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Sample records for retrotransposon intracisternal a-particle

  1. Genes Altered by Intracisternal A Particles in Mouse Mammary Tumorigenesis

    National Research Council Canada - National Science Library

    Crowley, Michael

    1997-01-01

    ...) in BALB/c mice which express high levels of intracistemal A-particles (IAP). Differential hybpridization and differential display strategies are being used to isolate transcripts which contained IAP LTR sequences...

  2. Expression of intracisternal A-particles in radiation-induced murine osteosarcomas

    International Nuclear Information System (INIS)

    Seidel, E.

    1989-01-01

    The expression of intracisternal A-type particles (IAPs) and the distribution of the corresponding type I and type II genes was investigated in radiation induced osteosarcomas of Balb/c, NMRI and CBA mice. The results can be summarized as follows: 1. Slot blot analysis showed that 9 out of 23 (i.e. 39%) of the examined tumours had enhanced IAP expression as compared to normal tissues. None of the CBA tumours were enhanced in IAP expression - only tumours of the strains Balb/c and NMRI expressed higher levels of IAP RNA. 2. Northern blot analysis of RNA from osteosarcomas revealed that the two IAP transcrips (7.2 kb and 5.4 kb) had the same mobility in these tissues as in normal tissue. Some tumours showed a higher level of expression of the 7.2 kb transcript as compared to normal tissues. This 7.2 kb transcript encodes the major structural protein p 73 of IAPs. 3. Hybridization of Southern blots of mouse DNA using the IAP type I specific probe revealed a unique fragment in three of the investigated Balb/c osteosarcomas. 4. Although it could not directly be shown that IAPs were involved in the genesis of osteosarcomas, the changes in IAP expression and the unique fragments suggest a possible correlation with tumour progression. In this light the level of IAP expression may serve as a marker for the degree of the malignancy of the tumour. (orig.) [de

  3. Genes Altered by Intracisternal A Particles in Mouse Mammary Tumorigenesis

    National Research Council Canada - National Science Library

    Crowley, Michael

    1999-01-01

    ...) and murine viral leukemia elements (MuLVs). Expression of MuLVs has lead to the appearance of novel restriction fragments associated with the ecotropic MuLV in D2 HANs and several D2 tumors from BALB/c mice...

  4. 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.

  5. 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.

  6. Intracisternal granules in the adipokinetic cells of locusts are not degraded and apparently function as supplementary stores of secretory material.

    Science.gov (United States)

    Harthoorn, L F; Diederen, J H; Oudejans, R C; Verstegen, M M; Vullings, H G; Van der Horst, D J

    2000-01-01

    The intracisternal granules in locust adipokinetic cells appear to represent accumulations of secretory material within cisternae of the rough endoplasmic reticulum. An important question is whether these granules are destined for degradation or represent stores of (pro)hormones. Two strategies were used to answer this question. First, cytochemistry was applied to elucidate the properties of intracisternal granules. The endocytic tracers horseradish peroxidase and wheat-germ agglutinin-conjugated horseradish peroxidase were used to facilitate the identification of endocytic, autophagic, and lysosomal organelles, which may be involved in the degradation of intracisternal granules. No intracisternal granules could be found within autophagosomes, and granules fused with endocytic and lysosomal organelles were not observed, nor could tracer be found within the granules. The lysosomal enzyme acid phosphatase was absent from the granules. Second, biochemical analysis of the content of intracisternal granules revealed that these granules contain prohormones as well as hormones. Prohormones were present in relatively higher amounts compared with ordinary secretory granules. Since the intracisternal granules in locust adipokinetic cells are not degraded and contain intact (pro)hormones it is concluded that they function as supplementary stores of secretory material.

  7. Detection of a human intracisternal A-type retroviral particle antigenically related to HIV

    Science.gov (United States)

    Garry, R. F.; Fermin, C. D.; Hart, D. J.; Alexander, S. S.; Donehower, L. A.; Luo-Zhang, H.

    1990-01-01

    Sjogren's syndrome is an autoimmune disease that is characterized by dryness of the mouth and eyes. The loss of salivary and lacrimal gland function is accompanied by lymphocytic infiltration. Because similar symptoms and glandular pathology are observed in certain persons infected with human immunodeficiency virus (HIV), a search was initiated for a possible retroviral etiology in this syndrome. A human intracisternal A-type retroviral particle that is antigenically related to HIV was detected in lymphoblastoid cells exposed to homogenates of salivary tissue from patients with Sjogren's syndrome. Comparison of this retroviral particle to HIV indicates that they are distinguishable by several ultrastructural, physical, and enzymatic criteria.

  8. Characterizing the glymphatic influx by utilizing intracisternal infusion of fluorescently conjugated cadaverine.

    Science.gov (United States)

    Zhang, Cui; Lin, Jun; Wei, Fang; Song, Jian; Chen, Wenyue; Shan, Lidong; Xue, Rong; Wang, Guoqing; Tao, Jin; Zhang, Guoxing; Xu, Guang-Yin; Wang, Linhui

    2018-05-15

    Accumulating evidence supports that cerebrospinal fluid (CSF) in the subarachnoid space (SAS) could reenter the brain parenchyma via the glymphatic influx. The present study was designed to characterize the detailed pathway of subarachnoid CSF influx by using a novel CSF tracer. Fluorescently conjugated cadaverine (A488-ca), for the first time, was employed to investigate CSF movement in the brain. Following intracisternal infusion of CSF tracers, mice brain was sliced and prepared for fluorescence imaging. Some brain sections were immunostained in order to observe tracer distribution and cellular uptake. A488-ca moved into the brain parenchyma rapidly, and the influx was time and region dependent. A488-ca entered the mice brain more readily and spread more widely than another commonly used CSF tracer-fluorescently conjugated ovalbumin (OA-45). Furthermore, A488-ca could enter the brain parenchyma either along the paravascular space or across the pial surface. Suppression of glymphatic transport by administration with acetazolamide strikingly reduced the influx of A488-ca. More importantly, relative to OA-45 largely remained in the extracellular space, A488-ca exhibited obvious cellular uptake by astrocytes surrounding the blood vessels and neurons in the cerebral cortex. Subarachnoid CSF could flow into the brain parenchyma via the glymphatic influx, in which the transcellular pathway was faithfully traced by intracisternal infusion with fluorescently conjugated cadaverine. These observations extend our comprehension on the glymphatic influx pathway. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. 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.

  10. [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.

  11. 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...

  12. 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

  13. 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 ...

  14. 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.

  15. [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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Reversibility of neurofilamentous inclusion formation following repeated sublethal intracisternal inoculums of AlCl3 in New Zealand white rabbits.

    Science.gov (United States)

    Strong, M J; Gaytan-Garcia, S; Jakowec, D M

    1995-01-01

    In this report, we describe the clinical, topographical and immunohistochemical characteristics of neurofilament (NF) inclusion formation induced by the intracisternal inoculation of young adult New Zealand white rabbits at 28-day intervals with 100 micrograms AlCl3 over the course of 267 days. The ability to recover following cessation of aluminum exposure has also been assessed. The extent of neurofilamentous inclusion formation was proportionate to the cumulative amount of AlCl3 inoculated and initially consisted of fusiform axonal distention in the ventral spinal cord at day 51 following the initial inoculum. Spinal motor neuron perikaryal inclusions and discrete axonal spheroids were observed at day 107 and supraspinal neurofilamentous pathology by day 156. Perikaryal inclusions were immunoreactive to antibodies recognizing both poorly phosphorylated (SMI 32) and more highly phosphorylated high molecular weight NF (NFH). In contrast, axonal spheroids were intensely immunoreactive at all stages with antibodies recognizing highly phosphorylated NFH and an age-dependent NFH phosphorylation state (SMI 34) with only faint SMI 32 immunoreactivity. Immunoreactivity to an antibody recognizing ubiquitin-protein conjugates did not appear until day 156, whereas inclusions were not immunoreactive to antibodies recognizing either phosphatase-dependent or -independent microtubule-associated protein tau at any stage. Upon withdrawal from further AlCl3 exposure after intervals of 51, 107 or 156 days following the initial inoculum, clinical recovery ensued in all rabbits. In all but the most severely affected rabbits, perikaryal neurofilamentous inclusions resolved. However, axonal spheroids continued to be prominent. These studies demonstrate that the repetitive intracisternal inoculation of AlCl3 in New Zealand white rabbits induces a reversible process of neurofilamentous inclusion formation that preferentially affects motor neurons, and in which recovery will occur in

  1. 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.

  2. 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.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. 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...

  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. 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

  13. 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.

  14. 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

  15. 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.

  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. 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.

  19. 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.

  20. 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.

  1. 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

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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...

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. MASiVEdb: the Sirevirus Plant Retrotransposon Database

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    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

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

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    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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

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

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    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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Restoration of central nervous system alpha-N-acetylglucosaminidase activity and therapeutic benefits in mucopolysaccharidosis IIIB mice by a single intracisternal recombinant adeno-associated viral type 2 vector delivery.

    Science.gov (United States)

    Fu, Haiyan; DiRosario, Julianne; Kang, Lu; Muenzer, Joseph; McCarty, Douglas M

    2010-07-01

    Finding efficient central nervous system (CNS) delivery approaches has been the major challenge facing therapeutic development for treating diseases with global neurological manifestation, such as mucopolysaccharidosis (MPS) IIIB, a lysosomal storage disease, caused by autosomal recessive defect of alpha-N-acetylglucosaminidase (NaGlu). Previously, we developed an approach, intracisternal (i.c.) injection, to deliver recombinant adeno-associated viral (rAAV) vector to the CNS of mice, leading to a widespread periventricular distribution of transduction. In the present study, we delivered rAAV2 vector expressing human NaGlu into the CNS of MPS IIIB mice by an i.c. injection approach, to test its therapeutic efficacy and feasibility for treating the neurological manifestation of the disease. We demonstrated significant functional neurological benefits of a single i.c. vector infusion in adult MPS IIIB mice. The treatment slowed the disease progression by mediating widespread recombinant NaGlu expression in the CNS, resulting in the reduction of brain lysosomal storage pathology, significantly improved cognitive function and prolonged survival. However, persisting motor function deficits suggested that pathology in areas outside the CNS contributes to the MPS IIIB behavioral phenotype. The therapeutic benefit of i.c. rAAV2 delivery was dose-dependent and could be attribute solely to the CNS transduction because the procedure did not lead to detectable transduction in somatic tissues. A single IC rAAV2 gene delivery is functionally beneficial for treating the CNS disease of MPS IIIB in mice. It is immediately clinically translatable, with the potential of improving the quality of life for patients with MPS IIIB.

  7. 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.

  8. 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.

  9. 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...

  10. 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.

  11. 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

  12. 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.

  13. 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.

  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. 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

  16. 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

  17. 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....

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  17. 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.

  18. 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...

  19. 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.

  20. Moving foil stripper for a particle accelerator

    International Nuclear Information System (INIS)

    Gorka, A.J. Jr.

    1975-01-01

    Thin foils for stripping a particle beam are stored on the edge of a disk spinning in the accelerator vacuum. Cutting a foil at one edge releases the foil to project beyond the disk for insertion into the beam at a time determined by controlling the phase of the disk. A wiper removes a spent foil from the disk. The foil release and wiper are operable from a remote location. (U.S.)

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Requirements and specifications for a particle database

    International Nuclear Information System (INIS)

    2015-01-01

    One of the tasks of WPEC Subgroup 38 (SG38) is to design a database structure for storing the particle information needed for nuclear reaction databases and transport codes. Since the same particle may appear many times in a reaction database (produced by many different reactions on different targets), one of the long-term goals for SG38 is to move towards a central database of particle information to reduce redundancy and ensure consistency among evaluations. The database structure must be general enough to describe all relevant particles and their properties, including mass, charge, spin and parity, half-life, decay properties, and so on. Furthermore, it must be broad enough to handle not only excited nuclear states but also excited atomic states that can de-excite through atomic relaxation. Databases built with this hierarchy will serve as central repositories for particle information that can be linked to from codes and other databases. It is hoped that the final product is general enough for use in other projects besides SG38. While this is called a 'particle database', the definition of a particle (as described in Section 2) is very broad. The database must describe nucleons, nuclei, excited nuclear states (and possibly atomic states) in addition to fundamental particles like photons, electrons, muons, etc. Under this definition the list of possible particles becomes quite large. To help organize them the database will need a way of grouping related particles (e.g., all the isotopes of an element, or all the excited levels of an isotope) together into particle 'groups'. The database will also need a way to classify particles that belong to the same 'family' (such as 'leptons', 'baryons', etc.). Each family of particles may have special requirements as to what properties are required. One important function of the particle database will be to provide an easy way for codes and external databases to look up any particle stored inside. In order to make access as

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. Magazine for handling stripping foils in a particle accelerator

    International Nuclear Information System (INIS)

    Gorka, A.J. Jr.

    1975-01-01

    Thin foils for stripping a particle beam are stored in a magazine that is operable remotely to display an individual foil, release it when it is spent, and repeat this process. The magazine is operable in the high-vacuum, high-radiation environment in the interior of a particle accelerator, and it uses the magnetic field of the accelerator to operate the display and dropping mechanism. (U.S.)

  2. Is an elementary particle really: (i) a particle? (ii) elementary?

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Is an elementary particle really: (i) a particle? (ii) elementary? Over centuries, naïve notions about this have turned out incorrect. Particles are not really pointlike. The word elementary is not necessarily well-defined. Notes:

  3. The Mathematical Formalism of a Particle in a Magnetic Field

    CERN Document Server

    Mantoiu, M

    2005-01-01

    In this review article we develop a basic part of the mathematical theory involved in the description of a particle (classical and quantal) placed in the Euclidean space $\\mathbb R^N$ under the influence of a magnetic field $B$, emphasising the structure of the family of observables.

  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. Early-life lead exposure results in dose- and sex-specific effects on weight and epigenetic gene regulation in weanling mice

    Science.gov (United States)

    Faulk, Christopher; Barks, Amanda; Liu, Kevin; Goodrich, Jaclyn M; Dolinoy, Dana C

    2013-01-01

    Aims Epidemiological and animal data suggest that the development of adult chronic conditions is influenced by early-life exposure-induced changes to the epigenome. This study investigates the effects of perinatal lead (Pb) exposure on DNA methylation and bodyweight in weanling mice. Materials & methods Viable yellow agouti (Avy) mouse dams were exposed to 0, 2.1, 16 and 32 ppm Pb acetate before conception through weaning. Epigenetic effects were evaluated by scoring coat color of Avy/a offspring and quantitative bisulfite sequencing of two retrotransposon-driven (Avy and CDK5 activator-binding protein intracisternal A particle element) and two imprinted (Igf2 and Igf2r) loci in tail DNA. Results Maternal blood Pb levels were below the limit of detection in controls, and 4.1, 25.1 and 32.1 μg/dl for each dose, respectively. Pb exposure was associated with a trend of increased wean bodyweight in males (p = 0.03) and altered coat color in Avy/a offspring. DNA methylation at Avy and the CDK5 activator-binding protein intracisternal A-particle element was significantly different from controls following a cubic trend (p = 0.04; p = 0.01), with male-specific effects at the Avy locus. Imprinted genes did not shift in methylation across exposures. Conclusion Dose- and sex-specific responses in bodyweight and DNA methylation indicate that Pb acts on the epigenome in a locus-specific fashion, dependent on the genomic feature hosting the CpG site of interest, and that sex is a factor in epigenetic response. PMID:24059796

  7. Stochastic Thermodynamics of a Particle in a Box.

    Science.gov (United States)

    Gong, Zongping; Lan, Yueheng; Quan, H T

    2016-10-28

    The piston system (particles in a box) is the simplest paradigmatic model in traditional thermodynamics. However, the recently established framework of stochastic thermodynamics (ST) fails to apply to this model system due to the embedded singularity in the potential. In this Letter, we study the ST of a particle in a box by adopting a novel coordinate transformation technique. Through comparing with the exact solution of a breathing harmonic oscillator, we obtain analytical results of work distribution for an arbitrary protocol in the linear response regime and verify various predictions of the fluctuation-dissipation relation. When applying to the Brownian Szilard engine model, we obtain the optimal protocol λ_{t}=λ_{0}2^{t/τ} for a given sufficiently long total time τ. Our study not only establishes a paradigm for studying ST of a particle in a box but also bridges the long-standing gap in the development of ST.

  8. A Program to Generate a Particle Distribution from Emittance Measurements

    CERN Document Server

    Bouma, DS; Lallement, JB

    2010-01-01

    We have written a program to generate a particle distribution based on emittance measurements in x-x’ and y-y’. The accuracy of this program has been tested using real and constructed emittance measurements. Based on these tests, the distribution generated by the program can be used to accurately simulate the beam in multi-particle tracking codes, as an alternative to a Gaussian or uniform distribution.

  9. Characterization of steady streaming for a particle manipulation system.

    Science.gov (United States)

    Amit, Roni; Abadi, Avi; Kosa, Gabor

    2016-04-01

    Accurate positioning of biological cells or microscopic particle without directly contacting them is a challenging task in biomedical engineering. Various trapping methods for controlling the position of a particle have been suggested. The common driving methods are based on laser and ultrasonic actuation principles. In this work we suggest a design for a hydrodynamic particle manoeuvring system. The system operates using steady streaming in a viscous fluid media induced by high frequency vibration of piezoelectric cantilevers. A particle within the workspace of the system can be trapped and manipulated to a desired position by the fairly unidirectional flow field created by the beams. In this paper, the flow field in the particle manipulation system is characterized numerically and experimentally. We find that the flow field resembles the analytical solutions of a flow field created by an oscillating sphere. Furthermore, we validate numerically the quadratic relation between the steady streaming velocity and the vibration amplitude of the beam. The calibration of the piezoelectric actuator's oscillation amplitudes enables effective positioning of particles with a diameter of 20 um to 1 mm. We find that a 30X0.8X2 mm(3) piezoelectric beam vibrating at its first resonance frequency, 200 Hz, is able to move a particle at a typical flow velocity ranging between 0.05 mm/sec and 0.13 mm/s in 430 cSt Si oil (Re=0.2).

  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. Dynamical groups of a particle in a periodic potential

    International Nuclear Information System (INIS)

    Yusuf, M.

    1992-09-01

    Solving the Schroedinger non-relativistic equation of a particle moving under the influence of the potential V(θ) = ω(1 - cosθ) leads to us to the standard Mathieu equation. Jahnke-Emde's(1938), the periodic solutions are Mathieu functions of even order. With an approximation we study two important limiting cases, a simple quantum rotator and one-dimensional linear oscillator. We show the dynamical groups of these special, and a further study of the real problem connects us an Euclidean group of 2D. An IRR of matrix elements give us the energy levels. The interface between the E 2 and Bessel Functions is showed. (author). 7 refs

  15. Dropping a particle out of a roller coaster

    International Nuclear Information System (INIS)

    Mungan, Carl E; Lipscombe, Trevor C

    2014-01-01

    A rider in a roller coaster lets go of a particle such as a small marble. How far does the marble travel horizontally from the point of release before hitting the ground, assuming the speed of the roller coaster is determined by conservation of mechanical energy starting from the highest hill up which it was pulled? Where should the marble be released along the track if one wishes to maximize the range of the marble? These questions constitute interesting variations on conventional problems in two-dimensional kinematics, appropriate for an undergraduate course in classical mechanics. Exploration of various shapes of tracks could form interesting student projects for numerical or experimental investigation. (paper)

  16. Feynman propagator for a particle with arbitrary spin

    International Nuclear Information System (INIS)

    Huang Shi-Zhong; Zhang Peng-Fei; Ruan Tu-Nan; Zhu Yu-Can; Zheng Zhi-Peng

    2005-01-01

    Based on the solution to the Rarita-Schwinger equations, a direct derivation of the projection operator and propagator for a particle with arbitrary spin is worked out. The projection operator constructed by Behrends and Fronsdal is re-deduced and confirmed, and simplified in the case of half-integral spin; the general commutation rules and Feynman propagator for a free particle of any spin are derived, and explicit expressions for the propagators for spins 3/2, 2, 5/2, 3, 7/2, 4 are provided. (orig.)

  17. Search for a particle with a long interaction length

    International Nuclear Information System (INIS)

    Barrowes, S.C.; Huggett, R.W.; Jones, W.V.; Levit, L.B.; Porter, L.G.

    1975-01-01

    A search has been carried out for a long-lived particle having an interaction length lambdasub(m) = 300 to 2,000 cm -2 in air. Such a particle, called the mandela, has been proposed by the Leeds group to explain an anomalous energy spectrum of particles observed near sea level with a shallow spectrometer. Data taken at mountain altitude with a deep spectrometer has been examined for compatibility with the existence of the mandela. Although the data tend to favor the mandela hypothesis the results are not conclusive and appear to be explainable by conventional means. (orig.) [de

  18. Dynamics of a particle attracted by a magnetized wire

    International Nuclear Information System (INIS)

    Lawson, W.F. Jr.; Simons, W.H.; Treat, R.P.

    1977-01-01

    The dynamics of a particle attracted by a magnetized wire is studied for nonvanishing gravitational forces and a broad range of Stokes number K. The Newtonian equation of motion for the particle is integrated for 10 -2 2 , a range which includes conditions where the particle inertia cannot be ignored. Families of trajectories, typical of low and high K, reveal the dominance of viscous forces at low K, as expected, and show oscillatory approach to capture for high K, where inertia is significant. Capture distances in the interval 1< or =X/sub c/< or =8 are given as a function of three independent dimensionless parameters which measure the strengths of the magnetic, viscous, and gravitational forces. The range of conditions is established for which it is permissible to neglect, for the purpose of computing capture distances, both the inertia and the radially attractive short-range part of the magnetic force. The equation of motion in which the inertia and the short-range term are neglected is studied. An integral of this equation is found which extends the trajectory equations of Zebel and Luborsky to include the gravitational force. A general approach to the construction of the integral of motion shows how to find the trajectory equation for a particle moving in a more complicated incompressible viscous flow with higher multipole contributions to the magnetic field of force

  19. Entanglement entropy for a particle coupled with its surrounding

    International Nuclear Information System (INIS)

    Puttarprom, C.; Yoo-Kong, S.; Tanasittikosol, M.; Liewrian, W.

    2014-01-01

    We investigate the entanglement for a model of a particle moving in the lattice (many-body system). The interaction between the particle and the lattice is modelled using Hooke's law. The Feynman path integral approach is applied to compute the density matrix of the system. The complexity of the problem is reduced by considering two-body system (bipartite system). The spatial entanglement of ground state is studied using the linear entropy. We find that increasing the confining potential implies a large spatial separation between the two particles. Thus the interaction between the particles increases according to Hooke's law. This results in the increase in the spatial entanglement

  20. Stochastic motion of a particle in a model fluctuating medium

    International Nuclear Information System (INIS)

    Moreau, M.; Gaveau, B.; Perera, A.; Frankowicz, M.

    1993-01-01

    We present several models of time fluctuating media with finite memory, consisting in one and two-dimensional lattices, the Modes of which fluctuate between two internal states according to a Poisson process. A particle moves on the lattice, the diffusion by the Modes depending on their internal state. Such models can be used for the microscopic theory of reaction constants in a dense phase, or for the study of diffusion or reactivity in a complex medium. In a number of cases, the transmission probability of the medium is computed exactly; it is shown that stochastic resonances can occur, an optimal transmission being obtained for a convenient choice of parameters. In more general situations, approximate solutions are given in the case of short and moderate memory of the obstacles. The diffusion in an infinite two-dimensional lattice is studied, and the memory is shown to affect the distribution of the particles rather than the diffusion law. (author). 25 refs, 5 figs

  1. Nonlinear data assimilation using synchronization in a particle filter

    Science.gov (United States)

    Rodrigues-Pinheiro, Flavia; Van Leeuwen, Peter Jan

    2017-04-01

    Current data assimilation methods still face problems in strongly nonlinear cases. A promising solution is a particle filter, which provides a representation of the model probability density function by a discrete set of particles. However, the basic particle filter does not work in high-dimensional cases. The performance can be improved by considering the proposal density freedom. A potential choice of proposal density might come from the synchronisation theory, in which one tries to synchronise the model with the true evolution of a system using one-way coupling via the observations. In practice, an extra term is added to the model equations that damps growth of instabilities on the synchronisation manifold. When only part of the system is observed synchronization can be achieved via a time embedding, similar to smoothers in data assimilation. In this work, two new ideas are tested. First, ensemble-based time embedding, similar to an ensemble smoother or 4DEnsVar is used on each particle, avoiding the need for tangent-linear models and adjoint calculations. Tests were performed using Lorenz96 model for 20, 100 and 1000-dimension systems. Results show state-averaged synchronisation errors smaller than observation errors even in partly observed systems, suggesting that the scheme is a promising tool to steer model states to the truth. Next, we combine these efficient particles using an extension of the Implicit Equal-Weights Particle Filter, a particle filter that ensures equal weights for all particles, avoiding filter degeneracy by construction. Promising results will be shown on low- and high-dimensional Lorenz96 models, and the pros and cons of these new ideas will be discussed.

  2. Model Adaptation for Prognostics in a Particle Filtering Framework

    Directory of Open Access Journals (Sweden)

    Bhaskar Saha

    2011-01-01

    Full Text Available One of the key motivating factors for using particle filters for prognostics is the ability to include model parameters as part of the state vector to be estimated. This performs model adaptation in conjunction with state tracking, and thus, produces a tuned model that can used for long term predictions. This feature of particle filters works in most part due to the fact that they are not subject to the “curse of dimensionality”, i.e. the exponential growth of computational complexity with state dimension. However, in practice, this property holds for “well-designed” particle filters only as dimensionality increases. This paper explores the notion of wellness of design in the context of predicting remaining useful life for individual discharge cycles of Li-ion and Li-Polymer batteries. Prognostic metrics are used to analyze the tradeoff between different model designs and prediction performance. Results demonstrate how sensitivity analysis may be used to arrive at a well-designed prognostic model that can take advantage of the model adaptation properties of a particle filter.

  3. Nonlinear Statistical Signal Processing: A Particle Filtering Approach

    International Nuclear Information System (INIS)

    Candy, J.

    2007-01-01

    A introduction to particle filtering is discussed starting with an overview of Bayesian inference from batch to sequential processors. Once the evolving Bayesian paradigm is established, simulation-based methods using sampling theory and Monte Carlo realizations are discussed. Here the usual limitations of nonlinear approximations and non-gaussian processes prevalent in classical nonlinear processing algorithms (e.g. Kalman filters) are no longer a restriction to perform Bayesian inference. It is shown how the underlying hidden or state variables are easily assimilated into this Bayesian construct. Importance sampling methods are then discussed and shown how they can be extended to sequential solutions implemented using Markovian state-space models as a natural evolution. With this in mind, the idea of a particle filter, which is a discrete representation of a probability distribution, is developed and shown how it can be implemented using sequential importance sampling/resampling methods. Finally, an application is briefly discussed comparing the performance of the particle filter designs with classical nonlinear filter implementations

  4. Model Adaptation for Prognostics in a Particle Filtering Framework

    Science.gov (United States)

    Saha, Bhaskar; Goebel, Kai Frank

    2011-01-01

    One of the key motivating factors for using particle filters for prognostics is the ability to include model parameters as part of the state vector to be estimated. This performs model adaptation in conjunction with state tracking, and thus, produces a tuned model that can used for long term predictions. This feature of particle filters works in most part due to the fact that they are not subject to the "curse of dimensionality", i.e. the exponential growth of computational complexity with state dimension. However, in practice, this property holds for "well-designed" particle filters only as dimensionality increases. This paper explores the notion of wellness of design in the context of predicting remaining useful life for individual discharge cycles of Li-ion batteries. Prognostic metrics are used to analyze the tradeoff between different model designs and prediction performance. Results demonstrate how sensitivity analysis may be used to arrive at a well-designed prognostic model that can take advantage of the model adaptation properties of a particle filter.

  5. Simulations of Shock Wave Interaction with a Particle Cloud

    Science.gov (United States)

    Koneru, Rahul; Rollin, Bertrand; Ouellet, Frederick; Annamalai, Subramanian; Balachandar, S.'Bala'

    2016-11-01

    Simulations of a shock wave interacting with a cloud of particles are performed in an attempt to understand similar phenomena observed in dispersal of solid particles under such extreme environment as an explosion. We conduct numerical experiments in which a particle curtain fills only 87% of the shock tube from bottom to top. As such, the particle curtain upon interaction with the shock wave is expected to experience Kelvin-Helmholtz (KH) and Richtmyer-Meshkov (RM) instabilities. In this study, the initial volume fraction profile matches with that of Sandia Multiphase Shock Tube experiments, and the shock Mach number is limited to M =1.66. In these simulations we use a Eulerian-Lagrangian approach along with state-of-the-art point-particle force and heat transfer models. Measurements of particle dispersion are made at different initial volume fractions of the particle cloud. A detailed analysis of the evolution of the particle curtain with respect to the initial conditions is presented. This work was supported by the U.S. Department of Energy, National Nuclear Security Administration, Advanced Simulation and Computing Program, as a Cooperative Agreement under the Predictive Science Academic Alliance Program, Contract No. DE-NA0002378.

  6. 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...

  7. A particle based simulation model for glacier dynamics

    Directory of Open Access Journals (Sweden)

    J. A. Åström

    2013-10-01

    Full Text Available A particle-based computer simulation model was developed for investigating the dynamics of glaciers. In the model, large ice bodies are made of discrete elastic particles which are bound together by massless elastic beams. These beams can break, which induces brittle behaviour. At loads below fracture, beams may also break and reform with small probabilities to incorporate slowly deforming viscous behaviour in the model. This model has the advantage that it can simulate important physical processes such as ice calving and fracturing in a more realistic way than traditional continuum models. For benchmarking purposes the deformation of an ice block on a slip-free surface was compared to that of a similar block simulated with a Finite Element full-Stokes continuum model. Two simulations were performed: (1 calving of an ice block partially supported in water, similar to a grounded marine glacier terminus, and (2 fracturing of an ice block on an inclined plane of varying basal friction, which could represent transition to fast flow or surging. Despite several approximations, including restriction to two-dimensions and simplified water-ice interaction, the model was able to reproduce the size distributions of the debris observed in calving, which may be approximated by universal scaling laws. On a moderate slope, a large ice block was stable and quiescent as long as there was enough of friction against the substrate. For a critical length of frictional contact, global sliding began, and the model block disintegrated in a manner suggestive of a surging glacier. In this case the fragment size distribution produced was typical of a grinding process.

  8. A Particle Batch Smoother Approach to Snow Water Equivalent Estimation

    Science.gov (United States)

    Margulis, Steven A.; Girotto, Manuela; Cortes, Gonzalo; Durand, Michael

    2015-01-01

    This paper presents a newly proposed data assimilation method for historical snow water equivalent SWE estimation using remotely sensed fractional snow-covered area fSCA. The newly proposed approach consists of a particle batch smoother (PBS), which is compared to a previously applied Kalman-based ensemble batch smoother (EnBS) approach. The methods were applied over the 27-yr Landsat 5 record at snow pillow and snow course in situ verification sites in the American River basin in the Sierra Nevada (United States). This basin is more densely vegetated and thus more challenging for SWE estimation than the previous applications of the EnBS. Both data assimilation methods provided significant improvement over the prior (modeling only) estimates, with both able to significantly reduce prior SWE biases. The prior RMSE values at the snow pillow and snow course sites were reduced by 68%-82% and 60%-68%, respectively, when applying the data assimilation methods. This result is encouraging for a basin like the American where the moderate to high forest cover will necessarily obscure more of the snow-covered ground surface than in previously examined, less-vegetated basins. The PBS generally outperformed the EnBS: for snow pillows the PBSRMSE was approx.54%of that seen in the EnBS, while for snow courses the PBSRMSE was approx.79%of the EnBS. Sensitivity tests show relative insensitivity for both the PBS and EnBS results to ensemble size and fSCA measurement error, but a higher sensitivity for the EnBS to the mean prior precipitation input, especially in the case where significant prior biases exist.

  9. An experimental and analytical study of a buoyancy driven cooling system for a particle accelerator

    International Nuclear Information System (INIS)

    Campbell, B.; Ranganathan, R.

    1993-05-01

    A buoyancy driven closed-loop cooling system that transports the heat generated in a particle accelerator to the ambient has been evaluated both through experiments performed earlier and analysis techniques developed elsewhere. Excellent comparisons between measurements and calculations have been obtained. The model illustrates the feasibility (from a heat transfer viewpoint) of such a cooling system for a particle accelerator

  10. An experimental and analytical study of a buoyancy driven cooling system for a particle accelerator

    International Nuclear Information System (INIS)

    Campbell, B.; Ranganathan, R.

    1993-01-01

    A buoyancy driven closed-loop cooling system that transports the heat generated in a particle accelerator to the ambient has been evaluated both through experiments performed earlier and analysis techniques developed elsewhere. Excellent comparisons between measurements and calculations have been obtained. The model illustrates the feasibility (from a heat transfer viewpoint) of such a cooling system for a particle accelerator

  11. CFD study of the minimum bubbling velocity of Geldart A particles in gas-fluidized beds

    NARCIS (Netherlands)

    Wang, Junwu; Hoef, van der M.A.; Kuipers, J.A.M.

    2010-01-01

    The minimum bubbling velocity, which demarcates the homogeneous and heterogeneous fluidization regimes, plays a pivotal role in gas fluidization of Geldart A particles. We systematically study the effect of gas and particle properties on the minimum bubbling velocity of Geldart A particles in

  12. Trapping of a particle in a short-range harmonic potential well

    OpenAIRE

    Castro, L. B.; de Castro, A. S.

    2012-01-01

    Eigenstates of a particle in a localized and unconfined harmonic potential well are investigated. Effects due to the variation of the potential parameters as well as certain results from asymptotic expansions are discussed.

  13. Differential radioautographic visualization of central catecholaminergic neurons following intracisternal or intraventricular injection of tritiated norepinephrine

    International Nuclear Information System (INIS)

    Nowaczyk, T.; Pujol, J.F.; Valatx, J.L.; Bobillier, P.

    1978-01-01

    The differential [ 3 H]NE labeling of CA groups following cerebrospinal fluid (CSF) injection procedures seems to be accounted by the dynamics of CSF formation and circulation, which is similar in the rat to that known in man. Following intraventricular injection there was a lack of labeling of CA neurons located at a distance from the cerebrospinal cavities. Labeled neurons were also visualized outside known CA groups, questioning the nature and functional significance of these cells. (C.F.)

  14. Isolated spinal accessory neuropathy and intracisternal schwannomas of the spinal accessory nerve

    Directory of Open Access Journals (Sweden)

    Abdullah M. Al-Ajmi

    2015-03-01

    Full Text Available We report a 40-year-old female patient presenting with isolated left spinal accessory neuropathy that developed insidiously over 6 years. She complained of ill-defined deep neck and shoulder pain. On examination, prominent sternocleidomastoid and trapezoid muscle weakness and atrophy, shoulder instability, and lateral scapular winging were observed. MRI identified a small mass of the cisternal portion of the spinal accessory nerve. Its appearance was typical of schwannoma. Surgical treatment was not offered because of the small tumor size, lack of mass effect and the questionable functional recovery in the presence of muscular atrophy.

  15. The Antiedema Effect of Intracisternal Hyperosmolar Albumine on Experimental Created Brain Edema

    Directory of Open Access Journals (Sweden)

    Ayhan Tekiner

    2010-01-01

    Full Text Available Aim: The brain edema caused by central nervous system diseases and trauma is an important reason of morbidity and mortality currently. Although the most of physiopathology of traumatic brain edema has been elucidated through many clinical and laboratory studies, the treatment of edema couldn?t been standardized. For this purpose, from past to the present although many treatment principles have been accepted, also different treatment agents are being used. Material and Methods: In this experimental study thirty six New Zealander rabbits weighing between 2.2 and 2.8 kg were used. Craniectomi was applied to the subjects and gravity was dropped from high in order to develop traumatic brain edema. The subjects were divided into six groups and hyperosmolar albumine was given to each group on different time periods. It was Aim: ed to resolve the edema by drawing the edema liquid to subarachnoid distance by giving human albumin a physiologic macromolecule through cysterna manga. The efficacy of tretment was evaluated through two parameters: the first cerebrospinal fluid osmolality and the second the rate of brain tissue fluid. Results: Cerebrospinal fluid osmolality and brain tissue fluid ratio gained at the result of the study were statistical evaluated by  Kruskal-Wallis nonparametric ANOVA test and Mann-Whitney U test. p value<0,05 was accepted statistical significant. Conclusions: When compared the Results : of the study groups the difference was significant between trauma and control group and the difference was relatively close to the control group at the treatment group. The treatment was significantly efficient at the groups which were applied hyperosmolar albumine two or three times in the first 72 hours after trauma. According to these Results : we can declare this experimental study has reached to the purpose and can contribute to future studies about the same subject.

  16. Variation in angular velocity and angular acceleration of a particle in rectilinear motion

    International Nuclear Information System (INIS)

    Mashood, K K; Singh, V A

    2012-01-01

    We discuss the angular velocity and angular acceleration associated with a particle in rectilinear motion with constant acceleration. The discussion was motivated by an observation that students and even teachers have difficulty in ascribing rotational motion concepts to a particle when the trajectory is a straight line. We present some details of our observations. A formal derivation of ω and α is presented which reveals ‘surprising’ and non-intuitive aspects, namely non-monotonic behaviour with an associated extremum. The special case of constant velocity is studied and we find that angular acceleration associated with it also has an extremum. We discuss a plausible source of difficulty. (paper)

  17. Academic Training Lectures | Black Holes from a Particle Physics Perspective | 18-19 November

    CERN Multimedia

    2014-01-01

    Black Holes from a Particle Physics Perspective by Georgi Dvali   Tuesday 18 and Wednesday 19 November 2014 from 11 am to 12 noon at CERN ( 40-S2-A01 - Salle Anderson ) Description: We will review the physics of black holes, both large and small, from a particle physicist's perspective, using particle physics tools for describing concepts such as entropy, temperature and quantum information processing. We will also discuss microscopic pictures of black hole formation in high energy particle scattering, potentially relevant for high-energy accelerator experiments, and some differences and similarities with the signatures of other BSM physics. See the Indico page here.

  18. From the Weyl quantization of a particle on the circle to number–phase Wigner functions

    International Nuclear Information System (INIS)

    Przanowski, Maciej; Brzykcy, Przemysław; Tosiek, Jaromir

    2014-01-01

    A generalized Weyl quantization formalism for a particle on the circle is shown to supply an effective method for defining the number–phase Wigner function in quantum optics. A Wigner function for the state ϱ ^ and the kernel K for a particle on the circle is defined and its properties are analysed. Then it is shown how this Wigner function can be easily modified to give the number–phase Wigner function in quantum optics. Some examples of such number–phase Wigner functions are considered

  19. Modeling the C. elegans nematode and its environment using a particle system.

    Science.gov (United States)

    Rönkkö, Mauno; Wong, Garry

    2008-07-21

    A particle system, as understood in computer science, is a novel technique for modeling living organisms in their environment. Such particle systems have traditionally been used for modeling the complex dynamics of fluids and gases. In the present study, a particle system was devised to model the movement and feeding behavior of the nematode Caenorhabditis elegans in three different virtual environments: gel, liquid, and soil. The results demonstrate that distinct movements of the nematode can be attributed to its mechanical interactions with the virtual environment. These results also revealed emergent properties associated with modeling organisms within environment-based systems.

  20. An Orthogonal Multi-Swarm Cooperative PSO Algorithm with a Particle Trajectory Knowledge Base

    Directory of Open Access Journals (Sweden)

    Jun Yang

    2017-01-01

    Full Text Available A novel orthogonal multi-swarm cooperative particle swarm optimization (PSO algorithm with a particle trajectory knowledge base is presented in this paper. Different from the traditional PSO algorithms and other variants of PSO, the proposed orthogonal multi-swarm cooperative PSO algorithm not only introduces an orthogonal initialization mechanism and a particle trajectory knowledge base for multi-dimensional optimization problems, but also conceives a new adaptive cooperation mechanism to accomplish the information interaction among swarms and particles. Experiments are conducted on a set of benchmark functions, and the results show its better performance compared with traditional PSO algorithm in aspects of convergence, computational efficiency and avoiding premature convergence.

  1. A method for the separation of non-ferrous metal containing particles from a particle stream

    NARCIS (Netherlands)

    Van der Weijden, R.D.; Rem, P.C.

    2004-01-01

    The invention relates to a method for the recovery of non-ferrous metal-comprising particles from a particle stream. According to the invention, the particle stream is put onto a conveyor belt in the form of a monolayer such that with the aid of a liquid, at least the non-ferrous metal comprising

  2. Simple One-Dimensional Quantum-Mechanical Model for a Particle Attached to a Surface

    Science.gov (United States)

    Fernandez, Francisco M.

    2010-01-01

    We present a simple one-dimensional quantum-mechanical model for a particle attached to a surface. It leads to the Schrodinger equation for a harmonic oscillator bounded on one side that we solve in terms of Weber functions and discuss the behaviour of the eigenvalues and eigenfunctions. We derive the virial theorem and other exact relationships…

  3. The current of a particle along a microtubule in microscopic plasma

    International Nuclear Information System (INIS)

    Li Wei; Chen Junfang; Wang Teng; Lai Xiuqiong

    2008-01-01

    Transport of a particle along the axis of a microtubule in a plasma-enhanced chemical vapor deposition (PECVD) system is investigated. The current, respectively, as a function of the temperature, the magnetic field and the external force is obtained. The value and direction of the current may be controlled by changing the above parameters

  4. A numerical study of fluidization behavior of Geldart A particles using a discrete particle model

    NARCIS (Netherlands)

    Ye, M.; van der Hoef, Martin Anton; Kuipers, J.A.M.

    2004-01-01

    This paper reports on a numerical study of fluidization behavior of Geldart A particles by use of a 2D soft-sphere discrete particle model (DPM). Some typical features, including the homogeneous expansion, gross particle circulation in the absence of bubbles, and fast bubbles, can be clearly

  5. Motion of a particle in a Coulomb plus Aharonov-Bohm potential

    International Nuclear Information System (INIS)

    Kibler, M.; Negadi, T.

    1987-05-01

    The motion of a particle in a Coulomb plus Aharonov-Bohm potential is investigated from a classical and a quantum mechanical viewpoint. The quantum bound states are derived by using the KS transformation. The grouping of certain levels is explained via the introduction of a SU(2) dynamical algebra. All classical finite trajectories are found to be periodic

  6. Equations of motion of a particle interacting with a scalar field

    International Nuclear Information System (INIS)

    Sato, N.K.

    1984-01-01

    The equations of motion of a particle (nucleon) interacting with a escalar (mesonic) field are derived by the energy momentum tensor moments method of Papapetrou. After a detailed study of the mesonic radiation field the expression of the reactive radiation force of the field upon the particle is established. (Author) [pt

  7. Eigenstates of a particle in an array of hexagons with periodic boundary condition

    Directory of Open Access Journals (Sweden)

    A Nemati

    2013-10-01

    Full Text Available In this paper the problem of a particle in an array of hexagons with periodic boundary condition is solved. Using the projection operators, we categorize eigenfunctions corresponding to each of the irreducible representations of the symmetry group . Based on these results, the Dirichlet and Neumann boundary conditions are discussed.

  8. Continuous Quantum Nondemolition Measurements of a Particle in Electromagnetic and Gravitational Fields

    International Nuclear Information System (INIS)

    Zhu Chunhua; Zha Chaozheng

    2005-01-01

    The detection of a particle in electromagnetic plus gravitational fields is investigated. We obtain a set of quantum nondemolition variables. The continuous measurements of these nondemolition parameters are analyzed in the framework of restricted path integral formalism. We manipulate the corresponding propagators, and deduce the probabilities associated with the possible measurement outputs.

  9. Man-made Black Holes? Can a particle collider be taken too far?

    CERN Multimedia

    Rupley, Sebastian

    2006-01-01

    "Can a particle collider be taken too far? That question is being raised about the next-generation Large Hadron Collider (LHC), shown in the photo here. The huge particle pulverizer and accelerator is located at the CERN particle physics laboratory, near Geneva, Switzerland." (1/2 page)

  10. Work distribution for a particle moving in an optical trap and non ...

    Indian Academy of Sciences (India)

    Administrator

    Work distribution for a particle moving in an optical trap and ... It is also observed that only at long time the total work is completely ...... speed ν and time t are varied but they are adjusted in ... the probability distribution P(W, t) for a given pull-.

  11. Transmission time of a particle in the reflectionless Sech-squared potential: Quantum clock approach

    International Nuclear Information System (INIS)

    Park, Chang-Soo

    2011-01-01

    We investigate the time for a particle to pass through the reflectionless Sech-squared potential. Using the Salecker-Wigner and Peres quantum clock an average transmission time of a Gaussian wave packet representing the particle is explicitly evaluated in terms of average momentum and travel distance. The average transmission time is shown to be shorter than the time of free-particle motion and very close to the classical time for wave packets with well-localized momentum states. Since the clock measures the duration of scattering process the average transmission time can be interpreted as the average dwell time. -- Highlights: → We examine the scattering of a particle in the Sech-squared potential. → We use quantum clock to find an average transmission time. → It is very close to the classical time. → It is shorter than the time of free particle. → It is interpreted as the average dwell time.

  12. Power System Stabilizer Design Based on a Particle Swarm Optimization Multiobjective Function Implemented Under Graphical Interface

    Directory of Open Access Journals (Sweden)

    Ghouraf Djamel Eddine

    2016-05-01

    Full Text Available Power system stability considered a necessary condition for normal functioning of an electrical network. The role of regulation and control systems is to ensure that stability by determining the essential elements that influence it. This paper proposes a Particle Swarm Optimization (PSO based multiobjective function to tuning optimal parameters of Power System Stabilizer (PSS; this later is used as auxiliary to generator excitation system in order to damp electro mechanicals oscillations of the rotor and consequently improve Power system stability. The computer simulation results obtained by developed graphical user interface (GUI have proved the efficiency of PSS optimized by a Particle Swarm Optimization, in comparison with a conventional PSS, showing stable   system   responses   almost   insensitive   to   large parameter variations.Our present study was performed using a GUI realized under MATLAB in our work.

  13. Three-dimensional investigation of recrystallization nucleation in a particle-containing Al alloy

    DEFF Research Database (Denmark)

    Zhang, Yonghao; Juul Jensen, Dorte; Zhang, Yubin

    2012-01-01

    The effects of an inhomogeneous distribution of second-phase particles on nucleation of recrystallization in a particle-containing aluminum alloy are investigated by 3-D serial sectioning. Clusters and bands of big intermetallic particles are the dominating nucleation sites, but other sites...... are also active. The effects of nucleation sites and the inhomogeneous particle distribution on the orientation and size of the nuclei are investigated and their relationships are discussed. 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved....

  14. Selection rules for the dematerialization of a particle into two photons

    International Nuclear Information System (INIS)

    Yang, C.N.

    1983-01-01

    Selection rules governing the disintegration of a particle into two photons are derived from the general principle of invariance under rotation and inversion. The polarization state of the photons is completely fixed by the selection rules for initial particles with spin less than 2. These results which are independent of any specific assumption about the interactions may possibly offer a method of deciding the symmetry nature of mesons which decay into two photons. 4 tables

  15. Quantum dynamics of a particle in a fermionic environment. Pt. 2

    International Nuclear Information System (INIS)

    Hedegard, P.; Caldeira, A.O.

    1985-09-01

    We study the ground state properties of a particle moving in a tight binding band and coupled to a Fermi sea of metal electrons. Using an effective Hamiltonian and a variational ground state, we find a band narrowing of Wsub(eff)/Wsub(o)approx.=(Wsub(o)/epsilonsub(F))sup(α/1-α), where α measures the coupling strength between particle and environment. A renormalization group analysis gives the same result for α 1, indicating a (zero-temperature) localization transition. (orig.)

  16. Transverse Motion of a Particle with an Oscillating Charge and Variable Mass in a Magnetic Field

    Science.gov (United States)

    Alisultanov, Z. Z.; Ragimkhanov, G. B.

    2018-03-01

    The problem of motion of a particle with an oscillating electric charge and variable mass in an uniform magnetic field has been solved. Three laws of mass variation have been considered: linear growth, oscillations, and stepwise growth. Analytical expressions for the particle velocity at different time dependences of the particle mass are obtained. It is established that simultaneous consideration of changes in the mass and charge leads to a significant change in the particle trajectory.

  17. Four-dimensional Hall mechanics as a particle on CP3

    International Nuclear Information System (INIS)

    Bellucci, Stefano; Casteill, Pierre-Yves; Nersessian, Armen

    2003-01-01

    In order to establish an explicit connection between four-dimensional Hall effect on S 4 and six-dimensional Hall effect on CP 3 , we perform the Hamiltonian reduction of a particle moving on CP 3 in a constant magnetic field to the four-dimensional Hall mechanics (i.e., a-bar particle on S 4 in a SU(2) instanton field). This reduction corresponds to fixing the isospin of the latter system

  18. Applying a Particle-only Model to the HL Tau Disk

    OpenAIRE

    Tabeshian, Maryam; Wiegert, Paul A.

    2018-01-01

    Observations have revealed rich structures in protoplanetary disks, offering clues about their embedded planets. Due to the complexities introduced by the abundance of gas in these disks, modeling their structure in detail is computationally intensive, requiring complex hydrodynamic codes and substantial computing power. It would be advantageous if computationally simpler models could provide some preliminary information on these disks. Here we apply a particle-only model (that we developed f...

  19. A particle bed reactor based NTP in the 112,500 N thrust class

    International Nuclear Information System (INIS)

    Ludewig, H.; Powell, J.R.; Lazareth, O.W. Jr.; Todosow, M.

    1993-01-01

    This paper discusses the application of a Particle Bed Reactor (PBR) to a 112,500 N thrust Nuclear Thermal Propulsion (NTP) Engine. The method of analysis is described, followed by a presentation of the results. It is concluded that the PBR would result in a very competitive NTP engine. In addition, due to the high power densities possible with a PBR, high thrust/weight ratios are possible. This conclusion can be used to satisfy a variety of mission goals

  20. A particle bed reactor based NTP in the 112,500 N thrust class

    Science.gov (United States)

    Ludewig, Hans; Powell, James R.; Lazareth, Otto W.; Todosow, Michael

    1993-01-01

    This paper discusses the application of a Particle Bed Reactor (PBR) to a 112,500 N thrust Nuclear Thermal Propulsion (NTP) Engine. The method of analysis is described, followed by a presentation of the results. It is concluded that the PBR would result in a very competitive NTP engine. In addition, due to the high power densities possible with a PBR, high thrust/weight ratios are possible. This conclusion can be used to satisfy a variety of mission goals.

  1. Considerations over the floating speed of a particle in vacuum pneumatic conveying sytems in flour milling

    Directory of Open Access Journals (Sweden)

    Tanase Tanase

    2016-06-01

    Full Text Available The present paper is a theoretical study aiming for to assess the influence of the different factors such as deviation from the spherical form of a particle, specific mass load of the pneumatic conveying pipe and the report between the particle diameter and the pipe diameter, over the floating speed of a particle. For a non-spherical particle, the Magnus force is affecting the floating speed of the given particle by increasing or decreasing it. The equation deducted within the present study, describes the movement of a particle or a fluid swirl under the resultant force with emphasis on the evaluation of the nature and magnitude of the Magnus force. The same Magnus Force explains the movement of the swirls in fluids, as for the wind swirls (hurricane or water swirls. The next part of the study relate the report between the particle diameter and the pipe diameter as well as the specific loads of the pipe, to the same floating speed. A differentiation in denominating the floating speed is proposed as well as that for the non-spherical particle the floating speed should be a domain, rather than a single value.

  2. Equilibrium without Friction of a Particle on a Mobile Surface with Bilateral Constraints

    Directory of Open Access Journals (Sweden)

    Nicolae–Doru Stănescu

    2015-09-01

    Full Text Available In this paper we will study the equilibrium of a particle on a mobile surface in the case characterized by bilateral constraints between the particle and the surface, and the absence of friction. Based on our previous work, the conditions for the equilibrium are obtained. We prove that the positions of equilibrium on a mobile surface are no longer the same with those obtained for a fixed surface, the system could have either other equilibrium positions, completely different, or some more equilibrium positions, or no equilibrium position.

  3. Combined Sewer Overflow pretreatment with chemical coagulation and a particle settler for improved peracetic acid disinfection

    DEFF Research Database (Denmark)

    Chhetri, Ravi Kumar; Bonnerup, Arne; Andersen, Henrik Rasmus

    2016-01-01

    Full scale disinfection by peracetic acid (PAA) was achieved on Combined Sewer Overflow (CSO) water, which was pre-treated physically by a fast settling-filtration unit. Disinfection of untreated CSO water using PAA was compared to treatment using a particle separator (Hydro......Separator®) and additional coagulation with poly-aluminum-chloride. Disinfection for Enterococcus increased with the applied dose of PAA and additional improvement was achieved when it was preceded by chemical coagulation with 5 mg L−1 poly-aluminum-chloride. When Enterococcus was reduced by treatment in the Hydro...

  4. Finite-temperature mobility of a particle coupled to a fermionic environment

    International Nuclear Information System (INIS)

    Castella, H.; Zotos, X.

    1996-01-01

    We study numerically the finite-temperature and frequency mobility of a particle coupled by a local interaction to a system of spinless fermions in one dimension. We find that when the model is integrable (particle mass equal to the mass of fermions) the static mobility diverges. Further, an enhanced mobility is observed over a finite parameter range away from the integrable point. We present an analysis of the finite-temperature static mobility based on a random matrix theory description of the many-body Hamiltonian. copyright 1996 The American Physical Society

  5. Numerical study of fundamental processes of severe accidents using a particle method

    International Nuclear Information System (INIS)

    Koshizuka, Seiichi

    2006-01-01

    A particle method has been developed for multiphase flows with large deformation of phase interfaces. The method is called Moving Particle Semi-implicit (MPS) which enables us to analyze incompressible fluid dynamics based on a semi-implicit algorithm. The MPS method has been applied to complex thermal-hydraulic problems in light water reactors and sodium-cooled fast reactors. The present paper provides the review of the past studies using MPS and an introduction of a new research project for severe accident analysis of fast reactors. (author)

  6. Statistical analysis of non-homogeneous Poisson processes. Statistical processing of a particle multidetector

    International Nuclear Information System (INIS)

    Lacombe, J.P.

    1985-12-01

    Statistic study of Poisson non-homogeneous and spatial processes is the first part of this thesis. A Neyman-Pearson type test is defined concerning the intensity measurement of these processes. Conditions are given for which consistency of the test is assured, and others giving the asymptotic normality of the test statistics. Then some techniques of statistic processing of Poisson fields and their applications to a particle multidetector study are given. Quality tests of the device are proposed togetherwith signal extraction methods [fr

  7. Hot gas path component cooling system having a particle collection chamber

    Science.gov (United States)

    Miranda, Carlos Miguel; Lacy, Benjamin Paul

    2018-02-20

    A cooling system for a hot gas path component includes a substrate having an outer surface and an inner surface. The inner surface defines at least one interior space. A passage is formed in the substrate between the outer surface and the inner surface. An access passage is formed in the substrate and extends from the outer surface to the inner space. The access passage is formed at a first acute angle to the passage and includes a particle collection chamber. The access passage is configured to channel a cooling fluid to the passage. Furthermore, the passage is configured to channel the cooling fluid therethrough to cool the substrate.

  8. Instanton Approach to the Langevin Motion of a Particle in a Random Potential

    International Nuclear Information System (INIS)

    Lopatin, A. V.; Vinokur, V. M.

    2001-01-01

    We develop an instanton approach to the nonequilibrium dynamics in one-dimensional random environments. The long time behavior is controlled by rare fluctuations of the disorder potential and, accordingly, by the tail of the distribution function for the time a particle needs to propagate along the system (the delay time). The proposed method allows us to find the tail of the delay time distribution function and delay time moments, providing thus an exact description of the long time dynamics. We analyze arbitrary environments covering different types of glassy dynamics: dynamics in a short-range random field, creep, and Sinai's motion

  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. A Particle Swarm Optimization of Natural Ventilation Parameters in a Greenhouse with Continuous Roof Vents

    Directory of Open Access Journals (Sweden)

    Abdelhafid HASNI

    2009-03-01

    Full Text Available Although natural ventilation plays an important role in the affecting greenhouse climate, as defined by temperature, humidity and CO2 concentration, particularly in Mediterranean countries, little information and data are presently available on full-scale greenhouse ventilation mechanisms. In this paper, we present a new method for selecting the parameters based on a particle swarm optimization (PSO algorithm which optimize the choice of parameters by minimizing a cost function. The simulator was based on a published model with some minor modifications as we were interested in the parameter of ventilation. The function is defined by a reduced model that could be used to simulate and predict the greenhouse environment, as well as the tuning methods to compute their parameters. This study focuses on the dynamic behavior of the inside air temperature and humidity during ventilation. Our approach is validated by comparison with some experimental results. Various experimental techniques were used to make full-scale measurements of the air exchange rate in a 400 m2 plastic greenhouse. The model which we propose based on natural ventilation parameters optimized by a particle swarm optimization was compared with the measurements results.

  11. FLIP-MHD: A particle-in-cell mehtod for magnetohydrodynamics

    International Nuclear Information System (INIS)

    Brackbill, J.U.

    1990-01-01

    A particle-in-cell (PIC) method, FLIP is extended to magnetohydrodynamic (MHD) flow in two dimensions. Particles are used to reduce computational diffusion of the magnetic field. FLIP is an extension of ''classical'' PIC, where particles have mass, but every other property of the fluid is stored on a grid. In FLIP, particles have every property of the fluid, so that they provide a complete Lagrangian description not only to resolve contact discontinuities but also to reduce computational diffusion of linear and angular momentum. The interactions among the particles are calculated on a grid, for convenience and economy. The present study extends FLIP to MHD, by including information about the magnetic field among the attributes of the particles. 6 refs

  12. LC HCAL Absorber And Active Media Comparisons Using a Particle-Flow Algorithm

    International Nuclear Information System (INIS)

    Magill, Steve; Kuhlmann, S.

    2006-01-01

    We compared Stainless Steel (SS) to Tungsten (W) as absorber for the HCAL in simulation using single particles (pions) and a Particle-Flow Algorithm applied to e + e - -> Z -> qqbar events. We then used the PFA to evaluate the performance characteristics of a LC HCAL using W absorber and comparing scintillator and RPC as active media. The W/Scintillator HCAL performs better than the SS/Scintillator version due to finer λ I sampling and narrower showers in the dense absorber. The W/Scintillator HCAL performs better than the W/RPC HCAL except in the number of unused hits in the PFA. Since this represents the confusion term in the PFA response, additional tuning and optimization of a W/RPC HCAL might significantly improve this HCAL configuration

  13. Quantum dynamics of a particle in a fermionic environment. Pt. 1

    International Nuclear Information System (INIS)

    Hedegard, P.; Caldeira, A.O.

    1985-09-01

    The reduced density operator of a particle coupled to a fermionic environment (metal electrons) is written in terms of a Feynman-Vernon influence functional. Two different approaches are used in order to achieve this goal. Firstly, the environmental interacting electron gas is treated in RPA and the coupling is correctly accounted for up to second order in perturbation theory. Then the local and tight-binding models are studied. For the latter a second approach for obtaining the influence functional is used in the narrow-band limit. It is found that the popular representation of the environment in terms of a single set of harmonic oscillators is not feasible unless the particle is confined to move in a local region of radial extension rapprox.=ksub(F) -1 . (orig.)

  14. Mobile Robot Positioning with 433-MHz Wireless Motes with Varying Transmission Powers and a Particle Filter.

    Science.gov (United States)

    Canedo-Rodriguez, Adrian; Rodriguez, Jose Manuel; Alvarez-Santos, Victor; Iglesias, Roberto; Regueiro, Carlos V

    2015-04-30

    In wireless positioning systems, the transmitter's power is usually fixed. In this paper, we explore the use of varying transmission powers to increase the performance of a wireless localization system. To this extent, we have designed a robot positioning system based on wireless motes. Our motes use an inexpensive, low-power sub-1-GHz system-on-chip (CC1110) working in the 433-MHz ISM band. Our localization algorithm is based on a particle filter and infers the robot position by: (1) comparing the power received with the expected one; and (2) integrating the robot displacement. We demonstrate that the use of transmitters that vary their transmission power over time improves the performance of the wireless positioning system significantly, with respect to a system that uses fixed power transmitters. This opens the door for applications where the robot can localize itself actively by requesting the transmitters to change their power in real time.

  15. The centripetal force law and the equation of motion for a particle on a curved hypersurface

    International Nuclear Information System (INIS)

    Hu, L.D.; Lian, D.K.; Liu, Q.H.

    2016-01-01

    It is pointed out that the current form of the extrinsic equation of motion for a particle constrained to remain on a hypersurface is in fact a half-finished version; for it is established without regard to the fact that the particle can never depart from the geodesics on the surface. Once this fact is taken into consideration, the equation takes the same form as that for the centripetal force law, provided that the symbols are re-interpreted so that the law is applicable for higher dimensions. The controversial issue of constructing operator forms of these equations is addressed, and our studies show the quantization of constrained system based on the extrinsic equation of motion is preferable. (orig.)

  16. An inventory on rotational kinematics of a particle: unravelling misconceptions and pitfalls in reasoning

    International Nuclear Information System (INIS)

    Mashood, K K; Singh, Vijay A

    2012-01-01

    Student difficulties regarding the angular velocity and angular acceleration of a particle have remained relatively unexplored in contrast to their linear counterparts. We present an inventory comprising multiple choice questions aimed at probing misconceptions and eliciting ill-suited reasoning patterns. The development of the inventory was based on interactions with students, teachers and experts. We report misconceptions, some of which are parallel to those found earlier in linear kinematics. Fixations with inappropriate prototypes were uncovered. Many students and even teachers mistakenly assume that all rotational motion is necessarily circular. A persistent notion that the direction of angular velocity and angular acceleration should be ‘along’ the motion exists. Instances of indiscriminate usage of equations were identified. (paper)

  17. PARTRACK - A particle tracking algorithm for transport and dispersion of solutes in a sparsely fractured rock

    International Nuclear Information System (INIS)

    Svensson, Urban

    2001-04-01

    A particle tracking algorithm, PARTRACK, that simulates transport and dispersion in a sparsely fractured rock is described. The main novel feature of the algorithm is the introduction of multiple particle states. It is demonstrated that the introduction of this feature allows for the simultaneous simulation of Taylor dispersion, sorption and matrix diffusion. A number of test cases are used to verify and demonstrate the features of PARTRACK. It is shown that PARTRACK can simulate the following processes, believed to be important for the problem addressed: the split up of a tracer cloud at a fracture intersection, channeling in a fracture plane, Taylor dispersion and matrix diffusion and sorption. From the results of the test cases, it is concluded that PARTRACK is an adequate framework for simulation of transport and dispersion of a solute in a sparsely fractured rock

  18. Expert system strategies for the diagnostic in a particle physics experiment

    International Nuclear Information System (INIS)

    D'Antone, I.; Mandrioli, G.; Matteuzzi, P.

    1990-01-01

    The maintenance of a particle detector functionality requires the knowledge of more experts: physicists and engineers for the detector and the electronic system. The integration of different knowledges and experiences can be easily done using an Expert System. A real-time Expert System allows us to diagnose the detector and data acquisition system anomalies; it makes an on-line diagnosis and, if an abnormal condition is identified, takes the appropriate action to reduce the unavailability of the apparatus. A method based on structural and behavioral reasoning is considered. Reasoning on the structure and on the functionality of the apparatus all the possible failures that can explain the sensor readings are searched. The behaviour of the apparatus components are described in qualitative terms to write the rules for the expert system

  19. Trajectory and velocity measurement of a particle in spray by digital holography

    Energy Technology Data Exchange (ETDEWEB)

    Lue Qieni; Chen Yiliang; Yuan Rui; Ge Baozhen; Gao Yan; Zhang Yimo

    2009-12-20

    We present a method for the trajectory and the velocity measurement of a particle in spray by digital holography. Based on multiple exposure digital in-line holography, a sequence of digital holograms of a dynamic spray particle field at different times are recorded with a CW laser and a high-speed CCD. The time evolution of the serial positions of particles, i.e., the motion trajectories of the particles, is obtained by numerically reconstructing the synthetic hologram of a sequence of digital holograms. The center coordinate (x,y) of each particle image can be extracted using a Hough transform and subpixel precision computing, and the velocity of an individual particle can also be obtained, which is then applied to measuring the velocity of diesel spray and alcohol spray. The research shows that the method presented in this paper for measuring spray field is feasible.

  20. A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding.

    Science.gov (United States)

    Yang, Cheng-Hong; Lin, Yu-Shiun; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2017-10-01

    The hydrophobic-polar (HP) model is commonly used for predicting protein folding structures and hydrophobic interactions. This study developed a particle swarm optimization (PSO)-based algorithm combined with local search algorithms; specifically, the high exploration PSO (HEPSO) algorithm (which can execute global search processes) was combined with three local search algorithms (hill-climbing algorithm, greedy algorithm, and Tabu table), yielding the proposed HE-L-PSO algorithm. By using 20 known protein structures, we evaluated the performance of the HE-L-PSO algorithm in predicting protein folding in the HP model. The proposed HE-L-PSO algorithm exhibited favorable performance in predicting both short and long amino acid sequences with high reproducibility and stability, compared with seven reported algorithms. The HE-L-PSO algorithm yielded optimal solutions for all predicted protein folding structures. All HE-L-PSO-predicted protein folding structures possessed a hydrophobic core that is similar to normal protein folding.

  1. Cloud a particle beam facility to investigate the influence of cosmic rays on clouds

    CERN Document Server

    Kirkby, Jasper

    2001-01-01

    Palaeoclimatic data provide extensive evidence for solar forcing of the climate during the Holocene and the last ice age, but the underlying mechanism remains a mystery. However recent observations suggest that cosmic rays may play a key role. Satellite data have revealed a surprising correlation between cosmic ray intensity and the fraction of the Earth covered by low clouds \\cite{svensmark97,marsh}. Since the cosmic ray intensity is modulated by the solar wind, this may be an important clue to the long-sought mechanism for solar-climate variability. In order to test whether cosmic rays and clouds are causally linked and, if so, to understand the microphysical mechanisms, a novel experiment known as CLOUD\\footnotemark\\ has been proposed \\cite{cloud_proposal}--\\cite{cloud_addendum_2}. CLOUD proposes to investigate ion-aerosol-cloud microphysics under controlled laboratory conditions using a beam from a particle accelerator, which provides a precisely adjustable and measurable artificial source of cosmic rays....

  2. Unusual equilibration of a particle in a potential with a thermal wall

    Science.gov (United States)

    Bhat, Deepak; Sabhapandit, Sanjib; Kundu, Anupam; Dhar, Abhishek

    2017-11-01

    We consider a particle in a one-dimensional box of length L, with a Maxwell bath at one end and a reflecting wall at the other end. Using a renewal approach, as well as directly solving the master equation, we show that the system exhibits a slow power law relaxation, with a logarithmic correction, towards the final equilibrium state. We extend the renewal approach to a class of confining potentials of the form U(x) \\propto x^α , x>0 , where we find that the relaxation is ∼ t-(α+2)/(α-2) for α >2 , with a logarithmic correction when (α+2)/(α-2) is an integer. For α <2 the relaxation is exponential. Interestingly for α=2 (harmonic potential) the localised bath cannot equilibrate the particle.

  3. Analysis of startup strategies for a particle bed reactor nuclear rocket engine

    Science.gov (United States)

    Suzuki, D. E.

    1993-06-01

    This paper develops and analyzes engine system startup strategies for a particle bed reactor (PBR) nuclear rocket engine. The strategies are designed to maintain stable flow through the PBR fuel element while reaching the design conditions as quickly as possible. The analyses are conducted using a computer model of a representative particle bed reactor and engine system. Elements of the startup strategy considered include: the coordinated control of reactor power and coolant flow; turbine inlet temperature and flow control; and use of an external starter system. The simulation results indicate that the use of an external starter system enables the engine to reach design conditions very quickly while maintaining the flow well away from the unstable regime. If a bootstrap start is used instead, the transient does not progress as fast and approaches closer to the unstable flow regime, but allows for greater engine reusability. These results can provide important information for engine designers and mission planners.

  4. Mobile Robot Positioning with 433-MHz Wireless Motes with Varying Transmission Powers and a Particle Filter

    Directory of Open Access Journals (Sweden)

    Adrian Canedo-Rodriguez

    2015-04-01

    Full Text Available In wireless positioning systems, the transmitter’s power is usually fixed. In this paper, we explore the use of varying transmission powers to increase the performance of a wireless localization system. To this extent, we have designed a robot positioning system based on wireless motes. Our motes use an inexpensive, low-power sub-1-GHz system-on-chip (CC1110 working in the 433-MHz ISM band. Our localization algorithm is based on a particle filter and infers the robot position by: (1 comparing the power received with the expected one; and (2 integrating the robot displacement. We demonstrate that the use of transmitters that vary their transmission power over time improves the performance of the wireless positioning system significantly, with respect to a system that uses fixed power transmitters. This opens the door for applications where the robot can localize itself actively by requesting the transmitters to change their power in real time.

  5. A particle swarm optimization algorithm for beam angle selection in intensity-modulated radiotherapy planning

    International Nuclear Information System (INIS)

    Li Yongjie; Yao Dezhong; Yao, Jonathan; Chen Wufan

    2005-01-01

    Automatic beam angle selection is an important but challenging problem for intensity-modulated radiation therapy (IMRT) planning. Though many efforts have been made, it is still not very satisfactory in clinical IMRT practice because of overextensive computation of the inverse problem. In this paper, a new technique named BASPSO (Beam Angle Selection with a Particle Swarm Optimization algorithm) is presented to improve the efficiency of the beam angle optimization problem. Originally developed as a tool for simulating social behaviour, the particle swarm optimization (PSO) algorithm is a relatively new population-based evolutionary optimization technique first introduced by Kennedy and Eberhart in 1995. In the proposed BASPSO, the beam angles are optimized using PSO by treating each beam configuration as a particle (individual), and the beam intensity maps for each beam configuration are optimized using the conjugate gradient (CG) algorithm. These two optimization processes are implemented iteratively. The performance of each individual is evaluated by a fitness value calculated with a physical objective function. A population of these individuals is evolved by cooperation and competition among the individuals themselves through generations. The optimization results of a simulated case with known optimal beam angles and two clinical cases (a prostate case and a head-and-neck case) show that PSO is valid and efficient and can speed up the beam angle optimization process. Furthermore, the performance comparisons based on the preliminary results indicate that, as a whole, the PSO-based algorithm seems to outperform, or at least compete with, the GA-based algorithm in computation time and robustness. In conclusion, the reported work suggested that the introduced PSO algorithm could act as a new promising solution to the beam angle optimization problem and potentially other optimization problems in IMRT, though further studies need to be investigated

  6. Vectorization of a particle code used in the simulation of rarefied hypersonic flow

    Science.gov (United States)

    Baganoff, D.

    1990-01-01

    A limitation of the direct simulation Monte Carlo (DSMC) method is that it does not allow efficient use of vector architectures that predominate in current supercomputers. Consequently, the problems that can be handled are limited to those of one- and two-dimensional flows. This work focuses on a reformulation of the DSMC method with the objective of designing a procedure that is optimized to the vector architectures found on machines such as the Cray-2. In addition, it focuses on finding a better balance between algorithmic complexity and the total number of particles employed in a simulation so that the overall performance of a particle simulation scheme can be greatly improved. Simulations of the flow about a 3D blunt body are performed with 10 to the 7th particles and 4 x 10 to the 5th mesh cells. Good statistics are obtained with time averaging over 800 time steps using 4.5 h of Cray-2 single-processor CPU time.

  7. PTRACK: A particle tracking program for evaluation travel path/travel time uncertainties

    International Nuclear Information System (INIS)

    Thompson, B.M.; Campbell, J.E.; Longsine, D.E.

    1987-12-01

    PTRACK is a model which tracks the path of a radionuclide particle released from a nuclear waste repository into a ground-water flow system in a two-dimensional representation of stratified geologic medium. The code calculates the time required for the particle to travel from the release point (the edge of the disturbed zone) to the specified horizontal or vertical boundary (the accessible environment). The physical properties of the geologic setting and the ground-water flow system can be treated as fixed values or as random variables sampled from their respective probability distributions. In the latter case, PTRACK assigns a sampled value for each parameter and tracks a particle for this trial (realization) of the system. Repeated realizations allow the effects of parameter uncertainty on travel paths/travel times to be quantified. The code can also calculate partial correlation coefficients between dependent variables and independent variables, which are useful in identifying important independent variables. This documentation describes the mathematical basis for the model, the algorithms and solution techniques used, and the computer code design. It also contains a detailed user's manual. The implementation of PTRACK is verified with several systems for which solutions have been calculated by hand. The integration of PTRACK with a Latin hypercube sampling (LHS) code is also discussed, although other sampling methods can be employed in place of LHS. 11 refs., 14 figs., 22 tabs

  8. Quantum dynamics of a particle with a spin-dependent velocity

    International Nuclear Information System (INIS)

    Aslangul, Claude

    2005-01-01

    We study the dynamics of a particle in continuous time and space, the displacement of which is governed by an internal degree of freedom (spin). In one definite limit, the so-called quantum random walk is recovered but, although quite simple, the model possesses a rich variety of dynamics and goes far beyond this problem. Generally speaking, our framework can describe the motion of an electron in a magnetic sea near the Fermi level when linearization of the dispersion law is possible, coupled to a transverse magnetic field. Quite unexpected behaviours are obtained. In particular, we find that when the initial wave packet is fully localized in space, the J z angular momentum component is frozen; this is an interesting example of an observable which, although it is not a constant of motion, has a constant expectation value. For a non-completely localized wave packet, the effect still occurs although less pronounced, and the spin keeps for ever memory of its initial state. Generally speaking, as time goes on, the spatial density profile looks rather complex, as a consequence of the competition between drift and precession, and displays various shapes according to the ratio between the Larmor period and the characteristic time of flight. The density profile gradually changes from a multimodal quickly moving distribution when the scattering rate is small, to a unimodal standing but flattening distribution in the opposite case

  9. Physical test of a particle simulation model in a sheared granular system.

    Science.gov (United States)

    Rycroft, Chris H; Orpe, Ashish V; Kudrolli, Arshad

    2009-09-01

    We report a detailed comparison of a slow gravity-driven sheared granular flow with a discrete-element simulation performed in the same geometry. In the experiments, grains flow inside a silo with a rectangular cross section and are sheared by a rough boundary on one side and smooth boundaries on the other sides. Individual grain position and motion are measured using a particle index-matching imaging technique where a fluorescent dye is added to the interstitial liquid which has the same refractive index as the glass beads. The simulations use a Cundall-Strack contact model between the grains using contact parameters that have been used in many other previous studies and ignore the hydrodynamic effects of the interstitial liquid. Computations are performed to understand the effect of particle coefficient of friction, elasticity, contact model, and polydispersity on mean flow properties. We then perform a detailed comparison of the particle fluctuation properties as measured by the displacement probability distribution function and the mean square displacement. All in all, our study suggests a high level of quantitative agreement between the simulations and experiments.

  10. A microcomputer real-time monitor for the control of a particle accelerator

    International Nuclear Information System (INIS)

    Ouali, M.

    1977-01-01

    The physical management of a particle accelerator requests the supervision and the control of a great number of parameters and various devices. A hierarchically structured multicomputer control system was implemented on the Synchrocyclotron of the 'Institut de Physique Nucleaire' at Orsay (France). A set of 3 microcomputers MICRAL (manufactured in France around an Intel 8080 microprocessor chip) is connected through a CAMAC link to an IBM 1130 central computer used for the general control. At the lowest level, measurements and supervisions are made by the means of special hardwired systems built in the Laboratory (the CSTIs). On the other hand, some measurements are done by using a conventional industrial data acquisition system. All these systems are managed by the 3 MICRALs, as also some independent devices (function generator, radioprotection beacons, beam profile encoders). A real-time monitor resident in the MICRAL computers is responsible for task activations, resource allocation and data exchange management, especially with the main control computer. It uses for the 6 interrupt levels of the MICRAL and it builds and manages in the memory a set of descriptive block and of data stacks [fr

  11. Comment on ‘Wigner function for a particle in an infinite lattice’

    International Nuclear Information System (INIS)

    Bizarro, João P S

    2013-01-01

    It is pointed out that in a recent paper (2012 New J. Phys. 14 103009) in which a Wigner function for a particle in an infinite lattice (a system described by an unbounded discrete coordinate and its conjugate angle-like momentum) has been introduced, no reference is made to previous, pioneering work on discrete Wigner distributions (more precisely, on the rotational Wigner function for a system described by a rotation angle and its unbounded discrete-conjugate angular momentum). Not only has the problem addressed in essence been solved for a long time (the discrete coordinate and angle-like conjugate momentum are the perfect dual of the rotation angle and discrete-conjugate angular momentum), but the solution advanced only in some distorted manner obeys two of the fundamental properties of a Wigner distribution (that, when integrated over one period of the momentum variable, it should yield the correct marginal distribution on the discrete position variable, and that it should be invariant with respect to translation). (comment)

  12. An extension theory-based maximum power tracker using a particle swarm optimization algorithm

    International Nuclear Information System (INIS)

    Chao, Kuei-Hsiang

    2014-01-01

    Highlights: • We propose an adaptive maximum power point tracking (MPPT) approach for PV systems. • Transient and steady state performances in tracking process are improved. • The proposed MPPT can automatically tune tracking step size along a P–V curve. • A PSO algorithm is used to determine the weighting values of extension theory. - Abstract: The aim of this work is to present an adaptive maximum power point tracking (MPPT) approach for photovoltaic (PV) power generation system. Integrating the extension theory as well as the conventional perturb and observe method, an maximum power point (MPP) tracker is made able to automatically tune tracking step size by way of the category recognition along a P–V characteristic curve. Accordingly, the transient and steady state performances in tracking process are improved. Furthermore, an optimization approach is proposed on the basis of a particle swarm optimization (PSO) algorithm for the complexity reduction in the determination of weighting values. At the end of this work, a simulated improvement in the tracking performance is experimentally validated by an MPP tracker with a programmable system-on-chip (PSoC) based controller

  13. A particle swarm-based algorithm for optimization of multi-layered and graded dental ceramics.

    Science.gov (United States)

    Askari, Ehsan; Flores, Paulo; Silva, Filipe

    2018-01-01

    The thermal residual stresses (TRSs) generated owing to the cooling down from the processing temperature in layered ceramic systems can lead to crack formation as well as influence the bending stress distribution and the strength of the structure. The purpose of this study is to minimize the thermal residual and bending stresses in dental ceramics to enhance their strength as well as to prevent the structure failure. Analytical parametric models are developed to evaluate thermal residual stresses in zirconia-porcelain multi-layered and graded discs and to simulate the piston-on-ring test. To identify optimal designs of zirconia-based dental restorations, a particle swarm optimizer is also developed. The thickness of each interlayer and compositional distribution are referred to as design variables. The effect of layers number constituting the interlayer between two based materials on the performance of graded prosthetic systems is also investigated. The developed methodology is validated against results available in literature and a finite element model constructed in the present study. Three different cases are considered to determine the optimal design of graded prosthesis based on minimizing (a) TRSs; (b) bending stresses; and (c) both TRS and bending stresses. It is demonstrated that each layer thickness and composition profile have important contributions into the resulting stress field and magnitude. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. A particle-based simplified swarm optimization algorithm for reliability redundancy allocation problems

    International Nuclear Information System (INIS)

    Huang, Chia-Ling

    2015-01-01

    This paper proposes a new swarm intelligence method known as the Particle-based Simplified Swarm Optimization (PSSO) algorithm while undertaking a modification of the Updating Mechanism (UM), called N-UM and R-UM, and simultaneously applying an Orthogonal Array Test (OA) to solve reliability–redundancy allocation problems (RRAPs) successfully. One difficulty of RRAP is the need to maximize system reliability in cases where the number of redundant components and the reliability of corresponding components in each subsystem are simultaneously decided with nonlinear constraints. In this paper, four RRAP benchmarks are used to display the applicability of the proposed PSSO that advances the strengths of both PSO and SSO to enable optimizing the RRAP that belongs to mixed-integer nonlinear programming. When the computational results are compared with those of previously developed algorithms in existing literature, the findings indicate that the proposed PSSO is highly competitive and performs well. - Highlights: • This paper proposes a particle-based simplified swarm optimization algorithm (PSSO) to optimize RRAP. • Furthermore, the UM and an OA are adapted to advance in optimizing RRAP. • Four systems are introduced and the results demonstrate the PSSO performs particularly well

  15. Data Assimilation in Air Contaminant Dispersion Using a Particle Filter and Expectation-Maximization Algorithm

    Directory of Open Access Journals (Sweden)

    Rongxiao Wang

    2017-09-01

    Full Text Available The accurate prediction of air contaminant dispersion is essential to air quality monitoring and the emergency management of contaminant gas leakage incidents in chemical industry parks. Conventional atmospheric dispersion models can seldom give accurate predictions due to inaccurate input parameters. In order to improve the prediction accuracy of dispersion models, two data assimilation methods (i.e., the typical particle filter & the combination of a particle filter and expectation-maximization algorithm are proposed to assimilate the virtual Unmanned Aerial Vehicle (UAV observations with measurement error into the atmospheric dispersion model. Two emission cases with different dimensions of state parameters are considered. To test the performances of the proposed methods, two numerical experiments corresponding to the two emission cases are designed and implemented. The results show that the particle filter can effectively estimate the model parameters and improve the accuracy of model predictions when the dimension of state parameters is relatively low. In contrast, when the dimension of state parameters becomes higher, the method of particle filter combining the expectation-maximization algorithm performs better in terms of the parameter estimation accuracy. Therefore, the proposed data assimilation methods are able to effectively support air quality monitoring and emergency management in chemical industry parks.

  16. Prediction of Skin Sensitization with a Particle Swarm Optimized Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Chenzhong Cao

    2009-07-01

    Full Text Available Skin sensitization is the most commonly reported occupational illness, causing much suffering to a wide range of people. Identification and labeling of environmental allergens is urgently required to protect people from skin sensitization. The guinea pig maximization test (GPMT and murine local lymph node assay (LLNA are the two most important in vivo models for identification of skin sensitizers. In order to reduce the number of animal tests, quantitative structure-activity relationships (QSARs are strongly encouraged in the assessment of skin sensitization of chemicals. This paper has investigated the skin sensitization potential of 162 compounds with LLNA results and 92 compounds with GPMT results using a support vector machine. A particle swarm optimization algorithm was implemented for feature selection from a large number of molecular descriptors calculated by Dragon. For the LLNA data set, the classification accuracies are 95.37% and 88.89% for the training and the test sets, respectively. For the GPMT data set, the classification accuracies are 91.80% and 90.32% for the training and the test sets, respectively. The classification performances were greatly improved compared to those reported in the literature, indicating that the support vector machine optimized by particle swarm in this paper is competent for the identification of skin sensitizers.

  17. Prediction of Skin Sensitization with a Particle Swarm Optimized Support Vector Machine

    Science.gov (United States)

    Yuan, Hua; Huang, Jianping; Cao, Chenzhong

    2009-01-01

    Skin sensitization is the most commonly reported occupational illness, causing much suffering to a wide range of people. Identification and labeling of environmental allergens is urgently required to protect people from skin sensitization. The guinea pig maximization test (GPMT) and murine local lymph node assay (LLNA) are the two most important in vivo models for identification of skin sensitizers. In order to reduce the number of animal tests, quantitative structure-activity relationships (QSARs) are strongly encouraged in the assessment of skin sensitization of chemicals. This paper has investigated the skin sensitization potential of 162 compounds with LLNA results and 92 compounds with GPMT results using a support vector machine. A particle swarm optimization algorithm was implemented for feature selection from a large number of molecular descriptors calculated by Dragon. For the LLNA data set, the classification accuracies are 95.37% and 88.89% for the training and the test sets, respectively. For the GPMT data set, the classification accuracies are 91.80% and 90.32% for the training and the test sets, respectively. The classification performances were greatly improved compared to those reported in the literature, indicating that the support vector machine optimized by particle swarm in this paper is competent for the identification of skin sensitizers. PMID:19742136

  18. Pairing vibrational and isospin rotational states in a particle number and isospin projected generator coordinate method

    International Nuclear Information System (INIS)

    Chen, H.T.; Muether, H.; Faessler, A.

    1978-01-01

    Pairing vibrational and isospin rotational states are described in different approximations based on particle number and isospin projected, proton-proton, neutron-neutron and proton-neutron pairing wave functions and on the generator coordinate method (GCM). The investigations are performed in models for which an exact group theoretical solution exists. It turns out that a particle number and isospin projection is essential to yield a good approximation to the ground state or isospin yrast state energies. For strong pairing correlations (pairing force constant equal to the single-particle level distance) isospin cranking (-ωTsub(x)) yields with particle number projected pairing wave function also good agreement with the exact energies. GCM wave functions generated by particle number and isospin projected BCS functions with different amounts of pairing correlations yield for the lowest T=0 and T=2 states energies which are practically indistinguishable from the exact solutions. But even the second and third lowest energies of charge-symmetric states are still very reliable. Thus it is concluded that also in realistic cases isospin rotational and pairing vibrational states may be described in the framework of the GCM method with isospin and particle number projected generating wave functions. (Auth.)

  19. Flow instability tests for a particle bed reactor nuclear thermal rocket fuel element

    Science.gov (United States)

    Lawrence, Timothy J.

    1993-05-01

    Recent analyses have focused on the flow stability characteristics of a particle bed reactor (PBR). These laminar flow instabilities may exist in reactors with parallel paths and are caused by the heating of the gas at low Reynolds numbers. This phenomena can be described as follows: several parallel channels are connected at the plenum regions and are stabilized by some inlet temperature and pressure; a perturbation in one channel causes the temperature to rise and increases the gas viscosity and reduces the gas density; the pressure drop is fixed by the plenum regions, therefore, the mass flow rate in the channel would decrease; the decrease in flow reduces the ability to remove the energy added and the temperature increases; and finally, this process could continue until the fuel element fails. Several analyses based on different methods have derived similar curves to show that these instabilities may exist at low Reynolds numbers and high phi's ((Tfinal Tinitial)/Tinitial). These analyses need to be experimentally verified.

  20. Development and application of a particle image velocimeter for high-speed flows

    Science.gov (United States)

    Molezzi, M. J.; Dutton, J. C.

    1992-01-01

    A particle image velocimetry (PIV) system has been developed for use in high-speed separated air flows. The image acquisition system uses two 550 mJ/pulse Nd:YAG lasers and is fully controlled by a host Macintosh computer. The interrogation system is also Macintosh-based and performs interrogations at approximately 2.3 sec/spot and 4.0 sec/spot when using the Young's fringe and autocorrelation methods, respectively. The system has been proven in preliminary experiments using known-displacement simulated PIV photographs and a simple axisymmetric jet flow. Further results have been obtained in a transonic wind tunnel operating at Mach 0.4 to 0.5 (135 m/s to 170 m/s). PIV experiments were done with an empty test section to provide uniform flow data for comparison with pressure and LDV data, then with a two-dimensional base model, revealing features of the von Karman vortex street wake and underlying small scale turbulence.

  1. Development of a particle method of characteristics (PMOC) for one-dimensional shock waves

    Science.gov (United States)

    Hwang, Y.-H.

    2018-03-01

    In the present study, a particle method of characteristics is put forward to simulate the evolution of one-dimensional shock waves in barotropic gaseous, closed-conduit, open-channel, and two-phase flows. All these flow phenomena can be described with the same set of governing equations. The proposed scheme is established based on the characteristic equations and formulated by assigning the computational particles to move along the characteristic curves. Both the right- and left-running characteristics are traced and represented by their associated computational particles. It inherits the computational merits from the conventional method of characteristics (MOC) and moving particle method, but without their individual deficiencies. In addition, special particles with dual states deduced to the enforcement of the Rankine-Hugoniot relation are deliberately imposed to emulate the shock structure. Numerical tests are carried out by solving some benchmark problems, and the computational results are compared with available analytical solutions. From the derivation procedure and obtained computational results, it is concluded that the proposed PMOC will be a useful tool to replicate one-dimensional shock waves.

  2. Dynamics of fibres in a turbulent flow field - A particle-level simulation technique

    International Nuclear Information System (INIS)

    Sasic, Srdjan; Almstedt, Alf-Erik

    2010-01-01

    A particle-level simulation technique has been developed for modelling the flow of fibres in a turbulent flow field. A single fibre is conceived here as a chain of segments, thus enabling the model fibre to have all the degrees of freedom (translation, rotation, bending and twisting) needed to realistically reproduce the dynamics of real fibres. Equations of motion are solved for each segment, accounting for the interaction forces with the fluid, the contact forces with other fibres and the forces that maintain integrity of the fibre. The motion of the fluid is resolved as a combination of 3D mean flow velocities obtained from a CFD code and fluctuating turbulent velocities derived from the Langevin equation. A case of homogeneous turbulence is treated in this paper. The results obtained show that fibre flocs in air-fibre flows can be created even when attractive forces are not present. In such a case, contacts between fibres, properties of an individual fibre (such as flexibility and equilibrium shapes) and properties of the flow of the carrying fluid are shown to govern the physics behind formation and breaking up of fibre flocs. Highly irregular fibre shapes and stiff fibres lead to strong flocculation. The modelling framework applied in this work aims at making possible a numerical model applicable for designing processes involving transport of fibres by air at industrial scale.

  3. Optimization of the Infrastructure of Reinforced Concrete Reservoirs by a Particle Swarm Algorithm

    Directory of Open Access Journals (Sweden)

    Kia Saeed

    2015-03-01

    Full Text Available Optimization techniques may be effective in finding the best modeling and shapes for reinforced concrete reservoirs (RCR to improve their durability and mechanical behavior, particularly for avoiding or reducing the bending moments in these structures. RCRs are one of the major structures applied for reserving fluids to be used in drinking water networks. Usually, these structures have fixed shapes which are designed and calculated based on input discharges, the conditions of the structure's topology, and geotechnical locations with various combinations of static and dynamic loads. In this research, the elements of reservoir walls are first typed according to the performance analyzed; then the range of the membrane based on the thickness and the minimum and maximum cross sections of the bar used are determined in each element. This is done by considering the variable constraints, which are estimated by the maximum stress capacity. In the next phase, based on the reservoir analysis and using the algorithm of the PARIS connector, the related information is combined with the code for the PSO algorithm, i.e., an algorithm for a swarming search, to determine the optimum thickness of the cross sections for the reservoir membrane’s elements and the optimum cross section of the bar used. Based on very complex mathematical linear models for the correct embedding and angles related to achain of peripheral strengthening membranes, which optimize the vibration of the structure, a mutual relation is selected between the modeling software and the code for a particle swarm optimization algorithm. Finally, the comparative weight of the concrete reservoir optimized by the peripheral strengthening membrane is analyzed using common methods. This analysis shows a 19% decrease in the bar’s weight, a 20% decrease in the concrete’s weight, and a minimum 13% saving in construction costs according to the items of a checklist for a concrete reservoir at 10,000 m3.

  4. ASME AG-1 Section FC Qualified HEPA Filters; a Particle Loading Comparison - 13435

    International Nuclear Information System (INIS)

    Stillo, Andrew; Ricketts, Craig I.

    2013-01-01

    High Efficiency Particulate Air (HEPA) Filters used to protect personnel, the public and the environment from airborne radioactive materials are designed, manufactured and qualified in accordance with ASME AG-1 Code section FC (HEPA Filters) [1]. The qualification process requires that filters manufactured in accordance with this ASME AG-1 code section must meet several performance requirements. These requirements include performance specifications for resistance to airflow, aerosol penetration, resistance to rough handling, resistance to pressure (includes high humidity and water droplet exposure), resistance to heated air, spot flame resistance and a visual/dimensional inspection. None of these requirements evaluate the particle loading capacity of a HEPA filter design. Concerns, over the particle loading capacity, of the different designs included within the ASME AG-1 section FC code[1], have been voiced in the recent past. Additionally, the ability of a filter to maintain its integrity, if subjected to severe operating conditions such as elevated relative humidity, fog conditions or elevated temperature, after loading in use over long service intervals is also a major concern. Although currently qualified HEPA filter media are likely to have similar loading characteristics when evaluated independently, filter pleat geometry can have a significant impact on the in-situ particle loading capacity of filter packs. Aerosol particle characteristics, such as size and composition, may also have a significant impact on filter loading capacity. Test results comparing filter loading capacities for three different aerosol particles and three different filter pack configurations are reviewed. The information presented represents an empirical performance comparison among the filter designs tested. The results may serve as a basis for further discussion toward the possible development of a particle loading test to be included in the qualification requirements of ASME AG-1

  5. A Particle Smoother with Sequential Importance Resampling for soil hydraulic parameter estimation: A lysimeter experiment

    Science.gov (United States)

    Montzka, Carsten; Hendricks Franssen, Harrie-Jan; Moradkhani, Hamid; Pütz, Thomas; Han, Xujun; Vereecken, Harry

    2013-04-01

    An adequate description of soil hydraulic properties is essential for a good performance of hydrological forecasts. So far, several studies showed that data assimilation could reduce the parameter uncertainty by considering soil moisture observations. However, these observations and also the model forcings were recorded with a specific measurement error. It seems a logical step to base state updating and parameter estimation on observations made at multiple time steps, in order to reduce the influence of outliers at single time steps given measurement errors and unknown model forcings. Such outliers could result in erroneous state estimation as well as inadequate parameters. This has been one of the reasons to use a smoothing technique as implemented for Bayesian data assimilation methods such as the Ensemble Kalman Filter (i.e. Ensemble Kalman Smoother). Recently, an ensemble-based smoother has been developed for state update with a SIR particle filter. However, this method has not been used for dual state-parameter estimation. In this contribution we present a Particle Smoother with sequentially smoothing of particle weights for state and parameter resampling within a time window as opposed to the single time step data assimilation used in filtering techniques. This can be seen as an intermediate variant between a parameter estimation technique using global optimization with estimation of single parameter sets valid for the whole period, and sequential Monte Carlo techniques with estimation of parameter sets evolving from one time step to another. The aims are i) to improve the forecast of evaporation and groundwater recharge by estimating hydraulic parameters, and ii) to reduce the impact of single erroneous model inputs/observations by a smoothing method. In order to validate the performance of the proposed method in a real world application, the experiment is conducted in a lysimeter environment.

  6. Applying a Particle-only Model to the HL Tau Disk

    Science.gov (United States)

    Tabeshian, Maryam; Wiegert, Paul A.

    2018-04-01

    Observations have revealed rich structures in protoplanetary disks, offering clues about their embedded planets. Due to the complexities introduced by the abundance of gas in these disks, modeling their structure in detail is computationally intensive, requiring complex hydrodynamic codes and substantial computing power. It would be advantageous if computationally simpler models could provide some preliminary information on these disks. Here we apply a particle-only model (that we developed for gas-poor debris disks) to the gas-rich disk, HL Tauri, to address the question of whether such simple models can inform the study of these systems. Assuming three potentially embedded planets, we match HL Tau’s radial profile fairly well and derive best-fit planetary masses and orbital radii (0.40, 0.02, 0.21 Jupiter masses for the planets orbiting a 0.55 M ⊙ star at 11.22, 29.67, 64.23 au). Our derived parameters are comparable to those estimated by others, except for the mass of the second planet. Our simulations also reproduce some narrower gaps seen in the ALMA image away from the orbits of the planets. The nature of these gaps is debated but, based on our simulations, we argue they could result from planet–disk interactions via mean-motion resonances, and need not contain planets. Our results suggest that a simple particle-only model can be used as a first step to understanding dynamical structures in gas disks, particularly those formed by planets, and determine some parameters of their hidden planets, serving as useful initial inputs to hydrodynamic models which are needed to investigate disk and planet properties more thoroughly.

  7. ASME AG-1 Section FC Qualified HEPA Filters; a Particle Loading Comparison - 13435

    Energy Technology Data Exchange (ETDEWEB)

    Stillo, Andrew [Camfil Farr, 1 North Corporate Drive, Riverdale, NJ 07457 (United States); Ricketts, Craig I. [New Mexico State University, Department of Engineering Technology and Surveying Engineering, P.O. Box 30001 MSC 3566, Las Cruces, NM 88003-8001 (United States)

    2013-07-01

    High Efficiency Particulate Air (HEPA) Filters used to protect personnel, the public and the environment from airborne radioactive materials are designed, manufactured and qualified in accordance with ASME AG-1 Code section FC (HEPA Filters) [1]. The qualification process requires that filters manufactured in accordance with this ASME AG-1 code section must meet several performance requirements. These requirements include performance specifications for resistance to airflow, aerosol penetration, resistance to rough handling, resistance to pressure (includes high humidity and water droplet exposure), resistance to heated air, spot flame resistance and a visual/dimensional inspection. None of these requirements evaluate the particle loading capacity of a HEPA filter design. Concerns, over the particle loading capacity, of the different designs included within the ASME AG-1 section FC code[1], have been voiced in the recent past. Additionally, the ability of a filter to maintain its integrity, if subjected to severe operating conditions such as elevated relative humidity, fog conditions or elevated temperature, after loading in use over long service intervals is also a major concern. Although currently qualified HEPA filter media are likely to have similar loading characteristics when evaluated independently, filter pleat geometry can have a significant impact on the in-situ particle loading capacity of filter packs. Aerosol particle characteristics, such as size and composition, may also have a significant impact on filter loading capacity. Test results comparing filter loading capacities for three different aerosol particles and three different filter pack configurations are reviewed. The information presented represents an empirical performance comparison among the filter designs tested. The results may serve as a basis for further discussion toward the possible development of a particle loading test to be included in the qualification requirements of ASME AG-1

  8. Development of a new approach to simulate a particle track under electrochemical etching in polymeric detectors

    International Nuclear Information System (INIS)

    Mostofizadeh, Ali; Huang, Yudong; Kardan, M. Reza; Babakhani, Asad; Sun Xiudong

    2012-01-01

    A numerical approach based on image processing was developed to simulate a particle track in a typical polymeric detector, e.g., polycarbonate, under electrochemical etching. The physical parameters such as applied voltage, detector thickness, track length, the radii of curvature at the tip of track, and the incidence angle of the particle were considered, and then the boundary condition of the problem was defined. A numerical method was developed to solve Laplace equation, and then the distribution of the applied voltage was obtained through the polymer volume. Subsequently, the electric field strengths in the detector elements were computed. In each step of the computation, an image processing technique was applied to convert the computed values to grayscale images. The results showed that a numerical solution to Laplace equation is dedicatedly an attractive approach to provide us the accurate values of electric field strength through the polymeric detector volume as well as the track area. According to the results, for a particular condition of the detector thickness equal to 445 μm, track length of 21 μm, the radii of 2.5 μm at track tip, the incidence angle of 90°, and the applied voltage of 2080 V, after computing Laplace equation for an extremely high population of 4000 × 4000 elements of detector, the average field strength at the tip of track was computed equal to 0.31 MV cm −1 which is in the range of dielectric strength for polymers. The results by our computation confirm Smythe’s model for estimating the ECE-tracks.

  9. Marrow stromal cells administrated intracisternally to rats after traumatic brain injury migrate into the brain and improve neurological function

    Institute of Scientific and Technical Information of China (English)

    胡德志; 周良辅; 朱剑虹

    2004-01-01

    @@ Marrow stromal cells(MSCs) have been reported to transplant into injured brain via intravenous or intraarterial or direct intracerebral administration.1-3 In the present study, we observed that MSCs migrated into the brain, survived and diffeneriated into neural cells after they were injected into the cisterna magna of rats, and that the behavior of the rats after traumatic brain injury (TBI) was improved.

  10. Physical test of a particle simulation model in a sheared granular system

    Energy Technology Data Exchange (ETDEWEB)

    Rycroft, Chris; Orpe, Ashish; Kudrolli, Arshad

    2009-01-15

    We report a detailed comparison of a slow gravity driven sheared granular flow with a computational model performed with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). To our knowledge, this is the first thorough test of the LAMMPS model with a laboratory granular flow. In the experiments, grains flow inside a silo with a rectangular cross-section, and are sheared by a rough boundary on one side and smooth boundaries on the other sides. Individual grain position and motion are measured using a particle index matching imaging technique where a fluorescent dye is added to the interstitial liquid which has the same refractive index as the glass beads. The boundary imposes a packing order, and the grains are observed to flow in layers which get progressively more disordered with distance from the walls. The computations use a Cundall--Strack contact model between the grains, using contact parameters that have been used in many other previous studies, and ignore the hydrodynamic effects of the interstitial liquid. Computations are performed to understand the effect of particle coefficient of friction, elasticity, contact model, and polydispersity on mean flow properties. After appropriate scaling, we find that the mean velocity of the grains and the number density as a function of flow cross-section observed in the experiments and the simulations are in excellent agreement. The mean flow profile is observed to be unchanged over a broad range of coefficient of friction, except near the smooth wall. We show that the flow profile is not sensitive to atleast 10\\percent polydispersity in particle size. Because the grain elasticity used is smaller in the computations as compared with glass grains, wave-like features can be noted over short time scales in the mean velocity and the velocity auto-correlations measured in the simulations. These wave features occur over an intermediate timescale larger than the particle interaction but smaller than the

  11. Radioactive Pollution Estimate for Fukushima Nuclear Power Plant by a Particle Model

    Science.gov (United States)

    Saito, Keisuke; Ogawa, Susumu

    2016-06-01

    On Mar 12, 2011, very wide radioactive pollution occurred by a hydrogen explosion in Fukushima Nuclear Power Plant. A large amount of radioisotopes started with four times of explosions. With traditional atmospheric diffusion models could not reconstruct radioactive pollution in Fukushima. Then, with a particle model, this accident was reconstructed from meteorological archive and Radar- AMeDAS. Calculations with the particle model were carried out for Mar 12, 15, 18 and 20 when east southeast winds blew for five hours continuously. Meteorological archive is expressed by wind speeds and directions in five-km grid every hour with eight classes of height till 3000 m. Radar- AMeDAS is precipitation data in one-km grid every thirty minutes. Particles are ten scales of 0.01 to 0.1 mm in diameter with specific weight of 2.65 and vertical speeds given by Stokes equation. But, on Mar 15, it rained from 16:30 and then the particles fell down at a moment as wet deposit in calculation. On the other hand, the altitudes on the ground were given by DEM with 1 km-grid. The spatial dose by emitted radioisotopes was referred to the observation data at monitoring posts of Tokyo Electric Power Company. The falling points of radioisotopes were expressed on the map using the particle model. As a result, the same distributions were obtained as the surface spatial dose of radioisotopes in aero-monitoring by Ministry of Education, Culture, Sports, Science and Technology. Especially, on Mar 15, the simulated pollution fitted to the observation, which extended to the northwest of Fukushima Daiichi Nuclear Power Plant and caused mainly sever pollution. By the particle model, the falling positions on the ground were estimated each particle size. Particles with more than 0.05 mm of size were affected by the topography and blocked by the mountains with the altitudes of more than 700 m. The particle model does not include the atmospheric stability, the source height, and deposit speeds. The

  12. Investigation of a Particle into Liquid Sampler to Study the Formation & Ageing of Secondary Organic Aerosol

    Science.gov (United States)

    Pereira, K. L.; Hamilton, J. F.; Rickard, A. R.; Bloss, W. J.; Alam, M. S.; Camredon, M.; Munoz, A.; Vazquez, M.; Rodenas, M.; Vera, T.; Borrás, E.

    2012-12-01

    The atmospheric oxidation of Volatile Organic Compounds (VOCs) in the presence of NOx results in the formation of tropospheric ozone and Secondary Organic Aerosol (SOA) [Hallquist et al., 2009]. Whilst SOA is known to affect both climate and human health, the VOC oxidation pathways leading to SOA formation are poorly understood [Solomon et al., 2007]. This is in part due to the vast number and the low concentration of SOA species present in the ambient atmosphere. It has been estimated as many as 10,000 to 100,000 VOCs have been detected in the atmosphere, all of which can undergo photo-chemical oxidation and contribute to SOA formation [Goldstein and Galbally, 2007]. Atmospheric simulation chambers such as the EUropean PHOtoREactor (EUPHORE) in Valencia, Spain, are often used to study SOA formation from a single VOC precursor under controlled conditions. SOA composition and formation can be studied using online techniques such as Aerosol Mass Spectrometry (AMS), which provide high time resolution but limited structural information [Zhang et al., 2007]. Offline techniques, such as collection onto filters, extraction and subsequent analysis, provide detailed SOA composition but only usually one or two samples per experiment. In this work we report time resolved SOA composition analysis using a Particle into Liquid Sampler (PILS) followed by Liquid Chromatography Ion-Trap Mass Spectrometry (LC-IT-MS/MS) and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS/MS). Experiments were performed at EUPHORE investigating the formation and composition of Methyl Chavicol SOA. Methyl Chavicol (also known as Estragole) was identified as the highest floral emission from an oil palm plantation in Malaysian Borneo and has also been observed in US pine forests [Bouvier-Brown et al., 2009; Misztal et al., 2010]. Previous studies indicate a high SOA yield from Methyl Chavicol at around 40 % [Lee et al., 2006], however currently there have been very few literature

  13. Diaphragm flange and method for lowering particle beam impedance at connected beam tubes of a particle accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Biallas, George Herman

    2017-07-04

    A diaphragm flange for connecting the tubes in a particle accelerator while minimizing beamline impedance. The diaphragm flange includes an outer flange and a thin diaphragm integral with the outer flange. Bolt holes in the outer flange provide a means for bolting the diaphragm flange to an adjacent flange or beam tube having a mating bolt-hole pattern. The diaphragm flange includes a first surface for connection to the tube of a particle accelerator beamline and a second surface for connection to a CF flange. The second surface includes a recessed surface therein and a knife-edge on the recessed surface. The diaphragm includes a thickness that enables flexing of the integral diaphragm during assembly of beamline components. The knife-edge enables compression of a soft metal gasket to provide a leak-tight seal.

  14. A Particle Swarm Optimization Algorithm for Optimal Operating Parameters of VMI Systems in a Two-Echelon Supply Chain

    Science.gov (United States)

    Sue-Ann, Goh; Ponnambalam, S. G.

    This paper focuses on the operational issues of a Two-echelon Single-Vendor-Multiple-Buyers Supply chain (TSVMBSC) under vendor managed inventory (VMI) mode of operation. To determine the optimal sales quantity for each buyer in TSVMBC, a mathematical model is formulated. Based on the optimal sales quantity can be obtained and the optimal sales price that will determine the optimal channel profit and contract price between the vendor and buyer. All this parameters depends upon the understanding of the revenue sharing between the vendor and buyers. A Particle Swarm Optimization (PSO) is proposed for this problem. Solutions obtained from PSO is compared with the best known results reported in literature.

  15. Search for a particle with a long interaction length. [particle mandela to explain anomalous energy spectra at mountain altitude

    Science.gov (United States)

    Barrowes, S. C.; Huggett, R. W.; Jones, W. V.; Levit, L. B.; Porter, L. G.

    1975-01-01

    A search has been carried out for a long-lived particle having an interaction length lambda sub m equals 300 to 2000 gm/sq cm in air. Such a particle, called the mandela, has been proposed to explain an anomalous energy spectrum of particles observed near sea level with a shallow spectrometer. Data taken at mountain altitude with a deep spectrometer has been examined for compatibility with the existence of the mandela. Although data tend to favor the mandela hypothesis the results are not conclusive and appear to be explainable by conventional means.

  16. Automatic fuel lattice design in a boiling water reactor using a particle swarm optimization algorithm and local search

    International Nuclear Information System (INIS)

    Lin Chaung; Lin, Tung-Hsien

    2012-01-01

    Highlights: ► The automatic procedure was developed to design the radial enrichment and gadolinia (Gd) distribution of fuel lattice. ► The method is based on a particle swarm optimization algorithm and local search. ► The design goal were to achieve the minimum local peaking factor. ► The number of fuel pins with Gd and Gd concentration are fixed to reduce search complexity. ► In this study, three axial sections are design and lattice performance is calculated using CASMO-4. - Abstract: The axial section of fuel assembly in a boiling water reactor (BWR) consists of five or six different distributions; this requires a radial lattice design. In this study, an automatic procedure based on a particle swarm optimization (PSO) algorithm and local search was developed to design the radial enrichment and gadolinia (Gd) distribution of the fuel lattice. The design goals were to achieve the minimum local peaking factor (LPF), and to come as close as possible to the specified target average enrichment and target infinite multiplication factor (k ∞ ), in which the number of fuel pins with Gd and Gd concentration are fixed. In this study, three axial sections are designed, and lattice performance is calculated using CASMO-4. Finally, the neutron cross section library of the designed lattice is established by CMSLINK; the core status during depletion, such as thermal limits, cold shutdown margin and cycle length, are then calculated using SIMULATE-3 in order to confirm that the lattice design satisfies the design requirements.

  17. Investigation of p,π+- charged particle correlations in π-C interactions at 5 GeV/c with emission of a particle in the backward direction

    International Nuclear Information System (INIS)

    Budagov, Yu.A.; Bayaramov, A.A.; Dzhelepov, V.P.; Dvornik, A.M.; Efremov, A.V.; Flyagin, V.B.; Lomakin, Yu.F.; Valkar, S.; Volodko, A.G.

    1976-01-01

    The π-C interactions at 5 GeV/c are studied. Angle correlation between two charged particles when a particle is emitted to the backward hemisphere has been investigated. Noticeable correlation appears if the angle between the two particles is 180 deg (lab.s.). It follows from this behaviour that the backward emission of a particle is due to the hard collision mechanism

  18. Geometric influences of a particle confined to a curved surface embedded in three-dimensional Euclidean space

    Science.gov (United States)

    Wang, Yong-Long; Jiang, Hua; Zong, Hong-Shi

    2017-08-01

    In the spirit of the thin-layer quantization approach, we give the formula of the geometric influences of a particle confined to a curved surface embedded in three-dimensional Euclidean space. The geometric contributions can result from the reduced commutation relation between the acted function depending on normal variable and the normal derivative. According to the formula, we obtain the geometric potential, geometric momentum, geometric orbital angular momentum, geometric linear Rashba, and cubic Dresselhaus spin-orbit couplings. As an example, a truncated cone surface is considered. We find that the geometric orbital angular momentum can provide an azimuthal polarization for spin, and the sign of the geometric Dresselhaus spin-orbit coupling can be flipped through the inclination angle of generatrix.

  19. Semiclassical Klein-Kramers and Smoluchowski equations for the Brownian motion of a particle in an external potential

    International Nuclear Information System (INIS)

    Coffey, W T; Kalmykov, Yu P; Titov, S V; Mulligan, B P

    2007-01-01

    The quantum Brownian motion of a particle in an external potential V(x) is treated using the master equation for the Wigner distribution function W(x, p, t) in phase space (x, p). A heuristic method of determination of diffusion coefficients in the master equation is proposed. The time evolution equation so obtained contains explicit quantum correction terms up to o(ℎ 4 ) and in the classical limit, ℎ → 0, reduces to the Klein-Kramers equation. For a quantum oscillator, the method yields an evolution equation for W(x, p, t) coinciding with that of Agarwal (1971 Phys. Rev. A 4 739). In the non-inertial regime, by applying the Brinkman expansion of the momentum distribution in Weber functions (Brinkman 1956 Physica 22 29), the corresponding semiclassical Smoluchowski equation is derived. (fast track communication)

  20. Contact forces between a particle and a wet wall at both quasi-static and dynamic state

    Directory of Open Access Journals (Sweden)

    Zhang Huang

    2017-01-01

    Full Text Available The contact regime of particle-wall is investigated by the atomic force microscope (AFM and theoretical models. First, AFM is used to measure the cohesive force between a micron-sized grain and a glass plate at quasi-static state under various humidity. It is found out that the cohesive force starts to grow slowly and suddenly increase rapidly beyond a critical Relative Humidity (RH. Second, mathematical models of contacting forces are presented to depict the dynamic process that a particle impacts on a wet wall. Then the energy loss of a falling grain is calculated in comparison with the models and the experimental data from the previous references. The simulation results show that the force models presented here are adaptive for both low and high viscosity fluid films with different thickness.

  1. X-ray and pressure conditions on the first wall of a particle beam inertial confinement reactor

    International Nuclear Information System (INIS)

    Magelssen, G.R.

    1979-01-01

    Because of the presence of a chamber gas in a particle beam reactor cavity, nonneutron target debris created from thermonuclear burn will be modified or stopped before it reaches the first reactor wall. The resulting modified spectra and pulse lengths of the debris need to be calculated to determine first wall effects. Further, the cavity overpressure created by the momentum and energy exchange between the debris and gas must also be calculated to determine its effect. The purpose of this paper is to present results of the debris-background gas problem obtained with a one fluid, two temperature plasma hydrodynamic computer code model which includes multifrequency radiation transport. Spherical symmetry, ideal gas equation of state, and LTE for each radiation frequency group were assumed. The transport of debris ions was not included and all the debris energy was assumed to be in radiation. The calculated x-ray spectra and pulse lengths and the background overpressure are presented

  2. Kalman filter with a linear state model for PDR+WLAN positioning and its application to assisting a particle filter

    Science.gov (United States)

    Raitoharju, Matti; Nurminen, Henri; Piché, Robert

    2015-12-01

    Indoor positioning based on wireless local area network (WLAN) signals is often enhanced using pedestrian dead reckoning (PDR) based on an inertial measurement unit. The state evolution model in PDR is usually nonlinear. We present a new linear state evolution model for PDR. In simulated-data and real-data tests of tightly coupled WLAN-PDR positioning, the positioning accuracy with this linear model is better than with the traditional models when the initial heading is not known, which is a common situation. The proposed method is computationally light and is also suitable for smoothing. Furthermore, we present modifications to WLAN positioning based on Gaussian coverage areas and show how a Kalman filter using the proposed model can be used for integrity monitoring and (re)initialization of a particle filter.

  3. Spin precession of a particle with an electric dipole moment: contributions from classical electrodynamics and from the Thomas effect

    International Nuclear Information System (INIS)

    Silenko, Alexander J

    2015-01-01

    The new derivation of the equation of the spin precession is given for a particle possessing electric and magnetic dipole moments. Contributions from classical electrodynamics and from the Thomas effect are explicitly separated. A fully covariant approach is used. The final equation is expressed in a very simple form in terms of the fields in the instantaneously accompanying frame. The Lorentz transformations of the electric and magnetic dipole moments and of the spin are derived from basic equations of classical electrodynamics. For this purpose, the Maxwell equations in matter are used and the result is confirmed by other methods. An antisymmetric four-tensor is correctly constructed from the electric and magnetic dipole moments. (article)

  4. A conceptual study of the use of a particle bed reactor nuclear propulsion module for the orbital maneuvering vehicle

    International Nuclear Information System (INIS)

    Malloy, J.; Potekhen, D.

    1989-01-01

    This paper examines the use of a particle bed reactor nuclear engine for direct thrust in a spacecraft based on the NASA/TRW orbital maneuvering vehicle (OMV). It presents the conceptual design of a 500 lb thrust engine that matches critical design features of the existing OMV bi-propellant propulsion system. This application contrasts with the usual tendency to consider a nuclear heat source either for high thrust direct propulsion or as a power source for electric propulsion. A nuclear propulsion module adapted to the OMV could potentially accomplish several Department of Defense missions, such as multiple round trips from a space-based support platform at 280 NM to service a constellation of satellites orbiting at 1800 NM

  5. When is a particle

    International Nuclear Information System (INIS)

    Drell, S.D.

    1978-01-01

    The concept of elementary constituents or ultimate building blocks of nature in recent years is reviewed. The quark hypothesis, neutrinos, color, hard collisions, psi and other recent resonances, flavor, quantum chromodynamics, the tau particle, and particle structure are among the ideas considered. 22 references

  6. The dynamics of nucleation and growth of a particle in the ternary alloy melt with anisotropic surface tension.

    Science.gov (United States)

    Chen, Ming-Wen; Li, Lin-Yan; Guo, Hui-Min

    2017-08-28

    The dynamics of nucleation and growth of a particle affected by anisotropic surface tension in the ternary alloy melt is studied. The uniformly valid asymptotic solution for temperature field, concentration field, and interface evolution of nucleation and particle growth is obtained by means of the multiple variable expansion method. The asymptotic solution reveals the critical radius of nucleation in the ternary alloy melt and an inward melting mechanism of the particle induced by the anisotropic effect of surface tension. The critical radius of nucleation is dependent on isotropic surface tension, temperature undercooling, and constitutional undercooling in the ternary alloy melt, and the solute diffusion melt decreases the critical radius of nucleation. Immediately after a nucleus forms in the initial stage of solidification, the anisotropic effect of surface tension makes some parts of its interface grow inward while some parts grow outward. Until the inward melting attains a certain distance (which is defined as "the melting depth"), these parts of interface start to grow outward with other parts. The interface of the particle evolves into an ear-like deformation, whose inner diameter may be less than two times the critical radius of nucleation within a short time in the initial stage of solidification. The solute diffusion in the ternary alloy melt decreases the effect of anisotropic surface tension on the interface deformation.

  7. Deadline pressure and human error: a study of human failures on a particle accelerator at Brookhaven National Laboratory

    International Nuclear Information System (INIS)

    Tiagha, E.A.

    1982-01-01

    The decline in industrial efficiency may be linked to decreased reliability of complex automatic systems. This decline threatens the viability of complex organizations in industrialized economies. Industrial engineering techniques that minimize system failure by increasing the reliability of systems hardware are well developed in comparison with those available to reduce human operator errors. The problem of system reliability and the associated costs of breakdown can be reduced if we understand how highly skilled technical personnel function in complex operations and systems. The purpose of this research is to investigate how human errors are affected by deadline pressures, technical communication and other socio-dynamic factors. Through the analysis of a technologically complex particle accelerator prototype at Brookhaven National Laboratory, two failure mechanisms: (1) physical defects in the production process and (2) human operator errors were identified. Two instruments were used to collect information on human failures: objective laboratory data and a human failure questionnaire. The results of human failures from the objective data were used to test for the deadline hypothesis and also to validate the human failure questionnaire. To explain why the human failures occurred, data were collected from a four-part, closed choice questionnaire administered to two groups of scientists, engineers, and technicians, working together against a deadline to produce an engineering prototype of a particle accelerator

  8. Structure of events with a particle at large transverse momentum in proton-proton collisions at the CERN ISR

    International Nuclear Information System (INIS)

    Herr, W.F.

    1985-01-01

    The structure of events with a particle with large transverse momentum has been studied for proton-proton collisions at a centre-of-mass energy of √s=62.2 GeV. The experiment was performed with the Split-Field-Magnet detector at the CERN Intersecting Storage Rings and events were recorded with high-psub(T) particles with psub(T)>2 GeV/c produced at polar angles around 45 0 and 20 0 . The distributions of charged particles in the jet recoiling against the high-psub(T) particle have been measured as a function of the fragmentation variable xsub(E)=psub(T)/psub(T)sup(tri). The production of high-psub(T) particles is usually interpreted in the quark parton model as the hard collision of proton constituents. The asymmetry and charge composition of the recoil jet and their correlation with the flavour of the high-psub(T) particle supports this qualitative picture. Model calculations using first order Quantum Chromodynamics (QCD) and phenomenological fragmentation model cannot explain the particle distribution in the recoil jet. (orig.) [de

  9. A Particle-in-Cell Simulation for the Traveling Wave Direct Energy Converter (TWDEC) for Fusion Propulsion

    Science.gov (United States)

    Chap, Andrew; Tarditi, Alfonso G.; Scott, John H.

    2013-01-01

    A Particle-in-cell simulation model has been developed to study the physics of the Traveling Wave Direct Energy Converter (TWDEC) applied to the conversion of charged fusion products into electricity. In this model the availability of a beam of collimated fusion products is assumed; the simulation is focused on the conversion of the beam kinetic energy into alternating current (AC) electric power. The model is electrostatic, as the electro-dynamics of the relatively slow ions can be treated in the quasistatic approximation. A two-dimensional, axisymmetric (radial-axial coordinates) geometry is considered. Ion beam particles are injected on one end and travel along the axis through ring-shaped electrodes with externally applied time-varying voltages, thus modulating the beam by forming a sinusoidal pattern in the beam density. Further downstream, the modulated beam passes through another set of ring electrodes, now electrically oating. The modulated beam induces a time alternating potential di erence between adjacent electrodes. Power can be drawn from the electrodes by connecting a resistive load. As energy is dissipated in the load, a corresponding drop in beam energy is measured. The simulation encapsulates the TWDEC process by reproducing the time-dependent transfer of energy and the particle deceleration due to the electric eld phase time variations.

  10. The effects of particle recycling on the divertor plasma: A particle-in-cell with Monte Carlo collision simulation

    Science.gov (United States)

    Chang, Mingyu; Sang, Chaofeng; Sun, Zhenyue; Hu, Wanpeng; Wang, Dezhen

    2018-05-01

    A Particle-In-Cell (PIC) with Monte Carlo Collision (MCC) model is applied to study the effects of particle recycling on divertor plasma in the present work. The simulation domain is the scrape-off layer of the tokamak in one-dimension along the magnetic field line. At the divertor plate, the reflected deuterium atoms (D) and thermally released deuterium molecules (D2) are considered. The collisions between the plasma particles (e and D+) and recycled neutral particles (D and D2) are described by the MCC method. It is found that the recycled neutral particles have a great impact on divertor plasma. The effects of different collisions on the plasma are simulated and discussed. Moreover, the impacts of target materials on the plasma are simulated by comparing the divertor with Carbon (C) and Tungsten (W) targets. The simulation results show that the energy and momentum losses of the C target are larger than those of the W target in the divertor region even without considering the impurity particles, whereas the W target has a more remarkable influence on the core plasma.

  11. Performance analysis and optimization for generalized quantum Stirling refrigeration cycle with working substance of a particle confined in a general 1D potential

    Science.gov (United States)

    Yin, Yong; Chen, Lingen; Wu, Feng

    2018-03-01

    A generalized irreversible quantum Stirling refrigeration cycle (GIQSRC) is proposed. The working substance of the GIQSRC is a particle confined in a general 1D potential which energy spectrum can be expressed as εn = ℏωnσ . Heat leakage and non-ideal regeneration loss are taken into account. The expressions of coefficient of performance (COP) and dimensionless cooling load are obtained. The different practical cases of the energy spectrum are analyzed. The results of this paper are meaningful to understand the quantum thermodynamics cycles with a particle confined in different potential as working substance.

  12. Effect of settling particles on the stability of a particle-laden flow in a vertical plane channel

    Science.gov (United States)

    Boronin, S. A.; Osiptsov, A. N.

    2018-03-01

    The stability of a viscous particle-laden flow in a vertical plane channel in the presence of the gravity force is studied. The flow is described using a two-fluid "dusty-gas" model with negligibly small volume fraction of fines and two-way coupling of the phases. Two different profiles of the particle number density in the main flow are considered: homogeneous and non-homogeneous in the form of two layers symmetric about the channel axis. The novel element of the linear-stability problem formulation is a particle velocity slip in the main flow caused by the gravity-induced settling of the dispersed phase. The eigenvalue problem for a linearized system of governing equations is solved using the orthonormalization and QZ algorithms. For a uniform particle number density distribution, it is found that there exists a domain in the plane of Froude and Stokes numbers, in which the two-phase flow in a vertical channel is stable for an arbitrary Reynolds number. This stability domain corresponds to relatively small-inertia particles and large velocity-slip in the main flow. In contrast to the flow with a uniform particle number density distribution, the stratified dusty-gas flow in a vertical channel is unstable over a wide range of governing parameters. The instability at small Reynolds numbers is determined by the gravitational mode characterized by small wavenumbers (long-wave instability), while at larger Reynolds numbers the instability is dominated by the shear mode with the time-amplification factor larger than that of the gravitational mode. The results of the study can be used for optimization of a large number of technological processes, including those in riser reactors, pneumatic conveying in pipeline systems, hydraulic fracturing, and well cementing.

  13. Why the two-fluid model fails to predict the bed expansion characteristics of Geldart A particles in gas-fluidized beds: A tentative answers

    NARCIS (Netherlands)

    Wang, J.; Hoef, van der M.A.; Kuipers, J.A.M.

    2009-01-01

    It is well known that two-fluid models (TFMs) can successfully predict the hydrodynamics of Geldart B and D particles. However, up to now, TFM have failed to accurately describe the hydrodynamics of Geldart A particles inside bubbling gas-fluidized beds: Researchers have reported that bed expansions

  14. Why the two-fluid model fails to predict the bed expansion characteristics of Geldart A particles in gas-fluidized beds: A tentative answer

    NARCIS (Netherlands)

    Wang, J.; van der Hoef, Martin Anton; Kuipers, J.A.M.

    2009-01-01

    It is well known that two-fluid models (TFMs) can successfully predict the hydrodynamics of Geldart B and D particles. However, up to now, TFM have failed to accurately describe the hydrodynamics of Geldart A particles inside bubbling gas-fluidized beds: Researchers have reported that bed expansions

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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-.

  4. Locality and nonlocality in geomorphic transport laws: Implications of a particle-based model of hillslope evolution

    Science.gov (United States)

    Tucker, G. E.; Bradley, D. N.

    2008-12-01

    Many geomorphic transport laws assume that the transport process is local, meaning that the space and time scales of particle displacement are short relative to those of the system as a whole. This assumption allows one to express sediment flux in terms of at-a-point properties such as the local surface gradient. However, while this assumption is quite reasonable for some processes (for example, grain displacement by raindrop impact), it is questionable for others (such as landsliding). Moreover, particle displacement distance may also depend on slope angle, becoming longer as gradient increases. For example, the average motion distance during sediment ravel events on very steep slopes may approach the length of the entire hillslope. In such cases, the mass flux through a given point may depend not only on the local topography but also on topography some distance upslope, thus violating the locality assumption. Here we use a stochastic, particle- based model of hillslope evolution to gain insight into the potential for, and consequences of, nonlocality in sediment transport. The model is designed as a simple analogy for a host of different processes that displace sediment grains on hillslopes. The hillslope is represented as a two-dimensional pile of particles. These particles undergo quasi-random motion according to the following rules: (1) during each iteration, a particle and a direction are selected at random; (2) the particle hops in the direction of motion with a probability that depends on the its height relative to that of its immediate neighbor; (3) the particle continues making hops in the same direction and with the same probability dependence, until coming to rest or exiting the base of the slope. The topography and motion statistics that emerge from these rules show a range of behavior that depends on a dimensionless relief parameter. At low relief, hillslope shape is parabolic, mean displacement length is on the order of two particle widths, and the

  5. A Novel Multi-Sensor Environmental Perception Method Using Low-Rank Representation and a Particle Filter for Vehicle Reversing Safety

    Directory of Open Access Journals (Sweden)

    Zutao Zhang

    2016-06-01

    Full Text Available Environmental perception and information processing are two key steps of active safety for vehicle reversing. Single-sensor environmental perception cannot meet the need for vehicle reversing safety due to its low reliability. In this paper, we present a novel multi-sensor environmental perception method using low-rank representation and a particle filter for vehicle reversing safety. The proposed system consists of four main steps, namely multi-sensor environmental perception, information fusion, target recognition and tracking using low-rank representation and a particle filter, and vehicle reversing speed control modules. First of all, the multi-sensor environmental perception module, based on a binocular-camera system and ultrasonic range finders, obtains the distance data for obstacles behind the vehicle when the vehicle is reversing. Secondly, the information fusion algorithm using an adaptive Kalman filter is used to process the data obtained with the multi-sensor environmental perception module, which greatly improves the robustness of the sensors. Then the framework of a particle filter and low-rank representation is used to track the main obstacles. The low-rank representation is used to optimize an objective particle template that has the smallest L-1 norm. Finally, the electronic throttle opening and automatic braking is under control of the proposed vehicle reversing control strategy prior to any potential collisions, making the reversing control safer and more reliable. The final system simulation and practical testing results demonstrate the validity of the proposed multi-sensor environmental perception method using low-rank representation and a particle filter for vehicle reversing safety.

  6. STOSS - A computer module which can be used in Monte-Carlo-calculation for determining the path of a particle in a heterogeneous medium in three dimensions

    International Nuclear Information System (INIS)

    Sdouz, G.

    1980-09-01

    The computer program STOSS determines the path of a particle in a heterogenous medium in three dimensions. The program can be used as a module in Monte-Carlo-calculations. The collision can be transferred from the centre-of-mass system into a fixed cartesian coordinate-system by means of appropriate transformations. Then the path length is determined and the location of the next collision is calculated. The computational details are discussed at some length. (auth.)

  7. Improved MECP2 Gene Therapy Extends the Survival of MeCP2-Null Mice without Apparent Toxicity after Intracisternal Delivery

    Directory of Open Access Journals (Sweden)

    Sarah E. Sinnett

    2017-06-01

    Full Text Available Intravenous administration of adeno-associated virus serotype 9 (AAV9/hMECP2 has been shown to extend the lifespan of Mecp2−/y mice, but this delivery route induces liver toxicity in wild-type (WT mice. To reduce peripheral transgene expression, we explored the safety and efficacy of AAV9/hMECP2 injected into the cisterna magna (ICM. AAV9/hMECP2 (1 × 1012 viral genomes [vg]; ICM extended Mecp2−/y survival but aggravated hindlimb clasping and abnormal gait phenotypes. In WT mice, 1 × 1012 vg of AAV9/hMECP2 induced clasping and abnormal gait. A lower dose mitigated these adverse phenotypes but failed to extend survival of Mecp2−/y mice. Thus, ICM delivery of this vector is impractical as a treatment for Rett syndrome (RTT. To improve the safety of MeCP2 gene therapy, the gene expression cassette was modified to include more endogenous regulatory elements believed to modulate MeCP2 expression in vivo. In Mecp2−/y mice, ICM injection of the modified vector extended lifespan and was well tolerated by the liver but did not rescue RTT behavioral phenotypes. In WT mice, these same doses of the modified vector had no adverse effects on survival or neurological phenotypes. In summary, we identified limitations of the original vector and demonstrated that an improved vector design extends Mecp2−/y survival, without apparent toxicity.

  8. Clustering of DSB in DNA by X-Ray and a-particle irradiation in MCF-7 cells studied with anti γ-H2AX

    International Nuclear Information System (INIS)

    Tapia, O.; Soto, J.; Castro, F.A.; Berciano, Ma T; Lafarga, M.; Cos, S.; Sanchez-Barcelo, E.

    2007-01-01

    Among the effects produced by the ionizing radiations in cellular DNA, double strand breaks (DSB) are considered particularly important. These ruptures and their grouping in certain points, clustering, are acknowledged as the cause for mutagenic effects and cellular death. In this work we present the methodology and the results of the application of the DSB - DNA marking technique by using anti γ-H2AX, taking human cancerous cells MCF-7 as model and X-rays and a particles as irradiation agents. The obtained results are showed in a qualitative way like a set of figures. Are shows the effects of a dose of 2 Gy X-rays in the DSB - DNA after 30 minutes of the irradiation that responds to a certain pattern in which a spatially homogenous irradiation interacts with the DNA. As in previous case, the effects of X-rays in the DSB - DNA shows a different pattern affecting the cells that are in mitosis. Also, the effects of a dose of 2 Gy X-rays obtained after 24 hours of irradiation shows a number of DSB smaller, which is indicative of the repairing process. The results of the irradiation with a dose of 0.1 Gy originated from a particles cause a smaller number of DSB. Nevertheless, the existence of a bigger clustering with the appearance of clearly more intense points is appraised. Also, the effect of the irradiation is showed as an aligned trace of clusters that is possible to attribute to the passing of a a particle through the cellular nucleus. (Author)

  9. On the dynamics aspects for the plane motion of a particle under the action of potential forces in the presence of a magnetic field

    Science.gov (United States)

    Mnasri, C.; Elmandouh, A. A.

    2018-06-01

    This article deals with the general motion of a particle moving in the Euclidean plane under the influence of a conservative potential force in the presence of a magnetic field perpendicular to the plane of the motion. We introduce the conditions for which this motion is not algebraically integrable by using Kowalevski's exponents. We present the equilibrium positions and study their stability and moreover, we clarify that the existence of the magnetic field acts as a stabilizer for maximum unstable equilibrium points for the effective potential. We employ Lyapunov theorem to construct the periodic solutions near the equilibrium points. The allowed regions of motion are specified and illustrated graphically.

  10. The enterovirus 71 A-particle forms a gateway to allow genome release: a cryoEM study of picornavirus uncoating.

    Directory of Open Access Journals (Sweden)

    Kristin L Shingler

    2013-03-01

    Full Text Available Since its discovery in 1969, enterovirus 71 (EV71 has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has the capacity to invade the central nervous system to cause severe disease and death. Upon binding to a host receptor on the cell surface, the virus begins a two-step uncoating process, first forming an expanded, altered "A-particle", which is primed for genome release. In a second step after endocytosis, an unknown trigger leads to RNA expulsion, generating an intact, empty capsid. Cryo-electron microscopy reconstructions of these two capsid states provide insight into the mechanics of genome release. The EV71 A-particle capsid interacts with the genome near the icosahedral two-fold axis of symmetry, which opens to the external environment via a channel ∼10 Å in diameter that is lined with patches of negatively charged residues. After the EV71 genome has been released, the two-fold channel shrinks, though the overall capsid dimensions are conserved. These structural characteristics identify the two-fold channel as the site where a gateway forms and regulates the process of genome release.

  11. Influence of the Molecular Adhesion Force on the Indentation Depth of a Particle into the Wafer Surface in the CMP Process

    Directory of Open Access Journals (Sweden)

    Zhou Jianhua

    2014-01-01

    Full Text Available By theoretical calculation, the external force on the particle conveyed by pad asperities and the molecular adhesion force between particle and wafer are compared and analyzed quantitatively. It is confirmed that the molecular adhesion force between particle and wafer has a great influence on the chemical mechanical polishing (CMP material removal process. Considering the molecular adhesion force between particle and wafer, a more precise model for the indentation of a particle into the wafer surface is developed in this paper, and the new model is compared with the former model which neglected the molecular adhesion force. Through theoretical analyses, an approach and corresponding critical values are applied to estimate whether the molecular adhesion force in CMP can be neglected. These methods can improve the precision of the material removal model of CMP.

  12. Analysis and Speed Ripple Mitigation of a Space Vector Pulse Width Modulation-Based Permanent Magnet Synchronous Motor with a Particle Swarm Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    Xing Liu

    2016-11-01

    Full Text Available A method is proposed for reducing speed ripple of permanent magnet synchronous motors (PMSMs controlled by space vector pulse width modulation (SVPWM. A flux graph and mathematics are used to analyze the speed ripple characteristics of the PMSM. Analysis indicates that the 6P (P refers to pole pairs of the PMSM time harmonic of rotor mechanical speed is the main harmonic component in the SVPWM control PMSM system. To reduce PMSM speed ripple, harmonics are superposed on a SVPWM reference signal. A particle swarm optimization (PSO algorithm is proposed to determine the optimal phase and multiplier coefficient of the superposed harmonics. The results of a Fourier decomposition and an optimized simulation model verified the accuracy of the analysis as well as the effectiveness of the speed ripple reduction methods, respectively.

  13. Investigation of the two-quasiparticle bands in the doubly-odd nucleus 166Ta using a particle-number conserving cranked shell model

    Science.gov (United States)

    Zhang, ZhenHua

    2016-07-01

    The high-spin rotational properties of two-quasiparticle bands in the doubly-odd 166Ta are analyzed using the cranked shell model with pairing correlations treated by a particle-number conserving method, in which the blocking effects are taken into account exactly. The experimental moments of inertia and alignments and their variations with the rotational frequency hω are reproduced very well by the particle-number conserving calculations, which provides a reliable support to the configuration assignments in previous works for these bands. The backbendings in these two-quasiparticle bands are analyzed by the calculated occupation probabilities and the contributions of each orbital to the total angular momentum alignments. The moments of inertia and alignments for the Gallagher-Moszkowski partners of these observed two-quasiparticle rotational bands are also predicted.

  14. On a criterion of incipient motion and entrainment into suspension of a particle from cuttings bed in shear flow of non-Newtonian fluid

    Science.gov (United States)

    Ignatenko, Yaroslav; Bocharov, Oleg; May, Roland

    2017-10-01

    Solids transport is a major issue in high angle wells. Bed-load forms by sediment while transport and accompanied by intermittent contact with stream-bed by rolling, sliding and bouncing. The study presents the results of a numerical simulation of a laminar steady-state flow around a particle at rest and in free motion in a shear flow of Herschel-Bulkley fluid. The simulation was performed using the OpenFOAM open-source CFD package. A criterion for particle incipient motion and entrainment into suspension from cuttings bed (Shields criteria) based on forces and torques balance is discussed. Deflection of the fluid parameters from the ones of Newtonian fluid leads to decreasing of the drag and lift forces and the hydrodynamic moment. Thus, the critical shear stress (Shields parameter) for the considered non-Newtonian fluid must be greater than the one for a Newtonian fluid.

  15. A particle accelerator probes artifacts

    International Nuclear Information System (INIS)

    Dran, J.C.; Calligaro, Th.; Salomon, J.

    2002-01-01

    The AGLAE system is made up of a 2 mega volts electrostatic accelerator and of 3 irradiation lines: one leads to a vacuum enclosure in which targets are irradiated and the 2 others lines are designed to irradiate targets under an air or helium atmosphere. The AGLAE system is located in the premises of the Louvre museum in Paris and is devoted to the study of cultural objects through ion beam analysis (IBA). 4 techniques are used: -) proton-induced X-ray emission (PIXE) -) proton-induced gamma ray (PIGE) -) Rutherford backscattering spectrometry (NRS) and -) nuclear reaction analysis (NRA). A decisive progress has permitted the direct analysis of artifacts without sampling. The object itself is set just a few millimeters away from the exit window of the beam in an air or helium atmosphere. The exit window must be resistant enough to bear the atmospheric pressure and the damages caused by the proton beam but must be thin enough to not deteriorate the quality of the beam. By using a 10 -7 m thick exit window made of Si 3 N 4 we get a beam whose diameter is 10 -5 m. This new technology presents 4 main advantages: 1) any object of any shape can be studied without sampling, 2) the analysis of very fragile artifacts that might be damaged by the vacuum setting is now possible, 3) a reduction of the thermal side-effects of the beam, and 4) the absence of accumulation of charges in isolating material allows to rid of covering the object with a conducting coating before irradiating it. (A.C.)

  16. A particle accelerator probes artifacts

    CERN Document Server

    Dran, J C; Salomon, J

    2002-01-01

    The AGLAE system is made up of a 2 mega volts electrostatic accelerator and of 3 irradiation lines: one leads to a vacuum enclosure in which targets are irradiated and the 2 others lines are designed to irradiate targets under an air or helium atmosphere. The AGLAE system is located in the premises of the Louvre museum in Paris and is devoted to the study of cultural objects through ion beam analysis (IBA). 4 techniques are used: -) proton-induced X-ray emission (PIXE) -) proton-induced gamma ray (PIGE) -) Rutherford backscattering spectrometry (NRS) and -) nuclear reaction analysis (NRA). A decisive progress has permitted the direct analysis of artifacts without sampling. The object itself is set just a few millimeters away from the exit window of the beam in an air or helium atmosphere. The exit window must be resistant enough to bear the atmospheric pressure and the damages caused by the proton beam but must be thin enough to not deteriorate the quality of the beam. By using a 10 sup - sup 7 m thick exit w...

  17. Electron microscopic study of spontaneous and experimentally induced leukemia in IRC mice

    International Nuclear Information System (INIS)

    Hiraki, S.; Ranadive, K.J.; Dmochowski, L.

    1974-01-01

    Spontaneous, serially transplanted, and experimentally induced leukemias of ICRC mice were studied by electron microscopy in an attempt to detect the presence of virus particles, if any, and to observe the influence of chemical and hormonal treatment on the presence of these virus particles. The first series of experiments included spontaneous, serially transplanted, and radiation-induced leukemia. The paucity of type C virus particles was quite conspicuous in spontaneous leukemia. Serially transplanted and radiation-accelerated leukemic lesions showed the presence of some type C and intracisternal type A particles. Found in two of these leukemic lesions (thymus and lymphosarcoma), in addition to type C virus particles, were budding and some mature type B virus particles, and numerous intracytoplasmic type A particles. ''Viropexis'' of type B virus particles has been observed in the lymphosarcoma and in a leukemic thymus gland. The second series of experiments included leukemia induced in ovariectomized ICRC mice with 20-methylcholanthrene (MCA), pituitary transplants, and ovarian hormones (estradiol and estradiol-progesterone). In ovariectomized ICRC mice, leukemic lesions induced by MCA or pituitary transplants, or by MCA and pituitary transplants, showed type C virus particles and, in most cases, intracisternal type A particles. In leukemia induced in ovariectomized ICRC mice by MCA and estradiol, numerous intracytoplasmic type A particles were observed but no type C virus particles

  18. From a particle in a box to the uncertainty relation in a quantum dot and to reflecting walls for relativistic fermions

    International Nuclear Information System (INIS)

    Al-Hashimi, M.H.; Wiese, U.-J.

    2012-01-01

    We consider a 1-parameter family of self-adjoint extensions of the Hamiltonian for a particle confined to a finite interval with perfectly reflecting boundary conditions. In some cases, one obtains negative energy states which seem to violate the Heisenberg uncertainty relation. We use this as a motivation to derive a generalized uncertainty relation valid for an arbitrarily shaped quantum dot with general perfectly reflecting walls in d dimensions. In addition, a general uncertainty relation for non-Hermitian operators is derived and applied to the non-Hermitian momentum operator in a quantum dot. We also consider minimal uncertainty wave packets in this situation, and we prove that the spectrum depends monotonically on the self-adjoint extension parameter. In addition, we construct the most general boundary conditions for semiconductor heterostructures such as quantum dots, quantum wires, and quantum wells, which are characterized by a 4-parameter family of self-adjoint extensions. Finally, we consider perfectly reflecting boundary conditions for relativistic fermions confined to a finite volume or localized on a domain wall, which are characterized by a 1-parameter family of self-adjoint extensions in the (1+1)-d and (2+1)-d cases, and by a 4-parameter family in the (3+1)-d and (4+1)-d cases. - Highlights: ► Finite volume Heisenberg uncertainty relation. ► General self-adjoint extensions for relativistic fermions. ► New prospective for the problem of particle in a box.

  19. Notes on T-invariance and polarization effects in the elastic scattering of a particle with spin 1/2 on the unpolarized target

    International Nuclear Information System (INIS)

    Lyuboshits, V.V.; Lyuboshits, V.L.

    1998-01-01

    In the frames of T-invariance the analysis of the general dependence of the elastic scattering effective cross section of a particle with spin 1/2 on the unpolarized target with arbitrary spin upon the initial and final polarizations of the particle has been performed. On the base of the T-symmetry of the differential scattering cross section only, without traditional consideration of the spin structure of scattering amplitudes, a simple proof of the Wolfenstein theorem is obtained (this theorem states that the degree of transverse polarization, arising in the elastic scattering of an unpolarized particle on the unpolarized target, is equal to the coefficient of left-right asymmetry in the elastic scattering of the same but transversally polarized particle on the same target). Meantime, it is ascertained that in the case of P-parity violation (conserving T-invariance) there exists no analogous universal relation between the degree of longitudinal polarization and the coefficient of P-odd spin asymmetry in the scattering of longitudinally polarized particles. It is shown, further, that under T-invariance the amplitude and cross section of 'backward' scattering of neutrons on zero-spin nuclei do not depend on spin, and the observation of such a dependence would testify unambiguously to the T-invariance violation. However, according to the fulfilled estimates, the T-noninvariant spin asymmetry in the 'backward' scattering is very small (about 10 -8 - 10 -7 )

  20. Evolution of metastable state molecules N2(A3Σu+) in a nanosecond pulsed discharge: A particle-in-cell/Monte Carlo collisions simulation

    International Nuclear Information System (INIS)

    Gao Liang; Sun Jizhong; Feng Chunlei; Bai Jing; Ding Hongbin

    2012-01-01

    A particle-in-cell plus Monte Carlo collisions method has been employed to investigate the nitrogen discharge driven by a nanosecond pulse power source. To assess whether the production of the metastable state N 2 (A 3 Σ u + ) can be efficiently enhanced in a nanosecond pulsed discharge, the evolutions of metastable state N 2 (A 3 Σ u + ) density and electron energy distribution function have been examined in detail. The simulation results indicate that the ultra short pulse can modulate the electron energy effectively: during the early pulse-on time, high energy electrons give rise to quick electron avalanche and rapid growth of the metastable state N 2 (A 3 Σ u + ) density. It is estimated that for a single pulse with amplitude of -9 kV and pulse width 30 ns, the metastable state N 2 (A 3 Σ u + ) density can achieve a value in the order of 10 9 cm -3 . The N 2 (A 3 Σ u + ) density at such a value could be easily detected by laser-based experimental methods.

  1. Evolution of metastable state molecules N2(A3 Σu+) in a nanosecond pulsed discharge: A particle-in-cell/Monte Carlo collisions simulation

    Science.gov (United States)

    Gao, Liang; Sun, Jizhong; Feng, Chunlei; Bai, Jing; Ding, Hongbin

    2012-01-01

    A particle-in-cell plus Monte Carlo collisions method has been employed to investigate the nitrogen discharge driven by a nanosecond pulse power source. To assess whether the production of the metastable state N2(A3 Σu+) can be efficiently enhanced in a nanosecond pulsed discharge, the evolutions of metastable state N2(A3 Σu+) density and electron energy distribution function have been examined in detail. The simulation results indicate that the ultra short pulse can modulate the electron energy effectively: during the early pulse-on time, high energy electrons give rise to quick electron avalanche and rapid growth of the metastable state N2(A3 Σu+) density. It is estimated that for a single pulse with amplitude of -9 kV and pulse width 30 ns, the metastable state N2(A3 Σu+) density can achieve a value in the order of 109 cm-3. The N2(A3 Σu+) density at such a value could be easily detected by laser-based experimental methods.

  2. One-parameter family of time-symmetric initial data for the radial infall of a particle into a Schwarzschild black hole

    International Nuclear Information System (INIS)

    Martel, Karl; Poisson, Eric

    2002-01-01

    A one-parameter family of time-symmetric initial data for the radial infall of a particle into a Schwarzschild black hole is constructed within the framework of black-hole perturbation theory. The parameter measures the amount of gravitational radiation present on the initial spacelike surface. These initial data sets are then evolved by integrating the Zerilli-Moncrief wave equation in the presence of the particle. Numerical results for the gravitational waveforms and their power spectra are presented; we show that the choice of initial data strongly influences the waveforms, both in their shapes and their frequency content. We also calculate the total energy radiated by the particle-black-hole system, as a function of the initial separation between the particle and the black hole, and as a function of the choice of initial data. Our results confirm that for large initial separations, a conformally flat initial three-geometry minimizes the initial gravitational-wave content, so that the total energy radiated is also minimized. For small initial separations, however, we show that the conformally flat solution no longer minimizes the energy radiated

  3. A Current Control Approach for an Abnormal Grid Supplied Ultra Sparse Z-Source Matrix Converter with a Particle Swarm Optimization Proportional-Integral Induction Motor Drive Controller

    Directory of Open Access Journals (Sweden)

    Seyed Sina Sebtahmadi

    2016-11-01

    Full Text Available A rotational d-q current control scheme based on a Particle Swarm Optimization- Proportional-Integral (PSO-PI controller, is used to drive an induction motor (IM through an Ultra Sparse Z-source Matrix Converter (USZSMC. To minimize the overall size of the system, the lowest feasible values of Z-source elements are calculated by considering the both timing and aspects of the circuit. A meta-heuristic method is integrated to the control system in order to find optimal coefficient values in a single multimodal problem. Henceforth, the effect of all coefficients in minimizing the total harmonic distortion (THD and balancing the stator current are considered simultaneously. Through changing the reference point of magnitude or frequency, the modulation index can be automatically adjusted and respond to changes without heavy computational cost. The focus of this research is on a reliable and lightweight system with low computational resources. The proposed scheme is validated through both simulation and experimental results.

  4. Application of a particle separation device to reduce inductively coupled plasma-enhanced elemental fractionation in laser ablation-inductively coupled plasma-mass spectrometry

    International Nuclear Information System (INIS)

    Guillong, Marcel; Kuhn, Hans-Rudolf; Guenther, Detlef

    2003-01-01

    The particle size distribution of laser ablation aerosols are a function of the wavelength, the energy density and the pulse duration of the laser, as well as the sample matrix and the gas environment. Further the size of the particles affects the vaporization and ionization efficiency in the inductively coupled plasma (ICP). Some matrices produce large particles, which are not completely vaporized and ionized in the ICP. The previous work has shown that analytical results such as matrix-independent calibration, accuracy and precision can be significantly influenced by the particle sizes of the particles. To minimize the particle size related incomplete conversion of the sample to ions in the ICP a particle separation device was developed, which allows effective particle separation using centrifugal forces in a thin coiled tube. In this device, the particle cut-off size is varied by changing the number of turns in the coil, as well as by changing the gas flow and the tube diameter. The interaction of the laser with the different samples leads to varying particle size distributions. When carrying out quantitative analysis with non-matrix matched calibration reference materials, it was shown that different particle cut-off sizes were required depending on the ICP conditions and the instrument used for analysis. Various sample materials were investigated in this study to demonstrate the applicability of the device. For silicate matrices, the capability of the ICP to produce ions was significantly reduced for particles larger than 0.5 μm, and was dependent on the element monitored. To reduce memory effects caused by the separated particles, a washout procedure was developed, which additionally allowed the analysis of the trapped particles. These results clearly demonstrate the very important particle size dependent ICP-MS signal response and the potential of the described particle size based separator for the reduction of ICP induced elemental fractionation

  5. Hydrodynamic description of the long-time tails of the linear and rotational velocity autocorrelation functions of a particle in a confined geometry.

    Science.gov (United States)

    Frydel, Derek; Rice, Stuart A

    2007-12-01

    We report a hydrodynamic analysis of the long-time behavior of the linear and angular velocity autocorrelation functions of an isolated colloid particle constrained to have quasi-two-dimensional motion, and compare the predicted behavior with the results of lattice-Boltzmann simulations. Our analysis uses the singularity method to characterize unsteady linear motion of an incompressible fluid. For bounded fluids we construct an image system with a discrete set of fundamental solutions of the Stokes equation from which we extract the long-time decay of the velocity. For the case that there are free slip boundary conditions at walls separated by H particle diameters, the time evolution of the parallel linear velocity and the perpendicular rotational velocity following impulsive excitation both correspond to the time evolution of a two-dimensional (2D) fluid with effective density rho_(2D)=rhoH. For the case that there are no slip boundary conditions at the walls, the same types of motion correspond to 2D fluid motions with a coefficient of friction xi=pi(2)nu/H(2) modulo a prefactor of order 1, with nu the kinematic viscosity. The linear particle motion perpendicular to the walls also experiences an effective frictional force, but the time dependence is proportional to t(-2) , which cannot be related to either pure 3D or pure 2D fluid motion. Our incompressible fluid model predicts correct self-diffusion constants but it does not capture all of the effects of the fluid confinement on the particle motion. In particular, the linear motion of a particle perpendicular to the walls is influenced by coupling between the density flux and the velocity field, which leads to damped velocity oscillations whose frequency is proportional to c_(s)/H , with c_(s) the velocity of sound. For particle motion parallel to no slip walls there is a slowing down of a density flux that spreads diffusively, which generates a long-time decay proportional to t(-1) .

  6. Retrotransposon-centered analysis of piRNA targeting shows a shift from active to passive retrotransposon transcription in developing mouse testes

    Directory of Open Access Journals (Sweden)

    Mourier Tobias

    2011-09-01

    Full Text Available Abstract Background Piwi-associated RNAs (piRNAs bind transcripts from retrotransposable elements (RTE in mouse germline cells and seemingly act as guides for genomic methylation, thereby repressing the activity of RTEs. It is currently unknown if and how Piwi proteins distinguish RTE transcripts from other cellular RNAs. During germline development, the main target of piRNAs switch between different types of RTEs. Using the piRNA targeting of RTEs as an indicator of RTE activity, and considering the entire population of genomic RTE loci along with their age and location, this study aims at further elucidating the dynamics of RTE activity during mouse germline development. Results Due to the inherent sequence redundancy between RTE loci, assigning piRNA targeting to specific loci is problematic. This limits the analysis, although certain features of piRNA targeting of RTE loci are apparent. As expected, young RTEs display a much higher level of piRNA targeting than old RTEs. Further, irrespective of age, RTE loci near protein-coding coding genes are targeted to a greater extent than RTE loci far from genes. During development, a shift in piRNA targeting is observed, with a clear increase in the relative piRNA targeting of RTEs residing within boundaries of protein-coding gene transcripts. Conclusions Reanalyzing published piRNA sequences and taking into account the features of individual RTE loci provide novel insight into the activity of RTEs during development. The obtained results are consistent with some degree of proportionality between what transcripts become substrates for Piwi protein complexes and the level by which the transcripts are present in the cell. A transition from active transcription of RTEs to passive co-transcription of RTE sequences residing within protein-coding transcripts appears to take place in postnatal development. Hence, the previously reported increase in piRNA targeting of SINEs in postnatal testis development does not necessitate widespread active transcription of SINEs, but may simply be explained by the prevalence of SINEs residing in introns.

  7. Use of mineral magnetic concentration data as a particle size proxy: a case study using marine, estuarine and fluvial sediments in the Carmarthen Bay area, South Wales, U.K.

    Science.gov (United States)

    Booth, C A; Walden, J; Neal, A; Smith, J P

    2005-07-15

    Compositional (non-magnetic) data can correlate strongly with particle size, which deems it appropriate as a particle size proxy and, therefore, a reliable means of normalising analytical data for particle size effects. Previous studies suggest magnetic concentration parameters represent an alternative means of normalising for these effects and, given the speed, low-cost and sensitivity of the measurements may, therefore, offer some advantages over other compositional signals. In this work, contemporary sediments from a range of depositional environments have been analysed with regard to their mineral magnetic concentration and textural characteristics, to observe if the strength and nature of the relationship identified in previous studies is universal. Our data shows magnetic parameters (chi(LF), chi(ARM) and SIRM) possess contrasting relationships with standard textural parameters for sediment samples collected from marine (Carmarthen Bay), estuarine (Gwendraeth Estuary) and fluvial (Rivers Gwendraeth Fach and Gwendraeth Fawr) settings. Magnetic concentrations of sediments from both the marine and estuarine environments are highly influenced by the magnetic contribution of finer particle sizes; Gwendraeth Fawr River sediments are influenced by the magnetic contribution of coarser particle sizes, while sediments from the Gwendraeth Fach River are not influenced significantly by any variations in textural properties. These results indicate mineral magnetic measurements have considerable potential as a particle size proxy for particular sedimentary environments, which in certain instances could be useful for geochemical, sediment transport, and sediment provenance studies. However, the data also highlight the importance of fully determining the nature of the relationship between sediment particle size and magnetic properties before applying mineral magnetic data as a particle size proxy.

  8. A retrotransposon-driven Dicer isoform directs endogenous small interfering RNA production in mouse oocytes

    Czech Academy of Sciences Publication Activity Database

    Flemr, Matyáš; Malík, Radek; Franke, V.; Nejepínská, Jana; Sedláček, Radislav; Vlahovicek, K.; Svoboda, Petr

    2013-01-01

    Roč. 155, č. 4 (2013), s. 807-816 ISSN 0092-8674 R&D Projects: GA ČR GAP305/10/2215; GA ČR(CZ) GBP305/12/G034; GA ČR GA204/09/0085; GA MŠk(CZ) LM2011032; GA MŠk ED1.1.00/02.0109 Grant - others:AV ČR(CZ) M200521202 Institutional support: RVO:68378050 Keywords : Dicer * miRNA * RNAi * mouse oocytes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 33.116, year: 2013

  9. Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2010-01-01

    of transcriptional activity are observed from both strands of solitary LTR sequences. Transcriptome data collected during meiosis suggests that transcription of solitary LTRs is correlated with the transcription of nearby protein-coding genes. CONCLUSIONS: Presumably, the host organism negatively regulates...

  10. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

    Czech Academy of Sciences Publication Activity Database

    Lexa, M.; Kejnovský, Eduard; Šteflová, Pavlína; Konvalinová, H.; Vorlíčková, Michaela; Vyskot, Boris

    2014-01-01

    Roč. 42, č. 2 (2014), s. 968-978 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GAP205/12/0466; GA ČR(CZ) GAP305/10/0930; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GA522/09/0083; GA ČR GPP501/10/P483 Institutional support: RVO:68081707 Keywords : INTRAMOLECULAR DNA QUADRUPLEXES * VIRUS TYPE-1 RNA * CIRCULAR-DICHROISM Subject RIV: BO - Biophysics Impact factor: 9.112, year: 2014

  11. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

    DEFF Research Database (Denmark)

    Fort, Alexandre; Hashimoto, Kosuke; Yamada, Daisuke

    2014-01-01

    The importance of microRNAs and long noncoding RNAs in the regulation of pluripotency has been documented; however, the noncoding components of stem cell gene networks remain largely unknown. Here we investigate the role of noncoding RNAs in the pluripotent state, with particular emphasis on nucl...

  12. Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice

    Czech Academy of Sciences Publication Activity Database

    Nagaki, K.; Neumann, Pavel; Zhang, D.; Ouyang, S.; Buell, C.R.; Cheng, Z.; Jiang, J.

    2005-01-01

    Roč. 22, - (2005), s. 845-855 ISSN 0737-4038 Institutional research plan: CEZ:AV0Z5051902 Keywords : rice * chromosomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.233, year: 2005

  13. A family of DNA repeats in Aspergillus nidulans has assimilated degenerated retrotransposons

    DEFF Research Database (Denmark)

    Nielsen, M.L.; Hermansen, T.D.; Aleksenko, Alexei Y.

    2001-01-01

    In the course of a chromosomal walk towards the centromere of chromosome IV of Aspergillus nidulans, several cross- hybridizing genomic cosmid clones were isolated. Restriction mapping of two such clones revealed that their restriction patterns were similar in a region of at least 15 kb, indicati......) phenomenon, first described in Neurospora crassa, may have operated in A. nidulans. The data indicate that this family of repeats has assimilated mobile elements that subsequently degenerated but then underwent further duplications as a part of the host repeats....... the presence of a large repeat. The nature of the repeat was further investigated by sequencing and Southern analysis. The study revealed a family of long dispersed repeats with a high degree of sequence similarity. The number and location of the repeats vary between wild isolates. Two copies of the repeat...

  14. Insertion polymorphisms of SINE200 retrotransposons within speciation islands of Anopheles gambiae molecular forms

    Directory of Open Access Journals (Sweden)

    Tu Zhijian

    2008-08-01

    Full Text Available Abstract Background SINEs (Short INterspersed Elements are homoplasy-free and co-dominant genetic markers which are considered to represent useful tools for population genetic studies, and could help clarifying the speciation processes ongoing within the major malaria vector in Africa, Anopheles gambiae s.s. Here, we report the results of the analysis of the insertion polymorphism of a nearly 200 bp-long SINE (SINE200 within genome areas of high differentiation (i.e. "speciation islands" of M and S A. gambiae molecular forms. Methods A SINE-PCR approach was carried out on thirteen SINE200 insertions in M and S females collected along the whole range of distribution of A. gambiae s.s. in sub-Saharan Africa. Ten specimens each for Anopheles arabiensis, Anopheles melas, Anopheles quadriannulatus A and 15 M/S hybrids from laboratory crosses were also analysed. Results Eight loci were successfully amplified and were found to be specific for A. gambiae s.s.: 5 on 2L chromosome and one on X chromosome resulted monomorphic, while two loci positioned respectively on 2R (i.e. S200 2R12D and X (i.e. S200 X6.1 chromosomes were found to be polymorphic. S200 2R12D was homozygote for the insertion in most S-form samples, while intermediate levels of polymorphism were shown in M-form, resulting in an overall high degree of genetic differentiation between molecular forms (Fst = 0.46 p S200 X6.1 was found to be fixed in all M- and absent in all S-specimens. This led to develop a novel easy-to-use PCR approach to straightforwardly identify A. gambiae molecular forms. This novel approach allows to overcome the constraints associated with markers on the rDNA region commonly used for M and S identification. In fact, it is based on a single copy and irreversible SINE200 insertion and, thus, is not subjected to peculiar evolutionary patterns affecting rDNA markers, e.g. incomplete homogenization of the arrays through concerted evolution and/or mixtures of M and S IGS-sequences among the arrays of single chromatids. Conclusion The approach utilized allowed to develop new easy-to-use co-dominant markers for the analysis of genetic differentiation between M and S-forms and opens new perspectives in the study of the speciation process ongoing within A. gambiae.

  15. Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome

    Czech Academy of Sciences Publication Activity Database

    Kubát, Z.; Žlůvová, J.; Vogel, I.; Kováčová, V.; Čermák, T.; Čegan, R.; Hobza, Roman; Vyskot, B.; Kejnovský, E.

    2014-01-01

    Roč. 202, č. 2 (2014), s. 662-678 ISSN 0028-646X R&D Projects: GA ČR GAP501/12/2220 Institutional support: RVO:61389030 Keywords : epigenetics * genome size * long terminal repeat Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.672, year: 2014

  16. Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome

    Czech Academy of Sciences Publication Activity Database

    Kubát, Zdeněk; Žlůvová, Jitka; Vogel, Ivan; Kováčová, Viera; Čermák, Tomáš; Čegan, Radim; Hobza, Roman; Vyskot, Boris; Kejnovský, Eduard

    2014-01-01

    Roč. 202, č. 2 (2014), s. 662-678 ISSN 0028-646X R&D Projects: GA ČR(CZ) GPP501/10/P483; GA ČR(CZ) GAP501/10/0102; GA MŠk(CZ) ED1.1.00/02.0068; GA MŠk(CZ) EE2.3.20.0045; GA MŠk LO1204 Institutional support: RVO:68081707 Keywords : epigenetics * genome size * long terminal repeat Subject RIV: BO - Biophysics Impact factor: 7.672, year: 2014

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

    KAUST Repository

    Chen, Jit Ern; Cui, Guoxin; Wang, Xin; Liew, Yi Jin; Aranda, Manuel

    2017-01-01

    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

  18. Identification of a Novel Retrotransposon with Sex Chromosome-Specific Distribution in Silene latifolia

    Czech Academy of Sciences Publication Activity Database

    Králová, Tereza; Čegan, Radim; Kubát, Zdeněk; Vrána, Jan; Vyskot, Boris; Vogel, Ivan; Kejnovský, Eduard; Hobza, Roman

    2014-01-01

    Roč. 143, 1-3 (2014), s. 87-95 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LM2010005; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GAP501/12/2220; GA ČR(CZ) GAP305/10/0930; GA ČR(CZ) GA522/09/0083; GA MŠk(CZ) LO1204 Institutional support: RVO:68081707 Keywords : Microdissection * Sex chromosomes * Silene latifolia (white campion) Subject RIV: BO - Biophysics; EF - Botanics (UEB-Q) Impact factor: 1.561, year: 2014

  19. PASSIVE CONTROL OF PARTICLE DISPERSION IN A PARTICLE-LADEN CIRCULAR JET USING ELLIPTIC CO-ANNULAR FLOW: A MEANS FOR IMPROVING UTILIZATION AND EMISSION REDUCTIONS IN PULVERIZED COAL BURNER

    Energy Technology Data Exchange (ETDEWEB)

    Ahsan R. Choudhuri

    2003-06-01

    A passive control technology utilizing elliptic co-flow to control the particle flinging and particle dispersion in a particle (coal)-laden flow was investigated using experimental and numerical techniques. Preferential concentration of particles occurs in particle-laden jets used in pulverized coal burner and causes uncontrollable NO{sub x} formation due to inhomogeneous local stoichiometry. This particular project was aimed at characterizing the near-field flow behavior of elliptic coaxial jets. The knowledge gained from the project will serve as the basis of further investigation on fluid-particle interactions in an asymmetric coaxial jet flow-field and thus is important to improve the design of pulverized coal burners where non-homogeneity of particle concentration causes increased NO{sub x} formation.

  20. A Particle X-ray Temporal Diagnostic (PXTD) for studies of kinetic, multi-ion effects, and ion-electron equilibration rates in Inertial Confinement Fusion plasmas at OMEGA (invited)

    International Nuclear Information System (INIS)

    Sio, H.; Frenje, J. A.; Katz, J.; Stoeckl, C.; Weiner, D.

    2016-01-01

    Here, a Particle X-ray Temporal Diagnostic (PXTD) has been implemented on OMEGA for simultaneous time-resolved measurements of several nuclear products as well as the x-ray continuum produced in High Energy Density Plasmas and Inertial Confinement Fusion implosions. The PXTD removes systematic timing uncertainties typically introduced by using multiple instruments, and it has been used to measure DD, DT, D"3He, and T"3He reaction histories and the emission history of the x-ray core continuum with relative timing uncertainties within ±10-20 ps. This enables, for the first time, accurate and simultaneous measurements of the x-ray emission histories, nuclear reaction histories, their time differences, and measurements of T_i(t) and T_e(t) from which an assessment of multiple-ion-fluid effects, kinetic effects during the shock-burn phase, and ion-electron equilibration rates can be made.

  1. Twistor theory a particle-physicist attitude

    International Nuclear Information System (INIS)

    Perjes, Z.

    1979-07-01

    Particle models in twistor theory are reviewed, starting with an introduction into the kinematical-twistor formalism which describes massive particles in Minkowski space-time. The internal transformations of constituent twistors are then discussed. The quantization rules available from a study of twistor scattering situations are used to construct quantum models of fundamental particles. The theory allows the introduction of an internal space with a Kaehlerian metric where hadron structure is described by ''spherical'' states of bound constituents. It is conjectured that the spectrum of successive families of hadrons might approach an accumulation point in energy. Above this threshold energy, the Kaehlerian analog of ionization could occur wherein the zero-mass constituents (twistors) of the particle break free. (author)

  2. Papa, a Particle Tracing Code in Pascal

    NARCIS (Netherlands)

    Haselhoff, E.H.; Haselhoff, Eltjo H.; Ernst, G.J.

    1990-01-01

    During the design of a 10 ¿m high-gain FEL oscillator (TEUFEL Project) we developed a new particle-tracing code to perform simulations of thermionic- and photo-cathode electron injectors/accelerators. The program allows predictions of current, energy and beam emittance in a user-specified linac

  3. ASYMPTOTICS OF a PARTICLES TRANSPORT PROBLEM

    Directory of Open Access Journals (Sweden)

    Kuzmina Ludmila Ivanovna

    2017-11-01

    Full Text Available Subject: a groundwater filtration affects the strength and stability of underground and hydro-technical constructions. Research objectives: the study of one-dimensional problem of displacement of suspension by the flow of pure water in a porous medium. Materials and methods: when filtering a suspension some particles pass through the porous medium, and some of them are stuck in the pores. It is assumed that size distributions of the solid particles and the pores overlap. In this case, the main mechanism of particle retention is a size-exclusion: the particles pass freely through the large pores and get stuck at the inlet of the tiny pores that are smaller than the particle diameter. The concentrations of suspended and retained particles satisfy two quasi-linear differential equations of the first order. To solve the filtration problem, methods of nonlinear asymptotic analysis are used. Results: in a mathematical model of filtration of suspensions, which takes into account the dependence of the porosity and permeability of the porous medium on concentration of retained particles, the boundary between two phases is moving with variable velocity. The asymptotic solution to the problem is constructed for a small filtration coefficient. The theorem of existence of the asymptotics is proved. Analytical expressions for the principal asymptotic terms are presented for the case of linear coefficients and initial conditions. The asymptotics of the boundary of two phases is given in explicit form. Conclusions: the filtration problem under study can be solved analytically.

  4. AMS, a particle spectrometer in space

    International Nuclear Information System (INIS)

    Buenerd, M.; Ohlsson-Malek, F.; Ren, Z.L.; Santos, D.; Thuillier, T.

    1997-01-01

    The Alpha Magnetic Spectrometer (AMS) is a detector designed for extraterrestrial study of anti-matter, matter and dark matter. A precursor flight and on the STS-91 flight of the shuttle is planned to take place on May 1998. AMS will be installed on the International Space Station in January 2002 where it will be operated next, for three to five years. The contributions of the ISN to the project on the shuttle (aerogel threshold Cherenkov counter) as well as the steps to build a RICH detector for AMS on the ISSA are explained here below. (authors)

  5. Process of dosimetry of a particle flux

    Energy Technology Data Exchange (ETDEWEB)

    Francois, H; Heilmann, C; Jacquot, C

    1976-06-25

    The main feature of this dosimetry process is that a nuclear emulsion plate with an emulsion of gelatine and silver bromide microcrystals is subjected to the flux of particles to be measured, that the plate is developed in a standard manner and that the amount of silver thus reduced to the metal state is then analysed by activation. The plate containing the nuclear emulsion irradiated in this way is then developed by the conventional temperature method, the effect of which is to cause traces to appear formed of metal silver particles at those places where ionising particles have penetrated into the emulsion and have given up therein all or part of their energy. Once the plates have been developed, like an ordinary photographic plate, they are then subjected to a neutron flux (nuclear reactor, accelerator, etc.) that activates the silver particles in the emulsion which then become emitters of ..gamma.. radiations which may then be detected to find out the amount of silver present in the plate, which finally is specific of the radiation flux dose received by this plate. A Geiger type gamma ray detector gives a global indication on the mass of silver contained in the emulsion. A more refined method consists in using a multi-channel gamma spectrometer and this makes it possible to have an energy selective dosimetry. The juxtaposition of several separate plates each having its own sensitivity in a given energy band enable a veritable 'sandwhich' of several plates to be made.

  6. Precision siting of a particle accelerator

    International Nuclear Information System (INIS)

    Cintra, Jorge Pimentel

    1996-01-01

    Precise location is a specific survey job that involves a high skilled work to avoid unrecoverable results at the project installation. As a function of the different process stages, different specifications can be applied, invoking different instruments: theodolite, measurement tape, distanciometer, invar wire. This paper, based on experience obtained at the installation of particle accelerator equipment, deals with general principles of precise location: tolerance definitions, increasing accuracy techniques, schedule of locations, sensitivity analysis, quality control methods. (author)

  7. Plasma memories associated to a particle detector

    International Nuclear Information System (INIS)

    Comby, G.; Mangeot, Ph.

    1978-01-01

    The realization of a localized and persisting memory of a detected particle which can be easily read out offers new possibilities for the detection of events with high multiplicity. The association of the plasma memory to a spark chamber allows the test of the principles of memorization and read-out. By means of one gap of plasma memories, one can read out without ambiguity the coordinates of a large number of memories. This device can be adapted to other types of detectors and also to larger geometries. (Auth.)

  8. Matter and Interactions: a particle physics perspective

    OpenAIRE

    Organtini, Giovanni

    2011-01-01

    In classical mechanics matter and fields are completely separated. Matter interacts with fields. For particle physicists this is not the case. Both matter and fields are represented by particles. Fundamental interactions are mediated by particles exchanged between matter particles. In this paper we explain why particle physicists believe in such a picture, introducing the technique of Feynman diagrams starting from very basic and popular analogies with classical mechanics, making the physics ...

  9. Desirable Elements for a Particle System Interface

    Directory of Open Access Journals (Sweden)

    Daniel Schroeder

    2014-01-01

    Full Text Available Particle systems have many applications, with the most popular being to produce special effects in video games and films. To permit particle systems to be created quickly and easily, Particle System Interfaces (PSIs have been developed. A PSI is a piece of software designed to perform common tasks related to particle systems for clients, while providing them with a set of parameters whose values can be adjusted to create different particle systems. Most PSIs are inflexible, and when clients require functionality that is not supported by the PSI they are using, they are forced to either find another PSI that meets their requirements or, more commonly, create their own particle system or PSI from scratch. This paper presents three original contributions. First, it identifies 18 features that a PSI should provide in order to be capable of creating diverse effects. If these features are implemented in a PSI, clients will be more likely to be able to accomplish all desired effects related to particle systems with one PSI. Secondly, it introduces a novel use of events to determine, at run time, which particle system code to execute in each frame. Thirdly, it describes a software architecture called the Dynamic Particle System Framework (DPSF. Simulation results show that DPSF possesses all 18 desirable features.

  10. Evolution of metastable state molecules N{sub 2}(A{sup 3}{Sigma}{sub u}{sup +}) in a nanosecond pulsed discharge: A particle-in-cell/Monte Carlo collisions simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gao Liang; Sun Jizhong; Feng Chunlei; Bai Jing; Ding Hongbin [School of Physics and Optical Electronic Technology, Key Laboratory of Materials Modification by Laser, Ion, and Electron Beams, Chinese Ministry of Education, Dalian University of Technology, Dalian 116024 (China)

    2012-01-15

    A particle-in-cell plus Monte Carlo collisions method has been employed to investigate the nitrogen discharge driven by a nanosecond pulse power source. To assess whether the production of the metastable state N{sub 2}(A{sup 3}{Sigma}{sub u}{sup +}) can be efficiently enhanced in a nanosecond pulsed discharge, the evolutions of metastable state N{sub 2}(A{sup 3}{Sigma}{sub u}{sup +}) density and electron energy distribution function have been examined in detail. The simulation results indicate that the ultra short pulse can modulate the electron energy effectively: during the early pulse-on time, high energy electrons give rise to quick electron avalanche and rapid growth of the metastable state N{sub 2}(A{sup 3}{Sigma}{sub u}{sup +}) density. It is estimated that for a single pulse with amplitude of -9 kV and pulse width 30 ns, the metastable state N{sub 2}(A{sup 3}{Sigma}{sub u}{sup +}) density can achieve a value in the order of 10{sup 9} cm{sup -3}. The N{sub 2}(A{sup 3}{Sigma}{sub u}{sup +}) density at such a value could be easily detected by laser-based experimental methods.

  11. Endogenous retroviruses mobilized during friend murine leukemia virus infection.

    Science.gov (United States)

    Boi, Stefano; Rosenke, Kyle; Hansen, Ethan; Hendrick, Duncan; Malik, Frank; Evans, Leonard H

    2016-12-01

    We have demonstrated in a mouse model that infection with a retrovirus can lead not only to the generation of recombinants between exogenous and endogenous gammaretrovirus, but also to the mobilization of endogenous proviruses by pseudotyping entire polytropic proviral transcripts and facilitating their infectious spread to new cells. However, the frequency of this occurrence, the kinetics, and the identity of mobilized endogenous proviruses was unclear. Here we find that these mobilized transcripts are detected after only one day of infection. They predominate over recombinant polytropic viruses early in infection, persist throughout the course of disease and are comprised of multiple different polytropic proviruses. Other endogenous retroviral elements such as intracisternal A particles (IAPs) were not detected. The integration of the endogenous transcripts into new cells could result in loss of transcriptional control and elevated expression which may facilitate pathogenesis, perhaps by contributing to the generation of polytropic recombinant viruses. Published by Elsevier Inc.

  12. Insertion of an SVA element, a nonautonomous retrotransposon, in PMS2 intron 7 as a novel cause of Lynch syndrome.

    Science.gov (United States)

    van der Klift, Heleen M; Tops, Carli M; Hes, Frederik J; Devilee, Peter; Wijnen, Juul T

    2012-07-01

    Heterozygous germline mutations in the mismatch repair gene PMS2 predispose carriers for Lynch syndrome, an autosomal dominant predisposition to cancer. Here, we present a LINE-1-mediated retrotranspositional insertion in PMS2 as a novel mutation type for Lynch syndrome. This insertion, detected with Southern blot analysis in the genomic DNA of the patient, is characterized as a 2.2 kb long 5' truncated SVA_F element. The insertion is not detectable by current diagnostic testing limited to MLPA and direct Sanger sequencing on genomic DNA. The molecular nature of this insertion could only be resolved in RNA from cultured lymphocytes in which nonsense-mediated RNA decay was inhibited. Our report illustrates the technical problems encountered in the detection of this mutation type. Especially large heterozygous insertions will remain unnoticed because of preferential amplification of the smaller wild-type allele in genomic DNA, and are probably underreported in the mutation spectra of autosomal dominant disorders. © 2012 Wiley Periodicals, Inc.

  13. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors

    DEFF Research Database (Denmark)

    Lennartsson, Andreas; Arner, Erik; Fagiolini, Michela

    2015-01-01

    BACKGROUND: The capacity for plasticity in the adult brain is limited by the anatomical traces laid down during early postnatal life. Removing certain molecular brakes, such as histone deacetylases (HDACs), has proven to be effective in recapitulating juvenile plasticity in the mature visual cortex...... and reactivate plasticity in the adult cortex. CONCLUSIONS: Treatment with HDAC inhibitors increases accessibility to enhancers and repetitive elements underlying brain-specific gene expression and reactivation of visual cortical plasticity....

  14. Linking Maternal and Somatic 5S rRNA types with Different Sequence-Specific Non-LTR Retrotransposons

    NARCIS (Netherlands)

    Locati, M.D.; Pagano, J.F.B.; Ensink, W.A.; van Olst, M.; van Leeuwen, S.; Nehrdich, U.; Zhu, K.; Spaink, H.P.; Girard, G.; Rauwerda, H.; Jonker, M.J.; Dekker, R.J.; Breit, T.M.

    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,

  15. Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer

    NARCIS (Netherlands)

    Stacey, S.N.; Kehr, B.; Gudmundsson, J.; Zink, F.; Jonasdottir, A.; Gudjonsson, S.A.; Sigurdsson, A.; Halldorsson, B.V.; Agnarsson, B.A.; Benediktsdottir, K.R.; Aben, K.K.; Vermeulen, S.H.; Cremers, R.G.; Panadero, A.; Helfand, B.T.; Cooper, P.R.; Donovan, J.L.; Hamdy, F.C.; Jinga, V.; Okamoto, I.; Jonasson, J.G.; Tryggvadottir, L.; Johannsdottir, H.; Kristinsdottir, A.M.; Masson, G.; Magnusson, O.T.; Iordache, P.D.; Helgason, A.; Helgason, H.; Sulem, P.; Gudbjartsson, D.F.; Kong, A.; Jonsson, E.; Barkardottir, R.B.; Einarsson, G.V.; Rafnar, T.; Thorsteinsdottir, U.; Mates, I.N.; Neal, D.E.; Catalona, W.J.; Mayordomo, J.I.; Kiemeney, L.A.; Thorleifsson, G.; Stefansson, K.

    2016-01-01

    Transcriptional and splicing anomalies have been observed in intron 8 of the CASP8 gene (encoding procaspase-8) in association with cutaneous basal-cell carcinoma (BCC) and linked to a germline SNP rs700635. Here, we show that the rs700635[C] allele, which is associated with increased risk of BCC

  16. Retrotransposon and gene activation in wheat in response to mycotoxigenic and non-mycotoxigenic-associated Fusarium stress

    DEFF Research Database (Denmark)

    Ansari, Khairul Islam; Walter, Stephanie; Brennan, Josephine M.

    2007-01-01

    Despite inhibition of protein synthesis being its mode of action, the trichothecene mycotoxin deoxynivalenol (DON) induced accumulation of transcripts encoding translation elongation factor 1 alpha (EF-1 alpha), class III plant peroxidase (POX), structure specific recognition protein, basic leuci...

  17. Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies

    Czech Academy of Sciences Publication Activity Database

    Ambrožová, K.; Mandáková, T.; Bureš, P.; Neumann, Pavel; Leitch, I. J.; Koblížková, Andrea; Macas, Jiří; Lysák, M.

    2011-01-01

    Roč. 107, č. 2 (2011), s. 255-268 ISSN 0305-7364 R&D Projects: GA ČR GA521/07/0284; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : Fritillaria * Liliaceae * repetitive DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.030, year: 2011

  18. A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation.

    Science.gov (United States)

    Pislariu, Catalina I; Murray, Jeremy D; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; Benedito, Vagner A; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S; Chen, Rujin; Udvardi, Michael K

    2012-08-01

    A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.

  19. Generalized study of the return to equilibrium of a particle in a plasma (Fokker-Planck formalism) (1961); Etude generale du retour a l'equilibre d'une particule au sein d'un plasma (formalisme de Fokker-Planck) (1961)

    Energy Technology Data Exchange (ETDEWEB)

    Salmon, J [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires; Faculte des Sciences de Caen, 14 (France)

    1961-07-01

    The author examines the problem of the return to equilibrium of a particle in a plasma and completely explains Fokker-Planck equation. After that, he studies the possibility of interpreting the return of the test particle to Maxwellian distribution, using the development - which is obtained. He discusses the validity limits of the Rosenbluth, MacDonald and Judd approximation. (author) [French] Examinant le probleme du retour a l'equilibre d'une particule test au sein d'un plasma en equilibre, l'auteur cherche a expliciter completement l'expression de l'operateur de Fokker-Planck. Il etudie ensuite les conditions de coherence, c'est-a-dire la possibilite pour le developpement obtenu de traduire le retour de la particule test a l'etat maxwellien et discute des limites de validite de la formule de 'Rosenbluth, Mac Donald et Judd'. (auteur)

  20. Vectorization of a particle simulation method for hypersonic rarefied flow

    Science.gov (United States)

    Mcdonald, Jeffrey D.; Baganoff, Donald

    1988-01-01

    An efficient particle simulation technique for hypersonic rarefied flows is presented at an algorithmic and implementation level. The implementation is for a vector computer architecture, specifically the Cray-2. The method models an ideal diatomic Maxwell molecule with three translational and two rotational degrees of freedom. Algorithms are designed specifically for compatibility with fine grain parallelism by reducing the number of data dependencies in the computation. By insisting on this compatibility, the method is capable of performing simulation on a much larger scale than previously possible. A two-dimensional simulation of supersonic flow over a wedge is carried out for the near-continuum limit where the gas is in equilibrium and the ideal solution can be used as a check on the accuracy of the gas model employed in the method. Also, a three-dimensional, Mach 8, rarefied flow about a finite-span flat plate at a 45 degree angle of attack was simulated. It utilized over 10 to the 7th particles carried through 400 discrete time steps in less than one hour of Cray-2 CPU time. This problem was chosen to exhibit the capability of the method in handling a large number of particles and a true three-dimensional geometry.

  1. Optimization of a particle optical system in a mutilprocessor environment

    International Nuclear Information System (INIS)

    Wei Lei; Yin Hanchun; Wang Baoping; Tong Linsu

    2002-01-01

    In the design of a charged particle optical system, many geometrical and electric parameters have to be optimized to improve the performance characteristics. In every optimization cycle, the electromagnetic field and particle trajectories have to be calculated. Therefore, the optimization of a charged particle optical system is limited by the computer resources seriously. Apart from this, numerical errors of calculation may also influence the convergence of merit function. This article studies how to improve the optimization of charged particle optical systems. A new method is used to determine the gradient matrix. With this method, the accuracy of the Jacobian matrix can be improved. In this paper, the charged particle optical system is optimized with a Message Passing Interface (MPI). The electromagnetic field, particle trajectories and gradients of optimization variables are calculated on networks of workstations. Therefore, the speed of optimization has been increased largely. It is possible to design a complicated charged particle optical system with optimum quality on a MPI environment. Finally, an electron gun for a cathode ray tube has been optimized on a MPI environment to verify the method proposed in this paper

  2. Quantum dynamics of a particle in a tracking chamber

    International Nuclear Information System (INIS)

    Figari, Rodolfo; INFN, Napoli; Teta, Alessandro

    2014-01-01

    In the original formulation of quantum mechanics the existence of a precise border between a microscopic world, governed by quantum mechanics, and a macroscopic world, described by classical mechanics was assumed. Modern theoretical and experimental physics has moved that border several times, carefully investigating its definition and making available to observation larger and larger quantum systems. The present book examines a paradigmatic case of the transition from quantum to classical behavior: A quantum particle is revealed in a tracking chamber as a trajectory obeying the laws of classical mechanics. The authors provide here a purely quantum-mechanical description of this behavior, thus helping to illuminate the nature of the border between the quantum and the classical.

  3. MCPLOTS: a particle physics resource based on volunteer computing

    CERN Document Server

    Karneyeu, A; Prestel, S; Skands, P Z

    2014-01-01

    The mcplots.cern.ch web site (MCPLOTS) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the HEPDATA online database of experimental results and on the RIVET Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the LHC@HOME platform.

  4. A particle-based method for granular flow simulation

    KAUST Repository

    Chang, Yuanzhang; Bao, Kai; Zhu, Jian; Wu, Enhua

    2012-01-01

    We present a new particle-based method for granular flow simulation. In the method, a new elastic stress term, which is derived from a modified form of the Hooke's law, is included in the momentum governing equation to handle the friction of granular materials. Viscosity force is also added to simulate the dynamic friction for the purpose of smoothing the velocity field and further maintaining the simulation stability. Benefiting from the Lagrangian nature of the SPH method, large flow deformation can be well handled easily and naturally. In addition, a signed distance field is also employed to enforce the solid boundary condition. The experimental results show that the proposed method is effective and efficient for handling the flow of granular materials, and different kinds of granular behaviors can be well simulated by adjusting just one parameter. © 2012 Science China Press and Springer-Verlag Berlin Heidelberg.

  5. SSCTRK: A particle tracking code for the SSC

    International Nuclear Information System (INIS)

    Ritson, D.

    1990-07-01

    While many indirect methods are available to evaluate dynamic aperture there appears at this time to be no reliable substitute to tracking particles through realistic machine lattices for a number of turns determined by the storage times. Machine lattices are generated by ''Monte Carlo'' techniques from the expected rms fabrication and survey errors. Any given generated machine can potentially be a lucky or unlucky fluctuation from the average. Therefore simulation to serve as a predictor of future performance must be done for an ensemble of generated machines. Further, several amplitudes and momenta are necessary to predict machine performance. Thus to make Monte Carlo type simulations for the SSC requires very considerable computer resources. Hitherto, it has been assumed that this was not feasible, and alternative indirect methods have been proposed or tried to answer the problem. We reexamined the feasibility of using direct computation. Previous codes have represented lattices by a succession of thin elements separated by bend-drifts. With ''kick-drift'' configurations, tracking time is linear in the multipole order included, and the code is symplectic. Modern vector processors simultaneously handle a large number of cases in parallel. Combining the efficiencies of kick drift tracking with vector processing, in fact, makes realistic Monte Carlo simulation entirely feasible. SSCTRK uses the above features. It is structured to have a very friendly interface, a very wide latitude of choice for cases to be run in parallel, and, by using pure FORTRAN 77, to interchangeably run on a wide variety of computers. We describe in this paper the program structure operational checks and results achieved

  6. Thermal contact resistance of a particle on a substrate

    International Nuclear Information System (INIS)

    Tan, J.; Safa, H.; Bonin, B.

    1996-01-01

    It has been formerly established that field emission in RF cavities is mainly die to contamination by small micron size particles lying on the surface. When applying the RF field, these particles can melt and stick to the surface making it harder to get rid of them. In order to understand the thermal process involved, a crucial physical quantity is needed: the thermal contact resistance between the particle and the substrate. In the present paper, an experimental method is described to measure this quantity, with the use of a scanning electron microscope. By defocusing the beam of the SEM, one can get enough power deposited in one particle to melt it. The power level at which the particle melts gives the thermal contact resistance. Therefore, using the measured value, thermal calculations yield some hints for understanding the violent thermal processes observed in RF fields. (author)

  7. Thermal contact resistance of a particle on a substrate

    International Nuclear Information System (INIS)

    Tan, J.; Safa, H.; Bonin, B.

    1996-01-01

    It has been formerly established that field emission in RF cavities is mainly due to contamination by small micron size particles lying on the surface. When applying the RF field, these particles can melt and stick to the surface making it harder to get rid of them. In order to understand the thermal process involved, a crucial physical quantity is needed: the thermal contact resistance between the particle and the substrate. An experimental method is described to measure this quantity, with the use of a scanning electron microscope. By defocusing the beam of the SEM, one can get enough power deposited in one particle to melt it. The power level at which the particle melts gives the thermal contact resistance. Therefore, using the measured value, thermal calculations yield some hints for understanding the violent thermal processes observed in RF fields. (author)

  8. Dynamics of a particle with friction and delay

    Science.gov (United States)

    Monteiro Marques, Manuel D. P.; Dzonou, Raoul

    2018-03-01

    We are interested in the motion of a simple mechanical system having a finite number of degrees of freedom subjected to a unilateral constraint with dry friction and delay effects (with maximal duration τ > 0). At the contact point, we characterize the friction by a Coulomb law associated with a friction cone. Starting from a formulation of the problem that was given by Jean-Jacques Moreau in the form of a second-order differential inclusion in the sense of measures, we consider a sweeping process algorithm that converges towards a solution to the dynamical contact problem. The mathematical machinery as well as the general plan of the existence proof may seem much too heavy in order to treat just this simple case, but they have proved useful in more complex settings. xml:lang="fr"

  9. Quantum interference of position and momentum: A particle propagation paradox

    Science.gov (United States)

    Hofmann, Holger F.

    2017-08-01

    Optimal simultaneous control of position and momentum can be achieved by maximizing the probabilities of finding their experimentally observed values within two well-defined intervals. The assumption that particles move along straight lines in free space can then be tested by deriving a lower limit for the probability of finding the particle in a corresponding spatial interval at any intermediate time t . Here, it is shown that this lower limit can be violated by quantum superpositions of states confined within the respective position and momentum intervals. These violations of the particle propagation inequality show that quantum mechanics changes the laws of motion at a fundamental level, providing a different perspective on causality relations and time evolution in quantum mechanics.

  10. A Particle of Indefiniteness in American Sign Language

    Directory of Open Access Journals (Sweden)

    Carol Neidle

    2003-01-01

    Full Text Available We describe here the characteristics of a very frequently-occurring ASL indefinite focus particle, which has not previously been recognized as such. We show here that, despite its similarity to the question sign "WHAT", the particle is distinct from that sign in terms of articulation, function, and distribution. The particle serves to express "uncertainty" in various ways, which can be formalized semantically in terms of a domain-widening effect of the same sort as that proposed for English "any" by Kadmon & Landman (1993. Its function is to widen the domain of possibilities under consideration from the typical to include the non-typical as well, along a dimension appropriate in the context.

  11. BOA, Beam Optics Analyzer A Particle-In-Cell Code

    International Nuclear Information System (INIS)

    Bui, Thuc

    2007-01-01

    The program was tasked with implementing time dependent analysis of charges particles into an existing finite element code with adaptive meshing, called Beam Optics Analyzer (BOA). BOA was initially funded by a DOE Phase II program to use the finite element method with adaptive meshing to track particles in unstructured meshes. It uses modern programming techniques, state-of-the-art data structures, so that new methods, features and capabilities are easily added and maintained. This Phase II program was funded to implement plasma simulations in BOA and extend its capabilities to model thermal electrons, secondary emissions, self magnetic field and implement a more comprehensive post-processing and feature-rich GUI. The program was successful in implementing thermal electrons, secondary emissions, and self magnetic field calculations. The BOA GUI was also upgraded significantly, and CCR is receiving interest from the microwave tube and semiconductor equipment industry for the code. Implementation of PIC analysis was partially successful. Computational resource requirements for modeling more than 2000 particles begin to exceed the capability of most readily available computers. Modern plasma analysis typically requires modeling of approximately 2 million particles or more. The problem is that tracking many particles in an unstructured mesh that is adapting becomes inefficient. In particular memory requirements become excessive. This probably makes particle tracking in unstructured meshes currently unfeasible with commonly available computer resources. Consequently, Calabazas Creek Research, Inc. is exploring hybrid codes where the electromagnetic fields are solved on the unstructured, adaptive mesh while particles are tracked on a fixed mesh. Efficient interpolation routines should be able to transfer information between nodes of the two meshes. If successfully developed, this could provide high accuracy and reasonable computational efficiency.

  12. Double layer -- a particle accelerator in the magnetosphere

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Xiangrong [Los Alamos National Laboratory

    2015-07-16

    Slides present the material under the following topics: Introduction (What is a double layer (DL)? Why is it important? Key unsolved problems); Theory -- time-independent solutions of 1D Vlasov--Poisson system; Particle-in-cell simulations (Current-driven DLs); and Electron acceleration by DL (Betatron acceleration). Key problems include the generation mechanism, stability, and electron acceleration. In summary, recent observations by Van Allen Probes show large number of DLs in the outer radiation belt, associated with enhanced flux of relativistic electrons. Simulations show that ion acoustic double layers can be generated by field-aligned currents. Thermal electrons can gain energy via betatron acceleration in a dipole magnetic field.

  13. Gone to Dust: Building and Deploying a Particle Sensor

    Science.gov (United States)

    Fibiger, D. L.; Wiley, C.

    2015-12-01

    Using an Arduino microcontroller board and a commercially available optical particle sensor, we built particulate sensors and walked them around the school to evaluate where the highest levels of particulate matter (PM) were. As part of the Earth Explorers outreach program in Boulder, Colorado, we worked with a group of middle school students to build and use these sensors. The students were in 6th and 7th grade, and we met three times. Once to introduce the scientist and science they will be working on, the second time to actually do the hand-on project and, finally, to review what they learned in the experiment. Arduino is an open-source electronics platform that is simple to program, using the Arduino programming language. There are example codes available for the particle sensors and they are easy to adapt to different uses. The sensor setup is straightforward and was built into a small footprint on a plastic toy brick with a handle for easy use. We pre-loaded the Arduino board with the necessary software, but had the students wire the sensor, Arduino, indicator lights and battery together and attached them to the brick. This gave the students an opportunity to learn about electricity and wiring, in addition to air pollution. The sensor is not calibrated or quantitative, so only qualitative data was obtained. The qualitative data, however, was sufficient to allow the students to make predictions and test their hypotheses. While most of the students predicted outside, near the parking lot would have the highest PM levels, they learned that indoor pollution can be much higher, particularly in carpeted areas.

  14. Complex dynamics of a particle in an oscillating potential field

    Indian Academy of Sciences (India)

    Barnali Pal

    2017-07-25

    Jul 25, 2017 ... ble spirals or stable nodes of the system depending on μ. If the time-dependent part of ... ble node for B > A or a stable node for B < A. If. 2 < 0, the equilibrium ...... of the controller. Therefore, the .... Signal Process. Control 15, 1.

  15. Model Adaptation for Prognostics in a Particle Filtering Framework

    Data.gov (United States)

    National Aeronautics and Space Administration — One of the key motivating factors for using particle filters for prognostics is the ability to include model parameters as part of the state vector to be estimated....

  16. PHITS-a particle and heavy ion transport code system

    International Nuclear Information System (INIS)

    Niita, Koji; Sato, Tatsuhiko; Iwase, Hiroshi; Nose, Hiroyuki; Nakashima, Hiroshi; Sihver, Lembit

    2006-01-01

    The paper presents a summary of the recent development of the multi-purpose Monte Carlo Particle and Heavy Ion Transport code System, PHITS. In particular, we discuss in detail the development of two new models, JAM and JQMD, for high energy particle interactions, incorporated in PHITS, and show comparisons between model calculations and experiments for the validations of these models. The paper presents three applications of the code including spallation neutron source, heavy ion therapy and space radiation. The results and examples shown indicate PHITS has great ability of carrying out the radiation transport analysis of almost all particles including heavy ions within a wide energy range

  17. A particle method for history-dependent materials

    Energy Technology Data Exchange (ETDEWEB)

    Sulsky, D.; Chen, Z.; Schreyer, H.L. [New Mexico Univ., Albuquerque, NM (United States)

    1993-06-01

    A broad class of engineering problems including penetration, impact and large rotations of solid bodies causes severe numerical problems. For these problems, the constitutive equations are history dependent so material points must be followed; this is difficult to implement in an Eulerian scheme. On the other hand, purely Lagrangian methods typically result in severe mesh distortion and the consequence is ill conditioning of the element stiffness matrix leading to mesh lockup or entanglement. Remeshing prevents the lockup and tangling but then interpolation must be performed for history dependent variables, a process which can introduce errors. Proposed here is an extension of the particle-in-cell method in which particles are interpreted to be material points that are followed through the complete loading process. A fixed Eulerian grid provides the means for determining a spatial gradient. Because the grid can also be interpreted as an updated Lagrangian frame, the usual convection term in the acceleration associated with Eulerian formulations does not appear. With the use of maps between material points and the grid, the advantages of both Eulerian and Lagrangian schemes are utilized so that mesh tangling is avoided while material variables are tracked through the complete deformation history. Example solutions in two dimensions are given to illustrate the robustness of the proposed convection algorithm and to show that typical elastic behavior can be reproduced. Also, it is shown that impact with no slip is handled without any special algorithm for bodies governed by elasticity and strain hardening plasticity.

  18. Multidimensional and memory effects on diffusion of a particle

    International Nuclear Information System (INIS)

    Bao, Jing-Dong

    2001-01-01

    The diffusion of an overdamped Brownian particle in the two-dimensional (2D) channel bounded periodically by a parabola is studied, where the particle is subject to an additive white or colored noise. The diffusion rate constant D * of the particle is evaluated by the quasi-2D approximation and the effective potential approach, and the theoretical result is compared with the Langevin simulation. The properties of the diffusion rate constant are stressed for weak and strong noise cases. It is shown that, in an entropy channel, the value of D * in units of Q decreases with increasing intensity of the colored noise. In the presence of energetic barriers, a nonmonotonic behavior of the reduced diffusion rate constant D * Q -1 as a function of the noise intensity is shown

  19. Go on a particle quest at the first CERN webfest

    CERN Multimedia

    Andrew Purcell

    2012-01-01

    From 3 to 5 August, CERN played host to its very first webfest. Organised by the Citizen Cyberscience Centre (CCC) and the Peer 2 Peer University, the 2012 CERN Webfest saw pizza-fuelled summer students hacking their way almost non-stop through an entire weekend to produce a host of weird and wonderful innovations. As each of the teams raced against time in the hope of winning the grand prize of a trip to the Mozilla festival in London, sleep was hard for the students to come by, but fortunately great ideas were not.   Particle quest sprites. Source: André-Pierre Olivier. Projects dreamt up by the students included a browser-based dashboard for the Large Hadron Collider (LHC), a new CERN open-data initiative, and a virtual world for the LHC@home platform.  However, the highlight of the event was the ParticleQuest game, which was selected by a panel of judges as the weekend’s overal...

  20. Beam collimator for a particle accelerator. [German patent

    Energy Technology Data Exchange (ETDEWEB)

    Benedetti, R

    1977-12-01

    The beam collimator for the electron beam coming from an electron accelerator consists of aperture plates and penumbra trimmers aligned parallel to them. To protect the patient from scattered radiation, additional tube plates are arranged between the radiation source and the patient. Continuous matching of the radiation field to the dimensions of a focus is achieved by providing a support plate outside the beam path which holds the tube plates. In this arrangement, the tube plates are aligned parallel to the edges of the aperture plates limiting the beam cone. The tube plates have different widths. They can be moved out of the beam path. Lining the inner walls of the tube plates with acrylic glass prevents the generation of secondary electrons and X-rays.

  1. MCPLOTS. A particle physics resource based on volunteer computing

    Energy Technology Data Exchange (ETDEWEB)

    Karneyeu, A. [Joint Inst. for Nuclear Research, Moscow (Russian Federation); Mijovic, L. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Irfu/SPP, CEA-Saclay, Gif-sur-Yvette (France); Prestel, S. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Lund Univ. (Sweden). Dept. of Astronomy and Theoretical Physics; Skands, P.Z. [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

    2013-07-15

    The mcplots.cern.ch web site (MCPLOTS) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the HEPDATA online database of experimental results and on the RIVET Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the LHC rate at HOME 2.0 platform.

  2. Study on a particle separator using ultrasonic wave

    International Nuclear Information System (INIS)

    Lee, Young Seop; Kwon, Jae Hwa; Seo, Dae Chul; Yun, Dong Jin

    2005-01-01

    This paper presents the theory, design and evaluation of a smart device for the enhanced separation of particles mixed in fluid. The smart device takes advantage of the ultrasonic standing wave, which was generated by the operation of a piezoceramic PZT patch installed in the smart device. The details of the device design including the electro-acoustical modelling for separation and PZT transducer are described at the first. Based on this design, the separation device was fabricated and evaluated. In the experiments, an optical camera with a zoom lense was used to monitor the position of interested particles within the separation channel layer in the device. The electric impedance of the PZT patch bonded on the separation device was measured. The device shows a strong levitation and separation force against 50m diameter particles mixed with water at the separation channel in the device. Experimental results also showed that the device can work at both heavy and light sand particles mixed with water due to the generated standing wave field in the separation channel.

  3. Gauge invariance of a particle in an external magnetic field

    International Nuclear Information System (INIS)

    Ekstein, H.

    1978-12-01

    In the accepted theory of a nonrelativistic particle in an external field, as well as in the Dirac equation, the canonical momentum p plays a strangely elusive role: contrary to the position q, it has no physical interpretation, yet it is a member of the algebra of observables; nor does it have a well-defined meaning as a translation generator. This paper proposes an observation procedure for p which entails a definite choice for the vector potential A: the radiation gauge divergence of A=0. The canonical momentum, so defined operationally, is shown to be the image of the generator of space translations, in the sense of presymmetry, as the position q is the image of the generator of Galilei boosts in nonrelativistic theories

  4. A particle finite element method for machining simulations

    Science.gov (United States)

    Sabel, Matthias; Sator, Christian; Müller, Ralf

    2014-07-01

    The particle finite element method (PFEM) appears to be a convenient technique for machining simulations, since the geometry and topology of the problem can undergo severe changes. In this work, a short outline of the PFEM-algorithm is given, which is followed by a detailed description of the involved operations. The -shape method, which is used to track the topology, is explained and tested by a simple example. Also the kinematics and a suitable finite element formulation are introduced. To validate the method simple settings without topological changes are considered and compared to the standard finite element method for large deformations. To examine the performance of the method, when dealing with separating material, a tensile loading is applied to a notched plate. This investigation includes a numerical analysis of the different meshing parameters, and the numerical convergence is studied. With regard to the cutting simulation it is found that only a sufficiently large number of particles (and thus a rather fine finite element discretisation) leads to converged results of process parameters, such as the cutting force.

  5. One century of cosmic rays – A particle physicist's view

    Directory of Open Access Journals (Sweden)

    Sutton Christine

    2015-01-01

    Full Text Available Experiments on cosmic rays and the elementary particles share a common history that dates back to the 19th century. Following the discovery of radioactivity in the 1890s, the paths of the two fields intertwined, especially during the decades after the discovery of cosmic rays. Experiments demonstrated that the primary cosmic rays are positively charged particles, while other studies of cosmic rays revealed various new sub-atomic particles, including the first antiparticle. Techniques developed in common led to the birth of neutrino astronomy in 1987 and the first observation of a cosmic γ-ray source by a ground-based cosmic-ray telescope in 1989.

  6. MCPLOTS: a particle physics resource based on volunteer computing

    International Nuclear Information System (INIS)

    Karneyeu, A.; Mijovic, L.; Prestel, S.; Skands, P.Z.

    2014-01-01

    The mcplots.cern.ch web site (mcplots) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the hepdata online database of experimental results and on the rivet Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the lhc rate at home 2.0 platform. (orig.)

  7. Vectorization of a particle simulation method for hypersonic rarefied flow

    International Nuclear Information System (INIS)

    Mcdonald, J.D.; Baganoff, D.

    1988-01-01

    An efficient particle simulation technique for hypersonic rarefied flows is presented at an algorithmic and implementation level. The implementation is for a vector computer architecture, specifically the Cray-2. The method models an ideal diatomic Maxwell molecule with three translational and two rotational degrees of freedom. Algorithms are designed specifically for compatibility with fine grain parallelism by reducing the number of data dependencies in the computation. By insisting on this compatibility, the method is capable of performing simulation on a much larger scale than previously possible. A two-dimensional simulation of supersonic flow over a wedge is carried out for the near-continuum limit where the gas is in equilibrium and the ideal solution can be used as a check on the accuracy of the gas model employed in the method. Also, a three-dimensional, Mach 8, rarefied flow about a finite-span flat plate at a 45 degree angle of attack was simulated. It utilized over 10 to the 7th particles carried through 400 discrete time steps in less than one hour of Cray-2 CPU time. This problem was chosen to exhibit the capability of the method in handling a large number of particles and a true three-dimensional geometry. 14 references

  8. Determination of Beam Intensity and Position in a Particle Accelerator

    CERN Document Server

    Kasprowicz, Grzegorz; Raich, Uli

    2011-10-04

    A subject of the thesis is conception, design, implementation, tests and deployment of new position measurement system of particle bunch in the CERN PS circular accelerator. The system is based on novel algorithms of particle position determination. The Proton Synchrotron accelerator (PS), installed at CERN†, although commissioned in 1959, still plays a central role in the production of beams for the Antiproton Decelerator, Super Proton Synchrotron, various experimental areas and for the Large Hadron Collider (LHC)‡. The PS produces beams of different types of particles, mainly protons, but also various species of ions. Almost all these particle beams pass through the PS. The quality of the beams delivered to the LHC has a direct impact on the effective luminosity, and therefore the performance of the instrumentation of the PS is of great importance. The old trajectory and orbit measurement system of the PS is dated back to 1988 and no longer fulfilled present day requirements. It used 40 beam posi...

  9. Determination of beam intensity and position in a particle accelerator

    CERN Document Server

    Kasprowicz, G

    2011-01-01

    A subject of the thesis is conception, design, implementation, tests and deployment of new position measurement system of particle bunch in the CERN PS circular accelerator. The system is based on novel algorithms of particle position determination. The Proton Synchrotron accelerator (PS), installed at CERN, although commissioned in 1959, still plays a central role in the production of beams for the Antiproton Decelerator, Super Proton Synchrotron, various experimental areas and for the Large Hadron Collider (LHC). The PS produces beams of different types of particles, mainly protons, but also various species of ions. Almost all these particle beams pass through the PS. The quality of the beams delivered to the LHC has a direct impact on the effective luminosity, and therefore the performance of the instrumentation of the PS is of great importance. The old trajectory and orbit measurement system of the PS is dated back to 1988 and no longer fulfilled present day requirements. It used 40 beam position monitors...

  10. Determination of Beam Intensity and Position in a Particle Accelerator

    CERN Document Server

    Kasprowicz, Grzegorz

    2010-01-01

    The Proton Synchrotron accelerator (PS), installed at CERN, although commissioned in 1959, still plays a central role in the production of beams for the Antiproton Decelerator, Super Proton Synchrotron, various experimental areas and for the Large Hadron Collider (LHC). The PS produces beams of different types of particles, mainly protons, but also various species of ions. Almost all these particle beams pass through the PS. The quality of the beams delivered to the LHC has a direct impact on the effective luminosity, and therefore the performance of the instrumentation of the PS is of great importance. The old trajec- tory and orbit measurement system of the PS dated back to 1988 and no longer fulfilled present day requirements. It used 40 beam position monitors (BPMs) and an analogue signal processing chain to acquire the trajectory of one single particle bunch out of many, over two consecutive turns at a maximum rate of once every 5ms. The BPMs were in good condition, however the electronics was aging and ...

  11. DIRC - a particle identification system for BaBar

    International Nuclear Information System (INIS)

    Hoecker, A.

    1999-10-01

    The DIRC (an acronym for Detection of Internally Reflected Cherenkov light) is a novel type of Cherenkov imaging device that has been developed, built and installed as part of the BaBar detector at the asymmetric B-factory PEP-II at SLAC. The DIRC is based on total internal reflection of Cherenkov photons produced and guided within thin, rectangular quartz bars covering the barrel region of BaBar. The photon detector is an array of photomultiplier tubes covering the photon phase space at the backward end of the bars. In its first few months of operation the DIRC performance has been found to achieve the design requirements. This note presents results from cosmic ray data and an analysis of the first beam collision runs. (author)

  12. A process of dosimetry of a particle flux

    International Nuclear Information System (INIS)

    Francois, Henri; Heilmann, Celine; Jacquot, Claude.

    1976-01-01

    The main feature of this dosimetry process is that a nuclear emulsion plate with an emulsion of gelatine and silver bromide microcrystals is subjected to the flux of particles to be measured, that the plate is developed in a standard manner and that the amount of silver thus reduced to the metal state is then analysed by activation. The plate containing the nuclear emulsion irradiated in this way is then developed by the conventional temperature method, the effect of which is to cause traces to appear formed of metal silver particles at those places where ionising particles have penetrated into the emulsion and have given up therein all or part of their energy. Once the plates have been developed, like an ordinary photographic plate, they are then subjected to a neutron flux (nuclear reactor, accelerator, etc.) that activates the silver particles in the emulsion which then become emitters of γ radiations which may then be detected to find out the amount of silver present in the plate, which finally is specific of the radiation flux dose received by this plate. A Geiger type gamma ray detector gives a global indication on the mass of silver contained in the emulsion. A more refined method consists in using a multi-channel gamma spectrometer and this makes it possible to have an energy selective dosimetry. The juxtaposition of several separate plates each having its own sensitivity in a given energy band enable a veritable 'sandwhich' of several plates to be made [fr

  13. APPLICATION OF A PARTICLE SWARM OPTIMIZATION IN AN ...

    African Journals Online (AJOL)

    programming, and meta-heuristic algorithms have been proposed for solving the OPF ... and it can be used to solve many complex optimization problems, which are nonlinear, .... This modification can be represented by the concept of velocity.

  14. Time evolution in a geometric model of a particle

    International Nuclear Information System (INIS)

    Atiyah, M.F.; Franchetti, G.; Schroers, B.J.

    2015-01-01

    We analyse the properties of a (4+1)-dimensional Ricci-flat spacetime which may be viewed as an evolving Taub-NUT geometry, and give exact solutions of the Maxwell and gauged Dirac equation on this background. We interpret these solutions in terms of a geometric model of the electron and its spin, and discuss links between the resulting picture and Dirac’s Large Number Hypothesis.

  15. The Aharonov-Bohm effect as a particle accelerator

    International Nuclear Information System (INIS)

    Costella, John.

    1990-01-01

    It is shown how the Aharonov-Bohm (AB) effect, as displayed conclusively in the experiment of Tonomura et. al., is calculated in classical electrodynamics. Comparison with the quantum prediction yields several new fundamental principles. It is also suggested that the properties of the AB effect may allow its use as a versatile particle accelerator. 14 refs

  16. Rapid spatial equilibration of a particle in a box.

    Science.gov (United States)

    Malabarba, Artur S L; Linden, Noah; Short, Anthony J

    2015-12-01

    We study the equilibration behavior of a quantum particle in a one-dimensional box, with respect to a coarse-grained position measurement (whether it lies in a certain spatial window or not). We show that equilibration in this context indeed takes place and does so very rapidly, in a time comparable to the time for the initial wave packet to reach the edges of the box. We also show that, for this situation, the equilibration behavior is relatively insensitive to the precise choice of position measurements or initial condition.

  17. The Quark Box--A Particle Physics Game.

    Science.gov (United States)

    Swedler, James A.

    This game is designed to be used in junior and senior high school science classes with the purpose of introducing quark theory to students. This material expands on atomic theory and subatomic structure. Quarks are the fundamental building blocks of protons and neutrons. The game will teach students about the standard model of elementary…

  18. A particle-based method for granular flow simulation

    KAUST Repository

    Chang, Yuanzhang

    2012-03-16

    We present a new particle-based method for granular flow simulation. In the method, a new elastic stress term, which is derived from a modified form of the Hooke\\'s law, is included in the momentum governing equation to handle the friction of granular materials. Viscosity force is also added to simulate the dynamic friction for the purpose of smoothing the velocity field and further maintaining the simulation stability. Benefiting from the Lagrangian nature of the SPH method, large flow deformation can be well handled easily and naturally. In addition, a signed distance field is also employed to enforce the solid boundary condition. The experimental results show that the proposed method is effective and efficient for handling the flow of granular materials, and different kinds of granular behaviors can be well simulated by adjusting just one parameter. © 2012 Science China Press and Springer-Verlag Berlin Heidelberg.

  19. A particle identification technique for large acceptance spectrometers

    International Nuclear Information System (INIS)

    Cappuzzello, F.; Cavallaro, M.; Cunsolo, A.; Foti, A.; Carbone, D.; Orrigo, S.E.A.; Rodrigues, M.R.D.

    2010-01-01

    A technique to identify the heavy ions produced in nuclear reactions is presented. It is based on the use of a hybrid detector, which measures the energy loss, the residual energy, the position and angle of the ions at the focal plane of a magnetic spectrometer. The key point is the use of a powerful algorithm for the reconstruction of the ion trajectory, which makes the technique reliable even with large acceptance optical devices. Experimental results with the MAGNEX spectrometer show a remarkable resolution of about 1/160 in the mass parameter.

  20. A particle system with cooperative branching and coalescence

    Czech Academy of Sciences Publication Activity Database

    Sturm, A.; Swart, Jan M.

    2015-01-01

    Roč. 25, č. 3 (2015), s. 1616-1649 ISSN 1050-5164 R&D Projects: GA ČR GAP201/10/0752 Institutional support: RVO:67985556 Keywords : interacting particle system * cooperative branching * coalescence * phase transition * upper invariant law * survival * extinction Subject RIV: BA - General Mathematics Impact factor: 1.755, year: 2015 http://library.utia.cas.cz/separaty/2015/SI/swart-0442871.pdf

  1. Quantum dynamics of a particle in a tracking chamber

    CERN Document Server

    Figari, Rodolfo

    2014-01-01

    In the original formulation of quantum mechanics the existence of a precise border between a microscopic world, governed by quantum mechanics, and a macroscopic world, described by classical mechanics was assumed. Modern theoretical and experimental physics has moved that border several times, carefully investigating its definition and making available to observation larger and larger quantum systems. The present book examines a paradigmatic case of the transition from quantum to classical behavior: A quantum particle is revealed in a tracking chamber as a trajectory obeying the laws of classical mechanics. The authors provide here a purely quantum-mechanical description of this behavior, thus helping to illuminate the nature of the border between the quantum and the classical.

  2. Zebrafish swimming in the flow: a particle image velocimetry study

    Directory of Open Access Journals (Sweden)

    Violet Mwaffo

    2017-11-01

    Full Text Available Zebrafish is emerging as a species of choice for the study of a number of biomechanics problems, including balance development, schooling, and neuromuscular transmission. The precise quantification of the flow physics around swimming zebrafish is critical toward a mechanistic understanding of the complex swimming style of this fresh-water species. Although previous studies have elucidated the vortical structures in the wake of zebrafish swimming in placid water, the flow physics of zebrafish swimming against a water current remains unexplored. In an effort to illuminate zebrafish swimming in a dynamic environment reminiscent of its natural habitat, we experimentally investigated the locomotion and hydrodynamics of a single zebrafish swimming in a miniature water tunnel using particle image velocimetry. Our results on zebrafish locomotion detail the role of flow speed on tail beat undulations, heading direction, and swimming speed. Our findings on zebrafish hydrodynamics offer a precise quantification of vortex shedding during zebrafish swimming and demonstrate that locomotory patterns play a central role on the flow physics. This knowledge may help clarify the evolutionary advantage of burst and cruise swimming movements in zebrafish.

  3. MCPLOTS. A particle physics resource based on volunteer computing

    International Nuclear Information System (INIS)

    Karneyeu, A.; Mijovic, L.; Prestel, S.

    2013-07-01

    The mcplots.cern.ch web site (MCPLOTS) provides a simple online repository of plots made with high-energy-physics event generators, comparing them to a wide variety of experimental data. The repository is based on the HEPDATA online database of experimental results and on the RIVET Monte Carlo analysis tool. The repository is continually updated and relies on computing power donated by volunteers, via the LHC rate at HOME 2.0 platform.

  4. A particle model of rolling grain ripples under waves

    DEFF Research Database (Denmark)

    Andersen, Ken Haste

    2001-01-01

    A simple model for the formation of rolling grain ripples on a flat sand bed by the oscillatory flow generated by a surface wave is presented. An equation of motion is derived for the individual ripples, seen as "particles," on the otherwise flat bed. The model accounts for the initial appearance...... of the ripples, the subsequent coarsening of the ripples, and the final equilibrium state. The model is related to the physical parameters of the problem, and an analytical approximation for the equilibrium spacing of the ripples is developed. It is found that the spacing between the ripples scales...

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

    NARCIS (Netherlands)

    J. Vogt (Julia); K. Bengesser (Kathrin); K.B.M. Claes (Kathleen B.M.); K. Wimmer (Katharina); V.-F. Mautner (Victor-Felix); R. van Minkelen (Rick); E. Legius (Eric); H. Brems (Hilde); M. Upadhyaya (Meena); J. Högel (Josef); C. Lazaro (Conxi); T. Rosenbaum (Thorsten); S. Bammert (Simone); L. Messiaen (Ludwine); D.N. Cooper (David); H. Kehrer-Sawatzki (Hildegard)

    2014-01-01

    textabstractBackground: 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

  6. 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

  7. The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons

    Czech Academy of Sciences Publication Activity Database

    Puterova, Janka; Kubát, Zdeněk; Kejnovský, Eduard; Jesionek, Wojciech; Čížková, Jana; Vyskot, Boris; Hobza, Roman

    2018-01-01

    Roč. 19, FEB2018 (2018) ISSN 1471-2164 R&D Projects: GA ČR GJ15-21523Y Institutional support: RVO:68081707 ; RVO:61389030 Keywords : sex-linked genes * plant silene * transposable elements Subject RIV: EF - Botanics; EF - Botanics (UEB-Q) OBOR OECD: Plant sciences, botany; Plant sciences, botany (UEB-Q) Impact factor: 3.729, year: 2016

  8. 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.

  9. A Medicago truncatula Tobacco Retrotransposon Insertion Mutant Collection with Defects in Nodule Development and Symbiotic Nitrogen Fixation1[W][OA

    Science.gov (United States)

    Pislariu, Catalina I.; D. Murray, Jeremy; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; A. Benedito, Vagner; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E.; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S.; Chen, Rujin; Udvardi, Michael K.

    2012-01-01

    A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod−), 51 mutants with totally ineffective nodules (Nod+ Fix−), 17 mutants with partially ineffective nodules (Nod+ Fix+/−), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/− Fix−), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/− Fix+), and 11 supernodulating mutants (Nod++Fix+/−). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN’T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod− lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging. PMID:22679222

  10. Expanding the Lotus japonicus reverse genetics toolbox – Development of LORE1 retrotransposon mutagenesis and artificial miRNA-mediated silencing

    DEFF Research Database (Denmark)

    Urbanski, Dorian Fabian

    2011-01-01

    . The protocols developed in the current project are now the cornerstone of a new LORE1 reverse genetics resource characterized by efficient mutant line generation and accurate mutation annotation. In parallel, artificial microRNAs (amiRNAs) were designed based on both Arabidopsis and Lotus backbones......Currently, the most common approach to studying Lotus japonicus (Lotus) genes is forward genetics in which a gene responsible for the studied phenotype is identified through map-based cloning. In reverse genetics, the activity of a gene of interest is modified to discover its mutant phenotype....... Prior to this project, the only reverse genetics resource available in Lotus was the TILLING resource. In an attempt to advance Lotus genetic studies, present study is focused on the development of two additional resources. The first is based on insertional mutagenesis and the second on harnessing post...

  11. Genome differentiation in a species pair of coregonine fishes: An extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications

    Czech Academy of Sciences Publication Activity Database

    Symonová, Radka; Majtánová, Zuzana; Sember, Alexandr; Staaks, G.B.O.; Bohlen, Jörg; Freyhof, J.; Rábová, Marie; Ráb, Petr

    2013-01-01

    Roč. 13, FEB 14 (2013), 42/1-42/21 ISSN 1471-2148 R&D Projects: GA ČR GA523/08/0824; GA MŠk LC06073; GA ČR(CZ) GPP506/11/P596 Institutional research plan: CEZ:AV0Z50450515 Keywords : species pairs Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.407, year: 2013

  12. Neurobehavioral Deficits in Progressive Experimental ...

    African Journals Online (AJOL)

    olayemitoyin

    Hydrocephalus was induced in three weeks old albino rats by intracisternal ... 0.71 crossings). Untreated hydrocephalus is accompanied by decline in motor functions which increase with duration and ..... Magnetic resonance imaging and.

  13. Pleiotropic effects of a methyl donor diet in a novel animal model.

    Directory of Open Access Journals (Sweden)

    Kimberly R Shorter

    Full Text Available Folate and other methyl-donor pathway components are widely supplemented due to their ability to prevent prenatal neural tube defects. Several lines of evidence suggest that these supplements act through epigenetic mechanisms (e.g. altering DNA methylation. Primary among these are the experiments on the mouse viable yellow allele of the agouti locus (A(vy. In the Avy allele, an Intracisternal A-particle retroelement has inserted into the genome adjacent to the agouti gene and is preferentially methylated. To further test these effects, we tested the same diet used in the Avy studies on wild-derived Peromyscus maniculatus, a native North American rodent. We collected tissues from neonatal offspring whose parents were fed the high-methyl donor diet as well as controls. In addition, we assayed coat-color of a natural variant (wide-band agouti = A(Nb that overexpresses agouti as a phenotypic biomarker. Our data indicate that these dietary components affected agouti protein production, despite the lack of a retroelement at this locus. Surprisingly, the methyl-donor diet was associated with defects (e.g. ovarian cysts, cataracts and increased mortality. We also assessed the effects of the diet on behavior: We scored animals in open field and social interaction tests. We observed significant increases in female repetitive behaviors. Thus these data add to a growing number of studies that suggest that these ubiquitously added nutrients may be a human health concern.

  14. Tests of a Particle Flow Algorithm with CALICE test beam data

    Czech Academy of Sciences Publication Activity Database

    Adloff, C.; Blaha, J.; Blaising, J.J.; Cvach, Jaroslav; Gallus, Petr; Havránek, Miroslav; Janata, Milan; Kvasnička, Jiří; Lednický, Denis; Marčišovský, Michal; Polák, Ivo; Popule, Jiří; Tomášek, Lukáš; Tomášek, Michal; Růžička, Pavel; Šícho, Petr; Smolík, Jan; Vrba, Václav; Zálešák, Jaroslav

    2011-01-01

    Roč. 6, č. 7 (2011), s. 1-15 ISSN 1748-0221 R&D Projects: GA MŠk LA09042; GA MŠk LA08032 Institutional research plan: CEZ:AV0Z10100502 Keywords : calorimeters * PFA * CALICE * calorimeter methods Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 1.869, year: 2011 http://iopscience.iop.org/1748-0221/6/07/P07005

  15. The polar cusp from a particle point of view: A statistical study based on Viking data

    International Nuclear Information System (INIS)

    Aparicio, B.; Thelin, B.; Lundin, R.

    1991-01-01

    The authors present results from the particle measurements made on board the Viking satellite. For the period of interest the Viking orbits covered at high latitudes the whole dayside sector. Data from the Viking V-3 particle experiment acquired during the Polar Region Outer Magnetospheric International Study period have been used to study the extension of the cusp and cleft in magnetic local time and invariant latitude, and furthermore, their dependence on solar wind and interplanetary magnetic field parameters. The study is limited to the MLT range from 0900 to 1500 and to invariant latitudes (ILAT) from 74 degree to 82 degree. This region is divided into bins of size. The authors concentrated on the region where magnetosheath solar wind plasma penetrates more directly into the magnetosphere and is measured at Viking altitudes. This region is called the cusp proper, to be distinguished from a broader region denoted the cleft, where more energetic particles are observed. Statistically, they find the cusp proper to extend from invariant latitudes of 75 degree to 82 degree and magnetic local times from 0930 to 1400 MLT. The width in ILAT is found to be on average ∼2 degree and in MLT ∼2 hours. It is shown that a clear correlation exists between the densities in the cusp proper calculated from the Viking V-3 experiment in the cusp proper and those in the solar wind calculated from IMP 8 measurements. It is also shown that the position of the cusp proper in MLT depends on the sense of the By component of the interplanetary magnetic field (IMF By), giving a well-defined displacement of the region of maximum occurrence toward earlier MLTs for IMF By 0

  16. A particle method with adjustable transport properties - the generalized consistent Boltzmann algorithm

    International Nuclear Information System (INIS)

    Garcia, A.L.; Alexander, F.J.; Alder, B.J.

    1997-01-01

    The consistent Boltzmann algorithm (CBA) for dense, hard-sphere gases is generalized to obtain the van der Waals equation of state and the corresponding exact viscosity at all densities except at the highest temperatures. A general scheme for adjusting any transport coefficients to higher values is presented

  17. Density matrix of a quantum field in a particle-creating background

    International Nuclear Information System (INIS)

    Gavrilov, S.P.; Gitman, D.M.; Tomazelli, J.L.

    2008-01-01

    We examine the time evolution of a quantized field in external backgrounds that violate the stability of vacuum (particle-creating backgrounds). Our purpose is to study the exact form of the final quantum state (the density operator at the final instant of time) that has emerged from a given arbitrary initial state (from a given arbitrary density operator at the initial time instant) in the course of evolution. We find a generating functional that allows one to obtain density operators for an arbitrary initial state. Averaging over states of the subsystem of antiparticles (particles), we obtain explicit forms of reduced density operators for the subsystem of particles (antiparticles). Analyzing one-particle correlation functions, we establish a one-to-one correspondence between these functions and the reduced density operators. It is shown that in the general case a presence of bosons (e.g., gluons) in the initial state increases the creation rate of the same type of bosons. We discuss the question (and its relation to the initial stage of quark-gluon plasma formation) whether a thermal form of one-particle distribution can appear even if the final state of the complete system is not in thermal equilibrium. In this respect, we discuss some cases when pair-creation by an electric-like field can mimic the one-particle thermal distribution. We apply our technics to some QFT problems in slowly varying electric-like backgrounds: electric, SU(3) chromoelectric, and metric. In particular, we analyze the time and temperature behavior of the mean numbers of created particles, provided that the effects of switching the external field on and off are negligible. It is demonstrated that at high temperatures and in slowly varying electric fields the rate of particle-creation is essentially time-dependent

  18. Coherent states of a particle in a magnetic field and the Stieltjes moment problem

    International Nuclear Information System (INIS)

    Gazeau, J.P.; Baldiotti, M.C.; Gitman, D.M.

    2009-01-01

    A solution to a version of the Stieltjes moment problem is presented. Using this solution, we construct a family of coherent states of a charged particle in a uniform magnetic field. We prove that these states form an overcomplete set that is normalized and resolves the unity. By the help of these coherent states we construct the Fock-Bergmann representation related to the particle quantization. This quantization procedure takes into account a circle topology of the classical motion.

  19. Density matrix of a quantum field in a particle-creating background

    Energy Technology Data Exchange (ETDEWEB)

    Gavrilov, S.P. [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318, CEP 05315-970 Sao Paulo, SP (Brazil)], E-mail: gavrilovsergeyp@yahoo.com; Gitman, D.M. [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318, CEP 05315-970 Sao Paulo, SP (Brazil)], E-mail: gitman@dfn.if.usp.br; Tomazelli, J.L. [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318, CEP 05315-970 Sao Paulo, SP (Brazil)], E-mail: tomazelli@fsc.ufsc.br

    2008-06-01

    We examine the time evolution of a quantized field in external backgrounds that violate the stability of vacuum (particle-creating backgrounds). Our purpose is to study the exact form of the final quantum state (the density operator at the final instant of time) that has emerged from a given arbitrary initial state (from a given arbitrary density operator at the initial time instant) in the course of evolution. We find a generating functional that allows one to obtain density operators for an arbitrary initial state. Averaging over states of the subsystem of antiparticles (particles), we obtain explicit forms of reduced density operators for the subsystem of particles (antiparticles). Analyzing one-particle correlation functions, we establish a one-to-one correspondence between these functions and the reduced density operators. It is shown that in the general case a presence of bosons (e.g., gluons) in the initial state increases the creation rate of the same type of bosons. We discuss the question (and its relation to the initial stage of quark-gluon plasma formation) whether a thermal form of one-particle distribution can appear even if the final state of the complete system is not in thermal equilibrium. In this respect, we discuss some cases when pair-creation by an electric-like field can mimic the one-particle thermal distribution. We apply our technics to some QFT problems in slowly varying electric-like backgrounds: electric, SU(3) chromoelectric, and metric. In particular, we analyze the time and temperature behavior of the mean numbers of created particles, provided that the effects of switching the external field on and off are negligible. It is demonstrated that at high temperatures and in slowly varying electric fields the rate of particle-creation is essentially time-dependent.

  20. Coherent states of a particle in a magnetic field and the Stieltjes moment problem

    Energy Technology Data Exchange (ETDEWEB)

    Gazeau, J.P. [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318-CEP, 05315-970 Sao Paulo, S.P. (Brazil)], E-mail: gazeau@apc.univ-paris7.fr; Baldiotti, M.C. [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318-CEP, 05315-970 Sao Paulo, S.P. (Brazil)], E-mail: baldiott@fma.if.usp.br; Gitman, D.M. [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318-CEP, 05315-970 Sao Paulo, S.P. (Brazil)], E-mail: gitman@dfn.if.usp.br

    2009-05-11

    A solution to a version of the Stieltjes moment problem is presented. Using this solution, we construct a family of coherent states of a charged particle in a uniform magnetic field. We prove that these states form an overcomplete set that is normalized and resolves the unity. By the help of these coherent states we construct the Fock-Bergmann representation related to the particle quantization. This quantization procedure takes into account a circle topology of the classical motion.

  1. Analysis of the start-up and control of a particle bed reactor

    International Nuclear Information System (INIS)

    Lazareth, O.W.; Araj, K.J.; Horn, F.L.; Ludewig, H.; Powell, J.R.

    1987-01-01

    This study describes the modeling of start-up transients in Particle Bed Reactors (PBR) for burst electric power. Two computer programs have been developed to analyze the start-up process. The first program (named KINETIC) analyzes the entire fuel element, calculating time dependent solutions for power and the temperature distribution in the packed bed. The second program (named SPHEAT, for Spherical Heating) calculates time-dependent temperatures inside individual, cladded fuel particles. The two programs provide powerful analytical tools for evaluation of material and geometrical options, power and time constraints, and conditions that could lead to element failures

  2. 18F-FDG positron autoradiography with a particle counting silicon pixel detector.

    Science.gov (United States)

    Russo, P; Lauria, A; Mettivier, G; Montesi, M C; Marotta, M; Aloj, L; Lastoria, S

    2008-11-07

    We report on tests of a room-temperature particle counting silicon pixel detector of the Medipix2 series as the detector unit of a positron autoradiography (AR) system, for samples labelled with (18)F-FDG radiopharmaceutical used in PET studies. The silicon detector (1.98 cm(2) sensitive area, 300 microm thick) has high intrinsic resolution (55 microm pitch) and works by counting all hits in a pixel above a certain energy threshold. The present work extends the detector characterization with (18)F-FDG of a previous paper. We analysed the system's linearity, dynamic range, sensitivity, background count rate, noise, and its imaging performance on biological samples. Tests have been performed in the laboratory with (18)F-FDG drops (37-37 000 Bq initial activity) and ex vivo in a rat injected with 88.8 MBq of (18)F-FDG. Particles interacting in the detector volume produced a hit in a cluster of pixels whose mean size was 4.3 pixels/event at 11 keV threshold and 2.2 pixels/event at 37 keV threshold. Results show a sensitivity for beta(+) of 0.377 cps Bq(-1), a dynamic range of at least five orders of magnitude and a lower detection limit of 0.0015 Bq mm(-2). Real-time (18)F-FDG positron AR images have been obtained in 500-1000 s exposure time of thin (10-20 microm) slices of a rat brain and compared with 20 h film autoradiography of adjacent slices. The analysis of the image contrast and signal-to-noise ratio in a rat brain slice indicated that Poisson noise-limited imaging can be approached in short (e.g. 100 s) exposures, with approximately 100 Bq slice activity, and that the silicon pixel detector produced a higher image quality than film-based AR.

  3. Prediction of the thermal behavior of a particle spherical fuel element using GITT

    International Nuclear Information System (INIS)

    Pessoa, C.V.; Oliveira, Claudio L. de; Jian, Su

    2008-01-01

    In this work, the transient and steady state heat conduction in a spherical fuel element of a pebble-bed high temperature were studied. This pebble element is composed by a particulate region with spherical inclusions, the fuel UO 2 particles, dispersed in a graphite matrix. A convective heat transfer by helium occurs on the outer surface of the fuel element. The two-energy equation model for the case of pure conduction was applied to this particulate spherical element, generating two macroscopic temperatures, respectively, of the inclusions and of the matrix. The transient analysis was carried out by using the Generalized Integral Transform Technique (GITT) that requires low computational efforts and allows a fast evaluation of the two macroscopic transient temperatures of the particulate region. The solution by GITT leads to a system of ordinary differential equations with the unknown transformed potentials. The mechanical properties (thermal conductivity and specific heat) of the materials were supposed not to depend on the temperature and to be uniform in each region. (author)

  4. A Particle Swarm Optimization Algorithm for Neural Networks in Recognition of Maize Leaf Diseases

    Directory of Open Access Journals (Sweden)

    Zhiyong ZHANG

    2014-03-01

    Full Text Available The neural networks have significance on recognition of crops disease diagnosis? but it has disadvantage of slow convergent speed and shortcoming of local optimum. In order to identify the maize leaf diseases by using machine vision more accurately, we propose an improved particle swarm optimization algorithm for neural networks. With the algorithm, the neural network property is improved. It reasonably confirms threshold and connection weight of neural network, and improves capability of solving problems in the image recognition. At last, an example of the emulation shows that neural network model based on recognizes significantly better than without optimization. Model accuracy has been improved to a certain extent to meet the actual needs of maize leaf diseases recognition.

  5. Diffusion and superdiffusion of a particle in a random potential with finite correlation time

    International Nuclear Information System (INIS)

    Lebedev, N.; Maass, P.; Feng, S.

    1995-01-01

    We study theoretically the long time asymptotic of a quantum particle moving in a random time-dependent potential with finite correlation time, in d=1. By applying a new unitary numerical scheme we first show the minor importance of quantum interference and then derive an effective Langevin-type equation for the corresponding clasical problem in the limit of weak potential. We find that on intermediate time scales E kin (t)∼t 2/5 , while the true long time asymptotic is determined by a new friction term, which gives rise to a stationary power law velocity distribution, multifractality of the velocity moments, and a slowing down of the superdiffusive behavior

  6. Impacts of radiation exposure on the experimental microbial ecosystem: a particle-based model simulation approach

    International Nuclear Information System (INIS)

    Doi, M.; Tanaka, N.; Fuma, S.; Kawabata, Z.

    2004-01-01

    Well-designed experimental model ecosystem could be a simple reference of the actual environment and complex ecological systems. For ecological toxicity test of radiation and other environmental toxicants, we investigated and aquatic microbial ecosystem (closed microcosm) in the test tube with initial substrates,autotroph flagellate algae (Euglena, G.), heterotroph ciliate protozoa (Tetrahymena T.) and saprotroph bacteria (E, coli). These species organizes by itself to construct the ecological system, that keeps the sustainable population dynamics for more than 2 years after inoculation only by adding light diurnally and controlling temperature at 25 degree Celsius. Objective of the study is to develop the particle-based computer simulation by reviewing interactions among microbes and environment, and analyze the ecological toxicities of radiation on the microcosm by replicating experimental results in the computer simulation. (Author) 14 refs

  7. Applying a particle filtering technique for canola crop growth stage estimation in Canada

    Science.gov (United States)

    Sinha, Abhijit; Tan, Weikai; Li, Yifeng; McNairn, Heather; Jiao, Xianfeng; Hosseini, Mehdi

    2017-10-01

    Accurate crop growth stage estimation is important in precision agriculture as it facilitates improved crop management, pest and disease mitigation and resource planning. Earth observation imagery, specifically Synthetic Aperture Radar (SAR) data, can provide field level growth estimates while covering regional scales. In this paper, RADARSAT-2 quad polarization and TerraSAR-X dual polarization SAR data and ground truth growth stage data are used to model the influence of canola growth stages on SAR imagery extracted parameters. The details of the growth stage modeling work are provided, including a) the development of a new crop growth stage indicator that is continuous and suitable as the state variable in the dynamic estimation procedure; b) a selection procedure for SAR polarimetric parameters that is sensitive to both linear and nonlinear dependency between variables; and c) procedures for compensation of SAR polarimetric parameters for different beam modes. The data was collected over three crop growth seasons in Manitoba, Canada, and the growth model provides the foundation of a novel dynamic filtering framework for real-time estimation of canola growth stages using the multi-sensor and multi-mode SAR data. A description of the dynamic filtering framework that uses particle filter as the estimator is also provided in this paper.

  8. Experimental study of a particle velocity immersed in a fluid in rotation

    International Nuclear Information System (INIS)

    Cesar, S.B.G.

    1981-12-01

    An incompressible viscous fluid is confined within a circular cylinder whose wall and top are fixed while the botton rotates with constant angular speed. The velocity components of a particule immersed in the fluid above, was determined. The method utilized employs filming the particle during its motion. Experimental measurements were made at rotational speeds between 50 and 190 rps, at inter-disc spacing between 10 and 40 cm, and the particle is let loose at distances between static disc and 5 cm above the inferior disc. The results show that the method utilized is valid in a radial region within the cylinder between 1.0 [pt

  9. A particle dark matter footprint on the first generation of stars

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, Ilídio [Centro Multidisciplinar de Astrofísica, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa (Portugal); Silk, Joseph, E-mail: ilidio.lopes@ist.utl.pt, E-mail: silk@astro.ox.ac.uk [Institut d' Astrophysique de Paris, F-75014 Paris (France)

    2014-05-01

    Dark matter particles with properties identical to those of dark matter candidates hinted at by several international collaborations dedicated to the experimental detection of dark matter (DAMA, COGENT, CRESST, and CDMS-II, although not, most notably, by LUX), which also have a dark matter asymmetry that is identical to the observed baryon asymmetry (Planck and Wilkinson Microwave Anisotropy Probe), may produce a significant impact on the evolution of the first generation of low-metallicity stars. The lifetimes of these stars in different phases of stellar evolution are significantly extended, namely, in the pre-main sequence, main sequence, and red giant phases. In particular, intermediate-mass stars in the red giant phase experience significant changes in their luminosity and chemical composition. The annihilations of dark matter particles affect the interior of the star in such a way that the 3α reaction becomes less efficient in the production of carbon and oxygen. This dark matter effect contradicts the excess of carbon and other metals observed today in stars of low mass and low metallicity. Hence, we can impose an upper limit on the dark matter halo density, and therefore on the redshift, at which the first generation of low-metallicity stars formed.

  10. Planet-Scale grid A particle collier leads data grid developers to unprecedented dimensions

    CERN Multimedia

    Thibodeau, Patrick

    2005-01-01

    In 2007, scientists will begin smashing protons and ions together in a massive, multinational experiment to understand what the universe looked like tiny fractions of a second after the Big Bang. The particle accelerator used in this test will release a vast flood of data on a scale unlike anything seen before, and for that scientists will need a computing grid of equally great capability

  11. Study of the equations of a particle in Non- Relativistic Quantum Mechanics

    International Nuclear Information System (INIS)

    Miltao, Milton Souza Ribeiro; Silva, Vanessa Santos Teles da

    2011-01-01

    Full text: The study of group theory is relevant to the treatment of physical problems, in which concepts of invariance and symmetry are important. In the field of Non-Relativistic Quantum Mechanics, we can do algebraic considerations taking into account the principles of symmetry, considering the framework of the study of Galileo transformations, which have characteristics of group. Therefore, we discuss the Stern-Gerlach experiment that had the historical importance of demonstrating that the electron has an intrinsic angular momentum. Through discussion of this experiment, we found that the spin appears in Non-Relativistic Quantum Mechanics as a feature of the algebraic structure underlying any physical theory represented by a group. From these studies, we have algebraic considerations for physical systems in non-relativistic domain, which are described by the Schroedinger and Pauli equations, describing the dynamics of particles of spin zero and 1/2 respectively, taking into account the structure of the transformations Galileo. Due to the operatorial, we represent Galileo's transformations by matrices by choosing an appropriate basis of space-time. Using these arrays, we saw group characteristics associated with these transformations, which we call the Galileo Group. We note the invariance of the Schroedinger and Pauli equations after these changes, as well as the physical state associated with it, which is represented by a radius vector in Hilbert space. (author)

  12. Optical forces induced behavior of a particle in a non-diffracting vortex beam

    Czech Academy of Sciences Publication Activity Database

    Šiler, Martin; Jákl, Petr; Brzobohatý, Oto; Zemánek, Pavel

    2012-01-01

    Roč. 20, č. 22 (2012), s. 24304-24319 ISSN 1094-4087 R&D Projects: GA ČR GPP205/11/P294; GA MŠk ED0017/01/01; GA MŠk LH12018 Institutional support: RVO:68081731 Keywords : optical vortex beam * tweezers * optical forces Subject RIV: BH - Optics, Masers, Lasers Impact factor: 3.546, year: 2012

  13. Seasonal characteristics of water exchange in Beibu Gulf based on a particle tracking model

    Science.gov (United States)

    Wang, L.; Pan, W.; Yan, X.

    2016-12-01

    A lagrangian particle tracking model coupled with a three-dimensional Marine Environmental Committee Ocean Model (MEC) is used to study the transport and seasonal characteristics of water exchange in Beibu Gulf. The hydrodynamic model (MEC), which is forced with the daily surface and lateral boundary fluxes, as well as tidal harmonics and monthly climatological river discharges, is applied to simulate the flow field in the gulf during 2014. Using these results, particle tracking method which includes tidal advection and random walk in the horizontal is used to determine the residence times of sub regions within the gulf in response of winter and summer wind forcing. The result shows water exchange processes in the gulf have a similar tendency with seasonal circulation structure. During the sourthwestly prevailing wind in summer, water particles are traped within the gulf that considerably increases the residence time of each sub region. On the contrary, the presence of strong northeastly prevailing wind in winter drives particles to move cyclonicly leading to shorter residence times and rather active water exchanges among sub regions. Similarly, particle tracking is applied to investigate the water transport in Beibu Gulf. As Qiongzhou Strait and the wide opening in the south of the gulf are two significant channels connecting with the open ocean, continuous particle releases are simulated to quantify the influence range and the pathways of these sources water flowing into Beibu Gulf. The results show that water particles originated from Qiongzhou Strait are moving westward due to the year-round strong westward flow transportation. Influencing range in the north of the Beibu Gulf is enlarged by winter northeastly wind, however, it is blocked to the Leizhou Peninsula coastal region by summer westly wind. In the south opening, water particles are transported northward into the gulf along Hainan Island and flushed from Vietnam coastal region to the ocean rapidly by the longshore currents.

  14. Application of a particle swarm optimization in an optimal power flow ...

    African Journals Online (AJOL)

    NR, Quasi Newton), and the intelligence heuristic algorithms such ac genetic algorithm, evolutionary programming. From simulation results it has been found that PSO method is highly competitive for its better general convergence performance.

  15. Fast shuttling of a particle under weak spring-constant noise of the moving trap

    Science.gov (United States)

    Lu, Xiao-Jing; Ruschhaupt, A.; Muga, J. G.

    2018-05-01

    We investigate the excitation of a quantum particle shuttled in a harmonic trap with weak spring-constant colored noise. The Ornstein-Uhlenbeck model for the noise correlation function describes a wide range of possible noises, in particular for short correlation times the white-noise limit examined by Lu et al. [Phys. Rev. A 89, 063414 (2014)], 10.1103/PhysRevA.89.063414 and, by averaging over correlation times, "1 /f flicker noise." We find expressions for the excitation energy in terms of static (independent of trap motion) and dynamical sensitivities, with opposite behavior with respect to shuttling time, and demonstrate that the excitation can be reduced by proper process timing and design of the trap trajectory.

  16. Dynamical properties of a particle in a time-dependent double-well potential

    International Nuclear Information System (INIS)

    Leonel, Edson D; McClintock, P V E

    2004-01-01

    Some chaotic properties of a classical particle interacting with a time-dependent double-square-well potential are studied. The dynamics of the system is characterized using a two-dimensional nonlinear area-preserving map. Scaling arguments are used to study the chaotic sea in the low-energy domain. It is shown that the distributions of successive reflections and of corresponding successive reflection times obey power laws with the same exponent. If one or both wells move randomly, the particle experiences the phenomenon of Fermi acceleration in the sense that it has unlimited energy growth

  17. Spectrum and Collapse of a Particle in a Nonlocal Field of Centrifugal Type

    CERN Document Server

    Pupyshev, V V

    2004-01-01

    The investigated problem is the one-dimensional Schrödinger equation with the zero boundary conditions at the ends of the segment $[0,\\pi/2]$, and the interaction equal to the product of the potential proportional to squared secant of the argument and the sum of the unity and integral operators. For this problem the dependence of the spectrum of real eigenvalues and the corresponding eigenfunctions on the real potential parameter is analyzed qualitatively and numerically. For analysis the Fourier- and spline-approximations of the searched eigenfunction are proposed and applied. Special attention is paid to the particle collapse.

  18. Jet milling from a particle perspective : predicting particle fracture based on mechanical material properties

    NARCIS (Netherlands)

    Vegt, Onno Martinus

    2007-01-01

    Milling is a very old discipline originated in milling agricultural products to flour. Despite the enormous literature on size reduction, milling is a unit operation which has no sound underlying theory comparable to those existing for other unit operations. The design of milling equipment for a

  19. Validation of a particle tracking analysis method for the size determination of nano- and microparticles

    Science.gov (United States)

    Kestens, Vikram; Bozatzidis, Vassili; De Temmerman, Pieter-Jan; Ramaye, Yannic; Roebben, Gert

    2017-08-01

    Particle tracking analysis (PTA) is an emerging technique suitable for size analysis of particles with external dimensions in the nano- and sub-micrometre scale range. Only limited attempts have so far been made to investigate and quantify the performance of the PTA method for particle size analysis. This article presents the results of a validation study during which selected colloidal silica and polystyrene latex reference materials with particle sizes in the range of 20 nm to 200 nm were analysed with NS500 and LM10-HSBF NanoSight instruments and video analysis software NTA 2.3 and NTA 3.0. Key performance characteristics such as working range, linearity, limit of detection, limit of quantification, sensitivity, robustness, precision and trueness were examined according to recommendations proposed by EURACHEM. A model for measurement uncertainty estimation following the principles described in ISO/IEC Guide 98-3 was used for quantifying random and systematic variations. For nominal 50 nm and 100 nm polystyrene and a nominal 80 nm silica reference materials, the relative expanded measurement uncertainties for the three measurands of interest, being the mode, median and arithmetic mean of the number-weighted particle size distribution, varied from about 10% to 12%. For the nominal 50 nm polystyrene material, the relative expanded uncertainty of the arithmetic mean of the particle size distributions increased up to 18% which was due to the presence of agglomerates. Data analysis was performed with software NTA 2.3 and NTA 3.0. The latter showed to be superior in terms of sensitivity and resolution.

  20. Realistic simulations of a cyclotron spiral inflector within a particle-in-cell framework

    Science.gov (United States)

    Winklehner, Daniel; Adelmann, Andreas; Gsell, Achim; Kaman, Tulin; Campo, Daniela

    2017-12-01

    We present an upgrade to the particle-in-cell ion beam simulation code opal that enables us to run highly realistic simulations of the spiral inflector system of a compact cyclotron. This upgrade includes a new geometry class and field solver that can handle the complicated boundary conditions posed by the electrode system in the central region of the cyclotron both in terms of particle termination, and calculation of self-fields. Results are benchmarked against the analytical solution of a coasting beam. As a practical example, the spiral inflector and the first revolution in a 1 MeV /amu test cyclotron, located at Best Cyclotron Systems, Inc., are modeled and compared to the simulation results. We find that opal can now handle arbitrary boundary geometries with relative ease. Simulated injection efficiencies and beam shape compare well with measured efficiencies and a preliminary measurement of the beam distribution after injection.

  1. State-of-charge estimation in lithium-ion batteries: A particle filter approach

    Science.gov (United States)

    Tulsyan, Aditya; Tsai, Yiting; Gopaluni, R. Bhushan; Braatz, Richard D.

    2016-11-01

    The dynamics of lithium-ion batteries are complex and are often approximated by models consisting of partial differential equations (PDEs) relating the internal ionic concentrations and potentials. The Pseudo two-dimensional model (P2D) is one model that performs sufficiently accurately under various operating conditions and battery chemistries. Despite its widespread use for prediction, this model is too complex for standard estimation and control applications. This article presents an original algorithm for state-of-charge estimation using the P2D model. Partial differential equations are discretized using implicit stable algorithms and reformulated into a nonlinear state-space model. This discrete, high-dimensional model (consisting of tens to hundreds of states) contains implicit, nonlinear algebraic equations. The uncertainty in the model is characterized by additive Gaussian noise. By exploiting the special structure of the pseudo two-dimensional model, a novel particle filter algorithm that sweeps in time and spatial coordinates independently is developed. This algorithm circumvents the degeneracy problems associated with high-dimensional state estimation and avoids the repetitive solution of implicit equations by defining a 'tether' particle. The approach is illustrated through extensive simulations.

  2. Influence of ECAP temperature on the formability of a particle reinforced 2017 aluminum alloy

    Science.gov (United States)

    Wagner, S.; Härtel, M.; Frint, P.; F-X Wagner, M.

    2017-03-01

    Severe plastic deformation methods are commonly used to increase the strength of materials by generating ultrafine-grained microstructures. The application of these methods to Al-Cu alloys is, however, difficult because of their poor formability at room temperature. An additional reduction of formability of such alloys occurs when ceramic particles are added as reinforcement: this often triggers shear localization and crack initiation during ECAP. This is the main reason why equal-channel angular pressing (ECAP) of aluminum matrix composites (AMCs) can generally only be performed at elevated temperatures and using ECAP dies with a channel angle larger than 90° (e.g. 120°). In this study we present a brief first report on an alternative approach for the improvement of the formability of an AMC (AA2017, 10 % SiC): ECAP at low temperatures. We show that, using a temperature of -60 °C and a channel angle of 90° (corresponding to an equivalent strain of 1.1), ECAP of the AMC can be successfully performed without material failure. The mechanical properties of the strongly deformed AMC are analyzed by tensile testing. Our results indicate that the increased formability of the AMC at low temperatures can be attributed to the suppression of unstable plastic flow that affects formability at room temperature.

  3. Calculation of the exit probability of a particle from a cylinder of matter

    International Nuclear Information System (INIS)

    Ertaud, A.; Mercier, C.

    1949-02-01

    In the elementary calculation of the ε coefficient and of the slowing down length inside a nuclear pile made of a network of cylindrical rods, it is necessary to know the exit probability of a neutron initially located inside a cylinder filled up with a given substance. This probability is the ratio between the number of output neutrons and the number of neutrons produced inside the surface of the cylinder. This report makes the resolution of this probabilistic equation (integral calculation) both for the cylindrical case and for the spherical case. (J.S.)

  4. A novel beam optics concept in a particle therapy gantry utilizing the advantages of superconducting magnets.

    Science.gov (United States)

    Gerbershagen, Alexander; Meer, David; Schippers, Jacobus Maarten; Seidel, Mike

    2016-09-01

    A first order design of the beam optics of a superconducting proton therapy gantry beam is presented. The possibilities of superconducting magnets with respect to the beam optics such as strong fields, large apertures and superposition of different multipole fields have been exploited for novel concepts in a gantry. Since various techniques used in existing gantries have been used in our first design steps, some examples of the existing superconducting gantry designs are described and the necessary requirements of such a gantry are explained. The study of a gantry beam optics design is based on superconducting combined function magnets. The simulations have been performed in first order with the conventional beam transport codes. The superposition of strong dipole and quadrupole fields generated by superconducting magnets enables the introduction of locally achromatic bending sections without increasing the gantry size. A rigorous implementation of such beam optics concepts into the proposed gantry design dramatically increases the momentum acceptance compared to gantries with normal conducting magnets. In our design this large acceptance has been exploited by the implementation of a degrader within the gantry and a potential possibility to use the same magnetic field for all energies used in a treatment, so that the superconducting magnets do not have to vary their fields during a treatment. This also enables very fast beam energy changes, which is beneficial for spreading the Bragg peak over the thickness of the tumor. The results show an improvement of its momentum acceptance. Large momentum acceptance in the gantry creates a possibility to implement faster dose application techniques. Copyright © 2016. Published by Elsevier GmbH.

  5. Developing a particle tracking surrogate model to improve inversion of ground water - Surface water models

    Science.gov (United States)

    Cousquer, Yohann; Pryet, Alexandre; Atteia, Olivier; Ferré, Ty P. A.; Delbart, Célestine; Valois, Rémi; Dupuy, Alain

    2018-03-01

    The inverse problem of groundwater models is often ill-posed and model parameters are likely to be poorly constrained. Identifiability is improved if diverse data types are used for parameter estimation. However, some models, including detailed solute transport models, are further limited by prohibitive computation times. This often precludes the use of concentration data for parameter estimation, even if those data are available. In the case of surface water-groundwater (SW-GW) models, concentration data can provide SW-GW mixing ratios, which efficiently constrain the estimate of exchange flow, but are rarely used. We propose to reduce computational limits by simulating SW-GW exchange at a sink (well or drain) based on particle tracking under steady state flow conditions. Particle tracking is used to simulate advective transport. A comparison between the particle tracking surrogate model and an advective-dispersive model shows that dispersion can often be neglected when the mixing ratio is computed for a sink, allowing for use of the particle tracking surrogate model. The surrogate model was implemented to solve the inverse problem for a real SW-GW transport problem with heads and concentrations combined in a weighted hybrid objective function. The resulting inversion showed markedly reduced uncertainty in the transmissivity field compared to calibration on head data alone.

  6. A Particle Swarm Optimization Algorithm with Variable Random Functions and Mutation

    Institute of Scientific and Technical Information of China (English)

    ZHOU Xiao-Jun; YANG Chun-Hua; GUI Wei-Hua; DONG Tian-Xue

    2014-01-01

    The convergence analysis of the standard particle swarm optimization (PSO) has shown that the changing of random functions, personal best and group best has the potential to improve the performance of the PSO. In this paper, a novel strategy with variable random functions and polynomial mutation is introduced into the PSO, which is called particle swarm optimization algorithm with variable random functions and mutation (PSO-RM). Random functions are adjusted with the density of the population so as to manipulate the weight of cognition part and social part. Mutation is executed on both personal best particle and group best particle to explore new areas. Experiment results have demonstrated the effectiveness of the strategy.

  7. Analytical and experimental investigation of the coaxial plasma gun for use as a particle accelerator

    Science.gov (United States)

    Shriver, E. L.

    1972-01-01

    The coaxial plasma accelerator for use as a projectile accelerator is discussed. The accelerator is described physically and analytically by solution of circuit equations, and by solving for the magnetic pressures which are formed by the j cross B vector forces on the plasma. It is shown that the plasma density must be increased if the accelerator is to be used as a projectile accelerator. Three different approaches to increasing plasma density are discussed. When a magnetic field containment scheme was used to increase the plasma density, glass beads of 0.66 millimeter diameter were accelerated to 7 to 8 kilometers per second velocities. Glass beads of smaller diameter were accelerated to more than twice this velocity.

  8. Tyre-road contact using a particle-envelope surface model

    Science.gov (United States)

    Pinnington, Roger J.

    2013-12-01

    Determination of the contact forces is the central problem in all aspects of road-tyre interaction: i.e. noise, energy loss and friction. A procedure to find the contact forces under a rolling tyre is presented in four stages. First, the contact stiffness of a uniform peak array from indentations in the rubber tread, and also tyre carcass deflection, is described by some new simplified expressions. Second, a routine divides a single surface profile into equal search intervals, in which the highest peaks are identified. These are used to obtain the parameters for the interval, i.e. the mean envelope and the mean interval. The process is repeated at geometrically decreasing search intervals until the level of the data resolution, thereby describing the profile by a set of envelopes. The ‘strip profile’ ultimately used to describe the surface, is obtained by selecting the highest points across the profiles of one stone's width. The third stage is to combine the strip profile envelopes with the contact stiffness expressions, yielding the nonlinear stiffness-displacement, and force-displacement relationships for the chosen road-tyre combination. Finally the contact pressure distribution from a steady-state rolling tyre model is applied to the strip profile, via the force-displacement relationship, giving the local tyre displacements on the road texture. This displacement pattern is shown to be proportional to the time and space varying contact pressure, which then is incorporated into a wave equation for rolling contact.

  9. A Particle-In-Cell approach to particle flux shaping with a surface mask

    Directory of Open Access Journals (Sweden)

    G. Kawamura

    2017-08-01

    Full Text Available The Particle-In-Cell simulation code PICS has been developed to study plasma in front of a surface with two types of masks, step-type and roof-type. Parameter scans with regard to magnetic field angle, electron density, and mask height were carried out to understand their influence on ion particle flux distribution on a surface. A roof-type mask with a small mask height yields short decay length in the flux distribution which is consistent with that estimated experimentally. A roof-type mask with a large height yields very long decay length and the flux value does not depend on a mask height or an electron density, but rather on a mask length and a biasing voltage of the surface. Mask height also changes the flux distribution apart from the mask because of the shading effect of the mask. Electron density changes the distribution near the mask edge according to the Debye length. Dependence of distribution on parameters are complicated especially for a roof-type mask, and simulation study with various parameters are useful to understand the physical reasons of dependence and also is useful as a tool for experiment studies.

  10. Third quantization: modeling the universe as a 'particle' in a quantum field theory of the minisuperspace

    International Nuclear Information System (INIS)

    Robles Pérez, S J

    2013-01-01

    The third quantization formalism of quantum cosmology adds simplicity and conceptual insight into the quantum description of the multiverse. Within such a formalism, the existence of squeezed and entangled states raises the question of whether the complementary principle of quantum mechanics has to be extended to the quantum description of the whole space-time manifold. If so, the particle description entails the consideration of a multiverse scenario and the wave description induces us to consider as well correlations and interactions among the universes of the multiverse.

  11. The influence of magnetic field on the inertial deposition of a particle on a rotating disk

    International Nuclear Information System (INIS)

    Tsatsin, P O; Beskachko, V P

    2008-01-01

    The problem of inertial deposition attracts considerable attention in the connection with the separating of detrimental impurities and the refining of liquid metals. In the present investigation the deposition of particles suspended in a conducting melt on the rotating disk in the presence of axial uniform magnetic field is considered. The field of the fluid velocities is computed by means of the MHD-analogue of Karman reduction, which makes possible to reduce initial governing nonlinear partial differential equations to a two-point boundary value problem for the set of ordinary differential equations. The influence of magnetic field on dia-and paramagnetic particle deposition effect was estimated. The results reveal that magnetic field has significant effect on particle parameters, especially for magnetic particles

  12. Correlation of A-particles emission with the speed of light

    International Nuclear Information System (INIS)

    Abbas, M.

    2004-01-01

    In this phenomenological research, a relation connecting α-particle energy and α-decay half-life for all isotopes emitting α-particles have been achieved, and the experimental data affirmed this tight correlation. Also a relation connecting α-decay rate with the speed of light has been established. Depending on this last relation and the hypothesis of increasing light speed as we go back in time, some mysterious phenomena discovered recently, concerning α-decay radioactivity, have also been interpreted. Thus, the increase of radioactivity as we go back in time was approved; which interpreted the enormous amount of α-particles in some positions on the earth that cannot be interpreted using known laws of radioactivity. (Author)

  13. Implementation of a Particle Image Velocimetry System for Wind Tunnel Flowfield Measurements

    Science.gov (United States)

    2014-12-01

    Instrumentation Wind tunnel speed was measured by two pitot probes mounted on opposite tunnel walls upstream of the model and above the ground...board. The pitot probes were connected differentially to Scanivalve 1-psi transducers. A secondary measurement of wind tunnel speed was made with the...Manf. Model Range 1 Tunnel Vel (south pitot ) Transducer Scanivalve CR24D 1 psi 2 Tunnel Vel (north pitot ) Transducer Scanivalve CR24D 1 psi 3

  14. Precision siting of a particle accelerator; Locacao de precisao de um acelerador de particulas

    Energy Technology Data Exchange (ETDEWEB)

    Cintra, Jorge Pimentel

    1996-07-01

    Precise location is a specific survey job that involves a high skilled work to avoid unrecoverable results at the project installation. As a function of the different process stages, different specifications can be applied, invoking different instruments: theodolite, measurement tape, distanciometer, invar wire. This paper, based on experience obtained at the installation of particle accelerator equipment, deals with general principles of precise location: tolerance definitions, increasing accuracy techniques, schedule of locations, sensitivity analysis, quality control methods. (author)

  15. Removal of divergences in the problem of scattering of a particle beam by a medium

    International Nuclear Information System (INIS)

    Kuz'min, V.L.

    1977-01-01

    Scattering of a beam of particles (neutrons) by a medium is considered. After the averaging according to the statistical mechanics rules, the cross-section of the process is represented in the form of the series including many-particle distribution functions. The series describes the scattering processes of arbitrary multiplicity. Disconnected parts of the distribution functions give rise to divergences. A method of the re-summation of the original series is proposed, which removes all the divergences completely

  16. Innovations in ILC detector design using a particle flow algorithm approach

    International Nuclear Information System (INIS)

    Magill, S.; High Energy Physics

    2007-01-01

    The International Linear Collider (ILC) is a future e + e - collider that will produce particles with masses up to the design center-of-mass (CM) energy of 500 GeV. The ILC complements the Large Hadron Collider (LHC) which, although colliding protons at 14 TeV in the CM, will be luminosity-limited to particle production with masses up to ∼1-2 TeV. At the ILC, interesting cross-sections are small, but there are no backgrounds from underlying events, so masses should be able to be measured by hadronic decays to dijets (∼80% BR) as well as in leptonic decay modes. The precise measurement of jets will require major detector innovations, in particular to the calorimeter, which will be optimized to reconstruct final state particle 4-vectors--called the particle flow algorithm approach to jet reconstruction

  17. Visualization of air flow around soccer ball using a particle image velocimetry

    Science.gov (United States)

    Hong, Sungchan; Asai, Takeshi; Seo, Kazuya

    2015-10-01

    A traditional soccer ball is constructed using 32 pentagonal and hexagonal panels. In recent years, however, the likes of the Teamgeist and Jabulani balls, constructed from 14 and 8 panels, respectively, have entered the field, marking a significant departure from conventionality in terms of shape and design. Moreover, the recently introduced Brazuca ball features a new 6-panel design and has already been adopted by many soccer leagues. However, the shapes of the constituent panels of these balls differ substantially from those of conventional balls. Therefore, this study set out to investigate the flight and aerodynamic characteristics of different orientations of the soccer ball, which is constructed from panels of different shapes. A wind tunnel test showed substantial differences in the aerodynamic forces acting on the ball, depending on its orientation. Substantial differences were also observed in the aerodynamic forces acting on the ball in different directions, corresponding to its orientation and rotation. Moreover, two-dimensional particle image velocimetry (2D-PIV) measurements showed that the boundary separation varies depending on the orientation of the ball. Based on these results, we can conclude that the shape of the panels of a soccer ball substantially affects its flight trajectory.

  18. Numerical and experimental validation of a particle Galerkin method for metal grinding simulation

    Science.gov (United States)

    Wu, C. T.; Bui, Tinh Quoc; Wu, Youcai; Luo, Tzui-Liang; Wang, Morris; Liao, Chien-Chih; Chen, Pei-Yin; Lai, Yu-Sheng

    2018-03-01

    In this paper, a numerical approach with an experimental validation is introduced for modelling high-speed metal grinding processes in 6061-T6 aluminum alloys. The derivation of the present numerical method starts with an establishment of a stabilized particle Galerkin approximation. A non-residual penalty term from strain smoothing is introduced as a means of stabilizing the particle Galerkin method. Additionally, second-order strain gradients are introduced to the penalized functional for the regularization of damage-induced strain localization problem. To handle the severe deformation in metal grinding simulation, an adaptive anisotropic Lagrangian kernel is employed. Finally, the formulation incorporates a bond-based failure criterion to bypass the prospective spurious damage growth issues in material failure and cutting debris simulation. A three-dimensional metal grinding problem is analyzed and compared with the experimental results to demonstrate the effectiveness and accuracy of the proposed numerical approach.

  19. Detectable elements in a particles pattern of suspended urban matter analysed by neutron activation

    International Nuclear Information System (INIS)

    Herrera, L.; Beltran, C.; Alemon, E.; Ortiz, M.E.

    2001-01-01

    The multielement composition of a Standard Reference Material 1648 pattern certified is reported and it is used for the suspended in air aerosol samples analysis from urban localities of the Valley of Mexico, which was irradiated in the same geometry of the sample. The bottom of laboratory is analysed where was made the gamma spectrometry and it is compared the ratio of country up of bottom photo peaks with pattern photo peaks in nearer interest regions. The bottom natural gamma transmitters were identified and those of the activated pattern in the TRIGA Mark III nuclear reactor. (Author)

  20. Diffusive real-time dynamics of a particle with Berry curvature

    Science.gov (United States)

    Misaki, Kou; Miyashita, Seiji; Nagaosa, Naoto

    2018-02-01

    We study theoretically the influence of Berry phase on the real-time dynamics of the single particle focusing on the diffusive dynamics, i.e., the time dependence of the distribution function. Our model can be applied to the real-time dynamics of intraband relaxation and diffusion of optically excited excitons, trions, or particle-hole pair. We found that the dynamics at the early stage is deeply influenced by the Berry curvature in real space (B ), momentum space (Ω ), and also the crossed space between these two (C ). For example, it is found that Ω induces the rotation of the wave packet and causes the time dependence of the mean square displacement of the particle to be linear in time t at the initial stage; it is qualitatively different from the t3 dependence in the absence of the Berry curvature. It is also found that Ω and C modify the characteristic time scale of the thermal equilibration of momentum distribution. Moreover, the dynamics under various combinations of B ,Ω , and C shows singular behaviors such as the critical slowing down or speeding up of the momentum equilibration and the reversals of the direction of rotations. The relevance of our model for time-resolved experiments in transition metal dichalcogenides is also discussed.

  1. A Particle System for Safety Verification of Free Flight in Air Traffic

    NARCIS (Netherlands)

    Blom, H.A.P.; Krystul, J.; Bakker, G.J.

    2006-01-01

    Under free flight, an aircrew has both the freedom to select their trajectory and the responsibility of resolving conflicts with other aircraft. The general belief is that free flight can be made safe under low traffic conditions. Increasing traffic, however, raises safety verification issues. This

  2. A particle-hole-rotator coupling model for the giant resonance of carbon-12

    International Nuclear Information System (INIS)

    McDougall, A.; Spicer, B.M.

    1975-01-01

    A collective correlations calculation has been made for the giant resonance of 12 C. The low-lying states are treated as members of two rotational bands, and higher energy low-lying states are included in the coupling procedure in an attempt to examine the connection of these states with structure in the 30-35 MeV region, and to examine a proposed rotational band of states built on the 7.65 MeV (0 + ) level. The calculation fails to transfer strength to the extent expected. (author)

  3. Application of a particle swarm optimization for shape optimization in hydraulic machinery

    Science.gov (United States)

    Moravec, Prokop; Rudolf, Pavel

    A study of shape optimization has become increasingly popular in academia and industry. A typical problem is to find an optimal shape, which minimizes (or maximizes) a certain cost function and satisfies given constraints. Particle Swarm Optimization (PSO) has received a lot of attention in past years and is inspired by social behaviour of some animals such as flocking behaviour of birds. This paper focuses on a possibility of a diffuser shape optimization using particle swarm optimization (PSO), which is coupled with CFD simulation. Influence of main parameters of PSO-algorithm and later diffuser shapes obtained with this method are discussed and advantages/disadvantages summarized.

  4. Application of a particle swarm optimization for shape optimization in hydraulic machinery

    Directory of Open Access Journals (Sweden)

    Moravec Prokop

    2017-01-01

    Full Text Available A study of shape optimization has become increasingly popular in academia and industry. A typical problem is to find an optimal shape, which minimizes (or maximizes a certain cost function and satisfies given constraints. Particle Swarm Optimization (PSO has received a lot of attention in past years and is inspired by social behaviour of some animals such as flocking behaviour of birds. This paper focuses on a possibility of a diffuser shape optimization using particle swarm optimization (PSO, which is coupled with CFD simulation. Influence of main parameters of PSO-algorithm and later diffuser shapes obtained with this method are discussed and advantages/disadvantages summarized.

  5. Method of measuring a profile of the density of charged particles in a particle beam

    International Nuclear Information System (INIS)

    Hyman, L.G.; Jankowski, D.J.

    1975-01-01

    A profile of the relative density of charged particles in a beam is obtained by disposing a number of rods parallel to each other in a plane perpendicular to the beam and shadowing the beam. A second number of rods is disposed perpendicular to the first rods in a plane perpendicular to the beam and also shadowing the beam. Irradiation of the rods by the beam of charged particles creates radioactive isotopes in a quantity proportional to the number of charged particles incident upon the rods. Measurement of the radioactivity of each of the rods provides a measure of the quantity of radioactive material generated thereby and, together with the location of the rods, provides information sufficient to identify a profile of the density of charged particles in the beam

  6. A Particle Swarm Optimization Approach to Composing Serial Test Sheets for Multiple Assessment Criteria

    Science.gov (United States)

    Yin, Peng-Yeng; Chang, Kuang-Cheng; Hwang, Gwo-Jen; Hwang, Gwo-Haur; Chan, Ying

    2006-01-01

    To accurately analyze the problems of students in learning, the composed test sheets must meet multiple assessment criteria, such as the ratio of relevant concepts to be evaluated, the average discrimination degree, difficulty degree and estimated testing time. Furthermore, to precisely evaluate the improvement of student's learning performance…

  7. Study of a Particle Based Films Cure Process by High-Frequency Eddy Current Spectroscopy

    Directory of Open Access Journals (Sweden)

    Iryna Patsora

    2016-12-01

    Full Text Available Particle-based films are today an important part of various designs and they are implemented in structures as conductive parts, i.e., conductive paste printing in the manufacture of Li-ion batteries, solar cells or resistive paste printing in IC. Recently, particle based films were also implemented in the 3D printing technique, and are particularly important for use in aircraft, wind power, and the automotive industry when incorporated onto the surface of composite structures for protection against damages caused by a lightning strike. A crucial issue for the lightning protection area is to realize films with high homogeneity of electrical resistance where an in-situ noninvasive method has to be elaborated for quality monitoring to avoid undesirable financial and time costs. In this work the drying process of particle based films was investigated by high-frequency eddy current (HFEC spectroscopy in order to work out an automated in-situ quality monitoring method with a focus on the electrical resistance of the films. Different types of particle based films deposited on dielectric and carbon fiber reinforced plastic substrates were investigated in the present study and results show that the HFEC method offers a good opportunity to monitor the overall drying process of particle based films. Based on that, an algorithm was developed, allowing prediction of the final electrical resistance of the particle based films throughout the drying process, and was successfully implemented in a prototype system based on the EddyCus® HFEC device platform presented in this work. This prototype is the first solution for a portable system allowing HFEC measurement on huge and uneven surfaces.

  8. Apparatus for observing a sample with a particle beam and an optical microscope

    NARCIS (Netherlands)

    2010-01-01

    An apparatus for observing a sample (1) with a TEM column and an optical high resolution scanning microscope (10). The sample position when observing the sample with the TEM column differs from the sample position when observing the sample with the optical microscope in that in the latter case the

  9. A unique nuclear thermal rocket engine using a particle bed reactor

    Science.gov (United States)

    Culver, Donald W.; Dahl, Wayne B.; McIlwain, Melvin C.

    1992-01-01

    Aerojet Propulsion Division (APD) studied 75-klb thrust Nuclear Thermal Rocket Engines (NTRE) with particle bed reactors (PBR) for application to NASA's manned Mars mission and prepared a conceptual design description of a unique engine that best satisfied mission-defined propulsion requirements and customer criteria. This paper describes the selection of a sprint-type Mars transfer mission and its impact on propulsion system design and operation. It shows how our NTRE concept was developed from this information. The resulting, unusual engine design is short, lightweight, and capable of high specific impulse operation, all factors that decrease Earth to orbit launch costs. Many unusual features of the NTRE are discussed, including nozzle area ratio variation and nozzle closure for closed loop after cooling. Mission performance calculations reveal that other well known engine options do not support this mission.

  10. Vortex ring formation at the open end of a shock tube: A particle image velocimetry study

    Science.gov (United States)

    Arakeri, J. H.; Das, D.; Krothapalli, A.; Lourenco, L.

    2004-04-01

    The vortex ring generated subsequent to the diffraction of a shock wave from the open end of a shock tube is studied using particle image velocimetry. We examine the early evolution of the compressible vortex ring for three-exit shock Mach numbers, 1.1, 1.2, and 1.3. For the three cases studied, the ring formation is complete at about tUb/D=2, where t is time, Ub is fluid velocity behind shock as it exits the tube and D is tube diameter. Unlike in the case of piston generated incompressible vortex rings where the piston velocity variation with time is usually trapezoidal, in the shock-generated vortex ring case the exit fluid velocity doubles from its initial value Ub before it slowly decays to zero. At the end of the ring formation, its translation speed is observed to be about 0.7 Ub. During initial formation and propagation, a jet-like flow exists behind the vortex ring. The vortex ring detachment from the tailing jet, commonly referred to as pinch-off, is briefly discussed.

  11. Radial rescaling approach for the eigenvalue problem of a particle in an arbitrarily shaped box.

    Science.gov (United States)

    Lijnen, Erwin; Chibotaru, Liviu F; Ceulemans, Arnout

    2008-01-01

    In the present work we introduce a methodology for solving a quantum billiard with Dirichlet boundary conditions. The procedure starts from the exactly known solutions for the particle in a circular disk, which are subsequently radially rescaled in such a way that they obey the new boundary conditions. In this way one constructs a complete basis set which can be used to obtain the eigenstates and eigenenergies of the corresponding quantum billiard to a high level of precision. Test calculations for several regular polygons show the efficiency of the method which often requires one or two basis functions to describe the lowest eigenstates with high accuracy.

  12. PREVENTING POLLUTION USING ISO 14001 AT A PARTICLE ACCELERATOR THE RELATIVISTIC HEAVY ION COLLIDER PROJECT

    International Nuclear Information System (INIS)

    BRIGGS, S.L.K.; MUSOLINO, S.V.

    2001-01-01

    In early 1997 Brookhaven National Laboratory (BNL) discovered that the spent fuel pool of their High Flux Beam Reactor was leaking tritium into the groundwater. Community members, activist groups, politicians and regulators were outraged with the poor environmental management practices at BNL. The reactor was shut down and the Department of Energy (DOE) terminated the contract with the existing Management Company. At this same time, a major new scientific facility, the Relativistic Heavy Ion Collider (RHIC), was nearing the end of construction and readying for commissioning. Although environmental considerations had been incorporated into the design of the facility; some interested parties were skeptical that this new facility would not cause significant environmental impacts. RHIC management recognized that the future of its operation was dependent on preventing pollution and allaying concerns of its stakeholders. Although never done at a DOE National Laboratory before Brookhaven Science Associates, the new management firm, committed to implementing an Environmental Management System (EMS) and RHIC managers volunteered to deploy it within their facility on an extremely aggressive schedule. Several of these IS0 requirements contribute directly to preventing pollution, an area where particular emphasis was placed. This paper describes how Brookhaven used the following key IS0 14001 elements to institutionalize Pollution Prevention concepts: Environmental Policy, Aspects, Objectives and Targets, Environmental Management Program, Structure and Responsibility, Operational Controls, Training, and Management Review. In addition, examples of implementation at the RHIC Project illustrate how BNL's premiere facility was able to demonstrate to interested parties that care had been taken to implement technological and administrative controls to minimize environmental impacts, while at the same time reduce the applicability of regulatory requirements to their operations

  13. A particle velocity based method for separating all multi incoherent sound sources

    NARCIS (Netherlands)

    Winkel, J.C.; Yntema, Doekle Reinder; Druyvesteyn, W.F.; de Bree, H.E.

    2006-01-01

    In this paper we present a method to separate the contributions of different uncorrelated sound sources to the total sound field. When the contribution of each sound source to the total sound field is known, techniques with array-applications like direct sound field measurements or inverse acoustics

  14. Geometrical optimization of a particle tracking system for proton computed tomography

    International Nuclear Information System (INIS)

    Penfold, S.N.; Rosenfeld, A.B.; Schulte, R.W.; Sadrozinksi, H.-F.W.

    2011-01-01

    Proton computed tomography (pCT) is currently being developed as an imaging modality for improving the accuracy of treatment planning in proton therapy. A tracking telescope comprising eight planes of single-sided silicon strip detectors (SSDs) forms an integral part of our present pCT design. Due to the currently maximum available Si wafer size, the sensitive area of 9 cm × 18 cm of the pCT tracker requires each tracking plane to be composed of two individual SSDs, which creates potential reconstruction problems due to overlap or gaps of the sensitive SSD areas. Furthermore, the spacing of the tracking planes creates competing design requirements between compactness and spatial resolution. Two Monte Carlo simulations were performed to study the effect of tracking detector location on pCT image quality. It was found that a “shingled” detector design suppressed reconstruction artefacts and, for the spatial resolution of the current detector hardware, reconstructed spatial resolution was not improved with a tracking separation of greater than 8 cm.

  15. A particle-in-cell method for modeling small angle Coulomb collisions in plasmas

    International Nuclear Information System (INIS)

    Parker, S.E.

    1989-01-01

    We propose a computational method to self-consistently model small angle collisional effects. This method may be added to standard Particle-In-Cell (PIC) plasma simulations to include collisions, or as an alternative to solving the Fokker-Planck (FP) equation using finite difference methods. The distribution function is represented by a large number of particles. The particle velocities change due to the drag force, and the diffusion in velocity is represented by a random process. This is similar to previous Monte-Carlo methods except we calculate the drag force and diffusion tensor self- consistently. The particles are weighted to a grid in velocity space and associated ''Poisson equations'' are solved for the Rosenbluth potentials. The motivation is to avoid the very time consuming method of Coulomb scattering pair by pair. First the approximation for small angle Coulomb collisions is discussed. Next, the FP-PIC collision method is outlined. Then we show a test of the particle advance modeling an electron beam scattering off a fixed ion background. 4 refs

  16. Relativistic equation of the orbit of a particle in a arbitrary central force field

    International Nuclear Information System (INIS)

    Aaron, Francisc D.

    2005-01-01

    The equation of the orbit of a relativistic particle moving in an arbitrary central force field is derived. Straightforward generalizations of well-known first and second order differential equations are given. It is pointed out that the relativistic equation of the orbit has the same form as in the non-relativistic case, the only changes consisting in the appearance of additional terms proportional to 1/c 2 in both potential and total energies. (author)

  17. Some considerations about the dynamic of a particle in Stueckelberg - Schroedinger formalism

    International Nuclear Information System (INIS)

    Horia, Radu

    2004-01-01

    Some time ago, E. C. G. Stueckelberg has demonstrated [Helv. Phys. Acta 14 (1941) 588, Helv. Phys. Acta 14 (1941) 322, Helv. Phys. Acta 15 (1942) 22, Phys. Rev. 10 (1957) 254] that it is possible to construct a classical and quantum relativistic mechanics theory considering electromagnetic and gravitational interactions if in the Einstein's theory time is considered as a dynamical variable. This theory forgot for many decades, is able to predict the pair particle production as well as the annihilation in classical relativistic mechanics without use of the quantum theory. The motion of an event in space-time is a free universe line. The interaction could bend this world line and then moves on to the possibility that world line can bend so much that it curves back in time. In this theory, an object moving backward in time would appear to have opposite charge if it is thought as having positive energy and therefore is identified as an antiparticle. This interpretation was used later by Feynman in his diagrams. Stueckelberg's theory contains some problems of interpretation, but some possible new consequences are remarkable. In this contribution, some phenomenological considerations of the theory are discussed in the frame of the classical hypothesis. If the time is a dynamical variable, thus the mass of particle must be also considered as independent dynamical variable. Thus it is possible to understand how gravity, electromagnetic and other possible interactions could influence the particle mass (and lifetime) and to estimate the differences between particle and antiparticle due to interactions, if they exist. (author)

  18. Trouble with diffusion: Reassessing hillslope erosion laws with a particle-based model

    Science.gov (United States)

    Tucker, Gregory E.; Bradley, D. Nathan

    2010-03-01

    Many geomorphic systems involve a broad distribution of grain motion length scales, ranging from a few particle diameters to the length of an entire hillslope or stream. Studies of analogous physical systems have revealed that such broad motion distributions can have a significant impact on macroscale dynamics and can violate the assumptions behind standard, local gradient flux laws. Here, a simple particle-based model of sediment transport on a hillslope is used to study the relationship between grain motion statistics and macroscopic landform evolution. Surface grains are dislodged by random disturbance events with probabilities and distances that depend on local microtopography. Despite its simplicity, the particle model reproduces a surprisingly broad range of slope forms, including asymmetric degrading scarps and cinder cone profiles. At low slope angles the dynamics are diffusion like, with a short-range, thin-tailed hop length distribution, a parabolic, convex upward equilibrium slope form, and a linear relationship between transport rate and gradient. As slope angle steepens, the characteristic grain motion length scale begins to approach the length of the slope, leading to planar equilibrium forms that show a strongly nonlinear correlation between transport rate and gradient. These high-probability, long-distance motions violate the locality assumption embedded in many common gradient-based geomorphic transport laws. The example of a degrading scarp illustrates the potential for grain motion dynamics to vary in space and time as topography evolves. This characteristic renders models based on independent, stationary statistics inapplicable. An accompanying analytical framework based on treating grain motion as a survival process is briefly outlined.

  19. HTS Dipole Magnet for a Particle Accelerator using a Twisted Stacked Cable

    CERN Document Server

    Himbele, John J.; Tixador, Pascal

    2016-01-01

    changes during the quench. Due to the large temperature margin between the operation and the current sharing temperatures, the normal zone does not propagate with the temperature front. This means that the temperature will rise in a considerably larger volume when compared to the quenched volume. Thus, the evolution of the temperature distribution below current sharing temperature Tcs after the quench onset affects the normal zone propagation velocity in HTS more than in LTS coils. This can be seen as an acceleration of the quench propagation velocities while the quench evolves when margin to Tcs is high. In this paper we scrutinize quench propagation in a stack of YBCO cables with an in-house finite element method software which solves the heat diffusion equation. We compute the longitudinal and transverse normal zone propagation velocities at various distances from the hot spot to demonstrate the distance-variation...

  20. Deconfinement and Phase Diagram of Bosons in a Linear Optical Lattice with a Particle Reservoir

    International Nuclear Information System (INIS)

    Majumdar, Kingshuk; Fertig, H.A.

    2005-01-01

    We investigate the zero-temperature phases of bosons in a one-dimensional optical lattice with an explicit tunnel coupling to a Bose-condensed particle reservoir. Renormalization group analysis of this system is shown to reveal three phases: one in which the linear system is fully phase locked to the reservoir; one in which Josephson vortices between the one-dimensional system and the particle reservoir deconfine due to quantum fluctuations, leading to a decoupled state in which the one-dimensional system is metallic; and one in which the one-dimensional system is in a Mott insulating state

  1. Preliminary results of oxygen isotope ratio measurement with a particle-gamma coincidence method

    Energy Technology Data Exchange (ETDEWEB)

    Borysiuk, Maciek, E-mail: maciek.borysiuk@pixe.lth.se; Kristiansson, Per; Ros, Linus; Abdel, Nassem S.; Elfman, Mikael; Nilsson, Charlotta; Pallon, Jan

    2015-04-01

    The possibility to study variations in the oxygen isotopic ratio with photon tagged nuclear reaction analysis (pNRA) is evaluated in the current work. The experiment described in the article was performed at Lund Ion Beam Analysis Facility (LIBAF) with a 2 MeV deuteron beam. Isotopic fractionation of light elements such as carbon, oxygen and nitrogen is the basis of many analytical tools in hydrology, geology, paleobiology and paleogeology. IBA methods provide one possible tool for measurement of isotopic content. During this experimental run we focused on measurement of the oxygen isotopic ratio. The measurement of stable isotopes of oxygen has a number of applications; the particular one driving the current investigation belongs to the field of astrogeology and specifically evaluation of fossil extraterrestrial material. There are three stable isotopes of oxygen: {sup 16}O, {sup 17}O and {sup 18}O. We procured samples highly enriched with all three isotopes. Isotopes {sup 16}O and {sup 18}O were easily detected in the enriched samples, but no significant signal from {sup 17}O was detected in the same samples. The measured yield was too low to detect {sup 18}O in a sample with natural abundances of oxygen isotopes, at least in the current experimental setup, but the spectral line from the reaction with {sup 16}O was clearly visible.

  2. A Particle Swarm Optimization Variant with an Inner Variable Learning Strategy

    Directory of Open Access Journals (Sweden)

    Guohua Wu

    2014-01-01

    Full Text Available Although Particle Swarm Optimization (PSO has demonstrated competitive performance in solving global optimization problems, it exhibits some limitations when dealing with optimization problems with high dimensionality and complex landscape. In this paper, we integrate some problem-oriented knowledge into the design of a certain PSO variant. The resulting novel PSO algorithm with an inner variable learning strategy (PSO-IVL is particularly efficient for optimizing functions with symmetric variables. Symmetric variables of the optimized function have to satisfy a certain quantitative relation. Based on this knowledge, the inner variable learning (IVL strategy helps the particle to inspect the relation among its inner variables, determine the exemplar variable for all other variables, and then make each variable learn from the exemplar variable in terms of their quantitative relations. In addition, we design a new trap detection and jumping out strategy to help particles escape from local optima. The trap detection operation is employed at the level of individual particles whereas the trap jumping out strategy is adaptive in its nature. Experimental simulations completed for some representative optimization functions demonstrate the excellent performance of PSO-IVL. The effectiveness of the PSO-IVL stresses a usefulness of augmenting evolutionary algorithms by problem-oriented domain knowledge.

  3. A Generalized Schwartz Model for Energy Spot Prices - Estimation using a Particle MCMC Method

    DEFF Research Database (Denmark)

    Lunde, Asger; Brix, Anne Floor; Wei, Wei

    structure. Instead of using various filtering techniques for splitting the two factors, as often found in the literature, we estimate the model in one step using an adaptive MCMC method with a Rao-Blackwellized particle filter. We fit the model to UK natural gas spot prices and investigate the importance......We propose an energy spot price model featuring a two-factor price process and a two-component stochastic volatility process. The first factor in the price process captures the normal variations; the second accounts for spikes. The two-component volatility allows for a flexible autocorrelation...... of spikes and stochastic volatility. We find that the inclusion of stochastic volatility is crucial and that it strongly impacts the jump intensity in the spike process. Furthermore, our estimation method enables us to consider both continuous and purely jump-driven volatility processes, and thereby assess...

  4. A cryogenic pump with a long continuous run without filling intended for a particle accelerator

    International Nuclear Information System (INIS)

    Bottiglioni, F.; Coutant, J.; Fois, M.; Duthil, R.; Gelebart, J.C.; Lottin, J.C.

    1977-06-01

    A cryogenic pump is described, specially designed to be used in an electrostatic particle accelerator. The same tubular liquid helium bath provides pumping in the accelerating tube and around the beam. The temperature of the bath can be adjusted between 2.2 and 4.2 deg K, the liquid helium level, in the low pressure bath, is keeped constant through a feeding system made of an heat exchanger and an expansion valve. An auxiliary container for liquid nitrogen and liquid helium, at atmospheric pressure, allows a several days continuous run without filling. This system allows refilling of the container without changing the pressure on the bath [fr

  5. Heat transfer to a particle exposed to a rarefield ionized-gas flow

    International Nuclear Information System (INIS)

    Chen, X.; He, P.

    1986-01-01

    Analytical results are presented concerning the heat transfer to a spherical particle exposed to a high temperature, ionized- gas flow for the extreme case of free-molecule flow regime. It has been shown that the presence of relative velocity between the particle and the ionized gas reduces the floating potential on the particle, enhances the heat flux and causes appreciably non-uniform distribution of the local heat flux. Pronounced difference is found between metallic and non-metallic particles in the floating potential and the local heat flux distributions, in particular for the case with high gas-flow temperature. Relative contribution of atoms to the total heat flux is dominant for the case of low gas-flow temperature, while the heat flux is mainly caused by ions and electrons for the case of high gas-flow temperature

  6. Characterization of scintillating plastic fibers and silicon photomultipliers for their usage in a particle telescope

    Energy Technology Data Exchange (ETDEWEB)

    Pruefer, Lea; Losekamm, Martin; Poeschl, Thomas; Greenwald, Daniel; Paul, Stephan [Technische Universitaet Muenchen, 85748 Garching (Germany)

    2016-07-01

    The Multi-purpose Active-target Particle Telescope (MAPT) is a newly developed compact charged-particle detector. It can be used for space applications, such as radiation monitoring on spacecraft or for stratospheric research balloons. Its core consists of scintillating plastic fibers coupled to silicon photomultiplier (SiPMs). The energy reconstruction of the incoming particles is based on an extended Bragg curve spectroscopy technique, requiring a good measurement of the energy deposition. Therefore, non-linearities of the measured light output -such as quenching effects of the scintillating material or saturation of the SiPMs at high light yields- have to be known quantitatively. To investigate these effects, two scaled-down prototypes were built, consisting of 128 and 16 channels. The first one was tested at a stationary proton beam at Paul Scherrer Institute. We determine Birk's coefficient describing the ionization quenching of the scintillator and calculate the characteristic photon detection efficiency of the SiPMs. We explain the results of the first prototype tests and the characterization of the SiPMs.

  7. No evidence of murine leukemia virus-related viruses in live attenuated human vaccines.

    Directory of Open Access Journals (Sweden)

    William M Switzer

    Full Text Available The association of xenotropic murine leukemia virus (MLV-related virus (XMRV in prostate cancer and chronic fatigue syndrome reported in previous studies remains controversial as these results have been questioned by recent data. Nonetheless, concerns have been raised regarding contamination of human vaccines as a possible source of introduction of XMRV and MLV into human populations. To address this possibility, we tested eight live attenuated human vaccines using generic PCR for XMRV and MLV sequences. Viral metagenomics using deep sequencing was also done to identify the possibility of other adventitious agents.All eight live attenuated vaccines, including Japanese encephalitis virus (JEV (SA-14-14-2, varicella (Varivax, measles, mumps, and rubella (MMR-II, measles (Attenuvax, rubella (Meruvax-II, rotavirus (Rotateq and Rotarix, and yellow fever virus were negative for XMRV and highly related MLV sequences. However, residual hamster DNA, but not RNA, containing novel endogenous gammaretrovirus sequences was detected in the JEV vaccine using PCR. Metagenomics analysis did not detect any adventitious viral sequences of public health concern. Intracisternal A particle sequences closest to those present in Syrian hamsters and not mice were also detected in the JEV SA-14-14-2 vaccine. Combined, these results are consistent with the production of the JEV vaccine in Syrian hamster cells.We found no evidence of XMRV and MLV in eight live attenuated human vaccines further supporting the safety of these vaccines. Our findings suggest that vaccines are an unlikely source of XMRV and MLV exposure in humans and are consistent with the mounting evidence on the absence of these viruses in humans.

  8. Alopecia in a viable phospholipase C delta 1 and phospholipase C delta 3 double mutant.

    Directory of Open Access Journals (Sweden)

    Fabian Runkel

    Full Text Available BACKGROUND: Inositol 1,4,5trisphosphate (IP(3 and diacylglycerol (DAG are important intracellular signalling molecules in various tissues. They are generated by the phospholipase C family of enzymes, of which phospholipase C delta (PLCD forms one class. Studies with functional inactivation of Plcd isozyme encoding genes in mice have revealed that loss of both Plcd1 and Plcd3 causes early embryonic death. Inactivation of Plcd1 alone causes loss of hair (alopecia, whereas inactivation of Plcd3 alone has no apparent phenotypic effect. To investigate a possible synergy of Plcd1 and Plcd3 in postnatal mice, novel mutations of these genes compatible with life after birth need to be found. METHODOLOGY/PRINCIPAL FINDINGS: We characterise a novel mouse mutant with a spontaneously arisen mutation in Plcd3 (Plcd3(mNab that resulted from the insertion of an intracisternal A particle (IAP into intron 2 of the Plcd3 gene. This mutation leads to the predominant expression of a truncated PLCD3 protein lacking the N-terminal PH domain. C3H mice that carry one or two mutant Plcd3(mNab alleles are phenotypically normal. However, the presence of one Plcd3(mNab allele exacerbates the alopecia caused by the loss of functional Plcd1 in Del(9olt1Pas mutant mice with respect to the number of hair follicles affected and the body region involved. Mice double homozygous for both the Del(9olt1Pas and the Plcd3(mNab mutations survive for several weeks and exhibit total alopecia associated with fragile hair shafts showing altered expression of some structural genes and shortened phases of proliferation in hair follicle matrix cells. CONCLUSIONS/SIGNIFICANCE: The Plcd3(mNab mutation is a novel hypomorphic mutation of Plcd3. Our investigations suggest that Plcd1 and Plcd3 have synergistic effects on the murine hair follicle in specific regions of the body surface.

  9. Molecular analysis of the mouse agouti gene and the role of dominant agouti-locus mutations in obesity and insulin resistance

    Energy Technology Data Exchange (ETDEWEB)

    Klebig, M.L.; Woychik, R.P. [Oak Ridge National Lab., TN (United States); Wilkinson, J.E. [Univ. of Tennessee, Knoxville, TN (United States)

    1994-09-01

    The lethal yellow (A{sup y/-}) and viable yellow (A{sup vy/-}) mouse agouti mutants have a predominantly yellow pelage and display a complex syndrome that includes obesity, hyperinsulinemia, and insulin resistance, hallmark features of obesity-associated noninsulin-dependent diabetes mellitus (NIDDM) in humans. A new dominant agouti allele, A{sup iapy}, has recently been identified; like the A{sup vy} allele, it is homozygous viable and confers obesity and yellow fur in heterozygotes. The agouti gene was cloned and characterized at the molecular level. The gene is expressed in the skin during hair growth and is predicted to encode a 131 amino acid protein, that is likely to be a secreted factor. In both Ay/- and A{sup iapy}/- mice, the obesity and other dominant pleiotropic effects are associated with an ectopic expression of agouti in many tissues where the gene product is normally not produced. In Ay, a 170-kb deletion has occurred that causes an upstream promoter to drive the ectopic expression of the wild-type agouti coding exons. In A{sup iapy}, the coding region of the gene is expressed from a cryptic promoter within the LTR of an intracisternal A-particle (IAP), which has integrated within the region just upstream of the first agouti coding exon. Transgenic mice ubiquitously expressing the cloned agouti gene under the influence of the beta-actin and phosphoglycerate kinase promoters display obesity, hyperinsulinemia, and yellow coat color. This demonstrates unequivocally that ectopic expression of agouti is responsible for the yellow obese syndrome.

  10. Levodopa acts centrally to induce an antinociceptive action against colonic distension through activation of D2 dopamine receptors and the orexinergic system in the brain in conscious rats

    Directory of Open Access Journals (Sweden)

    Toshikatsu Okumura

    2016-02-01

    Subcutaneously (80 mg/rat or intracisternally (2.5 μg/rat administered levodopa significantly increased the threshold of colonic distension-induced AWR in conscious rats. The dose difference to induce the antinociceptive action suggests levodopa acts centrally to exert its antinociceptive action against colonic distension. While neither sulpiride, a D2 dopamine receptor antagonist, nor SCH23390, a D1 dopamine receptor antagonist by itself changed the threshold of colonic distension-induced AWR, the intracisternally injected levodopa-induced antinociceptive action was significantly blocked by pretreatment with subcutaneously administered sulpiride but not SCH23390. Treatment with intracisternal SB334867, an orexin 1 receptor antagonist, significantly blocked the subcutaneously administered levodopa-induced antinociceptive action. These results suggest that levodopa acts centrally to induce an antinociceptive action against colonic distension through activation of D2 dopamine receptors and the orexinergic system in the brain.

  11. Antinociceptive Effects of Transcytosed Botulinum Neurotoxin Type A on Trigeminal Nociception in Rats

    Science.gov (United States)

    Kim, Hye-Jin; Lee, Geun-Woo; Kim, Min-Ji; Yang, Kui-Ye; Kim, Seong-Taek; Bae, Yong-Cheol

    2015-01-01

    We examined the effects of peripherally or centrally administered botulinum neurotoxin type A (BoNT-A) on orofacial inflammatory pain to evaluate the antinociceptive effect of BoNT-A and its underlying mechanisms. The experiments were carried out on male Sprague-Dawley rats. Subcutaneous (3 U/kg) or intracisternal (0.3 or 1 U/kg) administration of BoNT-A significantly inhibited the formalin-induced nociceptive response in the second phase. Both subcutaneous (1 or 3 U/kg) and intracisternal (0.3 or 1 U/kg) injection of BoNT-A increased the latency of head withdrawal response in the complete Freund's adjuvant (CFA)-treated rats. Intracisternal administration of N-methyl-D-aspartate (NMDA) evoked nociceptive behavior via the activation of trigeminal neurons, which was attenuated by the subcutaneous or intracisternal injection of BoNT-A. Intracisternal injection of NMDA up-regulated c-Fos expression in the trigeminal neurons of the medullary dorsal horn. Subcutaneous (3 U/kg) or intracisternal (1 U/kg) administration of BoNT-A significantly reduced the number of c-Fos immunoreactive neurons in the NMDA-treated rats. These results suggest that the central antinociceptive effects the peripherally or centrally administered BoNT-A are mediated by transcytosed BoNT-A or direct inhibition of trigeminal neurons. Our data suggest that central targets of BoNT-A might provide a new therapeutic tool for the treatment of orofacial chronic pain conditions. PMID:26170739

  12. 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.

  13. Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targets nucleosomal DNA near the H2A/H2B interface

    Directory of Open Access Journals (Sweden)

    Bridier-Nahmias Antoine

    2012-12-01

    Full Text Available Abstract Background Over the years, a number of reports have revealed that Ty1 integration occurs in a 1-kb window upstream of Pol III-transcribed genes with an approximate 80-bp periodicity between each integration hotspot and that this targeting requires active Pol III transcription at the site of integration. However, the molecular bases of Ty1 targeting are still not understood. Findings The publications by Baller et al. and Mularoni et al. in the April issue of Genome Res. report the first high-throughput sequencing analysis of Ty1 de novo insertion events. Their observations converge to the same conclusion, that Ty1 targets a specific surface of the nucleosome at he H2A/H2B interface. Conclusion This discovery is important, and should help identifying factor(s involved in Ty1 targeting. Recent data on transposable elements and retroviruses integration site choice obtained by large-scale analyses indicate that transcription and chromatin structure play an important role in this process. The studies reported in this commentary add a new evidence of the importance of chromatin in integration selectivity that should be of interest for everyone interested in transposable elements integration.

  14. ORF Alignment: Ca19AnnotatedDec2004aaSeq [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available retrotransposon Tca5 polyprotein [Candida albicans SC5314] ... Length = 221 ... Query: 556 QLHDSLGHTSTQQ...VSNVMKRFNVTTDNIGTDCETCRLGKAITQIPKISTHTISSHCLELL 615 ... QLHDSLGHTSTQQVSNVMKRFNVTTDNIGTDCETCRLGKAITQIP...KISTHTISSHCLELL Sbjct: 1 ... QLHDSLGHTSTQQVSNVMKRFNVTTDNIGTDCETCRLGKAITQIPKISTHTISS

  15. Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms?

    Science.gov (United States)

    Rodić, Nemanja; Burns, Kathleen H

    2013-03-01

    LINE-1 (L1) retrotransposons make up a significant portion of human genomes, with an estimated 500,000 copies per genome. Like other retrotransposons, L1 retrotransposons propagate through RNA sequences that are reverse transcribed into DNA sequences, which are integrated into new genomic loci. L1 somatic insertions have the potential to disrupt the transcriptome by inserting into or nearby genes. By mutating genes and playing a role in epigenetic dysregulation, L1 transposons may contribute to tumorigenesis. Studies of the "mobilome" have lagged behind other tumor characterizations at the sequence, transcript, and epigenetic levels. Here, we consider evidence that L1 retrotransposons may sometimes drive human tumorigenesis.

  16. Long interspersed element-1 (LINE-1: passenger or driver in human neoplasms?

    Directory of Open Access Journals (Sweden)

    Nemanja Rodić

    2013-03-01

    Full Text Available LINE-1 (L1 retrotransposons make up a significant portion of human genomes, with an estimated 500,000 copies per genome. Like other retrotransposons, L1 retrotransposons propagate through RNA sequences that are reverse transcribed into DNA sequences, which are integrated into new genomic loci. L1 somatic insertions have the potential to disrupt the transcriptome by inserting into or nearby genes. By mutating genes and playing a role in epigenetic dysregulation, L1 transposons may contribute to tumorigenesis. Studies of the "mobilome" have lagged behind other tumor characterizations at the sequence, transcript, and epigenetic levels. Here, we consider evidence that L1 retrotransposons may sometimes drive human tumorigenesis.

  17. CXC-chemokines KC and macrophage inflammatory protein-2 (MIP-2) synergistically induce leukocyte recruitment to the central nervous system in rats

    NARCIS (Netherlands)

    Zwijnenburg, Petra J. G.; Polfliet, Machteld M. J.; Florquin, Sandrine; van den Berg, Timo K.; Dijkstra, Christine D.; van Deventer, Sander J. H.; Roord, John J.; van der Poll, Tom; van Furth, A. Marceline

    2003-01-01

    Intracisternal injection of the CXC-chemokines KC or macrophage inflammatory protein (MIP)-2 induced a pleocytosis in the cerebrospinal fluid (CSF) of rats in a dose dependent way. MIP-2 was much more potent than KC. The concurrent injection of both chemokines revealed a profound synergistic effect

  18. Polymorphism and Mobilization of Rransposons in Bos taurus

    DEFF Research Database (Denmark)

    Guldbrandtsen, Bernt; Sahana, Goutam; Lund, Mogens Sandø

    The bovine genome assembly was explored to detect putative retrotransposon sequences. In total 87,310 such sites were detected. Four breeds of dairy cattle (Bos taurus) were examined with respect to the presence, segregation or complete absence of the putative retrotransposon. A total of 10...

  19. Somatic retrotransposition alters the genetic landscape of the human brain

    NARCIS (Netherlands)

    Baillie, J.K.; Barnett, M.W.; Upton, K.R.; Gerhardt, D.J.; Richmond, T.A.; De Sapio, F.; Brennan, P.; Rizzu, P.; Smith, S.; Fell, M.; Talbot, R.T.; Gustincich, S.; Freeman, T.C.; Mattick, J.S.; Hume, D.A.; Heutink, P.; Carninci, P.; Jeddeloh, J.A.; Faulkner, G.J.

    2011-01-01

    Retrotransposons are mobile genetic elements that use a germline 'copy-and-paste' mechanism to spread throughout metazoan genomes1. At least 50 per cent of the human genome is derived from retrotransposons, with three active families (L1, Alu and SVA) associated with insertional mutagenesis and

  20. AcEST: BP918427 [AcEST

    Lifescience Database Archive (English)

    Full Text Available tative uncharacterized protein OS=Vitis... 116 7e-25 tr|Q8RZ67|Q8RZ67_ORYSJ Putative rice retrotransposon retrofit... + Sbjct: 384 ATVRIILSLAVTSGLRLHKLDVKNAFLHGFLNEEVYMEQPPGYTDPY 430 >tr|Q8RZ67|Q8RZ67_ORYSJ Putative rice retrotransposon retrofit

  1. The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution

    Science.gov (United States)

    J.S. (Pat) Heslop-Harrison; Andrea Brandes; Shin Taketa; Thomas Schmidt; Alexander V. Vershinin; Elena G. Alkhimova; Anette Kamm; Robert L. Doudrick; . [and others

    1997-01-01

    Retrotransposons make up a major fraction - sometimes more than 40% - of all plant genomes investigated so far. We have isolated the reverse transcriptase domains of theTyl-copia group elements from several species, ranging in genome size from some 100 Mbp to 23,000 Mbp, and determined the distribution patterns of these retrotransposons on metaphase chromosomes and...

  2. Long range transport: Evaluation of a particle-in-cell model using sources in the US and USSR

    International Nuclear Information System (INIS)

    Rodriguez, D.J.

    1988-08-01

    After being informed that radioactive material from the Chernobyl nuclear power plant had been discovered on the clothing of workers at a Swedish reactor site, the United States Department of Energy requested that the Atmospheric Release Advisory Capability (ARAC) evaluate both the extent and the magnitude of the accident (Dickerson and Sullivan, 1987). ARAC is a real-time emergency response service that specializes in the regional assessment of radiological accidents using advanced dispersion models. While we possessed a sizable inventory of computer models with which to address this problem, we lacked an operational tool that could be used with confidence in determining the fate of airborne radioactivity beyond about 500 km. As an outgrowth of this experience, we began to explore the spatial limits of applicability of our Advection-Diffusion Particle-In-Cell (ADPIC) model (Lange, 1978). At the same time, we began testing a hybrid version of this model that uses the Air Force Global Weather Central's Northern Hemisphere Whole Mesh Grid of wind velocities as input. In combination, these models can provide, potentially, a response capability that extends from tens of kilometers to the entire Northern Hemisphere. 7 refs., 6 figs

  3. Preliminary investigations on a NTP cargo shuttle for earth to moon orbit payload transfer based on a particle bed reactor

    International Nuclear Information System (INIS)

    Raepsaet, X.; Proust, E.; Gervaise, F.; Baraer, L.; Naury, S.; Linet, F.L.

    1995-01-01

    MAPS, a 3-year study program on NTP has recently been launched at CEA following the conclusions of a preliminary scoping study of an NTP system for earth to moon orbit cargo shuttle missions. This paper presents the main results of this scoping study, and gives an outline of the MAPS program. (authors). 5 figs., 11 tabs., 7 refs

  4. Application of two component biodegradable carriers in a particle-fixed biofilm airlift suspension reactor: development and structure of biofilms.

    Science.gov (United States)

    Hille, Andrea; He, Mei; Ochmann, Clemens; Neu, Thomas R; Horn, Harald

    2009-01-01

    Two component biodegradable carriers for biofilm airlift suspension (BAS) reactors were investigated with respect to development of biofilm structure and oxygen transport inside the biofilm. The carriers were composed of PHB (polyhydroxybutyrate), which is easily degradable and PCL (caprolactone), which is less easily degradable by heterotrophic microorganisms. Cryosectioning combined with classical light microscopy and CLSM was used to identify the surface structure of the carrier material over a period of 250 days of biofilm cultivation in an airlift reactor. Pores of 50 to several hundred micrometers depth are formed due to the preferred degradation of PHB. Furthermore, microelectrode studies show the transport mechanism for different types of biofilm structures, which were generated under different substrate conditions. At high loading rates, the growth of a rather loosely structured biofilm with high penetration depths of oxygen was found. Strong changes of substrate concentration during fed-batch mode operation of the reactor enhance the growth of filamentous biofilms on the carriers. Mass transport in the outer regions of such biofilms was mainly driven by advection.

  5. Engineering survey planning for the alignment of a particle accelerator: part II. Design of a reference network and measurement strategy

    Science.gov (United States)

    Junqueira Leão, Rodrigo; Raffaelo Baldo, Crhistian; Collucci da Costa Reis, Maria Luisa; Alves Trabanco, Jorge Luiz

    2018-03-01

    The building blocks of particle accelerators are magnets responsible for keeping beams of charged particles at a desired trajectory. Magnets are commonly grouped in support structures named girders, which are mounted on vertical and horizontal stages. The performance of this type of machine is highly dependent on the relative alignment between its main components. The length of particle accelerators ranges from small machines to large-scale national or international facilities, with typical lengths of hundreds of meters to a few kilometers. This relatively large volume together with micrometric positioning tolerances make the alignment activity a classical large-scale dimensional metrology problem. The alignment concept relies on networks of fixed monuments installed on the building structure to which all accelerator components are referred. In this work, the Sirius accelerator is taken as a case study, and an alignment network is optimized via computational methods in terms of geometry, densification, and surveying procedure. Laser trackers are employed to guide the installation and measure the girders’ positions, using the optimized network as a reference and applying the metric developed in part I of this paper. Simulations demonstrate the feasibility of aligning the 220 girders of the Sirius synchrotron to better than 0.080 mm, at a coverage probability of 95%.

  6. Boundary conditions on the plasma emitter surface in the presence of a particle counter flow: I. Ion emitter

    Energy Technology Data Exchange (ETDEWEB)

    Astrelin, V. T., E-mail: V.T.Astrelin@inp.nsk.su; Kotelnikov, I. A. [Russian Academy of Sciences, Budker Institute of Nuclear Physics, Siberian Branch (Russian Federation)

    2017-02-15

    Emission of positively charged ions from a plasma emitter irradiated by a counterpropagating electron beam is studied theoretically. A bipolar diode with a plasma emitter in which the ion temperature is lower than the electron temperature and the counter electron flow is extracted from the ion collector is calculated in the one-dimensional model. An analog of Bohm’s criterion for ion emission in the presence of a counterpropagating electron beam is derived. The limiting density of the counterpropagating beam in a bipolar diode operating in the space-charge-limited-emission regime is calculated. The full set of boundary conditions on the plasma emitter surface that are required for operation of the high-current optics module in numerical codes used to simulate charged particle sources is formulated.

  7. Preliminary investigations on a NTP cargo shuttle for earth to moon orbit payload transfer based on a particle bed reactor

    Energy Technology Data Exchange (ETDEWEB)

    Raepsaet, X; Proust, E; Gervaise, F; Baraer, L; Naury, S; Linet, F L [CEA Centre d` Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. de Mecanique et de Technologie; Bresson, C F; Coriolis, C.C. de; Bergeron, I T.A.; Bourquin, L V; Clech, L V; Devaux, L V; Chevillot, L V; Augier, E V [EAMEA, 50 - Cherbourg (France)

    1995-12-01

    MAPS, a 3-year study program on NTP has recently been launched at CEA following the conclusions of a preliminary scoping study of an NTP system for earth to moon orbit cargo shuttle missions. This paper presents the main results of this scoping study, and gives an outline of the MAPS program. (authors). 5 figs., 11 tabs., 7 refs.

  8. A particle velocity sensor to measure the sound from a structure in the presence of background noise

    NARCIS (Netherlands)

    de Bree, H.E.; Druyvesteyn, W.F.

    2005-01-01

    The performance (or quality) of a product is often checked by measuring the radiated sound (noise) from the vibrating structure. Often this test has to be done in an environment with background noise, which makes the measurement difficult. When using a (pressure) microphone the background noise can

  9. Dynamical properties for the problem of a particle in an electric field of wave packet: Low velocity and relativistic approach

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Diego F.M., E-mail: diegofregolente@gmail.com [Institute for Multiscale Simulations, Friedrich-Alexander Universität, D-91052, Erlangen (Germany); Leonel, Edson D., E-mail: edleonel@rc.unesp.br [Departamento de Estatística, Matemática Aplicada e Computação, UNESP, Univ. Estadual Paulista, Av. 24A, 1515, Bela Vista, 13506-900, Rio Claro, SP (Brazil); Departamento de Física, UNESP, Univ. Estadual Paulista, Av. 24A, 1515, 13506-900, Rio Claro, SP (Brazil)

    2012-11-01

    We study some dynamical properties for the problem of a charged particle in an electric field considering both the low velocity and relativistic cases. The dynamics for both approaches is described in terms of a two-dimensional and nonlinear mapping. The structure of the phase spaces is mixed and we introduce a hole in the chaotic sea to let the particles to escape. By changing the size of the hole we show that the survival probability decays exponentially for both cases. Additionally, we show for the relativistic dynamics, that the introduction of dissipation changes the mixed phase space and attractors appear. We study the parameter space by using the Lyapunov exponent and the average energy over the orbit and show that the system has a very rich structure with infinite family of self-similar shrimp shaped embedded in a chaotic region.

  10. Analytical solution of settling behavior of a particle in incompressible Newtonian fluid by using Parameterized Perturbation Method

    Directory of Open Access Journals (Sweden)

    Reza Mohammadyari

    2015-08-01

    Full Text Available The problem of solid particle settling is a well known problem in mechanic of fluids. The parametrized Perturbation Method is applied to analytically solve the unsteady motion of a spherical particle falling in a Newtonian fluid using the drag of the form given by Oseen/Ferreira, for a range of Reynolds numbers. Particle equation of motion involved added mass term and ignored the Basset term. By using this new kind of perturbation method called parameterized perturbation method (PPM, analytical expressions for the instantaneous velocity, acceleration and position of the particle were derived. The presented results show the effectiveness of PPM and high rate of convergency of the method to achieve acceptable answers.

  11. Laser range finder model for autonomous navigation of a robot in a maize field using a particle filter

    NARCIS (Netherlands)

    Hiremath, S.A.; Heijden, van der G.W.A.M.; Evert, van F.K.; Stein, A.; Braak, ter C.J.F.

    2014-01-01

    Autonomous navigation of robots in an agricultural environment is a difficult task due to the inherent uncertainty in the environment. Many existing agricultural robots use computer vision and other sensors to supplement Global Positioning System (GPS) data when navigating. Vision based methods are

  12. Track calorimeter (TCAL) of alpha magnetic spectrometer (AMS) (a particle physics experiment on the international space station alpha)

    International Nuclear Information System (INIS)

    Anosov, V.; Baranov, S.; Bednyakov, V.

    1999-01-01

    Based on the simulation and R and D results the JINR project - to supplement AMS with a finely granulated scintillator calorimeter (TCAL) - is discussed. The project cost is about 1 million USD. TCAL would essentially increase the AMS potential in the studies of antimatter, matter and missing matter in the experiments in outer space

  13. A Particle Consistent with the Higgs Boson Observed with the ATLAS Detector at the Large Hadron Collider

    CERN Document Server

    Aad, Georges; Abbott, Brad; Abdallah, Jalal; Abdel Khalek, Samah; Abdelalim, Ahmed Ali; Abdinov, Ovsat; Aben, Rosemarie; Abi, Babak; Abolins, Maris; AbouZeid, Ossama; Abramowicz, Halina; Abreu, Henso; Acharya, Bobby Samir; Adamczyk, Leszek; Adams, David; Addy, Tetteh; Adelman, Jahred; Adomeit, Stefanie; Adragna, Paolo; Adye, Tim; Aefsky, Scott; Aguilar-Saavedra, Juan Antonio; Agustoni, Marco; Aharrouche, Mohamed; Ahlen, Steven; Ahles, Florian; Ahmad, Ashfaq; Ahsan, Mahsana; Aielli, Giulio; Akdogan, Taylan; Åkesson, Torsten Paul Ake; Akimoto, Ginga; Akimov, Andrei; Alam, Mohammad; Alam, Muhammad Aftab; Albert, Justin; Albrand, Solveig; Aleksa, Martin; Aleksandrov, Igor; Alessandria, Franco; Alexa, Calin; Alexander, Gideon; Alexandre, Gauthier; Alexopoulos, Theodoros; Alhroob, Muhammad; Aliev, Malik; Alimonti, Gianluca; Alison, John; Allbrooke, Benedict; Allport, Phillip; Allwood-Spiers, Sarah; Almond, John; Aloisio, Alberto; Alon, Raz; Alonso, Alejandro; Alonso, Francisco; Altheimer, Andrew David; Alvarez Gonzalez, Barbara; Alviggi, Mariagrazia; Amako, Katsuya; Amelung, Christoph; Ammosov, Vladimir; Amor Dos Santos, Susana Patricia; Amorim, Antonio; Amram, Nir; Anastopoulos, Christos; Ancu, Lucian Stefan; Andari, Nansi; Andeen, Timothy; Anders, Christoph Falk; Anders, Gabriel; Anderson, Kelby; Andreazza, Attilio; Andrei, George Victor; Andrieux, Marie-Laure; Anduaga, Xabier; Angelidakis, Stylianos; Anger, Philipp; Angerami, Aaron; Anghinolfi, Francis; Anisenkov, Alexey; Anjos, Nuno; Annovi, Alberto; Antonaki, Ariadni; Antonelli, Mario; Antonov, Alexey; Antos, Jaroslav; Anulli, Fabio; Aoki, Masato; Aoun, Sahar; Aperio Bella, Ludovica; Apolle, Rudi; Arabidze, Giorgi; Aracena, Ignacio; Arai, Yasuo; Arce, Ayana; Arfaoui, Samir; Arguin, Jean-Francois; Arik, Engin; Arik, Metin; Armbruster, Aaron James; Arnaez, Olivier; Arnal, Vanessa; Arnault, Christian; Artamonov, Andrei; Artoni, Giacomo; Arutinov, David; Asai, Shoji; Ask, Stefan; Åsman, Barbro; Asquith, Lily; Assamagan, Ketevi; Astbury, Alan; Atkinson, Markus; Aubert, Bernard; Auge, Etienne; Augsten, Kamil; Aurousseau, Mathieu; Avolio, Giuseppe; Avramidou, Rachel Maria; Axen, David; Azuelos, Georges; Azuma, Yuya; Baak, Max; Baccaglioni, Giuseppe; Bacci, Cesare; Bach, Andre; Bachacou, Henri; Bachas, Konstantinos; Backes, Moritz; Backhaus, Malte; Backus Mayes, John; Badescu, Elisabeta; Bagnaia, Paolo; Bahinipati, Seema; Bai, Yu; Bailey, David; Bain, Travis; Baines, John; Baker, Oliver Keith; Baker, Mark; Baker, Sarah; Balek, Petr; Banas, Elzbieta; Banerjee, Piyali; Banerjee, Swagato; Banfi, Danilo; Bangert, Andrea Michelle; Bansal, Vikas; Bansil, Hardeep Singh; Barak, Liron; Baranov, Sergei; Barbaro Galtieri, Angela; Barber, Tom; Barberio, Elisabetta Luigia; Barberis, Dario; Barbero, Marlon; Bardin, Dmitri; Barillari, Teresa; Barisonzi, Marcello; Barklow, Timothy; Barlow, Nick; Barnett, Bruce; Barnett, Michael; Baroncelli, Antonio; Barone, Gaetano; Barr, Alan; Barreiro, Fernando; Barreiro Guimarães da Costa, João; Barrillon, Pierre; Bartoldus, Rainer; Barton, Adam Edward; Bartsch, Valeria; Basye, Austin; Bates, Richard; Batkova, Lucia; Batley, Richard; Battaglia, Andreas; Battistin, Michele; Bauer, Florian; Bawa, Harinder Singh; Beale, Steven; Beau, Tristan; Beauchemin, Pierre-Hugues; Beccherle, Roberto; Bechtle, Philip; Beck, Hans Peter; Becker, Anne Kathrin; Becker, Sebastian; Beckingham, Matthew; Becks, Karl-Heinz; Beddall, Andrew; Beddall, Ayda; Bedikian, Sourpouhi; Bednyakov, Vadim; Bee, Christopher; Beemster, Lars; Begel, Michael; Behar Harpaz, Silvia; Behera, Prafulla; Beimforde, Michael; Belanger-Champagne, Camille; Bell, Paul; Bell, William; Bella, Gideon; Bellagamba, Lorenzo; Bellomo, Massimiliano; Belloni, Alberto; Beloborodova, Olga; Belotskiy, Konstantin; Beltramello, Olga; Benary, Odette; Benchekroun, Driss; Bendtz, Katarina; Benekos, Nektarios; Benhammou, Yan; Benhar Noccioli, Eleonora; Benitez Garcia, Jorge-Armando; Benjamin, Douglas; Benoit, Mathieu; Bensinger, James; Benslama, Kamal; Bentvelsen, Stan; Berge, David; Bergeaas Kuutmann, Elin; Berger, Nicolas; Berghaus, Frank; Berglund, Elina; Beringer, Jürg; Bernat, Pauline; Bernhard, Ralf; Bernius, Catrin; Bernlochner, Florian Urs; Berry, Tracey; Bertella, Claudia; Bertin, Antonio; Bertolucci, Federico; Besana, Maria Ilaria; Besjes, Geert-Jan; Besson, Nathalie; Bethke, Siegfried; Bhimji, Wahid; Bianchi, Riccardo-Maria; Bianco, Michele; Biebel, Otmar; Bieniek, Stephen Paul; Bierwagen, Katharina; Biesiada, Jed; Biglietti, Michela; Bilokon, Halina; Bindi, Marcello; Binet, Sebastien; Bingul, Ahmet; Bini, Cesare; Biscarat, Catherine; Bittner, Bernhard; Black, Kevin; Blair, Robert; Blanchard, Jean-Baptiste; Blanchot, Georges; Blazek, Tomas; Bloch, Ingo; Blocker, Craig; Blocki, Jacek; Blondel, Alain; Blum, Walter; Blumenschein, Ulrike; Bobbink, Gerjan; Bobrovnikov, Victor; Bocchetta, Simona Serena; Bocci, Andrea; Boddy, Christopher Richard; Boehler, Michael; Boek, Jennifer; Boelaert, Nele; Bogaerts, Joannes Andreas; Bogdanchikov, Alexander; Bogouch, Andrei; Bohm, Christian; Bohm, Jan; Boisvert, Veronique; Bold, Tomasz; Boldea, Venera; Bolnet, Nayanka Myriam; Bomben, Marco; Bona, Marcella; Boonekamp, Maarten; Bordoni, Stefania; Borer, Claudia; Borisov, Anatoly; Borissov, Guennadi; Borjanovic, Iris; Borri, Marcello; Borroni, Sara; Bortolotto, Valerio; Bos, Kors; Boscherini, Davide; Bosman, Martine; Boterenbrood, Hendrik; Bouchami, Jihene; Boudreau, Joseph; Bouhova-Thacker, Evelina Vassileva; Boumediene, Djamel Eddine; Bourdarios, Claire; Bousson, Nicolas; Boveia, Antonio; Boyd, James; Boyko, Igor; Bozovic-Jelisavcic, Ivanka; Bracinik, Juraj; Branchini, Paolo; Brandenburg, George; Brandt, Andrew; Brandt, Gerhard; Brandt, Oleg; Bratzler, Uwe; Brau, Benjamin; Brau, James; Braun, Helmut; Brazzale, Simone Federico; Brelier, Bertrand; Bremer, Johan; Brendlinger, Kurt; Brenner, Richard; Bressler, Shikma; Britton, Dave; Brochu, Frederic; Brock, Ian; Brock, Raymond; Broggi, Francesco; Bromberg, Carl; Bronner, Johanna; Brooijmans, Gustaaf; Brooks, Timothy; Brooks, William; Brown, Gareth; Brown, Heather; Bruckman de Renstrom, Pawel; Bruncko, Dusan; Bruneliere, Renaud; Brunet, Sylvie; Bruni, Alessia; Bruni, Graziano; Bruschi, Marco; Buanes, Trygve; Buat, Quentin; Bucci, Francesca; Buchanan, James; Buchholz, Peter; Buckingham, Ryan; Buckley, Andrew; Buda, Stelian Ioan; Budagov, Ioulian; Budick, Burton; Büscher, Volker; Bugge, Lars; Bulekov, Oleg; Bundock, Aaron Colin; Bunse, Moritz; Buran, Torleiv; Burckhart, Helfried; Burdin, Sergey; Burgess, Thomas; Burke, Stephen; Busato, Emmanuel; Bussey, Peter; Buszello, Claus-Peter; Butler, Bart; Butler, John; Buttar, Craig; Butterworth, Jonathan; Buttinger, William; Cabrera Urbán, Susana; Caforio, Davide; Cakir, Orhan; Calafiura, Paolo; Calderini, Giovanni; Calfayan, Philippe; Calkins, Robert; Caloba, Luiz; Caloi, Rita; Calvet, David; Calvet, Samuel; Camacho Toro, Reina; Camarri, Paolo; Cameron, David; Caminada, Lea Michaela; Caminal Armadans, Roger; Campana, Simone; Campanelli, Mario; Canale, Vincenzo; Canelli, Florencia; Canepa, Anadi; Cantero, Josu; Cantrill, Robert; Capasso, Luciano; Capeans Garrido, Maria Del Mar; Caprini, Irinel; Caprini, Mihai; Capriotti, Daniele; Capua, Marcella; Caputo, Regina; Cardarelli, Roberto; Carli, Tancredi; Carlino, Gianpaolo; Carminati, Leonardo; Caron, Bryan; Caron, Sascha; Carquin, Edson; Carrillo-Montoya, German D; Carter, Antony; Carter, Janet; Carvalho, João; Casadei, Diego; Casado, Maria Pilar; Cascella, Michele; Caso, Carlo; Castaneda Hernandez, Alfredo Martin; Castaneda-Miranda, Elizabeth; Castillo Gimenez, Victoria; Castro, Nuno Filipe; Cataldi, Gabriella; Catastini, Pierluigi; Catinaccio, Andrea; Catmore, James; Cattai, Ariella; Cattani, Giordano; Caughron, Seth; Cavaliere, Viviana; Cavalleri, Pietro; Cavalli, Donatella; Cavalli-Sforza, Matteo; Cavasinni, Vincenzo; Ceradini, Filippo; Cerqueira, Augusto Santiago; Cerri, Alessandro; Cerrito, Lucio; Cerutti, Fabio; Cetin, Serkant Ali; Chafaq, Aziz; Chakraborty, Dhiman; Chalupkova, Ina; Chan, Kevin; Chang, Philip; Chapleau, Bertrand; Chapman, John Derek; Chapman, John Wehrley; Chareyre, Eve; Charlton, Dave; Chavda, Vikash; Chavez Barajas, Carlos Alberto; Cheatham, Susan; Chekanov, Sergei; Chekulaev, Sergey; Chelkov, Gueorgui; Chelstowska, Magda Anna; Chen, Chunhui; Chen, Hucheng; Chen, Shenjian; Chen, Xin; Chen, Yujiao; Cheng, Yangyang; Cheplakov, Alexander; Cherkaoui El Moursli, Rajaa; Chernyatin, Valeriy; Cheu, Elliott; Cheung, Sing-Leung; Chevalier, Laurent; Chiefari, Giovanni; Chikovani, Leila; Childers, John Taylor; Chilingarov, Alexandre; Chiodini, Gabriele; Chisholm, Andrew; Chislett, Rebecca Thalatta; Chitan, Adrian; Chizhov, Mihail; Choudalakis, Georgios; Chouridou, Sofia; Christidi, Illectra-Athanasia; Christov, Asen; Chromek-Burckhart, Doris; Chu, Ming-Lee; Chudoba, Jiri; Ciapetti, Guido; Ciftci, Abbas Kenan; Ciftci, Rena; Cinca, Diane; Cindro, Vladimir; Ciocca, Claudia; Ciocio, Alessandra; Cirilli, Manuela; Cirkovic, Predrag; Citron, Zvi Hirsh; Citterio, Mauro; Ciubancan, Mihai; Clark, Allan G; Clark, Philip James; Clarke, Robert; Cleland, Bill; Clemens, Jean-Claude; Clement, Benoit; Clement, Christophe; Coadou, Yann; Cobal, Marina; Coccaro, Andrea; Cochran, James H; Coffey, Laurel; Cogan, Joshua Godfrey; Coggeshall, James; Cogneras, Eric; Colas, Jacques; Cole, Stephen; Colijn, Auke-Pieter; Collins, Neil; Collins-Tooth, Christopher; Collot, Johann; Colombo, Tommaso; Colon, German; Compostella, Gabriele; Conde Muiño, Patricia; Coniavitis, Elias; Conidi, Maria Chiara; Consonni, Sofia Maria; Consorti, Valerio; Constantinescu, Serban; Conta, Claudio; Conti, Geraldine; Conventi, Francesco; Cooke, Mark; Cooper, Ben; Cooper-Sarkar, Amanda; Cooper-Smith, Neil; Copic, Katherine; Cornelissen, Thijs; Corradi, Massimo; Corriveau, Francois; Cortes-Gonzalez, Arely; Cortiana, Giorgio; Costa, Giuseppe; Costa, María José; Costanzo, Davide; Côté, David; Courneyea, Lorraine; Cowan, Glen; Cowden, Christopher; Cox, Brian; Cranmer, Kyle; Crescioli, Francesco; Cristinziani, Markus; Crosetti, Giovanni; Crépé-Renaudin, Sabine; Cuciuc, Constantin-Mihai; Cuenca Almenar, Cristóbal; Cuhadar Donszelmann, Tulay; Curatolo, Maria; Curtis, Chris; Cuthbert, Cameron; Cwetanski, Peter; Czirr, Hendrik; Czodrowski, Patrick; Czyczula, Zofia; D'Auria, Saverio; D'Onofrio, Monica; D'Orazio, Alessia; Da Cunha Sargedas De Sousa, Mario Jose; Da Via, Cinzia; Dabrowski, Wladyslaw; Dafinca, Alexandru; Dai, Tiesheng; Dallapiccola, Carlo; Dam, Mogens; Dameri, Mauro; Damiani, Daniel; Danielsson, Hans Olof; Dao, Valerio; Darbo, Giovanni; Darlea, Georgiana Lavinia; Dassoulas, James; Davey, Will; Davidek, Tomas; Davidson, Nadia; Davidson, Ruth; Davies, Eleanor; Davies, Merlin; Davignon, Olivier; Davison, Adam; Davygora, Yuriy; Dawe, Edmund; Dawson, Ian; Daya-Ishmukhametova, Rozmin; De, Kaushik; de Asmundis, Riccardo; De Castro, Stefano; De Cecco, Sandro; de Graat, Julien; De Groot, Nicolo; de Jong, Paul; De La Taille, Christophe; De la Torre, Hector; De Lorenzi, Francesco; de Mora, Lee; De Nooij, Lucie; De Pedis, Daniele; De Salvo, Alessandro; De Sanctis, Umberto; De Santo, Antonella; De Vivie De Regie, Jean-Baptiste; De Zorzi, Guido; Dearnaley, William James; Debbe, Ramiro; Debenedetti, Chiara; Dechenaux, Benjamin; Dedovich, Dmitri; Degenhardt, James; Del Papa, Carlo; Del Peso, Jose; Del Prete, Tarcisio; Delemontex, Thomas; Deliyergiyev, Maksym; Dell'Acqua, Andrea; Dell'Asta, Lidia; Della Pietra, Massimo; della Volpe, Domenico; Delmastro, Marco; Delpierre, Pierre; Delsart, Pierre-Antoine; Deluca, Carolina; Demers, Sarah; Demichev, Mikhail; Demirkoz, Bilge; Deng, Jianrong; Denisov, Sergey; Derendarz, Dominik; Derkaoui, Jamal Eddine; Derue, Frederic; Dervan, Paul; Desch, Klaus Kurt; Devetak, Erik; Deviveiros, Pier-Olivier; Dewhurst, Alastair; DeWilde, Burton; Dhaliwal, Saminder; Dhullipudi, Ramasudhakar; Di Ciaccio, Anna; Di Ciaccio, Lucia; Di Donato, Camilla; Di Girolamo, Alessandro; Di Girolamo, Beniamino; Di Luise, Silvestro; Di Mattia, Alessandro; Di Micco, Biagio; Di Nardo, Roberto; Di Simone, Andrea; Di Sipio, Riccardo; Diaz, Marco Aurelio; Diehl, Edward; Dietrich, Janet; Dietzsch, Thorsten; Diglio, Sara; Dindar Yagci, Kamile; Dingfelder, Jochen; Dinut, Florin; Dionisi, Carlo; Dita, Petre; Dita, Sanda; Dittus, Fridolin; Djama, Fares; Djobava, Tamar; do Vale, Maria Aline Barros; Do Valle Wemans, André; Doan, Thi Kieu Oanh; Dobbs, Matt; Dobinson, Robert; Dobos, Daniel; Dobson, Ellie; Dodd, Jeremy; Doglioni, Caterina; Doherty, Tom; Doi, Yoshikuni; Dolejsi, Jiri; Dolenc, Irena; Dolezal, Zdenek; Dolgoshein, Boris; Dohmae, Takeshi; Donadelli, Marisilvia; Donini, Julien; Dopke, Jens; Doria, Alessandra; Dos Anjos, Andre; Dotti, Andrea; Dova, Maria-Teresa; Dowell, John; Doxiadis, Alexander; Doyle, Tony; Dressnandt, Nandor; Dris, Manolis; Dubbert, Jörg; Dube, Sourabh; Duchovni, Ehud; Duckeck, Guenter; Duda, Dominik; Dudarev, Alexey; Dudziak, Fanny; Dührssen, Michael; Duerdoth, Ian; Duflot, Laurent; Dufour, Marc-Andre; Duguid, Liam; Dunford, Monica; Duran Yildiz, Hatice; Duxfield, Robert; Dwuznik, Michal; Dydak, Friedrich; Düren, Michael; Ebenstein, William; Ebke, Johannes; Eckweiler, Sebastian; Edmonds, Keith; Edson, William; Edwards, Clive; Edwards, Nicholas Charles; Ehrenfeld, Wolfgang; Eifert, Till; Eigen, Gerald; Einsweiler, Kevin; Eisenhandler, Eric; Ekelof, Tord; El Kacimi, Mohamed; Ellert, Mattias; Elles, Sabine; Ellinghaus, Frank; Ellis, Katherine; Ellis, Nicolas; Elmsheuser, Johannes; Elsing, Markus; Emeliyanov, Dmitry; Engelmann, Roderich; Engl, Albert; Epp, Brigitte; Erdmann, Johannes; Ereditato, Antonio; Eriksson, Daniel; Ernst, Jesse; Ernst, Michael; Ernwein, Jean; Errede, Deborah; Errede, Steven; Ertel, Eugen; Escalier, Marc; Esch, Hendrik; Escobar, Carlos; Espinal Curull, Xavier; Esposito, Bellisario; Etienne, Francois; Etienvre, Anne-Isabelle; Etzion, Erez; Evangelakou, Despoina; Evans, Hal; Fabbri, Laura; Fabre, Caroline; Fakhrutdinov, Rinat; Falciano, Speranza; Fang, Yaquan; Fanti, Marcello; Farbin, Amir; Farilla, Addolorata; Farley, Jason; Farooque, Trisha; Farrell, Steven; Farrington, Sinead; Farthouat, Philippe; Fassi, Farida; Fassnacht, Patrick; Fassouliotis, Dimitrios; Fatholahzadeh, Baharak; Favareto, Andrea; Fayard, Louis; Fazio, Salvatore; Febbraro, Renato; Federic, Pavol; Fedin, Oleg; Fedorko, Wojciech; Fehling-Kaschek, Mirjam; Feligioni, Lorenzo; Fellmann, Denis; Feng, Cunfeng; Feng, Eric; Fenyuk, Alexander; Ferencei, Jozef; Fernando, Waruna; Ferrag, Samir; Ferrando, James; Ferrara, Valentina; Ferrari, Arnaud; Ferrari, Pamela; Ferrari, Roberto; Ferreira de Lima, Danilo Enoque; Ferrer, Antonio; Ferrere, Didier; Ferretti, Claudio; Ferretto Parodi, Andrea; Fiascaris, Maria; Fiedler, Frank; Filipčič, Andrej; Filthaut, Frank; Fincke-Keeler, Margret; Fiolhais, Miguel; Fiorini, Luca; Firan, Ana; Fischer, Gordon; Fisher, Matthew; Flechl, Martin; Fleck, Ivor; Fleckner, Johanna; Fleischmann, Philipp; Fleischmann, Sebastian; Flick, Tobias; Floderus, Anders; Flores Castillo, Luis; Flowerdew, Michael; Fonseca Martin, Teresa; Formica, Andrea; Forti, Alessandra; Fortin, Dominique; Fournier, Daniel; Fowler, Andrew; Fox, Harald; Francavilla, Paolo; Franchini, Matteo; Franchino, Silvia; Francis, David; Frank, Tal; Franklin, Melissa; Franz, Sebastien; Fraternali, Marco; Fratina, Sasa; French, Sky; Friedrich, Conrad; Friedrich, Felix; Froeschl, Robert; Froidevaux, Daniel; Frost, James; Fukunaga, Chikara; Fullana Torregrosa, Esteban; Fulsom, Bryan Gregory; Fuster, Juan; Gabaldon, Carolina; Gabizon, Ofir; Gadatsch, Stefan; Gadfort, Thomas; Gadomski, Szymon; Gagliardi, Guido; Gagnon, Pauline; Galea, Cristina; Galhardo, Bruno; Gallas, Elizabeth; Gallo, Valentina Santina; Gallop, Bruce; Gallus, Petr; Gan, KK; Gao, Yongsheng; Gaponenko, Andrei; Garberson, Ford; Garcia-Sciveres, Maurice; García, Carmen; García Navarro, José Enrique; Gardner, Robert; Garelli, Nicoletta; Garitaonandia, Hegoi; Garonne, Vincent; Gatti, Claudio; Gaudio, Gabriella; Gaur, Bakul; Gauthier, Lea; Gauzzi, Paolo; Gavrilenko, Igor; Gay, Colin; Gaycken, Goetz; Gazis, Evangelos; Ge, Peng; Gecse, Zoltan; Gee, Norman; Geerts, Daniël Alphonsus Adrianus; Geich-Gimbel, Christoph; Gellerstedt, Karl; Gemme, Claudia; Gemmell, Alistair; Genest, Marie-Hélène; Gentile, Simonetta; George, Matthias; George, Simon; Gerlach, Peter; Gershon, Avi; Geweniger, Christoph; Ghazlane, Hamid; Ghodbane, Nabil; Giacobbe, Benedetto; Giagu, Stefano; Giakoumopoulou, Victoria; Giangiobbe, Vincent; Gianotti, Fabiola; Gibbard, Bruce; Gibson, Adam; Gibson, Stephen; Gilchriese, Murdock; Gildemeister, Otto; Gillberg, Dag; Gillman, Tony; Gingrich, Douglas; Ginzburg, Jonatan; Giokaris, Nikos; Giordani, MarioPaolo; Giordano, Raffaele; Giorgi, Francesco Michelangelo; Giovannini, Paola; Giraud, Pierre-Francois; Giugni, Danilo; Giunta, Michele; Giusti, Paolo; Gjelsten, Børge Kile; Gladilin, Leonid; Glasman, Claudia; Glatzer, Julian; Glazov, Alexandre; Glitza, Karl-Walter; Glonti, George; Goddard, Jack Robert; Godfrey, Jennifer; Godlewski, Jan; Goebel, Martin; Göpfert, Thomas; Goeringer, Christian; Gössling, Claus; Goldfarb, Steven; Golling, Tobias; Gomes, Agostinho; Gomez Fajardo, Luz Stella; Gonçalo, Ricardo; Goncalves Pinto Firmino Da Costa, Joao; Gonella, Laura; González de la Hoz, Santiago; Gonzalez Parra, Garoe; Gonzalez Silva, Laura; Gonzalez-Sevilla, Sergio; Goodson, Jeremiah Jet; Goossens, Luc; Gorbounov, Petr Andreevich; Gordon, Howard; Gorelov, Igor; Gorfine, Grant; Gorini, Benedetto; Gorini, Edoardo; Gorišek, Andrej; Gornicki, Edward; Gosdzik, Bjoern; Goshaw, Alfred; Gosselink, Martijn; Gostkin, Mikhail Ivanovitch; Gough Eschrich, Ivo; Gouighri, Mohamed; Goujdami, Driss; Goulette, Marc Phillippe; Goussiou, Anna; Goy, Corinne; Gozpinar, Serdar; Grabowska-Bold, Iwona; Grafström, Per; Grahn, Karl-Johan; Gramstad, Eirik; Grancagnolo, Francesco; Grancagnolo, Sergio; Grassi, Valerio; Gratchev, Vadim; Grau, Nathan; Gray, Heather; Gray, Julia Ann; Graziani, Enrico; Grebenyuk, Oleg; Greenshaw, Timothy; Greenwood, Zeno Dixon; Gregersen, Kristian; Gregor, Ingrid-Maria; Grenier, Philippe; Griffiths, Justin; Grigalashvili, Nugzar; Grillo, Alexander; Grinstein, Sebastian; Gris, Philippe Luc Yves; Grishkevich, Yaroslav; Grivaz, Jean-Francois; Gross, Eilam; Grosse-Knetter, Joern; Groth-Jensen, Jacob; Grybel, Kai; Guest, Daniel; Guicheney, Christophe; Guillemin, Thibault; Guindon, Stefan; Gul, Umar; Gunther, Jaroslav; Guo, Bin; Guo, Jun; Gutierrez, Phillip; Guttman, Nir; Gutzwiller, Olivier; Guyot, Claude; Gwenlan, Claire; Gwilliam, Carl; Haas, Andy; Haas, Stefan; Haber, Carl; Hadavand, Haleh Khani; Hadley, David; Haefner, Petra; Hahn, Ferdinand; Haider, Stefan; Hajduk, Zbigniew; Hakobyan, Hrachya; Hall, David; Haller, Johannes; Hamacher, Klaus; Hamal, Petr; Hamano, Kenji; Hamer, Matthias; Hamilton, Andrew; Hamilton, Samuel; Han, Liang; Hanagaki, Kazunori; Hanawa, Keita; Hance, Michael; Handel, Carsten; Hanke, Paul; Hansen, John Renner; Hansen, Jørgen Beck; Hansen, Jorn Dines; Hansen, Peter Henrik; Hansson, Per; Hara, Kazuhiko; Hard, Andrew; Hare, Gabriel; Harenberg, Torsten; Harkusha, Siarhei; Harper, Devin; Harrington, Robert; Harris, Orin; Hartert, Jochen; Hartjes, Fred; Haruyama, Tomiyoshi; Harvey, Alex; Hasegawa, Satoshi; Hasegawa, Yoji; Hassani, Samira; Haug, Sigve; Hauschild, Michael; Hauser, Reiner; Havranek, Miroslav; Hawkes, Christopher; Hawkings, Richard John; Hawkins, Anthony David; Hayakawa, Takashi; Hayashi, Takayasu; Hayden, Daniel; Hays, Chris; Hayward, Helen; Haywood, Stephen; Head, Simon; Hedberg, Vincent; Heelan, Louise; Heim, Sarah; Heinemann, Beate; Heisterkamp, Simon; Helary, Louis; Heller, Claudio; Heller, Matthieu; Hellman, Sten; Hellmich, Dennis; Helsens, Clement; Henderson, Robert; Henke, Michael; Henrichs, Anna; Henriques Correia, Ana Maria; Henrot-Versille, Sophie; Hensel, Carsten; Henß, Tobias; Hernandez, Carlos Medina; Hernández Jiménez, Yesenia; Herrberg, Ruth; Herten, Gregor; Hertenberger, Ralf; Hervas, Luis; Hesketh, Gavin Grant; Hessey, Nigel; Higón-Rodriguez, Emilio; Hill, John; Hiller, Karl Heinz; Hillert, Sonja; Hillier, Stephen; Hinchliffe, Ian; Hines, Elizabeth; Hirose, Minoru; Hirsch, Florian; Hirschbuehl, Dominic; Hobbs, John; Hod, Noam; Hodgkinson, Mark; Hodgson, Paul; Hoecker, Andreas; Hoeferkamp, Martin; Hoffman, Julia; Hoffmann, Dirk; Hohlfeld, Marc; Holder, Martin; Holmgren, Sven-Olof; Holy, Tomas; Holzbauer, Jenny; Hong, Tae Min; Hooft van Huysduynen, Loek; Horner, Stephan; Hostachy, Jean-Yves; Hou, Suen; Hoummada, Abdeslam; Howard, Jacob; Howarth, James; Hristova, Ivana; Hrivnac, Julius; Hryn'ova, Tetiana; Hsu, Pai-hsien Jennifer; Hsu, Shih-Chieh; Hu, Diedi; Hubacek, Zdenek; Hubaut, Fabrice; Huegging, Fabian; Huettmann, Antje; Huffman, Todd Brian; Hughes, Emlyn; Hughes, Gareth; Huhtinen, Mika; Hurwitz, Martina; Huseynov, Nazim; Huston, Joey; Huth, John; Iacobucci, Giuseppe; Iakovidis, Georgios; Ibbotson, Michael; Ibragimov, Iskander; Iconomidou-Fayard, Lydia; Idarraga, John; Iengo, Paolo; Igonkina, Olga; Ikegami, Yoichi; Ikeno, Masahiro; Iliadis, Dimitrios; Ilic, Nikolina; Ince, Tayfun; Inigo-Golfin, Joaquin; Ioannou, Pavlos; Iodice, Mauro; Iordanidou, Kalliopi; Ippolito, Valerio; Irles Quiles, Adrian; Isaksson, Charlie; Ishino, Masaya; Ishitsuka, Masaki; Ishmukhametov, Renat; Issever, Cigdem; Istin, Serhat; Ivashin, Anton; Iwanski, Wieslaw; Iwasaki, Hiroyuki; Izen, Joseph; Izzo, Vincenzo; Jackson, Brett; Jackson, John; Jackson, Paul; Jaekel, Martin; Jain, Vivek; Jakobs, Karl; Jakobsen, Sune; Jakoubek, Tomas; Jakubek, Jan; Jamin, David Olivier; Jana, Dilip; Jansen, Eric; Jansen, Hendrik; Jantsch, Andreas; Janus, Michel; Jarlskog, Göran; Jeanty, Laura; Jen-La Plante, Imai; Jennens, David; Jenni, Peter; Loevschall-Jensen, Ask Emil; Jež, Pavel; Jézéquel, Stéphane; Jha, Manoj Kumar; Ji, Haoshuang; Ji, Weina; Jia, Jiangyong; Jiang, Yi; Jimenez Belenguer, Marcos; Jin, Shan; Jinnouchi, Osamu; Joergensen, Morten Dam; Joffe, David; Johansen, Marianne; Johansson, Erik; Johansson, Per; Johnert, Sebastian; Johns, Kenneth; Jon-And, Kerstin; Jones, Graham; Jones, Roger; Jones, Tim; Joram, Christian; Jorge, Pedro; Joshi, Kiran Daniel; Jovicevic, Jelena; Jovin, Tatjana; Ju, Xiangyang; Jung, Christian; Jungst, Ralph Markus; Juranek, Vojtech; Jussel, Patrick; Juste Rozas, Aurelio; Kabana, Sonja; Kaci, Mohammed; Kaczmarska, Anna; Kadlecik, Peter; Kado, Marumi; Kagan, Harris; Kagan, Michael; Kajomovitz, Enrique; Kalinin, Sergey; Kalinovskaya, Lidia; Kama, Sami; Kanaya, Naoko; Kaneda, Michiru; Kaneti, Steven; Kanno, Takayuki; Kantserov, Vadim; Kanzaki, Junichi; Kaplan, Benjamin; Kapliy, Anton; Kaplon, Jan; Kar, Deepak; Karagounis, Michael; Karakostas, Konstantinos; Karnevskiy, Mikhail; Kartvelishvili, Vakhtang; Karyukhin, Andrey; Kashif, Lashkar; Kasieczka, Gregor; Kass, Richard; Kastanas, Alex; Kataoka, Mayuko; Kataoka, Yousuke; Katsoufis, Elias; Katzy, Judith; Kaushik, Venkatesh; Kawagoe, Kiyotomo; Kawamoto, Tatsuo; Kawamura, Gen; Kayl, Manuel; Kazama, Shingo; Kazanin, Vassili; Kazarinov, Makhail; Keeler, Richard; Keener, Paul; Kehoe, Robert; Keil, Markus; Kekelidze, George; Keller, John; Kenyon, Mike; Kepka, Oldrich; Kerschen, Nicolas; Kerševan, Borut Paul; Kersten, Susanne; Kessoku, Kohei; Keung, Justin; Khalil-zada, Farkhad; Khandanyan, Hovhannes; Khanov, Alexander; Kharchenko, Dmitri; Khodinov, Alexander; Khomich, Andrei; Khoo, Teng Jian; Khoriauli, Gia; Khoroshilov, Andrey; Khovanskiy, Valery; Khramov, Evgeniy; Khubua, Jemal; Kim, Hyeon Jin; Kim, Shinhong; Kimura, Naoki; Kind, Oliver; King, Barry; King, Matthew; King, Robert Steven Beaufoy; Kirk, Julie; Kiryunin, Andrey; Kishimoto, Tomoe; Kisielewska, Danuta; Kitamura, Takumi; Kittelmann, Thomas; Kiuchi, Kenji; Kladiva, Eduard; Klein, Max; Klein, Uta; Kleinknecht, Konrad; Klemetti, Miika; Klier, Amit; Klimek, Pawel; Klimentov, Alexei; Klingenberg, Reiner; Klinger, Joel Alexander; Klinkby, Esben; Klioutchnikova, Tatiana; Klok, Peter; Klous, Sander; Kluge, Eike-Erik; Kluge, Thomas; Kluit, Peter; Kluth, Stefan; Kneringer, Emmerich; Knoops, Edith; Knue, Andrea; Ko, Byeong Rok; Kobayashi, Tomio; Kobel, Michael; Kocian, Martin; Kodys, Peter; Köneke, Karsten; König, Adriaan; Koenig, Sebastian; Köpke, Lutz; Koetsveld, Folkert; Koevesarki, Peter; Koffas, Thomas; Koffeman, Els; Kogan, Lucy Anne; Kohlmann, Simon; Kohn, Fabian; Kohout, Zdenek; Kohriki, Takashi; Koi, Tatsumi; Kolachev, Guennady; Kolanoski, Hermann; Kolesnikov, Vladimir; Koletsou, Iro; Koll, James; Komar, Aston; Komori, Yuto; Kondo, Takahiko; Kono, Takanori; Kononov, Anatoly; Konoplich, Rostislav; Konstantinidis, Nikolaos; Kopeliansky, Revital; Koperny, Stefan; Korcyl, Krzysztof; Kordas, Kostantinos; Korn, Andreas; Korol, Aleksandr; Korolkov, Ilya; Korolkova, Elena; Korotkov, Vladislav; Kortner, Oliver; Kortner, Sandra; Kostyukhin, Vadim; Kotov, Sergey; Kotov, Vladislav; Kotwal, Ashutosh; Kourkoumelis, Christine; Kouskoura, Vasiliki; Koutsman, Alex; Kowalewski, Robert Victor; Kowalski, Tadeusz; Kozanecki, Witold; Kozhin, Anatoly; Kral, Vlastimil; Kramarenko, Viktor; Kramberger, Gregor; Krasny, Mieczyslaw Witold; Krasznahorkay, Attila; Kraus, Jana; Kreiss, Sven; Krejci, Frantisek; Kretzschmar, Jan; Krieger, Nina; Krieger, Peter; Kroeninger, Kevin; Kroha, Hubert; Kroll, Joe; Kroseberg, Juergen; Krstic, Jelena; Kruchonak, Uladzimir; Krüger, Hans; Kruker, Tobias; Krumnack, Nils; Krumshteyn, Zinovii; Kruse, Amanda; Kubota, Takashi; Kuday, Sinan; Kuehn, Susanne; Kugel, Andreas; Kuhl, Thorsten; Kuhn, Dietmar; Kukhtin, Victor; Kulchitsky, Yuri; Kuleshov, Sergey; Kummer, Christian; Kuna, Marine; Kunkle, Joshua; Kupco, Alexander; Kurashige, Hisaya; Kurata, Masakazu; Kurochkin, Yurii; Kus, Vlastimil; Kuwertz, Emma Sian; Kuze, Masahiro; Kvita, Jiri; Kwee, Regina; La Rosa, Alessandro; La Rotonda, Laura; Labarga, Luis; Labbe, Julien; Lablak, Said; Lacasta, Carlos; Lacava, Francesco; Lacey, James; Lacker, Heiko; Lacour, Didier; Lacuesta, Vicente Ramón; Ladygin, Evgueni; Lafaye, Remi; Laforge, Bertrand; Lagouri, Theodota; Lai, Stanley; Laisne, Emmanuel; Lamanna, Massimo; Lambourne, Luke; Lampen, Caleb; Lampl, Walter; Lancon, Eric; Landgraf, Ulrich; Landon, Murrough; Lang, Valerie Susanne; Lange, Clemens; Lankford, Andrew; Lanni, Francesco; Lantzsch, Kerstin; Laplace, Sandrine; Lapoire, Cecile; Laporte, Jean-Francois; Lari, Tommaso; Larner, Aimee; Lassnig, Mario; Laurelli, Paolo; Lavorini, Vincenzo; Lavrijsen, Wim; Laycock, Paul; Lazovich, Tomo; Le Dortz, Olivier; Le Guirriec, Emmanuel; Le Menedeu, Eve; LeCompte, Thomas; Ledroit-Guillon, Fabienne Agnes Marie; Lee, Hurng-Chun; Lee, Jason; Lee, Shih-Chang; Lee, Lawrence; Lefebvre, Michel; Legendre, Marie; Legger, Federica; Leggett, Charles; Lehmacher, Marc; Lehmann Miotto, Giovanna; Lei, Xiaowen; Leite, Marco Aurelio Lisboa; Leitner, Rupert; Lellouch, Daniel; Lemmer, Boris; Lendermann, Victor; Leney, Katharine; Lenz, Tatiana; Lenzen, Georg; Lenzi, Bruno; Leonhardt, Kathrin; Leontsinis, Stefanos; Lepold, Florian; Leroy, Claude; Lessard, Jean-Raphael; Lester, Christopher; Lester, Christopher Michael; Levêque, Jessica; Levin, Daniel; Levinson, Lorne; Lewis, Adrian; Lewis, George; Leyko, Agnieszka; Leyton, Michael; Li, Bo; Li, Haifeng; Li, Ho Ling; Li, Shu; Li, Xuefei; Liang, Zhijun; Liao, Hongbo; Liberti, Barbara; Lichard, Peter; Lichtnecker, Markus; Lie, Ki; Liebig, Wolfgang; Limbach, Christian; Limosani, Antonio; Limper, Maaike; Lin, Simon; Linde, Frank; Linnemann, James; Lipeles, Elliot; Lipniacka, Anna; Liss, Tony; Lissauer, David; Lister, Alison; Litke, Alan; Liu, Chuanlei; Liu, Dong; Liu, Hao; Liu, Jianbei; Liu, Kun; Liu, Lulu; Liu, Minghui; Liu, Yanwen; Livan, Michele; Livermore, Sarah; Lleres, Annick; Llorente Merino, Javier; Lloyd, Stephen; Lobodzinska, Ewelina; Loch, Peter; Lockman, William; Loddenkoetter, Thomas; Loebinger, Fred; Loginov, Andrey; Loh, Chang Wei; Lohse, Thomas; Lohwasser, Kristin; Lokajicek, Milos; Lombardo, Vincenzo Paolo; Long, Jonathan; Long, Robin Eamonn; Lopes, Lourenco; Lopez Mateos, David; Lorenz, Jeanette; Lorenzo Martinez, Narei; Losada, Marta; Loscutoff, Peter; Lo Sterzo, Francesco; Losty, Michael; Lou, Xinchou; Lounis, Abdenour; Loureiro, Karina; Love, Jeremy; Love, Peter; Lowe, Andrew; Lu, Feng; Lubatti, Henry; Luci, Claudio; Lucotte, Arnaud; Ludwig, Andreas; Ludwig, Dörthe; Ludwig, Inga; Ludwig, Jens; Luehring, Frederick; Luijckx, Guy; Lukas, Wolfgang; Luminari, Lamberto; Lund, Esben; Lund-Jensen, Bengt; Lundberg, Björn; Lundberg, Johan; Lundberg, Olof; Lundquist, Johan; Lungwitz, Matthias; Lynn, David; Lytken, Else; Ma, Hong; Ma, Lian Liang; Maccarrone, Giovanni; Macchiolo, Anna; Maček, Boštjan; Machado Miguens, Joana; Mackeprang, Rasmus; Madaras, Ronald; Maddocks, Harvey Jonathan; Mader, Wolfgang; Maenner, Reinhard; Maeno, Tadashi; Mättig, Peter; Mättig, Stefan; Magnoni, Luca; Magradze, Erekle; Mahboubi, Kambiz; Mahlstedt, Joern; Mahmoud, Sara; Mahout, Gilles; Maiani, Camilla; Maidantchik, Carmen; Maio, Amélia; Majewski, Stephanie; Makida, Yasuhiro; Makovec, Nikola; Mal, Prolay; Malaescu, Bogdan; Malecki, Pawel; Malecki, Piotr; Maleev, Victor; Malek, Fairouz; Mallik, Usha; Malon, David; Malone, Caitlin; Maltezos, Stavros; Malyshev, Vladimir; Malyukov, Sergei; Mameghani, Raphael; Mamuzic, Judita; Manabe, Atsushi; Mandelli, Luciano; Mandić, Igor; Mandrysch, Rocco; Maneira, José; Manfredini, Alessandro; Mangeard, Pierre-Simon; Manhaes de Andrade Filho, Luciano; Manjarres Ramos, Joany Andreina; Mann, Alexander; Manning, Peter; Manousakis-Katsikakis, Arkadios; Mansoulie, Bruno; Mapelli, Alessandro; Mapelli, Livio; March, Luis; Marchand, Jean-Francois; Marchese, Fabrizio; Marchiori, Giovanni; Marcisovsky, Michal; Marino, Christopher; Marroquim, Fernando; Marshall, Zach; Martens, Kalen; Marti, Lukas Fritz; Marti-Garcia, Salvador; Martin, Brian; Martin, Brian; Martin, Jean-Pierre; Martin, Tim; Martin, Victoria Jane; Martin dit Latour, Bertrand; Martin-Haugh, Stewart; Martinez, Mario; Martinez Outschoorn, Verena; Martyniuk, Alex; Marx, Marilyn; Marzano, Francesco; Marzin, Antoine; Masetti, Lucia; Mashimo, Tetsuro; Mashinistov, Ruslan; Masik, Jiri; Maslennikov, Alexey; Massa, Ignazio; Massaro, Graziano; Massol, Nicolas; Mastrandrea, Paolo; Mastroberardino, Anna; Masubuchi, Tatsuya; Matricon, Pierre; Matsunaga, Hiroyuki; Matsushita, Takashi; Mattravers, Carly; Maurer, Julien; Maxfield, Stephen; Mayne, Anna; Mazini, Rachid; Mazur, Michael; Mazzaferro, Luca; Mazzanti, Marcello; Mc Donald, Jeffrey; Mc Kee, Shawn Patrick; McCarn, Allison; McCarthy, Robert; McCarthy, Tom; McCubbin, Norman; McFarlane, Kenneth; Mcfayden, Josh; Mchedlidze, Gvantsa; Mclaughlan, Tom; McMahon, Steve; McPherson, Robert; Meade, Andrew; Mechnich, Joerg; Mechtel, Markus; Medinnis, Mike; Meera-Lebbai, Razzak; Meguro, Tatsuma; Mehdiyev, Rashid; Mehlhase, Sascha; Mehta, Andrew; Meier, Karlheinz; Meirose, Bernhard; Melachrinos, Constantinos; Mellado Garcia, Bruce Rafael; Meloni, Federico; Mendoza Navas, Luis; Meng, Zhaoxia; Mengarelli, Alberto; Menke, Sven; Meoni, Evelin; Mercurio, Kevin Michael; Mermod, Philippe; Merola, Leonardo; Meroni, Chiara; Merritt, Frank; Merritt, Hayes; Messina, Andrea; Metcalfe, Jessica; Mete, Alaettin Serhan; Meyer, Carsten; Meyer, Christopher; Meyer, Jean-Pierre; Meyer, Jochen; Meyer, Joerg; Meyer, Thomas Christian; Michal, Sebastien; Micu, Liliana; Middleton, Robin; Migas, Sylwia; Mijović, Liza; Mikenberg, Giora; Mikestikova, Marcela; Mikuž, Marko; Miller, David; Miller, Robert; Mills, Bill; Mills, Corrinne; Milov, Alexander; Milstead, David; Milstein, Dmitry; Minaenko, Andrey; Miñano Moya, Mercedes; Minashvili, Irakli; Mincer, Allen; Mindur, Bartosz; Mineev, Mikhail; Ming, Yao; Mir, Lluisa-Maria; Mirabelli, Giovanni; Mitrevski, Jovan; Mitsou, Vasiliki A; Mitsui, Shingo; Miyagawa, Paul; Mjörnmark, Jan-Ulf; Moa, Torbjoern; Moeller, Victoria; Mönig, Klaus; Möser, Nicolas; Mohapatra, Soumya; Mohr, Wolfgang; Moles-Valls, Regina; Molfetas, Angelos; Monk, James; Monnier, Emmanuel; Montejo Berlingen, Javier; Monticelli, Fernando; Monzani, Simone; Moore, Roger; Moorhead, Gareth; Mora Herrera, Clemencia; Moraes, Arthur; Morange, Nicolas; Morel, Julien; Morello, Gianfranco; Moreno, Deywis; Moreno Llácer, María; Morettini, Paolo; Morgenstern, Marcus; Morii, Masahiro; Morley, Anthony Keith; Mornacchi, Giuseppe; Morris, John; Morvaj, Ljiljana; Moser, Hans-Guenther; Mosidze, Maia; Moss, Josh; Mount, Richard; Mountricha, Eleni; Mouraviev, Sergei; Moyse, Edward; Mueller, Felix; Mueller, James; Mueller, Klemens; Müller, Thomas; Mueller, Timo; Muenstermann, Daniel; Munwes, Yonathan; Murray, Bill; Mussche, Ido; Musto, Elisa; Myagkov, Alexey; Myska, Miroslav; Nackenhorst, Olaf; Nadal, Jordi; Nagai, Koichi; Nagai, Ryo; Nagano, Kunihiro; Nagarkar, Advait; Nagasaka, Yasushi; Nagel, Martin; Nairz, Armin Michael; Nakahama, Yu; Nakamura, Koji; Nakamura, Tomoaki; Nakano, Itsuo; Nanava, Gizo; Napier, Austin; Narayan, Rohin; Nash, Michael; Nattermann, Till; Naumann, Thomas; Navarro, Gabriela; Neal, Homer; Nechaeva, Polina; Neep, Thomas James; Negri, Andrea; Negri, Guido; Negrini, Matteo; Nektarijevic, Snezana; Nelson, Andrew; Nelson, Timothy Knight; Nemecek, Stanislav; Nemethy, Peter; Nepomuceno, Andre Asevedo; Nessi, Marzio; Neubauer, Mark; Neumann, Manuel; Neusiedl, Andrea; Neves, Ricardo; Nevski, Pavel; Newcomer, Mitchel; Newman, Paul; Nguyen Thi Hong, Van; Nickerson, Richard; Nicolaidou, Rosy; Nicquevert, Bertrand; Niedercorn, Francois; Nielsen, Jason; Nikiforou, Nikiforos; Nikiforov, Andriy; Nikolaenko, Vladimir; Nikolic-Audit, Irena; Nikolics, Katalin; Nikolopoulos, Konstantinos; Nilsen, Henrik; Nilsson, Paul; Ninomiya, Yoichi; Nisati, Aleandro; Nisius, Richard; Nobe, Takuya; Nodulman, Lawrence; Nomachi, Masaharu; Nomidis, Ioannis; Norberg, Scarlet; Nordberg, Markus; Norton, Peter; Novakova, Jana; Nozaki, Mitsuaki; Nozka, Libor; Nugent, Ian Michael; Nuncio-Quiroz, Adriana-Elizabeth; Nunes Hanninger, Guilherme; Nunnemann, Thomas; Nurse, Emily; O'Brien, Brendan Joseph; O'Neil, Dugan; O'Shea, Val; Oakes, Louise Beth; Oakham, Gerald; Oberlack, Horst; Ocariz, Jose; Ochi, Atsuhiko; Oda, Susumu; Odaka, Shigeru; Odier, Jerome; Ogren, Harold; Oh, Alexander; Oh, Seog; Ohm, Christian; Ohshima, Takayoshi; Okamura, Wataru; Okawa, Hideki; Okumura, Yasuyuki; Okuyama, Toyonobu; Olariu, Albert; Olchevski, Alexander; Olivares Pino, Sebastian Andres; Oliveira, Miguel Alfonso; Oliveira Damazio, Denis; Oliver Garcia, Elena; Olivito, Dominick; Olszewski, Andrzej; Olszowska, Jolanta; Onofre, António; Onyisi, Peter; Oram, Christopher; Oreglia, Mark; Oren, Yona; Orestano, Domizia; Orlando, Nicola; Orlov, Iliya; Oropeza Barrera, Cristina; Orr, Robert; Osculati, Bianca; Ospanov, Rustem; Osuna, Carlos; Otero y Garzon, Gustavo; Ottersbach, John; Ouchrif, Mohamed; Ouellette, Eric; Ould-Saada, Farid; Ouraou, Ahmimed; Ouyang, Qun; Ovcharova, Ana; Owen, Mark; Owen, Simon; Ozcan, Veysi Erkcan; Ozturk, Nurcan; Pacheco Pages, Andres; Padilla Aranda, Cristobal; Pagan Griso, Simone; Paganis, Efstathios; Pahl, Christoph; Paige, Frank; Pais, Preema; Pajchel, Katarina; Palacino, Gabriel; Paleari, Chiara; Palestini, Sandro; Pallin, Dominique; Palma, Alberto; Palmer, Jody; Pan, Yibin; Panagiotopoulou, Evgenia; Panduro Vazquez, William; Pani, Priscilla; Panikashvili, Natalia; Panitkin, Sergey; Pantea, Dan; Papadelis, Aras; Papadopoulou, Theodora; Paramonov, Alexander; Paredes Hernandez, Daniela; Park, Woochun; Parker, Andy; Parodi, Fabrizio; Parsons, John; Parzefall, Ulrich; Pashapour, Shabnaz; Pasqualucci, Enrico; Passaggio, Stefano; Passeri, Antonio; Pastore, Fernanda; Pastore, Francesca; Pásztor, Gabriella; Pataraia, Sophio; Patel, Nikhul; Pater, Joleen; Patricelli, Sergio; Pauly, Thilo; Pecsy, Martin; Pedraza Lopez, Sebastian; Pedraza Morales, Maria Isabel; Peleganchuk, Sergey; Pelikan, Daniel; Peng, Haiping; Penning, Bjoern; Penson, Alexander; Penwell, John; Perantoni, Marcelo; Perez, Kerstin; Perez Cavalcanti, Tiago; Perez Codina, Estel; Pérez García-Estañ, María Teresa; Perez Reale, Valeria; Perini, Laura; Pernegger, Heinz; Perrino, Roberto; Perrodo, Pascal; Peshekhonov, Vladimir; Peters, Krisztian; Petersen, Brian; Petersen, Jorgen; Petersen, Troels; Petit, Elisabeth; Petridis, Andreas; Petridou, Chariclia; Petrolo, Emilio; Petrucci, Fabrizio; Petschull, Dennis; Petteni, Michele; Pezoa, Raquel; Phan, Anna; Phillips, Peter William; Piacquadio, Giacinto; Picazio, Attilio; Piccaro, Elisa; Piccinini, Maurizio; Piec, Sebastian Marcin; Piegaia, Ricardo; Pignotti, David; Pilcher, James; Pilkington, Andrew; Pina, João Antonio; Pinamonti, Michele; Pinder, Alex; Pinfold, James; Pinto, Belmiro; Pizio, Caterina; Plamondon, Mathieu; Pleier, Marc-Andre; Plotnikova, Elena; Poblaguev, Andrei; Poddar, Sahill; Podlyski, Fabrice; Poggioli, Luc; Pohl, David-leon; Pohl, Martin; Polesello, Giacomo; Policicchio, Antonio; Polifka, Richard; Polini, Alessandro; Poll, James; Polychronakos, Venetios; Pomeroy, Daniel; Pommès, Kathy; Pontecorvo, Ludovico; Pope, Bernard; Popeneciu, Gabriel Alexandru; Popovic, Dragan; Poppleton, Alan; Portell Bueso, Xavier; Pospelov, Guennady; Pospisil, Stanislav; Potrap, Igor; Potter, Christina; Potter, Christopher; Poulard, Gilbert; Poveda, Joaquin; Pozdnyakov, Valery; Prabhu, Robindra; Pralavorio, Pascal; Pranko, Aliaksandr; Prasad, Srivas; Pravahan, Rishiraj; Prell, Soeren; Pretzl, Klaus Peter; Price, Darren; Price, Joe; Price, Lawrence; Prieur, Damien; Primavera, Margherita; Prokofiev, Kirill; Prokoshin, Fedor; Protopopescu, Serban; Proudfoot, James; Prudent, Xavier; Przybycien, Mariusz; Przysiezniak, Helenka; Psoroulas, Serena; Ptacek, Elizabeth; Pueschel, Elisa; Purdham, John; Purohit, Milind; Puzo, Patrick; Pylypchenko, Yuriy; Qian, Jianming; Quadt, Arnulf; Quarrie, David; Quayle, William; Quinonez, Fernando; Raas, Marcel; Raddum, Silje; Radeka, Veljko; Radescu, Voica; Radloff, Peter; Rador, Tonguc; Ragusa, Francesco; Rahal, Ghita; Rahimi, Amir; Rahm, David; Rajagopalan, Srinivasan; Rammensee, Michael; Rammes, Marcus; Randle-Conde, Aidan Sean; Randrianarivony, Koloina; Rauscher, Felix; Rave, Tobias Christian; Raymond, Michel; Read, Alexander Lincoln; Rebuzzi, Daniela; Redelbach, Andreas; Redlinger, George; Reece, Ryan; Reeves, Kendall; Reinherz-Aronis, Erez; Reinsch, Andreas; Reisinger, Ingo; Rembser, Christoph; Ren, Zhongliang; Renaud, Adrien; Rescigno, Marco; Resconi, Silvia; Resende, Bernardo; Reznicek, Pavel; Rezvani, Reyhaneh; Richter, Robert; Richter-Was, Elzbieta; Ridel, Melissa; Rijpstra, Manouk; Rijssenbeek, Michael; Rimoldi, Adele; Rinaldi, Lorenzo; Rios, Ryan Randy; Riu, Imma; Rivoltella, Giancesare; Rizatdinova, Flera; Rizvi, Eram; Robertson, Steven; Robichaud-Veronneau, Andree; Robinson, Dave; Robinson, James; Robson, Aidan; Rocha de Lima, Jose Guilherme; Roda, Chiara; Roda Dos Santos, Denis; Roe, Adam; Roe, Shaun; Røhne, Ole; Rolli, Simona; Romaniouk, Anatoli; Romano, Marino; Romeo, Gaston; Romero Adam, Elena; Rompotis, Nikolaos; Roos, Lydia; Ros, Eduardo; Rosati, Stefano; Rosbach, Kilian; Rose, Anthony; Rose, Matthew; Rosenbaum, Gabriel; Rosenberg, Eli; Rosendahl, Peter Lundgaard; Rosenthal, Oliver; Rosselet, Laurent; Rossetti, Valerio; Rossi, Elvira; Rossi, Leonardo Paolo; Rotaru, Marina; Roth, Itamar; Rothberg, Joseph; Rousseau, David; Royon, Christophe; Rozanov, Alexander; Rozen, Yoram; Ruan, Xifeng; Rubbo, Francesco; Rubinskiy, Igor; Ruckstuhl, Nicole; Rud, Viacheslav; Rudolph, Christian; Rudolph, Gerald; Rühr, Frederik; Ruiz-Martinez, Aranzazu; Rumyantsev, Leonid; Rurikova, Zuzana; Rusakovich, Nikolai; Rutherfoord, John; Ruzicka, Pavel; Ryabov, Yury; Rybar, Martin; Rybkin, Grigori; Ryder, Nick; Saavedra, Aldo; Sadeh, Iftach; Sadrozinski, Hartmut; Sadykov, Renat; Safai Tehrani, Francesco; Sakamoto, Hiroshi; Salamanna, Giuseppe; Salamon, Andrea; Saleem, Muhammad; Salek, David; Salihagic, Denis; Salnikov, Andrei; Salt, José; Salvachua Ferrando, Belén; Salvatore, Daniela; Salvatore, Pasquale Fabrizio; Salvucci, Antonio; Salzburger, Andreas; Sampsonidis, Dimitrios; Samset, Björn Hallvard; Sanchez, Arturo; Sanchez Martinez, Victoria; Sandaker, Heidi; Sander, Heinz Georg; Sanders, Michiel; Sandhoff, Marisa; Sandoval, Tanya; Sandoval, Carlos; Sandstroem, Rikard; Sankey, Dave; Sansoni, Andrea; Santamarina Rios, Cibran; Santoni, Claudio; Santonico, Rinaldo; Santos, Helena; Saraiva, João; Sarangi, Tapas; Sarkisyan-Grinbaum, Edward; Sarri, Francesca; Sartisohn, Georg; Sasaki, Osamu; Sasaki, Yuichi; Sasao, Noboru; Satsounkevitch, Igor; Sauvage, Gilles; Sauvan, Emmanuel; Sauvan, Jean-Baptiste; Savard, Pierre; Savinov, Vladimir; Savu, Dan Octavian; Sawyer, Lee; Saxon, David; Saxon, James; Sbarra, Carla; Sbrizzi, Antonio; Scannicchio, Diana; Scarcella, Mark; Schaarschmidt, Jana; Schacht, Peter; Schaefer, Douglas; Schäfer, Uli; Schaelicke, Andreas; Schaepe, Steffen; Schaetzel, Sebastian; Schaffer, Arthur; Schaile, Dorothee; Schamberger, R~Dean; Schamov, Andrey; Scharf, Veit; Schegelsky, Valery; Scheirich, Daniel; Schernau, Michael; Scherzer, Max; Schiavi, Carlo; Schieck, Jochen; Schioppa, Marco; Schlenker, Stefan; Schmid, Peter; Schmidt, Evelyn; Schmieden, Kristof; Schmitt, Christian; Schmitt, Sebastian; Schmitz, Martin; Schneider, Basil; Schnoor, Ulrike; Schoeffel, Laurent; Schoening, Andre; Schorlemmer, Andre Lukas; Schott, Matthias; Schouten, Doug; Schovancova, Jaroslava; Schram, Malachi; Schroeder, Christian; Schroer, Nicolai; Schultens, Martin Johannes; Schultes, Joachim; Schultz-Coulon, Hans-Christian; Schulz, Holger; Schumacher, Markus; Schumm, Bruce; Schune, Philippe; Schwanenberger, Christian; Schwartzman, Ariel; Schwegler, Philipp; Schwemling, Philippe; Schwienhorst, Reinhard; Schwierz, Rainer; Schwindling, Jerome; Schwindt, Thomas; Schwoerer, Maud; Sciolla, Gabriella; Scott, Bill; Searcy, Jacob; Sedov, George; Sedykh, Evgeny; Seidel, Sally; Seiden, Abraham; Seifert, Frank; Seixas, José; Sekhniaidze, Givi; Sekula, Stephen; Selbach, Karoline Elfriede; Seliverstov, Dmitry; Sellden, Bjoern; Sellers, Graham; Seman, Michal; Semprini-Cesari, Nicola; Serfon, Cedric; Serin, Laurent; Serkin, Leonid; Seuster, Rolf; Severini, Horst; Sfyrla, Anna; Shabalina, Elizaveta; Shamim, Mansoora; Shan, Lianyou; Shank, James; Shao, Qi Tao; Shapiro, Marjorie; Shatalov, Pavel; Shaw, Kate; Sherman, Daniel; Sherwood, Peter; Shimizu, Shima; Shimojima, Makoto; Shin, Taeksu; Shiyakova, Maria; Shmeleva, Alevtina; Shochet, Mel; Short, Daniel; Shrestha, Suyog; Shulga, Evgeny; Shupe, Michael; Sicho, Petr; Sidoti, Antonio; Siegert, Frank; Sijacki, Djordje; Silbert, Ohad; Silva, José; Silver, Yiftah; Silverstein, Daniel; Silverstein, Samuel; Simak, Vladislav; Simard, Olivier; Simic, Ljiljana; Simion, Stefan; Simioni, Eduard; Simmons, Brinick; Simoniello, Rosa; Simonyan, Margar; Sinervo, Pekka; Sinev, Nikolai; Sipica, Valentin; Siragusa, Giovanni; Sircar, Anirvan; Sisakyan, Alexei; Sivoklokov, Serguei; Sjölin, Jörgen; Sjursen, Therese; Skinnari, Louise Anastasia; Skottowe, Hugh Philip; Skovpen, Kirill; Skubic, Patrick; Slater, Mark; Slavicek, Tomas; Sliwa, Krzysztof; Smakhtin, Vladimir; Smart, Ben; Smestad, Lillian; Smirnov, Sergei; Smirnov, Yury; Smirnova, Lidia; Smirnova, Oxana; Smith, Ben Campbell; Smith, Douglas; Smith, Kenway; Smizanska, Maria; Smolek, Karel; Snesarev, Andrei; Snow, Steve; Snow, Joel; Snyder, Scott; Sobie, Randall; Sodomka, Jaromir; Soffer, Abner; Solans, Carlos; Solar, Michael; Solc, Jaroslav; Soldatov, Evgeny; Soldevila, Urmila; Solfaroli Camillocci, Elena; Solodkov, Alexander; Solovyanov, Oleg; Solovyev, Victor; Soni, Nitesh; Sopko, Vit; Sopko, Bruno; Sosebee, Mark; Soualah, Rachik; Soukharev, Andrey; Spagnolo, Stefania; Spanò, Francesco; Spearman, William Robert; Spighi, Roberto; Spigo, Giancarlo; Spiwoks, Ralf; Spousta, Martin; Spreitzer, Teresa; Spurlock, Barry; St Denis, Richard Dante; Stahlman, Jonathan; Stamen, Rainer; Stanecka, Ewa; Stanek, Robert; Stanescu, Cristian; Stanescu-Bellu, Madalina; Stanitzki, Marcel Michael; Stapnes, Steinar; Starchenko, Evgeny; Stark, Jan; Staroba, Pavel; Starovoitov, Pavel; Staszewski, Rafal; Staude, Arnold; Stavina, Pavel; Steele, Genevieve; Steinbach, Peter; Steinberg, Peter; Stekl, Ivan; Stelzer, Bernd; Stelzer, Harald Joerg; Stelzer-Chilton, Oliver; Stenzel, Hasko; Stern, Sebastian; Stewart, Graeme; Stillings, Jan Andre; Stockton, Mark; Stoerig, Kathrin; Stoicea, Gabriel; Stonjek, Stefan; Strachota, Pavel; Stradling, Alden; Straessner, Arno; Strandberg, Jonas; Strandberg, Sara; Strandlie, Are; Strang, Michael; Strauss, Emanuel; Strauss, Michael; Strizenec, Pavol; Ströhmer, Raimund; Strom, David; Strong, John; Stroynowski, Ryszard; Stugu, Bjarne; Stumer, Iuliu; Stupak, John; Sturm, Philipp; Styles, Nicholas Adam; Soh, Dart-yin; Su, Dong; Subramania, Halasya Siva; Subramaniam, Rajivalochan; Succurro, Antonella; Sugaya, Yorihito; Suhr, Chad; Suk, Michal; Sulin, Vladimir; Sultansoy, Saleh; Sumida, Toshi; Sun, Xiaohu; Sundermann, Jan Erik; Suruliz, Kerim; Susinno, Giancarlo; Sutton, Mark; Suzuki, Yu; Suzuki, Yuta; Svatos, Michal; Swedish, Stephen; Sykora, Ivan; Sykora, Tomas; Sánchez, Javier; Ta, Duc; Tackmann, Kerstin; Taffard, Anyes; Tafirout, Reda; Taiblum, Nimrod; Takahashi, Yuta; Takai, Helio; Takashima, Ryuichi; Takeda, Hiroshi; Takeshita, Tohru; Takubo, Yosuke; Talby, Mossadek; Talyshev, Alexey; Tamsett, Matthew; Tan, Kong Guan; Tanaka, Junichi; Tanaka, Reisaburo; Tanaka, Satoshi; Tanaka, Shuji; Tanasijczuk, Andres Jorge; Tani, Kazutoshi; Tannoury, Nancy; Tapprogge, Stefan; Tardif, Dominique; Tarem, Shlomit; Tarrade, Fabien; Tartarelli, Giuseppe Francesco; Tas, Petr; Tasevsky, Marek; Tassi, Enrico; Tatarkhanov, Mous; Tayalati, Yahya; Taylor, Christopher; Taylor, Frank; Taylor, Geoffrey; Taylor, Wendy; Teinturier, Marthe; Teischinger, Florian Alfred; Teixeira Dias Castanheira, Matilde; Teixeira-Dias, Pedro; Temming, Kim Katrin; Ten Kate, Herman; Teng, Ping-Kun; Terada, Susumu; Terashi, Koji; Terron, Juan; Testa, Marianna; Teuscher, Richard; Therhaag, Jan; Theveneaux-Pelzer, Timothée; Thoma, Sascha; Thomas, Juergen; Thompson, Emily; Thompson, Paul; Thompson, Peter; Thompson, Stan; Thomsen, Lotte Ansgaard; Thomson, Evelyn; Thomson, Mark; Thong, Wai Meng; Thun, Rudolf; Tian, Feng; Tibbetts, Mark James; Tic, Tomáš; Tikhomirov, Vladimir; Tikhonov, Yury; Timoshenko, Sergey; Tiouchichine, Elodie; Tipton, Paul; Tisserant, Sylvain; Todorov, Theodore; Todorova-Nova, Sharka; Toggerson, Brokk; Tojo, Junji; Tokár, Stanislav; Tokushuku, Katsuo; Tollefson, Kirsten; Tomoto, Makoto; Tompkins, Lauren; Toms, Konstantin; Tonoyan, Arshak; Topfel, Cyril; Topilin, Nikolai; Torchiani, Ingo; Torrence, Eric; Torres, Heberth; Torró Pastor, Emma; Toth, Jozsef; Touchard, Francois; Tovey, Daniel; Trefzger, Thomas; Tremblet, Louis; Tricoli, Alesandro; Trigger, Isabel Marian; Trilling, George; Trincaz-Duvoid, Sophie; Tripiana, Martin; Triplett, Nathan; Trischuk, William; Trocmé, Benjamin; Troncon, Clara; Trottier-McDonald, Michel; Trzebinski, Maciej; Trzupek, Adam; Tsarouchas, Charilaos; Tseng, Jeffrey; Tsiakiris, Menelaos; Tsiareshka, Pavel; Tsionou, Dimitra; Tsipolitis, Georgios; Tsiskaridze, Shota; Tsiskaridze, Vakhtang; Tskhadadze, Edisher; Tsukerman, Ilya; Tsulaia, Vakhtang; Tsung, Jieh-Wen; Tsuno, Soshi; Tsybychev, Dmitri; Tua, Alan; Tudorache, Alexandra; Tudorache, Valentina; Tuggle, Joseph; Turala, Michal; Turecek, Daniel; Turk Cakir, Ilkay; Turlay, Emmanuel; Turra, Ruggero; Tuts, Michael; Tykhonov, Andrii; Tylmad, Maja; Tyndel, Mike; Tzanakos, George; Uchida, Kirika; Ueda, Ikuo; Ueno, Ryuichi; Ugland, Maren; Uhlenbrock, Mathias; Uhrmacher, Michael; Ukegawa, Fumihiko; Unal, Guillaume; Undrus, Alexander; Unel, Gokhan; Unno, Yoshinobu; Urbaniec, Dustin; Urquijo, Phillip; Usai, Giulio; Uslenghi, Massimiliano; Vacavant, Laurent; Vacek, Vaclav; Vachon, Brigitte; Vahsen, Sven; Valenta, Jan; Valentinetti, Sara; Valero, Alberto; Valkar, Stefan; Valladolid Gallego, Eva; Vallecorsa, Sofia; Valls Ferrer, Juan Antonio; Van Berg, Richard; Van Der Deijl, Pieter; van der Geer, Rogier; van der Graaf, Harry; Van Der Leeuw, Robin; van der Poel, Egge; van der Ster, Daniel; van Eldik, Niels; van Gemmeren, Peter; van Vulpen, Ivo; Vanadia, Marco; Vandelli, Wainer; Vanguri, Rami; Vaniachine, Alexandre; Vankov, Peter; Vannucci, Francois; Vari, Riccardo; Varol, Tulin; Varouchas, Dimitris; Vartapetian, Armen; Varvell, Kevin; Vassilakopoulos, Vassilios; Vazeille, Francois; Vazquez Schroeder, Tamara; Vegni, Guido; Veillet, Jean-Jacques; Veloso, Filipe; Veness, Raymond; Veneziano, Stefano; Ventura, Andrea; Ventura, Daniel; Venturi, Manuela; Venturi, Nicola; Vercesi, Valerio; Verducci, Monica; Verkerke, Wouter; Vermeulen, Jos; Vest, Anja; Vetterli, Michel; Vichou, Irene; Vickey, Trevor; Vickey Boeriu, Oana Elena; Viehhauser, Georg; Viel, Simon; Villa, Mauro; Villaplana Perez, Miguel; Vilucchi, Elisabetta; Vincter, Manuella; Vinek, Elisabeth; Vinogradov, Vladimir; Virchaux, Marc; Virzi, Joseph; Vitells, Ofer; Viti, Michele; Vivarelli, Iacopo; Vives Vaque, Francesc; Vlachos, Sotirios; Vladoiu, Dan; Vlasak, Michal; Vogel, Adrian; Vokac, Petr; Volpi, Guido; Volpi, Matteo; Volpini, Giovanni; von der Schmitt, Hans; von Radziewski, Holger; von Toerne, Eckhard; Vorobel, Vit; Vorwerk, Volker; Vos, Marcel; Voss, Rudiger; Voss, Thorsten Tobias; Vossebeld, Joost; Vranjes, Nenad; Vranjes Milosavljevic, Marija; Vrba, Vaclav; Vreeswijk, Marcel; Vu Anh, Tuan; Vuillermet, Raphael; Vukotic, Ilija; Wagner, Wolfgang; Wagner, Peter; Wahlen, Helmut; Wahrmund, Sebastian; Wakabayashi, Jun; Walch, Shannon; Walder, James; Walker, Rodney; Walkowiak, Wolfgang; Wall, Richard; Waller, Peter; Walsh, Brian; Wang, Chiho; Wang, Fuquan; Wang, Haichen; Wang, Hulin; Wang, Jike; Wang, Jin; Wang, Rui; Wang, Song-Ming; Wang, Tan; Warburton, Andreas; Ward, Patricia; Wardrope, David Robert; Warsinsky, Markus; Washbrook, Andrew; Wasicki, Christoph; Watanabe, Ippei; Watkins, Peter; Watson, Alan; Watson, Ian; Watson, Miriam; Watts, Gordon; Watts, Stephen; Waugh, Anthony; Waugh, Ben; Weber, Michele; Weber, Pavel; Webster, Jordan S; Weidberg, Anthony; Weigell, Philipp; Weingarten, Jens; Weiser, Christian; Wells, Phillippa; Wenaus, Torre; Wendland, Dennis; Weng, Zhili; Wengler, Thorsten; Wenig, Siegfried; Wermes, Norbert; Werner, Matthias; Werner, Per; Werth, Michael; Wessels, Martin; Wetter, Jeffrey; Weydert, Carole; Whalen, Kathleen; Wheeler-Ellis, Sarah Jane; White, Andrew; White, Martin; White, Sebastian; Whitehead, Samuel Robert; Whiteson, Daniel; Whittington, Denver; Wicek, Francois; Wicke, Daniel; Wickens, Fred; Wiedenmann, Werner; Wielers, Monika; Wienemann, Peter; Wiglesworth, Craig; Wiik-Fuchs, Liv Antje Mari; Wijeratne, Peter Alexander; Wildauer, Andreas; Wildt, Martin Andre; Wilhelm, Ivan; Wilkens, Henric George; Will, Jonas Zacharias; Williams, Eric; Williams, Hugh; Willis, William; Willocq, Stephane; Wilson, John; Wilson, Michael Galante; Wilson, Alan; Wingerter-Seez, Isabelle; Winkelmann, Stefan; Winklmeier, Frank; Wittgen, Matthias; Wollstadt, Simon Jakob; Wolter, Marcin Wladyslaw; Wolters, Helmut; Wong, Wei-Cheng; Wooden, Gemma; Wosiek, Barbara; Wotschack, Jorg; Woudstra, Martin; Wozniak, Krzysztof; Wraight, Kenneth; Wright, Michael; Wrona, Bozydar; Wu, Sau Lan; Wu, Xin; Wu, Yusheng; Wulf, Evan; Wynne, Benjamin; Xella, Stefania; Xiao, Meng; Xie, Song; Xu, Chao; Xu, Da; Yabsley, Bruce; Yacoob, Sahal; Yamada, Miho; Yamaguchi, Hiroshi; Yamaguchi, Yohei; Yamamoto, Akira; Yamamoto, Kyoko; Yamamoto, Shimpei; Yamamura, Taiki; Yamanaka, Takashi; Yamazaki, Takayuki; Yamazaki, Yuji; Yan, Zhen; Yang, Haijun; Yang, Hongtao; Yang, Un-Ki; Yang, Yi; Yang, Zhaoyu; Yanush, Serguei; Yao, Liwen; Yao, Yushu; Yasu, Yoshiji; Ybeles Smit, Gabriel Valentijn; Ye, Jingbo; Ye, Shuwei; Yilmaz, Metin; Yoosoofmiya, Reza; Yorita, Kohei; Yoshida, Riktura; Yoshihara, Keisuke; Young, Charles; Young, Christopher John; Youssef, Saul; Yu, Dantong; Yu, Jaehoon; Yu, Jie; Yuan, Li; Yurkewicz, Adam; Byszewski, Marcin; Zabinski, Bartlomiej; Zaidan, Remi; Zaitsev, Alexander; Zajacova, Zuzana; Zanello, Lucia; Zanzi, Daniele; Zaytsev, Alexander; Zeitnitz, Christian; Zeman, Martin; Zemla, Andrzej; Zendler, Carolin; Zenin, Oleg; Ženiš, Tibor; Zinonos, Zinonas; Zerwas, Dirk; Zevi della Porta, Giovanni; Zhang, Dongliang; Zhang, Huaqiao; Zhang, Jinlong; Zhang, Xueyao; Zhang, Zhiqing; Zhao, Long; Zhao, Zhengguo; Zhemchugov, Alexey; Zhong, Jiahang; Zhou, Bing; Zhou, Ning; Zhou, Yue; Zhu, Cheng Guang; Zhu, Hongbo; Zhu, Junjie; Zhu, Yingchun; Zhuang, Xuai; Zhuravlov, Vadym; Zieminska, Daria; Zimin, Nikolai; Zimmermann, Robert; Zimmermann, Simone; Zimmermann, Stephanie; Ziolkowski, Michael; Zitoun, Robert; Živković, Lidija; Zmouchko, Viatcheslav; Zobernig, Georg; Zoccoli, Antonio; zur Nedden, Martin; Zutshi, Vishnu; Zwalinski, Lukasz

    2012-01-01

    Nearly 50 years ago, theoretical physicists proposed that a field permeates the universe and gives energy to the vacuum. This field was required to explain why some, but not all, fundamental particles have mass. Numerous precision measurements during recent decades have provided indirect support for the existence of this field, but one crucial prediction of this theory has remained unconfirmed despite 30 years of experimental searches: the existence of a massive particle, the standard model Higgs boson. The ATLAS experiment at the Large Hadron Collider at CERN has now observed the production of a new particle with a mass of 126 giga–electron volts and decay signatures consistent with those expected for the Higgs particle. This result is strong support for the standard model of particle physics, including the presence of this vacuum field. The existence and properties of the newly discovered particle may also have consequences beyond the standard model itself.

  14. A particle-number conserving microscopic approach to octupole deformation of normal deformed and superdeformed states in 194Pb

    International Nuclear Information System (INIS)

    Nhan Hao, T.V.; Phu Dat, D.H.; Hoang Tung, N.; Tran, H.N.

    2015-01-01

    The left–right asymmetric deformation of normal deformed (ND) and superdeformed (SD) states of 194 Pb has been investigated in the framework of the parity-symmetry projection of the highly truncated diagonalization approach (HTDA), which is suited to treat the correlations in an explicitly particle-number conserving microscopic approach. A Skyrme energy density functional using the SIII and SkM* interactions has been considered to treat the particle–hole channel, whereas a density-independent δ force has been adopted for the residual interaction. The obtained results are compared with previous approaches. The calculated octupole phonon excitation energy is found to be in good qualitative agreement with available data in the ND state. (author)

  15. Exact and quasi-classical density matrix and Wigner functions for a particle in the box and half space

    Science.gov (United States)

    Akhundova, E. A.; Dodonov, V. V.; Manko, V. I.

    1993-01-01

    The exact expressions for density matrix and Wigner functions of quantum systems are known only in special cases. Corresponding Hamiltonians are quadratic forms of Euclidean coordinates and momenta. In this paper we consider the problem of one-dimensional free particle movement in the bounded region 0 is less than x is less than a (including the case a = infinity).

  16. The Visualization of the Space Probability Distribution for a Particle Moving in a Double Ring-Shaped Coulomb Potential

    Directory of Open Access Journals (Sweden)

    Yuan You

    2018-01-01

    Full Text Available The analytical solutions to a double ring-shaped Coulomb potential (RSCP are presented. The visualizations of the space probability distribution (SPD are illustrated for the two- (contour and three-dimensional (isosurface cases. The quantum numbers (n,l,m are mainly relevant for those quasi-quantum numbers (n′,l′,m′ via the double RSCP parameter c. The SPDs are of circular ring shape in spherical coordinates. The properties for the relative probability values (RPVs P are also discussed. For example, when we consider the special case (n,l,m=(6,5,0, the SPD moves towards two poles of z-axis when P increases. Finally, we discuss the different cases for the potential parameter b, which is taken as negative and positive values for c>0. Compared with the particular case b=0, the SPDs are shrunk for b=-0.5, while they are spread out for b=0.5.

  17. On the radiation emitted by a particle falling into a black hole in the semi-relativistic approximation

    International Nuclear Information System (INIS)

    Coretti, C.; Ferrari, V.

    1986-01-01

    In this paper the limits of applicability of the semi-relativistic approximation for estimating the radiation emitted in processes of capture of particles by black holes are discussed. It is shown that it gives reliable estimates in the case of spherically symmetric black holes, but it fails in the case of rotating black holes

  18. A particle filter for ammonia coverage ratio and input simultaneous estimations in Diesel-engine SCR system.

    Science.gov (United States)

    Sun, Kangfeng; Ji, Fenzhu; Yan, Xiaoyu; Jiang, Kai; Yang, Shichun

    2018-01-01

    As NOx emissions legislation for Diesel-engines is becoming more stringent than ever before, an aftertreatment system has been widely used in many countries. Specifically, to reduce the NOx emissions, a selective catalytic reduction(SCR) system has become one of the most promising techniques for Diesel-engine vehicle applications. In the SCR system, input ammonia concentration and ammonia coverage ratio are regarded as essential states in the control-oriental model. Currently, an ammonia sensor placed before the SCR Can is a good strategy for the input ammonia concentration value. However, physical sensor would increase the SCR system cost and the ammonia coverage ratio information cannot be directly measured by physical sensor. Aiming to tackle this problem, an observer based on particle filter(PF) is investigated to estimate the input ammonia concentration and ammonia coverage ratio. Simulation results through the experimentally-validated full vehicle simulator cX-Emission show that the performance of observer based on PF is outstanding, and the estimation error is very small.

  19. Stochastic plasma heating by electrostatic waves: a comparison between a particle-in-cell simulation and a laboratory experiment

    International Nuclear Information System (INIS)

    Fivaz, M.; Fasoli, A.; Appert, K.; Trans, T.M.; Tran, M.Q.; Skiff, F.

    1993-08-01

    Dynamical chaos is produced by the interaction between plasma particles and two electrostatic waves. Experiments performed in a linear magnetized plasma and a 1D particle-in-cell simulation agree qualitatively: above a threshold wave amplitude, ion stochastic diffusion and heating occur on a fast time scale. Self-consistency appears to limit the extent of the heating process. (author) 5 figs., 18 refs

  20. A particle consistent with the Higgs Boson observed with the ATLAS detector at the Large Hadron Collider

    Czech Academy of Sciences Publication Activity Database

    Aad, G.; Abajyan, T.; Abbott, B.; Böhm, Jan; Chudoba, Jiří; Gallus, Petr; Gunther, Jaroslav; Havránek, Miroslav; Jakoubek, Tomáš; Juránek, Vojtěch; Kepka, Oldřich; Kupčo, Alexander; Kůs, Vlastimil; Lokajíček, Miloš; Marčišovský, Michal; Mikeštíková, Marcela; Myška, Miroslav; Němeček, Stanislav; Růžička, Pavel; Schovancová, Jaroslava; Šícho, Petr; Staroba, Pavel; Svatoš, Michal; Taševský, Marek; Tic, Tomáš; Vrba, Václav; Valenta, J.; Zeman, Martin

    2012-01-01

    Roč. 338, č. 6114 (2012), s. 1576-1582 ISSN 0036-8075 R&D Projects: GA MŠk LA08032 Institutional support: RVO:68378271 Keywords : Higgs particle * mass * ATLAS * CERN LHC Coll * interpretation of experiments Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 31.027, year: 2012