query, we discovered other Helitron insertions in maize BAC clones. Based on the comparison of the insertion site and PCR amplified genomic sequences, these elements inserted between AT dinucleotides. These putative non-autonomous Helitron insertions completely lacked sequences similar to RPA (replication protein A) and DNA Helicases reported in other species. A blastn analysis indicated that both the 5' and 3' termini of Helitrons are repeated in the maize genome. These data provide strong evidence that Helitron type transposable elements are active and may have played an essential role in the evolution and expansion of the maize genome.

  9. Enhancer/Suppressor mutator (En/Spm)-like transposable elements of cassava (Manihot esculenta) are transcriptionally inactive.

    Science.gov (United States)

    Gbadegesin, M A; Beeching, J R

    2010-04-13

    Transposable elements contribute to the size, structure, variation, and diversity of the genome and have major effects on gene function. Sequencing projects have revealed the diversity of transposable elements in many organisms and have shown that they constitute a high percentage of the genome. PCR-based techniques using degenerate primers designed from conserved enzyme domains of transposable elements can provide quick and extensive surveys, making study of diversity and abundance and their applications possible in species where full genome sequence data are not yet available. We studied cassava (Manihot esculenta) En/Spm-like transposons (Meens) with regard to genomic distribution, sequence diversity and methylation status. Cassava transposase fragments characteristic of En/Spm-like transposons were isolated, cloned and characterized. Sequence analysis showed that cassava En/Spm-like elements are highly conserved, with overall identity in the range of 68-98%. Southern hybridization supports the presence of multiple copies of En/Spm-like transposons integrated in the genome of all cassava cultivars that we tested. Hybridization patterns of HpaII- and MspI-digested cassava genomic DNA revealed highly methylated sequences. There were no clear differences in hybridization pattern between the cultivars. We did not detect RNA transcripts of Meens by Northern procedures. We examined the possibility of recent transposition activities of the cassava En/Spm-like elements.

  10. Differences of Skew Schur Functions of Staircases with Transposed Foundations

    CERN Document Server

    Morin, Matthew

    2010-01-01

    We consider the skew diagram $\\Delta_n$, which is the $180^\\circ$ rotation of the staircase diagram $\\delta_n = (n,n-1,n-2,...,2,1)$. We create a staircase with bad foundation by augmenting $\\Delta_n$ with another skew diagram, which we call the \\textit{foundation}. We consider pairs of staircases with bad foundation whose foundations are transposes of one another. Among these pairs, we show that the difference of the corresponding skew Schur functions is Schur-positive in the case when one of the foundations consists of either a one or two row diagram, or a hook diagram.

  11. Isolation and characterization of a potential transposable element from Wolbachia

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Wolbachia are a group of Rickettsia-like bacteria which parasitize the cells of a wide range of anthropoid. These microorganisms are associated with the reproductive and developmental abnormalities io their hosts. To study the molecular mechanism underlying such phenomena, we analyzed the genomic difference between Wolbachia with different cytoplasmic incompatibility (CI) phenotype using representational difference analysis method. A potential transposable element, which exists in the strong CI-inducing strain wRi, was isolated. This element was designated as Wolbachia insertion sequence element (WISE).

  12. Transpose symmetry of the Jones matrix and topological phases.

    Science.gov (United States)

    Bhandari, Rajendra

    2008-04-15

    The transmission Jones matrix of an arbitrary stack of reciprocal plane-parallel plates that has been turned through 180 degrees about an axis in the plane of the stack is, in an appropriate basis, the transpose of the transmission matrix of the unturned slab with a change in the sign of the off-diagonal elements. We prove this convention-free result for the case where reflection at the interfaces can be ignored and use it to devise an experimental scheme to separate isotropic and topological phase changes in a reciprocal optical medium.

  13. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.

    Science.gov (United States)

    Notwell, James H; Chung, Tisha; Heavner, Whitney; Bejerano, Gill

    2015-03-25

    The neocortex is a mammalian-specific structure that is responsible for higher functions such as cognition, emotion and perception. To gain insight into its evolution and the gene regulatory codes that pattern it, we studied the overlap of its active developmental enhancers with transposable element (TE) families and compared this overlap to uniformly shuffled enhancers. Here we show a striking enrichment of the MER130 repeat family among active enhancers in the mouse dorsal cerebral wall, which gives rise to the neocortex, at embryonic day 14.5. We show that MER130 instances preserve a common code of transcriptional regulatory logic, function as enhancers and are adjacent to critical neocortical genes. MER130, a nonautonomous interspersed TE, originates in the tetrapod or possibly Sarcopterygii ancestor, which far predates the appearance of the neocortex. Our results show that MER130 elements were recruited, likely through their common regulatory logic, as neocortical enhancers.

  14. Transposable elements and early evolution of sex chromosomes in fish.

    Science.gov (United States)

    Chalopin, Domitille; Volff, Jean-Nicolas; Galiana, Delphine; Anderson, Jennifer L; Schartl, Manfred

    2015-09-01

    In many organisms, the sex chromosome pair can be recognized due to heteromorphy; the Y and W chromosomes have often lost many genes due to the absence of recombination during meiosis and are frequently heterochromatic. Repetitive sequences are found at a high proportion on such heterochromatic sex chromosomes and the evolution and emergence of sex chromosomes has been connected to the dynamics of repeats and transposable elements. With an amazing plasticity of sex determination mechanisms and numerous instances of independent emergence of novel sex chromosomes, fish represent an excellent lineage to investigate the early stages of sex chromosome differentiation, where sex chromosomes often are homomorphic and not heterochromatic. We have analyzed the composition, distribution, and relative age of TEs from available sex chromosome sequences of seven teleost fish. We observed recent bursts of TEs and simple repeat accumulations around young sex determination loci. More strikingly, we detected transposable element (TE) amplifications not only on the sex determination regions of the Y and W sex chromosomes, but also on the corresponding regions of the X and Z chromosomes. In one species, we also clearly demonstrated that the observed TE-rich sex determination locus originated from a TE-poor genomic region, strengthening the link between TE accumulation and emergence of the sex determination locus. Altogether, our results highlight the role of TEs in the initial steps of differentiation and evolution of sex chromosomes.

  15. Transposed genes in Arabidopsis are often associated with flanking repeats.

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    Margaret R Woodhouse

    2010-05-01

    Full Text Available Much of the eukaryotic genome is known to be mobile, largely due to the movement of transposons and other parasitic elements. Recent work in plants and Drosophila suggests that mobility is also a feature of many nontransposon genes and gene families. Indeed, analysis of the Arabidopsis genome suggested that as many as half of all genes had moved to unlinked positions since Arabidopsis diverged from papaya roughly 72 million years ago, and that these mobile genes tend to fall into distinct gene families. However, the mechanism by which single gene transposition occurred was not deduced. By comparing two closely related species, Arabidopsis thaliana and Arabidopsis lyrata, we sought to determine the nature of gene transposition in Arabidopsis. We found that certain categories of genes are much more likely to have transposed than others, and that many of these transposed genes are flanked by direct repeat sequence that was homologous to sequence within the orthologous target site in A. lyrata and which was predominantly genic in identity. We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition.

  16. Evolutionary interaction between W/Y chromosome and transposable elements.

    Science.gov (United States)

    Śliwińska, Ewa B; Martyka, Rafał; Tryjanowski, Piotr

    2016-06-01

    The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.

  17. Genomic patterns associated with paternal/maternal distribution of transposable elements

    Science.gov (United States)

    Jurka, Jerzy

    2003-03-01

    Transposable elements (TEs) are specialized DNA or RNA fragments capable of surviving in intragenomic niches. They are commonly, perhaps unjustifiably referred to as "selfish" or "parasitic" elements. TEs can be divided in two major classes: retroelements and DNA transposons. The former include non-LTR retrotransposons and retrovirus-like elements, using reverse transriptase for their reproduction prior to integration into host DNA. The latter depend mostly on host DNA replication, with possible exception of rolling-circle transposons recently discovered by our team. I will review basic information on TEs, with emphasis on human Alu and L1 retroelements discussed in the context of genomic organization. TEs are non-randomly distributed in chromosomal DNA. In particular, human Alu elements tend to prefer GC-rich regions, whereas L1 accumulate in AT-rich regions. Current explanations of this phenomenon focus on the so called "target effects" and post-insertional selection. However, the proposed models appear to be unsatisfactory and alternative explanations invoking "channeling" to different chromosomal regions will be a major focus of my presentation. Transposable elements (TEs) can be expressed and integrated into host DNA in the male or female germlines, or both. Different models of expression and integration imply different proportions of TEs on sex chromosomes and autosomes. The density of recently retroposed human Alu elements is around three times higher on chromosome Y than on chromosome X, and over two times higher than the average density for all human autosomes. This implies Alu activity in paternal germlines. Analogous inter-chromosomal proportions for other repeat families should determine their compatibility with one of the three basic models describing the inheritance of TEs. Published evidence indicates that maternally and paternally imprinted genes roughly correspond to GC-rich and AT-rich DNA. This may explain the observed chromosomal distribution of

  18. Transposable element proliferation as a possible side effect of endosymbiont manipulations.

    Science.gov (United States)

    Kraaijeveld, Ken; Bast, Jens

    2012-09-01

    The mode of reproduction has been predicted to affect the proliferation of transposable elements (TEs). A population that switches from sexual to asexual reproduction could either accumulate TEs because purifying selection becomes less efficient, or a decrease in TE load because the opportunity for horizontal transmission is reduced. A third possibility is that the mechanism that induces asexual reproduction affects TE dynamics as a side effect. We propose two such mechanisms that might explain recently described patterns of TE abundance in sexual and asexual lineages of the parasitoid wasp Leptopilina clavipes. Asexual reproduction in this species is induced by endosymbiotic Wolbachia bacteria. In order to achieve parthenogenesis in its host, Wolbachia might remove methylation or interfere with Argonaute proteins. Both methylation and Argonaute proteins are known to control TE activity in other species. By interfering with either, Wolbachia might therefore secondarily hamper the control of specific TEs.

  19. An Ac transposon system based on maize chromosome 4S for isolating long-distance-transposed Ac tags in the maize genome.

    Science.gov (United States)

    Wang, Fei; Li, Zhaoying; Fan, Jun; Li, Pengfei; Hu, Wei; Wang, Gang; Xu, Zhengkai; Song, Rentao

    2010-12-01

    Transposon tagging is an important tool for gene isolation and functional studies. In maize, several transposon-tagging systems have been developed, mostly using Activator/Dissociation (Ac/Ds) and Mutator systems. Here, we establish another Ac-based transposon system with the donor Ac tightly linked with sugary1 (su1) on maize chromosome 4S. Newly transposed Ac (tr-Acs) were detected based on a negative dosage effect, and long-distance-transposed Ac events were identified and isolated from the donor Ac by a simple backcross scheme. In this study, we identified 208 independent long-distance-transposed Ac lines. Thirty-one flanking sequences of these tr-Acs were isolated and localized in the maize genome. As found in previous studies, the tr-Acs preferentially inserted into genic sequences. The distribution of tr-Acs is not random. In our study, the tr-Acs preferentially transposed into chromosomes 1, 2, 9 and 10. We discuss the preferential distribution of tr-Acs from Ac systems. Our system is complementary to two other Ac-based regional-mutagenesis systems in maize, and the combined use of these systems will achieve an even and high-density distribution of Ac elements throughout the maize genome for functional-genomics studies.

  20. Transposable elements: from DNA parasites to architects of metazoan evolution.

    Science.gov (United States)

    Piskurek, Oliver; Jackson, Daniel J

    2012-07-12

    One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.

  1. In Silico Methods to Identify Exapted Transposable Element Families.

    Science.gov (United States)

    Ramsay, LeeAnn; Bourque, Guillaume

    2016-01-01

    Transposable elements (TEs) have recently been shown to have many regulatory roles within the genome. In this chapter, we will examine two in silico methods for analyzing TEs and identifying families that may have acquired such functions. The first method will look at how the overrepresentation of a repeat family in a set of genomic features can be discovered. The example situation of OCT4 binding sites originating from LTR7 TE sequences will be used to show how this method could be applied. The second method will describe how to determine if a TE family exhibits a cell type-specific expression pattern. As an example, we will look at the expression of HERV-H, an endogenous retrovirus known to act as an lncRNA in embryonic stem cells. We will use this example to demonstrate how RNA-seq data can be used to compare cell type expression of repeats.

  2. Identification and frequency of transposable elements in Eucalyptus

    Directory of Open Access Journals (Sweden)

    Maurício Bacci Jr.

    2005-01-01

    Full Text Available Transposable elements (TE are major components of eukaryotic genomes and involved in cell regulation and organism evolution. We have analyzed 123,889 expressed sequence tags of the Eucalyptus Genome Project database and found 124 sequences representing 76 TE in 9 groups, of which copia, MuDR and FAR1 groups were the most abundant. The low amount of sequences of TE may reflect the high efficiency of repression of these elements, a process that is called TE silencing. Frequency of groups of TE in Eucalyptus libraries which were prepared with different tissues or physiologic conditions from seedlings or adult plants indicated that developing plants experience the expression of a much wider spectrum of TE groups than that seen in adult plants. These are preliminary results that identify the most relevant TE groups involved with Eucalyptus development, which is important for industrial wood production.

  3. Transposable Elements: From DNA Parasites to Architects of Metazoan Evolution

    Directory of Open Access Journals (Sweden)

    Oliver Piskurek

    2012-07-01

    Full Text Available One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs. Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.

  4. A blessing in disguise: Transposable elements are more than parasites.

    Science.gov (United States)

    Martin, Antoine; Bendahmane, Abdelhafid

    2010-07-01

    Transposable elements (TEs) are various DNA fragments inserted throughout genomes, which are able to move or duplicate themselves. Recent advances in genomics have placed them back at the center of genome dynamics. One of the emerging observations, especially in plants, is the importance of interactions between TEs and genes to generate or to participate in relevant functions essential for development, adaptation and/or life cycle. A recent publication illustrates the influence of TEs epigenetic control on the expression of a neighboring gene crucial for reproduction. Different reports lately showed that a fundamental mechanism such as imprinting is likely to be closely linked to the dynamics of TEs epigenetic control. Here we discuss and bring together these and others recent findings, to underline that the cis-vicinity or the trans-relation between TEs and genes could bring unexpected but positive outcomes.

  5. Transposable elements and small RNAs: Genomic fuel for species diversity.

    Science.gov (United States)

    Hoffmann, Federico G; McGuire, Liam P; Counterman, Brian A; Ray, David A

    2015-01-01

    While transposable elements (TE) have long been suspected of involvement in species diversification, identifying specific roles has been difficult. We recently found evidence of TE-derived regulatory RNAs in a species-rich family of bats. The TE-derived small RNAs are temporally associated with the burst of species diversification, suggesting that they may have been involved in the processes that led to the diversification. In this commentary, we expand on the ideas that were briefly touched upon in that manuscript. Specifically, we suggest avenues of research that may help to identify the roles that TEs may play in perturbing regulatory pathways. Such research endeavors may serve to inform evolutionary biologists of the ways that TEs have influenced the genomic and taxonomic diversity around us.

  6. Transposing, Transforming and Transcending Tradition in Creative Digital Media

    DEFF Research Database (Denmark)

    Prager, Phillip; Thomas, Maureen; Selsjord, Marianne

    2015-01-01

    How can digital media technologies, contemporary theories of creativity, and tradition combine to develop the aesthetics of computer-based art today and in the future? Through contextualised case-studies, this chapter investigates how games, information technologies, and traditional visual...... and storytelling arts combine to create rich, complex, and engaging moving-image based artworks with wide appeal. It examines how dramatist and interactive media artist Maureen Thomas and 3D media artist and conservator Marianne Selsjord deploy creative digital technologies to transpose, transform, and transcend...... of the aspirations and approaches of 20th-century avant-garde artists, revealing these as a potent source of conceptual riches for the digital media creators of today and tomorrow....

  7. Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

    Science.gov (United States)

    Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

    2012-01-01

    Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial

  8. Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria.

    Directory of Open Access Journals (Sweden)

    Lukasz Dziewit

    Full Text Available Several trap plasmids (enabling positive selection of transposition events were used to identify a pool of functional transposable elements (TEs residing in bacteria of the genus Paracoccus (Alphaproteobacteria. Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i 37 insertion sequences (ISs representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634, (ii a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv a transposable genomic island TnPpa1 (45 kb. Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1 and (ii structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family. We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value by horizontal gene transfer, which is considered the driving force of

  9. Useful parasites: the evolutionary biology and biotechnology applications of transposable elements

    Indian Academy of Sciences (India)

    GEORGI N. BONCHEV

    2016-12-01

    Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as ‘parasitic’ or ‘selfish’. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of theirhosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of ‘selfish’ DNA,play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobilefraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

  10. Useful parasites: the evolutionary biology and biotechnology applications of transposable elements.

    Science.gov (United States)

    Bonchev, Georgi N

    2016-12-01

    Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of 'selfish' DNA, play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobile fraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

  11. SoyTEdb: a comprehensive database of transposable elements in the soybean genome

    Directory of Open Access Journals (Sweden)

    Zhu Liucun

    2010-02-01

    Full Text Available Abstract Background Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop. Description Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I and 6,029 DNA transposons (Class II with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95% of these elements (particularly a few hundred low-copy-number families are first described in this study. Conclusion SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually

  12. A novel transposable Mu-like prophage in Bacillus alcalophilus CGMCC 1.3604(ATCC 27647)

    Institute of Scientific and Technical Information of China (English)

    Junjie; Yang; Yimeng; Kong; Xuan; Li; Sheng; Yang

    2015-01-01

    <正>Dear Editor,Transposable phages,which are reproduced by transposition(Harshey,2012;Taylor,1963),have been widely applied in the field of biotechnology to manipulate operon/gene fusions,in vivo cloning,randomion mutagenesis,and integration of DNA into bacterial genomes(Abalakina et al.,2008;Akhverdyan et al.,2011).One of the best-studied transposable phages is

  13. Multi-particle entanglement under asymptotic positive partial transpose preserving operations

    OpenAIRE

    Ishizaka, S; Plenio, M. B.

    2005-01-01

    We demonstrate that even under positive partial transpose preserving operations in an asymptotic setting GHZ and W states are not reversibly interconvertible. We investigate the structure of minimal reversible entanglement generating set (MREGS) for tri-partite states under positive partial transpose (ppt) preserving operations. We demonstrate that the set consisting of W and EPR states alone cannot be an MREGS. In this context we prove the surprising result that the relative entropy of entan...

  14. Transposable element influences on gene expression in plants.

    Science.gov (United States)

    Hirsch, Cory D; Springer, Nathan M

    2017-01-01

    Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

  15. Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Tuskan, Gerald A [ORNL; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

    2012-01-01

    Background: The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TEspecific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. Methodology/Principal Findings: TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. Conclusions: This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.

  16. Transposable-element associated small RNAs in Bombyx mori genome.

    Directory of Open Access Journals (Sweden)

    Yimei Cai

    Full Text Available Small RNAs are a group of regulatory RNA molecules that control gene expression at transcriptional or post-transcriptional levels among eukaryotes. The silkworm, Bombyx mori L., genome harbors abundant repetitive sequences derived from families of retrotransposons and transposons, which together constitute almost half of the genome space and provide ample resource for biogenesis of the three major small RNA families. We systematically discovered transposable-element (TE-associated small RNAs in B. mori genome based on a deep RNA-sequencing strategy and the effort yielded 182, 788 and 4,990 TE-associated small RNAs in the miRNA, siRNA and piRNA species, respectively. Our analysis suggested that the three small RNA species preferentially associate with different TEs to create sequence and functional diversity, and we also show evidence that a Bombyx non-LTR retrotransposon, bm1645, alone contributes to the generation of TE-associated small RNAs in a very significant way. The fact that bm1645-associated small RNAs partially overlap with each other implies a possibility that this element may be modulated by different mechanisms to generate different products with diverse functions. Taken together, these discoveries expand the small RNA pool in B. mori genome and lead to new knowledge on the diversity and functional significance of TE-associated small RNAs.

  17. Transposable element recruitments in the mammalian placenta: impacts and mechanisms.

    Science.gov (United States)

    Emera, Deena; Wagner, Günter P

    2012-07-01

    Transposable elements (TEs) are mobile DNA elements found at high frequency in mammalian genomes. Although these elements are generally perceived as genomic parasites, they have the potential to influence host genome function in many beneficial ways. This article discusses the role TEs have played in the evolution of the placenta and pregnancy in viviparous mammals. Using examples from our own research and the literature, we argue that frequent recruitment of TEs, in particular of retroelements, has facilitated the extreme diversification of tissues at the maternal-fetal interface. We also discuss the mechanisms by which TEs have been recruited for functions during pregnancy. We argue that retroelements are pre-adapted to becoming cis-regulatory elements for host genomes because they need to utilize host regulatory signals for their own life cycle. However, although TEs contain some of the signals necessary for host functions upon insertion, they often require modification before acquiring a biological role in a host tissue. We discuss the process by which one TE was transformed into a promoter for prolactin expression in the endometrium, describing a model for TE domestication called 'epistatic capture'.

  18. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Raquel S Linheiro

    Full Text Available Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes.

  19. The majority of primate-specific regulatory sequences are derived from transposable elements.

    Directory of Open Access Journals (Sweden)

    Pierre-Étienne Jacques

    2013-05-01

    Full Text Available Although emerging evidence suggests that transposable elements (TEs have contributed novel regulatory elements to the human genome, their global impact on transcriptional networks remains largely uncharacterized. Here we show that TEs have contributed to the human genome nearly half of its active elements. Using DNase I hypersensitivity data sets from ENCODE in normal, embryonic, and cancer cells, we found that 44% of open chromatin regions were in TEs and that this proportion reached 63% for primate-specific regions. We also showed that distinct subfamilies of endogenous retroviruses (ERVs contributed significantly more accessible regions than expected by chance, with up to 80% of their instances in open chromatin. Based on these results, we further characterized 2,150 TE subfamily-transcription factor pairs that were bound in vivo or enriched for specific binding motifs, and observed that TEs contributing to open chromatin had higher levels of sequence conservation. We also showed that thousands of ERV-derived sequences were activated in a cell type-specific manner, especially in embryonic and cancer cells, and we demonstrated that this activity was associated with cell type-specific expression of neighboring genes. Taken together, these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape.

  20. Detection of transposable elements by their compositional bias

    Directory of Open Access Journals (Sweden)

    Anxolabéhère Dominique

    2004-07-01

    Full Text Available Abstract Background Transposable elements (TE are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be used as a tool for detection and analysis of TE sequences. Results We compared the composition of TE sequences and host gene sequences using probabilistic models of nucleotide sequences. We used hidden Markov models (HMM, which take into account the base composition of the sequences (occurrences of words n nucleotides long, with n ranging here from 1 to 4 and the heterogeneity between coding and non-coding parts of sequences. We analyzed three sets of sequences containing class I TEs, class II TEs and genes respectively in three species: Drosophila melanogaster, Cænorhabditis elegans and Arabidopsis thaliana. Each of these sets had a distinct, homogeneous composition, enabling us to distinguish between the two classes of TE and the genes. However the particular base composition of the TEs differed in the three species studied. Conclusions This approach can be used to detect and annotate TEs in genomic sequences and complements the current homology-based TE detection methods. Furthermore, the HMM method is able to identify the parts of a sequence in which the nucleotide composition resembles that of a coding region of a TE. This is useful for the detailed annotation of TE sequences, which may contain an ancient, highly diverged coding region that is no longer fully functional.

  1. Characterization of new hAT transposable elements in 12 Drosophila genomes.

    Science.gov (United States)

    de Freitas Ortiz, Mauro; Loreto, Elgion Lucio Silva

    2009-01-01

    In silico searches for sequences homologous to hAT elements in 12 Drosophila genomes have allowed us to identify 37 new hAT elements (8 in D. ananassae, 11 in D. mojavensis, 2 in D. sechellia, 1 in D. simulans, 2 in D. virilis, 3 in D. yakuba, 3 in D. persimilis, 1 in D. grimshawi, 5 in D. willistoni and 1 in D. pseudobscura). The size of these elements varies from 2,359 to 4,962 bp and the terminal inverted repeats (TIRs) show lengths ranging from 10 to 24 bp. Several elements show intact transposase ORFs, suggesting that they are active. Conserved amino acid motifs were identified that correspond to those important for transposase activity. These elements are highly variable and phylogenetic analysis showed that they can be clustered into four different families. Incongruencies were observed between the phylogenies of the transposable elements and those of their hosts, suggesting that horizontal transfer may have occurred between some of the species.

  2. TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION.

    Science.gov (United States)

    Allen, Genevera I; Tibshirani, Robert

    2010-06-01

    Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable, meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal, in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility.

  3. Novel non-autonomous transposable elements onWchromosome of the silkworm, Bombyx mori

    Indian Academy of Sciences (India)

    Hiroaki Abe; Tsuguru Fujii; Toru Shimada; Kazuei Mita

    2010-09-01

    The sex chromosomes of the silkworm Bombyx mori are designated ZW(XY) for females and ZZ (XX) for males. Numerous long terminal repeat (LTR) and non-LTR retrotransposons, retroposons and DNA transposons have accumulated as strata on the W chromosome. However, there are nucleotide sequences that do not show the characteristics of typical transposable elements on the W chromosome. To analyse these uncharacterized nucleotide sequences on the W chromosome, we used whole-genome shotgun (WGS) data and assembled data that was obtained using male genome DNA. Through these analyses, we found that almost all of these uncharacterized sequences were non-autonomous transposable elements that do not fit into the conventional classification. It is notable that some of these transposable elements contained the Bombyx short interspersed element (Bm1) sequences in the elements. We designated them as secondary-Bm1 transposable elements (SBTEs). Because putative ancestral SBTE nucleotide sequences without Bm1 do not occur in theWGS data, we suggest that the Bm1 sequences of SBTEs are not carried on each element merely as a package but are components of each element. Therefore, we confirmed that SBTEs should be classified as a new group of transposable elements.

  4. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi

    Directory of Open Access Journals (Sweden)

    Kazimierz T. Tycowski

    2016-05-01

    Full Text Available The ENE (element for nuclear expression is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs from nuclear decay through triple-helix formation with the poly(A tail or 3′-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits.

  5. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.

    Science.gov (United States)

    Tycowski, Kazimierz T; Shu, Mei-Di; Steitz, Joan A

    2016-05-10

    The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs) from nuclear decay through triple-helix formation with the poly(A) tail or 3'-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits.

  6. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.

    Science.gov (United States)

    Wang, Lu; Rishishwar, Lavanya; Mariño-Ramírez, Leonardo; Jordan, I King

    2016-12-19

    Transposable element (TE) derived sequences are known to contribute to the regulation of the human genome. The majority of known TE-derived regulatory sequences correspond to relatively ancient insertions, which are fixed across human populations. The extent to which human genetic variation caused by recent TE activity leads to regulatory polymorphisms among populations has yet to be thoroughly explored. In this study, we searched for associations between polymorphic TE (polyTE) loci and human gene expression levels using an expression quantitative trait loci (eQTL) approach. We compared locus-specific polyTE insertion genotypes to B cell gene expression levels among 445 individuals from 5 human populations. Numerous human polyTE loci correspond to both cis and trans eQTL, and their regulatory effects are directly related to cell type-specific function in the immune system. PolyTE loci are associated with differences in expression between European and African population groups, and a single polyTE loci is indirectly associated with the expression of numerous genes via the regulation of the B cell-specific transcription factor PAX5 The polyTE-gene expression associations we found indicate that human TE genetic variation can have important phenotypic consequences. Our results reveal that TE-eQTL are involved in population-specific gene regulation as well as transcriptional network modification.

  7. Mobility of the maize transposable element En/Spm in Arabidopsis thaliana.

    Science.gov (United States)

    Cardon, G H; Frey, M; Saedler, H; Gierl, A

    1993-06-01

    The autonomous element En-1 of the maize En/Spm transposable element system is capable of frequent somatic and germinal excision in the heterologous host Arabidopsis thaliana. The pattern of En-homologous transcripts generated in transgenic Arabidopsis resembles En transcription in maize. An excision reporter construct based on NPT-II gene (pKEn2) can be used reliably for the isolation of En-1 germinal revertants by seed germination on kanamycin-containing medium. Re-insertion after germinal excision is apparently frequent. A dSpm receptor element can be efficiently trans-activated in Arabidopsis either by En-1 or by expressing cDNAs of tnpA and tnpD. Excision and re-insertion of En/Spm take place with similar characteristics as in maize. This is the first description of En/Spm transposition in Arabidopsis and the parameters analysed here suggest that transposon tagging with En should be feasible in this species.

  8. Effects of Un-transposed UHV Transmission Line on Fault Analysis of Power Systems

    Institute of Scientific and Technical Information of China (English)

    WANG Anning; CHEN Qing; ZHOU Zhanping

    2008-01-01

    The conventional fault analysis method based on symmetrical components supposes that the three-phase parameters of un-transposed transmission line are symmetrical in case of fault. The errors caused by the method with the symmetrical distributed parameter circuit model as the equivalent circuit of the un-transposed ultra high voltage (UHV) transmission line were studied under both normal operation and fault, and the corresponding problems arising were pointed out. By contrast with electromagnetic transient and power electronics (EMTPE) simulation results with the asymmetrical distributed parameter circuit model of un-transposed line, it is shown that the conventional method cannot show the existence of negative and zero sequences before fault happening and there are many errors on voltage and current after fault happening which are different with fault types. The error ranges of voltage and current are 2.13%-81.13% and -7.82%-86.15%, respectively.

  9. Holliday Junctions Are Associated with Transposable Element Sequences in the Human Genome.

    Science.gov (United States)

    Ladias, Paris; Markopoulos, Georgios; Lazaros, Leandros; Markoula, Sofia; Tzavaras, Theodore; Georgiou, Ioannis

    2016-02-13

    Holliday junctions (HJs) constitute important intermediate structures for many cell functions such as DNA recombination and DNA repair. They derive from a 10-nt degenerate sequence, with a 3-nt core motif. In this study, we explored the human genome whether the HJ degenerate sequence associates with transposable elements (TEs) and mainly with those of the active and inactive ALU, LINE, SVA and HERV families. We identified six different forms of the HJ sequence motif, and we located the genomic coordinates of sequences containing both HJs and TEs. From 2982 total HJs, a significant number of 1319 TE-associated HJs were found, with a median distribution of 1 per 2.4 Mb. The HJs with higher GC content were observed more frequently at the genome. A high percentage of HJs were associated with all main TE families, with specificity for particular active or inactive elements: DNA elements and the retroelements ALUs, LINEs and HERVs up to 41.94%, 72.72%, 42.94% and 84.5%, respectively. Phylogenetic analysis revealed that HJs occur in both active and inactive TEs. Furthermore, the TE-associated HJs were almost exclusively found within a distance less than 1 Mb from human genes, while only 23 were not associated with any genes. This is the first report associating human HJs, with mobile elements. Our data pinpoint that particular HJ forms show preference for specific active retrotransposon families of ALUs and LINEs, suggesting that retrotransposon-incorporated HJs may relocate or replicate in the genome through retrotransposition, contributing to recombination, genome plasticity and DNA repair.

  10. Evaluating the protein coding potential of exonized transposable element sequences

    Directory of Open Access Journals (Sweden)

    Borodovsky Mark

    2007-11-01

    Full Text Available Abstract Background Transposable element (TE sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons. Results We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently

  11. Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris

    Directory of Open Access Journals (Sweden)

    Scott eJackson

    2014-07-01

    Full Text Available Common bean (Phaseolus vulgaris is an important legume crop grown and consumed worldwide. With the availability of the common bean genome sequence, the next challenge is to annotate the genome and characterize functional DNA elements. Transposable elements (TEs are the most abundant component of plant genomes and can dramatically affect genome evolution and genetic variation. Thus, it is pivotal to identify TEs in the common bean genome. In this study, we performed a genome-wide transposon annotation in common bean using a combination of homology and sequence structure-based methods. We developed a 2.12-Mb transposon database which includes 791 representative transposon sequences and is available upon request or from www.phytozome.org. Of note, nearly all transposons in the database are previously unrecognized TEs. More than 5,000 transposon-related expressed sequence tags (ESTs were detected which indicates that some transposons may be transcriptionally active. Two Ty1-copia retrotransposon families were found to encode the envelope-like protein which has rarely been identified in plant genomes. Also, we identified an extra open reading frame (ORF termed ORF2 from 15 Ty3-gypsy families that was located between the ORF encoding the retrotransposase and the 3’LTR. The ORF2 was in opposite transcriptional orientation to retrotransposase. Sequence homology searches and phylogenetic analysis suggested that the ORF2 may have an ancient origin, but its function is not clear. This transposon data provides a useful resource for understanding the genome organization and evolution and may be used to identify active TEs for developing transposon-tagging system in common bean and other related genomes.

  12. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates.

    Science.gov (United States)

    Warren, Ian A; Naville, Magali; Chalopin, Domitille; Levin, Perrine; Berger, Chloé Suzanne; Galiana, Delphine; Volff, Jean-Nicolas

    2015-09-01

    Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.

  13. Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas].

    Directory of Open Access Journals (Sweden)

    Lang Yan

    Full Text Available BACKGROUND: Transposable elements (TEs are the most abundant genomic components in eukaryotes and affect the genome by their replications and movements to generate genetic plasticity. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization. Complete identification of TEs is essential for the study of genome evolution. However, the TEs of sweet potato are still poorly understood because of its complex hexaploid genome and difficulty in genome sequencing. The recent availability of the sweet potato transcriptome databases provides an opportunity for discovering and characterizing the expressed TEs. METHODOLOGY/PRINCIPAL FINDINGS: We first established the integrated-transcriptome database by de novo assembling four published sweet potato transcriptome databases from three cultivars in China. Using sequence-similarity search and analysis, a total of 1,405 TEs including 883 retrotransposons and 522 DNA transposons were predicted and categorized. Depending on mapping sets of RNA-Seq raw short reads to the predicted TEs, we compared the quantities, classifications and expression activities of TEs inter- and intra-cultivars. Moreover, the differential expressions of TEs in seven tissues of Xushu 18 cultivar were analyzed by using Illumina digital gene expression (DGE tag profiling. It was found that 417 TEs were expressed in one or more tissues and 107 in all seven tissues. Furthermore, the copy number of 11 transposase genes was determined to be 1-3 copies in the genome of sweet potato by Real-time PCR-based absolute quantification. CONCLUSIONS/SIGNIFICANCE: Our result provides a new method for TE searching on species with transcriptome sequences while lacking genome information. The searching, identification and expression analysis of TEs will provide useful TE information in sweet potato, which are valuable for the further studies of TE-mediated gene mutation and optimization in

  14. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates.

    Science.gov (United States)

    Chalopin, Domitille; Naville, Magali; Plard, Floriane; Galiana, Delphine; Volff, Jean-Nicolas

    2015-01-09

    Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages.

  15. Excision of transposable elements from the chalcone isomerase and dihydroflavonol 4-reductase genes may contribute to the variegation of the yellow-flowered carnation (Dianthus caryophyllus).

    Science.gov (United States)

    Itoh, Yoshio; Higeta, Daisuke; Suzuki, Akane; Yoshida, Hiroyuki; Ozeki, Yoshihiro

    2002-05-01

    In the "Rhapsody" cultivar of the carnation, which bears white flowers variegated with red flecks and sectors, a transposable element, dTdic1, belonging to the Ac/Ds superfamily, was found within the dihydroflavonol 4-reductase (DFR) gene. The red flecks and sectors of "Rhapsody" may be attributable to a reversion to DFR activity after the excision of dTdic1. The yellow color of the carnation petals is attributed to the synthesis and accumulation of chalcone 2'-glucoside. In several of the carnation cultivars that bear yellow flowers variegated with white flecks and sectors, both the chalcone isomerase (CHI) and DFR genes are disrupted by dTdic1.

  16. Reverted glutathione S-transferase-like genes that influence flower color intensity of carnation (Dianthus caryophyllus L.) originated from excision of a transposable element

    OpenAIRE

    Momose, Masaki; Itoh, Yoshio; Umemoto, Naoyuki; Nakayama, Masayoshi; Ozeki, Yoshihiro

    2013-01-01

    A glutathione S-transferase-like gene, DcGSTF2, is responsible for carnation (Dianthus caryophyllus L.) flower color intensity. Two defective genes, DcGSTF2mu with a nonsense mutation and DcGSTF2-dTac1 containing a transposable element dTac1, have been characterized in detail in this report. dTac1 is an active element that produces reverted functional genes by excision of the element. A pale-pink cultivar ‘Daisy’ carries both defective genes, whereas a spontaneous deep-colored mutant ‘Daisy-V...

  17. Structure and properties of the algebra of partially transposed permutation operators

    Energy Technology Data Exchange (ETDEWEB)

    Mozrzymas, Marek [Institute for Theoretical Physics, University of Wrocław, 50-204 Wrocław (Poland); Horodecki, Michał; Studziński, Michał [Institute for Theoretical Physics and Astrophysics, University of Gdańsk, 80-952 Gdańsk (Poland); National Quantum Information Centre of Gdańsk, 81-824 Sopot (Poland)

    2014-03-15

    We consider the structure of algebra of operators, acting in n-fold tensor product space, which are partially transposed on the last term. Using purely algebraical methods we show that this algebra is semi-simple and then, considering its regular representation, we derive basic properties of the algebra. In particular, we describe all irreducible representations of the algebra of partially transposed operators and derive expressions for matrix elements of the representations. It appears that there are two kinds of irreducible representations of the algebra. The first one is strictly connected with the representations of the group S(n − 1) induced by irreducible representations of the group S(n − 2). The second kind is structurally connected with irreducible representations of the group S(n − 1)

  18. Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.

    Science.gov (United States)

    Gohl, Daryl M; Freifeld, Limor; Silies, Marion; Hwa, Jennifer J; Horowitz, Mark; Clandinin, Thomas R

    2014-03-01

    Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.

  19. Survival of Tdc transposable elements of the En/Spm superfamily in the carrot genome.

    Science.gov (United States)

    Itoh, Y; Hasebe, M; Davies, E; Takeda, J; Ozeki, Y

    2003-04-01

    Three subfamilies of the En/Spm-type transposable element of carrot, Tdc A, B, and C, were characterized. It was supposed that the Tdc A subfamily may include autonomous elements which can produce transposases. Tdc B elements are defective, but still generate transcripts containing mutant open reading frame (ORF) sequences for transposases. The single member of the Tdc C group recovered seems to be a pseudogene. The sequences of the transposase ORFs of Tdc A and Tdc B elements are more highly conserved than those of the 5; and 3; untranslated regions and introns, as is found in other structural genes that are subject to selection. These observations indicate that the mutations in the nucleotide sequences of the Tdc elements occurred in the host genome. However, the mutations in the 5; and 3; untranslated regions and introns, which may not be sufficient to prevent transposition, accumulated in autonomous elements, which could transpose and produce copies. When the reproduction rate and the rate of disabling mutations reached an equilibrium, that is, when the birth rate of the transposable elements in the genome equalled the death rate, the population of elements achieved a stationary state in the genome, and could thus survive.

  20. Transposable element insertion location bias and the dynamics of gene drive in mosquito populations.

    Science.gov (United States)

    Rasgon, J L; Gould, F

    2005-10-01

    Some vector-borne disease control strategies using transgenic mosquitoes require transgene spread to high frequency in populations. Transposable elements (TEs) are DNA sequences that replicate and transpose within the genomes of other organisms and may therefore be represented in the next generation in higher frequencies than predicted by Mendelian segregation. This over-representation has allowed some TEs to spread through natural populations. Transgenes incorporated within a TE sequence are expected to be driven into populations as long as there is a positive balance between fitness costs and over-representation. Models have been used to examine parameters that affect this balance but did not take into account biased insertion of TEs to linked sites in the genome. A simulation model was created to examine the impact of insertion bias on TE spread in mosquito populations. TEs that induce no fitness costs are predicted to increase in frequency over a wide range of parameter values but spread is slower for lower levels of transposition and non-local movement. If TEs are costly, high proportions of local movement can slow or halt spread. To function as a robust transgene drive mechanism a TE should replicate and transpose > 10%/insert/generation, induce < 1% fitness cost/insert, and move preferentially to unlinked sites in the genome.

  1. The industrial melanism mutation in British peppered moths is a transposable element.

    Science.gov (United States)

    Van't Hof, Arjen E; Campagne, Pascal; Rigden, Daniel J; Yung, Carl J; Lingley, Jessica; Quail, Michael A; Hall, Neil; Darby, Alistair C; Saccheri, Ilik J

    2016-06-01

    Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria-typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of 'jumping genes' as a source of major phenotypic novelty.

  2. MicroRNA-Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells.

    Science.gov (United States)

    Mugat, Bruno; Akkouche, Abdou; Serrano, Vincent; Armenise, Claudia; Li, Blaise; Brun, Christine; Fulga, Tudor A; Van Vactor, David; Pélisson, Alain; Chambeyron, Séverine

    2015-05-01

    RNA interference-related silencing mechanisms concern very diverse and distinct biological processes, from gene regulation (via the microRNA pathway) to defense against molecular parasites (through the small interfering RNA and the Piwi-interacting RNA pathways). Small non-coding RNAs serve as specificity factors that guide effector proteins to ribonucleic acid targets via base-pairing interactions, to achieve transcriptional or post-transcriptional regulation. Because of the small sequence complementarity required for microRNA-dependent post-transcriptional regulation, thousands of microRNA (miRNA) putative targets have been annotated in Drosophila. In Drosophila somatic ovarian cells, genomic parasites, such as transposable elements (TEs), are transcriptionally repressed by chromatin changes induced by Piwi-interacting RNAs (piRNAs) that prevent them from invading the germinal genome. Here we show, for the first time, that a functional miRNA pathway is required for the piRNA-mediated transcriptional silencing of TEs in this tissue. Global miRNA depletion, caused by tissue- and stage-specific knock down of drosha (involved in miRNA biogenesis), AGO1 or gawky (both responsible for miRNA activity), resulted in loss of TE-derived piRNAs and chromatin-mediated transcriptional de-silencing of TEs. This specific TE de-repression was also observed upon individual titration (by expression of the complementary miRNA sponge) of two miRNAs (miR-14 and miR-34) as well as in a miR-14 loss-of-function mutant background. Interestingly, the miRNA defects differentially affected TE- and 3' UTR-derived piRNAs. To our knowledge, this is the first indication of possible differences in the biogenesis or stability of TE- and 3' UTR-derived piRNAs. This work is one of the examples of detectable phenotypes caused by loss of individual miRNAs in Drosophila and the first genetic evidence that miRNAs have a role in the maintenance of genome stability via piRNA-mediated TE repression.

  3. Orthographic Reading Deficits in Dyslexic Japanese Children: Examining the Transposed-Letter Effect in the Color-Word Stroop Paradigm

    Science.gov (United States)

    Ogawa, Shino; Shibasaki, Masahiro; Isomura, Tomoko; Masataka, Nobuo

    2016-01-01

    In orthographic reading, the transposed-letter effect (TLE) is the perception of a transposed-letter position word such as “cholocate” as the correct word “chocolate.” Although previous studies on dyslexic children using alphabetic languages have reported such orthographic reading deficits, the extent of orthographic reading impairment in dyslexic Japanese children has remained unknown. This study examined the TLE in dyslexic Japanese children using the color-word Stroop paradigm comprising congruent and incongruent Japanese hiragana words with correct and transposed-letter positions. We found that typically developed children exhibited Stroop effects in Japanese hiragana words with both correct and transposed-letter positions, thus indicating the presence of TLE. In contrast, dyslexic children indicated Stroop effects in correct letter positions in Japanese words but not in transposed, which indicated an absence of the TLE. These results suggest that dyslexic Japanese children, similar to dyslexic children using alphabetic languages, may also have a problem with orthographic reading. PMID:27303331

  4. On the structure of the body of states with positive partial transpose

    Energy Technology Data Exchange (ETDEWEB)

    Szarek, Stanislaw J [Case Western Reserve University, Cleveland, OH (United States); Universite Paris VI, Paris (France); Bengtsson, Ingemar [Fysikum, Stockholm University, Stockholm (Sweden); Zyczkowski, Karol [Perimeter Institute, Waterloo, Ontario (Canada); Institute of Physics, Jagiellonian University, Cracow (Poland); Center for Theoretical Physics, Polish Academy of Sciences, Warsaw (Poland)

    2006-02-03

    We show that the convex set of separable mixed states of the 2 x 2 system is a body of a constant height. This fact is used to prove that the probability of finding a random state to be separable equals twice the probability of finding a random boundary state to be separable, provided that the random states are generated uniformly with respect to the Hilbert-Schmidt (Euclidean) measure. An analogous property holds for the set of positive-partial-transpose states for an arbitrary bipartite system. (letter to the editor)

  5. On the structure of the body of states with positive partial transpose

    CERN Document Server

    Szarek, S; Zyczkowski, K; Szarek, Stanislaw; Bengtsson, Ingemar; Zyczkowski, Karol

    2005-01-01

    We show that the convex set of separable mixed states of the 2 x 2 system is a body of constant height. This fact is used to prove that the probability to find a random state to be separable equals 2 times the probability to find a random boundary state to be separable, provided the random states are generated uniformly with respect to the Hilbert-Schmidt (Euclidean) distance. An analogous property holds for the set of positive-partial-transpose states for an arbitrary bipartite system.

  6. LETTER TO THE EDITOR: On the structure of the body of states with positive partial transpose

    Science.gov (United States)

    Szarek, Stanislaw J.; Bengtsson, Ingemar; Zyczkowski, Karol

    2006-02-01

    We show that the convex set of separable mixed states of the 2 × 2 system is a body of a constant height. This fact is used to prove that the probability of finding a random state to be separable equals twice the probability of finding a random boundary state to be separable, provided that the random states are generated uniformly with respect to the Hilbert-Schmidt (Euclidean) measure. An analogous property holds for the set of positive-partial-transpose states for an arbitrary bipartite system.

  7. Distribution and insertion numbers of transposable elements in species of the Drosophila saltans group

    Directory of Open Access Journals (Sweden)

    Juliana P. de Castro

    2006-01-01

    Full Text Available Information about the distribution and insertion numbers of many transposable elements is restricted to few species of Drosophila, although these elements are widely distributed throughout the genus. The aim of this work was to describe the distribution and insertion numbers of four retrotransposons (copia, gypsy, micropia, I and four transposons (hobo, mariner, Minos and Bari-1 in the saltans group of Drosophila. Our data shows that, except for mariner, all the other elements are widespread within the saltans group and show variable insertion numbers of up to 24 copies.

  8. Germline transformation of Aedes fluviatilis (Diptera:Culicidae) with the piggyBac transposable element.

    Science.gov (United States)

    Rodrigues, Flávia Guimarães; Oliveira, Sabrina Barbosa; Rocha, Bruno Coelho; Moreira, Luciano Andrade

    2006-11-01

    The technique to generate transgenic mosquitoes requires adaptation for each target species because of aspects related to species biology, sensitivity to manipulation and rearing conditions. Here we tested different parameters on the microinjection procedure in order to obtain a transgenic Neotropical mosquito species. By using a transposon-based strategy we were able to successfully transform Aedes fluviatilis (Lutz), which can be used as an avian malaria model. These results demonstrate the usefulness of the piggyBac transposable element as a transformation vector for Neotropical mosquito species and opens up new research frontiers for South American mosquito vectors.

  9. Germline transformation of Aedes fluviatilis (Diptera:Culicidae with the piggyBac transposable element

    Directory of Open Access Journals (Sweden)

    Flávia Guimarães Rodrigues

    2006-11-01

    Full Text Available The technique to generate transgenic mosquitoes requires adaptation for each target species because of aspects related to species biology, sensitivity to manipulation and rearing conditions. Here we tested different parameters on the microinjection procedure in order to obtain a transgenic Neotropical mosquito species. By using a transposon-based strategy we were able to successfully transform Aedes fluviatilis (Lutz, which can be used as an avian malaria model. These results demonstrate the usefulness of the piggyBac transposable element as a transformation vector for Neotropical mosquito species and opens up new research frontiers for South American mosquito vectors.

  10. Distribution and conservation of the transposable element gypsy in drosophilid species

    Directory of Open Access Journals (Sweden)

    Fabiana Herédia

    2007-01-01

    Full Text Available In an attempt to understand the dynamics of transposable elements (T'S in the genome of host species, we investigated the distribution, representativeness and conservation of DNA sequences homologous to the Drosophila melanogaster gypsy retrotransposon in 42 drosophilid species. Our results extended the knowledge about the wide distribution of gypsy in the genus Drosophila, including several Neotropical species not previously studied. The gypsy-like sequences showed high divergence compared to the D. melanogaster gypsy element. Furthermore, the conservation of the restriction sites between gypsy sequences from phylogenetically unrelated species pointed to a more complex evolutionary picture, which includes the possibility of the horizontal transfer events already described for this retrotransposon.

  11. Detection transposable elements in Botrytis cinerea in latent infection stage from symptomless apples

    Directory of Open Access Journals (Sweden)

    Jorge G Fernández

    2014-02-01

    Full Text Available Objective: T o detect Botrytis cinerea ( B. cinerea latent infections on apples before storage, which is essential for effective control strategies in the fruit postharvest industry. Methods: I n the present study, a polymerase chain reaction detection method, based on primers designed on B. cinerea transposable elements ( boty and flipper and intergenic spacer region as internal control, were utilized to reveal the presence of symptomless infections on apple fruits. T his molecular method proved to be highly specific and sensitive in detecting latent infections. I t revealed the presence of the pathogen in 83 % of the samples from infected apples with 10 4 conidia/ m L , whereas those infected with 10 6 conidia/m L detected 94 % as compared to the traditional method that revealed the pathogen in 40 % and 66 % of the samples inoculated with 10 4 and 10 6 conidia/m L respectively. F urthermore, the method characterized B. cinerea as subpopulation transposa-type by the presence of the transposable elements boty and flipper Results: T he results obtained from DNA quantification method were compared with enzyme- linked immunosorbent assay and these studies showed good correlation. T herefore our method has important advantages compared with others detection methods for B. cinerea, because the proposed methodology allowed distinguishes between its two subpopulations ( vacuma and transposa and this would allow establish possible appropriate control strategies. Conclusions: F inally, the method can be an interesting alternative for its possible application in the phytosanitary programs of the fruit industry worldwide.

  12. Detection transposable elements in Botrytis cinerea in latent infection stage from symptomless apples

    Institute of Scientific and Technical Information of China (English)

    Jorge G Fernndez; Martn A Fernndez-Baldo; Claudio Muoz; Eloy Salinas; Julio Raba; Mara I Sanz

    2014-01-01

    Objective:To detect Botrytis cinerea (B. cinerea) latent infections on apples before storage, which is essential for effective control strategies in the fruit postharvest industry. Methods:In the present study, a polymerase chain reaction detection method, based on primers designed on B. cinerea transposable elements (boty and flipper) and intergenic spacer region as internal control, were utilized to reveal the presence of symptomless infections on apple fruits. This molecular method proved to be highly specific and sensitive in detecting latent infections. It revealed the presence of the pathogen in 83%of the samples from infected apples with 104 conidia/mL, whereas those infected with 106 conidia/mL detected 94%as compared to the traditional method that revealed the pathogen in 40%and 66%of the samples inoculated with 104 and 106 conidia/mL respectively. Furthermore, the method characterized B. cinerea as subpopulation transposa-type by the presence of the transposable elements boty and flipper Results:The results obtained from DNA quantification method were compared with enzyme-linked immunosorbent assay and these studies showed good correlation. Therefore our method has important advantages compared with others detection methods for B. cinerea, because the proposed methodology allowed distinguishes between its two subpopulations (vacuma and transposa) and this would allow establish possible appropriate control strategies. Conclusions:Finally, the method can be an interesting alternative for its possible application in the phytosanitary programs of the fruit industry worldwide.

  13. Tourist C transposable elements are closely associated with genes expressed in flowers of rice (Oryza sativa).

    Science.gov (United States)

    Iwamoto, M; Higo, K

    2003-03-01

    Tourist elements comprise a group of transposable elements in plants. One of these elements, Tourist-OsaCatA(a Tourist C element), has been found in the 5; flanking region of a catalase gene, CatA, in rice (Oryza sativa). Using reverse transcriptase-PCR (RT-PCR) analyses of leaves, roots, flowers and developing seeds of rice, we assessed the transcription levels of ten known genes containing Tourist C elements, and of three additional putative genes for which expressed sequence tags (ESTs) including Tourist C elements have been isolated. We found that nine of the ten known genes and two of the three represented by ESTs were expressed in at least one of the organs we analyzed, and all of the genes detected were expressed in flowers, usually in stamens or pistils. We also assessed the expression of the 29 Tourist C-containing hypothetical coding sequences (CDSs) obtained so far by high-throughput genomic sequencing. We found that CDSs of all 11 genes whose transcripts were detectable by RT-PCR were expressed in flowers, especially in stamens or pistils. In contrast, RT-PCR analyses of genes or CDSs associated with other miniature inverted-repeat transposable elements (MITEs), such as Tourist D, Gaijin, Explorer, and Castaway, showed that some of them were expressed only minimally or not at all in flowers. Therefore, compared with other MITEs, Tourist C elements seem to show a strong association with genes that are expressed in the flowers of rice.

  14. TEnest 2.0: computational annotation and visualization of nested transposable elements.

    Science.gov (United States)

    Kronmiller, Brent A; Wise, Roger P

    2013-01-01

    Grass genomes harbor a diverse and complex content of repeated sequences. Most of these repeats occur as abundant transposable elements (TEs), which present unique challenges to sequence, assemble, and annotate genomes. Multiple copies of Long Terminal Repeat (LTR) retrotransposons can hinder sequence assembly and also cause problems with gene annotation. TEs can also contain protein-encoding genes, the ancient remnants of which can mislead gene identification software if not correctly masked. Hence, accurate assembly is crucial for gene annotation. We present TEnest v2.0. TEnest computationally annotates and chronologically displays nested transposable elements. Utilizing organism-specific TE databases as a reference for reconstructing degraded TEs to their ancestral state, annotation of repeats is accomplished by iterative sequence alignment. Subsequently, an output consisting of a graphical display of the chronological nesting structure and coordinate positions of all TE insertions is the result. Both linux command line and Web versions of the TEnest software are available at www.wiselab.org and www.plantgdb.org/tool/, respectively.

  15. Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae.

    Science.gov (United States)

    Fléchard, Maud; Gilot, Philippe

    2014-07-01

    We have referenced and described Streptococcus agalactiae transposable elements encoding DDE transposases. These elements belonged to nine families of insertion sequences (ISs) and to a family of conjugative transposons (TnGBSs). An overview of the physiological impact of the insertion of all these elements is provided. DDE-transposable elements affect S. agalactiae in a number of aspects of its capability to adapt to various environments and modulate the expression of several virulence genes, the scpB-lmB genomic region and the genes involved in capsule expression and haemolysin transport being the targets of several different mobile elements. The referenced mobile elements modify S. agalactiae behaviour by transferring new gene(s) to its genome, by modifying the expression of neighbouring genes at the integration site or by promoting genomic rearrangements. Transposition of some of these elements occurs in vivo, suggesting that by dynamically regulating some adaptation and/or virulence genes, they improve the ability of S. agalactiae to reach different niches within its host and ensure the 'success' of the infectious process.

  16. A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana.

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    Zoé Joly-Lopez

    2012-09-01

    Full Text Available The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA, largely composed of transposable elements. Transposable elements persist through self-replication, but some genes once encoded by transposable elements have, through a process called molecular domestication, evolved new functions that increase fitness. Although they have conferred numerous adaptations, the number of such domesticated transposable element genes remains unknown, so their evolutionary and functional impact cannot be fully assessed. Systematic searches that exploit genomic signatures of natural selection have been employed to identify potential domesticated genes, but their predictions have yet to be experimentally verified. To this end, we investigated a family of domesticated genes called MUSTANG (MUG, identified in a previous bioinformatic search of plant genomes. We show that MUG genes are functional. Mutants of Arabidopsis thaliana MUG genes yield phenotypes with severely reduced plant fitness through decreased plant size, delayed flowering, abnormal development of floral organs, and markedly reduced fertility. MUG genes are present in all flowering plants, but not in any non-flowering plant lineages, such as gymnosperms, suggesting that the molecular domestication of MUG may have been an integral part of early angiosperm evolution. This study shows that systematic searches can be successful at identifying functional genetic elements in noncoding regions and demonstrates how to combine systematic searches with reverse genetics in a fruitful way to decipher eukaryotic genomes.

  17. Properties and construction of extreme bipartite states having positive partial transpose

    CERN Document Server

    Chen, Lin

    2012-01-01

    We investigate the set E of extreme points of the compact convex set of PPT states (i.e., the states having positive semidefinite partial transpose) of a bipartite MxN quantum system. Let E(M,N,r) denote the subset of E consisting of states of rank r which are supported on MxN. We show that for M,N>2 the sets E(M,N,M+N-2) are nonempty. On the other hand we show that for M,N>3 the sets E(M,N,N+1) are empty. It is known that the set E(M,N,MN) is empty, and we show that also the set E(M,N,MN-1) is empty. We divide the set of all states into the good and the bad states (the definition is too technical to be given here). We show that the good states have many good properties.

  18. Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification.

    Science.gov (United States)

    Becker, Kailey E; Thomas, Mary C; Martini, Samer; Shuipys, Tautvydas; Didorchuk, Volodymyr; Shanker, Rachyl M; Laten, Howard M

    2016-10-01

    Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.

  19. Genetic Innovation in Vertebrates: Gypsy Integrase Genes and Other Genes Derived from Transposable Elements

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    Domitille Chalopin

    2012-01-01

    Full Text Available Due to their ability to drive DNA rearrangements and to serve as a source of new coding and regulatory sequences, transposable elements (TEs are considered as powerful evolutionary agents within genomes. In this paper, we review the mechanism of molecular domestication, which corresponds to the formation of new genes derived from TE sequences. Many genes derived from retroelements and DNA transposons have been identified in mammals and other vertebrates, some of them fulfilling essential functions for the development and survival of their host organisms. We will particularly focus on the evolution and expression of Gypsy integrase (GIN genes, which have been formed from ancient event(s of molecular domestication and have evolved differentially in some vertebrate sublineages. What we describe here is probably only the tip of the evolutionary iceberg, and future genome analyses will certainly uncover new TE-derived genes and biological functions driving genetic innovation in vertebrates and other organisms.

  20. Transposable element distribution, abundance and role in genome size variation in the genus Oryza

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    Collura Kristi

    2007-08-01

    Full Text Available Abstract Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]. Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements in shaping these genomes and in their contributing to genome size variation. Results We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Conclusion Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys account for a significant portion of the genome size variations present in the Oryza genus.

  1. Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

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    Amyotte Stefan G

    2012-07-01

    Full Text Available Abstract Background Verticillium dahliae (Vd and Verticillium albo-atrum (Va are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs have contributed to the generation of four lineage-specific (LS regions in VdLs.17. Results We present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced Verticillium genomes. We report also of their distribution in other Vd and Va isolates from various geographic origins. In VdLs.17, we identified and characterized 56 complete retrotransposons of the Gypsy-, Copia- and LINE-like types, as well as 34 full-length elements of the “cut-and-paste” superfamilies Tc1/mariner, Activator and Mutator. While Copia and Tc1/mariner were present in multiple identical copies, Activator and Mutator sequences were highly divergent. Most elements comprised complete ORFs, had matching ESTs and showed active transcription in response to stress treatment. Noticeably, we found evidences of repeat-induced point mutation (RIP only in some of the Gypsy retroelements. While Copia-, Gypsy- and Tc1/mariner-like transposons were prominent, a large variation in presence of the other types of mobile elements was detected in the other Verticillium spp. strains surveyed. In particular, neither complete nor defective “cut-and-paste” TEs were found in VaMs.102. Conclusions Copia-, Gypsy- and Tc1/mariner-like transposons are the most wide-spread TEs in the phytopathogens V. dahliae and V. albo-atrum. In VdLs.17, we identified several retroelements and “cut-and-paste” transposons still potentially active. Some of these

  2. A tiger mouse and relatives. Variants caused by an activated transposable element?

    Science.gov (United States)

    Wallace, M E; Nash, H R

    1984-01-01

    In a laboratory-bred population of wild Peruvian house mice, one male had an excessive rate of non-pairing of the X and Y chromosomes. After crossing him with laboratory stock mice, a mouse of very unusual phenotype appeared from a yellow (AyA) mother. He was yellow with black dorsal stripes; hence Tiger. He was mated to many females, and inbred F2 and F3 generations were raised. There were no more tiger phenotypes, but his F1 contained an excess of black-and-tans over yellows, showing him to be a gonosomic mosaic Ayat/atat; the homozygous cell line probably arose from the heterozygous one. The mitotic karyotype was normal. Some of Tiger's mates were of known allozyme types and their progeny were scored. The allozyme segregations were normal, except at the Es-3 locus (esterase-3), for which Tiger was typed as homozygous. Several unusual events among Tiger's close relatives included a mutation to an unstable pattern mutant, three probable translocations, and several cases of somatic defect. All unusual mice derived from Tiger's yellow mother, whose genome was one-quarter Peruvian. Yellow is associated with an ecotropic murine leukemia virus. The Peru genome is characterized by a high occurrence of mutation and aberrant karyotypes. It is suggested that something from the Peru genome in Tiger's mother caused instability of the DNA sequence associated with yellow, with related disturbance at different locations thereafter. The nature of this instability, and of the Peru genome, is discussed.

  3. Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

    Directory of Open Access Journals (Sweden)

    Pupko Tal

    2008-10-01

    Full Text Available Abstract Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif. Reviewers This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers' Reports section.

  4. The Origin and Evolution of Six Miniature Inverted-Repeat Transposable Elements in Bombyx mori and Rhodnius prolixus

    OpenAIRE

    Zhang, Hua-Hao; Xu, Hong-En; Shen, Yi-Hong; Han, Min-Jin; Zhang, Ze

    2013-01-01

    Miniature inverted-repeat transposable elements (MITEs) are a specific group of nonautonomous DNA transposons, and they are distributed in a wide range of hosts. However, the origin and evolutionary history of MITEs in eukaryotic genomes remain unclear. In this study, six MITEs were identified in the silkworm (Bombyx mori). Five elements are grouped into four known superfamilies of DNA transposons, and one represents a novel class of MITEs. Unexpectedly, six similar MITEs are also present in ...

  5. Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System.

    Science.gov (United States)

    Singh, Harpreet; Maurya, Raj Kumar; Thakkar, Surbhi

    2016-12-01

    Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets.

  6. Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System

    Science.gov (United States)

    Singh, Harpreet; Thakkar, Surbhi

    2016-01-01

    Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets. PMID:28209017

  7. Somatic variegation and germinal mutability reflect the position of transposable element dissociation within the maize R gene

    Energy Technology Data Exchange (ETDEWEB)

    Alleman, M.; Kermicle, J.L. (Univ. of Wisconsin, Madison, WI (United States))

    1993-09-01

    The R gene regulates the timing and tissue-specificity of anthocyanin deposition during maize development. The Ac/Ds system of transposable elements was used to induce insertional mutants of the R-sc:124 allele during two cycles of mutagenesis. Of 43 unstable, spotted-aleurone mutants generated, 42 contain inserts of the Ds6 transposable element differing only in the position and orientation of the element. The remaining mutant, r-sc;ml, contained an insert of a Ds element of the approximate size of the Ds1 transposable element. The patterns of somatic variegation of these mutants, resulting from excision of Ds, define a spectrum of phenotypes ranging from sparse to dense variegation. The sparsely variegated mutants produce many germinal revertants and few stable null derivatives. Molecular analysis shows that the sparsely variegated alleles are caused by Ds6 insertions in protein coding regions of R-sc:124 whereas the densely variegated mutants result from insertions in introns or in flanking regions of the gene. The excision rate of Ds6 from R, estimated as the proportion of R genomic DNA restriction fragments lacking the element, was uniform regardless of position, orientation or whether the element was inserted in R-sc:124 or another R allele. The excision rate was greater, however, for the mutable alleles involving the Ds element from r-sc:m1. These data indicate that, although the excision rates are uniform for a given Ds element, the somatic and germinal mutability patterns of alleles associated with that element vary widely and depend primarily on the position of the transposable element within coding or noncoding regions of the gene.

  8. [The distributional clines in P susceptibility causing by the P family transposable element in Drosophila melanogaster population of China].

    Science.gov (United States)

    Hu, K; Wang, Q M

    1998-01-01

    An extensive survey of the P family transposable element of Drosophila melanogaster in China, from the far west as Xinjiang and Xizang (Tibet) to the east coast, covered all China was provided. Strains, sampling more than 70 localities, which were collected during 1980-1995. In the term of the PM system, the phenotypic property of it was mainly M type, including Taiwan. The molecular test determined, it was M type. There were three localities, the P activity of them were higher as Q type. They are: Dalian Peninsular. Chongming island, near Shanghai and Taizhong of Taiwan. For analyzed geographically, according to the east longitudes, grouped the country to four parts. After comparison, two dividing lines were found: 1. The East longitude of 115 degrees, it was between Area II and Area III, see Fig. 4, separating the coastal from inland. Except the P susceptibility of the northeastern three provinces was little higher, about 30.37%, the most part of the east coastal, the first line, its P susceptibility was very week. Seven strains were 0, fifteen strains were under 10%; its P activity was also low, never beyond 10%. Therefore, it was appeared neutral, its average was 7.23%. That was the major neutral property of the coastal areas. The second line of little increased P susceptibility averaged about 26.67%. Then, there was the third line was, when the line was the more westward, its P susceptibility was higher, up to 87%, closing to the highest score of middlewest part of the country. From the east coast to the west, there were three gradually increased P susceptibility lines pushing forward could be found. The E 115 degrees, it was between the lines of the second and the third. 2. Besides the East Longitude of 115 degrees, there is another natural geographic line shows its potentiality, that is the Tropic of Cancer. It divided the coastal to two parts, the localities at the south of this line, they did not show the coastal characteristic, instead of neutral or very

  9. Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes

    Science.gov (United States)

    Puterova, Janka; Razumova, Olga; Martinek, Tomas; Alexandrov, Oleg; Divashuk, Mikhail; Kubat, Zdenek; Hobza, Roman; Karlov, Gennady

    2017-01-01

    Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. PMID:28057732

  10. Identification and characterization of CACTA transposable elements capturing gene fragments in maize

    Institute of Scientific and Technical Information of China (English)

    LI Qing; LI Lin; DAI JingRui; LI JianSheng; YAN JianBing

    2009-01-01

    Transposable elements (TEs)-mediated gene sequence movement is thought to play an important role in genome expansion and origin of genes with novel functions. In this study, a gene, HGGT, involved in vitamin E synthesis was used in a case study to discover and characterize transposons carrying gene fragments in maize. A total of 69 transposons that are distributed across the 10 chromosomes and have an average length of 3689 bp were identified from the maize sequence database by using the BLAST search algorithm. Three of these carry gene fragments from the progenitor HGGT gene, while the rest (66) contain gene fragments from other cellular genes. Nine of the 69 transposons contain fragments derived from two locations in the genome. By querying the maize Expressed Sequence Tag (EST) da-tabase, we found that at least thirteen out of the 69 TEs had corresponding transcripts. More interest-ingly, two transposons that carry gene fragments from two different chromosomal loci could be ex-pressed as chimeric transcripts.

  11. Report of a chimeric origin of transposable elements in a bovine-coding gene.

    Science.gov (United States)

    Almeida, L M; Amaral, M E J; Silva, I T; Silva, W A; Riggs, P K; Carareto, C M

    2008-02-01

    Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is approximately 85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage.

  12. Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus.

    Science.gov (United States)

    Valente, Guilherme; Kocher, Thomas; Eickbush, Thomas; Simões, Rafael P; Martins, Cesar

    2016-06-01

    Integration of cytogenetics and genomics has become essential to a better view of architecture and function of genomes. Although the advances on genomic sequencing have contributed to study genes and genomes, the repetitive DNA fraction of the genome is still enigmatic and poorly understood. Among repeated DNAs, transposable elements (TEs) are major components of eukaryotic chromatin and their investigation has been hindered even after the availability of whole sequenced genomes. The cytogenetic mapping of TEs in chromosomes has proved to be of high value to integrate information from the micro level of nucleotide sequence to a cytological view of chromosomes. Different TEs have been cytogenetically mapped in cichlids; however, neither details about their genomic arrangement nor appropriated copy number are well defined by these approaches. The current study integrates TEs distribution in Nile tilapia Oreochromis niloticus genome based on cytogenetic and genomics/bioinformatics approach. The results showed that some elements are not randomly distributed and that some are genomic dependent on each other. Moreover, we found extensive overlap between genomics and cytogenetics data and that tandem duplication may be the major mechanism responsible for the genomic dynamics of TEs here analyzed. This paper provides insights in the genomic organization of TEs under an integrated view based on cytogenetics and genomics.

  13. Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data.

    Science.gov (United States)

    Li, Shu-Fen; Gao, Wu-Jun; Zhao, Xin-Peng; Dong, Tian-Yu; Deng, Chuan-Liang; Lu, Long-Dou

    2014-01-01

    Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.

  14. Transposable element insertions in long intergenic non-coding RNA genes

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    Sivakumar eKannan

    2015-06-01

    Full Text Available Transposable elements (TE are abundant in mammalian genomes and appear to have contributed to the evolution of their hosts by providing novel regulatory or coding sequences. We analyzed different regions of long intergenic non-coding RNA (lincRNA genes in human and mouse genomes to systematically assess the potential contribution of TEs to the evolution of the structure and regulation of expression of lincRNA genes. Introns of lincRNA genes contain the highest percentage of TE-derived sequences, followed by exons and then promoter regions although the density of TEs is not significantly different between exons and promoters. Higher frequencies of ancient TEs in promoters and exons compared to introns implies that many lincRNA genes emerged before the split of primates and rodents. The content of TE-derived sequences in lincRNA genes is substantially higher than that in protein-coding genes, especially in exons and promoter regions. A significant positive correlation was detected between the content of TEs and evolutionary rate of lincRNAs indicating that inserted TEs are preferentially fixed in fast-evolving lincRNA genes. These results are consistent with the RIDL (Repeat Insertion Domains of LncRNAs hypothesis under which TEs have substantially contributed to the origin, evolution, and in particular functional diversification, of lincRNA genes.

  15. Spatio-temporal requirements for transposable element piRNA-mediated silencing during Drosophila oogenesis.

    Science.gov (United States)

    Dufourt, Jérémy; Dennis, Cynthia; Boivin, Antoine; Gueguen, Nathalie; Théron, Emmanuelle; Goriaux, Coline; Pouchin, Pierre; Ronsseray, Stéphane; Brasset, Emilie; Vaury, Chantal

    2014-02-01

    During Drosophila oogenesis, transposable element (TE) repression involves the Piwi-interacting RNA (piRNA) pathway which ensures genome integrity for the next generation. We developed a transgenic model to study repression of the Idefix retrotransposon in the germline. Using a candidate gene KD-approach, we identified differences in the spatio-temporal requirements of the piRNA pathway components for piRNA-mediated silencing. Some of them (Aub, Vasa, Spn-E) are necessary in very early stages of oogenesis within the germarium and appear to be less important for efficient TE silencing thereafter. Others (Piwi, Ago3, Mael) are required at all stages of oogenesis. Moreover, during early oogenesis, in the dividing cysts within the germarium, Idefix anti-sense transgenes escape host control, and this is associated with very low piwi expression. Silencing of P-element-based transgenes is also strongly weakened in these cysts. This region, termed the 'Piwiless pocket' or Pilp, may ensure that new TE insertions occur and are transmitted to the next generation, thereby contributing to genome dynamics. In contrast, piRNA-mediated silencing is strong in germline stem cells in which TE mobilization is tightly repressed ensuring the continued production of viable germline cysts.

  16. The genomic proliferation of transposable elements in colonizing populations: Schistosoma mansoni in the new world.

    Science.gov (United States)

    Wijayawardena, Bhagya K; DeWoody, J Andrew; Minchella, Dennis J

    2015-06-01

    Transposable elements (TEs) are mobile genes with an inherent ability to move within and among genomes. Theory predicts that TEs proliferate extensively during physiological stress due to the breakdown of TE repression systems. We tested this hypothesis in Schistosoma mansoni, a widespread trematode parasite that causes the human disease schistosomiasis. According to phylogenetic analysis, S. mansoni invaded the new world during the last 500 years. We hypothesized that new world strains of S. mansoni would have more copies of TEs than old world strains due to the physiological stress associated with invasion of the new world. We quantified the copy number of six TEs (Saci-1, Saci-2 and Saci-3, Perere-1, Merlin-sm1, and SmTRC1) in the genome and the transcriptome of old world and new world strains of S. mansoni, using qPCR relative quantification. As predicted, the genomes of new world parasites contain significantly more copies of class I and class II TEs in both laboratory and field strains. However, such differences are not observed in the transcriptome suggesting that either TE silencing mechanisms have reactivated to control the expression of these elements or the presence of inactive truncated copies of TEs.

  17. Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

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    Vincent J. Lynch

    2015-02-01

    Full Text Available A major challenge in biology is determining how evolutionarily novel characters originate; however, mechanistic explanations for the origin of new characters are almost completely unknown. The evolution of pregnancy is an excellent system in which to study the origin of novelties because mammals preserve stages in the transition from egg laying to live birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved endometrial expression during the origins of mammalian pregnancy, including genes that mediate maternal-fetal communication and immunotolerance. Furthermore, thousands of cis-regulatory elements that mediate decidualization and cell-type identity in decidualized stromal cells are derived from ancient mammalian transposable elements (TEs. Our results indicate that one of the defining mammalian novelties evolved from DNA sequences derived from ancient mammalian TEs co-opted into hormone-responsive regulatory elements distributed throughout the genome.

  18. High genetic variation and recombination events in the vicinity of non-autonomous transposable elements from ‘Candidatus Liberibacter asiaticus’

    Institute of Scientific and Technical Information of China (English)

    WANG Xue-feng; CHEN Jiao-yue; TAN Jin; DUAN Suo; DENG Xiao-ling; CHEN Jian-chi; ZHOU Chang-yong

    2015-01-01

    Two miniature inverted-repeat transposable elements (MITEs), MCLas-A and MCLas-B, were recently identiifed from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yelow shoot disease). MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus’ isolates from China, the United States and Brazil. Out of the 12 sequence types, three (T4, T5-2, T6) were reported for the ifrst time. Recombination events were found in the two unique sequence types (T5-2 and T6) which were detected in al Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two wel supported clades including ifve subclades were identiifed, clearly relfecting the geographical origins of isolates, especialy that of Ruili isolates, São Paulo isolates and a few Florida isolates.

  19. Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements.

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    Szitenberg, Amir; Cha, Soyeon; Opperman, Charles H; Bird, David M; Blaxter, Mark L; Lunt, David H

    2016-10-05

    Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host's genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes.

  20. A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle.

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    Menzi, F; Besuchet-Schmutz, N; Fragnière, M; Hofstetter, S; Jagannathan, V; Mock, T; Raemy, A; Studer, E; Mehinagic, K; Regenscheit, N; Meylan, M; Schmitz-Hsu, F; Drögemüller, C

    2016-04-01

    Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle, has been recently reported to have an influence on the rearing success of calves. The affected animals show unresponsive diarrhea accompanied by hypocholesterolemia and usually die within the first weeks or months of life. Here, we show that whole genome sequencing combined with the knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred male carrying one copy of the critical 2.24-Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the non-affected carrier male. The genetic makeup of this key animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low-density lipoproteins, and therefore, the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia-1 (FHBL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle.

  1. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.

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    Aurélie Kapusta

    2013-04-01

    Full Text Available Advances in vertebrate genomics have uncovered thousands of loci encoding long noncoding RNAs (lncRNAs. While progress has been made in elucidating the regulatory functions of lncRNAs, little is known about their origins and evolution. Here we explore the contribution of transposable elements (TEs to the makeup and regulation of lncRNAs in human, mouse, and zebrafish. Surprisingly, TEs occur in more than two thirds of mature lncRNA transcripts and account for a substantial portion of total lncRNA sequence (~30% in human, whereas they seldom occur in protein-coding transcripts. While TEs contribute less to lncRNA exons than expected, several TE families are strongly enriched in lncRNAs. There is also substantial interspecific variation in the coverage and types of TEs embedded in lncRNAs, partially reflecting differences in the TE landscapes of the genomes surveyed. In human, TE sequences in lncRNAs evolve under greater evolutionary constraint than their non-TE sequences, than their intronic TEs, or than random DNA. Consistent with functional constraint, we found that TEs contribute signals essential for the biogenesis of many lncRNAs, including ~30,000 unique sites for transcription initiation, splicing, or polyadenylation in human. In addition, we identified ~35,000 TEs marked as open chromatin located within 10 kb upstream of lncRNA genes. The density of these marks in one cell type correlate with elevated expression of the downstream lncRNA in the same cell type, suggesting that these TEs contribute to cis-regulation. These global trends are recapitulated in several lncRNAs with established functions. Finally a subset of TEs embedded in lncRNAs are subject to RNA editing and predicted to form secondary structures likely important for function. In conclusion, TEs are nearly ubiquitous in lncRNAs and have played an important role in the lineage-specific diversification of vertebrate lncRNA repertoires.

  2. TEnest: automated chronological annotation and visualization of nested plant transposable elements.

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    Kronmiller, Brent A; Wise, Roger P

    2008-01-01

    Organisms with a high density of transposable elements (TEs) exhibit nesting, with subsequent repeats found inside previously inserted elements. Nesting splits the sequence structure of TEs and makes annotation of repetitive areas challenging. We present TEnest, a repeat identification and display tool made specifically for highly repetitive genomes. TEnest identifies repetitive sequences and reconstructs separated sections to provide full-length repeats and, for long-terminal repeat (LTR) retrotransposons, calculates age since insertion based on LTR divergence. TEnest provides a chronological insertion display to give an accurate visual representation of TE integration history showing timeline, location, and families of each TE identified, thus creating a framework from which evolutionary comparisons can be made among various regions of the genome. A database of repeats has been developed for maize (Zea mays), rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare) to illustrate the potential of TEnest software. All currently finished maize bacterial artificial chromosomes totaling 29.3 Mb were analyzed with TEnest to provide a characterization of the repeat insertions. Sixty-seven percent of the maize genome was found to be made up of TEs; of these, 95% are LTR retrotransposons. The rate of solo LTR formation is shown to be dissimilar across retrotransposon families. Phylogenetic analysis of TE families reveals specific events of extreme TE proliferation, which may explain the high quantities of certain TE families found throughout the maize genome. The TEnest software package is available for use on PlantGDB under the tools section (http://www.plantgdb.org/prj/TE_nest/TE_nest.html); the source code is available from (http://wiselab.org).

  3. Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements.

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    Amaury Herpin

    2010-02-01

    Full Text Available Control and coordination of eukaryotic gene expression rely on transcriptional and posttranscriptional regulatory networks. Evolutionary innovations and adaptations often require rapid changes of such networks. It has long been hypothesized that transposable elements (TE might contribute to the rewiring of regulatory interactions. More recently it emerged that TEs might bring in ready-to-use transcription factor binding sites to create alterations to the promoters by which they were captured. A process where the gene regulatory architecture is of remarkable plasticity is sex determination. While the more downstream components of the sex determination cascades are evolutionary conserved, the master regulators can switch between groups of organisms even on the interspecies level or between populations. In the medaka fish (Oryzias latipes a duplicated copy of dmrt1, designated dmrt1bY or DMY, on the Y chromosome was shown to be the master regulator of male development, similar to Sry in mammals. We found that the dmrt1bY gene has acquired a new feedback downregulation of its expression. Additionally, the autosomal dmrt1a gene is also able to regulate transcription of its duplicated paralog by binding to a unique target Dmrt1 site nested within the dmrt1bY proximal promoter region. We could trace back this novel regulatory element to a highly conserved sequence within a new type of TE that inserted into the upstream region of dmrt1bY shortly after the duplication event. Our data provide functional evidence for a role of TEs in transcriptional network rewiring for sub- and/or neo-functionalization of duplicated genes. In the particular case of dmrt1bY, this contributed to create new hierarchies of sex-determining genes.

  4. FB-NOF is a non-autonomous transposable element, expressed in Drosophila melanogaster and present only in the melanogaster group.

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    Badal, Martí; Xamena, Noel; Cabré, Oriol

    2013-09-10

    Most foldback elements are defective due to the lack of coding sequences but some are associated with coding sequences and may represent the entire element. This is the case of the NOF sequences found in the FB of Drosophila melanogaster, formerly considered as an autonomous TE and currently proposed as part of the so-called FB-NOF element, the transposon that would be complete and fully functional. NOF is always associated with FB and never seen apart from the FB inverted repeats (IR). This is the reason why the FB-NOF composite element can be considered the complete element. At least one of its ORFs encodes a protein that has always been considered its transposase, but no detailed studies have been carried out to verify this. In this work we test the hypothesis that FB-NOF is an active transposon nowadays. We search for its expression product, obtaining its cDNA, and propose the ORF and the sequence of its potential protein. We found that the NOF protein is not a transposase as it lacks any of the motifs of known transposases and also shows structural homology with hydrolases, therefore FB-NOF cannot belong to the superfamily MuDR/foldback, as up to now it has been classified, and can be considered as a non-autonomous transposable element. The alignment with the published genomes of 12 Drosophila species shows that NOF presence is restricted only to the 6 Drosophila species belonging to the melanogaster group.

  5. Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids.

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    Nicholas Delihas

    Full Text Available BACKGROUND: Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level. METHODOLOGY/PRINCIPAL FINDINGS: In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found "free-standing" and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3' ends of lipoprotein genes (PFam12 and PFam60, however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place. CONCLUSIONS/SIGNIFICANCE: Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in

  6. A transposable element within the Non-canonical telomerase RNA of Arabidopsis thaliana modulates telomerase in response to DNA damage [corrected].

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    Hengyi Xu

    2015-06-01

    Full Text Available Long noncoding RNAs (lncRNAs have emerged as critical factors in many biological processes, but little is known about how their regulatory functions evolved. One of the best-studied lncRNAs is TER, the essential RNA template for telomerase reverse transcriptase. We previously showed that Arabidopsis thaliana harbors three TER isoforms: TER1, TER2 and TER2S. TER1 serves as a canonical telomere template, while TER2 is a novel negative regulator of telomerase activity, induced in response to double-strand breaks (DSBs. TER2 contains a 529 nt intervening sequence that is removed along with 36 nt at the RNA 3' terminus to generate TER2S, an RNA of unknown function. Here we investigate how A. thaliana TER2 acquired its regulatory function. Using data from the 1,001 Arabidopsis genomes project, we report that the intervening sequence within TER2 is derived from a transposable element termed DSB responsive element (DRE. DRE is found in the TER2 loci of most but not all A. thaliana accessions. By analyzing accessions with (TER2 and without DRE (TER2Δ we demonstrate that this element is responsible for many of the unique properties of TER2, including its enhanced binding to TERT and telomerase inhibitory function. We show that DRE destabilizes TER2, and further that TER2 induction by DNA damage reflects increased RNA stability and not increased transcription. DRE-mediated changes in TER2 stability thus provide a rapid and sensitive switch to fine-tune telomerase enzyme activity. Altogether, our data shows that invasion of the TER2 locus by a small transposon converted this lncRNA into a DNA damage sensor that modulates telomerase enzyme activity in response to genome assault.

  7. Reverted glutathione S-transferase-like genes that influence flower color intensity of carnation (Dianthus caryophyllus L.) originated from excision of a transposable element.

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    Momose, Masaki; Itoh, Yoshio; Umemoto, Naoyuki; Nakayama, Masayoshi; Ozeki, Yoshihiro

    2013-12-01

    A glutathione S-transferase-like gene, DcGSTF2, is responsible for carnation (Dianthus caryophyllus L.) flower color intensity. Two defective genes, DcGSTF2mu with a nonsense mutation and DcGSTF2-dTac1 containing a transposable element dTac1, have been characterized in detail in this report. dTac1 is an active element that produces reverted functional genes by excision of the element. A pale-pink cultivar 'Daisy' carries both defective genes, whereas a spontaneous deep-colored mutant 'Daisy-VPR' lost the element from DcGSTF2-dTac1. This finding confirmed that dTac1 is active and that the resulting reverted gene, DcGSTF2rev1, missing the element is responsible for this color change. Crosses between the pale-colored cultivar '06-LA' and a deep-colored cultivar 'Spectrum' produced segregating progeny. Only the deep-colored progeny had DcGSTF2rev2 derived from the 'Spectrum' parent, whereas progeny with pale-colored flowers had defective forms from both parents, DcGSTF2mu and DcGSTF2-dTac1. Thus, DcGSTF2rev2 had functional activity and likely originated from excision of dTac1 since there was a footprint sequence at the vacated site of the dTac1 insertion. Characterizing the DcGSTF2 genes in several cultivars revealed that the two functional genes, DcGSTF2rev1 and DcGSTF2rev2, have been used for some time in carnation breeding with the latter in use for more than half a century.

  8. There is no direct generalization of positive partial transpose criterion to the three-by-three case

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    Skowronek, Łukasz

    2016-11-01

    We show that there cannot exist a straightforward generalization of the famous positive partial transpose criterion to three-by-three systems. We call straightforward generalizations that use a finite set of positive maps and arbitrary local rotations of the tested two-partite state. In particular, we show that a family of extreme positive maps discussed in a paper by Ha and Kye [Open Syst. Inf. Dyn. 18, 323-337 (2011)], cannot be replaced by a finite set of witnesses in the task of entanglement detection in three-by-three systems. In a more mathematically elegant parlance, our result says that the convex cone of positive maps of the set of three-dimensional matrices into itself is not finitely generated as a mapping cone.

  9. Genotype-dependent Burst of Transposable Element Expression in Crowns of Hexaploid Wheat (Triticum aestivum L. during Cold Acclimation

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    Debbie Laudencia-Chingcuanco

    2012-01-01

    Full Text Available The expression of 1,613 transposable elements (TEs represented in the Affymetrix Wheat Genome Chip was examined during cold treatment in crowns of four hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throughout the experiment in three of the genotypes. In winter Norstar, the most cold-hardy of the four genotypes, a subset of the TEs showed a burst of expression after vernalization saturation was achieved. About 47% of the TEs were expressed, and both Class I (retrotransposons and Class II (DNA transposons types were well represented. Gypsy and Copia were the most represented among the retrotransposons while CACTA and Mariner were the most represented DNA transposons. The data suggests that the Vrn-A1 region plays a role in the stage-specific induction of TE expression in this genotype.

  10. Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae

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    Fernández-Medina Rita D

    2012-06-01

    Full Text Available Abstract Background Transposable elements (TEs, both DNA transposons and retrotransposons, are genetic elements with the main characteristic of being able to mobilize and amplify their own representation within genomes, utilizing different mechanisms of transposition. An almost universal feature of TEs in eukaryotic genomes is their inability to transpose by themselves, mainly as the result of sequence degeneration (by either mutations or deletions. Most of the elements are thus either inactive or non-autonomous. Considering that the bulk of some eukaryotic genomes derive from TEs, they have been conceived as “TE graveyards.” It has been shown that once an element has been inactivated, it progressively accumulates mutations and deletions at neutral rates until completely losing its identity or being lost from the host genome; however, it has also been shown that these “neutral sequences” might serve as raw material for domestication by host genomes. Results We have analyzed the sequence structural variations, nucleotide divergence, and pattern of insertions and deletions of several superfamilies of TEs belonging to both class I (long terminal repeats [LTRs] and non-LTRs [NLTRs] and II in the genome of Anopheles gambiae, aiming at describing the landscape of deterioration of these elements in this particular genome. Our results describe a great diversity in patterns of deterioration, indicating lineage-specific differences including the presence of Solo-LTRs in the LTR lineage, 5′-deleted NLTRs, and several non-autonomous and MITEs in the class II families. Interestingly, we found fragments of NLTRs corresponding to the RT domain, which preserves high identity among them, suggesting a possible remaining genomic role for these domains. Conclusions We show here that the TEs in the An. gambiae genome deteriorate in different ways according to the class to which they belong. This diversity certainly has implications not only at the host

  11. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.

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    McCoy, Rajiv C; Taylor, Ryan W; Blauwkamp, Timothy A; Kelley, Joanna L; Kertesz, Michael; Pushkarev, Dmitry; Petrov, Dmitri A; Fiston-Lavier, Anna-Sophie

    2014-01-01

    High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or complex genomic arrangements. While TEs strongly affect genome function and evolution, most current de novo assembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly-parallel library preparation and local assembly of short read data and which achieve lengths of 1.5-18.5 Kbp with an extremely low error rate ([Formula: see text]0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organism Drosophila melanogaster (reference genome strain y; cn, bw, sp) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long-reads, and likely other methods that generate long-reads, offer a powerful approach to improve de novo assemblies of whole genomes.

  12. An immunity-triggering effector from the Barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution.

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    Ali, Shawkat; Laurie, John D; Linning, Rob; Cervantes-Chávez, José Antonio; Gaudet, Denis; Bakkeren, Guus

    2014-07-01

    The basidiomycete smut fungus Ustilago hordei was previously shown to comprise isolates that are avirulent on various barley host cultivars. Through genetic crosses we had revealed that a dominant avirulence locus UhAvr1 which triggers immunity in barley cultivar Hannchen harboring resistance gene Ruh1, resided within an 80-kb region. DNA sequence analysis of this genetically delimited region uncovered the presence of 7 candidate secreted effector proteins. Sequence comparison of their coding sequences among virulent and avirulent parental and field isolates could not distinguish UhAvr1 candidates. Systematic deletion and complementation analyses revealed that UhAvr1 is UHOR_10022 which codes for a small effector protein of 171 amino acids with a predicted 19 amino acid signal peptide. Virulence in the parental isolate is caused by the insertion of a fragment of 5.5 kb with similarity to a common U. hordei transposable element (TE), interrupting the promoter of UhAvr1 and thereby changing expression and hence recognition of UhAVR1p. This rearrangement is likely caused by activities of TEs and variation is seen among isolates. Using GFP-chimeric constructs we show that UhAvr1 is induced only in mated dikaryotic hyphae upon sensing and infecting barley coleoptile cells. When infecting Hannchen, UhAVR1p causes local callose deposition and the production of reactive oxygen species and necrosis indicative of the immune response. UhAvr1 does not contribute significantly to overall virulence. UhAvr1 is located in a cluster of ten effectors with several paralogs and over 50% of TEs. This cluster is syntenous with clusters in closely-related U. maydis and Sporisorium reilianum. In these corn-infecting species, these clusters harbor however more and further diversified homologous effector families but very few TEs. This increased variability may have resulted from past selection pressure by resistance genes since U. maydis is not known to trigger immunity in its corn host.

  13. Changes in DNA methylation and transgenerational mobilization of a transposable element (mPing by the Topoisomerase II inhibitor, Etoposide, in rice

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    Yang Xuejiao

    2012-04-01

    Full Text Available Abstract Background Etoposide (epipodophyllotoxin is a chemical commonly used as an anti-cancer drug which inhibits DNA synthesis by blocking topoisomerase II activity. Previous studies in animal cells have demonstrated that etoposide constitutes a genotoxic stress which may induce genomic instability including mobilization of normally quiescent transposable elements (TEs. However, it remained unknown whether similar genetically mutagenic effects could be imposed by etoposide in plant cells. Also, no information is available with regard to whether the drug may cause a perturbation of epigenetic stability in any organism. Results To investigate whether etoposide could generate genetic and/or epigenetic instability in plant cells, we applied etoposide to germinating seeds of six cultivated rice (Oryza sativa L. genotypes including both subspecies, japonica and indica. Based on the methylation-sensitive gel-blotting results, epigenetic changes in DNA methylation of three TEs (Tos17, Osr23 and Osr36 and two protein-encoding genes (Homeobox and CDPK-related genes were detected in the etoposide-treated plants (S0 generation in four of the six studied japonica cultivars, Nipponbare, RZ1, RZ2, and RZ35, but not in the rest japonica cultivar (Matsumae and the indica cultivar (93-11. DNA methylation changes in the etoposide-treated S0 rice plants were validated by bisulfite sequencing at both of two analyzed loci (Tos17 and Osr36. Transpositional activity was tested for eight TEs endogenous to the rice genome in both the S0 plants and their selfed progenies (S1 and S2 of one of the cultivars, RZ1, which manifested heritable phenotypic variations. Results indicated that no transposition occurred in the etoposide-treated S0 plants for any of the TEs. Nonetheless, a MITE transposon, mPing, showed rampant mobilization in the S1 and S2 progenies descended from the drug-treated S0 plants. Conclusions Our results demonstrate that etoposide imposes a similar

  14. Transcription of the rat testis-specific Rtdpoz-T1 and -T2 retrogenes during embryo development: co-transcription and frequent exonisation of transposable element sequences

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    Chang Che-Ming

    2009-07-01

    Full Text Available Abstract Background Retrotransposition is an important evolutionary force for the creation of new and potentially functional intronless genes which are collectively called retrogenes. Many retrogenes are expressed in the testis and the gene products have been shown to actively participate in spermatogenesis and other unique functions of the male germline. We have previously reported a cluster of retrogenes in the rat genome that encode putative TRAF- and POZ-domain proteins. Two of the genes, Rtdpoz-T1 and -T2 (abbreviated as T1 and T2, have further been shown to be expressed specifically in the rat testis. Results We show here that the T1 and T2 genes are also expressed in the rat embryo up to days 16–17 of development when the genes are silenced until being re-activated in the adult testis. On database interrogation, we find that some T1/T2 exons are chromosomally duplicated as cassettes of 2 or 3 exons consistent with retro-duplication. The embryonic T1/T2 transcripts, characterised by RT-PCR-cloning and rapid amplification of cDNA ends, are further found to have acquired one or more noncoding exons in the 5'-untranslated region (5'-UTR. Most importantly, the T1/T2 locus is embedded within a dense field of relics of transposable element (TE derived mainly from LINE1 and ERV sequences, and the TE sequences are frequently exonised through alternative splicing to form the 5'-UTR sequences of the T1/T2 transcripts. In a case of T1 transcript, the 3'-end is extended into and terminated within an L1 sequence. Since the two genes share a common exon 1 and are, therefore, regulated by a single promoter, a T2-to-T1 co-transcription model is proposed. We further demonstrate that the exonised 5'-UTR TE sequences could lead to the creation of upstream open reading frames resulting in translational repression. Conclusion Exonisation of TE sequences is a frequent event in the transcription of retrogenes during embryonic development and in the testis and

  15. A novel application of ecological analyses to assess transposable element distributions in the genome of the domestic cow, Bos taurus.

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    Saylor, Brent; Elliott, Tyler A; Linquist, Stefan; Kremer, Stefan C; Gregory, T Ryan; Cottenie, Karl

    2013-09-01

    Transposable elements (TEs) are among the most abundant components of many eukaryotic genomes. Efforts to explain TE abundance, as well as TE diversity among genomes, have led some researchers to draw an analogy between genomic and ecological processes. Adopting this perspective, we conducted an analysis of the cow (Bos taurus) genome using techniques developed by community ecologists to determine whether environmental factors influence community composition. Specifically, each chromosome within the Bos taurus genome was treated as a "linear transect", and a multivariate redundancy analysis (RDA) was used to identify large-scale spatial patterns in TE communities associated with 10 TE families. The position of each TE community on the chromosome accounted for ∼50% of the variation along the chromosome "transect". Multivariate analysis further revealed an effect of gene density on TE communities that is influenced by several other factors in the (genomic) environment, including chromosome length and TE density. The results of this analysis demonstrate that ecological methods can be applied successfully to help answer genomic questions.

  16. An adaptive transposable element insertion in the regulatory region of the EO gene in the domesticated silkworm, Bombyx mori.

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    Sun, Wei; Shen, Yi-Hong; Han, Min-Jin; Cao, Yun-Feng; Zhang, Ze

    2014-12-01

    Although there are many studies to show a key role of transposable elements (TEs) in adaptive evolution of higher organisms, little is known about the molecular mechanisms. In this study, we found that a partial TE (Taguchi) inserted in the cis-regulatory region of the silkworm ecdysone oxidase (EO) gene, which encodes a crucial enzyme to reduce the titer of molting hormone (20-hydroxyecdysone, 20E). The TE insertion occurred during domestication of silkworm and the frequency of the TE insertion in the domesticated silkworm (Bombyx mori) is high, 54.24%. The linkage disequilibrium in the TE inserted strains of the domesticated silkworm was elevated. Molecular population genetics analyses suggest that this TE insertion is adaptive for the domesticated silkworm. Luminescent reporter assay shows that the TE inserted in the cis-regulatory region of the EO gene functions as a 20E-induced enhancer of the gene expression. Further, phenotypic bioassay indicates that the silkworm with the TE insertion exhibited more stable developmental phenotype than the silkworm without the TE insertion when suffering from food shortage. Thus, the inserted TE in the cis-regulatory region of the EO gene increased developmental uniformity of silkworm individuals through regulating 20E metabolism, partially explaining transformation of a domestication developmental trait in the domesticated silkworm. Our results emphasize the exceptional role of gene expression regulation in developmental transition of domesticated animals.

  17. Heterochromatin and molecular characterization of DsmarMITE transposable element in the beetle Dichotomius schiffleri (Coleoptera: Scarabaeidae).

    Science.gov (United States)

    Xavier, Crislaine; Cabral-de-Mello, Diogo Cavalcanti; de Moura, Rita Cássia

    2014-12-01

    Cytogenetic studies of the Neotropical beetle genus Dichotomius (Scarabaeinae, Coleoptera) have shown dynamism for centromeric constitutive heterochromatin sequences. In the present work we studied the chromosomes and isolated repetitive sequences of Dichotomius schiffleri aiming to contribute to the understanding of coleopteran genome/chromosomal organization. Dichotomius schiffleri presented a conserved karyotype and heterochromatin distribution in comparison to other species of the genus with 2n = 18, biarmed chromosomes, and pericentromeric C-positive blocks. Similarly to heterochromatin distributional patterns, the highly and moderately repetitive DNA fraction (C 0 t-1 DNA) was detected in pericentromeric areas, contrasting with the euchromatic mapping of an isolated TE (named DsmarMITE). After structural analyses, the DsmarMITE was classified as a non-autonomous element of the type miniature inverted-repeat transposable element (MITE) with terminal inverted repeats similar to Mariner elements of insects from different orders. The euchromatic distribution for DsmarMITE indicates that it does not play a part in the dynamics of constitutive heterochromatin sequences.

  18. Spontaneous germline excision of Tol1, a DNA-based transposable element naturally occurring in the medaka fish genome.

    Science.gov (United States)

    Watanabe, Kohei; Koga, Hajime; Nakamura, Kodai; Fujita, Akiko; Hattori, Akimasa; Matsuda, Masaru; Koga, Akihiko

    2014-04-01

    DNA-based transposable elements are ubiquitous constituents of eukaryotic genomes. Vertebrates are, however, exceptional in that most of their DNA-based elements appear to be inactivated. The Tol1 element of the medaka fish, Oryzias latipes, is one of the few elements for which copies containing an undamaged gene have been found. Spontaneous transposition of this element in somatic cells has previously been demonstrated, but there is only indirect evidence for its germline transposition. Here, we show direct evidence of spontaneous excision in the germline. Tyrosinase is the key enzyme in melanin biosynthesis. In an albino laboratory strain of medaka fish, which is homozygous for a mutant tyrosinase gene in which a Tol1 copy is inserted, we identified de novo reversion mutations related to melanin pigmentation. The gamete-based reversion rate was as high as 0.4%. The revertant fish carried the tyrosinase gene from which the Tol1 copy had been excised. We previously reported the germline transposition of Tol2, another DNA-based element that is thought to be a recent invader of the medaka fish genome. Tol1 is an ancient resident of the genome. Our results indicate that even an old element can contribute to genetic variation in the host genome as a natural mutator.

  19. An Immunity-Triggering Effector from the Barley Smut Fungus Ustilago hordei Resides in an Ustilaginaceae-Specific Cluster Bearing Signs of Transposable Element-Assisted Evolution

    KAUST Repository

    Ali, Shawkat

    2014-07-03

    The basidiomycete smut fungus Ustilago hordei was previously shown to comprise isolates that are avirulent on various barley host cultivars. Through genetic crosses we had revealed that a dominant avirulence locus UhAvr1 which triggers immunity in barley cultivar Hannchen harboring resistance gene Ruh1, resided within an 80-kb region. DNA sequence analysis of this genetically delimited region uncovered the presence of 7 candidate secreted effector proteins. Sequence comparison of their coding sequences among virulent and avirulent parental and field isolates could not distinguish UhAvr1 candidates. Systematic deletion and complementation analyses revealed that UhAvr1 is UHOR_10022 which codes for a small effector protein of 171 amino acids with a predicted 19 amino acid signal peptide. Virulence in the parental isolate is caused by the insertion of a fragment of 5.5 kb with similarity to a common U. hordei transposable element (TE), interrupting the promoter of UhAvr1 and thereby changing expression and hence recognition of UhAVR1p. This rearrangement is likely caused by activities of TEs and variation is seen among isolates. Using GFP-chimeric constructs we show that UhAvr1 is induced only in mated dikaryotic hyphae upon sensing and infecting barley coleoptile cells. When infecting Hannchen, UhAVR1p causes local callose deposition and the production of reactive oxygen species and necrosis indicative of the immune response. UhAvr1 does not contribute significantly to overall virulence. UhAvr1 is located in a cluster of ten effectors with several paralogs and over 50% of TEs. This cluster is syntenous with clusters in closely-related U. maydis and Sporisorium reilianum. In these corn-infecting species, these clusters harbor however more and further diversified homologous effector families but very few TEs. This increased variability may have resulted from past selection pressure by resistance genes since U. maydis is not known to trigger immunity in its corn host.

  20. An immunity-triggering effector from the Barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution.

    Directory of Open Access Journals (Sweden)

    Shawkat Ali

    2014-07-01

    Full Text Available The basidiomycete smut fungus Ustilago hordei was previously shown to comprise isolates that are avirulent on various barley host cultivars. Through genetic crosses we had revealed that a dominant avirulence locus UhAvr1 which triggers immunity in barley cultivar Hannchen harboring resistance gene Ruh1, resided within an 80-kb region. DNA sequence analysis of this genetically delimited region uncovered the presence of 7 candidate secreted effector proteins. Sequence comparison of their coding sequences among virulent and avirulent parental and field isolates could not distinguish UhAvr1 candidates. Systematic deletion and complementation analyses revealed that UhAvr1 is UHOR_10022 which codes for a small effector protein of 171 amino acids with a predicted 19 amino acid signal peptide. Virulence in the parental isolate is caused by the insertion of a fragment of 5.5 kb with similarity to a common U. hordei transposable element (TE, interrupting the promoter of UhAvr1 and thereby changing expression and hence recognition of UhAVR1p. This rearrangement is likely caused by activities of TEs and variation is seen among isolates. Using GFP-chimeric constructs we show that UhAvr1 is induced only in mated dikaryotic hyphae upon sensing and infecting barley coleoptile cells. When infecting Hannchen, UhAVR1p causes local callose deposition and the production of reactive oxygen species and necrosis indicative of the immune response. UhAvr1 does not contribute significantly to overall virulence. UhAvr1 is located in a cluster of ten effectors with several paralogs and over 50% of TEs. This cluster is syntenous with clusters in closely-related U. maydis and Sporisorium reilianum. In these corn-infecting species, these clusters harbor however more and further diversified homologous effector families but very few TEs. This increased variability may have resulted from past selection pressure by resistance genes since U. maydis is not known to trigger immunity

  1. Functional identification of gene cluster for the aniline metabolic pathway mediated by transposable element

    Institute of Scientific and Technical Information of China (English)

    LIANG Quanfeng; Takeo Masahiro; LIN Min; CHEN Ming; XU Yuquan; ZHANG Wei; PING Shuzhen; LU Wei; SONG Xianlong; WANG Weiwei; GENG Lizhao

    2005-01-01

    A convenient and widely applicable method has been developed to clone aniline metabolic gene cluster in this study. Three positive recombinant plasmids pDA1, pDB2 and pDB11 were cloned from genomic library of aniline degradation strain AD9. The result of aniline dioxygenase (AD) activity and catechol 2,3-oxygenase (C23O) activity assay showed that pDA1 and pDB11 contain aniline dioxygenase genes and catechol 2,3-dioxygenase genes, respectively. The sequence analysis of the total 24.7-kb region revealed that this region contains 25 ORFs, of which 17 genes involve metabolism of aniline. In the gene cluster, the first five genes (tadQTA1A2B) and the subsequent gene (tadR1) were predicted to encode a multi-component aniline dioxygenase and a LysR-type regulator, respectively, while the others (tadD1C1D2C2EFGIJKL) were expected to encode meta- cleavage pathway enzymes for catechol degradation. The gene cluster was surrounded by two IS1071 sequences.

  2. Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements.

    Science.gov (United States)

    Åsman, Anna K M; Fogelqvist, Johan; Vetukuri, Ramesh R; Dixelius, Christina

    2016-08-01

    Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Recent evidence has suggested that pathogen-derived sRNAs can modulate the expression of plant defense genes. Here, we studied the sRNA classes and functions associated with Phytophthora infestans Argonaute (Ago) proteins. sRNAs were co-immunoprecipitated with three PiAgo proteins and deep sequenced. Twenty- to twenty-two-nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26-nt sRNAs was seen in the PiAgo4-bound sample. The frequencies and sizes of transposable element (TE)-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in the control of different TE classes. We further provide evidence for the involvement of PiAgo1 in the P. infestans microRNA (miRNA) pathway. Protein-coding genes are probably regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing Crinkler (CRN) effectors was bound to PiAgo1, implicating this protein in the regulation of the expanded CRN gene family. The data suggest that PiAgo1 plays an essential role in gene regulation and that at least two RNA silencing pathways regulate TEs in the plant-pathogenic oomycete P. infestans.

  3. Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis.

    Science.gov (United States)

    Fischer, Cécile; Bouneau, Laurence; Coutanceau, Jean-Pierre; Weissenbach, Jean; Volff, Jean-Nicolas; Ozouf-Costaz, Catherine

    2004-07-21

    Because of its unusual high degree of compaction and paucity of repetitive sequences, the genome of the smooth pufferfish Tetraodon nigroviridis is the subject of a well-advanced sequencing project. An astonishing diversity of transposable elements not found in the human and the mouse has been observed in the genome of T. nigroviridis. Due to the difficulty of assembling repeat-rich regions, the whole genome shotgun sequencing approach will probably fail to reveal the general organisation of this compact vertebrate genome. Therefore, in order to gain new insights into the global distribution pattern of repeated DNA in the genome of T. nigroviridis, we have reconstructed partial/complete repetitive sequences from data generated by the genome project and performed double-colour fluorescent in situ hybridization (FISH) analysis for representatives of three major categories of repeated sequences including two minisatellites (ms100 and ms104), two DNA transposons (Tol2 and Buffy1) and two non-long terminal repeat (LTR) retrotransposons (Rex3 and Babar). We show that DNA transposons and retroelements very frequently colocalize with minisatellites and mostly accumulate within heterochromatic regions. These results, which have not been reported so far for the fugu Takifugu rubripes, show that repeated elements are generally excluded from gene-rich regions in T. nigroviridis and underline the extreme degree of compartmentalization of this compact genome. The genome organization of the pufferfish is clearly different from that observed in humans, where repeated sequences make up an important fraction of euchromatic DNA, and is more similar to that observed in the fruit fly Drosophila melanogaster.

  4. Transposable prophage Mu is organized as a stable chromosomal domain of E. coli.

    Directory of Open Access Journals (Sweden)

    Rudra P Saha

    2013-11-01

    Full Text Available The E. coli chromosome is compacted by segregation into 400-500 supercoiled domains by both active and passive mechanisms, for example, transcription and DNA-protein association. We find that prophage Mu is organized as a stable domain bounded by the proximal location of Mu termini L and R, which are 37 kbp apart on the Mu genome. Formation/maintenance of the Mu 'domain' configuration, reported by Cre-loxP recombination and 3C (chromosome conformation capture, is dependent on a strong gyrase site (SGS at the center of Mu, the Mu L end and MuB protein, and the E. coli nucleoid proteins IHF, Fis and HU. The Mu domain was observed at two different chromosomal locations tested. By contrast, prophage λ does not form an independent domain. The establishment/maintenance of the Mu domain was promoted by low-level transcription from two phage promoters, one of which was domain dependent. We propose that the domain confers transposition readiness to Mu by fostering topological requirements of the reaction and the proximity of Mu ends. The potential benefits to the host cell from a subset of proteins expressed by the prophage may in turn help its long-term stability.

  5. La démarche RAROC utilisée en banque est-elle transposable à l’assurance-vie ?

    OpenAIRE

    Jean-Noël Ory

    2002-01-01

    L’objet de cet article est de dresser une tentative d’adaptation de la méthodologie RAROC (risk adjusted return on capital), utilisée en banque, au domaine de l’assurance-vie. Après avoir rappelé que la nécessité de constituer des fonds propres économiques est similaire pour une banque et pour une compagnie d’assurance-vie, nous rappelons la logique de construction de l’indicateur RAROC. Dans un deuxième temps, nous essayons de transposer cette logique à l’assurance-vie, en étudiant quels ser...

  6. Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat

    Directory of Open Access Journals (Sweden)

    Belyayev Alexander

    2010-02-01

    Full Text Available Abstract Background How new forms arise in nature has engaged evolutionary biologists since Darwin's seminal treatise on the origin of species. Transposable elements (TEs may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation. Results Significant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii the fluctuations in copy number are TE-family specific; (iii there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv a small percentage of TEs that increase in copy number can actually insert at novel locations and

  7. The transposability of the Mediterranean-type diet in non-Mediterranean regions: application to the physician/allied health team.

    Science.gov (United States)

    Speed, C

    2004-12-01

    Studies are consistently declaring that the Mediterranean-type diet is transposable to non-Mediterranean regions. The nutritional end points of Med-type eating appear to be achievable through foods from a variety of traditions and appear to support predetermined expectations surrounding food preparation, choice, taste and sensory appeal. The broad emphasis on minimally processed plants and their products (vegetables, fruit, legumes, wholegrains, nuts, seeds and oils); low fat dairy, fish, less emphasis on animal products and removal of partially hydrogenated fats has piqued the attention of health professionals who are interested in arresting the incidence of chronic disease. The theoretical underpinnings of Med-type eating have driven new understandings in dietary guidelines, which is especially timely as well-marketed fad diets loom large on the current health horizon.

  8. Activation of an endogenous retrotransposon associated with epigenetic changes in Lotus japonicus

    DEFF Research Database (Denmark)

    Fukai, Eigo; Stougaard, Jens; Hayashi, Makoto

    2013-01-01

    Long terminal repeat retrotransposons occupy a large portion of genomes in flowering plants. In spite of their abundance, the majority are silenced and rarely transpose. One of the examples of a highly active retrotransposon is Lotus Retrotransposon 1(LORE1), of the model legume Lotus japonicus (...

  9. Cytogenetic mapping of the retroelements Rex1, Rex3 and Rex6 among cichlid fish: new insights on the chromosomal distribution of transposable elements.

    Science.gov (United States)

    Valente, G T; Mazzuchelli, J; Ferreira, I A; Poletto, A B; Fantinatti, B E A; Martins, C

    2011-01-01

    To enhance our understanding of the organization of the genome and chromosome evolution of cichlid fish species, we have isolated and physically mapped onto the chromosomes the transposable elements (TEs) Rex1, Rex3 and Rex6, which are conserved in teleost fish, in the chromosomes of African and South American cichlid species. The physical mapping of different Rex elements showed that they are primarily compartmentalized in the pericentromeric heterochromatic regions, although dispersed or clustered signals in euchromatic regions were also observed. The presence of TEs in heterochromatin can be correlated with their role in the structure and organization of heterochromatic areas (such as centromeres) or with the lower selective pressure that act on these gene-poor regions. The Rex elements were also concentrated in the largest chromosome pair of the Nile tilapia, Oreochromis niloticus. This chromosome pair is supposed to have originated by fusions, demonstrating the possible involvement of TEs with chromosome rearrangements. Besides general patterns of chromosomal distribution, comparative analysis suggests that Rex elements could differ in their chromosomal distribution among different fish groups or species and that intrinsic aspects of the genomes could influence the spread, accumulation or elimination of TEs.

  10. Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.

    Science.gov (United States)

    Harding, Joanne L; Horswell, Stuart; Heliot, Claire; Armisen, Javier; Zimmerman, Lyle B; Luscombe, Nicholas M; Miska, Eric A; Hill, Caroline S

    2014-01-01

    Small RNA control of gene expression is critical for developmental processes in vertebrate embryos. To determine the dynamics of small RNA expression and to uncover novel small RNAs in the early vertebrate embryo, we performed high-throughput sequencing of all small RNAs in Xenopus tropicalis embryos at three developmental time points and in dissected halves of gastrula embryos. This analysis allowed us to identify novel microRNAs and we show that microRNA expression is highly dynamic and spatially localized in early embryos. In addition, we have developed a microRNA prediction pipeline and demonstrate that it has the power to predict new miRNAs that are experimentally detectable in frogs, mice, and humans. By combining the small RNA sequencing with mRNA profiling at the different developmental stages, we identify a new class of small noncoding RNAs that we name siteRNAs, which align in clusters to introns of protein-coding genes. We show that siteRNAs are derived from remnants of transposable elements present in the introns. We find that genes containing clusters of siteRNAs are transcriptionally repressed as compared with all genes. Furthermore, we show that this is true for individual genes containing siteRNA clusters, and that these genes are enriched in specific repressive histone modifications. Our data thus suggest a new mechanism of siteRNA-mediated gene silencing in vertebrates, and provide an example of how mobile elements can affect gene regulation.

  11. Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements.

    Science.gov (United States)

    Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; Kochko, Alexandre de; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

    2015-01-07

    A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes.

  12. Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements

    Science.gov (United States)

    Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; de Kochko, Alexandre; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

    2015-01-01

    A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes. PMID:25573958

  13. Differentiation of a Miniature Inverted Transposable Element (MITE) System in Asian Rice Cultivars and Its Inference for a Diphyletic Origin of Two Subspecies of Asian Cultivated Rice

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In the present study, we report a survey on a Miniature Inverted Transposable Element (MITE) system known as mPing in 102 varieties of Asian cultivated rice (Oryza sativa L.). We found that mPing populations could be generalized into two families, mping-1 and mPing-2, according to their sequence structures. Further analysis showed that these two families of mPing had significant bias in their distribution pattern in two subspecies of rice, namely O. sativa ssp. japonica and indica. O. sativa japonica has a higher proportion of mPing-1 as a general trait, whereas O. sativa indica has a higher proportion of mPing-2. We also examined the mPing system in a doubled haploid (DH) cross-breeding population of jingxi 17 (japonica) and zhaiyeqing 8 (indica) varieties and observed that the mPing system was not tightly linked to major subspecies-determining genes.Furthermore, we checked the mPing system in 28 accessions of Asian common wild rice O. rufipogon and found the mPing system in O. rufipogon. The distribution pattern of the mping system in O. rufipogon indicated a diphyletic origin of the Asian cultivated rice O. sativa species. We did not find the mPing system in another 20 Oryza species. These results substantiated a previous hypothesis that O. rufipogon and O. nivara species were the closest relatives of O. sativa and that the two extant subspecies of O. sativa were evolved independently from corresponding ecotypes of O. rufipogon.

  14. The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs

    Directory of Open Access Journals (Sweden)

    Arensburger Peter

    2011-12-01

    Full Text Available Abstract Background The piRNA pathway has been shown in model organisms to be involved in silencing of transposons thereby providing genome stability. In D. melanogaster the majority of piRNAs map to these sequences. The medically important mosquito species Aedes aegypti has a large genome size, a high transposon load which includes Miniature Inverted repeat Transposable Elements (MITES and an expansion of the piRNA biogenesis genes. Studies of transgenic lines of Ae. aegypti have indicated that introduced transposons are poorly remobilized and we sought to explore the basis of this. We wished to analyze the piRNA profile of Ae. aegypti and thereby determine if it is responsible for transposon silencing in this mosquito. Results Estimated piRNA sequence diversity was comparable between Ae. aegypti and D. melanogaster, but surprisingly only 19% of mosquito piRNAs mapped to transposons compared to 51% for D. melanogaster. Ae. aegypti piRNA clusters made up a larger percentage of the total genome than those of D. melanogaster but did not contain significantly higher percentages of transposon derived sequences than other regions of the genome. Ae. aegypti contains a number of protein coding genes that may be sources of piRNA biogenesis with two, traffic jam and maelstrom, implicated in this process in model organisms. Several genes of viral origin were also targeted by piRNAs. Examination of six mosquito libraries that had previously been transformed with transposon derived sequence revealed that new piRNA sequences had been generated to the transformed sequences, suggesting that they may have stimulated a transposon inactivation mechanism. Conclusions Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together the more uniform distribution of piRNA clusters throughout its genome, suggest that some aspects of the piRNA system differ between Ae. aegypti and D

  15. The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

    Directory of Open Access Journals (Sweden)

    de la Chaux Nicole

    2012-02-01

    Full Text Available Abstract Background Transposable elements (TEs are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata. This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that selfing species are likely to have fewer TEs.

  16. Orthodontic treatment of a transposed maxillary canine and first premolar in a young patient with Class III malocclusion.

    Science.gov (United States)

    Gracco, Antonio; Siviero, Laura; Perri, Alessandro; Favero, Lorenzo; Stellini, Edoardo

    2015-11-01

    A 12-year-old girl was referred to our clinic for evaluation of an unaesthetic dental appearance. All permanent teeth were erupted, while the deciduous maxillary right canine was retained. Cone-beam computed tomography revealed a complete transposition of the maxillary left canine and first premolar involving both the crowns and the roots. Initial cephalometric analysis showed a skeletal Class III pattern, with a slight maxillary retrusion and a compensated proclination of the upper incisors. The patient's teeth were considered to be in the correct position; therefore, we decided to attempt treatment by correcting the transposition and using only orthodontic compensation of the skeletal Class III malocclusion. After 25 months of active orthodontic treatment, the patient had a Class I molar and canine relationship on both sides, with ideal overbite and overjet values. Her profile was improved, her lips were competent, and cephalometric evaluation showed acceptable maxillary and mandibular incisor inclinations. The final panoramic radiograph showed that good root parallelism was achieved. Two-year follow-up intraoral photography showed stable results.

  17. Quality goals for energy resources - an innovative approach to transposing the EU requirements for energy efficiency and use of renewables to the national level; Energietraegerqualitaetsziele - ein innovativer Ansatz zur Weitergabe der Synergie von Energieeffizienz- und REN-Verpflichtungen

    Energy Technology Data Exchange (ETDEWEB)

    Luhmann, H.J.; Lechtenboehmer, S.; Venjakob, J. [Wuppertal Inst. fuer Klima, Umwelt, Energie GmbH (Germany). Forschungsgruppe 1 - Zukuenftige Energie- und Mobilitaetsstrukturen

    2008-06-15

    One of the main commitments contained in the EU package of 23 January 2008 for the realisation of the so-called 20-20-20 goals is to increase the share of renewable energies in the energy mix. This is to be achieved by means of a EU directive to be transposed into national law. The directive already exists as a draft. Although there is still some discussion about the alternatives of having either an EU-wide uniform system based on the trade in quotas or permits or national promotion systems, ultimately there is likely to be some form of coexistence at the national level of legislation similar to the German Electricity Feed Law on one side and quota-based systems on the other. With this situation in mind the following article explores innovative options for member states given the new legal situation at the EU level.

  18. A Study of Fractality and Long-Range Order in the Distribution of Transposable Elements in Eukaryotic Genomes Using the Scaling Properties of Block Entropy and Box-Counting

    Directory of Open Access Journals (Sweden)

    Labrini Athanasopoulou

    2014-03-01

    Full Text Available Repeats or Transposable Elements (TEs are highly repeated sequence stretches, present in virtually all eukaryotic genomes. We explore the distribution of representative TEs from all major classes in entire chromosomes across various organisms. We employ two complementary approaches, the scaling of block entropy and box-counting. Both converge to the conclusion that well-developed fractality is typical of small genomes while in large genomes it appears sporadically and in some cases is rudimentary. The human genome is particularly prone to develop this pattern, as TE chromosomal distributions therein are often highly clustered and inhomogeneous. Comparing with previous works, where occurrence of power-law-like size distributions in inter-repeat distances is studied, we conclude that fractality in entire chromosomes is a more stringent (thus less often encountered condition. We have formulated a simple evolutionary scenario for the genomic dynamics of TEs, which may account for their fractal distribution in real genomes. The observed fractality and long-range properties of TE genomic distributions have probably contributed to the formation of the “fractal globule”, a model for the confined chromatin organization of the eukaryotic nucleus proposed on the basis of experimental evidence.

  19. TamiR1123 originated from a family of miniature inverted-repeat transposable elements (MITE) including one inserted in the Vrn-A1a promoter in wheat.

    Science.gov (United States)

    Yu, Ming; Carver, Brett F; Yan, Liuling

    2014-02-01

    More than half of spring wheat cultivars have a dominant Vrn-A1a allele that has an insertion of a miniature inverted-repeat transposable element (MITE) in its promoter. In this study, we found that the MITE present in the Vrn-A1a gene (MITE_VRN) is a nearly perfect palindrome and it can form highly stable hairpin loops when expressed as RNA. MITE_VRN also possessed sequences of a microRNA in Triticum aestivum (TamiR1123). The P(32) labeled TamiR1123 probe detected two RNA molecules on a small RNA gel blot, one expected for MITE_VRN, and the other expected for TamiR1123. These results demonstrated that MITE_VRN was expressed as RNAs and TamiR1123 was originated from the MITE_VRN family. The isogenic line TDD carrying the dominant Vrn-A1a allele with MITE_VRN showed higher TamiR1123 and Vrn-A1a transcript levels than the isogenic line TDE carrying the recessive vrn-A1a allele without MITE_VRN. TamiR1123 were greatly up-regulated by plant age but slightly down-regulated by low temperature and short days. These findings have pointed to alternative regulatory mechanisms for plant development governed by Vrn-A1a in spring wheat.

  20. Picking the right tool for the job – phosphor-proteomics of egg activation

    Science.gov (United States)

    Wessel, Gary M.

    2016-01-01

    Eggs are the rarest cell in the human body, yet their study is essential for the fields of fertility, reproduction, and fetal health. Guo et al use a “surrogate” animal to discover the phophoproteomic pathways involved in egg activation. With datasets of several thousand phophosites on 2500 different proteins, these investigators have defined new pathways, connections to pathways, and priorities in searches for how eggs are activated at fertilization. These results in a sea urchin are now transposable to mammals for testing on a per candidate strategy. PMID:26573262

  1. Picking the right tool for the job--Phosphoproteomics of egg activation.

    Science.gov (United States)

    Wessel, Gary M

    2015-12-01

    Eggs are the rarest cell in the human body, yet their study is essential for the fields of fertility, reproduction, and fetal health. Guo et al. (Proteomics 2015, 15, 4080-4095) use a "surrogate" animal to discover the phosphoproteomic pathways involved in egg activation. With datasets of several thousand phosphosites on 2500 different proteins, these investigators have defined new pathways, connections to pathways, and priorities in searches for how eggs are activated at fertilization. These results in a sea urchin are now transposable to mammals for testing on a per candidate strategy.

  2. The Microprocessor controls the activity of mammalian retrotransposons

    DEFF Research Database (Denmark)

    Heras, Sara R.; Macias, Sara; Plass, Mireya

    2013-01-01

    More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for microRNA biogen......More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for micro......RNA biogenesis, also recognizes and binds RNAs derived from human long interspersed element 1 (LINE-1), Alu and SVA retrotransposons. Expression analyses demonstrate that cells lacking a functional Microprocessor accumulate LINE-1 mRNA and encoded proteins. Furthermore, we show that structured regions...... of the LINE-1 mRNA can be cleaved in vitro by Drosha. Additionally, we used a cell culture-based assay to show that the Microprocessor negatively regulates LINE-1 and Alu retrotransposition in vivo. Altogether, these data reveal a new role for the Microprocessor as a post-transcriptional repressor...

  3. A consolidated method for screening the endocrine activity of drinking water.

    Science.gov (United States)

    Chevolleau, Sylvie; Debrauwer, Laurent; Stroheker, Thomas; Viglino, Liza; Mourahib, Issam; Meireles, Maria-Helena; Grimaldi, Marina; Balaguer, Patrick; di Gioia, Lodovico

    2016-12-15

    Endocrine activity of drinking water is a matter of growing interest for scientists as well as health authorities. A concentration technique for endocrine activity screening was developed, optimized, and transposed from 200mL to 10L water samples. To avoid any contamination during concentration, the method was developed using exclusively glass, Teflon and stainless steel materials. Any potential losses were tracked using three model radiolabeled molecules, namely BPA, DEHP and 4n-NP. The final method allowed 10L water samples to be concentrated 5000-fold, with good recovery and repeatability. After validation, by concentrating spiked and non-spiked 10L samples of EVIAN natural mineral water, 14 different drinking water samples were concentrated and screened for endocrine disrupting activity using bioluminescent assays. Samples consisting of bottled water, conditioned in various materials (glass, PET) and subjected to different storage conditions, had no hormone-like activities whereas estrogenic activity was found in the filtered tap water.

  4. The Microprocessor controls the activity of mammalian retrotransposons.

    Science.gov (United States)

    Heras, Sara R; Macias, Sara; Plass, Mireya; Fernandez, Noemí; Cano, David; Eyras, Eduardo; Garcia-Perez, José L; Cáceres, Javier F

    2013-10-01

    More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for microRNA biogenesis, also recognizes and binds RNAs derived from human long interspersed element 1 (LINE-1), Alu and SVA retrotransposons. Expression analyses demonstrate that cells lacking a functional Microprocessor accumulate LINE-1 mRNA and encoded proteins. Furthermore, we show that structured regions of the LINE-1 mRNA can be cleaved in vitro by Drosha. Additionally, we used a cell culture-based assay to show that the Microprocessor negatively regulates LINE-1 and Alu retrotransposition in vivo. Altogether, these data reveal a new role for the Microprocessor as a post-transcriptional repressor of mammalian retrotransposons and a defender of human genome integrity.

  5. piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells.

    Science.gov (United States)

    Pezic, Dubravka; Manakov, Sergei A; Sachidanandam, Ravi; Aravin, Alexei A

    2014-07-01

    Transposable elements (TEs) occupy a large fraction of metazoan genomes and pose a constant threat to genomic integrity. This threat is particularly critical in germ cells, as changes in the genome that are induced by TEs will be transmitted to the next generation. Small noncoding piwi-interacting RNAs (piRNAs) recognize and silence a diverse set of TEs in germ cells. In mice, piRNA-guided transposon repression correlates with establishment of CpG DNA methylation on their sequences, yet the mechanism and the spectrum of genomic targets of piRNA silencing are unknown. Here we show that in addition to DNA methylation, the piRNA pathway is required to maintain a high level of the repressive H3K9me3 histone modification on long interspersed nuclear elements (LINEs) in germ cells. piRNA-dependent chromatin repression targets exclusively full-length elements of actively transposing LINE families, demonstrating the remarkable ability of the piRNA pathway to recognize active elements among the large number of genomic transposon fragments.

  6. Simulation and comparison of quarter-car passive suspension system with Bingham and Bouc-Wen MR semi-active suspension models

    Science.gov (United States)

    Perescu, A.; Bereteu, L.

    2013-11-01

    In this paper we want to transposion the suspension system in MATLAB, Simulink®, based on equation of motion. Consider only vertical movement of the car, neglecting roll and pitch. All movements of the car axes are modeled as having equal amplitude. The characteristic equations that describe the behavior of dynamical systems based on FBD (Free Body Diagram) of automotive suspension. It will make two models, one passive and one Bingham semi-active. Their responses will be compared between them, and with another Bouc-Wen semi-active model, more complex. Semi-active suspension systems have received significant attention in recent years because they offer the adaptability of active control devices without requiring large power sources. Given that both passive and semi-active dampers are in mass production will follow the normal parameters and their economic efficiency. These models are used for initial design of suspension system.

  7. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation.

    Science.gov (United States)

    Wang, Lu; Peng, Qian; Zhao, Jianbo; Ren, Fei; Zhou, Hui; Wang, Wei; Liao, Liao; Owiti, Albert; Jiang, Quan; Han, Yuepeng

    2016-05-01

    Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.

  8. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration.

    Science.gov (United States)

    Zhu, Wei; Kuo, Dwight; Nathanson, Jason; Satoh, Akira; Pao, Gerald M; Yeo, Gene W; Bryant, Susan V; Voss, S Randal; Gardiner, David M; Hunter, Tony

    2012-09-01

    Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes within the Mexican axolotl (Ambystoma mexicanum) that is indicative of cellular reprogramming of differentiated cells into a germline-like state. In this work, we focus on one of these genes, the long interspersed nucleotide element-1 (LINE-1) retrotransposon, which is usually active in germ cells and silent in most of the somatic tissues in other organisms. LINE-1 was found to be dramatically upregulated during regeneration. In addition, higher genomic LINE-1 content was also detected in the limb regenerate when compared to that before amputation indicating that LINE-1 retrotransposition is indeed active during regeneration. Active LINE-1 retrotransposition has been suggested to have a potentially deleterious impact on genomic integrity. Silencing of activated LINE-1 by small RNAs has been reported to be part of the machinery aiming to maintain genomic integrity. Indeed, we were able to identify putative LINE-1-related piRNAs in the limb blastema. Transposable element-related piRNAs have been identified frequently in the germline in other organisms. Thus, we present here a scenario in which a unique germline-like state is established during axolotl limb regeneration, and the re-activation of LINE-1 may serve as a marker for cellular dedifferentiation in the early-stage of limb regeneration.

  9. Analysis of energetically biased transcripts of viruses and transposable elements

    Directory of Open Access Journals (Sweden)

    Rodrigo Secolin

    2012-01-01

    Full Text Available RNA interference (RNAi is a natural endogenous process by which double-stranded RNA molecules trigger potent and specific gene silencing in eukaryotic cells and is characterized by target RNA cleavage. In mammals, small interfering RNAs (siRNAs are the trigger molecules of choice and constitute a new class of RNA-based antiviral agents. In an efficient RNAi response, the antisense strand of siRNAs must enter the RNA-induced silencing complex (RISC in a process mediated by thermodynamic features. In this report, we hypothesize that silent mutations capable of inverting thermodynamic properties can promote resistance to siRNAs. Extensive computational analyses were used to assess whether continuous selective pressure that promotes such mutations could lead to the emergence of viral strains completely resistant to RNAi (i.e., prone to transfer only the sense strands to RISC. Based on our findings, we propose that, although synonymous mutations may produce functional resistance, this strategy cannot be systematically adopted by viruses since the longest RNAi-refractory sequence is only 10 nt long. This finding also suggests that all mRNAs display fluctuating thermodynamic landscapes and that, in terms of thermodynamic features, RNAi is a very efficient antiviral system since there will always be sites susceptible to siRNAs.

  10. Is engineering O{sub 2}-tolerant hydrogenases just a matter of reproducing the active sites of the naturally occurring O{sub 2}-resistant enzymes?

    Energy Technology Data Exchange (ETDEWEB)

    Leroux, Fanny; Liebgott, Pierre-Pol; Kpebe, Arlette; Leger, Christophe; Rousset, Marc; Dementin, Sebastien [CNRS, Laboratoire de Bioenergetique et Ingenierie des Proteines, Institut de Microbiologie de la Mediterranee, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20 (France); Cournac, Laurent; Richaud, Pierre [CEA, DSV, IBEB, Laboratoire de Bioenergetique et Biotechnologie des Bacteries et Microalgues, 13108 Saint-Paul-lez-Durance (France); Aix-Marseille Universite, 3 place Victor-Hugo, 13331 Marseille (France); CNRS, UMR Biologie Vegetale et Microbiologie Environnementales, 13108 Saint-Paul-lez-Durance (France); Burlat, Benedicte; Guigliarelli, Bruno; Bertrand, Patrick [CNRS, Laboratoire de Bioenergetique et Ingenierie des Proteines, Institut de Microbiologie de la Mediterranee, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20 (France); Aix-Marseille Universite, 3 place Victor-Hugo, 13331 Marseille (France)

    2010-10-15

    Reproducing the naturally occurring O{sub 2}-tolerant hydrogenases is a potential strategy to make the oxygen sensitive enzymes, produced by organisms of biotechnological interest, more resistant. The search for resistance ''hotspots'' that could be transposed into sensitive hydrogenases is underway. Here, we replaced two residues (Y77 and V78) of the oxygen sensitive [NiFe] hydrogenase from Desulfovibrio fructosovorans with Gly and with Cys, respectively, to copy the active site pocket of the resistant membrane-bound [NiFe] enzyme from Ralstonia eutropha and we examined how this affected oxygen sensitivity. The results are discussed in the light of a short review of the recent results dealing with the reactivity of hydrogenases towards oxygen. (author)

  11. [Retrotransposons: selfish DNA or active epigenetic players in somatic cells?].

    Science.gov (United States)

    Guidez, Fabien

    2014-01-01

    Transposable elements (TE) represent around 40% of the human genome. They are endogenous mobile DNA sequences able to jump and duplicate in the host genome. TE have long been considered as "junk" DNA but are now believed to be important regulators of gene expression by participating to the establishment of the DNA methylation profile. Recent advances in genome sequencing reveals a higher transposition frequency and TE driven gene expression in somatic cells than previously thought. As TE propagation is deleterious and may be involved in oncogenic mechanisms, host cells have developed silencing mechanisms mainly described in germinal and embryonic cells. However, somatic cells are also proned to TE transposition and use specific mechanisms involving tumor suppressor proteins including p53, Rb and PLZF. These transcription factors specifically target genomic retrotransposon sequences, histone deacetylase and DNA methylase activities, inducing epigenetic modifications related to gene silencing. Thus, these transcription factors negatively regulate TE expression by the formation of DNA methylation profil in somatic cells possibly associated with oncogenic mechanisms.

  12. Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation.

    Science.gov (United States)

    Yamamuro, Chizuko; Miki, Daisuke; Zheng, Zhimin; Ma, Jun; Wang, Jing; Yang, Zhenbiao; Dong, Juan; Zhu, Jian-Kang

    2014-06-05

    DNA methylation is a reversible epigenetic mark regulating genome stability and function in many eukaryotes. In Arabidopsis, active DNA demethylation depends on the function of the ROS1 subfamily of genes that encode 5-methylcytosine DNA glycosylases/lyases. ROS1-mediated DNA demethylation plays a critical role in the regulation of transgenes, transposable elements and some endogenous genes; however, there have been no reports of clear developmental phenotypes in ros1 mutant plants. Here we report that, in the ros1 mutant, the promoter region of the peptide ligand gene EPF2 is hypermethylated, which greatly reduces EPF2 expression and thereby leads to a phenotype of overproduction of stomatal lineage cells. EPF2 gene expression in ros1 is restored and the defective epidermal cell patterning is suppressed by mutations in genes in the RNA-directed DNA methylation pathway. Our results show that active DNA demethylation combats the activity of RNA-directed DNA methylation to influence the initiation of stomatal lineage cells.

  13. Transposon display supports transpositional activity of elements in species of the saltans group of Drosophila

    Indian Academy of Sciences (India)

    Nathalia De Setta; Ana Paula Pimentel Costa; Fabrício Ramon Lopes; Marie-Anne Van Sluys; Cláudia Márcia Aparecida Carareto

    2007-01-01

    Mobilization of two element subfamilies (canonical and O-type) from Drosophila sturtevanti and D. saltans was evaluated for copy number and transposition activity using the transposon display (TD) technique. Pairwise distances between strains regarding the insertion polymorphism profile were estimated. Amplification of the element based on copy number estimates was highly variable among the strains (D. sturtevanti, canonical 20.11, O-type 9.00; D. saltans, canonical 16.4, O-type 12.60 insertions, on average). The larger values obtained by TD compared to our previous data by Southern blotting support the higher sensitivity of TD over Southern analysis for estimating transposable element copy numbers. The higher numbers of the canonical element and the greater divergence in its distribution within the genome of D. sturtevanti (24.8%) compared to the O-type (16.7%), as well as the greater divergence in the distribution of the canonical P element, between the D. sturtevanti (24.8%) and the D. saltans (18.3%) strains, suggest that the canonical element occupies more sites within the D. sturtevanti genome, most probably due to recent transposition activity. These data corroborate the hypothesis that the O-type is the oldest subfamily of elements in the saltans group and suggest that the canonical element is or has been transpositionally active until more recently in D. sturtevanti.

  14. Slow oscillation electrical brain stimulation during waking promotes EEG theta activity and memory encoding.

    Science.gov (United States)

    Kirov, Roumen; Weiss, Carsten; Siebner, Hartwig R; Born, Jan; Marshall, Lisa

    2009-09-08

    The application of transcranial slow oscillation stimulation (tSOS; 0.75 Hz) was previously shown to enhance widespread endogenous EEG slow oscillatory activity when applied during a sleep period characterized by emerging endogenous slow oscillatory activity. Processes of memory consolidation typically occurring during this state of sleep were also enhanced. Here, we show that the same tSOS applied in the waking brain also induced an increase in endogenous EEG slow oscillations (0.4-1.2 Hz), although in a topographically restricted fashion. Applied during wakefulness tSOS, additionally, resulted in a marked and widespread increase in EEG theta (4-8 Hz) activity. During wake, tSOS did not enhance consolidation of memories when applied after learning, but improved encoding of hippocampus-dependent memories when applied during learning. We conclude that the EEG frequency and related memory processes induced by tSOS critically depend on brain state. In response to tSOS during wakefulness the brain transposes stimulation by responding preferentially with theta oscillations and facilitated encoding.

  15. Compensatory signals associated with the activation of human GC 5' splice sites.

    Science.gov (United States)

    Kralovicova, Jana; Hwang, Gyulin; Asplund, A Charlotta; Churbanov, Alexander; Smith, C I Edvard; Vorechovsky, Igor

    2011-09-01

    GC 5' splice sites (5'ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5'ss activated by a mutation in BTK intron 3. This GC 5'ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5'ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5'ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5'ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5'ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5'ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5'ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.

  16. Repetitive and retinotopically restricted activation of the dorsal lateral geniculate nucleus with optogenetics.

    Directory of Open Access Journals (Sweden)

    Alexandre Castonguay

    Full Text Available Optogenetics allows the control of cellular activity using focused delivery of light pulses. In neuroscience, optogenetic protocols have been shown to efficiently inhibit or stimulate neuronal activity with a high temporal resolution. Among the technical challenges associated with the use of optogenetics, one is the ability to target a spatially specific population of neurons in a given brain structure. To address this issue, we developed a side-illuminating optical fiber capable of delivering light to specific sites in a target nucleus with added flexibility through rotation and translation of the fiber and by varying the output light power. The designed optical fiber was tested in vivo in visual structures of ChR2-expressing transgenic mice. To assess the spatial extent of neuronal activity modulation, we took advantage of the hallmark of the visual system: its retinotopic organization. Indeed, the relative position of ganglion cells in the retina is transposed in the cellular topography of both the dorsal lateral geniculate nucleus (LGN in the thalamus and the primary visual cortex (V1. The optical fiber was inserted in the LGN and by rotating it with a motor, it was possible to sequentially activate different neuronal populations within this structure. The activation of V1 neurons by LGN projections was recorded using intrinsic optical imaging. Increasing light intensity (from 1.4 to 8.9 mW/mm² led to increasing activation surfaces in V1. Optogenetic stimulation of the LGN at different translational and rotational positions was associated with different activation maps in V1. The position and/or orientation of the fiber inevitably varied across experiments, thus limiting the capacity to pool data. With the optogenetic design presented here, we demonstrate for the first time a transitory and spatially-concise activation of a deep neuronal structure. The optogenetic design presented here thus opens a promising avenue for studying the function

  17. Repetitive and retinotopically restricted activation of the dorsal lateral geniculate nucleus with optogenetics.

    Science.gov (United States)

    Castonguay, Alexandre; Thomas, Sébastien; Lesage, Frédéric; Casanova, Christian

    2014-01-01

    Optogenetics allows the control of cellular activity using focused delivery of light pulses. In neuroscience, optogenetic protocols have been shown to efficiently inhibit or stimulate neuronal activity with a high temporal resolution. Among the technical challenges associated with the use of optogenetics, one is the ability to target a spatially specific population of neurons in a given brain structure. To address this issue, we developed a side-illuminating optical fiber capable of delivering light to specific sites in a target nucleus with added flexibility through rotation and translation of the fiber and by varying the output light power. The designed optical fiber was tested in vivo in visual structures of ChR2-expressing transgenic mice. To assess the spatial extent of neuronal activity modulation, we took advantage of the hallmark of the visual system: its retinotopic organization. Indeed, the relative position of ganglion cells in the retina is transposed in the cellular topography of both the dorsal lateral geniculate nucleus (LGN) in the thalamus and the primary visual cortex (V1). The optical fiber was inserted in the LGN and by rotating it with a motor, it was possible to sequentially activate different neuronal populations within this structure. The activation of V1 neurons by LGN projections was recorded using intrinsic optical imaging. Increasing light intensity (from 1.4 to 8.9 mW/mm²) led to increasing activation surfaces in V1. Optogenetic stimulation of the LGN at different translational and rotational positions was associated with different activation maps in V1. The position and/or orientation of the fiber inevitably varied across experiments, thus limiting the capacity to pool data. With the optogenetic design presented here, we demonstrate for the first time a transitory and spatially-concise activation of a deep neuronal structure. The optogenetic design presented here thus opens a promising avenue for studying the function of deep brain

  18. A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Wataru eMatsunaga

    2015-02-01

    Full Text Available Transposable elements (TEs are key elements that facilitate genome evolution of the host organism. A number of studies have assessed the functions of TEs, which change gene expression in the host genome. Activation of TEs is controlled by epigenetic modifications such as DNA methylation and histone modifications. Several recent studies have reported that TEs can also be activated by biotic or abiotic stress in some plants. We focused on a Ty1/copia retrotransposon, ONSEN, that is activated by heat stress in Arabidopsis. We found that transcriptional activation of ONSEN was regulated by an siRNA-related pathway, and the activation could also be induced by oxidative stress. Mutants deficient in small interfering RNA (siRNA biogenesis that were exposed to heat stress at the initial stages of vegetative growth showed transgenerational transposition. The transposition was also detected in the progeny, which originated from tissue that had differentiated after exposure to the heat stress. The results indicated that in some undifferentiated cells, transpositional activity could be maintained quite long after exposure to the heat stress.

  19. Prioritization methodology for the monitoring of active pharmaceutical ingredients in hospital effluents.

    Science.gov (United States)

    Daouk, Silwan; Chèvre, Nathalie; Vernaz, Nathalie; Bonnabry, Pascal; Dayer, Pierre; Daali, Youssef; Fleury-Souverain, Sandrine

    2015-09-01

    The important number of active pharmaceutical ingredients (API) available on the market along with their potential adverse effects in the aquatic ecosystems, lead to the development of prioritization methods, which allow choosing priority molecules to monitor based on a set of selected criteria. Due to the large volumes of API used in hospitals, an increasing attention has been recently paid to their effluents as a source of environmental pollution. Based on the consumption data of a Swiss university hospital, about hundred of API has been prioritized following an OPBT approach (Occurrence, Persistence, Bioaccumulation and Toxicity). In addition, an Environmental Risk Assessment (ERA) allowed prioritizing API based on predicted concentrations and environmental toxicity data found in the literature for 71 compounds. Both prioritization approaches were compared. OPBT prioritization results highlight the high concern of some non steroidal anti-inflammatory drugs and antiviral drugs, whereas antibiotics are revealed by ERA as potentially problematic to the aquatic ecosystems. Nevertheless, according to the predicted risk quotient, only the hospital fraction of ciprofloxacin represents a risk to the aquatic organisms. Some compounds were highlighted as high-priority with both methods: ibuprofen, trimethoprim, sulfamethoxazole, ritonavir, gabapentin, amoxicillin, ciprofloxacin, raltegravir, propofol, etc. Analyzing consumption data and building prioritization lists helped choosing about 15 API to be monitored in hospital wastewaters. The API ranking approach adopted in this study can be easily transposed to any other hospitals, which have the will to look at the contamination of their effluents.

  20. Active Site Sharing and Subterminal Hairpin Recognition in a New Class of DNA Transposases

    Energy Technology Data Exchange (ETDEWEB)

    Ronning, Donald R.; Guynet, Catherine; Ton-Hoang, Bao; Perez, Zhanita N.; Ghirlando, Rodolfo; Chandler, Michael; Dyda, Fred (Centre Nat); (NIH)

    2010-07-20

    Many bacteria harbor simple transposable elements termed insertion sequences (IS). In Helicobacter pylori, the chimeric IS605 family elements are particularly interesting due to their proximity to genes encoding gastric epithelial invasion factors. Protein sequences of IS605 transposases do not bear the hallmarks of other well-characterized transposases. We have solved the crystal structure of full-length transposase (TnpA) of a representative member, ISHp608. Structurally, TnpA does not resemble any characterized transposase; rather, it is related to rolling circle replication (RCR) proteins. Consistent with RCR, Mg{sup 2+} and a conserved tyrosine, Tyr127, are essential for DNA nicking and the formation of a covalent intermediate between TnpA and DNA. TnpA is dimeric, contains two shared active sites, and binds two DNA stem loops representing the conserved inverted repeats near each end of ISHp608. The cocrystal structure with stem-loop DNA illustrates how this family of transposases specifically recognizes and pairs ends, necessary steps during transposition.

  1. Physical activity

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/001941.htm Physical activity To use the sharing features on this page, please enable JavaScript. Physical activity -- which includes an active lifestyle and routine exercise -- ...

  2. The Juan non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity

    Directory of Open Access Journals (Sweden)

    Tu Zhijian

    2007-07-01

    Full Text Available Abstract Background In contrast to DNA-mediated transposable elements (TEs, retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs, are generally considered to have a much lower propensity towards horizontal transfer. Detailed studies on site-specific non-LTR families have demonstrated strict vertical transmission. More studies are needed with non-site-specific non-LTR families to determine whether strict vertical transmission is a phenomenon related to site specificity or a more general characteristic of all non-LTRs. Juan is a Jockey clade non-LTR retrotransposon first discovered in mosquitoes that is widely distributed in the mosquito family Culicidae. Being a non-site specific non-LTR, Juan offers an opportunity to further investigate the hypothesis that non-LTRs are genomic elements that are primarily vertically transmitted. Results Systematic analysis of the ~1.3 Gbp Aedes aegypti (Ae. aegypti genome sequence suggests that Juan-A is the only Juan-type non-LTR in Aedes aegypti. Juan-A is highly reiterated and comprises approximately 3% of the genome. Using minimum cutoffs of 90% length and 70% nucleotide (nt identity, 663 copies were found by BLAST using the published Juan-A sequence as the query. All 663 copies are at least 95% identical to Juan-A, while 378 of these copies are 99% identical to Juan-A, indicating that the Juan-A family has been transposing recently in evolutionary history. Using the 0.34 Kb 5' UTR as the query, over 2000 copies were identified that may contain internal promoters, leading to questions on the genomic impact of Juan-A. Juan sequences were obtained by PCR, library screening, and database searches for 18 mosquito species of six genera including Aedes, Ochlerotatus, Psorophora, Culex, Deinocerites, and Wyeomyia. Comparison of host and Juan phylogenies shows overall congruence with few exceptions. Conclusion Juan-A is a major genomic component in Ae. aegypti and it has been

  3. The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements

    Directory of Open Access Journals (Sweden)

    Pereira Gonçalo AG

    2009-07-01

    Full Text Available Abstract Background For three decades the Mutator system was thought to be exclusive of plants, until the first homolog representatives were characterized in fungi and in early-diverging amoebas earlier in this decade. Results Here, we describe and characterize four families of Mutator-like elements in a new eukaryotic group, the Parabasalids. These Trichomonas vaginalis Mutator- like elements, or TvMULEs, are active in T. vaginalis and patchily distributed among 12 trichomonad species and isolates. Despite their relatively distinctive amino acid composition, the inclusion of the repeats TvMULE1, TvMULE2, TvMULE3 and TvMULE4 into the Mutator superfamily is justified by sequence, structural and phylogenetic analyses. In addition, we identified three new TvMULE-related sequences in the genome sequence of Candida albicans. While TvMULE1 is a member of the MuDR clade, predominantly from plants, the other three TvMULEs, together with the C. albicans elements, represent a new and quite distinct Mutator lineage, which we named TvCaMULEs. The finding of TvMULE1 sequence inserted into other putative repeat suggests the occurrence a novel TE family not yet described. Conclusion These findings expand the taxonomic distribution and the range of functional motif of MULEs among eukaryotes. The characterization of the dynamics of TvMULEs and other transposons in this organism is of particular interest because it is atypical for an asexual species to have such an extreme level of TE activity; this genetic landscape makes an interesting case study for causes and consequences of such activity. Finally, the extreme repetitiveness of the T. vaginalis genome and the remarkable degree of sequence identity within its repeat families highlights this species as an ideal system to characterize new transposable elements.

  4. Expression and enzyme activity determination of human cyclooxygenase-1 and -2 in a baculovirus-insect cell system

    Institute of Scientific and Technical Information of China (English)

    Wei-yu ZHANG; Xin-ning YANG; Dao-zhong JIN; Xing-zu ZHU

    2004-01-01

    AIM: To develop an in vitro intact cell-based assay for screening selective cyclooxygenase inhibitors. METHODS:Human cyclooxygenase-1 (hCOX-1) and cyclooxygenase-2 (hCOX-2) genes were cloned from human monocyte cell line THP-1 cells and expressed in Spodopterafrugiperda (sf9) insect cell line by Bac-to-Bac baculovirus expression systems. Infected sr9 cells were harvested 24 h post-infection (hpi), and distributed to a 24-well plate,preincubated with various nonsteroidal anti-inflammatory drugs, and challenged with 10 mmol/L arachidonic acid;the cyclooxygenase activity was assessed indirectly by prostaglandin E2-specific radioimmunoassay. RESULTS:Polymerase chain reaction detection demonstrated that hCOX-1 and hCOX-2 were transposed to the bacmid.Western blot analysis showed that infected sf9 cells could express hCOX-1 and hCOX-2 proteins. Radioimmunoassay demonstrated that both recombinant proteins functioned well in sf9 cells. CONCLUSION: Human cyclooxygenase-1 and cyclooxygenase-2 were successfully expressed in sf9 insect cell line. It can be utilized for the identification of potent and selective inhibitors of hCOX- 1 and/or hCOX-2.

  5. Activated Charcoal

    Science.gov (United States)

    Activated Carbon, Animal Charcoal, Carbo Vegetabilis, Carbon, Carbón Activado, Charbon Actif, Charbon Activé, Charbon Animal, Charbon Médicinal, Charbon Végétal, Charbon Végétal Activé, Charcoal, Gas Black, Lamp Black, Medicinal Charcoal, Noir de Gaz, ...

  6. Early Disruption of Maternal–Zygotic Interaction and Activation of Defense-Like Responses in Arabidopsis Interspecific Crosses[C][W][OPEN

    Science.gov (United States)

    Burkart-Waco, Diana; Ngo, Kathie; Dilkes, Brian; Josefsson, Caroline; Comai, Luca

    2013-01-01

    Seed death resulting from hybridization between Arabidopsis thaliana and Arabidopsis arenosa has complex genetic determination and involves deregulation 5 to 8 d after pollination (DAP) of AGAMOUS-LIKE genes and retroelements. To identify causal mechanisms, we compared transcriptomes of compatible and incompatible hybrids and parents at 3 DAP. Hybrids misexpressed endosperm and seed coat regulators and hyperactivated genes encoding ribosomal, photosynthetic, stress-related, and immune response proteins. Regulatory disruption was more severe in Columbia-0 hybrids than in C24 hybrids, consistent with the degree of incompatibility. Maternal loss-of-function alleles for endosperm growth factor TRANSPARENT TESTA GLABRA2 and HAIKU1 and defense response regulators NON-EXPRESSOR OF PATHOGENESIS RELATED1 and SALICYLIC ACID INDUCTION-DEFICIENT2 increased hybrid seed survival. The activation of presumed POLYCOMB REPRESSIVE COMPLEX (PRC) targets, together with a 20-fold reduction in expression of FERTILIZATION INDEPENDENT SEED2, indicated a PRC role. Proximity to transposable elements affected natural variation for gene regulation, but transposon activation did not differ from controls. Collectively, this investigation provides candidates for multigenic orchestration of the incompatibility response through disruption of endosperm development, a novel role for communication between endosperm and maternal tissues and for pathways previously connected to immunity, but, surprisingly, does not identify a role for transposons. PMID:23898028

  7. The reverse transcription inhibitor abacavir shows anticancer activity in prostate cancer cell lines.

    Directory of Open Access Journals (Sweden)

    Francesca Carlini

    Full Text Available BACKGROUND: Transposable Elements (TEs comprise nearly 45% of the entire genome and are part of sophisticated regulatory network systems that control developmental processes in normal and pathological conditions. The retroviral/retrotransposon gene machinery consists mainly of Long Interspersed Nuclear Elements (LINEs-1 and Human Endogenous Retroviruses (HERVs that code for their own endogenous reverse transcriptase (RT. Interestingly, RT is typically expressed at high levels in cancer cells. Recent studies report that RT inhibition by non-nucleoside reverse transcriptase inhibitors (NNRTIs induces growth arrest and cell differentiation in vitro and antagonizes growth of human tumors in animal model. In the present study we analyze the anticancer activity of Abacavir (ABC, a nucleoside reverse transcription inhibitor (NRTI, on PC3 and LNCaP prostate cancer cell lines. PRINCIPAL FINDINGS: ABC significantly reduces cell growth, migration and invasion processes, considerably slows S phase progression, induces senescence and cell death in prostate cancer cells. Consistent with these observations, microarray analysis on PC3 cells shows that ABC induces specific and dose-dependent changes in gene expression, involving multiple cellular pathways. Notably, by quantitative Real-Time PCR we found that LINE-1 ORF1 and ORF2 mRNA levels were significantly up-regulated by ABC treatment. CONCLUSIONS: Our results demonstrate the potential of ABC as anticancer agent able to induce antiproliferative activity and trigger senescence in prostate cancer cells. Noteworthy, we show that ABC elicits up-regulation of LINE-1 expression, suggesting the involvement of these elements in the observed cellular modifications.

  8. Physical Activity

    DEFF Research Database (Denmark)

    Andersen, Lars Bo; Anderssen, Sigmund Alfred; Wisløff, Ulrik

    2014-01-01

    Andersen LB, Anderssen SA, Wisløff U, Hellénius M-L, Fogelholm M, Ekelund U. (Expert Group) Nordic Nutrition Recommendations 2012. Integrating nutrition and physical activity. Chapter: Physical Activity p. 195-217.Nordic Counsil of Ministers.......Andersen LB, Anderssen SA, Wisløff U, Hellénius M-L, Fogelholm M, Ekelund U. (Expert Group) Nordic Nutrition Recommendations 2012. Integrating nutrition and physical activity. Chapter: Physical Activity p. 195-217.Nordic Counsil of Ministers....

  9. Activity Theory.

    Science.gov (United States)

    Koschmann, Timothy; Roschelle, Jeremy; Nardi, Bonnie A.

    1998-01-01

    Includes three articles that discuss activity theory, based on "Context and Consciousness." Topics include human-computer interaction; computer interfaces; hierarchical structuring; mediation; contradictions and development; failure analysis; and designing educational technology. (LRW)

  10. Variable transposition of eight maize activator (ac) elements located on the short arm of chromosome 1.

    Science.gov (United States)

    Sheridan, William F

    2011-09-01

    Eight Activator (Ac) transposable elements mapped to the maize chromosome arm 1S were assessed for Ac transposition rates. For each of the Ac stocks, plants homozygous for the single Ac element and the Ds reporter r1-sc:m3 on chromosome 10 were crossed as females by a homozygous r1-sc:m3 tester color-converted W22 line. The resulting ears produced mostly coarsely spotted kernels and a low frequency of either near-colorless fine-spotted kernels or nonspotted kernels. The relative frequency of these two types of near-colorless kernels differed among the eight Ac stocks. The extent to which increased Ac dosage results in nonspotted kernels may be Ac-specific. Although all of the Ac elements are in near-isogenic inbred W22 lines, they varied to a large extent in their transposition frequency. These differences might possibly result from structural differences among the Ac elements. Because one pair of Ac elements derived from Ac33 on chromosome arm 5S differed about 13-fold in transposition frequency and a second pair of Ac elements derived from Ac12 on chromosome arm 1S differed about 3-fold in transposition frequency, this is not a likely explanation for all eight Ac elements. The data presented here support the notion that the differences in transposition frequency of the eight Ac elements may be a reflection of variability in Ac transcription or accessibility of the transposase to the Ac element, resulting from differences in the chromatin environments wherein the Ac elements are located. This is the first report of variability in transposition rates among different Ac donor lines.

  11. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

    Directory of Open Access Journals (Sweden)

    Vardi Assaf

    2009-12-01

    Full Text Available Abstract Background Transposable elements (TEs are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions in genome dynamics and species evolution. Recent genomic data can now enlarge the identification and study of TEs to other branches of the eukaryotic tree of life. Diatoms, which belong to the heterokont group, are unicellular eukaryotic algae responsible for around 40% of marine primary productivity. The genomes of a centric diatom, Thalassiosira pseudonana, and a pennate diatom, Phaeodactylum tricornutum, that likely diverged around 90 Mya, have recently become available. Results In the present work, we establish that LTR retrotransposons (LTR-RTs are the most abundant TEs inhabiting these genomes, with a much higher presence in the P. tricornutum genome. We show that the LTR-RTs found in diatoms form two new phylogenetic lineages that appear to be diatom specific and are also found in environmental samples taken from different oceans. Comparative expression analysis in P. tricornutum cells cultured under 16 different conditions demonstrate high levels of transcriptional activity of LTR retrotransposons in response to nitrate limitation and upon exposure to diatom-derived reactive aldehydes, which are known to induce stress responses and cell death. Regulatory aspects of P. tricornutum retrotransposon transcription also include the occurrence of nitrate limitation sensitive cis-regulatory components within LTR elements and cytosine methylation dynamics. Differential insertion patterns in different P. tricornutum accessions isolated from around the world infer the role of LTR-RTs in generating intraspecific genetic variability. Conclusion Based on these findings we propose that LTR-RTs may have been important for promoting genome rearrangements in diatoms.

  12. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

    NARCIS (Netherlands)

    Willing, Eva Maria; Rawat, Vimal; Mandáková, Terezie; Maumus, Florian; James, Geo Velikkakam; Nordström, Karl J.V.; Becker, Claude; Warthmann, Norman; Chica, Claudia; Szarzynska, Bogna; Zytnicki, Matthias; Albani, Maria C.; Kiefer, Christiane; Bergonzi, Sara; Castaings, Loren; Mateos, Julieta L.; Berns, Markus C.; Bujdoso, Nora; Piofczyk, Thomas; Lorenzo, De Laura; Barrero-Sicilia, Cristina; Mateos, Isabel; Piednoël, Mathieu; Hagmann, Jörg; Chen-Min-Tao, Romy; Iglesias-Fernández, Raquel; Schuster, Stephan C.; Alonso-Blanco, Carlos; Roudier, François; Carbonero, Pilar; Paz-Ares, Javier; Davis, Seth J.; Pecinka, Ales; Quesneville, Hadi; Colot, Vincent; Lysak, Martin A.; Weigel, Detlef; Coupland, George; Schneeberger, Korbinian

    2015-01-01

    Despite evolutionary conserved mechanisms to silence transposable
    element activity, there are drastic differences in the
    abundance of transposable elements even among closely
    related plant species. We conducted a de novo assembly for the
    375 Mb genome of the perennial model plant, Ar

  13. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae.

    Science.gov (United States)

    Grandbastien, M-A; Audeon, C; Bonnivard, E; Casacuberta, J M; Chalhoub, B; Costa, A-P P; Le, Q H; Melayah, D; Petit, M; Poncet, C; Tam, S M; Van Sluys, M-A; Mhiri, C

    2005-01-01

    Tnt1 elements are a superfamily of LTR-retrotransposons distributed in the Solanaceae plant family and represent good model systems for studying regulatory and evolutionary controls established between hosts and transposable elements. Tnt1 retrotransposons tightly control their activation, by restricting expression to specific conditions. The Tnt1A element, originally discovered in tobacco, is expressed in response to stress, and its activation by microbial factors is followed by amplification, demonstrating that factors of pathogen origin can generate genetic diversity in plants. The Tnt1A promoter has the potential to be activated by various biotic and abiotic stimuli but a number of these are specifically repressed in tobacco and are revealed only when the LTR promoter is placed in a heterologous context. We propose that a tobacco- and stimulus-specific repression has been established in order to minimize activation in conditions that might generate germinal transposition. In addition to tight transcriptional controls, Tnt1A retrotransposons self-regulate their activity through gradual generation of defective copies that have reduced transcriptional activity. Tnt1 retrotransposons found in various Solanaceae species are characterized by a high level of variability in the LTR sequences involved in transcription, and have evolved by gaining new expression patterns, mostly associated with responses to diverse stress conditions. Tnt1A insertions associated with genic regions are initially favored but seem subsequently counter-selected, while insertions in repetitive DNA are maintained. On the other hand, amplification and loss of insertions may result from more brutal occurrences, as suggested by the large restructuring of Tnt1 populations observed in tobacco compared to each of its parental species. The distribution of Tnt1 elements thus appears as a dynamic flux, with amplification counterbalanced by loss of insertions. Tnt1 insertion polymorphisms are too high to

  14. Identifying Activity

    CERN Document Server

    Lewis, Adrian S

    2009-01-01

    Identification of active constraints in constrained optimization is of interest from both practical and theoretical viewpoints, as it holds the promise of reducing an inequality-constrained problem to an equality-constrained problem, in a neighborhood of a solution. We study this issue in the more general setting of composite nonsmooth minimization, in which the objective is a composition of a smooth vector function c with a lower semicontinuous function h, typically nonsmooth but structured. In this setting, the graph of the generalized gradient of h can often be decomposed into a union (nondisjoint) of simpler subsets. "Identification" amounts to deciding which subsets of the graph are "active" in the criticality conditions at a given solution. We give conditions under which any convergent sequence of approximate critical points finitely identifies the activity. Prominent among these properties is a condition akin to the Mangasarian-Fromovitz constraint qualification, which ensures boundedness of the set of...

  15. Activating schoolyards

    DEFF Research Database (Denmark)

    Andersen, Henriette Bondo; Pawlowski, Charlotte Skau; Scheller, Hanne Bebendorf;

    2015-01-01

    BACKGROUND: The aim of the Activating Schoolyards Study is to develop, implement, document and assess a comprehensive schoolyard intervention to promote physical activity (PA) during school recess for primary school children (grade 4-8). The intervention is designed to implement organizational...... to objectively determine where and how active the students are in the schoolyard, before and after the intervention. This provides a type of data that, to our knowledge, has not been used before in schoolyard interventions. Exploring the change in behavior in relation to specific intervention elements...... as well as quantitative methods can be seen as a strength, as the different types of data complement each other and results of one part of the study informed the following parts. A unique aspect of our study is the use of accelerometers in combination with GPS and GIS in the effect evaluation...

  16. Active house

    DEFF Research Database (Denmark)

    Eriksen, Kurt Emil; Olesen, Gitte Gylling Hammershøj

    2010-01-01

    Formålet med dette abstrakt er at illustrere, at huse kan være konstrueret til at basere sig udelukkende på vedvarende energikilder og samtidig være CO2-neutrale og producere mere energi end de forbruger. Active House Visionen undersøger disse muligheder i otte demonstration huse i fem forskellige...

  17. Get Active

    Science.gov (United States)

    ... Have fun with your family. If you have children, you can be a role model for making healthy choices. Encourage your whole family to get active outside . Go for a hike or organize a family soccer game. If someone you know has trouble making ...

  18. Active particles

    CERN Document Server

    Degond, Pierre; Tadmor, Eitan

    2017-01-01

    This volume collects ten surveys on the modeling, simulation, and applications of active particles using methods ranging from mathematical kinetic theory to nonequilibrium statistical mechanics. The contributing authors are leading experts working in this challenging field, and each of their chapters provides a review of the most recent results in their areas and looks ahead to future research directions. The approaches to studying active matter are presented here from many different perspectives, such as individual-based models, evolutionary games, Brownian motion, and continuum theories, as well as various combinations of these. Applications covered include biological network formation and network theory; opinion formation and social systems; control theory of sparse systems; theory and applications of mean field games; population learning; dynamics of flocking systems; vehicular traffic flow; and stochastic particles and mean field approximation. Mathematicians and other members of the scientific commu...

  19. Laboratory Activities

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Christopher F.; Serne, R. Jeffrey

    2008-01-17

    This chapter summarizes the laboratory activities performed by PNNL’s Vadose Zone Characterization Project in support of the Tank Farm Vadose Zone Program, led by CH2M HILL Hanford Group, Inc. The results of these studies are contained in numerous reports (Lindenmeier et al. 2002; Serne et al. 2002a, 2002b, 2002c, 2002d, 2002e; Lindenmeier et al. 2003; Serne et al. 2004a, 2004b; Brown et al. 2005, 2006a, 2007; Serne et al. 2007) and have generated much of the data reported in Chapter 22 (Geochemistry-Contaminant Movement), Appendix G (Geochemistry-Contaminant Movement), and Cantrell et al. (2007, SST WMA Geochemistry Data Package – in preparation). Sediment samples and characterization results from PNNL’s Vadose Zone Characterization Project are also shared with other science and technology (S&T) research projects, such as those summarized in Chapter 12 (Associated Science Activities).

  20. Antimicrobial Activity.

    Science.gov (United States)

    2016-01-01

    Natural products of higher plants may possess a new source of antimicrobial agents with possibly novel mechanisms of action. They are effective in the treatment of infectious diseases while simultaneously mitigating many of the side effects that are often associated with conventional antimicrobials. A method using scanning electron microscope (SEM) to study the morphology of the bacterial and fungal microbes and thus determining antimicrobial activity is presented in the chapter.

  1. Fumarase activity

    DEFF Research Database (Denmark)

    Nielsen, Per Mose; Eldirdiri, Abubakr; Bertelsen, Lotte Bonde

    2017-01-01

    ]fumarate conversion to [1,4-(13)C2]malate by fumarase has been proposed as a measure of necrosis in rat tumor models and in chemically induced AKI rats. Here we show that the degradation of cell membranes in connection with necrosis leads to elevated fumarase activity in plasma and urine and secondly...... that hyperpolarized [1,4-(13)C2]malate production 24 h after reperfusion correlates with renal necrosis in a 40-min unilateral ischemic rat model. Fumarase activity screening on bio-fluids can detect injury severity, in bilateral as well as unilateral AKI models, differentiating moderate and severe AKI as well...... as short- and long-term AKI. Furthermore after verification of renal injury by bio-fluid analysis the precise injury location can be monitored by in vivo measurements of the fumarase activity non-invasively by hyperpolarized [1,4-(13)C]fumarate MR imaging. The combined in vitro and in vivo biomarker of AKI...

  2. Glucokinase activators.

    Science.gov (United States)

    Filipski, Kevin J; Futatsugi, Kentaro; Pfefferkorn, Jeffrey A; Stevens, Benjamin D

    2012-07-01

    In this review we highlight recently disclosed progress in the field of small-molecule activators of the human glucokinase enzyme. Several of the reported chemotypes possess structural features that diverge from known leads; some of these modifications appear to be specifically designed to modulate tissue selectivity or discrete parameters of enzyme function (e.g., S0.5 v Vmax). This review will inform the reader of the extent of continued effort being directed toward discovery of a first-in-class drug for Type II diabetes mellitus that functions through this target. Patents were selected from those published in December 2009 up to November 2011; foreign filings were translated where possible to understand the claims and biological techniques utilized to characterize the reported glucokinase activators. Overall, there appears to be a recent trend leading to reduced patent filings for small-molecule glucokinase activators. There are many possible explanations for this trend; however, it is likely that the field has reached maturity and that the downturn of new disclosures represents the transition of many of these programs to the clinic.

  3. Active instruments

    DEFF Research Database (Denmark)

    Lim, Miguel Antonio; Ørberg, Jakob Williams

    2017-01-01

    themselves. We draw on two multi-year field studies of India and Denmark to investigate how national reforms and developments within the ranking industry interact in often surprising ways. Rankings do not always do what policy makers expect. We (1) highlight the activity of rankers in these two countries, (2......) show the dynamic nature of policy processes, and (3) consider the search for policy reference points among the different actors. We present rankers in motion, policies in motion, and finally the complex nature of the ranking device that needs to be both a relevant and malleable policy instrument...

  4. Active packaging with antifungal activities.

    Science.gov (United States)

    Nguyen Van Long, N; Joly, Catherine; Dantigny, Philippe

    2016-03-01

    There have been many reviews concerned with antimicrobial food packaging, and with the use of antifungal compounds, but none provided an exhaustive picture of the applications of active packaging to control fungal spoilage. Very recently, many studies have been done in these fields, therefore it is timely to review this topic. This article examines the effects of essential oils, preservatives, natural products, chemical fungicides, nanoparticles coated to different films, and chitosan in vitro on the growth of moulds, but also in vivo on the mould free shelf-life of bread, cheese, and fresh fruits and vegetables. A short section is also dedicated to yeasts. All the applications are described from a microbiological point of view, and these were sorted depending on the name of the species. Methods and results obtained are discussed. Essential oils and preservatives were ranked by increased efficacy on mould growth. For all the tested molecules, Penicillium species were shown more sensitive than Aspergillus species. However, comparison between the results was difficult because it appeared that the efficiency of active packaging depended greatly on the environmental factors of food such as water activity, pH, temperature, NaCl concentration, the nature, the size, and the mode of application of the films, in addition to the fact that the amount of released antifungal compounds was not constant with time.

  5. BAM! Physical Activity

    Science.gov (United States)

    ... Smarts Links Fuel Up for Fun Power Packing Physical Activity Xpert Opinion Activity Calendar Activity Cards Ballet Baseball ... Disaster - Are You at Risk? Disaster - Helping Hands Physical Activity - Questions Physical Activity - Active or Not, Here it ...

  6. Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of mPing in Rice

    Science.gov (United States)

    Li, Siyuan; Xia, Qiong; Wang, Fang; Yu, Xiaoming; Ma, Jian; Kou, Hongping; Lin, Xiuyun; Gao, Xiang; Liu, Bao

    2017-01-01

    DNA methylation is an integral component of the epigenetic code in most higher eukaryotes. Exploring the extent to which DNA methylation can be altered under a specific condition and its heritability is important for elucidating the biological functions of this epigenetic modification. Here, we conducted MSAP analysis of rice plants with altered phenotypes subsequent to a low-dose Nd3+YAG laser irradiation. We found that all four methylation patterns at the 5′-CCGG sites that are analyzable by MSAP showed substantial changes in the immediately treated M0 plants. Interestingly, the frequencies of hypo- and hypermethylation were of similar extents, which largely offset each other and render the total methylation levels unchanged. Further analysis revealed that the altered methylation patterns were meiotically heritable to at least the M2 generation but accompanied with further changes in each generation. The methylation changes and their heritability of the metastable epigenetic state were verified by bisulfite sequencing of portion of the retrotranspon, Tos17, an established locus for assessing DNA methylation liability in rice. Real-time PCR assay indicated that the expression of various methylation-related chromatin genes was perturbed, and a Pearson correlation analysis showed that many of these genes, especially two AGOs (AGO4-1 and AGO4-2), were significantly correlated with the methylation pattern alterations. In addition, excisions of a MITE transposon, mPing, occurred rampantly in the laser irradiated plants and their progenies. Together, our results indicate that heritable DNA methylation changes can be readily induced by low-dose laser irradiation, and which can be accompanied by transpostional activation of transposable elements.

  7. Intangible activities

    DEFF Research Database (Denmark)

    Hermansen, Jonathan

    2016-01-01

    ‘Informal helping’ is often associated with other types of prosocial behaviour such as formal voluntary work. Therefore, one could jump to the conclusion that it would be the same factors driving both types of activities. This article demonstrates that this is not the case. The study relies...... on a population survey on informal helping and volunteering in Denmark. The two contributions of this article are as follows: (1) it demonstrates that the sociodemographic indicators that are closely linked to formal volunteering are not related to informal helping in the same manner and (2) it demonstrates...... that it is necessary to separate the decision to help and the amount of hours that people help, a distinction that previous empirical studies on this topic fail to include. The results show that informal helping may not simply be compared to other instances of prosocial behaviour. In particular, the socio...

  8. Method of Lines Transpose an Implicit Vlasov Maxwell Solver for Plasmas

    Science.gov (United States)

    2015-04-17

    Numerical Analysis 52 (2014), no. 1, 220–235. 10. Roman Chapko, Rainer Kress, et al., Rothes method for the heat equation and boundary integral equations...collisionless plasma–sheath region, Physics of Fluids B: Plasma Physics (1989-1993) 2 (1990), no. 12, 3191–3205. 33. Erich Rothe , Zweidimensionale

  9. Transposing reform pedagogy into new contexts: complex instruction in remote Australia

    Science.gov (United States)

    Sullivan, Peter; Jorgensen, Robyn; Boaler, Jo; Lerman, Steve

    2013-03-01

    This article draws on the outcomes of a 4-year project where complex instruction was used as the basis for a reform in mathematics teaching in remote Aboriginal communities in Australia. The article describes the overall project in terms of the goals and aspirations for learning mathematics among remote Indigenous Australians. Knowing that the approach had been successful in a diverse setting in California, the project team sought to implement and evaluate the possibilities of such reform in a context in which the need for a culturally responsive pedagogy was critical. Elements of complex instruction offered considerable possibilities in aligning with the cultures of the remote communities, but with recognition of the possibility that some elements may not be workable in these contexts. Complex instruction also valued deep knowledge of mathematics rather than a tokenistic, impoverished mathematics. The strategies within complex instruction allowed for mathematical and cultural scaffolding to promote deep learning in mathematics. Such an approach was in line with current reforms in Indigenous education in Australia where there are high expectations of learners in order to break away from the deficit thinking that has permeated much education in remote Australia. The overall intent is to demonstrate what pedagogies are possible within the constraints of the remote context.

  10. Regulation of Metastasis and DNA Damage Resistance Pathways by Transposable Elements

    Science.gov (United States)

    2014-10-01

    Discovery Conference in Philadelphia. Philadelphia, PA. Sept. 2012 Interplay Between Chromatin Responses to DNA Double Strand Breaks and Transcription ...pathways. We have recently reported the phenomenon of Double Strand Break Induced Silencing in Cis (DISC), a process that relies on ATM and histone H2A... double - strand breaks (DSBs). Similar mechanisms of DSB silencing were involved in suppression of TEs following DNA damage, inspiring the hypothesis

  11. Characterization of Plys-proximal morphogenetic genes of transposable bacteriophage Mu.

    Science.gov (United States)

    Siboo, I R; Sieder, F; Kumar, K; Howe, M M; DuBow, M S

    2004-02-01

    Late during the bacteriophage Mu lytic cycle, Mu DNA must be matured and packaged from its dispersed integration sites in the host DNA in order to produce progeny virions. Whereas control of late gene transcription in Mu is becoming well understood, less is known about the phage morphogenetic process. To investigate the latter, we cloned and sequenced a approximately 4.3-kb region of the phage DNA beginning just upstream of the leftmost late promoter Plys. Previous mapping of amber mutations had located the lysis (lys) and proposed DNA maturation genes D and E in this region. When the DNA sequence was analyzed, seven potential open reading frames were found. DNA sequence analysis of amber mutations in genes D and E identified the sixth and seventh open reading frames as D and E, respectively. Cloning and expression of this region enabled production of cell-free protein extracts that specifically recognize the phage-encoded packaging sequence (pac), a characteristic exhibited by phage maturation enzymes. In addition, the E protein was found to share homology with the large subunit of many phage DNA maturation enzymes. These results support the hypothesis that D and E encode subunits of the Mu DNA maturation enzyme.

  12. Letter-Transposition Effects Are Not Universal: The Impact of Transposing Letters in Hebrew

    Science.gov (United States)

    Velan, Hadas; Frost, Ram

    2009-01-01

    We examined the effects of letter-transposition in Hebrew in three masked-priming experiments. Hebrew, like English has an alphabetic orthography where sequential and contiguous letter strings represent phonemes. However, being a Semitic language it has a non-concatenated morphology that is based on root derivations. Experiment 1 showed that…

  13. Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses.

    Science.gov (United States)

    Minaya, Miguel; Pimentel, Manuel; Mason-Gamer, Roberta; Catalan, Pilar

    2013-07-01

    The occurrence of Stowaway MITEs and their potential footprints in the grasses was assessed within an explicit phylogenetic framework. An organismal tree was used to analyze the distribution and evolutionary dynamics of these elements and their potential excision footprints in the fourth intron of the β-amylase gene and in other introns of several nuclear genes across the Poaceae. Megablast and discontiguous megablast searches in the Entrez nucleotide database were performed for the β-amylase, blz-1, dmc1, nuc, and xly genes MITEs. These elements and their potential footprints were distributed in introns and intergenic spacers of many other nuclear genes throughout the BEP lineages; however, they were absent in the studied PACCMAD lineages. A plausible underlying dynamic of successive acquisitions and deletions of β-amylase Stowaway MITEs in the temperate grasses could be explained by three alternative hypotheses: (i) a single early acquisition of a palindrome element, similar to Tc1-Mariner, in the fourth intron of the β-amylase gene in the ancestor of the Pooideae, followed by multiple independent losses, (ii) multiple independent acquisitions of MITEs in non-related pooid lineages or (iii) different waves of acquisition of MITEs, followed by multiple losses and horizontal transfers in the temperate grasses. This last hypothesis seems to fit best with the evidence found to date.

  14. Post-integration silencing of piggyBac transposable elements in Aedes aegypti.

    Directory of Open Access Journals (Sweden)

    Azhahianambi Palavesam

    Full Text Available The piggyBac transposon, originating in the genome of the Lepidoptera Trichoplusia ni, has a broad host range, making it useful for the development of a number of transposon-based functional genomic technologies including gene vectors, enhancer-, gene- and protein-traps. While capable of being used as a vector for the creation of transgenic insects and insect cell lines, piggyBac has very limited mobility once integrated into the genome of the yellow fever mosquito, Aedes aegypti. A transgenic Aedes aegypti cell line (AagPB8 was created containing three integrated piggyBac elements and the remobilization potential of the elements was tested. The integrated piggyBac elements in AagPB8 were transpositionally silent in the presence of functional transposase, which was shown to be capable of catalyzing the movement of plasmid-borne piggyBac elements in the same cells. The structural integrity of one of the integrated elements along with the quality of element-flanking DNA, which is known to influence transposition rates, were tested in D. melanogaster. The element was found to be structurally intact, capable of transposition and excision in the soma and germ-line of Drosophila melanogaster, and in a DNA sequence context highly conducive to element movement in Drosophila melanogaster. These data show that transpositional silencing of integrated piggyBac elements in the genome of Aedes aegypti appears to be a function of higher scale genome organization or perhaps epigenetic factors, and not due to structural defects or suboptimal integration sites.

  15. Significant reduction of AC losses in YBCO patterned coated conductors with transposed filaments

    Energy Technology Data Exchange (ETDEWEB)

    Abraimov, Dmytro; Gurevich, Alex; Polyanskii, Anatolii; Cai, X Y; Xu, Aixia; Larbalestier, David [Applied Superconductivity Center at the National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL (United States); Pamidi, Sastry [Center for Advanced Power Systems, Florida State University, Tallahassee, FL (United States); Thieme, C L H [American Superconductor Corporation, Devens, MA (United States)

    2008-08-15

    We report on a first implementation of a design which provides a significant reduction of AC losses in YB{sub 2}Cu{sub 3}O{sub 7-{delta}} (YBCO) coated conductors (CCs) without mechanical twisting. The conductor is composed of two diffusively bonded silver clad commercial CCs with zigzag patterned filaments partially separated by a dielectric layer. We produced three fully bonded samples with 500 {mu}m wide filaments using three-stage photolithography and wet chemical etching. A tenfold reduction of AC losses at frequencies between 20 and 400 Hz was observed, while transport measurements and magneto-optical imaging showed no degradation of T{sub c} and a low contact resistance of {approx_equal}10{sup -8} {omega}cm{sup 2} between Ag and YB{sub 2}Cu{sub 3}O{sub 7-{delta}}. (rapid communication)

  16. Transposable elements P and gypsy in natural populations of Drosophila willistoni

    Directory of Open Access Journals (Sweden)

    Adriana Koslovski Sassi

    2005-12-01

    Full Text Available The presence and integrity of the P transposon and the gypsy retrotransposon in the genome of 18 samples of natural Drosophila willistoni populations collected from a large area of South America were Southern blot screened using Drosophila melanogaster probes. The aim of this screening was provide further knowledge-base on the geographical distribution of D. willistoni and to carry out an inter-population analysis of the P and gypsy elements present in the genomes of the populations analyzed. The fragment patterns obtained indicate that both the P and gypsy elements are ancient in the D. willistoni genome, but whereas the gypsy retroelement appears to be invariable and stable the P element varies between populations and appears to still have some capacity for mobilization.

  17. An En/Spm based transposable element system for gene isolation in Arabidopsis thaliana.

    NARCIS (Netherlands)

    Aarts, M.G.M.

    1996-01-01

    At the start of the research described in this thesis, the main aim was to develop, study and apply an efficient En/Spm-I/dSpm based transposon tagging system in Arabidopsis thaliana to generate tagged mutants and to provide insights in the possibilities for future applications of such a transposon

  18. Dental anomalies in first-degree relatives of transposed canine probands

    Institute of Scientific and Technical Information of China (English)

    Adriana Bartolo; Neville Calleja; Fraser McDonald; Simon Camilleri

    2015-01-01

    The aim of this study was to investigate and compare the inheritance pattern and prevalence of inheritable dental anomalies in a sample of patients with maxillary canine—first premolar transposition and their first-degree relatives with a sample of palatally displaced canine families. Thirty-five consecutive maxillary canine—first premolar transposition probands and 111 first-degree relatives were matched to 35 consecutive palatally displaced canine probands and 115 first-degree relatives. These were assessed for palatally displaced canines and incisor-premolar hypodontia. Parental age at birth of the proband was also noted. The results revealed that (i) there is no difference in the overall prevalence of palatally displaced canine or incisor-premolar hypodontia between the groups of relatives; (ii) first-degree relatives of bilateral palatally displaced canine probands have a higher prevalence of palatally displaced canine and incisor-premolar hypodontia than those with unilateral palatally displaced canine; and (iii) maternal age at birth of the maxillary canine—first premolar transposition probands was significantly higher than that of the palatally displaced canine probands. The results suggest that maxillary canine—first premolar transposition and palatally displaced canine are unlikely to be different genetic entities and also indicate environmental or epigenetic influences on dental development.

  19. Dental anomalies in first-degree relatives of transposed canine probands

    Science.gov (United States)

    Bartolo, Adriana; Calleja, Neville; McDonald, Fraser; Camilleri, Simon

    2015-01-01

    The aim of this study was to investigate and compare the inheritance pattern and prevalence of inheritable dental anomalies in a sample of patients with maxillary canine—first premolar transposition and their first-degree relatives with a sample of palatally displaced canine families. Thirty-five consecutive maxillary canine—first premolar transposition probands and 111 first-degree relatives were matched to 35 consecutive palatally displaced canine probands and 115 first-degree relatives. These were assessed for palatally displaced canines and incisor-premolar hypodontia. Parental age at birth of the proband was also noted. The results revealed that (i) there is no difference in the overall prevalence of palatally displaced canine or incisor-premolar hypodontia between the groups of relatives; (ii) first-degree relatives of bilateral palatally displaced canine probands have a higher prevalence of palatally displaced canine and incisor-premolar hypodontia than those with unilateral palatally displaced canine; and (iii) maternal age at birth of the maxillary canine—first premolar transposition probands was significantly higher than that of the palatally displaced canine probands. The results suggest that maxillary canine—first premolar transposition and palatally displaced canine are unlikely to be different genetic entities and also indicate environmental or epigenetic influences on dental development. PMID:25634123

  20. Active sharing

    CERN Multimedia

    2012-01-01

    The big news this week is, of course, the conclusions from the LHC performance workshop held in Chamonix from 6 to 10 February . The main recommendation, endorsed by CERN’s Machine Advisory Committee and adopted by the Management, is that the LHC will run at 4 TeV per beam this year. You can find all the details from Chamonix in the slides presented on Wednesday at the summary session, which leaves me free to talk about another important development coming up soon.   In ten days time, a new kind of gathering will be taking place in Geneva, bringing together two previously separate conferences, one driven by physics, the other by the medical community, but both looking to apply physics to the advancement of health. The merger of the International Conference for Translational Research in Radio-Oncology and CERN’s workshop on Physics for Health in Europe (ICTR-PHE) makes for a very eclectic mix. Presentations range from active shielding for interplanetary flight to the rather...

  1. DAVIC activities

    Science.gov (United States)

    Fujiwara, Hiroshi

    1995-12-01

    DAVIC (Digital Audio Visual Council) is the defacto standardization organization established in Mar. 1994, based on international consensus for digital audio visual services. After completion of MPEG2 standardization, the broadcasting industry, the communication industry, the computer industry, and consumer electronics industry have started development of concrete services and products. Especially the interactive digital audio visual services, such as Video On Demand (VOD) or Near Video On Demand (NVOD), have become hot topics all over the world. Such interactive digital audio visual services are combined technologies of multi-media coding, digital transmission and computer networking. Therefore more than 150 organizations from all industry sectors have participated in DAVIC and are contributing from their own industrial contexts. DAVIC's basic policy is to use the available technologies specified by the other standards bodies as much as possible. So DAVIC's standardization activities have close relationship with ISO IEC/JTC1/SC29, ITU-T SG 9, ATM-Forum, IETF, IMA, DVB, etc. DAVIC is trying to specify Applications, Reference Models, Security, Usage Information Control, and the interfaces and protocols among the Content Provider, the Server, the core network, the access network, and the Set Top Unit. DAVIC's first goal is to specify DAVIC1.0 based on CFP1 (Call for Proposal) and CFP2 by Dec. 1995, and the next direction is under preparation for further progress based on CFP3 and CFP4.

  2. IASS Activity

    Science.gov (United States)

    Hojaev, Alisher S.; Ibragimova, Elvira M.

    2015-08-01

    It’s well known, astronomy in Uzbekistan has ancient roots and traditions (e.g., Mirzo Ulugh Beg, Abū al-Rayhān al-Bīrūnī, Abū ‘Abdallāh al-Khwārizmī) and astronomical heritage carefully preserved. Nowadays uzbek astronomers play a key role in scientific research but also in OAD and Decadal Plan activity in the Central Asia region. International Aerospace School (IASS) is an amazing and wonderful event held annually about 30 years. IASS is unique project in the region, and at the beginning we spent the Summer and Winter Schools. At present in the summer camp we gather about 50 teenage and undergraduate students over the country and abroad (France, Malaysia, Turkey, Azerbaijan, Pakistan, Russia, etc.). They are selected on the basis of tests of astronomy and space issues. During two weeks of IASS camp the invited scientists, cosmonauts and astronauts as well as other specialists give lectures and engage in practical exercises with IASS students in astronomy, including daily observations of the Sun and night sky observations with meniscus telescope, space research and exploration, aerospace modelling, preparation and presentation of original projects. This is important that IASS gives not theoretical grounds only but also practically train the students and the hands-on training is the major aims of IASS. Lectures and practice in the field of astronomy carried out with the direct involvement and generous assistance of Uranoscope Association (Paris, France). The current 26-th IASS is planned to held in July 2015.

  3. Activation Energy

    Science.gov (United States)

    Gadeken, Owen

    2002-01-01

    Teaming is so common in today's project management environment that most of us assume it comes naturally. We further assume that when presented with meaningful and challenging work, project teams will naturally engage in productive activity to complete their tasks. This assumption is expressed in the simple (but false) equation: Team + Work = Teamwork. Although this equation appears simple and straightforward, it is far from true for most project organizations whose reality is a complex web of institutional norms based on individual achievement and rewards. This is illustrated by the very first successful team experience from my early Air Force career. As a young lieutenant, I was sent to Squadron Officer School, which was the first in the series of Air Force professional military education courses I was required to complete during my career. We were immediately formed into teams of twelve officers. Much of the course featured competition between these teams. As the most junior member of my team, I quickly observed the tremendous pressure to show individual leadership capability. At one point early in the course, almost everyone in our group was vying to become the team leader. This conflict was so intense that it caused us to fail miserably in our first outdoor team building exercise. We spent so much time fighting over leadership that we were unable to complete any of the events on the outdoor obstacle course. This complete lack of success was so disheartening to me that I gave our team little hope for future success. What followed was a very intense period of bickering, conflict, and even shouting matches as our dysfunctional team tried to cope with our early failures and find some way to succeed. British physician and researcher Wilfred Bion (Experiences in Groups, 1961) discovered that there are powerful psychological forces inherent in all groups that divert from accomplishing their primary tasks. To overcome these restraining forces and use the potential

  4. Staying Active: Physical Activity and Exercise

    Science.gov (United States)

    ... Examples of muscle-strengthening activities include lifting weights, yoga, push-ups, and sit-ups. A “repetition” is one complete movement of an activity. To get health benefits, do muscle-strengthening activities until it is hard ...

  5. Physical Activity Assessment

    Science.gov (United States)

    Current evidence convincingly indicates that physical activity reduces the risk of colon and breast cancer. Physical activity may also reduce risk of prostate cancer. Scientists are also evaluating potential relationships between physical activity and other cancers.

  6. Immunizations: Active vs. Passive

    Science.gov (United States)

    ... Prevention > Immunizations > Immunizations: Active vs. Passive Safety & Prevention Listen Español Text Size Email Print Share Immunizations: Active vs. Passive Page Content Article Body Pediatricians can ...

  7. Political activity for physical activity: health advocacy for active transport.

    Science.gov (United States)

    Richards, Rosalina; Murdoch, Linda; Reeder, Anthony I; Amun, Qa-t-a

    2011-05-29

    Effective health advocacy is a priority for efforts to increase population participation in physical activity. Local councils are an important audience for this advocacy. The aim of the current study was to describe features of advocacy for active transport via submissions to city council annual plans in New Zealand, and the impact of an information sheet to encourage the health sector to be involved in this process. Written submissions to city council's annual consultation process were requested for 16 city councils over the period of three years (2007/08, 2008/09, and 2009/10). Submissions were reviewed and categories of responses were created. An advocacy information sheet encouraging health sector participation and summarising some of the evidence-base related to physical activity, active transport and health was released just prior to the 2009/10 submission time. Over the period of the study, city councils received 47,392 submissions, 17% of which were related to active transport. Most submissions came from city residents, with a small proportion (2%) from the health sector. The largest category of submissions was in support of pedestrian and cycling infrastructure, design and maintenance of facilities and additional features to support use of these transport modes. Health arguments featured prominently in justifications for active transport initiatives, including concerns about injury risk, obesity, physical inactivity, personal safety and facilities for people with disabilities. There was evidence that the information sheet was utilised by some health sector submitters (12.5%), providing tentative support for initiatives of this nature. In conclusion, the study provides novel information about the current nature of health advocacy for active transport and informs future advocacy efforts about areas for emphasis, such as health benefits of active transport, and potential alliances with other sectors such as environmental sustainability, transport and urban

  8. Criminalisation of Activism

    DEFF Research Database (Denmark)

    Uldam, Julie

    Different forms of political participation involve different challenges. This paper focuses on challenges to radical activism and particularly the criminalisation of activism.......Different forms of political participation involve different challenges. This paper focuses on challenges to radical activism and particularly the criminalisation of activism....

  9. Active commuting to school

    Science.gov (United States)

    Declines in physical activity levels have coincided with increasing rates of obesity in children. This is problematic because physical activity has been shown to attenuate weight gain in children. Active commuting to school is one way of increasing children's physical activity. However, given the hi...

  10. Physical Activity During School

    DEFF Research Database (Denmark)

    Østergaard, Lars Domino

    It is important, not only on health grounds, to exercise and to be physically active. In school, physical activities have shown to improve the students’ academic behaviour resulting in improved attention and information processing as well as enhanced coping. To stimulate and motivate students...... to be even more active during school hours further enhancing their academic behaviour, it is important to know when, why and how they are active, and their attitude towards different types of physical activities. Therefore, the aim of this study was to categorize the physical activities attended by students...... during school hours and to elucidate their attitude towards the different types of activities. The data consisted of observations of lessons followed by group interviews. Analyses of the observations revealed six categories of physical activities, varying from mandatory physical activities, activities...

  11. Cultural Activation of Consumers.

    Science.gov (United States)

    Siegel, Carole E; Reid-Rose, Lenora; Joseph, Adriana M; Hernandez, Jennifer C; Haugland, Gary

    2016-02-01

    This column discusses "cultural activation," defined as a consumer's recognition of the importance of providing cultural information to providers about cultural affiliations, challenges, views about, and attitudes toward behavioral health and general medical health care, as well as the consumer's confidence in his or her ability to provide this information. An aid to activation, "Cultural Activation Prompts," and a scale that measures a consumer's level of activation, the Cultural Activation Measurement Scale, are described. Suggestions are made about ways to introduce cultural activation as a component of usual care.

  12. Self-regulated growth of supermassive black holes by a dual jet-heating active galactic nucleus feedback mechanism: methods, tests and implications for cosmological simulations

    Science.gov (United States)

    Dubois, Yohan; Devriendt, Julien; Slyz, Adrianne; Teyssier, Romain

    2012-03-01

    We develop a subgrid model for the growth of supermassive black holes (BHs) and their associated active galactic nucleus (AGN) feedback in hydrodynamical cosmological simulations. This model transposes previous attempts to describe BH accretion and AGN feedback with the smoothed particle hydrodynamics (SPH) technique to the adaptive mesh refinement framework. It also furthers their development by implementing a new jet-like outflow treatment of the AGN feedback which we combine with the heating mode traditionally used in the SPH approach. Thus, our approach allows one to test the robustness of the conclusions derived from simulating the impact of self-regulated AGN feedback on galaxy formation vis-à-vis the numerical method. Assuming that BHs are created in the early stages of galaxy formation, they grow by mergers and accretion of gas at a Eddington-limited Bondi accretion rate. However this growth is regulated by AGN feedback which we model using two different modes: a quasar-heating mode when accretion rates on to the BHs are comparable to the Eddington rate, and a radio-jet mode at lower accretion rates which not only deposits energy, but also deposits mass and momentum on the grid. In other words, our feedback model deposits energy as a succession of thermal bursts and jet outflows depending on the properties of the gas surrounding the BHs. We assess the plausibility of such a model by comparing our results to observational measurements of the co-evolution of BHs and their host galaxy properties, and check their robustness with respect to numerical resolution. We show that AGN feedback must be a crucial physical ingredient for the formation of massive galaxies as it appears to be able to efficiently prevent the accumulation of and/or expel cold gas out of haloes/galaxies and significantly suppress star formation. Our model predicts that the relationship between BHs and their host galaxy mass evolves as a function of redshift, because of the vigorous accretion

  13. Major operations and activities

    Energy Technology Data Exchange (ETDEWEB)

    Black, D.G.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the major operations and activities on the site. These operations and activities include site management, waste management, environmental restoration and corrective actions, and research and technology development.

  14. ACS Community Activities Contests

    Science.gov (United States)

    Burgener, Marisa

    2007-08-01

    The Committee on Community Activities and the Office of Community Activities announce the winners of the Illustrated Haiku Contest, Earth Day 2007 and the Poster Contest, National Chemistry Week 2006.

  15. Active Marine Station Metadata

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Active Marine Station Metadata is a daily metadata report for active marine bouy and C-MAN (Coastal Marine Automated Network) platforms from the National Data...

  16. USAID Activity Locatons

    Data.gov (United States)

    US Agency for International Development — The USAID Activities dataset is a snapshot of activities supported by USAID including their geographical locations within countries at the time of the snapshot. The...

  17. Active magnetic regenerator

    Science.gov (United States)

    Barclay, John A.; Steyert, William A.

    1982-01-01

    The disclosure is directed to an active magnetic regenerator apparatus and method. Brayton, Stirling, Ericsson, and Carnot cycles and the like may be utilized in an active magnetic regenerator to provide efficient refrigeration over relatively large temperature ranges.

  18. Physical Activity (Exercise)

    Science.gov (United States)

    ... page Subscribe to ePublications email updates. Enter email address Submit Home > ePublications > Our ePublications > Physical activity (exercise) fact sheet ePublications Physical activity (exercise) ...

  19. Guide to Physical Activity

    Science.gov (United States)

    ... minutes Stairwalking for 15 minutes Sporting Activities Playing volleyball for 45–60 minutes Playing touch football for ... strenuous activities. Competitive sports, such as tennis and volleyball, can provide an enjoyable form of exercise for ...

  20. Italian active volcanoes

    Institute of Scientific and Technical Information of China (English)

    RobertoSantacroce; RenawCristofolini; LuigiLaVolpe; GiovanniOrsi; MauroRosi

    2003-01-01

    The eruptive histories, styles of activity and general modes of operation of the main active Italian volcanoes,Etna, Vulcano, Stromboli, Vesuvio, Campi Flegrei and Ischia, are described in a short summary.

  1. Facts about Physical Activity

    Science.gov (United States)

    ... Nutrition Physical Activity Overweight & Obesity Healthy Weight Breastfeeding Micronutrient Malnutrition State and Local Programs Facts about Physical ... Nutrition Physical Activity Overweight & Obesity Healthy Weight Breastfeeding Micronutrient Malnutrition State and Local Programs File Formats Help: ...

  2. Family Activities for Fitness

    Science.gov (United States)

    Grosse, Susan J.

    2009-01-01

    This article discusses how families can increase family togetherness and improve physical fitness. The author provides easy ways to implement family friendly activities for improving and maintaining physical health. These activities include: walking, backyard games, and fitness challenges.

  3. Activity Theory and Ontology

    Science.gov (United States)

    Peim, Nick

    2009-01-01

    This paper seeks to re-examine Yrio Engestrom's activity theory as a technology of knowledge designed to enable positive transformations of specific practices. The paper focuses on a key paper where Engestrom defines the nature and present state of activity theory. Beginning with a brief account of the relations between activity theory and…

  4. Measurement of Physical Activity.

    Science.gov (United States)

    Dishman, Rod K.; Washburn, Richard A.; Schoeller, Dale A.

    2001-01-01

    Valid assessment of physical activity must be unobtrusive, practical to administer, and specific about physical activity type, frequency, duration, and intensity. Assessment methods can be categorized according to whether they provide direct or indirect (e.g., self-report) observation of physical activity, body motion, physiological response…

  5. Ras activation by SOS

    DEFF Research Database (Denmark)

    Iversen, Lars; Tu, Hsiung-Lin; Lin, Wan-Chen;

    2014-01-01

    Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual ...

  6. Proteolytic activities in yeast.

    Science.gov (United States)

    Saheki, T; Holzer, H

    1975-03-28

    Studies on the mechanism and time course of the activation of proteinases A (EC 3.4.23.8), B (EC 3.4.22.9) and C (EC 3.4.12.--) in crude yeast extracts at pH 5.1 and 25 degrees C showed that the increase in proteinase B activity is paralleled with the disappearance of proteinase B inhibitor. Addition of purified proteinase A to fresh crude extracts accelerates the inactivation of the proteinase B inhibitor and the appearance of maximal activities of proteinases B and C. The decrease of proteinase B inhibitor activity and the increase of proteinase B activity are markedly retarded by the addition of pepstatin. Because 10-minus 7 M pepstatin completely inhibits proteinase A without affecting proteinase B activity, this is another indication for the role of proteinase A during the activation of proteinase B. Whereas extracts of yeast grown on minimal medium reached maximal activation of proteinases B and C after 20 h of incubation at pH 5.1 and 25 degrees C, extracts of yeast grown on complete medium had to be incubated for about 100 h. In the latter case, the addition of proteinas A results in maximal activation of proteinases B and C and disappearance of proteinase B inhibitor activity only after 10--20 h of incubation. With the optimal conditions, the maximal activities of proteinases A, B and C, as well as of the proteinase B inhibitor, were determined in crude extracts of yeast that had been grown batchwise for different lengths of time either on minimal or on complete medium. Upon incubation, all three proteinases were activated by several times their initial activity. This reflects the existence of proteolytically degradable inhibitors of the three proteinases and together with the above mentioned observations it demonstrates that the "activation" of yeast proteinases A, B and C upon incubation results from the proteolytic digestion of inhibitors rather than from activation of inactive zymogens by limited proteolysis.

  7. Recurrent radio activity in active galactic nuclei

    Directory of Open Access Journals (Sweden)

    Jamrozy M.

    2012-12-01

    Full Text Available There has been a growing body of persuasive evidence to indicate that AGN activity, powered by mass accretion onto a supermassive black hole, can involve multiple episodes. Thus thinking of jet activity as occurring within a unique brief period in the life of a galaxy is no longer valid. The most striking examples of AGNs with recurrent jet activity are the double-double radio sources, which contain two or more pairs of distinct lobes on the opposite sides of a parent optical object. On the other hand, we have now conclusive arguments that galaxy mergers and interactions are principal triggers for AGNs. Quite a number of examples of powerful radio sources hosted by galaxies with peculiar optical morphologies (tails, shells, dust-lanes, etc. can be cited to support such a scenario. The structure and spectra of extended radio emission from radio galaxies, with sizes ranging up to a few Mpc, can provide a lot of information on the history of the central AGN activity, while the spectral and dynamical ages of these extended radio lobes could be used to constrain the time scales of recurrent AGN activity.

  8. Active ageing technologies

    DEFF Research Database (Denmark)

    Lassen, Aske Juul

    the elderly. As part of this rearticulation of old age, many new technologies take form. This paper uses a wide concept of technologies (devices, regimes, strategies and ways of doing) and argues that technologies form active aging subjectivities, and on the other hand, that these subjectivities...... ‘sites of active aging’ in Denmark. By presenting three technologies of active aging (billiards at an activity center for elderly persons, dancing tiles for rehabilitation after falls and an online fitness community for elderly persons) the paper suggests that active aging is more than regimes...

  9. Non-GPS Navigation Using Vision-Aiding and Active Radio Range Measurements

    Science.gov (United States)

    2011-03-01

    technology has advanced to use ring laser gyros which are described in this paragraph. The inertia of a spinning mass causes it to resist changes in...Next, the INS body DCM is transposed, Cn ′ b = C bT n′ , to rotate the accelerometer specific force measurements, f b = [fx, fy, fz], from the INS b...65 IV. Results This chapter presents results and analysis for the data collections outlined inSection 3.2. Results from the stationary data collected

  10. Accessibility, activity participation and location of activities

    DEFF Research Database (Denmark)

    Næss, Petter

    2006-01-01

    By investigating relationships between residential location and the availability of facilities, location of activities, trip distances, activity participation and trip frequencies, this paper seeks to contribute to a more detailed and nuanced understanding of the relationships between residential...... outweigh each other. However, differences in trip distances due to the location of the dwelling relative to concentrations of facilities translate into substantially longer total travelling distances among suburbanites than among inner-city residents....... location and the amount of daily-life travel in an urban region. The empirical data are from a comprehensive study of residential location and travel in Copenhagen Metropolitan Area. Differences between inner- and outer-area residents in activity frequencies and trip frequencies are modest and partly...

  11. Marine Biology Activities. Ocean Related Curriculum Activities.

    Science.gov (United States)

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…

  12. Active knee joint flexibility and sports activity

    DEFF Research Database (Denmark)

    Hahn, Thomas; Foldspang, Anders; Vestergaard, E

    1999-01-01

    was significantly higher in women than in men and significantly positively associated with weekly hours of swimming and weekly hours of competitive gymnastics. Active knee flexion was significantly positively associated with participation in basketball, and significantly negatively associated with age and weekly...

  13. [Biomedical activity of biosurfactants].

    Science.gov (United States)

    Krasowska, Anna

    2010-07-23

    Biosurfactants, amphiphilic compounds, synthesized by microorganisms have surface, antimicrobial and antitumor properties. Biosurfactants prevent adhesion and biofilms formation by bacteria and fungi on various surfaces. For many years microbial surfactants are used as antibiotics with board spectrum of activity against microorganisms. Biosurfactants act as antiviral compounds and their antitumor activities are mediated through induction of apoptosis. This work presents the current state of knowledge related to biomedical activity of biosurfactants.

  14. CDBG Economic Development Activity

    Data.gov (United States)

    Department of Housing and Urban Development — CDBG activity related to economic development, including commercial or industrial rehab, commercial or industrial land acquisition, commercial or industrial...

  15. CDBG Housing Activity

    Data.gov (United States)

    Department of Housing and Urban Development — CDBG activity related to housing, including multifamily rehab, housing services, code enforcement, operation and repair of foreclosed property and public housing...

  16. CDBG Public Services Activity

    Data.gov (United States)

    Department of Housing and Urban Development — CDBG activity related to public services, including senior services, legal services, youth services, employment training, health services, homebuyer counseling, food...

  17. REACTIVATION POTENTIAL OF EPIGENETICALLY INACTIVE MU TRANSPOSABLE ELEMENTS OF ZEA MAYS L. DECREASES IN SUCCESSIVE GENERATIONS. (R824900)

    Science.gov (United States)

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  18. Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats.

    Science.gov (United States)

    Vera, Manuel; Bello, Xabier; Álvarez-Dios, Jose-Antonio; Pardo, Belen G; Sánchez, Laura; Carlsson, Jens; Carlsson, Jeanette E L; Bartolomé, Carolina; Maside, Xulio; Martinez, Paulino

    2015-12-01

    The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but its production has been greatly reduced by the parasite Bonamia ostreae. Here, new generation genomic resources were used to analyse the repetitive fraction of the oyster genome, with the aim of developing molecular markers to face this main oyster production challenge. The resulting oyster database, consists of two sets of 10,318 and 7159 unique contigs (4.8 Mbp and 6.8 Mbp in total length) representing the oyster's genome (WG) and haemocyte transcriptome (HT), respectively. A total of 1083 sequences were identified as TE-derived, which corresponded to 4.0% of WG and 1.1% of HT. They were clustered into 142 homology groups, most of which were assigned to the Penelope order of retrotransposons, and to the Helitron and TIR DNA-transposons. Simple repeats and rRNA pseudogenes, also made a significant contribution to the oyster's genome (0.5% and 0.3% of WG and HT, respectively).The most frequent short tandem repeats identified in WG were tetranucleotide motifs while trinucleotide motifs were in HT. Forty identified microsatellite loci, 20 from each database, were selected for technical validation. Success was much lower among WG than HT microsatellites (15% vs 55%), which could reflect higher variation in anonymous regions interfering with primer annealing. All microsatellites developed adjusted to Hardy-Weinberg proportions and represent a useful tool to support future breeding programmes and to manage genetic resources of natural flat oyster beds.

  19. Mapping of a Leishmania major gene/locus that confers pentamidine resistance by deletion and insertion of transposable element

    Directory of Open Access Journals (Sweden)

    Coelho Adriano C.

    2004-01-01

    Full Text Available Pentamidine (PEN is an alternative compound to treat antimony-resistant leishmaniasis patients, which cellular target remains unclear. One approach to the identification of prospective targets is to identify genes able to mediate PEN resistance following overexpression. Starting from a genomic library of transfected parasites bearing a multicopy episomal cosmid vector containing wild-type Leishmania major DNA, we isolated one locus capable to render PEN resistance to wild type cells after DNA transfection. In order to map this Leishmania locus, cosmid insert was deleted by two successive sets of partial digestion with restriction enzymes, followed by transfection into wild type cells, overexpression, induction and functional tests in the presence of PEN. To determine the Leishmania gene related to PEN resistance, nucleotide sequencing experiments were done through insertion of the transposon Mariner element of Drosophila melanogaster (mosK into the deleted insert to work as primer island. Using general molecular techniques, we described here this method that permits a quickly identification of a functional gene facilitating nucleotide sequence experiments from large DNA fragments. Followed experiments revealed the presence of a P-Glycoprotein gene in this locus which role in Leishmania metabolism has now been analyzed.

  20. Substituted-Letter and Transposed-Letter Effects in a Masked Priming Paradigm with French Developing Readers and Dyslexics

    Science.gov (United States)

    Lete, Bernard; Fayol, Michel

    2013-01-01

    The aim of the study was to undertake a behavioral investigation of the development of automatic orthographic processing during reading acquisition in French. Following Castles and colleagues' 2007 study ("Journal of Experimental Child Psychology, 97," 165-182) and their lexical tuning hypothesis framework, substituted-letter and…

  1. Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements

    Science.gov (United States)

    Gowda, Malali

    2016-01-01

    Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets. This study was aimed at generating genomic information for rice and non-rice Magnaporthe isolates to understand the extent of genetic variation. We have sequenced the whole genome of the Magnaporthe isolates, infecting rice (leaf and neck), finger millet (leaf and neck), foxtail millet (leaf) and buffel grass (leaf). Rice and finger millet isolates infecting both leaf and neck tissues were sequenced, since the damage and yield loss caused due to neck blast is much higher as compared to leaf blast. The genome-wide comparison was carried out to study the variability in gene content, candidate effectors, repeat element distribution, genes involved in carbohydrate metabolism and SNPs. The analysis of repeat element footprints revealed some genes such as naringenin, 2-oxoglutarate 3-dioxygenase being targeted by Pot2 and Occan, in isolates from different host species. Some repeat insertions were host-specific while other insertions were randomly shared between isolates. The distributions of repeat elements, secretory proteins, CAZymes and SNPs showed significant variation across host-specific lineages of Magnaporthe indicating an independent genome evolution orchestrated by multiple genomic factors. PMID:27658241

  2. Transposed-Letter Priming Effects with Masked Subset Primes: A Re-Examination of the "Relative Position Priming Constraint"

    Science.gov (United States)

    Stinchcombe, Eric J.; Lupker, Stephen J.; Davis, Colin J.

    2012-01-01

    Three experiments are reported investigating the role of letter order in orthographic subset priming (e.g., "grdn"-GARDEN) using both the conventional masked priming technique as well as the sandwich priming technique in a lexical decision task. In all three experiments, subset primes produced priming with the effect being considerably…

  3. Activity Book: Ocean Ecology.

    Science.gov (United States)

    Learning, 1992

    1992-01-01

    Presents a collection of activities to help elementary students study ocean ecology. The activities have students investigate ocean inhabitants, analyze animal adaptations, examine how temperature and saltiness affect ocean creatures, and learn about safeguarding the sea. Student pages offer reproducible learning sheets. (SM)

  4. Reflections on Activity Theory

    Science.gov (United States)

    Bakhurst, David

    2009-01-01

    It is sometimes suggested that activity theory represents the most important legacy of Soviet philosophy and psychology. But what exactly "is" activity theory? The canonical account in the West is given by Engestrom, who identifies three stages in the theory's development: from Vygotsky's insights, through Leontiev's articulation of the…

  5. The Activity of Play

    DEFF Research Database (Denmark)

    Pichlmair, Martin

    2016-01-01

    This paper presents Activity Theory as a framework for understanding the action of playing games with the intention of building a foundation for the creation of new game design tools and methods. Activity Theory, an epistemological framework rooted in Soviet psychology of the first half of the 20...

  6. Physical Activity Questionnaire

    Directory of Open Access Journals (Sweden)

    Kostencka Alicja

    2016-11-01

    Full Text Available Study aim: The aim of the study was to determine the weekly energy expenditure measuring MET/min/week based on data collected through the Canada Fitness Survey (CFS, according to the classification used in the International Physical Activity Questionnaire (IPAQ, and to verify the adopted method to assess the level of physical activity in students of physical education.

  7. Active and Healthy Schools

    Science.gov (United States)

    Ball, Stephen; Kovarik, Jessica; Leidy, Heather

    2015-01-01

    The Active and Healthy School Program (AHS) can be used to alter the culture and environment of a school to help children make healthier choices. The purpose of this study was to determine the effectiveness of AHS to increase physical activity while decreasing total screen time, increase healthy food choices, and improve knowledge about physical…

  8. Activating Event Knowledge

    Science.gov (United States)

    Hare, Mary; Jones, Michael; Thomson, Caroline; Kelly, Sarah; McRae, Ken

    2009-01-01

    An increasing number of results in sentence and discourse processing demonstrate that comprehension relies on rich pragmatic knowledge about real-world events, and that incoming words incrementally activate such knowledge. If so, then even outside of any larger context, nouns should activate knowledge of the generalized events that they denote or…

  9. Emotionally Intense Science Activities

    Science.gov (United States)

    King, Donna; Ritchie, Stephen; Sandhu, Maryam; Henderson, Senka

    2015-01-01

    Science activities that evoke positive emotional responses make a difference to students' emotional experience of science. In this study, we explored 8th Grade students' discrete emotions expressed during science activities in a unit on Energy. Multiple data sources including classroom videos, interviews and emotion diaries completed at the end of…

  10. Peak Longevity Physical Activity

    Science.gov (United States)

    People who engage in three to five times the recommended minimum level of leisure-time physical activity derive the greatest benefit in terms of mortality reduction when compared with people who do not engage in leisure-time physical activity.

  11. Activities of the ILO.

    Science.gov (United States)

    Labour Education, 1984

    1984-01-01

    Seven articles on International Labour Organization (ILO) activities cover study groups at ILO headquarters, a Philippine rural workers seminar, women's participation in Central American union activities, worksite courses in India, and seminars and symposia in Cape Verde, Mauritius, and Sierra Leone. (SK)

  12. Choreography of AMPK activation.

    Science.gov (United States)

    Langendorf, Christopher G; Kemp, Bruce E

    2015-01-01

    A recent study published in Cell Research by Li and colleagues reports a detailed biophysical and structural study of AMPK's intra-molecular interactions during activation. By employing subunit tagging and proximity analysis with the aid of AlphaScreen instrumentation, Li et al. add to our understanding of the choreography of activation of AMPK by both nucleotides and phosphorylation.

  13. Obesity, Physical Activity - Children.

    Science.gov (United States)

    Gilliam, Thomas B.

    Childhood obesity starts at a very early age, and preventive measures taken early enough may retard the development of fat cells. It appears that physical activity plays an important role in reducing obesity. The activity program must start early, in preschool days. It is felt that screening children for obesity when they first enter school and…

  14. Active at Any Size

    Science.gov (United States)

    ... go to the gym all the time to benefit from being active. To make physical activity more fun, try something you enjoy doing, such as dancing to the radio or taking a yoga class with friends. Many people find they start ...

  15. Global physical activity levels

    DEFF Research Database (Denmark)

    Hallal, Pedro C; Andersen, Lars Bo; Bull, Fiona C

    2012-01-01

    To implement effective non-communicable disease prevention programmes, policy makers need data for physical activity levels and trends. In this report, we describe physical activity levels worldwide with data for adults (15 years or older) from 122 countries and for adolescents (13-15-years-old) ...

  16. Biomedical activity of biosurfactants

    OpenAIRE

    Anna Krasowska

    2010-01-01

    Biosurfactants, amphiphilic compounds, synthesized by microorganisms have surface, antimicrobial and antitumor properties. Biosurfactants prevent adhesion and biofilms formation by bacteria and fungi on various surfaces. For many years microbial surfactants are used as antibiotics with board spectrum of activity against microorganisms. Biosurfactants act as antiviral compounds and their antitumor activities are mediated through induction of apoptosis. This work presents the current state of k...

  17. Activity-based design

    DEFF Research Database (Denmark)

    Andersen, Peter Bøgh

    2006-01-01

    : what you can do depends upon where you are. Finally, human and automatic machinery alternate in filling certain roles in the activity: sometime the officer maintains the course, sometimes the autopilot. Such activities require us to rethink the traditional oppositions between communication...

  18. Determinants of Physical Activity in Active and Low-Active, Sixth Grade African-American Youth.

    Science.gov (United States)

    Trost, Stewart G.; Pate, Russell R.; Ward, Dianne S.; Saunders, Ruth; Riner, William

    1999-01-01

    Compared determinants of physical activity in active and low-active African-American sixth graders, surveying students and making objective assessments of physical activity over seven days. Results indicated that physical activity self-efficacy, beliefs about physical activity outcomes, involvement in community-based physical activity, perception…

  19. Intracellular light-activation of riboswitch activity.

    Science.gov (United States)

    Walsh, Steven; Gardner, Laura; Deiters, Alexander; Williams, Gavin J

    2014-06-16

    By combining a riboswitch with a cell-permeable photocaged small-molecule ligand, an optochemical gene control element was constructed that enabled spatial and temporal control of gene expression in bacterial cells. The simplicity of this strategy, coupled with the ability to create synthetic riboswitches with tailored ligand specificities and output in a variety of microorganisms, plants, and fungi might afford a general strategy to photocontrol gene expression in vivo. The ability to activate riboswitches by using light enables the interrogation and manipulation of a wide range of biological processes with high precision, and will have broad utility in the regulation of artificial genetic circuits.

  20. Biological activities of alginate.

    Science.gov (United States)

    Ueno, Mikinori; Oda, Tatsuya

    2014-01-01

    To gain insight into the structure-activity relationship of alginate, we examined the effect of alginates with varying molecular weights and M/G ratio on murine macrophage cell line, RAW264.7 cells in terms of induction of tumor necrosis factor-α (TNF-α) secretion. Among the alginates tested, alginate with the highest molecular weight (MW 38,000, M/G 2.24) showed the most potent TNF-α-inducing activity. Alginates having higher M/G ratio tended to show higher activity. These results suggest that molecular size and M/G ratio are important structural parameters influencing the TNF-α-inducing activity. Interestingly, enzymatic depolymerization of alginate with bacterial alginate lyase resulted in dramatic increase in the TNF-α-inducing activity. The higher activity of enzymatically digested alginate oligomers to induce nitric oxide production from RAW264.7 cells than alginate polymer was also observed. On the other hand, alginate polymer and oligomer showed nearly equal hydroxyl radical scavenging activities.

  1. Emotionally Intense Science Activities

    Science.gov (United States)

    King, Donna; Ritchie, Stephen; Sandhu, Maryam; Henderson, Senka

    2015-08-01

    Science activities that evoke positive emotional responses make a difference to students' emotional experience of science. In this study, we explored 8th Grade students' discrete emotions expressed during science activities in a unit on Energy. Multiple data sources including classroom videos, interviews and emotion diaries completed at the end of each lesson were analysed to identify individual student's emotions. Results from two representative students are presented as case studies. Using a theoretical perspective drawn from theories of emotions founded in sociology, two assertions emerged. First, during the demonstration activity, students experienced the emotions of wonder and surprise; second, during a laboratory activity, students experienced the intense positive emotions of happiness/joy. Characteristics of these activities that contributed to students' positive experiences are highlighted. The study found that choosing activities that evoked strong positive emotional experiences, focused students' attention on the phenomenon they were learning, and the activities were recalled positively. Furthermore, such positive experiences may contribute to students' interest and engagement in science and longer term memorability. Finally, implications for science teachers and pre-service teacher education are suggested.

  2. Active optical zoom system

    Science.gov (United States)

    Wick, David V.

    2005-12-20

    An active optical zoom system changes the magnification (or effective focal length) of an optical imaging system by utilizing two or more active optics in a conventional optical system. The system can create relatively large changes in system magnification with very small changes in the focal lengths of individual active elements by leveraging the optical power of the conventional optical elements (e.g., passive lenses and mirrors) surrounding the active optics. The active optics serve primarily as variable focal-length lenses or mirrors, although adding other aberrations enables increased utility. The active optics can either be LC SLMs, used in a transmissive optical zoom system, or DMs, used in a reflective optical zoom system. By appropriately designing the optical system, the variable focal-length lenses or mirrors can provide the flexibility necessary to change the overall system focal length (i.e., effective focal length), and therefore magnification, that is normally accomplished with mechanical motion in conventional zoom lenses. The active optics can provide additional flexibility by allowing magnification to occur anywhere within the FOV of the system, not just on-axis as in a conventional system.

  3. A universe of activities

    Science.gov (United States)

    Armentia, J.; Jáuregui, F.; Gordón, N.; Manzanal, R.

    Since its opening back in november 1993 the Planetarium of Pamplona has gone a long way creating activities related to teaching and communicating Astronomy, Science and other areas of what we call Culture. In this poster we present a summary of some of the most relevant activities that have had an special relevance throughout these years. We will refer to our “School of Stars” in which more than 400 000 students have already been involved and other activities that have been very appreciated by our visitors.

  4. Physics of solar activity

    Science.gov (United States)

    Sturrock, Peter A.

    1993-01-01

    The aim of the research activity was to increase our understanding of solar activity through data analysis, theoretical analysis, and computer modeling. Because the research subjects were diverse and many researchers were supported by this grant, a select few key areas of research are described in detail. Areas of research include: (1) energy storage and force-free magnetic field; (2) energy release and particle acceleration; (3) radiation by nonthermal electrons; (4) coronal loops; (5) flare classification; (6) longitude distributions of flares; (7) periodicities detected in the solar activity; (8) coronal heating and related problems; and (9) plasma processes.

  5. China's Space Activities

    Institute of Scientific and Technical Information of China (English)

    China National Space Administration

    2004-01-01

    @@ Currently, space activities are very active around the world. Space technologies continuously expand to various areas of human activities, and space technology and applications are becoming an indispensable part of modern information society,while the development of space science brings a brand-new view to the development of science and technology. The development of space law is not only an important approach to improving people' s quality of lives, expanding the living space of human being, and exploiting new resources, but also an important symbol of the comprehensive strength and civilization of a nation.

  6. Active Directory cookbook

    CERN Document Server

    Hunter, Laura

    2008-01-01

    When you need practical hands-on support for Active Directory, the updated edition of this extremely popular Cookbook provides quick solutions to more than 300 common (and uncommon) problems you might encounter when deploying, administering, and automating Microsoft's network directory service. For the third edition, Active Directory expert Laura E. Hunter offers troubleshooting recipes based on valuable input from Windows administrators, in addition to her own experience. You'll find solutions for the Lightweight Directory Access Protocol (LDAP), ADAM (Active Directory Application Mode), m

  7. Creative activity and inclusion

    Directory of Open Access Journals (Sweden)

    Shemanov A.Yu.

    2013-09-01

    Full Text Available The aim of the article was to analyze the inclusion potential of art creative activity, namely of theatre performance, in people with disabilities. The article provides examples of disagreements in understanding the significance of these art activities for exercising the rights of people with disabilities to contribute to culture and art and some problems arising here. The conclusion is made that theatre art performed by people with disabilities is gradually changing its function: from being a means of self-affirmation to the determination of its specific place in overall theatre process. These changes confirm the inclusion potential of theatre art activity.

  8. Active Packaging Coatings

    Directory of Open Access Journals (Sweden)

    Luis J. Bastarrachea

    2015-11-01

    Full Text Available Active food packaging involves the packaging of foods with materials that provide an enhanced functionality, such as antimicrobial, antioxidant or biocatalytic functions. This can be achieved through the incorporation of active compounds into the matrix of the commonly used packaging materials, or by the application of coatings with the corresponding functionality through surface modification. The latter option offers the advantage of preserving the packaging materials’ bulk properties nearly intact. Herein, different coating technologies like embedding for controlled release, immobilization, layer-by-layer deposition, and photografting are explained and their potential application for active food packaging is explored and discussed.

  9. Creating Art Appreciation Activities.

    Science.gov (United States)

    Heidt, Ann H.

    1986-01-01

    The experiences of college students enrolled as majors in elementary education in designing art appreciation activities for use in elementary classrooms are described. The college students had no art background. (RM)

  10. Active flows on trees

    CERN Document Server

    Forrow, Aden; Dunkel, Jörn

    2016-01-01

    Coherent, large scale dynamics in many nonequilibrium physical, biological, or information transport networks are driven by small-scale local energy input. We introduce and explore a generic model for compressible active flows on tree networks. In contrast to thermally-driven systems, active friction selects discrete states with only a small number of oscillation modes activated at distinct fixed amplitudes. This state selection interacts with graph topology to produce different localized dynamical time scales in separate regions of large networks. Using perturbation theory, we systematically predict the stationary states of noisy networks and find good agreement with a Bayesian state estimation based on a hidden Markov model applied to simulated time series data on binary trees. While the number of stable states per tree scales exponentially with the number of edges, the mean number of activated modes in each state averages $\\sim 1/4$ the number of edges. More broadly, these results suggest that the macrosco...

  11. Tanzania - Kigoma Solar Activity

    Data.gov (United States)

    Millennium Challenge Corporation — The performance evaluation of the Kigoma solar activity was designed to answer questions about the implementation of the program and about outcomes that may have...

  12. Physical activity: genes & health

    CERN Multimedia

    2002-01-01

    Carl Johan SUNDBERG is an Associate Professor in Physiology and Licenced Physician. His research focus is Molecular mechanisms involved in the adaptation of human skeletal muscle to physical activity.

  13. Homebuyer Activities Report

    Data.gov (United States)

    Department of Housing and Urban Development — This monthly report is an Excel spreadsheet. PJs can use this report to view homebuyer activities with the 2012 or 2013 program year in IDIS that are in final draw,...

  14. Math Lab Activities

    Science.gov (United States)

    Brumbaugh, Douglas K.; Hynes, Michael C.

    1974-01-01

    The goals, objects, materials and grade levels are specified in this description of a laboratory activity involving analytic geometry concepts. Students mark out bicycle gymkhana courses in which directions to participants are given by Cartesian coordinates. (JP)

  15. PRCR Classes and Activities

    Data.gov (United States)

    Town of Cary, North Carolina — This data is specific to Parks and Recreation classes, workshops, and activities within the course catalog. It contains an entry for upcoming classes.*This data set...

  16. Habitats, activities, and signs

    DEFF Research Database (Denmark)

    Andersen, Peter Bøgh; Brynskov, Martin

    2004-01-01

    Digital habitats is a framework for designing and modeling environments for activities that involve mobile and embedded computing systems. This paper 1) introduces the basic concepts of the framework, i.e. activity, thematic role, and the three ‘dimensions’ of a habitat: physical, informational, ......, and pragmatic, 2) proposes a notation, and 3) sketches a method and exemplifies areas of application using authentic cases from hospital work, primary school education, the maritime domain, and other areas......Digital habitats is a framework for designing and modeling environments for activities that involve mobile and embedded computing systems. This paper 1) introduces the basic concepts of the framework, i.e. activity, thematic role, and the three ‘dimensions’ of a habitat: physical, informational...

  17. Active Photonic Crystal Waveguides

    DEFF Research Database (Denmark)

    Ek, Sara

    This thesis deals with the fabrication and characterization of active photonic crystal waveguides, realized in III-V semiconductor material with embedded active layers. The platform offering active photonic crystal waveguides has many potential applications. One of these is a compact photonic...... crystal semiconductor optical amplier. As a step towards such a component, photonic crystal waveguides with a single quantum well, 10 quantum wells and three layers of quantum dots are fabricated and characterized. An experimental study of the amplied spontaneous emission and a implied transmission...... due to photonic crystal dispersion. The observations are explained by the enhancement of net gain by light slow down. Another application based on active photonic crystal waveguides is micro lasers. Measurements on quantum dot micro laser cavities with different mirror configurations and photonic...

  18. CDBG Public Improvements Activity

    Data.gov (United States)

    Department of Housing and Urban Development — CDBG activity related to public improvements, including senior centers, youth centers, parks, street improvements, water/sewer improvements, child care centers, fire...

  19. Extravehicular activity technology discipline

    Science.gov (United States)

    Webbon, Bruce W.

    1990-01-01

    Viewgraphs on extravehicular activity technology discipline for Space Station Freedom are presented. Topics covered include: extravehicular mobility unit; airlock and EMU support equipment; tools, mobility aids, and workstations; and telerobotic work aids interfaces.

  20. MARIHUANA ACTIVITY OF CANNABINOL.

    Science.gov (United States)

    Loewe, S

    1945-12-14

    Cannabinol, generally believed to be an inert component of hemp oil, is shown to have marihuana activity. The significance of this observation with regard to the relationship between structure and mamactivity in the class of cannabinols is discussed.

  1. OTI Activity Database

    Data.gov (United States)

    US Agency for International Development — OTI's worldwide activity database is a simple and effective information system that serves as a program management, tracking, and reporting tool. In each country,...

  2. Vessel Activity Record

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Vessel Activity Record is a bi-weekly spreadsheet that shows the status of fishing vessels. It records whether fishing vessels are fishing without an observer...

  3. RAVEN Quality Assurance Activities

    Energy Technology Data Exchange (ETDEWEB)

    Cogliati, Joshua Joseph [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-09-01

    This report discusses the quality assurance activities needed to raise the Quality Level of Risk Analysis in a Virtual Environment (RAVEN) from Quality Level 3 to Quality Level 2. This report also describes the general RAVEN quality assurance activities. For improving the quality, reviews of code changes have been instituted, more parts of testing have been automated, and improved packaging has been created. For upgrading the quality level, requirements have been created and the workflow has been improved.

  4. Intercreativity: Mapping Online Activism

    Science.gov (United States)

    Meikle, Graham

    How do activists use the Internet? This article maps a wide range of activist practice and research by applying and developing Tim Berners-Lee's concept of ‘intercreativity' (1999). It identifies four dimensions of Net activism: intercreative texts, tactics, strategies and networks. It develops these through examples of manifestations of Net activism around one cluster of issues: support campaigns for refugees and asylum seekers.

  5. TPR And TPR Activities

    Institute of Scientific and Technical Information of China (English)

    宋丽萍

    2008-01-01

    This paper presents the definition of Total Physical Response(TPR),elaborates the process and the principles of it 80 that more and more TPR activities can be created according to them.The use of TPR shows us an interesting and effective way of teaching and learning English.TPR activities are interesting,challenging and motivating that almost all the students enjoy them.

  6. Toroidal optical activity

    CERN Document Server

    Raybould, T A; Papasimakis, N; Kuprov, I; Youngs, I; Chen, W T; Tsai, D P; Zheludev, N I

    2015-01-01

    Optical activity is ubiquitous across natural and artificial media and is conventionally understood in terms of scattering from electric and magnetic moments. Here we demonstrate experimentally and confirm numerically a type of optical activity that cannot be attributed to electric and magnetic multipoles. We show that our observations can only be accounted for by the inclusion of the toroidal dipole moment, the first term of the recently established peculiar family of toroidal multipoles.

  7. Phytase activity in lichens.

    Science.gov (United States)

    Higgins, Niall F; Crittenden, Peter D

    2015-10-01

    Phytase activity was investigated in 13 lichen species using a novel assay method. The work tested the hypothesis that phytase is a component of the suite of surface-bound lichen enzymes that hydrolyse simple organic forms of phosphorus (P) and nitrogen (N) deposited onto the thallus surface. Hydrolysis of inositol hexaphosphate (InsP6 , the substrate for phytase) and appearance of lower-order inositol phosphates (InsP5 -InsP1 ), the hydrolysis products, were measured by ion chromatography. Phytase activity in Evernia prunastri was compared among locations with contrasting rates of N deposition. Phytase activity was readily measurable in epiphytic lichens (e.g. 11.3 μmol InsP6 hydrolysed g(-1)  h(-1) in Bryoria fuscescens) but low in two terricolous species tested (Cladonia portentosa and Peltigera membranacea). Phytase and phosphomonoesterase activities were positively correlated amongst species. In E. prunastri both enzyme activities were promoted by N enrichment and phytase activity was readily released into thallus washings. InsP6 was not detected in tree canopy throughfall but was present in pollen leachate. Capacity to hydrolyse InsP6 appears widespread amongst lichens potentially promoting P capture from atmospheric deposits and plant leachates, and P cycling in forest canopies. The enzyme assay used here might find wider application in studies on plant root-fungal-soil systems.

  8. Antimicrobial activity of flavonoids.

    Science.gov (United States)

    Cushnie, T P Tim; Lamb, Andrew J

    2005-11-01

    Flavonoids are ubiquitous in photosynthesising cells and are commonly found in fruit, vegetables, nuts, seeds, stems, flowers, tea, wine, propolis and honey. For centuries, preparations containing these compounds as the principal physiologically active constituents have been used to treat human diseases. Increasingly, this class of natural products is becoming the subject of anti-infective research, and many groups have isolated and identified the structures of flavonoids possessing antifungal, antiviral and antibacterial activity. Moreover, several groups have demonstrated synergy between active flavonoids as well as between flavonoids and existing chemotherapeutics. Reports of activity in the field of antibacterial flavonoid research are widely conflicting, probably owing to inter- and intra-assay variation in susceptibility testing. However, several high-quality investigations have examined the relationship between flavonoid structure and antibacterial activity and these are in close agreement. In addition, numerous research groups have sought to elucidate the antibacterial mechanisms of action of selected flavonoids. The activity of quercetin, for example, has been at least partially attributed to inhibition of DNA gyrase. It has also been proposed that sophoraflavone G and (-)-epigallocatechin gallate inhibit cytoplasmic membrane function, and that licochalcones A and C inhibit energy metabolism. Other flavonoids whose mechanisms of action have been investigated include robinetin, myricetin, apigenin, rutin, galangin, 2,4,2'-trihydroxy-5'-methylchalcone and lonchocarpol A. These compounds represent novel leads, and future studies may allow the development of a pharmacologically acceptable antimicrobial agent or class of agents.

  9. Hypoglycemic Activity of Jatrorrhizine

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The hypoglycemic activity and its mechanism of Jatrorrhizine (Jat) were studied. The normal mice and alloxan-induced hyperglycemic mice were given with different doses of Jat. Blood glucose and liver glycogen levels were determined by spectrophotometry with glucose-oxidase and iodine reagents respectively. The levels of blood lactic acid (LC) and liver lactate dehydrogenase (LDH) activity were measured to explore the effect of Jat on anaerobic glycolysis. Succinate dehydrogenase (SDH) activity in liver was measured to evaluate the effect of Jat on aerobic glycolysis in liver. It was found that Jat (50 mg/kg, 100 mg/kg) could significantly decrease blood glucose level in a dose- and time-dependent manner in both normal and alloxan-diabetic mice, increase the activity of SDH, but had no significant effects on the LC level and LDH activity. Jat could significantly reduce the content of liver glycogen in normal mice. Moreover, Jat could inhibit the platelet aggregation in rabbits in vitro in a dose-effect relationship. It was concluded that Jat induced the pronounced decrease in blood glucose in normal and hyperglycemic mice. The hypoglycemic activity of Jat may be attributed to the enhancement of aerobic glycolysis.

  10. Psychomotor activities with seniors

    Directory of Open Access Journals (Sweden)

    Jitka Kopřivová

    2015-07-01

    Full Text Available BACKGROUND: Given that the population all over the world is aging, it is necessary to fi nd ways to help maintain or improve the quality of life of seniors. The main goal of this paper is to show how appropriate physical activity programs contribute to the improvement of the functionality and psychosocial wellbeing of seniors. We are particularly interested in the possibilities of preserving self-suffi ciency and self-service, independence and the ability to perform everyday activities. One of the most eff ective forms of physical activity is psychomotr activity.OBJECTIVE: The aim of our paper is to present basic information concerning the meaning and the application of the psychomotr activities in intervention movement programmes in order to improve seniors’ life quality.METHODS: We defi ne the term psychomotr activities according to Adamírová (1995 and Novotná (2010. In this paper we present some results of research that stress the positive eff ect of psychomotor exercises and games on the life satisfaction of the elderly (Stará 2011; Stará & Kopřivová, 2011.DESCRIPTION: According to the results of our research and practical experience gained from working with the elderly it is strongly recommended to include suitable psychomotor exercises and games focusing on the development of manual dexterity in training programs in order to improve the balance abilities and the psychosocial area. In terms of prevention, because of the growing number of neurological disorders at an old age it is appropriate to include psychomotor exercises that encourage the development of cognitive functions in the physical interventions.CONCLUSION: We were able to positively infl uence the emotional aspect from performing physical activities, to enhance self-esteem of the exercising subjects and to create new social relationships. Motion programs, which also included psychomotor exercises and games, had a positive eff ect on the physical assessment of the

  11. Antimutagenic activity of spearmint.

    Science.gov (United States)

    Yu, Tian-Wei; Xu, Meirong; Dashwood, Roderick H

    2004-01-01

    The antimutagenic activity of spearmint (Mentha spicata), a popular food flavoring agent, was studied in the Salmonella assay. Spearmint leaves were brewed in hot water for 5 min at concentrations up to 5% (w/v), and the water extracts were tested against the direct-acting mutagens 4-nitro-1,2-phenylenediamine (NPD) and 2-hydroxyamino-3-methyl-3H-imidazo[4,5-f]quinoline (N-OH-IQ) using Salmonella typhimurium strain TA98. Nontoxic concentrations of spearmint extract inhibited the mutagenic activity of N-OH-IQ in a concentration-dependent fashion, but had no effect against NPD. These experiments by design focused on the water extract consumed commonly as an herbal tea, but chloroform and methanol extracts of spearmint also possessed antimutagenic activity against N-OH-IQ. Water extract of spearmint inhibited the mutagenic activity of the parent compound, 2-amino-3-methyl-3H-imidazo[4,5-f]quinoline (IQ), in the presence of rat liver S9; however, the concentration for 50% inhibition (IC50) against IQ was approximately 10-fold higher than in assays with N-OH-IQ minus S9. At concentrations similar to those used in the Salmonella assays, spearmint extract inhibited two of the major enzymes that play a role in the metabolic activation of IQ, namely, cytochromes P4501A1 and 1A2, based on ethoxyresorufin O-deethylase and methoxyresorufin O-demethylase assays in vitro. In vivo, rats were given spearmint water extract (2%; w/v) as the sole source of drinking fluid before, during, and after 2-week treatment with IQ; colonic aberrant crypt foci were inhibited significantly at 8 weeks (P < 0.05, compared with rats given IQ alone). Collectively, these findings suggest that spearmint tea protects against IQ and possibly other heterocyclic amines through inhibition of carcinogen activation and via direct effects on the activated metabolite(s).

  12. ACTIVATION ENERGY OF DESORPTION OF DIBENZOFURAN ON ACTIVATED CARBONS

    Institute of Scientific and Technical Information of China (English)

    LI Xiang; LI Zhong; XI Hongxia; LUO Lingai

    2004-01-01

    Three kinds of commercial activated carbons, such as Norit RB1, Monolith and Chemviron activated carbons, were used as adsorbents for adsorption of dibenzofuran. The average pore size and specific surface area of these activated carbons were measured. Temperature Programmed Desorption (TPD) experiments were conducted to measure the TPD curves of dibenzofuran on the activated carbons, and then the activation energy for desorption of dibenzofuran on the activated carbons was estimated. The results showed that the Chemviron and the Norit RB1 activated carbon maintained higher specific surface area and larger micropore pore volume in comparison with the Monolith activated carbon, and the activation energy for the desorption of dibenzofuran on these two activated carbons was higher than that on the Monolith activated carbon. The smaller the pore of the activated carbon was, the higher the activated energy of dibenzofuran desorption was.

  13. Interpreting EEG alpha activity.

    Science.gov (United States)

    Bazanova, O M; Vernon, D

    2014-07-01

    Exploring EEG alpha oscillations has generated considerable interest, in particular with regards to the role they play in cognitive, psychomotor, psycho-emotional and physiological aspects of human life. However, there is no clearly agreed upon definition of what constitutes 'alpha activity' or which of the many indices should be used to characterize it. To address these issues this review attempts to delineate EEG alpha-activity, its physical, molecular and morphological nature, and examine the following indices: (1) the individual alpha peak frequency; (2) activation magnitude, as measured by alpha amplitude suppression across the individual alpha bandwidth in response to eyes opening, and (3) alpha "auto-rhythmicity" indices: which include intra-spindle amplitude variability, spindle length and steepness. Throughout, the article offers a number of suggestions regarding the mechanism(s) of alpha activity related to inter and intra-individual variability. In addition, it provides some insights into the various psychophysiological indices of alpha activity and highlights their role in optimal functioning and behavior.

  14. Active flows on trees

    Science.gov (United States)

    Forrow, Aden; Woodhouse, Francis G.; Dunkel, Jörn

    2016-11-01

    Coherent, large scale dynamics in many nonequilibrium physical, biological, or information transport networks are driven by small-scale local energy input. We introduce and explore a generic model for compressible active flows on tree networks. In contrast to thermally-driven systems, active friction selects discrete states with only a small number of oscillation modes activated at distinct fixed amplitudes. This state selection can interact with graph topology to produce different localized dynamical time scales in separate regions of large networks. Using perturbation theory, we systematically predict the stationary states of noisy networks. Our analytical predictions agree well with a Bayesian state estimation based on a hidden Markov model applied to simulated time series data on binary trees. While the number of stable states per tree scales exponentially with the number of edges, the mean number of activated modes in each state averages 1 / 4 the number of edges. More broadly, these results suggest that the macroscopic response of active networks, from actin-myosin networks in cells to flow networks in Physarum polycephalum, can be dominated by a few select modes.

  15. Active noise control primer

    CERN Document Server

    Snyder, Scott D

    2000-01-01

    Active noise control - the reduction of noise by generating an acoustic signal that actively interferes with the noise - has become an active area of basic research and engineering applications. The aim of this book is to present all of the basic knowledge one needs for assessing how useful active noise control will be for a given problem and then to provide some guidance for designing, setting up, and tuning an active noise-control system. Written for students who have no prior knowledge of acoustics, signal processing, or noise control but who do have a reasonable grasp of basic physics and mathematics, the book is short and descriptive. It leaves for more advanced texts or research monographs all mathematical details and proofs concerning vibrations, signal processing and the like. The book can thus be used in independent study, in a classroom with laboratories, or in conjunction with a kit for experiment or demonstration. Topics covered include: basic acoustics; human perception and sound; sound intensity...

  16. Software Activation Using Multithreading

    Directory of Open Access Journals (Sweden)

    Jianrui Zhang

    2012-11-01

    Full Text Available Software activation is an anti-piracy technology designed to verify that software products have been legitimately licensed. Activation should be quick and simple while simultaneously being secure and protecting customer privacy. The most common form of software activation is for the user to enter a legitimate product serial number. However, software activation based on serial numbers appears to be weak, since cracks for many programs are readily available on the Internet. Users can employ such cracks to bypass software activation.Serial number verification logic usually executes sequentially in a single thread. Such an approach is relatively easy to break since attackers can trace the code to understand how the logic works. In this paper, we develop a practical multi-threaded verification design. Our results show that by proper use of multi-threading, the amount of traceable code in a debugger can be reduced to a low percentage of the total and the traceable code in each run can differ as well. This makes it significantly more difficult for an attacker to reverse engineer the code as a means of bypassing a security check. Finally, we attempt to quantify the increased effort needed to break our verification logic.

  17. Chromatin as active matter

    Science.gov (United States)

    Agrawal, Ankit; Ganai, Nirmalendu; Sengupta, Surajit; Menon, Gautam I.

    2017-01-01

    Active matter models describe a number of biophysical phenomena at the cell and tissue scale. Such models explore the macroscopic consequences of driving specific soft condensed matter systems of biological relevance out of equilibrium through ‘active’ processes. Here, we describe how active matter models can be used to study the large-scale properties of chromosomes contained within the nuclei of human cells in interphase. We show that polymer models for chromosomes that incorporate inhomogeneous activity reproduce many general, yet little understood, features of large-scale nuclear architecture. These include: (i) the spatial separation of gene-rich, low-density euchromatin, predominantly found towards the centre of the nucleus, vis a vis. gene-poor, denser heterochromatin, typically enriched in proximity to the nuclear periphery, (ii) the differential positioning of individual gene-rich and gene-poor chromosomes, (iii) the formation of chromosome territories, as well as (iv), the weak size-dependence of the positions of individual chromosome centres-of-mass relative to the nuclear centre that is seen in some cell types. Such structuring is induced purely by the combination of activity and confinement and is absent in thermal equilibrium. We systematically explore active matter models for chromosomes, discussing how our model can be generalized to study variations in chromosome positioning across different cell types. The approach and model we outline here represent a preliminary attempt towards a quantitative, first-principles description of the large-scale architecture of the cell nucleus.

  18. [Inflammasome: activation mechanisms].

    Science.gov (United States)

    Suárez, Raibel; Buelvas, Neudo

    2015-03-01

    Inflammation is a rapid biologic response of the immune system in vascular tissues, directed to eliminate stimuli capable of causing damage and begin the process of repair. The macromolecular complexes known as "inflammasomes" are formed by a receptor, either NOD (NLR) or ALR, the receptor absent in melanoma 2 (AIM2). In addition, the inflammasome is formed by the speck-like protein associated to apoptosis (ASC) and procaspase-1, that may be activated by variations in the ionic and intracellular and extracellular ATP concentrations; and the loss of stabilization of the fagolisosomme by internalization of insoluble crystals and redox mechanisms. As a result, there is activation of the molecular platform and the processing of inflammatory prointerleukins to their active forms. There are two modalities of activation of the inflammasome: canonical and non-canonical, both capable of generating effector responses. Recent data associate NLRP 3, IL-1β and IL-18 in the pathogenesis of a variety of diseases, including atherosclerosis, type II diabetes, hyperhomocysteinemia, gout, malaria and hypertension. The inflammasome cascade is emerging as a new chemotherapeutic target in these diseases. In this review we shall discuss the mechanisms of activation and regulation of the inflammasome that stimulate, modulate and resolve inflammation.

  19. Regulating prefrontal cortex activation

    DEFF Research Database (Denmark)

    Aznar, Susana; Klein, Anders Bue

    2013-01-01

    of emotion-based actions, such as addiction and other impulse-related behaviors. In this review, we give an overview of the 5-HT2A receptor distribution (neuronal, intracellular, and anatomical) along with its functional and physiological effect on PFC activation, and how that relates to more recent findings......The prefrontal cortex (PFC) is involved in mediating important higher-order cognitive processes such as decision making, prompting thereby our actions. At the same time, PFC activation is strongly influenced by emotional reactions through its functional interaction with the amygdala...... is highly expressed in the prefrontal cortex areas, playing an important role in modulating cortical activity and neural oscillations (brain waves). This makes it an interesting potential pharmacological target for the treatment of neuropsychiatric modes characterized by lack of inhibitory control...

  20. IHY activities in Brazil

    Science.gov (United States)

    Dal Lago, Alisson

    The International Heliophysical Year is a program of international scientific colaboration planned to be held in the period from 2007-2009. Many brazilian institutions have shown interest in participating in the IHY activities. All of them provided information about their instrumental facilities and contact person. A list of institutions and their information is shown in the Latin-American IHY webpage (http://www.alage.org/IHYLA/ihyla.html), hosted by the Latin American Association on Space Geophysics - ALAGE. IHY Brazilian activities are being conducted in close colaboration with Latin-American Institutions. Five Coordinated Investigation programs (CIPs) have been proposed by scientists from brazilian institutions. Recentely, in February 2008, there has been the Latin American IHY School in Sao Paulo (Brazil), with the participation of 80 students from Brazil, Argentina, Peru, Mexico and Cuba. In this work, a report on the brazilian activities will be presented.

  1. Lesion activity assessment

    DEFF Research Database (Denmark)

    Ekstrand, K R; Zero, D T; Martignon, S;

    2009-01-01

    . The literature suggests that there is a fair agreement between visual/tactile external scripts of caries and the severity/depth of the lesion. The reproducibility of the different systems is, in general, substantial. No single clinical predictor is able to reliably assess activity. However, a combination......This chapter focusses on the probability of a caries lesion detected during a clinical examination being active (progressing) or arrested. Visual and tactile methods to assess primary coronal lesions and primary root lesions are considered. The evidence level is rated as low (R...... in response to cariogenic plaque as well as lesion arrest. Based on this understanding, different clinical scoring systems have been developed to assess the severity/depth and activity of lesions. A recent system has been devised by the International Caries Detection and Assessment System Committee...

  2. Active Elbow Orthosis

    Directory of Open Access Journals (Sweden)

    Tomas Ripel

    2014-09-01

    Full Text Available This paper presents a novel approach to the design of a motorized rehabilitation device – active elbow orthosis (AEO – inspired by the principles of robotic exoskeletons. The device is currently designed for the elbow joint, but can be easily modified for other joints as well. AEO determines the motion activity of the patient using a strain gauge and utilizes this measurement to control the actuator that drives the forearm part of the orthosis. Patient activity level is related to a free arm measurement obtained via a calibration procedure prior to the exercise. A high-level control module offers several types of exercises mimicking the physiotherapist. The device was successfully verified by tests on a number of patients, resulting in extended range of elbow-joint motion.

  3. Adapted Active Appearance Models

    Directory of Open Access Journals (Sweden)

    Renaud Séguier

    2009-01-01

    Full Text Available Active Appearance Models (AAMs are able to align efficiently known faces under duress, when face pose and illumination are controlled. We propose Adapted Active Appearance Models to align unknown faces in unknown poses and illuminations. Our proposal is based on the one hand on a specific transformation of the active model texture in an oriented map, which changes the AAM normalization process; on the other hand on the research made in a set of different precomputed models related to the most adapted AAM for an unknown face. Tests on public and private databases show the interest of our approach. It becomes possible to align unknown faces in real-time situations, in which light and pose are not controlled.

  4. Correlates of physical activity

    DEFF Research Database (Denmark)

    Bauman, Adrian E; Reis, Rodrigo S; Sallis, James F

    2012-01-01

    that age, sex, health status, self-efficacy, and motivation are associated with physical activity. Ecological models take a broad view of health behaviour causation, with the social and physical environment included as contributors to physical inactivity, particularly those outside the health sector......Physical inactivity is an important contributor to non-communicable diseases in countries of high income, and increasingly so in those of low and middle income. Understanding why people are physically active or inactive contributes to evidence-based planning of public health interventions, because......, such as urban planning, transportation systems, and parks and trails. New areas of determinants research have identified genetic factors contributing to the propensity to be physically active, and evolutionary factors and obesity that might predispose to inactivity, and have explored the longitudinal tracking...

  5. General human activity patterns

    CERN Document Server

    Mollgaard, Anders; Mathiesen, Joachim

    2016-01-01

    We investigate the dynamics and interplay between human communication, movement, and social proximity by analyzing data collected from smartphones distributed among 638 individuals. The main question we consider is: to what extent do individuals act according to patterns shared across an entire population? Based on statistics of the entire population, we successfully predict 71\\% of the activity and 85\\% of the inactivity involved in communication, movement, and social proximity. We find that individual level statistics only result in marginally better predictions, indicating a high degree of shared activity patterns across the population. Finally, we predict short-term activity patterns using a generalized linear model, which suggests that a simple linear description might be sufficient to explain a wide range of actions, whether they be of social or of physical character.

  6. SCOR announces new activities

    Science.gov (United States)

    Urban, Edward R., Jr.

    Roger Revelle had many good ideas during his long and productive career. One of them came to fruition in 1957 in the form of the Scientific Committee on Oceanic Research (SCOR), which the International Council for Science created as its first interdisciplinary body, to promote international activities in oceanography. Revelle served as SCOR's first president from 1957 to 1960. SCOR offers opportunities for scientists from different countries to cooperate in planning and executing international programs in ocean sciences. Over its 44 years in existence, SCOR has sponsored 120 working groups and has actively participated in many of the major international oceanographic projects. Thirty-six nations presently participate as SCOR members.

  7. Actively coupled optical waveguides

    OpenAIRE

    Alexeeva, N. V.; Barashenkov, I. V.; Rayanov, K.; Flach, S.

    2013-01-01

    We consider light propagation through a pair of nonlinear optical waveguides with absorption, placed in a medium with power gain. The active medium boosts the in-phase component of the overlapping evanescent fields of the guides, while the nonlinearity of the guides couples it to the damped out-of-phase component creating a feedback loop. As a result, the structure exhibits stable stationary and oscillatory regimes in a wide range of gain-loss ratios. We show that the pair of actively-coupled...

  8. Actively coupled optical waveguides

    Science.gov (United States)

    Alexeeva, N. V.; Barashenkov, I. V.; Rayanov, K.; Flach, S.

    2014-01-01

    We consider light propagation through a pair of nonlinear optical waveguides with absorption, placed in a medium with power gain. The active medium boosts the in-phase component of the overlapping evanescent fields of the guides, while the nonlinearity of the guides couples it to the damped out-of-phase component creating a feedback loop. As a result, the structure exhibits stable stationary and oscillatory regimes in a wide range of gain-loss ratios. We show that the pair of actively coupled (AC) waveguides can act as a stationary or integrate-and-fire comparator sensitive to tiny differences in their input powers.

  9. Antibacterial Activity of Grepafloxacin

    Directory of Open Access Journals (Sweden)

    B Wiedemann

    1998-01-01

    Full Text Available Grepafloxin has an extremely broad spectrum of activity. Its activity against Gram-positive bacteria exceeds that of currently available quinolones. Grepafloxacin-resistant mutants seem to occur less frequently than ciprofloxacin - or ofloxacin-resistant mutants, and the increase in minimum inhibitory concentration (MIC against the former mutants is less than that of the latter. This applies only to the relative differences (in dilution steps; the absolute values are similar. Grepafloxacin kills Gram-positive bacteria at concentrations little above the MIC. Its pharmacodynamic profile against pneumococci is promising, favouring use of this drug for respiratory tract infections.

  10. Measuring children's physical activity

    DEFF Research Database (Denmark)

    Schneller, Mikkel Bo; Bentsen, Peter; Nielsen, Glen

    2017-01-01

    INTRODUCTION: Accelerometer-based physical activity monitoring has become the method of choice in many large-scale physical activity (PA) studies. However, there is an ongoing debate regarding the placement of the device, the determination of device wear time, and how to solve a lack of participant...... on the thigh (n=903) and one on the lower back (n= 856), for up to ten consecutive days. Participants were instructed not to reattach an accelerometer should it fall off. Simple and multiple linear regression were used to determine associations between accelerometer wear time and age, sex, BMI percentiles...

  11. Antifungal activity of diethyldithiocarbamate.

    Science.gov (United States)

    Allerberger, F; Reisinger, E C; Söldner, B; Dierich, M P

    1989-10-01

    Sodium diethyldithiocarbamate (DTC) was evaluated for its ability to combat four different species of fungi in vitro. Using a microtiter-broth-dilution method we were able to demonstrate an antifungal activity against Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus and Mucor mucedo in doses achievable by intravenous administration in man.

  12. Atherosclerosis and Physical Activity

    OpenAIRE

    Al-Mamari, Ali

    2009-01-01

    Atherosclerosis and coronary heart disease have been considered as major health problem worldwide. Abnormalities in lipids and lipoprotein metabolism and impairment of endothelial function have been implicated as the main contributing factors in atherosclerosis and its progression. Physical activity has been recognized as a preventive measure for atherosclerosis.

  13. Bonus Activity Book.

    Science.gov (United States)

    Learning, 1993

    1993-01-01

    Elementary level activity book presents suggestions for teaching students about endangered and threatened species worldwide. Students learn about what is causing the rapid extinction rate and what needs to be done. They also discover the value of rainforests and why conservationists are fighting to save them. (SM)

  14. Asteroseismic stellar activity relations

    CERN Document Server

    Bonanno, A; Karoff, C

    2014-01-01

    In asteroseismology an important diagnostic of the evolutionary status of a star is the small frequency separation which is sensitive to the gradient of the mean molecular weight in the stellar interior. It is thus interesting to discuss the classical age-activity relations in terms of this quantity. Moreover, as the photospheric magnetic field tends to suppress the amplitudes of acoustic oscillations, it is important to quantify the importance of this effect by considering various activity indicators. We propose a new class of age-activity relations that connects the Mt. Wilson $S$ index and the average scatter in the light curve with the small frequency separation and the amplitude of the p-mode oscillations. We used a Bayesian inference to compute the posterior probability of various empirical laws for a sample of 19 solar-like active stars observed by the Kepler telescope. We demonstrate the presence of a clear correlation between the Mt. Wilson $S$ index and the relative age of the stars as indicated by ...

  15. [Biological activity of Spirulina].

    Science.gov (United States)

    Blinkova, L P; Gorobets, O B; Baturo, A P

    2001-01-01

    In this review information of Spirulina platensis (SP), a blue-green alga (photosynthesizing cyanobacterium) having diverse biological activity is presented. Due to high content of highly valuable proteins, indispensable amino acids, vitamins, beta-carotene and other pigments, mineral substances, indispensable fatty acids and polysaccharides, PS has been found suitable for use as bioactive additive. SP produces an immunostimulating effect by enhancing the resistance of humans, mammals, chickens and fish to infections, the capacity of influencing hemopoiesis, stimulating the production of antibodies and cytokines. Under the influence of SP macrophages, T and B cells are activated. SP sulfolipids have proved to be effective against HIV. Preparations obtained from SP biomass have also been found active against herpesvirus, cytomegalovirus, influenza virus, etc. SP extracts are capable in inhibiting cancerogenesis. SP preparations are regarded as functional products contributing to the preservation of the resident intestinal microflora, especially lactic acid bacilli and bifidobacteria, and to a decrease in the level of Candida albicans. The biological activity of SP with respect to microorganisms holds good promise for using these microalgae as components of culture media.

  16. Activation force splines

    DEFF Research Database (Denmark)

    Engell-Nørregård, Morten Pol; Erleben, Kenny

    dimensional 2D/3D deformable model. Our activation splines are easy to set up and can be used for physics based animation of deformable models such as snake motion and locomotion of characters. Our approach generalises easily to both 2D and 3D simulations and is applicable in physics based games or animations...

  17. Mechanism of charity activity

    Directory of Open Access Journals (Sweden)

    Roman B. Golovkin

    2015-12-01

    Full Text Available Objective to establish the essential properties of the mechanism of charitable activities and to formulate the concept of quotmechanism of charitable activityquot. Methods the objective of the study is achieved using the complex of methods which are based on the interaction of dialectical and metaphysical analysis the epistemological properties of which allowed to reveal various aspects of the charitable activities mechanism functioning taking into account the principles of comprehensiveness complexity specificity and objectivity of the research. Results the rules are stated of using the term quotmechanismquot to characterize actions of state and law the essence of the charity mechanism is defined the definition of quotthe mechanism of charitable activity quot is formulated. Scientific novelty for the first time at theoretical level in legal science the definition of quotthe mechanism of charitable activityquot is formulated and its essential properties are set. Practical significance the research will contribute to improving the legal regulation in the field of philanthropy as well as to improving the efficiency and quality of charitable activity in the Russian Federation. nbsp

  18. Active surveillance: Oncologic outcome

    NARCIS (Netherlands)

    L.D.F. Venderbos (Lionne); L.P. Bokhorst (Leonard); C.H. Bangma (Chris); M.J. Roobol-Bouts (Monique)

    2013-01-01

    textabstractPURPOSE OF REVIEW: To give insight into recent literature (during the past 12-18 months) reporting on oncologic outcomes of men on active surveillance. RECENT FINDINGS: From recent published trials comparing radical prostatectomy vs. watchful waiting, we learn that radical treatment only

  19. Low activity aluminum blanket

    Energy Technology Data Exchange (ETDEWEB)

    Benenati, R.; Tichler, P.; Powell, J.R.

    1976-03-01

    The basic design of the breeding blanket consists of cylindrical aluminium canisters filled with a ceramic bed of moderating, shielding, and breeding materials all suitably cooled. A technical analysis of the blanket for an EPR design is given. Activation studies are presented. The effect of pulsed magnetic fields on module structure is investigated. (MOW)

  20. Seismology of active stars

    NARCIS (Netherlands)

    Hekker, S.; García, R.A.

    2012-01-01

    In this review we will discuss the current standing and open questions of seismology in active stars. With the longer photometric time series data that are, and will become, available from space-missions such as Kepler we foresee significant progress in our understanding of stellar internal structur

  1. 'Active' Thin Sections

    NARCIS (Netherlands)

    De Rooij, M.R.; Bijen, J.M.J.M.

    1999-01-01

    Optical microscopy using thin sections has become more and more important over the last decade to study concrete. Unfortunately, this technique is not capable of studying actually hydrating cement paste. At Delft University of Technology a new technique has been developed using 'active' thin section

  2. Sexual activity and aging.

    Science.gov (United States)

    Ni Lochlainn, Mary; Kenny, Rose Anne

    2013-08-01

    Sexuality is an important component of emotional and physical intimacy that men and women experience throughout their lives. Research suggesting that a high proportion of men and women remain sexually active well into later life refutes the prevailing myth that aging and sexual dysfunction are inexorably linked. Age-related physiological changes do not render a meaningful sexual relationship impossible or even necessarily difficult. Many of these physiological changes are modifiable. There are various therapeutic options available to patients to achieve maximum sexual capacity in old age. This article reviews the prevalence of sexual activity among older adults, the problems these adults encounter with sexual activity, and the role of the health care professional in addressing these problems. The physiological sex-related changes that occur as part of the normal aging process in men and women are reviewed, as well as the effect of age-related physical and psychological illness on sexual function. The attitudes and perceptions of the media and general public toward sexual activity and aging are summarized. An understanding of the sexual changes that accompany the aging process may help general practitioners and other doctors to give practical and useful advice on sexuality as well as refute the misconception that aging equates to celibacy. A thorough awareness of this aspect of older people's quality of life can raise meaningful expectations for aging patients.

  3. Elusive active galactic nuclei

    NARCIS (Netherlands)

    Maiolino, R; Comastri, A; Gilli, R; Nagar, NM; Bianchi, S; Boker, T; Colbert, E; Krabbe, A; Marconi, A; Matt, G; Salvati, M

    2003-01-01

    A fraction of active galactic nuclei do not show the classical Seyfert-type signatures in their optical spectra, i.e. they are optically 'elusive'. X-ray observations are an optimal tool to identify this class of objects. We combine new Chandra observations with archival X-ray data in order to obtai

  4. Activated Sludge Rheology

    DEFF Research Database (Denmark)

    Ratkovich, Nicolas Rios; Horn, Willi; Helmus, Frank

    2013-01-01

    Rheological behaviour is an important fluid property that severely impacts its flow behaviour and many aspects related to this. In the case of activated sludge, the apparent viscosity has an influence on e.g. pumping, hydrodynamics, mass transfer rates, sludge-water separation (settling and filtr...

  5. Regional Activities Division. Papers.

    Science.gov (United States)

    International Federation of Library Associations, The Hague (Netherlands).

    Papers on library network activities in Canada, the Third World, Japan, Malaysia, Brazil, and Sweden which were presented at the 1982 International Federation of Library Associations (IFLA) conference include: (1) "Canada: A Voluntary and Flexible Network," a review by Guy Sylvestre of the political, social, and economic structures affecting…

  6. Active Math Learning

    DEFF Research Database (Denmark)

    The presentation is concerned with general course planning philosophy and a specific case study (boomerang flight geometro-dynamics) for active learning of mathematics via computer assisted and hands-on unfolding of first principles - in this case the understanding of rotations and Eulers equatio...

  7. Marketing coprovided activities.

    Science.gov (United States)

    Dickerson, Pamela S

    2014-05-01

    Coproviding is a wonderful way for two or more organizations to work together to provide continuing nursing education. To be transparent to the learners, marketing materials identify the parties involved and prominently note the name of the organization accountable for developing the activity and awarding the contact hours.

  8. An electrochemical active valve

    NARCIS (Netherlands)

    Neagu, C.R.; Gardeniers, J.G.E.; Elwenspoek, M.; Kelly, J.J.

    1997-01-01

    A novel electrochemical microactuator was developed, which operates as an active valve. The microactuator consists of an electrochemical cell and a membrane that deflects because of the pressure of oxygen gas generated by electrolysis. Relatively large pressures (up to tens of bars) can be reached w

  9. Access and Fishing Activities

    DEFF Research Database (Denmark)

    Høst, Jeppe Engset

    2015-01-01

    In this chapter, I look at the implications of transferable quotas on the organization of production; that is, how fishing activities are structured around access to the individual and transferable quotas and how, in turn, the quotas structure the production. Therefore, this chapter will give...

  10. Grooming. Learning Activity Package.

    Science.gov (United States)

    Stark, Pamela

    This learning activity package on grooming for health workers is one of a series of 12 titles developed for use in health occupations education programs. Materials in the package include objectives, a list of materials needed, information sheets, reviews (self evaluations) of portions of the content, and answers to reviews. These topics are…

  11. CMMs Development Activities

    Institute of Scientific and Technical Information of China (English)

    HU Jun; HU Yefa; HUANG Anyi

    2006-01-01

    The coordinate measuring machine (CMM) has been an important role in the digital manufacturing. This paper reviews CMM early stage development history and current activities. The authors provide some ideas about the areas that academic research can help to the CMMs development.

  12. Shark Tagging Activities.

    Science.gov (United States)

    Current: The Journal of Marine Education, 1998

    1998-01-01

    In this group activity, children learn about the purpose of tagging and how scientists tag a shark. Using a cut-out of a shark, students identify, measure, record data, read coordinates, and tag a shark. Includes introductory information about the purpose of tagging and the procedure, a data sheet showing original tagging data from Tampa Bay, and…

  13. Antimalarial activity of cedronin.

    Science.gov (United States)

    Moretti, C; Deharo, E; Sauvain, M; Jardel, C; David, P T; Gasquet, M

    1994-06-01

    Cedronin was isolated from Simaba cedron Planchon (Simaroubaceae), a species popularly believed in South America to have antimalarial properties. It was examined for in vitro and in vivo antimalarial activities and for cytotoxicity against KB cells. Experimental results showed that cedronin was active against chloroquine-sensitive and resistant strain, with an IC50 of 0.25 micrograms/ml (0.65 mumol/ml). It was also found to be active in vivo against Plasmodium vinkei with an IC50 of 1.8 mg/kg (4.7 nM/kg) in the classic 4-day test. Cedronin belongs to the small group of quassinoids with a C19 basic skeleton and shows a rather low cytotoxicity against KB cells (IC50 = 4 micrograms/ml, 10.4 microM) as compared with C20 biologically active quassinoids; however its toxic/therapeutic ratio (10/1.8) remains lower than chloroquine (10/0.5).

  14. Interdisciplinary Astronomy Activities

    Science.gov (United States)

    Nerantzis, Nikolaos; Mitrouda, Aikaterini; Reizopoulou, Ioanna; Sidiropoulou, Eirini; Hatzidimitriou, Antonios

    2016-04-01

    On November 9th, 2015, three didactical hours were dedicated to Interdisciplinary Astronomy Activities (http://wp.me/p6Hte2-1I). Our students and their teachers formed three groups and in rotation, were engaged with the following activities: (a) viewing unique images of the Cosmos in the mobile planetarium STARLAB (http://www.planitario.gr/tholos-starlab-classic-standard.html), (b) watching the following videos: Journey to the end of the universe (https://youtu.be/Ufl_Nwbl8xs), Rosetta update (https://youtu.be/nQ9ivd7wv30), The Solar System (https://youtu.be/d66dsagrTa0), Ambition the film (https://youtu.be/H08tGjXNHO4) in the school's library. Students and teachers were informed about our solar system, the Rosetta mission, the universe, etc. and (c) tactile activities such as Meet our home and Meet our neighbors (http://astroedu.iau.org, http://nuclio.org/astroneighbours/resources) and the creation of planets' 3D models (Geology-Geography A' Class Student's book, pg.15). With the activities above we had the pleasure to join the Cosmic Light Edu Kit / International Year of Light 2015 program. After our Interdisciplinary Astronomy Activities, we did a "small" research: our students had to fill an evaluation about their educational gains and the results can be found here http://wp.me/p6Hte2-2q. Moreover, we discussed about Big Ideas of Science (http://wp.me/p3oRiZ-dm) and through the "big" impact of the Rosetta mission & the infinity of our universe, we print posters with relevant topics and place them to the classrooms. We thank Rosa Doran (Nuclio - President of the Executive Council) for her continuous assistance and support on innovative science teaching proposals. She is an inspiration.

  15. Activities. Inductive and Deductive Reasoning.

    Science.gov (United States)

    O'Daffer, Phares G.; And Others

    1990-01-01

    Provided are the activity sheets for students and the teaching guide for this middle school geometry activity. Materials, prerequisites, objectives, and procedures are listed. Extension activities are suggested. An answer key is included. (CW)

  16. Is Enhanced Physical Activity Possible Using Active Videogames?

    OpenAIRE

    Baranowski, Tom; Baranowski, Janice; O'Connor, Teresia; Lu, Amy Shirong; Thompson, Debbe

    2012-01-01

    Our research indicated that 10–12-year-old children receiving two active Wii™ (Nintendo®; Nintendo of America, Inc., Redmond, WA) console videogames were no more physically active than children receiving two inactive videogames. Research is needed on how active videogames may increase physical activity.

  17. Is Enhanced Physical Activity Possible Using Active Videogames?

    Science.gov (United States)

    Baranowski, Tom; Baranowski, Janice; O'Connor, Teresia; Lu, Amy Shirong; Thompson, Debbe

    2012-06-01

    Our research indicated that 10-12-year-old children receiving two active Wii(™) (Nintendo(®); Nintendo of America, Inc., Redmond, WA) console videogames were no more physically active than children receiving two inactive videogames. Research is needed on how active videogames may increase physical activity.

  18. Integration of Active Video Games in Extracurricular Activity at Schools

    Science.gov (United States)

    Lee, Jung Eun; Huang, Charles; Pope, Zachary; Gao, Zan

    2015-01-01

    Active video games require players to be physically active. Dance Dance Revolution (DDR) is an interactive dancing game that requires fast-foot movement coordinated with energetic music and visuals. The Wii and Xbox Kinect games have also become good active video games for the promotion of physical activity participation. These games are much more…

  19. Active microchannel heat exchanger

    Science.gov (United States)

    Tonkovich, Anna Lee Y [Pasco, WA; Roberts, Gary L [West Richland, WA; Call, Charles J [Pasco, WA; Wegeng, Robert S [Richland, WA; Wang, Yong [Richland, WA

    2001-01-01

    The present invention is an active microchannel heat exchanger with an active heat source and with microchannel architecture. The microchannel heat exchanger has (a) an exothermic reaction chamber; (b) an exhaust chamber; and (c) a heat exchanger chamber in thermal contact with the exhaust chamber, wherein (d) heat from the exothermic reaction chamber is convected by an exothermic reaction exhaust through the exhaust chamber and by conduction through a containment wall to the working fluid in the heat exchanger chamber thereby raising a temperature of the working fluid. The invention is particularly useful as a liquid fuel vaporizer and/or a steam generator for fuel cell power systems, and as a heat source for sustaining endothermic chemical reactions and initiating exothermic reactions.

  20. Nematicidal activity of terpenoids.

    Science.gov (United States)

    Abdel-Rahman, Fawzia H; Alaniz, Nina M; Saleh, Mahmoud A

    2013-01-01

    Thirty four phytoterpenoids were evaluated for their nematicidal effect using the model nematode Caenorhabditis elegans. Nematicidal activities of the tested compounds at concentrations of 50 μg/mL showed wide variation in their effects ranging from no effect, weak, moderate and strong effects. Terpenoids exerting 50% or higher mortality at 50 μg/mL were further tested at five different concentrations to calculate the concentration that will kill 50% of the nematode population (LC(50)). Among the most effective terpenoids were carvacrol, thymol, nerolidol, α-terpinene, geraniol, citronellol, farnesol, limonene, pseudoionone and eugenol in a descending order. These compounds exhibited a dose-dependent effect. The results suggest that the selected monoterpenoids and essential oils with a high concentration of these compounds mayprovide potential natural nematicides and merit further study as botanical nematicides for the control of both plant and animal parasitic nematodes. In general, oxygenated terpenoids and phenolic terpenoids exhibited higher nematicidal activity than hydrocarbons terpenoids.

  1. Apheresis activity in Venezuela.

    Science.gov (United States)

    Saltiel, Christiane

    2005-07-01

    Interest for apheresis activity has been growing in Venezuela. In 1976 there were only a few devices; in 2003, 80 apheresis machines performed 27,675 donor apheresis procedures and 547 therapeutic procedures countrywide. We report the activity at the Metropolitan Blood Bank (the largest one of the country) in the period 1999-2003: 597 therapeutic procedures were performed in 171 patients, during 212 crisis episodes. The average age was 38 +/- 16 years, 65% male and 35% female. Most of the therapeutic procedures were therapeutic plasma exchange for hematology diseases (mainly thrombotic thrombocitopenic purpura and hemophilia inhibitors), including 184 therapeutic procedures with the Autopheresis-C (Baxter Healthcare Corp., Deerfield, IL). Most common adverse effects (3.9%) were hypotension and allergic reactions to the plasma.

  2. Active optical clock

    Institute of Scientific and Technical Information of China (English)

    CHEN JingBiao

    2009-01-01

    This article presents the principles and techniques of active optical clock, a special laser combining the laser physics of one-atom laser, bad-cavity gas laser, super-cavity stabilized laser and optical atomic clock together. As a simple example, an active optical clock based on thermal strontium atomic beam shows a quantum-limited linewidth of 0.51 Hz, which is insensitive to laser cavity-length noise, and may surpass the recorded narrowest 6.7 Hz of Hg ion optical clock and 1.5 Hz of very recent optical lattice clock. The estimated 0.1 Hz one-second instability and 0.27 Hz uncertainty are limited only by the rela-tivistic Doppler effect, and can be improved by cold atoms.

  3. LANSCE Activity Report

    Energy Technology Data Exchange (ETDEWEB)

    Amy Robinson; Audrey Archuleta; Barbara Maes; Dan Strottman; Earl Hoffman; Garth Tietjen; Gene Farnum; Geoff Greene; Joyce Roberts; Ken Johnson; Paul Lewis; Roger Pynn; Stan Schriber; Steve Sterbenz; Steve Wender; Sue Harper

    1999-02-01

    The Los Alamos Neutron Science Center Activity Report describes scientific and technological progress and achievements in LANSCE Division during the period of 1995 to 1998. This report includes a message from the Division Director, an overview of LANSCE, sponsor overviews, research highlights, advanced projects and facility upgrades achievements, experimental and user program accomplishments, news and events, and a list of publications. The research highlights cover the areas of condensed-matter science and engineering, accelerator science, nuclear science, and radiography. This report also contains a compact disk that includes an overview, the Activity Report itself, LANSCE operations progress reports for 1996 and 1997, experiment reports from LANSCE users, as well as a search capability.

  4. Stellar Chromospheric Activity

    Directory of Open Access Journals (Sweden)

    Hall Jeffrey C.

    2008-03-01

    Full Text Available The Sun, stars similar to it, and many rather dissimilar to it, have chromospheres, regions classically viewed as lying above the brilliant photosphere and characterized by a positive temperature gradient and a marked departure from radiative equilibrium. Stellar chromospheres exhibit a wide range of phenomena collectively called activity, stemming largely from the time evolution of their magnetic fields and the mass flux and transfer of radiation through the complex magnetic topology and the increasingly optically thin plasma of the outer stellar atmosphere. In this review, I will (1 outline the development of our understanding of chromospheric structure from 1960 to the present, (2 discuss the major observational programs and theoretical lines of inquiry, (3 review the origin and nature of both solar and stellar chromospheric activity and its relationship to, and effect on, stellar parameters including total energy output, and (4 summarize the outstanding problems today.

  5. Techniques for active passivation

    Energy Technology Data Exchange (ETDEWEB)

    Roscioli, Joseph R.; Herndon, Scott C.; Nelson, Jr., David D.

    2016-12-20

    In one embodiment, active (continuous or intermittent) passivation may be employed to prevent interaction of sticky molecules with interfaces inside of an instrument (e.g., an infrared absorption spectrometer) and thereby improve response time. A passivation species may be continuously or intermittently applied to an inlet of the instrument while a sample gas stream is being applied. The passivation species may have a highly polar functional group that strongly binds to either water or polar groups of the interfaces, and once bound presents a non-polar group to the gas phase in order to prevent further binding of polar molecules. The instrument may be actively used to detect the sticky molecules while the passivation species is being applied.

  6. Cisplatin triggers platelet activation.

    Science.gov (United States)

    Togna, G I; Togna, A R; Franconi, M; Caprino, L

    2000-09-01

    Clinical observations suggest that anticancer drugs could contribute to the thrombotic complications of malignancy in treated patients. Thrombotic microangiopathy, myocardial infarction, and cerebrovascular thrombotic events have been reported for cisplatin, a drug widely used in the treatment of many solid tumours. The aim of this study is to explore in vitro cisplatin effect on human platelet reactivity in order to define the potentially active role of platelets in the pathogenesis of cisplatin-induced thrombotic complications. Our results demonstrate that cisplatin increases human platelet reactivity (onset of platelet aggregation wave and thromboxane production) to non-aggregating concentrations of the agonists involving arachidonic acid metabolism. Direct or indirect activation of platelet phospholipase A(2) appears to be implicated. This finding contributes to a better understanding of the pathogenesis of thrombotic complications occurring during cisplatin-based chemotherapy.

  7. The Active Asteroids

    CERN Document Server

    Jewitt, Dave

    2011-01-01

    Some asteroids eject dust, unexpectedly producing transient, comet-like comae and tails. First ascribed to the sublimation of near-surface water ice, mass losing asteroids (also called "main-belt comets") can in fact be driven by a surprising diversity of mechanisms. In this paper, we consider eleven dynamical asteroids losing mass, in nine of which the ejected material is spatially resolved. We address mechanisms for producing mass loss including rotational instability, impact ejection, electrostatic repulsion, radiation pressure sweeping, dehydration stresses and thermal fracture, in addition to the sublimation of ice. In two objects (133P and 238P) the repetitive nature of the observed activity leaves ice sublimation as the only reasonable explanation while, in a third ((596) Scheila), a recent impact is the cause. Another impact may account for activity in P/2010 A2 but this tiny object can also be explained as having shed mass after reaching rotational instability. Mass loss from (3200) Phaethon is proba...

  8. Myofilament length dependent activation

    Energy Technology Data Exchange (ETDEWEB)

    de Tombe, Pieter P.; Mateja, Ryan D.; Tachampa, Kittipong; Mou, Younss Ait; Farman, Gerrie P.; Irving, Thomas C. (IIT); (Loyola)

    2010-05-25

    The Frank-Starling law of the heart describes the interrelationship between end-diastolic volume and cardiac ejection volume, a regulatory system that operates on a beat-to-beat basis. The main cellular mechanism that underlies this phenomenon is an increase in the responsiveness of cardiac myofilaments to activating Ca{sup 2+} ions at a longer sarcomere length, commonly referred to as myofilament length-dependent activation. This review focuses on what molecular mechanisms may underlie myofilament length dependency. Specifically, the roles of inter-filament spacing, thick and thin filament based regulation, as well as sarcomeric regulatory proteins are discussed. Although the 'Frank-Starling law of the heart' constitutes a fundamental cardiac property that has been appreciated for well over a century, it is still not known in muscle how the contractile apparatus transduces the information concerning sarcomere length to modulate ventricular pressure development.

  9. L'analyse de l'expertise du point de vue de l'ergonomie cognitive

    CERN Document Server

    Visser, Willemien

    2006-01-01

    This paper presents a review of methods for collecting and analysing data on complex activities. Starting with methods developed for design, we examine the possibility to transpose them to other complex activities, especially activities referring to sensorial expertise. ----- R\\'esum\\'e Ce texte pr\\'esente une revue de m\\'ethodes pour recueillir et analyser des donn\\'ees sur des actvit\\'es complexes. A partir de m\\'ethodes d\\'evelopp\\'ees pour des actvit\\'es de conception, nous examinons la possibilit\\'e de les transposer \\`a d'autres actvit\\'es complexes, notamment des actvit\\'es faisant \\`a appel \\`a des expertises sensorielles.

  10. Sesterterpenoids with Anticancer Activity.

    Science.gov (United States)

    Evidente, Antonio; Kornienko, Alexander; Lefranc, Florence; Cimmino, Alessio; Dasari, Ramesh; Evidente, Marco; Mathieu, Véronique; Kiss, Robert

    2015-01-01

    Terpenes have received a great deal of attention in the scientific literature due to complex, synthetically challenging structures and diverse biological activities associated with this class of natural products. Based on the number of C5 isoprene units they are generated from, terpenes are classified as hemi- (C5), mono- (C10), sesqui- (C15), di- (C20), sester- (C25), tri (C30), and tetraterpenes (C40). Among these, sesterterpenes and their derivatives known as sesterterpenoids, are ubiquitous secondary metabolites in fungi, marine organisms, and plants. Their structural diversity encompasses carbotricyclic ophiobolanes, polycyclic anthracenones, polycyclic furan-2-ones, polycyclic hydroquinones, among many other carbon skeletons. Furthermore, many of them possess promising biological activities including cytotoxicity and the associated potential as anticancer agents. This review discusses the natural sources that produce sesterterpenoids, provides sesterterpenoid names and their chemical structures, biological properties with the focus on anticancer activities and literature references associated with these metabolites. A critical summary of the potential of various sesterterpenoids as anticancer agents concludes the review.

  11. Human neutrophil antimicrobial activity.

    Science.gov (United States)

    Thomas, E L; Lehrer, R I; Rest, R F

    1988-01-01

    Polymorphonuclear neutrophilic leukocytes (PMNs) take up opsonized microorganisms into phagosomes that fuse with secretory granules in the PMN cytoplasm to form phagolysosomes. Killing and digestion of microorganisms take place within phagolysosomes. Antimicrobial activities in phagolysosomes are divided into two classes. Oxygen (O2)-dependent mechanisms are expressed when PMNs undergo the "respiratory burst." An NADPH oxidase in the phagolysosome membrane is activated and reduces O2 to superoxide (O2-). O2 reduction is the first step in a series of reactions that produce toxic oxidants. For example, .O2- dismutases to hydrogen peroxide (H2O2), and the azurophil granule enzyme myeloperoxidase catalyzes the oxidation of Cl- by H2O2 to yield hypochlorous acid (HOCl). The reaction of HOCl with ammonia and amines modulates the toxicity of this oxidant. O2-independent antimicrobial mechanisms include the activities of lysosomal proteases, other hydrolytic enzymes, and proteins and peptides that bind to microorganisms and disrupt essential processes or structural components. For example, the bactericidal/permeability-increasing protein, cathepsin G, and the defensins are released into phagolysosomes from the azurophil granules. Proposed mechanisms of action of neutrophil antimicrobial agents, their range of microbial targets, and their possible interactions within phagolysosomes are discussed.

  12. Amphoteric surface active agents

    Directory of Open Access Journals (Sweden)

    Eissa, A.M. F.

    1995-10-01

    Full Text Available 2-[trimethyl ammonium, triethyl ammonium, pyridinium and 2-amino pyridinium] alkanoates, four series of surface active agents containing carbon chain C12, C14, C16 and C18carbon atoms, were prepared. Their structures were characterized by microanalysis, infrared (IR and nuclear magnetic resonance (NMR. Surface and interfacial tension, Krafft point, wetting time, emulsification power, foaming height and critical micelle concentration (cmc were determined and a comparative study was made between their chemical structure and surface active properties. Antimicrobial activity of these surfactants was also determined.

    Se prepararon cuatro series de agentes tensioactivos del tipo 2-[trimetil amonio, trietil amonio, piridinio y 2-amino piridinio] alcanoatos, que contienen cadenas carbonadas con C12, C14, C16 y C18 átomos de carbono.
    Se determinaron la tensión superficial e interfacial, el punto de Krafft, el tiempo humectante, el poder de emulsionamiento, la altura espumante y la concentración critica de miscela (cmc y se hizo un estudio comparativo entre la estructura química y sus propiedades tensioactivas. Se determinó también la actividad antimicrobiana de estos tensioactivos. Estas estructuras se caracterizaron por microanálisis, infrarrojo (IR y resonancia magnética nuclear (RMN.

  13. Thermal activity on Enceladus

    Science.gov (United States)

    Tobie, G.; Besserer, J.; Behounkova, M.; Cadek, O.; Choblet, G.; Sotin, C.

    2009-04-01

    Observations by Cassini have revealed that Enceladus' souh pole is highly active, with jets of icy particles and water vapour emanated from narrow tectonic ridges, called "tiger stripes". This jet activity is associated to a very high thermal emission mainly focused along the tectonic ridges. Heat power required to sustain such an activity is probably related to the dissipation of mechanical energy due to tidal forces exerted by Saturn. However, the dissipation process and its relation to the tectonic features are not clearly established. Both shear heating along the tectonic ridges and viscous dissipation in the convective part of the ice shell could contribute to the energy budget (Nimmo et al. 2007, Tobie et al. 2008). Tobie et al. (2008) pointed out that only interior models with a liquid water layer at depth, covering at least ~2/3 of the southern hemisphere, can explain the observed magnitude of dissipation and its particular location at the south pole. However, the long term stability of such a liquid reservoir remains problematic (Roberts and Nimmo 2007) and the possible link between the liquid reservoir and the surface activities is unknown. Concentration of tidal stresses along the tiger ridges have also been invoked as a mechanism to trigger the eruptive processes (Hurtford et al. 2007, Smith-Konter et al. 2008). However, those models do not take into account a realistic rheological structure for the ice shell when computing the fluctuating stress field. Moreover, the effect of the faults on the background tidal stress is neglected. In particular, low viscosity values are expected to be associated with the shear zone along the tiger stripes and may have a significant impact of the global tidal stress field. In order to self-consistently determine the tidal deformation and its impact on the thermal activity on Enceladus, we are currently developing a 3D model that combines a thermal convection code in spherical geometry (Choblet et al. 2007) and a

  14. Adaptable typologies for active roofs

    NARCIS (Netherlands)

    Quanjel, E.M.C.J.; Zeiler, W.

    2006-01-01

    The main objective of this part of the 6th framework Pan-European EUR-ACTIVE ROOF-er project is to improve the interaction between design participants of dynamic adaptable Active Roofs in product development and Active Roofs from an architects/ customers perspective. Improvements in Active Roof desi

  15. Spontaneous Plasticity of Multineuronal Activity Patterns in Activated Hippocampal Networks

    Directory of Open Access Journals (Sweden)

    Atsushi Usami

    2008-01-01

    Full Text Available Using functional multineuron imaging with single-cell resolution, we examined how hippocampal networks by themselves change the spatiotemporal patterns of spontaneous activity during the course of emitting spontaneous activity. When extracellular ionic concentrations were changed to those that mimicked in vivo conditions, spontaneous activity was increased in active cell number and activity frequency. When ionic compositions were restored to the control conditions, the activity level returned to baseline, but the weighted spatial dispersion of active cells, as assessed by entropy-based metrics, did not. Thus, the networks can modify themselves by altering the internal structure of their correlated activity, even though they as a whole maintained the same level of activity in space and time.

  16. Enzyme Activities in Waste Water and Activated Sludge

    DEFF Research Database (Denmark)

    Nybroe, Ole; Jørgensen, Per Elberg; Henze, Mogens

    1992-01-01

    The purpose of the present study was to evaluate the potential of selected enzyme activity assays to determine microbial abundance and heterotrophic activity in waste water and activated sludge. In waste water, esterase and dehydrogenase activities were found to correlate with microbial abundance...... measured as colony forming units of heterotrophic bacteria. A panel of four enzyme activity assays, α-glucosidase, alanine-aminopeptidase, esterase and dehydrogenase were used to characterize activated sludge and anaerobic hydrolysis sludge from a pilot scale plant. The enzymatic activity profiles were...... distinctly different, suggesting that microbial populations were different, or had different physiological properties, in the two types of sludge. Enzyme activity profiles in activated sludge from four full-scale plants seemed to be highly influenced by the composition of the inlet. Addition of hydrolysed...

  17. Advances in Activity Cliff Research.

    Science.gov (United States)

    Dimova, Dilyana; Bajorath, Jürgen

    2016-05-01

    Activity cliffs, i.e. similar compounds with large potency differences, are of interest from a chemical and informatics viewpoint; as a source of structure-activity relationship information, for compound optimization, and activity prediction. Herein, recent highlights of activity cliff research are discussed including studies that have further extended our understanding of activity cliffs, yielded unprecedented insights, or paved the way for practical applications.

  18. AMS Prototyping Activities

    Science.gov (United States)

    Burleigh, Scott

    2008-01-01

    This slide presentation reviews the activity around the Asynchronous Message Service (AMS) prototype. An AMS reference implementation has been available since late 2005. It is aimed at supporting message exchange both in on-board environments and over space links. The implementation incoroporates all mandatory elements of the draft recommendation from July 2007: (1) MAMS, AMS, and RAMS protocols. (2) Failover, heartbeats, resync. (3) "Hooks" for security, but no cipher suites included in the distribution. The performance is reviewed, and a Benchmark latency test over VxWorks Message Queues is shown as histograms of a count vs microseconds per 1000-byte message

  19. Athena: Assessment Phase Activities

    Science.gov (United States)

    Lumb, David; Ayre, Mark

    2015-09-01

    The Athena mission concept has been proposed by the community in response to science themes of the Hot and Energetic Universe. Unlike other, competitive, mission selection exercises this "Large" class observatory mission has essentially been pre-selected. Nevertheless it has to be demonstrated that Athena meets the programmatic constraints of 1Bn euro cost cap, and a readiness level appropriate for formal mission adoption by the end 2019. This should be confirmed through a Phase A study conducted with two parallel industry activities. We describe the technical and programmatic content of these and latest progress in space and ground segment definition.

  20. Topological Active Volumes

    Directory of Open Access Journals (Sweden)

    Barreira N

    2005-01-01

    Full Text Available The topological active volumes (TAVs model is a general model for 3D image segmentation. It is based on deformable models and integrates features of region-based and boundary-based segmentation techniques. Besides segmentation, it can also be used for surface reconstruction and topological analysis of the inside of detected objects. The TAV structure is flexible and allows topological changes in order to improve the adjustment to object's local characteristics, find several objects in the scene, and identify and delimit holes in detected structures. This paper describes the main features of the TAV model and shows its ability to segment volumes in an automated manner.

  1. System of Volcanic activity

    Directory of Open Access Journals (Sweden)

    P. HÉDERVARI

    1972-06-01

    Full Text Available A comparison is made among the systems of B. G.
    Escher (3, of R. W. van Bemmelen (1 and that of the author (4. In this
    connection, on the basis of Esclier's classification, the terms of "constructiv
    e " and "destructive" eruptions are introduced into the author's system and
    at the same time Escher's concept on the possible relation between the depth
    of magma-chamber and the measure of the gas-pressure is discussed briefly.
    Three complementary remarks to the first paper (4 011 the subject of system
    of volcanic activity are added.

  2. COMPANY ACTIVITY FINANCIAL RISK

    Directory of Open Access Journals (Sweden)

    Caruntu Genu Alexandru

    2012-12-01

    Full Text Available In economic and financial activity, risk is an inherent financial decisions, encountered in daily agenda of managers of companies. Unexpected changes in the price of a product development not only affect the financial results of a company, but can cause even bankruptcy. In fact, the nature of financial decisions involve uncertainty. Financial decisions are made based on cash flows under future contracts, which are par excellence incerte.Activitatea an enterprise that holds any weight in the industry is subject to risks, since it can not predict with certainty different components of its outcome (cost, quantity, price and operating cycle (purchase, processing, sales.

  3. Active galactic nuclei

    CERN Document Server

    Blandford, RD; Woltjer, L

    1990-01-01

    Starting with this volume, the Lecture Notes of the renowned Advanced Courses of the Swiss Society for Astrophysics and Astronomy will be published annually. In each course, three extensive lectures given by leading experts in their respective fields cover different and essential aspects of the subject. The 20th course, held at Les Diablerets in April 1990, dealt with current research on active galactic nuclei; it represents the most up-to-date views on the subject, presented with particular regard for clarity. The previous courses considered a wide variety of subjects, beginning with ""Theory

  4. Active terahertz metamaterials

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hou-tong [Los Alamos National Laboratory; O' Hara, John F [Los Alamos National Laboratory; Taylor, Antoinette J [Los Alamos National Laboratory

    2009-01-01

    In this paper we present an overview of research in our group in terahertz (THz) metamaterials and their applications. We have developed a series of planar metamaterials operating at THz frequencies, all of which exhibit a strong resonant response. By incorporating natural materials, e.g. semiconductors, as the substrates or as critical regions of metamaterial elements, we are able to effectively control the metamaterial resonance by the application of external stimuli, e.g., photoexcitation and electrical bias. Such actively controllable metamaterials provide novel functionalities for solid-state device applications with unprecedented performance, such as THz spectroscopy, imaging, and many others.

  5. Reuse of activated alumina

    Energy Technology Data Exchange (ETDEWEB)

    Hobensack, J.E. [Martin Marietta Energy Systems, Inc., Piketon, OH (United States)

    1991-12-31

    Activated alumina is used as a trapping media to remove trace quantities of UF{sub 6} from process vent streams. The current uranium recovery method employs concentrated nitric acid which destroys the alumina pellets and forms a sludge which is a storage and disposal problem. A recently developed technique using a distilled water rinse followed by three dilute acid rinses removes on average 97% of the uranium, and leaves the pellets intact with crush strength and surface area values comparable with new material. Trapping tests confirm the effectiveness of the recycled alumina as UF{sub 6} trapping media.

  6. Diagramming Complex Activities

    DEFF Research Database (Denmark)

    Andersen, Peter Bøgh

    2005-01-01

    We increasingly live in heterogeneous ever-changing webs of activities where human actions are intertwined with events created by automatic machines.  In order to make such webs understandable to its human participants, their structure should be represented by displays emphasizing their action as...... aspect. The paper suggests thematic roles as a semantics for actions, argues that a selection of well-known diagramming techniques can be defined within this theory, and uses the theory to discuss new issues related to process control and mobile technology....

  7. Miscarriage and occupational activity

    DEFF Research Database (Denmark)

    Bonde, Jens Peter; Jørgensen, Kristian Tore; Bonzini, Matteo

    2013-01-01

    . METHODS: A search in Medline and EMBASE 1966-2012 identified 30 primary papers reporting the relative risk (RR) of miscarriage according to ≥1 of 5 occupational activities of interest. Following an assessment of completeness of reporting, confounding, and bias, each risk estimate was characterized as more......, N=10). RR for working hours and standing became smaller when analyses were restricted to higher quality studies. CONCLUSIONS: These largely reassuring findings do not provide a strong case for mandatory restrictions in relation to shift work, long working hours, occupational lifting, standing...

  8. Physical activity in elderly

    Directory of Open Access Journals (Sweden)

    Jan Cvecka

    2015-08-01

    Full Text Available Aging is a multifactorial irreversible process associated with significant decline in muscle mass and neuromuscular functions. One of the most efficient methods to counteract age-related changes in muscle mass and function is physical exercise. An alternative effective intervention to improve muscle structure and performance is electrical stimulation. In the present work we present the positive effects of physical activity in elderly and a study where the effects of a 8-week period of functional electrical stimulation and strength training with proprioceptive stimulation in elderly are compared.

  9. Physical Activity in Elderly

    Science.gov (United States)

    Tirpakova, Veronika; Sedliak, Milan; Kern, Helmut; Mayr, Winfried; Hamar, Dušan

    2015-01-01

    Aging is a multifactorial irreversible process associated with significant decline in muscle mass and neuromuscular functions. One of the most efficient methods to counteract age-related changes in muscle mass and function is physical exercise. An alternative effective intervention to improve muscle structure and performance is electrical stimulation. In the present work we present the positive effects of physical activity in elderly and a study where the effects of a 8-week period of functional electrical stimulation and strength training with proprioceptive stimulation in elderly are compared. PMID:26913164

  10. The Active Muon Shield

    CERN Document Server

    Bezshyiko, Iaroslava

    2016-01-01

    In the SHiP beam-dump of the order of 1011 muons will be produced per second. An active muon-shield is used to magnetically deflect these muons out of the acceptance of the spectrom- eter. This note describes how this shield is modelled and optimized. The SHiP spectrometer is being re-optimized using a conical decay-vessel, and utilizing the possibility to magnetize part of the beam-dump shielding iron. A shield adapted to these new conditions is presented which is significantly shorter and lighter than the shield used in the Technical Proposal (TP), while showing a similar performance.

  11. Active galactic nuclei

    CERN Document Server

    Beckmann, Volker

    2012-01-01

    This AGN textbook includes phenomena based on new results in the X-Ray domain from new telescopes such as Chandra and XMM Newton not mentioned in any other book. Furthermore, it considers also the Fermi Gamma Ray Space Telescope with its revolutionary advances of unprecedented sensitivity, field of view and all-sky monitoring. Those and other new developments as well as simulations of AGN merging events and formations, enabled through latest super-computing capabilities. The book gives an overview on the current knowledge of the Active Galacitc Nuclei phenomenon. The spectral energy d

  12. Direct Activation Of Methane

    KAUST Repository

    Basset, Jean-Marie

    2013-07-15

    Heteropolyacids (HPAs) can activate methane at ambient temperature (e.g., 20.degree. C.) and atmospheric pressure, and transform methane to acetic acid, in the absence of any noble metal such as Pd). The HPAs can be, for example, those with Keggin structure: H.sub.4SiW.sub.12O.sub.40, H.sub.3PW.sub.12O.sub.40, H.sub.4SiMo.sub.12O.sub.40, or H.sub.3PMo.sub.12O.sub.40, can be when supported on silica.

  13. Rationales for regulatory activity

    Energy Technology Data Exchange (ETDEWEB)

    Perhac, R.M. [Univ. of Tennessee, Knoxville, TN (United States)

    1997-02-01

    The author provides an outline which touches on the types of concerns about risk evaluation which are addressed in the process of establishing regulatory guides. Broadly he says regulatory activity serves three broad constituents: (1) Paternalism (private risk); (2) Promotion of social welfare (public risks); (3) Protection of individual rights (public risks). He then discusses some of the major issues encountered in reaching a decision on what is an acceptable level of risk within each of these areas, and how one establishes such a level.

  14. Microbiologically active nanocomposite media

    Science.gov (United States)

    Petranovskii, Vitalii; Panina, Lyudmila; Bogomolova, Eugenia; Belostotskaya, Galina

    2003-07-01

    The most recent approach to the development of novel antimicrobial and antifungal agents is based on the application of synthetic and natural zeolites, because zeolites are known to be the carrier and slow releaser of the heavy metals with olygodynamic properties. The microbiological activity of the ion-exchanged zeolites is attributed to the ionic state of the metal sreleased from the zeolites by ion re-exchange. In the present work we used low cost natural clinoptilolite (Cli) as a substrate for copper and silver in different states. The state of oxidation of the exchanged metal in zeolite with supported Cu and Ag species (in the form of cations, small clusters, sub-coloidal particles, large particles) in order to fit them to fulfill the following criteria: to demonstrate their high protective abilities against fungi and long-term stability. The study of structure of samples with XRD, UV-visible spectroscopy, FTIR, their stability with temperature and during storage was carried out for obtaining the correct correlation with microbiological activity.

  15. The Active Solid Earth

    Science.gov (United States)

    Ebinger, Cynthia

    2016-04-01

    Dynamic processes in Earth's crust, mantle and core shape Earth's surface and magnetic field over time scales of seconds to millennia, and even longer time scales as recorded in the ca. 4 Ga rock record. Our focus is the earthquake-volcano deformation cycles that occur over human time scales, and their comparison with time-averaged deformation studies, with emphasis on mantle plume provinces where magma and volatile release and vertical tectonics are readily detectable. Active deformation processes at continental and oceanic rift and back arc zones provide critical constraints on mantle dynamics, the role of fluids (volatiles, magma, water), and plate rheology. For example, recent studies of the East African rift zone, which formed above one of Earth's largest mantle upwellings reveal that magma production and volatile release rates are comparable to those of magmatic arcs, the archetypal zones of continental crustal creation. Finite-length faults achieve some plate deformation, but magma intrusion in the form of dikes accommodates extension in continental, back-arc, and oceanic rifts, and intrusion as sills causes permanent uplift that modulates the local time-space scales of earthquakes and volcanoes. Volatile release from magma intrusion may reduce fault friction and permeability, facilitating aseismic slip and creating magma pathways. We explore the implications of active deformation studies to models of the time-averaged structure of plume and extensional provinces in continental and oceanic plate settings.

  16. Active Optics in LAMOST

    Institute of Scientific and Technical Information of China (English)

    Ding-Qiang Su; Xiang-Qun Cui

    2004-01-01

    Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST)is one of the major national projects under construction in China. Active optics is one of the most important technologies for new large telescopes. It is used for correcting telescope errors generated by gravitational and thermal changes. Here,however, we use this technology to realize the configuration of LAMOST, -a task that cannot be done in the traditional way. A comprehensive and intensive research on the active optics used in LAMOST is also reported, including an open-loop control method and an auxiliary closed-loop control method. Another important development is in our pre-calibration method of open-loop control, which is with some new features: simultaneous calculation of the forces and displacements of force actuators and displacement actuators; the profile of mirror can be arbitrary;the mirror surface shape is not expressed by a fitting polynomial, but is derived from the mirror surface shape formula which is highly accurate; a proof is given that the solution of the pre-calibration method is the same as the least squares solution.

  17. Active Astronomy Roadshow Haiti

    Science.gov (United States)

    Laycock, Silas; Oram, Kathleen; Alabre, Dayana; Douyon, Ralph; UMass Lowell Haiti Development Studies Center

    2016-01-01

    College-age Haitian students working with advisors and volunteers from UMass Lowell in 2015 developed and tested an activity-based K-8 curriculum in astronomy, space, and earth science. Our partner school is located in Les Cayes, Haiti a city where only 65% of children attend school, and only half of those will complete 6th grade. Astronomy provides an accessible and non-intimidating entry into science, and activity-based learning contrasts with the predominant traditional teaching techniques in use in Haiti, to reach and inspire a different cohort of learners. Teachers are predominantly women in Haiti, so part of the effort involves connecting them with scientists, engineers and teacher peers in the US. As a developing nation, it is vital for Haitian (as for all) children to grow up viewing women as leaders in science. Meanwhile in the US, few are aware of the reality of getting an education in a 3rd world nation (i.e. most of the world), so we also joined with teachers in Massachusetts to give US school children a peek at what daily life is like for their peers living in our vibrant but impoverished neighbor. Our Haitian partners are committed to helping their sister-schools with curriculum and educator workshops, so that the overall quality of education can rise, and not be limited to the very few schools with access to resources. We will describe the activites, motivation, and and the lessons learned from our first year of the project.

  18. Leadership Development Activities

    Directory of Open Access Journals (Sweden)

    Malikeh Beheshtifar

    2012-07-01

    Full Text Available Nowadays, human resource development is considered as a developed concept in HR field. It is a process for helping personnel to conduct their duties better. Most organizations tend to leadership development as a separable subject and as areas of responsibility within organization. Whereas the leadership development plans have been unsuccessful. This article aim to draw attention to the fact that leadership development is crucial in organizations. A literature review was conducted by searching journal databases, textbooks, and relevant reports. A categorization of the evidence allowed informed discussions on the key themes surrounding leadership development activities. Leadership development is caused to employees' promotion and progress via nurture of new talents, stimulus in employees by persuade to do individual development, save time and cost, and increase customers' satisfaction by relations improvement. Accordingly, the development systems can cover a wide scope in organization. They are effective to career management, training and development, performance management, strategic human resource planning, recruitment and selection, and succession planning activities. Despite the need for further scientific and validated studies, organizations should be urged to devote sufficient resources and attention towards leadership development for promoting long-term survival and prosperity.

  19. Involvement in Physical Activity

    Directory of Open Access Journals (Sweden)

    James Gavin

    2013-04-01

    Full Text Available A total of 1,096 adolescents participated in 123 focus groups regarding the perceived outcomes of their involvement in sports and physical activity (PA. The groups, segmented by grade level, sex, and school types, were conducted in both public and private high schools in Montreal, Quebec. We sought to understand, through the participants’ own words, their perception of the outcome matrix of involvement in sports and PA. Focus group questions emphasized changes that adolescents associated with such engagement. In particular, participants were asked how sports and PA might influence behaviors, emotional states, personal characteristics, and other outcomes. Twelve themes were identified in the responses: Positive Health and Physical Changes (18.5%, Activity-Related Positive Emotions (15.6%, and Personal Learning (11.3% were most prevalent in the discussions. A cluster of deeper personal changes thematically described as Self-Identity, Autonomy, and Positive Character Development accounted for another 16.5% of the responses. Relatively few commentaries emphasized negative effects (7.1%. Converting the proportions of qualitative data into a quantitative index allowed us to analyze potential differences in emphasis according to sex, age, and school type. Though a few significant findings emerged, the larger pattern was of a uniform perceptual map across the variables for this adolescent sample. Implications drawn from this investigation highlight the need to clearly articulate concrete pathways to positive nonphysical changes (e.g., mood states, autonomy, positive character development from engagements in sports and PA.

  20. CBP Active Dumping and Active Countervailing (AD/CVD) Cases

    Data.gov (United States)

    Department of Homeland Security — The datasets provide information from CBP's reference files on active anti-dumping and active countervailing cases. This data includes associated case numbers (if...

  1. Sedentary activity associated with metabolic syndrome independent of physical activity

    DEFF Research Database (Denmark)

    Bankoski, Andrea; Harris, Tamara B; McClain, James J

    2011-01-01

    This study examined the association between objectively measured sedentary activity and metabolic syndrome among older adults.......This study examined the association between objectively measured sedentary activity and metabolic syndrome among older adults....

  2. Characterization and distribution of esterase activity in activated sludge

    NARCIS (Netherlands)

    Boczar, BA; Forney, LJ; Begley, WM; Larson, RJ; Federle, TW

    2001-01-01

    The location and activity of esterase enzymes in activated Sludge from three Municipal wastewater treatment plants were characterized using model Substrate, and denaturing and nondenaturing polyacrylamide gel electrophoresis (PAGE) Of particulate, freeze thaw (primarily periplasmic enzymes and those

  3. The active video games' narrative impact on children's physical activities

    Science.gov (United States)

    Active video games (AVGs) capable of inducing physical activity offer an innovative approach to combating childhood obesity. Unfortunately, children's AVG game play decreases quickly, underscoring the need to identify novel methods for player engagement. Narratives have been demonstrated to influenc...

  4. INFLUENCE OF SELECTED PHARMACEUTICALS ON ACTIVATED SLUDGE DEHYDROGENASE ACTIVITY

    Directory of Open Access Journals (Sweden)

    Agnieszka Tomska

    2016-06-01

    The aim of this work was to evaluate the effect of selected antibiotics - sulfanilamide and erythromycin on activated sludge dehydrogenase activity with use of trifenyltetrazolinum chloride (TTC test. Dehydrogenases activity is an indicator of biochemical activity of microorganisms present in activated sludge or the ability to degrade organic compounds in waste water. TTC test is particularly useful for the regularity of the course of treatment, in which the presence of inhibitors of biochemical reactions and toxic compounds are present. It was observed that the dehydrogenase activity decreases with the increase of a antibiotics concentration. The lowest value of the dehydrogenase activity equal to 32.4 μmol TF / gMLSS obtained at sulfanilamide concentration 150mg / l. For this sample, an inhibition of dehydrogenase activity was 31%.

  5. How Active Are Older Americans?

    Directory of Open Access Journals (Sweden)

    Judy Kruger, PhD

    2007-07-01

    Full Text Available IntroductionRegular physical activity can reduce age-related functional decline, as well people’s risk for chronic diseases such as coronary heart disease, hypertension, colon cancer, and diabetes. The objective of this study was to estimate the level of participation in aerobic, muscle-strengthening, and flexibility activities among Americans aged 50 years or older.MethodsUsing population-based data from the 2001 National Health Interview Survey, we classified qualified respondents (N = 11,969 according to whether they met the activity criteria used in Healthy People 2010 goals for leisure-time participation in regular aerobic physical activity, vigorous-intensity aerobic activity, strength-training activity, and flexibility activity. We also classified respondents according to their level of aerobic activity (i.e., inactive, insufficiently active, and regularly active.ResultsWe estimated that 46.4% of older Americans engaged in no leisure-time aerobic activity; that 26.1% were regularly active (participated in light- to moderate-intensity aerobic activities at least 5 days per week for at least 30 minutes or vigorous-intensity activities at least 3 days per week for at least 20 minutes; that 16.2% participated in vigorous-intensity aerobic activities at least 3 days per week for at least 20 minutes; that 13.7% participated in strength-training activities at least 2 days per week; and that 24.5% participated in flexibility activities at least 1 day per week. Among the 26.1% of older Americans who were regularly active, 30.5% engaged in strengthen-training activities at least 2 days per week. Overall, only 8.2% of older Americans met the criteria for both aerobic and strength-training activity.ConclusionAs of 2001, the percentage of older Americans who met recommended activity levels of physical activity were well below the goals for U.S. adults in Healthy People 2010. Further efforts are needed to encourage older Americans to engage in

  6. Active Magnetic Regenerative Liquefier

    Energy Technology Data Exchange (ETDEWEB)

    Barclay, John A. [Heracles Energy Corporation d.b.a. Prometheus Energy, Washington, DC (United States); Oseen-Send, Kathryn [Heracles Energy Corporation d.b.a. Prometheus Energy, Washington, DC (United States); Ferguson, Luke [Heracles Energy Corporation d.b.a. Prometheus Energy, Washington, DC (United States); Pouresfandiary, Jamshid [Heracles Energy Corporation d.b.a. Prometheus Energy, Washington, DC (United States); Cousins, Anand [Heracles Energy Corporation d.b.a. Prometheus Energy, Washington, DC (United States); Ralph, Heather [Heracles Energy Corporation d.b.a. Prometheus Energy, Washington, DC (United States); Hampto, Tom [Heracles Energy Corporation d.b.a. Prometheus Energy, Washington, DC (United States)

    2016-01-12

    This final report for the DOE Project entitled Active Magnetic Regenerative Liquefier (AMRL) funded under Grant DE-FG36-08GO18064 to Heracles Energy Corporation d.b.a. Prometheus Energy (Heracles/Prometheus) describes an active magnetic regenerative refrigerator (AMRR) prototype designed and built during the period from July 2008 through May 2011. The primary goal of this project was to make significant technical advances toward highly efficient liquefaction of hydrogen. Conventional hydrogen liquefiers at any scale have a maximum FOM of ~0.35 due primarily to the intrinsic difficulty of rapid, efficient compression of either hydrogen or helium working gases. Numerical simulation modeling of high performance AMRL designs indicates certain designs have promise to increase thermodynamic efficiency from a FOM of ~0.35 toward ~0.5 to ~0.6. The technical approach was the use of solid magnetic working refrigerants cycled in and out of high magnetic fields to build an efficient active regenerative magnetic refrigeration module providing cooling power for AMRL. A single-stage reciprocating AMRR with a design temperature span from ~290 K to ~120 K was built and tested with dual magnetic regenerators moving in and out of the conductively-cooled superconducting magnet subsystem. The heat transfer fluid (helium) was coupled to the process stream (refrigeration/liquefaction load) via high performance heat exchangers. In order to maximize AMRR efficiency a helium bypass loop with adjustable flow was incorporated in the design because the thermal mass of magnetic refrigerants is higher in low magnetic field than in high magnetic field. Heracles/Prometheus designed experiments to measure AMRR performance under a variety of different operational parameters such as cycle frequency, magnetic field strength, heat transfer fluid flow rate, amount of bypass flow of the heat transfer fluid while measuring work input, temperature span, cooling capability as a function of cold temperature

  7. Examining Activism in Practice: A Qualitative Study of Archival Activism

    Science.gov (United States)

    Novak, Joy Rainbow

    2013-01-01

    While archival literature has increasingly discussed activism in the context of archives, there has been little examination of the extent to which archivists in the field have accepted or incorporated archival activism into practice. Scholarship that has explored the practical application of archival activism has predominately focused on case…

  8. Youth Physical Activity Resource Use and Activity Measured by Accelerometry

    Science.gov (United States)

    Maslow, Andra L.; Colabianchi, Natalie

    2011-01-01

    Objectives: To examine whether use of physical activity resources (e.g., parks) was associated with daily physical activity measured by accelerometry. Methods: One hundred eleven adolescents completed a travel diary with concurrent accelerometry. The main exposure was self-reported use of a physical activity resource (none /1 resources). The main…

  9. Project origami activities for exploring mathematics

    CERN Document Server

    Hull, Thomas

    2012-01-01

    IntroductionActivity 1 Folding Equilateral Triangles in a Square Activity 2 Origami Trigonometry Activity 3 Dividing a Length into Equal Nths: Fujimoto Approximation Activity 4 Dividing a Length into Equal Nths Exactly Activity 5 Origami Helix Activity 6 Folding a Parabola Activity 7 Can Origami Trisect an Angle?Activity 8 Solving Cubic Equations Activity 9 Lill's Method Activity 10 Folding Strips into Knots Activity 11 Haga's ""Origamics"" Activity 12 Modular Star Ring Activity 13 Folding a Butterfly Bomb Activity 14 Molly's Hexahedron Activity 15 Business Card Modulars Activity 16 Five Inter

  10. Active Ageing: An Analysis

    Directory of Open Access Journals (Sweden)

    Alina-Cristina Nuta

    2011-10-01

    Full Text Available The problem of ageing is a highly topical for Romania and for European Union. In this framework, to create and implement some strategies for active ageing is an important objective. The international and regional forums set (supported by official statistics that the number of older people growing rapidly. Romania needs some programmes (with labour, social, economic, health care aspects to deal with the demographic changes, programs that will reform the existing working life structures and legislation. Despite the actual pension reform, which tries to close the opportunity of early retirement (by penalizing the total pension flows, or increasing the retirement age, etc., the labour system does not sets some important targets for this area.

  11. DPAL activities in Japan

    Science.gov (United States)

    Endo, Masamori; Wani, Fumio

    2015-02-01

    Activities on diode pumped alkali laser (DPAL) in Japan is reviewed. We have started alkali laser works in 2011, and currently, we are the only players in Japan. Our interests are application oriented, and it is not only defense but also industrial. DPAL is a good candidate as a source of remote laser machining, thanks to its scalability and extremely good beam quality. We are studying on scientific and engineering problems of Cs DPAL with a small-scale apparatus. A commercial diode laser with volume Bragg grating outcoupler is used to pump the gain cell longitudinally. A 6.5 W continuous-wave output with optical to optical efficiency of 56% (based on the absorbed power) has been achieved. Numerical simulation codes are developed to understand the physics of DPAL and to help future developments.

  12. SPORTS ACTIVITIES SPONSORSHIP

    Directory of Open Access Journals (Sweden)

    DURBĂCEA - BOLOVAN MARIAN

    2016-12-01

    Full Text Available Sports and economy have discovered each other, hoping to serve common interests. In view of transferring in a more efficient way the information about their products or services to consumers, the business operator finances sports activities for advertising purposes. A company involved in sports sponsorship can instantly transmit the message about its products to millions of potential buyers, thus increasing the market share and hence the profit that it generates. By sponsoring sport it is meant any agreement / convention, under which one party the sponsor makes available to the beneficiary the material resources, financial and / or other benefits in exchange for its association with a sport or sportsman and especially the promise to use this association with sport or sportsman for the purpose of advertising, especially TV advertising. The growing use of athletes as spokespersons for a product is largely due to the ability of athletes to attract public attention and the credibility they enjoy

  13. The sound of activism.

    Science.gov (United States)

    Sandstrom, B; Vetter, C

    2001-01-01

    ABSTRACT A longtime advocate for female empowerment and equality, Boden Sandstrom has worked for political change in many arenas. In the 1960s, she began a career as a librarian, but soon made activism her full-time job, working for feminist, leftist and socialist causes. In the 1970s, she found a way to turn her lifelong passion for music into a career as a sound engineer. Once established in that profession, she began donating her services to political events, marches, demonstrations, and rallies. After thirteen years of running her own company, called Woman Sound,Inc. (later City Sound Productions,Inc.), she turned to the study of ethnomusicology. She is now Program Manager and Lecturer for the Ethnomusicology Program at the University of Maryland, where she is also working on her doctorate in that subject. She continues to freelance as a sound engineer and serve as a technical producer for major events.

  14. Actively stressed marginal networks

    CERN Document Server

    Sheinman, M; MacKintosh, F C

    2012-01-01

    We study the effects of motor-generated stresses in disordered three dimensional fiber networks using a combination of a mean-field, effective medium theory, scaling analysis and a computational model. We find that motor activity controls the elasticity in an anomalous fashion close to the point of marginal stability by coupling to critical network fluctuations. We also show that motor stresses can stabilize initially floppy networks, extending the range of critical behavior to a broad regime of network connectivities below the marginal point. Away from this regime, or at high stress, motors give rise to a linear increase in stiffness with stress. Finally, we demonstrate that our results are captured by a simple, constitutive scaling relation highlighting the important role of non-affine strain fluctuations as a susceptibility to motor stress.

  15. Actively stressed marginal networks.

    Science.gov (United States)

    Sheinman, M; Broedersz, C P; MacKintosh, F C

    2012-12-07

    We study the effects of motor-generated stresses in disordered three-dimensional fiber networks using a combination of a mean-field theory, scaling analysis, and a computational model. We find that motor activity controls the elasticity in an anomalous fashion close to the point of marginal stability by coupling to critical network fluctuations. We also show that motor stresses can stabilize initially floppy networks, extending the range of critical behavior to a broad regime of network connectivities below the marginal point. Away from this regime, or at high stress, motors give rise to a linear increase in stiffness with stress. Finally, we demonstrate that our results are captured by a simple, constitutive scaling relation highlighting the important role of nonaffine strain fluctuations as a susceptibility to motor stress.

  16. Active Flow Control

    Science.gov (United States)

    FFOWCS WILLIAMS, J. E.

    2001-01-01

    This paper considers the two-dimensional problem of a plane vortex sheet disturbed by an impulsive line source. A previous incorrect treatment of this problem is examined in detail. Instabilities of the vortex sheet are triggered by the source and grow exponentially in space and time. The Green function is constructed for the problem and it is shown that a point source properly positioned and delayed will induce a field that cancels the unstable growing modes. The resulting displacement of the vortex sheet is expressed in simple terms. The instabilities are checked by the anti-source which combines with the field of the primary source into a vortex sheet response which decays with time at large time. This paper is a contribution to the study of active control of shear layer instabilities, the main contribution being to clear up a previous paper with peculiar results that are, in fact, wrong.

  17. Respiratory active mitochondrial supercomplexes.

    Science.gov (United States)

    Acín-Pérez, Rebeca; Fernández-Silva, Patricio; Peleato, Maria Luisa; Pérez-Martos, Acisclo; Enriquez, Jose Antonio

    2008-11-21

    The structural organization of the mitochondrial respiratory complexes as four big independently moving entities connected by the mobile carriers CoQ and cytochrome c has been challenged recently. Blue native gel electrophoresis reveals the presence of high-molecular-weight bands containing several respiratory complexes and suggesting an in vivo assembly status of these structures (respirasomes). However, no functional evidence of the activity of supercomplexes as true respirasomes has been provided yet. We have observed that (1) supercomplexes are not formed when one of their component complexes is absent; (2) there is a temporal gap between the formation of the individual complexes and that of the supercomplexes; (3) some putative respirasomes contain CoQ and cytochrome c; (4) isolated respirasomes can transfer electrons from NADH to O(2), that is, they respire. Therefore, we have demonstrated the existence of a functional respirasome and propose a structural organization model that accommodates these findings.

  18. Plasminogen activation and cancer

    DEFF Research Database (Denmark)

    Danø, Keld; Behrendt, N.; Hoyer-Hansen, G.

    2005-01-01

    Breakdown of the extracellular matrix is crucial for cancer invasion and metastasis. It is accomplished by the concerted action of several proteases, including the serine protease plasmin and a number of matrix metalloproteases.The activity of each of these proteases is regulated by an array......, the regulation of extracellular proteolysis in cancer involves a complex interplay between cancer cells and non-malignant stromal cells in the expression of the molecular components involved. For some types of cancer, this cellular interplay mimics that observed in the tissue of ori- gin during non......-neoplastic tissue remodelling processes.We propose that cancer invasion can be considered as uncontrolled tissue remodelling. Inhibition of extracellular proteases is an attractive approach to cancer therapy. Because proteases have many different functions in the normal organism, efficient inhibition will have...

  19. Physical activity among adolescents

    DEFF Research Database (Denmark)

    Henriksen, P W; Ingholt, L; Rasmussen, M

    2016-01-01

    The objectives of this study were (a) to examine the association between various kinds of parental social support and adolescents' physical activity (PA) and (b) to examine whether various kinds of social support from mothers and fathers were differently associated with boys' and girls' PA. Data...... during leisure time. We used logistic regression analyses to estimate the associations for girls and boys separately, adjusted by age group, parents' occupational social class, family structure, and migration status. There were significant and graded associations between adolescents' PA and all four...... dimensions of parental support for PA. The association patterns were similar for mothers' and fathers' social support and similar for girls and boys. Social processes in the family are important for adolescents' participation in PA. It is important to continue to explore these social processes in order...

  20. Existing chemicals: international activities.

    Science.gov (United States)

    Purchase, J F

    1989-01-01

    The standards of care used in the protection of the health and safety of people exposed to chemicals has increased dramatically in the last decade. Standards imposed by regulation and those adopted by industry have required a greater level of knowledge about the hazards of chemicals. In the E.E.C., the 6th amendment of the dangerous substances directive imposed the requirement that al new chemicals should be tested according to prescribed programme before introduction on to the market. The development of a European inventory of existing chemicals was an integral part of the 6th amendment. It has now become clear that increased standards of care referred to above must be applied to the chemicals on the inventory list. There is, however, a considerable amount of activity already under way in various international agencies. The OECD Chemicals Programme has been involved in considering the problem of existing chemicals for some time, and is producing a priority list and action programme. The International Programme on Chemical Safety produces international chemical safety cards, health and safety guides and environmental health criteria documents. The international register of potentially toxic compounds (part of UNEP) has prepared chemical data profiles on 990 compounds. The International Agency for Research on Cancer prepared monographs on the carcinogenic risk of chemicals to man. So far 42 volumes have been prepared covering about 900 substances. IARC and IPCS also prepare periodic reports on ongoing research on carcinogenicity or toxicity (respectively) of chemicals. The chemical industry through ECETOC (the European Chemical Industry Ecology and Toxicology Centre) has mounted a major initiative on existing chemicals. Comprehensive reviews of the toxicity of selected chemicals are published (Joint Assessment of Commodity Chemicals). In its technical report no. 30 ECETOC lists reviews and evaluations by major national and international organisations, which provides

  1. Diabetes Diet, Eating, & Physical Activity

    Science.gov (United States)

    ... Disease, & Other Dental Problems Diabetes & Sexual & Urologic Problems Diabetes Diet, Eating, & Physical Activity Nutrition and physical activity ... What foods can I eat if I have diabetes? You may worry that having diabetes means going ...

  2. Consolidated Human Activities Database (CHAD)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Consolidated Human Activity Database (CHAD) contains data obtained from human activity studies that were collected at city, state, and national levels. CHAD is...

  3. Motivating Kids to Be Active

    Science.gov (United States)

    ... set healthy patterns that will last into adulthood. Benefits of Being Active When kids are active, their ... school sports to after-school interests, such as yoga or skateboarding. It's important to remember that physical ...

  4. Physical Activity and Your Heart

    Science.gov (United States)

    ... more energy than resting. Walking, running, dancing, swimming, yoga, and gardening are a few examples of physical activity. According to the Department of Health and Human Services' 2008 Physical Activity Guidelines for ...

  5. Physical activity extends life expectancy

    Science.gov (United States)

    Leisure-time physical activity is associated with longer life expectancy, even at relatively low levels of activity and regardless of body weight, according to a study by a team of researchers led by the NCI.

  6. Advanced Active Acoustics Lab (AAAL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Active Acoustics Lab (AAAL) is a state-of-the-art Undersea Warfare (USW) acoustic data analysis facility capable of both active and passive underwater...

  7. Physical active rest in education of active personality of students

    Directory of Open Access Journals (Sweden)

    Zaycev V.P.

    2010-10-01

    Full Text Available Meaningfulness of physical recreation is rotined in education of active personality of students. Research material is literary sources on this issue. Factors which influence on an educate function of personality of students are considered. Application of physical recreation is grounded for education of active personality of students. It is marked that physical recreation in pedagogical process decides educate, educational, health and social tasks. It positively influences on education of active personality of students. It is rotined that in education of active personality of students an important role is played by their research activity.

  8. Automated activity-aware prompting for activity initiation.

    Science.gov (United States)

    Holder, Lawrence B; Cook, Diane J

    2013-01-01

    Performing daily activities without assistance is important to maintaining an independent functional lifestyle. As a result, automated activity prompting systems can potentially extend the period of time that adults can age in place. In this paper we introduce AP, an algorithm to automate activity prompting based on smart home technology. AP learns prompt rules based on the time when activities are typically performed as well as the relationship between activities that normally occur in a sequence. We evaluate the AP algorithm based on smart home datasets and demonstrate its ability to operate within a physical smart environment.

  9. Writing clear animal activity proposals.

    Science.gov (United States)

    Pinson, David M

    2011-06-01

    Although IACUC-related topics are frequently discussed in the literature, there is little published information about how to write animal activity proposals. In this article, the author discusses key considerations in the writing and review of animal activity proposals. The author then describes a framework for developing and writing clear animal activity proposals that highlight animal welfare concerns. Though these recommendations are aimed at individuals writing and reviewing research proposals, the framework can be modified for other types of animal activity proposals.

  10. Danish Labour Market Activation Policies

    DEFF Research Database (Denmark)

    Kvist, Jon; Pedersen, LIsbeth

    2007-01-01

    transformation over the past fifteen years. From the initial curbing of unemployment among the insured unemployed through standard activation offers, the aim today is also to increase labour supply among non-economic active groups using individually tailored programmes. Danish activation policies this embrace...

  11. Assessing and Increasing Physical Activity

    Science.gov (United States)

    Van Camp, Carole M.; Hayes, Lynda B.

    2012-01-01

    Increasing physical activity is a crucial component of any comprehensive approach to combat the growing obesity epidemic. This review summarizes recent behavioral research on the measurement of physical activity and interventions aimed at increasing physical activity and provides directions for future research.

  12. Water-Related Teaching Activities.

    Science.gov (United States)

    Coon, Herbert L.; Price, Charles L.

    This publication is designed to provide interested teachers with teaching activities for all grade levels and subject areas that can be used to help students learn about water resources. For each activity, the purpose, level, subject, and concept are given. Activities are organized by grade level. Most of these water related learning activities…

  13. TCUP: A novel hAT transposon active in maize tissue culture

    Directory of Open Access Journals (Sweden)

    Alan eSmith

    2012-01-01

    Full Text Available Transposable elements are capable of inducing heritable de novo genetic variation. The sequences capable of reactivation, and environmental factors that induce mobilization, remain poorly defined even in well-studied genomes such as maize. We treated maize tissue culture with the demethylating agent 5-aza-2-deoxcytidine and examined long-term tissue culture lines to discover silenced transposable elements that have the potential to induce heritable genetic variation. Through these screens we have identified a novel low copy number hAT transposon, Tissue Culture Up-Regulated (TCUP, which is transcribed at high levels in long-term maize Black Mexican Sweet (BMS tissue culture and up-regulated in response to treatment with 5-aza-2-deoxycytidine. Analysis of the TIGR Maize Gene Index revealed that this element is the most frequently represented EST from the BMS cell culture library and is not represented in other tissue libraries, which is the basis for its name. A full-length sequence was assembled in inbred B73 that contains the putative functional motifs required for autonomous movement of a hAT transposon. Transposon display detected movement of TCUP in two long-term tissue cultured cell lines of the genotype Hi-II AxB and BMS. This research implicates TCUP as a transposon that is capable of reactivation and which may also be particularly sensitive to the stress of the tissue culture environment. Our findings are consistent with the hypothesis that epigenetic alterations potentiate genomic responses to stress during clonal propagation of plants.

  14. Optically active quantum dots

    Science.gov (United States)

    Gerard, Valerie; Govan, Joseph; Loudon, Alexander; Baranov, Alexander V.; Fedorov, Anatoly V.; Gun'ko, Yurii K.

    2015-10-01

    The main goal of our research is to develop new types of technologically important optically active quantum dot (QD) based materials, study their properties and explore their biological applications. For the first time chiral II-VI QDs have been prepared by us using microwave induced heating with the racemic (Rac), D- and L-enantiomeric forms of penicillamine as stabilisers. Circular dichroism (CD) studies of these QDs have shown that D- and L-penicillamine stabilised particles produced mirror image CD spectra, while the particles prepared with a Rac mixture showed only a weak signal. It was also demonstrated that these QDs show very broad emission bands between 400 and 700 nm due to defects or trap states on the surfaces of the nanocrystals. These QDs have demonstrated highly specific chiral recognition of various biological species including aminoacids. The utilisation of chiral stabilisers also allowed the preparation of new water soluble white emitting CdS nano-tetrapods, which demonstrated circular dichroism in the band-edge region of the spectrum. Biological testing of chiral CdS nanotetrapods displayed a chiral bias for an uptake of the D- penicillamine stabilised nano-tetrapods by cancer cells. It is expected that this research will open new horizons in the chemistry of chiral nanomaterials and their application in nanobiotechnology, medicine and optical chemo- and bio-sensing.

  15. [Active management of labor].

    Science.gov (United States)

    Ruiz Ortiz, E; Villalobos Román, M; Flores Murrieta, G; Sotomayor Alvarado, L

    1991-01-01

    Eighty three primigravidae patients at the end of latency labor, erased cervix, 3 cm dilation, vertex presentation and adequate pelvis, were studied. Two groups were formed: 53 patients in the study group, who received active management of labor, and 30 patients in the control group, treated in the traditional way. In all the patients a graphic recording of labor, was carried out; it included all the events, and as labor advanced, a signoidal curve of cervical dilatation, was registered, as well as the hyperbolic one for presentation descent. The study group received the method in a systematized manner, as follows: 1. Peridular block. 2. Amniotomy. 3. IV oxytocin one hour after amniotomy. 4. FCR monitoring. 5. Detection of dystocia origin. Materno-fetal morbidity was registered in both groups, as well as cesarean section rate, instrumental delivery and its indications, labor duration, and time of stay in labor room. Diminution of above intems and opportune detection of dystocia, were determined. It was concluded that a constructive action plan, starting at hospital admission in most healthy women, allows a normal delivery of brief duration.

  16. Surface Active Components: Review

    Directory of Open Access Journals (Sweden)

    Z. Shafiei

    2014-03-01

    Full Text Available Biosurfactant or surface active components are produced by many different microorganisms. Biosurfactants are amphiphilic molecules with both hydrophilic and hydrophobic (generally hydrocarbon moieties that partition preferentially a within the interface between fluid phases with some other degrees of polarity and hydrogen bonding including oil/water or air/water interfaces. These properties render surfactants able to reducing surface and interfacial tension and forming microemulsion where hydrocarbons can solubilize in water or where water can solubilize in hydrocarbons, the majority of surfactants have gained importance in the fields of enhanced oil recovery, environmental bioremediation, food processing and pharmaceuticals. However, large-scale production of these molecules has not been realized as a result of low yields in production processes and high recovery and purification costs. This review article represents a classification of biosurfactant in addition to their microbial origin and effect of some nutrition and environmental factor for high production of biosurfactant. The nitrogen, carbon sources and environmental factors can make a difference key to the regulating biosurfactants synthesis Fascination with microbial surfactants have been steadily increasing recently because of advantages over the chemical surfactants for example environmentally friendly nature, lower toxicity, higher biodegradability, higher selectivity and specific gravity at extreme temperature, pH and salinity. For this reason the demand of biosurfactant are increasing day by day.

  17. Elusive Active Galactic Nuclei

    CERN Document Server

    Maiolino, R; Gilli, R; Nagar, N M; Bianchi, S; Böker, T; Colbert, E; Krabbe, A; Marconi, A; Matt, G; Salvati, M

    2003-01-01

    A fraction of active galactic nuclei do not show the classical Seyfert-type signatures in their optical spectra, i.e. they are optically "elusive". X-ray observations are an optimal tool to identify this class of objects. We combine new Chandra observations with archival X-ray data in order to obtain a first estimate of the fraction of elusive AGN in local galaxies and to constrain their nature. Our results suggest that elusive AGN have a local density comparable to or even higher than optically classified Seyfert nuclei. Most elusive AGN are heavily absorbed in the X-rays, with gas column densities exceeding 10^24 cm^-2, suggesting that their peculiar nature is associated with obscuration. It is likely that in elusive AGN, the nuclear UV source is completely embedded and the ionizing photons cannot escape, which prevents the formation of a classical Narrow Line Region. Elusive AGN may contribute significantly to the 30 keV bump of the X-ray background.

  18. ADASY (Active Daylighting System)

    Science.gov (United States)

    Vázquez-Moliní, Daniel; González-Montes, Mario; Fernández-Balbuena, Antonio Á.; Bernabéu, Eusebio; García-Botella, Ángel; García-Rodríguez, Lucas; Pohl, Wilfried

    2009-08-01

    The main objective of ADASY (Active Daylighting System) work is to design a façade static daylighting system oriented to office applications, mainly. The goal of the project is to save energy by guiding daylight into a building for lighting purpose. With this approach we can reduce the electrical load for artificial lighting, completing it with sustainable energy. The collector of the system is integrated on a vertical façade and its distribution guide is always horizontal inside of the false ceiling. ADASY is designed with a specific patent pending caption system, a modular light-guide and light extractor luminaire system. Special care has been put on the final cost of the system and its building integration purpose. The current ADASY configuration is able to illuminate 40 m2 area with a 300lx-400lx level in the mid time work hours; furthermore it has a good enough spatial uniformity distribution and a controlled glare. The data presented in this study are the result of simulation models and have been confirmed by a physical scaled prototype. ADASY's main advantages over regular illumination systems are: -Low maintenance; it has not mobile pieces and therefore it lasts for a long time and require little attention once installed. - No energy consumption; solar light continue working even if there has been a power outage. - High quality of light: the colour rendering of light is very high - Psychological benefits: People working with daylight get less stress and more comfort, increasing productivity. - Health benefits

  19. Barriers for recess physical activity

    DEFF Research Database (Denmark)

    Pawlowski, Charlotte Skau; Tjørnhøj-Thomsen, Tine; Schipperijn, Jasper

    2014-01-01

    BACKGROUND: Many children, in particular girls, do not reach the recommended amount of daily physical activity. School recess provides an opportunity for both boys and girls to be physically active, but barriers to recess physical activity are not well understood. This study explores gender...... differences in children's perceptions of barriers to recess physical activity. Based on the socio-ecological model four types of environmental barriers were distinguished: natural, social, physical and organizational environment. METHODS: Data were collected through 17 focus groups (at 17 different schools...... this study, we recommend promoting recess physical activity through a combination of actions, addressing barriers within the natural, social, physical and organizational environment....

  20. Perspectives in active liquid crystals.

    Science.gov (United States)

    Majumdar, Apala; Cristina, Marchetti M; Virga, Epifanio G

    2014-11-28

    Active soft matter is a young, growing field, with potential applications to a wide variety of systems. This Theme Issue explores this emerging new field by highlighting active liquid crystals. The collected contributions bridge theory to experiment, mathematical theories of passive and active nematics, spontaneous flows to defect dynamics, microscopic to continuum levels of description, spontaneous activity to biological activation. While the perspectives offered here only span a small part of this rapidly evolving field, we trust that they might provide the interested reader with a taste for this new class of non-equilibrium systems and their rich behaviour.

  1. In vivo imaging of protease activity by Probody therapeutic activation.

    Science.gov (United States)

    Wong, Kenneth R; Menendez, Elizabeth; Craik, Charles S; Kavanaugh, W Michael; Vasiljeva, Olga

    2016-03-01

    Probody™ therapeutics are recombinant, proteolytically-activated antibody prodrugs, engineered to remain inert until activated locally by tumor-associated proteases. Probody therapeutics exploit the fundamental dysregulation of extracellular protease activity that exists in tumors relative to healthy tissue. Leveraging the ability of a Probody therapeutic to bind its target at the site of disease after proteolytic cleavage, we developed a novel method for profiling protease activity in living animals. Using NIR optical imaging, we demonstrated that a non-labeled anti-EGFR Probody therapeutic can become activated and compete for binding to tumor cells in vivo with a labeled anti-EGFR monoclonal antibody. Furthermore, by inhibiting matriptase activity in vivo with a blocking-matriptase antibody, we show that the ability of the Probody therapeutic to bind EGFR in vivo was dependent on protease activity. These results demonstrate that in vivo imaging of Probody therapeutic activation can be used for screening and characterization of protease activity in living animals, and provide a method that avoids some of the limitations of prior methods. This approach can improve our understanding of the activity of proteases in disease models and help to develop efficient strategies for cancer diagnosis and treatment.

  2. Global optogenetic activation of inhibitory interneurons during epileptiform activity.

    Science.gov (United States)

    Ledri, Marco; Madsen, Marita Grønning; Nikitidou, Litsa; Kirik, Deniz; Kokaia, Merab

    2014-02-26

    Optogenetic techniques provide powerful tools for bidirectional control of neuronal activity and investigating alterations occurring in excitability disorders, such as epilepsy. In particular, the possibility to specifically activate by light-determined interneuron populations expressing channelrhodopsin-2 provides an unprecedented opportunity of exploring their contribution to physiological and pathological network activity. There are several subclasses of interneurons in cortical areas with different functional connectivity to the principal neurons (e.g., targeting their perisomatic or dendritic compartments). Therefore, one could optogenetically activate specific or a mixed population of interneurons and dissect their selective or concerted inhibitory action on principal cells. We chose to explore a conceptually novel strategy involving simultaneous activation of mixed populations of interneurons by optogenetics and study their impact on ongoing epileptiform activity in mouse acute hippocampal slices. Here we demonstrate that such approach results in a brief initial action potential discharge in CA3 pyramidal neurons, followed by prolonged suppression of ongoing epileptiform activity during light exposure. Such sequence of events was caused by massive light-induced release of GABA from ChR2-expressing interneurons. The inhibition of epileptiform activity was less pronounced if only parvalbumin- or somatostatin-expressing interneurons were activated by light. Our data suggest that global optogenetic activation of mixed interneuron populations is a more effective approach for development of novel therapeutic strategies for epilepsy, but the initial action potential generation in principal neurons needs to be taken in consideration.

  3. Evaluating Active U: an internet-mediated physical activity program

    Directory of Open Access Journals (Sweden)

    Goodrich David E

    2009-09-01

    Full Text Available Abstract Background Engaging in regular physical activity can be challenging, particularly during the winter months. To promote physical activity at the University of Michigan during the winter months, an eight-week Internet-mediated program (Active U was developed providing participants with an online physical activity log, goal setting, motivational emails, and optional team participation and competition. Methods This study is a program evaluation of Active U. Approximately 47,000 faculty, staff, and graduate students were invited to participate in the online Active U intervention in the winter of 2007. Participants were assigned a physical activity goal and were asked to record each physical activity episode into the activity log for eight weeks. Statistics for program reach, effectiveness, adoption, and implementation were calculated using the Re-Aim framework. Multilevel regression analyses were used to assess the decline in rates of data entry and goal attainment during the program, to assess the likelihood of joining a team by demographic characteristics, to test the association between various predictors and the number of weeks an individual met his or her goal, and to analyze server load. Results Overall, 7,483 individuals registered with the Active U website (≈16% of eligible, and 79% participated in the program by logging valid data at least once. Staff members, older participants, and those with a BMI P Conclusion Internet-mediated physical activity interventions that focus on physical activity logging and goal setting while incorporating team competition may help a significant percentage of the target population maintain their physical activity during the winter months.

  4. Resources Management in Active Networks

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    In an active network, users can insert customized active codes into active nodes to execute. Thus it needs more resources than those required by conventional networks, and these resources must be effectively monitored and managed. Management policies in existing OSs are too complicated to apply to simple active packets. In this paper, we present new resources management policies that are mainly adoped to manage CPU, storage and transmission bandwidth. Namely, we use SPF algorithm to schedule and process active packets, and import an interval queue method to allocate transmission bandwidth, and use feedback mechanism to control congestion. At the same time, we design some experiments on prototype systems with and without resources management policies respectively. The experiments results show that management policies presented by us can effectively manage resources in active nodes and can improve the performance of active networks.

  5. Activity cliffs and activity cliff generators based on chemotype-related activity landscapes.

    Science.gov (United States)

    Pérez-Villanueva, Jaime; Méndez-Lucio, Oscar; Soria-Arteche, Olivia; Medina-Franco, José L

    2015-11-01

    Activity cliffs have large impact in drug discovery; therefore, their detection and quantification are of major importance. This work introduces the metric activity cliff enrichment factor and expands the previously reported activity cliff generator concept by adding chemotype information to representations of the activity landscape. To exemplify these concepts, three molecular databases with multiple biological activities were characterized. Compounds in each database were grouped into chemotype classes. Then, pairwise comparisons of structure similarities and activity differences were calculated for each compound and used to construct chemotype-based structure-activity similarity (SAS) maps. Different landscape distributions among four major regions of the SAS maps were observed for different subsets of molecules grouped in chemotypes. Based on this observation, the activity cliff enrichment factor was calculated to numerically detect chemotypes enriched in activity cliffs. Several chemotype classes were detected having major proportion of activity cliffs than the entire database. In addition, some chemotype classes comprising compounds with smooth structure activity relationships (SAR) were detected. Finally, the activity cliff generator concept was applied to compounds grouped in chemotypes to extract valuable SAR information.

  6. Atmospheric neutrino data Active-Active x Active-Sterile oscillations

    CERN Document Server

    Peres, O L G

    1998-01-01

    I summarize here the results of a global fit to the full data set corresponding to 33.0 kt-yr of data of the Super-Kamiokande experiment as well as to all other experiments in order to compare the active-active and active-sterile neutrinos oscillation channels to the atmospheric neutrino anomaly.

  7. UV activity indicators

    Science.gov (United States)

    Buccino, A. P.; Mauas, P. J. D.

    In Order to continue the work displayed in Buccino & Mauas(2003) and Buccino (2003), we have calculated the index Mg II (Xhk) on 1640 high resolution IUE spectra of 269 main sequence stars of spectral classes F, G and K. From this set of observations, we found an exponential relation between the continuum UV flux and the color (B-V). Contrary to Schrijver et al (1989), who assumed that the continuum UV flux depended on the color following the relation found by Rutten (1984) for the visible one, i.e. the logarithm of the flux is proportional to a polynomial of third order with the color. Nevertheless, the exponential relation flux in the continuous UV and the color (B-V) fits far better to our data that the given one by Rutten (1984). Obtained this dependency for the ultraviolet continuum flux, the index Xhk can be obtained from the single flux in the lines core, allowing to calculate the index of Mg II for those spectra where the continuum is very dark and so the relation signal noise is very low. As it were already reported in previous works (Rutten (1991), Schrijver (1992)), we found a minimum basal flux in the Mg II h and k lines core due to the cromospheric heating by disipation of acustics waves. From this minimum flux, we calculated minimum index of activity that satisfactorily fits to the minimum values of the indexes calculated on the 1640 spectra like quotient between the flux in the line core and the continuous one.

  8. Strategy as active waiting.

    Science.gov (United States)

    Sull, Donald N

    2005-09-01

    Successful executives who cut their teeth in stable industries or in developed countries often stumble when they face more volatile markets. They falter, in part, because they assume they can gaze deep into the future and develop a long-term strategy that will confer a sustainable competitive advantage. But visibility into the future of volatile markets is sharply limited because so many different variables are in play. Factors such as technological innovation, customers' evolving needs, government policy, and changes in the capital markets interact with one another to create unexpected outcomes. Over the past six years, Donald Sull, an associate professor at London Business School, has led a research project examining some of the world's most volatile markets, from national markets like China and Brazil to industries like enterprise software, telecommunications, and airlines. One of the most striking findings from this research is the importance of taking action during comparative lulls in the storm. Huge business opportunities are relatively rare; they come along only once or twice in a decade. And, for the most part, companies can't manufacture those opportunities; changes in the external environment converge to make them happen. What managers can do is prepare for these golden opportunities by managing smart during the comparative calm of business as usual. During these periods of active waiting, leaders must probe the future and remain alert to anomalies that signal potential threats or opportunities; exercise restraint to preserve their war chests; and maintain discipline to keep the troops battle ready. When a golden opportunity or"sudden death"threat emerges, managers must have the courage to declare the main effort and concentrate resources to seize the moment.

  9. Genotoxic activity of praziquantel.

    Science.gov (United States)

    Montero, R; Ostrosky, P

    1997-12-01

    Praziquantel is a synthetic drug with a remarkable activity against parasites, particularly treamatodes and cestodes. Initial genotoxicity tests used a spectrum of endpoints including tests in bacteria, yeasts, mammalian cells and Drosophila and each one gave negative results. Effects on reproductive cells of mice were negative as well. However, host mediated studies in mice and humans were contradictory and a comutagenic effect with several mutagens and carcinogens was found. Later studies, including monitoring in humans and pigs have shown that Praziquantel induces a greater frequency of hyperploid lymphocytes as well as structural chromosomal aberrations, but not in all the individuals treated. In vitro studies have demonstrated that Praziquantel can induce micronuclei in syrian hamster embryonic (SHE) cells and in lymphocytes of some individuals. The same was found about structural chromosomal aberrations. Fetal death and fetal resorption were found when Praziquantel was administered in high doses to pregnant rats between the 6th and 10th day of gestation. Due to its efficiency as a parasiticide, Praziquantel is in use in Latin-American, Asiatic, African and East-European countries where infections by trematodes and cestodes are frequent. However, the extensive use of Praziquantel in multiple reinfections, in non-infected and non-diagnosed individuals for prevention, in higher doses or repeated doses for cysticercosis treatment and in individuals exposed to environmental mutagens, in conjunction with new findings about its metabolism and genotoxic properties, make it necessary to further evaluate the potential of this drug not only to be mutagenic per se, but to contribute in the development of neoplasm.

  10. Active Beam Spectroscopy

    Science.gov (United States)

    von Hellermann, M. G.; Delabie, E.; Jaspers, R. J. E.; Biel, W.; Marchuk, O.; Summers, H. P.; Whiteford, A.; Giroud, C.; Hawkes, N. C.; Zastrow, K. D.

    2008-03-01

    Charge eXchange Recombination Spectroscopy (CXRS) plays a pivotal role in the diagnostics of hot fusion plasmas and is implemented currently in most of the operating devices. In the present report the main features of CXRS are summarized and supporting software packages encompassing "Spectral Analysis Code CXSFIT", "Charge Exchange Analysis Package CHEAP", and finally "Forward Prediction of Spectral Features" are described. Beam Emission Spectroscopy (BES) is proposed as indispensable cross-calibration tool for absolute local impurity density measurements and also for the continuous monitoring of the neutral beam power deposition profile. Finally, a full exploitation of the `Motional Stark Effect' pattern is proposed to deduce local pitch angles, total magnetic fields and possibly radial electric fields. For the proposed active beam spectroscopy diagnostic on ITER comprehensive performance studies have been carried out. Estimates of expected spectral signal-to-noise ratios are based on atomic modelling of neutral beam stopping and emissivities for CXRS, BES and background continuum radiation as well as extrapolations from present CXRS diagnostic systems on JET, Tore Supra, TEXTOR and ASDEX-UG. Supplementary to thermal features a further promising application of CXRS has been proposed recently for ITER, that is a study of slowing-down alpha particles in the energy range up to 2 MeV making use of the 100 keV/amu DNB (Diagnostic Neutral Beam) and the 500 keV/amu HNB (Heating Neutral Beam). Synthetic Fast Ion Slowing-Down spectra are evaluated in terms of source rates and slowing-down parameters

  11. IDENTIFICATION AND ECOPHYSIOLOGY OF ACTIVE DENITRIFIERS IN ACTIVATED SLUDGE

    DEFF Research Database (Denmark)

    Hansen, Aviaja Anna; Le-Quy, Vang; Nielsen, Kåre Lehmann;

    and when external carbon sources were supplemented to the activated sludge the composition of the denitrifying communities was significantly affected. Transcriptome profiling provided detailed insight in the metabolic pathways in several of the active denitrifiers in activated sludge. In conclusion...... reactor studies. To obtain better identification of active denitrifying communities in full-scale wastewater treatment plants (WWTPs) we applied DNA-SIP with 13C-labelled substrates, and RT-PCR of expressed denitrification genes (nirS, nirK and nosZ) upon various substrate-inductions. To come around...... were determined with quantitative FISH, while their active metabolic pathways were investigated directly in activated sludge with a tag-based metatranscriptomic approach under acetate-utilizing and denitrifying conditions. The different methods revealed a majority of denitrifiers in all WWTPs belonging...

  12. Fluidization and Active Thinning by Molecular Kinetics in Active Gels.

    Science.gov (United States)

    Oriola, David; Alert, Ricard; Casademunt, Jaume

    2017-02-24

    We derive the constitutive equations of an active polar gel from a model for the dynamics of elastic molecules that link polar elements. Molecular binding kinetics induces the fluidization of the material, giving rise to Maxwell viscoelasticity and, provided that detailed balance is broken, to the generation of active stresses. We give explicit expressions for the transport coefficients of active gels in terms of molecular properties, including nonlinear contributions on the departure from equilibrium. In particular, when activity favors linker unbinding, we predict a decrease of viscosity with activity-active thinning-of kinetic origin, which could explain some experimental results on the cell cortex. By bridging the molecular and hydrodynamic scales, our results could help understand the interplay between molecular perturbations and the mechanics of cells and tissues.

  13. Negotiating active ageing at a Danish activity centre

    DEFF Research Database (Denmark)

    Lassen, Aske Juul

    and practices active ageing. The paper uses an activity centre in Copenhagen as its site of negotiation. Methods: These questions have been explored with the use of ethnographic fieldwork and through a documentary study. The ethnographic fieldwork has been conducted at an activity centre with 4 months...... of participatory observation in 2011 and 2012, as well as 11 semi-structured, in-depth interviews with users of the centre. 4 of these users have been followed around during everyday activities such as doing groceries, picking up grandchildren, etc. The documentary study consists of documents and statements...

  14. Activated coconut shell charcoal carbon using chemical-physical activation

    Science.gov (United States)

    Budi, Esmar; Umiatin, Nasbey, Hadi; Bintoro, Ridho Akbar; Wulandari, Futri; Erlina

    2016-02-01

    The use of activated carbon from natural material such as coconut shell charcoal as metal absorbance of the wastewater is a new trend. The activation of coconut shell charcoal carbon by using chemical-physical activation has been investigated. Coconut shell was pyrolized in kiln at temperature about 75 - 150 °C for about 6 hours in producing charcoal. The charcoal as the sample was shieved into milimeter sized granule particle and chemically activated by immersing in various concentration of HCl, H3PO4, KOH and NaOH solutions. The samples then was physically activated using horizontal furnace at 400°C for 1 hours in argon gas environment with flow rate of 200 kg/m3. The surface morphology and carbon content of activated carbon were characterized by using SEM/EDS. The result shows that the pores of activated carbon are openned wider as the chemical activator concentration is increased due to an excessive chemical attack. However, the pores tend to be closed as further increasing in chemical activator concentration due to carbon collapsing.

  15. Production and characterization of granular activated carbon from activated sludge

    Directory of Open Access Journals (Sweden)

    Z. Al-Qodah

    2009-03-01

    Full Text Available In this study, activated sludge was used as a precursor to prepare activated carbon using sulfuric acid as a chemical activation agent. The effect of preparation conditions on the produced activated carbon characteristics as an adsorbent was investigated. The results indicate that the produced activated carbon has a highly porous structure and a specific surface area of 580 m²/g. The FT-IR analysis depicts the presence of a variety of functional groups which explain its improved adsorption behavior against pesticides. The XRD analysis reveals that the produced activated carbon has low content of inorganic constituents compared with the precursor. The adsorption isotherm data were fitted to three adsorption isotherm models and found to closely fit the BET model with R² equal 0.948 at pH 3, indicating a multilayer of pesticide adsorption. The maximum loading capacity of the produced activated carbon was 110 mg pesticides/g adsorbent and was obtained at this pH value. This maximum loading was found experimentally to steeply decrease as the solution pH increases. The obtained results show that activated sludge is a promising low cost precursor for the production of activated carbon.

  16. Silicon active photonic devices

    Science.gov (United States)

    Dimitropoulos, Dimitrios

    Active photonic devices utilizing the optical nonlinearities of silicon have emerged in the last 5 years and the effort for commercial photonic devices in the material that has been the workhorse of electronics has been building up since. This dissertation presents the theory for some of these devices. We are concerned herein with CW lasers, amplifiers and wavelength converters that are based on the Raman effect. There have already been cursory experimental demonstrations of these devices and some of their limitations are already apparent. Most of the limitations observed are because of the appearance of effects that are competing with stimulated Raman scattering. Under the high optical powers that are necessary for the Raman effect (tens to hundrends of mW's) the process of optical two-photon (TPA) absorption occurs. The absorption of optical power that it causes itself is weak but in the process electrons and holes are generated which can further absorb light through the free-carrier absorption effect (FCA). The effective "lifetime" that these carriers have determines the magnitude of the FCA loss. We present a model for the carrier lifetime in Silicon-On-Insulator (SOI) waveguides and numerical simulations to understand how this critical parameter varies and how it can be controlled. A p-i-n junction built along SOI waveguides can help achieve lifetime of the order of 20--100 ps but the price one has to pay is on-chip electrical power consumption on the order of 100's of mWs. We model CW Raman lasers and we find that the carrier lifetime reduces the output power. If the carrier lifetime exceeds a certain "critical" value optical losses become overwhelming and lasing is impossible. As we show, in amplifiers, the nonlinear loss does not only result in diminished gain, but also in a higher noise figure. Finally the effect of Coherent anti-Stokes Raman scattering (CARS) is examined. The effect is important because with a pump frequency at 1434nm coherent power

  17. Permanent active longitudes and activity cycles on RS CVn stars

    Science.gov (United States)

    Berdyugina, Svetlana V.; Tuominen, Ilkka

    1998-08-01

    A new analysis of the published long-term photometric observations has revealed permanent active-longitude structures in four RS CVn stars: EI Eri, II Peg, sigma Gem, and HR 7275. Two active longitudes separated by half of the period are found to dominate on the surface during all available seasons. The positions of the longitudes on three stars (EI Eri, II Peg, HR 7275) are migrating in the orbital reference frame, and there is no preferred orientation with respect to the line of centres in the binaries. The rate of migration is approximately constant. In case of sigma Gem the active longitude migration is synchronized with the orbital motion in the direction of the line of centres in the binary. The active region lifetimes can be longer than the time span of the observations (>=15 yr). The periods of the active longitude rotation are determined: for EI Eri 1fd 9510, for II Peg 6fd 7066, for sigma Gem 19fd 604, for HR 7275 28fd 263. Long-term activity cycles of the stars are discovered from the analysis of the relative contribution of the two longitudes to the photometric variability. One longitude is found to be usually more active than the other at a given moment, and the change of the activity level between the longitudes is cyclic with periods of years. The switch of the activity takes a much shorter time, about a few months, similar to the ``flip-flop'' phenomenon found for FK Com stars. Moments of switching are regarded as new tracers of the activity, and total cycles, which return activity to the same longitude, are found to be for EI Eri 9.0 yr, for II Peg 9.3 yr, for sigma Gem 14.9 yr, for HR 7275 17.5 yr.

  18. Tyrosine phosphorylation of NEDD4 activates its ubiquitin ligase activity.

    Science.gov (United States)

    Persaud, Avinash; Alberts, Philipp; Mari, Sara; Tong, Jiefei; Murchie, Ryan; Maspero, Elena; Safi, Frozan; Moran, Michael F; Polo, Simona; Rotin, Daniela

    2014-10-07

    Ligand binding to the receptor tyrosine kinase fibroblast growth factor (FGF) receptor 1 (FGFR1) causes dimerization and activation by transphosphorylation of tyrosine residues in the kinase domain. FGFR1 is ubiquitylated by the E3 ligase NEDD4 (also known as NEDD4-1), which promotes FGFR1 internalization and degradation. Although phosphorylation of FGFR1 is required for NEDD4-dependent endocytosis, NEDD4 directly binds to a nonphosphorylated region of FGFR1. We found that activation of FGFR1 led to activation of c-Src kinase-dependent tyrosine phosphorylation of NEDD4, enhancing the ubiquitin ligase activity of NEDD4. Using mass spectrometry, we identified several FGF-dependent phosphorylated tyrosines in NEDD4, including Tyr(43) in the C2 domain and Tyr(585) in the HECT domain. Mutating these tyrosines to phenylalanine to prevent phosphorylation inhibited FGF-dependent NEDD4 activity and FGFR1 endocytosis and enhanced cell proliferation. Mutating the tyrosines to glutamic acid to mimic phosphorylation enhanced NEDD4 activity. Moreover, the NEDD4 C2 domain bound the HECT domain, and the presence of phosphomimetic mutations inhibited this interaction, suggesting that phosphorylation of NEDD4 relieves an inhibitory intra- or intermolecular interaction. Accordingly, activation of FGFR1 was not required for activation of NEDD4 that lacked its C2 domain. Activation of c-Src by epidermal growth factor (EGF) also promoted tyrosine phosphorylation and enhanced the activity of NEDD4. Thus, we identified a feedback mechanism by which receptor tyrosine kinases promote catalytic activation of NEDD4 and that may represent a mechanism of receptor crosstalk.

  19. CDPK Activation in PRR Signaling.

    Science.gov (United States)

    Seybold, Heike; Boudsocq, Marie; Romeis, Tina

    2017-01-01

    Calcium-dependent protein kinases undergo a rapid biochemical activation in response to an intracellular Ca increase induced by the PRR-dependent perception of a pathogen-related stimulus. Based on SDS gel resolution, the in-gel kinase assay allows the analysis of multiple in vivo protein samples in parallel, combining the advantage of protein separation according to molecular mass with the activity read-out of a protein kinase assay. It thus enables to follow the transient CDPK activation and inactivation in response to in vivo elicitation with a time-wise resolution. In addition, changes of CDPK phosphorylation activity often correlate with slight shifts in the enzyme's apparent molecular mass, indicating posttranslational modifications and a conformational change of the active enzyme compared to its inactive resting form. These band shifts can be detected by a simple immunoblotting to monitor CDPK activation.

  20. Swim pressure of active matter

    Science.gov (United States)

    Takatori, Sho; Yan, Wen; Brady, John; Caltech Team

    2014-11-01

    Through their self-motion, all active matter systems generate a unique ``swim pressure'' that is entirely athermal in origin. This new source for the active stress exists at all scales in both living and nonliving active systems, and also applies to larger organisms where inertia is important (i.e., the Stokes number is not small). Here we explain the origin of the swim stress and develop a simple thermodynamic model to study the self-assembly and phase separation in active soft matter. Our new swim stress perspective can help analyze and exploit a wide class of active soft matter, from swimming bacteria and catalytic nanobots, schools of fish and birds, and molecular motors that activate the cellular cytoskeleton.

  1. Enhanced NIF neutron activation diagnostics.

    Science.gov (United States)

    Yeamans, C B; Bleuel, D L; Bernstein, L A

    2012-10-01

    The NIF neutron activation diagnostic suite relies on removable activation samples, leading to operational inefficiencies and a fundamental lower limit on the half-life of the activated product that can be observed. A neutron diagnostic system measuring activation of permanently installed samples could remove these limitations and significantly enhance overall neutron diagnostic capabilities. The physics and engineering aspects of two proposed systems are considered: one measuring the (89)Zr/(89 m)Zr isomer ratio in the existing Zr activation medium and the other using potassium zirconate as the activation medium. Both proposed systems could improve the signal-to-noise ratio of the current system by at least a factor of 5 and would allow independent measurement of fusion core velocity and fuel areal density.

  2. Catalytic activity of Au nanoparticles

    DEFF Research Database (Denmark)

    Larsen, Britt Hvolbæk; Janssens, Ton V.W.; Clausen, Bjerne;

    2007-01-01

    Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change with par......Au is usually viewed as an inert metal, but surprisingly it has been found that Au nanoparticles less than 3–5 nm in diameter are catalytically active for several chemical reactions. We discuss the origin of this effect, focusing on the way in which the chemical activity of Au may change...... with particle size. We find that the fraction of low-coordinated Au atoms scales approximately with the catalytic activity, suggesting that atoms on the corners and edges of Au nanoparticles are the active sites. This effect is explained using density functional calculations....

  3. Social activity and healthy aging

    DEFF Research Database (Denmark)

    McGue, Matt; Christensen, Kaare

    2007-01-01

    with late-life physical functioning, cognitive functioning, and depression symptomatology using data from 1112 pairs of like-sex twins who participated in the Longitudinal Study of Aging Danish Twins. Consistent with previous research, we found that social activity was significantly correlated with overall...... level of physical functioning, cognitive functioning, and depression symptomatology. We also found that social activity was significantly and moderately heritable (estimate of .36), raising the possibility that its association with late-life functioning might reflect selection processes. Further, social...... activity did not predict change in functioning and in monozygotic twin pairs discordant on level of social activity, the more socially active twin was not less susceptible to age decreases in physical and cognitive functioning and increases in depression symptomatology than the less socially active twin...

  4. Activated sludge inhibition capacity index

    Directory of Open Access Journals (Sweden)

    V. Surerus

    2014-06-01

    Full Text Available Toxic compounds in sewage or industrial wastewater may inhibit the biological activity of activated sludge impairing the treatment process. This paper evaluates the Inhibition Capacity Index (ICI for the assessment of activated sludge in the presence of toxicants. In this study, activated sludge was obtained from industrial treatment plants and was also synthetically produced. Continuous respirometric measurements were carried out in a reactor, and the oxygen uptake rate profile obtained was used to evaluate the impact of inhibiting toxicants, such as dissolved copper, phenol, sodium alkylbenzene sulfonate and amoxicillin, on activated sludge. The results indicate that ICI is an efficient tool to quantify the intoxication capacity. The activated sludge from the pharmaceutical industry showed higher resistance than the sludge from other sources, since toxicants are widely discharged in the biological treatment system. The ICI range was from 58 to 81% when compared to the synthetic effluent with no toxic substances.

  5. Japanese activities in refrigeration technology

    Science.gov (United States)

    Fujita, T.; Ohtsuka, T.; Ishizaki, Y.

    This paper reviews recent activities in refrigeration technology in Japan. The projects described are stimulated by growing industrial needs or form part of large national projects. The JNR project on the MAGLEV train is currently the most powerful activity and it demands knowledge in all the different disciplines of cryogenics in particular on various scales of refrigeration. Research activities are also directed towards the development of Stirling cycle and magnetic refrigerators for applications in a wider area.

  6. L3 Study Team Activities

    Science.gov (United States)

    Shoemaker, David; L3ST Team

    2017-01-01

    The NASA-Chartered L3 Study Team is working to develop the US community participation and to support NASA's contribution to the ESA-led LISA mission to observe gravitational waves via space-based detectors. The present activities of the L3ST will be described, and the next steps for the Study Team will also be given. NASA supports travel activities and support for the Study Team activities.

  7. INNOVATIONS AND TOURISTIC ACTIVITY EVOLUTION

    Directory of Open Access Journals (Sweden)

    V. S. Novikov

    2012-01-01

    Full Text Available Fundamental and applied innovations impact activities in the tourist industry and evolution thereof. More and more sophisticated technologies and communication techniques are practically used to serve tourists. Basically, innovative tourist activity development concept represents innovation of values and in particular means that tourist’s impression is taken into account to higher extent and tourist product personification changes the products’ consumer value. Discussed in the article are tourist activity, tourist cluster, destination and glocalization development prospects.

  8. Activity Recognition in Social Media

    Science.gov (United States)

    2015-12-29

    activity is splitting. 6 Crowd video classification Ability to identify crowd behavior enables crowd management systems to design and manage public...characterize group activities . We then showed the effectiveness of group level features in crowd video classification . 9 List of Publications 1. N. Bhargava, S...AFRL-AFOSR-JP-TR-2016-0044 Activity Recognition in Social Media Subhasis Chaudhuri INDIAN INSTITUTE OF TECHNOLOGY BOMBAY Final Report 05/09/2016

  9. Activating Teaching for Quality Learning

    DEFF Research Database (Denmark)

    Zhurbenko, Vitaliy

    2013-01-01

    Activating teaching is an educational concept which is based on active participation of students in the study process. It is becoming an alternative to more typical approach where the teacher will just lecture and the students will take notes. The study described in this paper considers student...... activating teaching methods focusing on those based on knowledge dissemination. The practical aspects of the implemented teaching method are considered, and employed assessment methods and tools are discussed....

  10. Spanish Young Generation (JJNN) Activities

    Energy Technology Data Exchange (ETDEWEB)

    Millan, Miguel [INITEC Nuclear- Westinghouse, Padilla 17, 28006 Madrid (Spain)

    2008-07-01

    Spanish Young Generation has been very active during 2006-2008. JJNN have mainly focused on communication activities, as conferences at universities, schools and nuclear companies. Lately, becoming in referent of the young politics, journalist and the young people in Nuclear Subjects is the new and most challenging target of the Spanish Young Generation. In order to accomplish with their objects and commitments with their members, JJNN are developing all kinds of activities focused in the young people and the JJNN members. (authors)

  11. Architectural Design Activities for JAS

    CERN Document Server

    Khaled, Lena

    2009-01-01

    The critical part for building any software system is its architecture. Architectural design is a design at a higher level of abstraction. A good architecture ensures that software will satisfy its requirement. This paper defines the most important activities of architectural design that used through building any software; also it applies these activities on one type of Electronic Commerce (EC) applications that is Job Agency System(JAS) to show how these activities can work through these types of applications.

  12. Biological Activities of Hydrazone Derivatives

    Directory of Open Access Journals (Sweden)

    S. Güniz Küçükgüzel

    2007-08-01

    Full Text Available There has been considerable interest in the development of novel compounds with anticonvulsant, antidepressant, analgesic, antiinflammatory, antiplatelet, antimalarial, antimicrobial, antimycobacterial, antitumoral, vasodilator, antiviral and antischistosomiasis activities. Hydrazones possessing an azometine -NHN=CH- proton constitute an important class of compounds for new drug development. Therefore, many researchers have synthesized these compounds as target structures and evaluated their biological activities. These observations have been guiding for the development of new hydrazones that possess varied biological activities.

  13. Active Combustion Control Valve Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Over the past decade, research into active combustion control has yielded impressive results in suppressing thermoacoustic instabilities and widening the...

  14. Studies in geophysics: Active tectonics

    Science.gov (United States)

    1986-01-01

    Active tectonics is defined within the study as tectonic movements that are expected to occur within a future time span of concern to society. Such movements and their associated hazards include earthquakes, volcanic eruptions, and land subsidence and emergence. The entire range of geology, geophysics, and geodesy is, to some extent, pertinent to this topic. The needs for useful forecasts of tectonic activity, so that actions may be taken to mitigate hazards, call for special attention to ongoing tectonic activity. Further progress in understanding active tectonics depends on continued research. Particularly important is improvement in the accuracy of dating techniques for recent geologic materials.

  15. Physical Activity in the Classroom

    DEFF Research Database (Denmark)

    Réol, Lise Andersen

    2016-01-01

    physical activity during each school day from 0th to 10th school year, as a tool to facilitate health, motivation and academic performance. A qualitative study on pupils in 6th grade (N=8) and teachers’ (N=3) experience of movement and physical activities in school gives support to the idea, that physical...... activities in school enhance positive emotions and support an inclusive and safe learning environment. Thought it does also point to the fact, that it is indeed not that simple. Teachers’ sport-specific educational competences, their own experience of well-being and fun related to physical activities...

  16. THERMAL ACTIVATION OF IMMOBILIZED PAPAIN

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    Papain (Papainase, EC 3.4.22.2) was immobilized on porous silica beads by cross linking with glutaraldehyde. The thermal activation of this immobilized papain in aqueous system was found at a temperature range from 50 to 90℃. The higher the temperature, the more active the immobilized papain will possess. At the same time,the durability of the immobilized papain on heating was greatly improved. The effect of additives and salts on the activity of the immobilized papain were also studied. The results showed that the additives and some of the salts studied could markedly enhance the activity of the immobilized papain at elevated temperature.

  17. CDBG Activity Funding by Tract

    Data.gov (United States)

    Department of Housing and Urban Development — All CDBG activities in the categories of acquisition, economic development, housing, public improvements, public services, and other summarized by Census Tract.

  18. Physical activity and human health

    Directory of Open Access Journals (Sweden)

    Paulina Wojciechowska

    2015-01-01

    Full Text Available Introduction: The dynamic development of the automotive industry, transport, and the media means that human life has become much easier. At the same time, the comfortable living conditions have decreased physical activity. Biologically conditioned, the need of activity has been minimised by the ever-increasing pace of life. As a result, it may lead to the loss of physical and mental health. Active recreation is not only an excellent source of activity, but also a source of satisfaction. Youths and adults should therefore spend their free time primarily on various forms of physical activity. Aim of the research : To evaluate the physical fitness of students who regularly practice physical exercise, those who occasionally practice, and those not practicing any form of physical activity. Material and methods : In the research we used a questionnaire of the Ruffier test and an orthostatic test. The study involved a group of 15 people aged 20–25 years. Participation in the study was entirely voluntary and anonymous. The study group consisted only of women. Results obtained from the questionnaire survey were fully reflected during exercise tests performed. Results and conclusions: Only regularly practiced physical activity has an effect on our body. Regular exercise increases our body’s physical capacity. Activity is the best means of prevention of lifestyle diseases. Youths and adults should spend their free time mainly doing various forms of physical activity.

  19. Active Combustion Control Valve Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Over the past decade, research into active combustion control has yielded impressive results in suppressing thermoacoustic instabilities and widening the operational...

  20. Active Gas Regenerative Liquefier Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We offer a novel liquefier that has the potential to simultaneously increase thermodynamic efficiency and significantly reduce complexity. The ?active gas...