WorldWideScience

Sample records for relics including retrotransposons

  1. Retrotransposon Domestication and Control in Dictyostelium discoideum

    Directory of Open Access Journals (Sweden)

    Marek Malicki

    2017-10-01

    Full Text Available Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition. Several of its contemporary retrotransposons display intrinsic integration preferences, for example by inserting next to transfer RNA genes or other retroelements. Likely, any retrotransposons that invaded the genome of the amoeba in a non-directed manner were lost during evolution, as this would result in decreased fitness of the organism. Thus, the positional preference of the Dictyostelium retroelements might represent a domestication of the selfish elements. Likewise, the reduced danger of such domesticated transposable elements led to their accumulation, and they represent about 10% of the current genome of D. discoideum. To prevent the uncontrolled spreading of retrotransposons, the amoeba employs control mechanisms including RNA interference and heterochromatization. Here, we review TRE5-A, DIRS-1 and Skipper-1, as representatives of the three retrotransposon classes in D. discoideum, which make up 5.7% of the Dictyostelium genome. We compile open questions with respect to their mobility and cellular regulation, and suggest strategies, how these questions might be addressed experimentally.

  2. [Non-LTR retrotransposons: LINEs and SINEs in plant genome].

    Science.gov (United States)

    Cheng, Xu-Dong; Ling, Hong-Qing

    2006-06-01

    Retrotransposons are one of the drivers of genome evolution. They include LTR (long terminal repeat) retrotransposons, which widespread in Eukaryotagenomes, show structural similarity to retroviruses. Non-LTR retrotransposons were first discovered in animal genomes and then identified as ubiquitous components of nuclear genomes in many species across the plant kingdom. They constitute a large fraction of the repetitive DNA. Non-LTR retrotransposons are divided into LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements). Transposition of non-LTR retrotransposons is rarely observed in plants indicating that most of them are inactive and/or under regulation of the host genome. Transposition is poorly understood, but experimental evidence from other genetic systems shows that LINEs are able to transpose autonomously while non-autonomous SINEs depend on the reverse transcription machinery of other retrotransposons. Phylogenic analysis shows LINEs are probably the most ancient class of retrotransposons in plant genomes, while the origin of SINEs is unknown. This review sums up the above data and wants to show readers a clear picture of non-LTR retrotransposons.

  3. Identification of retrotransposon-like sequences in Iranian river buffalo

    African Journals Online (AJOL)

    ONOS

    2010-03-29

    % of a genome (Waterston et al., 2002). Mobile elements can be divided into two classes: Class I includes retrotransposons and class II includes DNA tran- sposons ... including dog, cat, horse, cattle, donkey, kangaroo, etc.

  4. LTR retrotransposons in fungi.

    Directory of Open Access Journals (Sweden)

    Anna Muszewska

    Full Text Available Transposable elements with long terminal direct repeats (LTR TEs are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (8000 elements. The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other.

  5. Retrotransposons and non-protein coding RNAs

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2009-01-01

    does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review...

  6. The number density of a charged relic

    International Nuclear Information System (INIS)

    Berger, C.F.; Kraml, S.; Palorini, F.

    2008-07-01

    We investigate scenarios in which a charged, long-lived scalar particle decouples from the primordial plasma in the Early Universe. We compute the number density at time of freeze-out considering both the cases of abelian and non-abelian interactions and including the effect of Sommerfeld enhancement at low initial velocity. We also discuss as extreme case the maximal cross section that fulfils the unitarity bound. We then compare these number densities to the exotic nuclei searches for stable relics and to the BBN bounds on unstable relics and draw conclusions for the cases of a stau or stop NLSP in supersymmetric models with a gravitino or axino LSP. (orig.)

  7. The number density of a charged relic

    Energy Technology Data Exchange (ETDEWEB)

    Berger, C.F. [Massachusetts Institute of Technology, Cambridge, MA (United States). Center for Theoretical Physics]|[California Univ., Santa Barbara, CA (United States). Kavli Inst. for Theoretical Physics; Covi, L. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Kraml, S. [CNRS/IN2P3, Grenoble (France). Lab. de Physique Subatomique et de Cosmologie; Palorini, F. [Lyon Univ., UCBL, CNRS/IN2P3, Villeurbanne (France). IPN de Lyon

    2008-07-15

    We investigate scenarios in which a charged, long-lived scalar particle decouples from the primordial plasma in the Early Universe. We compute the number density at time of freeze-out considering both the cases of abelian and non-abelian interactions and including the effect of Sommerfeld enhancement at low initial velocity. We also discuss as extreme case the maximal cross section that fulfils the unitarity bound. We then compare these number densities to the exotic nuclei searches for stable relics and to the BBN bounds on unstable relics and draw conclusions for the cases of a stau or stop NLSP in supersymmetric models with a gravitino or axino LSP. (orig.)

  8. Drosophila: Retrotransposons Making up Telomeres.

    Science.gov (United States)

    Casacuberta, Elena

    2017-07-19

    Drosophila and extant species are the best-studied telomerase exception. In this organism, telomere elongation is coupled with targeted retrotransposition of Healing Transposon (HeT-A) and Telomere Associated Retrotransposon (TART) with sporadic additions of Telomere Associated and HeT-A Related (TAHRE), all three specialized non-Long Terminal Repeat (non-LTR) retrotransposons. These three very special retroelements transpose in head to tail arrays, always in the same orientation at the end of the chromosomes but never in interior locations. Apparently, retrotransposon and telomerase telomeres might seem very different, but a detailed view of their mechanisms reveals similarities explaining how the loss of telomerase in a Drosophila ancestor could successfully have been replaced by the telomere retrotransposons. In this review, we will discover that although HeT-A, TART, and TAHRE are still the only examples to date where their targeted transposition is perfectly tamed into the telomere biology of Drosophila, there are other examples of retrotransposons that manage to successfully integrate inside and at the end of telomeres. Because the aim of this special issue is viral integration at telomeres, understanding the base of the telomerase exceptions will help to obtain clues on similar strategies that mobile elements and viruses could have acquired in order to ensure their survival in the host genome.

  9. The physics of relic neutrinos

    International Nuclear Information System (INIS)

    Dighe, A.; Pastor, S.; Smirnov, A.

    1998-12-01

    We report on the main results presented at the workshop on the Physics of Relic Neutrinos. The study of relic neutrinos involves a broad spectrum of problems in particle physics, astrophysics and cosmology. Features of baryogenesis and leptogenesis could be imprinted in the properties of the relic neutrino sea. Relic neutrinos played a crucial role in the big bang nucleosynthesis. Being the hot component of the dark matter, they have participated in the structure formation in the universe. Although the direct detection of the sea seems impossible at this stage, there could be various indirect manifestations of these neutrinos which would allow us to study the properties of the sea both in the past and at the present epoch. (author)

  10. Relic gravitational waves and cosmology

    International Nuclear Information System (INIS)

    Grishchuk, Leonid P

    2005-01-01

    The paper begins with a brief recollection of interactions of the author with Ya B Zeldovich in the context of the study of relic gravitational waves. The principles and early results on the quantum-mechanical generation of cosmological perturbations are then summarized. The expected amplitudes of relic gravitational waves differ in various frequency windows, and therefore the techniques and prospects of their detection are distinct. One section of the paper describes the present state of efforts in direct detection of relic gravitational waves. Another section is devoted to indirect detection via the anisotropy and polarization measurements of the cosmic microwave background (CMB) radiation. It is emphasized throughout the paper that the inference about the existence and expected amount of relic gravitational waves is based on a solid theoretical foundation and the best available cosmological observations. It is also explained in great detail what went wrong with the so-called 'inflationary gravitational waves', whose amount is predicted by inflationary theorists to be negligibly small, thus depriving them of any observational significance. (reviews of topical problems)

  11. Relics in galaxy clusters at high radio frequencies

    Science.gov (United States)

    Kierdorf, M.; Beck, R.; Hoeft, M.; Klein, U.; van Weeren, R. J.; Forman, W. R.; Jones, C.

    2017-04-01

    Aims: We investigated the magnetic properties of radio relics located at the peripheries of galaxy clusters at high radio frequencies, where the emission is expected to be free of Faraday depolarization. The degree of polarization is a measure of the magnetic field compression and, hence, the Mach number. Polarization observations can also be used to confirm relic candidates. Methods: We observed three radio relics in galaxy clusters and one radio relic candidate at 4.85 and 8.35 GHz in total emission and linearly polarized emission with the Effelsberg 100-m telescope. In addition, we observed one radio relic candidate in X-rays with the Chandra telescope. We derived maps of polarization angle, polarization degree, and Faraday rotation measures. Results: The radio spectra of the integrated emission below 8.35 GHz can be well fitted by single power laws for all four relics. The flat spectra (spectral indices of 0.9 and 1.0) for the so-called Sausage relic in cluster CIZA J2242+53 and the so-called Toothbrush relic in cluster 1RXS 06+42 indicate that models describing the origin of relics have to include effects beyond the assumptions of diffuse shock acceleration. The spectra of the radio relics in ZwCl 0008+52 and in Abell 1612 are steep, as expected from weak shocks (Mach number ≈2.4). Polarization observations of radio relics offer a method of measuring the strength and geometry of the shock front. We find polarization degrees of more than 50% in the two prominent Mpc-sized radio relics, the Sausage and the Toothbrush, which are among the highest percentages of linear polarization detected in any extragalactic radio source to date. This is remarkable because the large beam size of the Effelsberg single-dish telescope corresponds to linear extensions of about 300 kpc at 8.35 GHz at the distances of the relics. The high degree of polarization indicates that the magnetic field vectors are almost perfectly aligned along the relic structure, as expected for shock

  12. Modeling the amplification dynamics of human Alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    Dale J Hedges

    2005-09-01

    Full Text Available Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.

  13. Modeling the amplification dynamics of human alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.

  14. Prediction of retrotransposons and assessment of genetic variability based on developed retrotransposon-based insertion polymorphism (RBIP) markers in Pyrus L.

    Science.gov (United States)

    Jiang, Shuang; Zong, Yu; Yue, Xiaoyan; Postman, Joseph; Teng, Yuanwen; Cai, Danying

    2015-02-01

    Interspecific hybridization has been considered the major mode of evolution in Pyrus (pear), and thus, the genetic relationships within this genus have not been well documented. Retrotransposons are ubiquitous components of plant genomes and 42.4 % of the pear genome was reported to be long terminal repeat (LTR) retrotransposons, implying that retrotransposons might be significant in the evolution of Pyrus. In this study, 1,836 putative full-length LTR retrotransposons were isolated and 196 retrotransposon-based insertion polymorphism (RBIP) primers were developed, of which 24 pairs to the Ppcr1 subfamily of copia retrotransposons were used to analyze genetic diversity among 110 Pyrus accessions from Eurasia. Our results showed that Ppcr1 replicated many times in the development of cultivated Asian pears. The genetic structure analysis and the unweighted pair group method with arithmetic mean (UPGMA) dendrogram indicated that all accessions could be divided into Oriental and Occidental groups. In Oriental pears, wild pea pears clustered separately into independent groups in accordance with their morphological classifications. Cultivars of P. ussuriensis Maxim, P. pyrifolia Nakai, and P. pyrifolia Chinese white pear were mingled together, which inferred that hybridization events occurred during the development of the cultivated Asian pears. In Occidental pears, two clades were obtained in the UPGMA dendrogram in accordance with their geographical distribution; one contained the European species and the other included species from North Africa and West Asia. New findings in this study will be important to further understand the phylogeny of Pyrus and origins of cultivated pears.

  15. Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants

    Directory of Open Access Journals (Sweden)

    Blinov Alexander

    2010-04-01

    Full Text Available Abstract Background Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes. Results In present study we preformed in silico analysis of chromodomain-containing LTR retrotransposons in 25 diverse fungi and a number of plant species including spikemoss Selaginella moellendorffii (Lycopodiophyta coupled with an experimental survey of chromodomain-containing Gypsy LTR retrotransposons from diverse non-seed vascular plants (lycophytes, ferns, and horsetails. Our mining of Gypsy LTR retrotransposons in genomic sequences allowed identification of numerous families which have not been described previously in fungi. Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes. It appeared that one of the clades, namely Tcn1 clade, was present in basidiomycetes and non-seed plants including mosses (Bryophyta and lycophytes (genus Selaginella. Conclusions The interkingdom distribution is not typical for chromodomain-containing LTR retrotransposons clades which are usually very specific for a particular taxonomic group. Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the

  16. Prospects for relic neutrino detection

    International Nuclear Information System (INIS)

    Smith, P.F.

    1991-03-01

    The standard big bang model predicts a universal background of relic neutrinos, comparable in number density to the background microwave photons. This neutrino background is undetectable at the present time firstly because the neutrino energy is very low (10 -4 -10 -5 eV) resulting in a very low energy transfer to any conceivable detector, and secondly the low energy gives a lower interaction cross section and hence a very low event rate per unit mass. These obstacles have so far precluded any realistic proposal for relic neutrino detection. The aim of this paper is to illustrate the difficulties in detecting these neutrinos by summarizing six detection ideas which have been previously considered, indicating in each case the problems which have prevented the idea being developed into an experimental proposal. The most promising direction for further study would appear to be that of coherent interactions. So far, no investigations of this idea have resulted in a practical detection scheme, but in this paper one new variation is suggested which could in principle give an observable effect, if the necessary stringent experimental conditions could be created. It is suggested that this may become possible with the aid of foreseeable 21st century developments in nanotechnology. (author)

  17. Relic gravitons and viscous cosmologies

    International Nuclear Information System (INIS)

    Cataldo, Mauricio; Mella, Patricio

    2006-01-01

    Previously it was shown that there exists a class of viscous cosmological models which violate the dominant energy condition for a limited amount of time after which they are smoothly connected to the ordinary radiation era (which preserves the dominant energy conditions). This violation of the dominant energy condition at an early cosmological epoch may influence the slopes of energy spectra of relic gravitons that might be of experimental relevance. However, the bulk viscosity coefficient of these cosmologies became negative during the ordinary radiation era, and then the entropy of the sources driving the geometry decreases with time. We show that in the presence of viscous sources with a linear barotropic equation of state p=γρ we get viscous cosmological models with positive bulk viscous stress during all their evolution, and hence the matter entropy increases with the expansion time. In other words, in the framework of viscous cosmologies, there exist isotropic models compatible with the standard second law of thermodynamics which also may influence the slopes of energy spectra of relic gravitons

  18. Cosmic relics from the big bang

    International Nuclear Information System (INIS)

    Hall, L.J.

    1988-12-01

    A brief introduction to the big bang picture of the early universe is given. Dark matter is discussed; particularly its implications for elementary particle physics. A classification scheme for dark matter relics is given. 21 refs., 11 figs., 1 tab

  19. Cosmic relics from the big bang

    Energy Technology Data Exchange (ETDEWEB)

    Hall, L.J.

    1988-12-01

    A brief introduction to the big bang picture of the early universe is given. Dark matter is discussed; particularly its implications for elementary particle physics. A classification scheme for dark matter relics is given. 21 refs., 11 figs., 1 tab.

  20. [Ulysses retrotransposon aspartate proteinase (Drosophila virilis)].

    Science.gov (United States)

    Volkov, D A; Savvateeva, L V; Dergousova, N I; Rumsh, L D

    2002-01-01

    Retrotransposones are mobile genetic elements occurring in genomes of bacteria, plants or animals. Retrotransposones were found to contain nucleotide sequences encoding proteins which are homological to retroviral aspartic proteinases. Our research has been focused on Ulysses which is mobile genetic element found in Drosophila virilis. We suggested a primary structure of Ulysses proteinase using comparative analysis of amino acid sequences of retroviral proteinases and proteinases from retrotransposones. The appropriate cDNA fragment has been cloned and expressed in E. coli. The purification of recombinant protein (12 kD) has been carried out by affinity chromatography using pepstatine-agarose. The obtained protein has proteolytic activity at optimum pH 5.5 like the majority of aspartic proteinases.

  1. RELICS of the Cosmic Dawn

    Science.gov (United States)

    Bradac, Marusa; Coe, Dan; Strait, Victoria; Salmon, Brett; Hoag, Austin; Bradley, Larry; Ryan, Russell; Dawson, Will; Zitrin, Adi; Jones, Christine; Sharon, Keren; Trenti, Michele; Stark, Daniel; Oesch, Pascal; Lam, Danel; Carrasco Nunez, Daniela Patricia; Paterno-Mahler, Rachel; Frye, Brenda

    2018-05-01

    When did galaxies start forming stars? What is the role of distant galaxies in galaxy formation models and epoch of reionization? Recent observations indicate at least two critical puzzles in these studies. (1) First galaxies might have started forming stars earlier than previously thought (knowledge of stellar masses, ages, and star formation rates at this epoch requires measuring both rest-frame UV and optical light, which only Spitzer and HST can probe at z 6-11 for a large enough sample of typical galaxies. To address this cosmic puzzle, we propose to complete deep Spitzer imaging of the fields behind the 10 most powerful cosmic telescopes selected using HST, Spitzer, and Planck data from the RELICS and SRELICS programs (Reionization Lensing Cluster Survey; 41 clusters, 190 HST orbits, 440 Spitzer hours). 6 clusters out of 10 are still lacking deep data. This proposal will be a valuable Legacy complement to the existing IRAC deep surveys, and it will open up a new parameter space by probing the ordinary yet magnified population with much improved sample variance. The program will allow us to study stellar properties of a large number, 60 galaxies at z 6-11. Deep Spitzer data will be crucial to unambiguously measure their stellar properties (age, SFR, M*). Finally this proposal will establish the presence (or absence) of an unusually early established stellar population, as was recently observed in MACS1149JD at z 9. If confirmed in a larger sample, this result will require a paradigm shift in our understanding of the earliest star formation.

  2. RELICS of the Cosmic Dawn

    Science.gov (United States)

    Bradac, Marusa; Coe, Dan; Huang, Kuang-Han; Salmon, Brett; Hoag, Austin; Bradley, Larry; Ryan, Russell; Dawson, Will; Zitrin, Adi; Jones, Christine; Sharon, Keren; Trentu, Michele; Stark, Daniel; Bouwens, Rychard; Oesch, Pascal; Lam, Daniel; Patricia Carasco Nunez, Daniela; Paterno-Mahler, Rachel; Strait, Victoria

    2017-10-01

    When did galaxies start forming stars? What is the role of distant galaxies in galaxy formation models and epoch of reionization? Recent observations indicate at least two critical puzzles in these studies. (1) First galaxies might have started forming stars earlier than previously thought (Big Bang). (2) It is still unclear what is their star formation history and whether these galaxies can reionize the Universe. Accurate knowledge of stellar masses, ages, and star formation rates at this epoch requires measuring both rest-frame UV and optical light, which only Spitzer and HST can probe at z 6-11 for a large enough sample of typical galaxies. To address this cosmic puzzle, we propose Spitzer imaging of the fields behind the most powerful cosmic telescopes selected using HST, Spitzer, and Planck data from the RELICS and SRELICS programs (Reionization Lensing Cluster Survey; 41 clusters, 190 HST orbits, 550 Spitzer hours). This proposal will be a valuable Legacy complement to the existing IRAC deep surveys, and it will open up a new parameter space by probing the ordinary yet magnified population with much improved sample variance. The program will allow us to study stellar properties of a large number, 20 galaxies at z 6-11. Deep Spitzer data will be crucial to unambiguously measure their stellar properties (age, SFR, M*). Finally this proposal is a unique opportunity to establish the presence (or absence) of an unusually early established stellar population, as was recently observed in MACS1149JD at z 9. If confirmed, this result will require a paradigm shift in our understanding of the earliest star formation.

  3. Citrus and Prunuscopia-like retrotransposons.

    Science.gov (United States)

    Asíns, M J; Monforte, A J; Mestre, P F; Carbonell, E A

    1999-08-01

    Many of the world's most important citrus cultivars ("Washington Navel", satsumas, clementines) have arisen through somatic mutation. This phenomenon occurs fairly often in the various species and varieties of the genus.The presence of copia-like retrotransposons has been investigated in fruit trees, especially citrus, by using a PCR assay designed to detect copia-like reverse transcriptase (RT) sequences. Amplification products from a genotype of each the following species Citrus sinensis, Citrus grandis, Citrus clementina, Prunus armeniaca and Prunus amygdalus, were cloned and some of them sequenced. Southern-blot hybridization using RT clones as probes showed that multiple copies are integrated throughout the citrus genome, while only 1-3 copies are detected in the P. armeniaca genome, which is in accordance with the Citrus and Prunus genome sizes. Sequence analysis of RT clones allowed a search for homologous sequences within three gene banks. The most similar ones correspond to RT domains of copia-like retrotransposons from unrelated plant species. Cluster analysis of these sequences has shown a great heterogeneity among RT domains cloned from the same genotype. This finding supports the hypothesis that horizontal transmission of retrotransposons has occurred in the past. The species presenting a RT sequence most similar to citrus RT clones is Gnetum montanum, a gymnosperm whose distribution area coincides with two of the main centers of origin of Citrus spp. A new C-methylated restriction DNA fragment containing a RT sequence is present in navel sweet oranges, but not in Valencia oranges from which the former originated suggesting, that retrotransposon activity might be, at least in part, involved in the genetic variability among sweet orange cultivars. Given that retrotransposons are quite abundant throughout the citrus genome, their activity should be investigated thoroughly before commercializing any transgenic citrus plant where the transgene(s) is part

  4. Human Retrotransposon Insertion Polymorphisms Are Associated with Health and Disease via Gene Regulatory Phenotypes

    Directory of Open Access Journals (Sweden)

    Lu Wang

    2017-08-01

    Full Text Available The human genome hosts several active families of transposable elements (TEs, including the Alu, LINE-1, and SVA retrotransposons that are mobilized via reverse transcription of RNA intermediates. We evaluated how insertion polymorphisms generated by human retrotransposon activity may be related to common health and disease phenotypes that have been previously interrogated through genome-wide association studies (GWAS. To address this question, we performed a genome-wide screen for retrotransposon polymorphism disease associations that are linked to TE induced gene regulatory changes. Our screen first identified polymorphic retrotransposon insertions found in linkage disequilibrium (LD with single nucleotide polymorphisms that were previously associated with common complex diseases by GWAS. We further narrowed this set of candidate disease associated retrotransposon polymorphisms by identifying insertions that are located within tissue-specific enhancer elements. We then performed expression quantitative trait loci analysis on the remaining set of candidates in order to identify polymorphic retrotransposon insertions that are associated with gene expression changes in B-cells of the human immune system. This progressive and stringent screen yielded a list of six retrotransposon insertions as the strongest candidates for TE polymorphisms that lead to disease via enhancer-mediated changes in gene regulation. For example, we found an SVA insertion within a cell-type specific enhancer located in the second intron of the B4GALT1 gene. B4GALT1 encodes a glycosyltransferase that functions in the glycosylation of the Immunoglobulin G (IgG antibody in such a way as to convert its activity from pro- to anti-inflammatory. The disruption of the B4GALT1 enhancer by the SVA insertion is associated with down-regulation of the gene in B-cells, which would serve to keep the IgG molecule in a pro-inflammatory state. Consistent with this idea, the B4GALT1 enhancer

  5. The 'relics of Joan of Arc'

    DEFF Research Database (Denmark)

    Charlier, P.; Poupon, J.; Eb, A.

    2010-01-01

    Archaeological remains can provide concrete cases, making it possible to develop, refine or validate medico-legal techniques. In the case of the so-called 'Joan of Arc's relics' (a group of bone and archaeological remains known as the 'Bottle of Chinon'), 14 specialists analysed the samples such ...

  6. Neutrino Coannihilation on Dark-Matter Relics?

    Energy Technology Data Exchange (ETDEWEB)

    Barenboim, Gabriela; /Valencia U.; Mena Requejo, Olga; Quigg, Chris; /Fermilab

    2006-04-01

    High-energy neutrinos may resonate with relic background neutralinos to form short-lived sneutrinos. In some circumstances, the decay chain that leads back to the lightest supersymmetric particle would yield few-GeV gamma rays or charged-particle signals. Although resonant coannihilation would occur at an appreciable rate in our galaxy, the signal in any foreseeable detector is unobservably small.

  7. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers.

    Science.gov (United States)

    Smýkal, P; Bačová-Kerteszová, N; Kalendar, R; Corander, J; Schulman, A H; Pavelek, M

    2011-05-01

    Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70-100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics.

  8. Research on Splicing Method of Digital Relic Fragment Model

    Science.gov (United States)

    Yan, X.; Hu, Y.; Hou, M.

    2018-04-01

    In the course of archaeological excavation, a large number of pieces of cultural relics were unearthed, and the restoration of these fragments was done manually by traditional arts and crafts experts. In this process, cultural relics experts often try to splice the existing cultural relics, and then use adhesive to stick together the fragments of correct location, which will cause irreversible secondary damage to cultural relics. In order to minimize such damage, the surveyors combine 3D laser scanning with computer technology, and use the method of establishing digital cultural relics fragments model to make virtual splicing of cultural relics. The 3D software on the common market can basically achieve the model translation and rotation, using this two functions can be achieved manually splicing between models, mosaic records after the completion of the specific location of each piece of fragments, so as to effectively reduce the damage to the relics had tried splicing process.

  9. Full Length Research Paper LTR-retrotransposons-based molecular ...

    African Journals Online (AJOL)

    LTR-retrotransposons possess unique properties that make them appropriate for investigating relationships between closely related species and populations. The aim of the current study was to employ Ty1-copia group retrotransposons as molecular markers in cultivated Egyptian cottons, G. barbadense L. Restriction site ...

  10. Convergent evolution of ribonuclease h in LTR retrotransposons and retroviruses.

    Science.gov (United States)

    Ustyantsev, Kirill; Novikova, Olga; Blinov, Alexander; Smyshlyaev, Georgy

    2015-05-01

    Ty3/Gypsy long terminals repeat (LTR) retrotransposons are structurally and phylogenetically close to retroviruses. Two notable structural differences between these groups of genetic elements are 1) the presence in retroviruses of an additional envelope gene, env, which mediates infection, and 2) a specific dual ribonuclease H (RNH) domain encoded by the retroviral pol gene. However, similar to retroviruses, many Ty3/Gypsy LTR retrotransposons harbor additional env-like genes, promoting concepts of the infective mode of these retrotransposons. Here, we provide a further line of evidence of similarity between retroviruses and some Ty3/Gypsy LTR retrotransposons. We identify that, together with their additional genes, plant Ty3/Gypsy LTR retrotransposons of the Tat group have a second RNH, as do retroviruses. Most importantly, we show that the resulting dual RNHs of Tat LTR retrotransposons and retroviruses emerged independently, providing strong evidence for their convergent evolution. The convergent resemblance of Tat LTR retrotransposons and retroviruses may indicate similar selection pressures acting on these diverse groups of elements and reveal potential evolutionary constraints on their structure. We speculate that dual RNH is required to accelerate retrotransposon evolution through increased rates of strand transfer events and subsequent recombination events. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.)

    Science.gov (United States)

    2009-01-01

    Background Retrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. Copia- and Gypsy-like retrotransposons are the two main classes of retroelements shown to be ubiquitous in plant genomes. Ideally, the retrotransposons life cycle results in the synthesis of a messenger RNA and then self-encoded proteins to process retrotransposon mRNA in double stranded extra-chromosomal cDNA copies which may integrate in new chromosomal locations. Results The RT-PCR and IRAP protocol were applied to detect the presence of Copia and Gypsy retrotransposon transcripts and of new events of integration in unstressed plants of a sunflower (Helianthus annuus L.) selfed line. Results show that in sunflower retrotransposons transcription occurs in all analyzed organs (embryos, leaves, roots, and flowers). In one out of sixty-four individuals analyzed, retrotransposons transcription resulted in the integration of a new element into the genome. Conclusion These results indicate that the retrotransposon life cycle is firmly controlled at a post transcriptional level. A possible silencing mechanism is discussed. PMID:20030800

  12. LTR-retrotransposons-based molecular markers in cultivated ...

    African Journals Online (AJOL)

    GRACE

    2006-07-03

    Jul 3, 2006 ... LTR-retrotransposons represent a standard component of the Gossypium Genome (Zaki and Abdel Ghany,. 2003). The analysis of the molecular existence and distribution of ancient and active LTR-retrotransposons, therefore, provides a comprehensive evaluation of the evolutionary history of Gossypium.

  13. Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants.

    Directory of Open Access Journals (Sweden)

    Sophie Lanciano

    2017-02-01

    Full Text Available Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.

  14. Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants.

    Science.gov (United States)

    Lanciano, Sophie; Carpentier, Marie-Christine; Llauro, Christel; Jobet, Edouard; Robakowska-Hyzorek, Dagmara; Lasserre, Eric; Ghesquière, Alain; Panaud, Olivier; Mirouze, Marie

    2017-02-01

    Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.

  15. Relic neutrino asymmetry evolution from first principles

    International Nuclear Information System (INIS)

    Bell, N.F.; Volkas, R.R.; Wong, Y.Y.Y.

    1998-09-01

    The exact Quantum Kinetic Equations for a two-flavour active-sterile neutrino system are used to provide a systematic derivation of approximate evolution equations for the relic neutrino asymmetry. An extension of the adiabatic approximation for matter-affected neutrino oscillations is developed which incorporates decoherence due to collisions. Exact and approximate expressions for the decoherence and repopulation functions are discussed. A first pass is made over the exact treatment of multi-flavour partially incoherent oscillations. (authors)

  16. Supernova relic electron neutrinos and anti-neutrinos in future large-scale observatories

    International Nuclear Information System (INIS)

    Volpe, C.; Welzel, J.

    2007-01-01

    We investigate the signal from supernova relic neutrinos in future large scale observatories, such as MEMPHYS (UNO, Hyper-K), LENA and GLACIER, at present under study. We discuss that complementary information might be gained from the observation of supernova relic electron antineutrinos and neutrinos using the scattering on protons on one hand, and on nuclei such as oxygen, carbon or argon on the other hand. When determining the relic neutrino fluxes we also include, for the first time, the coupling of the neutrino magnetic moment to magnetic fields within the core collapse supernova. We present numerical results on both the relic ν e and ν-bar e fluxes and on the number of events for ν e + C 12 , ν e + O 16 , ν e + Ar 40 and ν-bar e + p for various oscillation scenarios. The observation of supernova relic neutrinos might provide us with unique information on core-collapse supernova explosions, on the star formation history and on neutrino properties, that still remain unknown. (authors)

  17. Supernova relic electron neutrinos and anti-neutrinos in future large-scale observatories

    Energy Technology Data Exchange (ETDEWEB)

    Volpe, C.; Welzel, J. [Institut de Physique Nuclueaire, 91 - Orsay (France)

    2007-07-01

    We investigate the signal from supernova relic neutrinos in future large scale observatories, such as MEMPHYS (UNO, Hyper-K), LENA and GLACIER, at present under study. We discuss that complementary information might be gained from the observation of supernova relic electron antineutrinos and neutrinos using the scattering on protons on one hand, and on nuclei such as oxygen, carbon or argon on the other hand. When determining the relic neutrino fluxes we also include, for the first time, the coupling of the neutrino magnetic moment to magnetic fields within the core collapse supernova. We present numerical results on both the relic {nu}{sub e} and {nu}-bar{sub e} fluxes and on the number of events for {nu}{sub e} + C{sup 12}, {nu}{sub e} + O{sup 16}, {nu}{sub e} + Ar{sup 40} and {nu}-bar{sub e} + p for various oscillation scenarios. The observation of supernova relic neutrinos might provide us with unique information on core-collapse supernova explosions, on the star formation history and on neutrino properties, that still remain unknown. (authors)

  18. Retrotransposon Targeting of Tumor Cells

    National Research Council Canada - National Science Library

    Wu, Dongdong; DeVaux, George

    2005-01-01

    .... Cancer gene therapy techniques include oncogene inactivation, tumor suppressor gene replacement, inhibition of angiogenesis, immunopotentiation, molecular chemotherapy, and transfer of drug resistance genes...

  19. The Smell of Relics: Authenticating Saintly Bones and the Role of Scent in the Sensory Experience of Medieval Christian Veneration

    Directory of Open Access Journals (Sweden)

    Paul Anthony Brazinski

    2013-09-01

    Full Text Available ''The archaeology of smell is a burgeoning field in recent scholarship. This paper adds to existing literature by investigating the function of smell in relation to relic sales and veneration in medieval Europe, a hitherto understudied area of research. Collating historical texts concerning the translatio of saintly relics in Western Europe and the Byzantine Empire with archaeological sources associated with relic veneration and religious worship (including ampullae, unguentaria, sarcophagi, holy oils, pillow graves, and silk, this paper suggests that (1 smell was used in the medieval world as a means to challenge or confirm a relic’s authenticity, and (2 olfactory liquids that imbued or permeated material objects in the context of worship functioned as a means of focusing attention on relic veneration and were an essential part of the cult and/or pilgrimage experience.

  20. Effects of QCD bound states on dark matter relic abundance

    Energy Technology Data Exchange (ETDEWEB)

    Liew, Seng Pei [Department of Physics, The University of Tokyo,Bunkyo-ku, Tokyo 113-0033 (Japan); Luo, Feng [Kavli IPMU (WPI), UTIAS, The University of Tokyo,Kashiwa, Chiba 277-8583 (Japan)

    2017-02-17

    We study scenarios where there exists an exotic massive particle charged under QCD in the early Universe. We calculate the formation and dissociation rates of bound states formed by pairs of these particles, and apply the results in dark matter (DM) coannihilation scenarios, including also the Sommerfeld effect. We find that on top of the Sommerfeld enhancement, bound-state effects can further significantly increase the largest possible DM masses which can give the observed DM relic abundance, by ∼30–100% with respect to values obtained by considering the Sommerfeld effect only, for the color triplet or octet exotic particles we consider. In particular, it indicates that the Bino DM mass in the right-handed stop-Bino coannihilation scenario in the Minimal Supersymmetric extension of the Standard Model (MSSM) can reach ∼2.5 TeV, even though the potential between the stop and antistop prior to forming a bound state is repulsive. We also apply the bound-state effects in the calculations of relic abundance of long-lived or metastable massive colored particles, and discuss the implications on the BBN constraints and the abundance of a super-weakly interacting DM. The corrections for the bound-state effect when the exotic massive colored particles also carry electric charges, and the collider bounds are also discussed.

  1. Cosmic selection rule for the glueball dark matter relic density

    Science.gov (United States)

    Soni, Amarjit; Xiao, Huangyu; Zhang, Yue

    2017-10-01

    We point out a unique mechanism to produce the relic abundance for the glueball dark matter from a gauged SU (N )d hidden sector which is bridged to the standard model sector through heavy vectorlike quarks colored under gauge interactions from both sides. A necessary ingredient of our assumption is that the vectorlike quarks, produced either thermally or nonthermally, are abundant enough to dominate the universe for some time in the early universe. They later undergo dark color confinement and form unstable vectorlike-quarkonium states which annihilate decay and reheat the visible and dark sectors. The ratio of entropy dumped into two sectors and the final energy budget in the dark glueballs is only determined by low energy parameters, including the intrinsic scale of the dark SU (N )d , Λd, and number of dark colors, Nd, but depend weakly on parameters in the ultraviolet such as the vectorlike quark mass or the initial condition. We call this a cosmic selection rule for the glueball dark matter relic density.

  2. The Shroud of Turin: Relic or icon?

    International Nuclear Information System (INIS)

    Dale, W.S.A.

    1987-01-01

    The Shroud of Turin, a linen cloth on which appear the imprints of the front and back of a crucified man, can be historically traced to ca. 1354 A.D. Many believe it to be a true relic of the Passion of Christ. Many others regard it as a fake. This paper suggests a third alternative, that it is an icon dating from the 11th century. If future scientific tests, of which radiocarbon dating will be the most important, support this theory, the Shroud of Turin may well be recognized as one of the masterpieces of Christian art. (orig.)

  3. Relic gravitational waves and extended inflation

    International Nuclear Information System (INIS)

    Turner, M.S.; Wilczek, F.

    1990-01-01

    In extended inflation, a new version of inflation where the transition from an inflationary to a radiation-dominated Universe is accomplished by bubble nucleation, bubble collisions supply a potent---and potentially detectable---source of gravitational waves. The energy density in relic gravitons from bubble collisions is expected to be about 10 -5 of closure density. Their characteristic wavelength depends upon the reheating temperature T RH: λ∼(10 4 cm)[(10 14 GeV)/T RH ]. If black holes are produced by bubble collisions, they will evaporate producing shorter-wavelength gravitons

  4. Retrotransposons as regulators of gene expression.

    Science.gov (United States)

    Elbarbary, Reyad A; Lucas, Bronwyn A; Maquat, Lynne E

    2016-02-12

    Transposable elements (TEs) are both a boon and a bane to eukaryotic organisms, depending on where they integrate into the genome and how their sequences function once integrated. We focus on two types of TEs: long interspersed elements (LINEs) and short interspersed elements (SINEs). LINEs and SINEs are retrotransposons; that is, they transpose via an RNA intermediate. We discuss how LINEs and SINEs have expanded in eukaryotic genomes and contribute to genome evolution. An emerging body of evidence indicates that LINEs and SINEs function to regulate gene expression by affecting chromatin structure, gene transcription, pre-mRNA processing, or aspects of mRNA metabolism. We also describe how adenosine-to-inosine editing influences SINE function and how ongoing retrotransposition is countered by the body's defense mechanisms. Copyright © 2016, American Association for the Advancement of Science.

  5. Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants

    OpenAIRE

    Lanciano, Sophie; Carpentier, M. C.; Llauro, C.; Jobet, E.; Robakowska-Hyzorek, D.; Lasserre, E.; Ghesquière, Alain; Panaud, O.; Mirouze, Marie

    2017-01-01

    Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposon...

  6. a Method of 3d Measurement and Reconstruction for Cultural Relics in Museums

    Science.gov (United States)

    Zheng, S.; Zhou, Y.; Huang, R.; Zhou, L.; Xu, X.; Wang, C.

    2012-07-01

    Three-dimensional measurement and reconstruction during conservation and restoration of cultural relics have become an essential part of a modem museum regular work. Although many kinds of methods including laser scanning, computer vision and close-range photogrammetry have been put forward, but problems still exist, such as contradiction between cost and good result, time and fine effect. Aimed at these problems, this paper proposed a structure-light based method for 3D measurement and reconstruction of cultural relics in museums. Firstly, based on structure-light principle, digitalization hardware has been built and with its help, dense point cloud of cultural relics' surface can be easily acquired. To produce accurate 3D geometry model from point cloud data, multi processing algorithms have been developed and corresponding software has been implemented whose functions include blunder detection and removal, point cloud alignment and merge, 3D mesh construction and simplification. Finally, high-resolution images are captured and the alignment of these images and 3D geometry model is conducted and realistic, accurate 3D model is constructed. Based on such method, a complete system including hardware and software are built. Multi-kinds of cultural relics have been used to test this method and results prove its own feature such as high efficiency, high accuracy, easy operation and so on.

  7. Evolutionary characterization of Ty3/gypsy-like LTR retrotransposons in the parasitic cestode Echinococcus granulosus.

    Science.gov (United States)

    Bae, Young-An

    2016-11-01

    Cyclophyllidean cestodes including Echinococcus granulosus have a smaller genome and show characteristics such as loss of the gut, a segmented body plan, and accelerated growth rate in hosts compared with other tissue-invading helminths. In an effort to address the molecular mechanism relevant to genome shrinkage, the evolutionary status of long-terminal-repeat (LTR) retrotransposons, which are known as the most potent genomic modulators, was investigated in the E. granulosus draft genome. A majority of the E. granulosus LTR retrotransposons were classified into a novel characteristic clade, named Saci-2, of the Ty3/gypsy family, while the remaining elements belonged to the CsRn1 clade of identical family. Their nucleotide sequences were heavily corrupted by frequent base substitutions and segmental losses. The ceased mobile activity of the major retrotransposons and the following intrinsic DNA loss in their inactive progenies might have contributed to decrease in genome size. Apart from the degenerate copies, a gag gene originating from a CsRn1-like element exhibited substantial evidences suggesting its domestication including a preserved coding profile and transcriptional activity, the presence of syntenic orthologues in cestodes, and selective pressure acting on the gene. To my knowledge, the endogenized gag gene is reported for the first time in invertebrates, though its biological function remains elusive.

  8. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.

    Directory of Open Access Journals (Sweden)

    Sudhir Kumar Rai

    2017-12-01

    Full Text Available Retroviruses and Long Terminal Repeat (LTR-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.

  9. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.

    Science.gov (United States)

    Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak; Levin, Henry L

    2017-12-01

    Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.

  10. Scalar modes of the relic gravitons

    CERN Document Server

    Giovannini, Massimo

    2015-01-01

    In conformally flat background geometries the long wavelength gravitons can be described in the fluid approximation and they induce scalar fluctuations both during inflation and in the subsequent radiation-dominated epoch. While this effect is minute and suppressed for a de Sitter stage of expansion, the fluctuations of the energy-momentum pseudo-tensor of the graviton fluid lead to curvature perturbations that increase with time all along the post-inflationary evolution. An explicit calculation of these effects is presented for a standard thermal history and it is shown that the growth of the curvature perturbations caused by the long wavelength modes is approximately compensated by the slope of the power spectra of the energy density, pressure and anisotropic stress of the relic gravitons.

  11. Relic gravitational waves and extended inflation

    International Nuclear Information System (INIS)

    Turner, M.S.; Wilczek, F.

    1990-08-01

    In extended inflation, a new version of inflation where the transition from the false-vacuum phase to a radiation-dominated Universe is accomplished by bubble nucleation and percolation, bubble collisions supply a potent-and potentially detectable-source of gravitational waves. The present energy density in relic gravity waves from bubble collisions is expected to be about 10(exp -5) of closure density-many orders of magnitude greater than that of the gravity waves produced by quantum fluctuations. Their characteristic wavelength depends upon the reheating temperature T(sub RH): lambda is approximately 10(exp 4) cm (10(exp 14) GeV/T(sub RH)). If large numbers of black holes are produced, a not implausible outcome, they will evaporate producing comparable amounts of shorter wavelength waves, lambda is approximately 10(exp -6) cm (T(sub RH)/10(exp 14) GeV)

  12. The refractive index of relic gravitons

    CERN Document Server

    Giovannini, Massimo

    2016-01-01

    The dynamical evolution of the refractive index of the tensor modes of the geometry produces a specific class of power spectra characterized by a blue (i.e. slightly increasing) slope which is directly determined by the competition of the slow-roll parameter and of the rate of variation of the refractive index. Throughout the conventional stages of the inflationary and post-inflationary evolution, the microwave background anisotropies measurements, the pulsar timing limits and the big-bang nucleosythesis constraints set stringent bounds on the refractive index and on its rate of variation. Within the physically allowed region of the parameter space the cosmic background of relic gravitons leads to a potentially large signal for the ground based detectors (in their advanced version) and for the proposed space-borne interferometers. Conversely, the lack of direct detection of the signal will set a qualitatively new bound on the dynamical variation of the refractive index.

  13. Stochastic backgrounds of relic gravitons: a theoretical appraisal

    CERN Document Server

    Giovannini, Massimo

    2010-01-01

    Stochastic backgrounds or relic gravitons, if ever detected, will constitute a prima facie evidence of physical processes taking place during the earliest stages of the evolution of the plasma. The essentials of the stochastic backgrounds of relic gravitons are hereby introduced and reviewed. The pivotal observables customarily employed to infer the properties of the relic gravitons are discussed both in the framework of the $\\Lambda$CDM paradigm as well as in neighboring contexts. The complementarity between experiments measuring the polarization of the Cosmic Microwave Background (such as, for instance, WMAP, Capmap, Quad, Cbi, just to mention a few) and wide band interferometers (e.g. Virgo, Ligo, Geo, Tama) is emphasized. While the analysis of the microwave sky strongly constrains the low-frequency tail of the relic graviton spectrum, wide-band detectors are sensitive to much higher frequencies where the spectral energy density depends chiefly upon the (poorly known) rate of post-inflationary expansion.

  14. Relic gravitational waves in the accelerating Universe

    International Nuclear Information System (INIS)

    Zhang Yang; Yuan Yefei; Zhao Wen; Chen Yingtian

    2005-01-01

    Recent observations have indicated that the Universe at the present stage is in an accelerating expansion, a process that has great implications. We evaluate the spectrum of relic gravitational waves in the current accelerating Universe and find that there are new features appearing in the resulting spectrum as compared to the decelerating models. In the low-frequency range the peak of the spectrum is now located at a frequency ν E ∼ (OMEGA m /OMEGA Λ ) 1/3 ν H , where ν H is the Hubble frequency, and there appears a new segment of spectrum between ν E and ν H . In all other intervals of frequencies ≥ν H , the spectral amplitude acquires an extra factor (OMEGA m /OMEGA Λ ), due to the current acceleration; otherwise the shape of the spectrum is similar to that in the decelerating models. The recent WMAP result of CMB anisotropies is used to normalize the amplitude for gravitational waves. The slope of the power spectrum depends sensitively on the scale factor a(τ) ∝ vertical bar τ vertical bar 1+β during the inflationary stage with β = -2 for the exact de Sitter space. With increasing β, the resulting spectrum is tilted to be flatter with more power at high frequencies, and the sensitivity of the second science run of the LIGO detectors puts a restriction on the parameter β ≤ -1.8. We also give a numerical solution which confirms these features

  15. Relic gravity waves from braneworld inflation

    International Nuclear Information System (INIS)

    Sahni, Varun; Sami, M.; Souradeep, Tarun

    2002-01-01

    We discuss a scenario in which extra dimensional effects allow a scalar field with a steep potential to play the dual role of the inflaton as well as dark energy (quintessence). The post-inflationary evolution of the universe in this scenario is generically characterized by a 'kinetic regime' during which the kinetic energy of the scalar field greatly exceeds its potential energy resulting in a 'stiff' equation of state for scalar field matter P φ ≅ρ φ . The kinetic regime precedes the radiation dominated epoch and introduces an important new feature into the spectrum of relic gravity waves created quantum mechanically during inflation. The amplitude of the gravity wave spectrum increases with the wave number for wavelengths shorter than the comoving horizon scale at the commencement of the radiative regime. This 'blue tilt' is a generic feature of models with steep potentials and imposes strong constraints on a class of inflationary braneworld models. Prospects for detection of the gravity wave background by terrestrial and space-borne gravity wave observatories such as LIGO II and LISA are discussed

  16. RNA Relics and Origin of Life

    Directory of Open Access Journals (Sweden)

    Laurent Vial

    2009-07-01

    Full Text Available A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.

  17. RNA Relics and Origin of Life

    Science.gov (United States)

    Demongeot, Jacques; Glade, Nicolas; Moreira, Andrés; Vial, Laurent

    2009-01-01

    A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells. PMID:20111682

  18. Transferability of retrotransposon primers derived from Persimmon (Diospyros kaki Thunb.) across other plant species.

    Science.gov (United States)

    Du, X Y; Hu, Q N; Zhang, Q L; Wang, Y B; Luo, Z R

    2013-06-06

    Retrotransposon-based molecular markers are powerful molecular tools. However, these markers are not readily available due to the difficulty in obtaining species-specific retrotransposon primers. Although recent techniques enabling the rapid isolation of retrotransposon sequences have facilitated primer development, this process nonetheless remains time-consuming and costly. Therefore, research into the transferability of retrotransposon primers developed from one plant species onto others would be of great value. The present study investigated the transferability of retrotransposon primers derived from 'Luotian-tianshi' persimmon (Diospyros kaki Thunb.) across other fruit crops, as well as within the genus using inter-retrotransposon amplified polymorphism molecular marker. Fourteen of the 26 retrotransposon primers tested (53.85%) produced robust and reproducible amplification products across all fruit crops tested, indicating their applicability across plant species. Four of the 13 fruit crops showed the best transferability performances: persimmon, grape, citrus, and peach. Furthermore, similarity coefficients and UPGMA clustering indicated that these primers could further offer a potential tool for germplasm differentiation, parentage identification, genetic diversity assessment, classification, and phylogenetic studies across a variety of plant species. Transferability was further confirmed by examining published primers derived from Rosaceae, Gramineae, and Solanaceae. This study is one of the few currently available studies concerning the transferability of retrotransposon primers across plant species in general, and is the first successful study of the transferability of retrotransposon primers derived from persimmon. The primers presented here will help reduce costs for future retrotransposon primer development and therefore contribute to the popularization of retrotransposon molecular markers.

  19. Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration.

    Science.gov (United States)

    Bridier-Nahmias, Antoine; Tchalikian-Cosson, Aurélie; Baller, Joshua A; Menouni, Rachid; Fayol, Hélène; Flores, Amando; Saïb, Ali; Werner, Michel; Voytas, Daniel F; Lesage, Pascale

    2015-05-01

    Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of RNA polymerase III (Pol III)-transcribed genes, yet the primary determinant of target specificity has remained elusive. Here we describe an interaction between Ty1 integrase and the AC40 subunit of Pol III and demonstrate that AC40 is the predominant determinant targeting Ty1 integration upstream of Pol III-transcribed genes. Lack of an integrase-AC40 interaction dramatically alters target site choice, leading to a redistribution of Ty1 insertions in the genome, mainly to chromosome ends. The mechanism of target specificity allows Ty1 to proliferate and yet minimizes genetic damage to its host. Copyright © 2015, American Association for the Advancement of Science.

  20. Relic abundance of WIMPs in non-standard cosmological scenarios

    International Nuclear Information System (INIS)

    Yimingniyazi, W.

    2007-01-01

    In this thesis we study the relic density n χ of non--relativistic long--lived or stable particles χ in various non--standard cosmological scenarios. First, we discuss the relic density in the non--standard cosmological scenario in which the temperature is too low for the particles χ to achieve full chemical equilibrium. We also investigated the case where χ particles are non--thermally produced from the decay of heavier particles in addition to the usual thermal production. In low temperature scenario, we calculate the relic abundance starting from arbitrary initial temperatures T 0 of the radiation--dominated epoch and derive approximate solutions for the temperature dependence of the relic density which can accurately reproduces numerical results when full thermal equilibrium is not achieved. If full equilibrium is reached, our ansatz no longer reproduces the correct temperature dependence of the χ number density. However, we can contrive a semi-analytic formula which gives the correct final relic density, to an accuracy of about 3% or better, for all cross sections and initial temperatures. We also derive the lower bound on the initial temperature T 0 , assuming that the relic particle accounts for the dark matter energy density in the universe. The observed cold dark matter abundance constrains the initial temperature T 0 ≥m χ /23, where m χ is the mass of χ. Second, we discuss the χ density in the scenario where the the Hubble parameter is modified. Even in this case, an approximate formula similar to the standard one is found to be capable of predicting the final relic abundance correctly. Choosing the χ annihilation cross section such that the observed cold dark matter abundance is reproduced in standard cosmology, we constrain possible modifications of the expansion rate at T ∝m χ /20, well before Big Bang Nucleosynthesis. (orig.)

  1. Relic abundance of WIMPs in non-standard cosmological scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Yimingniyazi, W.

    2007-08-06

    In this thesis we study the relic density n{sub {chi}} of non--relativistic long--lived or stable particles {chi} in various non--standard cosmological scenarios. First, we discuss the relic density in the non--standard cosmological scenario in which the temperature is too low for the particles {chi} to achieve full chemical equilibrium. We also investigated the case where {chi} particles are non--thermally produced from the decay of heavier particles in addition to the usual thermal production. In low temperature scenario, we calculate the relic abundance starting from arbitrary initial temperatures T{sub 0} of the radiation--dominated epoch and derive approximate solutions for the temperature dependence of the relic density which can accurately reproduces numerical results when full thermal equilibrium is not achieved. If full equilibrium is reached, our ansatz no longer reproduces the correct temperature dependence of the {chi} number density. However, we can contrive a semi-analytic formula which gives the correct final relic density, to an accuracy of about 3% or better, for all cross sections and initial temperatures. We also derive the lower bound on the initial temperature T{sub 0}, assuming that the relic particle accounts for the dark matter energy density in the universe. The observed cold dark matter abundance constrains the initial temperature T{sub 0} {>=}m{sub {chi}}/23, where m{sub {chi}} is the mass of {chi}. Second, we discuss the {chi} density in the scenario where the the Hubble parameter is modified. Even in this case, an approximate formula similar to the standard one is found to be capable of predicting the final relic abundance correctly. Choosing the {chi} annihilation cross section such that the observed cold dark matter abundance is reproduced in standard cosmology, we constrain possible modifications of the expansion rate at T {proportional_to}m{sub {chi}}/20, well before Big Bang Nucleosynthesis. (orig.)

  2. BARE retrotransposons are translated and replicated via distinct RNA pools.

    Directory of Open Access Journals (Sweden)

    Wei Chang

    Full Text Available The replication of Long Terminal Repeat (LTR retrotransposons, which can constitute over 80% of higher plant genomes, resembles that of retroviruses. A major question for retrotransposons and retroviruses is how the two conflicting roles of their transcripts, in translation and reverse transcription, are balanced. Here, we show that the BARE retrotransposon, despite its organization into just one open reading frame, produces three distinct classes of transcripts. One is capped, polyadenylated, and translated, but cannot be copied into cDNA. The second is not capped or polyadenylated, but is destined for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor production of a subgenomic RNA encoding only Gag, the protein forming virus-like particles. Moreover, the BARE2 subfamily, which cannot synthesize Gag and is parasitic on BARE1, does not produce the spliced sub-genomic RNA for translation but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.

  3. The Microprocessor controls the activity of mammalian retrotransposons

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...

  4. Forward and reverse genetics: The LORE1 retrotransposon insertion mutants

    DEFF Research Database (Denmark)

    Fukai, Eigo; Malolepszy, Anna; Sandal, Niels Nørgaard

    2014-01-01

    The endogenous Lotus retrotransposon 1 (LORE1) transposes in the germ line of Lotus japonicus plants that carry an active element. This feature of LORE1 has been exploited for generation of a large non-transgenic insertion mutant population, where insertions have been annotated using next-generat...

  5. Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.).

    Science.gov (United States)

    Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling

    2014-06-04

    Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes.

    Science.gov (United States)

    Vitte, C; Estep, M C; Leebens-Mack, J; Bennetzen, J L

    2013-09-01

    Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots. To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4-5 % (asparagus) or 3-4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.

  7. Calculation of the local density of relic neutrinos

    Energy Technology Data Exchange (ETDEWEB)

    De Salas, P.F.; Gariazzo, S.; Pastor, S. [Instituto de Física Corpuscular (CSIC-Universitat de València), Parc Científic UV, C/ Catedrático José Beltrán, 2, E-46980 Paterna (Valencia) (Spain); Lesgourgues, J., E-mail: pabferde@ific.uv.es, E-mail: gariazzo@ific.uv.es, E-mail: Julien.Lesgourgues@physik.rwth-aachen.de, E-mail: pastor@ific.uv.es [Institute for Theoretical Particle Physics and Cosmology (TTK), RWTH Aachen University, D-52056 Aachen (Germany)

    2017-09-01

    Nonzero neutrino masses are required by the existence of flavour oscillations, with values of the order of at least 50 meV . We consider the gravitational clustering of relic neutrinos within the Milky Way, and used the N -one-body simulation technique to compute their density enhancement factor in the neighbourhood of the Earth with respect to the average cosmic density. Compared to previous similar studies, we pushed the simulation down to smaller neutrino masses, and included an improved treatment of the baryonic and dark matter distributions in the Milky Way. Our results are important for future experiments aiming at detecting the cosmic neutrino background, such as the Princeton Tritium Observatory for Light, Early-universe, Massive-neutrino Yield (PTOLEMY) proposal. We calculate the impact of neutrino clustering in the Milky Way on the expected event rate for a PTOLEMY-like experiment. We find that the effect of clustering remains negligible for the minimal normal hierarchy scenario, while it enhances the event rate by 10 to 20% (resp. a factor 1.7 to 2.5) for the minimal inverted hierarchy scenario (resp. a degenerate scenario with 150 meV masses). Finally we compute the impact on the event rate of a possible fourth sterile neutrino with a mass of 1.3 eV.

  8. Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway.

    Directory of Open Access Journals (Sweden)

    John Karijolich

    Full Text Available Short interspersed nuclear elements (SINEs are highly abundant, RNA polymerase III-transcribed noncoding retrotransposons that are silenced in somatic cells but activated during certain stresses including viral infection. How these induced SINE RNAs impact the host-pathogen interaction is unknown. Here we reveal that during murine gammaherpesvirus 68 (MHV68 infection, rapidly induced SINE RNAs activate the antiviral NF-κB signaling pathway through both mitochondrial antiviral-signaling protein (MAVS-dependent and independent mechanisms. However, SINE RNA-based signaling is hijacked by the virus to enhance viral gene expression and replication. B2 RNA expression stimulates IKKβ-dependent phosphorylation of the major viral lytic cycle transactivator protein RTA, thereby enhancing its activity and increasing progeny virion production. Collectively, these findings suggest that SINE RNAs participate in the innate pathogen response mechanism, but that herpesviruses have evolved to co-opt retrotransposon activation for viral benefit.

  9. Dark matter relic abundance and light sterile neutrinos

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yi-Lei [Center for High Energy Physics,Peking University, Beijing 100871 (China); Zhu, Shou-hua [Center for High Energy Physics,Peking University, Beijing 100871 (China); Institute of Theoretical Physics & State Key Laboratory of Nuclear Physics and Technology,Peking University, Beijing 100871 (China); Collaborative Innovation Center of Quantum Matter,Beijing 100871 (China)

    2017-01-09

    In this paper, we calculate the relic abundance of the dark matter particles when they can annihilate into sterile neutrinos with the mass ≲100 GeV in a simple model. Unlike the usual standard calculations, the sterile neutrino may fall out of the thermal equilibrium with the thermal bath before the dark matter freezes out. In such a case, if the Yukawa coupling y{sub N} between the Higgs and the sterile neutrino is small, this process gives rise to a larger Ω{sub DM}h{sup 2} so we need a larger coupling between the dark matter and the sterile neutrino for a correct relic abundance.

  10. Thermal relic dark matter beyond the unitarity limit

    Energy Technology Data Exchange (ETDEWEB)

    Harigaya, Keisuke [Berkeley Center for Theoretical Physics, Department of Physics, University of California,Berkeley, CA 94720 (United States); Theoretical Physics Group, Lawrence Berkeley National Laboratory,Berkeley, CA 94720 (United States); Ibe, Masahiro [Kavli IPMU (WPI), UTIAS, The University of Tokyo,Kashiwa, Chiba 277-8583 (Japan); ICRR, The University of Tokyo,Kashiwa, Chiba 277-8582 (Japan); Kaneta, Kunio [Center for Theoretical Physics of the Universe, Institute for Basic Science (IBS),Daejeon 34051 (Korea, Republic of); Nakano, Wakutaka; Suzuki, Motoo [Kavli IPMU (WPI), UTIAS, The University of Tokyo,Kashiwa, Chiba 277-8583 (Japan); ICRR, The University of Tokyo,Kashiwa, Chiba 277-8582 (Japan)

    2016-08-25

    We discuss a simple model of thermal relic dark matter whose mass can be much larger than the so-called unitarity limit on the mass of point-like particle dark matter. The model consists of new strong dynamics with one flavor of fermions in the fundamental representation which is much heavier than the dynamical scale of the new strong dynamics. Dark matter is identified with the lightest baryonic hadron of the new dynamics. The baryonic hadrons annihilate into the mesonic hadrons of the new strong dynamics when they have large radii. Resultantly, thermal relic dark matter with a mass in the PeV range is possible.

  11. 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...... significance of LORE1 as a member of chromovirus, a chromodomain containing clade of the Gypsy superfamily. Then we discuss possibilities and methodologies for using endogenous transposable elements as mutagens to generate gene tagging populations in plants...

  12. APPLICATION OF 3D MODEL OF CULTURAL RELICS IN VIRTUAL RESTORATION

    Directory of Open Access Journals (Sweden)

    S. Zhao

    2018-04-01

    Full Text Available In the traditional cultural relics splicing process, in order to identify the correct spatial location of the cultural relics debris, experts need to manually splice the existing debris. The repeated contact between debris can easily cause secondary damage to the cultural relics. In this paper, the application process of 3D model of cultural relic in virtual restoration is put forward, and the relevant processes and ideas are verified with the example of Terracotta Warriors data. Through the combination of traditional cultural relics restoration methods and computer virtual reality technology, virtual restoration of high-precision 3D models of cultural relics can provide a scientific reference for virtual restoration, avoiding the secondary damage to the cultural relics caused by improper restoration. The efficiency and safety of the preservation and restoration of cultural relics have been improved.

  13. Application of 3d Model of Cultural Relics in Virtual Restoration

    Science.gov (United States)

    Zhao, S.; Hou, M.; Hu, Y.; Zhao, Q.

    2018-04-01

    In the traditional cultural relics splicing process, in order to identify the correct spatial location of the cultural relics debris, experts need to manually splice the existing debris. The repeated contact between debris can easily cause secondary damage to the cultural relics. In this paper, the application process of 3D model of cultural relic in virtual restoration is put forward, and the relevant processes and ideas are verified with the example of Terracotta Warriors data. Through the combination of traditional cultural relics restoration methods and computer virtual reality technology, virtual restoration of high-precision 3D models of cultural relics can provide a scientific reference for virtual restoration, avoiding the secondary damage to the cultural relics caused by improper restoration. The efficiency and safety of the preservation and restoration of cultural relics have been improved.

  14. Mammalian-specific genomic functions: Newly acquired traits generated by genomic imprinting and LTR retrotransposon-derived genes in mammals.

    Science.gov (United States)

    Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2015-01-01

    Mammals, including human beings, have evolved a unique viviparous reproductive system and a highly developed central nervous system. How did these unique characteristics emerge in mammalian evolution, and what kinds of changes did occur in the mammalian genomes as evolution proceeded? A key conceptual term in approaching these issues is "mammalian-specific genomic functions", a concept covering both mammalian-specific epigenetics and genetics. Genomic imprinting and LTR retrotransposon-derived genes are reviewed as the representative, mammalian-specific genomic functions that are essential not only for the current mammalian developmental system, but also mammalian evolution itself. First, the essential roles of genomic imprinting in mammalian development, especially related to viviparous reproduction via placental function, as well as the emergence of genomic imprinting in mammalian evolution, are discussed. Second, we introduce the novel concept of "mammalian-specific traits generated by mammalian-specific genes from LTR retrotransposons", based on the finding that LTR retrotransposons served as a critical driving force in the mammalian evolution via generating mammalian-specific genes.

  15. Plant centromeric retrotransposons: a structural and cytogenetic perspective

    Czech Academy of Sciences Publication Activity Database

    Neumann, Pavel; Navrátilová, Alice; Koblížková, Andrea; Kejnovský, Eduard; Hřibová, Eva; Hobza, Roman; Widmer, A.; Doležel, Jaroslav; Macas, Jiří

    2011-01-01

    Roč. 2, č. 4 (2011), s. 1-16 ISSN 1759-8753 R&D Projects: GA AV ČR KJB500960802; GA MŠk(CZ) LC06004; GA ČR GA522/09/0083 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z50380511 Keywords : plant chromosomes * retrotransposons * cytogenetic perspective Subject RIV: EB - Genetics ; Molecular Biology

  16. Relic abundance of mass-varying cold dark matter particles

    International Nuclear Information System (INIS)

    Rosenfeld, Rogerio

    2005-01-01

    In models of coupled dark energy and dark matter the mass of the dark matter particle depends on the cosmological evolution of the dark energy field. In this Letter we exemplify in a simple model the effects of this mass variation on the relic abundance of cold dark matter

  17. Quantum state correction of relic gravitons from quantum gravity

    OpenAIRE

    Rosales, Jose-Luis

    1996-01-01

    The semiclassical approach to quantum gravity would yield the Schroedinger formalism for the wave function of metric perturbations or gravitons plus quantum gravity correcting terms in pure gravity; thus, in the inflationary scenario, we should expect correcting effects to the relic graviton (Zel'dovich) spectrum of the order (H/mPl)^2.

  18. Radiological data acquisition, investigation and evaluation of mining relics

    International Nuclear Information System (INIS)

    1992-01-01

    Within the scope of a Federal Project, the environmental radioactivity and the radon concentration in buildings caused by mining relics in the new Federal Lands of Germany are investigated. In the first phase of the project, about 8000 relics of former mining were identified by analysing existing documents, categorised, and recorded in a special data bank. Thereby, 'areas of suspicion' of 1500 km 2 spaciously defined in the beginning could be reduced to 'areas of investigation' of 250 km 2 now to be examined in close coordination with the land and district authorities by a programme gradually adapted to the radiological significance of the relics. Experience with site-specific measuring programmes have already been gained through three pilot projects at typical sites of former mining activities. Recommendations of the German Radiation Protection Commission serve for the evaluation of the results. By the measuring programme for radon in buildings of mining and geological predestined regions more than 25000 buildings of 210 communities have been investigated. The results confirm the expected prevailing influence of the geologic underground on the radon concentration. Extreme values are observed where direct connections additionally exist to mining relics in the ground. (orig./HP) With 11 figs. in annex [de

  19. Late Quaternary sea level and environmental changes from relic ...

    Indian Academy of Sciences (India)

    Relic carbonate deposits along the western margin of India occur as dolomite crusts, aragonite sands (pelletal / oolitic) and aragonite-cemented limestones, oyster shells, corals, encrusted coralline algal and foraminiferal-dominated nodules. The petrology and mineralogy of the deposits indicate that except for aragonite ...

  20. Dusty Relic to Shining Treasure: Embedded in a Multicultural Environment

    Science.gov (United States)

    Avery, Beth Fuseler; Batman, Cindy

    2014-01-01

    Far from being dusty old relics who are guardians of the book, embedded librarians need to be proactively leading students through the digital maze of the virtual library. Working with students more than 7,000 miles away changed perceptions of how to teach and learn, and how people interact online. We will share how as embedded librarians we…

  1. Cold dark matter plus not-so-clumpy dark relics

    NARCIS (Netherlands)

    Diamanti, R.; Ando, S.; Gariazzo, S.; Mena, O.; Weniger, C.

    Various particle physics models suggest that, besides the (nearly) cold dark matter that accounts for current observations, additional but sub-dominant dark relics might exist. These could be warm, hot, or even contribute as dark radiation. We present here a comprehensive study of two-component dark

  2. Proto-ribosome: a theoretical approach based on RNA relics

    OpenAIRE

    Demongeot, Jacques

    2017-01-01

    We describe in this paper, based on already published articles, a contribution to the theory postulating the existence of a proto-ribosome, which could have appeared early at the origin of life and we discuss the interest of this notion in an evolutionary perspective, taking into account the existence of possible RNA relics of this proto-ribosome.

  3. Relic gravitational waves and the generalized second law

    International Nuclear Information System (INIS)

    Izquierdo, German; Pavon, Diego

    2004-01-01

    The generalized second law of gravitational thermodynamics is applied to the present era of accelerated expansion of the Universe. In spite of the fact that the entropy of matter and relic gravitational waves inside the event horizon diminish, the mentioned law is fulfilled provided that the expression for the entropy density of the gravitational waves satisfies a certain condition

  4. Stress-induced rearrangement of Fusarium retrotransposon sequences.

    Science.gov (United States)

    Anaya, N; Roncero, M I

    1996-11-27

    Rearrangement of fusarium oxysporum retrotransposon skippy was induced by growth in the presence of potassium chlorate. Three fungal strains, one sensitive to chlorate (Co60) and two resistant to chlorate and deficient for nitrate reductase (Co65 and Co94), were studied by Southern analysis of their genomic DNA. Polymorphism was detected in their hybridization banding pattern, relative to the wild type grown in the absence of chlorate, using various enzymes with or without restriction sites within the retrotransposon. Results were consistent with the assumption that three different events had occurred in strain Co60: genomic amplification of skippy yielding tandem arrays of the element, generation of new skippy sequences, and deletion of skippy sequences. Amplification of Co60 genomic DNA using the polymerase chain reaction and divergent primers derived from the retrotransposon generated a new band, corresponding to one long terminal repeat plus flanking sequences, that was not present in the wild-type strain. Molecular analysis of nitrate reductase-deficient mutants showed that generation and deletion of skippy sequences, but not genomic amplification in tandem repeats, had occurred in their genomes.

  5. A Zoo of Radio Relics: Cluster Cores to Filaments Ruta Kale1,2 ...

    Indian Academy of Sciences (India)

    Abstract. Radio relics in galaxy clusters can be electrons accelerated at cluster merger shocks or adiabatically compressed fossil radio cocoons or dying radio galaxies. The spectral evolution of radio relics is affected by the surrounding thermal plasma. We present a low frequency study of three radio relics representing ...

  6. GALAXY CLUSTER RADIO RELICS IN ADAPTIVE MESH REFINEMENT COSMOLOGICAL SIMULATIONS: RELIC PROPERTIES AND SCALING RELATIONSHIPS

    International Nuclear Information System (INIS)

    Skillman, Samuel W.; Hallman, Eric J.; Burns, Jack O.; Smith, Britton D.; O'Shea, Brian W.; Turk, Matthew J.

    2011-01-01

    Cosmological shocks are a critical part of large-scale structure formation, and are responsible for heating the intracluster medium in galaxy clusters. In addition, they are capable of accelerating non-thermal electrons and protons. In this work, we focus on the acceleration of electrons at shock fronts, which is thought to be responsible for radio relics-extended radio features in the vicinity of merging galaxy clusters. By combining high-resolution adaptive mesh refinement/N-body cosmological simulations with an accurate shock-finding algorithm and a model for electron acceleration, we calculate the expected synchrotron emission resulting from cosmological structure formation. We produce synthetic radio maps of a large sample of galaxy clusters and present luminosity functions and scaling relationships. With upcoming long-wavelength radio telescopes, we expect to see an abundance of radio emission associated with merger shocks in the intracluster medium. By producing observationally motivated statistics, we provide predictions that can be compared with observations to further improve our understanding of magnetic fields and electron shock acceleration.

  7. Imprints of relic gravitational waves in cosmic microwave background radiation

    International Nuclear Information System (INIS)

    Baskaran, D.; Grishchuk, L. P.; Polnarev, A. G.

    2006-01-01

    A strong variable gravitational field of the very early Universe inevitably generates relic gravitational waves by amplifying their zero-point quantum oscillations. We begin our discussion by contrasting the concepts of relic gravitational waves and inflationary 'tensor modes'. We explain and summarize the properties of relic gravitational waves that are needed to derive their effects on cosmic microwave background (CMB) temperature and polarization anisotropies. The radiation field is characterized by four invariants I, V, E, B. We reduce the radiative transfer equations to a single integral equation of Voltairre type and solve it analytically and numerically. We formulate the correlation functions C l XX ' for X, X ' =T, E, B and derive their amplitudes, shapes and oscillatory features. Although all of our main conclusions are supported by exact numerical calculations, we obtain them, in effect, analytically by developing and using accurate approximations. We show that the TE correlation at lower l's must be negative (i.e. an anticorrelation), if it is caused by gravitational waves, and positive if it is caused by density perturbations. This difference in TE correlation may be a signature more valuable observationally than the lack or presence of the BB correlation, since the TE signal is about 100 times stronger than the expected BB signal. We discuss the detection by WMAP of the TE anticorrelation at l≅30 and show that such an anticorrelation is possible only in the presence of a significant amount of relic gravitational waves (within the framework of all other common assumptions). We propose models containing considerable amounts of relic gravitational waves that are consistent with the measured TT, TE and EE correlations

  8. MASiVEdb: the Sirevirus Plant Retrotransposon Database

    Directory of Open Access Journals (Sweden)

    Bousios Alexandros

    2012-04-01

    Full Text Available Abstract Background Sireviruses are an ancient genus of the Copia superfamily of LTR retrotransposons, and the only one that has exclusively proliferated within plant genomes. Based on experimental data and phylogenetic analyses, Sireviruses have successfully infiltrated many branches of the plant kingdom, extensively colonizing the genomes of grass species. Notably, it was recently shown that they have been a major force in the make-up and evolution of the maize genome, where they currently occupy ~21% of the nuclear content and ~90% of the Copia population. It is highly likely, therefore, that their life dynamics have been fundamental in the genome composition and organization of a plethora of plant hosts. To assist studies into their impact on plant genome evolution and also facilitate accurate identification and annotation of transposable elements in sequencing projects, we developed MASiVEdb (Mapping and Analysis of SireVirus Elements Database, a collective and systematic resource of Sireviruses in plants. Description Taking advantage of the increasing availability of plant genomic sequences, and using an updated version of MASiVE, an algorithm specifically designed to identify Sireviruses based on their highly conserved genome structure, we populated MASiVEdb (http://bat.infspire.org/databases/masivedb/ with data on 16,243 intact Sireviruses (total length >158Mb discovered in 11 fully-sequenced plant genomes. MASiVEdb is unlike any other transposable element database, providing a multitude of highly curated and detailed information on a specific genus across its hosts, such as complete set of coordinates, insertion age, and an analytical breakdown of the structure and gene complement of each element. All data are readily available through basic and advanced query interfaces, batch retrieval, and downloadable files. A purpose-built system is also offered for detecting and visualizing similarity between user sequences and Sireviruses, as

  9. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

    NARCIS (Netherlands)

    Jacobs, F.M.J.; Greenberg, D.; Nguyen, N.; Haeussler, M.; Ewing, A.D.; Katzman, S.; Paten, B.; Salama, S.R.; Haussler, D.

    2014-01-01

    Throughout evolution primate genomes have been modified by waves of retrotransposon insertions1, 2, 3. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons

  10. Cosmic background radiation spectral distortion and radiative decays of relic neutral particles

    International Nuclear Information System (INIS)

    Berezhiani, Z.G.; Doroshkevich, A.G.; Khlopov, M.Yu.; Yurov, V.P.; Vysotskij, M.I.

    1989-01-01

    The recently observed excess of photons on a short wavelength side of the peak of a cosmic background radiation spectrum can be described by radiative decays of relic neutral particles. The lifetime and mass of a decaying particle must satisfy the following conditions: 2x10 9 s 14 s, 0.4 eV -9 -8x10 -8 ) μ b , and the interaction of new particles with the usual matter must be rather strong. The generalization of the standard SU(3)xSU(2)xU(1) model is presented which includes new particles with the desired properties. 18 refs.; 3 figs.; 2 tabs

  11. arXiv Squeezed relic photons beyond the horizon

    CERN Document Server

    Giovannini, Massimo

    2017-11-14

    Owing to the analogy with the ordinary photons in the visible range of the electromagnetic spectrum, the Glauber theory is generalized to address the quantum coherence of the gauge field fluctuations parametrically amplified during an inflationary stage of expansion. The first and second degrees of quantum coherence of relic photons are then computed beyond the effective horizon defined by the evolution of the susceptibility. In the zero-delay limit the Hanbury Brown-Twiss correlations exhibit a super-Poissonian statistics which is however different from the conventional results of the single-mode approximation customarily employed, in quantum optics, to classify the coherence properties of visible light. While in the case of large-scale curvature perturbations the degrees of quantum coherence coincide with the naive expectation of the single-mode approximation, the net degree of second-order coherence computed for the relic photons diminishes thanks to the effect of the polarizations. We suggest that the Han...

  12. Cosmological constraints on the amplitude of relic gravitational waves

    International Nuclear Information System (INIS)

    Novosyadlij, B.; Apunevich, S.

    2005-01-01

    The evolution of the amplitude of relic gravitational waves (RGW) generated in early Universe has been analyzed. The analytical approximation is presented for angular power spectrum of cosmic microwave background anisotropies caused by gravitational waves through Sachs-Wolfe effect. The estimate of the most probable value for this amplitude was obtained on the basis of observation data on cosmic microwave background anisotropies from COBE, WMAP and BOOMERanG experiments along with large-scale structure observations

  13. Could unstable relic particles distort the microwave background radiation?

    International Nuclear Information System (INIS)

    Dar, A.; Loeb, A.; Nussinov, S.

    1989-01-01

    Three general classes of possible scenarios for the recently reported distortion of the microwave background radiation (MBR) via decaying relic weakly interacting particles are analyzed. The analysis shows that such particles could not reheat the universe and cause the spectral distortion of the MBR. Gravitational processes such as the early formation of massive black holes may still be plausible energy sources for producing the reported spectral distortion of the MBR at an early cosmological epoch. 24 references

  14. Radiative corrections for the direct detection of neutralino dark matter and its relic density

    Energy Technology Data Exchange (ETDEWEB)

    Steppeler, Patrick Norbert

    2016-07-01

    entering the Boltzmann equation in many scenarios of the MSSM. The Boltzmann equation allows to determine the neutralino relic density, i.e. to predict their present abundance. This prediction can be checked experimentally and is thus of great phenomenological relevance. Measurements of the temperature fluctuations of the cosmic microwave background permit to determine the relic density precisely. Comparing the theoretical prediction with the experimental finding allows to exclude large fractions of the MSSM parameter space. In order to maximally benefit from the experimental precision, it is necessary to minimise theoretical uncertainties and to include the aforementioned radiative corrections. The radiative corrections to the elastic neutralino-nucleon scattering and the corresponding relic density have been implemented into the numerical package Dark matter at next-to-leading order. With the help of this program, we perform a phenomenological investigation and analyse the impact of the radiative corrections. It turns out that the neutralino relic density depends not on a single but a multitude of gaugino (co)annihilation processes in parallel quite often. The calculated radiative corrections lead to a relative shift of the relic density of up to 10%, which is significantly larger than the experimental uncertainty (±2% at the 1σ confidence level) and demonstrates that these corrections should be included when identifying the cosmologically preferred region of the MSSM. Moreover, we investigate the relation between the relic density and the neutralino-nucleon cross sections. In the spin-independent case, the inclusion of radiative corrections leads to a relative shift roughly +14% in comparison to a tree-level calculation. This shift is comparable to typical recent nuclear uncertainties, which influence the prediction as well. The spin-dependent cross section is subject to even larger shifts and modified by up to -50% by radiative corrections.

  15. Recognizing the SINEs of Infection: Regulation of Retrotransposon Expression and Modulation of Host Cell Processes

    Directory of Open Access Journals (Sweden)

    William Dunker

    2017-12-01

    Full Text Available Short interspersed elements (SINEs are a family of retrotransposons evolutionarily derived from cellular RNA polymerase III transcripts. Over evolutionary time, SINEs have expanded throughout the human genome and today comprise ~11% of total chromosomal DNA. While generally transcriptionally silent in healthy somatic cells, SINE expression increases during a variety of types of stresses, including DNA virus infection. The relevance of SINE expression to viral infection was largely unexplored, however, recent years have seen great progress towards defining the impact of SINE expression on viral replication and host gene expression. Here we review the origin and diversity of SINE elements and their transcriptional control, with an emphasis on how their expression impacts host cell biology during viral infection.

  16. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting.

    Directory of Open Access Journals (Sweden)

    Shunsuke Suzuki

    2007-04-01

    Full Text Available Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10 is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii, but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus, suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 5' region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation.

  17. Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

    Science.gov (United States)

    Harkess, Alex; Mercati, Francesco; Abbate, Loredana; McKain, Michael; Pires, J Chris; Sala, Tea; Sunseri, Francesco; Falavigna, Agostino; Leebens-Mack, Jim

    2016-09-08

    Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once, or possibly twice, in the genus Asparagus Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n = 2× = 20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here, we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion, or to retrotransposon proliferation in dioecious species. We first estimate genome sizes, or use published values, for four hermaphrodites and four dioecious species distributed across the phylogeny, and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach, we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication (WGD) event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing, and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements, in particular, have undergone a marked proliferation in dioecious species. In the absence of a detectable WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species. Copyright © 2016 Harkess et al.

  18. Detection of a Double Relic in the Torpedo Cluster: SPT-CL J0245-5302

    Science.gov (United States)

    Zheng, Q.; Johnston-Hollitt, M.; Duchesne, S. W.; Li, W. T.

    2018-06-01

    The Torpedo cluster, SPT-CL J0245-5302 (S0295) is a massive, merging cluster at a redshift of z = 0.300, which exhibits a strikingly similar morphology to the Bullet cluster 1E 0657-55.8 (z = 0.296), including a classic bow shock in the cluster's intra-cluster medium revealed by Chandra X-ray observations. We present Australia Telescope Compact Array data centred at 2.1 GHz and Murchison Widefield Array data at frequencies between 72 MHz and 231 MHz which we use to study the properties of the cluster. We characterise a number of discrete and diffuse radio sources in the cluster, including the detection of two previously unknown radio relics on the cluster periphery. The average spectral index of the diffuse emission between 70 MHz and 3.1 GHz is α =-1.63_{-0.10}^{+0.10} and a radio-derived Mach number for the shock in the west of the cluster is calculated as M = 2.04. The Torpedo cluster is thus a double relic system at moderate redshift.

  19. VizieR Online Data Catalog: Galaxy clusters: radio halos, relics and parameters (Yuan+, 2015)

    Science.gov (United States)

    Yuan, Z. S.; Han, J. L.; Wen, Z. L.

    2017-10-01

    A large number of radio halos, relics, and mini-halos have been discovered and measured in recent decades through observations with VLA (e.g., Giovannini & Feretti 2000NewA....5..335G; van Weeren et al. 2011A&A...533A..35V), GMRT (e.g., Venturi et al. 2007A&A...463..937V; Kale et al. 2015A&A...579A..92K), WSRT (e.g., van Weeren et al. 2010Sci...330..347V; Trasatti et al. 2015A&A...575A..45T), and also ATCA (e.g., Shimwell et al. 2014MNRAS.440.2901S, 2015MNRAS.449.1486S). We have checked the radio images of radio halos, relics, and mini-halos in the literature and collected in Table 1 the radio flux Sν at frequencies within a few per cent around 1.4 GHz, 610 MHz, and 325 MHz; we have interpolated the flux at an intermediate frequency if measurements are available at higher and lower frequencies. To establish reliable scaling relations, we include only the very firm detection of diffuse radio emission in galaxy clusters, and omit questionable detections or flux estimates due to problematic point-source subtraction. (3 data files).

  20. Exploration and implementation of ontology-based cultural relic knowledge map integration platform

    Science.gov (United States)

    Yang, Weiqiang; Dong, Yiqiang

    2018-05-01

    To help designers to better carry out creative design and improve the ability of searching traditional cultural relic information, the ontology-based knowledge map construction method was explored and an integrated platform for cultural relic knowledge map was developed. First of all, the construction method of the ontology of cultural relics was put forward, and the construction of the knowledge map of cultural relics was completed based on the constructed cultural relic otology. Then, a personalized semantic retrieval framework for creative design was proposed. Finally, the integrated platform of the knowledge map of cultural relics was designed and realized. The platform was divided into two parts. One was the foreground display system, which was used for designers to search and browse cultural relics. The other was the background management system, which was for cultural experts to manage cultural relics' knowledge. The research results showed that the platform designed could improve the retrieval ability of cultural relic information. To sum up, the platform can provide a good support for the designer's creative design.

  1. Cold dark matter plus not-so-clumpy dark relics

    International Nuclear Information System (INIS)

    Diamanti, Roberta; Ando, Shin'ichiro; Weniger, Christoph; Gariazzo, Stefano; Mena, Olga

    2017-01-01

    Various particle physics models suggest that, besides the (nearly) cold dark matter that accounts for current observations, additional but sub-dominant dark relics might exist. These could be warm, hot, or even contribute as dark radiation. We present here a comprehensive study of two-component dark matter scenarios, where the first component is assumed to be cold, and the second is a non-cold thermal relic. Considering the cases where the non-cold dark matter species could be either a fermion or a boson, we derive consistent upper limits on the non-cold dark relic energy density for a very large range of velocity dispersions, covering the entire range from dark radiation to cold dark matter. To this end, we employ the latest Planck Cosmic Microwave Background data, the recent BOSS DR11 and other Baryon Acoustic Oscillation measurements, and also constraints on the number of Milky Way satellites, the latter of which provides a measure of the suppression of the matter power spectrum at the smallest scales due to the free-streaming of the non-cold dark matter component. We present the results on the fraction f ncdm of non-cold dark matter with respect to the total dark matter for different ranges of the non-cold dark matter masses. We find that the 2σ limits for non-cold dark matter particles with masses in the range 1–10 keV are f ncdm ≤0.29 (0.23) for fermions (bosons), and for masses in the 10–100 keV range they are f ncdm ≤0.43 (0.45), respectively.

  2. Cold dark matter plus not-so-clumpy dark relics

    Energy Technology Data Exchange (ETDEWEB)

    Diamanti, Roberta; Ando, Shin' ichiro; Weniger, Christoph [GRAPPA, Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam (Netherlands); Gariazzo, Stefano; Mena, Olga, E-mail: r.diamanti@uva.nl, E-mail: s.ando@uva.nl, E-mail: gariazzo@to.infn.it, E-mail: omena@ific.uv.es, E-mail: c.weniger@uva.nl [Instituto de Física Corpuscular (IFIC), CSIC-Universitat de Valencia, Apartado de Correos 22085, E-46071, Valencia (Spain)

    2017-06-01

    Various particle physics models suggest that, besides the (nearly) cold dark matter that accounts for current observations, additional but sub-dominant dark relics might exist. These could be warm, hot, or even contribute as dark radiation. We present here a comprehensive study of two-component dark matter scenarios, where the first component is assumed to be cold, and the second is a non-cold thermal relic. Considering the cases where the non-cold dark matter species could be either a fermion or a boson, we derive consistent upper limits on the non-cold dark relic energy density for a very large range of velocity dispersions, covering the entire range from dark radiation to cold dark matter. To this end, we employ the latest Planck Cosmic Microwave Background data, the recent BOSS DR11 and other Baryon Acoustic Oscillation measurements, and also constraints on the number of Milky Way satellites, the latter of which provides a measure of the suppression of the matter power spectrum at the smallest scales due to the free-streaming of the non-cold dark matter component. We present the results on the fraction f {sub ncdm} of non-cold dark matter with respect to the total dark matter for different ranges of the non-cold dark matter masses. We find that the 2σ limits for non-cold dark matter particles with masses in the range 1–10 keV are f {sub ncdm}≤0.29 (0.23) for fermions (bosons), and for masses in the 10–100 keV range they are f {sub ncdm}≤0.43 (0.45), respectively.

  3. Higgs enhancement for the dark matter relic density

    Science.gov (United States)

    Harz, Julia; Petraki, Kalliopi

    2018-04-01

    We consider the long-range effect of the Higgs on the density of thermal-relic dark matter. While the electroweak gauge boson and gluon exchange have been previously studied, the Higgs is typically thought to mediate only contact interactions. We show that the Sommerfeld enhancement due to a 125 GeV Higgs can deplete TeV-scale dark matter significantly and describe how the interplay between the Higgs and other mediators influences this effect. We discuss the importance of the Higgs enhancement in the minimal supersymmetric standard model and its implications for experiments.

  4. Investigation of laser cleaning on bronze cultural relics

    International Nuclear Information System (INIS)

    Ling, Xiulan; Wang, Gao; Zhang, Chen

    2016-01-01

    The effects of laser cleaning on the corrosion layers of bronze cultural relics were studied using a pulsed fiber laser. The laser cleaning threshold value of the corrosion layers was obtained. It was found that the corrosion layer was removed successfully by employing a laser fluence value of 0.32 J cm −2 and scanning for three times. To obtain experimental evidence, laser con-focal scanning microscopy, scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDS), laser induced breakdown spectroscopy (LIBS) and laser Raman spectroscopy were employed to investigate the cleaning efficiency of corrosion layers on specimens. (paper)

  5. SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast.

    Directory of Open Access Journals (Sweden)

    Alfica Sehgal

    2007-08-01

    Full Text Available Retrotransposons are mobile genetic elements that proliferate through an RNA intermediate. Transposons do not encode transcription factors and thus rely on host factors for mRNA expression and survival. Despite information regarding conditions under which elements are upregulated, much remains to be learned about the regulatory mechanisms or factors controlling retrotransposon expression. Here, we report that low oxygen activates the fission yeast Tf2 family of retrotransposons. Sre1, the yeast ortholog of the mammalian membrane-bound transcription factor sterol regulatory element binding protein (SREBP, directly induces the expression and mobilization of Tf2 retrotransposons under low oxygen. Sre1 binds to DNA sequences in the Tf2 long terminal repeat that functions as an oxygen-dependent promoter. We find that Tf2 solo long terminal repeats throughout the genome direct oxygen-dependent expression of adjacent coding and noncoding sequences, providing a potential mechanism for the generation of oxygen-dependent gene expression.

  6. New aspartic proteinase of Ulysses retrotransposon from Drosophila virilis.

    Science.gov (United States)

    Volkov, D A; Dergousova, N I; Rumsh, L D

    2004-06-01

    This work is focused on the investigation of a proteinase of Ulysses mobile genetic element from Drosophila virilis. The primary structure of this proteinase is suggested based on comparative analysis of amino acid sequences of aspartic proteinases from retroviruses and retrotransposons. The corresponding cDNA fragment has been cloned and expressed in E. coli. The protein accumulated in inclusion bodies. The recombinant protein (12 kD) was subjected to refolding and purified by affinity chromatography on pepstatin-agarose. Proteolytic activity of the protein was determined using oligopeptide substrates melittin and insulin B-chain. It was found that the maximum of the proteolytic activity is displayed at pH 5.5 as for the majority of aspartic proteinases. We observed that hydrolysis of B-chain of insulin was totally inhibited by pepstatin A in the micromolar concentration range. The molecular weight of the monomer of the Ulysses proteinase was determined by MALDI-TOF mass-spectrometry.

  7. Perspectives for Detection of a Higgsino-like Relic Neutralino

    CERN Document Server

    Bottino, A; Mignola, G; Olechowski, M; Scopel, S

    1996-01-01

    It has been conjectured by Ambrosanio, Kane, Kribs, Martin and Mrenna (AKM) that the CDF event $p \\bar p \\to e^+ e^- \\gamma \\gamma + missing E_T$ is due to a decay chain involving two neutralino states (the lightest and the next-to-lightest ones). The lightest neutralino ($\\chi_{AKM}$) has been further considered by Kane and Wells as a candidate for cold dark matter. In this paper we examine the properties of relic $\\chi_{AKM}$'s in their full parameter space, and examine the perspectives for detection by comparing theoretical predictions to sensitivities of various experimental searches. We find that for most regions of the parameter space the detectability of a relic $\\chi_{AKM}$ would require quite substantial improvements in current experimental sensitivities. The measurements of neutrino fluxes from the center of the Earth and of an excess of $\\bar{p}/p$ in cosmic rays are shown to offer some favorable perspectives for investigating a region of the the model.

  8. SCRMS: An RFID and Sensor Web-Enabled Smart Cultural Relics Management System.

    Science.gov (United States)

    Xiao, Changjiang; Chen, Nengcheng; Li, Dandan; Lv, You; Gong, Jianya

    2016-12-30

    Cultural relics represent national or even global resources of inestimable value. How to efficiently manage and preserve these cultural relics is a vitally important issue. To achieve this goal, this study proposed, designed, and implemented an RFID and Sensor Web-enabled smart cultural relics management system (SCRMS). In this system, active photovoltaic subtle energy-powered Radio Frequency Identification (RFID) is used for long-range contactless identification and lifecycle management of cultural relics during their storage and circulation. In addition, different types of ambient sensors are integrated with the RFID tags and deployed around cultural relics to monitor their environmental parameters, helping to ensure that they remain in good condition. An Android-based smart mobile application, as middleware, is used in collaboration with RFID readers to collect information and provide convenient management for the circulation of cultural relics. Moreover, multiple sensing techniques are taken advantage of simultaneously for preservation of cultural relics. The proposed system was successfully applied to a museum in the Yongding District, Fujian Province, China, demonstrating its feasibility and advantages for smart and efficient management and preservation of cultural relics.

  9. SCRMS: An RFID and Sensor Web-Enabled Smart Cultural Relics Management System

    Directory of Open Access Journals (Sweden)

    Changjiang Xiao

    2016-12-01

    Full Text Available Cultural relics represent national or even global resources of inestimable value. How to efficiently manage and preserve these cultural relics is a vitally important issue. To achieve this goal, this study proposed, designed, and implemented an RFID and Sensor Web–enabled smart cultural relics management system (SCRMS. In this system, active photovoltaic subtle energy-powered Radio Frequency Identification (RFID is used for long-range contactless identification and lifecycle management of cultural relics during their storage and circulation. In addition, different types of ambient sensors are integrated with the RFID tags and deployed around cultural relics to monitor their environmental parameters, helping to ensure that they remain in good condition. An Android-based smart mobile application, as middleware, is used in collaboration with RFID readers to collect information and provide convenient management for the circulation of cultural relics. Moreover, multiple sensing techniques are taken advantage of simultaneously for preservation of cultural relics. The proposed system was successfully applied to a museum in the Yongding District, Fujian Province, China, demonstrating its feasibility and advantages for smart and efficient management and preservation of cultural relics.

  10. Recurrent emergence of structural variants of LTR retrotransposon CsRn1 evolving novel expression strategy and their selective expansion in a carcinogenic liver fluke, Clonorchis sinensis.

    Science.gov (United States)

    Kim, Seon-Hee; Kong, Yoon; Bae, Young-An

    2017-06-01

    Autonomous retrotransposons, in which replication and transcription are coupled, encode the essential gag and pol genes as a fusion or separate overlapping form(s) that are expressed in single transcripts regulated by a common upstream promoter. The element-specific expression strategies have driven development of relevant translational recoding mechanisms including ribosomal frameshifting to satisfy the protein stoichiometry critical for the assembly of infectious virus-like particles. Retrotransposons with different recoding strategies exhibit a mosaic distribution pattern across the diverse families of reverse transcribing elements, even though their respective distributions are substantially skewed towards certain family groups. However, only a few investigations to date have focused on the emergence of retrotransposons evolving novel expression strategy and causal genetic drivers of the structural variants. In this study, the bulk of genomic and transcribed sequences of a Ty3/gypsy-like CsRn1 retrotransposon in Clonorchis sinensis were analyzed for the comprehensive examination of its expression strategy. Our results demonstrated that structural variants with single open reading frame (ORF) have recurrently emerged from precedential CsRn1 copies encoding overlapping gag-pol ORFs by a single-nucleotide insertion in an upstream region of gag stop codon. In the parasite genome, some of the newly evolved variants appeared to undergo proliferative burst as active master lineages together with their ancestral copies. The genetic event was similarly observed in Opisthorchis viverrini, the closest neighbor of C. sinensis, whereas the resulting structural variants might have failed to overcome purifying selection and comprised minor remnant copies in the Opisthorchis genome. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Twin radio relics in the nearby low-mass galaxy cluster Abell 168

    Science.gov (United States)

    Dwarakanath, K. S.; Parekh, V.; Kale, R.; George, L. T.

    2018-06-01

    We report the discovery of twin radio relics in the outskirts of the low-mass merging galaxy cluster Abell 168 (redshift=0.045). One of the relics is elongated with a linear extent ˜800 kpc and projected width of ˜80 kpc and is located ˜900 kpc towards the north of the cluster centre, oriented roughly perpendicular to the major axis of the X-ray emission. The second relic is ring-shaped with a size ˜220 kpc and is located near the inner edge of the elongated relic at a distance of ˜600 kpc from the cluster centre. These radio sources were imaged at 323 and 608 MHz with the Giant Meterwave Radio Telescope and at 1520 MHz with the Karl G. Jansky Very Large Array (VLA). The elongated relic was detected at all frequencies, with a radio power of 1.38 ± 0.14 × 1023 W Hz-1 at 1.4 GHz and a power law in the frequency range 70-1500 MHz (S ∝ να, α = -1.1 ± 0.04). This radio power is in good agreement with that expected from the known empirical relation between the radio powers of relics and host cluster masses. This is the lowest mass (M500 = 1.24 × 1014 M⊙) cluster in which relics due to merger shocks are detected. The ring-shaped relic has a steeper spectral index (α) of -1.74 ± 0.29 in the frequency range 100-600 MHz. We propose this relic to be an old plasma, revived due to adiabatic compression by the outgoing shock that produced the elongated relic.

  12. Life of saint Spiridon and history on relic to the bishop of Tremithus

    Directory of Open Access Journals (Sweden)

    Adam Magruk

    2015-11-01

    Full Text Available In the last few years Saint Spyridon – the great hierarch of Greek Orthodox Church, is becoming increasingly known, glorified and praised by Orthodox Christians from all over the world including slavic territories. In Russia, for instance, St Spyridon is honored on a par with St Nikolaos the Wonderworker. Therefore, his biography is truly admirable, e.g. occurrences before the ordination to the priesthood and even more interestingly facts after he was made Bishop of Trimythous. St Spyridon participated in the sessions of the Firts Ecumenical Council, where he played a significant and remarkable role. Special attention deserve also the history of St Spyridon’s relics, which repose on the Greek island of Corfu to this day as well as his miraculous right hand returned to Orthodox Greeks by Catholic Church after c. 800 years.

  13. Molecular relics from chemical evolution and the origin of life

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1994-04-01

    The main hypothesis proposed in this work intends to remove the difficulty that arises from the conjecture that the RNA world may have left molecular relics that may still be extant in the angiosperms. We discuss whether it is possible to envisage a possible evolutionary pathway of the RNA replicators spanning the vast time span separating the first appearance of the angiosperms, late in the Mesozoic era (the Lower Cretaceous), from the most likely suberas in which the RNA world may have occurred, namely the Hadean/Early Archean. In order to address this question we suggest that through horizontal gene transfer, as well as through a series of symbiosis of the precursor cell of the land plants, the genes of the replicases (RNA-directed RNA polymerases) associated with putative DNA-independent RNA replicators may have been transferred vertically, eventually becoming specific to the angiosperms. (author). Refs, 7 tabs

  14. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation.

    Science.gov (United States)

    Kalendar, Ruslan; Antonius, Kristiina; Smýkal, Petr; Schulman, Alan H

    2010-11-01

    Molecular markers are essential in plant and animal breeding and biodiversity applications, in human forensics, and for map-based cloning of genes. The long terminal repeat (LTR) retrotransposons are well suited as molecular markers. As dispersed and ubiquitous transposable elements, their "copy and paste" life cycle of replicative transposition leads to new genome insertions without excision of the original element. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Nevertheless, up to a year has been required to develop a retrotransposon marker system in a new species, involving cloning and sequencing steps as well as the development of custom primers. Here, we describe a novel PCR-based method useful both as a marker system in its own right and for the rapid isolation of retrotransposon termini and full-length elements, making it ideal for "orphan crops" and other species with underdeveloped marker systems. The method, iPBS amplification, is based on the virtually universal presence of a tRNA complement as a reverse transcriptase primer binding site (PBS) in LTR retrotransposons. The method differs from earlier retrotransposon isolation methods because it is applicable not only to endogenous retroviruses and retroviruses, but also to both Gypsy and Copia LTR retrotransposons, as well as to non-autonomous LARD and TRIM elements, throughout the plant kingdom and to animals. Furthermore, the inter-PBS amplification technique as such has proved to be a powerful DNA fingerprinting technology without the need for prior sequence knowledge.

  15. Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice.

    Directory of Open Access Journals (Sweden)

    Kota Inoue

    2017-07-01

    Full Text Available Mammalian genomes harbor millions of retrotransposon copies, some of which are transpositionally active. In mouse prospermatogonia, PIWI-interacting small RNAs (piRNAs combat retrotransposon activity to maintain the genomic integrity. The piRNA system destroys retrotransposon-derived RNAs and guides de novo DNA methylation at some retrotransposon promoters. However, it remains unclear whether DNA methylation contributes to retrotransposon silencing in prospermatogonia. We have performed comprehensive studies of DNA methylation and polyA(+ RNAs (transcriptome in developing male germ cells from Pld6/Mitopld and Dnmt3l knockout mice, which are defective in piRNA biogenesis and de novo DNA methylation, respectively. The Dnmt3l mutation greatly reduced DNA methylation levels at most retrotransposons, but its impact on their RNA abundance was limited in prospermatogonia. In Pld6 mutant germ cells, although only a few retrotransposons exhibited reduced DNA methylation, many showed increased expression at the RNA level. More detailed analysis of RNA sequencing, nascent RNA quantification, profiling of cleaved RNA ends, and the results obtained from double knockout mice suggest that PLD6 works mainly at the posttranscriptional level. The increase in retrotransposon expression was larger in Pld6 mutants than it was in Dnmt3l mutants, suggesting that RNA degradation by the piRNA system plays a more important role than does DNA methylation in prospermatogonia. However, DNA methylation had a long-term effect: hypomethylation caused by the Pld6 or Dnmt3l mutation resulted in increased retrotransposon expression in meiotic spermatocytes. Thus, posttranscriptional silencing plays an important role in the early stage of germ cell development, then transcriptional silencing becomes important in later stages. In addition, intergenic and intronic retrotransposon sequences, in particular those containing the antisense L1 promoters, drove ectopic expression of nearby

  16. Accurate estimate of the relic density and the kinetic decoupling in nonthermal dark matter models

    International Nuclear Information System (INIS)

    Arcadi, Giorgio; Ullio, Piero

    2011-01-01

    Nonthermal dark matter generation is an appealing alternative to the standard paradigm of thermal WIMP dark matter. We reconsider nonthermal production mechanisms in a systematic way, and develop a numerical code for accurate computations of the dark matter relic density. We discuss, in particular, scenarios with long-lived massive states decaying into dark matter particles, appearing naturally in several beyond the standard model theories, such as supergravity and superstring frameworks. Since nonthermal production favors dark matter candidates with large pair annihilation rates, we analyze the possible connection with the anomalies detected in the lepton cosmic-ray flux by Pamela and Fermi. Concentrating on supersymmetric models, we consider the effect of these nonstandard cosmologies in selecting a preferred mass scale for the lightest supersymmetric particle as a dark matter candidate, and the consequent impact on the interpretation of new physics discovered or excluded at the LHC. Finally, we examine a rather predictive model, the G2-MSSM, investigating some of the standard assumptions usually implemented in the solution of the Boltzmann equation for the dark matter component, including coannihilations. We question the hypothesis that kinetic equilibrium holds along the whole phase of dark matter generation, and the validity of the factorization usually implemented to rewrite the system of a coupled Boltzmann equation for each coannihilating species as a single equation for the sum of all the number densities. As a byproduct we develop here a formalism to compute the kinetic decoupling temperature in case of coannihilating particles, which can also be applied to other particle physics frameworks, and also to standard thermal relics within a standard cosmology.

  17. RELICS: Strong Lens Models for Five Galaxy Clusters from the Reionization Lensing Cluster Survey

    Science.gov (United States)

    Cerny, Catherine; Sharon, Keren; Andrade-Santos, Felipe; Avila, Roberto J.; Bradač, Maruša; Bradley, Larry D.; Carrasco, Daniela; Coe, Dan; Czakon, Nicole G.; Dawson, William A.; Frye, Brenda L.; Hoag, Austin; Huang, Kuang-Han; Johnson, Traci L.; Jones, Christine; Lam, Daniel; Lovisari, Lorenzo; Mainali, Ramesh; Oesch, Pascal A.; Ogaz, Sara; Past, Matthew; Paterno-Mahler, Rachel; Peterson, Avery; Riess, Adam G.; Rodney, Steven A.; Ryan, Russell E.; Salmon, Brett; Sendra-Server, Irene; Stark, Daniel P.; Strolger, Louis-Gregory; Trenti, Michele; Umetsu, Keiichi; Vulcani, Benedetta; Zitrin, Adi

    2018-06-01

    Strong gravitational lensing by galaxy clusters magnifies background galaxies, enhancing our ability to discover statistically significant samples of galaxies at {\\boldsymbol{z}}> 6, in order to constrain the high-redshift galaxy luminosity functions. Here, we present the first five lens models out of the Reionization Lensing Cluster Survey (RELICS) Hubble Treasury Program, based on new HST WFC3/IR and ACS imaging of the clusters RXC J0142.9+4438, Abell 2537, Abell 2163, RXC J2211.7–0349, and ACT-CLJ0102–49151. The derived lensing magnification is essential for estimating the intrinsic properties of high-redshift galaxy candidates, and properly accounting for the survey volume. We report on new spectroscopic redshifts of multiply imaged lensed galaxies behind these clusters, which are used as constraints, and detail our strategy to reduce systematic uncertainties due to lack of spectroscopic information. In addition, we quantify the uncertainty on the lensing magnification due to statistical and systematic errors related to the lens modeling process, and find that in all but one cluster, the magnification is constrained to better than 20% in at least 80% of the field of view, including statistical and systematic uncertainties. The five clusters presented in this paper span the range of masses and redshifts of the clusters in the RELICS program. We find that they exhibit similar strong lensing efficiencies to the clusters targeted by the Hubble Frontier Fields within the WFC3/IR field of view. Outputs of the lens models are made available to the community through the Mikulski Archive for Space Telescopes.

  18. Another shock for the Bullet cluster, and the source of seed electrons for radio relics

    Science.gov (United States)

    Shimwell, Timothy W.; Markevitch, Maxim; Brown, Shea; Feretti, Luigina; Gaensler, B. M.; Johnston-Hollitt, M.; Lage, Craig; Srinivasan, Raghav

    2015-05-01

    With Australia Telescope Compact Array observations, we detect a highly elongated Mpc-scale diffuse radio source on the eastern periphery of the Bullet cluster 1E 0657-55.8, which we argue has the positional, spectral and polarimetric characteristics of a radio relic. This powerful relic (2.3 ± 0.1 × 1025 W Hz-1) consists of a bright northern bulb and a faint linear tail. The bulb emits 94 per cent of the observed radio flux and has the highest surface brightness of any known relic. Exactly coincident with the linear tail, we find a sharp X-ray surface brightness edge in the deep Chandra image of the cluster - a signature of a shock front in the hot intracluster medium (ICM), located on the opposite side of the cluster to the famous bow shock. This new example of an X-ray shock coincident with a relic further supports the hypothesis that shocks in the outer regions of clusters can form relics via diffusive shock (re-)acceleration. Intriguingly, our new relic suggests that seed electrons for reacceleration are coming from a local remnant of a radio galaxy, which we are lucky to catch before its complete disruption. If this scenario, in which a relic forms when a shock crosses a well-defined region of the ICM polluted with aged relativistic plasma - as opposed to the usual assumption that seeds are uniformly mixed in the ICM - is also the case for other relics, this may explain a number of peculiar properties of peripheral relics.

  19. Analysis of Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons in rice

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    Gozde Yuzbasioglu

    2016-03-01

    Full Text Available We investigated Hopi/Osr27 (gypsy and Houba/Tos5/Osr13 (copy retrotransposon movements in 10-day-old roots and leaves of Oryza sativa cvs. Ipsala, Beser and Osmancik-97. Seeds from these three cultivars were germinated between filter papers in Petri dishes for 10 days. Three biologically independent (nonrelated seeds were germinated for each cultivar. Then, roots and leaves grown from the same rice plant were harvested and used for genomic DNA isolation. Inter-retrotransposon amplified polymorphism–polymerase chain reaction with suitable primers was performed with each DNA template to analyze the movements of Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons. Polymorphism ratios were evaluated both among cultivars and among roots and leaves from the same cultivar. The polymorphism ratios ranged from 0% to 17% for Hopi/Osr27 and from 10% to 87% for Houba/Tos5/Osr13. The obtained results at retrotransposon and varietal levels indicated that the retrotransposon type and genotype dependence are responsible for the occurrence of different variations. Transposable elements are very important for understanding the relationship between cultivars and evolution. Our findings are expected to contribute to the understanding of spontaneous genomic insertion events and their effects on the genetic and epigenetic changes during rice development.

  20. Retrotransposon hypomethylation in melanoma and expression of a placenta-specific gene.

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    Erin C Macaulay

    Full Text Available In the human placenta, DNA hypomethylation permits the expression of retrotransposon-derived genes that are normally silenced by methylation in somatic tissues. We previously identified hypomethylation of a retrotransposon-derived transcript of the voltage-gated potassium channel gene KCNH5 that is expressed only in human placenta. However, an RNA sequence from this placental-specific transcript has been reported in melanoma. This study examined the promoter methylation and expression of the retrotransposon-derived KCNH5 transcript in 25 melanoma cell lines to determine whether the acquisition of 'placental' epigenetic marks is a feature of melanoma. Methylation and gene expression analysis revealed hypomethylation of this retrotransposon in melanoma cell lines, particularly in those samples that express the placental KCNH5 transcript. Therefore we propose that hypomethylation of the placental-specific KCNH5 promoter is frequently associated with KCNH5 expression in melanoma cells. Our findings show that melanoma can develop hypomethylation of a retrotransposon-derived gene; a characteristic notably shared with the normal placenta.

  1. PpRT1: the first complete gypsy-like retrotransposon isolated in Pinus pinaster.

    Science.gov (United States)

    Rocheta, Margarida; Cordeiro, Jorge; Oliveira, M; Miguel, Célia

    2007-02-01

    We have isolated and characterized a complete retrotransposon sequence, named PpRT1, from the genome of Pinus pinaster. PpRT1 is 5,966 bp long and is closely related to IFG7 gypsy retrotransposon from Pinus radiata. The long terminal repeats (LTRs) have 333 bp each and show a 5.4% sequence divergence between them. In addition to the characteristic polypurine tract (PPT) and the primer binding site (PBS), PpRT1 carries internal regions with homology to retroviral genes gag and pol. The pol region contains sequence motifs related to the enzymes protease, reverse transcriptase, RNAseH and integrase in the same typical order known for Ty3/gypsy-like retrotransposons. PpRT1 was extended from an EST database sequence indicating that its transcription is occurring in pine tissues. Southern blot analyses indicate however, that PpRT1 is present in a unique or a low number of copies in the P. pinaster genome. The differences in nucleotide sequence found between PpRT1 and IFG7 may explain the strikingly different copy number in the two pine species genome. Based on the homologies observed when comparing LTR region among different gypsy elements we propose that the highly conserved LTR regions may be useful to amplify other retrotransposon sequences of the same or close retrotransposon family.

  2. Diaspora, a large family of Ty3-gypsy retrotransposons in Glycine max, is an envelope-less member of an endogenous plant retrovirus lineage.

    Science.gov (United States)

    Yano, Sho T; Panbehi, Bahman; Das, Arpita; Laten, Howard M

    2005-05-05

    The chromosomes of higher plants are littered with retrotransposons that, in many cases, constitute as much as 80% of plant genomes. Long terminal repeat retrotransposons have been especially successful colonizers of the chromosomes of higher plants and examinations of their function, evolution, and dispersal are essential to understanding the evolution of eukaryotic genomes. In soybean, several families of retrotransposons have been identified, including at least two that, by virtue of the presence of an envelope-like gene, may constitute endogenous retroviruses. However, most elements are highly degenerate and are often sequestered in regions of the genome that sequencing projects initially shun. In addition, finding potentially functional copies from genomic DNA is rare. This study provides a mechanism to surmount these issues to generate a consensus sequence that can then be functionally and phylogenetically evaluated. Diaspora is a multicopy member of the Ty3-gypsy-like family of LTR retrotransposons and comprises at least 0.5% of the soybean genome. Although the Diaspora family is highly degenerate, and with the exception of this report, is not represented in the Genbank nr database, a full-length consensus sequence was generated from short overlapping sequences using a combination of experimental and in silico methods. Diaspora is 11,737 bp in length and contains a single 1892-codon ORF that encodes a gag-pol polyprotein. Phylogenetic analysis indicates that it is closely related to Athila and Calypso retroelements from Arabidopsis and soybean, respectively. These in turn form the framework of an endogenous retrovirus lineage whose members possess an envelope-like gene. Diaspora appears to lack any trace of this coding region. A combination of empirical sequencing and retrieval of unannotated Genome Survey Sequence database entries was successfully used to construct a full-length representative of the Diaspora family in Glycine max. Diaspora is presently the

  3. Discussion of impact of relics activation on protection and utilization approaches-take the old summer palace as an example

    Science.gov (United States)

    Xiaoqi, J.

    2015-08-01

    As the popularization of cultural relics and the rapid development of cultural tourism industry, a large number of cultural relic tourism resources goes into public eyes. Activation of relics has became an important way for tourist to contact and understand culture relics. The way of how to properly interpret the historical sense and cultural uniqueness to the masses of tourists in order to achieve social service functions of relic resources has always been research focal point of site protection and utilization, so nowadays it has important significance to protection and utilization of heritage resources in our country. From the point of activation of relics and based on the analysis of resource characteristic, the paper in depth discuss ways of activation of relics of the Old Summer Palace, in order to provide reference for sustainable development of sites tourism in China.

  4. Analysis on the environment of cultural relic as tourist attraction--take Yungang Grottoes as an example

    Science.gov (United States)

    Xiangdong, Zhu; Jie, Bai

    2018-03-01

    Cultural relic resources are precious non-renewable resources and an important cornerstone for the development of cultural relic tourism. With the rapid development of tourism industry, the native environment of cultural relics is being squeezed constantly. Meanwhile, under the economic interests, cultural relic’s protection and heritage tourism contradictions continue to intensify. The present era which the architectural style is convergence, cultural relics protection is simplistic, restore historical sites blindly and other. In the historical process of economic development and the acceleration of new-type urbanization, the heritage industry faces the dual tasks and development challenges. As cultural relic protection workers, investigation of the utilization of cultural relic’s tourist attractions, investigation and analysis of the Yungang Grottoes, indicating cultural relics as a tourist attraction, not only to strengthen the protection of ontology, also should attach importance to the coordinated development of the protection of cultural relics and the utilization of tourism.

  5. Identification and chromosomal distribution of copia-like retrotransposon sequences in the coffee (Coffea L. genome

    Directory of Open Access Journals (Sweden)

    Juan-Carlos Herrera

    2013-12-01

    Full Text Available The presence of copia-like transposable elements in seven coffee (Coffea sp. species, including the cultivated Coffea arabica, was investigated. The highly conserved domains of the reverse transcriptase (RT present in the copia retrotransposons were amplified by PCR using degenerated primers. Fragments of roughly 300 bp were obtained and the nucleotide sequence was determined for 36 clones, 19 of which showed good quality. The deduced amino acid sequences were compared by multiple alignment analysis. The data suggested two distinct coffee RT groups, designated as CRTG1 and CRTG2. The sequence identities among the groups ranged from 52 to 60% for CRTG1 and 74 to 85% for CRTG2. The multiple alignment analysis revealed that some of the clones in CRTG1 were closely related to the representative elements present in other plant species such as Brassica napus, Populus ciliata and Picea abis. Furthermore, the chromosomal localization of the RT domains in C. arabica and their putative ancestors was investigated by fluorescence in situ hybridization (FISH analysis. FISH signals were observed throughout the chromosomes following a similar dispersed pattern with some localized regions exhibiting higher concentrations of those elements, providing new evidence of their relative conservation and stability in the coffee genome

  6. An Account of Translation of Relics: the Writings of Alonso de Cartagena

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    Luis Fernández Gallardo

    2018-01-01

    Full Text Available The narratives of translation of relics is a genre of devotional literature that didn´t develop extensively in Medieval Castile. But Alonso de Cartagena contributed to it remarkably. In 1453, during a pastoral visit, he decided to move the relics of St. Juliana to a more honorable place. He wrote an account of these facts that adjusts strictly to the features of the genre. This vernacular text contains an exposition about the cult of saints and their relics, which has an intense Thomist inspiration: it sets theological questions with precision and clarity. The provisions on the decoration of the chapel of the relics offer an interesting testimony of the debate on religious image which is then developed in Castile.

  7. a Review of Digital Watermarking and Copyright Control Technology for Cultural Relics

    Science.gov (United States)

    Liu, H.; Hou, M.; Hu, Y.

    2018-04-01

    With the rapid growth of the application and sharing of the 3-D model data in the protection of cultural relics, the problem of Shared security and copyright control of the three-dimensional model of cultural relics is becoming increasingly prominent. Followed by a digital watermarking copyright control has become the frontier technology of 3-D model security protection of cultural relics and effective means, related technology research and application in recent years also got further development. 3-D model based on cultural relics digital watermarking and copyright control technology, introduces the research background and demand, its unique characteristics were described, and its development and application of the algorithm are discussed, and the prospects of the future development trend and some problems and the solution.

  8. “The Godly Greedy Appetite”: New Relic Circulation in the Early Modern World

    Directory of Open Access Journals (Sweden)

    Igor Pérez Tostado

    2017-05-01

    Full Text Available Having lost all monasteries and a good deal of its medieval Christian movable assets, England became one of the greatest producers of new Catholic relics during the sixteenth and seventeenth centuries. This article aims to look, from a material point of view, at the circulation and consumption of English relics on the Catholic continent. In this case, these products were created because of violence and circulated as an answer to it. Gifts and the exchange of relics served to obtain support for the exiled Catholics and for the institutions providing for their education created in the continent, and allowed them to participate in the necropolitics of the Spanish Monarchy. Relics, artifacts and printed and manuscript narratives brought back from all over the world helped construct a selfimage of an English Catholic as a necrocommunity imbued by a sense of historical continuity and connected to a global imagined community.

  9. Gravitino dark matter from increased thermal relic particles

    International Nuclear Information System (INIS)

    Okada, Nobuchika; Seto, Osamu

    2008-01-01

    We investigate the so-called superWIMP scenario with the gravitino as the lightest supersymmetric particle (LSP) in the context of nonstandard cosmology, in particular, brane world cosmology. As a candidate of the next-to-LSP (NLSP), we examine the slepton and the sneutrino. Brane world cosmological effects dramatically enhance the relic density of the slepton or sneutrino NLSP, so that the NLSP with mass of order 100 GeV can provide the correct abundance of gravitino dark matter through its decay. We find that with an appropriate five-dimensional Planck mass, this scenario can be realized consistently with the constraints from big bang nucleosynthesis for both NLSP candidates of the slepton and the sneutrino. The big bang nucleosynthesis constraints for the slepton NLSP are more stringent than that for the sneutrino; as the result, the gravitino must be rather warm in the slepton NLSP case. The energy density of the gravitino produced by thermal scattering is highly suppressed and negligible due to the brane world cosmological effects

  10. Relic gravitational waves from light primordial black holes

    International Nuclear Information System (INIS)

    Dolgov, Alexander D.; Ejlli, Damian

    2011-01-01

    The energy density of relic gravitational waves (GWs) emitted by primordial black holes (PBHs) is calculated. We estimate the intensity of GWs produced at quantum and classical scattering of PBHs, the classical graviton emission from the PBH binaries in the early Universe, and the graviton emission due to PBH evaporation. If nonrelativistic PBHs dominated the cosmological energy density prior to their evaporation, the probability of formation of dense clusters of PBHs and their binaries in such clusters would be significant and the energy density of the generated gravitational waves in the present-day universe could exceed that produced by other known mechanisms. The intensity of these gravitational waves would be maximal in the GHz frequency band of the spectrum or higher and makes their observation very difficult by present detectors but also gives a rather good possibility to investigate it by present and future high-frequency gravitational waves electromagnetic detectors. However, the low-frequency part of the spectrum in the range f∼0.1-10 Hz may be detectable by the planned space interferometers DECIGO/BBO. For sufficiently long duration of the PBH matter-dominated stage, the cosmological energy fraction of GWs from inflation would be noticeably diluted.

  11. Mapping the ecological dimensions and potential distributions of endangered relic shrubs in western Ordos biodiversity center.

    Science.gov (United States)

    Zhu, Geng-Ping; Li, Hui-Qi; Zhao, Li; Man, Liang; Liu, Qiang

    2016-05-20

    Potential distributions of endemic relic shrubs in western Ordos were poorly mapped, which hindered our implementation of proper conservation. Here we investigated the applicability of ecological niche modeling for endangered relic shrubs to detect areas of priority for biodiversity conservation and analyze differences in ecological niche spaces used by relic shrubs. We applied ordination and niche modeling techniques to assess main environmental drivers of five endemic relic shrubs in western Ordos, namely, Ammopiptanthus mongolicus, Amygdalus mongolica, Helianthemum songaricum, Potaninia mongolica, and Tetraena mongolica. We calculated niche overlap metrics in gridded environmental spaces and compared geographical projections of ecological niches to determine similarities and differences of niches occupied by relic shrubs. All studied taxa presented different responses to environmental factors, which resulted in a unique combination of niche conditions. Precipitation availability and soil quality characteristics play important roles in the distributions of most shrubs. Each relic shrub is constrained by a unique set of environmental conditions, the distribution of one species cannot be implied by the distribution of another, highlighting the inadequacy of one-fits-all type of conservation measure. Our stacked habitat suitability maps revealed regions around Yellow River, which are highly suitable for most species, thereby providing high conservation value.

  12. Flower symbolism and the cult of relics in medieval Serbia

    Directory of Open Access Journals (Sweden)

    Popović Danica

    2008-01-01

    Full Text Available The Life of archbishop Eustathios I [Jevstatije] (1279-1286, deserving head of the medieval Serbian Church and a saint, is a very interesting source for studying the cult of relics with the Serbs. This is not surprising considering that the Life was penned by one of the most illustrious of Eustathios' successors on the church throne, Daniel II [Danilo], a learned Athonite and unquestionable master of the hagiographie literary genre. In his account of the life of his distinguished predecessor, Daniel describes extensively the events constituting the key stage in the glorification of a saint, namely Eustathios' death and posthumous occurrences at his grave. As most holy men, Eustathios foresaw his own death, and he departed from this world serenely. He was buried, with due honours, in the 'marble grave' he had prepared for himself in the cathedral church of Holy Saviour at Žiča. In keeping with the well-established saint-making process, a few years after the funeral 'extraordinary signs' began to occur at the archbishop's grave, in this particular case, candlelight and a multitude of murmuring voices followed by the miraculous cure of an incurably ill person. These occurrences preceded the great miracle which, to the best of my knowledge, is unparalleled in the medieval Serbian practice of relic veneration. Namely, 'one day they found growing from his marble grave three flowers endowed with wondrous beauty and impossible to liken to anything else. For, indeed, they were not of earthly humidity or of union with flowers that grow from earth; but, o wonder, how a dry stone standing for so long in the church could send forth fragrant flowers, to the renewal of the sanctified one's body'. Flower metaphors occur in the Service to the holy archbishop Eustathios, yet another piece penned by Daniel II, notably in his paraphrases of Psalm 92, 12-14 ('The righteous shall flourish like the palm tree: he shall grow like a cedar in Lebanon. These that be

  13. An evaluation of a SVA retrotransposon in the FUS promoter as a transcriptional regulator and its association to ALS.

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    Abigail L Savage

    Full Text Available Genetic mutations of FUS have been linked to many diseases including Amyotrophic Lateral Sclerosis (ALS and Frontotemporal Lobar Degeneration. A primate specific and polymorphic retrotransposon of the SINE-VNTR-Alu (SVA family is present upstream of the FUS gene. Here we have demonstrated that this retrotransposon can act as a classical transcriptional regulatory domain in the context of a reporter gene construct both in vitro in the human SK-N-AS neuroblastoma cell line and in vivo in a chick embryo model. We have also demonstrated that the SVA is composed of multiple distinct regulatory domains, one of which is a variable number tandem repeat (VNTR. The ability of the SVA and its component parts to direct reporter gene expression supported a hypothesis that this region could direct differential FUS expression in vivo. The SVA may therefore contribute to the modulation of FUS expression exhibited in and associated with neurological disorders including ALS where FUS regulation may be an important parameter in progression of the disease. As VNTRs are often clinical associates for disease progression we determined the extent of polymorphism within the SVA. In total 2 variants of the SVA were identified based within a central VNTR. Preliminary analysis addressed the association of these SVA variants within a small sporadic ALS cohort but did not reach statistical significance, although we did not include other parameters such as SNPs within the SVA or an environmental factor in this analysis. The latter may be particularly important as the transcriptional and epigenetic properties of the SVA are likely to be directed by the environment of the cell.

  14. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.

    Science.gov (United States)

    Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H; Cavallini, Andrea; Natali, Lucia

    2015-11-24

    The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Relics of the cosmological quark-hadron phase transition

    International Nuclear Information System (INIS)

    Sinha, Bikash

    2001-01-01

    In this talk I will not dwell further on the nature of the Q -> H transition, Instead, I will simply assume that it is a phase transition, and further, a first-order phase transition, in which case, there is a possibility that a particular kind of relics called quark nuggets (QNs) containing a large fraction of the net baryon number of the universe may have been formed at the end of such a phase transition. The QNs would have tremendous implications for cosmology and astrophysics. In particular, they can be a good candidate for the baryonic dark matter in the universe provided they can survive up to the present epoch. The QNs which survived and floating around the universe, is there any connection with the recently discovered MACHOs between the earth and the Large Magellanic clouds. The QNs are hypothesized to be made of 'strange matter' which is composed of a roughly equal mixture of u, d, and s quarks at a density ≥ nuclear density. It has been hypothesized that at zero temperature and zero pressure the true ground state of hadronic matter could be SM rather than 56 Fe, the energy per baryon in SM could be lower that in ordinary nuclear matter. The latter would, however, still be effectively stable against decay would require high order simultaneous weak interaction process with a life-time much greater than the age of the universe. For certain ranges of values of parameters involved, namely, the QCD fine structure constant (α c ), mass of the strange quark (m s ), the vacuum bag energy (B), the hypothesis of SM being the absolutely stable of hadronic matter has been found to be quite plausible. (author)

  16. Envelope-like retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster).

    Science.gov (United States)

    Miguel, Célia; Simões, Marta; Oliveira, Maria Margarida; Rocheta, Margarida

    2008-11-01

    Retroviruses differ from retrotransposons due to their infective capacity, which depends critically on the encoded envelope. Some plant retroelements contain domains reminiscent of the env of animal retroviruses but the number of such elements described to date is restricted to angiosperms. We show here the first evidence of the presence of putative env-like gene sequences in a gymnosperm species, Pinus pinaster (maritime pine). Using a degenerate primer approach for conserved domains of RNaseH gene, three clones from putative envelope-like retrotransposons (PpRT2, PpRT3, and PpRT4) were identified. The env-like sequences of P. pinaster clones are predicted to encode proteins with transmembrane domains. These sequences showed identity scores of up to 30% with env-like sequences belonging to different organisms. A phylogenetic analysis based on protein alignment of deduced aminoacid sequences revealed that these clones clustered with env-containing plant retrotransposons, as well as with retrotransposons from invertebrate organisms. The differences found among the sequences of maritime pine clones isolated here suggest the existence of different putative classes of env-like retroelements. The identification for the first time of env-like genes in a gymnosperm species may support the ancestrality of retroviruses among plants shedding light on their role in plant evolution.

  17. Identification of a non-LTR retrotransposon from the gypsy moth

    Science.gov (United States)

    K.J. Garner; J.M. Slavicek

    1999-01-01

    A family of highly repetitive elements, named LDT1, has been identified in the gypsy moth, Lymantria dispar. The complete element is 5.4 kb in length and lacks long-terminal repeats, The element contains two open reading frames with a significant amino acid sequence similarity to several non-LTR retrotransposons. The first open reading frame contains...

  18. How a retrotransposon exploits the plant's heat stress response for its activation.

    Directory of Open Access Journals (Sweden)

    Vladimir V Cavrak

    2014-01-01

    Full Text Available Retrotransposons are major components of plant and animal genomes. They amplify by reverse transcription and reintegration into the host genome but their activity is usually epigenetically silenced. In plants, genomic copies of retrotransposons are typically associated with repressive chromatin modifications installed and maintained by RNA-directed DNA methylation. To escape this tight control, retrotransposons employ various strategies to avoid epigenetic silencing. Here we describe the mechanism developed by ONSEN, an LTR-copia type retrotransposon in Arabidopsis thaliana. ONSEN has acquired a heat-responsive element recognized by plant-derived heat stress defense factors, resulting in transcription and production of full length extrachromosomal DNA under elevated temperatures. Further, the ONSEN promoter is free of CG and CHG sites, and the reduction of DNA methylation at the CHH sites is not sufficient to activate the element. Since dividing cells have a more pronounced heat response, the extrachromosomal ONSEN DNA, capable of reintegrating into the genome, accumulates preferentially in the meristematic tissue of the shoot. The recruitment of a major plant heat shock transcription factor in periods of heat stress exploits the plant's heat stress response to achieve the transposon's activation, making it impossible for the host to respond appropriately to stress without losing control over the invader.

  19. Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic.

    Science.gov (United States)

    Marcon, Helena Sanches; Domingues, Douglas Silva; Silva, Juliana Costa; Borges, Rafael Junqueira; Matioli, Fábio Filippi; Fontes, Marcos Roberto de Mattos; Marino, Celso Luis

    2015-08-14

    In Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome. We characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values. Our strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.

  20. The role of retrotransposons in gene family expansions in the human and mouse genomes

    Czech Academy of Sciences Publication Activity Database

    Janoušek, Václav; Laukaitis, C. M.; Yanchukov, Alexey; Karn, R. C.

    2016-01-01

    Roč. 8, č. 9 (2016), s. 2632-2650 ISSN 1759-6653 R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 Keywords : gene families * transposable elements * retrotransposons * LINE * LTR * SINE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.979, year: 2016

  1. A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons

    Czech Academy of Sciences Publication Activity Database

    Steinbauerová, Veronika; Neumann, Pavel; Novák, Petr; Macas, Jiří

    2011-01-01

    Roč. 139, 11-12 (2011), s. 1543-1555 ISSN 0016-6707 Institutional research plan: CEZ:AV0Z50510513 Keywords : Additional ORFs * LTR retrotransposons * Repetitive DNA * Plant genome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.148, year: 2011

  2. LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

    Czech Academy of Sciences Publication Activity Database

    Barghini, E.; Natali, L.; Giordani, T.; Cossu, R.M.; Scalabrin, S.; Cattonaro, F.; Šimková, Hana; Vrána, Jan; Doležel, Jaroslav; Morgante, M.; Cavallini, A.

    2015-01-01

    Roč. 22, č. 1 (2015), s. 91-100 ISSN 1340-2838 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : LTR retrotransposons * next-generation sequencing * olive Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.267, year: 2015

  3. TURBULENT COSMIC-RAY REACCELERATION AT RADIO RELICS AND HALOS IN CLUSTERS OF GALAXIES

    International Nuclear Information System (INIS)

    Fujita, Yutaka; Takizawa, Motokazu; Yamazaki, Ryo; Akamatsu, Hiroki; Ohno, Hiroshi

    2015-01-01

    Radio relics are synchrotron emission found on the periphery of galaxy clusters. From the position and the morphology, it is often believed that the relics are generated by cosmic-ray (CR) electrons accelerated at shocks through a diffusive shock acceleration (DSA) mechanism. However, some radio relics have harder spectra than the prediction of the standard DSA model. One example is observed in the cluster 1RXS J0603.3+4214, which is often called the “Toothbrush Cluster.” Interestingly, the position of the relic is shifted from that of a possible shock. In this study, we show that these discrepancies in the spectrum and the position can be solved if turbulent (re)acceleration is very effective behind the shock. This means that for some relics turbulent reacceleration may be the main mechanism to produce high-energy electrons, contrary to the common belief that it is the DSA. Moreover, we show that for efficient reacceleration, the effective mean free path of the electrons has to be much smaller than their Coulomb mean free path. We also study the merging cluster 1E 0657−56, or the “Bullet Cluster,” in which a radio relic has not been found at the position of the prominent shock ahead of the bullet. We indicate that a possible relic at the shock is obscured by the observed large radio halo that is generated by strong turbulence behind the shock. We propose a simple explanation of the morphological differences of radio emission among the Toothbrush, the Bullet, and the Sausage (CIZA J2242.8+5301) Clusters

  4. Saints' Relics in Scuola di S. Giorgio degli Schiavoni: An Anti-Ottoman Pantheon

    Directory of Open Access Journals (Sweden)

    Ana Marinković

    2018-04-01

    Full Text Available The intensified military campaigns against the Ottomans in the second half of the fifteenth century palpably influenced the cult of saints venerated in Scuola di S. Giorgio degli Schiavoni, both by assimilating new saints, as well as strenghtening the existing cults through indulgences and relic acquisitions. The initial pair of patron saints – St George and St Tryphon, the city patrons of Bar and Kotor – delineated the geographical area where the majority of confraternity members originated from, that is, the Venetian Albania. The inclusion of St Jerome, the patron of Dalmatia, to the confraternal pantheon by Cardinal Bessarion's indulgence issued in 1464, in addition to rounding up the holy patronage to all the Eastern Adriatic Venetian dependencies, also marked the beginning of a strong anti-Ottoman motivation in the scuola's hagiographic horizon. The triple endowment of the Scuola in 1502 – relic acquisition, granting of indulgence, and commission of Carpaccio's monumental cycle – continued to work on the same line, and added to the practical aspect of spiritual support to the members of Venetian troops provenient of the Eastern Adriatic. However, the saints whose relics are today kept in the altar of the lower hall, including the patron saint of the Republic of Dubrovnik, point to an even wider devotional agenda, possibly arranged after the Battle of Lepanto, as the comparative analysis of the reliquaries show.   Le campagne militari contro gli Ottomani intensificatesi nella seconda metà del XV secolo influenzarono palesemente il culto dei santi venerati nella Scuola di S. Giorgio degli Schiavoni, sia attraverso l'assimilazione di nuovi santi, sia tramite il rafforzamento del culto già esistente verso le indulgenze e l'impulso all'acquisizione di reliquie. La prima coppia di santi patroni - San Giorgio e San Trifone, patroni della città di Bar e Cattaro - delimitano l'area geografica da cui proviene la maggior parte dei membri

  5. The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition.

    Directory of Open Access Journals (Sweden)

    Maria J Aristizabal

    2015-10-01

    Full Text Available RNA polymerase II (RNAPII contains a unique C-terminal domain that is composed of heptapeptide repeats and which plays important regulatory roles during gene expression. RNAPII is responsible for the transcription of most protein-coding genes, a subset of non-coding genes, and retrotransposons. Retrotransposon transcription is the first step in their multiplication cycle, given that the RNA intermediate is required for the synthesis of cDNA, the material that is ultimately incorporated into a new genomic location. Retrotransposition can have grave consequences to genome integrity, as integration events can change the gene expression landscape or lead to alteration or loss of genetic information. Given that RNAPII transcribes retrotransposons, we sought to investigate if the RNAPII-CTD played a role in the regulation of retrotransposon gene expression. Importantly, we found that the RNAPII-CTD functioned to maintaining genome integrity through inhibition of retrotransposon gene expression, as reducing CTD length significantly increased expression and transposition rates of Ty1 elements. Mechanistically, the increased Ty1 mRNA levels in the rpb1-CTD11 mutant were partly due to Cdk8-dependent alterations to the RNAPII-CTD phosphorylation status. In addition, Cdk8 alone contributed to Ty1 gene expression regulation by altering the occupancy of the gene-specific transcription factor Ste12. Loss of STE12 and TEC1 suppressed growth phenotypes of the RNAPII-CTD truncation mutant. Collectively, our results implicate Ste12 and Tec1 as general and important contributors to the Cdk8, RNAPII-CTD regulatory circuitry as it relates to the maintenance of genome integrity.

  6. PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy

    Directory of Open Access Journals (Sweden)

    Kong Yoon

    2008-10-01

    Full Text Available Abstract Background Retrotransposons have been known to involve in the remodeling and evolution of host genome. These reverse transcribing elements, which show a complex evolutionary pathway with diverse intermediate forms, have been comprehensively analyzed from a wide range of host genomes, while the information remains limited to only a few species in the phylum Platyhelminthes. Results A LTR retrotransposon and its homologs with a strong phylogenetic affinity toward CsRn1 of Clonorchis sinensis were isolated from a trematode parasite Paragonimus westermani via a degenerate PCR method and from an insect species Anopheles gambiae by in silico analysis of the whole mosquito genome, respectively. These elements, designated PwRn1 and AgCR-1 – AgCR-14 conserved unique features including a t-RNATrp primer binding site and the unusual CHCC signature of Gag proteins. Their flanking LTRs displayed >97% nucleotide identities and thus, these elements were likely to have expanded recently in the trematode and insect genomes. They evolved heterogeneous expression strategies: a single fused ORF, two separate ORFs with an identical reading frame and two ORFs overlapped by -1 frameshifting. Phylogenetic analyses suggested that the elements with the separate ORFs had evolved from an ancestral form(s with the overlapped ORFs. The mobile potential of PwRn1 was likely to be maintained differentially in association with the karyotype of host genomes, as was examined by the presence/absence of intergenomic polymorphism and mRNA transcripts. Conclusion Our results on the structural diversity of CsRn1-like elements can provide a molecular tool to dissect a more detailed evolutionary episode of LTR retrotransposons. The PwRn1-associated genomic polymorphism, which is substantial in diploids, will also be informative in addressing genomic diversification following inter-/intra-specific hybridization in P. westermani populations.

  7. Review of the analysis of relics associated with the HMAS Sydney II

    Energy Technology Data Exchange (ETDEWEB)

    Treasure, Alana, E-mail: alana.treasure@awm.gov.a [Collection Services, Australian War Memorial, Canberra (Australia); Bailey, George; Challenor, Catherine [Collection Services, Australian War Memorial, Canberra (Australia); Otieno-Alego, Vincent [Forensic and Data Centres, Australian Federal Police, Canberra (Australia); Creagh, Dudley [Faculty of Applied Science, University of Canberra, Canberra (Australia)

    2010-07-21

    The 1941 sinking of the HMAS Sydney II in action with the German raider KSN Kormoran off the coast of Western Australia has been a source of mystery and speculation for more than 60 years. HMAS Sydney II was lost with all hands. The largest item of flotsam found in the vicinity was a Carley float, which was riddled with holes some of which contained small metallic items. The float was subjected to various physical and elemental examination methods in 1992 in an attempt to determine what may have happened. Three months after sinking, the unidentified body of a man washed ashore at Christmas Island in another Carley float. Relics found in his unmarked grave in 2006 included several degraded and corroded press-studs, some containing fragments of fabric. A metal fragment was recovered from the man's skull. XRF, SEM-EDS, Raman and FTIR spectroscopy, and X-ray tomography analysis of these items was conducted in an attempt to determine what link the sailor may have to the HMAS Sydney II.

  8. Effects of As2O3 on DNA methylation, genomic instability, and LTR retrotransposon polymorphism in Zea mays.

    Science.gov (United States)

    Erturk, Filiz Aygun; Aydin, Murat; Sigmaz, Burcu; Taspinar, M Sinan; Arslan, Esra; Agar, Guleray; Yagci, Semra

    2015-12-01

    Arsenic is a well-known toxic substance on the living organisms. However, limited efforts have been made to study its DNA methylation, genomic instability, and long terminal repeat (LTR) retrotransposon polymorphism causing properties in different crops. In the present study, effects of As2O3 (arsenic trioxide) on LTR retrotransposon polymorphism and DNA methylation as well as DNA damage in Zea mays seedlings were investigated. The results showed that all of arsenic doses caused a decreasing genomic template stability (GTS) and an increasing Random Amplified Polymorphic DNAs (RAPDs) profile changes (DNA damage). In addition, increasing DNA methylation and LTR retrotransposon polymorphism characterized a model to explain the epigenetically changes in the gene expression were also found. The results of this experiment have clearly shown that arsenic has epigenetic effect as well as its genotoxic effect. Especially, the increasing of polymorphism of some LTR retrotransposon under arsenic stress may be a part of the defense system against the stress.

  9. The first observations of wide-band interferometers and the spectra of relic gravitons

    CERN Document Server

    Giovannini, Massimo

    2016-01-01

    Stochastic backgrounds of relic gravitons of cosmological origin extend from frequencies of the order of the aHz up to the GHz range. Since the temperature and polarization anisotropies constrain the low frequency normalization of the spectra, in the concordance paradigm the strain amplitude corresponding to the frequency window of wide-band interferometers turns out to be, approximately, nine orders of magnitude smaller than the astounding signal recently reported and attributed to a binary black hole merger. The backgrounds of relic gravitons expected from the early Universe are compared with the stochastic foregrounds stemming from the estimated multiplicity of the astrophysical sources. It is suggested that while the astrophysical foregrounds are likely to dominate between few Hz and 10 kHz, relic gravitons with frequencies exceeding 100 kHz represent a potentially uncontaminated signal for the next generation of high-frequency detectors currently under scrutiny.

  10. Radio observations of the double-relic galaxy cluster Abell 1240

    Science.gov (United States)

    Hoang, D. N.; Shimwell, T. W.; van Weeren, R. J.; Intema, H. T.; Röttgering, H. J. A.; Andrade-Santos, F.; Akamatsu, H.; Bonafede, A.; Brunetti, G.; Dawson, W. A.; Golovich, N.; Best, P. N.; Botteon, A.; Brüggen, M.; Cassano, R.; de Gasperin, F.; Hoeft, M.; Stroe, A.; White, G. J.

    2018-05-01

    We present LOFAR 120 - 168 MHz images of the merging galaxy cluster Abell 1240 that hosts double radio relics. In combination with the GMRT 595 - 629 MHz and VLA 2 - 4 GHz data, we characterised the spectral and polarimetric properties of the radio emission. The spectral indices for the relics steepen from their outer edges towards the cluster centre and the electric field vectors are approximately perpendicular to the major axes of the relics. The results are consistent with the picture that these relics trace large-scale shocks propagating outwards during the merger. Assuming diffusive shock acceleration (DSA), we obtain shock Mach numbers of M=2.4 and 2.3 for the northern and southern shocks, respectively. For M≲ 3 shocks, a pre-existing population of mildly relativistic electrons is required to explain the brightness of the relics due to the high (>10 per cent) particle acceleration efficiency required. However, for M≳ 4 shocks the required efficiency is ≳ 1% and ≳ 0.5%, respectively, which is low enough for shock acceleration directly from the thermal pool. We used the fractional polarization to constrain the viewing angle to ≥53 ± 3° and ≥39 ± 5° for the northern and southern shocks, respectively. We found no evidence for diffuse emission in the cluster central region. If the halo spans the entire region between the relics (˜1.8 Mpc) our upper limit on the power is P1.4GHz = (1.4 ± 0.6) × 1023 W Hz-1 which is approximately equal to the anticipated flux from a cluster of this mass. However, if the halo is smaller than this, our constraints on the power imply that the halo is underluminous.

  11. Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification.

    Science.gov (United States)

    Smýkal, Petr

    2006-01-01

    Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.

  12. Genome-wide analysis of LTR-retrotransposons in oil palm.

    Science.gov (United States)

    Beulé, Thierry; Agbessi, Mawussé Dt; Dussert, Stephane; Jaligot, Estelle; Guyot, Romain

    2015-10-15

    The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world's largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences. In this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data. Our results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome. Considering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution

  13. LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin.

    Directory of Open Access Journals (Sweden)

    Anderly C Chueh

    2009-01-01

    Full Text Available We have previously identified and characterized the phenomenon of ectopic human centromeres, known as neocentromeres. Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres. Recent studies have indicated that neocentromere formation provides a major mechanism for centromere repositioning, karyotype evolution, and speciation. Using a marker chromosome mardel(10 containing a neocentromere formed at the normal chromosomal 10q25 region, we have previously mapped a 330-kb CENP-A-binding domain and described an increased prevalence of L1 retrotransposons in the underlying DNA sequences of the CENP-A-binding clusters. Here, we investigated the potential role of the L1 retrotransposons in the regulation of neocentromere activity. Determination of the transcriptional activity of a panel of full-length L1s (FL-L1s across a 6-Mb region spanning the 10q25 neocentromere chromatin identified one of the FL-L1 retrotransposons, designated FL-L1b and residing centrally within the CENP-A-binding clusters, to be transcriptionally active. We demonstrated the direct incorporation of the FL-L1b RNA transcripts into the CENP-A-associated chromatin. RNAi-mediated knockdown of the FL-L1b RNA transcripts led to a reduction in CENP-A binding and an impaired mitotic function of the 10q25 neocentromere. These results indicate that LINE retrotransposon RNA is a previously undescribed essential structural and functional component of the neocentromeric chromatin and that retrotransposable elements may serve as a critical epigenetic determinant in the chromatin remodelling events leading to neocentromere formation.

  14. Retrotransposon-associated long non-coding RNAs in mice and men

    Czech Academy of Sciences Publication Activity Database

    Ganesh, Sravya; Svoboda, Petr

    2016-01-01

    Roč. 468, č. 6 (2016), s. 1049-1060 ISSN 0031-6768 R&D Projects: GA ČR(CZ) GBP305/12/G034; GA MŠk LO1419 EU Projects: European Commission 647403; European Commission 607720 Institutional support: RVO:68378050 Keywords : lncRNA * Retrotransposon * line * sine * ltr * MaLR Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.156, year: 2016

  15. The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes.

    Science.gov (United States)

    Richardson, Sandra R; Doucet, Aurélien J; Kopera, Huira C; Moldovan, John B; Garcia-Perez, José Luis; Moran, John V

    2015-04-01

    Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.

  16. Identification and chromosomal localization of the monkey retrotransposon in Mesa sp

    Czech Academy of Sciences Publication Activity Database

    Balint-Kurti, P.; Clendennen, S.; Doleželová, Marie; Valárik, Miroslav; Doležel, Jaroslav; Beetham, G. M.

    2000-01-01

    Roč. 263, č. 6 (2000), s. 908-915 ISSN 0026-8925 R&D Projects: GA ČR GV521/96/K117; GA AV ČR IAA5020803; GA MŠk ME 376 Institutional research plan: CEZ:AV0Z5038910 Keywords : In situ hybridization * chromosomal localization * monkey retrotransposon Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.462, year: 2000

  17. Links between human LINE-1 retrotransposons and hepatitis virus-related hepatocellular carcinoma

    Science.gov (United States)

    Honda, Tomoyuki

    2016-05-01

    Hepatocellular carcinoma (HCC) accounts for approximately 80% of liver cancers, the third most frequent cause of cancer mortality. The most prevalent risk factors for HCC are infections by hepatitis B or hepatitis C virus. Findings suggest that hepatitis virus-related HCC might be a cancer in which LINE-1 retrotransposons, often termed L1, activity plays a potential role. Firstly, hepatitis viruses can suppress host defense factors that also control L1 mobilization. Secondly, many recent studies also have indicated that hypomethylation of L1 affects the prognosis of HCC patients. Thirdly, endogenous L1 retrotransposition was demonstrated to activate oncogenic pathways in HCC. Fourthly, several L1 chimeric transcripts with host or viral genes are found in hepatitis virus-related HCC. Such lines of evidence suggest a linkage between L1 retrotransposons and hepatitis virus-related HCC. Here, I briefly summarize current understandings of the association between hepatitis virus-related HCC and L1. Then, I discuss potential mechanisms of how hepatitis viruses drive the development of HCC via L1 retrotransposons. An increased understanding of the contribution of L1 to hepatitis virus-related HCC may provide unique insights related to the development of novel therapeutics for this disease.

  18. Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum

    Science.gov (United States)

    Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Zelenin, Alexander V.; Lakunina, Valentina A.; Yurkevich, Olga Yu.; Speranskaya, Anna S.; Dmitriev, Alexey A.; Krinitsina, Anastasia A.; Belenikin, Maxim S.; Uroshlev, Leonid A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Koroban, Nadezda V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Guzenko, Elena V.; Lemesh, Valentina A.; Savilova, Anastasya M.; Rachinskaia, Olga A.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Bolsheva, Nadezhda L.; Muravenko, Olga V.

    2014-01-01

    SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

  19. Different histories of two highly variable LTR retrotransposons in sunflower species.

    Science.gov (United States)

    Mascagni, Flavia; Cavallini, Andrea; Giordani, Tommaso; Natali, Lucia

    2017-11-15

    In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data

    Directory of Open Access Journals (Sweden)

    Ramos Kenneth

    2010-10-01

    Full Text Available Abstract Background In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1 retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of transcripts from genes that span or neighbor the LINE-1 insertion site. Results In this work, newly released pilot data from the 1000 Genomes Project is analyzed to detect previously unreported full length insertions of the retrotransposon LINE-1. By direct analysis of the sequence data, we have identified 22 previously unreported LINE-1 insertion sites within the sequence data reported for a mother/father/daughter trio. Conclusions It is demonstrated here that next generation sequencing data, as well as emerging high quality datasets from individual genome projects allow us to assess the amount of heterogeneity with respect to the LINE-1 retrotransposon amongst humans, and provide us with a wealth of testable hypotheses as to the impact that this diversity may have on the health of individuals and populations.

  1. Retrotransposon-Encoded Reverse Transcriptase in the Genesis, Progression and Cellular Plasticity of Human Cancer

    International Nuclear Information System (INIS)

    Sinibaldi-Vallebona, Paola; Matteucci, Claudia; Spadafora, Corrado

    2011-01-01

    LINE-1 (Long Interspersed Nuclear Elements) and HERVs (Human Endogenous Retroviruses) are two families of autonomously replicating retrotransposons that together account for about 28% of the human genome. Genes harbored within LINE-1 and HERV retrotransposons, particularly those encoding the reverse transcriptase (RT) enzyme, are generally expressed at low levels in differentiated cells, but their expression is upregulated in transformed cells and embryonic tissues. Here we discuss a recently discovered RT-dependent mechanism that operates in tumorigenesis and reversibly modulates phenotypic and functional variations associated with tumor progression. Downregulation of active LINE-1 elements drastically reduces the tumorigenic potential of cancer cells, paralleled by reduced proliferation and increased differentiation. Pharmacological RT inhibitors (e.g., nevirapine and efavirenz) exert similar effects on tumorigenic cell lines, both in culture and in animal models. The HERV-K family play a distinct complementary role in stress-dependent transition of melanoma cells from an adherent, non-aggressive, to a non-adherent, highly malignant, growth phenotype. In synthesis, the retrotransposon-encoded RT is increasingly emerging as a key regulator of tumor progression and a promising target in a novel anti-cancer therapy

  2. Relating the baryon asymmetry to the thermal relic dark matter density

    International Nuclear Information System (INIS)

    McDonald, John

    2011-01-01

    We present a generic framework, baryomorphosis, which modifies the baryon asymmetry to be naturally of the order of a typical thermal relic weakly interacting massive particle (WIMP) density. We consider a simple scalar-based model to show how this is possible. This model introduces a sector in which a large initial baryon asymmetry is injected into particles ('annihilons'), φ B , φ-circumflex B , of mass ∼100 GeV-1 TeV. φ B φ-circumflex B annihilations convert the initial φ B , φ-circumflex B asymmetry to a final asymmetry with a thermal relic WIMP-like density. This subsequently decays to a conventional baryon asymmetry whose magnitude is naturally related to the density of thermal relic WIMP dark matter. In this way the two coincidences of baryons and dark matter, i.e. why their densities are similar to each other and why they are both similar to a WIMP thermal relic density (the 'WIMP miracle'), may be understood. The model may be tested by the production of annihilons at colliders.

  3. The Variable and Changing Status of Performance Art Relics and Artifacts in Museum Collections

    DEFF Research Database (Denmark)

    Cone, Louise

    2017-01-01

    The status of an artwork in a museum collection is variable and contingent upon factors and parameters that are specific not only to the logic of the museum world but also to factors extrinsic to the museum. In particular older performance art 'relics' are subject to contextual interpretations...

  4. Relics of short distance effects for the neutron electric dipole moment

    International Nuclear Information System (INIS)

    Eeg, J.O.

    1982-12-01

    The Feynman diagrams which dominate the estimates of the electric dipole moment of the neutron with Kobayashi-Maskawa CP violation are considered. The extracted long distance contributions and the relics of short distance contributions are shown to be complementary and of the same magnitude, resulting in mod(Dsub(n)/e) approximately = (10 - 31 - 10 - 30 ) cm. (Auth.)

  5. Ultra-cold WIMPs relics of non-standard pre-BBN cosmologies

    CERN Document Server

    Gelmini, Graciela B

    2008-01-01

    We point out that in scenarios in which the Universe evolves in a non-standard manner during and after the kinetic decoupling of weakly interacting massive particles (WIMPs), these relics can be much colder than in standard cosmological scenarios (i.e. can be ultra-cold), possibly leading to the formation of smaller first objects in hierarchical structure formation scenarios.

  6. On the absence of radio haloes in clusters with double relics

    Science.gov (United States)

    Bonafede, A.; Cassano, R.; Brüggen, M.; Ogrean, G. A.; Riseley, C. J.; Cuciti, V.; de Gasperin, F.; Golovich, N.; Kale, R.; Venturi, T.; van Weeren, R. J.; Wik, D. R.; Wittman, D.

    2017-09-01

    Pairs of radio relics are believed to form during cluster mergers, and are best observed when the merger occurs in the plane of the sky. Mergers can also produce radio haloes, through complex processes likely linked to turbulent re-acceleration of cosmic ray electrons. However, only some clusters with double relics also show a radio halo. Here, we present a novel method to derive upper limits on the radio halo emission, and analyse archival X-ray Chandra data, as well as galaxy velocity dispersions and lensing data, in order to understand the key parameter that switches on radio halo emission. We place upper limits on the halo power below the P1.4 GHz-M500 correlation for some clusters, confirming that clusters with double relics have different radio properties. Computing X-ray morphological indicators, we find that clusters with double relics are associated with the most disturbed clusters. We also investigate the role of different mass-ratios and time-since-merger. Data do not indicate that the merger mass-ratio has an impact on the presence or absence of radio haloes (the null hypothesis that the clusters belong to the same group cannot be rejected). However, the data suggest that the absence of radio haloes could be associated with early and late mergers, but the sample is too small to perform a statistical test. Our study is limited by the small number of clusters with double relics. Future surveys with LOFAR, ASKAP, MeerKat and SKA will provide larger samples to better address this issue.

  7. LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice

    Directory of Open Access Journals (Sweden)

    Liu Jin-Song

    2008-08-01

    Full Text Available Abstract Background Long terminal repeat retrotransposons (LTR elements are ubiquitous Eukaryotic TEs that transpose through RNA intermediates. Accounting for significant proportion of many plant genomes, LTR elements have been well established as one of the major forces underlying the evolution of plant genome size, structure and function. The accessibility of more than 40% of genomic sequences of the model legume Medicago truncatula (Mt has made the comprehensive study of its LTR elements possible. Results We use a newly developed tool LTR_FINDER to identify LTR retrotransposons in the Mt genome and detect 526 full-length elements as well as a great number of copies related to them. These elements constitute about 9.6% of currently available genomic sequences. They are classified into 85 families of which 64 are reported for the first time. The majority of the LTR retrotransposons belong to either Copia or Gypsy superfamily and the others are categorized as TRIMs or LARDs by their length. We find that the copy-number of Copia-like families is 3 times more than that of Gypsy-like ones but the latter contribute more to the genome. The analysis of PBS and protein-coding domain structure of the LTR families reveals that they tend to use only 4–5 types of tRNAs and many families have quite conservative ORFs besides known TE domains. For several important families, we describe in detail their abundance, conservation, insertion time and structure. We investigate the amplification-deletion pattern of the elements and find that the detectable full-length elements are relatively young and most of them were inserted within the last 0.52 MY. We also estimate that more than ten million bp of the Mt genomic sequences have been removed by the deletion of LTR elements and the removal of the full-length structures in Mt has been more rapid than in rice. Conclusion This report is the first comprehensive description and analysis of LTR retrotransposons in the

  8. MULTI-FREQUENCY STUDIES OF RADIO RELICS IN THE GALAXY CLUSTERS A4038, A1664, AND A786

    Energy Technology Data Exchange (ETDEWEB)

    Kale, Ruta; Dwarakanath, K. S., E-mail: ruta@iucaa.ernet.in [Raman Research Institute, C. V. Raman Avenue, Sadashivanagar, Bangalore 560 080 (India)

    2012-01-01

    We present a multi-frequency study of radio relics associated with the galaxy clusters A4038, A1664, and A786. Radio images, integrated spectra, spectral index maps, and fits to the integrated spectra in the framework of the adiabatic compression model are presented. Images of the relic in A4038 at 150, 240, and 606 MHz with the Giant Meterwave Radio Telescope have revealed extended ultra-steep spectrum ({alpha} {approx} -1.8 to -2.7) emission of extent 210 Multiplication-Sign 80 kpc{sup 2}. The model of passively evolving radio lobes compressed by a shock fits the integrated spectrum best. The relic with a circular morphology at the outskirts of the cluster A1664 has an integrated spectral index of {approx} - 1.10 {+-} 0.06 and is best fit by the model of radio lobes lurking for {approx}4 Multiplication-Sign 10{sup 7} yr. The relic near A786 has a curved spectrum and is best fit by a model of radio lobes lurking for {approx}3 Multiplication-Sign 10{sup 7} yr. At 4.7 GHz, a compact radio source, possibly the progenitor of the A786 relic, is detected near the center of the radio relic. The A786 radio relic is thus likely a lurking radio galaxy rather than a site of cosmological shock as has been considered in earlier studies.

  9. Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

    Science.gov (United States)

    Tetreault, Hannah M.; Ungerer, Mark C.

    2016-01-01

    The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny. PMID:27233667

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

    Directory of Open Access Journals (Sweden)

    Katarzyna Pachulska-Wieczorek

    2016-07-01

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

  11. Hybridogenesis and a potential case of R2 non-LTR retrotransposon horizontal transmission in Bacillus stick insects (Insecta Phasmida).

    Science.gov (United States)

    Scavariello, Claudia; Luchetti, Andrea; Martoni, Francesco; Bonandin, Livia; Mantovani, Barbara

    2017-02-06

    Horizontal transfer (HT) is an event in which the genetic material is transferred from one species to another, even if distantly related, and it has been demonstrated as a possible essential part of the lifecycle of transposable elements (TEs). However, previous studies on the non-LTR R2 retrotransposon, a metazoan-wide distributed element, indicated its vertical transmission since the Radiata-Bilateria split. Here we present the first possible instances of R2 HT in stick insects of the genus Bacillus (Phasmida). Six R2 elements were characterized in the strictly bisexual subspecies B. grandii grandii, B. grandii benazzii and B. grandii maretimi and in the obligatory parthenogenetic taxon B. atticus. These elements were compared with those previously retrieved in the facultative parthenogenetic species B. rossius. Phylogenetic inconsistencies between element and host taxa, and age versus divergence analyses agree and support at least two HT events. These HT events can be explained by taking into consideration the complex Bacillus reproductive biology, which includes also hybridogenesis, gynogenesis and androgenesis. Through these non-canonical reproductive modes, R2 elements may have been transferred between Bacillus genomes. Our data suggest, therefore, a possible role of hybridization for TEs survival and the consequent reshaping of involved genomes.

  12. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates.

    Science.gov (United States)

    Naville, M; Warren, I A; Haftek-Terreau, Z; Chalopin, D; Brunet, F; Levin, P; Galiana, D; Volff, J-N

    2016-04-01

    Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  13. Direct detection of projectile relics from the end of the lunar basin-forming epoch.

    Science.gov (United States)

    Joy, Katherine H; Zolensky, Michael E; Nagashima, Kazuhide; Huss, Gary R; Ross, D Kent; McKay, David S; Kring, David A

    2012-06-15

    The lunar surface, a key proxy for the early Earth, contains relics of asteroids and comets that have pummeled terrestrial planetary surfaces. Surviving fragments of projectiles in the lunar regolith provide a direct measure of the types and thus the sources of exogenous material delivered to the Earth-Moon system. In ancient [>3.4 billion years ago (Ga)] regolith breccias from the Apollo 16 landing site, we located mineral and lithologic relics of magnesian chondrules from chondritic impactors. These ancient impactor fragments are not nearly as diverse as those found in younger (3.4 Ga to today) regolith breccias and soils from the Moon or that presently fall as meteorites to Earth. This suggests that primitive chondritic asteroids, originating from a similar source region, were common Earth-Moon-crossing impactors during the latter stages of the basin-forming epoch.

  14. Bound-state formation for thermal relic dark matter and unitarity

    International Nuclear Information System (INIS)

    Harling, Benedict von; Petraki, Kalliopi

    2014-01-01

    We show that the relic abundance of thermal dark matter annihilating via a long-range interaction, is significantly affected by the formation and decay of dark matter bound states in the early universe, if the dark matter mass is above a few TeV . We determine the coupling required to obtain the observed dark matter density, taking into account both the direct 2-to-2 annihilations and the formation of bound states, and provide an analytical fit. We argue that the unitarity limit on the inelastic cross-section is realized only if dark matter annihilates via a long-range interaction, and we determine the upper bound on the mass of thermal-relic dark matter to be about 197 (139) TeV for (non)-self-conjugate dark matter

  15. Detecting relic gravitational waves in the CMB: The contamination caused by the cosmological birefringence

    Directory of Open Access Journals (Sweden)

    Wen Zhao

    2014-10-01

    Full Text Available The B-mode polarization of the cosmic microwave background (CMB radiation is an excellent information channel for the detection of relic gravitational waves. However, the detection is contaminated by the B-mode polarization generated by some other effects. In this paper, we discuss the contaminations caused by the cosmological birefringence, which converts the CMB E-mode to the B-mode, and forms the effective noise for the detection of gravitational waves. We find that this contamination is significant, if the rotation angle is large. However, this kind of B-mode can be properly de-rotated, and the effective noises can be greatly reduced. We find that, comparing with the contaminations caused by cosmic weak lensing, the residual polarization generated by the cosmological birefringence is negligible for the detection of relic gravitational waves in the CMB.

  16. Stochastic Background of Relic Scalar Gravitational Waves tuned by Extended Gravity

    International Nuclear Information System (INIS)

    De Laurentis, Mariafelicia; Capozziello, Salvatore

    2009-01-01

    A stochastic background of relic gravitational waves is achieved by the so called adiabatically-amplified zero-point fluctuations process derived from early inflation. It provides a distinctive spectrum of relic gravitational waves. In the framework of scalar-tensor gravity, we discuss the scalar modes of gravitational waves and the primordial production of this scalar component which is generated beside tensorial one. Then analyze seven different viable f(R)-gravities towards the Solar System tests and stochastic gravitational waves background. It is demonstrated that seven viable f(R)-gravities under consideration not only satisfy the local tests, but additionally, pass the above PPN-and stochastic gravitational waves bounds for large classes of parameters.

  17. Quintessential inflation on the brane and the relic gravity wave background

    International Nuclear Information System (INIS)

    Sami, M.; Sahni, V.

    2004-01-01

    Quintessential inflation describes a scenario in which both inflation and dark energy (quintessence) are described by the same scalar field. In conventional braneworld models of quintessential inflation gravitational particle-production is used to reheat the universe. This reheating mechanism is very inefficient and results in an excessive production of gravity waves which violate nucleosynthesis constraints and invalidate the model. We describe a new method of realizing quintessential inflation on the brane in which inflation is followed by 'instant preheating' (Felder, Kofman and Linde 1999). The larger reheating temperature in this model results in a smaller amplitude of relic gravity waves which is consistent with nucleosynthesis bounds. The relic gravity wave background has a 'blue' spectrum at high frequencies and is a generic byproduct of successful quintessential inflation on the brane

  18. Dark matter relics and the expansion rate in scalar-tensor theories

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Bhaskar; Jimenez, Esteban [Mitchell Institute for Fundamental Physics and Astronomy, Department of Physics and Astronomy, Texas A and M University, College Station, TX 77843 (United States); Zavala, Ivonne, E-mail: dutta@physics.tamu.edu, E-mail: este1985@physics.tamu.edu, E-mail: e.i.zavalacarrasco@swansea.ac.uk [Department of Physics, Swansea University, Singleton Park, Swansea, SA2 8PP (United Kingdom)

    2017-06-01

    We study the impact of a modified expansion rate on the dark matter relic abundance in a class of scalar-tensor theories. The scalar-tensor theories we consider are motivated from string theory constructions, which have conformal as well as disformally coupled matter to the scalar. We investigate the effects of such a conformal coupling to the dark matter relic abundance for a wide range of initial conditions, masses and cross-sections. We find that exploiting all possible initial conditions, the annihilation cross-section required to satisfy the dark matter content can differ from the thermal average cross-section in the standard case. We also study the expansion rate in the disformal case and find that physically relevant solutions require a nontrivial relation between the conformal and disformal functions. We study the effects of the disformal coupling in an explicit example where the disformal function is quadratic.

  19. Late Quaternary sea level and environmental changes from relic carbonate deposits of the western margin of India

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, V.P.; Rajagopalan, G.; Vora, K.H.; Almeida, F.

    . The petrology and mineralogy of the deposits indicate that except for aragonite sands and foraminiferal nodules, the others were formed in shallow marine conditions and serve as sea level indicators. Radiocarbon dates were measured for 62 relic deposits covering...

  20. Constructing Teaching Model for Training English Guides of Stone In-scription Relics

    Institute of Scientific and Technical Information of China (English)

    李慧

    2016-01-01

    A teaching model based on constructivism is proposed in this paper. The model contains five teaching steps, e.g. inter-pretation teaching, questioning-dialogue, knowledge and skills teaching, discussion-collaboration and field training. Practice proves that it can effectively improve the training efficiency of the training of English guides of stone inscription relics and en-hance their interpretation quality and English skills.

  1. Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.

    Science.gov (United States)

    Frahry, Matthew Blake; Sun, Cheng; Chong, Rebecca A; Mueller, Rachel Lockridge

    2015-02-01

    Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.

  2. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip.

    Science.gov (United States)

    Xu, Zongli; Langie, Sabine A S; De Boever, Patrick; Taylor, Jack A; Niu, Liang

    2017-01-03

    The Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in epigenome-wide association studies. Both arrays use two fluorescent dyes (Cy3-green/Cy5-red) to measure methylation level at CpG sites. However, performance difference between dyes can result in biased estimates of methylation levels. Here we describe a novel method, called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels. We evaluate the method in several datasets against other widely used dye-bias correction methods. Results on data quality improvement showed that RELIC correction statistically significantly outperforms alternative dye-bias correction methods. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website ( https://www.bioconductor.org/packages/release/bioc/html/ENmix.html ). RELIC is an efficient and robust method to correct for dye-bias in Illumina Methylation BeadChip data. It outperforms other alternative methods and conveniently implemented in R package ENmix to facilitate DNA methylation studies.

  3. THE SCALING RELATIONS AND THE FUNDAMENTAL PLANE FOR RADIO HALOS AND RELICS OF GALAXY CLUSTERS

    International Nuclear Information System (INIS)

    Yuan, Z. S.; Han, J. L.; Wen, Z. L.

    2015-01-01

    Diffuse radio emission in galaxy clusters is known to be related to cluster mass and cluster dynamical state. We collect the observed fluxes of radio halos, relics, and mini-halos for a sample of galaxy clusters from the literature, and calculate their radio powers. We then obtain the values of cluster mass or mass proxies from previous observations, and also obtain the various dynamical parameters of these galaxy clusters from optical and X-ray data. The radio powers of relics, halos, and mini-halos are correlated with the cluster masses or mass proxies, as found by previous authors, while the correlations concerning giant radio halos are in general the strongest. We found that the inclusion of dynamical parameters as the third dimension can significantly reduce the data scatter for the scaling relations, especially for radio halos. We therefore conclude that the substructures in X-ray images of galaxy clusters and the irregular distributions of optical brightness of member galaxies can be used to quantitatively characterize the shock waves and turbulence in the intracluster medium responsible for re-accelerating particles to generate the observed diffuse radio emission. The power of radio halos and relics is correlated with cluster mass proxies and dynamical parameters in the form of a fundamental plane

  4. Detecting relic gravitational waves in the CMB: Optimal parameters and their constraints

    International Nuclear Information System (INIS)

    Zhao, W.; Baskaran, D.

    2009-01-01

    The prospect of detecting relic gravitational waves, through their imprint in the cosmic microwave background radiation, provides an excellent opportunity to study the very early Universe. In the simplest viable theoretical models the relic gravitational wave background is characterized by two parameters, the tensor-to-scalar ratio r and the tensor spectral index n t . In this paper, we analyze the potential joint constraints on these two parameters, r and n t , using the data from the upcoming cosmic microwave background radiation experiments. Introducing the notion of the best-pivot multipole l t *, we find that at this pivot multipole the parameters r and n t are uncorrelated, and have the smallest variances. We derive the analytical formulas for the best-pivot multipole number l t *, and the variances of the parameters r and n t . We verify these analytical calculations using numerical simulation methods, and find agreement to within 20%. The analytical results provide a simple way to estimate the detection ability for the relic gravitational waves by the future observations of the cosmic microwave background radiation.

  5. Superpixel segmentation and pigment identification of colored relics based on visible spectral image

    Science.gov (United States)

    Li, Junfeng; Wan, Xiaoxia

    2018-01-01

    To enrich the contents of digital archive and to guide the copy and restoration of colored relics, non-invasive methods for extraction of painting boundary and identification of pigment composition are proposed in this study based on the visible spectral images of colored relics. Superpixel concept is applied for the first time to the field of oversegmentation of visible spectral images and implemented on the visible spectral images of colored relics to extract their painting boundary. Since different pigments are characterized by their own spectrum and the same kind of pigment has the similar geometric profile in spectrum, an automatic identification method is established by comparing the proximity between the geometric profiles of the unknown spectrum from each superpixel and the pre-known spectrum from a deliberately prepared database. The methods are validated using the visible spectral images of the ancient wall paintings in Mogao Grottoes. By the way, the visible spectral images are captured by a multispectral imaging system consisting of two broadband filters and a RGB camera with high spatial resolution.

  6. Characterization of active reverse transcriptase and nucleoprotein complexes of the yeast retrotransposon Ty3 in vitro.

    Science.gov (United States)

    Cristofari, G; Gabus, C; Ficheux, D; Bona, M; Le Grice, S F; Darlix, J L

    1999-12-17

    Human immunodeficiency virus (HIV) and the distantly related yeast Ty3 retrotransposon encode reverse transcriptase (RT) and a nucleic acid-binding protein designated nucleocapsid protein (NCp) with either one or two zinc fingers, required for HIV-1 replication and Ty3 transposition, respectively. In vitro binding of HIV-1 NCp7 to viral 5' RNA and primer tRNA(3)(Lys) catalyzes formation of nucleoprotein complexes resembling the virion nucleocapsid. Nucleocapsid complex formation functions in viral RNA dimerization and tRNA annealing to the primer binding site (PBS). RT is recruited in these nucleoprotein complexes and synthesizes minus-strand cDNA initiated at the PBS. Recent results on yeast Ty3 have shown that the homologous NCp9 promotes annealing of primer tRNA(i)(Met) to a 5'-3' bipartite PBS, allowing RNA:tRNA dimer formation and initiation of cDNA synthesis at the 5' PBS (). To compare specific cDNA synthesis in a retrotransposon and HIV-1, we have established a Ty3 model system comprising Ty3 RNA with the 5'-3' PBS, primer tRNA(i)(Met), NCp9, and for the first time, highly purified Ty3 RT. Here we report that Ty3 RT is as active as retroviral HIV-1 or murine leukemia virus RT using a synthetic template-primer system. Moreover, and in contrast to what was found with retroviral RTs, retrotransposon Ty3 RT was unable to direct cDNA synthesis by self-priming. We also show that Ty3 nucleoprotein complexes were formed in vitro and that the N terminus of NCp9, but not the zinc finger, is required for complex formation, tRNA annealing to the PBS, RNA dimerization, and primer tRNA-directed cDNA synthesis by Ty3 RT. These results indicate that NCp9 chaperones bona fide cDNA synthesis by RT in the yeast Ty3 retrotransposon, as illustrated for NCp7 in HIV-1, reinforcing the notion that Ty3 NCp9 is an ancestor of HIV-1 NCp7.

  7. The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family.

    Science.gov (United States)

    Janoušek, Václav; Karn, Robert C; Laukaitis, Christina M

    2013-05-29

    Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes. Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the duplication arose as a result of NAHR using L1 elements as substrates. L1 and ERVII retrotransposons are considerably denser in the Abp regions than in one Mb flanking regions, while other repeat types are depleted in the Abp regions compared to flanking regions. L1 retrotransposons preferentially accumulated in the Abp gene regions after lineage separation and roughly followed the pattern of Abp gene expansion. By contrast, the proportion of shared vs. lineage-specific ERVII repeats in the Abp region resembles the rest of the genome. We confirmed the role of L1 repeats in Abp gene duplication with the identification of recombinant L1Md_T elements at the edges of the most recent mouse Abp gene duplication. High densities of L1 and ERVII repeats were found in the Abp gene region with abrupt transitions at the region boundaries, suggesting that their higher densities are tightly associated with Abp gene duplication. We observed that the major accumulation of L1 elements occurred after the split of the mouse and rat lineages and that there is a striking overlap between the timing of L1 accumulation and expansion of the Abp gene family in the mouse genome. Establishing a link between the accumulation of L1 elements and the expansion of the Abp gene family and identification of an NAHR-related breakpoint in

  8. Making the most of the relic density for dark matter searches at the LHC 14 TeV Run

    International Nuclear Information System (INIS)

    Busoni, Giorgio; Simone, Andrea De; Jacques, Thomas; Morgante, Enrico; Riotto, Antonio

    2015-01-01

    As the LHC continues to search for new weakly interacting particles, it is important to remember that the search is strongly motivated by the existence of dark matter. In view of a possible positive signal, it is essential to ask whether the newly discovered weakly interacting particle can be be assigned the label 'dark matter'. Within a given set of simplified models and modest working assumptions, we reinterpret the relic abundance bound as a relic abundance range, and compare the parameter space yielding the correct relic abundance with projections of the Run II exclusion regions. Assuming that dark matter is within the reach of the LHC, we also make the comparison with the potential 5σ discovery regions. Reversing the logic, relic density calculations can be used to optimize dark matter searches by motivating choices of parameters where the LHC can probe most deeply into the dark matter parameter space. In the event that DM is seen outside of the region giving the correct relic abundance, we will learn that either thermal relic DM is ruled out in that model, or the DM-quark coupling is suppressed relative to the DM coupling strength to other SM particles

  9. The radio relics and halo of El Gordo, a massive z = 0.870 cluster merger

    Energy Technology Data Exchange (ETDEWEB)

    Lindner, Robert R.; Baker, Andrew J.; Hughes, John P. [Rutgers, The State University of New Jersey, 136 Frelinghuysen Road, Piscataway, NJ 08854-8019 (United States); Battaglia, Nick [McWilliams Center for Cosmology, Wean Hall, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213 (United States); Gupta, Neeraj [ASTRON, the Netherlands Institute for Radio Astronomy, Postbus 2, 7990 AA Dwingeloo (Netherlands); Knowles, Kenda; Moodley, Kavilan [Astrophysics and Cosmology Research Unit, University of KwaZulu-Natal, Durban 4041 (South Africa); Marriage, Tobias A. [Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2686 (United States); Menanteau, Felipe [National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W. Clark St., Urbana, IL 61801 (United States); Reese, Erik D. [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd St., Philadelphia, PA 19104 (United States); Srianand, Raghunathan, E-mail: rlindner@astro.wisc.edu [IUCAA, Ganeshkhind, Pune 411007 (India)

    2014-05-01

    We present 610 MHz and 2.1 GHz imaging of the massive Sunyaev-Zel'dovich Effect selected z = 0.870 cluster merger ACT-CL J0102–4915 ({sup E}l Gordo{sup )}, obtained with the Giant Metrewave Radio Telescope and the Australia Telescope Compact Array (ATCA), respectively. We detect two complexes of radio relics separated by 3.'4 (1.6 Mpc) along the system's northwest-to-southeast collision axis that have high integrated polarization fractions (33%) and steep spectral indices (α between 1 and 2; S {sub ν}∝ν{sup –α}), consistent with creation via Fermi acceleration by shocks in the intracluster medium triggered by the cluster collision. From the spectral index of the relics, we compute a Mach number M=2.5{sub −0.3}{sup +0.7} and shock speed of 2500{sub −300}{sup +400} km s{sup −1}. With our wide-bandwidth, full-polarization ATCA data, we compute the Faraday depth φ across the northwest relic and find a range of values spanning Δφ = 30 rad m{sup –2}, with a mean value of (φ) = 11 rad m{sup –2} and standard deviation σ{sub φ} = 6 rad m{sup –2}. With the integrated line-of-sight gas density derived from new Chandra X-ray observations, our Faraday depth measurement implies B {sub ∥} ∼ 0.01 μG in the cluster outskirts. The extremely narrow shock widths in the relics (d {sub shock} ≤ 23 kpc), caused by the short synchrotron cooling timescale of relativistic electrons at z = 0.870, prevent us from placing a meaningful constraint on the magnetic field strength B using cooling time arguments. In addition to the relics, we detect a large (r {sub H} ≅ 1.1 Mpc radius), powerful (log (L {sub 1.4}/W Hz{sup –1}) = 25.66 ± 0.12) radio halo with a shape similar to El Gordo's 'bullet'-like X-ray morphology. The spatially resolved spectral-index map of the halo shows the synchrotron spectrum is flattest near the relics, along the system's collision axis, and in regions of high T {sub gas}, all locations associated

  10. Recent expansion of heat-activated retrotransposons in the coral symbiont Symbiodinium microadriaticum

    KAUST Repository

    Chen, Jit Ern

    2017-10-20

    Rising sea surface temperature is the main cause of global coral reef decline. Abnormally high temperatures trigger the breakdown of the symbiotic association between corals and their photosynthetic symbionts in the genus Symbiodinium. Higher genetic variation resulting from shorter generation times has previously been proposed to provide increased adaptability to Symbiodinium compared to the host. Retrotransposition is a significant source of genetic variation in eukaryotes and some transposable elements are specifically expressed under adverse environmental conditions. We present transcriptomic and phylogenetic evidence for the existence of heat stress-activated Ty1-copia-type LTR retrotransposons in the coral symbiont Symbiodinium microadriaticum. Genome-wide analyses of emergence patterns of these elements further indicate recent expansion events in the genome of S. microadriaticum. Our findings suggest that acute temperature increases can activate specific retrotransposons in the Symbiodinium genome with potential impacts on the rate of retrotransposition and the generation of genetic variation under heat stress.The ISME Journal advance online publication, 20 October 2017; doi:10.1038/ismej.2017.179.

  11. Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons.

    Directory of Open Access Journals (Sweden)

    Soledad Sacristán

    2009-10-01

    Full Text Available Parasites are able to evolve rapidly and overcome host defense mechanisms, but the molecular basis of this adaptation is poorly understood. Powdery mildew fungi (Erysiphales, Ascomycota are obligate biotrophic parasites infecting nearly 10,000 plant genera. They obtain their nutrients from host plants through specialized feeding structures known as haustoria. We previously identified the AVR(k1 powdery mildew-specific gene family encoding effectors that contribute to the successful establishment of haustoria. Here, we report the extensive proliferation of the AVR(k1 gene family throughout the genome of B. graminis, with sequences diverging in formae speciales adapted to infect different hosts. Also, importantly, we have discovered that the effectors have coevolved with a particular family of LINE-1 retrotransposons, named TE1a. The coevolution of these two entities indicates a mutual benefit to the association, which could ultimately contribute to parasite adaptation and success. We propose that the association would benefit 1 the powdery mildew fungus, by providing a mechanism for amplifying and diversifying effectors and 2 the associated retrotransposons, by providing a basis for their maintenance through selection in the fungal genome.

  12. Regulation of rice root development by a retrotransposon acting as a microRNA sponge.

    Science.gov (United States)

    Cho, Jungnam; Paszkowski, Jerzy

    2017-08-26

    It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.

  13. Cosmic backgrounds of relic gravitons and their absolute normalization

    CERN Document Server

    Giovannini, Massimo

    2014-01-01

    Provided the consistency relations are not violated, the recent Bicep2 observations pin down the absolute normalization, the spectral slope and the maximal frequency of the cosmic graviton background produced during inflation. The properly normalized spectra are hereby computed from the lowest frequencies (of the order of the present Hubble rate) up to the highest frequency range in the GHz region. Deviations from the conventional paradigm cannot be excluded and are examined by allowing for different physical possibilities including, in particular, a running of the tensor spectral index, an explicit breaking of the consistency relations and a spike in the high-frequency tail of the spectrum coming either from a post-inflationary phase dominated by a stiff fluid of from the contribution of waterfall fields in a hybrid inflationary context. The direct determinations of the tensor to scalar ratio at low frequencies, if confirmed by the forthcoming observations, will also affect and constrain the high-frequencies...

  14. DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms

    Directory of Open Access Journals (Sweden)

    Bonnivard Eric

    2009-04-01

    Full Text Available Abstract Background Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. Considering their mutational abilities, TEs can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. DIRS1-like retrotransposons are a particular group of retrotransposons according to their mode of transposition that implies a tyrosine recombinase. To date, they have been described in a restricted number of species in comparison with the LTR retrotransposons. In this paper, we determine the distribution of DIRS1-like elements among 25 decapod species, 10 of them living in hydrothermal vents that correspond to particularly unstable environments. Results Using PCR approaches, we have identified 15 new DIRS1-like families in 15 diverse decapod species (shrimps, lobsters, crabs and galatheid crabs. Hydrothermal organisms show a particularly great diversity of DIRS1-like elements with 5 families characterized among Alvinocarididae shrimps and 3 in the galatheid crab Munidopsis recta. Phylogenic analyses show that these elements are divergent toward the DIRS1-like families previously described in other crustaceans and arthropods and form a new clade called AlDIRS1. At larger scale, the distribution of DIRS1-like retrotransposons appears more or less patchy depending on the taxa considered. Indeed, a scattered distribution can be observed in the infraorder Brachyura whereas all the species tested in infraorders Caridea and Astacidea harbor some DIRS1-like elements. Conclusion Our results lead to nearly double both the number of DIRS1-like elements described to date, and the number of species known to harbor these ones. In this study, we provide the first degenerate primers designed to look specifically for DIRS1-like retrotransposons. They

  15. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons

    Directory of Open Access Journals (Sweden)

    Steinbiss Sascha

    2012-11-01

    Full Text Available Abstract Background Long terminal repeat (LTR retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets, making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. Results We have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. Conclusions LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining

  16. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.

    Science.gov (United States)

    Steinbiss, Sascha; Kastens, Sascha; Kurtz, Stefan

    2012-11-07

    Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets), making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. We have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining the output of software for predicting LTR

  17. Nonuniform multiview color texture mapping of image sequence and three-dimensional model for faded cultural relics with sift feature points

    Science.gov (United States)

    Li, Na; Gong, Xingyu; Li, Hongan; Jia, Pengtao

    2018-01-01

    For faded relics, such as Terracotta Army, the 2D-3D registration between an optical camera and point cloud model is an important part for color texture reconstruction and further applications. This paper proposes a nonuniform multiview color texture mapping for the image sequence and the three-dimensional (3D) model of point cloud collected by Handyscan3D. We first introduce nonuniform multiview calibration, including the explanation of its algorithm principle and the analysis of its advantages. We then establish transformation equations based on sift feature points for the multiview image sequence. At the same time, the selection of nonuniform multiview sift feature points is introduced in detail. Finally, the solving process of the collinear equations based on multiview perspective projection is given with three steps and the flowchart. In the experiment, this method is applied to the color reconstruction of the kneeling figurine, Tangsancai lady, and general figurine. These results demonstrate that the proposed method provides an effective support for the color reconstruction of the faded cultural relics and be able to improve the accuracy of 2D-3D registration between the image sequence and the point cloud model.

  18. [Research Progress of Raman Spectroscopy on Dyestuff Identification of Ancient Relics and Artifacts].

    Science.gov (United States)

    He, Qiu-ju; Wang, Li-qin

    2016-02-01

    As the birthplace of Silk Road, China has a long dyeing history. The valuable information about the production time, the source of dyeing material, dyeing process and preservation status were existed in organic dyestuff deriving from cultural relics and artifacts. However, because of the low contents, complex compositions and easily degraded of dyestuff, it is always a challenging task to identify the dyestuff in relics analyzing field. As a finger-print spectrum, Raman spectroscopy owns unique superiorities in dyestuff identification. Thus, the principle, characteristic, limitation, progress and development direction of micro-Raman spectroscopy (MRS/µ-Raman), near infrared reflection and Fourier transform Raman spectroscopy (NIR-FT-Raman), surface-enhanced Raman spectroscopy (SERS) and resonance raman spectroscopy (RRS) have been introduced in this paper. Furthermore, the features of Raman spectra of gardenia, curcumin and other natural dyestuffs were classified by MRS technology, and then the fluorescence phenomena of purpurin excitated with different wavelength laser was compared and analyzed. At last, gray green silver colloidal particles were made as the base, then the colorant of madder was identified combining with thin layer chromatography (TLC) separation technology and SERS, the result showed that the surface enhancement effect of silver colloidal particles could significantly reduce fluorescence background of the Raman spectra. It is pointed out that Raman spectroscopy is a rapid and convenient molecular structure qualitative methodology, which has broad application prospect in dyestuff analysis of cultural relics and artifacts. We propose that the combination of multi-Raman spectroscopy, separation technology and long distance transmission technology are the development trends of Raman spectroscopy.

  19. NGC 1277: A MASSIVE COMPACT RELIC GALAXY IN THE NEARBY UNIVERSE

    Energy Technology Data Exchange (ETDEWEB)

    Trujillo, Ignacio; Vazdekis, Alexandre [Instituto de Astrofísica de Canarias, c/Vía Láctea s/n, E-38205-La Laguna, Tenerife (Spain); Ferré-Mateu, Anna [Subaru Telescope, 650 North A' ohoku Place, Hilo, HI 96720 (United States); Balcells, Marc [Isaac Newton Group of Telescopes, E-38700 Santa Cruz de La Palma, Canary Islands (Spain); Sánchez-Blázquez, Patricia, E-mail: trujillo@iac.es [Departamento de Física Teórica, Universidad Autónoma de Madrid, E-28049, Cantoblanco, Madrid (Spain)

    2014-01-10

    As early as 10 Gyr ago, galaxies with more than 10{sup 11} M {sub ☉} of stars already existed. While most of these massive galaxies must have subsequently transformed through on-going star formation and mergers with other galaxies, a small fraction (≲0.1%) may have survived untouched until today. Searches for such relic galaxies, useful windows to explore the early universe, have been inconclusive to date: galaxies with masses and sizes like those observed at high redshift (M {sub *} ≳ 10{sup 11} M {sub ☉}; R{sub e} ≲ 1.5 kpc) have been found in the local universe, but their stars are far too young for the galaxy to be a relic galaxy. This paper explores the first case of a nearby galaxy, NGC 1277 (at a distance of 73 Mpc in the Perseus galaxy cluster), which fulfills many criteria to be considered a relic galaxy. Using deep optical spectroscopy, we derive the star formation history along the structure of the galaxy: the stellar populations are uniformly old (>10 Gyr) with no evidence for more recent star formation episodes. The metallicity of their stars is super-solar ([Fe/H] = 0.20 ± 0.04 with a smooth decline toward the outer regions) and α-enriched ([α/Fe] = 0.4 ± 0.1). This suggests a very short formation time scale for the bulk of the stars in this galaxy. This object also rotates very fast (V {sub rot} ∼ 300 km s{sup –1}) and has a large central velocity dispersion (σ > 300 km s{sup –1}). NGC 1277 allows the exploration in full detail of properties such as the structure, internal dynamics, metallicity, and initial mass function as they were at ∼10-12 Gyr ago when the first massive galaxies were built.

  20. Overexpression of LINE-1 Retrotransposons in Autism Brain.

    Science.gov (United States)

    Shpyleva, Svitlana; Melnyk, Stepan; Pavliv, Oleksandra; Pogribny, Igor; Jill James, S

    2018-02-01

    Long interspersed nuclear elements-1 (LINE-1 or L1) are mobile DNA sequences that are capable of duplication and insertion (retrotransposition) within the genome. Recently, retrotransposition of L1 was shown to occur within human brain leading to somatic mosaicism in hippocampus and cerebellum. Because unregulated L1 activity can promote genomic instability and mutagenesis, multiple mechanisms including epigenetic chromatin condensation have evolved to effectively repress L1 expression. Nonetheless, L1 expression has been shown to be increased in patients with Rett syndrome and schizophrenia. Based on this evidence and our reports of oxidative stress and epigenetic dysregulation in autism cerebellum, we sought to determine whether L1 expression was increased in autism brain. The results indicated that L1 expression was significantly elevated in the autism cerebellum but not in BA9, BA22, or BA24. The binding of repressive MeCP2 and histone H3K9me3 to L1 sequences was significantly lower in autism cerebellum suggesting that relaxation of epigenetic repression may have contributed to increased expression. Further, the increase in L1 expression was inversely correlated with glutathione redox status consistent with reports indicating that L1 expression is increased under pro-oxidant conditions. Finally, the expression of transcription factor FOXO3, sensor of oxidative stress, was significantly increased and positively associated with L1 expression and negatively associated with glutathione redox status. While these novel results are an important first step, future understanding of the contribution of elevated L1 expression to neuronal CNVs and genomic instability in autism will depend on emerging cell-specific genomic technologies, a challenge that warrants future investigation.

  1. DNA methylation inhibits expression and transposition of the Neurospora Tad retrotransposon.

    Science.gov (United States)

    Zhou, Y; Cambareri, E B; Kinsey, J A

    2001-06-01

    Tad is a LINE-like retrotransposon of the filamentous fungus Neurospora crassa. We have analyzed both expression and transposition of this element using strains with a single copy of Tad located in the 5' noncoding sequences of the am (glutamate dehydrogenase) gene. Tad in this position has been shown to carry a de novo cytosine methylation signal which causes reversible methylation of both Tad and am upstream sequences. Here we find that methylation of the Tad sequences inhibits both Tad expression and transposition. This inhibition can be relieved by the use of 5-azacytidine, a drug which reduces cytosine methylation, or by placing the Tad/am sequences in a dim-2 genetic background.

  2. Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform

    OpenAIRE

    Monden, Yuki; Yamamoto, Ayaka; Shindo, Akiko; Tahara, Makoto

    2014-01-01

    In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LI...

  3. PeV IceCube signals and Dark Matter relic abundance in modified cosmologies

    Science.gov (United States)

    Lambiase, G.; Mohanty, S.; Stabile, An.

    2018-04-01

    The discovery by the IceCube experiment of a high-energy astrophysical neutrino flux with energies of the order of PeV, has opened new scenarios in astroparticles physics. A possibility to explain this phenomenon is to consider the minimal models of Dark Matter (DM) decay, the 4-dimensional operator ˜ y_{α χ }\\overline{{L_{L_{α }}}} H χ , which is also able to generate the correct abundance of DM in the Universe. Assuming that the cosmological background evolves according to the standard cosmological model, it follows that the rate of DM decay Γ _χ ˜ |y_{α χ }|^2 needed to get the correct DM relic abundance (Γ _χ ˜ 10^{-58}) differs by many orders of magnitude with respect that one needed to explain the IceCube data (Γ _χ ˜ 10^{-25}), making the four-dimensional operator unsuitable. In this paper we show that assuming that the early Universe evolution is governed by a modified cosmology, the discrepancy between the two the DM decay rates can be reconciled, and both the IceCube neutrino rate and relic density can be explained in a minimal model.

  4. Radiative corrections in supersymmetry and application to relic density calculation beyond leading order

    International Nuclear Information System (INIS)

    Chalons, G.

    2010-07-01

    This thesis focuses on the evaluation of supersymmetric radiative corrections for processes involved in the calculation of the relic density of dark matter, in the MSSM (Minimal Supersymmetric Standard Model) and the standard cosmological scenario, as well as the impact of the choice renormalisation scheme in the neutralino/chargino sector based on the measure of three physical masses. This study has been carried out with the help of an automatic program dedicated the the computation of physical observables at one-loop in the MSSM, called SloopS. For the relic density calculation we investigated scenarios where the most studied dark matter candidate, the neutralino, annihilates into gauge boson pair. We covered cases where its mass was of the order of hundreds of GeV to 2 TeV. The full set of electroweak and strong corrections has been taken into account, involved in sub-leading channels with quarks. In the case of very heavy neutralinos, two important effects were outlined: the Sommerfeld enhancement due to massive gauge bosons and maybe even more important some corrections of Sudakov type. (authors)

  5. English Water Meadows: historic relics or focus for environmental management and inter-disciplinary research?

    Science.gov (United States)

    Cook, Hadrian

    2015-04-01

    Irrigated water meadows are found across Europe, from southern Scandinavia to Spain and in the Alpine regions and Italy. While the practice of engineering 'floated' meadow land for deliberate irrigation on hillsides and floodplains is widespread and ancient, since about 1600 AD the practice was widely adopted on floodplains in southern England where they improved the timing and productivity of grazing land and produced hay crops. They also became a part of English consciousness through art and literature. To some, water meadows are a relic of an agrarian past, to others they are the object of a range of foci for conservation, education, sustainable grass production, community engagement and recent research suggests water returned from meadow irrigation is beneficial to river water quality. Historically floodplain 'bedwork' water meadows grew from, and were integral in, the farming system of 'Wessex' involving sheep which produced dung for arable land and later supporting dairy and beef production, as well as hay. Where systems remain, this is largely due to the whim of individuals, the outcome of agri-environmental schemes. Water meadows may be managed by public, voluntary or private sector bodies. What is needed is a fresh look at how land owners, or communities, might micro-target them for heritage, habitat and grassland management. There are therefore interesting questions concerning their future: Who might invest in their restoration and maintenance? How might they be integrated into commercial farming? Are they of sufficient interest to restore en masse to become (once more) a major feature of the English chalk stream valleys? Do they provide a way into academic and public perception, combining environmental science, history, cultural heritage and environmental management? How might restoration and management become vehicles for public engagement? While each of these questions represents a major topic for discussion, this paper is an attempt to consolidate

  6. Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).

    Science.gov (United States)

    Mascagni, Flavia; Giordani, Tommaso; Ceccarelli, Marilena; Cavallini, Andrea; Natali, Lucia

    2017-08-18

    Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial

  7. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons.

    Science.gov (United States)

    Locati, Mauro D; Pagano, Johanna F B; Ensink, Wim A; van Olst, Marina; van Leeuwen, Selina; Nehrdich, Ulrike; Zhu, Kongju; Spaink, Herman P; Girard, Geneviève; Rauwerda, Han; Jonker, Martijs J; Dekker, Rob J; Breit, Timo M

    2017-04-01

    5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci. © 2017 Locati et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. Finger of a saint, thumb of a priest: medieval relics in the Diocese of Turku, and the archaeology of lived bodies

    Directory of Open Access Journals (Sweden)

    Visa Immonen

    2011-01-01

    Full Text Available The relics of Turku Cathedral are remains belonging to the bodies of holy persons, different from ours, even today, although the cathedral is the see for the archbishop of the Evangelical Lutheran Church of Finland, and relics are not on public display. Among the relics of the cathedral, there is a fragment of a radius, which according to its authentica, belongs to St Henry. Relics and reliquaries were in the core of medieval piety, and the cult of saints had infused throughout the society. Due to their central position in culture, relics offer glimpses at a range of material, social and cultural phenomena related to medieval embodiment.The Department of Archaeology at the University of Turku began to study the finger relic of St Eric and other items in the assemblage of Turku Cathedral in 2007. Relics and reliquaries are being opened and documented and organic as well as inorganic samples are being taken for a range of scientific analyses. So far the project has concentrated on building a chronological chart of individual artefacts. The majority of the relics date to the fourteenth century, although much more recent datings have also been obtained. The challenge of the project is not to stop when a better understanding of materials, their origins and age has been accomplished, but to use the results as a steppingstone into a study of the practices of medieval relic veneration. Medieval bodies and those material processes which authenticate relics, or distinguish saints’ bodies from other human remains, are thus at the heart of this article discussing embodiment.

  9. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.

    Science.gov (United States)

    Kojima, Kenji K; Jurka, Jerzy

    2015-01-01

    Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes.

  10. Relic gravitons from the pre-big bang: what we know and what we do not know

    OpenAIRE

    Gasperini, M.

    1996-01-01

    I discuss the status of present knowledge about a possible background of relic gravitons left by an early, pre-big bang cosmological epoch, whose existence in the past of our Universe is suggested by the duality symmetries of string theory.

  11. Can Planck-mass relics of evaporating black holes close the Universe

    International Nuclear Information System (INIS)

    MacGibbon, J.H.

    1987-01-01

    The authors propose that the cosmological dark matter consists of the Planck-mass remnants of evaporating primordial black holes. Such remnants would be expected to have close to the critical density if the black holes evaporating at the present epoch have the maximum density consistent with cosmic-ray constraints. Primordial black holes of the required density may form naturally at the end of an inflationary epoch. Planck-mass relics would behave dynamically just like 'cold dark matter' and would therefore share the attractions of other 'cold' candidates. In addition, because the baryonic matter in black holes cannot participate in nucleosynthesis the limits on the baryonic content of the Universe set by primordial nucleosynthesis are circumvented. (author)

  12. Mechanism for thermal relic dark matter of strongly interacting massive particles.

    Science.gov (United States)

    Hochberg, Yonit; Kuflik, Eric; Volansky, Tomer; Wacker, Jay G

    2014-10-24

    We present a new paradigm for achieving thermal relic dark matter. The mechanism arises when a nearly secluded dark sector is thermalized with the standard model after reheating. The freeze-out process is a number-changing 3→2 annihilation of strongly interacting massive particles (SIMPs) in the dark sector, and points to sub-GeV dark matter. The couplings to the visible sector, necessary for maintaining thermal equilibrium with the standard model, imply measurable signals that will allow coverage of a significant part of the parameter space with future indirect- and direct-detection experiments and via direct production of dark matter at colliders. Moreover, 3→2 annihilations typically predict sizable 2→2 self-interactions which naturally address the "core versus cusp" and "too-big-to-fail" small-scale structure formation problems.

  13. Relic excavated in western India is probably of Georgian Queen Ketevan.

    Science.gov (United States)

    Rai, Niraj; Taher, Nizamuddin; Singh, Manvendra; Chaubey, Gyaneshwer; Jha, Aditya Nath; Singh, Lalji; Thangaraj, Kumarasamy

    2014-01-01

    History has well documented the execution of Queen Ketevan of Georgia by the Persian Emperor of modern day Iran. Based on historical records, in 1624 two Augustinian friars unearthed the queen's remains and one of them brought the relic to the St. Augustine convent in Goa, India. We carried out ancient DNA analysis on the human bone remains excavated from the St. Augustine convent by sequencing and genotyping of the mitochondrial DNA. The investigations of the remains revealed a unique mtDNA haplogroup U1b, which is absent in India, but present in Georgia and surrounding regions. Since our genetic analysis corroborates archaeological and literary evidence, it is likely that the excavated bone belongs to Queen Ketevan of Georgia. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. arXiv The propagating speed of relic gravitational waves and their refractive index during inflation

    CERN Document Server

    Giovannini, Massimo

    2018-06-02

    If the refractive index of the tensor modes increases during a conventional inflationary stage of expansion the relic graviton spectrum is tilted towards high frequencies. Two apparently diverse parametrizations of this effect are shown to be related by a rescaling of the four-dimensional metric through a conformal factor that involves the refractive index itself. Non-monotonic spectra with a maximum in the MHz region correspond to a limited variation of the refractive index terminating well before the end of inflation. After exploring a general approach encompassing the ones proposed so far, we estimate the required sensitivity for the direct detection of the predicted gravitational radiation and demonstrate that the allowed regions of the parameter space are within reach for some of the planned detectors operating either in the audio band (like Ligo/Virgo and Kagra) or in the mHz band (like Lisa, Bbo and Decigo).

  15. Constraints upon the spectral indices of relic gravitational waves by LIGO S5

    International Nuclear Information System (INIS)

    Zhang, Y.; Tong, M. L.; Fu, Z. W.

    2010-01-01

    With LIGO having achieved its design sensitivity and the LIGO S5 strain data being available, constraints on the relic gravitational waves (RGWs) become realistic. The analytical spectrum of RGWs generated during inflation depends sensitively on the initial condition, which is generically described by the index β, the running index α t , and the tensor-to-scalar ratio r. By the LIGO S5 data of the cross-correlated two detectors, we obtain constraints on the parameters (β,α t ,r). As a main result, we have computed the theoretical signal-to-noise ratio of RGWs for various values of (β,α t ,r), using the cross-correlation for the given pair of LIGO detectors. The constraints by the indirect bound on the energy density of RGWs by big bang nucleosynthesis and cosmic microwave background have been obtained, which turn out to be still more stringent than LIGO S5.

  16. Relic gravitational wave spectrum, the trans-Planckian physics and Horava-Lifshitz gravity

    International Nuclear Information System (INIS)

    Koh, Seoktae

    2010-01-01

    We calculate the spectrum of the relic gravitational wave due to the trans-Planckian effect in which the standard linear dispersion relations may be modified. Of the modified dispersion relations suggested in the literature which has investigated the trans-Planckian effect, we especially use the Corley-Jacobson dispersion relations. The Corley-Jacobson-type modified dispersion relations can be obtained from Horava-Lifshitz gravity which is non-relativistic and UV complete. Although it is not clear how the transitions from Horava-Lifshitz gravity in the UV regime to Einstein gravity in the IR limit occur, we assume that the Horava-Lifshitz gravity regime is followed by the inflationary phase in Einstein gravity.

  17. Stochastic backgrounds of relic gravitons, T$\\Lambda$CDM paradigm and the stiff ages

    CERN Document Server

    Giovannini, Massimo

    2008-01-01

    Absent any indirect tests on the thermal history of the Universe prior to the formation of light nuclear elements, it is legitimate to investigate situations where, before nucleosyntheis, the sound speed of the plasma was larger than $c/\\sqrt{3}$, at most equalling the speed of light $c$. In this plausible extension of the current cosmological paradigm, hereby dubbed Tensor-$\\Lambda$CDM (i.e. T$\\Lambda$CDM) scenario, high-frequency gravitons are copiously produced. Without conflicting with the bounds on the tensor to scalar ratio stemming from the combined analysis of the three standard cosmological data sets (i.e. cosmic microwave background anisotropies, large-scale structure and supenovae), the spectral energy density of the relic gravitons in the T$\\Lambda$CDM scenario can be potentially observable by wide-band interferometers (in their advanced version) operating in a frequency window which ranges between few Hz and few kHz.

  18. Impact of Low-Energy Ion Beam Implantation on the Expression of Ty1-copia-like Retrotransposons in Wheat (Triticum aestivum)

    International Nuclear Information System (INIS)

    Ya Huiyuan; Jiao Zhen; Gu Yunhong; Wang Weidong; Qin Guangyong; Huo Yuping

    2007-01-01

    Retrotransposon-like elements are major constituents of most eukaryotic genomes. For example, they account for roughly 90% of the wheat (Triticum aestivum) genome. Previous study on a wheat strain treated by low-energy N + ions indicated the variations in AFLP (Amplified Fragment Length Polymorphism ) markers. One such variation was caused by the re-activation of Ty1-copia-like retrotransposons, implying that the mutagenic effects of low-energy ions might work through elevated activation of retrotransposons. In this paper an expression profile of Ty1-copia-like retrotransposons in wheat treated by low-energy N + ions is reported. The reverse transcriptase (RT) domains of these retrotransposons were amplified by reverse-transcriptional polymerase chain reaction (RT-PCR) and sequentially cloned. 42 and 65 clones were obtained from the treated (CL) and control materials (CK), respectively. Sequence analysis of each clone was performed by software. Phylogeny and classification were calculated responding to the sequences of the RT domains. All the results show that there is much difference in the RT domain between the control sample and the treated sample. Especially, the RT domains from the treated group encode significantly more functional ORF (open reading frames) than those from the control sample. This observation suggests that the treated sample has higher activation of retrotransposons, possibly as a consequence of low-energy ion beam irradiation. It also suggests that retrotransposons in the two groups impact the host gene expression in two different ways and carry out different functions in wheat cells

  19. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

    Directory of Open Access Journals (Sweden)

    Palhares Alessandra C

    2012-06-01

    Full Text Available Abstract Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’ contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs. Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56 were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60

  20. Mobilization of retrotransposons as a cause of chromosomal diversification and rapid speciation: the case for the Antarctic teleost genus Trematomus.

    Science.gov (United States)

    Auvinet, J; Graça, P; Belkadi, L; Petit, L; Bonnivard, E; Dettaï, A; Detrich, W H; Ozouf-Costaz, C; Higuet, D

    2018-05-09

    The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus Trematomus (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity. Here we apply a multi-strategy approach to determine the role of large-scale TE mobilization in chromosomal diversification within Trematomus species. Despite the extensive chromosomal rearrangements observed in Trematomus species, our measurements revealed strong interspecific genome size conservation. After identifying the DIRS1, Gypsy and Copia retrotransposon superfamilies in genomes of 13 nototheniid species, we evaluated their diversity, abundance (copy numbers) and chromosomal distribution. Four families of DIRS1, nine of Gypsy, and two of Copia were highly conserved in these genomes; DIRS1 being the most represented within Trematomus genomes. Fluorescence in situ hybridization mapping showed preferential accumulation of DIRS1 in centromeric and pericentromeric regions, both in Trematomus and other nototheniid species, but not in outgroups: species of the Sub-Antarctic notothenioid families Bovichtidae and Eleginopsidae, and the non-notothenioid family Percidae. In contrast to the outgroups, High-Antarctic notothenioid species, including the genus Trematomus, were subjected to strong environmental stresses involving repeated bouts of warming above the freezing point of seawater and cooling to sub-zero temperatures on the Antarctic continental shelf during the past 40 millions of years (My). As a consequence of these repetitive environmental changes, including thermal shocks; a breakdown of epigenetic regulation that

  1. Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus

    DEFF Research Database (Denmark)

    Urbanski, Dorian Fabian; Malolepszy, Anna; Stougaard, Jens

    2012-01-01

    Insertion mutants facilitate functional analysis of genes, but for most plant species it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics. The main challenge is developing efficient high-throughput procedures for both mutagenesis and insert......Insertion mutants facilitate functional analysis of genes, but for most plant species it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics. The main challenge is developing efficient high-throughput procedures for both mutagenesis...... plants. The identified insertions showed that the endogenous LORE1 retrotransposon is well suited for insertion mutagenesis due to its homogenous gene targeting and exonic insertion preference. Since LORE1 transposition occurs in the germline, harvesting seeds from a single founder line and cultivating...... progeny generates a complete mutant population. This ease of LORE1 mutagenesis combined with the efficient FSTpoolit protocol, which exploits 2D pooling, Illumina sequencing, and automated data analysis, allows highly cost-efficient development of a comprehensive reverse genetic resource....

  2. A LTR copia retrotransposon and Mutator transposons interrupt Pgip genes in cultivated and wild wheats.

    Science.gov (United States)

    Di Giovanni, Michela; Cenci, Alberto; Janni, Michela; D'Ovidio, Renato

    2008-04-01

    Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. Wheat pgip genes have been isolated from the B (Tapgip1) and D (Tapgip2) genomes, and now we report the identification of pgip genes from the A genomes of wild and cultivated wheats. By Southern blots and sequence analysis of BAC clones we demonstrated that wheat contains a single copy pgip gene per genome and the one from the A genome, pgip3, is inactivated by the insertion of a long terminal repeat copia retrotranspon within the fourth LRR. We demonstrated also that this retrotransposon insertion is present in Triticum urartu and all the polyploidy wheats assayed, but is absent in T. monococcum (Tmpgip3), suggesting that this insertion took place after the divergence between T. monococcum and T. urartu, but before the formation of the polyploid wheats. We identified also two independent insertion events of new Class II transposable elements, Vacuna, belonging to the Mutator superfamily, that interrupted the Tdipgip1 gene of T. turgidum ssp. dicoccoides. The occurrence of these transposons within the coding region of Tdipgip1 facilitated the mapping of the Pgip locus in the pericentric region of the short arm of chromosome group 7. We speculate that the inactivation of pgip genes are tolerated because of redundancy of PGIP activities in the wheat genome.

  3. Insertion of a solo LTR retrotransposon associates with spur mutations in 'Red Delicious' apple (Malus × domestica).

    Science.gov (United States)

    Han, Mengxue; Sun, Qibao; Zhou, Junyong; Qiu, Huarong; Guo, Jing; Lu, Lijuan; Mu, Wenlei; Sun, Jun

    2017-09-01

    Insertion of a solo LTR, which possesses strong bidirectional, stem-specific promoter activities, is associated with the evolution of a dwarfing apple spur mutation. Spur mutations in apple scions revolutionized global apple production. Since long terminal repeat (LTR) retrotransposons are tightly related to natural mutations, inter-retrotransposon-amplified polymorphism technique and genome walking were used to find sequences in the apple genome based on these LTRs. In 'Red Delicious' spur mutants, a novel, 2190-bp insertion was identified as a spur-specific, solo LTR (sLTR) located at the 1038th nucleotide of another sLTR, which was 1536 bp in length. This insertion-within-an-insertion was localized within a preexisting Gypsy-50 retrotransposon at position 3,762,767 on chromosome 4. The analysis of transcriptional activity of the two sLTRs (the 2190- and 1536-bp inserts) indicated that the 2190-bp sLTR is a promoter, capable of bidirectional transcription. GUS expression in the 2190-bp-sense and 2190-bp-antisense transgenic lines was prominent in stems. In contrast, no promoter activity from either the sense or the antisense strand of the 1536-bp sLTR was detected. From ~150 kb of DNA on each side of the 2190 bp, sLTR insertion site, corresponding to 300 kb of the 'Golden Delicious' genome, 23 genes were predicted. Ten genes had predicted functions that could affect shoot development. This first report, of a sLTR insertion associated with the evolution of apple spur mutation, will facilitate apple breeding, cloning of spur-related genes, and discovery of mechanisms behind dwarf habit.

  4. Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae).

    Science.gov (United States)

    Kolano, Bozena; Bednara, Edyta; Weiss-Schneeweiss, Hanna

    2013-10-01

    High heterogeneity was observed among conserved domains of reverse transcriptase ( rt ) isolated from quinoa. Only one Ty1- copia rt was highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes. The heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics.

  5. Stable indications of relic gravitational waves in Wilkinson Microwave Anisotropy Probe data and forecasts for the Planck mission

    International Nuclear Information System (INIS)

    Zhao, W.; Baskaran, D.; Grishchuk, L. P.

    2009-01-01

    The relic gravitational waves are the cleanest probe of the violent times in the very early history of the Universe. They are expected to leave signatures in the observed cosmic microwave background anisotropies. We significantly improved our previous analysis [W. Zhao, D. Baskaran, and L. P. Grishchuk, Phys. Rev. D 79, 023002 (2009)] of the 5-year WMAP TT and TE data at lower multipoles l. This more general analysis returned essentially the same maximum likelihood result (unfortunately, surrounded by large remaining uncertainties): The relic gravitational waves are present and they are responsible for approximately 20% of the temperature quadrupole. We identify and discuss the reasons by which the contribution of gravitational waves can be overlooked in a data analysis. One of the reasons is a misleading reliance on data from very high multipoles l and another a too narrow understanding of the problem as the search for B modes of polarization, rather than the detection of relic gravitational waves with the help of all correlation functions. Our analysis of WMAP5 data has led to the identification of a whole family of models characterized by relatively high values of the likelihood function. Using the Fisher matrix formalism we formulated forecasts for Planck mission in the context of this family of models. We explore in detail various 'optimistic', 'pessimistic', and 'dream case' scenarios. We show that in some circumstances the B-mode detection may be very inconclusive, at the level of signal-to-noise ratio S/N=1.75, whereas a smarter data analysis can reveal the same gravitational wave signal at S/N=6.48. The final result is encouraging. Even under unfavorable conditions in terms of instrumental noises and foregrounds, the relic gravitational waves, if they are characterized by the maximum likelihood parameters that we found from WMAP5 data, will be detected by Planck at the level S/N=3.65.

  6. Shrines and relics between Late Antiquity and Middle Ages: Christianization of the space or sacralization of the Christianity?

    Directory of Open Access Journals (Sweden)

    Luigi Canetti

    2002-12-01

    Full Text Available This essay analyzes the importance of relics and sanctuaries against the backdrop of the sacralization of Christianity and the latter’s re-elaboration into a religious system that occurred in urban milieux in the late ancient times. The main steps of this process, which came to a climax in the 4th century, are the Christianization of time and space as well as the reinterpretation of Christ’s death in terms of a sacrifice.

  7. Are Brands Postmodern Relics? Taking a Closer Look at New Sacred Objects

    Directory of Open Access Journals (Sweden)

    Stéphane DUFOUR

    2011-01-01

    Full Text Available Ever since the Church lost its monopoly on the sacred, no longer able to solely determine its form or contents, the social sphere has gradually taken over this value, applying it to new human and social objects. As a result, the modes of expression of the sacred have multiplied, along with the subjective and intimate experiences of modern individualism. Among the vast number of potential manifestations of this value, to which almost everything now seems to aspire, this paper will concentrate on commercial brands as vectors of meaning, with the hypothesis that some of them seek to position themselves, in postmodern society, as new figures of the sacred. This area of study is close to that of the sociologist Adam Arvidsson, when he describes brands as religious objects. If brands are less interested in selling products than in creating an affective experience, Arvidsson assimilates them to modern relics. However, this paper goes beyond metaphors, to examine the rhetorical strategies (discourse, rituals, representations, imagery through which brands construct meaning around sacred objects. Situated between a branch of marketing which concentrates on sacralising commercial products, and a theory popular in the English-speaking world, which has illustrated how the media work to sacralise products and brands, this paper uses a communicational approach to analyse the construction of meaning, by brands looking to make themselves (appear sacred.

  8. Understanding the radio spectral indices of galaxy cluster relics by superdiffusive shock acceleration

    Science.gov (United States)

    Zimbardo, Gaetano; Perri, Silvia

    2018-06-01

    Galaxy cluster merger shocks are the likely source of relativistic electrons, but many observations do not fit into the standard acceleration models. In particular, there is a long-standing discrepancy between the radio derived Mach numbers M_radio and the Mach numbers derived from X-ray measurements, M_X. Here, we show how superdiffusive electron transport and superdiffusive shock acceleration (SSA) can help to solve this problem. We present a heuristic derivation of the superlinear time growth of the mean square displacement of particles, ⟨Δx2⟩∝tβ, and of the particle energy spectral index in the framework of SSA. The resulting expression for the radio spectral index α is then used to determine the superdiffusive exponent β from the observed values of α and of the compression ratio for a number of radio relics. Therefore, the fact that M_radio>M_X can be explained by SSA without the need to make assumptions on the energy spectrum of the seed electrons to be re-accelerated. We also consider the acceleration times obtained in the diffusive case, based both on the Bohm diffusion coefficient and on the quasilinear diffusion coefficient. While in the latter case the acceleration time is consistent with the estimated electron energy loss time, the former case it is much shorter.

  9. X-ray fluorescence in investigations of cultural relics and archaeological finds

    Energy Technology Data Exchange (ETDEWEB)

    Musilek, Ladislav, E-mail: musilek@fjfi.cvut.cz [Czech Technical University in Prague, Faculty of Nuclear Sciences and Physical Engineering, Brehova 7, 115 19 Praha 1 (Czech Republic); Cechak, Tomas; Trojek, Tomas [Czech Technical University in Prague, Faculty of Nuclear Sciences and Physical Engineering, Brehova 7, 115 19 Praha 1 (Czech Republic)

    2012-07-15

    Some characteristic features of X-ray fluorescence (XRF) analysis make it an ideal method for investigations of cultural relics and archaeological finds. It has therefore become a standard method used in archaeometry. Paintings, frescos, manuscripts, pottery, metalwork, glass, and many other objects are analysed with the aim of recognising their materials, production technologies and origin, and for identifying counterfeits. This paper reviews various techniques used in XRF analyses of works of art, summarises the advantages and limitations of the method, and presents some typical examples of its use. The general review is supplemented by some techniques used and some results achieved at CTU-FNSPE in Prague. - Highlights: Black-Right-Pointing-Pointer Review of XRF analysis in archaeometry. Black-Right-Pointing-Pointer Instrumentation for XRF analysis with various sources of radiation. Black-Right-Pointing-Pointer Materials and artefacts, which can be measured and information, which can be obtained. Black-Right-Pointing-Pointer XRF analysis of artworks at the CTU Prague.

  10. RELICS: A Candidate Galaxy Arc at z~10 and Other Brightly Lensed z>6 Galaxies

    Science.gov (United States)

    Salmon, Brett; Coe, Dan; Bradley, Larry; Bradac, Marusa; Huang, Kuang-Han; Oesch, Pascal; Brammer, Gabriel; Stark, Daniel P.; Sharon, Keren; Trenti, Michele; Avila, Roberto J.; Ogaz, Sara; Acebron, Ana; Andrade-Santos, Felipe; Carrasco, Daniela; Cerny, Catherine; Cibirka, Nathália; Dawson, William; Frye, Brenda; Hoag, Austin; Jones, Christine; Mainali, Ramesh; Ouchi, Masami; Paterno-Mahler, Rachel; Rodney, Steven; Umetsu, Keiichi; Zitrin, Adi; RELICS

    2018-01-01

    Massive foreground galaxy clusters magnify and distort the light of objects behind them, permitting a view into both the extremely distant and intrinsically faint galaxy populations. We present here some of the most brightly lensed z>6 galaxy candidates known from the Reionization Lensing Cluster Survey (RELICS) and the discovery of a particularly fortuitous z~10 galaxy candidate which has been arced by the effects of strong gravitational lensing. The z~10 candidate has a lensed H-band magnitude of 25.8 AB mag and a high lensing magnification (~4-7). The inferred upper limits on the stellar mass (log [M_star /M_Sun]=9.5) and star formation rate (log [SFR/(M_Sun/yr)]=1.5) indicate that this candidate is a typical star-forming galaxy on the z>6 SFR-M_star relation. We rule out the only low-z solution as unphysical based on the required stellar mass, dust attenuation, size, and [OIII] EW needed for a z~2 SED to match the data. Finally, we reconstruct the source-plane image and estimate the candidate's physical size at z~10, finding a half-light radius of r_e 9 candidates. While the James Webb Space Telescope will detect z>10 with ease, this rare candidate offers the potential for unprecedented spatial resolution less than 500 Myr after the Big Bang.

  11. Relic density and CMB constraints on dark matter annihilation with Sommerfeld enhancement

    International Nuclear Information System (INIS)

    Zavala, Jesus; White, Simon D. M.; Vogelsberger, Mark

    2010-01-01

    We calculate how the relic density of dark matter particles is altered when their annihilation is enhanced by the Sommerfeld mechanism due to a Yukawa interaction between the annihilating particles. Maintaining a dark matter abundance consistent with current observational bounds requires the normalization of the s-wave annihilation cross section to be decreased compared to a model without enhancement. The level of suppression depends on the specific parameters of the particle model, with the kinetic decoupling temperature having the most effect. We find that the cross section can be reduced by as much as an order of magnitude for extreme cases. We also compute the μ-type distortion of the CMB energy spectrum caused by energy injection from such Sommerfeld-enhanced annihilation. Our results indicate that in the vicinity of resonances, associated with bound states, distortions can be large enough to be excluded by the upper limit |μ|≤9.0x10 -5 found by the FIRAS (Far Infrared Absolute Spectrophotometer) instrument on the COBE (Cosmic Background Explorer) satellite.

  12. Relic gravitational waves with a running spectral index and its constraints at high frequencies

    International Nuclear Information System (INIS)

    Tong, M. L.; Zhang, Y.

    2009-01-01

    We study the impact of a running index α t on the spectrum of relic gravitational waves (RGWs) over the whole range of frequency (10 -18 ∼10 10 ) Hz and reveal its implications in RGWs detections and in cosmology. Analytical calculations show that, although the spectrum of RGWs on low frequencies is less affected by α t ≠0, on high frequencies, the spectrum is modified substantially. Investigations are made toward potential detections of the α t -modified RGWs for several kinds of current and planned detectors. The Advanced LIGO will likely be able to detect RGWs with α t ≥0 for inflationary models with the inflation index β=-1.956 and the tensor-scalar ratio r=0.55. The future LISA can detect RGWs for a much broader range of (α t ,β,r), and will have a better chance to break a degeneracy between them. Constraints on α t are estimated from several detections and cosmological observations. Among them, the most stringent one is from the bound of the big bang nucleosynthesis, and requires α t s to be of the same magnitude as α t , if both RGWs and scalar perturbations are generated by the same scalar inflation.

  13. AMS radiocarbon dating of medieval textile relics: The frocks and the pillow of St. Francis of Assisi

    Energy Technology Data Exchange (ETDEWEB)

    Fedi, M.E. [Dipartimento di Fisica dell' Universita di Firenze and INFN Sezione di Firenze, via Sansone 1, 50019 Sesto Fiorentino (Italy)], E-mail: fedi@fi.infn.it; Cartocci, A.; Taccetti, F.; Mando, P.A. [Dipartimento di Fisica dell' Universita di Firenze and INFN Sezione di Firenze, via Sansone 1, 50019 Sesto Fiorentino (Italy)

    2008-05-15

    Since natural textiles usually originate from short-lived organisms, they can represent a useful material to date samples from historical periods with a good accuracy. In this work, we present a set of radiocarbon measurements on medieval textile relics: two woollen habits and a pillow traditionally associated with St. Francis of Assisi, the saint patron of Italy. The strategy in choosing samples for radiocarbon dating is first discussed and the procedures for measurements - performed at the 3 MV Tandetron accelerator of Laboratorio di Tecniche Nucleari per i Beni Culturali (LABEC), Florence - are described; AMS results for the two frocks showed that only one of them, presently kept in the church of St. Francis in Cortona, is compatible with the Saint's period of life, as is the pillow also kept in Cortona. Another frock attributed to St. Francis appears to date from at least 80 years after his death. However, the goal of these measurements was not a bare authentication/disconfirmation of the relics; they just represent an example of how scientific analysis can integrate with humanistic studies. Indeed, AMS results, combined with a thorough analysis of the textiles typologies, confirmed the historical hypotheses based on documentary studies and on tradition. The overall conclusions contributed to the decisions taken for conservation, and have as a whole enhanced the religious importance of the relics.

  14. AMS radiocarbon dating of medieval textile relics: The frocks and the pillow of St. Francis of Assisi

    International Nuclear Information System (INIS)

    Fedi, M.E.; Cartocci, A.; Taccetti, F.; Mando, P.A.

    2008-01-01

    Since natural textiles usually originate from short-lived organisms, they can represent a useful material to date samples from historical periods with a good accuracy. In this work, we present a set of radiocarbon measurements on medieval textile relics: two woollen habits and a pillow traditionally associated with St. Francis of Assisi, the saint patron of Italy. The strategy in choosing samples for radiocarbon dating is first discussed and the procedures for measurements - performed at the 3 MV Tandetron accelerator of Laboratorio di Tecniche Nucleari per i Beni Culturali (LABEC), Florence - are described; AMS results for the two frocks showed that only one of them, presently kept in the church of St. Francis in Cortona, is compatible with the Saint's period of life, as is the pillow also kept in Cortona. Another frock attributed to St. Francis appears to date from at least 80 years after his death. However, the goal of these measurements was not a bare authentication/disconfirmation of the relics; they just represent an example of how scientific analysis can integrate with humanistic studies. Indeed, AMS results, combined with a thorough analysis of the textiles typologies, confirmed the historical hypotheses based on documentary studies and on tradition. The overall conclusions contributed to the decisions taken for conservation, and have as a whole enhanced the religious importance of the relics

  15. AMS radiocarbon dating of medieval textile relics: The frocks and the pillow of St. Francis of Assisi

    Science.gov (United States)

    Fedi, M. E.; Cartocci, A.; Taccetti, F.; Mandò, P. A.

    2008-05-01

    Since natural textiles usually originate from short-lived organisms, they can represent a useful material to date samples from historical periods with a good accuracy. In this work, we present a set of radiocarbon measurements on medieval textile relics: two woollen habits and a pillow traditionally associated with St. Francis of Assisi, the saint patron of Italy. The strategy in choosing samples for radiocarbon dating is first discussed and the procedures for measurements - performed at the 3 MV Tandetron accelerator of Laboratorio di Tecniche Nucleari per i Beni Culturali (LABEC), Florence - are described; AMS results for the two frocks showed that only one of them, presently kept in the church of St. Francis in Cortona, is compatible with the Saint's period of life, as is the pillow also kept in Cortona. Another frock attributed to St. Francis appears to date from at least 80 years after his death. However, the goal of these measurements was not a bare authentication/disconfirmation of the relics; they just represent an example of how scientific analysis can integrate with humanistic studies. Indeed, AMS results, combined with a thorough analysis of the textiles typologies, confirmed the historical hypotheses based on documentary studies and on tradition. The overall conclusions contributed to the decisions taken for conservation, and have as a whole enhanced the religious importance of the relics.

  16. Isolation of two new retrotransposon sequences and development of molecular and cytological markers for Dasypyrum villosum (L.).

    Science.gov (United States)

    Zhang, Jie; Jiang, Yun; Xuan, Pu; Guo, Yuanlin; Deng, Guangbing; Yu, Maoqun; Long, Hai

    2017-10-01

    Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D. villosum accessions. The two SCAR markers and FISH karyotype of D. villosum could be used for efficient and precise identification of D. villosum chromatin in wheat breeding.

  17. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.

    Science.gov (United States)

    Leung, Wilson; Shaffer, Christopher D; Chen, Elizabeth J; Quisenberry, Thomas J; Ko, Kevin; Braverman, John M; Giarla, Thomas C; Mortimer, Nathan T; Reed, Laura K; Smith, Sheryl T; Robic, Srebrenka; McCartha, Shannon R; Perry, Danielle R; Prescod, Lindsay M; Sheppard, Zenyth A; Saville, Ken J; McClish, Allison; Morlock, Emily A; Sochor, Victoria R; Stanton, Brittney; Veysey-White, Isaac C; Revie, Dennis; Jimenez, Luis A; Palomino, Jennifer J; Patao, Melissa D; Patao, Shane M; Himelblau, Edward T; Campbell, Jaclyn D; Hertz, Alexandra L; McEvilly, Maddison F; Wagner, Allison R; Youngblom, James; Bedi, Baljit; Bettincourt, Jeffery; Duso, Erin; Her, Maiye; Hilton, William; House, Samantha; Karimi, Masud; Kumimoto, Kevin; Lee, Rebekah; Lopez, Darryl; Odisho, George; Prasad, Ricky; Robbins, Holly Lyn; Sandhu, Tanveer; Selfridge, Tracy; Tsukashima, Kara; Yosif, Hani; Kokan, Nighat P; Britt, Latia; Zoellner, Alycia; Spana, Eric P; Chlebina, Ben T; Chong, Insun; Friedman, Harrison; Mammo, Danny A; Ng, Chun L; Nikam, Vinayak S; Schwartz, Nicholas U; Xu, Thomas Q; Burg, Martin G; Batten, Spencer M; Corbeill, Lindsay M; Enoch, Erica; Ensign, Jesse J; Franks, Mary E; Haiker, Breanna; Ingles, Judith A; Kirkland, Lyndsay D; Lorenz-Guertin, Joshua M; Matthews, Jordan; Mittig, Cody M; Monsma, Nicholaus; Olson, Katherine J; Perez-Aragon, Guillermo; Ramic, Alen; Ramirez, Jordan R; Scheiber, Christopher; Schneider, Patrick A; Schultz, Devon E; Simon, Matthew; Spencer, Eric; Wernette, Adam C; Wykle, Maxine E; Zavala-Arellano, Elizabeth; McDonald, Mitchell J; Ostby, Kristine; Wendland, Peter; DiAngelo, Justin R; Ceasrine, Alexis M; Cox, Amanda H; Docherty, James E B; Gingras, Robert M; Grieb, Stephanie M; Pavia, Michael J; Personius, Casey L; Polak, Grzegorz L; Beach, Dale L; Cerritos, Heaven L; Horansky, Edward A; Sharif, Karim A; Moran, Ryan; Parrish, Susan; Bickford, Kirsten; Bland, Jennifer; Broussard, Juliana; Campbell, Kerry; Deibel, Katelynn E; Forka, Richard; Lemke, Monika C; Nelson, Marlee B; O'Keeffe, Catherine; Ramey, S Mariel; Schmidt, Luke; Villegas, Paola; Jones, Christopher J; Christ, Stephanie L; Mamari, Sami; Rinaldi, Adam S; Stity, Ghazal; Hark, Amy T; Scheuerman, Mark; Silver Key, S Catherine; McRae, Briana D; Haberman, Adam S; Asinof, Sam; Carrington, Harriette; Drumm, Kelly; Embry, Terrance; McGuire, Richard; Miller-Foreman, Drew; Rosen, Stella; Safa, Nadia; Schultz, Darrin; Segal, Matt; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Skuse, Gary; Paetkau, Don W; Bridgman, Rachael K; Brown, Charlotte M; Carroll, Alicia R; Gifford, Francesca M; Gillespie, Julie Beth; Herman, Susan E; Holtcamp, Krystal L; Host, Misha A; Hussey, Gabrielle; Kramer, Danielle M; Lawrence, Joan Q; Martin, Madeline M; Niemiec, Ellen N; O'Reilly, Ashleigh P; Pahl, Olivia A; Quintana, Guadalupe; Rettie, Elizabeth A S; Richardson, Torie L; Rodriguez, Arianne E; Rodriguez, Mona O; Schiraldi, Laura; Smith, Joanna J; Sugrue, Kelsey F; Suriano, Lindsey J; Takach, Kaitlyn E; Vasquez, Arielle M; Velez, Ximena; Villafuerte, Elizabeth J; Vives, Laura T; Zellmer, Victoria R; Hauke, Jeanette; Hauser, Charles R; Barker, Karolyn; Cannon, Laurie; Parsamian, Perouza; Parsons, Samantha; Wichman, Zachariah; Bazinet, Christopher W; Johnson, Diana E; Bangura, Abubakarr; Black, Jordan A; Chevee, Victoria; Einsteen, Sarah A; Hilton, Sarah K; Kollmer, Max; Nadendla, Rahul; Stamm, Joyce; Fafara-Thompson, Antoinette E; Gygi, Amber M; Ogawa, Emmy E; Van Camp, Matt; Kocsisova, Zuzana; Leatherman, Judith L; Modahl, Cassie M; Rubin, Michael R; Apiz-Saab, Susana S; Arias-Mejias, Suzette M; Carrion-Ortiz, Carlos F; Claudio-Vazquez, Patricia N; Espada-Green, Debbie M; Feliciano-Camacho, Marium; Gonzalez-Bonilla, Karina M; Taboas-Arroyo, Mariela; Vargas-Franco, Dorianmarie; Montañez-Gonzalez, Raquel; Perez-Otero, Joseph; Rivera-Burgos, Myrielis; Rivera-Rosario, Francisco J; Eisler, Heather L; Alexander, Jackie; Begley, Samatha K; Gabbard, Deana; Allen, Robert J; Aung, Wint Yan; Barshop, William D; Boozalis, Amanda; Chu, Vanessa P; Davis, Jeremy S; Duggal, Ryan N; Franklin, Robert; Gavinski, Katherine; Gebreyesus, Heran; Gong, Henry Z; Greenstein, Rachel A; Guo, Averill D; Hanson, Casey; Homa, Kaitlin E; Hsu, Simon C; Huang, Yi; Huo, Lucy; Jacobs, Sarah; Jia, Sasha; Jung, Kyle L; Wai-Chee Kong, Sarah; Kroll, Matthew R; Lee, Brandon M; Lee, Paul F; Levine, Kevin M; Li, Amy S; Liu, Chengyu; Liu, Max Mian; Lousararian, Adam P; Lowery, Peter B; Mallya, Allyson P; Marcus, Joseph E; Ng, Patrick C; Nguyen, Hien P; Patel, Ruchik; Precht, Hashini; Rastogi, Suchita; Sarezky, Jonathan M; Schefkind, Adam; Schultz, Michael B; Shen, Delia; Skorupa, Tara; Spies, Nicholas C; Stancu, Gabriel; Vivian Tsang, Hiu Man; Turski, Alice L; Venkat, Rohit; Waldman, Leah E; Wang, Kaidi; Wang, Tracy; Wei, Jeffrey W; Wu, Dennis Y; Xiong, David D; Yu, Jack; Zhou, Karen; McNeil, Gerard P; Fernandez, Robert W; Menzies, Patrick Gomez; Gu, Tingting; Buhler, Jeremy; Mardis, Elaine R; Elgin, Sarah C R

    2017-08-07

    The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster , but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes ( e.g. , larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster , the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains. Copyright © 2017 Leung et al.

  18. The reverse transcriptase encoded by LINE-1 retrotransposons in the genesis, progression and therapy of cancer

    Directory of Open Access Journals (Sweden)

    Ilaria eSciamanna

    2016-02-01

    Full Text Available In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1 retrotransposons represent a large family of repeated genomic elements. They transpose using a reverse transcriptase (RT, which they encode as part of the ORF2p product. RT inhibition in cancer cells, either via RNA interference-dependent silencing of active LINE-1 elements, or using RT inhibitory drugs, reduces cancer cell proliferation, promotes their differentiation and antagonizes tumor progression in animal models. Indeed, the nonnucleoside RT inhibitor efavirenz has recently been tested in a phase II clinical trial with metastatic prostate cancer patients. An in-depth analysis of ORF2p in a mouse model of breast cancer showed ORF2p to be precociously expressed in precancerous lesions and highly abundant in advanced cancer stages, while being barely detectable in normal breast tissue, providing a rationale for the finding that RT-expressing tumours are therapeutically sensitive to RT inhibitors. We summarise mechanistic and gene profiling studies indicating that highly abundant LINE-1-derived RT can sequester RNA substrates for reverse transcription in tumor cells, entailing the formation of RNA:DNA hybrid molecules and impairing the overall production of regulatory miRNAs, with a global impact on the cell transcriptome. Based on these data, LINE-1-ORF2 encoded RT has a tumor-promoting potential that is exerted at an epigenetic level. We propose a model whereby LINE1-RT drives a previously unrecognized global regulatory process, the deregulation of which drives cell transformation and tumorigenesis and possibly implicated in cancer cell heterogeneity.

  19. The reverse transcriptase encoded by LINE-1 retrotransposons in the genesis, progression and therapy of cancer

    Science.gov (United States)

    Sciamanna, Ilaria; De Luca, Chiara; Spadafora, Corrado

    2016-02-01

    In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons represent a large family of repeated genomic elements. They transpose using a reverse transcriptase (RT), which they encode as part of the ORF2p product. RT inhibition in cancer cells, either via RNA interference-dependent silencing of active LINE-1 elements, or using RT inhibitory drugs, reduces cancer cell proliferation, promotes their differentiation and antagonizes tumor progression in animal models. Indeed, the nonnucleoside RT inhibitor efavirenz has recently been tested in a phase II clinical trial with metastatic prostate cancer patients. An in-depth analysis of ORF2p in a mouse model of breast cancer showed ORF2p to be precociously expressed in precancerous lesions and highly abundant in advanced cancer stages, while being barely detectable in normal breast tissue, providing a rationale for the finding that RT-expressing tumours are therapeutically sensitive to RT inhibitors. We summarise mechanistic and gene profiling studies indicating that highly abundant LINE-1-derived RT can “sequester” RNA substrates for reverse transcription in tumor cells, entailing the formation of RNA:DNA hybrid molecules and impairing the overall production of regulatory miRNAs, with a global impact on the cell transcriptome. Based on these data, LINE-1-ORF2 encoded RT has a tumor-promoting potential that is exerted at an epigenetic level. We propose a model whereby LINE1-RT drives a previously unrecognized global regulatory process, the deregulation of which drives cell transformation and tumorigenesis and possibly implicated in cancer cell heterogeneity.

  20. 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

    2012-01-01

    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. PMID:22913491

  1. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

    Directory of Open Access Journals (Sweden)

    Wilson Leung

    2017-08-01

    Full Text Available The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons are major contributors to this expansion (78.6%, while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%. Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias, but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5′ ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2, while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.

  2. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

    Science.gov (United States)

    Shaffer, Christopher D.; Chen, Elizabeth J.; Quisenberry, Thomas J.; Ko, Kevin; Braverman, John M.; Giarla, Thomas C.; Mortimer, Nathan T.; Reed, Laura K.; Smith, Sheryl T.; Robic, Srebrenka; McCartha, Shannon R.; Perry, Danielle R.; Prescod, Lindsay M.; Sheppard, Zenyth A.; Saville, Ken J.; McClish, Allison; Morlock, Emily A.; Sochor, Victoria R.; Stanton, Brittney; Veysey-White, Isaac C.; Revie, Dennis; Jimenez, Luis A.; Palomino, Jennifer J.; Patao, Melissa D.; Patao, Shane M.; Himelblau, Edward T.; Campbell, Jaclyn D.; Hertz, Alexandra L.; McEvilly, Maddison F.; Wagner, Allison R.; Youngblom, James; Bedi, Baljit; Bettincourt, Jeffery; Duso, Erin; Her, Maiye; Hilton, William; House, Samantha; Karimi, Masud; Kumimoto, Kevin; Lee, Rebekah; Lopez, Darryl; Odisho, George; Prasad, Ricky; Robbins, Holly Lyn; Sandhu, Tanveer; Selfridge, Tracy; Tsukashima, Kara; Yosif, Hani; Kokan, Nighat P.; Britt, Latia; Zoellner, Alycia; Spana, Eric P.; Chlebina, Ben T.; Chong, Insun; Friedman, Harrison; Mammo, Danny A.; Ng, Chun L.; Nikam, Vinayak S.; Schwartz, Nicholas U.; Xu, Thomas Q.; Burg, Martin G.; Batten, Spencer M.; Corbeill, Lindsay M.; Enoch, Erica; Ensign, Jesse J.; Franks, Mary E.; Haiker, Breanna; Ingles, Judith A.; Kirkland, Lyndsay D.; Lorenz-Guertin, Joshua M.; Matthews, Jordan; Mittig, Cody M.; Monsma, Nicholaus; Olson, Katherine J.; Perez-Aragon, Guillermo; Ramic, Alen; Ramirez, Jordan R.; Scheiber, Christopher; Schneider, Patrick A.; Schultz, Devon E.; Simon, Matthew; Spencer, Eric; Wernette, Adam C.; Wykle, Maxine E.; Zavala-Arellano, Elizabeth; McDonald, Mitchell J.; Ostby, Kristine; Wendland, Peter; DiAngelo, Justin R.; Ceasrine, Alexis M.; Cox, Amanda H.; Docherty, James E.B.; Gingras, Robert M.; Grieb, Stephanie M.; Pavia, Michael J.; Personius, Casey L.; Polak, Grzegorz L.; Beach, Dale L.; Cerritos, Heaven L.; Horansky, Edward A.; Sharif, Karim A.; Moran, Ryan; Parrish, Susan; Bickford, Kirsten; Bland, Jennifer; Broussard, Juliana; Campbell, Kerry; Deibel, Katelynn E.; Forka, Richard; Lemke, Monika C.; Nelson, Marlee B.; O'Keeffe, Catherine; Ramey, S. Mariel; Schmidt, Luke; Villegas, Paola; Jones, Christopher J.; Christ, Stephanie L.; Mamari, Sami; Rinaldi, Adam S.; Stity, Ghazal; Hark, Amy T.; Scheuerman, Mark; Silver Key, S. Catherine; McRae, Briana D.; Haberman, Adam S.; Asinof, Sam; Carrington, Harriette; Drumm, Kelly; Embry, Terrance; McGuire, Richard; Miller-Foreman, Drew; Rosen, Stella; Safa, Nadia; Schultz, Darrin; Segal, Matt; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Skuse, Gary; Paetkau, Don W.; Bridgman, Rachael K.; Brown, Charlotte M.; Carroll, Alicia R.; Gifford, Francesca M.; Gillespie, Julie Beth; Herman, Susan E.; Holtcamp, Krystal L.; Host, Misha A.; Hussey, Gabrielle; Kramer, Danielle M.; Lawrence, Joan Q.; Martin, Madeline M.; Niemiec, Ellen N.; O'Reilly, Ashleigh P.; Pahl, Olivia A.; Quintana, Guadalupe; Rettie, Elizabeth A.S.; Richardson, Torie L.; Rodriguez, Arianne E.; Rodriguez, Mona O.; Schiraldi, Laura; Smith, Joanna J.; Sugrue, Kelsey F.; Suriano, Lindsey J.; Takach, Kaitlyn E.; Vasquez, Arielle M.; Velez, Ximena; Villafuerte, Elizabeth J.; Vives, Laura T.; Zellmer, Victoria R.; Hauke, Jeanette; Hauser, Charles R.; Barker, Karolyn; Cannon, Laurie; Parsamian, Perouza; Parsons, Samantha; Wichman, Zachariah; Bazinet, Christopher W.; Johnson, Diana E.; Bangura, Abubakarr; Black, Jordan A.; Chevee, Victoria; Einsteen, Sarah A.; Hilton, Sarah K.; Kollmer, Max; Nadendla, Rahul; Stamm, Joyce; Fafara-Thompson, Antoinette E.; Gygi, Amber M.; Ogawa, Emmy E.; Van Camp, Matt; Kocsisova, Zuzana; Leatherman, Judith L.; Modahl, Cassie M.; Rubin, Michael R.; Apiz-Saab, Susana S.; Arias-Mejias, Suzette M.; Carrion-Ortiz, Carlos F.; Claudio-Vazquez, Patricia N.; Espada-Green, Debbie M.; Feliciano-Camacho, Marium; Gonzalez-Bonilla, Karina M.; Taboas-Arroyo, Mariela; Vargas-Franco, Dorianmarie; Montañez-Gonzalez, Raquel; Perez-Otero, Joseph; Rivera-Burgos, Myrielis; Rivera-Rosario, Francisco J.; Eisler, Heather L.; Alexander, Jackie; Begley, Samatha K.; Gabbard, Deana; Allen, Robert J.; Aung, Wint Yan; Barshop, William D.; Boozalis, Amanda; Chu, Vanessa P.; Davis, Jeremy S.; Duggal, Ryan N.; Franklin, Robert; Gavinski, Katherine; Gebreyesus, Heran; Gong, Henry Z.; Greenstein, Rachel A.; Guo, Averill D.; Hanson, Casey; Homa, Kaitlin E.; Hsu, Simon C.; Huang, Yi; Huo, Lucy; Jacobs, Sarah; Jia, Sasha; Jung, Kyle L.; Wai-Chee Kong, Sarah; Kroll, Matthew R.; Lee, Brandon M.; Lee, Paul F.; Levine, Kevin M.; Li, Amy S.; Liu, Chengyu; Liu, Max Mian; Lousararian, Adam P.; Lowery, Peter B.; Mallya, Allyson P.; Marcus, Joseph E.; Ng, Patrick C.; Nguyen, Hien P.; Patel, Ruchik; Precht, Hashini; Rastogi, Suchita; Sarezky, Jonathan M.; Schefkind, Adam; Schultz, Michael B.; Shen, Delia; Skorupa, Tara; Spies, Nicholas C.; Stancu, Gabriel; Vivian Tsang, Hiu Man; Turski, Alice L.; Venkat, Rohit; Waldman, Leah E.; Wang, Kaidi; Wang, Tracy; Wei, Jeffrey W.; Wu, Dennis Y.; Xiong, David D.; Yu, Jack; Zhou, Karen; McNeil, Gerard P.; Fernandez, Robert W.; Menzies, Patrick Gomez; Gu, Tingting; Buhler, Jeremy; Mardis, Elaine R.; Elgin, Sarah C.R.

    2017-01-01

    The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5′ ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains. PMID:28667019

  3. Advances in research on protection of stone relics by science and technology methods%石质文物科技保护研究进展

    Institute of Scientific and Technical Information of China (English)

    叶良; 李强强; 孙平平

    2016-01-01

    总结了石质文物病害机理研究及病害检测技术、石质文物清洗方法、石质文物保护材料、石质文物监测方法、现代化信息技术,在石质文物科技保护中的应用等方面的研究现状和取得的重要成就,并针对石质文物科技保护在保护材料、仪器设备等方面现存的问题提出了一些建议。%This paper summarized research situation and great achievements obtained in stone cultural relics disease mechanism research and disease detection technology ,stone cultural relics cleaning method ,materials for stone cultural relics conservation ,stone cultural relics monitoring method ,the application of modern information technology in stone cultural relics protection . Based on that ,some suggestions are put forward for the problems existed in protection of stone relics by science and technology methods in protective materials ,equipment and other aspects .

  4. Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

    Directory of Open Access Journals (Sweden)

    Xueli Zhang

    Full Text Available Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP, sequence-specific amplification polymorphism (SSAP and methylation-sensitive amplified polymorphism (MSAP were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8% and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

  5. Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

    Science.gov (United States)

    Zhang, Xueli; Ge, Xianhong; Shao, Yujiao; Sun, Genlou; Li, Zaiyun

    2013-01-01

    Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

  6. Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress.

    Science.gov (United States)

    Servant, Géraldine; Pinson, Benoit; Tchalikian-Cosson, Aurélie; Coulpier, Fanny; Lemoine, Sophie; Pennetier, Carole; Bridier-Nahmias, Antoine; Todeschini, Anne Laure; Fayol, Hélène; Daignan-Fornier, Bertrand; Lesage, Pascale

    2012-07-01

    Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.

  7. A population of relic intermediate-mass black holes in the halo of the Milky Way

    International Nuclear Information System (INIS)

    Rashkov, Valery; Madau, Piero

    2014-01-01

    If 'seed' central black holes were common in the subgalactic building blocks that merged to form present-day massive galaxies, then relic intermediate-mass black holes (IMBHs) should be present in the Galactic bulge and halo. We use a particle tagging technique to dynamically populate the N-body Via Lactea II high-resolution simulation with black holes, and assess the size, properties, and detectability of the leftover population. The method assigns a black hole to the most tightly bound central particle of each subhalo at infall according to an extrapolation of the M BH -σ * relation, and self-consistently follows the accretion and disruption of Milky Way progenitor dwarfs and their holes in a cosmological 'live' host from high redshift to today. We show that, depending on the minimum stellar velocity dispersion, σ m , below which central black holes are assumed to be increasingly rare, as many as ∼2000 (σ m = 3 km s –1 ) or as few as ∼70 (σ m = 12 km s –1 ) IMBHs may be left wandering in the halo of the Milky Way today. The fraction of IMBHs forced from their hosts by gravitational recoil is ≲ 20%. We identify two main Galactic subpopulations, 'naked' IMBHs, whose host subhalos were totally destroyed after infall, and 'clothed' IMBHs residing in dark matter satellites that survived tidal stripping. Naked IMBHs typically constitute 40%-50% of the total and are more centrally concentrated. We show that, in the σ m = 12 km s –1 scenario, the clusters of tightly bound stars that should accompany naked IMBHs would be fainter than m V = 16 mag, spatially resolvable, and have proper motions of 0.1-10 mas yr –1 . Their detection may provide an observational tool to constrain the formation history of massive black holes in the early universe.

  8. Relic right-handed Dirac neutrinos and implications for detection of cosmic neutrino background

    Directory of Open Access Journals (Sweden)

    Jue Zhang

    2016-02-01

    Full Text Available It remains to be determined experimentally if massive neutrinos are Majorana or Dirac particles. In this connection, it has been recently suggested that the detection of cosmic neutrino background of left-handed neutrinos νL and right-handed antineutrinos ν‾R in future experiments of neutrino capture on beta-decaying nuclei (e.g., νe+H3→He3+e− for the PTOLEMY experiment is likely to distinguish between Majorana and Dirac neutrinos, since the capture rate is twice larger in the former case. In this paper, we investigate the possible impact of right-handed neutrinos on the capture rate, assuming that massive neutrinos are Dirac particles and both right-handed neutrinos νR and left-handed antineutrinos ν‾L can be efficiently produced in the early Universe. It turns out that the capture rate can be enhanced at most by 28% due to the presence of relic νR and ν‾L with a total number density of 95 cm−3, which should be compared to the number density 336 cm−3 of cosmic neutrino background. The enhancement has actually been limited by the latest cosmological and astrophysical bounds on the effective number of neutrino generations Neff=3.14−0.43+0.44 at the 95% confidence level. For illustration, two possible scenarios have been proposed for thermal production of right-handed neutrinos in the early Universe.

  9. Digging for red nuggets: discovery of hot halos surrounding massive, compact, relic galaxies

    Science.gov (United States)

    Werner, N.; Lakhchaura, K.; Canning, R. E. A.; Gaspari, M.; Simionescu, A.

    2018-04-01

    We present the results of Chandra X-ray observations of the isolated, massive, compact, relic galaxies MRK 1216 and PGC 032873. Compact massive galaxies observed at z > 2, also called red nuggets, formed in quick dissipative events and later grew by dry mergers into the local giant ellipticals. Due to the stochastic nature of mergers, a few of the primordial massive galaxies avoided the mergers and remained untouched over cosmic time. We find that the hot atmosphere surrounding MRK 1216 extends far beyond the stellar population and has an 0.5-7 keV X-ray luminosity of LX = (7.0 ± 0.2) × 1041 erg s-1, which is similar to the nearby X-ray bright giant ellipticals. The hot gas has a short central cooling time of ˜50 Myr and the galaxy has a ˜13 Gyr old stellar population. The presence of an X-ray atmosphere with a short nominal cooling time and the lack of young stars indicate the presence of a sustained heating source, which prevented star formation since the dissipative origin of the galaxy 13 Gyrs ago. The central temperature peak and the presence of radio emission in the core of the galaxy indicate that the heating source is radio-mechanical AGN feedback. Given that both MRK 1216 and PGC 032873 appear to have evolved in isolation, the order of magnitude difference in their current X-ray luminosity could be traced back to a difference in the ferocity of the AGN outbursts in these systems. Finally, we discuss the potential connection between the presence of hot halos around such massive galaxies and the growth of super/over-massive black holes via chaotic cold accretion.

  10. The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements

    Directory of Open Access Journals (Sweden)

    Morales Maria E

    2005-02-01

    Full Text Available Abstract Background Of the major families of long terminal repeat (LTR retrotransposons, the Pao/BEL family is probably the least well studied. It is becoming apparent that numerous LTR retrotransposons and other mobile genetic elements have colonized the genome of the human blood fluke, Schistosoma mansoni. Results A proviral form of Sinbad, a new LTR retrotransposon, was identified in the genome of S. mansoni. Phylogenetic analysis indicated that Sinbad belongs to one of five discreet subfamilies of Pao/BEL like elements. BLAST searches of whole genomes and EST databases indicated that members of this clade occurred in species of the Insecta, Nematoda, Echinodermata and Chordata, as well as Platyhelminthes, but were absent from all plants, fungi and lower eukaryotes examined. Among the deuterostomes examined, only aquatic species harbored these types of elements. All four species of nematode examined were positive for Sinbad sequences, although among insect and vertebrate genomes, some were positive and some negative. The full length, consensus Sinbad retrotransposon was 6,287 bp long and was flanked at its 5'- and 3'-ends by identical LTRs of 386 bp. Sinbad displayed a triple Cys-His RNA binding motif characteristic of Gag of Pao/BEL-like elements, followed by the enzymatic domains of protease, reverse transcriptase (RT, RNAseH, and integrase, in that order. A phylogenetic tree of deduced RT sequences from 26 elements revealed that Sinbad was most closely related to an unnamed element from the zebrafish Danio rerio and to Saci-1, also from S. mansoni. It was also closely related to Pao from Bombyx mori and to Ninja of Drosophila simulans. Sinbad was only distantly related to the other schistosome LTR retrotransposons Boudicca, Gulliver, Saci-2, Saci-3, and Fugitive, which are gypsy-like. Southern hybridization and bioinformatics analyses indicated that there were about 50 copies of Sinbad in the S. mansoni genome. The presence of ESTs

  11. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L.

    Science.gov (United States)

    2013-01-01

    Background Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features of copia-type retrotransposons as ideal genetic tools for gene tagging, mutagenesis, and marker-assisted selection, they have not been characterized in the jatropha genome yet. Here, we examined the diversity, evolution, and genome-wide organization of copia-type retrotransposons in the Asian, African, and Mesoamerican accessions of jatropha, then introduced a retrotransposon-based marker for this biofuel crop. Results In total, 157 PCR fragments that were amplified using the degenerate primers for the reverse transcriptase (RT) domain of copia-type retroelements were sequenced and aligned to construct the neighbor-joining tree. Phylogenetic analysis demonstrated that isolated copia RT sequences were classified into ten families, which were then grouped into three lineages. An in-depth study of the jatropha genome for the RT sequences of each family led to the characterization of full consensus sequences of the jatropha copia-type families. Estimated copy numbers of target sequences were largely different among families, as was presence of genes within 5 kb flanking regions for each family. Five copia-type families were as appealing candidates for the development of DNA marker systems. A candidate marker from family Jc7 was particularly capable of detecting genetic variation among different jatropha accessions. Fluorescence in situ hybridization (FISH) to metaphase chromosomes reveals that copia-type retrotransposons are scattered across chromosomes mainly located in the distal part regions. Conclusion This is the first report on genome-wide analysis and the cytogenetic mapping of copia-type retrotransposons of jatropha, leading to the discovery of families bearing high potential as DNA

  12. Relics, miracles and furta sacra: A contribution to the study of Serbo-Bulgarian relations in the 1230s

    Directory of Open Access Journals (Sweden)

    Marjanović-Dušanić Smilja

    2009-01-01

    Full Text Available A contribution to the study of Serbo-Bulgarian relations in the 1230s The enquiry into the cult of relics and its manifestations such as miracle working, transfer of mortal remains and the act of translatio that involves the topos of furta sacra relies on two lives of St Sava of Serbia, one penned by Domentijan (Domentianus, the other by Teodosije (Theodosius. The hagiographic episodes most relevant to this enquiry are certainly those describing Sava's stay in Tirnovo, his death (1236 and the translation of his remains to his homeland (1237. The narrative about the future saint's stay and death in Tirnovo gives conscious hints of the hero's sanctity using various hagiographic devices. Especially interesting to us is the account of the miracle Sava worked in Tirnovo while officiating the Epiphany service at the church of the Forty Martyrs. According to our analysis, the reference to the Epiphany service and the association of the miracle with that particular feast are certainly not an accident. The ideology of the Second Bulgarian Empire attached great importance to the epic victory over the Romaioi at the Battle of Tryavna in 1190, which was commemorated annually on the Day of Epiphany. The Byzantine historians Niketas Choniates and George Akropolites report that the Bulgarians seized the imperial insignia during the battle. It is irrelevant whether Sava's two hagiographers were aware of the importance of the feast or simply reiterated the well-known information about the service celebrated on that day at the church of the Forty Martyrs; what is quite certain is that the great honour of officiating the service-a celebration pregnant with symbolism-was bestowed upon the most distinguished guest and that it was then that, we believe not at all by chance, his miracle-working power was manifested in public-in front of the Bulgarian tsar, all clergy and the notables. As a natural consequence of the power of working miracles manifested in one

  13. Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.

    Science.gov (United States)

    Sharma, Vishakha; Nandineni, Madhusudan R

    2014-04-01

    Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485-0.971) as compared to IRAP (0.69-0.911) and REMAP (0.713-0.947). A Mantel's matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0

  14. Updated Reach of the CERN LHC and Constraints from Relic Density, $b \\to s\\gamma$ and $a_{\\mu}$ in the mSUGRA Model

    CERN Document Server

    Baer, Howard W; Belyaev, A; Krupovnickas, T; Tata, Xerxes; Baer, Howard; Balazs, Csaba; Belyaev, Alexander; Krupovnickas, Tadas; Tata, Xerxes

    2003-01-01

    We present an updated assessment of the reach of the CERN LHC pp collider for supersymmetric matter in the context of the minimal supergravity (mSUGRA) model. In addition to previously examined channels, we also include signals with an isolated photon or with a leptonically decaying Z boson. For an integrated luminosity of 100 fb-1, values of m_{1/2}\\sim 1400 GeV can be probed for small m_0, corresponding to a gluino mass of m_{\\tg}\\sim 3 TeV. For large m_0, in the hyperbolic branch/focus point region, m_{1/2}\\sim 700 GeV can be probed, corresponding to m_{\\tg}\\sim 1800 GeV. We also map out parameter space regions preferred by the measured values of the dark matter relic density, the b\\to s\\gamma decay rate, and the muon anomalous magnetic moment a_\\mu, and discuss how SUSY might reveal itself in these regions.

  15. From direct detection to relic abundance: the case of proton-philic spin-dependent inelastic Dark Matter

    Energy Technology Data Exchange (ETDEWEB)

    Scopel, Stefano; Yu, Hyeonhye, E-mail: scopel@sogang.ac.kr, E-mail: skyh2yu@gmail.com [Department of Physics, Sogang University, Seoul (Korea, Republic of)

    2017-04-01

    We discuss strategies to make inferences on the thermal relic abundance of a Weakly Interacting Massive Particle (WIMP) when the same effective dimension-six operator that explains an experimental excess in direct detection is assumed to drive decoupling at freeze-out, and apply them to the explicit scenario of WIMP inelastic up-scattering with spin-dependent couplings to protons (proton-philic Spin-dependent Inelastic Dark Matter, pSIDM), a phenomenological set-up containing two Dark Matter (DM) particles χ{sub 1} and χ{sub 2} with masses m {sub χ}= m {sub χ{sub 1}} and m {sub χ{sub 2}}= m {sub χ}+δ that we have shown in a previous paper to explain the DAMA effect in compliance with the constraints from other detectors. We also update experimental constraints on pSIDM, extend the analysis to the most general spin-dependent momentum-dependent interactions allowed by non-relativistic Effective Field Theory (EFT), and consider for the WIMP velocity distribution in our Galaxy f ( v ) both a halo-independent approach and a standard Maxwellian. Under these conditions we find that the DAMA effect can be explained in terms of the particle χ{sub 1} in compliance with all the other constraints for all the analyzed EFT couplings and also for a Maxwellian f ( v ). As far as the relic abundance is concerned, we show that the problem of calculating it by using direct detection data to fix the model parameters is affected by a strong sensitivity on f ( v ) and by the degeneracy between the WIMP local density ρ{sub χ} and the WIMP-nucleon scattering cross section, since ρ{sub χ} must be rescaled with respect to the observed DM density in the neighborhood of the Sun when the calculated relic density Ω is smaller than the observed one Ω{sub 0}. As a consequence, a DM direct detection experiment is not directly sensitive to the physical cut-off scale of the EFT, but on some dimensional combination that does not depend on the actual value of Ω. However, such degeneracy

  16. micrOMEGAs 2.0.7: a program to calculate the relic density of dark matter in a generic model

    Science.gov (United States)

    Bélanger, G.; Boudjema, F.; Pukhov, A.; Semenov, A.

    2007-12-01

    micrOMEGAs2.0.7 is a code which calculates the relic density of a stable massive particle in an arbitrary model. The underlying assumption is that there is a conservation law like R-parity in supersymmetry which guarantees the stability of the lightest odd particle. The new physics model must be incorporated in the notation of CalcHEP, a package for the automatic generation of squared matrix elements. Once this is done, all annihilation and coannihilation channels are included automatically in any model. Cross-sections at v=0, relevant for indirect detection of dark matter, are also computed automatically. The package includes three sample models: the minimal supersymmetric standard model (MSSM), the MSSM with complex phases and the NMSSM. Extension to other models, including non supersymmetric models, is described. Program summaryTitle of program:micrOMEGAs2.0.7 Catalogue identifier:ADQR_v2_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADQR_v2_1.html Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.:216 529 No. of bytes in distributed program, including test data, etc.:1 848 816 Distribution format:tar.gz Programming language used:C and Fortran Computer:PC, Alpha, Mac, Sun Operating system:UNIX (Linux, OSF1, SunOS, Darwin, Cygwin) RAM:17 MB depending on the number of processes required Classification:1.9, 11.6 Catalogue identifier of previous version:ADQR_v2_0 Journal version of previous version:Comput. Phys. Comm. 176 (2007) 367 Does the new version supersede the previous version?:Yes Nature of problem:Calculation of the relic density of the lightest stable particle in a generic new model of particle physics. Solution method:In numerically solving the evolution equation for the density of dark matter, relativistic formulae for the thermal average are used. All tree

  17. The Effect of Pulsed Streamer-like Discharge in Liquid on Transcriptional Activation of Retrotransposon Genes of a Red Alga, Porphyra Yezoensis

    OpenAIRE

    Ohno, T.; Li, Z.; Lin, X.F.; Zhang, W.B.; Takano, H.; Takio, S.; Namihira, T.; Akiyama, H.; オオノ, ツヨシ; ナミヒラ, タカオ; アキヤマ, ヒデノリ; 大野, 剛史; 浪平, 隆男; 秋山, 秀典

    2007-01-01

    Retrotransposons are mobile genetic elements thataccomplished transposition via an RNA intermediate.These elements can be transcriptionally activated by stressfactors, such as UV light, ozone, pathogens, woundingand drought. A red alga, porphyra yezoensis has recentlybeen recognized as a model plant for fundamental andapplied study in marine biological science. In this paper,pulsed streamer-like discharge in liquid was used as a newstress condition, and the transcription level of a copia-like...

  18. Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform.

    Science.gov (United States)

    Monden, Yuki; Yamamoto, Ayaka; Shindo, Akiko; Tahara, Makoto

    2014-10-01

    In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2,024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  19. The relic Criollo cacao in Belize- genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad

    Science.gov (United States)

    Cacao (Theobroma cacao L.) is native to the South American rainforest but it was domesticated in Mesoamerica. The relic Criollo cocoa in Belize has been well known in the premium chocolate market for its high-quality. Knowledge of genetic diversity in this variety is essential for efficient conserva...

  20. Impact of SUSY-QCD corrections on neutralino-stop co-annihilation and the neutralino relic density

    Energy Technology Data Exchange (ETDEWEB)

    Harz, Julia [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Herrmann, Bjoern [Savoie Univ./CNRS, Annecy-le-Vieux (France). LAPTh; Klasen, Michael [Muenster Univ. (Germany). Inst. fuer Theoretische Physik 1; Kovarik, Karol [Karlsruher Institut fuer Technologie, Karlsruhe (Germany). Inst. fuer Theoretische Physik; Le Boulc' h, Quentin [Grenoble Univ./CNRS-IN2P3/INPG, Grenoble (France). Lab. de Physique Subatomique et de Cosmologie

    2013-02-15

    We have calculated the full O({alpha}{sub s}) supersymmetric QCD corrections to neutralino-stop coannihilation into electroweak vector and Higgs bosons within the Minimal Supersymmetric Standard Model (MSSM).We performed a parameter study within the phenomenological MSSM and demonstrated that the studied co-annihilation processes are phenomenologically relevant, especially in the context of a 126 GeV Higgs-like particle. By means of an example scenario we discuss the effect of the full next-to-leading order corrections on the co-annihilation cross section and show their impact on the predicted neutralino relic density. We demonstrate that the impact of these corrections on the cosmologically preferred region of parameter space is larger than the current experimental uncertainty of WMAP data.

  1. Detection of relic gravitational waves in thermal case by using Adv.LIGO data of GW150914

    Energy Technology Data Exchange (ETDEWEB)

    Ghayour, Basem [University of Hyderabad, School of Physics, Hyderabad (India); Khodagholizadeh, Jafar [Farhangian University, Tehran (Iran, Islamic Republic of)

    2017-08-15

    The thermal spectrum of relic gravitational waves enhances the usual spectrum. Our analysis shows that there exist some chances for detection of the thermal spectrum in addition to the usual spectrum by comparison with sensitivity of Adv.LIGO of GW150914 and detector based on the maser light. The behavior of the inflation and reheating stages are often known as power law expansion like S(η) ∝ η{sup 1+β}, S(η) ∝ η{sup 1+β{sub s}}, respectively, with constraints 1 + β < 0, 1 + β{sub s} > 0. The β and β{sub s} have an unique effect on the shape of the spectrum. We find some values of the β and β{sub s} by considering the mentioned comparison. As obtained, the results give us more information as regards the evolution of inflation and reheating stages. (orig.)

  2. Big-bang nucleosynthesis and the relic abundance of dark matter in a stau-neutralino coannihilation scenario

    International Nuclear Information System (INIS)

    Jittoh, Toshifumi; Koike, Masafumi; Sato, Joe; Yamanaka, Masato; Kohri, Kazunori; Shimomura, Takashi

    2008-01-01

    A scenario of the big-bang nucleosynthesis is analyzed within the minimal supersymmetric standard model, which is consistent with a stau-neutralino coannihilation scenario to explain the relic abundance of dark matter. We find that we can account for the possible discrepancy of the abundance of 7 Li between the observation and the prediction of the big-bang nucleosynthesis by taking the mass of the neutralino as 300 GeV and the mass difference between the stau and the neutralino as (100-120) MeV. We can therefore simultaneously explain the abundance of the dark matter and that of 7 Li by these values of parameters. The lifetime of staus in this scenario is predicted to be O(100-1000) sec.

  3. Detection of relic gravitational waves in thermal case by using Adv.LIGO data of GW150914

    International Nuclear Information System (INIS)

    Ghayour, Basem; Khodagholizadeh, Jafar

    2017-01-01

    The thermal spectrum of relic gravitational waves enhances the usual spectrum. Our analysis shows that there exist some chances for detection of the thermal spectrum in addition to the usual spectrum by comparison with sensitivity of Adv.LIGO of GW150914 and detector based on the maser light. The behavior of the inflation and reheating stages are often known as power law expansion like S(η) ∝ η"1"+"β, S(η) ∝ η"1"+"β"_s, respectively, with constraints 1 + β 0. The β and β_s have an unique effect on the shape of the spectrum. We find some values of the β and β_s by considering the mentioned comparison. As obtained, the results give us more information as regards the evolution of inflation and reheating stages. (orig.)

  4. Strong lensing analysis of PLCK G004.5-19.5, a Planck-discovered cluster hosting a radio relic at z = 0.52

    Science.gov (United States)

    Sifón, Cristóbal; Menanteau, Felipe; Hughes, John P.; Carrasco, Mauricio; Barrientos, L. Felipe

    2014-02-01

    Context. The recent discovery of a large number of galaxy clusters using the Sunyaev-Zel'dovich (SZ) effect has opened a new era on the study of the most massive clusters in the Universe. Multiwavelength analyses are required to understand the properties of these new sets of clusters, which are a sensitive probe of cosmology. Aims: We aim for a multiwavelength characterization of PLCK G004.5-19.5, one of the most massive X-ray validated SZ effect-selected galaxy clusters discovered by the Planck satellite. Methods: We have observed PLCK G004.5-19.5 with GMOS on the 8.1 m-Gemini South Telescope for optical imaging and spectroscopy, and performed a strong lensing analysis. We also searched for associated radio emission in published catalogs. Results: An analysis of the optical images confirms that this is a massive cluster, with a dominant central galaxy and an accompanying red sequence of galaxies, plus a 14″-long strong lensing arc. Longslit spectroscopy of six cluster members shows that the cluster is at z = 0.516 ± 0.002. We also targeted the strongly lensed arc, and found zarc = 1.601. We use LensTool to carry out a strong lensing analysis, from which we measure a median Einstein radius θE(zs = 1.6) ≃ 30″ and estimate an enclosed mass ME = 2.45-0.47+0.45 × 1014 M⊙. By extrapolating a Navarro-Frenk-White profile, we find a total mass M500SL = 4.0-1.0+2.1 × 1014 M⊙. We also include a constraint on the mass from previous X-ray observations, which yields a slightly higher mass, M500SL+X = 6.7-1.3+2.6 × 1014 M⊙, consistent with the value from strong lensing alone. Intermediate-resolution radio images from the TIFR GMRT Sky Survey at 150 MHz reveal that PLCK G004.5-19.5 hosts a powerful radio relic on scales ≲500 kpc. Emission at the same location is also detected in low-resolution images at 843 MHz and 1.4 GHz. This is one of the higher redshift radio relics known to date. Based on observations obtained at the Gemini Observatory, which is operated

  5. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

    KAUST Repository

    La, Honggui; Ding, Bo; Mishra, Gyan Prakash; Zhou, Bo; Yang, Hongmei; Bellizzi, Maria Del Rosario; Chen, Songbiao; Meyers, Blake C.; Peng, Zhaohua; Zhu, Jian-Kang; Wang, Guoliang

    2011-01-01

    DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counter-act transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.

  6. Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction.

    Science.gov (United States)

    Sookdeo, Akash; Hepp, Crystal M; Boissinot, Stéphane

    2018-01-01

    LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1. We found that multiple L1 lineages, carrying different 5'UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time. The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms.

  7. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

    KAUST Repository

    La, Honggui

    2011-09-06

    DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counter-act transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.

  8. On the Relics of Scytho-Sarmato-Alanian Vocabulary in the Toponymy of Ossetia Voprosy onomastiki, 2018, Volume 15, Issu

    Directory of Open Access Journals (Sweden)

    Yuri A. Dzitstsoity

    2018-03-01

    Full Text Available The article undertakes to pick out the oldest Scythian-Sarmatian-Alanian element in Ossetian toponymy where the appellative lexis that was lost in the language is partly retained. The reconstruction of the ancient Iranian etymons is based on strict data recordings of historical phonetics and historical morphology of the Ossetian language. As a result of the work carried out, such stems as *æf- ‘water, river’, *æfsæn- ‘the top of a mountain’, *dæj- ‘settlement’, *fi jjag- ‘(wild onion’, *fi jjag- ‘running (about water’, *ke- ‘house’, *mærg- ‘meadow’, *zæræ- ‘grass’ and others were reconstructed. Some of them are also present in the appellative lexis as elements of compounds. The analyzed information verifi es the remarkable capacity of toponymy as a keeper of the ancient lexis. And although this line of research is barely touched upon, it is already clear that the relics of the ancient Iranian lexis in the Ossetian toponymy are important both for the history of the Ossetian language and the ethnic history of Ossetia. Common Iranian lexis retained in the Ossetian toponymy came out of use at different times and for various reasons. In most cases, it was replaced by Ossetian neologisms, but some of these stems were substituted by ancient Iranian lexemes which had the status of dialectical words in the ancestor language. Therefore, the Ossetian toponymy, along with compounds and the Nart Epic language, is one of the sources for reconstruction of the ancient Iranian lexis. The geography of relic lexis is another feature of interest: these word forms are equally distributed all over the Ossetian mountain zone, regardless of the contemporary dialect variations of the Ossetian language: the toponym Zæræmæg is present both in Digoria and the Alagir gorge, the hydronym Æræf is attested in Digoria and in South Ossetia.

  9. Stau relic density at the big-bang nucleosynthesis era in the coannihilation scenario and a solution to the Li7 problem

    Science.gov (United States)

    Jittoh, Toshifumi; Kohri, Kazunori; Koike, Masafumi; Sato, Joe; Shimomura, Takashi; Yamanaka, Masato

    2010-12-01

    We calculate the relic density of stau at the big-bang nucleosynthesis era in the coannihilation scenario of the minimal supersymmetric standard model. In this scenario, stau can be long lived and have significance in the remediation of light elements abundances. The freeze-out of stau is corroborated by solving the Boltzmann equation numerically, and the parameter dependence of the relic density is investigated. The possibility of solving the Li7 problem is examined by taking account into the long-lived stau. By adopting an observational value of Li7 in [J. Meléndez and I. Ramírez, Astrophys. J. 615, L33 (2004).ASJOAB0004-637X10.1086/425962], we get minimal supersymmetric standard model parameter space in which abundances of both dark matter and all of the light elements are reproduced in accordance with observations. We also address the influence of intergenerational mixing on our calculation.

  10. Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunfl ower (Helianthus annuus L.) under natural and water-limited states.

    Science.gov (United States)

    Ali, Soleimani Gezeljeh; Darvishzadeh, Reza; Ebrahimi, Asa; Bihamta, Mohammad Reza

    2018-03-01

    Sunflower is an important source of edible oil. Drought is known as an important factor limiting the growth and productivity of field crops in most parts of the world. Agricultural biotechnology mainly aims at developing crops with higher tolerance to the challenging environmental conditions, such as drought. This study examined a number of morphological characters, along with relative water content (RWC) in 100 inbred sunflower lines. A 10 × 10 simple lattice design with two replications was employed to measure the mentioned parameters under natural and water-limited states during two successive years. In molecular trial, 30 simple sequence repeat (SSR) primer pairs, as well as 14 inter-retrotransposon amplified polymorphism (IRAP) and 14 retrotransposon-microsatellite amplified polymorphism (REMAP) primer combinations were used for DNA fingerprinting of the lines. Most of the examined characters had lower average values under water-limited than natural states. Maximum and minimum reductions were observed in the cases of yield and oil percentage, respectively. The broad-sense heritabilities for all the examined characters were 0.20-0.73 and 0.10-0.34 under natural and water-limited states, respectively. In the studied samples, 8.97% of the 435 possible locus pairs of the SSRs represented significant linkage disequilibrium (LD) levels. In the association analysis using SSR markers, 22 and 21 markers were identified (P ≤ 0.05) for the studied characters under natural and water-limited states, respectively. The corresponding values were 50 and 37 using retrotransposon-based molecular markers. Some detected markers were communal between the characters under water-limited and natural states. This was in line with the phenotypic correlations detected between the characters. Communal markers facilitate the simultaneous selection of several characters and can thus improve the efficacy of selection based on markers in the plant-breeding activities.

  11. Comparative studies of the endonucleases from two related Xenopus laevis retrotransposons, Tx1L and Tx2L: target site specificity and evolutionary implications.

    Science.gov (United States)

    Christensen, S; Pont-Kingdon, G; Carroll, D

    2000-01-01

    In the genome of the South African frog, Xenopus laevis, there are two complex families of transposable elements, Tx1 and Tx2, that have identical overall structures, but distinct sequences. In each family there are approximately 1500 copies of an apparent DNA-based element (Tx1D and Tx2D). Roughly 10% of these elements in each family are interrupted by a non-LTR retrotransposon (Tx1L and Tx2L). Each retrotransposon is flanked by a 23-bp target duplication of a specific D element sequence. In earlier work, we showed that the endonuclease domain (Tx1L EN) located in the second open reading frame (ORF2) of Tx1L encodes a protein that makes a single-strand cut precisely at the expected site within its target sequence, supporting the idea that Tx1L is a site-specific retrotransposon. In this study, we express the endonuclease domain of Tx2L (Tx2L EN) and compare the target preferences of the two enzymes. Each endonuclease shows some preference for its cognate target, on the order of 5-fold over the non-cognate target. The observed discrimination is not sufficient, however, to explain the observation that no cross-occupancy is observed - that is, L elements of one family have never been found within D elements of the other family. Possible sources of additional specificity are discussed. We also compare two hypotheses regarding the genome duplication event that led to the contemporary pseudotetraploid character of Xenopus laevis in light of the Tx1L and Tx2L data.

  12. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation.

    Directory of Open Access Journals (Sweden)

    Kristel Kaer

    Full Text Available Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown.Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals.Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.

  13. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

    Directory of Open Access Journals (Sweden)

    Domingues Douglas S

    2012-04-01

    Full Text Available Abstract Background Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Results Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Conclusions Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

  14. Cisovka - the relic population of Abies alba and its relationship to man-made silver-fir stands in Białowieża primeval forest

    Directory of Open Access Journals (Sweden)

    Leon Mejnartowicz

    2014-01-01

    Full Text Available In Białowieża Primeval Forest, in 1823 Stanisław Górski discovered on the Cisovka Hag, a relic population of European silver-fir (Abies alba Mill.. This population is isolated and most away, 120 km to the North-East, from the border of European-silver-fir distribution. Besides the natural population Cisovka, there are also man-made silver fir stands and clumps in the Polish and Belorussian part of Białowieża Primeval Forest. In the Polish part there are four such artificial stands. If the seed-producing silver-fir stands really originated from the Cisovka population, then they are a very valuable part of the declining population and an easy accessible seed source. However, if these populations were introduced to the Białowieża Primeval Forest, then they are a potential source of dangerous genetic pollution of the Cisovka population. The relationship of the genetic structure of the Cisovka population to man-made silver-fir-stands in Białowieża Forest was investigated with the help of 17 loci of 1 1 enzyme systems. Genetic diversity of Cisovka population is characterized by the smallest mean number of alleles per locus (Mal= 1.353, includes all loci studied and per polimorphic locus Malp = 2.00. In Cisovka population there is very low-grade of polimorphic loci (Pp = 11.765 with the mean 37.255 for all studied populations. Expected heterozygosity, He = 0.079 revealed very low-grade of genetic diversity in the population. The observed heterozygosity (Ho = 0.123 was similar to this characterictic in other populations. A dendrogram based on Neis genetic distance coefficient (D among 9 silver-fir populations was constructed. Cisovka in the UPGMA dendrogram is a distinct population separated from other ones by a very great genetic distance (D = 0.06. Also two man-made silver-fir (B I and 132 stands are separated from others. Only populations B3 and B4 are combined into one subgroup linked to the population Tomaszów Lubelski. Basing on the

  15. Complete sequence of Tvv1, a family of Ty 1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking.

    Science.gov (United States)

    Pelsy, F.; Merdinoglu, D.

    2002-09-01

    A chromosome-walking strategy was used to sequence and characterize retrotransposons in the grapevine genome. The reconstitution of a family of retroelements, named Tvv1, was achieved by six successive steps. These elements share a single, highly conserved open reading frame 4,153 nucleotides-long, putatively encoding the gag, pro, int, rt and rh proteins. Comparison of the Tvv1 open reading frame coding potential with those of drosophila copia and tobacco Tnt1, revealed that Tvv1 is closely related to Ty 1 copia-like retrotransposons. A highly variable untranslated leader region, upstream of the open reading frame, allowed us to differentiate Tvv1 variants, which represent a family of at least 28 copies, in varying sizes. This internal region is flanked by two long terminal repeats in direct orientation, sized between 149 and 157 bp. Among elements theoretically sized from 4,970 to 5,550 bp, we describe the full-length sequence of a reference element Tvv1-1, 5,343 nucleotides-long. The full-length sequence of Tvv1-1 compared to pea PDR1 shows a 53.3% identity. In addition, both elements contain long terminal repeats of nearly the same size in which the U5 region could be entirely absent. Therefore, we assume that Tvv1 and PDR1 could constitute a particular class of short LTRs retroelements.

  16. Identification of an Internal Ribosome Entry Segment in the 5′ Region of the Mouse VL30 Retrotransposon and Its Use in the Development of Retroviral Vectors

    Science.gov (United States)

    López-Lastra, Marcelo; Ulrici, Sandrine; Gabus, Caroline; Darlix, Jean-Luc

    1999-01-01

    Mouse virus-like 30S RNAs (VL30m) constitute a family of retrotransposons, present at 100 to 200 copies, dispersed in the mouse genome. They display little sequence homology to Moloney murine leukemia virus (MoMLV), do not encode virus-like proteins, and have not been implicated in retroviral carcinogenesis. However, VL30 RNAs are efficiently packaged into MLV particles that are propagated in cell culture. In this study, we addressed whether the 5′ region of VL30m could replace the 5′ leader of MoMLV functionally in a recombinant vector construct. Our data confirm that the putative packaging sequence of VL30 is located within the 5′ region (nucleotides 362 to 1149 with respect to the cap structure) and that it can replace the packaging sequence of MoMLV. We also show that VL30m contains an internal ribosome entry segment (IRES) in the 5′ region, as do MoMLV, Friend murine leukemia virus, Harvey murine sarcoma virus, and avian reticuloendotheliosis virus type A. Our data show that both the packaging and IRES functions of the 5′ region of VL30m RNA can be efficiently used to develop retrotransposon-based vectors. PMID:10482590

  17. Identification of an internal ribosome entry segment in the 5' region of the mouse VL30 retrotransposon and its use in the development of retroviral vectors.

    Science.gov (United States)

    López-Lastra, M; Ulrici, S; Gabus, C; Darlix, J L

    1999-10-01

    Mouse virus-like 30S RNAs (VL30m) constitute a family of retrotransposons, present at 100 to 200 copies, dispersed in the mouse genome. They display little sequence homology to Moloney murine leukemia virus (MoMLV), do not encode virus-like proteins, and have not been implicated in retroviral carcinogenesis. However, VL30 RNAs are efficiently packaged into MLV particles that are propagated in cell culture. In this study, we addressed whether the 5' region of VL30m could replace the 5' leader of MoMLV functionally in a recombinant vector construct. Our data confirm that the putative packaging sequence of VL30 is located within the 5' region (nucleotides 362 to 1149 with respect to the cap structure) and that it can replace the packaging sequence of MoMLV. We also show that VL30m contains an internal ribosome entry segment (IRES) in the 5' region, as do MoMLV, Friend murine leukemia virus, Harvey murine sarcoma virus, and avian reticuloendotheliosis virus type A. Our data show that both the packaging and IRES functions of the 5' region of VL30m RNA can be efficiently used to develop retrotransposon-based vectors.

  18. Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion.

    Science.gov (United States)

    Leprinc, A S; Grandbastien, M A; Christian, M

    2001-11-01

    Active retrotransposons have been identified in Nicotiana plumbaginifolia by their ability to disrupt the nitrate reductase gene in chlorate-resistant mutants selected from protoplast-derived cultures. In mutants E23 and F97, two independent insertions of Tnp2, a new retrotransposon closely related to the tobacco Tnt1 elements, were detected in the nitrate reductase gene. These two Tnp2 elements are members of the Tnt1B subfamily which shows that Tnt1B elements can be active and mutagenic in the N. plumbaginifolia genome. Furthermore, these results suggest that Tnt1B is the most active family of Tntl elements in N. plumbaginifolia, whereas in tobacco only members of the Tnt1A subfamily were found inserted in the nitrate reductase gene. The transcriptional regulations of Tnp2 and Tnt1A elements are most probably different due to non-conserved U3 regions. Our results thus support the hypothesis that different Nicotiana species contain different active Tntl subfamilies and that only one active Tntl subfamily might be maintained in each of these species. The Tnp2 insertion found in the F97 mutant was found to be spliced out of the nitrate reductase mRNA by activation of cryptic donor and acceptor sites in the nitrate reductase and the Tnp2 sequences respectively.

  19. Asymmetric thermal-relic dark matter: Sommerfeld-enhanced freeze-out, annihilation signals and unitarity bounds

    Energy Technology Data Exchange (ETDEWEB)

    Baldes, Iason [DESY, Notkestraße 85, Hamburg, D-22607 Germany (Germany); Petraki, Kalliopi, E-mail: iason.baldes@desy.de, E-mail: kpetraki@lpthe.jussieu.fr [Laboratoire de Physique Théorique et Hautes Energies (LPTHE), UMR 7589 CNRS and UPMC, 4 Place Jussieu, Paris, F-75252 France (France)

    2017-09-01

    Dark matter that possesses a particle-antiparticle asymmetry and has thermalised in the early universe, requires a larger annihilation cross-section compared to symmetric dark matter, in order to deplete the dark antiparticles and account for the observed dark matter density. The annihilation cross-section determines the residual symmetric component of dark matter, which may give rise to annihilation signals during CMB and inside haloes today. We consider dark matter with long-range interactions, in particular dark matter coupled to a light vector or scalar force mediator. We compute the couplings required to attain a final antiparticle-to-particle ratio after the thermal freeze-out of the annihilation processes in the early universe, and then estimate the late-time annihilation signals. We show that, due to the Sommerfeld enhancement, highly asymmetric dark matter with long-range interactions can have a significant annihilation rate, potentially larger than symmetric dark matter of the same mass with contact interactions. We discuss caveats in this estimation, relating to the formation of stable bound states. Finally, we consider the non-relativistic partial-wave unitarity bound on the inelastic cross-section, we discuss why it can be realised only by long-range interactions, and showcase the importance of higher partial waves in this regime of large inelasticity. We derive upper bounds on the mass of symmetric and asymmetric thermal-relic dark matter for s -wave and p -wave annihilation, and exhibit how these bounds strengthen as the dark asymmetry increases.

  20. Asymmetric thermal-relic dark matter. Sommerfeld-enhanced freeze-out, annihilation signals and unitarity bounds

    International Nuclear Information System (INIS)

    Baldes, Iason; Petraki, Kalliopi

    2017-03-01

    Dark matter that possesses a particle-antiparticle asymmetry and has thermalised in the early universe, requires a larger annihilation cross-section compared to symmetric dark matter, in order to deplete the dark antiparticles and account for the observed dark matter density. The annihilation cross-section determines the residual symmetric component of dark matter, which may give rise to annihilation signals during CMB and inside haloes today. We consider dark matter with long-range interactions, in particular dark matter coupled to a light vector or scalar force mediator. We compute the couplings required to attain a final antiparticle-to-particle ratio after the thermal freeze-out of the annihilation processes in the early universe, and then estimate the late-time annihilation signals. We show that, due to the Sommerfeld enhancement, highly asymmetric dark matter with long-range interactions can have a significant annihilation rate, potentially larger than symmetric dark matter of the same mass with contact interactions. We discuss caveats in this estimation, relating to the formation of stable bound states. Finally, we consider the non-relativistic partial-wave unitarity bound on the inelastic cross-section, we discuss why it can be realised only by long-range interactions, and showcase the importance of higher partial waves in this regime of large inelasticity. We derive upper bounds on the mass of symmetric and asymmetric thermal-relic dark matter for s-wave and p-wave annihilation, and exhibit how these bounds strengthen as the dark asymmetry increases.

  1. Asymmetric thermal-relic dark matter. Sommerfeld-enhanced freeze-out, annihilation signals and unitarity bounds

    Energy Technology Data Exchange (ETDEWEB)

    Baldes, Iason [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Petraki, Kalliopi [Nationaal Instuut voor Kernfysica en Hoge-Energiefysica (NIKHEF), Amsterdam (Netherlands); UMR 7589 CNRS et UPMC, Paris (France). Laboratoire de Physique Theorique et Hautes Energies (LPTHE)

    2017-03-15

    Dark matter that possesses a particle-antiparticle asymmetry and has thermalised in the early universe, requires a larger annihilation cross-section compared to symmetric dark matter, in order to deplete the dark antiparticles and account for the observed dark matter density. The annihilation cross-section determines the residual symmetric component of dark matter, which may give rise to annihilation signals during CMB and inside haloes today. We consider dark matter with long-range interactions, in particular dark matter coupled to a light vector or scalar force mediator. We compute the couplings required to attain a final antiparticle-to-particle ratio after the thermal freeze-out of the annihilation processes in the early universe, and then estimate the late-time annihilation signals. We show that, due to the Sommerfeld enhancement, highly asymmetric dark matter with long-range interactions can have a significant annihilation rate, potentially larger than symmetric dark matter of the same mass with contact interactions. We discuss caveats in this estimation, relating to the formation of stable bound states. Finally, we consider the non-relativistic partial-wave unitarity bound on the inelastic cross-section, we discuss why it can be realised only by long-range interactions, and showcase the importance of higher partial waves in this regime of large inelasticity. We derive upper bounds on the mass of symmetric and asymmetric thermal-relic dark matter for s-wave and p-wave annihilation, and exhibit how these bounds strengthen as the dark asymmetry increases.

  2. Relocation of Intermediate-depth Seismicity in the Relic Alboran Slab: Clustering and Relationship to Tearing and Dehydration Embrittlement.

    Science.gov (United States)

    Sun, M.; Bezada, M.

    2017-12-01

    Intermediate-depth seismicity outside active subduction zones is rare. However, there is a well-known occurrence of such events in a N-S elongated volume between Spain and Morocco, within what most researchers consider to be the relic Alboran slab. Partial subduction of, and tearing from the adjoining continental lithosphere have been suggested in this area. We investigate whether dehydration embrittlement or shear instability is more consistent with the Alboran intermediate depth seismicity by considering their location relative to the expected thermal structure and expected areas of high strain rate associated with thinning or tearing of the slab. We use a dense temporary seismograph deployment in Spain and Morocco to relocate 65 intermediate-depth events occurring between 2010 and 2013 in this region. The relocation procedure is realized by a grid-search approach that minimizes the normalized misfit between the picked times and travel times calculated using a regional 3D velocity model. Results indicate that, compared with catalog results, hypocenters after relocation are more concentrated in space; they tend to shift southward and eastward while no systematic shift in depth is observed. Relocated hypocenters concentrate at a depth range between 50-100 km and along a narrow longitude range around 4.5W. Investigation of the earthquake density distribution indicates these earthquakes concentrate into several clusters. One such cluster sits above the spain-arm of the Alboran slab and beneath the Spain continental lithosphere, indicating that it is likely associated to the thinning process of the Alboran slab. The other four clusters all lie within the interior of the slab. Interestingly, two of them are near the middle of the subducted lithosphere and the other two lie near its base. This observation seems at odds with expectations based on the two leading hypotheses for enabling brittle failure at intermediate depths.

  3. Asymmetric thermal-relic dark matter: Sommerfeld-enhanced freeze-out, annihilation signals and unitarity bounds

    International Nuclear Information System (INIS)

    Baldes, Iason; Petraki, Kalliopi

    2017-01-01

    Dark matter that possesses a particle-antiparticle asymmetry and has thermalised in the early universe, requires a larger annihilation cross-section compared to symmetric dark matter, in order to deplete the dark antiparticles and account for the observed dark matter density. The annihilation cross-section determines the residual symmetric component of dark matter, which may give rise to annihilation signals during CMB and inside haloes today. We consider dark matter with long-range interactions, in particular dark matter coupled to a light vector or scalar force mediator. We compute the couplings required to attain a final antiparticle-to-particle ratio after the thermal freeze-out of the annihilation processes in the early universe, and then estimate the late-time annihilation signals. We show that, due to the Sommerfeld enhancement, highly asymmetric dark matter with long-range interactions can have a significant annihilation rate, potentially larger than symmetric dark matter of the same mass with contact interactions. We discuss caveats in this estimation, relating to the formation of stable bound states. Finally, we consider the non-relativistic partial-wave unitarity bound on the inelastic cross-section, we discuss why it can be realised only by long-range interactions, and showcase the importance of higher partial waves in this regime of large inelasticity. We derive upper bounds on the mass of symmetric and asymmetric thermal-relic dark matter for s -wave and p -wave annihilation, and exhibit how these bounds strengthen as the dark asymmetry increases.

  4. [Effects of relic microorganism B. sp. on development, gaseous exchange, spontaneous motor activity, stress resistance and survival of Drosophila melanogaster].

    Science.gov (United States)

    Brushkov, A V; Bezrukov, V V; Griva, G I; Muradian, Kh K

    2011-01-01

    The effect of relic microorganism B. sp., living in severe environment of Siberian permafrost during thousands and millions of years, on development and stress resistance of Drosophila melanogaster has been studied. In manipulating with such objects with practically "eternal life span", molecular carriers of the unprecedented longevity potential and possibilities of their transmission to other biological objects should primarily be addressed. Here we discuss for the first time the influence of B. sp. application on development, survival, stress resistance and the gross physiological predictors of aging rate in D. melanogaster. To establish optimal and toxic doses, wide range of B. sp. concentrations were tested (1-500 million cells of B. sp. per 1 ml of the flies feeding medium). Surprisingly, no toxic effects of B. sp. could be registered even on such a "sensitive" model as the developing larvae. In fact, the rate of development, survival and body mass gradually increased with elevation of B. sp. concentration. The gain of higher body mass within shorter periods of development could indicate enhanced anabolic and/ or declined catabolic effects of B. sp. Higher motor activity and gaseous exchange rates were observed in imagoes developed on the mediums with B. sp. application. Survival of these flies at the heat shock (30 min at 38 degrees C) and ultraviolet irradiation (60 min, 50W UV lamp) was increased, indicating elevated stress resistance, apparently due to stimulation of DNA-repair and chaperone-mediated protection of macromolecules. Further research is clearly warranted to identify more efficient anti-stress and antiaging preparations and schemes of B. sp. application on models of laboratory mammals and human cell cultures.

  5. Biomorphology and rhythm of seasonal development of the relic species Lobelia dortmanna in oligotrophic lakes of Tver region

    Directory of Open Access Journals (Sweden)

    A. G. Lapirov

    2017-07-01

    Full Text Available This article covers the morphology of the vegetative and generative sphere of a rare relic species, Lobelia dortmanna L. (Lobelioideae. This is the first time that using the modular approach a study has analysed the shoot system of this species and described the structures of all three categories: elementary (EM, universal (UM and basic (OM. This paper describes the life form and analyses the rhythm of seasonal development of the species in the lakes of Tver oblast, and provides data on the seed productivity. As a life form, L. dortmanna is a herbaceous polycarpic, un clearly polycentric shallow-rooted plant with a fibrous root system and non-specialized morphological disintegration. The sympodially growing shoot-system of the plant is formed by two types of different-aged anisotropic replacement shoots: dicyclic vegetative-generative semirosette and annual vegetative rosette shoots. The indicator of actual seed productivity equals on average up to 1621 ± 451 seeds per single vegetative-generative shoot. The module structure of L. dortmanna is presented by 10 variants of elementary modules. The main modules are formed on the basis of a monocarpic dicyclic anisotropic monopodial shoot with the following morpho-functional zones distinguished: 1 the lower zone of inhibition; 2 the recovery zone; 3 the upper zone of inhibition 4 the latent generative zone; 5 the main inflorescence. The functional role of the first three morpho-functional zones of a monocarpic shoot is performed by a minimum number of variants of elementary modules. In the rhythm of seasonal development, the authors distinguished 7 consecutive stages: 1 the period of relative rest; 2 vegetative phase; 3 the phase of budding; 4 flowering; 5 frui ting; 6 secondary activities. By the character of rhythm of seasonal development, L. dortmanna belongs to the group of evergreen plants with a long growing season and middle-late summer flowering.

  6. Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins

    Science.gov (United States)

    Nikitin, Daniil; Penzar, Dmitry; Garazha, Andrew; Sorokin, Maxim; Tkachev, Victor; Borisov, Nicolas; Poltorak, Alexander; Prassolov, Vladimir; Buzdin, Anton A.

    2018-01-01

    Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS). Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged) elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle progression and

  7. Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins

    Directory of Open Access Journals (Sweden)

    Daniil Nikitin

    2018-01-01

    Full Text Available Endogenous retroviruses and retrotransposons also termed retroelements (REs are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs. We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS. Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle

  8. Near Surface Magnetic Survey for Investigating the Cultural Relics in Suchon, Gongju, Korea

    Science.gov (United States)

    Islam, M. R.; Tiampo, K.; Suh, M.; Abdallatif, T. F.

    2009-05-01

    A magnetic study by the FM256 Fluxgate Gradiometer was conducted in Suchon, Gongju to measure the vertical magnetic gradient of the Earth's magnetic field and to give further details of the shallow section. The region was divided into two separate areas. The first study area measured 40m by 20m while the second study area was 20m x 20m. Each was subsequently divided into four grids of dimension 20m by 10m and 10m by 10m respectively. Measurements of the vertical magnetic gradient were conducted through successive zigzag traverses. The sample-interval and the traverse-interval were set to specifically record small anomalies at a high resolution. A total of 3200 readings were measured at the first study area and 1600 at the second study area. The data have been downloaded, presented and processed through the Geoplot software to remove the spikes, grid discontinuities, and traverses stripes, and also to enhance the display and smooth the data using the Gaussian low-pass filtering techniques. The vertical gradient of the processed data over the second study area ranges from -34nT to + 21nT, while it ranges from -36nT to + 62nT at the first study area. The gradiometer results defined several positive and negative magnetic anomalies, which revealed the existence of several subsurface features of different shapes and sizes. A comparison between the processed magnetic images suggest that the subsurface features may include a room structure (e.g. hut), a cave-shaped stone chamber tomb, an accumulation of potteries and porcelains common in the Baekje period in the ancient Korean history. The biggest anomaly (3 m in diameter) may illuminate a quartzite tomb chamber. As a result, the study area has great archaeological interest.

  9. Hybridization relics complicate barcode-based identification of species in earthworms.

    Science.gov (United States)

    Dupont, L; Porco, D; Symondson, W O C; Roy, V

    2016-07-01

    Introgressive hybridization results in mito-nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early-generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation. © 2016 John Wiley & Sons Ltd.

  10. A Virtual Reconstruction Methodology for Archaeological Heritage in East Asia – Practical Experience from the Re-relic Program in China

    Directory of Open Access Journals (Sweden)

    Yan He

    2013-11-01

    Full Text Available There is as much abundance of archaeological heritage in East Asia as there is diversity in the methodology for its reconstruction and representation. The Re-relic program in China recognizes the uniqueness of archaeological heritage in East Asia and has developed a tailored virtual reconstruction methodology that is both scientifically robust and popular for public interpretation. The theoretical consideration and field experience over the years shall contribute to the global understanding of the value and technique in virtual reconstruction, while testifying to the very principles of Seville Charter.

  11. Spectrum of perturbations arising in a nonsingular model of the Universe with the initial de Sitter stage and the anisotropy of the relic radiation

    International Nuclear Information System (INIS)

    Starobinskij, A.A.

    1983-01-01

    Spectrum of primary adiabatic perturbations and gravitational waves formed in the proposed earlier by the author nonsingular cosmological model with the initial quantum de Sitter stage generated by gravitational vacuum polarization is calculated. The spectrum of gravitational waves appears to be flat, the spectrum of adiabatic perturbations is close to the flat one. The large-scale anisotropy of the temperature T of the relic electromagnetic radiation due to these fluctuations is found. It is shown that the most promising way to detect the anisotropy in the case of a flat perturbation spectrum is the investigation of correlations of ΔT/T at the angles of 5 deg - 10 deg

  12. Relics of the Past

    DEFF Research Database (Denmark)

    Eskildsen, Kasper Risbjerg

    2016-01-01

    , they insisted, were not only more reliable than eyewitness accounts, but also better historical evidence than all other material remains of the past. The use of these sources in historical research also helped shape the modern ideal of the historian as an archival researcher. To illustrate these changes......, the paper focuses upon the example of the Göttingen historian Johann Christoph Gatterer, who is often considered one of the founders of modern critical historical research....

  13. Containment: Relevant or Relic?

    Science.gov (United States)

    2011-06-10

    demonstration of killing multiple birds with a single stone: in one speech Reagan managed simultaneously to pre-empt the nuclear freeze movement, to...Aideed and his forces tragically led to the famous battle on 3 October 1993 that resulted in the deaths of 18 Americans, one Malaysian , and between 500

  14. Dark Relics in Cosmology

    DEFF Research Database (Denmark)

    Tram, Thomas

    2012-01-01

    For 13,7 milliarder år siden befandt Universet sig i en meget varm og tæt tilstand, og siden da har det udvidet sig og er blevet afkølet. Kosmologi forsøger at forklare hvordan vores Univers har udviklet sig fra Big Bang og frem til i dag. Udviklingen afhænger af de fundamentale naturlove, så der...

  15. Transcriptional analysis of the HeT-A retrotransposon in mutant and wild type stocks reveals high sequence variability at Drosophila telomeres and other unusual features

    Directory of Open Access Journals (Sweden)

    Piñeyro David

    2011-11-01

    Full Text Available Abstract Background Telomere replication in Drosophila depends on the transposition of a domesticated retroelement, the HeT-A retrotransposon. The sequence of the HeT-A retrotransposon changes rapidly resulting in differentiated subfamilies. This pattern of sequence change contrasts with the essential function with which the HeT-A is entrusted and brings about questions concerning the extent of sequence variability, the telomere contribution of different subfamilies, and whether wild type and mutant Drosophila stocks show different HeT-A scenarios. Results A detailed study on the variability of HeT-A reveals that both the level of variability and the number of subfamilies are higher than previously reported. Comparisons between GIII, a strain with longer telomeres, and its parental strain Oregon-R indicate that both strains have the same set of HeT-A subfamilies. Finally, the presence of a highly conserved splicing pattern only in its antisense transcripts indicates a putative regulatory, functional or structural role for the HeT-A RNA. Interestingly, our results also suggest that most HeT-A copies are actively expressed regardless of which telomere and where in the telomere they are located. Conclusions Our study demonstrates how the HeT-A sequence changes much faster than previously reported resulting in at least nine different subfamilies most of which could actively contribute to telomere extension in Drosophila. Interestingly, the only significant difference observed between Oregon-R and GIII resides in the nature and proportion of the antisense transcripts, suggesting a possible mechanism that would in part explain the longer telomeres of the GIII stock.

  16. A New Method of Gold Foil Damage Detection in Stone Carving Relics Based on Multi-Temporal 3D LiDAR Point Clouds

    Directory of Open Access Journals (Sweden)

    Miaole Hou

    2016-05-01

    Full Text Available The timely detection of gold foil damage in gold-overlaid stone carvings and the associated maintenance of these relics pose several challenges to both the research and heritage protection communities internationally. This paper presents a new method for detecting gold foil damage by making use of multi-temporal 3D LiDAR point clouds. By analyzing the errors involved in the detection process, a formula is developed for calculation of the damage detection threshold. An improved division method for the linear octree that only allocates memory to the non-blank nodes, is proposed, which improves storage and retrieval efficiency for the point clouds. Meanwhile, the damage-occurrence regions are determined according to Hausdorff distances. Using a triangular mesh, damaged regions can be identified and measured in order to determine the relic’s total damaged area. Results demonstrate that this method can effectively detect gold foil damage in stone carvings. The identified surface area of damaged regions can provide the information needed for subsequent restoration and protection of relics of this type.

  17. Lensing substructure quantification in RXJ1131-1231: a 2 keV lower bound on dark matter thermal relic mass

    Energy Technology Data Exchange (ETDEWEB)

    Birrer, Simon; Amara, Adam; Refregier, Alexandre, E-mail: simon.birrer@phys.ethz.ch, E-mail: adam.amara@phys.ethz.ch, E-mail: alexandre.refregier@phys.ethz.ch [Institute for Astronomy, Department of Physics, ETH Zurich, Wolfgang-Pauli-Strasse 27, 8093, Zurich (Switzerland)

    2017-05-01

    We study the substructure content of the strong gravitational lens RXJ1131-1231 through a forward modelling approach that relies on generating an extensive suite of realistic simulations. We use a semi-analytic merger tree prescription that allows us to stochastically generate substructure populations whose properties depend on the dark matter particle mass. These synthetic halos are then used as lenses to produce realistic mock images that have the same features, e.g. luminous arcs, quasar positions, instrumental noise and PSF, as the data. We then analyse the data and the simulations in the same way with summary statistics that are sensitive to the signal being targeted and are able to constrain models of dark matter statistically using Approximate Bayesian Computing (ABC) techniques. (In this work, we focus on the thermal relic mass estimate and fix the semi-analytic descriptions of the substructure evolution based on recent literature.) We are able, based on the HST data for RXJ1131-1231, to rule out a warm dark matter thermal relic mass below 2 keV at the 2σ confidence level.

  18. (N)LSP decays and gravitino dark matter relic abundance in big divisor (nearly) SLagy D3/D7μ-split SUSY

    Science.gov (United States)

    Dhuria, Mansi; Misra, Aalok

    2013-02-01

    Using the (nearly) Ricci-flat Swiss-Cheese metric of Misra (2012) [1], in the context of a mobile space-time filling D3-brane restricted to a nearly special Lagrangian sub-manifold (in the large volume limit, the pull-back of the Kähler form close to zero and the real part of the pull-back of e, θ=π/2 times the nowhere-vanishing holomorphic three-form providing the volume form on the three-cycle) of the "big" divisor with (fluxed stacks of) space-time filling D7-branes also wrapping the "big" divisor (corresponding to a local minimum), we provide an explicit identification of the electron and the u-quark, as well as their SU (2-singlet cousins, with fermionic superpartners of four Wilson line moduli; their superpartners turn out to be very heavy, the Higgsino-mass parameter turns out to be large, one obtains one light (with a mass of 125 GeV) and one heavy Higgs and the gluino is long lived (from a collider point of view) providing a possible realization of "μ-Split Supersymmetry". By explicitly calculating the lifetimes of decays of the co-NLSPs - the first generation squark/slepton and a neutralino - to the LSP - the gravitino - as well as gravitino decays, we verify that BBN constraints relevant to the former as well as the requirement of the latter to be (more than) the age of the universe, are satisfied. For the purpose of calculation of the gravitino relic density in terms of the neutralino/slepton relic density, we evaluate the latter by evaluating the neutralino/slepton (co-)annihilation cross sections and hence show that the former satisfies the requirement for a dark matter candidate.

  19. (N)LSP decays and gravitino dark matter relic abundance in big divisor (nearly) SLagy D3/D7μ-split SUSY

    International Nuclear Information System (INIS)

    Dhuria, Mansi; Misra, Aalok

    2013-01-01

    Using the (nearly) Ricci-flat Swiss-Cheese metric of Misra (2012) [1], in the context of a mobile space–time filling D3-brane restricted to a nearly special Lagrangian sub-manifold (in the large volume limit, the pull-back of the Kähler form close to zero and the real part of the pull-back of e −iθ , θ=(π)/2 times the nowhere-vanishing holomorphic three-form providing the volume form on the three-cycle) of the “big” divisor with (fluxed stacks of) space–time filling D7-branes also wrapping the “big” divisor (corresponding to a local minimum), we provide an explicit identification of the electron and the u-quark, as well as their SU(2) L -singlet cousins, with fermionic superpartners of four Wilson line moduli; their superpartners turn out to be very heavy, the Higgsino-mass parameter turns out to be large, one obtains one light (with a mass of 125 GeV) and one heavy Higgs and the gluino is long lived (from a collider point of view) providing a possible realization of “μ-Split Supersymmetry”. By explicitly calculating the lifetimes of decays of the co-NLSPs – the first generation squark/slepton and a neutralino – to the LSP – the gravitino – as well as gravitino decays, we verify that BBN constraints relevant to the former as well as the requirement of the latter to be (more than) the age of the universe, are satisfied. For the purpose of calculation of the gravitino relic density in terms of the neutralino/slepton relic density, we evaluate the latter by evaluating the neutralino/slepton (co-)annihilation cross sections and hence show that the former satisfies the requirement for a dark matter candidate.

  20. (N)LSP decays and gravitino dark matter relic abundance in big divisor (nearly) SLagy D3/D7{mu}-split SUSY

    Energy Technology Data Exchange (ETDEWEB)

    Dhuria, Mansi, E-mail: mansidph@iitr.ernet.in [Department of Physics, Indian Institute of Technology, Roorkee 247 667, Uttaranchal (India); Misra, Aalok, E-mail: aalokfph@iitr.ernet.in [Department of Physics, Indian Institute of Technology, Roorkee 247 667, Uttaranchal (India)

    2013-02-21

    Using the (nearly) Ricci-flat Swiss-Cheese metric of Misra (2012) [1], in the context of a mobile space-time filling D3-brane restricted to a nearly special Lagrangian sub-manifold (in the large volume limit, the pull-back of the Kaehler form close to zero and the real part of the pull-back of e{sup -i{theta}}, {theta}=({pi})/2 times the nowhere-vanishing holomorphic three-form providing the volume form on the three-cycle) of the 'big' divisor with (fluxed stacks of) space-time filling D7-branes also wrapping the 'big' divisor (corresponding to a local minimum), we provide an explicit identification of the electron and the u-quark, as well as their SU(2){sub L}-singlet cousins, with fermionic superpartners of four Wilson line moduli; their superpartners turn out to be very heavy, the Higgsino-mass parameter turns out to be large, one obtains one light (with a mass of 125 GeV) and one heavy Higgs and the gluino is long lived (from a collider point of view) providing a possible realization of '{mu}-Split Supersymmetry'. By explicitly calculating the lifetimes of decays of the co-NLSPs - the first generation squark/slepton and a neutralino - to the LSP - the gravitino - as well as gravitino decays, we verify that BBN constraints relevant to the former as well as the requirement of the latter to be (more than) the age of the universe, are satisfied. For the purpose of calculation of the gravitino relic density in terms of the neutralino/slepton relic density, we evaluate the latter by evaluating the neutralino/slepton (co-)annihilation cross sections and hence show that the former satisfies the requirement for a dark matter candidate.

  1. New seismograph includes filters

    Energy Technology Data Exchange (ETDEWEB)

    1979-11-02

    The new Nimbus ES-1210 multichannel signal enhancement seismograph from EG and G geometrics has recently been redesigned to include multimode signal fillers on each amplifier. The ES-1210F is a shallow exploration seismograph for near subsurface exploration such as in depth-to-bedrock, geological hazard location, mineral exploration, and landslide investigations.

  2. Analytic device including nanostructures

    KAUST Repository

    Di Fabrizio, Enzo M.; Fratalocchi, Andrea; Totero Gongora, Juan Sebastian; Coluccio, Maria Laura; Candeloro, Patrizio; Cuda, Gianni

    2015-01-01

    A device for detecting an analyte in a sample comprising: an array including a plurality of pixels, each pixel including a nanochain comprising: a first nanostructure, a second nanostructure, and a third nanostructure, wherein size of the first nanostructure is larger than that of the second nanostructure, and size of the second nanostructure is larger than that of the third nanostructure, and wherein the first nanostructure, the second nanostructure, and the third nanostructure are positioned on a substrate such that when the nanochain is excited by an energy, an optical field between the second nanostructure and the third nanostructure is stronger than an optical field between the first nanostructure and the second nanostructure, wherein the array is configured to receive a sample; and a detector arranged to collect spectral data from a plurality of pixels of the array.

  3. Saskatchewan resources. [including uranium

    Energy Technology Data Exchange (ETDEWEB)

    1979-09-01

    The production of chemicals and minerals for the chemical industry in Saskatchewan are featured, with some discussion of resource taxation. The commodities mentioned include potash, fatty amines, uranium, heavy oil, sodium sulfate, chlorine, sodium hydroxide, sodium chlorate and bentonite. Following the successful outcome of the Cluff Lake inquiry, the uranium industry is booming. Some developments and production figures for Gulf Minerals, Amok, Cenex and Eldorado are mentioned.

  4. Identification and characterization of REC66, a Ty1-copia-like retrotransposon in the genome of red flower of Mirabilis jalapa L.

    Directory of Open Access Journals (Sweden)

    Shunri Jiang

    2017-01-01

    Full Text Available Mirabilis jalapa Lis the most commonly grown ornamental species of Mirabilis and is available in a range of brilliant colors. However, genetic research on Mirabilis jalapa Lis limited. Using fluorescent differential display (FDD screening, we report the identification of a novel Ty1-copia-like retrotransposon in the genome of the red flower of Mirabilis jalapa L, and we named it REC66based on its sequence homology to the GAG protein from Ty1-copiaretrotransposon. Using degenerate primers based on the DNA sequence of REC66, a total of fourteen different variants in reverse transcriptase (RT sequence were recovered from the genomic DNA. These RT sequences show a high degree of heterogeneity characterized mainly by deletion mutation; they can be divided into three subfamilies, of which the majority encode defective RT. This is the first report of a Ty1-copiaretrotransposon in Mirabilis jalapa L. The finding could be helpful for the development of new molecular markers for genetic studies, particularly on the origin and evolutionary relationships of M. jalapa L, and the study of Ty1-copiaretrotransposons and plant genome evolution in the genus Mirabilisor family Nyctaginaceae.

  5. A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla).

    Science.gov (United States)

    Gallus, S; Kumar, V; Bertelsen, M F; Janke, A; Nilsson, M A

    2015-10-25

    Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Being Included and Excluded

    DEFF Research Database (Denmark)

    Korzenevica, Marina

    2016-01-01

    Following the civil war of 1996–2006, there was a dramatic increase in the labor mobility of young men and the inclusion of young women in formal education, which led to the transformation of the political landscape of rural Nepal. Mobility and schooling represent a level of prestige that rural...... politics. It analyzes how formal education and mobility either challenge or reinforce traditional gendered norms which dictate a lowly position for young married women in the household and their absence from community politics. The article concludes that women are simultaneously excluded and included from...... community politics. On the one hand, their mobility and decision-making powers decrease with the increase in the labor mobility of men and their newly gained education is politically devalued when compared to the informal education that men gain through mobility, but on the other hand, schooling strengthens...

  7. Eclogite facies relics and a multistage breakdown in metabasites of the KTB pilot hole, NE Bavaria: implications for the Variscan tectonometamorphic evolution of the NW Bohemian Massif

    Science.gov (United States)

    O'Brien, Patrick J.; Röhr, Christian; Okrusch, Martin; Patzak, Margarete

    1992-11-01

    Complex reaction textures in coronitic metagabbros and retrograded eclogites of the KTB pilot and an adjacent drilling provide evidence for a multistage metamorphic history in the Variscan basement of the NW Bohemian Massif. The eclogites show complete metamorphic recrystallization leaving no textural or mineral relics of their igneous precursors. In contrast, textural relics of the igneous protolith are still preserved in the metagabbros where the metamorphic overprint under high pressure conditions achieved only partial replacement of the initial assemblage plagioclase + augite + amphibole (+olivine or orthopyroxene?) + ilmenite to form the eclogite facies assemblage garnet + omphacite + kyanite + zoisite + quartz+rutile. The garnets in the metagabbros occur in the typical ‘necklace’ fashion at the borders between the original plagioclase and mafic phase domains. In the same rocks, omphacite formed by a topotactic reaction mechanism replacing igneous augite as well as in smaller grains at the margins of the texturally igneous clinopyroxene where it occurs without fixed orientation with respect to the relict phase. Both eclogites and metagabbros show a partial breakdown under high pressure granulite (transitional to high pressure amphibolite) facies conditions during which omphacite broke down to vermicular symplectites of diopside + plagioclase. A later pervasive medium pressure metamorphism under amphibolite facies conditions led to the development of assemblages dominated by hornblende + plagioclase+titanite: phases prevailing in the overwhelming majority of the surrounding metabasites. Subsequent vein-associated retrogression produced minerals typical of the greenschist to zeolite facies. All metamorphic stages may be represented in a single thin section but although the overall reaction sequence is apparent, the obvious disequilibrium in the rocks makes the use of conventional geothermobarometry difficult. However, calculations made by assuming an

  8. Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

    Science.gov (United States)

    Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

    2013-10-01

    Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.

  9. Sri Dalada Maligawa - 3D-Scanning and Documentation of the Temple of the Sacred Tooth Relic at Kandy, Sri Lanka

    Science.gov (United States)

    Rahrig, M.; Luib, A.

    2017-08-01

    Sri Dalada Maligawa - the Temple of the Sacred Tooth Relic - is one of the most important pilgrim sites in Buddhist culture. It is the main part of the UNESCO World Heritage Site Sacred City of Kandy. Since the end of the 17th century the temple has been keeping the sacred tooth of the Buddha. Until now an accurate documentation of the temple with all its rich decorations is missing. The Temple is built in an area vulnerable to environmental factors like earthquakes or monsoon rains and was the target of terrorist attacks. To help preserving this important cultural heritage a research project was carried out. Main part of the project was a 3D-documentation of the entire temple by using Terrestrial-Laser-Scanning (TLS) and the creating of CAD-Plans. In addition to the documentation of the architecture several details were taken in high resolution by Structured-Light-Scanning (SLS). All data will be part of the digital archive of the temple and were used as a base for a general site monitoring, especially to observe cracks. Next to the mere documentation a transfer of knowledge was another aim of the project. In future most of the analysis of the scan data can be done by local specialists.

  10. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

    Science.gov (United States)

    2014-01-01

    Background Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated. Results We analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites. Conclusions Since active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome. PMID:24958239

  11. A retrotransposon insertion in the 5' regulatory domain of Ptf1a results in ectopic gene expression and multiple congenital defects in Danforth's short tail mouse.

    Directory of Open Access Journals (Sweden)

    Francesca Lugani

    Full Text Available Danforth's short tail mutant (Sd mouse, first described in 1930, is a classic spontaneous mutant exhibiting defects of the axial skeleton, hindgut, and urogenital system. We used meiotic mapping in 1,497 segregants to localize the mutation to a 42.8-kb intergenic segment on chromosome 2. Resequencing of this region identified an 8.5-kb early retrotransposon (ETn insertion within the highly conserved regulatory sequences upstream of Pancreas Specific Transcription Factor, 1a (Ptf1a. This mutation resulted in up to tenfold increased expression of Ptf1a as compared to wild-type embryos at E9.5 but no detectable changes in the expression levels of other neighboring genes. At E9.5, Sd mutants exhibit ectopic Ptf1a expression in embryonic progenitors of every organ that will manifest a developmental defect: the notochord, the hindgut, and the mesonephric ducts. Moreover, at E 8.5, Sd mutant mice exhibit ectopic Ptf1a expression in the lateral plate mesoderm, tail bud mesenchyme, and in the notochord, preceding the onset of visible defects such as notochord degeneration. The Sd heterozygote phenotype was not ameliorated by Ptf1a haploinsufficiency, further suggesting that the developmental defects result from ectopic expression of Ptf1a. These data identify disruption of the spatio-temporal pattern of Ptf1a expression as the unifying mechanism underlying the multiple congenital defects in Danforth's short tail mouse. This striking example of an enhancer mutation resulting in profound developmental defects suggests that disruption of conserved regulatory elements may also contribute to human malformation syndromes.

  12. Proteolytic Processing and Assembly of gag and gag-pol Proteins of TED, a Baculovirus-Associated Retrotransposon of the Gypsy Family

    Science.gov (United States)

    Hajek, Kathryn L.; Friesen, Paul D.

    1998-01-01

    TED (transposable element D) is an env-containing member of the gypsy family of retrotransposons that represents a possible retrovirus of invertebrates. This lepidopteran (moth) retroelement contains gag and pol genes that encode proteins capable of forming viruslike particles (VLP) with reverse transcriptase. Since VLP are likely intermediates in TED transposition, we investigated the roles of gag and pol in TED capsid assembly and maturation. By using constructed baculovirus vectors and TED Gag-specific antiserum, we show that the principal translation product of gag (Pr55gag) is cleaved to produce a single VLP structural protein, p37gag. Replacement of Asp436 within the retrovirus-like active site of the pol-encoded protease (PR) abolished Pr55gag cleavage and demonstrated the requirement for PR in capsid processing. As shown by expression of an in-frame fusion of TED gag and pol, PR is derived from the Gag-Pol polyprotein Pr195gag-pol. The PR cleavage site within Pr55gag was mapped to a position near the junction of a basic, nucleocapsid-like domain and a C-terminal acidic domain. Once released by cleavage, the C-terminal fragment was not detected. This acidic fragment was dispensable for VLP assembly, as demonstrated by the formation of VLP by C-terminal Pr55gag truncation proteins and replacement of the acidic domain with a heterologous protein. In contrast, C-terminal deletions that extended into the adjacent nucleocapsid-like domain of Pr55gag abolished VLP recovery and demonstrated that this central region contributes to VLP assembly or stability, or both. Collectively, these data suggest that the single TED protein p37gag provides both capsid and nucleocapsid functions. TED may therefore use a simple processing strategy for VLP assembly and genome packaging. PMID:9765414

  13. Internal validation of two new retrotransposons-based kits (InnoQuant® HY and InnoTyper® 21) at a forensic lab.

    Science.gov (United States)

    Martins, Cátia; Ferreira, Paulo Miguel; Carvalho, Raquel; Costa, Sandra Cristina; Farinha, Carlos; Azevedo, Luísa; Amorim, António; Oliveira, Manuela

    2018-02-01

    Obtaining a genetic profile from pieces of evidence collected at a crime scene is the primary objective of forensic laboratories. New procedures, methods, kits, software or equipment must be carefully evaluated and validated before its implementation. The constant development of new methodologies for DNA testing leads to a steady process of validation, which consists of demonstrating that the technology is robust, reproducible, and reliable throughout a defined range of conditions. The present work aims to internally validate two new retrotransposon-based kits (InnoQuant ® HY and InnoTyper ® 21), under the working conditions of the Laboratório de Polícia Científica da Polícia Judiciária (LPC-PJ). For the internal validation of InnoQuant ® HY and InnoTyper ® 21 sensitivity, repeatability, reproducibility, and mixture tests and a concordance study between these new kits and those currently in use at LPC-PJ (Quantifiler ® Duo and GlobalFiler™) were performed. The results obtained for sensitivity, repeatability, and reproducibility tests demonstrated that both InnoQuant ® HY and InnoTyper ® 21 are robust, reproducible, and reliable. The results of the concordance studies demonstrate that InnoQuant ® HY produced quantification results in nearly 29% more than Quantifiler ® Duo (indicating that this new kit is more effective in challenging samples), while the differences observed between InnoTyper ® 21 and GlobalFiler™ are not significant. Therefore, the utility of InnoTyper ® 21 has been proven, especially by the successful amplification of a greater number of complete genetic profiles (27 vs. 21). The results herein presented allowed the internal validation of both InnoQuant ® HY and InnoTyper ® 21, and their implementation in the LPC-PJ laboratory routine for the treatment of challenging samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. SMSS J130522.47-293113.0: a high-latitude stellar X-ray source with pc-scale outflow relics?

    Science.gov (United States)

    Da Costa, G. S.; Soria, R.; Farrell, S. A.; Bayliss, D.; Bessell, M. S.; Vogt, F. P. A.; Zhou, G.; Points, S. D.; Beers, T. C.; López-Sánchez, Á. R.; Bannister, K. W.; Bell, M.; Hancock, P. J.; Burlon, D.; Gaensler, B. M.; Sadler, E. M.; Tingay, S.; Keller, S. C.; Schmidt, B. P.; Tisserand, P.

    2018-06-01

    We report the discovery of an unusual stellar system SMSS J130522.47-293113.0. The optical spectrum is dominated by a blue continuum together with emission lines of hydrogen, neutral, and ionized helium, and the N III, C III blend at ˜4640-4650 Å. The emission-line profiles vary in strength and position on time-scales as short as 1 d, while optical photometry reveals fluctuations of as much as ˜0.2 mag in g on time-scales as short as 10-15 min. The system is a weak X-ray source (f0.3-10 = (1.2 ± 0.1) × 10-13 ergs cm2 s-1 in the 0.3-10 keV band) but is not detected at radio wavelengths (3σ upper limit of 50 μJy at 5.5 GHz). The most intriguing property of the system, however, is the existence of two `blobs', a few arcsec in size, that are symmetrically located 3{^'.}8 (2.2 pc for our preferred system distance of ˜2 kpc) each side of the central object. The blobs are detected in optical and near-IR broad-band images but do not show any excess emission in H α images. We discuss the interpretation of the system, suggesting that the central object is most likely a nova-like CV, and that the blobs are relics of a pc-scale accretion-powered collimated outflow.

  15. Human occupation and environmental change in Holocene from a case of XDW2 relic site in the Tibetan Plateau at above 4000 meters above sea level.

    Science.gov (United States)

    Hou, G.; Li, F.; Zhu, Y.

    2017-12-01

    XDW2 is an important microlithic cultural relics with continuous stratum that is located in the the Tibetan plateau at above 4,000 masl, wich is a window of revealing the evolution of early human activities and the response and adaptation to extreme environmental in the principal part of Tibetan plateau. So it has important research significance. The analysis on human activity indicator(stoneware, potsherds) and environmental indicators(magnetic susceptibility, color, granularity and pollen) showed: the winter wind and dust storm intensity is weak in this area during 7.0-6 cal. Ka BP, pedogenesis is strong, the climate is humid, environment is suitable relatively, when is Holocene Megathermal; the active phase of microlithic human activities occurred during 7.2-6 cal. ka BP, and quickly weakened after 6 cal. ka BP. The number of stone tools reveal that human activities are concentrated before and after 7-6.2 cal. ka BP, charcoal fragmental concentration indicates that microlithic human activity reached the peak at around 6.7 cal. ka BP. Thus relatively suitable environment during Holocene Megathermal is the important motivating factor of active hunter-gatherer activities in the principal part of Tibetan plateau. After 6 cal. ka BP, summer monsoon weakened rapidly, agricultural growers in the Loess Plateau began to expand towards the plateau, under the effect of environmental degradation and new technologies, microlithic hunter-gatherers in the principal part of plateau moved towards the river valley at low altitude, and learnt settlement and plantation, microlithic activity in the main plateau began to decline.

  16. Cloning the uteroglobin gene promoter from the relic volcano rabbit (Romerolagus diazi) reveals an ancient estrogen-response element.

    Science.gov (United States)

    Acosta-MontesdeOca, Adriana; Zariñán, Teresa; Macías, Héctor; Pérez-Solís, Marco A; Ulloa-Aguirre, Alfredo; Gutiérrez-Sagal, Rubén

    2012-05-01

    To gain further insight on the estrogen-dependent transcriptional regulation of the uteroglobin (UG) gene, we cloned the 5'-flanking region of the UG gene from the phylogenetically ancient volcano rabbit (Romerolagus diazi; Rd). The cloned region spans 812 base pairs (bp; -812/-1) and contains a noncanonical TATA box (TACA). The translation start site is 48 bp downstream from the putative transcription initiation site (AGA), and is preceded by a consensus Kozak box. Comparison of the Rd-UG gene with that previously isolated from rabbits (Oryctolagus cuniculus) showed 93% in sequence identity as well as a number of conserved cis-acting elements, including the estrogen-response element (ERE; -265/-251), which differs from the consensus by two nucleotides. In MCF-7 cells, 17β-estradiol (E(2)) induced transcription of a luciferase reporter driven by the Rd-UG promoter in a similar manner as in an equivalent rabbit UG reporter; the Rd-UG promoter was 30% more responsive to E(2) than the rabbit promoter. Mutagenesis studies on the Rd-ERE confirmed this cis-element as a target of E(2) as two luciferase mutant reporters of the Rd-promoter, one with the rabbit and the other with the consensus ERE, were more responsive to the hormone than the wild-type reporter. Gel shift and super-shift assays showed that estrogen receptor-α indeed binds to the imperfect palindromic sequence of the Rd-ERE. Copyright © 2012 Wiley Periodicals, Inc.

  17. [Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants].

    Science.gov (United States)

    Boronnikova, S V; Kalendar', R N

    2010-01-01

    Species-specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm' region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP-markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

  18. American uranium: Relic or reality?

    International Nuclear Information System (INIS)

    Anon.

    1994-01-01

    This article is a review of the American Uranium industry. Historical aspects are presented as the industry's history is outlined from the mid-1950's to the present day. Present capabilities are noted, as are a current comparison of American production costs vs. world costs. Future trends are analyzed

  19. (including travel dates) Proposed itinerary

    Indian Academy of Sciences (India)

    Ashok

    31 July to 22 August 2012 (including travel dates). Proposed itinerary: Arrival in Bangalore on 1 August. 1-5 August: Bangalore, Karnataka. Suggested institutions: Indian Institute of Science, Bangalore. St Johns Medical College & Hospital, Bangalore. Jawaharlal Nehru Centre, Bangalore. 6-8 August: Chennai, TN.

  20. Theory including future not excluded

    DEFF Research Database (Denmark)

    Nagao, K.; Nielsen, H.B.

    2013-01-01

    We study a complex action theory (CAT) whose path runs over not only past but also future. We show that, if we regard a matrix element defined in terms of the future state at time T and the past state at time TA as an expectation value in the CAT, then we are allowed to have the Heisenberg equation......, Ehrenfest's theorem, and the conserved probability current density. In addition,we showthat the expectation value at the present time t of a future-included theory for large T - t and large t - T corresponds to that of a future-not-included theory with a proper inner product for large t - T. Hence, the CAT...

  1. Device including a contact detector

    DEFF Research Database (Denmark)

    2011-01-01

    arms (12) may extend from the supporting body in co-planar relationship with the first surface. The plurality of cantilever arms (12) may extend substantially parallel to each other and each of the plurality of cantilever arms (12) may include an electrical conductive tip for contacting the area......The present invention relates to a probe for determining an electrical property of an area of a surface of a test sample, the probe is intended to be in a specific orientation relative to the test sample. The probe may comprise a supporting body defining a first surface. A plurality of cantilever...... of the test sample by movement of the probe relative to the surface of the test sample into the specific orientation.; The probe may further comprise a contact detector (14) extending from the supporting body arranged so as to contact the surface of the test sample prior to any one of the plurality...

  2. Neoclassical transport including collisional nonlinearity.

    Science.gov (United States)

    Candy, J; Belli, E A

    2011-06-10

    In the standard δf theory of neoclassical transport, the zeroth-order (Maxwellian) solution is obtained analytically via the solution of a nonlinear equation. The first-order correction δf is subsequently computed as the solution of a linear, inhomogeneous equation that includes the linearized Fokker-Planck collision operator. This equation admits analytic solutions only in extreme asymptotic limits (banana, plateau, Pfirsch-Schlüter), and so must be solved numerically for realistic plasma parameters. Recently, numerical codes have appeared which attempt to compute the total distribution f more accurately than in the standard ordering by retaining some nonlinear terms related to finite-orbit width, while simultaneously reusing some form of the linearized collision operator. In this work we show that higher-order corrections to the distribution function may be unphysical if collisional nonlinearities are ignored.

  3. “Viimne reliikvia” ja “Kolme katku vahel”: ruumist eesti ajalookirjanduse ekraniseeringutes / The Last Relic and Between Three Plagues: On Space in Film Adaptations of Estonian Historical Fiction

    Directory of Open Access Journals (Sweden)

    Eva Näripea

    2015-06-01

    Full Text Available Teesid: Artikkel keskendub kahele ajalooromaani ekraniseeringule Nõukogude Eesti filmikunstis: „Viimne reliikvia“ (1969, rež Grigori Kromanov, Tallinnfilm, mis põhineb Eduard Bornhöhe romaanil „Vürst Gabriel ehk Pirita kloostri viimsed päevad“ (1893, ning „Kolme katku vahel“ (1970, rež Virve Aruoja, Eesti Telefilm, mille seosed oma kirjandusliku allikaga (Jaan Krossi samanimelise romaaniga on oluliselt keerulisemad. Ekraniseeringuid käsitletakse ruumirepresentatsioonide perspektiivist, uurides, missuguseid strateegiaid kasutati filmiruumide loomisel, kuidas suhestuti kirjandusliku (lähtematerjaliga ning millised ajaloonarratiivi ja rahvusliku identiteedi vahekorrad neis kangastuvad. SU M M A R Y This article examines two Soviet Estonian screen adaptations of historical novels: The Last Relic (Viimne reliikvia, Tallinnfilm, 1969, directed by Grigori Kromanov, based on Eduard Bornhöhe’s novel Prince Gabriel or The Last Days of Pirita Monastery (1893, which became a box-office hit throughout the Soviet Union and even beyond; and Between Three Plagues (Kolme katku vahel, Eesti Telefilm, 1970, directed by Virve Aruoja which reached much more limited TV-audiences; the connections between this film and its literary „source“ (a novel of the same name by Jaan Kross are much more complicated. These screen adaptations are considered from the perspective of spatial representations. I examine which strategies and devices the scriptwriters, directors and production designers drew upon when constructing these cinematic spaces and how they related to their literary hypotexts. As generally for adaptations of historical novels to other media, both The Last Relic and Between Three Plagues speak (perhaps even primarily about their time of production, about the present rather than the past. In this regard, it is important to recall the role of Tallinn’s Old Town as a locus of resistance in Soviet Estonian culture. Arguably

  4. The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7.

    Science.gov (United States)

    Gabus, C; Ficheux, D; Rau, M; Keith, G; Sandmeyer, S; Darlix, J L

    1998-08-17

    Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3' PBS for primer tRNAiMet annealing to the genomic RNA, and the 5' PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNAiMet bound to the PBS was found to direct dimerization of Ty3 RNA-tRNAiMet. Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs.

  5. Possible interaction between B1 retrotransposon-containing sequences and β(major) globin gene transcriptional activation during MEL cell erythroid differentiation.

    Science.gov (United States)

    Vizirianakis, Ioannis S; Tezias, Sotirios S; Amanatiadou, Elsa P; Tsiftsoglou, Asterios S

    2012-01-01

    Repetitive sequences consist of >50% of mammalian genomic DNAs and among these SINEs (short interspersed nuclear elements), e.g. B1 elements, account for 8% of the mouse genome. In an effort to delineate the molecular mechanism(s) involved in the blockade of the in vitro differentiation program of MEL (murine erythroleukaemia) cells by treatment with methylation inhibitors, we detected a DNA region of 559 bp in chromosome 7 located downstream of the 3'-end of the β(major) globin gene (designated B1-559) with unique characteristics. We have fully characterized this B1-559 region that includes a B1 element, several repeats of ATG initiation codons and consensus DNA-binding sites for erythroid-specific transcription factors NF-E2 (nuclear factor-erythroid-derived 2), GATA-1 and EKLF (erythroid Krüppel-like factor). Fragments derived from B1-559 incubated with nuclear extracts form protein complexes in both undifferentiated and differentiated MEL cells. Transient reporter-gene experiments in MEL and human erythroleukaemia K-562 cells with recombinant constructs containing B1-559 fragments linked to HS-2 (hypersensitive site-2) sequences of human β-globin gene LCR (locus control region) indicated potential cooperation upon erythropoiesis and globin gene expression. The possible interaction between the B1-559 region and β(major) globin gene transcriptional activation upon execution of erythroid MEL cell differentiation programme is discussed. © The Author(s) Journal compilation © 2012 Portland Press Limited

  6. Historical Relics and Qing Rule Over Tibet

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    In October 1720, when the Qing troops had driven the Zungar forces out of Tibet, the Qing court started to reform the govemment system of the region that was geared to control by Tibetans of the upper ruling class.

  7. Pre-Inflationary Relics in the CMB?

    CERN Document Server

    Gruppuso, A.; Mandolesi, N.; Natoli, P.; Sagnotti, A.

    String Theory and Supergravity allow, in principle, to follow the transition of the inflaton from pre-inflationary fast roll to slow roll. This introduces an infrared depression in the primordial power spectrum that might have left an imprint in the CMB anisotropy, if it occurred at accessible wavelengths. We model the effect extending $\\Lambda$CDM with a scale $\\Delta$ related to the infrared depression and explore the constraints allowed by {\\sc Planck} data, employing also more conservative, wider Galactic masks in the low resolution CMB likelihood. In an extended mask with $f_{sky}=39\\%$, we thus find $\\Delta = (0.351 \\pm 0.114) \\times 10^{-3} \\, \\mbox{Mpc}^{-1}$, at $99.4\\%$ confidence level, to be compared with a nearby value at $88.5\\%$ with the standard $f_{sky}=94\\%$ mask. With about 64 $e$--folds of inflation, these values for $\\Delta$ would translate into primordial energy scales ${\\cal O}(10^{14})$ GeV.

  8. 42 CFR 410.100 - Included services.

    Science.gov (United States)

    2010-10-01

    ... service; however, maintenance therapy itself is not covered as part of these services. (c) Occupational... increase respiratory function, such as graded activity services; these services include physiologic... rehabilitation plan of treatment, including physical therapy services, occupational therapy services, speech...

  9. Mobilization of retrotransposons in synthetic allotetraploid tobacco

    Czech Academy of Sciences Publication Activity Database

    Petit, M.; Guidat, C.; Daniel, J.; Montoriol, E.; Bui, Q.T.; Lim, K.Y.; Kovařík, Aleš; Leitch, A.R.; Grandbastien, M.-A.; Mhiri, C.

    2010-01-01

    Roč. 186, č. 1 (2010), s. 135-147 ISSN 0028-646X R&D Projects: GA MŠk(CZ) MEB020823; GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : allopolyploidy * evolution * retrotransposition Subject RIV: AQ - Safety, Health Protection, Human - Machine Impact factor: 6.516, year: 2010

  10. Static, Lightweight Includes Resolution for PHP

    NARCIS (Netherlands)

    M.A. Hills (Mark); P. Klint (Paul); J.J. Vinju (Jurgen)

    2014-01-01

    htmlabstractDynamic languages include a number of features that are challenging to model properly in static analysis tools. In PHP, one of these features is the include expression, where an arbitrary expression provides the path of the file to include at runtime. In this paper we present two

  11. Article Including Environmental Barrier Coating System

    Science.gov (United States)

    Lee, Kang N. (Inventor)

    2015-01-01

    An enhanced environmental barrier coating for a silicon containing substrate. The enhanced barrier coating may include a bond coat doped with at least one of an alkali metal oxide and an alkali earth metal oxide. The enhanced barrier coating may include a composite mullite bond coat including BSAS and another distinct second phase oxide applied over said surface.

  12. Rare thoracic cancers, including peritoneum mesothelioma

    NARCIS (Netherlands)

    Siesling, Sabine; van der Zwan, Jan Maarten; Izarzugaza, Isabel; Jaal, Jana; Treasure, Tom; Foschi, Roberto; Ricardi, Umberto; Groen, Harry; Tavilla, Andrea; Ardanaz, Eva

    Rare thoracic cancers include those of the trachea, thymus and mesothelioma (including peritoneum mesothelioma). The aim of this study was to describe the incidence, prevalence and survival of rare thoracic tumours using a large database, which includes cancer patients diagnosed from 1978 to 2002,

  13. Rare thoracic cancers, including peritoneum mesothelioma

    NARCIS (Netherlands)

    Siesling, Sabine; Zwan, J.M.V.D.; Izarzugaza, I.; Jaal, J.; Treasure, T.; Foschi, R.; Ricardi, U.; Groen, H.; Tavilla, A.; Ardanaz, E.

    2012-01-01

    Rare thoracic cancers include those of the trachea, thymus and mesothelioma (including peritoneum mesothelioma). The aim of this study was to describe the incidence, prevalence and survival of rare thoracic tumours using a large database, which includes cancer patients diagnosed from 1978 to 2002,

  14. Births and deaths including fetal deaths

    Data.gov (United States)

    U.S. Department of Health & Human Services — Access to a variety of United States birth and death files including fetal deaths: Birth Files, 1968-2009; 1995-2005; Fetal death file, 1982-2005; Mortality files,...

  15. Including Indigenous Minorities in Decision-Making

    DEFF Research Database (Denmark)

    Pristed Nielsen, Helene

    Based on theories of public sphere participation and deliberative democracy, this book presents empirical results from a study of experiences with including Aboriginal and Maori groups in political decision-making in respectively Western Australia and New Zealand......Based on theories of public sphere participation and deliberative democracy, this book presents empirical results from a study of experiences with including Aboriginal and Maori groups in political decision-making in respectively Western Australia and New Zealand...

  16. Gas storage materials, including hydrogen storage materials

    Science.gov (United States)

    Mohtadi, Rana F; Wicks, George G; Heung, Leung K; Nakamura, Kenji

    2013-02-19

    A material for the storage and release of gases comprises a plurality of hollow elements, each hollow element comprising a porous wall enclosing an interior cavity, the interior cavity including structures of a solid-state storage material. In particular examples, the storage material is a hydrogen storage material such as a solid state hydride. An improved method for forming such materials includes the solution diffusion of a storage material solution through a porous wall of a hollow element into an interior cavity.

  17. Electric Power Monthly, August 1990. [Glossary included

    Energy Technology Data Exchange (ETDEWEB)

    1990-11-29

    The Electric Power Monthly (EPM) presents monthly summaries of electric utility statistics at the national, Census division, and State level. The purpose of this publication is to provide energy decisionmakers with accurate and timely information that may be used in forming various perspectives on electric issues that lie ahead. Data includes generation by energy source (coal, oil, gas, hydroelectric, and nuclear); generation by region; consumption of fossil fuels for power generation; sales of electric power, cost data; and unusual occurrences. A glossary is included.

  18. Electrochemical cell structure including an ionomeric barrier

    Science.gov (United States)

    Lambert, Timothy N.; Hibbs, Michael

    2017-06-20

    An apparatus includes an electrochemical half-cell comprising: an electrolyte, an anode; and an ionomeric barrier positioned between the electrolyte and the anode. The anode may comprise a multi-electron vanadium phosphorous alloy, such as VP.sub.x, wherein x is 1-5. The electrochemical half-cell is configured to oxidize the vanadium and phosphorous alloy to release electrons. A method of mitigating corrosion in an electrochemical cell includes disposing an ionomeric barrier in a path of electrolyte or ion flow to an anode and mitigating anion accumulation on the surface of the anode.

  19. Isolators Including Main Spring Linear Guide Systems

    Science.gov (United States)

    Goold, Ryan (Inventor); Buchele, Paul (Inventor); Hindle, Timothy (Inventor); Ruebsamen, Dale Thomas (Inventor)

    2017-01-01

    Embodiments of isolators, such as three parameter isolators, including a main spring linear guide system are provided. In one embodiment, the isolator includes first and second opposing end portions, a main spring mechanically coupled between the first and second end portions, and a linear guide system extending from the first end portion, across the main spring, and toward the second end portion. The linear guide system expands and contracts in conjunction with deflection of the main spring along the working axis, while restricting displacement and rotation of the main spring along first and second axes orthogonal to the working axis.

  20. 28 CFR 20.32 - Includable offenses.

    Science.gov (United States)

    2010-07-01

    ... Exchange of Criminal History Record Information § 20.32 Includable offenses. (a) Criminal history record... vehicular manslaughter, driving under the influence of drugs or liquor, and hit and run), when unaccompanied by a § 20.32(a) offense. These exclusions may not be applicable to criminal history records...

  1. Including Students with Visual Impairments: Softball

    Science.gov (United States)

    Brian, Ali; Haegele, Justin A.

    2014-01-01

    Research has shown that while students with visual impairments are likely to be included in general physical education programs, they may not be as active as their typically developing peers. This article provides ideas for equipment modifications and game-like progressions for one popular physical education unit, softball. The purpose of these…

  2. Extending flood damage assessment methodology to include ...

    African Journals Online (AJOL)

    Optimal and sustainable flood plain management, including flood control, can only be achieved when the impacts of flood control measures are considered for both the man-made and natural environments, and the sociological aspects are fully considered. Until now, methods/models developed to determine the influences ...

  3. BIOLOGIC AND ECONOMIC EFFECTS OF INCLUDING DIFFERENT ...

    African Journals Online (AJOL)

    The biologic and economic effects of including three agro-industrial by-products as ingredients in turkey poult diets were investigated using 48 turkey poults in a completely randomised design experiment. Diets were formulated to contain the three by-products – wheat offal, rice husk and palm kernel meal, each at 20% level ...

  4. Including Children Dependent on Ventilators in School.

    Science.gov (United States)

    Levine, Jack M.

    1996-01-01

    Guidelines for including ventilator-dependent children in school are offered, based on experience with six such students at a New York State school. Guidelines stress adherence to the medical management plan, the school-family partnership, roles of the social worker and psychologist, orientation, transportation, classroom issues, and steps toward…

  5. Photoactive devices including porphyrinoids with coordinating additives

    Science.gov (United States)

    Forrest, Stephen R; Zimmerman, Jeramy; Yu, Eric K; Thompson, Mark E; Trinh, Cong; Whited, Matthew; Diev, Vlacheslav

    2015-05-12

    Coordinating additives are included in porphyrinoid-based materials to promote intermolecular organization and improve one or more photoelectric characteristics of the materials. The coordinating additives are selected from fullerene compounds and organic compounds having free electron pairs. Combinations of different coordinating additives can be used to tailor the characteristic properties of such porphyrinoid-based materials, including porphyrin oligomers. Bidentate ligands are one type of coordinating additive that can form coordination bonds with a central metal ion of two different porphyrinoid compounds to promote porphyrinoid alignment and/or pi-stacking. The coordinating additives can shift the absorption spectrum of a photoactive material toward higher wavelengths, increase the external quantum efficiency of the material, or both.

  6. Electric power monthly, September 1990. [Glossary included

    Energy Technology Data Exchange (ETDEWEB)

    1990-12-17

    The purpose of this report is to provide energy decision makers with accurate and timely information that may be used in forming various perspectives on electric issues. The power plants considered include coal, petroleum, natural gas, hydroelectric, and nuclear power plants. Data are presented for power generation, fuel consumption, fuel receipts and cost, sales of electricity, and unusual occurrences at power plants. Data are compared at the national, Census division, and state levels. 4 figs., 52 tabs. (CK)

  7. Nuclear reactor shield including magnesium oxide

    International Nuclear Information System (INIS)

    Rouse, C.A.; Simnad, M.T.

    1981-01-01

    An improvement is described for nuclear reactor shielding of a type used in reactor applications involving significant amounts of fast neutron flux. The reactor shielding includes means providing structural support, neutron moderator material, neutron absorber material and other components, wherein at least a portion of the neutron moderator material is magnesium in the form of magnesium oxide either alone or in combination with other moderator materials such as graphite and iron

  8. Model for safety reports including descriptive examples

    International Nuclear Information System (INIS)

    1995-12-01

    Several safety reports will be produced in the process of planning and constructing the system for disposal of high-level radioactive waste in Sweden. The present report gives a model, with detailed examples, of how these reports should be organized and what steps they should include. In the near future safety reports will deal with the encapsulation plant and the repository. Later reports will treat operation of the handling systems and the repository

  9. Jet-calculus approach including coherence effects

    International Nuclear Information System (INIS)

    Jones, L.M.; Migneron, R.; Narayanan, K.S.S.

    1987-01-01

    We show how integrodifferential equations typical of jet calculus can be combined with an averaging procedure to obtain jet-calculus-based results including the Mueller interference graphs. Results in longitudinal-momentum fraction x for physical quantities are higher at intermediate x and lower at large x than with the conventional ''incoherent'' jet calculus. These results resemble those of Marchesini and Webber, who used a Monte Carlo approach based on the same dynamics

  10. [Renal patient's diet: Can fish be included?].

    Science.gov (United States)

    Castro González, M I; Maafs Rodríguez, A G; Galindo Gómez, C

    2012-01-01

    Medical and nutritional treatment for renal disease, now a major public health issue, is highly complicated. Nutritional therapy must seek to retard renal dysfunction, maintain an optimal nutritional status and prevent the development of underlying pathologies. To analyze ten fish species to identify those that, because of their low phosphorus content, high biological value protein and elevated n-3 fatty acids EPA and DHA, could be included in renal patient's diet. The following fish species (Litte tunny, Red drum, Spotted eagleray, Escolar, Swordfish, Big-scale pomfret, Cortez flounder, Largemouth blackbass, Periche mojarra, Florida Pompano) were analyzed according to the AOAC and Keller techniques to determine their protein, phosphorus, sodium, potassium, cholesterol, vitamins D(3) and E, and n-3 EPA+DHA content. These results were used to calculate relations between nutrients. The protein in the analyzed species ranged from 16.5 g/100 g of fillet (Largemouth black bass) to 27.2 g/100 g (Red drum); the lowest phosphorus value was 28.6 mg/100 g (Periche mojarra) and the highest 216.3 mg/100 g (Spotted eagle ray). 80% of the fish presented > 100 mg EPA + DHA in 100 g of fillet. By its Phosphorus/gProtein ratio, Escolar and Swordfish could not be included in the renal diet; Little tunny, Escolar, Big-scale pomfret, Largemouth black-bass, Periche mojarra and Florida Pompano presented a lower Phosphorus/EPA + DHA ratio. Florida pompano is the most recommended specie for renal patients, due to its optimal nutrient relations. However, all analyzed species, except Escolar and Swordfish, could be included in renal diets.

  11. MOS modeling hierarchy including radiation effects

    International Nuclear Information System (INIS)

    Alexander, D.R.; Turfler, R.M.

    1975-01-01

    A hierarchy of modeling procedures has been developed for MOS transistors, circuit blocks, and integrated circuits which include the effects of total dose radiation and photocurrent response. The models were developed for use with the SCEPTRE circuit analysis program, but the techniques are suitable for other modern computer aided analysis programs. The modeling hierarchy permits the designer or analyst to select the level of modeling complexity consistent with circuit size, parametric information, and accuracy requirements. Improvements have been made in the implementation of important second order effects in the transistor MOS model, in the definition of MOS building block models, and in the development of composite terminal models for MOS integrated circuits

  12. Drug delivery device including electrolytic pump

    KAUST Repository

    Foulds, Ian G.; Buttner, Ulrich; Yi, Ying

    2016-01-01

    Systems and methods are provided for a drug delivery device and use of the device for drug delivery. In various aspects, the drug delivery device combines a “solid drug in reservoir” (SDR) system with an electrolytic pump. In various aspects an improved electrolytic pump is provided including, in particular, an improved electrolytic pump for use with a drug delivery device, for example an implantable drug delivery device. A catalytic reformer can be incorporated in a periodically pulsed electrolytic pump to provide stable pumping performance and reduced actuation cycle.

  13. Drug delivery device including electrolytic pump

    KAUST Repository

    Foulds, Ian G.

    2016-03-31

    Systems and methods are provided for a drug delivery device and use of the device for drug delivery. In various aspects, the drug delivery device combines a “solid drug in reservoir” (SDR) system with an electrolytic pump. In various aspects an improved electrolytic pump is provided including, in particular, an improved electrolytic pump for use with a drug delivery device, for example an implantable drug delivery device. A catalytic reformer can be incorporated in a periodically pulsed electrolytic pump to provide stable pumping performance and reduced actuation cycle.

  14. Energy principle with included boundary conditions

    International Nuclear Information System (INIS)

    Lehnert, B.

    1994-01-01

    Earlier comments by the author on the limitations of the classical form of the extended energy principle are supported by a complementary analysis on the potential energy change arising from free-boundary displacements of a magnetically confined plasma. In the final formulation of the extended principle, restricted displacements, satisfying pressure continuity by means of plasma volume currents in a thin boundary layer, are replaced by unrestricted (arbitrary) displacements which can give rise to induced surface currents. It is found that these currents contribute to the change in potential energy, and that their contribution is not taken into account by such a formulation. A general expression is further given for surface currents induced by arbitrary displacements. The expression is used to reformulate the energy principle for the class of displacements which satisfy all necessary boundary conditions, including that of the pressure balance. This makes a minimization procedure of the potential energy possible, for the class of all physically relevant test functions which include the constraints imposed by the boundary conditions. Such a procedure is also consistent with a corresponding variational calculus. (Author)

  15. Aerosol simulation including chemical and nuclear reactions

    International Nuclear Information System (INIS)

    Marwil, E.S.; Lemmon, E.C.

    1985-01-01

    The numerical simulation of aerosol transport, including the effects of chemical and nuclear reactions presents a challenging dynamic accounting problem. Particles of different sizes agglomerate and settle out due to various mechanisms, such as diffusion, diffusiophoresis, thermophoresis, gravitational settling, turbulent acceleration, and centrifugal acceleration. Particles also change size, due to the condensation and evaporation of materials on the particle. Heterogeneous chemical reactions occur at the interface between a particle and the suspending medium, or a surface and the gas in the aerosol. Homogeneous chemical reactions occur within the aersol suspending medium, within a particle, and on a surface. These reactions may include a phase change. Nuclear reactions occur in all locations. These spontaneous transmutations from one element form to another occur at greatly varying rates and may result in phase or chemical changes which complicate the accounting process. This paper presents an approach for inclusion of these effects on the transport of aerosols. The accounting system is very complex and results in a large set of stiff ordinary differential equations (ODEs). The techniques for numerical solution of these ODEs require special attention to achieve their solution in an efficient and affordable manner. 4 refs

  16. Addressing Stillbirth in India Must Include Men.

    Science.gov (United States)

    Roberts, Lisa; Montgomery, Susanne; Ganesh, Gayatri; Kaur, Harinder Pal; Singh, Ratan

    2017-07-01

    Millennium Development Goal 4, to reduce child mortality, can only be achieved by reducing stillbirths globally. A confluence of medical and sociocultural factors contribute to the high stillbirth rates in India. The psychosocial aftermath of stillbirth is a well-documented public health problem, though less is known of the experience for men, particularly outside of the Western context. Therefore, men's perceptions and knowledge regarding reproductive health, as well as maternal-child health are important. Key informant interviews (n = 5) were analyzed and 28 structured interviews were conducted using a survey based on qualitative themes. Qualitative themes included men's dual burden and right to medical and reproductive decision making power. Wives were discouraged from expressing grief and pushed to conceive again. If not successful, particularly if a son was not conceived, a second wife was considered a solution. Quantitative data revealed that men with a history of stillbirths had greater anxiety and depression, perceived less social support, but had more egalitarian views towards women than men without stillbirth experience. At the same time fathers of stillbirths were more likely to be emotionally or physically abusive. Predictors of mental health, attitudes towards women, and perceived support are discussed. Patriarchal societal values, son preference, deficient women's autonomy, and sex-selective abortion perpetuate the risk for future poor infant outcomes, including stillbirth, and compounds the already higher risk of stillbirth for males. Grief interventions should explore and take into account men's perceptions, attitudes, and behaviors towards reproductive decision making.

  17. Including gauge corrections to thermal leptogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Huetig, Janine

    2013-05-17

    This thesis provides the first approach of a systematic inclusion of gauge corrections to leading order to the ansatz of thermal leptogenesis. We have derived a complete expression for the integrated lepton number matrix including all resummations needed. For this purpose, a new class of diagram has been invented, namely the cylindrical diagram, which allows diverse investigations into the topic of leptogenesis such as the case of resonant leptogenesis. After a brief introduction of the topic of the baryon asymmetry in the universe and a discussion of its most promising solutions as well as their advantages and disadvantages, we have presented our framework of thermal leptogenesis. An effective model was described as well as the associated Feynman rules. The basis for using nonequilibrium quantum field theory has been built in chapter 3. At first, the main definitions have been presented for equilibrium thermal field theory, afterwards we have discussed the Kadanoff-Baym equations for systems out of equilibrium using the example of the Majorana neutrino. The equations have also been solved in the context of leptogenesis in chapter 4. Since gauge corrections play a crucial role throughout this thesis, we have also repeated the naive ansatz by replacing the free equilibrium propagator by propagators including thermal damping rates due to the Standard Model damping widths for lepton and Higgs fields. It is shown that this leads to a comparable result to the solutions of the Boltzmann equations for thermal leptogenesis. Thus it becomes obvious that Standard Model corrections are not negligible for thermal leptogenesis and therefore need to be included systematically from first principles. In order to achieve this we have started discussing the calculation of ladder rung diagrams for Majorana neutrinos using the HTL and the CTL approach in chapter 5. All gauge corrections are included in this framework and thus it has become the basis for the following considerations

  18. Including gauge corrections to thermal leptogenesis

    International Nuclear Information System (INIS)

    Huetig, Janine

    2013-01-01

    This thesis provides the first approach of a systematic inclusion of gauge corrections to leading order to the ansatz of thermal leptogenesis. We have derived a complete expression for the integrated lepton number matrix including all resummations needed. For this purpose, a new class of diagram has been invented, namely the cylindrical diagram, which allows diverse investigations into the topic of leptogenesis such as the case of resonant leptogenesis. After a brief introduction of the topic of the baryon asymmetry in the universe and a discussion of its most promising solutions as well as their advantages and disadvantages, we have presented our framework of thermal leptogenesis. An effective model was described as well as the associated Feynman rules. The basis for using nonequilibrium quantum field theory has been built in chapter 3. At first, the main definitions have been presented for equilibrium thermal field theory, afterwards we have discussed the Kadanoff-Baym equations for systems out of equilibrium using the example of the Majorana neutrino. The equations have also been solved in the context of leptogenesis in chapter 4. Since gauge corrections play a crucial role throughout this thesis, we have also repeated the naive ansatz by replacing the free equilibrium propagator by propagators including thermal damping rates due to the Standard Model damping widths for lepton and Higgs fields. It is shown that this leads to a comparable result to the solutions of the Boltzmann equations for thermal leptogenesis. Thus it becomes obvious that Standard Model corrections are not negligible for thermal leptogenesis and therefore need to be included systematically from first principles. In order to achieve this we have started discussing the calculation of ladder rung diagrams for Majorana neutrinos using the HTL and the CTL approach in chapter 5. All gauge corrections are included in this framework and thus it has become the basis for the following considerations

  19. The surgery of peripheral nerves (including tumors)

    DEFF Research Database (Denmark)

    Fugleholm, Kåre

    2013-01-01

    Surgical pathology of the peripheral nervous system includes traumatic injury, entrapment syndromes, and tumors. The recent significant advances in the understanding of the pathophysiology and cellular biology of peripheral nerve degeneration and regeneration has yet to be translated into improved...... surgical techniques and better outcome after peripheral nerve injury. Decision making in peripheral nerve surgery continues to be a complex challenge, where the mechanism of injury, repeated clinical evaluation, neuroradiological and neurophysiological examination, and detailed knowledge of the peripheral...... nervous system response to injury are prerequisite to obtain the best possible outcome. Surgery continues to be the primary treatment modality for peripheral nerve tumors and advances in adjuvant oncological treatment has improved outcome after malignant peripheral nerve tumors. The present chapter...

  20. AMS at the ANU including biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Fifield, L K; Allan, G L; Cresswell, R G; Ophel, T R [Australian National Univ., Canberra, ACT (Australia); King, S J; Day, J P [Manchester Univ. (United Kingdom). Dept. of Chemistry

    1994-12-31

    An extensive accelerator mass spectrometry program has been conducted on the 14UD accelerator at the Australian National University since 1986. In the two years since the previous conference, the research program has expanded significantly to include biomedical applications of {sup 26}Al and studies of landform evolution using isotopes produced in situ in surface rocks by cosmic ray bombardment. The system is now used for the measurement of {sup 10}Be, {sup 14}C, {sup 26}Al, {sup 36}Cl, {sup 59}Ni and {sup 129}I, and research is being undertaken in hydrology, environmental geochemistry, archaeology and biomedicine. On the technical side, a new test system has permitted the successful off-line development of a high-intensity ion source. A new injection line to the 14UD has been established and the new source is now in position and providing beams to the accelerator. 4 refs.

  1. AMS at the ANU including biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Fifield, L.K.; Allan, G.L.; Cresswell, R.G.; Ophel, T.R. [Australian National Univ., Canberra, ACT (Australia); King, S.J.; Day, J.P. [Manchester Univ. (United Kingdom). Dept. of Chemistry

    1993-12-31

    An extensive accelerator mass spectrometry program has been conducted on the 14UD accelerator at the Australian National University since 1986. In the two years since the previous conference, the research program has expanded significantly to include biomedical applications of {sup 26}Al and studies of landform evolution using isotopes produced in situ in surface rocks by cosmic ray bombardment. The system is now used for the measurement of {sup 10}Be, {sup 14}C, {sup 26}Al, {sup 36}Cl, {sup 59}Ni and {sup 129}I, and research is being undertaken in hydrology, environmental geochemistry, archaeology and biomedicine. On the technical side, a new test system has permitted the successful off-line development of a high-intensity ion source. A new injection line to the 14UD has been established and the new source is now in position and providing beams to the accelerator. 4 refs.

  2. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of the "LabView Basic I" and "LabView Intermediate II" courses have recently been changed to include, respectively, an introduction to and expert training in the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to developing expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course pr...

  3. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of the "LabView Basic I" and "LabView Intermediate II" courses have recently been changed to include, respectively, an introduction to and expert training in the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to developing expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course prepares participants to develop test and measurement, da...

  4. CERN Technical Training: LABVIEW courses include RADE

    CERN Multimedia

    HR Department

    2009-01-01

    The contents of "LabView Basic I" and "LabView Intermediate II" trainings have been recently changed to include, respectively, an introduction and an expert training on the Rapid Application Development Environment (RADE). RADE is a LabView-based application developed at CERN to integrate LabView in the accelerator and experiment control infrastructure. It is a suitable solution to develop expert tools, machine development analysis and independent test facilities. The course names have also been changed to "LabVIEW Basics I with RADE Introduction" and "LabVIEW Intermediate II with Advanced RADE Application". " LabVIEW Basics I with RADE Introduction" is designed for: Users preparing to develop applications using LabVIEW, or NI Developer Suite; users and technical managers evaluating LabVIEW or NI Developer Suite in purchasing decisions; users pursuing the Certified LabVIEW Developer certification. The course prepare...

  5. Critical point anomalies include expansion shock waves

    Energy Technology Data Exchange (ETDEWEB)

    Nannan, N. R., E-mail: ryan.nannan@uvs.edu [Mechanical Engineering Discipline, Anton de Kom University of Suriname, Leysweg 86, PO Box 9212, Paramaribo, Suriname and Process and Energy Department, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft (Netherlands); Guardone, A., E-mail: alberto.guardone@polimi.it [Department of Aerospace Science and Technology, Politecnico di Milano, Via La Masa 34, 20156 Milano (Italy); Colonna, P., E-mail: p.colonna@tudelft.nl [Propulsion and Power, Delft University of Technology, Kluyverweg 1, 2629 HS Delft (Netherlands)

    2014-02-15

    From first-principle fluid dynamics, complemented by a rigorous state equation accounting for critical anomalies, we discovered that expansion shock waves may occur in the vicinity of the liquid-vapor critical point in the two-phase region. Due to universality of near-critical thermodynamics, the result is valid for any common pure fluid in which molecular interactions are only short-range, namely, for so-called 3-dimensional Ising-like systems, and under the assumption of thermodynamic equilibrium. In addition to rarefaction shock waves, diverse non-classical effects are admissible, including composite compressive shock-fan-shock waves, due to the change of sign of the fundamental derivative of gasdynamics.

  6. CLIC expands to include the Southern Hemisphere

    CERN Multimedia

    Roberto Cantoni

    2010-01-01

    Australia has recently joined the CLIC collaboration: the enlargement will bring new expertise and resources to the project, and is especially welcome in the wake of CERN budget redistributions following the recent adoption of the Medium Term Plan.   The countries involved in CLIC collaboration With the signing of a Memorandum of Understanding on 26 August 2010, the ACAS network (Australian Collaboration for Accelerator Science) became the 40th member of in the multilateral CLIC collaboration making Australia the 22nd country to join the collaboration. “The new MoU was signed by the ACAS network, which includes the Australian Synchrotron and the University of Melbourne”, explains Jean-Pierre Delahaye, CLIC Study Leader. “Thanks to their expertise, the Australian institutes will contribute greatly to the CLIC damping rings and the two-beam test modules." Institutes from any country wishing to join the CLIC collaboration are invited to assume responsibility o...

  7. Should Broca's area include Brodmann area 47?

    Science.gov (United States)

    Ardila, Alfredo; Bernal, Byron; Rosselli, Monica

    2017-02-01

    Understanding brain organization of speech production has been a principal goal of neuroscience. Historically, brain speech production has been associated with so-called Broca’s area (Brodmann area –BA- 44 and 45), however, modern neuroimaging developments suggest speech production is associated with networks rather than with areas. The purpose of this paper was to analyze the connectivity of BA47 ( pars orbitalis) in relation to language . A meta-analysis was conducted to assess the language network in which BA47 is involved. The Brainmap database was used. Twenty papers corresponding to 29 experimental conditions with a total of 373 subjects were included. Our results suggest that BA47 participates in a “frontal language production system” (or extended Broca’s system). The BA47  connectivity found is also concordant with a minor role in language semantics. BA47 plays a central role in the language production system.

  8. Musculoskeletal ultrasound including definitions for ultrasonographic pathology

    DEFF Research Database (Denmark)

    Wakefield, RJ; Balint, PV; Szkudlarek, Marcin

    2005-01-01

    Ultrasound (US) has great potential as an outcome in rheumatoid arthritis trials for detecting bone erosions, synovitis, tendon disease, and enthesopathy. It has a number of distinct advantages over magnetic resonance imaging, including good patient tolerability and ability to scan multiple joints...... in a short period of time. However, there are scarce data regarding its validity, reproducibility, and responsiveness to change, making interpretation and comparison of studies difficult. In particular, there are limited data describing standardized scanning methodology and standardized definitions of US...... pathologies. This article presents the first report from the OMERACT ultrasound special interest group, which has compared US against the criteria of the OMERACT filter. Also proposed for the first time are consensus US definitions for common pathological lesions seen in patients with inflammatory arthritis....

  9. Grand unified models including extra Z bosons

    International Nuclear Information System (INIS)

    Li Tiezhong

    1989-01-01

    The grand unified theories (GUT) of the simple Lie groups including extra Z bosons are discussed. Under authors's hypothesis there are only SU 5+m SO 6+4n and E 6 groups. The general discussion of SU 5+m is given, then the SU 6 and SU 7 are considered. In SU 6 the 15+6 * +6 * fermion representations are used, which are not same as others in fermion content, Yukawa coupling and broken scales. A conception of clans of particles, which are not families, is suggested. These clans consist of extra Z bosons and the corresponding fermions of the scale. The all of fermions in the clans are down quarks except for the standard model which consists of Z bosons and 15 fermions, therefore, the spectrum of the hadrons which are composed of these down quarks are different from hadrons at present

  10. Including climate change in energy investment decisions

    International Nuclear Information System (INIS)

    Ybema, J.R.; Boonekamp, P.G.M.; Smit, J.T.J.

    1995-08-01

    To properly take climate change into account in the analysis of energy investment decisions, it is required to apply decision analysis methods that are capable of considering the specific characteristics of climate change (large uncertainties, long term horizon). Such decision analysis methods do exist. They can explicitly include evolving uncertainties, multi-stage decisions, cumulative effects and risk averse attitudes. Various methods are considered in this report and two of these methods have been selected: hedging calculations and sensitivity analysis. These methods are applied to illustrative examples, and its limitations are discussed. The examples are (1a) space heating and hot water for new houses from a private investor perspective and (1b) as example (1a) but from a government perspective, (2) electricity production with an integrated coal gasification combined cycle (ICGCC) with or without CO 2 removal, and (3) national energy strategy to hedge for climate change. 9 figs., 21 tabs., 42 refs., 1 appendix

  11. Education Program on Fossil Resources Including Coal

    Science.gov (United States)

    Usami, Masahiro

    Fossil fuels including coal play a key role as crucial energies in contributing to economic development in Asia. On the other hand, its limited quantity and the environmental problems causing from its usage have become a serious global issue and a countermeasure to solve such problems is very much demanded. Along with the pursuit of sustainable development, environmentally-friendly use of highly efficient fossil resources should be therefore, accompanied. Kyushu-university‧s sophisticated research through long years of accumulated experience on the fossil resources and environmental sectors together with the advanced large-scale commercial and empirical equipments will enable us to foster cooperative research and provide internship program for the future researchers. Then, this program is executed as a consignment business from the Ministry of Economy, Trade and Industry from 2007 fiscal year to 2009 fiscal year. The lecture that uses the textbooks developed by this program is scheduled to be started a course in fiscal year 2010.

  12. Analysis of Smart Composite Structures Including Debonding

    Science.gov (United States)

    Chattopadhyay, Aditi; Seeley, Charles E.

    1997-01-01

    Smart composite structures with distributed sensors and actuators have the capability to actively respond to a changing environment while offering significant weight savings and additional passive controllability through ply tailoring. Piezoelectric sensing and actuation of composite laminates is the most promising concept due to the static and dynamic control capabilities. Essential to the implementation of these smart composites are the development of accurate and efficient modeling techniques and experimental validation. This research addresses each of these important topics. A refined higher order theory is developed to model composite structures with surface bonded or embedded piezoelectric transducers. These transducers are used as both sensors and actuators for closed loop control. The theory accurately captures the transverse shear deformation through the thickness of the smart composite laminate while satisfying stress free boundary conditions on the free surfaces. The theory is extended to include the effect of debonding at the actuator-laminate interface. The developed analytical model is implemented using the finite element method utilizing an induced strain approach for computational efficiency. This allows general laminate geometries and boundary conditions to be analyzed. The state space control equations are developed to allow flexibility in the design of the control system. Circuit concepts are also discussed. Static and dynamic results of smart composite structures, obtained using the higher order theory, are correlated with available analytical data. Comparisons, including debonded laminates, are also made with a general purpose finite element code and available experimental data. Overall, very good agreement is observed. Convergence of the finite element implementation of the higher order theory is shown with exact solutions. Additional results demonstrate the utility of the developed theory to study piezoelectric actuation of composite

  13. Zγ production at NNLO including anomalous couplings

    Science.gov (United States)

    Campbell, John M.; Neumann, Tobias; Williams, Ciaran

    2017-11-01

    In this paper we present a next-to-next-to-leading order (NNLO) QCD calculation of the processes pp → l + l -γ and pp\\to ν \\overline{ν}γ that we have implemented in MCFM. Our calculation includes QCD corrections at NNLO both for the Standard Model (SM) and additionally in the presence of Zγγ and ZZγ anomalous couplings. We compare our implementation, obtained using the jettiness slicing approach, with a previous SM calculation and find broad agreement. Focusing on the sensitivity of our results to the slicing parameter, we show that using our setup we are able to compute NNLO cross sections with numerical uncertainties of about 0.1%, which is small compared to residual scale uncertainties of a few percent. We study potential improvements using two different jettiness definitions and the inclusion of power corrections. At √{s}=13 TeV we present phenomenological results and consider Zγ as a background to H → Zγ production. We find that, with typical cuts, the inclusion of NNLO corrections represents a small effect and loosens the extraction of limits on anomalous couplings by about 10%.

  14. Alternating phase focussing including space charge

    International Nuclear Information System (INIS)

    Cheng, W.H.; Gluckstern, R.L.

    1992-01-01

    Longitudinal stability can be obtained in a non-relativistic drift tube accelerator by traversing each gap as the rf accelerating field rises. However, the rising accelerating field leads to a transverse defocusing force which is usually overcome by magnetic focussing inside the drift tubes. The radio frequency quadrupole is one way of providing simultaneous longitudinal and transverse focusing without the use of magnets. One can also avoid the use of magnets by traversing alternate gaps between drift tubes as the field is rising and falling, thus providing an alternation of focussing and defocusing forces in both the longitudinal and transverse directions. The stable longitudinal phase space area is quite small, but recent efforts suggest that alternating phase focussing (APF) may permit low velocity acceleration of currents in the 100-300 ma range. This paper presents a study of the parameter space and a test of crude analytic predictions by adapting the code PARMILA, which includes space charge, to APF. 6 refs., 3 figs

  15. Probabilistic production simulation including CHP plants

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, H.V.; Palsson, H.; Ravn, H.F.

    1997-04-01

    A probabilistic production simulation method is presented for an energy system containing combined heat and power plants. The method permits incorporation of stochastic failures (forced outages) of the plants and is well suited for analysis of the dimensioning of the system, that is, for finding the appropriate types and capacities of production plants in relation to expansion planning. The method is in the tradition of similar approaches for the analysis of power systems, based on the load duration curve. The present method extends on this by considering a two-dimensional load duration curve where the two dimensions represent heat and power. The method permits the analysis of a combined heat and power system which includes all the basic relevant types of plants, viz., condensing plants, back pressure plants, extraction plants and heat plants. The focus of the method is on the situation where the heat side has priority. This implies that on the power side there may be imbalances between demand and production. The method permits quantification of the expected power overflow, the expected unserviced power demand, and the expected unserviced heat demand. It is shown that a discretization method as well as double Fourier series may be applied in algorithms based on the method. (au) 1 tab., 28 ills., 21 refs.

  16. Langevin simulations of QCD, including fermions

    International Nuclear Information System (INIS)

    Kronfeld, A.S.

    1986-02-01

    We encounter critical slow down in updating when xi/a -> infinite and in matrix inversion (needed to include fermions) when msub(q)a -> 0. A simulation that purports to solve QCD numerically will encounter these limits, so to face the challenge in the title of this workshop, we must cure the disease of critical slow down. Physically, this critical slow down is due to the reluctance of changes at short distances to propagate to large distances. Numerically, the stability of an algorithm at short wavelengths requires a (moderately) small step size; critical slow down occurs when the effective long wavelength step size becomes tiny. The remedy for this disease is an algorithm that propagates signals quickly throughout the system; i.e. one whose effective step size is not reduced for the long wavelength conponents of the fields. (Here the effective ''step size'' is essentially an inverse decorrelation time.) To do so one must resolve various wavelengths of the system and modify the dynamics (in CPU time) of the simulation so that all modes evolve at roughly the same rate. This can be achieved by introducing Fourier transforms. I show how to implement Fourier acceleration for Langevin updating and for conjugate gradient matrix inversion. The crucial feature of these algorithms that lends them to Fourier acceleration is that they update the lattice globally; hence the Fourier transforms are computed once per sweep rather than once per hit. (orig./HSI)

  17. SEEPAGE MODEL FOR PA INCLUDING DRIFT COLLAPSE

    International Nuclear Information System (INIS)

    C. Tsang

    2004-01-01

    The purpose of this report is to document the predictions and analyses performed using the seepage model for performance assessment (SMPA) for both the Topopah Spring middle nonlithophysal (Tptpmn) and lower lithophysal (Tptpll) lithostratigraphic units at Yucca Mountain, Nevada. Look-up tables of seepage flow rates into a drift (and their uncertainty) are generated by performing numerical simulations with the seepage model for many combinations of the three most important seepage-relevant parameters: the fracture permeability, the capillary-strength parameter 1/a, and the percolation flux. The percolation flux values chosen take into account flow focusing effects, which are evaluated based on a flow-focusing model. Moreover, multiple realizations of the underlying stochastic permeability field are conducted. Selected sensitivity studies are performed, including the effects of an alternative drift geometry representing a partially collapsed drift from an independent drift-degradation analysis (BSC 2004 [DIRS 166107]). The intended purpose of the seepage model is to provide results of drift-scale seepage rates under a series of parameters and scenarios in support of the Total System Performance Assessment for License Application (TSPA-LA). The SMPA is intended for the evaluation of drift-scale seepage rates under the full range of parameter values for three parameters found to be key (fracture permeability, the van Genuchten 1/a parameter, and percolation flux) and drift degradation shape scenarios in support of the TSPA-LA during the period of compliance for postclosure performance [Technical Work Plan for: Performance Assessment Unsaturated Zone (BSC 2002 [DIRS 160819], Section I-4-2-1)]. The flow-focusing model in the Topopah Spring welded (TSw) unit is intended to provide an estimate of flow focusing factors (FFFs) that (1) bridge the gap between the mountain-scale and drift-scale models, and (2) account for variability in local percolation flux due to

  18. An Integrated Biochemistry Laboratory, Including Molecular Modeling

    Science.gov (United States)

    Hall, Adele J. Wolfson Mona L.; Branham, Thomas R.

    1996-11-01

    The dilemma of designing an advanced undergraduate laboratory lies in the desire to teach and reinforce basic principles and techniques while at the same time exposing students to the excitement of research. We report here on a one-semester, project-based biochemistry laboratory that combines the best features of a cookbook approach (high success rate, achievement of defined goals) with those of an investigative, discovery-based approach (student involvement in the experimental design, excitement of real research). Individual modules may be selected and combined to meet the needs of different courses and different institutions. The central theme of this lab is protein purification and design. This laboratory accompanies the first semester of biochemistry (Structure and Function of Macromolecules, a course taken mainly by junior and senior chemistry and biological chemistry majors). The protein chosen as the object of study is the enzyme lysozyme, which is utilized in all projects. It is suitable for a student lab because it is easily and inexpensively obtained from egg white and is extremely stable, and its high isoelectric point (pI = 11) allows for efficient separation from other proteins by ion-exchange chromatography. Furthermore, a literature search conducted by the resourceful student reveals a wealth of information, since lysozyme has been the subject of numerous studies. It was the first enzyme whose structure was determined by crystallography (1). Hendrickson et al. (2) have previously described an intensive one-month laboratory course centered around lysozyme, although their emphasis is on protein stability rather than purification and engineering. Lysozyme continues to be the focus of much exciting new work on protein folding and dynamics, structure and activity (3 - 5). This lab course includes the following features: (i) reinforcement of basic techniques, such as preparation of buffers, simple enzyme kinetics, and absorption spectroscopy; (ii

  19. Ionic liquids, electrolyte solutions including the ionic liquids, and energy storage devices including the ionic liquids

    Science.gov (United States)

    Gering, Kevin L.; Harrup, Mason K.; Rollins, Harry W.

    2015-12-08

    An ionic liquid including a phosphazene compound that has a plurality of phosphorus-nitrogen units and at least one pendant group bonded to each phosphorus atom of the plurality of phosphorus-nitrogen units. One pendant group of the at least one pendant group comprises a positively charged pendant group. Additional embodiments of ionic liquids are disclosed, as are electrolyte solutions and energy storage devices including the embodiments of the ionic liquid.

  20. Catalyst support structure, catalyst including the structure, reactor including a catalyst, and methods of forming same

    Science.gov (United States)

    Van Norman, Staci A.; Aston, Victoria J.; Weimer, Alan W.

    2017-05-09

    Structures, catalysts, and reactors suitable for use for a variety of applications, including gas-to-liquid and coal-to-liquid processes and methods of forming the structures, catalysts, and reactors are disclosed. The catalyst material can be deposited onto an inner wall of a microtubular reactor and/or onto porous tungsten support structures using atomic layer deposition techniques.

  1. Launch Lock Assemblies Including Axial Gap Amplification Devices and Spacecraft Isolation Systems Including the Same

    Science.gov (United States)

    Barber, Tim Daniel (Inventor); Hindle, Timothy (Inventor); Young, Ken (Inventor); Davis, Torey (Inventor)

    2014-01-01

    Embodiments of a launch lock assembly are provided, as are embodiments of a spacecraft isolation system including one or more launch lock assemblies. In one embodiment, the launch lock assembly includes first and second mount pieces, a releasable clamp device, and an axial gap amplification device. The releasable clamp device normally maintains the first and second mount pieces in clamped engagement; and, when actuated, releases the first and second mount pieces from clamped engagement to allow relative axial motion there between. The axial gap amplification device normally residing in a blocking position wherein the gap amplification device obstructs relative axial motion between the first and second mount pieces. The axial gap amplification device moves into a non-blocking position when the first and second mount pieces are released from clamped engagement to increase the range of axial motion between the first and second mount pieces.

  2. Electrolyte solutions including a phosphoranimine compound, and energy storage devices including same

    Science.gov (United States)

    Klaehn, John R.; Dufek, Eric J.; Rollins, Harry W.; Harrup, Mason K.; Gering, Kevin L.

    2017-09-12

    An electrolyte solution comprising at least one phosphoranimine compound and a metal salt. The at least one phosphoranimine compound comprises a compound of the chemical structure ##STR00001## where X is an organosilyl group or a tert-butyl group and each of R.sup.1, R.sup.2, and R.sup.3 is independently selected from the group consisting of an alkyl group, an aryl group, an alkoxy group, or an aryloxy group. An energy storage device including the electrolyte solution is also disclosed.

  3. Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis in Both Haematological Malignancies and Solid Tumours: The Extraordinary Case of MYEOV Gene

    Directory of Open Access Journals (Sweden)

    Spyros I. Papamichos

    2015-01-01

    Full Text Available The incidence of cancer in human is high as compared to chimpanzee. However previous analysis has documented that numerous human cancer-related genes are highly conserved in chimpanzee. Till date whether human genome includes species-specific cancer-related genes that could potentially contribute to a higher cancer susceptibility remains obscure. This study focuses on MYEOV, an oncogene encoding for two protein isoforms, reported as causally involved in promoting cancer cell proliferation and metastasis in both haematological malignancies and solid tumours. First we document, via stringent in silico analysis, that MYEOV arose de novo in Catarrhini. We show that MYEOV short-isoform start codon was evolutionarily acquired after Catarrhini/Platyrrhini divergence. Throughout the course of Catarrhini evolution MYEOV acquired a gradually elongated translatable open reading frame (ORF, a gradually shortened translation-regulatory upstream ORF, and alternatively spliced mRNA variants. A point mutation introduced in human allowed for the acquisition of MYEOV long-isoform start codon. Second, we demonstrate the precious impact of exonized transposable elements on the creation of MYEOV gene structure. Third, we highlight that the initial part of MYEOV long-isoform coding DNA sequence was under positive selection pressure during Catarrhini evolution. MYEOV represents a Primate Orphan Gene that acquired, via ORF expansion, a human-protein-specific coding potential.

  4. Dictionary of scientific units including dimensionless numbers and scales

    National Research Council Canada - National Science Library

    Jerrard, H.G; McNeill, D.B

    1992-01-01

    .... The text includes the most recently accepted values of all units. Several disciplines, which have in the past employed few scientific principles and the dictionary has been extended to include examples of these.

  5. Should Relational Aggression Be Included in DSM-V?

    Science.gov (United States)

    Keenan, Kate; Coyne, Claire; Lahey, Benjamin B.

    2008-01-01

    The study examines whether relational aggression should be included in DSM-V disruptive behavior disorders. The results conclude that some additional information is gathered from assessing relational aggression but not enough to be included in DSM-V.

  6. Partially ionized plasmas including the third symposium on uranium plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, M. [ed.

    1976-09-01

    Separate abstracts are included for 28 papers on electrically generated plasmas, fission generated plasmas, nuclear pumped lasers, gaseous fuel reactor research, and applications. Five papers have been previously abstracted and included in ERA.

  7. 48 CFR 536.213-371 - Bids that include options.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Bids that include options... Contracting for Construction 536.213-371 Bids that include options. (a) Subject to the limitations in paragraph (c) of this section, you may include options in contracts if it is in the Government's interest...

  8. 29 CFR 780.616 - Operations included in raising livestock.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Operations included in raising livestock. 780.616 Section... Employment in Agriculture and Livestock Auction Operations Under the Section 13(b)(13) Exemption Requirements for Exemption § 780.616 Operations included in raising livestock. Raising livestock includes such...

  9. Stable Superstring Relics and Ultrahigh Energy Cosmic Rays

    CERN Document Server

    Coriano, Claudio; Plumacher, Michael; Coriano, Claudio; Faraggi, Alon E.; Plumacher, Michael

    2001-01-01

    One of the most intriguing experimental results of recent years is the observation of Ultrahigh Energy Cosmic Rays (UHECRs) above the GZK cutoff. Plausible candidates for the UHECR primaries are the decay products of a meta--stable matter state with mass of order O(10^{12-15 GeV}), which simultaneously is a good cold dark matter candidate. We study possible meta-stable matter states that arise from Wilson line breaking of GUT symmetries in semi-realistic heterotic string models. In the models that we study the exotic matter states can be classified according to patterns of SO(10) symmetry breaking. We show that cryptons, which are states that carry fractional electric charge $\\pm1/2$, and are confined by a hidden gauge group cannot produce viable dark matter. This is due to the fact that, in addition to the lightest neutral bound state, cryptons give rise to meta-stable charged bound states. However, these states may still account for the UHECR events. We argue that the uniton, which is an exotic Standard Mod...

  10. Late Quaternary sea level and environmental changes from relic ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Keywords. Late Quaternary sea level; western margin of India; subsidence; uplift; depositional environment. ...... sea level rise by about 80m (between 12,000 and. 7,000 yr BP) or, .... from the Florida Keys; Palaentology 28 189–206. Carballo ...

  11. EC infuses Serbian nuclear relic cleanup with critical donation

    International Nuclear Information System (INIS)

    2008-01-01

    Full text: As part of the Vinca Institute Nuclear Decommissioning (VIND) Programme, the Serbian government and the IAEA recently signed an $8.63 million (EUR 5.46 million) framework agreement with the European Commission to help fund activities related to decommissioning of the aging Cold War-era nuclear reactor. The European donation is the largest in the project's history, and the infusion of funds is vital to complete a crucial stage of the decommissioning programme. 'Thanks to the impressive contribution by the European Commission, we're one step closer to completing this important and complex project,' said John J. Kelly, the IAEA's Special Programme Manager for VIND. 'With radioactive waste, disused sources, and leaking spent fuel that's almost 45 years old, the Vinca site presents huge radiological challenges.' The task at Vinca is a mammoth undertaking, and the work is split into three major projects. In the first and most expensive project, old Soviet fuel, some of which is high-enriched uranium (HEU) that could be converted to weapons-grade material, must be safely repackaged and then prepared and repatriated to Russia for reprocessing. Once completed, the VIND spent fuel shipment will comprise the largest shipment of spent research reactor fuel in the European theatre, and extra shipping casks have already been built for the project through funding received from the USA. In the second VIND project, thousands of containers of unprocessed radioactive waste and disused sealed radioactive sources must be removed from old, degraded storage buildings, conditioned and packaged for safe, secure storage, and placed into new storage facilities, The new storage facilities are currently under construction and should be ready later this year. The third VIND project focuses on decommissioning of the research reactor. The reactor's draft decommissioning plan is almost finished, and plans are in place to begin some decommissioning and dismantlement activities in 2009. In addition to the radiological legacy at Vinca, security had long been a source of concern. The reactor has been offline since 1984, and much of the dangerous material and facilities were inadequately protected. Thanks to funding and other support activities provided by the Serbian government and the USA for security upgrades and police support, overall site security has been substantially improved over the past two years. Yet more needs to be done, and time is running out. Along with the EC's recent donation, an additional $25 million must be raised by 2010 to meet a crucial deadline. The fuel needs to be shipped back to Russia by the end of 2010 or the job falls off the shipping schedule, and potential funding for VIND would also dry up should the 2010 target date be missed. VIND is the largest one-house programme within the IAEA, and the EC contribution is the largest single contribution ever received for a Technical Cooperation (TC) national project. 'The EC support was absolutely crucial to the life of the programme, but we have quite a way to go to find the remaining $25 million for the project,' said Kelly. 'The EC contribution serves as a great example and encourages other potential donors to invest in an important and successful project.' Background: Located on the outskirts of Belgrade, the 'Institute for Nuclear Sciences (Vinca)' was set up as a research centre in the former Yugoslavia in the 1950s. A civilian nuclear research reactor loaded with high-enriched uranium was housed at the site. The area was also a central radioactive waste collection and consolidation centre for the former Yugoslavia. The grounds at Vinca accumulated all the former country's dangerous radioactive waste and other radioactive sources for nearly 45 years, and though the reactor went offline in 1984, the radioactive waste and sources received from around the country continued to pile up. International concern about Vinca mushroomed in the 1990s after the break-up of the former Yugoslavia, which led to increased international cooperation to remediate the site and reduce the radiological risk. Initial seed funding of $5 million to tackle the situation at Vinca was put forth in 2004 by the Nuclear Threat Initiative (NTI), a non-governmental organization dedicated to non-proliferation. VIND is part of the Russian Research Reactor Fuel Return Programme, a project borne out of the Global Threat Reduction Initiative. (IAEA)

  12. Diffusion theory in biology: a relic of mechanistic materialism.

    Science.gov (United States)

    Agutter, P S; Malone, P C; Wheatley, D N

    2000-01-01

    Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metalbolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science.

  13. Estimating relic magnetic fields from CMB temperature correlations

    International Nuclear Information System (INIS)

    Giovannini, Massimo

    2009-01-01

    The temperature and polarization inhomogeneities of the cosmic microwave background might bear the mark of predecoupling magnetism. The parameters of a putative magnetized background are hereby estimated, for the first time, from the observed temperature autocorrelation as well as from the measured temperature-polarization cross correlation.

  14. Estimating relic magnetic fields from CMB temperature correlations

    CERN Document Server

    Giovannini, Massimo

    2009-01-01

    The temperature and polarization inhomogeneities of the Cosmic Microwave Background might bear the mark of pre-decoupling magnetism. The parameters of a putative magnetized background are hereby estimated from the observed temperature autocorrelation as well as from the measured temperature-polarization cross-correlation.

  15. From Patrimonial Relics to Materialized Memories in the National Museum

    Directory of Open Access Journals (Sweden)

    Sandra Carolina Pulido Chaparro

    2015-02-01

    Full Text Available The following paper comes from an ethnographic work in the National Museum of Colombia, and it aims to analyze the objects exhibited in its halls and the store in order to understand the connection between patrimony and consumption. In this sense, the representation of the National Museum consolidates in the creation of a national identity based on the official history of the national heroes and their descendants, which is expressed in most of the objects displayed in the exhibit halls. On the other hand, another narrative guided by the neoliberal economy is constructed in the museum store. It takes afro, indigenous and rural representations that have been marginalized in most of the museum halls, strenghtened by the ethnic economy and promoted by tourism and advertising. This duality leads the museum visitors to consume both representations: the ones built by the State as well as the ones positioned by companies and multinationals.

  16. Is the ATPase from halobacterium saccharovorum an evolutionary relic?

    Science.gov (United States)

    Hochstein, L. I.; Altekar, W.; Kristjansson, H.

    1986-01-01

    The ATP Synthase Complex present in the membranes of mitochondria, chloroplasts or bacteria is composed of 2 sectors: FO, an integral membrane protein consisting of 3 subunits mediating proton translocation across the membrane and F1, the catalytic component composed of 5 non-identical subunits. The apparent early origin of the ATP Synthase Complex, as implied by its ubiquitous distribution, seems inconsistent with its structural and functional complexity and raises the question if simpler versions of the ATP Synthase exist. Such an ATP Synthase has been searched for in various Archaebacteria. A purified halobacterial ATPase activity which possesses certain properties consistent with those of an ATP Synthase but which has a different subunit structure is described.

  17. Relic dark energy from the trans-Planckian regime

    International Nuclear Information System (INIS)

    Mersini, Laura; Bastero-Gil, Mar; Kanti, Panagiota

    2001-01-01

    As yet, there is no underlying fundamental theory for the trans-Planckian regime. There is a need to address the issue of how the observables in our present Universe are affected by processes that may have occurred at super-Planckian energies (referred to as the trans-Planckian regime). Specifically, we focus on the impact the trans-Planckian regime has on two observables: namely, dark energy and the cosmic microwave background radiation (CMBR) spectrum. We model the trans-Planckian regime by introducing a 1-parameter family of smooth non-linear dispersion relations which modify the frequencies at very short distances. A particular feature of the family of dispersion functions chosen is the production of ultralow frequencies at very high momenta k (for k>M P ). We name the range of the ultralow energy modes (of very short distances) that have frequencies equal to or less than the current Hubble rate H 0 as the tail modes. These modes are still frozen today due to the expansion of the Universe. We calculate their energy today and show that the tail provides a strong candidate for the dark energy of the Universe. During inflation, their energy is about 122 to 123 orders of magnitude smaller than the total energy, for any random value of the free parameter in the family of dispersion relations. For this family of dispersions, we present the exact solutions and show that the CMBR spectrum is that of a (nearly) blackbody, and that the adiabatic vacuum is the only choice for the initial conditions

  18. Crumbs, Thieves, and Relics: Translation and Alien Humanism

    Science.gov (United States)

    McAlhany, Joseph

    2014-01-01

    Terence's famous humanistic motto, "homo sum: humani nil a me alienum puto," was transmitted from antiquity to modernity as an isolated fragment of a surviving play, and was subjected to various forms of translation and interpretation. In this essay, Joseph McAlhany argues that fragments and translation, by their nature, resist…

  19. Stellar Relics from the Early Galaxy T. Sivarani

    Indian Academy of Sciences (India)

    metal-poor stars is used to study the chemical history of the galaxy. Apart from this,. 5 .... They fit a color-magnitude diagram in order to trace different stellar population and derived a ... distinctly different stellar population with a different origin.

  20. The long-lived stau as a thermal relic

    Energy Technology Data Exchange (ETDEWEB)

    Pradler, Josef

    2009-07-20

    We consider physics beyond the Standard Model which implies the existence a of long-lived electromagnetically charged massive particle species (CHAMP) which we denote by X{sup {+-}}. We discuss in detail the unique sensitivity the early Universe exhibits on the mere presence and on the decay of such a particle. We carry out a detailed study of gravitino (G) dark matter scenarios in which the lighter scalar tau (stau, {tau}{sub 1}) is the lightest Standard Model superpartner so that {tau}{sub 1}=X. We also provide a thorough investigation of the thermal freeze-out process of {tau}{sub 1}. The thesis is divided into three parts: Part I: In this part we consider a generic but weak-scale CHAMP. In Chapter 1 we set the stage for the coming investigations by shortly reviewing the framework of Big Bang Nucleosynthesis (BBN), by working out the typical CHAMP freeze-out abundance, and by reviewing the stringent constraints arising from such a decaying component during/after BBN. In Chapter 2 we discuss the physics which emerges when the light elements fused in BBN are captured by X{sup -} at the time of primordial nucleosynthesis. In the remainder of this chapter we focus on the catalytic production of {sup 6}Li and {sup 9}Be. The second part is devoted to scenarios in which G is the lightest supersymmetric particle (LSP) and {tau}{sub 1} is the next-to-lightest SUSY particle (NLSP). In Chapter 3 we focus on the gravitino LSP as a dark matter candidate. In Chapter 4 we then focus on gravitino dark matter scenarios in which {tau}{sub 1} is the NLSP. In Part III we take an in-depth look into the chemical decoupling process of the long-lived {tau}{sub 1} from the primordial plasma. The quantity of interest is the thermal freeze-out abundance of the stau. We identify its dependence on the crucial SUSY parameters and also show that it sensitively depends on the details of the Higgs sector. Stau annihilation into final state Higgses as well as resonant annihilation via the heavy CP even Higgs boson can substantially deplete the decoupling yield. (orig.)

  1. 76 FR 61741 - Bmc Software, Inc. Including On-Site Leased Workers From COMSYS ITS Including Remote Workers...

    Science.gov (United States)

    2011-10-05

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-74,540] Bmc Software, Inc... November 23, 2010, applicable to workers of BMC Software, Inc., including on-site leased workers from... BMC Software, inc., including on-site leased workers from Comsys ITS, and including remote workers...

  2. Characterization of a genome-specific Gypsy-like retrotransposon ...

    Indian Academy of Sciences (India)

    2013-04-12

    Apr 12, 2013 ... E-mail: Guangbing Deng, denggb@cib.ac.cn; ... characterized using FISH image. ... CAAAA (invert) motif is boxed, and the 12-mer direct nucleotide repeats are under- lined. ... The fixed root tips were squashed on microscope.

  3. Characterization of a genome-specific Gypsy-like retrotransposon ...

    Indian Academy of Sciences (India)

    Aegilops ventricosa. As 106. DvDvMvMv. Ae. uniaristata. As136. M. Ae. tauschii. 38. D. T. durum - D. villosum amphipoild. Th1w, Th2w, Th3w, Th1,Th3. ABV. T. aestivum (CS) - D. villorum additional lines. Add. *. 1V-7V. ABDV. *. Add. indicates wheat - D. villosum addition lines. Journal of Genetics, Vol. 92, No. 1, April 2013.

  4. Insertional mutagenesis using Tnt1 retrotransposon in potato

    Science.gov (United States)

    Potato is the third most important food crop in the world. However, genetics and genomics research of potato has lagged behind many major crop species due to its autotetraploidy and a highly heterogeneous genome. Insertional mutagenesis using T-DNA or transposable elements, which is available in sev...

  5. Genomic and phylogenetic evidence of VIPER retrotransposon domestication in trypanosomatids

    Directory of Open Access Journals (Sweden)

    Adriana Ludwig

    Full Text Available Transposable elements are important residents of eukaryotic genomes and eventually the host can domesticate them to serve cellular functions. We reported here a possible domestication event of the vestigial interposed retroelement (VIPER in trypanosomatids. We found a large gene in a syntenic location in Leishmania braziliensis, L. panamensis, Leptomanas pyrrhocoris, and Crithidia fasciculata whose products share similarity in the C-terminal portion with the third protein of VIPER. No remnants of other VIPER regions surrounding the gene sequence were found. We hypothesise that the domestication event occurred more than 50 mya and the conservation of this gene suggests it might perform some function in the host species.

  6. Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins

    International Nuclear Information System (INIS)

    Montoya-Durango, Diego E.; Liu, Yongqing; Teneng, Ivo; Kalbfleisch, Ted; Lacy, Mary E.; Steffen, Marlene C.; Ramos, Kenneth S.

    2009-01-01

    Long interspersed nuclear elements (LINEs or L1 elements) are targeted for epigenetic silencing during early embryonic development and remain inactive in most cells and tissues. Here we show that E2F-Rb family complexes participate in L1 elements epigenetic regulation via nucleosomal histone modifications and recruitment of histone deacetylases (HDACs) HDAC1 and HDAC2. Our experiments demonstrated that (i) Rb and E2F interact with human and mouse L1 elements, (ii) L1 elements are deficient in both heterochromatin-associated histone marks H3 tri methyl K9 and H4 tri methyl K20 in Rb family triple knock out (Rb, p107, and p130) fibroblasts (TKO), (iii) L1 promoter exhibits increased histone H3 acetylation in the absence of HDAC1 and HDAC2 recruitment, (iv) L1 expression in TKO fibroblasts is upregulated compared to wild type counterparts, (v) L1 expression increases in the presence of the HDAC inhibitor TSA. On the basis of these findings we propose a model in which L1 sequences throughout the genome serve as centers for heterochromatin formation in an Rb family-dependent manner. As such, Rb proteins and L1 elements may play key roles in heterochromatin formation beyond pericentromeric chromosomal regions. These findings describe a novel mechanism of L1 reactivation in mammalian cells mediated by failure of corepressor protein recruitment by Rb, loss of histone epigenetic marks, heterochromatin formation, and increased histone H3 acetylation.

  7. Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins

    Energy Technology Data Exchange (ETDEWEB)

    Montoya-Durango, Diego E. [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Liu, Yongqing [James Graham Brown Cancer Center and Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Teneng, Ivo; Kalbfleisch, Ted; Lacy, Mary E.; Steffen, Marlene C. [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States); Ramos, Kenneth S., E-mail: kenneth.ramos@louisville.edu [Department of Biochemistry and Molecular Biology and Center for Genetics and Molecular Medicine, University of Louisville School of Medicine Health Sciences Center, Louisville, KY 40202 (United States)

    2009-06-01

    Long interspersed nuclear elements (LINEs or L1 elements) are targeted for epigenetic silencing during early embryonic development and remain inactive in most cells and tissues. Here we show that E2F-Rb family complexes participate in L1 elements epigenetic regulation via nucleosomal histone modifications and recruitment of histone deacetylases (HDACs) HDAC1 and HDAC2. Our experiments demonstrated that (i) Rb and E2F interact with human and mouse L1 elements, (ii) L1 elements are deficient in both heterochromatin-associated histone marks H3 tri methyl K9 and H4 tri methyl K20 in Rb family triple knock out (Rb, p107, and p130) fibroblasts (TKO), (iii) L1 promoter exhibits increased histone H3 acetylation in the absence of HDAC1 and HDAC2 recruitment, (iv) L1 expression in TKO fibroblasts is upregulated compared to wild type counterparts, (v) L1 expression increases in the presence of the HDAC inhibitor TSA. On the basis of these findings we propose a model in which L1 sequences throughout the genome serve as centers for heterochromatin formation in an Rb family-dependent manner. As such, Rb proteins and L1 elements may play key roles in heterochromatin formation beyond pericentromeric chromosomal regions. These findings describe a novel mechanism of L1 reactivation in mammalian cells mediated by failure of corepressor protein recruitment by Rb, loss of histone epigenetic marks, heterochromatin formation, and increased histone H3 acetylation.

  8. Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

    Directory of Open Access Journals (Sweden)

    Ma Bi

    2017-10-01

    Full Text Available Copia and Gypsy play important roles in structural, functional and evolutionary dynamics of plant genomes. In this study, a total of 106 and 101, Copia and Gypsy reverse transcriptase (rt were amplified respectively in the Morus notabilis genome using degenerate primers. All sequences exhibited high levels of heterogeneity, were rich in AT and possessed higher sequence divergence of Copia rt in comparison to Gypsy rt. Two reasons are likely to account for this phenomenon: a these elements often experience deletions or fragmentation by illegitimate or unequal homologous recombination in the transposition process; b strong purifying selective pressure drives the evolution of these elements through “selective silencing” with random mutation and eventual deletion from the host genome. Interestingly, mulberry rt clustered with other rt from distantly related taxa according to the phylogenetic analysis. This phenomenon did not result from horizontal transposable element transfer. Results obtained from fluorescence in situ hybridization revealed that most of the hybridization signals were preferentially concentrated in pericentromeric and distal regions of chromosomes, and these elements may play important roles in the regions in which they are found. Results of this study support the continued pursuit of further functional studies of Copia and Gypsy in the mulberry genome.

  9. Identification of SSR and retrotransposon-based molecular markers ...

    Indian Academy of Sciences (India)

    SOLEIMANI GEZELJEH ALI

    2018-03-13

    Mar 13, 2018 ... A 10 × 10 simple lattice design with two replications was employed to measure the ..... was applied for the analysis population structure by using a software package of ... polygenic system (figures 1 and 2). The minimum, max-.

  10. 26 CFR 1.1013-1 - Property included in inventory.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 11 2010-04-01 2010-04-01 true Property included in inventory. 1.1013-1 Section... inventory. The basis of property required to be included in inventory is the last inventory value of such property in the hands of the taxpayer. The requirements with respect to the valuation of an inventory are...

  11. 31 CFR 103.51 - Dollars as including foreign currency.

    Science.gov (United States)

    2010-07-01

    ... RECORDKEEPING AND REPORTING OF CURRENCY AND FOREIGN TRANSACTIONS General Provisions § 103.51 Dollars as including foreign currency. Wherever in this part an amount is stated in dollars, it shall be deemed to mean... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Dollars as including foreign currency...

  12. Microfluidic devices and methods including porous polymer monoliths

    Science.gov (United States)

    Hatch, Anson V; Sommer, Gregory J; Singh, Anup K; Wang, Ying-Chih; Abhyankar, Vinay V

    2014-04-22

    Microfluidic devices and methods including porous polymer monoliths are described. Polymerization techniques may be used to generate porous polymer monoliths having pores defined by a liquid component of a fluid mixture. The fluid mixture may contain iniferters and the resulting porous polymer monolith may include surfaces terminated with iniferter species. Capture molecules may then be grafted to the monolith pores.

  13. 7 CFR 1437.303 - Aquaculture, including ornamental fish.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Aquaculture, including ornamental fish. 1437.303... ASSISTANCE PROGRAM Determining Coverage Using Value § 1437.303 Aquaculture, including ornamental fish. (a... human consumption as determined by CCC. (2) Fish raised as feed for other fish that are consumed by...

  14. Solar Energy Education. Reader, Part II. Sun story. [Includes glossary

    Energy Technology Data Exchange (ETDEWEB)

    1981-05-01

    Magazine articles which focus on the subject of solar energy are presented. The booklet prepared is the second of a four part series of the Solar Energy Reader. Excerpts from the magazines include the history of solar energy, mythology and tales, and selected poetry on the sun. A glossary of energy related terms is included. (BCS)

  15. A framework for including family health spillovers in economic evaluation

    NARCIS (Netherlands)

    H. Al-Janabi (Hareth); N.J.A. van Exel (Job); W.B.F. Brouwer (Werner); J. Coast (Joanna)

    2016-01-01

    textabstractHealth care interventions may affect the health of patients' family networks. It has been suggested that these health spillovers? should be included in economic evaluation, but there is not a systematic method for doing this. In this article, we develop a framework for including health

  16. Articles which include chevron film cooling holes, and related processes

    Science.gov (United States)

    Bunker, Ronald Scott; Lacy, Benjamin Paul

    2014-12-09

    An article is described, including an inner surface which can be exposed to a first fluid; an inlet; and an outer surface spaced from the inner surface, which can be exposed to a hotter second fluid. The article further includes at least one row or other pattern of passage holes. Each passage hole includes an inlet bore extending through the substrate from the inlet at the inner surface to a passage hole-exit proximate to the outer surface, with the inlet bore terminating in a chevron outlet adjacent the hole-exit. The chevron outlet includes a pair of wing troughs having a common surface region between them. The common surface region includes a valley which is adjacent the hole-exit; and a plateau adjacent the valley. The article can be an airfoil. Related methods for preparing the passage holes are also described.

  17. Electric drive systems including smoothing capacitor cooling devices and systems

    Energy Technology Data Exchange (ETDEWEB)

    Dede, Ercan Mehmet; Zhou, Feng

    2017-02-28

    An electric drive system includes a smoothing capacitor including at least one terminal, a bus bar electrically coupled to the at least one terminal, a thermoelectric device including a first side and a second side positioned opposite the first side, where the first side is thermally coupled to at least one of the at least one terminal and the bus bar, and a cooling element thermally coupled to the second side of the thermoelectric device, where the cooling element dissipates heat from the thermoelectric device.

  18. Diabetes Nutrition: Including Sweets in Your Meal Plan

    Science.gov (United States)

    Diabetes nutrition: Including sweets in your meal plan Diabetes nutrition focuses on healthy foods, but sweets aren't necessarily ... your meal plan. By Mayo Clinic Staff Diabetes nutrition focuses on healthy foods. But you can eat ...

  19. Initiation devices, initiation systems including initiation devices and related methods

    Energy Technology Data Exchange (ETDEWEB)

    Daniels, Michael A.; Condit, Reston A.; Rasmussen, Nikki; Wallace, Ronald S.

    2018-04-10

    Initiation devices may include at least one substrate, an initiation element positioned on a first side of the at least one substrate, and a spark gap electrically coupled to the initiation element and positioned on a second side of the at least one substrate. Initiation devices may include a plurality of substrates where at least one substrate of the plurality of substrates is electrically connected to at least one adjacent substrate of the plurality of substrates with at least one via extending through the at least one substrate. Initiation systems may include such initiation devices. Methods of igniting energetic materials include passing a current through a spark gap formed on at least one substrate of the initiation device, passing the current through at least one via formed through the at least one substrate, and passing the current through an explosive bridge wire of the initiation device.

  20. Chronic Obstructive Pulmonary Disease (COPD) Includes: Chronic Bronchitis and Emphysema

    Science.gov (United States)

    ... Submit Button NCHS Home Chronic Obstructive Pulmonary Disease (COPD) Includes: Chronic Bronchitis and Emphysema Recommend on Facebook ... Percent of visits to office-based physicians with COPD indicated on the medical record: 3.2% Source: ...

  1. Including estimates of the future in today's financial statements

    OpenAIRE

    Mary Barth

    2006-01-01

    This paper explains why the question is how, not if, today's financial statements should include estimates of the future. Including such estimates is not new, but their use is increasing. This increase results primarily because standard setters believe asset and liability measures that reflect current economic conditions and up-to-date expectations of the future will result in more useful information for making economic decisions, which is the objective of financial reporting. This is why sta...

  2. 75 FR 16513 - B&C Corporation, JR Engineering Division, Including B&C Distribution Center, Including On-Site...

    Science.gov (United States)

    2010-04-01

    ... Engineering Division, Including B&C Distribution Center, Including On-Site Leased Workers From B&C Services... occurred during the relevant time period at the B&C Distribution Center, Inc. of the B&C Corporation, JR Engineering Division, Barberton, Ohio. The B&C Distribution Center provides distribution and logistical...

  3. [Origin of sennosides in health teas including Malva leaves].

    Science.gov (United States)

    Kojima, T; Kishi, M; Sekita, S; Satake, M

    2001-06-01

    The aim of this study is to clarify whether sennosides are contained in the leaf of Malva verticillata L., and then to clarify the source of sennosides in health teas including malva leaves. The identification and determination of sennosides were performed with thin layer chromatography and high performance liquid chromatography. The leaf of Malva verticillata L. did not contain sennosides A or B and could be easily distinguished from senna leaf. Our previous report showed that sennosides are contained in weight-reducing herbal teas including malva leaves, and that senna leaf is a herbal component in some teas. Furthermore, in 10 samples of health tea including malva leaves that were bought last year, the smallest amount of sennosides was 6.1 mg/bag, and all health teas including malva leaves contained the leaf and midrib of senna. We suggest that sennosides A and B are not contained in the leaf of Malva verticillata L., and that the sennosides in health teas including malva leaves are not derived from malva leaf but from senna leaf.

  4. Classical mechanics including an introduction to the theory of elasticity

    CERN Document Server

    Hentschke, Reinhard

    2017-01-01

    This textbook teaches classical mechanics as one of the foundations of physics. It describes the mechanical stability and motion in physical systems ranging from the molecular to the galactic scale. Aside from the standard topics of mechanics in the physics curriculum, this book includes an introduction to the theory of elasticity and its use in selected modern engineering applications, e.g. dynamic mechanical analysis of viscoelastic materials. The text also covers many aspects of numerical mechanics, ranging from the solution of ordinary differential equations, including molecular dynamics simulation of many particle systems, to the finite element method. Attendant Mathematica programs or parts thereof are provided in conjunction with selected examples. Numerous links allow the reader to connect to related subjects and research topics. Among others this includes statistical mechanics (separate chapter), quantum mechanics, space flight, galactic dynamics, friction, and vibration spectroscopy. An introductory...

  5. Internet addiction neuroscientific approaches and therapeutical implications including smartphone addiction

    CERN Document Server

    Reuter, Martin

    2017-01-01

    The second edition of this successful book provides further and in-depth insight into theoretical models dealing with Internet addiction, as well as includes new therapeutical approaches. The editors also broach the emerging topic of smartphone addiction. This book combines a scholarly introduction with state-of-the-art research in the characterization of Internet addiction. It is intended for a broad audience including scientists, students and practitioners. The first part of the book contains an introduction to Internet addiction and their pathogenesis. The second part of the book is dedicated to an in-depth review of neuroscientific findings which cover studies using a variety of biological techniques including brain imaging and molecular genetics. The third part of the book focuses on therapeutic interventions for Internet addiction. The fourth part of the present book is an extension to the first edition and deals with a new emerging potential disorder related to Internet addiction – smartphone addicti...

  6. Ceramic substrate including thin film multilayer surface conductor

    Science.gov (United States)

    Wolf, Joseph Ambrose; Peterson, Kenneth A.

    2017-05-09

    A ceramic substrate comprises a plurality of ceramic sheets, a plurality of inner conductive layers, a plurality of vias, and an upper conductive layer. The ceramic sheets are stacked one on top of another and include a top ceramic sheet. The inner conductive layers include electrically conductive material that forms electrically conductive features on an upper surface of each ceramic sheet excluding the top ceramic sheet. The vias are formed in each of the ceramic sheets with each via being filled with electrically conductive material. The upper conductive layer includes electrically conductive material that forms electrically conductive features on an upper surface of the top ceramic sheet. The upper conductive layer is constructed from a stack of four sublayers. A first sublayer is formed from titanium. A second sublayer is formed from copper. A third sublayer is formed from platinum. A fourth sublayer is formed from gold.

  7. Tunable cavity resonator including a plurality of MEMS beams

    Science.gov (United States)

    Peroulis, Dimitrios; Fruehling, Adam; Small, Joshua Azariah; Liu, Xiaoguang; Irshad, Wasim; Arif, Muhammad Shoaib

    2015-10-20

    A tunable cavity resonator includes a substrate, a cap structure, and a tuning assembly. The cap structure extends from the substrate, and at least one of the substrate and the cap structure defines a resonator cavity. The tuning assembly is positioned at least partially within the resonator cavity. The tuning assembly includes a plurality of fixed-fixed MEMS beams configured for controllable movement relative to the substrate between an activated position and a deactivated position in order to tune a resonant frequency of the tunable cavity resonator.

  8. Meta-structure and tunable optical device including the same

    Science.gov (United States)

    Han, Seunghoon; Papadakis, Georgia Theano; Atwater, Harry

    2017-12-26

    A meta-structure and a tunable optical device including the same are provided. The meta-structure includes a plurality of metal layers spaced apart from one another, an active layer spaced apart from the plurality of metal layers and having a carrier concentration that is tuned according to an electric signal applied to the active layer and the plurality of metal layers, and a plurality of dielectric layers spaced apart from one another and each having one surface contacting a metal layer among the plurality of metal layers and another surface contacting the active layer.

  9. EC6 safety enhancement - including impact of Fukushima lessons learned

    Energy Technology Data Exchange (ETDEWEB)

    Yu, S.; Zemdegs, R.; Boyle, S.; Soulard, M., E-mail: stephen.yu@candu.com [Candu Energy Inc., Mississauga, Ontario (Canada)

    2012-09-15

    The Enhanced CANDU 6 (EC6) is the new Generation III CANDU reactor design that meets the most up to date regulatory requirements and customer expectations. EC6 builds on the proven high performance design inch as the Qinshan CANDU 6 units and has made improvements to safety and operational performance, and has incorporated extensive operational feedback including Fukushima. The Fukushima Dai-ichi March 11, 2011 event has demonstrated the importance of defence-in-depth considerations for beyond-design basis events, including severe accidents. The EC6 design is based on the defence-in-depth principles and provides further design features that address the lessons learned from Fukushima. (author)

  10. Solar Energy Education. Renewable energy: a background text. [Includes glossary

    Energy Technology Data Exchange (ETDEWEB)

    1985-01-01

    Some of the most common forms of renewable energy are presented in this textbook for students. The topics include solar energy, wind power hydroelectric power, biomass ocean thermal energy, and tidal and geothermal energy. The main emphasis of the text is on the sun and the solar energy that it yields. Discussions on the sun's composition and the relationship between the earth, sun and atmosphere are provided. Insolation, active and passive solar systems, and solar collectors are the subtopics included under solar energy. (BCS)

  11. Methods of producing adsorption media including a metal oxide

    Science.gov (United States)

    Mann, Nicholas R; Tranter, Troy J

    2014-03-04

    Methods of producing a metal oxide are disclosed. The method comprises dissolving a metal salt in a reaction solvent to form a metal salt/reaction solvent solution. The metal salt is converted to a metal oxide and a caustic solution is added to the metal oxide/reaction solvent solution to adjust the pH of the metal oxide/reaction solvent solution to less than approximately 7.0. The metal oxide is precipitated and recovered. A method of producing adsorption media including the metal oxide is also disclosed, as is a precursor of an active component including particles of a metal oxide.

  12. Calculation of Permeability inside the Basket including one Fuel Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Seung Hwan; Bang, Kyung Sik; Lee, Ju an; Choi, Woo Seok [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    In general, the porous media model and the effective thermal conductivity were used to simply the fuel assembly. The methods of calculating permeability were compared considering the flow inside a basket which includes a nuclear fuel. Detailed fuel assembly was a computational modeling and the flow characteristics were investigated. The flow inside the basket which included a fuel assembly is analyzed by CFD. As the height of the fuel assembly increases, the pressure drop linearly increased. The inertia resistance could be neglected. Three methods to calculate the permeability were compared. The permeability by the friction factor is 50% less than the permeability by wall shear stress and pressure drop.

  13. 36 CFR 1254.94 - What must my request include?

    Science.gov (United States)

    2010-07-01

    ... includes the following elements: (1) Record group number or agency of origin or, for donated historical... volume in number of pages or cubic feet. (b) The estimated amount of time (work-days) that the microfilm... who would require training (see § 1254.108(b)). (c) The number and a description of the equipment that...

  14. 20 CFR 404.1013 - Included-excluded rule.

    Science.gov (United States)

    2010-04-01

    ... least one-half of your time in the pay period is in covered work. If you spend most of your time in a... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Included-excluded rule. 404.1013 Section 404.1013 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL OLD-AGE, SURVIVORS AND DISABILITY...

  15. Including Critical Thinking and Problem Solving in Physical Education

    Science.gov (United States)

    Pill, Shane; SueSee, Brendan

    2017-01-01

    Many physical education curriculum frameworks include statements about the inclusion of critical inquiry processes and the development of creativity and problem-solving skills. The learning environment created by physical education can encourage or limit the application and development of the learners' cognitive resources for critical and creative…

  16. Modelling a linear PM motor including magnetic saturation

    NARCIS (Netherlands)

    Polinder, H.; Slootweg, J.G.; Compter, J.C.; Hoeijmakers, M.J.

    2002-01-01

    The use of linear permanent-magnet (PM) actuators increases in a wide variety of applications because of the high force density, robustness and accuracy. The paper describes the modelling of a linear PM motor applied in, for example, wafer steppers, including magnetic saturation. This is important

  17. Sexually transmitted infections, including HIV, in the Netherlands in 2006

    NARCIS (Netherlands)

    MG van Veen; FDH Koedijk; IVF van der Broek; ELM Op de Coul; IM de Boer; AI van Sighem; MAB van der Sande; soa-centra; Stichting HIV Monitoring; EPI/Cib

    2007-01-01

    The nationally covered low threshold STI centres offering STI care targeted at high risk groups, provide surveillance data to monitor national trends in STI, including HIV. In 2006, chlamydia remained the most commonly diagnosed bacterial STI in the Netherlands in the STI centres, in spite of

  18. 40 CFR 1502.14 - Alternatives including the proposed action.

    Science.gov (United States)

    2010-07-01

    ... impacts of the proposal and the alternatives in comparative form, thus sharply defining the issues and... action so that reviewers may evaluate their comparative merits. (c) Include reasonable alternatives not... identify such alternative in the final statement unless another law prohibits the expression of such a...

  19. 31 CFR 306.87 - Partnerships (including nominee partnerships).

    Science.gov (United States)

    2010-07-01

    ... (including nominee partnerships). An assignment of a security registered in the name of or assigned to a... appropriate for winding up partnership affairs. In those cases where assignments by or in behalf of all... dissolution. Upon voluntary dissolution, for any jurisdiction where a general partner may not act in winding...

  20. 10 CFR 905.11 - What must an IRP include?

    Science.gov (United States)

    2010-01-01

    ..., energy conservation and efficiency, cogeneration and district heating and cooling applications, and..., consumer preferences, environmental impacts, demand or energy impacts, implementation issues, revenue... 10 Energy 4 2010-01-01 2010-01-01 false What must an IRP include? 905.11 Section 905.11 Energy...

  1. Smart Antenna Skins, including Conformal Array, MMICs and Applications

    NARCIS (Netherlands)

    Bogaart, F.L.M. van den

    2000-01-01

    Low-cost technologies are presented for future space-borne and airborne SAR systems. These technologies include state-of-the art highly integrated circuits to miniaturise front-end, solutions to lower-cost interconnection technologies, new beamforming aspects and new architectures. The MMICs address

  2. LTRACK: Beam-transport calculation including wakefield effects

    International Nuclear Information System (INIS)

    Chan, K.C.D.; Cooper, R.K.

    1988-01-01

    LTRACK is a first-order beam-transport code that includes wakefield effects up to quadrupole modes. This paper will introduce the readers to this computer code by describing the history, the method of calculations, and a brief summary of the input/output information. Future plans for the code will also be described

  3. Towards a general framework for including noise impacts in LCA

    NARCIS (Netherlands)

    Cucurachi, Stefano; Heijungs, Reinout; Ohlau, Katrin

    Purpose Several damages have been associated with the exposure of human beings to noise. These include auditory effects, i.e., hearing impairment, but also non-auditory physiological ones such as hypertension and ischemic heart disease, or psychological ones such as annoyance, depression, sleep

  4. 30 CFR 250.1007 - What to include in applications.

    Science.gov (United States)

    2010-07-01

    ... features and other pertinent data including area, lease, and block designations; water depths; route...) submitted for a pipeline right-of-way shall bear a signed certificate upon its face by the engineer who made... additional design precautions you took to enable the pipeline to withstand the effects of water currents...

  5. cDNA encoding a polypeptide including a hevein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

  6. Synthetic pulse radar including a microprocessor based controller

    International Nuclear Information System (INIS)

    Fowler, J.C.; Rubin, L.A.; Still, W.L.

    1980-01-01

    This invention relates to pulse radar detection of targets in extended media, including natural phenomena such as oil, coal and ore deposits within the earth. In particular, this invention relates to a pulse radar system employing a synthetic pulse formed from a fourier spectrum of frequencies generated and detected by a digitally controlled transmitter and receiver circuits

  7. Methodological challenges when doing research that includes ethnic minorities

    DEFF Research Database (Denmark)

    Morville, Anne-Le; Erlandsson, Lena-Karin

    2016-01-01

    minorities are included. Method: A thorough literature search yielded 21 articles obtained from the scientific databases PubMed, Cinahl, Web of Science and PsychInfo. Analysis followed Arksey and O’Malley’s framework for scoping reviews, applying content analysis. Results: The results showed methodological...

  8. Including patients’ perspectives in patient information leaflets: A polyocular approach

    DEFF Research Database (Denmark)

    Fage-Butler, Antoinette Mary

    2013-01-01

    Existing research reveals that patients’ perspectives are missing from mandatory patient information leaflets (PILs). At the same time, there is overwhelming consensus that they should be included in this genre, and a corresponding need for potential approaches to tackle this problem. This paper ...

  9. Prototype solar heating and cooling systems including potable hot water

    Science.gov (United States)

    1978-01-01

    Progress is reviewed in the development, delivery, and support of two prototype solar heating and cooling systems including potable hot water. The system consisted of the following subsystems: collector, auxiliary heating, potable hot water, storage, control, transport, and government-furnished site data acquisition.

  10. A Guide to Running a Recycling Project. [Includes Recycling Handbook].

    Science.gov (United States)

    Oregon Recycling Information and Organizing Network, Portland.

    This guide, designed for both students and adults, is intended for individuals who feel they might be interested in establishing a recycling depot. The guide includes such pertinent information as deciding how to set up a depot, markets and transportation, preparation of materials, where to place the depot and when to operate it, publicity and…

  11. 25 CFR 20.403 - What do protective services include?

    Science.gov (United States)

    2010-04-01

    ....403 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR HUMAN SERVICES FINANCIAL ASSISTANCE AND SOCIAL SERVICES PROGRAMS Services to Children, Elderly, and Families § 20.403 What do protective services include? Protective services provided to a child, family or elderly person will be documented in...

  12. Unsteady panel method for complex configurations including wake modeling

    CSIR Research Space (South Africa)

    Van Zyl, Lourens H

    2008-01-01

    Full Text Available implementations of the DLM are however not very versatile in terms of geometries that can be modeled. The ZONA6 code offers a versatile surface panel body model including a separated wake model, but uses a pressure panel method for lifting surfaces. This paper...

  13. Interviewing Objects: Including Educational Technologies as Qualitative Research Participants

    Science.gov (United States)

    Adams, Catherine A.; Thompson, Terrie Lynn

    2011-01-01

    This article argues the importance of including significant technologies-in-use as key qualitative research participants when studying today's digitally enhanced learning environments. We gather a set of eight heuristics to assist qualitative researchers in "interviewing" technologies-in-use (or other relevant objects), drawing on concrete…

  14. Towards ligand docking including explicit interface water molecules.

    Directory of Open Access Journals (Sweden)

    Gordon Lemmon

    Full Text Available Small molecule docking predicts the interaction of a small molecule ligand with a protein at atomic-detail accuracy including position and conformation the ligand but also conformational changes of the protein upon ligand binding. While successful in the majority of cases, docking algorithms including RosettaLigand fail in some cases to predict the correct protein/ligand complex structure. In this study we show that simultaneous docking of explicit interface water molecules greatly improves Rosetta's ability to distinguish correct from incorrect ligand poses. This result holds true for both protein-centric water docking wherein waters are located relative to the protein binding site and ligand-centric water docking wherein waters move with the ligand during docking. Protein-centric docking is used to model 99 HIV-1 protease/protease inhibitor structures. We find protease inhibitor placement improving at a ratio of 9:1 when one critical interface water molecule is included in the docking simulation. Ligand-centric docking is applied to 341 structures from the CSAR benchmark of diverse protein/ligand complexes [1]. Across this diverse dataset we see up to 56% recovery of failed docking studies, when waters are included in the docking simulation.

  15. 25 CFR 20.308 - What does earned income include?

    Science.gov (United States)

    2010-04-01

    ... self-employment, total profit from a business enterprise (i.e., gross receipts less expenses incurred in producing the goods or services). Business expenses do not include depreciation, personal business and entertainment expenses, personal transportation, capital equipment purchases, or principal...

  16. Visual Impairments, "Including Blindness." NICHCY Disability Fact Sheet #13

    Science.gov (United States)

    National Dissemination Center for Children with Disabilities, 2012

    2012-01-01

    Vision is one of the five senses. Being able to see gives tremendous access to learning about the world around--people's faces and the subtleties of expression, what different things look like and how big they are, and the physical environments, including approaching hazards. When a child has a visual impairment, it is cause for immediate…

  17. Truck Drivers And Risk Of STDs Including HIV

    Directory of Open Access Journals (Sweden)

    Bansal R.K

    1995-01-01

    Full Text Available Research Question: Whether long distance truck drivers are at a higher risk of contracting and transmitting STDs including HIV? Objectives: i To study the degree of knowledge of HIV and AIDS among long- distance truck drivers. ii Assess their sexual behaviour including condom use. iii Explore their prevailing social influences and substance abuse patterns. iv Explore their treatment seeking bahaviour as regards STDs. v Deduce their risk of contracting and transmitting STDs including HIV. Study Design: Cross- sectional interview. Setting: Transport Nagar, Indore (M.P Participants: 210 senior drivers (First drivers and 210 junior drivers (Second drivers. Study Variables: Extra-Marital sexual intercourse, condom usage, past and present history of STDs, treatment and counseling, substance abuse, social â€" cultural milieu. Outcome Variables: Risk of contraction of STDs. Statistical Analysis: Univariate analysis. Results: 94% of the drivers were totally ignorant about AIDS. 82.9% and 43.8 % of the senior and junior drivers had a history of extra- marital sex and of these only 2 regularly used condoms. 13.8% and 3.3 % of the senior and junior drivers had a past or present history suggestive of STD infection. Alcohol and Opium were regularly used by them. Conclusion: The studied drivers are at a high risk of contracting and transmitting STDs including HIV.

  18. Including Students with Severe Disabilities in General Education Settings.

    Science.gov (United States)

    Wisniewski, Lech; Alper, Sandra

    1994-01-01

    This paper presents five systematic phases for bringing about successful regular education inclusion of students with severe disabilities. Phases include develop networks within the community, assess school and community resources, review strategies for integration, install strategies that lead to integration, and develop a system of feedback and…

  19. Simple suggestions for including vertical physics in oil spill models

    International Nuclear Information System (INIS)

    D'Asaro, Eric; University of Washington, Seatle, WA

    2001-01-01

    Current models of oil spills include no vertical physics. They neglect the effect of vertical water motions on the transport and concentration of floating oil. Some simple ways to introduce vertical physics are suggested here. The major suggestion is to routinely measure the density stratification of the upper ocean during oil spills in order to develop a database on the effect of stratification. (Author)

  20. 27 CFR 53.181 - Further manufacture included.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2010-04-01 2010-04-01 false Further manufacture... Further manufacture included. (a) In general. The payment of tax imposed by chapter 32 of the Code on the... of any use in further manufacture, or sale as part of a second manufactured article, described in...

  1. Energy storage device including a redox-enhanced electrolyte

    Science.gov (United States)

    Stucky, Galen; Evanko, Brian; Parker, Nicholas; Vonlanthen, David; Auston, David; Boettcher, Shannon; Chun, Sang-Eun; Ji, Xiulei; Wang, Bao; Wang, Xingfeng; Chandrabose, Raghu Subash

    2017-08-08

    An electrical double layer capacitor (EDLC) energy storage device is provided that includes at least two electrodes and a redox-enhanced electrolyte including two redox couples such that there is a different one of the redox couples for each of the electrodes. When charged, the charge is stored in Faradaic reactions with the at least two redox couples in the electrolyte and in a double-layer capacitance of a porous carbon material that comprises at least one of the electrodes, and a self-discharge of the energy storage device is mitigated by at least one of electrostatic attraction, adsorption, physisorption, and chemisorption of a redox couple onto the porous carbon material.

  2. Progressive IRP Models for Power Resources Including EPP

    Directory of Open Access Journals (Sweden)

    Yiping Zhu

    2017-01-01

    Full Text Available In the view of optimizing regional power supply and demand, the paper makes effective planning scheduling of supply and demand side resources including energy efficiency power plant (EPP, to achieve the target of benefit, cost, and environmental constraints. In order to highlight the characteristics of different supply and demand resources in economic, environmental, and carbon constraints, three planning models with progressive constraints are constructed. Results of three models by the same example show that the best solutions to different models are different. The planning model including EPP has obvious advantages considering pollutant and carbon emission constraints, which confirms the advantages of low cost and emissions of EPP. The construction of progressive IRP models for power resources considering EPP has a certain reference value for guiding the planning and layout of EPP within other power resources and achieving cost and environmental objectives.

  3. 3D integrated HYDRA simulations of hohlraums including fill tubes

    Science.gov (United States)

    Marinak, M. M.; Milovich, J.; Hammel, B. A.; Macphee, A. G.; Smalyuk, V. A.; Kerbel, G. D.; Sepke, S.; Patel, M. V.

    2017-10-01

    Measurements of fill tube perturbations from hydro growth radiography (HGR) experiments on the National Ignition Facility show spoke perturbations in the ablator radiating from the base of the tube. These correspond to the shadow of the 10 μm diameter glass fill tube cast by hot spots at early time. We present 3D integrated HYDRA simulations of these experiments which include the fill tube. Meshing techniques are described which were employed to resolve the fill tube structure and associated perturbations in the simulations. We examine the extent to which the specific illumination geometry necessary to accommodate a backlighter in the HGR experiment contributes to the spoke pattern. Simulations presented include high resolution calculations run on the Trinity machine operated by the Alliance for Computing at Extreme Scale (ACES) partnership. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.

  4. Management of radioactive waste from reprocessing including disposal aspects

    International Nuclear Information System (INIS)

    Malherbe, J.

    1991-01-01

    Based on a hypothetical scenario including a reactor park of 20 GWe consisting of Pressurised-Water-Reactors with a resulting annual production of 600 tonnes of heavy metal of spent fuel, all aspects of management of resulting wastes are studied. Waste streams from reprocessing include gaseous and liquid effluents, and a number of solid conditioned waste types. Disposal of waste is supposed to be performed either in a near-surface engineered repository, as long as the content of alpha-emitting radionuclides is low enough, and in a deep geological granite formation. After having estimated quantities, cost and radiological consequences, the sensitivity of results to modification in reactor park size, burn-up and the introduction of mixed-oxide fuel (MOX) is evaluated

  5. Improving the strength of amalgams by including steel fibers

    Energy Technology Data Exchange (ETDEWEB)

    Cochran, Calvin T. [Hendrix College, Conway, AR 72032 (United States); Van Hoose, James R. [Siemens, Orlando, FL 32826 (United States); McGill, Preston B. [Marshall Space Flight Center, EM20, Huntsville, AL 35812 (United States); Grugel, Richard N., E-mail: richard.n.grugel@nasa.gov [Marshall Space Flight Center, EM30, Huntsville, AL 35812 (United States)

    2012-05-30

    Highlights: Black-Right-Pointing-Pointer A room temperature liquid Ga-In alloy was successfully substituted for mercury. Black-Right-Pointing-Pointer Physically sound amalgams with included steel fibers can be made. Black-Right-Pointing-Pointer A small volume fraction inclusion of fibers increased strength by {approx}20%. - Abstract: Mercury amalgams, due to their material properties, are widely and successfully used in dental practice. They are, however, also well recognized as having poor tensile strength. With the possibility of expanding amalgam applications it is demonstrated that tensile strength can be increased some 20% by including a small amount of steel fibers. Furthermore, it is shown that mercury can be replaced with a room temperature liquid gallium-indium alloy. Processing, microstructures, and mechanical test results of these novel amalgams are presented and discussed in view of means to further improve their properties.

  6. Microfluidic System Simulation Including the Electro-Viscous Effect

    Science.gov (United States)

    Rojas, Eileen; Chen, C. P.; Majumdar, Alok

    2007-01-01

    This paper describes a practical approach using a general purpose lumped-parameter computer program, GFSSP (Generalized Fluid System Simulation Program) for calculating flow distribution in a network of micro-channels including electro-viscous effects due to the existence of electrical double layer (EDL). In this study, an empirical formulation for calculating an effective viscosity of ionic solutions based on dimensional analysis is described to account for surface charge and bulk fluid conductivity, which give rise to electro-viscous effect in microfluidics network. Two dimensional slit micro flow data was used to determine the model coefficients. Geometry effect is then included through a Poiseuille number correlation in GFSSP. The bi-power model was used to calculate flow distribution of isotropically etched straight channel and T-junction microflows involving ionic solutions. Performance of the proposed model is assessed against experimental test data.

  7. Including investment risk in large-scale power market models

    DEFF Research Database (Denmark)

    Lemming, Jørgen Kjærgaard; Meibom, P.

    2003-01-01

    Long-term energy market models can be used to examine investments in production technologies, however, with market liberalisation it is crucial that such models include investment risks and investor behaviour. This paper analyses how the effect of investment risk on production technology selection...... can be included in large-scale partial equilibrium models of the power market. The analyses are divided into a part about risk measures appropriate for power market investors and a more technical part about the combination of a risk-adjustment model and a partial-equilibrium model. To illustrate...... the analyses quantitatively, a framework based on an iterative interaction between the equilibrium model and a separate risk-adjustment module was constructed. To illustrate the features of the proposed modelling approach we examined how uncertainty in demand and variable costs affects the optimal choice...

  8. Suddenly included: cultural differences in experiencing re-inclusion.

    Science.gov (United States)

    Pfundmair, Michaela; Graupmann, Verena; Du, Hongfei; Frey, Dieter; Aydin, Nilüfer

    2015-03-01

    In the current research, we examined whether re-inclusion (i.e. the change from a previous state of exclusion to a new state of inclusion) was perceived differently by people with individualistic and collectivistic cultural backgrounds. Individualists (German and Austrian participants) but not collectivists (Chinese participants) experienced re-inclusion differently than continued inclusion: While collectivistic participants did not differentiate between both kinds of inclusion, individualistic participants showed reduced fulfilment of their psychological needs under re-inclusion compared to continued inclusion. The results moreover revealed that only participants from individualistic cultures expressed more feelings of exclusion when re-included than when continually included. These exclusionary feelings partially mediated the relationship between the different states of inclusion and basic need fulfilment. © 2014 International Union of Psychological Science.

  9. MODEL OF THE TOKAMAK EDGE DENSITY PEDESTAL INCLUDING DIFFUSIVE NEUTRALS

    International Nuclear Information System (INIS)

    BURRELL, K.H.

    2003-01-01

    OAK-B135 Several previous analytic models of the tokamak edge density pedestal have been based on diffusive transport of plasma plus free-streaming of neutrals. This latter neutral model includes only the effect of ionization and neglects charge exchange. The present work models the edge density pedestal using diffusive transport for both the plasma and the neutrals. In contrast to the free-streaming model, a diffusion model for the neutrals includes the effect of both charge exchange and ionization and is valid when charge exchange is the dominant interaction. Surprisingly, the functional forms for the electron and neutral density profiles from the present calculation are identical to the results of the previous analytic models. There are some differences in the detailed definition of various parameters in the solution. For experimentally relevant cases where ionization and charge exchange rate are comparable, both models predict approximately the same width for the edge density pedestal

  10. Positron scattering by atomic hydrogen including positronium formation

    International Nuclear Information System (INIS)

    Higgins, K.; Burke, P.G.

    1993-01-01

    Positron scattering by atomic hydrogen including positronium formation has been formulated using the R-matrix method and a general computer code written. Partial wave elastic and ground state positronium formation cross sections have been calculated for L ≤ 6 using a six-state approximation which includes the ground state and the 2s and 2p pseudostates of both hydrogen and positronium. The elastic scattering results obtained are in good agreement with those derived from a highly accurate calculation based upon the intermediate energy R-matrix approach. As in a previous coupled-channel static calculation, resonance effects are observed at intermediate energies in the S-wave positronium formation cross section. However, in the present results, the dominant resonance arises in the P-wave cross sections at an energy of 2.73 Ryd and with a width of 0.19 Ryd. (author)

  11. XFEL OSCILLATOR SIMULATION INCLUDING ANGLE-DEPENDENT CRYSTAL REFLECTIVITY

    International Nuclear Information System (INIS)

    Fawley, William; Lindberg, Ryan; Kim, K.-J.; Shvyd'ko, Yuri

    2010-01-01

    The oscillator package within the GINGER FEL simulation code has now been extended to include angle-dependent reflectivity properties of Bragg crystals. Previously, the package was modified to include frequencydependent reflectivity in order to model x-ray FEL oscillators from start-up from shot noise through to saturation. We present a summary of the algorithms used for modeling the crystal reflectivity and radiation propagation outside the undulator, discussing various numerical issues relevant to the domain of high Fresnel number and efficient Hankel transforms. We give some sample XFEL-O simulation results obtained with the angle-dependent reflectivity model, with particular attention directed to the longitudinal and transverse coherence of the radiation output.

  12. QCD Reggeon field theory for every day: Pomeron loops included

    International Nuclear Information System (INIS)

    Altinoluk, Tolga; Kovner, Alex; Peressutti, Javier; Lublinsky, Michael

    2009-01-01

    We derive the evolution equation for hadronic scattering amplitude at high energy. Our derivation includes the nonlinear effects of finite partonic density in the hadronic wave function as well as the effect of multiple scatterings for scattering on dense hadronic target. It thus includes Pomeron loops. It is based on the evolution of the hadronic wave function derived in /cite{foam}. The kernel of the evolution equation defines the second quantized Hamiltonian of the QCD Reggeon Field Theory, H RFT beyond the limits considered so far. The two previously known limits of the evolution: dilute target (JIMWLK limit) and dilute projectile (KLWMIJ limit) are recovered directly from our final result. The Hamiltonian H RFT is applicable for the evolution of scattering amplitude for arbitrarily dense hadronic projectiles/targets - from 'dipole-dipole' to 'nucleus-nucleus' scattering processes.

  13. The Physics of Semiconductors An Introduction Including Devices and Nanophysics

    CERN Document Server

    Grundmann, Marius

    2006-01-01

    The Physics of Semiconductors provides material for a comprehensive upper-level-undergrauate and graduate course on the subject, guiding readers to the point where they can choose a special topic and begin supervised research. The textbook provides a balance between essential aspects of solid-state and semiconductor physics, on the one hand, and the principles of various semiconductor devices and their applications in electronic and photonic devices, on the other. It highlights many practical aspects of semiconductors such as alloys, strain, heterostructures, nanostructures, that are necessary in modern semiconductor research but typically omitted in textbooks. For the interested reader some additional advanced topics are included, such as Bragg mirrors, resonators, polarized and magnetic semiconductors are included. Also supplied are explicit formulas for many results, to support better understanding. The Physics of Semiconductors requires little or no prior knowledge of solid-state physics and evolved from ...

  14. Smart Farming: Including Rights Holders for Responsible Agricultural Innovation

    OpenAIRE

    Kelly Bronson

    2018-01-01

    This article draws on the literature of responsible innovation to suggest concrete processes for including rights holders in the “smart” agricultural revolution. It first draws upon historical agricultural research in Canada to highlight how productivist values drove seed innovations with particular consequences for the distribution of power in the food system. Next, the article uses document analysis to suggest that a similar value framework is motivating public investment in smart farming i...

  15. Aggregated Demand Modelling Including Distributed Generation, Storage and Demand Response

    OpenAIRE

    Marzooghi, Hesamoddin; Hill, David J.; Verbic, Gregor

    2014-01-01

    It is anticipated that penetration of renewable energy sources (RESs) in power systems will increase further in the next decades mainly due to environmental issues. In the long term of several decades, which we refer to in terms of the future grid (FG), balancing between supply and demand will become dependent on demand actions including demand response (DR) and energy storage. So far, FG feasibility studies have not considered these new demand-side developments for modelling future demand. I...

  16. Stochastic modelling of two-phase flows including phase change

    International Nuclear Information System (INIS)

    Hurisse, O.; Minier, J.P.

    2011-01-01

    Stochastic modelling has already been developed and applied for single-phase flows and incompressible two-phase flows. In this article, we propose an extension of this modelling approach to two-phase flows including phase change (e.g. for steam-water flows). Two aspects are emphasised: a stochastic model accounting for phase transition and a modelling constraint which arises from volume conservation. To illustrate the whole approach, some remarks are eventually proposed for two-fluid models. (authors)

  17. Production, control and utilization of radioisotopes including radiopharmaceuticals

    International Nuclear Information System (INIS)

    Muenze, R.

    1985-05-01

    From April 29th to May 5th, 1984 27 participants from 21 developing countries stayed within an IAEA Study Tour ('Production, Control and Utilization of Radioisotopes including Radiopharmaceuticals') in the GDR. In the CINR, Rossendorf the reactor, the cyclotron, the technological centre as well as the animal test laboratory were visited. The participants were made familiar by 10 papers with the development, production and control of radiopharmaceuticals in the CINR, Rossendorf. (author)

  18. Reliability evaluation of containments including soil-structure interaction

    International Nuclear Information System (INIS)

    Pires, J.; Hwang, H.; Reich, M.

    1985-12-01

    Soil-structure interaction effects on the reliability assessment of containment structures are examined. The probability-based method for reliability evaluation of nuclear structures developed at Brookhaven National Laboratory is extended to include soil-structure interaction effects. In this method, reliability of structures is expressed in terms of limit state probabilities. Furthermore, random vibration theory is utilized to calculate limit state probabilities under random seismic loads. Earthquake ground motion is modeled by a segment of a zero-mean, stationary, filtered Gaussian white noise random process, represented by its power spectrum. All possible seismic hazards at a site, represented by a hazard curve, are also included in the analysis. The soil-foundation system is represented by a rigid surface foundation on an elastic halfspace. Random and other uncertainties in the strength properties of the structure, in the stiffness and internal damping of the soil, are also included in the analysis. Finally, a realistic reinforced concrete containment is analyzed to demonstrate the application of the method. For this containment, the soil-structure interaction effects on; (1) limit state probabilities, (2) structural fragility curves, (3) floor response spectra with probabilistic content, and (4) correlation coefficients for total acceleration response at specified structural locations, are examined in detail. 25 refs., 21 figs., 12 tabs

  19. Electrolytes including fluorinated solvents for use in electrochemical cells

    Science.gov (United States)

    Tikhonov, Konstantin; Yip, Ka Ki; Lin, Tzu-Yuan

    2015-07-07

    Provided are electrochemical cells and electrolytes used to build such cells. The electrolytes include ion-supplying salts and fluorinated solvents capable of maintaining single phase solutions with the salts at between about -30.degree. C. to about 80.degree. C. The fluorinated solvents, such as fluorinated carbonates, fluorinated esters, and fluorinated esters, are less flammable than their non-fluorinated counterparts and increase safety characteristics of cells containing these solvents. The amount of fluorinated solvents in electrolytes may be between about 30% and 80% by weight not accounting weight of the salts. Fluorinated salts, such as fluoroalkyl-substituted LiPF.sub.6, fluoroalkyl-substituted LiBF.sub.4 salts, linear and cyclic imide salts as well as methide salts including fluorinated alkyl groups, may be used due to their solubility in the fluorinated solvents. In some embodiments, the electrolyte may also include a flame retardant, such as a phosphazene or, more specifically, a cyclic phosphazene and/or one or more ionic liquids.

  20. A Framework for Including Family Health Spillovers in Economic Evaluation.

    Science.gov (United States)

    Al-Janabi, Hareth; van Exel, Job; Brouwer, Werner; Coast, Joanna

    2016-02-01

    Health care interventions may affect the health of patients' family networks. It has been suggested that these "health spillovers" should be included in economic evaluation, but there is not a systematic method for doing this. In this article, we develop a framework for including health spillovers in economic evaluation. We focus on extra-welfarist economic evaluations where the objective is to maximize health benefits from a health care budget (the "health care perspective"). Our framework involves adapting the conventional cost-effectiveness decision rule to include 2 multiplier effects to internalize the spillover effects. These multiplier effects express the ratio of total health effects (for patients and their family networks) to patient health effects. One multiplier effect is specified for health benefit generated from providing a new intervention, one for health benefit displaced by funding this intervention. We show that using multiplier effects to internalize health spillovers could change the optimal funding decisions and generate additional health benefits to society. © The Author(s) 2015.

  1. The COG database: an updated version includes eukaryotes

    Directory of Open Access Journals (Sweden)

    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  2. Global anthropogenic emissions of particulate matter including black carbon

    Science.gov (United States)

    Klimont, Zbigniew; Kupiainen, Kaarle; Heyes, Chris; Purohit, Pallav; Cofala, Janusz; Rafaj, Peter; Borken-Kleefeld, Jens; Schöpp, Wolfgang

    2017-07-01

    This paper presents a comprehensive assessment of historical (1990-2010) global anthropogenic particulate matter (PM) emissions including the consistent and harmonized calculation of mass-based size distribution (PM1, PM2. 5, PM10), as well as primary carbonaceous aerosols including black carbon (BC) and organic carbon (OC). The estimates were developed with the integrated assessment model GAINS, where source- and region-specific technology characteristics are explicitly included. This assessment includes a number of previously unaccounted or often misallocated emission sources, i.e. kerosene lamps, gas flaring, diesel generators, refuse burning; some of them were reported in the past for selected regions or in the context of a particular pollutant or sector but not included as part of a total estimate. Spatially, emissions were calculated for 172 source regions (as well as international shipping), presented for 25 global regions, and allocated to 0.5° × 0.5° longitude-latitude grids. No independent estimates of emissions from forest fires and savannah burning are provided and neither windblown dust nor unpaved roads emissions are included. We estimate that global emissions of PM have not changed significantly between 1990 and 2010, showing a strong decoupling from the global increase in energy consumption and, consequently, CO2 emissions, but there are significantly different regional trends, with a particularly strong increase in East Asia and Africa and a strong decline in Europe, North America, and the Pacific region. This in turn resulted in important changes in the spatial pattern of PM burden, e.g. European, North American, and Pacific contributions to global emissions dropped from nearly 30 % in 1990 to well below 15 % in 2010, while Asia's contribution grew from just over 50 % to nearly two-thirds of the global total in 2010. For all PM species considered, Asian sources represented over 60 % of the global anthropogenic total, and residential combustion

  3. Global anthropogenic emissions of particulate matter including black carbon

    Directory of Open Access Journals (Sweden)

    Z. Klimont

    2017-07-01

    Full Text Available This paper presents a comprehensive assessment of historical (1990–2010 global anthropogenic particulate matter (PM emissions including the consistent and harmonized calculation of mass-based size distribution (PM1, PM2. 5, PM10, as well as primary carbonaceous aerosols including black carbon (BC and organic carbon (OC. The estimates were developed with the integrated assessment model GAINS, where source- and region-specific technology characteristics are explicitly included. This assessment includes a number of previously unaccounted or often misallocated emission sources, i.e. kerosene lamps, gas flaring, diesel generators, refuse burning; some of them were reported in the past for selected regions or in the context of a particular pollutant or sector but not included as part of a total estimate. Spatially, emissions were calculated for 172 source regions (as well as international shipping, presented for 25 global regions, and allocated to 0.5°  ×  0.5° longitude–latitude grids. No independent estimates of emissions from forest fires and savannah burning are provided and neither windblown dust nor unpaved roads emissions are included. We estimate that global emissions of PM have not changed significantly between 1990 and 2010, showing a strong decoupling from the global increase in energy consumption and, consequently, CO2 emissions, but there are significantly different regional trends, with a particularly strong increase in East Asia and Africa and a strong decline in Europe, North America, and the Pacific region. This in turn resulted in important changes in the spatial pattern of PM burden, e.g. European, North American, and Pacific contributions to global emissions dropped from nearly 30 % in 1990 to well below 15 % in 2010, while Asia's contribution grew from just over 50 % to nearly two-thirds of the global total in 2010. For all PM species considered, Asian sources represented over 60 % of the global

  4. Phenotypes in defined genotypes including siblings with Usher syndrome.

    Science.gov (United States)

    Malm, Eva; Ponjavic, Vesna; Möller, Claes; Kimberling, William J; Andréasson, Sten

    2011-06-01

    To characterize visual function in defined genotypes including siblings with Usher syndrome. Thirteen patients with phenotypically different subtypes of Usher syndrome, including 3 families with affected siblings, were selected. Genetic analysis and ophthalmological examinations including visual fields, full-field electroretinography (ERG), multifocal electroretinography (mf ERG), and optical coherence tomography (OCT) were assessed. The patients' degree of visual handicap was evaluated by a questionnaire (ADL). Twelve of thirteen patients were genotyped as Usher 1B, 1D, 1F, 2A, 2C or 3A. In 12 of 13 patients examined with ERG the 30 Hz flickering light response revealed remaining cone function. In 3 of the patients with Usher type 1 mf ERG demonstrated a specific pattern, with a sharp distinction between the area with reduced function and the central area with remaining macular function and normal peak time. OCT demonstrated loss of foveal depression with distortion of the foveal architecture in the macula in all patients. The foveal thickness ranged from 159 to 384 µm and was not correlated to retinal function. Three siblings shared the same mutation for Usher 2C but in contrast to previous reports regarding this genotype, 1 of them diverged in phenotype with substantially normal visual fields, almost normal OCT and mf ERG findings, and only moderately reduced rod and cone function according to ERG. Evaluation of visual function comprising both the severity of the rod cone degeneration and the function in the macular region confirm phenotypical heterogeneity within siblings and between different genotypes of Usher syndrome.

  5. Developing HYDMN code to include the transient of MNSR

    International Nuclear Information System (INIS)

    Al-Barhoum, M.

    2000-11-01

    A description of the programs added to HYDMN code (a code for thermal-hydraulic steady state of MNSR) to include the transient of the same MNSR is presented. The code asks the initial conditions for the power (in k W) and the cold initial core inlet temperature (in degrees centigrade). A time-dependent study of the coolant inlet and outlet temperature, its speed, pool and tank temperatures is done for MNSR in general and for the Syrian MNSR in particular. The study solves the differential equations taken from reference (1) by using some numerical methods found in reference (3). The code becomes this way independent of any external information source. (Author)

  6. Modification of SKYSHINE-III to include cask array shadowing

    Energy Technology Data Exchange (ETDEWEB)

    Hertel, N.E. [Georgia Institute of Technology, Atlanta, GA (United States); Pfeifer, H.J. [NAC International, Norcross, GA (United States); Napolitano, D.G. [NISYS Corporation, Duluth, GA (United States)

    2000-03-01

    The NAC International version of SKYSHINE-III has been expanded to represent the radiation emissions from ISFSI (Interim Spent Fuel Storage Installations) dry storage casks using surface source descriptions. In addition, this modification includes a shadow shielding algorithm of the casks in the array. The resultant code is a flexible design tool which can be used to rapidly assess the impact of various cask loadings and arrangements. An example of its use in calculating dose rates for a 10x8 cask array is presented. (author)

  7. Composite material including nanocrystals and methods of making

    Science.gov (United States)

    Bawendi, Moungi G.; Sundar, Vikram C.

    2010-04-06

    Temperature-sensing compositions can include an inorganic material, such as a semiconductor nanocrystal. The nanocrystal can be a dependable and accurate indicator of temperature. The intensity of emission of the nanocrystal varies with temperature and can be highly sensitive to surface temperature. The nanocrystals can be processed with a binder to form a matrix, which can be varied by altering the chemical nature of the surface of the nanocrystal. A nanocrystal with a compatibilizing outer layer can be incorporated into a coating formulation and retain its temperature sensitive emissive properties.

  8. Endoscopic Management of Vascular Sinonasal Tumors, Including Angiofibroma.

    Science.gov (United States)

    Snyderman, Carl H; Pant, Harshita

    2016-06-01

    The greatest challenge in the surgical treatment of angiofibromas is dealing with the hypervascularity of these tumors. Staging systems that take into account the vascularity of the tumor may be more prognostic. A variety of treatment strategies are used to deal with the vascularity of angiofibromas, including preoperative embolization, segmentation of the tumor into vascular territories, use of hemostatic tools, and staging of surgery. Even large angiofibromas with intracranial extension and residual vascularity can be successfully managed by a skull base team using endoscopic techniques. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Solution of neutron slowing down equation including multiple inelastic scattering

    International Nuclear Information System (INIS)

    El-Wakil, S.A.; Saad, A.E.

    1977-01-01

    The present work is devoted the presentation of an analytical method for the calculation of elastically and inelastically slowed down neutrons in an infinite non absorbing homogeneous medium. On the basis of the Central limit theory (CLT) and the integral transform technique the slowing down equation including inelastic scattering in terms of the Green function of elastic scattering is solved. The Green function is decomposed according to the number of collisions. A formula for the flux at any lethargy O (u) after any number of collisions is derived. An equation for the asymptotic flux is also obtained

  10. cDNA encoding a polypeptide including a hevein sequence

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, Natasha V. (Okemos, MI); Broekaert, Willem F. (Dilbeek, BE); Chua, Nam-Hai (Scarsdale, NY); Kush, Anil (New York, NY)

    1993-02-16

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a pu GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.

  11. Smart Farming: Including Rights Holders for Responsible Agricultural Innovation

    Directory of Open Access Journals (Sweden)

    Kelly Bronson

    2018-02-01

    Full Text Available This article draws on the literature of responsible innovation to suggest concrete processes for including rights holders in the “smart” agricultural revolution. It first draws upon historical agricultural research in Canada to highlight how productivist values drove seed innovations with particular consequences for the distribution of power in the food system. Next, the article uses document analysis to suggest that a similar value framework is motivating public investment in smart farming innovations. The article is of interest to smart farming’s decision makers (from farmers to governance actors and a broader audience – anyone interested in engendering equity through innovation-led societal transitions.

  12. Clinton administration budget includes mixed bag for science

    Science.gov (United States)

    Showstack, Randy

    The $1,766 trillion federal budget proposal that the Clinton Administration rolled out on February 1—which promises to protect Social Security and Medicare and work within mandated budget caps—generally provides favorable news for federally funded science research and development.Within the 17% ($592 billion) of the federal budget earmarked for discretionary spending, the Administration's budget proposal increases funding for nondefense research and development for the seventh year in a row. This includes increased funding for a number of science accounts and money for a series of new science initiatives.

  13. TOOLS TO INCLUDE BLIND STUDENTS IN SCHOOL BUILDING PERFORMANCE ASSESSMENTS

    Directory of Open Access Journals (Sweden)

    Tania Pietzschke Abate

    2016-05-01

    Full Text Available This article discusses the design of data collection instruments that include the opinions of blind students, in accordance with the principles of Universal Design (UD. The aim of this study is to understand the importance of adapting data collection instruments for the inclusion of disabled persons in field research in Architecture and Design, among other fields. The data collection instruments developed were a play interview with a tactile map and a 3D survey with the use of tactile models. These instruments sought to assess the school environment experienced by blind students. The study involved students from the early years of a school for the blind who had not yet mastered the Braille system. The participation of these students was evaluated. A multidisciplinary team consisting of architects, designers, educators, and psychologists lent support to the study. The results showed that the data collection instruments adapted to blind students were successful in making the group of authors examine questions regarding UD. An analysis of the participatory phase showed that the limitations resulting from blindness determine the specificities in the adaptation and implementation process of the instruments in schools. Practical recommendations for future studies related to instruments in the UD thematic are presented. This approach is in line with the global trend of including disabled persons in society based on these users’ opinions concerning what was designed by architects and designers.

  14. Kabuki syndrome: expanding the phenotype to include microphthalmia and anophthalmia.

    Science.gov (United States)

    McVeigh, Terri P; Banka, Siddharth; Reardon, William

    2015-10-01

    Kabuki syndrome is a rare genetic malformation syndrome that is characterized by distinct facies, structural defects and intellectual disability. Kabuki syndrome may be caused by mutations in one of two histone methyltransferase genes: KMT2D and KDM6A. We describe a male child of nonconsanguineous Irish parents presenting with multiple malformations, including bilateral extreme microphthalmia; cleft palate; congenital diaphragmatic hernia; duplex kidney; as well as facial features of Kabuki syndrome, including interrupted eyebrows and lower lid ectropion. A de-novo germline mutation in KMT2D was identified. Whole-exome sequencing failed to reveal mutations in any of the known microphthalmia/anopthalmia genes. We also identified four other patients with Kabuki syndrome and microphthalmia. We postulate that Kabuki syndrome may produce this type of ocular phenotype as a result of extensive interaction between KMT2D, WAR complex proteins and PAXIP1. Children presenting with microphthalmia/anophthalmia should be examined closely for other signs of Kabuki syndrome, especially at an age where the facial gestalt might be less readily appreciable.

  15. Risk Factors for Breast Cancer, Including Occupational Exposures

    Directory of Open Access Journals (Sweden)

    Elisabete Weiderpass

    2011-03-01

    Full Text Available The knowledge on the etiology of breast cancer has advanced substantially in recent years, and several etiological factors are now firmly established. However, very few new discoveries have been made in relation to occupational risk factors. The International Agency for Research on Cancer has evaluated over 900 different exposures or agents to-date to determine whether they are carcinogenic to humans. These evaluations are published as a series of Monographs (www.iarc.fr. For breast cancer the following substances have been classified as “carcinogenic to humans” (Group 1: alcoholic beverages, exposure to diethylstilbestrol, estrogen-progestogen contraceptives, estrogen-progestogen hormone replacement therapy and exposure to X-radiation and gamma-radiation (in special populations such as atomic bomb survivors, medical patients, and in-utero exposure. Ethylene oxide is also classified as a Group 1 carcinogen, although the evidence for carcinogenicity in epidemiologic studies, and specifically for the human breast, is limited. The classification “probably carcinogenic to humans” (Group 2A includes estrogen hormone replacement therapy, tobacco smoking, and shift work involving circadian disruption, including work as a flight attendant. If the association between shift work and breast cancer, the most common female cancer, is confirmed, shift work could become the leading cause of occupational cancer in women.

  16. Proposal to Include Electrical Energy in the Industrial Return Statistics

    CERN Document Server

    2003-01-01

    At its 108th session on the 20 June 1997, the Council approved the Report of the Finance Committee Working Group on the Review of CERN Purchasing Policy and Procedures. Among other topics, the report recommended the inclusion of utility supplies in the calculation of the return statistics as soon as the relevant markets were deregulated, without reaching a consensus on the exact method of calculation. At its 296th meeting on the 18 June 2003, the Finance Committee approved a proposal to award a contract for the supply of electrical energy (CERN/FC/4693). The purpose of the proposal in this document is to clarify the way electrical energy will be included in future calculations of the return statistics. The Finance Committee is invited: 1. to agree that the full cost to CERN of electrical energy (excluding the cost of transport) be included in the Industrial Service return statistics; 2. to recommend that the Council approves the corresponding amendment to the Financial Rules set out in section 2 of this docum...

  17. Exclusive queueing model including the choice of service windows

    Science.gov (United States)

    Tanaka, Masahiro; Yanagisawa, Daichi; Nishinari, Katsuhiro

    2018-01-01

    In a queueing system involving multiple service windows, choice behavior is a significant concern. This paper incorporates the choice of service windows into a queueing model with a floor represented by discrete cells. We contrived a logit-based choice algorithm for agents considering the numbers of agents and the distances to all service windows. Simulations were conducted with various parameters of agent choice preference for these two elements and for different floor configurations, including the floor length and the number of service windows. We investigated the model from the viewpoint of transit times and entrance block rates. The influences of the parameters on these factors were surveyed in detail and we determined that there are optimum floor lengths that minimize the transit times. In addition, we observed that the transit times were determined almost entirely by the entrance block rates. The results of the presented model are relevant to understanding queueing systems including the choice of service windows and can be employed to optimize facility design and floor management.

  18. Impact of a pain protocol including hypnosis in major burns.

    Science.gov (United States)

    Berger, Mette M; Davadant, Maryse; Marin, Christian; Wasserfallen, Jean-Blaise; Pinget, Christophe; Maravic, Philippe; Koch, Nathalie; Raffoul, Wassim; Chiolero, René L

    2010-08-01

    Pain is a major issue after burns even when large doses of opioids are prescribed. The study focused on the impact of a pain protocol using hypnosis on pain intensity, anxiety, clinical course, and costs. All patients admitted to the ICU, aged >18 years, with an ICU stay >24h, accepting to try hypnosis, and treated according to standardized pain protocol were included. Pain was scaled on the Visual Analog Scale (VAS) (mean of daily multiple recordings), and basal and procedural opioid doses were recorded. Clinical outcome and economical data were retrieved from hospital charts and information system, respectively. Treated patients were matched with controls for sex, age, and the burned surface area. Forty patients were admitted from 2006 to 2007: 17 met exclusion criteria, leaving 23 patients, who were matched with 23 historical controls. Altogether patients were 36+/-14 years old and burned 27+/-15%BSA. The first hypnosis session was performed after a median of 9 days. The protocol resulted in the early delivery of higher opioid doses/24h (ppatient. A pain protocol including hypnosis reduced pain intensity, improved opioid efficiency, reduced anxiety, improved wound outcome while reducing costs. The protocol guided use of opioids improved patient care without side effects, while hypnosis had significant psychological benefits.

  19. Study on 'Tannix' an absorbent for heavy metals including uranium

    International Nuclear Information System (INIS)

    Nakamura, Yasuo

    1997-01-01

    To treat radioactive wastes including uranium and transuranic elements such as plutonium, americium etc., development of an absorbent which can be used to absorb and isolate these elements without producing secondary wastes after treatment was attempted. And an absorbent has been successfully developed by polymerizing tannin, a natural product. It is known that tannin binds heavy metals including uranium resulting to produce their precipitates. There are some reports suggesting its absorption ability for uranium. However, tannin has not been used to isolate a heavy metal from a solution because it is soluble in water. Here, insolubilization of tannin was attempted and a manufacturing method for a gelatinized insoluble tannin named as ''Tannix'' was established. Wattle tannin extracted from Mimosa pudica produced in Africa was dissolved in an alkaline solution and gelatinized by heating after the addition of formalin. Thus obtained insoluble tannin was used after crushing and sieving. This product, ''Tannix'' was able to absorb more than 99% of uranium in the waste. And the absorbed Tannin could be degraded by incineration even at a low temperature, leaving only uranium, but not producing any secondary product. (M.N.)

  20. Global Analysis of Solar Neutrino Oscillations Including SNO CC Measurement

    CERN Document Server

    Bahcall, J N; Peña-Garay, C; Bahcall, John N; Peña-Garay, Carlos

    2001-01-01

    For active and sterile neutrinos, we present the globally allowed solutions for two neutrino oscillations. We include the SNO CC measurement and all other relevant solar neutrino and reactor data. Five active neutrino oscillation solutions (LMA, LOW, SMA, VAC, and Just So2) are currently allowed at 3 sigma; three sterile neutrino solutions (Just So2, SMA, and VAC) are allowed at 3 sigma. The goodness of fit is satisfactory for all eight solutions. We also investigate the robustness of the allowed solutions by carrying out global analyses with and without: 1) imposing solar model constraints on the 8B neutrino flux, 2) including the Super-Kamiokande spectral energy distribution and day-night data, 3) using an enhanced CC cross section for deuterium (due to radiative corrections), and 4) a optimistic, hypothetical reduction by a factor of three of the error of the SNO CC rate. For every analysis strategy used in this paper, the most favored solutions all involve large mixing angles: LMA, LOW, or VAC. The favore...