WorldWideScience

Sample records for non-ltr retrotransposon r2

  1. The Wide Distribution and Change of Target Specificity of R2 Non-LTR Retrotransposons in Animals

    Science.gov (United States)

    Seto, Yosuke; Fujiwara, Haruhiko

    2016-01-01

    Transposons, or transposable elements, are the major components of genomes in most eukaryotes. Some groups of transposons have developed target specificity that limits the integration sites to a specific nonessential sequence or a genomic region to avoid gene disruption caused by insertion into an essential gene. R2 is one of the most intensively investigated groups of sequence-specific non-LTR retrotransposons and is inserted at a specific site inside of 28S ribosomal RNA (rRNA) genes. R2 is known to be distributed among at least six animal phyla even though its occurrence is reported to be patchy. Here, in order to obtain a more detailed picture of the distribution of R2, we surveyed R2 using both in silico screening and degenerate PCR, particularly focusing on actinopterygian fish. We found two families of the R2C lineage from vertebrates, although it has previously only been found in platyhelminthes. We also revealed the apparent movement of insertion sites of a lineage of actinopterygian R2, which was likely concurrent with the acquisition of a 28S rRNA-derived sequence in their 3′ UTR. Outside of actinopterygian fish, we revealed the maintenance of a single R2 lineage in birds; the co-existence of four lineages of R2 in the leafcutter bee Megachile rotundata; the first examples of R2 in Ctenophora, Mollusca, and Hemichordata; and two families of R2 showing no target specificity. These findings indicate that R2 is relatively stable and universal, while differences in the distribution and maintenance of R2 lineages probably reflect characteristics of some combination of both R2 lineages and host organisms. PMID:27662593

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

    Science.gov (United States)

    Cheng, Xu-Dong; Ling, Hong-Qing

    2006-06-01

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

  3. Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Brindley Paul J

    2005-11-01

    Full Text Available Abstract Background It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of the schistosome genome. Of more than 12 recognized clades of non-LTR retrotransposons, only members of the CR1, RTE, and R2 clades have been reported from the schistosome genome. Results Inspection of the nucleotide sequence of bacterial artificial chromosome number 49_J_14 from chromosome 1 of the genome of Schistosoma mansoni (GenBank AC093105 revealed the likely presence of several RTE-like retrotransposons. Among these, a new non-LTR retrotransposon designated SR3 was identified and is characterized here. Analysis of gene structure and phylogenetic analysis of both the reverse transcriptase and endonuclease domains of the mobile element indicated that SR3 represented a new family of RTE-like non-LTR retrotransposons. Remarkably, two full-length copies of SR3-like elements were present in BAC 49-J-14, and one of 3,211 bp in length appeared to be intact, indicating SR3 to be an active non-LTR retrotransposon. Both were flanked by target site duplications of 10–12 bp. Southern hybridization and bioinformatics analyses indicated the presence of numerous copies (probably >1,000 of SR3 interspersed throughout the genome of S. mansoni. Bioinformatics analyses also revealed SR3 to be transcribed in both larval and adult developmental stages of S. mansoni and to be also present in the genomes of the other major schistosome parasites of humans, Schistosoma haematobium and S. japonicum. Conclusion Numerous copies of SR3, a novel non-LTR retrotransposon of the RTE clade are present in the genome of S. mansoni. Non-LTR retrotransposons of the RTE clade including SR3 appear to have been remarkably successful in colonizing, and

  4. Recent CR1 non-LTR retrotransposon activity in coscoroba reveals an insertion site preference

    Directory of Open Access Journals (Sweden)

    Quinn Thomas W

    2008-11-01

    Full Text Available Abstract Background Chicken repeat 1 (CR1 is a taxonomically widespread non-LTR retrotransposon. Insertion site bias, or lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site. Results Elucidation of the exact octomer repeat sequence (TTCTGTGA allowed for the identification of younger insertion events. The number of octomer repeats associated with a CR1 element increases after insertion with CR1s having one octomer being youngest. These young CR1s are flanked by regions of low GC content (38%. Furthermore, a bias for specific bases within the first four positions at the site of insertion was revealed. Conclusion This study focused on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events. Our data suggest that CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, preferentially inserting into regions of lower GC content. Furthermore, there appears to be a base preference (TTCT for the insertion site. The results of this study increase the current level of understanding regarding the elusive CR1 non-LTR retrotransposon.

  5. An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris.

    Science.gov (United States)

    Wenke, Torsten; Holtgräwe, Daniela; Horn, Axel V; Weisshaar, Bernd; Schmidt, Thomas

    2009-12-01

    We describe a non-LTR retrotransposon family,BvL, of the long interspersed nuclear elements L1 clade isolated from sugar beet (Beta vulgaris). Characteristic molecular domains of three full-length BvL elements were determined in detail, showing that coding sequences are interrupted and most likely non-functionally. In addition,eight highly conserved endonuclease regions were defined by comparison with other plant LINEs. The abundant BvL family is widespread within the genus Beta, however, the vast majority of BvL copies are extremely 50 truncated indicating an error-prone reverse transcriptase activity. The dispersed distribution of BvL copies on all sugar beet chromosomes with exclusion of most heterochromatic regions was shown by fluorescent in situ hybridization. The analysis of BvL 30 end sequences and corresponding flanking regions, respectively, revealed the preferred integration of BvL into A/T-rich regions of the sugar beet genome, but no specific target sequences.

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

    Directory of Open Access Journals (Sweden)

    Kenji K Kojima

    Full Text Available 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.

  7. 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.

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

    Directory of Open Access Journals (Sweden)

    Tu Zhijian

    2007-07-01

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

  9. Hominoid composite non-LTR retrotransposons-variety, assembly, evolution, and structural determinants of mobilization.

    Science.gov (United States)

    Ianc, Bianca; Ochis, Cornelia; Persch, Robert; Popescu, Octavian; Damert, Annette

    2014-11-01

    SVA (SINE-R-VNTR-Alu) elements constitute the youngest family of composite non-LTR retrotransposons in hominoid primates. The sequence of their assembly, however, remains unclear. Recently, a second family of VNTR-containing composites, LAVA (L1-Alu-VNTR-Alu), has been identified in gibbons. We now report the existence of two additional VNTR composite families, PVA (PTGR2-VNTR-Alu) and FVA (FRAM-VNTR-Alu), in the genome of Nomascus leucogenys. Like LAVA, they share the 5'-Alu-like region and VNTR with SVA, but differ at their 3'-ends. The 3'-end of PVA comprises part of the PTGR2 gene, whereas FVA is characterized by the presence of a partial FRAM element in its 3'-domain. Splicing could be identified as the mechanism of acquisition of the variant 3'-ends in all four families of VNTR composites. SVAs have been shown to be mobilized by the L1 protein machinery in trans. A critical role in this process has been ascribed to their 5'-hexameric repeat/ Alu-like region. The Alu-like region displays specific features in each of the VNTR composite families/subfamilies with characteristic deletions found in the evolutionary younger subfamilies. Using reciprocal exchanges between SVA_E and PVA/FVA elements, we demonstrate that the structure, not the presence of the (CCCTCT)n/ Alu-like region determines mobilization capacity. Combination of LAVA and SVA_E domains does not yield any active elements-suggesting the use of different combinations of host factors for the two major groups of VNTR composites. Finally, we demonstrate that the LAVA 3'-L1ME5 fragment attenuates mobilization capacity. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Vertical evolution and horizontal transfer of CR1 non-LTR retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species.

    Science.gov (United States)

    Sormacheva, Irina; Smyshlyaev, Georgiy; Mayorov, Vladimir; Blinov, Alexander; Novikov, Anton; Novikova, Olga

    2012-12-01

    Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long terminal repeat (LTR) retrotransposons, non-LTR retrotransposons rarely undergo HT, and their phylogenies are largely congruent to those of their hosts. Previously, we described HT of CR1-like non-LTR retrotransposons between butterflies (Maculinea) and moths (Bombyx), which occurred less than 5 million years ago (Novikova O, Sliwinska E, Fet V, Settele J, Blinov A, Woyciechowski M. 2007. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol. 7:93). In this study, we continued to explore the diversity of CR1 non-LTR retrotransposons among lepidopterans providing additional evidences to support HT hypothesis. We also hypothesized that DNA transposons could be involved in HT of non-LTR retrotransposons. Thus, we performed analysis of one of the groups of DNA transposons, mariner-like DNA elements, as potential vectors for HT of non-LTR retrotransposons. Our results demonstrate multiple HTs between Maculinea and Bombyx genera. Although we did not find strong evidence for our hypothesis of the involvement of DNA transposons in HT of non-LTR retrotransposons, we demonstrated that recurrent and/or simultaneous flow of TEs took place between distantly related moths and butterflies.

  11. The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals.

    Science.gov (United States)

    Novick, Peter A; Basta, Holly; Floumanhaft, Mark; McClure, Marcella A; Boissinot, Stéphane

    2009-08-01

    The genome of the lizard Anolis carolinensis (the green anole) is the first nonavian reptilian genome sequenced. It offers a unique opportunity to comparatively examine the evolution of amniote genomes. We analyzed the abundance and diversity of non-LTR (long terminal repeat) retrotransposons in the anole using the Genome Parsing Suite. We found that the anole genome contains an extraordinary diversity of elements. We identified 46 families of elements representing five clades (L1, L2, CR1, RTE, and R4). Within most families, elements are very similar to each other suggesting that they have been inserted recently. The rarity of old elements suggests a high rate of turnover, the insertion of new elements being offset by the loss of element-containing loci. Consequently, non-LTR retrotransposons accumulate in the anole at a low rate and are found in low copy number. This pattern of diversity shows some striking similarity with the genome of teleostean fish but contrasts greatly with the low diversity and high copy number of mammalian L1 elements, suggesting a fundamental difference in the way mammals and nonmammalian vertebrates interact with their genomic parasites. The scarcity of divergent elements in anoles suggests that insertions have a deleterious effect and are eliminated by natural selection. We propose that the low abundance of non-LTR retrotransposons in the anole is related directly or indirectly to a higher rate of ectopic recombination in the anole relative to mammals.

  12. A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5' truncations

    Directory of Open Access Journals (Sweden)

    Gladyshev Eugene A

    2010-04-01

    Full Text Available Abstract Background Rotifers of the class Bdelloidea are microscopic freshwater invertebrates best known for: their capacity for anhydrobiosis; the lack of males and meiosis; and for the ability to capture genes from other non-metazoan species. Although genetic exchange between these animals might take place by non-canonical means, the overall lack of meiosis and syngamy should greatly impair the ability of transposable elements (TEs to spread in bdelloid populations. Previous studies demonstrated that bdelloid chromosome ends, in contrast to gene-rich regions, harbour various kinds of TEs, including specialized telomere-associated retroelements, as well as DNA TEs and retrovirus-like retrotransposons which are prone to horizontal transmission. Vertically-transmitted retrotransposons have not previously been reported in bdelloids and their identification and studies of the patterns of their distribution and evolution could help in the understanding of the high degree of TE compartmentalization within bdelloid genomes. Results We identified and characterized a non-long terminal repeat (LTR retrotransposon residing primarily in subtelomeric regions of the genome in the bdelloid rotifer Adineta vaga. Contrary to the currently prevailing views on the mode of proliferation of non-LTR retrotransposons, which results in frequent formation of 5'-truncated ('dead-on-arrival' copies due to the premature disengagement of the element-encoded reverse transcriptase from its template, this non-LTR element, Hebe, is represented only by non-5'-truncated copies. Most of these copies, however, were subject to internal deletions associated with microhomologies, a hallmark of non-homologous end-joining events. Conclusions The non-LTR retrotransposon Hebe from the bdelloid rotifer A. vaga was found to undergo frequent microhomology-associated deletions, rather than 5'-terminal truncations characteristic of this class of retrotransposons, and to exhibit preference for

  13. RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN.

    Science.gov (United States)

    Naik, Pradeep Kumar; Mittal, Vinay Kumar; Gupta, Sumit

    2008-01-27

    The problem of predicting non-long terminal repeats (LTR) like long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) from the DNA sequence is still an open problem in bioinformatics. To elevate the quality of annotations of LINES and SINEs an automated tool "RetroPred" was developed. The pipeline allowed rapid and thorough annotation of non-LTR retrotransposons. The non-LTR retrotransposable elements were initially predicted by Pairwise Aligner for Long Sequences (PALS) and Parsimonious Inference of a Library of Elementary Repeats (PILER). Predicted non-LTR elements were automatically classified into LINEs and SINEs using ANN based on the position specific probability matrix (PSPM) generated by Multiple EM for Motif Elicitation (MEME). The ANN model revealed a superior model (accuracy = 78.79 +/- 6.86 %, Q(pred) = 74.734 +/- 17.08 %, sensitivity = 84.48 +/- 6.73 %, specificity = 77.13 +/- 13.39 %) using four-fold cross validation. As proof of principle, we have thoroughly annotated the location of LINEs and SINEs in rice and Arabidopsis genome using the tool and is proved to be very useful with good accuracy. Our tool is accessible at http://www.juit.ac.in/RepeatPred/home.html.

  14. Non-LTR R2 element evolutionary patterns: phylogenetic incongruences, rapid radiation and the maintenance of multiple lineages.

    Directory of Open Access Journals (Sweden)

    Andrea Luchetti

    Full Text Available Retrotransposons of the R2 superclade specifically insert within the 28S ribosomal gene. They have been isolated from a variety of metazoan genomes and were found vertically inherited even if their phylogeny does not always agree with that of the host species. This was explained with the diversification/extinction of paralogous lineages, being proved the absence of horizontal transfer. We here analyze the widest available collection of R2 sequences, either newly isolated from recently sequenced genomes or drawn from public databases, in a phylogenetic framework. Results are congruent with previous analyses, but new important issues emerge. First, the N-terminal end of the R2-B clade protein, so far unknown, presents a new zinc fingers configuration. Second, the phylogenetic pattern is consistent with an ancient, rapid radiation of R2 lineages: being the estimated time of R2 origin (850-600 Million years ago placed just before the metazoan Cambrian explosion, the wide element diversity and the incongruence with the host phylogeny could be attributable to the sudden expansion of available niches represented by host's 28S ribosomal genes. Finally, we detect instances of coexisting multiple R2 lineages showing a non-random phylogenetic pattern, strongly similar to that of the "library" model known for tandem repeats: a collection of R2s were present in the ancestral genome and then differentially activated/repressed in the derived species. Models for activation/repression as well as mechanisms for sequence maintenance are also discussed within this framework.

  15. 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.

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

    Science.gov (United States)

    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.

    2017-01-01

    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. PMID:28003516

  17. A yeast model for target-primed (non-LTR retrotransposition

    Directory of Open Access Journals (Sweden)

    Busby Jason N

    2007-08-01

    Full Text Available Abstract Background Target-primed (non-LTR retrotransposons, such as the human L1 element, are mobile genetic elements found in many eukaryotic genomes. They are often present in large numbers and their retrotransposition can cause mutations and genomic rearrangements. Despite their importance, many aspects of their replication are not well understood. Results We have developed a yeast model system for studying target-primed retrotransposons. This system uses the Zorro3 element from Candida albicans. A cloned copy of Zorro3, tagged with a retrotransposition indicator gene, retrotransposes at a high frequency when introduced into an appropriate C. albicans host strain. Retrotransposed copies of the tagged element exhibit similar features to the native copies, indicating that the natural retrotransposition pathway is being used. Retrotransposition is dependent on the products of the tagged element's own genes and is highly temperature-regulated. The new assay permits the analysis of the effects of specific mutations introduced into the cloned element. Conclusion This Zorro3 retrotransposition assay system complements previously available target-primed retrotransposition assays. Due to the relative simplicity of the growth, manipulation and analysis of yeast cells, the system should advance our understanding of target-primed retrotransposition.

  18. Preferential occupancy of R2 retroelements on the B chromosomes of the grasshopper Eyprepocnemis plorans.

    Directory of Open Access Journals (Sweden)

    Eugenia E Montiel

    Full Text Available R2 non-LTR retrotransposons exclusively insert into the 28S rRNA genes of their host, and are expressed by co-transcription with the rDNA unit. The grasshopper Eyprepocnemis plorans contains transcribed rDNA clusters on most of its A chromosomes, as well as non-transcribed rDNA clusters on the parasitic B chromosomes found in many populations. Here the structure of the E. plorans R2 element, its abundance relative to the number of rDNA units and its retrotransposition activity were determined. Animals screened from five populations contained on average over 12,000 rDNA units on their A chromosomes, but surprisingly only about 100 R2 elements. Monitoring the patterns of R2 insertions in individuals from these populations revealed only low levels of retrotransposition. The low rates of R2 insertion observed in E. plorans differ from the high levels of R2 insertion previously observed in insect species that have many fewer rDNA units. It is proposed that high levels of R2 are strongly selected against in E. plorans, because the rDNA transcription machinery in this species is unable to differentiate between R2-inserted and uninserted units. The B chromosomes of E. plorans contain an additional 7,000 to 15,000 rDNA units, but in contrast to the A chromosomes, from 150 to over 1,500 R2 elements. The higher concentration of R2 in the inactive B chromosomes rDNA clusters suggests these chromosomes can act as a sink for R2 insertions thus further reducing the level of insertions on the A chromosomes. These studies suggest an interesting evolutionary relationship between the parasitic B chromosomes and R2 elements.

  19. Preferential occupancy of R2 retroelements on the B chromosomes of the grasshopper Eyprepocnemis plorans.

    Science.gov (United States)

    Montiel, Eugenia E; Cabrero, Josefa; Ruiz-Estévez, Mercedes; Burke, William D; Eickbush, Thomas H; Camacho, Juan Pedro M; López-León, María Dolores

    2014-01-01

    R2 non-LTR retrotransposons exclusively insert into the 28S rRNA genes of their host, and are expressed by co-transcription with the rDNA unit. The grasshopper Eyprepocnemis plorans contains transcribed rDNA clusters on most of its A chromosomes, as well as non-transcribed rDNA clusters on the parasitic B chromosomes found in many populations. Here the structure of the E. plorans R2 element, its abundance relative to the number of rDNA units and its retrotransposition activity were determined. Animals screened from five populations contained on average over 12,000 rDNA units on their A chromosomes, but surprisingly only about 100 R2 elements. Monitoring the patterns of R2 insertions in individuals from these populations revealed only low levels of retrotransposition. The low rates of R2 insertion observed in E. plorans differ from the high levels of R2 insertion previously observed in insect species that have many fewer rDNA units. It is proposed that high levels of R2 are strongly selected against in E. plorans, because the rDNA transcription machinery in this species is unable to differentiate between R2-inserted and uninserted units. The B chromosomes of E. plorans contain an additional 7,000 to 15,000 rDNA units, but in contrast to the A chromosomes, from 150 to over 1,500 R2 elements. The higher concentration of R2 in the inactive B chromosomes rDNA clusters suggests these chromosomes can act as a sink for R2 insertions thus further reducing the level of insertions on the A chromosomes. These studies suggest an interesting evolutionary relationship between the parasitic B chromosomes and R2 elements.

  20. 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,

  1. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia: e0140084

    National Research Council Canada - National Science Library

    Kenji K Kojima; Jerzy Jurka[dagger

    2015-01-01

    .... 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...

  2. Dead element replicating: degenerate R2 element replication and rDNA genomic turnover in the Bacillus rossius stick insect (Insecta: Phasmida.

    Directory of Open Access Journals (Sweden)

    Francesco Martoni

    Full Text Available R2 is an extensively investigated non-LTR retrotransposon that specifically inserts into the 28S rRNA gene sequences of a wide range of metazoans, disrupting its functionality. During R2 integration, first strand synthesis can be incomplete so that 5' end deleted copies are occasionally inserted. While active R2 copies repopulate the locus by retrotransposing, the non-functional truncated elements should frequently be eliminated by molecular drive processes leading to the concerted evolution of the rDNA array(s. Although, multiple R2 lineages have been discovered in the genome of many animals, the rDNA of the stick insect Bacillus rossius exhibits a peculiar situation: it harbors both a canonical, functional R2 element (R2Brfun as well as a full-length but degenerate element (R2Brdeg. An intensive sequencing survey in the present study reveals that all truncated variants in stick insects are present in multiple copies suggesting they were duplicated by unequal recombination. Sequencing results also demonstrate that all R2Brdeg copies are full-length, i. e. they have no associated 5' end deletions, and functional assays indicate they have lost the active ribozyme necessary for R2 RNA maturation. Although it cannot be completely ruled out, it seems unlikely that the degenerate elements replicate via reverse transcription, exploiting the R2Brfun element enzymatic machinery, but rather via genomic amplification of inserted 28S by unequal recombination. That inactive copies (both R2Brdeg or 5'-truncated elements are not eliminated in a short term in stick insects contrasts with findings for the Drosophila R2, suggesting a widely different management of rDNA loci and a lower efficiency of the molecular drive while achieving the concerted evolution.

  3. Retrotransposon OV-RTE-1 from the carcinogenic liver fluke Opisthorchis viverrini: potential target for DNA-based diagnosis.

    Science.gov (United States)

    Thi Phung, Luyen; Loukas, Alex; Brindley, Paul J; Sripa, Banchob; Laha, Thewarach

    2014-01-01

    Infections by the fish-borne liver flukes Opisthorchis viverrini and Clonorchis sinensis can lead to bile duct cancer. These neglected tropical disease pathogens occur in East Asia, with O. viverrini primarily in Thailand and Laos and C. sinensis in Cambodia, Vietnam, and China. Genomic information about these pathogens holds the potential to improve disease treatment and control. Transcriptome analysis indicates that mobile genetic elements are active in O. viverrini, including a novel non-Long Terminal Repeat (LTR) retrotransposon. A consensus sequence of this element, termed OV-RTE-1, was assembled from expressed sequence tags and PCR amplified genomic DNA. OV-RTE-1 was 3330 bp in length, encoded 1101 amino acid residues and exhibited hallmark structures and sequences of non-LTR retrotransposons including a single open reading frame encoding apurinic-apyrimidinic endonuclease (EN) and reverse transcriptase (RT). Phylogenetic analyses confirmed that OV-RTE-1 was member of the RTE clade of non-LTR retrotransposons. OV-RTE-1 is the first non-LTR retrotransposon characterized from the trematode family Opisthorchiidae. Sequences of OV-RTE-1 were targeted to develop a diagnostic tool for detection of infection by O. viverrini. PCR specific primers for detection of O. viverrini DNA showed 100% specificity and sensitivity for detection of as little as 5 fg of O. viverrini DNA whereas the PCR based approach showed 62% sensitivity and 100% specificity with clinical stool samples. The OV-RTE-1 specific PCR could be developed as a molecular diagnostic for Opisthorchis infection targeting parasite eggs in stool samples, especially in regions of mixed infection of O. viverrini and/or C. sinensis and minute intestinal flukes.

  4. How retrotransposons shape genome regulation.

    Science.gov (United States)

    Mita, Paolo; Boeke, Jef D

    2016-04-01

    Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.

  5. Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

    Directory of Open Access Journals (Sweden)

    Bao Weidong

    2010-01-01

    Full Text Available Abstract Background In eukaryotes, long terminal repeat (LTR retrotransposons such as Copia, BEL and Gypsy integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT. The Gypsy INT-like transposase is also conserved in the Polinton/Maverick self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as TDD-4 and TDD-5. Moreover, it is known that INT is similar to bacterial transposases that belong to the IS3, IS481, IS30 and IS630 families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons. Results A new diverse eukaryotic superfamily of DNA transposons, named Ginger (for 'Gypsy INteGrasE Related' DNA transposons is defined and analyzed. Analogously to the IS3 and IS481 bacterial transposons, the Ginger termini resemble those of the Gypsy LTR retrotransposons. Currently, Ginger transposons can be divided into two distinct groups named Ginger1 and Ginger2/Tdd. Elements from the Ginger1 group are characterized by approximately 40 to 270 base pair (bp terminal inverted repeats (TIRs, and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD sequences. The Ginger1-encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire Gypsy-encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of Gypsy and endogenous retrovirus (ERV integrases. Ginger1 transposases also contain additional C-terminal domains: ovarian tumor (OTU-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from

  6. 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.

  7. ${\\cal R}^2$ Supergravity

    CERN Document Server

    Ferrara, Sergio; Porrati, Massimo

    2015-01-01

    We formulate $R^2$ pure supergravity as a scale invariant theory built only in terms of superfields describing the geometry of curved superspace. The standard supergravity duals are obtained in both "old" and "new" minimal formulations of auxiliary fields. These theories have massless fields in de Sitter space as they do in their non supersymmetric counterpart. Remarkably, the dual theory of $R^2$ supergravity in the new minimal formulation is an extension of the Freedman model, describing a massless gauge field and a massless chiral multiplet in de Sitter space, with inverse radius proportional to the Fayet-Iliopoulos term. This model can be interpreted as the "de-Higgsed" phase of the dual companion theory of $R+R^2$ supergravity.

  8. R^2 Dark Matter

    CERN Document Server

    Cembranos, Jose A R

    2010-01-01

    There is a non-trivial four-derivative extension of the gravitational spectrum that is free of ghosts and phenomenologically viable. It is the so called $R^2$-gravity since it is defined by the only addition of a term proportional to the square of the scalar curvature. Just the presence of this term does not improve the ultraviolet behaviour of Einstein gravity but introduces one additional scalar degree of freedom that can account for the dark matter of our Universe.

  9. Lineage specific evolution of the VNTR composite retrotransposon central domain and its role in retrotransposition of gibbon LAVA elements.

    Science.gov (United States)

    Lupan, Iulia; Bulzu, Paul; Popescu, Octavian; Damert, Annette

    2015-05-16

    VNTR (Variable Number of Tandem Repeats) composite retrotransposons - SVA (SINE-R-VNTR-Alu), LAVA (LINE-1-Alu-VNTR-Alu), PVA (PTGR2-VNTR-Alu) and FVA (FRAM-VNTR-Alu) - are specific to hominoid primates. Their assembly, the evolution of their 5' and 3' domains, and the functional significance of the shared 5' Alu-like region are well understood. The central VNTR domain, by contrast, has long been assumed to represent a more or less random collection of 30-50 bp GC-rich repeats. It is only recently that it attracted attention in the context of regulation of SVA expression. Here we provide evidence that the organization of the VNTR is non-random, with conserved repeat unit (RU) arrays at both the 5' and 3' ends of the VNTRs of human, chimpanzee and orangutan SVA and gibbon LAVA. The younger SVA subfamilies harbour highly organized internal RU arrays. The composition of these arrays is specific to the human/chimpanzee and orangutan lineages, respectively. Tracing the development of the VNTR through evolution we show for the first time how tandem repeats evolve within the constraints set by a functional, non-autonomous non-LTR retrotransposon in two different families - LAVA and SVA - in different hominoid lineages. Our analysis revealed that a microhomology-driven mechanism mediates expansion/contraction of the VNTR domain at the DNA level. Elements of all four VNTR composite families have been shown to be mobilized by the autonomous LINE1 retrotransposon in trans. In case of SVA, key determinants of mobilization are found in the 5' hexameric repeat/Alu-like region. We now demonstrate that in LAVA, by contrast, the VNTR domain determines mobilization efficiency in the context of domain swaps between active and inactive elements. The central domain of VNTR composites evolves in a lineage-specific manner which gives rise to distinct structures in gibbon LAVA, orangutan SVA, and human/chimpanzee SVA. The differences observed between the families and lineages are likely to

  10. DIRS and Ngaro Retrotransposons in Fungi.

    Directory of Open Access Journals (Sweden)

    Anna Muszewska

    Full Text Available Retrotransposons with a tyrosine recombinase (YR have been discovered recently and lack thorough annotation in fungi. YR retrotransposons are divided into 3 groups: DIRS, Ngaro and VIPER (known only from kinetoplastida. We used comparative genomics to investigate the evolutionary patterns of retrotransposons in the fungal kingdom. The identification of both functional and remnant elements provides a unique view on both recent and past transposition activity. Our searches covering a wide range of fungal genomes allowed us to identify 2241 YR retrotransposons. Based on CLANS clustering of concatenated sequences of the reverse transcriptase (RT, RNase H (RH, DNA N-6-adenine-methyltransferase (MT and YR protein domains we propose a revised classification of YR elements expanded by two new categories of Ngaro elements. A phylogenetic analysis of 477 representatives supports this observation and additionally demonstrates that DIRS and Ngaro abundance changed independently in Basidiomycota and Blastocladiomycota/Mucoromycotina/Kixellomycotina. Interestingly, a single remnant Ngaro element could be identified in an Ascomycota genome. Our analysis revealed also that 3 Pucciniomycotina taxa, known for their overall mobile element abundance and big genome size, encode an elevated number of Ngaro retrotransposons. Considering the presence of DIRS elements in all analyzed Mucoromycotina, Kickxellomycotina and Blastocladiomycota genomes one might assume a common origin of fungal DIRS retrotransposons with a loss in Dicarya. Ngaro elements described to date from Opisthokonta, seem to have invaded the common ancestor of Agaricomycotina and Pucciniomycotina after Ustilagomycotina divergence. Yet, most of analyzed genomes are devoid of YR elements and most identified retrotransposons are incomplete.

  11. Identification and characterization of jute LTR retrotransposons:

    Science.gov (United States)

    Ahmed, Salim; Shafiuddin, MD; Azam, Muhammad Shafiul; Islam, Md. Shahidul; Ghosh, Ajit

    2011-01-01

    Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome. PMID:22016842

  12. 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...

  13. Domesticated DNA transposon proteins mediate retrotransposon control

    Institute of Scientific and Technical Information of China (English)

    Kathryn A O'Donnell; Jef D Boeke

    2008-01-01

    @@ The Schizosaccharomyces pontbe genome, like those of many eukaryotes, contains a number of retrotransposable repeat sequences. The pombe elements, termed Tfl (transposon of fission yeast 1) and Tf2 possess long terminal repeats (LTRs) and belong to the gypsy family of retrotransposons [1].

  14. Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Judith Reichmann

    Full Text Available Retrotransposons are highly prevalent in mammalian genomes due to their ability to amplify in pluripotent cells or developing germ cells. Host mechanisms that silence retrotransposons in germ cells and pluripotent cells are important for limiting the accumulation of the repetitive elements in the genome during evolution. However, although silencing of selected individual retrotransposons can be relatively well-studied, many mammalian retrotransposons are seldom analysed and their silencing in germ cells, pluripotent cells or somatic cells remains poorly understood. Here we show, and experimentally verify, that cryptic repetitive element probes present in Illumina and Affymetrix gene expression microarray platforms can accurately and sensitively monitor repetitive element expression data. This computational approach to genome-wide retrotransposon expression has allowed us to identify the histone deacetylase Hdac1 as a component of the retrotransposon silencing machinery in mouse embryonic stem cells, and to determine the retrotransposon targets of Hdac1 in these cells. We also identify retrotransposons that are targets of other retrotransposon silencing mechanisms such as DNA methylation, Eset-mediated histone modification, and Ring1B/Eed-containing polycomb repressive complexes in mouse embryonic stem cells. Furthermore, our computational analysis of retrotransposon silencing suggests that multiple silencing mechanisms are independently targeted to retrotransposons in embryonic stem cells, that different genomic copies of the same retrotransposon can be differentially sensitive to these silencing mechanisms, and helps define retrotransposon sequence elements that are targeted by silencing machineries. Thus repeat annotation of gene expression microarray data suggests that a complex interplay between silencing mechanisms represses retrotransposon loci in germ cells and embryonic stem cells.

  15. Evolution of Centromeric Retrotransposons in Grasses

    Science.gov (United States)

    Sharma, Anupma; Presting, Gernot G.

    2014-01-01

    Centromeric retrotransposons (CRs) constitute a family of plant retroelements, some of which have the ability to target their insertion almost exclusively to the functional centromeres. Our exhaustive analysis of CR family members in four grass genomes revealed not only horizontal transfer (HT) of CR elements between the oryzoid and panicoid grass lineages but also their subsequent recombination with endogenous elements that in some cases created prolific recombinants in foxtail millet and sorghum. HT events are easily identifiable only in cases where host genome divergence significantly predates HT, thus documented HT events likely represent only a fraction of the total. If the more difficult to detect ancient HT events occurred at frequencies similar to those observable in present day grasses, the extant long terminal repeat retrotransposons represent the mosaic products of HT and recombination that are optimized for retrotransposition in their host genomes. This complicates not only phylogenetic analysis but also the establishment of a meaningful retrotransposon nomenclature, which we have nevertheless attempted to implement here. In contrast to the plant-centric naming convention used currently for CR elements, we classify elements primarily based on their phylogenetic relationships regardless of host plant, using the exhaustively studied maize elements assigned to six different subfamilies as a standard. The CR2 subfamily is the most widely distributed of the six CR subfamilies discovered in grass genomes to date and thus the most likely to play a functional role at grass centromeres. PMID:24814286

  16. Retrotransposon vectors for gene delivery in plants

    Directory of Open Access Journals (Sweden)

    Hou Yi

    2010-08-01

    Full Text Available Abstract Background Retrotransposons are abundant components of plant genomes, and although some plant retrotransposons have been used as insertional mutagens, these mobile genetic elements have not been widely exploited for plant genome manipulation. In vertebrates and yeast, retrotransposons and retroviruses are routinely altered to carry additional genes that are copied into complementary (cDNA through reverse transcription. Integration of cDNA results in gene delivery; recombination of cDNA with homologous chromosomal sequences can create targeted gene modifications. Plant retrotransposon-based vectors, therefore, may provide new opportunities for plant genome engineering. Results A retrotransposon vector system was developed for gene delivery in plants based on the Tnt1 element from Nicotiana tabacum. Mini-Tnt1 transfer vectors were constructed that lack coding sequences yet retain the 5' and 3' long terminal repeats (LTRs and adjacent cis sequences required for reverse transcription. The internal coding region of Tnt1 was replaced with a neomycin phosphotransferase gene to monitor replication by reverse transcription. Two different mini-Tnt1 s were developed: one with the native 5' LTR and the other with a chimeric 5' LTR that had the first 233 bp replaced by the CaMV 35 S promoter. After transfer into tobacco protoplasts, both vectors undergo retrotransposition using GAG and POL proteins provided in trans by endogenous Tnt1 elements. The transposition frequencies of mini-Tnt1 vectors are comparable with native Tnt1 elements, and like the native elements, insertion sites are within or near coding sequences. In this paper, we provide evidence that template switching occurs during mini-Tnt1 reverse transcription, indicating that multiple copies of Tnt1 mRNA are packaged into virus-like particles. Conclusions Our data demonstrate that mini-Tnt1 vectors can replicate efficiently in tobacco cells using GAG and POL proteins provided in trans by

  17. Differential regulation of genes by retrotransposons in rice promoters.

    Science.gov (United States)

    Dhadi, Surendar Reddy; Xu, Zijun; Shaik, Rafi; Driscoll, Kyle; Ramakrishna, Wusirika

    2015-04-01

    Rice genome harbors genes and promoters with retrotransposon insertions. There is very little information about their function. The effect of retrotransposon insertions in four rice promoter regions on gene regulation, was investigated using promoter-reporter gene constructs with and without retrotransposons. Differences in expression levels of gus and egfp reporter genes in forward orientation and rfp in reverse orientation were evaluated in rice plants with transient expression employing quantitative RT-PCR analysis, histochemical GUS staining, and eGFP and RFP fluorescent microscopy. The presence of SINE in the promoter 1 (P1) resulted in higher expression levels of the reporter genes, whereas the presence of LINE in P2 or gypsy LTR retrotransposon in P3 reduced expression of the reporter genes. Furthermore, the SINE in P1 acts as an enhancer in contrast with the LINE in P2 and the gypsy LTR retrotransposon in P3 which act as silencers. CTAA and CGG motifs in these retrotransposons are the likely candidates for the downregulation compared to TCTT motif (SINE) which is a candidate for the upregulation of gene expression. The effect of retrotransposons on gene regulation correlated with the earlier investigation of conservation patterns of these four retrotransposon insertions in several rice accessions implying their evolutionary significance.

  18. 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.

  19. The evolution of Ty1-copia group retrotransposons in gymnosperms.

    Science.gov (United States)

    Stuart-Rogers, C; Flavell, A J

    2001-02-01

    A diverse collection of Ty1-copia group retrotransposons has been characterized from the genome of Picea abies (Norway spruce) by degenerate PCR amplification of a region of the reverse transcriptase gene. The occurrence of these retrotransposable elements in the gymnosperms was investigated by Southern blot hybridization analysis. The distribution of the different retrotransposons across the gymnosperms varies greatly. All of the retrotransposon clones isolated are highly conserved within the Picea (spruce) genus, many are also present in Pinus (pine) and/or Abies (fir) genera, and some share strongly homologous sequences with one or more of cedar, larch, Sequoia, cypress, and Ginkgo. Further subclones of one of the most strongly conserved retrotransposon sequences, Tpa28, were obtained from Ginkgo and P. abies. Comparisons of individual sequence pairs between the two species show nucleotide cross-homologies of around 80%-85%, corresponding to nucleotide substitution rates similar to those of nuclear protein-coding genes. Analysis of Tpa28 consensus sequences reveals that strong purifying selection has acted on this retrotransposon in the lineages connecting Ginkgo and Picea. Collectively, these data suggest, first, that the evolution of the Ty1-copia retrotransposon group in the gymnosperms is dominated by germ line vertical transmission, with strong selection for reverse transcriptase sequence, and, second, that extinction of individual retrotransposon types has been comparatively rare in gymnosperm species lineages compared with angiosperms. If this very high level of sequence conservation is a general property of the retrotransposons, then their extreme sequence diversity implies that they are extremely ancient, and the major element lineages seen today may have arisen early in eukaryote evolution. The data are also consistent with horizontal transmission of particular retrotransposons between species, but such a mechanism is unnecessary to explain the results.

  20. BEL/Pao retrotransposons in metazoan genomes

    Directory of Open Access Journals (Sweden)

    de la Chaux Nicole

    2011-06-01

    Full Text Available Abstract Background Long terminal repeat (LTR retrotransposons are a widespread kind of transposable element present in eukaryotic genomes. They are a major factor in genome evolution due to their ability to create large scale mutations and genome rearrangements. Compared to other transposable elements, little attention has been paid to elements belonging to the metazoan BEL/Pao subclass of LTR retrotransposons. No comprehensive characterization of these elements is available so far. The aim of this study was to describe all BEL/Pao elements in a set of 62 sequenced metazoan genomes, and to analyze their phylogenetic relationship. Results We identified a total of 7,861 BEL/Pao elements in 53 of our 62 study genomes. We identified BEL/Pao elements in 20 genomes where such elements had not been found so far. Our analysis shows that BEL/Pao elements are the second-most abundant class of LTR retrotransposons in the genomes we study, more abundant than Ty1/Copia elements, and second only to Ty3/Gypsy elements. They occur in multiple phyla, including basal metazoan phyla, suggesting that BEL/Pao elements arose early in animal evolution. We confirm findings from previous studies that BEL/Pao elements do not occur in mammals. The elements we found can be grouped into more than 1725 families, 1623 of which are new, previously unknown families. These families fall into seven superfamilies, only five of which have been characterized so far. One new superfamily is a major subdivision of the Pao superfamily which we propose to call Dan, because it is restricted to the genome of the zebrafish Danio rerio. The other new superfamily comprises 83 elements and is restricted to lower aquatic eumetazoans. We propose to call this superfamily Flow. BEL/Pao elements do not show any signs of recent horizontal gene transfer between distantly related species. Conclusions In sum, our analysis identifies thousands of new BEL/Pao elements and provides new insights into

  1. Atrx promotes heterochromatin formation at retrotransposons.

    Science.gov (United States)

    Sadic, Dennis; Schmidt, Katharina; Groh, Sophia; Kondofersky, Ivan; Ellwart, Joachim; Fuchs, Christiane; Theis, Fabian J; Schotta, Gunnar

    2015-07-01

    More than 50% of mammalian genomes consist of retrotransposon sequences. Silencing of retrotransposons by heterochromatin is essential to ensure genomic stability and transcriptional integrity. Here, we identified a short sequence element in intracisternal A particle (IAP) retrotransposons that is sufficient to trigger heterochromatin formation. We used this sequence in a genome-wide shRNA screen and identified the chromatin remodeler Atrx as a novel regulator of IAP silencing. Atrx binds to IAP elements and is necessary for efficient heterochromatin formation. In addition, Atrx facilitates a robust and largely inaccessible heterochromatin structure as Atrx knockout cells display increased chromatin accessibility at retrotransposons and non-repetitive heterochromatic loci. In summary, we demonstrate a direct role of Atrx in the establishment and robust maintenance of heterochromatin.

  2. Reverse Transcription of Retroviruses and LTR Retrotransposons.

    Science.gov (United States)

    Hughes, Stephen H

    2015-04-01

    The enzyme reverse transcriptase (RT) was discovered in retroviruses almost 50 years ago. The demonstration that other types of viruses, and what are now called retrotransposons, also replicated using an enzyme that could copy RNA into DNA came a few years later. The intensity of the research in both the process of reverse transcription and the enzyme RT was greatly stimulated by the recognition, in the mid-1980s, that human immunodeficiency virus (HIV) was a retrovirus and by the fact that the first successful anti-HIV drug, azidothymidine (AZT), is a substrate for RT. Although AZT monotherapy is a thing of the past, the most commonly prescribed, and most successful, combination therapies still involve one or both of the two major classes of anti-RT drugs. Although the basic mechanics of reverse transcription were worked out many years ago, and the first high-resolution structures of HIV RT are now more than 20 years old, we still have much to learn, particularly about the roles played by the host and viral factors that make the process of reverse transcription much more efficient in the cell than in the test tube. Moreover, we are only now beginning to understand how various host factors that are part of the innate immunity system interact with the process of reverse transcription to protect the host-cell genome, the host cell, and the whole host, from retroviral infection, and from unwanted retrotransposition.

  3. LTR-retrotransposons in plants: Engines of evolution.

    Science.gov (United States)

    Galindo-González, Leonardo; Mhiri, Corinne; Deyholos, Michael K; Grandbastien, Marie-Angèle

    2017-08-30

    LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    The endogenous Lotus retrotransposon 1 (LORE1) transposes in the germ line of Lotus japonicus plants that carry an active element. This feature of LORE1 has been exploited for generation of a large non-transgenic insertion mutant population, where insertions have been annotated using next......-generation sequencing approaches. The LORE1 mutant lines are freely available and can be ordered online. Endogenous retrotransposons are also active in many other plant species. Based on the methods developed for LORE1 mutagenesis, it should be simple to establish similar systems in other species, once an appropriate...

  5. The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles

    Science.gov (United States)

    Lim, Ai Khim; Lorthongpanich, Chanchao; Chew, Ting Gang; Tan, Chin Wee Godwin; Shue, Yan Ting; Balu, Sathish; Gounko, Natalia; Kuramochi-Miyagawa, Satomi; Matzuk, Martin M.; Chuma, Shinichiro; Messerschmidt, Daniel M.; Solter, Davor; Knowles, Barbara B.

    2013-01-01

    Mobilization of endogenous retrotransposons can destabilize the genome, an imminent danger during epigenetic reprogramming of cells in the germline. The P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway is known to silence retrotransposons in the mouse testes. Several piRNA pathway components localize to the unique, germline structure known as the nuage. In this study, we surveyed mouse ovaries and found, for the first time, transient appearance of nuage-like structures in oocytes of primordial follicles. Mouse vasa homolog (MVH), Piwi-like 2 (PIWIL2/MILI) and tudor domain-containing 9 (TDRD9) are present in these structures, whereas aggregates of germ cell protein with ankyrin repeats, sterile alpha motif and leucine zipper (GASZ) localize separately in the cytoplasm. Retrotransposons are silenced in primordial ovarian follicles, and de-repressed upon reduction of piRNA expression in Mvh, Mili or Gasz mutants. However, these null-mutant females, unlike their male counterparts, are fertile, uncoupling retrotransposon activation from sterility. PMID:23924633

  6. Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.).

    Science.gov (United States)

    Nakatsuka, Akira; Iwami, Naoko; Matsumoto, Shigehito; Itamura, Hiroyuki; Yamagishi, Masumi

    2002-04-01

    We cloned and characterized Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.). Genomic DNA or methyl jasmonate (MJA)-treated cDNA were used as templates to amplify the reverse transcriptase region of Ty1-copia group retrotransposons. About 280 bp fragments were amplified and cloned, and 97 clones were sequenced. Forty-nine clones included frameshift or the stop codon, or both. Among 48 clones containing complete reading frames, 42 clones had unique nucleotide sequences. Alignment and phylogenetic analysis of putative amino acid sequences in the 42 clones indicated that these clones (named Tdk; retroTransposon in Diospyros kaki) fell into seven subgroups and six ungrouped sequences, indicating high sequence heterogeneity in Tdk clones. Phylogenetic analysis comparing unrelated plant species shows that some Tdk clones are more closely related to Ty1-copia group retrotransposons in the orders Solanales and Sapindales rather than to other Tdk clones. Southern blot analysis using Tdk2B, Tdk4c, Tdk6Ac, Tdk12K and Tdk13G clones as probes showed that persimmon and its related species, D. lotus, D. lotus var. glabba, D. oleifera, D. rhombifolia and D. virginiana, contained multiple Tdk-like sequences, indicating that homologous elements exist in other Diospyros species.

  7. Presence of env-like sequences in Quercus suber retrotransposons.

    Science.gov (United States)

    Carvalho, M; Ribeiro, T; Viegas, W; Morais-Cecilio, L; Rocheta, M

    2010-01-01

    The main difference between LTR retrotransposons and retroviruses is the presence of the envelope (env) gene in the latter, downstream of the pol gene. The env gene is involved in their infectious capacity. Here we report the presence of env-like sequences in the genome of Quercus suber (cork oak), one of the most economically important Portuguese species. These gene sequences were isolated through DNA amplification between RNaseH conserved motifs and 3' LTR, based on the structure of copia retrotransposons. Phylogenetic analysis revealed that almost all the clones isolated are clustered with Cyclops-2, a Ty3-gypsy element identified in Pisum sativum, except one clustered with gypsy and copia retroelements found in different species. This suggests the existence of a potential ancestral sequence of the env gene, prior to the separation of Ty3-gypsy and Ty1-copia retrotransposons. Additionally, the isolated env-like sequences showed 26-39% of homology with env-like sequences characterized in viruses. The origin of env-like sequences in retrotransposons from host plant taxa is discussed.

  8. 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.

  9. 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.

  10. Mastering Virtual Machine Manager 2008 R2

    CERN Document Server

    Michael, Michael

    2009-01-01

    One-of-a-kind guide from Microsoft insiders on Virtual Machine Manager 2008 R2!. What better way to learn VMM 2008 R2 than from the high-powered Microsoft program managers themselves? This stellar author team takes you under the hood of VMM 2008 R2, providing intermediate and advanced coverage of all features.: Walks you through Microsoft's new System Center Virtual Machine Manager 2008, a unified system for managing all virtual and physical assets; VMM 2008 not only supports Windows Server 2008 Hyper-V, but also VMware ESXas well!; Features a winning author team behind the new VMM; Describes

  11. R/2R DAC Nonlinearity Compensation

    OpenAIRE

    Kulig, Gabriel; Wallin, Gustav

    2012-01-01

    The resistor ladder (R/2R) digital-to-analogue converter (DAC) architecture is often used in high performance audio solutions due to its low-noise performance. Even high-end R/2R DACs suffer from static nonlinearity distortions. It was suspected that compensating for these nonlinearities would be possible. It was also suspected that this could improve audio quality in audio systems using R/2R DACs for digital-to-analogue (A/D) conversion. Through the use of models of the resistor ladder archi...

  12. Plant centromeric retrotransposons: a structural and cytogenetic perspective

    Directory of Open Access Journals (Sweden)

    Neumann Pavel

    2011-03-01

    Full Text Available Abstract Background The centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity. Results We have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD. A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active. Conclusions Comprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A. These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their

  13. Condensin II subunit dCAP-D3 restricts retrotransposon mobilization in Drosophila somatic cells.

    Directory of Open Access Journals (Sweden)

    Andrew T Schuster

    2013-10-01

    Full Text Available Retrotransposon sequences are positioned throughout the genome of almost every eukaryote that has been sequenced. As mobilization of these elements can have detrimental effects on the transcriptional regulation and stability of an organism's genome, most organisms have evolved mechanisms to repress their movement. Here, we identify a novel role for the Drosophila melanogaster Condensin II subunit, dCAP-D3 in preventing the mobilization of retrotransposons located in somatic cell euchromatin. dCAP-D3 regulates transcription of euchromatic gene clusters which contain or are proximal to retrotransposon sequence. ChIP experiments demonstrate that dCAP-D3 binds to these loci and is important for maintaining a repressed chromatin structure within the boundaries of the retrotransposon and for repressing retrotransposon transcription. We show that dCAP-D3 prevents accumulation of double stranded DNA breaks within retrotransposon sequence, and decreased dCAP-D3 levels leads to a precise loss of retrotransposon sequence at some dCAP-D3 regulated gene clusters and a gain of sequence elsewhere in the genome. Homologous chromosomes exhibit high levels of pairing in Drosophila somatic cells, and our FISH analyses demonstrate that retrotransposon-containing euchromatic loci are regions which are actually less paired than euchromatic regions devoid of retrotransposon sequences. Decreased dCAP-D3 expression increases pairing of homologous retrotransposon-containing loci in tissue culture cells. We propose that the combined effects of dCAP-D3 deficiency on double strand break levels, chromatin structure, transcription and pairing at retrotransposon-containing loci may lead to 1 higher levels of homologous recombination between repeats flanking retrotransposons in dCAP-D3 deficient cells and 2 increased retrotransposition. These findings identify a novel role for the anti-pairing activities of dCAP-D3/Condensin II and uncover a new way in which dCAP-D3/Condensin

  14. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

    Directory of Open Access Journals (Sweden)

    Ganko Eric W

    2004-03-01

    Full Text Available Abstract Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (

  15. The Microprocessor controls the activity of mammalian retrotransposons.

    Science.gov (United States)

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

    2013-10-01

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

  16. The application of LTR retrotransposons as molecular markers in plants.

    Science.gov (United States)

    Schulman, Alan H; Flavell, Andrew J; Paux, Etienne; Ellis, T H Noel

    2012-01-01

    Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction.

  17. Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences

    Science.gov (United States)

    Balaj, Leonora; Lessard, Ryan; Dai, Lixin; Cho, Yoon-Jae; Pomeroy, Scott L.; Breakefield, Xandra O.; Skog, Johan

    2011-01-01

    Tumour cells release an abundance of microvesicles containing a selected set of proteins and RNAs. Here, we show that tumour microvesicles also carry DNA, which reflects the genetic status of the tumour, including amplification of the oncogene c-Myc. We also find amplified c-Myc in serum microvesicles from tumour-bearing mice. Further, we find remarkably high levels of retrotransposon RNA transcripts, especially for some human endogenous retroviruses, such as LINE-1 and Alu retrotransposon elements, in tumour microvesicles and these transposable elements could be transferred to normal cells. These findings expand the nucleic acid content of tumour microvesicles to include: elevated levels of specific coding and non-coding RNA and DNA, mutated and amplified oncogene sequences and transposable elements. Thus, tumour microvesicles contain a repertoire of genetic information available for horizontal gene transfer and potential use as blood biomarkers for cancer. PMID:21285958

  18. Meiosis and retrotransposon silencing during germ cell development in mice.

    Science.gov (United States)

    Ollinger, Rupert; Reichmann, Judith; Adams, Ian R

    2010-03-01

    In mammals, germ cells derive from the pluripotent cells that are present early in embryogenesis, and then differentiate into male sperm or female eggs as development proceeds. Fusion between an egg and a sperm at fertilization allows genetic information from both parents to be transmitted to the next generation, and produces a pluripotent zygote to initiate the next round of embryogenesis. Meiosis is a central event in this self-perpetuating cycle that creates genetic diversity by generating new combinations of existing genetic alleles, and halves the number of chromosomes in the developing male and female germ cells to allow chromosome number to be maintained through successive generations. The developing germ cells also help to maintain genetic and chromosomal stability through the generations by protecting the genome from excessive de novo mutation. Several mouse mutants have recently been characterised whose germ cells exhibit defects in silencing the potentially mutagenic endogenous retroviruses and other retrotransposons that are prevalent in mammalian genomes, and these germ cells also exhibit defects in progression through meiosis. Here we review how mouse germ cells develop and proceed through meiosis, how mouse germ cells silence endogenous retroviruses and other retrotransposons, and discuss why silencing of endogenous retroviruses and other retrotransposons may be required for meiotic progression in mice.

  19. Windows Server 2012 R2 administrator cookbook

    CERN Document Server

    Krause, Jordan

    2015-01-01

    This book is intended for system administrators and IT professionals with experience in Windows Server 2008 or Windows Server 2012 environments who are looking to acquire the skills and knowledge necessary to manage and maintain the core infrastructure required for a Windows Server 2012 and Windows Server 2012 R2 environment.

  20. Mastering Windows Server 2012 R2

    CERN Document Server

    Minasi, Mark; Booth, Christian; Butler, Robert; McCabe, John; Panek, Robert; Rice, Michael; Roth, Stefan

    2013-01-01

    Check out the new Hyper-V, find new and easier ways to remotely connect back into the office, or learn all about Storage Spaces-these are just a few of the features in Windows Server 2012 R2 that are explained in this updated edition from Windows authority Mark Minasi and a team of Windows Server experts led by Kevin Greene. This book gets you up to speed on all of the new features and functions of Windows Server, and includes real-world scenarios to put them in perspective. If you're a system administrator upgrading to, migrating to, or managing Windows Server 2012 R2, find what you need to

  1. Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian.

    Science.gov (United States)

    Cao, Liping; Yin, Guojun; Cao, Zheming; Bing, Xuwen; Ding, Weidong

    2016-06-01

    A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.

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

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2010-01-01

    transcriptional activity from Long Terminal Repeat (LTR) retrotransposons. LTR retrotransposons are normally flanked by two LTR sequences. However, the majority of LTR sequences in S. pombe exist as solitary LTRs, i.e. as single terminal repeat sequences not flanking a retrotransposon. Transcriptional activity...... 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...... proliferation of LTR retrotransposons. The finding of considerable transcriptional activity of retrotransposons suggests that part of this regulation is likely to take place at a posttranscriptional level. Alternatively, the transcriptional activity may signify a hitherto unrecognized activity level...

  3. CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome.

    Science.gov (United States)

    Göke, Jonathan; Ng, Huck Hui

    2016-08-01

    The human genome contains millions of fragments from retrotransposons-highly repetitive DNA sequences that were once able to "copy and paste" themselves to other regions in the genome. However, the majority of retrotransposons have lost this capacity through acquisition of mutations or through endogenous silencing mechanisms. Without this imminent threat of transposition, retrotransposons have the potential to act as a major source of genomic innovation. Indeed, large numbers of retrotransposons have been found to be active in specific contexts: as gene regulatory elements and promoters for protein-coding genes or long noncoding RNAs, among others. In this review, we summarise recent findings about retrotransposons, with implications in gene expression regulation, the expansion of gene isoform diversity and the generation of long noncoding RNAs. We highlight key examples that demonstrate their role in cellular identity and their versatility as markers of cell states, and we discuss how their dysregulation may contribute to the formation of and possibly therapeutic response in human cancers.

  4. Expanding Lorentzian Wormholes in R2 Gravity

    Science.gov (United States)

    Sajadi, S. N.; Riazi, N.

    2011-10-01

    We present traversable, Lorentzian wormholes in the framework of R^{2} gravity. These wormholes are obtained by assuming constant Ricci scalar and trace-less equation of state. The metric is asymptotically RW, and locally that of a Lorentzian wormhole. Dynamics of the cosmological background, as well as the expanding wormhole are discussed. Weak energy condition near the wormhole throat is also examined. It is shown that the positive energy density condition can be satisfied all-over a spacelike hypersurface at large enough cosmological times and small enough, positive cosmological constant.

  5. LINEing germ and embryonic stem cells' silencing of retrotransposons.

    Science.gov (United States)

    Ishiuchi, Takashi; Torres-Padilla, Maria-Elena

    2014-07-01

    Almost half of our genome is occupied by transposable elements. Although most of them are inactive, one type of non-long terminal repeat (LTR) retrotransposon, long interspersed nuclear element 1 (LINE1), is capable of retrotransposition. Two studies in this issue, Pezic and colleagues (pp. 1410-1428) and Castro-Diaz and colleagues (pp. 1397-1409), provide novel insight into the regulation of LINE1s in human embryonic stem cells and mouse germ cells and shed new light on the conservation of complex mechanisms to ensure silencing of transposable elements in mammals.

  6. R + R$^{2}$ gravity as R + backreaction

    CERN Document Server

    Kung, J H

    1995-01-01

    Quadratic theory of gravity is a complicated constraint system. We investigate some consequences of treating quadratic terms perturbatively (higher derivative version of backreaction effects). This approach is shown to overcome some well known problems associated with higher derivative theories, i.e., the physical gravitational degree of freedom remains unchanged from those of Einstein gravity. Using such an interpretation of R + \\beta R^2 gravity, we investigate a classical and Wheeler DeWitt evolution of R + \\beta R^2 gravity for a particular sign of \\beta, corresponding to non- tachyon case. Matter is described by a phenomenological \\rho \\propto a(t)^{-n}. It is concluded that both the Friedmann potential U(a) ( {\\dot a}^2 + 2U(a) = 0 ) and the Wheeler DeWitt potential W(a) (\\left[-{\\partial^2\\over \\partial a^2} + 2W(a)\\right]\\psi (a) =0 ) develop repulsive barriers near a\\approx 0 for n>4 (i.e., p > {1\\over 3}\\rho ). The interpretations is clear. Repulsive barrier in U(a) implies that a contracting FRW un...

  7. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

    Science.gov (United States)

    Sun, Cheng; Shepard, Donald B; Chong, Rebecca A; López Arriaza, José; Hall, Kathryn; Castoe, Todd A; Feschotte, Cédric; Pollock, David D; Mueller, Rachel Lockridge

    2012-01-01

    Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

  8. 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

    2016-01-01

    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. PMID:27342737

  9. Submicron R2Fe14B particles

    Directory of Open Access Journals (Sweden)

    O. Koylu-Alkan

    2016-05-01

    Full Text Available Mechanochemical synthesis of submicron R2Fe14B particles with R = Dy, Nd, Pr has been performed successfully via high energy ball milling of rare-earth oxides, iron oxide and boron oxide in the presence of a reducing agent (Ca and a dispersant material (CaO, followed by annealing at 800 - 900 °C. In the R = Nd system, we were able to fabricate particles embedded in a CaO matrix with coercivity (Hc of 10.3 kOe after annealing at 900 °C for 5 min. After washing off the dispersant, the Hc was decreased to below 1 kOe because of hydrogen absorption that leads to the formation of the hydrated R2Fe14BHx phase that has a lower anisotropy. Upon removal of the hydrogen the coercivity was increased to 3.3 kOe. The average size of the Nd2Fe14B particles increases from 100 nm in a sample synthesized at 800 °C to 158 nm at 900 °C. The isotropic Dy2Fe14B particles showed a higher coercivity of 21 kOe in washed samples after annealing at 900 °C for 5 min. An average size of 71 nm is measured in samples synthesized at 800 °C and 107 nm at 900 °C. Fitting the high field M(H measurements in Nd2Fe14B to the law of approach to saturation gave values for the magnetocrystalline anisotropy for the washed sample 2.23 × 107 erg/cm3 and for the vacuum annealed sample 4.15 × 107 erg/cm3, both of which are lower than the bulk values. This would explain the lower values of Hc observed in the particles.

  10. 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.

  11. Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline.

    Science.gov (United States)

    Crichton, James H; Dunican, Donncha S; Maclennan, Marie; Meehan, Richard R; Adams, Ian R

    2014-05-01

    The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline.

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

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2010-01-01

    BACKGROUND: Retrotransposons are transposable elements that proliferate within eukaryotic genomes through a process involving reverse transcription. The numbers of retrotransposons within genomes and differences between closely related species may yield insight into the evolutionary history...... 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...

  13. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters.

    Science.gov (United States)

    Estécio, Marcos R H; Gallegos, Juan; Dekmezian, Mhair; Lu, Yue; Liang, Shoudan; Issa, Jean-Pierre J

    2012-10-01

    Almost half of the human genome and as much as 40% of the mouse genome is composed of repetitive DNA sequences. The majority of these repeats are retrotransposons of the SINE and LINE families, and such repeats are generally repressed by epigenetic mechanisms. It has been proposed that these elements can act as methylation centers from which DNA methylation spreads into gene promoters in cancer. Contradictory to a methylation center function, we have found that retrotransposons are enriched near promoter CpG islands that stay methylation-free in cancer. Clearly, it is important to determine which influence, if any, these repetitive elements have on nearby gene promoters. Using an in vitro system, we confirm here that SINE B1 elements can influence the activity of downstream gene promoters, with acquisition of DNA methylation and loss of activating histone marks, thus resulting in a repressed state. SINE sequences themselves did not immediately acquire DNA methylation but were marked by H3K9me2 and H3K27me3. Moreover, our bisulfite sequencing data did not support that gain of DNA methylation in gene promoters occurred by methylation spreading from SINE B1 repeats. Genome-wide analysis of SINE repeats distribution showed that their enrichment is directly correlated with the presence of USF1, USF2, and CTCF binding, proteins with insulator function. In summary, our work supports the concept that SINE repeats interfere negatively with gene expression and that their presence near gene promoters is counter-selected, except when the promoter is protected by an insulator element.

  14. Multicenter R2* mapping in the healthy brain

    DEFF Research Database (Denmark)

    Ropele, Stefan; Wattjes, Mike P; Langkammer, Christian;

    2014-01-01

    PURPOSE: The R2* relaxation rate constant has been suggested as a sensitive measure for iron accumulation. The aim of this multi-center study was to assess the inter-scanner and inter-subject variability of R2* mapping and to investigate the relationship between brain volume and R2* in specific...

  15. Synthesis and Structure of Mixed Distannoxane Dimers [ClR2SnOSnR'2Cl]2

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Mixed distannoxane dimers [ClR2SnOSnR'2Cl]2 were synthesized by the reaction of R2SnO (R = Bu, Pr) and R2SnCl2 (R = Me, Ph, Cy, Oct). The crystal structures of compound 1 and 5 show they are ladder-type dimers that contain a central planar Sn2O2 four-membered ring. Both endo- and exo-Sn atoms are five-coordinate.

  16. 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

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

    Science.gov (United States)

    Stacey, Simon N; Kehr, Birte; Gudmundsson, Julius; Zink, Florian; Jonasdottir, Aslaug; Gudjonsson, Sigurjon A; Sigurdsson, Asgeir; Halldorsson, Bjarni V; Agnarsson, Bjarni A; Benediktsdottir, Kristrun R; Aben, Katja K H; Vermeulen, Sita H; Cremers, Ruben G; Panadero, Angeles; Helfand, Brian T; Cooper, Phillip R; Donovan, Jenny L; Hamdy, Freddie C; Jinga, Viorel; Okamoto, Ichiro; Jonasson, Jon G; Tryggvadottir, Laufey; Johannsdottir, Hrefna; Kristinsdottir, Anna M; Masson, Gisli; Magnusson, Olafur T; Iordache, Paul D; Helgason, Agnar; Helgason, Hannes; Sulem, Patrick; Gudbjartsson, Daniel F; Kong, Augustine; Jonsson, Eirikur; Barkardottir, Rosa B; Einarsson, Gudmundur V; Rafnar, Thorunn; Thorsteinsdottir, Unnur; Mates, Ioan N; Neal, David E; Catalona, William J; Mayordomo, José I; Kiemeney, Lambertus A; Thorleifsson, Gudmar; Stefansson, Kari

    2016-03-01

    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 and breast cancer, is protective against prostate cancer [odds ratio (OR) = 0.91, P = 1.0 × 10(-6)]. rs700635[C] is also associated with failures to correctly splice out CASP8 intron 8 in breast and prostate tumours and in corresponding normal tissues. Investigation of rs700635[C] carriers revealed that they have a human-specific short interspersed element-variable number of tandem repeat-Alu (SINE-VNTR-Alu), subfamily-E retrotransposon (SVA-E) inserted into CASP8 intron 8. The SVA-E shows evidence of prior activity, because it has transduced some CASP8 sequences during subsequent retrotransposition events. Whole-genome sequence (WGS) data were used to tag the SVA-E with a surrogate SNP rs1035142[T] (r(2) = 0.999), which showed associations with both the splicing anomalies (P = 6.5 × 10(-32)) and with protection against prostate cancer (OR = 0.91, P = 3.8 × 10(-7)).

  18. Identification and characterization of jute LTR retrotransposons:: Their abundance, heterogeneity and transcriptional activity.

    Science.gov (United States)

    Ahmed, Salim; Shafiuddin, Md; Azam, Muhammad Shafiul; Islam, Md Shahidul; Ghosh, Ajit; Khan, Haseena

    2011-05-01

    Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.

  19. Identification of retrotransposon families and analysis of their transcriptional activation in wheat

    Institute of Scientific and Technical Information of China (English)

    TANG Yimiao; MA Youzhi; LI Liancheng; XIN Zhiyong

    2005-01-01

    Variations in the reverse transcriptase (RT) domain were analyzed to clarify retrotransposon family structure and their evolution in wheat genome. RT-PCR was conducted by using primers based on the conserved RT peptide motifs of plant retrotransposons to amplify the RT domain of retrotransposons in the seedlings of wheat line Pm97034 treated with powdery mildew fungus. High level of heterogeneity was detected in 51 (RT1-51) clones randomly selected and the identity of nucleotide sequence among them ranged from 75.4% to 97.9%. These sequences, in combination with previously identified seven representatives from wheat retrotransposon families (families 1―7), were used to construct a composite phylogenetic tree. Three new families, designated family 8 to family 10, were identified. Famliy 8 formed before divergence of the Pooideae subfamily and was regarged as an ancient retrotransposon family. Some members of family 4 and family 7 had transcriptional activativity, and were present with multiple copies in wheat and its related species.

  20. A supersymmetric R2-action in six dimensions and torsion

    NARCIS (Netherlands)

    Bergshoeff, E.; Salam, Abdus; Sezgin, E.

    1986-01-01

    The superconformal extension of (Rµνab)2 is given in six dimensions. It is shown that in a superconformal gauge the three-form field Hµν� has a natural torsion interpretation. Also partial results are given on the superconformal extension of the Gauss-Bonnet combination R2µνab - 4R2µa + R2.

  1. The Microprocessor controls the activity of mammalian retrotransposons

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  2. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons.

    Directory of Open Access Journals (Sweden)

    Jungnam Lee

    Full Text Available The long interspersed element-1 (LINE-1 or L1 and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI, that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution.

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

    Science.gov (United States)

    Guidez, Fabien

    2014-01-01

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

  4. Genome-wide Characterization of Long Terminal Repeat-retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1-copia and Ty3-gypsy Retrotransposons

    Institute of Scientific and Technical Information of China (English)

    Hai-Yue Sun; Hong-Yan Dai; Gui-Ling Zhao; Yue Ma; Chun-Qing Ou; He Li; Lin-Guang Li; Zhi-Hong Zhang

    2008-01-01

    The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers.Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame.High heterogeneity among RT sequences of both Tyl-copia and Ty3-gypsy group retrotransposons was observed,but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements.Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (~500O) and Ty3-gypsy ( ~26000).All elements of the two types of LTR retrotransposons comprise approximately 38% of the M.domestica genome,with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%).Transcription was not detected by reverse transcription-polymerase chain reaction for either Tyl.copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine.This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome.Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon,but the latter has a higher copy number,which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution.

  5. 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...... (Regel) K. Larsen (syn. Lotus corniculatus L. var. japonicus Regel). LORE1 has several unusual characteristics that are interesting both for studying evolutional genomics and for the use of LORE1 as a genetic tool. In this review, we present the characteristics of LORE1 and discuss the biological...... 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...

  6. Regulating retrotransposon activity through the use of alternative transcription start sites

    DEFF Research Database (Denmark)

    Persson, Jenna; Steglich, Babett; Smialowska, Agata

    2016-01-01

    a new mechanism of retrotransposon regulation through transcription start site (TSS) selection by altered nucleosome occupancy. We show that Fun30 chromatin remodelers cooperate to maintain a high level of nucleosome occupancy at retrotransposon-flanking long terminal repeat (LTR) elements......Retrotransposons, the ancestors of retroviruses, have the potential for gene disruption and genomic takeover if not kept in check. Paradoxically, although host cells repress these elements by multiple mechanisms, they are transcribed and are even activated under stress conditions. Here, we describe....... This enforces the use of a downstream TSS and the production of a truncated RNA incapable of reverse transcription and retrotransposition. However, in stressed cells, nucleosome occupancy at LTR elements is reduced, and the TSS shifts to allow for productive transcription. We propose that controlled...

  7. Identification and Characterization of Reverse Transcriptase Domain of Transcriptionally Active Retrotransposons in Wheat Genomes

    Institute of Scientific and Technical Information of China (English)

    Yi-Miao TANG; You-Zhi MA; Lian-Cheng LI; Xing-Guo YE

    2005-01-01

    To clarify activation characterization of wheat (Triticum aestivum L.) retrotransposons, transcriptionally active Ty1-copia retrotransposons were found in wheat by using RT-PCR to amplify the RT domain. Sequence analysis of random RT-PCR clones reveals that Ty1-copia retrotransposons are highly heterogeneous and can be divided into at least four groups, which are tentatively named TaRT-1 to TaRT-4.Dot blot hybridization indicates that TaRT- 1 exists in the wheat genome as multiple copies (at 30 000 copies/a hexaploid genome (ABD)). Northern blot hybridization showed that TaRT-1 is only expressed at a low level under normal conditions in seedlings, but at a high level when induced by powdery mildew fungus, jasmonic acid (JA) and salicylic acid (SA). These results suggest that the TaRT-1 expression is highly sensitive to biotic and abiotic stresses.

  8. Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon.

    Science.gov (United States)

    Purugganan, M D; Wessler, S R

    1994-11-22

    The magellan transposable element is responsible for a spontaneous 5.7-kb insertion in the maize wx-M allele. This element has the sequence and structural characteristics of a Ty3/gypsy-like retrotransposon. The magellan element is present in all Zea species and Tripsacum andersonii; it is absent, however, in the genomes of all other Tripsacum species analyzed. The genetic distances between magellan elements suggest that this retrotransposon is evolving faster than other Zea nuclear loci. The phylogeny of magellan within Zea and T. andersonii also reveals a pattern of interspecies transfers, resulting in the movement of magellan subfamilies between different species genomes. Interspecific hybridization may be a major mechanism by which this retrotransposon invades and establishes itself in new taxa.

  9. 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

  10. Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species.

    Science.gov (United States)

    Kuipers, A G; Heslop-Harrison, J S; Jacobsen, E

    1998-06-01

    The genus Alstroemeria contains species with large genomes (2C = 36.5-78.9 pg (17,600-38,000 Mb) in those species with 2n = 2x = 16). We investigated the diversity and genomic and chromosomal organisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Analysis of 33 PCR-amplified sequences corresponding to a conserved domain of the Ty1-copia reverse transcriptase (rt) gene showed high heterogeneity among predicted amino acid sequences; no two sequences were identical, but most fell into one of five subgroups. Levels of inter- and intra-specific heterogeneity of sequences were similar. HaeIII-digested genomic DNA of various Alstroemeria species contained distinct bands upon hybridisation with individual rt gene fragments. Hybridisation with the heterogeneous PCR pool of rt fragments (retrotransposon pool) revealed additional bands; some minor bands were characteristic of either Brazilian or Chilean species. In situ hybridisation of the retrotransposon pool from three species to metaphase chromosomes from the same species showed a dispersed distribution of the retrotransposon pool with exclusion from rDNA and other chromosomal sites. Alstroemeria pelegrina, which is without major heterochromatic sites, showed some clustering and small negative bands. The retrotransposon pool was excluded from major DAPI-staining bands in Alstroemeria aurea, but in contrast, the sites of the major tandemly repeated sequences in Alstroemeria inodora showed a hybridisation signal similar to that in the rest of the chromosomes. The data are discussed in the context of the contribution of Ty1-copia-like retrotransposons to plant genome size, their evolution, and their value for phylogenetic and biodiversity studies.

  11. Regulating retrotransposon activity through the use of alternative transcription start sites

    DEFF Research Database (Denmark)

    Persson, Jenna; Steglich, Babett; Smialowska, Agata;

    2016-01-01

    a new mechanism of retrotransposon regulation through transcription start site (TSS) selection by altered nucleosome occupancy. We show that Fun30 chromatin remodelers cooperate to maintain a high level of nucleosome occupancy at retrotransposon-flanking long terminal repeat (LTR) elements....... This enforces the use of a downstream TSS and the production of a truncated RNA incapable of reverse transcription and retrotransposition. However, in stressed cells, nucleosome occupancy at LTR elements is reduced, and the TSS shifts to allow for productive transcription. We propose that controlled...

  12. Strong energy condition in R + R$^{2}$ gravity

    CERN Document Server

    Kung, J H

    1996-01-01

    In this paper, we study Raychaudhuri's equation in the background of R + \\beta R^2 gravity with a phenomenological matter (\\rho \\propto a(t)^{-n}). We conclude that even though the Strong Energy Condition (S.E.C.) for Einstein's gravity, which guarantees singularity, is n\\geq 2 for \\rho \\propto a(t)^{-n}, a perturbative analysis of Raychaudhuri's equation in the background of R + \\beta R^2 gravity reveals that the big bang singularity may not be guaranteed for n > 4. We derive the following Strong Energy Conditions for R + \\beta R^2 (\\beta \

  13. [Retrotransposon MDG4 and its role in genetic instability of a mutator strain of Drosophila melanogaster].

    Science.gov (United States)

    Liubomirskaia, N V; Kim, A I; Il'in, Iu V

    2003-02-01

    This article summarizes the results of a ten-year study of genetic instability of a mutator strain of Drosophila melanogaster caused by transposition of the gypsy retrotransposon. The results of other authors working with an analogous system are analyzed. Possible mechanisms are suggested for the interaction of gypsy with the cell gene flamenco that participates in transposition control of this mobile element.

  14. 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.

  15. Analysis of genetic diversity in pigeon pea germplasm using retrotransposon-based molecular markers

    Indian Academy of Sciences (India)

    MANEESHA; KAILASH C. UPADHYAYA

    2017-09-01

    Pigeon pea (Cajanus cajan), an important legume crop is predominantly cultivated in tropical and subtropical regions of Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes.We have analysed genetic polymorphism of domesticated pigeon pea germplasm (47 accessions) across the world using earlier characterized panzee retrotransposon-based molecularmarkers. Itwas conjectured that since retrotransposons are interspersed throughout the genome, retroelements-based markers would be able to uncover polymorphism possibly inherent in the diversity of retroelement sequences. Two PCR-based techniques, sequence-specific amplified polymorphism (SSAP) and retrotransposon microsatellite amplified polymorphism (REMAP) were utilized for the analyses.We show that a considerable degree of polymorphism could be detected using these techniques. Three primer combinations in SSAP generated 297 amplified products across 47 accessionswith an average of 99 amplicons per assay. Degree of polymorphism varied from 84–95%. In the REMAP assays, the number of amplicons was much less but up to 73% polymorphism could be detected. On the basis of similarity coefficients, dendrograms were constructed. The results demonstrate that the retrotransposon-based markers could serve as a better alternative for the assessment of genetic diversity in crops with apparent low genetic base.

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

    Science.gov (United States)

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

    2008-11-01

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

  17. Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons.

    Science.gov (United States)

    Shpiz, Sergey; Olovnikov, Ivan; Sergeeva, Anna; Lavrov, Sergey; Abramov, Yuri; Savitsky, Mikhail; Kalmykova, Alla

    2011-11-01

    In the Drosophila germline, retrotransposons are silenced by the PIWI-interacting RNA (piRNA) pathway. Telomeric retroelements HeT-A, TART and TAHRE, which are involved in telomere maintenance in Drosophila, are also the targets of piRNA-mediated silencing. We have demonstrated that expression of reporter genes driven by the HeT-A promoter is under the control of the piRNA silencing pathway independent of the transgene location. In order to test directly whether piRNAs affect the transcriptional state of retrotransposons we performed a nuclear run-on (NRO) assay and revealed increased density of the active RNA polymerase complexes at the sequences of endogenous HeT-A and TART telomeric retroelements as well as HeT-A-containing constructs in the ovaries of spn-E mutants and in flies with piwi knockdown. This strongly correlates with enrichment of two histone H3 modifications (dimethylation of lysine 79 and dimethylation of lysine 4), which mark transcriptionally active chromatin, on the same sequences in the piRNA pathway mutants. spn-E mutation and piwi knockdown results in transcriptional activation of some other non-telomeric retrotransposons in the ovaries, such as I-element and HMS Beagle. Therefore piRNA-mediated transcriptional mode of silencing is involved in the control of retrotransposon expression in the Drosophila germline.

  18. Isolation and Characterization of Copia-like Retrotransposons from 12 Sweet Orange (Citrus sinensis Osbeck) Cultivars

    Institute of Scientific and Technical Information of China (English)

    Neng-Guo TAO; Juan XU; Yun-Jiang CHENG; Liu HONG; Wen-Wu GUO; Hua-Lin YI; Xiu-Xin DENG

    2005-01-01

    As the largest transposable element in the plant genome, retrotransposons are thought to be involved in citrus genetic instability and genome evolution, especially in sweet orange, which is prone to bud mutation. In the present study, the presence of copia-like retrotransposons, their heterogeneity, genomic distribution, and transcriptional activities in Citrus were investigated in 12 sweet orange (Citrus sinensis Osbeck) cultivars using a PCR assay designed to detect copia-like reverse transcriptase (RT)sequences. Twelve amplification products from each cultivar were cloned and sequenced. The cloned sequences showed great heterogeneity, except "Dream" navel and "Hamlin", both of which shared the same sequence. Frame shifting, termination, deletion, and substitution accounted for the heterogeneity of RT sequences. Southern blot hybridization using the RT1 clone from the "Cara Cara" navel as a probe showed that multiple copies were integrated throughout the sweet orange genomes, which made the retrotransposon possible an effective molecular marker to detect citrus evolution events and to reveal its relationship with bud mutation. No transcriptional activities of the retrotransposon were detected by RT-PCR and Northern analysis in the fruits and leaves of either "Cara Cara" or "Seike" navels.

  19. Evolution of brain functions in mammals and LTR retrotransposon-derived genes.

    Science.gov (United States)

    Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2016-01-01

    In the human genome, there are approximately 30 LTR retrotransposon-derived genes, such as the sushi-ichi retrotransposon homologues (SIRH) and the paraneoplastic Ma antigen (PNMA) family genes. They are derivatives from the original LTR retrotransposons and each gene seems to have its own unique function. PEG10/SIRH1 as well as PEG11/RTL1/SIRH2 and SIRH7/LDOC1 play essential roles in placenta formation, maintenance of fetal capillaries and the differentiation/maturation of a variety of placental cells, respectively. All of this evidence provides strong support for their contribution to the evolution of viviparity in mammals via their eutherian-specific functions. SIRH11/ZCCHC16 is an X-linked gene that encodes a CCHC type of zinc-finger protein that exhibits high sequence identity to the LTR retrotransposon Gag protein and its deletion causes abnormal behavior related to cognition, including attention, impulsivity and working memory, possibly via the locus coeruleus noradrenaergic system in mice. Therefore, we have suggested that the acquisition of SIRH11/ZCCHC16 was involved in eutherian brain evolution. Interestingly, SIRH11/ZCCHC16 displays lineage-specific structural and putative species-specific functional variations in eutherians, suggesting that it contributed to the diversification of eutherians via increasing evolutionary fitness by these changes.

  20. Analysis of heterogeneity of Copia-like retrotransposons in the genome of cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Gbadegesin, Micheal A; Beeching, John R

    2011-12-20

    Retrotransposons are ubiquitous in eukaryotic genomes and now proving to be useful genetic tools for genetic diversity and phylogenetic analyses, especially in plants. In order to assess the diversity of Ty1/Copia-like retrotransposons of cassava, we used PCR primers anchored on the conserved domains of reverse transcriptases (RTs) to amplify cassava Ty1/Copia-like RT. The PCR product was cloned and sequenced. Sequences analysis of the clones revealed the presence of 69 families of Ty1/Copia-like retrotransposon in the genome of cassava. Comparative analyses of the predicted amino acid sequences of these clones with those of other plants showed that retroelements of this class are very heterogeneous in cassava. Cassava is widely grown for its edible roots in the tropical and subtropical regions of the world. Cassava roots, though poor in protein, are rich in starch (makes up about 80% of the dry matter), vitamin C, carotenes, calcium and potassium. It has a great commercial importance as a source of starch and starch based products. Realizing the importance of cassava, it stands out as a crop to benefit from biotechnology development. Heterogeneity of Mecops (Manihot esculenta copia-like Retrotransposons) showed that they may be useful for genetic diversity and phylogenetic analyses of cassava germplasm.

  1. Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation.

    Science.gov (United States)

    Chen, Long; Dahlstrom, Jane E; Lee, Sung-Hun; Rangasamy, Danny

    2012-07-01

    Long interspersed nuclear element 1 (LINE-1) retrotransposons are mutagens that are capable of generating deleterious mutations by inserting themselves into genes and affecting gene function in the human genome. In normal cells, the activity of LINE-1 retrotransposon is mostly repressed, maintaining a stable genome structure. In contrast, cancer cells are characterized by aberrant expression of LINE-1 retrotransposons, which, in principle, have the potential to contribute to genomic instability. The mechanistic pathways that regulate LINE-1 expression remain unclear. Using deep-sequencing small RNA analysis, we identified a subset of differentially expressed endo-siRNAs that directly regulate LINE-1 expression. Detailed analyses suggest that these endo-siRNAs are significantly depleted in human breast cancer cells compared with normal breast cells. The overexpression of these endo-siRNAs in cancer cells markedly silences endogenous LINE-1 expression through increased DNA methylation of the LINE-1 5'-UTR promoter. The finding that endo-siRNAs can silence LINE-1 activity through DNA methylation suggests that a functional link exists between the expression of endo-siRNAs and LINE-1 retrotransposons in human cells.

  2. HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Buti, M; Giordani, T; Vukich, M; Gentzbittel, L; Pistelli, L; Cattonaro, F; Morgante, M; Cavallini, A; Natali, L

    2009-11-01

    In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5' and 3' long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5' LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last approximately 84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions.

  3. The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution.

    Science.gov (United States)

    Estep, M C; DeBarry, J D; Bennetzen, J L

    2013-02-01

    Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with >5-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.

  4. Microsoft System Center 2012 R2 Operations Manager cookbook

    CERN Document Server

    Beaumont (MVP), Steve; Odika, Chiyo; Ryan, Robert

    2015-01-01

    If you are tasked with monitoring the IT infrastructure within your organization, this book demonstrates how System Center 2012 R2 Operations Manager offers a radical and exciting solution to modern administration.

  5. MASiVEdb: the Sirevirus Plant Retrotransposon Database

    Directory of Open Access Journals (Sweden)

    Bousios Alexandros

    2012-04-01

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

  6. Kinetic pathway of pyrophosphorolysis by a retrotransposon reverse transcriptase.

    Directory of Open Access Journals (Sweden)

    Manjula Pandey

    Full Text Available DNA and RNA polymerases use a common phosphoryl transfer mechanism for base addition that requires two or three acidic amino acid residues at their active sites. We previously showed, for the reverse transcriptase (RT encoded by the yeast retrotransposon Ty1, that one of the three conserved active site aspartates (D(211 can be substituted by asparagine and still retain in vitro polymerase activity, although in vivo transposition is lost. Transposition is partially restored by second site suppressor mutations in the RNAse H domain. The novel properties of this amino acid substitution led us to express the WT and D(211N mutant enzymes, and study their pre-steady state kinetic parameters. We found that the k(pol was reduced by a factor of 223 in the mutant, although the K(d for nucleotide binding was unaltered. Further, the mutant enzyme had a marked preference for Mn(2+ over Mg(2+. To better understand the functions of this residue within the Ty1 RT active site, we have now examined the in vitro properties of WT and D(211N mutant Ty1 RTs in carrying out pyrophosphorolysis, the reverse reaction to polymerization, where pyrophosphate is the substrate and dNTPs are the product. We find that pyrophosphorolysis is efficient only when the base-paired primer template region is >14 bases, and that activity increases when the primer end is blunt-ended or recessed by only a few bases. Using pre-steady state kinetic analysis, we find that the rate of pyrophosphorolysis (k(pyro in the D(211N mutant is nearly 320 fold lower than the WT enzyme, and that the mutant enzyme has an approximately 170 fold lower apparent K(d for pyrophosphate. These findings indicate that subtle substrate differences can strongly affect the enzyme's ability to properly position the primer-end to carry out pyrophosphorolysis. Further the kinetic data suggests that the D(211 residue has a role in pyrophosphate binding and release, which could affect polymerase translocation, and help

  7. DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.).

    Science.gov (United States)

    Zakrzewski, Falk; Schmidt, Martin; Van Lijsebettens, Mieke; Schmidt, Thomas

    2017-03-03

    The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses activity of transposable elements (TEs), affects gene expression, and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of the worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%) in particular, satellite DNA, retrotransposons, and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H=A, C, and T), and CHH sites, whereas the TE pattern differed, depending on the classes 1 (retrotransposons) and 2 (DNA transposons), respectively. Along genes and TEs, the CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing toward a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared to leaves. This article is protected by copyright. All rights reserved.

  8. Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding.

    Science.gov (United States)

    Thieme, Michael; Lanciano, Sophie; Balzergue, Sandrine; Daccord, Nicolas; Mirouze, Marie; Bucher, Etienne

    2017-07-07

    Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on transcriptional activity of the host RNA polymerase II (Pol II) for their mobility, it was so far unclear whether Pol II is directly involved in repressing their activity. Here we show that plants defective in Pol II activity lose DNA methylation at repeat sequences and produce more extrachromosomal retrotransposon DNA upon stress in Arabidopsis and rice. We demonstrate that combined inhibition of both DNA methylation and Pol II activity leads to a strong stress-dependent mobilization of the heat responsive ONSEN retrotransposon in Arabidopsis seedlings. The progenies of these treated plants contain up to 75 new ONSEN insertions in their genome which are stably inherited over three generations of selfing. Repeated application of heat stress in progeny plants containing increased numbers of ONSEN copies does not result in increased activation of this transposon compared to control lines. Progenies with additional ONSEN copies show a broad panel of environment-dependent phenotypic diversity. We demonstrate that Pol II acts at the root of transposon silencing. This is important because it suggests that Pol II can regulate the speed of plant evolution by fine-tuning the amplitude of transposon mobility. Our findings show that it is now possible to study induced transposon bursts in plants and unlock their use to induce epigenetic and genetic diversity for crop breeding.

  9. EPA Region 2 SEMS_CERCLIS Sites All [R2] and SEMS_CERCLIS Sites NPL [R2] GIS Layers

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Region 2 SEMS_CERCLIS Sites All [R2] GIS layer contains unique Superfund Enterprise Management System (SEMS) site records. These records have the following...

  10. Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration

    National Research Council Canada - National Science Library

    Manoj Kannan; Jingfeng Li; Sarah E Fritz; Kathryn E Husarek; Jonathan C Sanford; Teresa L Sullivan; Pawan Kumar Tiwary; Wenfeng An; Jef D Boeke; David E Symer

    2017-01-01

    ... retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human...

  11. 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.

  12. Cognitive Function Related to the Sirh11/Zcchc16 Gene Acquired from an LTR Retrotransposon in Eutherians

    OpenAIRE

    Masahito Irie; Masanobu Yoshikawa; Ryuichi Ono; Hirotaka Iwafune; Tamio Furuse; Ikuko Yamada; Shigeharu Wakana; Yui Yamashita; Takaya Abe; Fumitoshi Ishino; Tomoko Kaneko-Ishino

    2015-01-01

    Author Summary Retrotransposon-derived DNA sequences occupy approximately 40% of the mammalian genome, compared with only 1.5% of protein coding genes. They have been commonly considered “junk DNA” and even potentially harmful for host organisms. However, a series of knockout (KO) mouse analyses demonstrated that at least some of the LTR retrotransposon- and retrovirus-derived sequences play essential roles in the current mammalian developmental system as endogenous genes, such as Peg10, Peg1...

  13. 322-R2U2 Engineering Assessment - August 2015

    Energy Technology Data Exchange (ETDEWEB)

    Abri, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Griffin, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-08-13

    This Engineering Assessment and Certification of Integrity of retention tank system 322-R2 has been prepared for tank systems that store and neutralizes hazardous waste and have secondary containment. The regulations require that this assessment be completed periodically and certified by an independent, qualified, California-registered professional engineer. Abri Environmental Engineering performed an inspection of the 322-R2 Tank system at the Lawrence Livermore National Laboratory (LLNL) in Livermore, CA. Mr. William W. Moore, P.E., conducted this inspection on March 16, 2015. Mr. Moore is a California Registered Civil Engineer, with extensive experience in civil engineering, and hazardous waste management.

  14. 在2008 R2中安装Nero9

    Institute of Scientific and Technical Information of China (English)

    李明

    2010-01-01

    WindowsServer2008 R2.是Windows Server 2008 Release 2即Windows Server 2008的第二个发行版,虽然是Windows Server 2008的第二个发行版本,但相比Windows Server 2008还是有非常大的改动的。Windows Server 2008 R2在2009年10月22日发布.2009年9月14日发售。

  15. Oracle JDeveloper 11gR2 Cookbook

    CERN Document Server

    Haralabidis, Nick

    2012-01-01

    "Oracle JDeveloper 11gR2 Cookbook" is a practical cookbook which goes beyond the basics with immediately applicable recipes for building ADF applications at an intermediate-to-advanced level. If you are a JavaEE developer who wants to go beyond the basics of building ADF applications with Oracle JDeveloper 11gR2 and get hands on with practical recipes, this book is for you. You should be comfortable with general Java development principles, the JDeveloper IDE, and ADF basics

  16. R2E – identifying problems, mitigating risks

    CERN Multimedia

    Anaïs Schaeffer

    2013-01-01

    During LS1, the R2E project team will be working on a task as painstaking as it is crucial: to achieve a sixfold reduction in the number of electronic malfunctions caused by radiation. On their success depends the ability of the accelerator to function correctly at nominal energy. No mean challenge, considering it comes on top of the tenfold reduction already achieved since 2009.   The graph plots the rate of LHC beam dumps due to single-event effects against beam luminosity. An indication of the challenge that faces the R2E project teams during LS1! The origins of the project known as R2E (Radiation to Electronics) go back to 2007, when the CNGS (CERN Neutrinos to Gran Sasso) experiment was being commissioned. "Right from the outset, some CNGS control systems were causing problems. They would regularly break down in operations with beam," recalls Markus Brugger, head of the R2E project. "Even though the beam intensity was very low, we began to suspect that radiati...

  17. Structures and physical properties of R2TX3 compounds

    Institute of Scientific and Technical Information of China (English)

    Pan Zhi-Yan; Cao Chong-De; Bai Xiao-Jun; Song Rui-Bo; Zheng Jian-Bang; Duan Li-Bing

    2013-01-01

    Rare-earth compounds have been an attractive subject based on the unique electronic structures of the rare-earth elements.Novel ternary intermetallic compounds R2TX3 (R =rare-earth element or U,T =transition-metal element,X =Si,Ge,Ga,In) are a significant branch of this research field due to their complex and intriguing physical properties,such as magnetic order at low temperature,spin-glass behavior,Kondo effect,heavy fermion behavior,and so on.The unique physical properties of R2TX3 compounds are related to distinctive electronic structures,crystal structures,microinteraction,and external environment.Most R2TX3 compounds crystallize in AlB2-type or derived AlB2-type structures and exhibit many similar properties.This paper gives a concise review of the structures and physical properties of these compounds.Spin glass,magnetic susceptibility,resistivity,and specific heat of R2TX3 compounds are discussed.

  18. GluR2 ligand-binding core complexes

    DEFF Research Database (Denmark)

    Kasper, C; Lunn, M-L; Liljefors, T

    2002-01-01

    X-ray structures of the GluR2 ligand-binding core in complex with (S)-Des-Me-AMPA and in the presence and absence of zinc ions have been determined. (S)-Des-Me-AMPA, which is devoid of a substituent in the 5-position of the isoxazolol ring, only has limited interactions with the partly hydrophobic...

  19. Microsoft System Center Data Protection Manager 2012 R2 cookbook

    CERN Document Server

    Hedblom, Robert

    2015-01-01

    If you are a DPM administrator, this book will help you verify your knowledge and provide you with everything you need to know about the 2012 R2 release. No prior knowledge about System Center DPM is required, however some experience of running backups will come in handy.

  20. A sensitive RNase protection assay to detect transcripts from potentially functional human endogenous L1 retrotransposons

    DEFF Research Database (Denmark)

    Woodcock, D M; Williamson, M R; Doherty, J P

    1996-01-01

    A high background of read-through transcripts from degenerate human L1 retrotransposons is present in almost all human cell types. This prevents the detection of RNA transcripts from potentially functional elements. To overcome this, we have developed an RNase protection assay based on the recons...... transcripts from divergent L1 families but are either discrete shorter transcripts or specifically processed products from longer initial transcripts....

  1. Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.

    Directory of Open Access Journals (Sweden)

    Alexandra Olarte

    Full Text Available Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.

  2. 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.

  3. Comparison of a retrotransposon-based marker with microsatellite markers for discriminating accessions of Vitis vinifera.

    Science.gov (United States)

    Sant'Ana, G C; Ferreira, J L; Rocha, H S; Borém, A; Pasqual, M; Cançado, G M A

    2012-05-21

    Identification and knowledge concerning genetic diversity are fundamental for efficient management and use of grapevine germplasm. Recently, new types of molecular markers have been developed, such as retrotransposon-based markers. Because of their multilocus pattern, retrotransposon-based markers might be able to differentiate grapevine accessions with just one pair of primers. In order to evaluate the efficiency of this type of marker, we compared retrotransposon marker Tvv1 with seven microsatellite markers frequently used for genotyping of the genus Vitis (VVMD7, VVMD25, VVMD5, VVMD27, VVMD31, VVS2, and VZAG62). The reference population that we used consisted of 26 accessions of Vitis, including seven European varieties of Vitis vinifera, four North American varieties and hybrids of Vitis labrusca, and 15 rootstock hybrids obtained from crosses of several Vitis species. Individually, the Tvv1 and the group of seven SSR markers were capable of distinguishing all accessions except 'White Niagara' compared to 'Red Niagara'. Using the Structure software, the retrotransposon marker Tvv1 generated two clusters: one with V. vinifera plus North American varieties and the other comprising rootstocks. The seven SSR markers generated five clusters: V. vinifera, the North American varieties, and three groups of rootstock hybrids. The percentages of variation explained by the first two components in the principal coordinate analysis were 65.21 (Tvv1) and 50.42 (SSR markers) while the Mantel correlation between the distance matrixes generated by the two types of markers was 42.5%. We conclude that the Tvv1 marker is useful for DNA fingerprinting, but it lacks efficiency for discrimination of structured groups.

  4. Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species

    Science.gov (United States)

    Olarte, Alexandra; Mantri, Nitin; Nugent, Gregory; Pang, Edwin C. K.

    2013-01-01

    Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea. PMID:23940565

  5. New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

    Institute of Scientific and Technical Information of China (English)

    Lijuan Wei; Meili Xiao; Zeshan An; Bi Ma; Annaliese S.Mason; Wei Qian; Jiana Li

    2013-01-01

    Long terminal repeat (LTR) retrotransposons,one of the foremost types of transposons,continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation.Many LTR-TEs preferentially insert within other LTR-TEs,but the cause and evolutionary significance of these nested LTR-TEs are not well understood.In this study,a total of 1.52 Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned,and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density:7.24/kb)were selected for further analysis.The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions,with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23 Mya.LTR-TEs also preferably inserted into TA-rich repeat regions.Gene prediction by Genescan identified 207 genes in the 0.84 Mb of total BAC sequences.Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database,indicating that most genes were inactive after retrotransposon insertion.Five of the six BACs were putatively centromeric.Hence,nested LTR-TEs in centromere regions are rapidly duplicated,repeatedly inserted,and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences.Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions,and that these nested LTR-TEs play a role in the formation of centromeres.

  6. An epi [c] genetic battle: LINE-1 retrotransposons and intragenomic conflict in humans

    OpenAIRE

    Muñoz-Lopez, Martin; Macia, Angela; Garcia-Cañadas, Marta; Badge, Richard M.; Garcia-Perez, Jose L

    2011-01-01

    The ongoing activity of the human retrotransposon Long Interspersed Element 1 (LINE-1 or L1) continues to impact the human genome in various ways. Throughout evolution, mammalian and primate genomes have been under selection to generate strategies to reduce the activity of selfish DNA like L1. Similarly, selfish DNA has evolved to elude these containment systems. This intragenomic conflict has left many inactive versions of LINEs and other Transposable Elements (TEs) littering the human genom...

  7. 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.

  8. 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., 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.

  9. Development and Characterisation of Irap Markers From Expressed Retrotransposon-like sequences in Pinus sylvestris L.

    Directory of Open Access Journals (Sweden)

    Voronova Angelika

    2014-07-01

    Full Text Available Conifer genomes are large and stably diploid, in contrast to angiosperms, which are more variable both in genome size and ploidy. Conifer genomes are characterised by multiple gene families and pseudogenes, contain large inter-gene regions and a considerable proportion of repetitive sequences. All members of plant retrotransposon orders have been identified in gymnosperm genomes, however active elements have not been described. Investigation of transposable elements in Scots pine (Pinus sylvestris L. could offer insights into transposon-mediated reorganisation under stress conditions in complex and ancient plant genomes. Nine Pinus sylvestris specific markers were developed to hypothetical long terminal repeats (LTRs from differentially expressed retrotransposon-like fragments after heat stress and insect damage. Genetic diversity of 150 trees from a naturally regenerated pine stand was investigated using the IRAP method. The developed markers revealed high levels of genetic diversity and were able to distinguish subpopulations growing in long-term differential environmental conditions. Somaclonal variation was also investigated using these markers and polymorphic fragments were identified between ramets of Scots pine clones growing in two different plantations, possibly indicating evidence of recent transposition events. Sequencing of the polymorphic fragments identified two groups of sequences containing LTR sequences of an unknown retrotransposon with homology to the LTRs of the Copia-17-PAb-I element.

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

    Directory of Open Access Journals (Sweden)

    Jason W. Rausch

    2017-03-01

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

  11. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sinibaldi-Vallebona, Paola; Matteucci, Claudia [Department of Experimental Medicine and Biochemical Sciences, University ‘Tor Vergata’, Rome (Italy); Spadafora, Corrado, E-mail: cspadaf@tin.it [Italian National Institute of Health (ISS), Rome (Italy)

    2011-03-07

    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. Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta).

    Science.gov (United States)

    Kuhn, B C; Mangolin, C A; Souto, E R; Vicient, C M; Machado, M F P S

    2016-04-07

    Retrotransposons are abundant in the genomes of plants. In the present study, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers were developed for the cassava genome (Manihot esculenta Crantz). Four cassava cultivars (Fécula Branca, IPR-União, Olho Junto, and Tamboara, two samples per cultivar) were used to obtain IRAP and REMAP fingerprints. Twelve designed primers were amplified alone and in combinations. The 42 IRAP/REMAP primer combinations amplified 431 DNA segments (bands; markers) of which 36 (8.36%) were polymorphic. The largest number of informative markers (16) was detected using the primers AYF2 and AYF2xAYF4. The number of bands for each primer varied from 3 to 16, with an average of 10.26 amplified segments per primer. The size of the amplified products ranged between 100 and 7000 bp. The AYF2 primer generated the highest number of amplified segments and showed the highest number of polymorphic bands (68.75%). Two samples of each cassava cultivar were used to illustrate the usefulness and the polymorphism of IRAP/REMAP markers. IRAP and REMAP markers produced a high number of reproducible bands, and might be informative and reliable for investigation of genetic diversity and relationships among cassava cultivars.

  14. R2-Based Multi/Many-Objective Particle Swarm Optimization

    Science.gov (United States)

    Toscano, Gregorio; Barron-Zambrano, Jose Hugo; Tello-Leal, Edgar

    2016-01-01

    We propose to couple the R2 performance measure and Particle Swarm Optimization in order to handle multi/many-objective problems. Our proposal shows that through a well-designed interaction process we could maintain the metaheuristic almost inalterable and through the R2 performance measure we did not use neither an external archive nor Pareto dominance to guide the search. The proposed approach is validated using several test problems and performance measures commonly adopted in the specialized literature. Results indicate that the proposed algorithm produces results that are competitive with respect to those obtained by four well-known MOEAs. Additionally, we validate our proposal in many-objective optimization problems. In these problems, our approach showed its main strength, since it could outperform another well-known indicator-based MOEA. PMID:27656200

  15. Spherical collapse for the Starobinsky $R^2$ model

    CERN Document Server

    Guo, Jun-Qi

    2015-01-01

    Spherical scalar collapse for the Starobinsky $R^2$ model is simulated to explore the black hole and singularity formation scenarios. This model was obtained by considering quantum-gravitational effects and would admit some cases of singularity-free cosmological spacetimes. It is found, however, that in gravitational collapse situations, when the matter field is strong enough, a black hole including central singularity can be formed. The nature of this singularity is examined, and it is seen that near the central singularity gravity dominates the repulsion from the $R^2$ term, so that in some circumstances the Ricci scalar $R$ is pushed to infinity by gravity. Therefore, the semi-classical effects as included here do not avoid the singularity problem in general relativity.

  16. 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

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

    Science.gov (United States)

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

    2005-01-01

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

  18. Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis.

    Science.gov (United States)

    Zedek, František; Smerda, Jakub; Smarda, Petr; Bureš, Petr

    2010-11-30

    Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus Eleocharis (Cyperaceae), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-copia and Ty3-gypsy in relation to changes in both genome size and karyotype in Eleocharis. We also examined how this relationship is reflected in the phylogeny of Eleocharis. Using flow cytometry, we measured the genome sizes of members of the genus Eleocharis (Cyperaceae). We found positive correlation between the independent phylogenetic contrasts of genome size and chromosome number in Eleocharis. We analyzed PCR-amplified sequences of various reverse transcriptases of the LTR retrotransposons Ty1-copia and Ty3-gypsy (762 sequences in total). Using real-time PCR and dot blot approaches, we quantified the densities of Ty1-copia and Ty3-gypsy within the genomes of the analyzed species. We detected an increasing density of Ty1-copia elements in evolutionarily younger Eleocharis species and found a positive correlation between Ty1-copia densities and C/n-values (an alternative measure of monoploid genome size) in the genus phylogeny. In addition, our analysis of Ty1-copia sequences identified a novel retrotransposon family named Helos1, which is responsible for the increasing density of Ty1-copia. The transition:transversion ratio of Helos1 sequences suggests that Helos1 recently transposed in later

  19. Robotic Range Clearance Competition (R2C2)

    Science.gov (United States)

    2011-10-01

    Paddock. Meals—Breakfast, Lunch and Dinner will be available in the mess tent (See Schedule, Section 2.1). Snacks – Snack foods and bottled water...ROBOTIC RANGE CLEARANCE COMPETITION (R2C2) Final Report DISTRIBUTION A: AIR FORCE RESEARCH LABORATORY MATERIALS AND MANUFACTURING DIRECTORATE Air...other person or corporation; or convey any rights or permission to manufacture , use, or sell any patented invention that may relate to them. This

  20. System Center 2012 R2 Virtual Machine Manager cookbook

    CERN Document Server

    Cardoso, Edvaldo Alessandro

    2014-01-01

    This book is a step-by-step guide packed with recipes that cover architecture design and planning. The book is also full of deployment tips, techniques, and solutions. If you are a solutions architect, technical consultant, administrator, or any other virtualization enthusiast who needs to use Microsoft System Center Virtual Machine Manager in a real-world environment, then this is the book for you. We assume that you have previous experience with Windows 2012 R2 and Hyper-V.

  1. 全面掌控Windows Server 2012 R2

    Institute of Scientific and Technical Information of China (English)

    顾武雄

    2015-01-01

    想要全面掌控Windows Server 2012 R2核心的IT维运技术,有三项网络服务器内建的强大功能,是所有网络管理员都必须学习的,分别是HyDer-V服务器虚拟化、iSCSI网络储存管理和IPAM网络管理。

  2. Gravitational luminosity of a hot plasma in R^2 gravity

    CERN Document Server

    Niri, B Nadiri; Corda, C

    2016-01-01

    The R^{2}-gravity contribution to energy loss of a hot plasma due to the gravitational bremsstrahlung is calculated in the linearized theory on the basis of classical Coulomb scattering of plasma constituents in small-angle scattering approximation. The explicit dependence of the gravitational luminosity on the plasma temperature is derived and its relevance to the Einstein gravity is demonstrated. The result when applied to the Sun as a hot plasma, shows very good agreement with available data.

  3. Age-associated de-repression of retrotransposons in the Drosophila fat body, its potential cause and consequence.

    Science.gov (United States)

    Chen, Haiyang; Zheng, Xiaobin; Xiao, Danqing; Zheng, Yixian

    2016-06-01

    Eukaryotic genomes contain transposable elements (TE) that can move into new locations upon activation. Since uncontrolled transposition of TEs, including the retrotransposons and DNA transposons, can lead to DNA breaks and genomic instability, multiple mechanisms, including heterochromatin-mediated repression, have evolved to repress TE activation. Studies in model organisms have shown that TEs become activated upon aging as a result of age-associated deregulation of heterochromatin. Considering that different organisms or cell types may undergo distinct heterochromatin changes upon aging, it is important to identify pathways that lead to TE activation in specific tissues and cell types. Through deep sequencing of isolated RNAs, we report an increased expression of many retrotransposons in the old Drosophila fat body, an organ equivalent to the mammalian liver and adipose tissue. This de-repression correlates with an increased number of DNA damage foci and decreased level of Drosophila lamin-B in the old fat body cells. Depletion of the Drosophila lamin-B in the young or larval fat body results in a reduction of heterochromatin and a corresponding increase in retrotransposon expression and DNA damage. Further manipulations of lamin-B and retrotransposon expression suggest a role of the nuclear lamina in maintaining the genome integrity of the Drosophila fat body by repressing retrotransposons.

  4. Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers.

    Science.gov (United States)

    Vukich, M; Schulman, A H; Giordani, T; Natali, L; Kalendar, R; Cavallini, A

    2009-10-01

    The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied for the first time within the genus Helianthus to assess intraspecific variability based on retrotransposon sequences among 36 wild accessions and 26 cultivars of Helianthus annuus L., and interspecific variability among 39 species of Helianthus. Two groups of LTRs, one belonging to a Copia-like retroelement and the other to a putative retrotransposon of unknown nature (SURE) have been isolated, sequenced and primers were designed to obtain IRAP fingerprints. The number of polymorphic bands in H. annuus wild accessions is as high as in Helianthus species. If we assume that a polymorphic band can be related to a retrotransposon insertion, this result suggests that retrotransposon activity continued after Helianthus speciation. Calculation of similarity indices from binary matrices (Shannon's and Jaccard's indices) show that variability is reduced among domesticated H. annuus. On the contrary, similarity indices among Helianthus species were as large as those observed among wild H. annuus accessions, probably related to their scattered geographic distribution. Principal component analysis of IRAP fingerprints allows the distinction between perennial and annual Helianthus species especially when the SURE element is concerned.

  5. Chiral Discrimination of Tryptophan Enantiomers via (1R, 2R-2-Amino-1, 2-Diphenyl Ethanol Modified Interface

    Directory of Open Access Journals (Sweden)

    Juan Zhou

    2011-01-01

    Full Text Available The paper reported that a simple chiral selective interface constructed by (1R, 2R-2-amino-1, 2-diphenyl ethanol had been developed to discriminate tryptophan enantiomers. Cyclic voltammetry (CV and electrochemical impedance spectroscopy (EIS were used for the characteristic analysis of the electrode. The results indicated that the interface showed stable and sensitive property to determine the tryptophan enantiomers. Moreover, it exhibited the better stereoselectivity for L-tryptophan than that for D-tryptophan. The discrimination characteristics of the chiral selective interface for discriminating tryptophan enantiomers, including the response time, the effect of tryptophan enantiomers concentration, and the stability, were investigated in detail. In addition, the chiral selective interface was used to determine the enantiomeric composition of L- and D-tryptophan enantiomer mixtures by measuring the relative change of the peak current as well as in pure enantiomeric solutions. These results suggested that the chiral selective interface has the potential for enantiomeric discrimination of tryptophan enantiomers.

  6. The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story

    NARCIS (Netherlands)

    Bousios, A.; Kourmpetis, Y.I.A.; Pavlidis, P.; Minga, E.; Tsaftaris, A.; Darzentas, N.

    2012-01-01

    Sireviruses are one of the three genera of Copia long terminal repeat (LTR) retrotransposons, exclusive to and highly abundant in plants, and with a unique, among retrotransposons, genome structure. Yet, perhaps due to the few references to the Sirevirus origin of some families, compounded by the di

  7. Foundations of SQL Server 2008 R2 Business Intelligence

    CERN Document Server

    Fouche, Guy

    2011-01-01

    Foundations of SQL Server 2008 R2 Business Intelligence introduces the entire exciting gamut of business intelligence tools included with SQL Server 2008. Microsoft has designed SQL Server 2008 to be more than just a database. It's a complete business intelligence (BI) platform. The database is at its core, and surrounding the core are tools for data mining, modeling, reporting, analyzing, charting, and integration with other enterprise-level software packages. SQL Server 2008 puts an incredible amount of BI functionality at your disposal. But how do you take advantage of it? That's what this

  8. Microsoft Windows Server 2008 R2 Administration Instant Reference

    CERN Document Server

    Hester, Matthew

    2010-01-01

    Windows Server 2008 R2 Administration Instant Reference provides quick referencing for the day-to-day tasks of administrating Microsoft's newest version of Windows Server. This book uses design features such as thumb tabs, secondary and tertiary tables of contents, and special heading treatments to provide quick and easy lookup, as well as quick-reference tables and lists to provide answers on the spot. Covering the essentials of day-to-day tasks Windows Server administrators perform, key topics include: Hyper-V 2.0; DirectAccess; LiveMigration; Automation; Core Active Directory administration

  9. Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges[W][OA

    Science.gov (United States)

    Butelli, Eugenio; Licciardello, Concetta; Zhang, Yang; Liu, Jianjun; Mackay, Steve; Bailey, Paul; Reforgiato-Recupero, Giuseppe; Martin, Cathie

    2012-01-01

    Traditionally, Sicilian blood oranges (Citrus sinensis) have been associated with cardiovascular health, and consumption has been shown to prevent obesity in mice fed a high-fat diet. Despite increasing consumer interest in these health-promoting attributes, production of blood oranges remains unreliable due largely to a dependency on cold for full color formation. We show that Sicilian blood orange arose by insertion of a Copia-like retrotransposon adjacent to a gene encoding Ruby, a MYB transcriptional activator of anthocyanin production. The retrotransposon controls Ruby expression, and cold dependency reflects the induction of the retroelement by stress. A blood orange of Chinese origin results from an independent insertion of a similar retrotransposon, and color formation in its fruit is also cold dependent. Our results suggest that transposition and recombination of retroelements are likely important sources of variation in Citrus. PMID:22427337

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

    Directory of Open Access Journals (Sweden)

    Katarzyna Pachulska-Wieczorek

    2016-07-01

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

  11. $R^2\\log R$ quantum corrections and the inflationary observables

    CERN Document Server

    Ben-Dayan, Ido; Torabian, Mahdi; Westphal, Alexander; Zarate, Lucila

    2014-01-01

    We study a model of inflation with terms quadratic and logarithmic in the Ricci scalar, where the gravitational action is $f(R)=R+\\alpha R^2+\\beta R^2 \\ln R$. These terms are expected to arise from one loop corrections involving matter fields in curved space-time. The spectral index $n_s$ and the tensor to scalar ratio yield $10^{-4}\\lesssim r\\lesssim0.03$ and $0.94\\lesssim n_s \\lesssim 0.99$. i.e. $r$ is an order of magnitude bigger or smaller than the original Starobinsky model which predicted $r\\sim 10^{-3}$. Further enhancement of $r$ gives a scale invariant $n_s\\sim 1$ or higher. Other inflationary observables are $d n_s/d\\ln k \\gtrsim -5.2 \\times 10^{-4},\\, \\mu \\lesssim 2.1 \\times 10^{-8} ,\\, y \\lesssim 2.6 \\times 10^{-9}$. Despite the enhancement in $r$, if the recent BICEP2 measurement stands, this model is disfavoured.

  12. Deuteration around the ultracompact HII region Mon R2

    CERN Document Server

    Treviño-Morales, S P; Fuente, A; Kramer, C; Roueff, E; González-García, M; Cernicharo, J; Gerin, M; Goicoechea, J R; Pety, J; Berné, O; Ossenkopf, V; Ginard, D; García-Burillo, S; Rizzo, J R; Viti, S

    2014-01-01

    The massive star-forming region Mon R2 hosts the closest ultra-compact HII region that can be spatially resolved with current single-dish telescopes. We used the IRAM-30m telescope to carry out an unbiased spectral survey toward two important positions (namely IF and MP2), in order to studying the chemistry of deuterated molecules toward Mon R2. We found a rich chemistry of deuterated species at both positions, with detections of C2D, DCN, DNC, DCO+, D2CO, HDCO, NH2D, and N2D+ and their corresponding hydrogenated species and isotopologs. Our high spectral resolution observations allowed us to resolve three velocity components: the component at 10 km/s is detected at both positions and seems associated with the layer most exposed to the UV radiation from IRS 1; the component at 12 km/s is found toward the IF position and seems related to the molecular gas; finally, a component at 8.5 km/s is only detected toward the MP2 position, most likely related to a low-UV irradiated PDR. We derived the column density of ...

  13. Inflationary Magnetogenesis in $R^{2}$-Inflation after Planck 2015

    CERN Document Server

    AlMuhammad, Anwar Saleh

    2015-01-01

    We study the primordial magnetic field generated by the simple model $f^2 FF$ in Starobinsky, $R^2$-inflationary, model. The scale invariant PMF is achieved at relatively high power index of the coupling function, $\\left| \\alpha \\right| \\approx 7.44$. This model does not suffer from the backreaction problem as long as, the rate of inflationary expansion, $H$, is in the order of or less than the upper bound reported by Planck ($\\le 3.6 \\times 10^{-5} M_\\rm{Pl}$) in both de Sitter and power law expansion, which show similar results. We calculate the lower limit of the reheating parameter, $R_\\rm{rad} > 6.888$ in $R^2$-inflation. Based on the upper limit obtained from CMB, we find that the upper limits of magnetic field and reheating energy density as, $\\left(\\rho_{B_\\rm{end}} \\right)_\\rm{CMB} < 1.184 \\times 10^{-20} M_\\rm{Pl}^4$ and $\\left(\\rho_\\rm{reh} \\right)_\\rm{CMB} < 8.480 \\times 10^{-22} M_\\rm{Pl}^4$. All of foregoing results are well more than the lower limit derived from WMAP7 for both large and s...

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

    Directory of Open Access Journals (Sweden)

    Vardi Assaf

    2009-12-01

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

  15. Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain.

    Science.gov (United States)

    Nandi, Sayan; Chandramohan, Dhruva; Fioriti, Luana; Melnick, Ari M; Hébert, Jean M; Mason, Christopher E; Rajasethupathy, Priyamvada; Kandel, Eric R

    2016-10-24

    Piwi-interacting RNAs (piRNAs), long thought to be restricted to germline, have recently been discovered in neurons of Aplysia, with a role in the epigenetic regulation of gene expression underlying long-term memory. We here ask whether piwi/piRNAs are also expressed and have functional roles in the mammalian brain. Large-scale RNA sequencing and subsequent analysis of protein expression revealed the presence in brain of several piRNA biogenesis factors including a mouse piwi (Mili), as well as small RNAs, albeit at low levels, resembling conserved piRNAs in mouse testes [primarily LINE1 (long interspersed nuclear element1) retrotransposon-derived]. Despite the seeming low expression of these putative piRNAs, single-base pair CpG methylation analyses across the genome of Mili/piRNA-deficient (Mili(-/-)) mice demonstrate that brain genomic DNA is preferentially hypomethylated within intergenic areas and LINE1 promoter areas of the genome. Furthermore, Mili mutant mice exhibit behavioral deficits such as hyperactivity and reduced anxiety. These results suggest that putative piRNAs exist in mammalian brain, and similar to the role of piRNAs in testes, they may be involved in the silencing of retrotransposons, which in brain have critical roles in contributing to genomic heterogeneity underlying adaptation, stress response, and brain pathology. We also describe the presence of another class of small RNAs in the brain, with features of endogenous siRNAs, which may have taken over the role of invertebrate piRNAs in their capacity to target both transposons, as well as protein-coding genes. Thus, RNA interference through gene and retrotransposon silencing previously encountered in Aplysia may also have potential roles in the mammalian brain.

  16. Serum cholesterol and nigrostriatal R2* values in Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Guangwei Du

    Full Text Available BACKGROUND: The occurrence of Parkinson's disease (PD is known to be associated both with increased nigrostriatal iron content and with low serum cholesterol and PD, but there has been no study to determine a potential relationship between these two factors. METHODS: High-resolution MRI (T1-, T2, and multiple echo T2*-weighted imaging and fasting lipid levels were obtained from 40 patients with PD and 29 healthy controls. Iron content was estimated from mean R2* values (R2* = 1/T2* calculated for each nigrostriatal structure including substantia nigra, caudate, putamen, and globus pallidus. This was correlated with serum cholesterol levels after controlling for age, gender, and statin use. RESULTS: In patients with PD, higher serum cholesterol levels were associated with lower iron content in the substantia nigra (R = -0.43, p = 0.011 for total-cholesterol, R = -0.31, p = 0.080 for low-density lipoprotein and globus pallidus (R = -0.38, p = 0.028 for total-cholesterol, R = -0.27, p = 0.127 for low-density lipoprotein, but only a trend toward significant association of higher total-cholesterol with lower iron content in the striatum (R = -0.34, p = 0.052 for caudate; R = -0.32, p = 0.061 for putamen. After adjusting for clinical measures, the cholesterol-iron relationships held or became even stronger in the substantia nigra and globus pallidus, but weaker in the caudate and putamen. There was no significant association between serum cholesterol levels and nigrostriatal iron content for controls. CONCLUSIONS: The data show that higher serum total-cholesterol concentration is associated with lower iron content in substantia nigra and globus pallidus in Parkinson's disease patients. Further studies should investigate whether this is mechanistic or epiphenomenological relationship.

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

    Institute of Scientific and Technical Information of China (English)

    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 Tyl-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 Tyl-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.

  18. The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice.

    Science.gov (United States)

    Reichmann, Judith; Reddington, James P; Best, Diana; Read, David; Ollinger, Rupert; Meehan, Richard R; Adams, Ian R

    2013-05-01

    DNA methylation plays an important role in suppressing retrotransposon activity in mammalian genomes, yet there are stages of mammalian development where global hypomethylation puts the genome at risk of retrotransposition-mediated genetic instability. Hypomethylated primordial germ cells appear to limit this risk by expressing a cohort of retrotransposon-suppressing genome-defence genes whose silencing depends on promoter DNA methylation. Here, we investigate whether similar mechanisms operate in hypomethylated trophectoderm-derived components of the mammalian placenta to couple expression of genome-defence genes to the potential for retrotransposon activity. We show that the hypomethylated state of the mouse placenta results in activation of only one of the hypomethylation-sensitive germline genome-defence genes: Tex19.1. Tex19.1 appears to play an important role in placenta function as Tex19.1(-/-) mouse embryos exhibit intra-uterine growth retardation and have small placentas due to a reduction in the number of spongiotrophoblast, glycogen trophoblast and sinusoidal trophoblast giant cells. Furthermore, we show that retrotransposon mRNAs are derepressed in Tex19.1(-/-) placentas and that protein encoded by the LINE-1 retrotransposon is upregulated in hypomethylated trophectoderm-derived cells that normally express Tex19.1. This study suggests that post-transcriptional genome-defence mechanisms are operating in the placenta to protect the hypomethylated cells in this tissue from retrotransposons and suggests that imbalances between retrotransposon activity and genome-defence mechanisms could contribute to placenta dysfunction and disease.

  19. GENETIC DIVERSITY OF TRITICALE CULTIVARS BASED ON MICROSATELLITE AND RETROTRANSPOSON-BASED MARKERS

    Directory of Open Access Journals (Sweden)

    Želmíra Balážová

    2014-02-01

    Full Text Available The aim of our work was to detect genetic variability in the set of 59 winter and spring triticale (x Triticosecale Witt. varieties using combination of 4 wheat SSR and 4 retrotransposon-based markers. The number of alleles for SSR markers ranged from 8 to 10 with an average number of 8,75 alleles per locus. For IRAP markers the number of alleles ranged from 9 to 10 with an average number of 9,25 alleles per locus Totally, 72 alleles were detected, 37 alleles for IRAP markers and 35 alleles for SSR markers. For the assessment of genetic diversity the dendrogram, based on the hierarchical cluster analysis using UPGMA algorithm was prepared. Fifty nine triticale cultivars were grouped into two major groups. The first group contained all winter triticale varieties and in the second cluster were included all spring triticale varieties. The closest relationship was found out between two Polish winter triticale cultivars, Alekto and Pizarro. Results showed the utility of combination of microsatellite and retrotransposon-based markers for estimation of genetic diversity of triticale genotypes leading to genotype identification.

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

    Directory of Open Access Journals (Sweden)

    Soledad Sacristán

    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.

  1. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes.

    Directory of Open Access Journals (Sweden)

    Virginia Bilanchone

    Full Text Available Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5' to 3' exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs.

  2. GASZ Is Essential for Male Meiosis and Suppression of Retrotransposon Expression in the Male Germline

    Science.gov (United States)

    Greenbaum, Michael P.; Roy, Angshumoy; Burns, Kathleen H.; Zhu, Huifeng; Han, Derek Y.; Harris, R. Alan; Coarfa, Cristian; Gunaratne, Preethi H.; Yan, Wei; Matzuk, Martin M.

    2009-01-01

    Nuage are amorphous ultrastructural granules in the cytoplasm of male germ cells as divergent as Drosophila, Xenopus, and Homo sapiens. Most nuage are cytoplasmic ribonucleoprotein structures implicated in diverse RNA metabolism including the regulation of PIWI-interacting RNA (piRNA) synthesis by the PIWI family (i.e., MILI, MIWI2, and MIWI). MILI is prominent in embryonic and early post-natal germ cells in nuage also called germinal granules that are often associated with mitochondria and called intermitochondrial cement. We find that GASZ (Germ cell protein with Ankyrin repeats, Sterile alpha motif, and leucine Zipper) co-localizes with MILI in intermitochondrial cement. Knockout of Gasz in mice results in a dramatic downregulation of MILI, and phenocopies the zygotene–pachytene spermatocyte block and male sterility defect observed in MILI null mice. In Gasz null testes, we observe increased hypomethylation and expression of retrotransposons similar to MILI null testes. We also find global shifts in the small RNAome, including down-regulation of repeat-associated, known, and novel piRNAs. These studies provide the first evidence for an essential structural role for GASZ in male fertility and epigenetic and post-transcriptional silencing of retrotransposons by stabilizing MILI in nuage. PMID:19730684

  3. GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline.

    Directory of Open Access Journals (Sweden)

    Lang Ma

    2009-09-01

    Full Text Available Nuage are amorphous ultrastructural granules in the cytoplasm of male germ cells as divergent as Drosophila, Xenopus, and Homo sapiens. Most nuage are cytoplasmic ribonucleoprotein structures implicated in diverse RNA metabolism including the regulation of PIWI-interacting RNA (piRNA synthesis by the PIWI family (i.e., MILI, MIWI2, and MIWI. MILI is prominent in embryonic and early post-natal germ cells in nuage also called germinal granules that are often associated with mitochondria and called intermitochondrial cement. We find that GASZ (Germ cell protein with Ankyrin repeats, Sterile alpha motif, and leucine Zipper co-localizes with MILI in intermitochondrial cement. Knockout of Gasz in mice results in a dramatic downregulation of MILI, and phenocopies the zygotene-pachytene spermatocyte block and male sterility defect observed in MILI null mice. In Gasz null testes, we observe increased hypomethylation and expression of retrotransposons similar to MILI null testes. We also find global shifts in the small RNAome, including down-regulation of repeat-associated, known, and novel piRNAs. These studies provide the first evidence for an essential structural role for GASZ in male fertility and epigenetic and post-transcriptional silencing of retrotransposons by stabilizing MILI in nuage.

  4. [Chromosomal organization of centromeric Ty3/gypsy retrotransposons in Allium cepa L. and Allium fistulosum L].

    Science.gov (United States)

    Kiseleva, A V; Kirov, I V; Khrustaleva, L I

    2014-06-01

    This is the first report on the presence of Ty3/gypsy-like retrotransposons in the centromeric region of Allium cepa and Allium fistulosum. The paper identifies the putative Ty3/gypsy centromeric retrotransposons (CR) among the DNA sequences of A. cepa present in the NCBI database and evaluates their copy number in the genomes of Allium cepa and Allium fistulosum. The putative copy number of Ty3/gypsy CR constituted about 26000 for A. cepa and about 7000 for A. fistulosum. The chromosomal organization of Ty3/gypsy CR was analyzed with the help of fluorescent in situ hybridization (FISH). The 300-bp PCR products synthesized with genomic DNA of Allium cepa and Allium fistulosum and primers designed for the sequence ET645811 of A. cepa (Genome Survey Sequence database), displaying similarity to the reverse transcriptase of the CR Ty3/gypsy family, served as FISH hybridization probes. On the chromosomes of A. cepa, hybridization signals were mainly localized in the centromeric region. On the chromosomes of A. fistulosum the signals were less expressed in the centromeric regions, though they were abundant in other chromosomal regions. The pathways of evolution in these closely related species are discussed.

  5. Mono-allelic retrotransposon insertion addresses epigenetic transcriptional repression in human genome

    Directory of Open Access Journals (Sweden)

    Byun Hyang-Min

    2012-02-01

    Full Text Available Abstract Background Retrotransposons have been extensively studied in plants and animals and have been shown to have an impact on human genome dynamics and evolution. Their ability to move within genomes gives retrotransposons to affect genome instability. Methods we examined the polymorphic inserted AluYa5, evolutionary young Alu, in the progesterone receptor gene to determine the effects of Alu insertion on molecular environment. We used mono-allelic inserted cell lines which carry both Alu-present and Alu-absent alleles. To determine the epigenetic change and gene expression, we performed restriction enzyme digestion, Pyrosequencing, and Chromatin Immunoprecipitation. Results We observed that the polymorphic insertion of evolutionally young Alu causes increasing levels of DNA methylation in the surrounding genomic area and generates inactive histone tail modifications. Consequently the Alu insertion deleteriously inactivates the neighboring gene expression. Conclusion The mono-allelic Alu insertion cell line clearly showed that polymorphic inserted repetitive elements cause the inactivation of neighboring gene expression, bringing aberrant epigenetic changes.

  6. Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Henrik D. Møller

    2016-02-01

    Full Text Available Extrachromosomal circular DNA (eccDNA derived from chromosomal Ty retrotransposons in yeast can be generated in multiple ways. Ty eccDNA can arise from the circularization of extrachromosomal linear DNA during the transpositional life cycle of retrotransposons, or from circularization of genomic Ty DNA. Circularization may happen through nonhomologous end-joining (NHEJ of long terminal repeats (LTRs flanking Ty elements, by Ty autointegration, or by LTR–LTR recombination. By performing an in-depth investigation of sequence reads stemming from Ty eccDNAs obtained from populations of Saccharomyces cerevisiae S288c, we find that eccDNAs predominantly correspond to full-length Ty1 elements. Analyses of sequence junctions reveal no signs of NHEJ or autointegration events. We detect recombination junctions that are consistent with yeast Ty eccDNAs being generated through recombination events within the genome. This opens the possibility that retrotransposable elements could move around in the genome without an RNA intermediate directly through DNA circularization.

  7. Corky, a gypsy-like retrotransposon is differentially transcribed in Quercus suber tissues

    Directory of Open Access Journals (Sweden)

    Rocheta Margarida

    2012-08-01

    Full Text Available Abstract Background Transposable elements (TEs make up a large part of eukaryotic genomes. Due to their repetitive nature and to the fact that they harbour regulatory signals, TEs can be responsible for chromosomal rearrangements, movement of gene sequences and evolution of gene regulation and function. Retrotransposon ubiquity raises the question about their function in genomes and most are transcriptionally inactive due to rearrangements that compromise their activity. However, the activity of TEs is currently considered to have been one of the major processes in genome evolution. Findings We report on the characterization of a transcriptionally active gypsy-like retrotransposon (named Corky from Quercus suber, in a comparative and quantitative study of expression levels in different tissues and distinct developmental stages through RT-qPCR. We observed Corky’s differential transcription levels in all the tissues analysed. Conclusions These results document that Corky’s transcription levels are not constant. Nevertheless, they depend upon the developmental stage, the tissue analysed and the potential occurring events during an individuals’ life span. This modulation brought upon by different developmental and environmental influences suggests an involvement of Corky in stress response and during development.

  8. piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline.

    Science.gov (United States)

    Chambeyron, Séverine; Popkova, Anna; Payen-Groschêne, Geneviève; Brun, Christine; Laouini, Dorsaf; Pelisson, Alain; Bucheton, Alain

    2008-09-30

    Germline silencing of transposable elements is essential for the maintenance of genome integrity. Recent results indicate that this repression is largely achieved through a RNA silencing pathway that involves Piwi-interacting RNAs (piRNAs). However the repressive mechanisms are not well understood. To address this question, we used the possibility to disrupt the repression of the Drosophila I element retrotransposon by hybrid dysgenesis. We show here that the repression of the functional I elements that are located in euchromatin requires proteins of the piRNA pathway, and that the amount of ovarian I element piRNAs correlates with the strength of the repression in the female germline. Antisense RNAs, which are likely used to produce antisense piRNAs, are transcribed by heterochromatic defective I elements, but efficient production of these antisense small RNAs requires the presence in the genome of euchromatic functional I elements. Finally, we demonstrate that the piRNA-induced silencing of the functional I elements is at least partially posttranscriptional. In a repressive background, these elements are still transcribed, but some of their sense transcripts are kept in nurse cell nuclear foci together with those of the Doc retrotransposon. In the absence of I element piRNAs, either in dysgenic females or in mutants of the piRNA silencing pathway, sense I element transcripts are transported toward the oocyte where retrotransposition occurs. Our results indicate that piRNAs are involved in a posttranscriptional gene-silencing mechanism resulting in RNA nuclear accumulation.

  9. Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor

    Science.gov (United States)

    Morales-Hernández, Antonio; González-Rico, Francisco J.; Román, Angel C.; Rico-Leo, Eva; Alvarez-Barrientos, Alberto; Sánchez, Laura; Macia, Ángela; Heras, Sara R.; García-Pérez, José L.; Merino, Jaime M.; Fernández-Salguero, Pedro M.

    2016-01-01

    Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, their role in gene regulation is poorly understood. Here, we show that the dioxin receptor (AHR) leads to differentiation of human carcinoma cells through the transcriptional upregulation of Alu retrotransposons, whose RNA transcripts can repress pluripotency genes. Despite the genome-wide presence of Alu elements, we provide evidences that those located at the NANOG and OCT4 promoters bind AHR, are transcribed by RNA polymerase-III and repress NANOG and OCT4 in differentiated cells. OCT4 and NANOG repression likely involves processing of Alu-derived transcripts through the miRNA machinery involving the Microprocessor and RISC. Consistently, stable AHR knockdown led to basal undifferentiation, impaired Alus transcription and blockade of OCT4 and NANOG repression. We suggest that transcripts produced from AHR-regulated Alu retrotransposons may control the expression of stemness genes OCT4 and NANOG during differentiation of carcinoma cells. The control of discrete Alu elements by specific transcription factors may have a dynamic role in genome regulation under physiological and diseased conditions. PMID:26883630

  10. Mobilization of LINE-1 retrotransposons is restricted by Tex19.1 in mouse embryonic stem cells

    Science.gov (United States)

    MacLennan, Marie; García-Cañadas, Marta; Reichmann, Judith; Khazina, Elena; Wagner, Gabriele; Playfoot, Christopher J; Salvador-Palomeque, Carmen; Mann, Abigail R; Peressini, Paula; Sanchez, Laura; Dobie, Karen; Read, David; Hung, Chao-Chun; Eskeland, Ragnhild; Meehan, Richard R; Weichenrieder, Oliver; García-Pérez, Jose Luis; Adams, Ian R

    2017-01-01

    Mobilization of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution, but these mutagenic events can also cause genetic disorders. In humans, retrotransposon mobilization is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilize in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilization. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, loss of Tex19.1 increases L1-ORF1p levels and L1 mobilization in pluripotent mouse embryonic stem cells, implying that Tex19.1 prevents de novo retrotransposition in the pluripotent phase of the germline cycle. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in mammals. DOI: http://dx.doi.org/10.7554/eLife.26152.001 PMID:28806172

  11. Isolation of Ty1-copia retrotransposon in myrtle genome and development of S-SAP molecular marker.

    Science.gov (United States)

    Woodrow, Pasqualina; Pontecorvo, Giovanni; Ciarmiello, Loredana F

    2012-04-01

    Long terminal repeat (LTR)-retrotransposons are mobile genetic elements that are ubiquitous in plants and constitute a major portion of their nuclear genomes. LTR- retrotransposons possess unique properties that make them appropriate for investigating relationships between populations, varieties and closely related species. Myrtus communis L. is an evergreen shrub growing spontaneously throughout the Mediterranean area. Accessions show significant variations for agriculturally important traits, so the development of specific molecular markers for conservation and characterization of myrtle germplasm is desirable to conserve biodiversity. In this study, we isolated the first retrotransposon Ty1-copia-like element (Tmc1) in Myrtus communis L. genome and used this as a molecular marker. We successfully employed the S-SAP marker system to specifically characterize four myrtle accessions belonging to different areas in the province of Caserta (Italy). The high level of polymorphism detected in isolated LTRs, make Tmc1 a good molecular marker for this species. Our findings confirm that retrotransposon-based molecular markers are particularly valuable tools for plant molecular characterization studies.

  12. Activation of the promoter of the Tnt1 retrotransposon in tomato after inoculation with the fungal pathogen Cladosporium fulvum

    NARCIS (Netherlands)

    Mhiri, C.; Wit, de P.J.G.M.; Grandbastien, M.A.

    1999-01-01

    The copia-like Tnt1 element of tobacco is one of the few active plant retrotransposons and is transcriptionally activated, in tobacco and in heterologous species, by biotic and abiotic stress factors. In order to establish more precisely the link between Tnt1 activation and plant defense responses,

  13. Exploiting the power of LINE-1 retrotransposon mutagenesis for identification of genes involved in embryonic stem cell differentiation.

    Science.gov (United States)

    Lenka, Nibedita; Krishnan, Shruthi; Board, Philip; Rangasamy, Danny

    2014-06-01

    Identifying the genes or epigenetic factors that control the self-renewal and differentiation of stem cells is critical to understanding the molecular basis of cell commitment. Although a number of insertional mutagenesis vectors have been developed for identifying gene functions in animal models, the L1 retrotransposition system offers additional advantages as a tool to disrupt genes in embryonic stem cells in order to identify their functions and the phenotypes associated with them. Recent advances in producing synthetic versions of L1 retrotransposon vector system and the optimization of techniques to accurately identify retrotransposon integration sites have increased their utility for gene discovery applications. We have developed a novel episomal, nonviral L1 retrotransposon vector using scaffold/matrix attachment regions that provides stable, sustained levels of retrotransposition in cell cultures without being affected by epigenetic silencing or from some of the common problems of vector integration. This modified vector contains a GFP marker whose expression occurs only after successful gene disruption events and thus the cells with disrupted genes can be easily picked for functional analysis. Here we present a method to disrupt gene function in embryonic stem cells that aid in the identification of genes involved in stem cell differentiation processes. The methods presented here can be easily adapted to the study of other types of cancer stem cells or induced pluripotent stem cells using the L1 retrotransposon as an insertional mutagen.

  14. Dark energy and dimensional transmutation in $R^2$ gravity

    CERN Document Server

    Maggiore, Michele

    2015-01-01

    Recent work has shown that non-local modifications of gravity involving terms such as $m^2R\\Box^{-2}R$ (and no cosmological constant) provide a phenomenologically viable alternative to $\\Lambda$CDM. We discuss the possibility that such non-local terms emerge in the far infrared from the running of the coupling constant associated to the $R^2$ term in higher-derivative gravity, which is asymptotically free in the ultraviolet and strongly coupled in the infrared. In this scenario the mass scale $m$ of the non-local model emerges from dimensional transmutation, similarly to $\\Lambda_{\\rm QCD}$ for strong interactions, leading to a technically natural value of the scale associated to dark energy. We also argue that the emergence of the non-local term can be understood as a dynamical mass generation for the conformal mode, as a response of the vacuum to the strong infrared fluctuations that are generated by the anomaly-induced effective action.

  15. Dyadic Bivariate Wavelet Multipliers in L2(R2)

    Institute of Scientific and Technical Information of China (English)

    Zhong Yan LI; Xian Liang SHI

    2011-01-01

    The single 2 dilation wavelet multipliers in one-dimensional case and single A-dilation (where A is any expansive matrix with integer entries and |detA|=2)wavelet multipliers in twodimensional case were completely characterized by Wutam Consortium(1998)and Li Z.,et al.(2010).But there exist no results on multivariate wavelet multipliers corresponding to integer expansive dilation.matrix with the absolute value of determinant not 2 in L2(R2).In this paper,we choose 2I2=(0202)as the dilation matrix and consider the 2I2-dilation multivariate wavelet Ψ={ψ1,ψ2,ψ3}(which is called a dyadic bivariate wavelet)multipliers.Here we call a measurable function family f={f1,f2,f3}a dyadic bivariate wavelet multiplier if Ψ1={F-1(f1ψ1),F-1(f2ψ2),F-1(f3ψ3)} is a dyadic bivariate wavelet for any dyadic bivariate wavelet Ψ={ψ1,ψ2,ψ3},where(f)and,F-1 denote the Fourier transform and the inverse transform of function f respectively.We study dyadic bivariate wavelet multipliers,and give some conditions for dyadic bivariate wavelet multipliers.We also give concrete forms of linear phases of dyadic MRA bivariate wavelets.

  16. Inflation in R2 supergravity with non-minimal superpotentials

    Directory of Open Access Journals (Sweden)

    G.A. Diamandis

    2015-05-01

    Full Text Available We investigate the cosmological inflation in a class of supergravity models that are generalizations of non-supersymmetric R2 models. Although such models have been extensively studied recently, especially after the launch of the PLANCK and BICEP2 data, the class of models that can be constructed has not been exhausted. In this note, working in a supergravity model that is a generalization of Cecotti's model, we show that the appearance of new superpotential terms, which are quadratic in the superfield Λ that couples to the Ricci supermultiplet, alters substantially the form of the scalar potential. The arising potential has the form of the Starobinsky potential times a factor that is exponential in the inflaton field and dominates for large inflaton values. We show that the well-known Starobinsky inflation scenario is maintained only for unnaturally small fine-tuned values of the coupling describing the Λ2 superpotential terms. A welcome feature is the possible increase of the tensor to scalar ratio r, within the limits set by the new Planck and BICEP2 data.

  17. Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene

    Directory of Open Access Journals (Sweden)

    Rodriguez Jose M

    2002-03-01

    Full Text Available Abstract Background The potential adaptive significance of transposable elements (TEs to the host genomes in which they reside is a topic that has been hotly debated by molecular evolutionists for more than two decades. Recent genomic analyses have demonstrated that TE fragments are associated with functional genes in plants and animals. These findings suggest that TEs may contribute significantly to gene evolution. Results We have analyzed two transposable elements associated with genes in the sequenced Drosophila melanogaster y; cn bw sp strain. A fragment of the Antonia long terminal repeat (LTR retrotransposon is present in the intron of Chitinase 3 (Cht3, a gene located within the constitutive heterochromatin of chromosome 2L. Within the euchromatin of chromosome 2R a full-length Burdock LTR retrotransposon is located immediately 3' to cathD, a gene encoding cathepsin D. We tested for the presence of these two TE/gene associations in strains representing 12 geographically diverse populations of D. melanogaster. While the cathD insertion variant was detected only in the sequenced y; cn bw sp strain, the insertion variant present in the heterochromatic Cht3 gene was found to be fixed throughout twelve D. melanogaster populations and in a D. mauritiana strain suggesting that it maybe of adaptive significance. To further test this hypothesis, we sequenced a 685bp region spanning the LTR fragment in the intron of Cht3 in strains representative of the two sibling species D. melanogaster and D. mauritiana (~2.7 million years divergent. The level of sequence divergence between the two species within this region was significantly lower than expected from the neutral substitution rate and lower than the divergence observed between a randomly selected intron of the Drosophila Alcohol dehydrogenase gene (Adh. Conclusions Our results suggest that a 359 bp fragment of an Antonia retrotransposon (complete LTR is 659 bp located within the intron of the

  18. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus

    OpenAIRE

    Petit, J.; Bourgeois, E; Stenger, W.; Bes, M.; Droc, G.; Meynard, D.; Courtois, B.; Ghesquière, Alain; Sabot, François; Panaud, O.; Guiderdoni, E.

    2009-01-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the eleme...

  19. 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

    including software for automated data analysis, which take full advantage of high next-generation sequencing throughput. Here we address these challenges by developing the FSTpoolit protocol and software package and we demonstrate its efficacy by detecting 8,935 LORE1 insertions in 3,744 Lotus japonicus...... 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....

  20. Acquisition of full-length viral helicase domains by insect retrotransposon-encoded polypeptides

    Directory of Open Access Journals (Sweden)

    Ekaterina eLazareva

    2015-12-01

    Full Text Available Recent metagenomic studies in insects identified many sequences unexpectedly closely related to plant virus genes. Here we describe a new example of this kind, insect R1 LINEs with an additional C-terminal domain in their open reading frame 2. This domain is similar to NTPase/helicase (SF1H domains, which are found in replicative proteins encoded by plant viruses of the genus Tobamovirus. We hypothesize that the SF1H domain could be acquired by LINEs, directly or indirectly, upon insect feeding on virus-infected plants. Possible functions of this domain in LINE transposition and involvement in LINEs counteraction the silencing-based cell defense against retrotransposons are discussed.

  1. Polymorphic L1 retrotransposons are frequently in strong linkage disequilibrium with neighboring SNPs.

    Science.gov (United States)

    Higashino, Saneyuki; Ohno, Tomoyuki; Ishiguro, Koichi; Aizawa, Yasunori

    2014-05-10

    L1 retrotransposons have been the major driver of structural variation of the human genome. L1 insertion polymorphism (LIP)-mediated genomic variation can alter the transcriptome and contribute to the divergence of human phenotypes. To assess this possibility, a genome-wide association study (GWAS) including LIPs is required. Toward this ultimate goal, the present study examined linkage disequilibrium between six LIPs and their neighboring single nucleotide polymorphisms (SNPs). Genomic PCR and sequencing of L1-plus and -minus alleles from different donors revealed that all six LIPs were in strong linkage disequilibrium with at least one SNP. In addition, comparison of syntenic regions containing the identified SNP nucleotides was performed among modern humans (L1-plus and -minus alleles), archaic humans and non-human primates, revealing two different evolutionary schemes that might have resulted in the observed strong SNP-LIP linkage disequilibria. This study provides an experimental framework and guidance for a future SNP-LIP integrative GWAS.

  2. Burdock, a novel retrotransposon in Drosophila melanogaster, integrates into the coding region of the cut locus.

    Science.gov (United States)

    Ponomarenko, N A; Bannikov, V M; Anashchenko, V A; Tchurikov, N A

    1997-08-11

    The burdock element is known to be the 2.6-kb insertion into the same region of the cut locus in 12 independently obtained ct-lethal mutants. Here we have determined the complete sequences of this insertion and of the hot spot region. It was found that the burdock is a short retrotransposon with long terminal repeats and a single open reading frame (ORF). The polypeptide encoded by the burdock ORF contains two adjacent regions homologous to the gag and pol polyproteins of the gypsy mobile element. The burdock insertion interrupts the short ORF of the cut locus. The target site sequence of the burdock insertions is similar to the Drosophila topoisomerase II cleavage site.

  3. An epi [c] genetic battle: LINE-1 retrotransposons and intragenomic conflict in humans.

    Science.gov (United States)

    Muñoz-Lopez, Martin; Macia, Angela; Garcia-Cañadas, Marta; Badge, Richard M; Garcia-Perez, Jose L

    2011-07-01

    The ongoing activity of the human retrotransposon Long Interspersed Element 1 (LINE-1 or L1) continues to impact the human genome in various ways. Throughout evolution, mammalian and primate genomes have been under selection to generate strategies to reduce the activity of selfish DNA like L1. Similarly, selfish DNA has evolved to elude these containment systems. This intragenomic conflict has left many inactive versions of LINEs and other Transposable Elements (TEs) littering the human genome, which together account for roughly half of our DNA. Here, we survey the distinct mechanisms operating in the human genome that seem to reduce the mobility of L1s. In addition, we discuss recent findings that strongly suggest epigenetic mechanisms specifically regulate L1 activity in pluripotent human cells.

  4. Characterization and cloning of p11, a transrepressor of Drosophila melanogaster retrotransposon 1731.

    Science.gov (United States)

    Lacoste, J; Codani-Simonart, S; Best-Belpomme, M; Peronnet, F

    1995-01-01

    The NssBF element has been characterized as a 26 nt sequence in the long terminal repeat of Drosophila melanogaster retrotransposon 1731. This sequence has been shown to be implicated in transcriptional repression of the 1731 promoter. We here report the cloning of a cDNA encoding a nuclear DNA binding protein named p11 that binds specifically to the NssBF element. P11 is a 98 amino acid polypeptide. It exhibits similarities with the mouse p9 single-stranded DNA binding protein, raising the possibility of a very general family of protein factors. Co-transfection experiments in human U937 cells showed repression of the 1731 promoter by overexpression of p11. Images PMID:8559667

  5. 再探究x0^x+y0y=r^2与x^2+y^2=r^2的关系

    Institute of Scientific and Technical Information of China (English)

    杨华

    2011-01-01

    贵刊文[1]给出了直线x0^x+y0y=r^2与x^2+y^2=r^2圆的关系:结论1 已知圆O:x^+y^2=r^2,点P(x0,y0).(1)若点P(x0,y0)在圆上,过点P的圆切线方程为x0x+y0y=r^2;(2)若点P(x0,y0)在圆外,过点P向圆引两条切线,两切点A、B两点,过A、B两点的两条切线交点的轨迹方程为x0x+y0y=r^2.

  6. Identification of rtl1, a retrotransposon-derived imprinted gene, as a novel driver of hepatocarcinogenesis.

    Directory of Open Access Journals (Sweden)

    Jesse D Riordan

    2013-04-01

    Full Text Available We previously utilized a Sleeping Beauty (SB transposon mutagenesis screen to discover novel drivers of HCC. This approach identified recurrent mutations within the Dlk1-Dio3 imprinted domain, indicating that alteration of one or more elements within the domain provides a selective advantage to cells during the process of hepatocarcinogenesis. For the current study, we performed transcriptome and small RNA sequencing to profile gene expression in SB-induced HCCs in an attempt to clarify the genetic element(s contributing to tumorigenesis. We identified strong induction of Retrotransposon-like 1 (Rtl1 expression as the only consistent alteration detected in all SB-induced tumors with Dlk1-Dio3 integrations, suggesting that Rtl1 activation serves as a driver of HCC. While previous studies have identified correlations between disrupted expression of multiple Dlk1-Dio3 domain members and HCC, we show here that direct modulation of a single domain member, Rtl1, can promote hepatocarcinogenesis in vivo. Overexpression of Rtl1 in the livers of adult mice using a hydrodynamic gene delivery technique resulted in highly penetrant (86% tumor formation. Additionally, we detected overexpression of RTL1 in 30% of analyzed human HCC samples, indicating the potential relevance of this locus as a therapeutic target for patients. The Rtl1 locus is evolutionarily derived from the domestication of a retrotransposon. In addition to identifying Rtl1 as a novel driver of HCC, our study represents one of the first direct in vivo demonstrations of a role for such a co-opted genetic element in promoting carcinogenesis.

  7. Gag Proteins of Drosophila Telomeric Retrotransposons: Collaborative Targeting to Chromosome Ends

    Science.gov (United States)

    Fuller, Adelaide M.; Cook, Elizabeth G.; Kelley, Kerry J.; Pardue, Mary-Lou

    2010-01-01

    TAHRE, the least abundant of the three retrotransposons forming telomeres in Drosophila melanogaster, has high sequence similarity to the gag gene and untranslated regions of HeT-A, the most abundant telomere-specific retrotransposon. Despite TAHRE's apparent evolutionary relationship to HeT-A, we find TAHRE Gag cannot locate to telomere-associated “Het dots” unless collaborating with HeT-A Gag. TAHRE Gag is carried into nuclei by HeT-A or TART Gag, but both TART and TAHRE Gags need HeT-A Gag to localize to Het dots. When coexpressed with the appropriate fragment of HeT-A and/or TART Gags, TAHRE Gag multimerizes with either protein. HeT-A and TART Gags form homo- and heteromultimers using a region containing major homology region (MHR) and zinc knuckle (CCHC) motifs, separated by a pre_C2HC motif (motifs common to other retroelements). This region's sequence is strongly conserved among the three telomeric Gags, with precise spacing of conserved residues. Nontelomeric Gags neither interact with the telomeric Gags nor have this conserved spacing. TAHRE Gag is much less able to enter the nucleus by itself than HeT-A or TART Gags. The overall telomeric localization efficiency for each of the three telomeric Gag proteins correlates with the relative abundance of that element in telomere arrays, suggesting an explanation for the relative rarity of TAHRE elements in telomere arrays and supporting the hypothesis that Gag targeting to telomeres is important for the telomere-specific transposition of these elements. PMID:20026680

  8. Isolation of Ty1-copia-like Retrotransposon Sequences from the Apple Genome by Chromosome Walking Based on Modified SiteFinding-polymerase Chain Reaction

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Long terminal repeat (LTR) retrotransposons are powerful tools for studying genetic biodiversity,genome evolution, gene mutation, gene cloning and gene expression. The scarcity of retrotransposon sequence information restricts the development of these studies in higher plants. In the present study, 31 reverse transcriptase (RT) genes of Tyl-copia-like retrotransposons were identified from the apple genome by amplifying the RT coding region using degenerate primers. Nineteen RT genes showed extreme heterogeneity in terms of fragment size, base pair composition and open reading frame integrality. Originating from one 266 bp cloned RT gene, a 1966 bp Ty1-copia-like retrotransposon (named Tcrm1), including RT-ribonuclease H-LTR domain sequences, was achieved by chromosome walking based on modified SiteFinding-polymerase chain reaction. The comparison between Tcrm1 and other LTR retrotransposons in gene structure and sequence homology shows that Tcrm1 is the first Ty1-copia-like retrotransposon including an LTR domain in the apple genome. Dot blot analysis revealed that Tcrm1 copy number in the apple was approximately 1×103 copies per haploid genome.

  9. R2* and R2 mapping for quantifying recruitment of superparamagnetic iron oxide-tagged endothelial progenitor cells to injured liver: tracking in vitro and in vivo

    Directory of Open Access Journals (Sweden)

    Wang Q

    2014-04-01

    Full Text Available Qingguo Wang, Kangan Li, Qimeng Quan, Guixiang ZhangDepartment of Radiology, Shanghai Jiaotong University Affiliated First People’s Hospital, Hongkou District, Shanghai, People’s Republic of ChinaObjective: To evaluate clinical 3.0T magnetic resonance for tracking and quantifying superparamagnetic iron oxide (SPIO–labeled endothelial progenitor cells (EPCs in vitro and homing to liver with acute injury in vivo.Methods: The bone marrow-derived EPCs were isolated and cultured for 4 days and examined in vitro for lineage markers. Then the cultured cells were labeled with a ferumoxides-protamine sulfate complex. Iron uptake was analyzed with an electron microscope and Prussian blue staining. Agarose gel phantoms containing different amounts of EPCs (0–2.5 × 106 cells per milliliter of 1.0% agarose gel were analyzed with 3.0T R2 and R2* relaxometry. For in vivo tracking, liver injury was induced in healthy C57 mice (female, 6 weeks old, weight 19–20 g by administration of carbon tetrachloride by single intraperitoneal injection. The R2* and R2 mapping of injured and normal livers of C57 mice were conducted by using 3.0T magnetic resonance on Days 0, 1, 4, and 8 after intravenous SPIO-tagged cells transplantation.Results: Electron microscope and Perls Prussian blue stain revealed the efficiency of SPIO particles uptake was more than 95% and no structural changes of labeled cells were found compared with control group. R2 and R2* values were linearly correlated with the number of iron-loaded cells in the agarose gel phantoms, and R2* values were significantly greater than R2 (P<0.01. R2* values in all groups were obviously greater than R2 (P<0.01. The R2* values of the injured livers were greater than normal on Days 1 and 4 (P<0.01. No significant difference of R2 values could be found among the three groups.Conclusion: Quantitative R2* mapping provides a useful method for quantifying intravascular administered SPIO-tagged EPCs homing to

  10. [Study of the transcriptional and transpositional activities of the Tirant retrotransposon in Drosophila melanogaster strains mutant for the flamenco locus].

    Science.gov (United States)

    Nefedova, L N; Urusov, F A; Romanova, N I; Shmel'kova, A O; Kim, A I

    2012-11-01

    Transpositions of the gypsy retrotransposon in the Drosophila melanogaster genome are controlled by the flamenco locus, which is represented as an accumulation of defective copies of transposable elements. In the present work, genetic control by the flamenco locus of the transcriptional and transpositional activities of the Tirant retrotransposon from the gypsy group was studied. Tissue-specific expression of Tirant was detected in the tissues of ovaries in a strain mutant for the flamenco locus. Tirant was found to be transpositionally active in isogenic D. melanogaster strains mutant for the flamenco locus. The sites of two new insertions have been localized by the method of subtractive hybridization. It has been concluded from the results obtained that the flamenco locus is involved in the genetic control of Tirant transpositions.

  11. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  13. 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

  14. Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum.

    Directory of Open Access Journals (Sweden)

    Shu-Ye Jiang

    Full Text Available Long terminal repeat (LTR retrotransposons are the major class I mobile elements in plants. They play crucial roles in gene expansion, diversification and evolution. However, their captured genes are yet to be genome-widely identified and characterized in most of plants although many genomes have been completely sequenced. In this study, we have identified 7,043 and 23,915 full-length LTR retrotransposons in the rice and sorghum genomes, respectively. High percentages of rice full-length LTR retrotransposons were distributed near centromeric region in each of the chromosomes. In contrast, sorghum full-length LTR retrotransposons were not enriched in centromere regions. This dissimilarity could be due to the discrepant retrotransposition during and after divergence from their common ancestor thus might be contributing to species divergence. A total of 672 and 1,343 genes have been captured by these elements in rice and sorghum, respectively. Gene Ontology (GO and gene set enrichment analysis (GSEA showed that no over-represented GO term was identified in LTR captured rice genes. For LTR captured sorghum genes, GO terms with functions in DNA/RNA metabolism and chromatin organization were over-represented. Only 36% of LTR captured rice genes were expressed and expression divergence was estimated as 11.9%. Higher percentage of LTR captured rice genes have evolved into pseudogenes under neutral selection. On the contrary, higher percentage of LTR captured sorghum genes were under purifying selection and 72.4% of them were expressed. Thus, higher percentage of LTR captured sorghum genes was functional. Small RNA analysis suggested that some of LTR captured genes in rice and sorghum might have been involved in negative regulation. On the other hand, positive selection has been observed in both rice and sorghum LTR captured genes and some of them were still expressed and functional. The data suggest that some of these LTR captured genes might have

  15. MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs

    Science.gov (United States)

    Frost, Robert J. A.; Hamra, F. Kent; Richardson, James A.; Qi, Xiaoxia; Bassel-Duby, Rhonda; Olson, Eric N.

    2010-01-01

    Piwi-interacting RNAs (piRNAs) comprise a broad class of small noncoding RNAs that function as an endogenous defense system against transposable elements. Here we show that the putative DExD-box helicase MOV10-like-1 (MOV10L1) is essential for silencing retrotransposons in the mouse male germline. Mov10l1 is specifically expressed in germ cells with increasing expression from gonocytes/type A spermatogonia to pachytene spermatocytes. Primary spermatocytes of Mov10l1−/− mice show activation of LTR and LINE-1 retrotransposons, followed by cell death, causing male infertility and a complete block of spermatogenesis at early prophase of meiosis I. Despite the early expression of Mov10l1, germline stem cell maintenance appears unaffected in Mov10l1−/− mice. MOV10L1 interacts with the Piwi proteins MILI and MIWI. MOV10L1 also interacts with heat shock 70-kDa protein 2 (HSPA2), a testis-enriched chaperone expressed in pachytene spermatocytes and also essential for male fertility. These studies reveal a crucial role of MOV10L1 in male fertility and piRNA-directed retrotransposon silencing in male germ cells and suggest that MOV10L1 functions as a key component of a safeguard mechanism for the genetic information in male germ cells of mammals. PMID:20547853

  16. Genomic Rearrangement in Endogenous Long Terminal Repeat Retrotransposons of Rice Lines Introgressed by Wild Rice (Zizania latifolia Griseb.)

    Institute of Scientific and Technical Information of China (English)

    Ye SHEN; Xiu-Yun LIN; Xiao-Hui SHAN; Chun-Jing LIN; Fang-Pu HAN; Jin-Song PANG; Bao LIU

    2005-01-01

    Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome.Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, low-copy, and potentially active long terminal repeat (LTR) retrotransposons occurred in one or more of threerice lines studied that were introgressed by wild rice (Zizania latifolia Griseb.). For nine retrotransposons inwhich both the reverse-transcriptase (RT) region and the LTR region were available, largely concordantrearrangements occurred at both regions in five elements and at the RT region only in the remaining fourelements. A marked proportion of the genomic changes was shared by two or all three introgression linesthat were derived from a single F1 plant. This indicates that most of the genomic changes occurred at earlydevelopmental stages of the F1 somatic cells, which then gave rise to germline cells, and, hence, ensuredinheritance of the changes to later generations. Possible causes and potential implications of the introgres-sion-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant ge-nome evolution and breeding.

  17. Crystal field analysis of the magnetization curves of R2Fe17 and R2Fe17H3 (R=Tb,Ho,Er)

    Institute of Scientific and Technical Information of China (English)

    Ma Ru-Gui; Yan Yu; Zhang Yan-Xiang; Du Xiao-Bo; Wang Xiang-Qun; Su Feng; Jin Han-Min

    2006-01-01

    In this paper the values of the crystalline-electric-field parameters Anm for R2Fe17 and R2Fe17H3 (R=Tb,Ho,Er)are evaluated by fitting calculations to the magnetization curves measured on the single crystal at several temperatures.The fitted Anm for R2Fe17 are strikingly different from those for the corresponding R2Fe17H3. The energy gaps between the lowest four energy levels for Ho ions in Ho2Fe17 can be reproduced by using the fitted Anm and exchange field 2μBHex, which estimated from the fit of the temperature dependence of the spontaneous magnetization combined with inelastic neutron scattering experiment.

  18. Phosphorylation of RyR2 and shortening of RyR2 cluster spacing in spontaneously hypertensive rat with heart failure.

    Science.gov (United States)

    Chen-Izu, Ye; Ward, Christopher W; Stark, Wayne; Banyasz, Tamas; Sumandea, Marius P; Balke, C William; Izu, Leighton T; Wehrens, Xander H T

    2007-10-01

    As a critical step toward understanding the role of abnormal intracellular Ca(2+) release via the ryanodine receptor (RyR(2)) during the development of hypertension-induced cardiac hypertrophy and heart failure, this study examines two questions: 1) At what stage, if ever, in the development of hypertrophy and heart failure is RyR(2) hyperphosphorylated at Ser(2808)? 2) Does the spatial distribution of RyR(2) clusters change in failing hearts? Using a newly developed semiquantitative immunohistochemistry method and Western blotting, we measured phosphorylation of RyR(2) at Ser(2808) in the spontaneously hypertensive rat (SHR) at four distinct disease stages. A major finding is that hyperphosphorylation of RyR(2) at Ser(2808) occurred only at late-stage heart failure in SHR, but not in age-matched controls. Furthermore, the spacing between RyR(2) clusters was shortened in failing hearts, as predicted by quantitative model simulation to increase spontaneous Ca(2+) wave generation and arrhythmias.

  19. Structure and Mechanism of Receptoe Sharing by the IL-10R2 Common Chain

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Sung-il; Jones, Brandi C.; Logsdon, Naomi J.; Harris, Bethany D.; Deshpande, Ashlesha; Radaeva, Svetlana; Halloran, Brian A.; Gao, Bin; Walter, Mark R. (NIH); (UAB)

    2010-06-14

    IL-10R2 is a shared cell surface receptor required for the activation of five class 2 cytokines (IL-10, IL-22, IL-26, IL-28, and IL-29) that play critical roles in host defense. To define the molecular mechanisms that regulate its promiscuous binding, we have determined the crystal structure of the IL-10R2 ectodomain at 2.14 {angstrom} resolution. IL-10R2 residues required for binding were identified by alanine scanning and used to derive computational models of IL-10/IL-10R1/IL-10R2 and IL-22/IL-22R1/IL-10R2 ternary complexes. The models reveal a conserved binding epitope that is surrounded by two clefts that accommodate the structural and chemical diversity of the cytokines. These results provide a structural framework for interpreting IL-10R2 single nucleotide polymorphisms associated with human disease.

  20. Structure and Mechanism of Receptor Sharing by the IL-10R2 Common Chain

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Sung-il; Jones, Brandi C.; Logsdon, Naomi J.; Harris, Bethany D.; Deshpande, Ashlesha; Radaeva, Svetlana; Halloran, Brian A.; Gao, Bin; Walter, Mark R. (NIH); (UAB)

    2010-07-19

    IL-10R2 is a shared cell surface receptor required for the activation of five class 2 cytokines (IL-10, IL-22, IL-26, IL-28, and IL-29) that play critical roles in host defense. To define the molecular mechanisms that regulate its promiscuous binding, we have determined the crystal structure of the IL-10R2 ectodomain at 2.14 {angstrom} resolution. IL-10R2 residues required for binding were identified by alanine scanning and used to derive computational models of IL-10/IL-10R1/IL-10R2 and IL-22/IL-22R1/IL-10R2 ternary complexes. The models reveal a conserved binding epitope that is surrounded by two clefts that accommodate the structural and chemical diversity of the cytokines. These results provide a structural framework for interpreting IL-10R2 single nucleotide polymorphisms associated with human disease.

  1. R2*-relaxometry of the pancreas in patients with human hemochromatosis protein associated hereditary hemochromatosis.

    Science.gov (United States)

    Henninger, B; Rauch, S; Zoller, H; Plaikner, M; Jaschke, W; Kremser, C

    2017-04-01

    To evaluate pancreatic iron in patients with human hemochromatosis protein associated hereditary hemochromatosis (HHC) using R2* relaxometry. 81 patients (58 male, 23 female; median age 49.5, range 10-81 years) with HHC were retrospectively studied. All underwent 1.5T magnetic resonance imaging (MRI) of the abdomen. A fat-saturated multi-gradient echo sequence with 12 echoes (TR=200ms; TE-initial 0.99ms; Delta-TE 1.41ms; 12 echoes; flip-angle: 20°) was used for the R2* quantification of the liver and the pancreas. Parameter maps were analyzed using regions of interest (3 in the liver and 2 in the pancreas) and R2* values were correlated. 59/81 patients had a liver R2*≥70 1/s of which 10/59 patients had a pancreas R2*≥50 1/s. No patient presented with a liver R2*pancreas R2*≥50 1/s. All patients with pancreas R2* values≥50 1/s had liver R2* values≥70 1/s. ROC analysis resulted in a threshold of 209.4 1/s for liver R2* values to identify HFE positive patients with pancreas R2* values≥50 1/s with a median specificity of 78.87% and a median sensitivity of 90%. In patients with HHC R2* relaxometry of the pancreas should be performed when liver iron overload is present and can be omitted in cases with no sign of hepatic iron. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. The Implementation of C-ID, R2D2 Model on Learning Reading Comprehension

    Science.gov (United States)

    Rayanto, Yudi Hari; Rusmawan, Putu Ngurah

    2016-01-01

    The purposes of this research are to find out, (1) whether C-ID, R2D2 model is effective to be implemented on learning Reading comprehension, (2) college students' activity during the implementation of C-ID, R2D2 model on learning Reading comprehension, and 3) college students' learning achievement during the implementation of C-ID, R2D2 model on…

  3. Calcium release channel RyR2 regulates insulin release and glucose homeostasis

    OpenAIRE

    Santulli, Gaetano; Pagano, Gennaro; Sardu, Celestino; Xie, Wenjun; Reiken, Steven; D’Ascia, Salvatore Luca; Cannone, Michele; Marziliano, Nicola; Trimarco, Bruno; Guise, Theresa A.; Lacampagne, Alain; Marks, Andrew R.

    2015-01-01

    The type 2 ryanodine receptor (RyR2) is a Ca2+ release channel on the endoplasmic reticulum (ER) of several types of cells, including cardiomyocytes and pancreatic β cells. In cardiomyocytes, RyR2-dependent Ca2+ release is critical for excitation-contraction coupling; however, a functional role for RyR2 in β cell insulin secretion and diabetes mellitus remains controversial. Here, we took advantage of rare RyR2 mutations that were identified in patients with a genetic form of exercise-induced...

  4. MCSA Windows Server 2012 R2 installation and configuration study guide exam 70-410

    CERN Document Server

    Panek, William

    2015-01-01

    Master Windows Server installation and configuration withhands-on practice and interactive study aids for the MCSA: WindowsServer 2012 R2 exam 70-410 MCSA: Windows Server 2012 R2 Installation and ConfigurationStudy Guide: Exam 70-410 provides complete preparationfor exam 70-410: Installing and Configuring Windows Server 2012 R2.With comprehensive coverage of all exam topics and plenty ofhands-on practice, this self-paced guide is the ideal resource forthose preparing for the MCSA on Windows Server 2012 R2. Real-worldscenarios demonstrate how the lessons are applied in everydaysettings. Reader

  5. Calcium release channel RyR2 regulates insulin release and glucose homeostasis.

    Science.gov (United States)

    Santulli, Gaetano; Pagano, Gennaro; Sardu, Celestino; Xie, Wenjun; Reiken, Steven; D'Ascia, Salvatore Luca; Cannone, Michele; Marziliano, Nicola; Trimarco, Bruno; Guise, Theresa A; Lacampagne, Alain; Marks, Andrew R

    2015-05-01

    The type 2 ryanodine receptor (RyR2) is a Ca2+ release channel on the endoplasmic reticulum (ER) of several types of cells, including cardiomyocytes and pancreatic β cells. In cardiomyocytes, RyR2-dependent Ca2+ release is critical for excitation-contraction coupling; however, a functional role for RyR2 in β cell insulin secretion and diabetes mellitus remains controversial. Here, we took advantage of rare RyR2 mutations that were identified in patients with a genetic form of exercise-induced sudden death (catecholaminergic polymorphic ventricular tachycardia [CPVT]). As these mutations result in a "leaky" RyR2 channel, we exploited them to assess RyR2 channel function in β cell dynamics. We discovered that CPVT patients with mutant leaky RyR2 present with glucose intolerance, which was heretofore unappreciated. In mice, transgenic expression of CPVT-associated RyR2 resulted in impaired glucose homeostasis, and an in-depth evaluation of pancreatic islets and β cells from these animals revealed intracellular Ca2+ leak via oxidized and nitrosylated RyR2 channels, activated ER stress response, mitochondrial dysfunction, and decreased fuel-stimulated insulin release. Additionally, we verified the effects of the pharmacological inhibition of intracellular Ca2+ leak in CPVT-associated RyR2-expressing mice, in human islets from diabetic patients, and in an established murine model of type 2 diabetes mellitus. Taken together, our data indicate that RyR2 channels play a crucial role in the regulation of insulin secretion and glucose homeostasis.

  6. 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.

  7. Hypomethylation of L1 retrotransposons in colorectal cancer and adjacent normal tissue.

    Science.gov (United States)

    Suter, Catherine M; Martin, David I; Ward, Robyn L

    2004-03-01

    Malignant cells often exhibit perturbations in the pattern of cytosine methylation. Hypermethylation of CpG islands has been extensively documented, but genome-wide hypomethylation is also a common feature of malignant cells. The bulk of cytosine methylation in the mammalian genome occurs on repetitive elements. This study analysed the methylation status of L1 retrotransposons in colorectal cancer. Methylation-sensitive Southern blotting was used to determine L1 promoter methylation in colon tumours, adjacent normal tissue, and normal colonic mucosa from healthy individuals. Hypomethylation of L1 promoter sequences was detected in all tumours but was also detected in the histologically normal colonic mucosa of 6 of 19 cancer patients, even at a considerable distance from the tumour. L1 hypomethylation was not detected in matched normal peripheral blood, lymph node or smooth muscle tissue from cancer patients or in the colonic mucosa of 14 healthy individuals. We also assayed for the total proportion of methylated CpG in normal bowel specimens from normal and colon cancer patients. Normal mucosa from cancer patients exhibited lower levels of genomic methylation than the mucosa from healthy individuals, and levels were significantly lower in those patients exhibiting L1 promoter hypomethylation. These results suggest that genomic hypomethylation is an early event in tumourigenesis. Progressive demethylation of L1 promoter sequences could lead to disturbance of normal gene expression and facilitate the process of neoplastic progression.

  8. 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

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

    Science.gov (United States)

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

    2012-09-01

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

  10. Promoter competition as a mechanism of transcriptional interference mediated by retrotransposons.

    Science.gov (United States)

    Conte, Caroline; Dastugue, Bernard; Vaury, Chantal

    2002-07-15

    Enhancers can function over great distances and interact with almost any kind of promoter, but insulators or promoter competition generally limit their effect to a single gene. We provide in vivo evidence that retroelements may establish promoter competition with their neighboring genes and restrict the range of action of an enhancer. We report that the retroelement Idefix from Drosophila melanogaster inhibits white gene expression in testes by a promoter competition mechanism that does not occur in the eyes. The sequence specificity of the two TATA-less promoters of white and Idefix is a prime determinant in the competition that takes place in tissues where both are transcriptionally active. This study brings to light a novel mechanism whereby transcriptional interference by an active retrotransposon may perturb expression of neighboring genes. This capacity to interfere with the transcriptional regulation of their host, together with the facts that retroelements preferentially move within the germline and do not excise to replicate, suggest that these elements are cis-regulatory sequences able to imprint specific and heritable controls essential for eukaryotic gene regulation.

  11. Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture.

    Science.gov (United States)

    Masuta, Yukari; Nozawa, Kosuke; Takagi, Hiroki; Yaegashi, Hiroki; Tanaka, Keisuke; Ito, Tasuku; Saito, Hideyuki; Kobayashi, Hisato; Matsunaga, Wataru; Masuda, Seiji; Kato, Atsushi; Ito, Hidetaka

    2016-12-23

    A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation. The heat activation of ONSEN transcripts was not significantly up-regulated in tissue culture compared with that in heat-stressed seedlings, indicating that the transposition of ONSEN was regulated independently of the transcript level. RdDM-related genes were up-regulated by heat stress in both tissue culture and seedlings. The level of DNA methylation of ONSEN did not show any change in tissue culture, and the amount of ONSEN-derived small RNAs was not affected by heat stress. The results indicated that the transposition of ONSEN was regulated by an alternative mechanism in addition to the RdDM-mediated epigenetic regulation in tissue culture. We applied the tissue culture-induced transposition of ONSEN to Japanese radish, an important breeding species of the family Brassicaceae. Several new insertions were detected in a regenerated plant derived from heat-stressed tissues and its self-fertilized progeny, revealing the possibility of molecular breeding without genetic modification.

  12. Serial number tagging reveals a prominent sequence preference of retrotransposon integration.

    Science.gov (United States)

    Chatterjee, Atreyi Ghatak; Esnault, Caroline; Guo, Yabin; Hung, Stevephen; McQueen, Philip G; Levin, Henry L

    2014-07-01

    Transposable elements (TE) have both negative and positive impact on the biology of their host. As a result, a balance is struck between the host and the TE that relies on directing integration to specific genome territories. The extraordinary capacity of DNA sequencing can create ultra dense maps of integration that are being used to study the mechanisms that position integration. Unfortunately, the great increase in the numbers of insertion sites detected comes with the cost of not knowing which positions are rare targets and which sustain high numbers of insertions. To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions. We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position. Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration. The serial number system is a general method that can be applied to determine precise integration maps for retroviruses and gene therapy vectors.

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

    Science.gov (United States)

    Urbański, Dorian Fabian; Małolepszy, Anna; Stougaard, Jens; Andersen, Stig Uggerhøj

    2012-02-01

    Use of insertion mutants facilitates functional analysis of genes, but it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics in most plant species. The main challenge is developing efficient high-throughput procedures for both mutagenesis and identification of insertion sites. To date, only floral-dip T-DNA transformation of Arabidopsis has produced independent germinal insertions, thereby allowing generation of mutant populations from seeds of single plants. In addition, advances in insertion detection have been hampered by a lack of protocols, including software for automated data analysis, that take full advantage of high-throughput next-generation sequencing. We have addressed these challenges by developing the FSTpoolit protocol and software package, and here we demonstrate its efficacy by detecting 8935 LORE1 insertions in 3744 Lotus japonicus plants. The identified insertions show that the endogenous LORE1 retrotransposon is well suited for insertion mutagenesis due to homogenous gene targeting and exonic insertion preference. As 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.

  14. Inverse changes in L1 retrotransposons between blood and brain in major depressive disorder.

    Science.gov (United States)

    Liu, Shu; Du, Tingfu; Liu, Zeyue; Shen, Yan; Xiu, Jianbo; Xu, Qi

    2016-11-22

    Long interspersed nuclear element-1 (LINE-1 or L1) is a type of retrotransposons comprising 17% of the human and mouse genome, and has been found to be associated with several types of neurological disorders. Previous post-mortem brain studies reveal increased L1 copy number in the prefrontal cortex from schizophrenia patients. However, whether L1 retrotransposition occurs similarly in major depressive disorder (MDD) is unknown. Here, L1 copy number was measured by quantitative PCR analysis in peripheral blood of MDD patients (n = 105) and healthy controls (n = 105). The results showed that L1 copy number was increased in MDD patients possibly due to its hypomethylation. Furthermore, L1 copy number in peripheral blood and five brain regions (prefrontal cortex, hippocampus, amygdala, nucleus accumbens and paraventricular hypothalamic nucleus) was measured in the chronic unpredictable mild stress (CUMS) model of depression in mice. Intriguingly, increased L1 copy number in blood and the decreased L1 copy number in the prefrontal cortex were observed in stressed mice, while no change was found in other brain regions. Our results suggest that the changes of L1 may be associated with the pathophysiology of MDD, but the biological mechanism behind dysfunction of L1 retrotransposition in MDD remains to be further investigated.

  15. TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice.

    Science.gov (United States)

    Yabuta, Yukihiro; Ohta, Hiroshi; Abe, Takaya; Kurimoto, Kazuki; Chuma, Shinichiro; Saitou, Mitinori

    2011-03-01

    The Tudor domain-containing proteins (TDRDs) are an evolutionarily conserved family of proteins involved in germ cell development. We show here that in mice, TDRD5 is a novel component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Tdrd5-deficient males are sterile because of spermiogenic arrest at the round spermatid stage, with occasional failure in meiotic prophase. Without TDRD5, IMCs and CBs are disorganized, with mislocalization of their key components, including TDRD1/6/7/9 and MIWI/MILI/MIWI2. In addition, Tdrd5-deficient germ cells fail to repress LINE-1 retrotransposons with DNA-demethylated promoters. Cyclic adenosine monophosphate response element modulator (CREM) and TRF2, key transcription factors for spermiogenesis, are expressed in Tdrd5-deficient round spermatids, but their targets, including Prm1/Prm2/Tnp1, are severely down-regulated, which indicates the importance of IMC/CB-mediated regulation for postmeiotic gene expression. Strikingly, Tdrd5-deficient round spermatids injected into oocytes contribute to fertile offspring, demonstrating that acquisition of a functional haploid genome may be uncoupled from TDRD5 function.

  16. Data of evolutionary structure change: 1AIJL-1R2CM [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1AIJL-1R2CM 1AIJ 1R2C L M -----ALLSFERKYRVPGGTLVGGNLFD----FWVGP--...HHHHHHHHH ----HHHHHHH HHHH 0 1AIJ... L 1AIJL GLU CA 293 ARG CA 285 1AIJ L 1AIJL AANPEKGKEMRTPDH

  17. High nigral iron deposition in LRRK2 and Parkin mutation carriers using R2* relaxometry

    DEFF Research Database (Denmark)

    Pyatigorskaya, Nadya; Sharman, Michael; Corvol, Jean-Christophe

    2015-01-01

    symptomatic and two asymptomatic Parkin subjects, nine symptomatic and five asymptomatic LRRK2 subjects) were compared with 20 patients with idiopathic PD (IPD) and 20 healthy subjects. Images were obtained at 3 teslas, using multi-echo T2 and T2* sequences. R2 and R2* values were calculated in the substantia...

  18. Identification of a New Allergen from Amaranthus retroflexus Pollen, Ama r 2

    Directory of Open Access Journals (Sweden)

    Mohsen Tehrani

    2011-01-01

    Conclusions: The profilin from the A. retroflexus pollen, Ama r 2, was firstly identified as an allergen. Moreover, rAma r 2 was produced in E. coli as a soluble immunoreactive protein with an IgE-reactivity similar to that of its natural counterpart.

  19. How do uncertainties in NCEP R2 and CFSR surface fluxes impact tropical ocean simulations?

    Science.gov (United States)

    Wen, Caihong; Xue, Yan; Kumar, Arun; Behringer, David; Yu, Lisan

    2017-01-01

    NCEP/DOE reanalysis (R2) and Climate Forecast System Reanalysis (CFSR) surface fluxes are widely used by the research community to understand surface flux climate variability, and to drive ocean models as surface forcings. However, large discrepancies exist between these two products, including (1) stronger trade winds in CFSR than in R2 over the tropical Pacific prior 2000; (2) excessive net surface heat fluxes into ocean in CFSR than in R2 with an increase in difference after 2000. The goals of this study are to examine the sensitivity of ocean simulations to discrepancies between CFSR and R2 surface fluxes, and to assess the fidelity of the two products. A set of experiments, where an ocean model was driven by a combination of surface flux components from R2 and CFSR, were carried out. The model simulations were contrasted to identify sensitivity to different component of the surface fluxes in R2 and CFSR. The accuracy of the model simulations was validated against the tropical moorings data, altimetry SSH and SST reanalysis products. Sensitivity of ocean simulations showed that temperature bias difference in the upper 100 m is mostly sensitive to the differences in surface heat fluxes, while depth of 20 °C (D20) bias difference is mainly determined by the discrepancies in momentum fluxes. D20 simulations with CFSR winds agree with observation well in the western equatorial Pacific prior 2000, but have large negative bias similar to those with R2 winds after 2000, partly because easterly winds over the central Pacific were underestimated in both CFSR and R2. On the other hand, the observed temperature variability is well reproduced in the tropical Pacific by simulations with both R2 and CFSR fluxes. Relative to the R2 fluxes, the CFSR fluxes improve simulation of interannual variability in all three tropical oceans to a varying degree. The improvement in the tropical Atlantic is most significant and is largely attributed to differences in surface winds.

  20. An ODIP Effort to Map R2R Ocean Data Terms to International Vocabularies

    Science.gov (United States)

    Ferreira, R.; Stocks, K. I.; Arko, R. A.

    2014-12-01

    The diverseness of terminology used in describing ocean data creates a barrier to efficient discovery and re-use of data, particularly across institutional, programmatic, and disciplinary boundaries. Here we explore the outcomes of a student project to crosswalk terms between the Rolling Deck to Repository (R2R) program and other international systems, as part of the Ocean Data Interoperability Platform (ODIP). R2R is a U.S. program developing and implementing an information management system to preserve and provide access to routine underway data collected by U.S. academic research vessels. R2R participates in ODIP, an international forum for improving interoperability and effective sharing of marine data resources through technical workshops and joint prototypes. The vocabulary mapping effort lays a foundation for future ocean data portals through which users search and access ocean data using familiar terms. R2R describes its data with a suite of controlled vocabularies (http://www.rvdata.us/voc) some of which were developed within R2R or are specific to the U.S. The goal of this student project is to crosswalk local/national vocabularies to authoritative international ones, where they exist, or to vocabularies widely used by ODIP partners. Specifically, R2R developed the following crosswalks: UNOLS ports to SeaDataNet Ports Gazetteer, R2R Device Models to NVS SeaVoX Device Catalog, R2R Organizations to the European Directory of Marine Organizations (EDMO), and R2R chief scientist names to well known professional identifiers such as ORCID, Research Gate, Linkedin, etc. Mappings were done in simple spreadsheets using synonymy relationships, and will be published as part of the R2R Linked Data resources. The level of success in crosswalking was variable. All ports are successfully mapped. Both organizations and device models have initial mappings and R2R has added new terms to EDMO and SeaVoX Device Catalog vocabularies allowing for nearly complete coverage of

  1. LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like copia elements.

    Directory of Open Access Journals (Sweden)

    Mathieu Piednoël

    Full Text Available Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They 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. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a "domino days spreading" branching process in which successive amplifications may interact positively.

  2. Diversity of LTR-retrotransposons and Enhancer/Suppressor Mutator-like transposons in cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Gbadegesin, Michael A; Wills, Matthew A; Beeching, John R

    2008-10-01

    Cassava (Manihot esculenta Crantz), though a major world crop with enormous potential, is very under studied. Little is known about its genome structure and organisation. Transposable elements have a key role in the evolution of genome structure, and can be used as important tools in applied genetics. This paper sets out to survey the diversity of members of three major classes of transposable element within the cassava genome and in relation to similar elements in other plants. Members of two classes of LTR-retrotransposons, Ty1/copia-like and Ty3/gypsy-like, and of Enhancer/Suppressor Mutator (En/Spm)-like transposons were isolated and characterised. Analyses revealed 59 families of Ty1/copia, 26 families of Ty3/gypsy retrotransposons, and 40 families of En/Spm in the cassava genome. In the comparative analyses, the predicted amino acid sequences for these transposon classes were compared with those of related elements from other plant species. These revealed that there were multiple lineages of Ty1/copia-like retrotransposons in the genome of cassava and suggested that vertical and horizontal transmission as the source of cassava Mecops may not be mutually exclusive. For the Ty3/gypsy elements network, two groups of cassava Megyps were evident including the Arabidopsis Athila lineage. However, cassava En/Spm-like elements (Meens) constituted a single group within a network of plant En/Spm-like elements. Hybridisation analysis supported the presence of transposons in the genome of cassava in medium (Ty3/gypsy and En/Spm) to high (Ty1/copia) copy numbers. Thus the cassava genome was shown to contain diverse members of three major classes of transposable element; however, the different classes exhibited contrasting evolutionary histories.

  3. 26 CFR 31.3306(r)(2)-1 - Treatment of amounts deferred under certain nonqualified deferred compensation plans.

    Science.gov (United States)

    2010-04-01

    ... nonqualified deferred compensation plans. 31.3306(r)(2)-1 Section 31.3306(r)(2)-1 Internal Revenue INTERNAL..., Internal Revenue Code of 1954) § 31.3306(r)(2)-1 Treatment of amounts deferred under certain nonqualified deferred compensation plans. (a) In general. Section 3306(r)(2) provides a special timing rule for the...

  4. Retrospective comparison of gradient recalled echo R2* and spin-echo R2 magnetic resonance analysis methods for estimating liver iron content in children and adolescents

    Energy Technology Data Exchange (ETDEWEB)

    Serai, Suraj D.; Fleck, Robert J. [Cincinnati Children' s Hospital Medical Center, Department of Radiology, MLC 5031, Cincinnati, OH (United States); Quinn, Charles T. [Cincinnati Children' s Hospital Medical Center, Division of Hematology, Cincinnati, OH (United States); Zhang, Bin [Cincinnati Children' s Hospital Medical Center, Division of Biostatistics and Epidemiology, Cincinnati, OH (United States); Podberesky, Daniel J. [Nemours Children' s Health System Nemours Children' s Hospital, Department of Radiology, Orlando, FL (United States)

    2015-10-15

    Serial surveillance of liver iron concentration (LIC) provides guidance for chelation therapy in patients with iron overload. The diagnosis of iron overload traditionally relies on core liver biopsy, which is limited by invasiveness, sampling error, cost and general poor acceptance by pediatric patients and parents. Thus noninvasive diagnostic methods such as MRI are highly attractive for quantification of liver iron concentration. To compare two MRI-based methods for liver iron quantification in children. 64 studies on 48 children and young adults (age range 4-21 years) were examined by gradient recalled echo (GRE) R2* and spin-echo R2 MRI at 1.5T to evaluate liver iron concentration. Scatter plots and Bland-Altman difference plots were generated to display and assess the relationship between the methods. With the protocols used in this investigation, Bland-Altman agreement between the methods is best when LIC is <20 mg/g dry tissue. Scatter plots show that all values with LIC <20 mg/g dry tissue fall within the 95% prediction limits. Liver iron concentration as determined by the R2* and R2 MR methods is statistically comparable, with no statistical difference between these methods for LIC <20 mg/g. (orig.)

  5. ChR2 transgenic animals in peripheral sensory system: Sensing light as various sensations.

    Science.gov (United States)

    Ji, Zhi-Gang; Wang, Hongxia

    2016-04-01

    Since the introduction of Channelrhodopsin-2 (ChR2) to neuroscience, optogenetics technology was developed, making it possible to activate specific neurons or circuits with spatial and temporal precision. Various ChR2 transgenic animal models have been generated and are playing important roles in revealing the mechanisms of neural activities, mapping neural circuits, controlling the behaviors of animals as well as exploring new strategy for treating the neurological diseases in both central and peripheral nervous system. An animal including humans senses environments through Aristotle's five senses (sight, hearing, smell, taste and touch). Usually, each sense is associated with a kind of sensory organ (eyes, ears, nose, tongue and skin). Is it possible that one could hear light, smell light, taste light and touch light? When ChR2 is targeted to different peripheral sensory neurons by viral vectors or generating ChR2 transgenic animals, the animals can sense the light as various sensations such as hearing, touch, pain, smell and taste. In this review, we focus on ChR2 transgenic animals in the peripheral nervous system. Firstly the working principle of ChR2 as an optogenetic actuator is simply described. Then the current transgenic animal lines where ChR2 was expressed in peripheral sensory neurons are presented and the findings obtained by these animal models are reviewed.

  6. Methoxychlor and fenvalerate induce neuronal death by reducing GluR2 expression.

    Science.gov (United States)

    Umeda, Kanae; Kotake, Yaichiro; Miyara, Masatsugu; Ishida, Keishi; Sanoh, Seigo; Ohta, Shigeru

    2016-04-01

    GluR2, an α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor subunit, plays important roles in neuronal survival. We previously showed that exposure of cultured rat cortical neurons to several chemicals decreases GluR2 protein expression, leading to neuronal toxicity. Methoxychlor, the bis-p-methoxy derivative of dichlorodiphenyltrichloroethane, and fenvalerate, a synthetic pyrethroid chemical, have been used commercially as agricultural pesticides in several countries. In this study, we investigated the effects of long-term methoxychlor and fenvalerate exposure on neuronal glutamate receptors. Treatment of cultured rat cortical neurons with 1 or 10 µM methoxychlor and fenvalerate for 9 days selectively decreased GluR2 protein expression; the expression of other AMPA receptor subunits GluR1, GluR3, and GluR4 did not change under the same conditions. Importantly, the decreases in GluR2 protein expression were also observed on the cell surface membrane where AMPA receptors typically function. In addition, both chemicals decreased neuronal viability, which was blocked by pretreatment with 1-naphtylacetylspermine, an antagonist of GluR2-lacking AMPA receptors, and MK-801, an N-methyl-d-aspartate (NMDA) receptor antagonist. These results suggest that long-term exposure to methoxychlor and fenvalerate decreases GluR2 protein expression, leading to neuronal death via overactivation of GluR2-lacking AMPA and NMDA receptors.

  7. Delivery of continuously-varying stimuli using ChR2

    Directory of Open Access Journals (Sweden)

    Tatjana eTchumatchenko

    2013-12-01

    Full Text Available To study sensory processing, stimuli are delivered to the sensory organs of animals and evoked neural activity is recorded downstream. However, noise and uncontrolled modulatory input can interfere with repeatable delivery of sensory stimuli to higher brain regions. Here we show how channelrhodopsin-2 (ChR2 can be used to deliver continuous time-varying currents to neurons at any point along the sensory-motor pathway. To do this, we first deduce the frequency response function of ChR2 using a Markov model of channel kinetics. We confirm ChR2's frequency response characteristics using continuously-varying optical stimulation of neurons that express one of three ChR2 variants. We find that wild-type ChR2 and the E123T/H134R mutant (`CheTA' can pass continuously-varying stimuli with frequencies up to 70 Hz. Additionally, we find that wild-type ChR2 exhibits a strong resonance at 6-10 Hz. Together, these results indicate that ChR2-derived optogenetic tools are useful for delivering highly repeatable artificial stimuli that mimic in-vivo synaptic bombardment.

  8. 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

    2017-06-21

    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.

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

    Science.gov (United States)

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

    2015-01-07

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

  10. The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats

    Directory of Open Access Journals (Sweden)

    Huneau Cecile

    2011-06-01

    Full Text Available Abstract Background Transposable elements (TEs are a rapidly evolving fraction of the eukaryotic genomes and the main contributors to genome plasticity and divergence. Recently, occupation of the A- and D-genomes of allopolyploid wheat by specific TE families was demonstrated. Here, we investigated the impact of the well-represented family of gypsy LTR-retrotransposons, Fatima, on B-genome divergence of allopolyploid wheat using the fluorescent in situ hybridisation (FISH method and phylogenetic analysis. Results FISH analysis of a BAC clone (BAC_2383A24 initially screened with Spelt1 repeats demonstrated its predominant localisation to chromosomes of the B-genome and its putative diploid progenitor Aegilops speltoides in hexaploid (genomic formula, BBAADD and tetraploid (genomic formula, BBAA wheats as well as their diploid progenitors. Analysis of the complete BAC_2383A24 nucleotide sequence (113 605 bp demonstrated that it contains 55.6% TEs, 0.9% subtelomeric tandem repeats (Spelt1, and five genes. LTR retrotransposons are predominant, representing 50.7% of the total nucleotide sequence. Three elements of the gypsy LTR retrotransposon family Fatima make up 47.2% of all the LTR retrotransposons in this BAC. In situ hybridisation of the Fatima_2383A24-3 subclone suggests that individual representatives of the Fatima family contribute to the majority of the B-genome specific FISH pattern for BAC_2383A24. Phylogenetic analysis of various Fatima elements available from databases in combination with the data on their insertion dates demonstrated that the Fatima elements fall into several groups. One of these groups, containing Fatima_2383A24-3, is more specific to the B-genome and proliferated around 0.5-2.5 MYA, prior to allopolyploid wheat formation. Conclusion The B-genome specificity of the gypsy-like Fatima, as determined by FISH, is explained to a great degree by the appearance of a genome-specific element within this family for Ae

  11. MCSA Windows Server 2012 R2 administration study guide exam 70-411

    CERN Document Server

    Panek, William

    2015-01-01

    Complete exam coverage, hands-on practice, and interactive studytools for the MCSA: Administering Windows Server 2012 R2 exam70-411 MCSA: Windows Server 2012 R2 Administration Study Guide: Exam70-411 provides comprehensive preparation for exam 70-411:Administering Windows Server 2012 R2. With full coverage of allexam domains, this guide contains everything you need to know to befully prepared on test day. Real-world scenarios illustrate thepractical applications of the lessons, and hands-on exercises allowyou to test yourself against everyday tasks. You get access to aninteractive practice te

  12. 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

    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.

  13. Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider.

    Science.gov (United States)

    Jiang, Ning; Gao, Dongying; Xiao, Han; van der Knaap, Esther

    2009-10-01

    DNA sequences provide useful insights into genome structure and organization as well as evolution of species. We report on a detailed analysis of the locus surrounding the tomato (Solanum lycopersicum) fruit-shape gene SUN to determine the driving force and genome environment that foster the appearance of novel phenotypes. The gene density at the sun locus is similar to that described in other euchromatic portions of the tomato genome despite the relatively high number of transposable elements. Genes at the sun locus include protein-coding as well as RNA genes, are small in size, and belong to families that were duplicated at the locus an estimated 5-74 million years ago. In general, the DNA transposons at the sun locus are older than the RNA transposons, and their insertion pre-dates the speciation of S. lycopersicum and S. pimpinellifolium. Gene redundancy and large intergenic regions may explain the tolerance of the sun locus to frequent rearrangements and transpositions. The most recent transposition event at the sun locus involved Rider, a recently discovered high-copy retrotransposon. Rider probably arose early during the speciation of tomato. The element inserts into or near to genes and may still be active, which are unusual features for a high-copy element. Rider full-length and read-through transcripts past the typical transcription termination stop are detected, and the latter are required for mobilizing nearby sequences. Rider activity has resulted in an altered phenotype in three known cases, and may therefore have played an important role in tomato evolution and domestication.

  14. 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

  15. Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae.

    Directory of Open Access Journals (Sweden)

    Jose Manuel C Tubio

    Full Text Available Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis.

  16. A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons.

    Science.gov (United States)

    Hamilton, Russell S; Hartswood, Eve; Vendra, Georgia; Jones, Cheryl; Van De Bor, Veronique; Finnegan, David; Davis, Ilan

    2009-02-01

    mRNA localization is a widespread mode of delivering proteins to their site of function. The embryonic axes in Drosophila are determined in the oocyte, through Dynein-dependent transport of gurken/TGF-alpha mRNA, containing a small localization signal that assigns its destination. A signal with a similar secondary structure, but lacking significant sequence similarity, is present in the I factor retrotransposon mRNA, also transported by Dynein. It is currently unclear whether other mRNAs exist that are localized to the same site using similar signals. Moreover, searches for other genes containing similar elements have not been possible due to a lack of suitable bioinformatics methods for searches of secondary structure elements and the difficulty of experimentally testing all the possible candidates. We have developed a bioinformatics approach for searching across the genome for small RNA elements that are similar to the secondary structures of particular localization signals. We have uncovered 48 candidates, of which we were able to test 22 for their localization potential using injection assays for Dynein mediated RNA localization. We found that G2 and Jockey transposons each contain a gurken/I factor-like RNA stem-loop required for Dynein-dependent localization to the anterior and dorso-anterior corner of the oocyte. We conclude that I factor, G2, and Jockey are members of a "family" of transposable elements sharing a gurken-like mRNA localization signal and Dynein-dependent mechanism of transport. The bioinformatics pipeline we have developed will have broader utility in fields where small RNA signals play important roles.

  17. Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao

    Directory of Open Access Journals (Sweden)

    Li Xuanyang

    2009-06-01

    Full Text Available Abstract Background We recently discovered two composite long terminal repeat (LTR-retrotransposon-like elements which we named DA (~300 kb and Xiao (~30 kb, meaning big and small in Chinese respectively. Xiao and DA (three types of DA identified were found to have been derived from several donor sites and have spread to 30 loci in the human genome, totaling to 5 Mb. Our bioinformatics analyses with the released human, chimp, rhesus macaque, orangutan, and marmoset genomic sequences indicate that DA and Xiao emerged ~25 million years (Myr ago. Results To better understand the evolution of these two complex elements, we investigated various internal junctions of DA and Xiao as well as orthologous genomic sites of the 30 DA/Xiao loci in non-human primates including great apes, lesser apes, Old World monkeys, New World monkeys, and a prosimian. We found that Xiao and type I DA first emerged in the genome between 25 and 18 Myr ago, whereas type II and Type III DAs emerged between 14 and 7 Myr ago. Xiao and DA were most active in great apes, with their amplification peaking during 25-14 and 14-7 Myr ago, respectively. Neither DA nor Xiao seem to have been active in the human and chimp genomes during last 6 Myr. Conclusion The study has led to a more accurate age determination of the DA and Xiao elements than our previous bioinformatics analyses, and indicates that the amplification activity of the elements coincided with that of group I HERV-Es during evolution. It has also illustrated an evolutionary path with stepwise structural changes for the elements during past 25 Myr, and in doing so has shed more light on these two intriguing and complex elements that have reshaped our genome.

  18. 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.

  19. Diagnostic use of computational retrotransposon detection: Successful definition of pathogenetic mechanism in a ciliopathy phenotype.

    Science.gov (United States)

    Takenouchi, Toshiki; Kuchikata, Tomu; Yoshihashi, Hiroshi; Fujiwara, Mineko; Uehara, Tomoko; Miyama, Sahoko; Yamada, Shiro; Kosaki, Kenjiro

    2017-05-01

    Among more than 5,000 human monogenic disorders with known causative genes, transposable element insertion of a Long Interspersed Nuclear Element 1 (LINE1, L1) is known as the mechanistic basis in only 13 genetic conditions. Meckel-Gruber syndrome is a rare ciliopathy characterized by occipital encephalocele and cystic kidney disease. Here, we document a boy with occipital encephalocele, post-axial polydactyly, and multicystic renal disease. A medical exome analysis detected a heterozygous frameshift mutation, c.4582_4583delCG p.(Arg1528Serfs*17) in CC2D2A in the maternally derived allele. The further use of a dedicated bioinformatics algorithm for detecting retrotransposon insertions led to the detection of an L1 insertion affecting exon 7 in the paternally derived allele. The complete sequencing and sequence homology analysis of the inserted L1 element showed that the L1 element was classified as L1HS (L1 human specific) and that the element had intact open reading frames in the two L1-encoded proteins. This observation ranks Meckel-Gruber syndrome as only the 14th disorder to be caused by an L1 insertion among more than 5,000 known human genetic disorders. Although a transposable element detection algorithm is not included in the current best-practice next-generation sequencing analysis, the present observation illustrates the utility of such an algorithm, which would require modest computational time and resources. Whether the seemingly infrequent recognition of L1 insertion in the pathogenesis of human genetic diseases might simply reflect a lack of appropriate detection methods remains to be seen. © 2017 Wiley Periodicals, Inc.

  20. 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.

  1. Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs

    Science.gov (United States)

    RUSCHAK, AMY M.; MATHEWS, DAVID H.; BIBILLO, ARKADIUSZ; SPINELLI, SHERRY L.; CHILDS, JESSICA L.; EICKBUSH, THOMAS H.; TURNER, DOUGLAS H.

    2004-01-01

    The RNA structure of the 3′ untranslated region (UTR) of the R2 retrotransposable element is recognized by the R2-encoded reverse transcriptase in a reaction called target primed reverse transcription (TPRT). To provide insight into structure–function relationships important for TPRT, we have created alignments that reveal the secondary structure for 22 Drosophila and five silkmoth 3′ UTR R2 sequences. In addition, free energy minimization has been used to predict the secondary structure for the 3′ UTR R2 RNA of Forficula auricularia. The predicted structures for Bombyx mori and F. auricularia are consistent with chemical modification data obtained with β-ethoxy-α-ketobutyraldehyde (kethoxal), dimethyl sulfate, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate. The structures appear to have common helices that are likely important for function. PMID:15146081

  2. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Weinberg Zasha

    2011-01-01

    Full Text Available Abstract Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

  3. On the limit cycle for the 1/r^2 potential in momentum space

    OpenAIRE

    Hammer, H. -W.; Swingle, Brian G.

    2005-01-01

    The renormalization of the attractive 1/r^2 potential has recently been studied using a variety of regulators. In particular, it was shown that renormalization with a square well in position space allows multiple solutions for the depth of the square well, including, but not requiring a renormalization group limit cycle. Here, we consider the renormalization of the 1/r^2 potential in momentum space. We regulate the problem with a momentum cutoff and absorb the cutoff dependence using a moment...

  4. 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. PMID:26666304

  5. Cognitive Function Related to the Sirh11/Zcchc16 Gene Acquired from an LTR Retrotransposon in Eutherians.

    Directory of Open Access Journals (Sweden)

    Masahito Irie

    2015-09-01

    Full Text Available Gene targeting of mouse Sushi-ichi-related retrotransposon homologue 11/Zinc finger CCHC domain-containing 16 (Sirh11/Zcchc16 causes abnormal behaviors related to cognition, including attention, impulsivity and working memory. Sirh11/Zcchc16 encodes a CCHC type of zinc-finger protein that exhibits high homology to an LTR retrotransposon Gag protein. Upon microdialysis analysis of the prefrontal cortex region, the recovery rate of noradrenaline (NA was reduced compared with dopamine (DA after perfusion of high potassium-containing artificial cerebrospinal fluid in knockout (KO mice. These data indicate that Sirh11/Zcchc16 is involved in cognitive function in the brain, possibly via the noradrenergic system, in the contemporary mouse developmental systems. Interestingly, it is highly conserved in three out of the four major groups of the eutherians, euarchontoglires, laurasiatheria and afrotheria, but is heavily mutated in xenarthran species such as the sloth and armadillo, suggesting that it has contributed to brain evolution in the three major eutherian lineages, including humans and mice. Sirh11/Zcchc16 is the first SIRH gene to be involved in brain function, instead of just the placenta, as seen in the case of Peg10, Peg11/Rtl1 and Sirh7/Ldoc1.

  6. Variation in Copy Number of Ty3/Gypsy Centromeric Retrotransposons in the Genomes of Thinopyrum intermedium and Its Diploid Progenitors.

    Directory of Open Access Journals (Sweden)

    Mikhail G Divashuk

    Full Text Available Speciation and allopolyploidization in cereals may be accompanied by dramatic changes in abundance of centromeric repeated transposable elements. Here we demonstrate that the reverse transcriptase part of Ty3/gypsy centromeric retrotransposon (RT-CR is highly conservative in the segmental hexaploid Thinopyrum intermedium (JrJvsSt and its possible diploid progenitors Th. bessarabicum (Jb, Pseudoroegneria spicata (St and Dasypyrum villosum (V but the abundance of the repeats varied to a large extent. Fluorescence in situ hybridization (FISH showed hybridization signals in centromeric region of all chromosomes in the studied species, although the intensity of the signals drastically differed. In Th. intermedium, the strongest signal of RT-CR probe was detected on the chromosomes of Jv, intermediate on Jr and faint on Js and St subgenome suggesting different abundance of RT-CR on the individual chromosomes rather than the sequence specificity of RT-CRs of the subgenomes. RT-CR quantification using real-time PCR revealed that its content per genome in Th. bessarabicum is ~ 2 times and P. spicata is ~ 1,5 times higher than in genome of D. villosum. The possible burst of Ty3/gypsy centromeric retrotransposon in Th. intermedium during allopolyploidization and its role in proper mitotic and meiotic chromosome behavior in a nascent allopolyploid is discussed.

  7. Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons.

    Directory of Open Access Journals (Sweden)

    Guilherme M Q Cruz

    Full Text Available Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.

  8. On the Adjacency Matrix of RyR2 Cluster Structures.

    Science.gov (United States)

    Walker, Mark A; Kohl, Tobias; Lehnart, Stephan E; Greenstein, Joseph L; Lederer, W J; Winslow, Raimond L

    2015-11-01

    In the heart, electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells. This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors (RyR2). Their openings cause cell-wide release of Ca2+, which in turn causes muscle contraction and the generation of the mechanical force required to pump blood. In resting myocytes, RyR2s can also open spontaneously giving rise to spatially-confined Ca2+ release events known as "sparks." RyR2s are organized in a lattice to form clusters in the junctional sarcoplasmic reticulum membrane. Our recent work has shown that the spatial arrangement of RyR2s within clusters strongly influences the frequency of Ca2+ sparks. We showed that the probability of a Ca2+ spark occurring when a single RyR2 in the cluster opens spontaneously can be predicted from the precise spatial arrangements of the RyR2s. Thus, "function" follows from "structure." This probability is related to the maximum eigenvalue (λ1) of the adjacency matrix of the RyR2 cluster lattice. In this work, we develop a theoretical framework for understanding this relationship. We present a stochastic contact network model of the Ca2+ spark initiation process. We show that λ1 determines a stability threshold for the formation of Ca2+ sparks in terms of the RyR2 gating transition rates. We recapitulate these results by applying the model to realistic RyR2 cluster structures informed by super-resolution stimulated emission depletion (STED) microscopy. Eigendecomposition of the linearized mean-field contact network model reveals functional subdomains within RyR2 clusters with distinct sensitivities to Ca2+. This work provides novel perspectives on the cardiac Ca2+ release process and a general method for inferring the functional properties of transmembrane receptor clusters from their structure.

  9. On the Adjacency Matrix of RyR2 Cluster Structures.

    Directory of Open Access Journals (Sweden)

    Mark A Walker

    2015-11-01

    Full Text Available In the heart, electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells. This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors (RyR2. Their openings cause cell-wide release of Ca2+, which in turn causes muscle contraction and the generation of the mechanical force required to pump blood. In resting myocytes, RyR2s can also open spontaneously giving rise to spatially-confined Ca2+ release events known as "sparks." RyR2s are organized in a lattice to form clusters in the junctional sarcoplasmic reticulum membrane. Our recent work has shown that the spatial arrangement of RyR2s within clusters strongly influences the frequency of Ca2+ sparks. We showed that the probability of a Ca2+ spark occurring when a single RyR2 in the cluster opens spontaneously can be predicted from the precise spatial arrangements of the RyR2s. Thus, "function" follows from "structure." This probability is related to the maximum eigenvalue (λ1 of the adjacency matrix of the RyR2 cluster lattice. In this work, we develop a theoretical framework for understanding this relationship. We present a stochastic contact network model of the Ca2+ spark initiation process. We show that λ1 determines a stability threshold for the formation of Ca2+ sparks in terms of the RyR2 gating transition rates. We recapitulate these results by applying the model to realistic RyR2 cluster structures informed by super-resolution stimulated emission depletion (STED microscopy. Eigendecomposition of the linearized mean-field contact network model reveals functional subdomains within RyR2 clusters with distinct sensitivities to Ca2+. This work provides novel perspectives on the cardiac Ca2+ release process and a general method for inferring the functional properties of transmembrane receptor clusters from their structure.

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

    DEFF Research Database (Denmark)

    Gallus, S; Kumar, V; Bertelsen, Mads Frost

    2015-01-01

    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...

  11. Supersymmetric R2 actions, conformal invariance and the Lorentz Chern-Simons term in 6 and 10 dimensions

    NARCIS (Netherlands)

    Bergshoeff, E.; Salam, Abdus; Sezgin, E.

    1987-01-01

    We consider the superconformal extension of R2 actions in 6 and 10 dimensions. We show that the fields of the conformal multiplet alone admit a one parameter family of R2 actions of the form φ[R2µνab + α(R2µνab - 4R2µa + R2)]. In d=6 we give the supersymmetric action for α = 0, while for α

  12. 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

  13. RyR2 modulates a Ca2+-activated K+ current in mouse cardiac myocytes.

    Directory of Open Access Journals (Sweden)

    Yong-Hui Mu

    Full Text Available In cardiomyocytes, Ca2+ entry through voltage-dependent Ca2+ channels (VDCCs binds to and activates RyR2 channels, resulting in subsequent Ca2+ release from the sarcoplasmic reticulum (SR and cardiac contraction. Previous research has documented the molecular coupling of small-conductance Ca2+-activated K+ channels (SK channels to VDCCs in mouse cardiac muscle. Little is known regarding the role of RyRs-sensitive Ca2+ release in the SK channels in cardiac muscle. In this study, using whole-cell patch clamp techniques, we observed that a Ca2+-activated K+ current (IK,Ca recorded from isolated adult C57B/L mouse atrial myocytes was significantly decreased by ryanodine, an inhibitor of ryanodine receptor type 2 (RyR2, or by the co-application of ryanodine and thapsigargin, an inhibitor of the sarcoplasmic reticulum calcium ATPase (SERCA (p<0.05, p<0.01, respectively. The activation of RyR2 by caffeine increased the IK,Ca in the cardiac cells (p<0.05, p<0.01, respectively. We further analyzed the effect of RyR2 knockdown on IK,Ca and Ca2+ in isolated adult mouse cardiomyocytes using a whole-cell patch clamp technique and confocal imaging. RyR2 knockdown in mouse atrial cells transduced with lentivirus-mediated small hairpin interference RNA (shRNA exhibited a significant decrease in IK,Ca (p<0.05 and [Ca2+]i fluorescence intensity (p<0.01. An immunoprecipitated complex of SK2 and RyR2 was identified in native cardiac tissue by co-immunoprecipitation assays. Our findings indicate that RyR2-mediated Ca2+ release is responsible for the activation and modulation of SK channels in cardiac myocytes.

  14. TNF-R2 expression in acquired middle ear cholesteatoma Expressão do TNF-R2 no colesteatoma adquirido da orelha média

    Directory of Open Access Journals (Sweden)

    Rodrigo Faller Vitale

    2011-08-01

    Full Text Available Acquired middle ear cholesteatoma is a disease which promotes bone erosion resulting in potentially serious complications. The tumor necrosis factor alpha (TNF-α is present in cholesteatoma and it is related to bone erosion, as shown by different authors. To understand the aggressiveness characteristics of cholesteatoma is necessary, however, to better address the presence and distribution of their receptors. OBJECTIVE: To evaluate the expression of type 2 TNF-α receptor (TNF-R2 in fragments of cholesteatoma and correlate it to the degree of inflammation present. MATERIAL AND METHODS: observational cross-sectional study, which analyzed 33 fragments of cholesteatomas through histological analysis and immunohistochemistry (using as primary antibody to TNF-R2 LabVision® brand. The evaluation was performed by means of a qualitative and semi-quantitative agreement with the observed intensity. For statistical analysis we used the Fisher exact test and Spearman´s correlation coefficient (considered statistically significant when p O colesteatoma adquirido da orelha média promove erosão óssea, ocasionando complicações potencialmente graves. O fator de necrose tumoral alfa (TNF-α está presente no colesteatoma adquirido da orelha média e relaciona-se com a erosão óssea, como demonstraram diferentes autores. Para que se compreenda as características de agressividade do colesteatoma, é necessário que se estude a presença e a distribuição seus receptores. OBJETIVO: Avaliar a expressão do receptor tipo dois do TNF-α (TNF-R2 em fragmentos de colesteatoma e relacioná-lo com o grau de inflamação. MATERIAL E MÉTODOS: Estudo observacional do tipo transversal. Foram analisados 33 fragmentos de colesteatomas, submetidos à análise histológica e imunoistoquímica (utilizando o TNF-R2 da marca Labvision®. A avaliação foi realizada de forma qualitativa e semiquantitativa, de acordo com a intensidade observada. Para a análise estat

  15. High-throughput retrotransposon-based fluorescent markers: improved information content and allele discrimination

    Directory of Open Access Journals (Sweden)

    Baker David

    2009-07-01

    Full Text Available Abstract Background Dense genetic maps, together with the efficiency and accuracy of their construction, are integral to genetic studies and marker assisted selection for plant breeding. High-throughput multiplex markers that are robust and reproducible can contribute to both efficiency and accuracy. Multiplex markers are often dominant and so have low information content, this coupled with the pressure to find alternatives to radio-labelling, has led us to adapt the SSAP (sequence specific amplified polymorphism marker method from a 33P labelling procedure to fluorescently tagged markers analysed from an automated ABI 3730 xl platform. This method is illustrated for multiplexed SSAP markers based on retrotransposon insertions of pea and is applicable for the rapid and efficient generation of markers from genomes where repetitive element sequence information is available for primer design. We cross-reference SSAP markers previously generated using the 33P manual PAGE system to fluorescent peaks, and use these high-throughput fluorescent SSAP markers for further genetic studies in Pisum. Results The optimal conditions for the fluorescent-labelling method used a triplex set of primers in the PCR. These included a fluorescently labelled specific primer together with its unlabelled counterpart, plus an adapter-based primer with two bases of selection on the 3' end. The introduction of the unlabelled specific primer helped to optimise the fluorescent signal across the range of fragment sizes expected, and eliminated the need for extensive dilutions of PCR amplicons. The software (GeneMarker Version 1.6 used for the high-throughput data analysis provided an assessment of amplicon size in nucleotides, peak areas and fluorescence intensity in a table format, so providing additional information content for each marker. The method has been tested in a small-scale study with 12 pea accessions resulting in 467 polymorphic fluorescent SSAP markers of which

  16. C. elegans germ cells show temperature and age-dependent expression of Cer1, a Gypsy/Ty3-related retrotransposon.

    Directory of Open Access Journals (Sweden)

    Shannon Dennis

    Full Text Available Virus-like particles (VLPs have not been observed in Caenorhabditis germ cells, although nematode genomes contain low numbers of retrotransposon and retroviral sequences. We used electron microscopy to search for VLPs in various wild strains of Caenorhabditis, and observed very rare candidate VLPs in some strains, including the standard laboratory strain of C. elegans, N2. We identified the N2 VLPs as capsids produced by Cer1, a retrotransposon in the Gypsy/Ty3 family of retroviruses/retrotransposons. Cer1 expression is age and temperature dependent, with abundant expression at 15°C and no detectable expression at 25°C, explaining how VLPs escaped detection in previous studies. Similar age and temperature-dependent expression of Cer1 retrotransposons was observed for several other wild strains, indicating that these properties are common, if not integral, features of this retroelement. Retrotransposons, in contrast to DNA transposons, have a cytoplasmic stage in replication, and those that infect non-dividing cells must pass their genomic material through nuclear pores. In most C. elegans germ cells, nuclear pores are largely covered by germline-specific organelles called P granules. Our results suggest that Cer1 capsids target meiotic germ cells exiting pachytene, when free nuclear pores are added to the nuclear envelope and existing P granules begin to be removed. In pachytene germ cells, Cer1 capsids concentrate away from nuclei on a subset of microtubules that are exceptionally resistant to microtubule inhibitors; the capsids can aggregate these stable microtubules in older adults, which exhibit a temperature-dependent decrease in egg viability. When germ cells exit pachytene, the stable microtubules disappear and capsids redistribute close to nuclei that have P granule-free nuclear pores. This redistribution is microtubule dependent, suggesting that capsids that are released from stable microtubules transfer onto new, dynamic microtubules

  17. Occurrence of exact R 2 inflation in non-local UV-complete gravity

    Science.gov (United States)

    Koshelev, Alexey S.; Modesto, Leonardo; Rachwal, Leslaw; Starobinsky, Alexei A.

    2016-11-01

    The R + R 2, shortly named " R 2" ("Starobinsky") inflationary model, represents a fully consistent example of a one-parameter inflationary scenario. This model has a "graceful exit" from inflation and provides a mechanism for subsequent creation and final thermalization of the standard matter. Moreover, it produces a very good fit of the observed spectrum of primordial perturbations. In the present paper we show explicitly that the R 2 inflationary spacetime is an exact solution of a range of weakly non-local (quasi-polynomial) gravitational theories, which provide an ultraviolet completion of the R 2 theory. These theories are ghost-free, super-renormalizable or finite at quantum level, and perturbatively unitary. Their spectrum consists of the graviton and the scalaron that is responsible for driving the inflation. Notably, any further extension of the spectrum leads to propagating ghost degrees of freedom. We are aimed at presenting a detailed construction of such theories in the so called Weyl basis. Further, we give a special account to the cosmological implications of this theory by considering perturbations during inflation. The highlight of the non-local model is the prediction of a modified, in comparison to a local R 2 model, value for the ratio of tensor and scalar power spectra r, depending on the parameters of the theory. The relevant parameters are under control to be successfully confronted with existing observational data. Furthermore, the modified r can surely meet future observational constraints.

  18. Glutamate signals through mGluR2 to control Schwann cell differentiation and proliferation

    Science.gov (United States)

    Saitoh, Fuminori; Wakatsuki, Shuji; Tokunaga, Shinji; Fujieda, Hiroki; Araki, Toshiyuki

    2016-01-01

    Rapid saltatory nerve conduction is facilitated by myelin structure, which is produced by Schwann cells (SC) in the peripheral nervous system (PNS). Proper development and degeneration/regeneration after injury requires regulated phenotypic changes of SC. We have previously shown that glutamate can induce SC proliferation in culture. Here we show that glutamate signals through metabotropic glutamate receptor 2 (mGluR2) to induce Erk phosphorylation in SC. mGluR2-elicited Erk phosphorylation requires ErbB2/3 receptor tyrosine kinase phosphorylation to limit the signaling cascade that promotes phosphorylation of Erk, but not Akt. We found that Gβγ and Src are involved in subcellular signaling downstream of mGluR2. We also found that glutamate can transform myelinating SC to proliferating SC, while inhibition of mGluR2 signaling can inhibit demyelination of injured nerves in vivo. These data suggest pathophysiological significance of mGluR2 signaling in PNS and its possible therapeutic importance to combat demyelinating disorders including Charcot-Marie-Tooth disease. PMID:27432639

  19. Direct interaction between GluR2 and GAPDH regulates AMPAR-mediated excitotoxicity

    Directory of Open Access Journals (Sweden)

    Wang Min

    2012-04-01

    Full Text Available Abstract Over-activation of AMPARs (α−amino-3-hydroxy-5-methylisoxazole-4-propionic acid subtype glutamate receptors is implicated in excitotoxic neuronal death associated with acute brain insults, such as ischemic stroke. However, the specific molecular mechanism by which AMPARs, especially the calcium-impermeable AMPARs, induce neuronal death remains poorly understood. Here we report the identification of a previously unrecognized molecular pathway involving a direct protein-protein interaction that underlies GluR2-containing AMPAR-mediated excitotoxicity. Agonist stimulation of AMPARs promotes GluR2/GAPDH (glyceraldehyde-3-phosphate dehydrogenase complex formation and subsequent internalization. Disruption of GluR2/GAPDH interaction by administration of an interfering peptide prevents AMPAR-mediated excitotoxicity and protects against damage induced by oxygen-glucose deprivation (OGD, an in vitro model of brain ischemia.

  20. Reducing U2R and R2L category false negative rates with support vector machines

    Directory of Open Access Journals (Sweden)

    Maček Nemanja

    2014-01-01

    Full Text Available The KDD Cup '99 is commonly used dataset for training and testing IDS machine learning algorithms. Some of the major downsides of the dataset are the distribution and the proportions of U2R and R2L instances, which represent the most dangerous attack types, as well as the existence of R2L attack instances identical to normal traffic. This enforces minor category detection complexity and causes problems while building a machine learning model capable of detecting these attacks with sufficiently low false negative rate. This paper presents a new support vector machine based intrusion detection system that classifies unknown data instances according both to the feature values and weight factors that represent importance of features towards the classification. Increased detection rate and significantly decreased false negative rate for U2R and R2L categories, that have a very few instances in the training set, have been empirically proven.

  1. Data Retrieved by ARCADE-R2 Experiment On Board the BEXUS-17 Balloon

    Science.gov (United States)

    Barbetta, M.; Branz, F.; Carron, A.; Olivieri, L.; Prendin, J.; Sansone, F.; Savioli, L.; Spinello, F.; Francesconi, A.

    2015-09-01

    The Autonomous Rendezvous, Control And Docking Experiment — Reflight 2 (ARCADE-R2) is a technology demonstrator aiming to prove automatic attitude determination and control, rendezvous and docking capabilities for small scale spacecraft and aircraft. The development of such capabilities could be fundamental to create, in the near future, fleets of cooperative, autonomous unmanned aerial vehicles for mapping, surveillance, inspection and remote observation of hazardous environments; small-class satellites could also benefit from the employment of docking systems to extend and reconfigure their mission profiles. ARCADE-R2 is designed to test these technologies on a stratospheric flight on board the BEXUS-17 balloon, allowing to demonstrate them in a harsh environment subjected to gusty winds and high pressure and temperature variations. In this paper, ARCADE-R2 architecture is introduced and the main results obtained from a stratospheric balloon flight are presented.

  2. Statistical mechanics of the $N$-point vortex system with random intensities on $R^2$

    Directory of Open Access Journals (Sweden)

    Cassio Neri

    2005-01-01

    Full Text Available The system of N -point vortices on $mathbb{R}^2$ is considered under the hypothesis that vortex intensities are independent and identically distributed random variables with respect to a law $P$ supported on $(0,1]$. It is shown that, in the limit as $N$ approaches $infty$, the 1-vortex distribution is a minimizer of the free energy functional and is associated to (some solutions of the following non-linear Poisson Equation:$$ -Delta u(x = C^{-1}int_{(0,1]} rhbox{e}^{-eta ru(x- gamma r|x|^2}P(hbox{d}r, quadforall xin mathbb{R}^2, $$where $displaystyle C = int_{(0,1]}int_{mathbb{R}^2}hbox{e}^{-eta ru(y - gamma r|y|^2}hbox{d} yP(hbox{d}r$

  3. Windows Server 2008 R2 Hyper-V Insiders Guide to Microsoft's Hypervisor

    CERN Document Server

    Kelbley, John

    2010-01-01

    Get the inside scoop on Hyper-V for Windows Server 2008 R2. Virtualization is a top priority for thousands of companies all over the world. Written by an author team that is part of the Windows virtualization group at Microsoft, Windows Server 2008 R2 Hyper-V will walk you through Hyper-V essentials so you can get you up to speed and down to business with Hyper-V. Now fully updated for Windows Server 2008 R2 Hyper-V, you will find additional content on new features and capabilities such as Live Migration and support for 64 Logical Processors (LP).: Teaches how to manage virtual machines with t

  4. 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

  5. Rolling Deck to Repository (R2R): Automated Magnetic and Gravity Quality Assessment and Data Reduction

    Science.gov (United States)

    Morton, J. J.; O'Hara, S.; Ferrini, V.; Arko, R. A.

    2010-12-01

    With its global capability and diverse array of sensors, the academic research fleet is an integral component of ocean exploration. The Rolling Deck to Repository (R2R) Program provides a central shore-side gateway for underway data from the U.S. academic research fleet. In addition to ensuring preservation and documentation of routine underway data, R2R is also developing automated quality assessment (QA) tools for a variety of underway data types. Routine post-cruise QA will enable prompt feedback to shipboard operators and to provide the science community with sufficient background information for data analysis. Based on community feedback, R2R will perform data reduction to generate enhanced data products for select data types including gravity and magnetics. In the development of these tools, R2R seeks input from the scientific community, engaging specialists for each data type and requesting feedback from operators and scientists to deliver the most relevant and useful metadata. Development of data acquisition best practices that are being assembled within the community for some data types will also be important components of R2R QA development. Protocols for gravity and magnetics QA will include the development of guidelines for minimal and optimal metadata for each data type that will enable data reduction and optimize data re-use. Metadata including instrument specifications, navigational offsets, and calibration information will be important inputs for both data reduction and QA. Data reduction will include merging these geophysical data types with high-quality R2R-generated navigation data products, cleaning the data and applying instrument corrections. Automated routines that are being developed will then be used to assess data quality, ultimately producing a Quality Assessment Certificate (QAC) that will provide the science community with quality information in an easily accessible and understandable format. We present progress to date and invite

  6. Rolling Deck to Repository (R2R): Standards and Semantics for Open Access to Research Data

    Science.gov (United States)

    Arko, Robert; Carbotte, Suzanne; Chandler, Cynthia; Smith, Shawn; Stocks, Karen

    2015-04-01

    In recent years, a growing number of funding agencies and professional societies have issued policies calling for open access to research data. The Rolling Deck to Repository (R2R) program is working to ensure open access to the environmental sensor data routinely acquired by the U.S. academic research fleet. Currently 25 vessels deliver 7 terabytes of data to R2R each year, acquired from a suite of geophysical, oceanographic, meteorological, and navigational sensors on over 400 cruises worldwide. R2R is working to ensure these data are preserved in trusted repositories, discoverable via standard protocols, and adequately documented for reuse. R2R maintains a master catalog of cruises for the U.S. academic research fleet, currently holding essential documentation for over 3,800 expeditions including vessel and cruise identifiers, start/end dates and ports, project titles and funding awards, science parties, dataset inventories with instrument types and file formats, data quality assessments, and links to related content at other repositories. A Digital Object Identifier (DOI) is published for 1) each cruise, 2) each original field sensor dataset, 3) each post-field data product such as quality-controlled shiptrack navigation produced by the R2R program, and 4) each document such as a cruise report submitted by the science party. Scientists are linked to personal identifiers, such as the Open Researcher and Contributor ID (ORCID), where known. Using standard global identifiers such as DOIs and ORCIDs facilitates linking with journal publications and generation of citation metrics. Since its inception, the R2R program has worked in close collaboration with other data repositories in the development of shared semantics for oceanographic research. The R2R cruise catalog uses community-standard terms and definitions hosted by the NERC Vocabulary Server, and publishes ISO metadata records for each cruise that use community-standard profiles developed with the NOAA Data

  7. MCSA Windows Server 2012 R2 configuring advanced services study guide exam 70-412

    CERN Document Server

    Panek, William

    2015-01-01

    The bestselling MCSA study guide, with expert instruction andhands-on practice MCSA Windows Server 2012 R2 Configuring Advanced ServicesStudy Guide provides focused preparation for exam 70-412 and isfully updated to align with the latest Windows Server 2012 R2objectives. This comprehensive guide covers 100 percent of all examobjective domains, and includes hundreds of practice questions andanswers. You get access to video demonstrations, electronicflashcards, and practice exams, and hands-on exercises based onreal-world scenarios allow you to apply your skills to everydaytasks. Organized by o

  8. Pro EDI in BizTalk Server 2006 R2 electronic document interchange solutions

    CERN Document Server

    Beckner, Mark

    2008-01-01

    As business becomes more dependent on working with partners, suppliers, and other organizations in a streamlined way, Electronic Data Interchange (EDI) is one of the next big waves in connected systems. Microsoft BizTalk Server 2006 R2 offers an efficient, integrated way to deploy EDI solutions, and with the help of this book, readers will see how EDI can be used in their business and how best to get it set up with BizTalk. This book offers insights into the brand-new Biztalk 2006 R2--based EDI functionality, including the far greater flexibility in handling interchange. It gives advice coveri

  9. 三星YP-R2多媒体播放器

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    三星YP-R2多媒体播放器提供对MP3HD音乐格式的支持,是全球首款MP3HD播放器,用户还可以通过韩国SK电讯推出的无线音乐服务"MelOn"下载丰富的正版音乐。三星YP-R2外形尺寸为50.9mm×90.9mm×8.6mm,重约52g,提供蓝、

  10. Rolling Deck to Repository (R2R): Fleetwide Standard Underway Data Products

    Science.gov (United States)

    Sweeney, A. D.; Clark, P. D.; Miller, S. P.; Stocks, K.; Arko, R. A.; Ferrini, V.

    2009-12-01

    The Rolling Deck to Repository (R2R) project was recently launched with the ambitious goal of documenting “routine underway data” from the US academic research fleet and delivering those data to established national archives. Data distributions will be submitted by 18 operating institutions for 30 vessels, from hundreds of cruises per year. R2R will be responsible for digital data collected with instruments that are part of the ship’s permanent equipment and are routinely operated and recorded by the ship’s technicians. Examples include navigation, multibeam, subbottom, gravimeter, magnetics, ADCP, CTD, meteorology, etc. It is anticipated that most underway data will be promptly and publicly released. However R2R will have the ability to securely embargo any specific datasets identified in advance by the chief scientist, for a proprietary hold period of up to two years as mandated by the NSF 04-004 Division of Ocean Sciences Data and Sample Policy. It is important to note that there are data types that R2R will not address. For example, the chief scientist will continue to be responsible for the documentation and archiving of data from specific instruments brought on board by the scientific party, not part of the ship’s standard equipment. Similarly, data collected with National Facility assets including the National Deep Submergence Facility (NDSF), Ocean Bottom Seismograph Instrument Pool (OBSIP) and the National Marine Seismic Facility (NMSF) will continue to be submitted to the appropriate archiving facility directly by those facilities, rather than through R2R. Soon after the shipboard data is received by R2R, the entire original distribution will be safely stored in a deep archive for long-term preservation, and a cataloging process will be undertaken to assemble data sets for delivery to National Data Centers, as described more fully in the invited presentation by Robert Arko, “Rolling Deck to Repository: Technical Design - Experiences and

  11. On a nonlinear elliptic problem with critical potential in R2

    Institute of Scientific and Technical Information of China (English)

    SHEN; Yaotian; YAO; Yangxin; HEN; Zhihui

    2004-01-01

    Consider the existence of nontrivial solutions of homogeneous Dirichlet problem for a nonlinear elliptic equation with the critical potential in R2. By establishing a weighted inequality with the best constant, determine the critical potential in R2, and study the eigenvalues of Laplace equation with the critical potential. By the Pohozaev identity of a solution with a singular point and the Cauchy-Kovalevskaya theorem, obtain the nonexistence result of solutions with singular points to the nonlinear elliptic equation. Moreover, for the same problem, the existence results of multiple solutions are proved by the mountain pass theorem.

  12. Oracle Data Guard 11gR2 administration beginner's guide

    CERN Document Server

    Baransel, Emre

    2013-01-01

    Using real-world examples and hands-on tasks, Oracle Data Guard 11gR2 Administration Beginner's Guide will give you a solid foundation in Oracle Data Guard. It has been designed to teach you everything you need to know to successfully create and operate Data Guard environments with maximum flexibility, compatibility, and effectiveness.If you are an Oracle database administrator who wants to configure and administer Data Guard configurations, then ""Oracle Data Guard 11gR2 Administration Beginner's Guide"" is for you. With a basic understanding of Oracle database administration, you'll be able

  13. Windows Server 2008 R2的活动目录回收站

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Windows Server 2008 R2的活动目录回收站可以让你恢复意外删除的活动目录(AD)对象。而要使用回收站功能,你必须把林功能级别升级到Windows Server 2008 R2而不只是Windows Server 2008,这也就意味着无法在老的域控制器上使用该功能。

  14. A new role for plant R2R3-MYB transcription factors in cell cycle regulation

    Institute of Scientific and Technical Information of China (English)

    Eleonora Cominelli; Chiara Tonelli

    2009-01-01

    @@ MYB proteins are transcription factors present in all eukaryotes,sharing a common DNA-binding domain that consists of one to three imperfect helix-helix-turn-helix repeats of about 50 amino acids,called RI,R2,and R3 respectively [1].In animals and yeast these proteins represent a small gene family [1].Animal R1R2R3-MYB proteins have been described for their role in cell cycle regulation mainly at the G1/S,but also at the G2/M transition,as firstly demonstrated in Drosophila [2].

  15. Microsoft® Office Communications Server 2007 R2 Resource Kit

    CERN Document Server

    Maximo, Rui; Ramanathan, Rajesh; Kamdar, Nirav

    2009-01-01

    In-depth, comprehensive, and fully revised for R2-this RESOURCE KIT delivers the information you need to deploy, manage, and troubleshoot Microsoft Office Communications Server 2007 R2. Get technical insights, scenarios, and best practices from those who know the technology best-the engineers who designed and developed it-along with 90+ Windows PowerShell™ scripts, bonus references, and other essential resources on CD. Get expert advice on how to: Plan server roles, infrastructure, topology, and securityDesign and manage enterprise instant messaging (IM), presence, and conferencing solutio

  16. SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age

    Science.gov (United States)

    Van Meter, Michael; Kashyap, Mehr; Rezazadeh, Sarallah; Geneva, Anthony J.; Morello, Timothy D.; Seluanov, Andrei; Gorbunova, Vera

    2014-01-01

    L1 retrotransposons are an abundant class of transposable elements which pose a threat to genome stability and may play a role in age-related pathologies such as cancer. Recent evidence indicates that L1s become more active in somatic tissues during the course of aging; the mechanisms underlying this phenomenon remain unknown, however. Here we report that the longevity regulating protein, SIRT6, is a powerful repressor of L1 activity. Specifically, SIRT6 binds to the 5′UTR of L1 loci, where it mono-ADP ribosylates the nuclear corepressor protein, KAP1, and facilitates KAP1 interaction with the heterochromatin factor, HP1α, thereby contributing to the packaging of L1 elements into transcriptionally repressive heterochromatin. During the course of aging, and also in response to DNA damage, however, we find that SIRT6 is depleted from L1 loci, allowing for the activation of these previously silenced retroelements. PMID:25247314

  17. Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription.

    Science.gov (United States)

    Huang, Qing; Purzycka, Katarzyna J; Lusvarghi, Sabrina; Li, Donghui; Legrice, Stuart F J; Boeke, Jef D

    2013-03-01

    Ty1 retrotransposon RNA has the potential to fold into a variety of distinct structures, mutation of which affects retrotransposition frequencies. We show here that one potential functional structure is located at the 5' end of the genome and can assume a pseudoknot conformation. Chemoenzymatic probing of wild-type and mutant mini-Ty1 RNAs supports the existence of such a structure, while molecular genetic analyses show that mutations disrupting pseudoknot formation interfere with retrotransposition, indicating that it provides a critical biological function. These defects are enhanced at higher temperatures. When these mutants are combined with compensatory changes, retrotransposition is restored, consistent with pseudoknot architecture. Analyses of mutants suggest a defect in Ty1 reverse transcription. Collectively, our data allow modeling of a three-dimensional structure for this novel critical cis-acting signal of the Ty1 genome.

  18. 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.

  19. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting.

    Science.gov (United States)

    Youngson, Neil A; Kocialkowski, Sylvia; Peel, Nina; Ferguson-Smith, Anne C

    2005-10-01

    Ty3/gypsy retrotransposons are rare in mammalian genomes despite their abundance in invertebrate and other vertebrate classes. Here we identify a family of nine conserved mammalian genes with homology to Ty3/gypsy retrotransposons but which have lost their ability to autonomously retrotranspose. Of these, five map to the X chromosome while the remaining four are autosomal. Comparative phylogenetic analyses show them to have strongest homology to the sushi-ichi element from Fugu rubripes. Two of the autosomal gene members, Peg10 and Rtl1, are known to be imprinted, being expressed from the paternally inherited chromosome homologue. This suggests, consistent with the host-parasite response theory of the evolution of the imprinting mechanism, that parental-origin specific epigenetic control may be mediated by genomic "parasitic" elements such as these. Alternatively, these elements may preferentially integrate into regions that are differentially modified on the two homologous chromosomes such as imprinted domains and the X chromosome and acquire monoallelic expression. We assess the imprinting status of the remaining autosomal members of this family and show them to be biallelically expressed in embryo and placenta. Furthermore, the methylation status of Rtl1 was assayed throughout development and was found to resemble that of actively, silenced repetitive elements rather than imprinted sequences. This indicates that the ability to undergo genomic imprinting is not an inherent property of all members of this family of retroelements. Nonetheless, the conservation but functional divergence between the different members suggests that they have undergone positive selection and acquired distinct endogenous functions within their mammalian hosts.

  20. Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae).

    Science.gov (United States)

    Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

    2013-07-01

    The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.

  1. Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs.

    Science.gov (United States)

    Cervera, Amelia; Urbina, Denisse; de la Peña, Marcos

    2016-06-23

    Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA pathogens. Recent data, however, indicate that small self-cleaving ribozymes are widespread in genomes, although their functions are still unknown. We reveal that hammerhead ribozyme sequences in plant genomes form part of a new family of small non-autonomous retrotransposons with hammerhead ribozymes, referred to as retrozymes. These elements contain two long terminal repeats of approximately 350 bp, each harbouring a hammerhead ribozyme that delimitates a variable region of 600-1000 bp with no coding capacity. Retrozymes are actively transcribed, which gives rise to heterogeneous linear and circular RNAs that accumulate differentially depending on the tissue or developmental stage of the plant. Genomic and transcriptomic retrozyme sequences are highly heterogeneous and share almost no sequence homology among species except the hammerhead ribozyme motif and two small conserved domains typical of Ty3-gypsy long terminal repeat retrotransposons. Moreover, we detected the presence of RNAs of both retrozyme polarities, which suggests events of independent RNA-RNA rolling-circle replication and evolution, similarly to that of infectious circular RNAs like viroids and viral satellite RNAs. Our work reveals that circular RNAs with hammerhead ribozymes are frequently occurring molecules in plant and, most likely, metazoan transcriptomes, which explains the ubiquity of these genomic ribozymes and suggests a feasible source for the emergence of circular RNA plant pathogens.

  2. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines

    Science.gov (United States)

    Sciamanna, Ilaria; Gualtieri, Alberto; Cossetti, Cristina; Osimo, Emanuele Felice; Ferracin, Manuela; Macchia, Gianfranco; Aricò, Eleonora; Prosseda, Gianni; Vitullo, Patrizia; Misteli, Tom; Spadafora, Corrado

    2013-01-01

    LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the

  3. 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.

  4. Inhibition of LINE-1 retrotransposon-encoded reverse transcriptase modulates the expression of cell differentiation genes in breast cancer cells.

    Science.gov (United States)

    Patnala, Radhika; Lee, Sung-Hun; Dahlstrom, Jane E; Ohms, Stephen; Chen, Long; Dheen, S Thameem; Rangasamy, Danny

    2014-01-01

    Long Interspersed Elements (L1 elements) are biologically active retrotransposons that are capable of autonomous replication using their own reverse transcriptase (RT) enzyme. Expression of the normally repressed RT has been implicated in cancer cell growth. However, at present, little is known about the expression of L1-encoded RT activity or the molecular changes that are associated with RT activity in the development of breast cancer. Here, we report that RT activity is widespread in breast cancer cells. The expression of RT protein decreased markedly in breast cancer cells after treatment with the antiretroviral drug, efavirenz. While the majority of cells showed a significant reduction in proliferation, inhibition of RT was also accompanied by cell-specific differences in morphology. MCF7 cells displayed elongated microtubule extensions that adhered tightly to their substrate, while a large fraction of the T47D cells that we studied formed long filopodia projections. These morphological changes were reversible upon cessation of RT inhibition, confirming their dependence on RT activity. We also carried out gene expression profiling with microarrays and determined the genes that were differentially expressed during the process of cellular differentiation. Genes involved in proliferation, cell migration, and invasive activity were repressed in RT-inhibited cells. Concomitantly, genes involved in cell projection, formation of vacuolar membranes, and cell-to-cell junctions were significantly upregulated in RT-inhibited cells. qRT-PCR examination of the mRNA expression of these genes in additional cell lines yielded close correlation between their differential expression and the degree of cellular differentiation. Our study demonstrates that the inhibition of L1-encoded RT can reduce the rate of proliferation and promote differentiation of breast cancer cells. Together, these results provide a direct functional link between the expression of L1 retrotransposons and

  5. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines.

    Science.gov (United States)

    Sciamanna, Ilaria; Gualtieri, Alberto; Cossetti, Cristina; Osimo, Emanuele Felice; Ferracin, Manuela; Macchia, Gianfranco; Aricò, Eleonora; Prosseda, Gianni; Vitullo, Patrizia; Misteli, Tom; Spadafora, Corrado

    2013-12-01

    LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the 'normal' small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the

  6. The construction of R2 actions in D = 4, N = 1 supergravity

    NARCIS (Netherlands)

    Roo, M. de; Wiedemann, A.; Zijlstra, E.

    1990-01-01

    Actions containing R2 terms in d = 4, N = 1 supergravity are constructed in the on-shell and the new minimal formulation of the theory. The basic feature in both cases is an analogy between supersymmetric Yang-Mills theory and supergravity. This analogy is also used to construct supersymmetric Loren

  7. Consideration of R2Fe14B layers as targets with polarized electrons

    NARCIS (Netherlands)

    Hoogduin, JM; van Klinken, J

    1998-01-01

    Thin layers of R2Fe14B magnets (R = rare earth) can be magnetized perpendicularly to their planes and can be used as targets of polarized electrons with polarization of approximate to 4% to facilitate Moller/Bhabha and Compton polarimetry of electrons/positrons and photons, respectively. (C) 1998 El

  8. A note on Lagrangian cobordisms between Legendrian submanifolds of R^{2n+1}

    CERN Document Server

    Golovko, Roman

    2011-01-01

    We study the relation of an embedded Lagrangian cobordism between two closed orientable Legendrian submanifolds of R^{2n+1}. More precisely, we invesigate the behavior of the Thurston-Bennequin number and linearized Legendrian contact homology under this relation. The result about the Thurston-Bennequin number can be considered as a generalization of the result of Chantraine which holds when n=1.

  9. Spectral line survey of the ultracompact HII region Monoceros R2

    NARCIS (Netherlands)

    Ginard, D.; Gonzalez-Garcia, M.; Fuente, A.; Cernicharo, J.; Alonso-Albi, T.; Pilleri, P.; Gerin, M.; Garcia-Burillo, S.; Ossenkopf, V.; Rizzo, J. R.; Kramer, C.; Goicoechea, J. R.; Pety, J.; Berne, O.; Joblin, C.

    2012-01-01

    Context. Ultracompact (UC) HII regions constitute one of the earliest phases in the formation of a massive star and are characterized by extreme physical conditions (G(0) > 10(5) Habing field and n > 10(6) cm(-3)). The UC HII Mon R2 is the closest example and an excellent target to study the chemist

  10. Genome-wide identification and characterization of R2R3MYB family in Rosaceae.

    Science.gov (United States)

    González, Máximo; Carrasco, Basilio; Salazar, Erika

    2016-09-01

    Transcription factors R2R3MYB family have been associated with the control of secondary metabolites, development of structures, cold tolerance and response to biotic and abiotic stress, among others. In recent years, genomes of Rosaceae botanical family are available. Although this information has been used to study the karyotype evolution of these species from an ancestral genome, there are no studies that treat the evolution and diversity of gene families present in these species or in the botanical family. Here we present the first comparative study of the R2R3MYB subfamily of transcription factors in three species of Rosaceae family (Malus domestica, Prunus persica and Fragaria vesca). We described 186, 98 and 86 non-redundant gene models for apple, peach and strawberry, respectively. In this research, we analyzed the intron-exon structure and genomic distribution of R2R3MYB families mentioned above. The phylogenetic comparisons revealed putative functions of some R2R3MYB transcription factors. This analysis found 44 functional subgroups, seven of which were unique for Rosaceae. In addition, our results showed a highly collinearity among some genes revealing the existence of conserved gene models between the three species studied. Although some gene models in these species have been validated under several approaches, more research in the Rosaceae family is necessary to determine gene expression patterns in specific tissues and development stages to facilitate understanding of the regulatory and biochemical mechanism in this botanical family.

  11. Instant migration from Windows Server 2008 and 2008 R2 to 2012 how-to

    CERN Document Server

    Sivarajan, Santhosh

    2013-01-01

    Presented in a hands-on reference manual style, with real-world scenarios to lead you through each process. This book is intended for Windows server administrators who are performing migrations from their existing Windows Server 2008 / 2008 R2 environment to Windows Server 2012. The reader must be familiar with Windows Server 2008.

  12. Consideration of R2Fe14B layers as targets with polarized electrons

    NARCIS (Netherlands)

    Hoogduin, JM; van Klinken, J

    1998-01-01

    Thin layers of R2Fe14B magnets (R = rare earth) can be magnetized perpendicularly to their planes and can be used as targets of polarized electrons with polarization of approximate to 4% to facilitate Moller/Bhabha and Compton polarimetry of electrons/positrons and photons, respectively. (C) 1998 El

  13. On Local Smooth Solutions for the Vlasov Equation with the Potential of Interactions {\\pm} r^{-2}

    CERN Document Server

    Zhidkov, P E

    2003-01-01

    For the initial value problem for the Vlasov equation with the potential of interactions {\\pm} r^{-2} we prove the existence and uniqueness of a local solution with values in the Schwartz space S of infinitely differentiable functions rapidly decaying at infinity.

  14. Chiral recognition in electron scattering by S- and R-2-butanol

    DEFF Research Database (Denmark)

    Jones, Nykola C.; Hoffmann, Søren Vrønning; Field, David

    2015-01-01

    Experiments are described involving the low energy scattering of electrons from the two optical enantiomers S- and R- 2-butanol. Using a synchrotron radiation photoionization source on the ASTRID storage ring, scattering spectra are reported between a few meV and 140 meV at an electron energy...

  15. B(A)CKLUND TRANSFORMATION ON SURFACES WITH CONSTANT MEAN CURVATURE IN R2'1

    Institute of Scientific and Technical Information of China (English)

    田畴; 周扣华; 田涌波

    2003-01-01

    In this paper,the authors obtain the Backlund transformation on time-like surfaces with constant mean curvature in R2,1.Using this transformation,families of surfaces with constant mean curvature from known ones can be constructed.

  16. Examples of stationary BPS solutions in N=2 supergravity theories with $R^{2}$-interactions

    CERN Document Server

    Lópes-Cardoso, G; Käppeli, J; Mohaupt, T

    2001-01-01

    We discuss explicit examples of BPS solutions in four-dimensional N=2 supergravity with R^2-interactions. We demonstrate how to construct solutions by iteration. Generically, the presence of higher-curvature interactions leads to non-static spacetime line elements. We comment on the existence of horizons for multi-centered solutions.

  17. Consideration of R2Fe14B layers as targets with polarized electrons

    NARCIS (Netherlands)

    Hoogduin, JM; van Klinken, J

    Thin layers of R2Fe14B magnets (R = rare earth) can be magnetized perpendicularly to their planes and can be used as targets of polarized electrons with polarization of approximate to 4% to facilitate Moller/Bhabha and Compton polarimetry of electrons/positrons and photons, respectively. (C) 1998

  18. Occurrence of exact $R^2$ inflation in non-local UV-complete gravity

    CERN Document Server

    Koshelev, Alexey S; Rachwal, Leslaw; Starobinsky, Alexei A

    2016-01-01

    The $R+R^2$, shortly named "$R^2$" ("Starobinsky") inflationary model, represents a fully consistent example of a one-parameter inflationary scenario. This model has a "graceful exit" from inflation and provides a mechanism for subsequent creation and final thermalization of the standard matter. Moreover, it produces a very good fit of the observed spectrum of primordial perturbations. In the present paper we show explicitly that the $R^2$ inflationary spacetime is an exact solution of a range of weakly non-local (quasi-polynomial) gravitational theories, which provide an ultraviolet completion of the $R^2$ theory. These theories are ghost-free, super-renormalizable or finite at quantum level, and perturbatively unitary. Their spectrum consists of the graviton and the scalaron that is responsible for driving the inflation. Notably, any further extension of the spectrum leads to propagating ghost degrees of freedom. We are aimed at presenting a detailed construction of such theories in the so called Weyl basis...

  19. Beware of R2: simple, unambiguous assessment of the prediction accuracy of QSAR and QSPR models

    OpenAIRE

    Alexander, D. L. J.; Tropsha, A; Winkler, David A.

    2015-01-01

    The statistical metrics used to characterize the external predictivity of a model, i.e., how well it predicts the properties of an independent test set, have proliferated over the past decade. This paper clarifies some apparent confusion over the use of the coefficient of determination, R2, as a measure of model fit and predictive power in QSAR and QSPR modelling.

  20. Kinematics of the ionized-to-neutral interfaces in Monoceros R2

    CERN Document Server

    Pilleri, P; Gerin, M; Cernicharo, J; Goicoechea, J R; Ossenkopf, V; Joblin, C; González-García, M; Treviño-Morales, S P; Sánchez-Monge, Á; Pety, J; Berné, O; Kramer, C

    2013-01-01

    Context. Monoceros R2 (Mon R2), at a distance of 830 pc, is the only ultra-compact H ii region (UC H ii) where its associated photon-dominated region (PDR) can be resolved with the Herschel Space Observatory. Aims. Our aim is to investigate observationally the kinematical patterns in the interface regions (i.e., the transition from atomic to molecular gas) associated with Mon R2. Methods. We used the HIFI instrument onboard Herschel to observe the line profiles of the reactive ions CH+, OH+ and H2O+ toward different positions in Mon R2. We derive the column density of these molecules and compare them with gas-phase chemistry models. Results. The reactive ion CH+ is detected both in emission (at central and red-shifted velocities) and in absorption (at blue-shifted velocities). OH+ is detected in absorption at both blue- and red-shifted velocities, with similar column densities. H2O+ is not detected at any of the positions, down to a rms of 40 mK toward the molecular peak. At this position, we find that the OH...

  1. The take and give between retrotransposable elements and their hosts.

    Science.gov (United States)

    Beauregard, Arthur; Curcio, M Joan; Belfort, Marlene

    2008-01-01

    Retrotransposons mobilize via RNA intermediates and usually carry with them the agent of their mobility, reverse transcriptase. Retrotransposons are streamlined, and therefore rely on host factors to proliferate. However, retrotransposons are exposed to cellular forces that block their paths. For this review, we have selected for our focus elements from among target-primed (TP) retrotransposons, also called non-LTR retrotransposons, and extrachromosomally-primed (EP) retrotransposons, also called LTR retrotransposons. The TP retrotransposons considered here are group II introns, LINEs and SINEs, whereas the EP elements considered are the Ty and Tf retrotransposons, with a brief comparison to retroviruses. Recurring themes for these elements, in hosts ranging from bacteria to humans, are tie-ins of the retrotransposons to RNA metabolism, DNA replication and repair, and cellular stress. Likewise, there are parallels among host-cell defenses to combat rampant retrotransposon spread. The interactions between the retrotransposon and the host, and their coevolution to balance the tension between retrotransposon proliferation and host survival, form the basis of this review.

  2. Response of rice gypsy retrotransposons to different stress conditions%水稻gypsy类逆转座子对不同胁迫条件的响应

    Institute of Scientific and Technical Information of China (English)

    徐玲; 杨静; 刘林; 李成云

    2012-01-01

    LTR retrotransposons are the largest and most widely distributed transposable elements in rice, of which Ty3-gypsy class are more numerous. Using degenerate primers based on conserved region of reverse transcriptase gene in Ty3-gypsy retrotransposons, transcript fragments were amplified by RT-PCR and sequenced respectively from cDNAs of rice variety Acuche treated by 5 different stresses (M oryza, SA, 2,4-D, high-salt and tissue culture) to analyze the characteristics of Ty3-gypsy retrotransposons activated by different stresses. The results showed that all the 5 different stresses could activate Tyl-gypsy retrotransposon; amino acid sequences of reverse transcriptase of retrotransposons responding to different stresses were highly conserved and distributed crossly, only few of them showed specificity of stress response, suggesting that many Ty3-gy/wy retrotransposons could respond to different stresses.%LTR类逆转座子是水稻基因组中数量最多、分布最广的转座元件,其中Ty3-ypsy类所占比例较大.根据Ty3-gypsy类逆转座子逆转录酶的保守区域,采用简并引物,通过RT-PCR,对5种胁迫处理(稻瘟菌、水杨酸、2,4-D、高盐及组织培养)后的云南地方水稻品种月亮谷的cDNA进行扩增,并测序获得了一批转录片段,分析不同胁迫条件诱导激活的Ty3-ypsy类逆转座子的特点.结果表明:5种胁迫处理都能诱导月亮谷中Ty3-gypsy类逆转座子的表达;对不同胁迫响应的逆转座子序列大部分同源性较高,且呈交叉分布,仅有少部分具有胁迫响应的特异性,说明很多Ty3-gypsy类逆转座子能对不同胁迫进行响应.

  3. R2R Eventlogger: Community-wide Recording of Oceanographic Cruise Science Events

    Science.gov (United States)

    Maffei, A. R.; Chandler, C. L.; Stolp, L.; Lerner, S.; Avery, J.; Thiel, T.

    2012-12-01

    Methods used by researchers to track science events during a science research cruise - and to note when and where these occur - varies widely. Handwritten notebooks, printed forms, watch-keeper logbooks, data-logging software, and customized software have all been employed. The quality of scientific results is affected by the consistency and care with which such events are recorded and integration of multi-cruise results is hampered because recording methods vary widely from cruise to cruise. The Rolling Deck to Repository (R2R) program has developed an Eventlogger system that will eventually be deployed on most vessels in the academic research fleet. It is based on the open software package called ELOG (http://midas.psi.ch/elog/) originally authored by Stefan Ritt and enhanced by our team. Lessons have been learned in its development and use on several research cruises. We have worked hard to find approaches that encourage cruise participants to use tools like the eventlogger. We examine these lessons and several eventlogger datasets from past cruises. We further describe how the R2R Science Eventlogger works in concert with the other R2R program elements to help coordinate research vessels into a coordinated mobile observing fleet. Making use of data collected on different research cruises is enabled by adopting common ways of describing science events, the science instruments employed, the data collected, etc. The use of controlled vocabularies and the practice of mapping these local vocabularies to accepted oceanographic community vocabularies helps to bind shipboard research events from different cruises into a more cohesive set of fleet-wide events that can be queried and examined in a cross-cruise manner. Examples of the use of the eventlogger during multi-cruise oceanographic research programs along with examples of resultant eventlogger data will be presented. Additionally we will highlight the importance of vocabulary use strategies to the success of the

  4. Voltage-dependent modulation of cardiac ryanodine receptors (RyR2 by protamine.

    Directory of Open Access Journals (Sweden)

    Paula L Diaz-Sylvester

    Full Text Available It has been reported that protamine (>10 microg/ml blocks single skeletal RyR1 channels and inhibits RyR1-mediated Ca2+ release from sarcoplasmic reticulum microsomes. We extended these studies to cardiac RyR2 reconstituted into planar lipid bilayers. We found that protamine (0.02-20 microg/ml added to the cytosolic surface of fully activated RyR2 affected channel activity in a voltage-dependent manner. At membrane voltage (V(m; SR lumen-cytosol = 0 mV, protamine induced conductance transitions to several intermediate states (substates as well as full block of RyR2. At V(m>10 mV, the substate with the highest level of conductance was predominant. Increasing V(m from 0 to +80 mV, decreased the number of transitions and residence of the channel in this substate. The drop in current amplitude (full opening to substate had the same magnitude at 0 and +80 mV despite the approximately 3-fold increase in amplitude of the full opening. This is more similar to rectification of channel conductance induced by other polycations than to the action of selective conductance modifiers (ryanoids, imperatoxin. A distinctive effect of protamine (which might be shared with polylysines and histones but not with non-peptidic polycations is the activation of RyR2 in the presence of nanomolar cytosolic Ca2+ and millimolar Mg2+ levels. Our results suggest that RyRs would be subject to dual modulation (activation and block by polycationic domains of neighboring proteins via electrostatic interactions. Understanding these interactions could be important as such anomalies may be associated with the increased RyR2-mediated Ca2+ leak observed in cardiac diseases.

  5. Cytotoxicity of platinum(IV) and platinum(II) complexes containing 1R,2R-cyclohexanediamine as a ligand.

    Science.gov (United States)

    Yamashita, T; Hirose, J; Noji, M; Saito, R; Tomida, H; Kidani, Y

    1993-10-01

    Several Pt(IV) and Pt(II) complexes containing 1R,2R-cyclohexanediamine (1R,2R-dach) as a carrier ligand were synthesized. The cytotoxicities and the uptake of the platinum complexes by leukemia L1210 cells were compared in order to study the correlation between their structures and cytotoxicities. [Pt(II)Cl2(1R,2R-dach)], [(Pt(II)(oxalato)(1R,2R-dach)], and [Pt(II)(malonato)(1R,2R-dach)], which have excellent anticancer properties, exhibited very high cytotoxicities and were easily taken up by leukemia L1210 cells. [Pt(IV)Cl4(1R,2R-dach)], trans(Cl)-[Pt(IV)Cl2(oxalato)(1R,2R-dach)], and trans(Cl)-[Pt(IV)Cl2(malonato)(1R,2R-dach)] also had high cytotoxicities. After a short incubation time, the uptake of [Pt(II)Cl2(1R,2R-dach)], [Pt(II)(oxalato)(1R,2R-dach)], and [Pt(II)(malonato)(1R,2R-dach)] by leukemia L1210 cells were respectively very similar to those of [Pt(IV)Cl4(1R,2R-dach)], trans(Cl)-[Pt(IV)Cl2(oxalato)(1R,2R-dach)], and trans(Cl)-[Pt(IV)Cl2(malonato)(1R,2R-dach)]. In addition, trans(OH)-[Pt(IV)(OH)2Y2(1R,2R-dach)] (Y2: oxalato or malonato) did not exhibit cytotoxicity towards leukemia L1210 cells, whereas trans(Cl)-[Pt(IV)Cl2Y2(1R,2R-dach)] (Y2: oxalato or malonato) were highly cytotoxic. The accumulation of trans(OH)-[Pt(IV)(OH)2Y2(1R,2R-dach)] in leukemia L1210 cells was much lower than that of trans(Cl)-[Pt(IV)Cl2Y2(1R,2R-dach)]. Platinum(IV) complexes, in which leaving groups are replaced by hydroxide groups, have decreased cytotoxic activity, because the hydroxide groups of the platinum(IV) complex reduce the uptake of platinum by the cells. trans(OH),cis(Cl)-[Pt(IV)(OH)2Cl2(1R,2R-dach)], which has hydroxide and chloride groups, was easily incorporated into the cells and exhibited the high cytotoxic activity. This behavior indicates that the chloride group apparently overcomes the ameliorating effect of the hydroxide group.

  6. piRNA-associated proteins and retrotransposons are differentially expressed in murine testis and ovary of aryl hydrocarbon receptor deficient mice

    Science.gov (United States)

    Rico-Leo, Eva M.; Moreno-Marín, Nuria; González-Rico, Francisco J.; Barrasa, Eva; Ortega-Ferrusola, Cristina; Martín-Muñoz, Patricia; Sánchez-Guardado, Luis O.; Llano, Elena; Alvarez-Barrientos, Alberto; Infante-Campos, Ascensión; Catalina-Fernández, Inmaculada; Hidalgo-Sánchez, Matías; de Rooij, Dirk G.; Pendás, Alberto M.; Peña, Fernando J.; Merino, Jaime M.

    2016-01-01

    Previous studies suggested that the aryl hydrocarbon receptor (AhR) contributes to mice reproduction and fertility. However, the mechanisms involved remain mostly unknown. Retrotransposon silencing by Piwi-interacting RNAs (piRNAs) is essential for germ cell maturation and, remarkably, AhR has been identified as a regulator of murine B1-SINE retrotransposons. Here, using littermate AhR+/+ and AhR−/− mice, we report that AhR regulates the general course of spermatogenesis and oogenesis by a mechanism likely to be associated with piRNA-associated proteins, piRNAs and retrotransposons. piRNA-associated proteins MVH and Miwi are upregulated in leptotene to pachytene spermatocytes with a more precocious timing in AhR−/− than in AhR+/+ testes. piRNAs and transcripts from B1-SINE, LINE-1 and IAP retrotransposons increased at these meiotic stages in AhR-null testes. Moreover, B1-SINE transcripts colocalize with MVH and Miwi in leptonema and pachynema spermatocytes. Unexpectedly, AhR−/− males have increased sperm counts, higher sperm functionality and enhanced fertility than AhR+/+ mice. In contrast, piRNA-associated proteins and B1-SINE and IAP-derived transcripts are reduced in adult AhR−/− ovaries. Accordingly, AhR-null female mice have lower numbers of follicles when compared with AhR+/+ mice. Thus, AhR deficiency differentially affects testis and ovary development possibly by a process involving piRNA-associated proteins, piRNAs and transposable elements. PMID:28003471

  7. In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways.

    Directory of Open Access Journals (Sweden)

    Sophie Desset

    Full Text Available BACKGROUND: In the Drosophila germ line, repeat-associated small interfering RNAs (rasiRNAs ensure genomic stability by silencing endogenous transposable elements. This RNA silencing involves small RNAs of 26-30 nucleotides that are mainly produced from the antisense strand and function through the Piwi protein. Piwi belongs to the subclass of the Argonaute family of RNA interference effector proteins, which are expressed in the germline and in surrounding somatic tissues of the reproductive apparatus. In addition to this germ-line expression, Piwi has also been implicated in diverse functions in somatic cells. PRINCIPAL FINDINGS: Here, we show that two LTR retrotransposons from Drosophila melanogaster, ZAM and Idefix, are silenced by an RNA silencing pathway that has characteristics of the rasiRNA pathway and that specifically recognizes and destroys the sense-strand RNAs of the retrotransposons. This silencing depends on Piwi in the follicle cells surrounding the oocyte. Interestingly, this silencing is active in all the somatic tissues examined from embryos to adult flies. In these somatic cells, while the silencing still involves the strict recognition of sense-strand transcripts, it displays the marked difference of being independent of the Piwi protein. Finally, we present evidence that in all the tissues examined, the repression is controlled by the heterochromatic COM locus. CONCLUSION: Our data shed further light on the silencing mechanism that acts to target Drosophila LTR retrotransposons in somatic cells throughout fly development. They demonstrate that different RNA silencing pathways are involved in ovarian versus other somatic tissues, since Piwi is necessary for silencing in the former tissues but is dispensable in the latter. They further demonstrate that these pathways are controlled by the heterochromatic COM locus which ensures the overall protection of Drosophila against the detrimental effects of random retrotransposon

  8. Apoptosis Induction by Targeting Interferon Gamma Receptor 2 (IFNgammaR2) in Prostate Cancer: Ligand (IFNgamma)-Independent Novel Function of IFNgammaR2 as a Bax Inhibitor

    Science.gov (United States)

    2015-08-01

    in Mitochondria and ER membranes! Cell Death ER# Bax! Bax! Bax! Mitochondria ! IFNγR 2! IFNγR1! IFNγ" Jak! STA T! Gene Expression! (IFNγ Response...planned to determine what kind of cell type(s) in prostate cancer tissue expresses IFNγR2 by performing immunohistochemistry. Another important...proposed experiment is to determine whether IFNγR2 expression profile (expression levels and expression type (cytosol or membrane expression, or cell type

  9. 平面停止域族{FTzz R2+} 满足条件F1-- F4%Families of Stopping--fields {FTZZ} R2+ on Plane .1inSatisfy F1--F4 Conditions

    Institute of Scientific and Technical Information of China (English)

    周新全

    2000-01-01

    This paper first presents families ofstopping --fields on plane and proves that families of stopping--fields FTZZ R2+ satisfy F1--F4 conditions.%本文首次提出平面停止域族FTZ Z R2+,证明了停止域族F2T2 R+2满足F1--F4条件.

  10. Exchange Server2010只能安装在Windows Server2008R2上,这是真的吗?Windows Server2008R2支持Exchange Server2007P~?

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Windows Server 2008 SP2 64位版本和Windows Server 2008 R2都支持Exchange Server2010。Windows Server 2008 R2不支持Exchange Server2007和Exchange Server 2007 SP1。Windows Server 2008 R2预计也不会增加对Exchange Server 2007 SP2的支持。

  11. On the limit cycle for the 1/r^2 potential in momentum space

    CERN Document Server

    Hammer, H W; Swingle, Brian G.

    2006-01-01

    The renormalization of the attractive 1/r^2 potential has recently been studied using a variety of regulators. In particular, it was shown that renormalization with a square well in position space allows multiple solutions for the depth of the square well, including, but not requiring a renormalization group limit cycle. Here, we consider the renormalization of the 1/r^2 potential in momentum space. We regulate the problem with a momentum cutoff and absorb the cutoff dependence using a momentum-independent counterterm potential. The strength of this counterterm is uniquely determined and runs on a limit cycle. We also calculate the bound state spectrum and scattering observables, emphasizing the manifestation of the limit cycle in these observables.

  12. R2 Correction and Its Implication of Present Cosmic Accelerating Behavior

    Institute of Scientific and Technical Information of China (English)

    LI Hui; XU Jian-Jun

    2004-01-01

    In this work we show an R + αR2 model of the universe in which certain quadratic correction is considered. Our results indicate that the R2 term can act as the present impetus of cosmic acceleration, but there may be a future collapsing universe with this component damped. This model can also tolerate a negative cosmological constant A,although there seems to be no need for a non-vanishing one. In our simplification, this curvature component has a stationary equation of state, which is similar to radiation. Unlike other dark energy models, this "missing" energy has a negative density. Some details and effects on cold dark matter and A-relevant model have been discussed in the frame of curvature-squared gravity theories.

  13. On Supersymmetric Geometric Flows and $\\mathcal{R}^2$ Inflation From Scale Invariant Supergravity

    CERN Document Server

    Rajpoot, Subhash

    2016-01-01

    Models of geometric flows pertaining to $\\mathcal{R}^2$ scale invariant (super) gravity theories coupled to conformally invariant matter fields are investigated. Related to this work are supersymmetric scalar manifolds that are isomorphic to the K\\"{a}hlerian spaces $\\mathcal{M}_n=SU(1,1+k)/U(1)\\times SU(1+k)$ as generalizations of the non-supersymmetric analogs with $SO(1,1+k)/SO(1+k)$ manifolds. For curved superspaces with geometric evolution of physical objects, a complete supersymmetric theory has to be elaborated on nonholonomic (super) manifolds and bundles determined by non-integrable superdistributions with additional constraints on (super) field dynamics and geometric evolution equations. We also consider generalizations of Perelman's functionals using such nonholonomic variables which result in the decoupling of geometric flow equations and Ricci soliton equations with supergravity modifications of the $R^2$ gravity theory. As such, it is possible to construct exact non-homogeneous and locally aniso...

  14. 浅析Windows Server 2008 R2新增功能

    Institute of Scientific and Technical Information of China (English)

    卢印海

    2012-01-01

    Windows Server 2008R2用于在虚拟化工作负载、支持应用程序和保护网络方面向组织提供最高效的平台。它为开发和可靠地承载Web应用程序和服务提供了一个安全,易于管理的平台。从工作组到数据中心,Windows Server 2008R2都提供了令人兴奋且很有价值的新功能,对基本操作系统做出了重大改进

  15. 4-bit digital to analog converter using R-2R ladder and binary weighted resistors

    Science.gov (United States)

    Diosanto, J.; Batac, M. L.; Pereda, K. J.; Caldo, R.

    2017-06-01

    The use of a 4-bit digital-to-analog converter using two methods; Binary Weighted Resistors and R-2R Ladder is designed and presented in this paper. The main components that were used in constructing both circuits were different resistor values, operational amplifier (LM741) and single pole double throw switches. Both circuits were designed using MULTISIM software to be able to test the circuit for its ideal application and FRITZING software for the layout designing and fabrication to the printed circuit board. The implementation of both systems in an actual circuit benefits in determining and comparing the advantages and disadvantages of each. It was realized that the binary weighted circuit is more efficient DAC, having lower percentage error of 0.267% compared to R-2R ladder circuit which has a minimum of percentage error of 4.16%.

  16. Apoptosis Induction by Targeting Interferon Gamma Receptor 2 (IFNgammaR2) in Prostate Cancer: Ligand (IFNgamma)-Independent Novel Function of IFNgammaR2 as a Bax Inhibitor

    Science.gov (United States)

    2015-08-01

    inhibitor of Bax. Bax is a key mediator of apoptosis. We found that IFNγR2 is overexpressed in prostate cancer, and we hypothesize that abnormally high...We found that IFNγR2 levels are abnormally elevated in prostate cancer cell lines. Short hairpin (sh) RNA- mediated knockdown of IFNγR2 was able to... enhances Bax activation. (Months 1-24) Task 2: To identify the subtype of prostate cancer that can be effectively treated by IFNγR2-targeting

  17. Rolling Deck to Repository (R2R): Building a Reference Cruise Catalog for the Research Fleet

    Science.gov (United States)

    Arko, R. A.; Clark, P. D.; Chandler, C. L.; Smith, S. R.

    2012-12-01

    The Rolling Deck to Repository (R2R) program is developing infrastructure to ensure the underway sensor data from NSF-supported oceanographic research vessels are routinely and consistently documented, preserved in long-term archives, and disseminated to the science community. A core element of this infrastructure is a master catalog of research vessels, cruises, sensor systems, underway datasets, navigation products, field reports, event logs, file formats, people, organizations, and funding awards that is maintained uniformly across the research fleet. All NSF-supported vessel operators now submit their underway cruise data and documentation directly to R2R, per the revised Division of Ocean Sciences (OCE) Sample and Data Policy published in 2011. R2R ingests this content into the fleet catalog, assigning globally unique and persistent identifiers at the cruise, dataset, and file (granule) levels. The catalog is aligned with community-standard vocabularies, working collaboratively with the NOAA Data Centers, UNOLS Office, and pan-European SeaDataNet project; and includes links to related data at other inter/national repositories. In response to community demand, we are extending the catalog to include instrument-specific metadata such as installation details, patch tests, and calibration results. The entire R2R catalog is published on the Web as "Linked Data", making it easily accessible to encourage integration with other repositories. Selected content is also published in formal metadata records according to ISO and W3C standards, suitable for submission to long-term archives. We are deploying both faceted (classification/filter) and Web map-based browse and search interfaces.

  18. Universal correlations in random matrices quantum chaos, the $1\\/r^2$ integrable model, and quantum gravity

    CERN Document Server

    Jain, S

    1996-01-01

    Random matrix theory (RMT) provides a common mathematical formulation of distinct physical questions in three different areas: quantum chaos, the 1-d integrable model with the $1/r^2$ interaction (the Calogero-Sutherland-Moser system), and 2-d quantum gravity. We review the connection of RMT with these areas. We also discuss the method of loop equations for determining correlation functions in RMT, and smoothed global eigenvalue correlators in the 2-matrix model for gaussian orthogonal, unitary and symplectic ensembles.

  19. Decreased placental and maternal serum TRAIL-R2 levels are associated with placenta accreta.

    Science.gov (United States)

    Oztas, Efser; Ozler, Sibel; Ersoy, Ali Ozgur; Ersoy, Ebru; Caglar, Ali Turhan; Uygur, Dilek; Yucel, Aykan; Ergin, Merve; Danisman, Nuri

    2016-03-01

    TNF-related apoptosis-inducing ligand receptor-2 (TRAIL-R2) is produced both by decidual and trophoblast cells during pregnancy and known to participate in apoptosis. In this study, we aimed to determine and to compare maternal serum and placental TRAIL-R2 levels in patients with placenta accreta, non-adherent placenta previa and in healthy pregnancies. We also aimed to analyze the association of placenta accreta with the occurrence of previous C-sections. A total of 82 pregnant women were enrolled in this case-control study (27 placenta accreta patients, 26 non-adherent placenta previa patients and 29 age-, and BMI-matched healthy, uncomplicated pregnant controls). TRAIL-R2 levels were studied in both maternal serum and placental tissue homogenates. Determining the best predictor(s) which discriminate placenta accreta was analyzed by multiple logistic regression analyses. Adjusted odds ratios and 95% confidence intervals were also calculated. Both placental and serum TRAIL-R2 levels were significantly lower in placenta accreta group (median 34.82 pg/mg and 19.85 pg/mL, respectively) when compared with both non-adherent placenta previa (median 39.24 pg/mg and 25.99 pg/mL, respectively) and the control groups (median 41.62 pg/mg and 25.87 pg/mL, respectively) (p placenta accreta (OR: 0.934 95% CI 0.883-0.987, p = 0.016 and OR:7.725 95% CI: 2.717-21.965, p placenta accreta, suggesting a possible role of apoptosis in abnormal trophoblast invasion. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Rolling Deck to Repository (R2R): Collaborative Development of Linked Data for Oceanographic Research

    Science.gov (United States)

    Arko, Robert; Chandler, Cynthia; Stocks, Karen; Smith, Shawn; Clark, Paul; Shepherd, Adam; Moore, Carla; Beaulieu, Stace

    2013-04-01

    The Rolling Deck to Repository (R2R) program is developing infrastructure to ensure the underway sensor data from U.S. academic oceanographic research vessels are routinely and consistently documented, preserved in long-term archives, and disseminated to the science community. The entire R2R Catalog is published online as a Linked Data collection, making it easily accessible to encourage discovery and integration with data at other repositories. We are developing the R2R Linked Data collection with specific goals in mind: 1.) We facilitate data access and reuse by publishing the richest possible collection of resources to describe vessels, cruises, instruments, and datasets from the U.S. academic fleet, including data quality assessment results and clean trackline navigation; 2.) We facilitate data citation through the entire lifecycle from field acquisition to shoreside archiving to journal articles and global syntheses, by publishing Digital Object Identifiers (DOIs) for datasets and encoding them directly into our Linked Data resources; and 3.) We facilitate federation with other repositories such as the Biological and Chemical Oceanography Data Management Office (BCO-DMO), InterRidge Vents Database, and Index to Marine and Lacustrine Geological Samples (IMLGS), by reciprocal linking between RDF resources and supporting the RDF Query Language. R2R participates in the Ocean Data Interoperability Platform (ODIP), a joint European-U.S.-Australian partnership to facilitate the sharing of data and documentation across international borders. We publish our controlled vocabularies as a Simple Knowledge Organization System (SKOS) concept collection, and are working toward alignment with SeaDataNet and other community-standard terms using the NERC Vocabulary Server (NVS). http://rvdata.us/

  1. Identification of a novel PNMA-MS1 gene in marsupials suggests the LTR retrotransposon-derived PNMA genes evolved differently in marsupials and eutherians.

    Science.gov (United States)

    Iwasaki, Sawa; Suzuki, Shunsuke; Pelekanos, Matthew; Clark, Helen; Ono, Ryuichi; Shaw, Geoff; Renfree, Marilyn B; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2013-10-01

    Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians.

  2. The Renormalization Group Limit Cycle for the 1/r^2 Potential

    CERN Document Server

    Braaten, E; Braaten, Eric; Phillips, Demian

    2004-01-01

    Previous work has shown that if an attractive 1/r^2 potential is regularized at short distances by a spherical square-well potential, renormalization allows multiple solutions for the depth of the square well. The depth can be chosen to be a continuous function of the short-distance cutoff R, but it can also be a log-periodic function of R with finite discontinuities, corresponding to a renormalization group (RG) limit cycle. We consider the regularization with a delta-shell potential. In this case, the coupling constant is uniquely determined to be a log-periodic function of R with infinite discontinuities, and an RG limit cycle is unavoidable. In general, a regularization with an RG limit cycle is selected as the correct renormalization of the 1/r^2 potential by the conditions that the cutoff radius R can be made arbitrarily small and that physical observables are reproduced accurately at all energies much less than hbar^2/mR^2.

  3. Antifungal potential of Bacillus vallismortis R2 against different phytopathogenic fungi

    Energy Technology Data Exchange (ETDEWEB)

    Kaur, P.K.; Kaur, J.; Saini, H.S.

    2015-07-01

    The cash crops grown in an agro-climatic region are prone to infection by various fungal pathogens. The use of chemical fungicides over the years has resulted in emergence of resistant fungal strains, thereby necessitating the development of effective and environmental friendly alternatives. The natural antagonistic interactions among different microbial populations have been exploited as an eco-friendly approach for controlling fungal pathogens resistant to synthetic chemicals. Morphologically distinct bacterial cultures (150), isolated from rhizospheric soils of wheat, rice, onion and tomato plants were screened for their antifungal potential against seven phytopathogenic fungi prevalent in the State of Punjab (India). The bacterial isolate R2, identified as Bacillus vallismortis, supported more than 50% inhibition of different phytopathogenic fungi (Alternaria alternata, Rhizoctonia oryzae, Fusarium oxysporum, Fusarium moniliforme, Colletotrichum sp, Helminthosporium sp and Magnaporthe grisea) in dual culture plate assay. The thin layer chromatography based bio-autography of acid-precipitated biomolecules (APB) indicated the presence of more than one type of antifungal molecule, as evidenced from zones of inhibition against the respective fungal pathogen. The initial analytical studies indicated the presence of surfactin, iturin A and fengycin-like compounds in APB. The antifungal activity of whole cells and APB of isolate R2 was evaluated by light and scanning electron microscopy. The wheat grains treated with APB and exposed to spores of A. alternata showed resistance to the development of black point disease, thereby indicating the potential application of R2 and its biomolecules at field scale level. (Author)

  4. ERP44 inhibits human lung cancer cell migration mainly via IP3R2.

    Science.gov (United States)

    Huang, Xue; Jin, Meng; Chen, Ying-Xiao; Wang, Jun; Zhai, Kui; Chang, Yan; Yuan, Qi; Yao, Kai-Tai; Ji, Guangju

    2016-06-01

    Cancer cell migration is involved in tumour metastasis. However, the relationship between calcium signalling and cancer migration is not well elucidated. In this study, we used the human lung adenocarcinoma A549 cell line to examine the role of endoplasmic reticulum protein 44 (ERP44), which has been reported to regulate calcium release inside of the endoplasmic reticulum (ER), in cell migration. We found that the inositol 1,4,5-trisphosphate receptors (IP3Rs/ITPRs) inhibitor 2-APB significantly inhibited A549 cell migration by inhibiting cell polarization and pseudopodium protrusion, which suggests that Ca2+ is necessary for A549 cell migration. Similarly, the overexpression of ERP44 reduced intracellular Ca2+ release via IP3Rs, altered cell morphology and significantly inhibited the migration of A549 cells. These phenomena were primarily dependent on IP3R2 because wound healing in A549 cells with IP3R2 rather than IP3R1 or IP3R3 siRNA was markedly inhibited. Moreover, the overexpression of ERP44 did not affect the migration of the human neuroblastoma cell line SH-SY5Y, which mainly expresses IP3R1. Based on the above observations, we conclude that ERP44 regulates A549 cell migration mainly via an IP3R2-dependent pathway.

  5. R2MLwiN: A Package to Run MLwiN from within R

    Directory of Open Access Journals (Sweden)

    Zhengzheng Zhang

    2016-09-01

    Full Text Available R2MLwiN is a new package designed to run the multilevel modeling software program MLwiN from within the R environment. It allows for a large range of models to be specified which take account of a multilevel structure, including continuous, binary, proportion, count, ordinal and nominal responses for data structures which are nested, cross-classified and/or exhibit multiple membership. Estimation is available via iterative generalized least squares (IGLS, which yields maximum likelihood estimates, and also via Markov chain Monte Carlo (MCMC estimation for Bayesian inference. As well as employing MLwiN's own MCMC engine, users can request that MLwiN write BUGS model, data and initial values statements for use with WinBUGS or OpenBUGS (which R2MLwiN automatically calls via rbugs, employing IGLS starting values from MLwiN. Users can also take advantage of MLwiN's graphical user interface: for example to specify models and inspect plots via its interactive equations and graphics windows. R2MLwiN is supported by a large number of examples, reproducing all the analyses conducted in MLwiN's IGLS and MCMC manuals.

  6. R2* mapping for brain iron: associations with cognition in normal aging.

    Science.gov (United States)

    Ghadery, Christine; Pirpamer, Lukas; Hofer, Edith; Langkammer, Christian; Petrovic, Katja; Loitfelder, Marisa; Schwingenschuh, Petra; Seiler, Stephan; Duering, Marco; Jouvent, Eric; Schmidt, Helena; Fazekas, Franz; Mangin, Jean-Francois; Chabriat, Hugues; Dichgans, Martin; Ropele, Stefan; Schmidt, Reinhold

    2015-02-01

    Brain iron accumulates during aging and has been associated with neurodegenerative disorders including Alzheimer's disease. Magnetic resonance (MR)-based R2* mapping enables the in vivo detection of iron content in brain tissue. We investigated if during normal brain aging iron load relates to cognitive impairment in region-specific patterns in a community-dwelling cohort of 336 healthy, middle aged, and older adults from the Austrian Stroke Prevention Family Study. MR imaging and R2* mapping in the basal ganglia and neocortex were done at 3T. Comprehensive neuropsychological testing assessed memory, executive function, and psychomotor speed. We found the highest iron concentration in the globus pallidus, and pallidal and putaminal iron was significantly and inversely associated with cognitive performance in all cognitive domains, except memory. These associations were iron load dependent. Vascular brain lesions and brain volume did not mediate the relationship between iron and cognitive performance. We conclude that higher R2*-determined iron in the basal ganglia correlates with cognitive impairment during brain aging independent of concomitant brain abnormalities. The prognostic significance of this finding needs to be determined.

  7. Antifungal potential of Bacillus vallismortis R2 against different phytopathogenic fungi

    Directory of Open Access Journals (Sweden)

    Preet K. Kaur

    2015-06-01

    Full Text Available The cash crops grown in an agro-climatic region are prone to infection by various fungal pathogens. The use of chemical fungicides over the years has resulted in emergence of resistant fungal strains, thereby necessitating the development of effective and environmental friendly alternatives. The natural antagonistic interactions among different microbial populations have been exploited as an eco-friendly approach for controlling fungal pathogens resistant to synthetic chemicals. Morphologically distinct bacterial cultures (150, isolated from rhizospheric soils of wheat, rice, onion and tomato plants were screened for their antifungal potential against seven phytopathogenic fungi prevalent in the State of Punjab (India. The bacterial isolate R2, identified as Bacillus vallismortis, supported more than 50% inhibition of different phytopathogenic fungi (Alternaria alternata, Rhizoctonia oryzae, Fusarium oxysporum, Fusarium moniliforme, Colletotrichum sp, Helminthosporium sp and Magnaporthe griseain dual culture plate assay. The thin layer chromatography based bio-autography of acid-precipitated biomolecules (APB indicated the presence of more than one type of antifungal molecule, as evidenced from zones of inhibition against the respective fungal pathogen. The initial analytical studies indicated the presence of surfactin, iturin A and fengycin-like compounds in APB. The antifungal activity of whole cells and APB of isolate R2 was evaluated by light and scanning electron microscopy. The wheat grains treated with APB and exposed to spores of A. alternata showed resistance to the development of black point disease, thereby indicating the potential application of R2 and its biomolecules at field scale level.

  8. Rolling Deck to Repository (R2R): Building the Data Pipeline - Initial Results

    Science.gov (United States)

    Arko, R. A.; Clark, P. D.; Rioux, M. A.; McGovern, T. M.; Deering, T. W.; Hagg, R. K.; Payne, A. A.; Fischman, D. E.; Ferrini, V.

    2009-12-01

    The NSF-funded Rolling Deck to Repository (R2R) project is working with U.S. academic research vessel operators to ensure the documentation and preservation of data from routine “underway” (meteorological, geophysical, and oceanographic) sensor systems. A standard pipeline is being developed in which data are submitted by vessel operators directly to a central repository; inventoried in an integrated fleet-wide catalog; organized into discrete data sets with persistent unique identifiers; associated with essential cruise-level metadata; and delivered to the National Data Centers for archiving and dissemination. Several vessels including Atlantis, Healy, Hugh R. Sharp, Ka'imikai-O-Kanaloa, Kilo Moana, Knorr, Marcus G. Langseth, Melville, Oceanus, Roger Revelle, and Thomas G. Thompson began submitting data and documentation to R2R during the project’s pilot phase, and a repository infrastructure has been established. Cruise metadata, track maps, and data inventories are published at the R2R Web portal, with controlled vocabularies drawn from community standards (e.g. International Council for the Exploration of the Sea (ICES) ship codes). A direct connection has been established to the University-National Oceanographic Laboratory System (UNOLS) Ship Time Request and Scheduling System (STRS) via Web services to synchronize port codes and cruise schedules. A secure portal is being developed where operators may login to upload sailing orders, review data inventories, and create vessel profiles. R2R has established a standard procedure for submission of data to the National Geophysical Data Center (NGDC) that incorporates persistent unique identifiers for cruises, data sets, and individual files, using multibeam data as a test bed. Once proprietary holds are cleared and a data set is delivered to NGDC, the R2R catalog record is updated with the URL for direct download and it becomes immediately available to integration and synthesis projects such as the NSF

  9. Rolling Deck to Repository (R2R): Research Cruise Event Logger

    Science.gov (United States)

    Chandler, C. L.; Maffei, A. R.; Stolp, L.; Dubois, D. L.

    2011-12-01

    Scientific event logs, used by the science party to record scientific sampling events that occur during a research cruise, have been used in various ways for decades. An event log is very important for documenting the occurrence of a sampling event and its location, time, relative sequence, and related details. Event logging, done well, can provide important documentation about scientific data collected during a cruise, and enable more efficient use of those data by cruise participants and future researchers. When the resultant event log is a digital data file, with content generated programmatically and controlled by term vocabularies, it becomes an even more valuable addition to the full complement of data sets generated during the cruise. However, such a tool is only effective if it is used. Through field testing, several key factors were identified that encourage the use of such a tool: the ability to customize the tool to represent the science implementation plan, proposed sampling scheme, cruise personnel and instrumentation; the ability to retrieve date, time and location data automatically from the shipboard network and the ability to enter events quickly and from any location on the ship. This presentation provides an overview of both the current version 1 and soon to be released version 2 of the Rolling Deck to Repository (R2R) research cruise Event Logger system. The R2R Event Logger application is built upon a pre-existing, open-source, weblog product called ELOG (ELOG URL: http://midas.psi.ch/elog/). We provide an oceanographer's view of the full process by which: 1) the R2R Event Logger application is configured and tested to meet the unique needs of a research cruise; 2) the R2R project works with the ship operator to install the Event Logger on the ship designated for the cruise, 3) the Event Logger is configured to automatically retrieve location, time, and other pertinent information from the shipboard network; 4) a copy of the event log file is

  10. Synaptic AMPA receptor subunit trafficking is independent of the C terminus in the GluR2-lacking mouse.

    Science.gov (United States)

    Panicker, Sandip; Brown, Keith; Nicoll, Roger A

    2008-01-22

    Glutamate is the primary excitatory neurotransmitter in the brain, and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) type glutamate receptors mediate most fast synaptic transmission. AMPA receptors are tetrameric assemblies composed from four possible subunits (GluR1-4). In hippocampal pyramidal cells, AMPA receptors are heteromeric receptors containing the GluR2 subunit and either GluR1 or GluR3. It is generally accepted that the trafficking of GluR1/GluR2 receptors to synapses requires activity, whereas GluR2/GluR3 receptors traffic constitutively. It has been suggested that the trafficking is governed by the cytoplasmic C termini of the subunits. Because the basis for this theory relied on the introduction of unnatural, homomeric, calcium-permeable AMPA receptors, we have used the GluR2(-/-) knock out mouse to determine whether the expression of mutated forms of GluR2 can rescue WT synaptic responses. We find that GluR2, lacking its entire C terminus, or a GluR2 chimera containing the C terminus of GluR1, is capable of trafficking to the synapse in the absence of activity. These findings suggest that the GluR2 C terminus is not required for GluR2 synaptic insertion.

  11. Development of a simple measurement method for GluR2 protein expression as an index of neuronal vulnerability

    Directory of Open Access Journals (Sweden)

    Chihiro Sugiyama

    2015-01-01

    Full Text Available In vitro estimating strategies for potential neurotoxicity are required to screen multiple substances. In a previous study, we showed that exposure to low-concentrations of some chemicals, such as organotin, decreased the expression of GluR2 protein, which is a subunit of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA-type glutamate receptors, and led to neuronal vulnerability. This result suggested that GluR2 decreases as an index of neuronal cell sensitivity and vulnerability to various toxic insults. Accordingly, we developed a versatile method that is a large scale determination of GluR2 protein expression in the presence of environmental chemicals by means of AlphaLISA technology. Various analytical conditions were optimized, and then GluR2 protein amount was measured by the method using AlphaLISA. The GluR2 amounts were strongly correlated with that of measured by western blotting, which is currently used to determine GluR2 expression. An ideal standard curve could be written with the authentic GluR2 protein from 0 ng to 100 ng. Subsequently, twenty environmental chemicals were screened and nitenpyram was identified as a chemical which lead to decrease in GluR2 protein expression. This assay may provide a tool for detecting neurotoxic chemicals according to decreases in GluR2 protein expression.

  12. Decommissioning of the Nuclear Reactors R2 and R2-0 at Studsvik, Sweden. General Data as called for under Article 37 of the Euratom Treaty

    Energy Technology Data Exchange (ETDEWEB)

    2009-01-15

    This document describes the plans for decommissioning of the nuclear research and material test reactors R2 and R2-0, situated at the Studsvik site close to the city of Nykoeping, Sweden. The purpose of the document is to serve as information for the European Commission, and to fulfil the requirements of Article 37 of the Euratom Treaty. Studsvik is situated on the Baltic coast, about 20 km east of Nykoeping and 80 km southwest of Stockholm. The site comprises the reactors R2 and R2-0 and several facilities for material investigation and radioactive waste treatment and storage. The reactors were used for a number of different purposes from 1960 until June 2005, when they were shut down following a decision by the operator. Decommissioning of the reactor facility is planned to be completed in 2016 after dismantling and conditioning of radioactive parts and demolition of the facility. Solid and liquid radioactive wastes from the dismantling activities will be treated and stored on-site awaiting final disposal. The waste treatment facilities, which are situated in other buildings at the Studsvik site, are planned to continue operation during and after the decommissioning of the reactor facility. All nuclear fuel has been transferred to a separate storage facility and is being shipped to the US according to existing agreements. The objective of the planned dismantling activities is to achieve clearance of the facility to make it possible to either demolish the buildings or use them for other purposes. The operator has divided the planning for dismantling and demolition of the facility into three phases [1]: Dismantling 1, including primary system decontamination, dismantling of the reactors with systems in the reactor pool, draining, cleaning and temporary covering of the reactor pool. This phase has begun and is due to last till approximately December 2009. Dismantling 2, including dismantling of systems in the reactor facility, removal of equipment, radiological

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

    Directory of Open Access Journals (Sweden)

    Das Arpita

    2005-05-01

    Full Text Available Abstract Background 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. Results 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. Conclusion A combination of empirical sequencing and retrieval of unannotated Genome Survey Sequence database entries was successfully used to construct a full-length representative of

  14. E2C(R2) Periodic Benefit-Risk Evaluation Report and E2C(R2) Periodic Benefit-Risk Evaluation Report--Questions and Answers; International Council for Harmonisation; Guidances for Industry; Availability. Notice.

    Science.gov (United States)

    2016-07-19

    The Food and Drug Administration (FDA or Agency) is announcing the availability of guidances for industry entitled ``E2C(R2) Periodic Benefit-Risk Evaluation'' (E2C(R2) guidance) and ``E2C(R2) Periodic Benefit-Risk Evaluation Report--Questions and Answers'' (E2C(R2) Q&A guidance). These guidances were prepared under the auspices of the International Council for Harmonisation (ICH), formerly the International Conference on Harmonisation. The E2C(R2) draft guidance, issued April 11, 2012, updated and combined two ICH guidances, ``E2C Clinical Safety Data Management: Periodic Safety Update Reports for Marketed Drugs'' (E2C guidance) and ``Addendum to E2C Clinical Safety Data Management: Periodic Safety Update Reports for Marketed Drugs'' (addendum to the E2C guidance). The E2C(R2) guidance is intended to describe the format, content, and timing of a Periodic Benefit-Risk Evaluation Report (PBRER) for an approved drug or biologic, and it finalizes the draft guidance. The E2C(R2) Q&A guidance is a supplementary guidance that is intended to clarify key issues in the E2C(R2) guidance.

  15. A sugarcane R2R3-MYB transcription factor gene is alternatively spliced during drought stress

    Science.gov (United States)

    Guo, Jinlong; Ling, Hui; Ma, Jingjing; Chen, Yun; Su, Yachun; Lin, Qingliang; Gao, Shiwu; Wang, Hengbo; Que, Youxiong; Xu, Liping

    2017-01-01

    MYB transcription factors of the R2R3-MYB family have been shown to play important roles in many plant processes. A sugarcane R2R3-MYB gene (ScMYB2) and its two alternative forms of transcript (ScMYB2S1 and ScMYB2S2) were identified in this study. The deduced protein of ScMYB2S1 is a typical plant R2R3-MYB protein, while ScMYB2S2 encodes a truncated protein. Real-time qPCR analysis revealed that ScMYB2S1 is suppressed under PEG-simulated drought stress in sugarcane, while ScMYB2S2 is induced at later treatment stage. A senescence symptom was observed when ScMYB2S1 was injected into tobacco leaves mediated by Agrobacterium, but no symptom for ScMYB2S2. Further investigation showed that the expression levels of 4 senescence-associated genes, NtPR-1a, NtNYC1, NtCAT3 and NtABRE, were markedly induced in tobacco leaves after ScMYB2S1-injection, while they were not sensitive to ScMYB2S2-injection. Moreover, MDA and proline were also investigated after injection. Similarly, MDA and proline levels were induced by ABA and ScMYB2S1, while inhibited by ScMYB2S2. We propose that ScMYB2, by alternatively splicing two transcripts (ScMYB2S1 and ScMYB2S2), is involved in an ABA-mediated leaf senescence signaling pathway and play positive role in respond to drought-induced senescence in sugarcane. The results of this study provide information for further research in sugarcane stress processes. PMID:28167824

  16. The Onion (Allium cepa L.) R2R3-MYB Gene MYB1 Regulates Anthocyanin Biosynthesis.

    Science.gov (United States)

    Schwinn, Kathy E; Ngo, Hanh; Kenel, Fernand; Brummell, David A; Albert, Nick W; McCallum, John A; Pither-Joyce, Meeghan; Crowhurst, Ross N; Eady, Colin; Davies, Kevin M

    2016-01-01

    Bulb color is an important consumer trait for onion (Allium cepa L., Allioideae, Asparagales). The bulbs accumulate a range of flavonoid compounds, including anthocyanins (red), flavonols (pale yellow), and chalcones (bright yellow). Flavonoid regulation is poorly characterized in onion and in other plants belonging to the Asparagales, despite being a major plant order containing many important crop and ornamental species. R2R3-MYB transcription factors associated with the regulation of distinct branches of the flavonoid pathway were isolated from onion. These belonged to sub-groups (SGs) that commonly activate anthocyanin (SG6, MYB1) or flavonol (SG7, MYB29) production, or repress phenylpropanoid/flavonoid synthesis (SG4, MYB4, MYB5). MYB1 was demonstrated to be a positive regulator of anthocyanin biosynthesis by the induction of anthocyanin production in onion tissue when transiently overexpressed and by reduction of pigmentation when transiently repressed via RNAi. Furthermore, ectopic red pigmentation was observed in garlic (Allium sativum L.) plants stably transformed with a construct for co-overexpression of MYB1 and a bHLH partner. MYB1 also was able to complement the acyanic petal phenotype of a defined R2R3-MYB anthocyanin mutant in Antirrhinum majus of the asterid clade of eudicots. The availability of sequence information for flavonoid-related MYBs from onion enabled phylogenetic groupings to be determined across monocotyledonous and dicotyledonous species, including the identification of characteristic amino acid motifs. This analysis suggests that divergent evolution of the R2R3-MYB family has occurred between Poaceae/Orchidaceae and Allioideae species. The DNA sequences identified will be valuable for future analysis of classical flavonoid genetic loci in Allium crops and will assist the breeding of these important crop species.

  17. The Onion (Allium cepa L.) R2R3-MYB Gene MYB1 Regulates Anthocyanin Biosynthesis

    Science.gov (United States)

    Schwinn, Kathy E.; Ngo, Hanh; Kenel, Fernand; Brummell, David A.; Albert, Nick W.; McCallum, John A.; Pither-Joyce, Meeghan; Crowhurst, Ross N.; Eady, Colin; Davies, Kevin M.

    2016-01-01

    Bulb color is an important consumer trait for onion (Allium cepa L., Allioideae, Asparagales). The bulbs accumulate a range of flavonoid compounds, including anthocyanins (red), flavonols (pale yellow), and chalcones (bright yellow). Flavonoid regulation is poorly characterized in onion and in other plants belonging to the Asparagales, despite being a major plant order containing many important crop and ornamental species. R2R3-MYB transcription factors associated with the regulation of distinct branches of the flavonoid pathway were isolated from onion. These belonged to sub-groups (SGs) that commonly activate anthocyanin (SG6, MYB1) or flavonol (SG7, MYB29) production, or repress phenylpropanoid/flavonoid synthesis (SG4, MYB4, MYB5). MYB1 was demonstrated to be a positive regulator of anthocyanin biosynthesis by the induction of anthocyanin production in onion tissue when transiently overexpressed and by reduction of pigmentation when transiently repressed via RNAi. Furthermore, ectopic red pigmentation was observed in garlic (Allium sativum L.) plants stably transformed with a construct for co-overexpression of MYB1 and a bHLH partner. MYB1 also was able to complement the acyanic petal phenotype of a defined R2R3-MYB anthocyanin mutant in Antirrhinum majus of the asterid clade of eudicots. The availability of sequence information for flavonoid-related MYBs from onion enabled phylogenetic groupings to be determined across monocotyledonous and dicotyledonous species, including the identification of characteristic amino acid motifs. This analysis suggests that divergent evolution of the R2R3-MYB family has occurred between Poaceae/Orchidaceae and Allioideae species. The DNA sequences identified will be valuable for future analysis of classical flavonoid genetic loci in Allium crops and will assist the breeding of these important crop species. PMID:28018399

  18. Quantum gravity corrections to the standard model Higgs in Einstein and $R^2$ gravity

    CERN Document Server

    Abe, Yugo; Inami, Takeo

    2016-01-01

    We evaluate quantum gravity corrections to the standard model Higgs potential $V(\\phi)$ a la Coleman-Weinberg and examine the stability question of $V(\\phi)$ at scales of Planck mass $M_{\\rm Pl}$. We compute the gravity one-loop corrections by using the momentum cut-off in Einstein gravity. The gravity corrections affect the potential in a significant manner for the value of $\\Lambda= (1 - 3)M_{\\rm Pl}.$ In view of reducing the UV cut-off dependence we also make a similar study in the $R^2$ gravity.

  19. Accretion disks around neutron and strange stars in $\\mathcal{R}^2$ gravity

    CERN Document Server

    Staykov, Kalin V; Yazadjiev, Stoytcho S

    2016-01-01

    We study the electromagnetic spectrum of accretion disks around neutron and strange stars in $\\mathcal{R}^2$ gravity. Both static and rapidly rotating models are investigated. The results are compared with the General Relativistic results. We found difference between the results in both theories of about 50\\% for the electromagnetic flux and about 20\\% in the luminosity for models with equal mass and angular velocity in both theories. The observed differences are much lower for models rotating with Kelperian velocity and with equal masses.

  20. Rolling Deck to Repository (R2R): Big Data and Standard Services for the Fleet Community

    Science.gov (United States)

    Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Smith, S. R.; Stocks, K. I.

    2014-12-01

    The Rolling Deck to Repository (R2R; http://rvdata.us/) program curates underway environmental sensor data from the U.S. academic oceanographic research fleet, ensuring data sets are routinely and consistently documented, preserved in long-term archives, and disseminated to the science community. Currently 25 in-service vessels contribute 7 terabytes of data to R2R each year, acquired from a full suite of geophysical, oceanographic, meteorological, and navigational sensors on over 400 cruises worldwide. To accommodate this large volume and variety of data, R2R has developed highly efficient stewardship procedures. These include scripted "break out" of cruise data packages from each vessel based on standard filename and directory patterns; automated harvest of cruise metadata from the UNOLS Office via Web Services and from OpenXML-based forms submitted by vessel operators; scripted quality assessment routines that calculate statistical summaries and standard ratings for selected data types; adoption of community-standard controlled vocabularies for vessel codes, instrument types, etc, provided by the NERC Vocabulary Server, in lieu of maintaining custom local term lists; and a standard package structure based on the IETF BagIt format for delivering data to long-term archives. Documentation and standard post-field products, including quality-controlled shiptrack navigation data for every cruise, are published in multiple services and formats to satisfy a diverse range of clients. These include Catalog Service for Web (CSW), GeoRSS, and OAI-PMH discovery services via a GeoNetwork portal; OGC Web Map and Feature Services for GIS clients; a citable Digital Object Identifier (DOI) for each dataset; ISO 19115-2 standard geospatial metadata records suitable for submission to long-term archives as well as the POGO global catalog; and Linked Open Data resources with a SPARQL query endpoint for Semantic Web clients. R2R participates in initiatives such as the Ocean Data

  1. Degradation and stability of R2R manufactured polymer solar cells

    DEFF Research Database (Denmark)

    Norrman, Kion; Krebs, Frederik C

    2009-01-01

    Polymer solar cells have many advantages such as light weight, flexibility, environmental friendliness, low thermal budget, low cost and most notably very fast modes of production by printing techniques. Production experiments have shown that it is highly feasible with existing technology to mass...... produce polymer solar cells at a very low cost. We have employed state-of-the-art analytical techniques to address the challenging issues of degradation and stability of R2R manufactured devices. We have specifically studied the relative effect of oxygen and water on the operational devices in regard...

  2. Optimum Kinematic Design of the 4R 2-DOF Parallel Mechanism

    Institute of Scientific and Technical Information of China (English)

    XIE Fugui; LIU Xinjun; WANG Liping; WANG Jinsong

    2009-01-01

    This paper analyzes the kinematic optimization design of the 4R 2-DOF parallel mechanism taking into account the force transmissibility. Three indices are introduced to reflect the force transmissibility. Based on these indices and their performance charts, the optimization design process with respect to the work-space is presented in detail. The results show that the designed mechanism is not only far from every sin-gularity but also has good force transmissibility in its workspace. These kinematic optimization indices can be extended to other parallel mechanisms.

  3. Recursion Formulae for Obtaining Surfaces with Constant Mean Curvature in R2,1

    Institute of Scientific and Technical Information of China (English)

    TIAN Yong-Bo; NAN Zhi-Jie; TIAN Chou

    2007-01-01

    Though the B(a)cklund transformation on time-like surfaces with constant mean curvature surfaces in R2,1 has been obtained,it is not easy to obtain corresponding surfaces because the procedure of solving the related integrable system cannot be avoided when the B(a)cklund transformation is used.For sake of this,in this article,some special work is done to reform the B(a)cklund transformation to a recursion formula,by which we can construct time-like surfaces with constant mean curvature form known ones just by quadrature procedure.

  4. The cumulative influence of hyperoxia and hypercapnia on blood oxygenation and R2*

    Science.gov (United States)

    Faraco, Carlos C; Strother, Megan K; Siero, Jeroen CW; Arteaga, Daniel F; Scott, Allison O; Jordan, Lori C; Donahue, Manus J

    2015-01-01

    Cerebrovascular reactivity (CVR)-weighted blood-oxygenation-level-dependent magnetic resonance imaging (BOLD-MRI) experiments are frequently used in conjunction with hyperoxia. Owing to complex interactions between hyperoxia and hypercapnia, quantitative effects of these gas mixtures on BOLD responses, blood and tissue R2*, and blood oxygenation are incompletely understood. Here we performed BOLD imaging (3 T; TE/TR=35/2,000 ms; spatial resolution=3 × 3 × 3.5 mm3) in healthy volunteers (n=12; age=29±4.1 years) breathing (i) room air (RA), (ii) normocapnic–hyperoxia (95% O2/5% N2, HO), (iii) hypercapnic–normoxia (5% CO2/21% O2/74% N2, HC-NO), and (iv) hypercapnic–hyperoxia (5% CO2/95% O2, HC-HO). For HC-HO, experiments were performed with separate RA and HO baselines to control for changes in O2. T2-relaxation-under-spin-tagging MRI was used to calculate basal venous oxygenation. Signal changes were quantified and established hemodynamic models were applied to quantify vasoactive blood oxygenation, blood–water R2*, and tissue–water R2*. In the cortex, fractional BOLD changes (stimulus/baseline) were HO/RA=0.011±0.007; HC-NO/RA=0.014±0.004; HC-HO/HO=0.020±0.008; and HC-HO/RA=0.035±0.010; for the measured basal venous oxygenation level of 0.632, this led to venous blood oxygenation levels of 0.660 (HO), 0.665 (HC-NO), and 0.712 (HC-HO). Interleaving a HC-HO stimulus with HO baseline provided a smaller but significantly elevated BOLD response compared with a HC-NO stimulus. Results provide an outline for how blood oxygenation differs for several gas stimuli and provides quantitative information on how hypercapnic BOLD CVR and R2* are altered during hyperoxia. PMID:26174329

  5. R2R-koneen rainanohjausjärjestelmän kehittäminen

    OpenAIRE

    Tervo, Jarno

    2015-01-01

    Tässä opinnäytetyössä kehitettiin Oulun Ammattikorkeakoulu Oy:n Prinlab-osaston painettavan elektroniikan R2R-painokoneen rainanohjausjärjestelmää. Painokoneessa esiintyi materiaalirainan sivuttaissuuntaista siirtymää ja vääntymää, jotka vaikuttivat rainan kelauksen laatuun. Työn tavoitteena oli tuottaa rainanohjausmenetelmistä esiselvitykset ja niiden kustannusarviointi, joita työn tilaaja voi käyttää tulevien projektien arvioinnin tukena. Ongelmaa ratkaistiin haastattelemalla ensin...

  6. Rolling Deck to Repository (R2R): Linking and Integrating Data for Oceanographic Research

    Science.gov (United States)

    Arko, R. A.; Chandler, C. L.; Clark, P. D.; Shepherd, A.; Moore, C.

    2012-12-01

    The Rolling Deck to Repository (R2R) program is developing infrastructure to ensure the underway sensor data from NSF-supported oceanographic research vessels are routinely and consistently documented, preserved in long-term archives, and disseminated to the science community. We have published the entire R2R Catalog as a Linked Data collection, making it easily accessible to encourage linking and integration with data at other repositories. We are developing the R2R Linked Data collection with specific goals in mind: 1.) We facilitate data access and reuse by providing the richest possible collection of resources to describe vessels, cruises, instruments, and datasets from the U.S. academic fleet, including data quality assessment results and clean trackline navigation. We are leveraging or adopting existing community-standard concepts and vocabularies, particularly concepts from the Biological and Chemical Oceanography Data Management Office (BCO-DMO) ontology and terms from the pan-European SeaDataNet vocabularies, and continually re-publish resources as new concepts and terms are mapped. 2.) We facilitate data citation through the entire data lifecycle from field acquisition to shoreside archiving to (ultimately) global syntheses and journal articles. We are implementing globally unique and persistent identifiers at the collection, dataset, and granule levels, and encoding these citable identifiers directly into the Linked Data resources. 3.) We facilitate linking and integration with other repositories that publish Linked Data collections for the U.S. academic fleet, such as BCO-DMO and the Index to Marine and Lacustrine Geological Samples (IMLGS). We are initially mapping datasets at the resource level, and plan to eventually implement rule-based mapping at the concept level. We work collaboratively with partner repositories to develop best practices for URI patterns and consensus on shared vocabularies. The R2R Linked Data collection is implemented as a

  7. Lagrangian Submanifolds Foliated by (n-1)-spheres in R2n

    Institute of Scientific and Technical Information of China (English)

    Henri ANCIAUX; Ildefonso CASTRO; Pascal ROMON

    2006-01-01

    We study Lagrangian submanifolds foliated by (n-1)-spheres in R2n for n≥3. We give a general parametrization for such submanifolds, and refine that description when the submanifold is special Lagrangian, self-similar, Hamiltonian stationary or has mean curvature vector of constant length. In all these cases, the submanifold is centered, i.e. invariant under the action of SO(n). It suffices then to solve a simple ODE in two variables to describe the geometry of the solutions.

  8. Synthesis of Quinolone Analogues:7-[(2S, 4R)-2-Aminomethyl-4- hydroxypyrrolidin-1-yl] Quinolones

    Institute of Scientific and Technical Information of China (English)

    Jiu Yu LIU; Hui Yuan GUO

    2004-01-01

    New quinolone derivatives of 7-[(2S, 4R)-2-aminomethyl-4-hydroxypyrrolidin-1-yl] quinolone-3-carboxylic acids were synthesized by condensation of 7-halo substituted quinolone-3-carboxylic acids with (2S, 4R)-2-aminomethyl-4-hydroxypyrrolidine. These compounds were characterized by FAB-MS and 1H NMR.

  9. Evaluation of Role 2 (R2) Medical Resources in the Afghanistan Combat Theater: Past, Present and Future

    Science.gov (United States)

    2016-10-01

    doctrine 39 describes R2 (E) MTFs as: small field hospital providing basic secondary health care, built around primary surgery, ICU and nursed beds. It... nurses , other licensed professionals, medics) deployed to the R2 environment. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...10 Special Reporting Requirements

  10. Practical evaluation of organic polymer thermoelectrics by large-area R2R processing on flexible substrates

    DEFF Research Database (Denmark)

    Søndergaard, Roar R.; Hösel, Markus; Espinosa Martinez, Nieves

    2013-01-01

    Here, we present a process based on roll-to-roll (R2R) technology which allows for very fast processing of polymer thermoelectric (TE) devices and we furthermore demonstrate a simplified but more efficient way of serially connecting these devices by means of R2R thin-film processing. The new device...

  11. Modulation of Sweet Taste by Umami Compounds via Sweet Taste Receptor Subunit hT1R2: e0124030

    National Research Council Canada - National Science Library

    Jaewon Shim; Hee Jin Son; Yiseul Kim; Ki Hwa Kim; Jung Tae Kim; Hana Moon; Min Jung Kim; Takumi Misaka; Mee-Ra Rhyu

    2015-01-01

    ...), in human sweet taste receptor hT1R2/hT1R3-expressing cells. The sensitivity of sucrose to hT1R2/hT1R3 was significantly attenuated by MSG and umami active peptides but not by umami active nucleotides...

  12. Natural epigenetic protection against the I-factor, a Drosophila LINE retrotransposon, by remnants of ancestral invasions.

    Science.gov (United States)

    Dramard, Xavier; Heidmann, Thierry; Jensen, Silke

    2007-03-21

    Transposable elements are major components of most eukaryotic genomes. Such sequences are generally defective for transposition and have little or no coding capacity. Because transposition can be highly mutagenic, mobile elements that remain functional are tightly repressed in all living species. Drosophila pericentromeric heterochromatin naturally contains transposition-defective, non-coding derivatives of a LINE retrotransposon related to the I-factor. The I-factor is a good model to study the regulation of transposition in vivo because, under specific conditions, current functional copies of this mobile element can transpose at high frequency, specifically in female germ cells, with deleterious effects including female sterility. However, this high transpositional activity becomes spontaneously repressed upon ageing or heat treatment, by a maternally transmitted, transgenerational epigenetic mechanism of unknown nature. We have analyzed, by quantitative real time RT-PCR, the RNA profile of the transposition-defective I-related sequences, in the Drosophila ovary during ageing and upon heat treatment, and also in female somatic tissues and in males, which are not permissive for I-factor transposition. We found evidence for a role of transcripts from these ancestral remnants in the natural epigenetic protection of the Drosophila melanogaster genome against the deleterious effects of new invasions by functional I-factors. These results provide a molecular basis for a probably widespread natural protection against transposable elements by persisting vestiges of ancient invasions.

  13. Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters.

    Science.gov (United States)

    Zanni, Vanessa; Eymery, Angéline; Coiffet, Michael; Zytnicki, Matthias; Luyten, Isabelle; Quesneville, Hadi; Vaury, Chantal; Jensen, Silke

    2013-12-03

    Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin's structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be responsible for the control of at least three transposable elements (TEs). We report its detailed structure in three different Drosophila lines chosen according to their capacity to repress or not to repress the expression of two retrotransposons named ZAM and Idefix, and we show that they display high structural diversity. Numerous rearrangements due to homologous and nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are diverse sources of active genomic variation at this locus. Notably, we evidence a correlation between the presence of ZAM and Idefix in this piRNA cluster and their silencing. They are absent from flam in the strain where they are derepressed. We show that, unexpectedly, more than half of the flam locus results from recent TE insertions and that most of the elements concerned are prone to horizontal transfer between species of the melanogaster subgroup. We build a model showing how such high and constant dynamics of a piRNA master locus open the way to continual emergence of new patterns of piRNA biogenesis leading to changes in the level of transposition control.

  14. Two variants of the Drosophila melanogaster retrotransposon gypsy (mdg4): structural and functional differences, and distribution in fly stocks.

    Science.gov (United States)

    Lyubomirskaya, N V; Smirnova, J B; Razorenova, O V; Karpova, N N; Surkov, S A; Avedisov, S N; Kim, A I; Ilyin, Y V

    2001-04-01

    Two variants of the Drosophila melanogaster retrotransposon gypsy were subjected to detailed structural and functional analysis. A series of hybrid constructs containing various combinations of "active" and "inactive" gypsy copies were tested for their ability to produce new DNA copies in cultured cells by means of reverse transcription. It was shown that the previously demonstrated variations in retrotranspositional activity are associated with either one or both of two amino acid substitutions at the beginning of ORF2. The first substitution is located at the boundary between the putative protease and reverse transcriptase domains and, hence, may influence the processing of the polyprotein. The other substitution may alter reverse transcriptase activity since it is located in the second of the seven conserved domains of the RT gene. To address the question of the evolutionary relationship between the two gypsy variants, their distribution was analyzed in among various fly stocks. Southern analysis revealed that all D. melanogaster strains studied so far contain the "inactive" gypsy variant, while the "active" copies are present only in some strains; most of the latter were established from flies recently isolated from natural populations. Finally, in stocks carrying the flamenco mutation the "active" gypsy variant is much more abundant than the "inactive" form. Possible scenarios for the orgin of the "active" form of gypsy are discussed.

  15. Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes.

    Science.gov (United States)

    Conte, Caroline; Dastugue, Bernard; Vaury, Chantal

    2002-03-01

    We recently reported a novel transposition system in which two retroelements from Drosophila melanogaster, ZAM and Idefix, are highly mobilized and preferentially insert within intergenic regions. Among the loci where new copies are detected, a hot spot for their insertion was identified at the white locus, where up to three elements occurred within a 3-kb fragment upstream of the transcriptional start site of white. We have used these insertions as molecular entry points to throw light on the mutagenic effect exerted by multiple insertions of retrotransposons within intergenic regions of a genome. Analysis of the molecular mechanisms by which ZAM and Idefix elements interfere with the regulation of the white gene has shown that ZAM bears cis-acting regulatory sequences able to enhance transcription of the white gene in the eyes of the flies. This activation may be counteracted by Idefix, which acts as an insulator able to isolate the white gene from the upstream ZAM enhancer. In addition to revealing a novel insulator sequence with its own specific features, our data clearly illustrate how retroelements can act as epigenetic factors able to interfere with the transcriptional regulation of their host.

  16. Precise excision of the retrotransposon gypsy from the forked and cut loci in a genetically unstable D. melanogaster strain.

    Science.gov (United States)

    Kuzin, A B; Lyubomirskaya, N V; Khudaibergenova, B M; Ilyin, Y V; Kim, A I

    1994-11-11

    The genetically unstable Mutator Strain of D. melanogaster is characterised by a high frequency of spontaneous mutations and their reversions. Three forked mutants were obtained independently and several reversions arose spontaneously with frequency of 10(-3)-10(-4). The sites of integration and excision of the gypsy retrotransposon were analysed by Southern blot analysis and sequencing of PCR fragments. In all cases gypsy had inserted at the end of the third exon of the major transcript of the forked gene, causing the duplication of TCCA target sequence. All the reversions resulted from precise excision of the gypsy. A double mutant containing ct6 and f1, caused by gypsy insertions into untranslated regions of the corresponding genes, was constructed. Two spontaneous ct6f+ revertants as well as one ct+f1 revertant were obtained from this line. Sequence analysis of gypsy integration and excision sites revealed that in all cases gypsy excision was also precise. These experiments constitute the first demonstration of precise excision of LTR-containing elements from their host genomes.

  17. Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups

    Directory of Open Access Journals (Sweden)

    Carareto Claudia MA

    2006-09-01

    Full Text Available Abstract Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5'LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. On the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families.

  18. 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.

  19. Distinct human and mouse membrane trafficking systems for sweet taste receptors T1r2 and T1r3.

    Science.gov (United States)

    Shimizu, Madoka; Goto, Masao; Kawai, Takayuki; Yamashita, Atsuko; Kusakabe, Yuko

    2014-01-01

    The sweet taste receptors T1r2 and T1r3 are included in the T1r taste receptor family that belongs to class C of the G protein-coupled receptors. Heterodimerization of T1r2 and T1r3 is required for the perception of sweet substances, but little is known about the mechanisms underlying this heterodimerization, including membrane trafficking. We developed tagged mouse T1r2 and T1r3, and human T1R2 and T1R3 and evaluated membrane trafficking in human embryonic kidney 293 (HEK293) cells. We found that human T1R3 surface expression was only observed when human T1R3 was coexpressed with human T1R2, whereas mouse T1r3 was expressed without mouse T1r2 expression. A domain-swapped chimera and truncated human T1R3 mutant showed that the Venus flytrap module and cysteine-rich domain (CRD) of human T1R3 contain a region related to the inhibition of human T1R3 membrane trafficking and coordinated regulation of human T1R3 membrane trafficking. We also found that the Venus flytrap module of both human T1R2 and T1R3 are needed for membrane trafficking, suggesting that the coexpression of human T1R2 and T1R3 is required for this event. These results suggest that the Venus flytrap module and CRD receive taste substances and play roles in membrane trafficking of human T1R2 and T1R3. These features are different from those of mouse receptors, indicating that human T1R2 and T1R3 are likely to have a novel membrane trafficking system.

  20. Feasibility of noninvasive quantitative measurements of intrarenal R(2) ' in humans using an asymmetric spin echo echo planar imaging sequence.

    Science.gov (United States)

    Zhang, Xiaodong; Zhang, Yudong; Yang, Xuedong; Wang, Xiaoying; An, Hongyu; Zhang, Jue; Fang, Jing

    2013-01-01

    The purpose of this study was to demonstrate the feasibility of an asymmetric spin echo (ASE) single-shot echo planar imaging (EPI) sequence for the noninvasive quantitative measurement of intrarenal R(2) ' in humans within 20 s. The reproducibility of R(2) ' measurements with the ASE-EPI sequence was assessed in nine healthy young subjects in repeated studies conducted over three consecutive days. Moreover, we also evaluated whether the ASE-EPI sequence-measured R(2) ' reflected the intrarenal oxygenation changes induced by furosemide in another group of normal human subjects (n = 10). Different flow attenuation gradients (b = 0, 40 and 80 s/mm(2) ) were utilized to examine the impact of the intravascular signal contribution on the estimation of intrarenal R(2) '. In the absence of flow dephasing gradients (b = 0 s/mm(2) ), the computed coefficient of variation (CV) of R(2) ' was 21.31 ± 4.52%, and the estimated R(2) ' value decreased slightly, but not statistically significantly (p > 0.05), after the administration of furosemide in the medullary region. However, CV of R(2) ' was much smaller in the presence of flow dephasing gradients (9.68 ± 3.58% with b = 40 s/mm(2) and 10.50 ± 3.62% with b = 80 s/mm(2) ). Moreover, a significant reduction in R(2) ' in the renal medulla was obtained (p R(2) ' measurements did not differ between the b = 40 s/mm(2) and b = 80 s/mm(2) scans, suggesting that small diffusion gradients were sufficient to minimize the intravascular signal contribution. In summary, we have demonstrated that renal R(2) ' can be obtained rapidly using an ASE-EPI sequence. The measurement was highly reproducible and reflected the expected intrarenal oxygenation changes induced by furosemide.

  1. Structural Synthesis of a Class of 2R2T Hybrid Mechanisms

    Institute of Scientific and Technical Information of China (English)

    TIAN Chunxu; FANG Yuefa; GUO Sheng

    2016-01-01

    Conventional overconstrained parallel manipulators have been widely studied both in industry and academia, however the structural synthesis of hybrid mechanisms with additional constraints is seldom studied, especially for the four degrees of freedom(DOF) hybrid mechanisms. In order to develop a manipulator with additional constraints, a class of important spatial mechanisms with coupling chains(CCs) whose motion type is two rotations and two translations(2R2T) is presented. Based on screw theory, the combination of different types of limbs which are used to construct parallel mechanisms and coupling chains is proposed. The basic types of the general parallel mechanisms and geometric conditions of the kinematic chains are given using constraint synthesis method. Moreover, the 2R2T motion pattern hybrid mechanisms which are derived by adding coupling chains between different serial kinematic chains(SKCs) of the corresponding parallel mechanisms are presented. According to the constraint analysis of the mechanisms, the movement relationship of the moving platform and the kinematic chains is derived by disassembling the coupling chains. At last, fourteen novel hybrid mechanisms with two or three serial kinematic chains are presented. The proposed novel hybrid mechanisms and construction method enrich the family of the spatial mechanisms and provide an instruction to design more complex hybrid mechanisms.

  2. Dark matter and inflation in R + ζR2 supergravity

    Science.gov (United States)

    Addazi, Andrea; Khlopov, Maxim Yu.

    2017-03-01

    As is well known, the gravitational degrees of freedom contained in R + ζR2 (super)gravity lead to Starobinsky's potential, in a one-field setting for inflationary Cosmology that appears favored by Planck data. In this letter we discuss another interesting aspect of this model, related to gravitino production, with emphasis on the corresponding mass spectrum. Assuming that supersymmetry is broken at a very high scale, Super Heavy Gravitino Dark Matter (SHGDM) and Starobinsky's inflation can be coherently unified in a R + ζR2 supergravity. Gravitinos are assumed to be the Lightest Supersymmetric Particles (LSP) and are non-thermally produced during inflation, in turn originated by a scalar with a Starobinsky's potential. Gravitino mass runs with the inflaton field, so that a continuous spectrum of superheavy gravitinos emerges. The theory is implemented with a U(1)R gauge symmetry. However, in a string UV completion, U(1)R-symmetry can be broken by non-perturbative string instantons, while for consistency of our scenario U(1)R gauge symmetry breaking must be broken in order to generate a soft mass terms for the gravitino and gauginos. R-parity violating operators can be generated at non-perturbative level. Gravitinos can decay into very energetic neutrinos and photons in cosmological time scale, with intriguing implications for high energy cosmic rays experiments.

  3. Crystallographic superstructure in R2PdSi3 compounds (R=heavy rare earth)

    Science.gov (United States)

    Tang, Fei; Frontzek, Matthias; Dshemuchadse, Julia; Leisegang, Tilmann; Zschornak, Matthias; Mietrach, Robert; Hoffmann, Jens-Uwe; Löser, Wolfgang; Gemming, Sibylle; Meyer, Dirk C.; Loewenhaupt, Michael

    2011-09-01

    The R2PdSi3 intermetallic compounds have been reported to crystallize in a hexagonal AlB2-derived structure, with the rare earth atoms on the Al sites and Pd and Si atoms randomly distributed on the B sites. However, the intricate magnetic properties observed in the series of compounds have always suggested complications to the assumed structure. To clarify the situation, x-ray and neutron diffraction measurements were performed on the heavy rare earth compounds with R=Gd, Tb, Dy, Ho, Er, Tm, which revealed the existence of a crystallographic superstructure. The superstructure features a doubled unit cell in the hexagonal basal plane and an octuplication along the perpendicular c direction with respect to the primitive cell. No structural transition was observed between 300 and 1.5 K. Extended x-ray absorption fine structure (EXAFS) analysis as well as density functional theory (DFT) calculations were utilized to investigate the local environments of the respective atoms. In this paper the various experimental results will be presented and it will be shown that the superstructure is mainly due to the Pd-Si order on the B sites. A structure model will be proposed to fully describe the superstructure of Pd-Si order in R2PdSi3. The connection between the crystallographic superstructure and the magnetic properties will be discussed in the framework of the presented model.

  4. ARCADE-R2 experiment on board BEXUS 17 stratospheric balloon

    Science.gov (United States)

    Barbetta, Marco; Boesso, Alessandro; Branz, Francesco; Carron, Andrea; Olivieri, Lorenzo; Prendin, Jacopo; Rodeghiero, Gabriele; Sansone, Francesco; Savioli, Livia; Spinello, Fabio; Francesconi, Alessandro

    2015-09-01

    This paper provides an overview of the ARCADE-R2 experiment, a technology demonstrator that aimed to prove the feasibility of small-scale satellite and/or aircraft systems with automatic (a) attitude determination, (b) control and (c) docking capabilities. The experiment embodies a simplified scenario in which an unmanned vehicle mock-up performs rendezvous and docking operations with a fixed complementary unit. The experiment is composed by a supporting structure, which holds a small vehicle with one translational and one rotational degree of freedom, and its fixed target. The dual system features three main custom subsystems: a relative infrared navigation sensor, an attitude control system based on a reaction wheel and a small-scale docking mechanism. The experiment bus is equipped with pressure and temperature sensors, and wind probes to monitor the external environmental conditions. The experiment flew on board the BEXUS 17 stratospheric balloon on October 10, 2013, where several navigation-control-docking sequences were executed and data on the external pressure, temperature, wind speed and direction were collected, characterizing the atmospheric loads applied to the vehicle. This paper describes the critical components of ARCADE-R2 as well as the main results obtained from the balloon flight.

  5. Structural synthesis of a class of 2R2T hybrid mechanisms

    Science.gov (United States)

    Tian, Chunxu; Fang, Yuefa; Guo, Sheng

    2016-07-01

    Conventional overconstrained parallel manipulators have been widely studied both in industry and academia, however the structural synthesis of hybrid mechanisms with additional constraints is seldom studied, especially for the four degrees of freedom(DOF) hybrid mechanisms. In order to develop a manipulator with additional constraints, a class of important spatial mechanisms with coupling chains(CCs) whose motion type is two rotations and two translations(2R2T) is presented. Based on screw theory, the combination of different types of limbs which are used to construct parallel mechanisms and coupling chains is proposed. The basic types of the general parallel mechanisms and geometric conditions of the kinematic chains are given using constraint synthesis method. Moreover, the 2R2T motion pattern hybrid mechanisms which are derived by adding coupling chains between different serial kinematic chains(SKCs) of the corresponding parallel mechanisms are presented. According to the constraint analysis of the mechanisms, the movement relationship of the moving platform and the kinematic chains is derived by disassembling the coupling chains. At last, fourteen novel hybrid mechanisms with two or three serial kinematic chains are presented. The proposed novel hybrid mechanisms and construction method enrich the family of the spatial mechanisms and provide an instruction to design more complex hybrid mechanisms.

  6. The star forming region Monoceros R2 as a gamma-ray source

    CERN Document Server

    Martí, Josep; Muñoz-Arjonilla, Álvaro J; Sánchez-Ayaso, Estrella; Munar-Adrover, Pere; Sánchez-Sutil, Juan R; Romero, Gustavo E; Paredes, Josep M; Combi, Jorge A

    2013-01-01

    Context. After the release of the gamma-ray source catalog produced by the Fermi satellite during its first two years of operation, a significant fraction of sources still remain unassociated at lower energies. In addition to well-known high-energy emitters (pulsars, blazars, supernova remnants, etc.) theoretical expectations predict new classes of gamma-ray sources. In particular, gamma-ray emission could be associated with some of the early phases of stellar evolution, but this interesting possibility is still poorly understood. Aims. The aim of this paper is to assess the possibility of the Fermi gamma-ray source 2FGL J0607.5-0618c being associated with the massive star forming region Monoceros R2. Methods. A multi-wavelength analysis of the Monoceros R2 region is carried out using archival data at radio, infrared, X-ray, and gamma-ray wavelengths. The resulting observational properties are used to estimate the physical parameters needed to test the different physical scenarios. Results. We confirm the 2FG...

  7. Design Concepts of Emergency Response Robot Platform K-R2D2

    Energy Technology Data Exchange (ETDEWEB)

    Noh, Sun Young; Jeong, Kyungmin [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-10-15

    From the analysis for various mobile robots competed in DARPA Robotics Challenge, there are some drawbacks in using two or four legs because bipedal locomotion is not yet suitable for maintaining stability and quadrupedal locomotion is difficult to go through narrow aisles. Motivated by the above observations, we propose a K-R2D2 robot platform with three legs arranged in the form of a triangle like as R2-D2 robot which is a fictional robot character in the Star Wars movies. This robot has 3 legs with tracks in each sole of the leg. It is statically stable since there are three contact points to ground. In addition, three legs are also possible to design a structure walking stairs that can expand and contract in the vertical direction. This paper has presented the conceptual design, it is developed on the purpose of quick response instead of emergent workers to the extreme conditions disasters. This robot is emergency response robot platform KR2D2 with three legs, which is statically stable to walk or wheel depending on the terrains and move quickly as possible as on uneven terrain or stairs.

  8. Spectral line survey of the ultracompact HII region Mon R2

    CERN Document Server

    Ginard, D; Fuente, A; Cernicharo, J; Alonso-Albi, T; Pilleri, P; Gerin, M; García-Burillo, S; Ossenkopf, V; Rizzo, J R; Kramer, C; Goicoechea, J R; Pety, J; Berné, O; Joblin, C

    2012-01-01

    Ultracompact (UC) HII regions constitute one of the earliest phases in the formation of a massive star and are characterized by extreme physical conditions (Go>10^5 Habing field and n>10^6 cm^-3). The UC HII Mon R2 is the closest one and therefore an excellent target to study the chemistry in these complex regions. We carried out a 3mm and 1mm spectral survey using the IRAM 30-m telescope towards three positions that represent different physical environments in Mon R2: (i) the ionization front (IF) at (0",0"); two peaks in the molecular cloud (ii) MP1 at the offset (+15",-15") and (iii) MP2 at the farther offset (0",40"). In addition, we carried out extensive modeling to explain the chemical differences between the three observed regions. We detected more than thirty different species. We detected SO+ and C4H suggesting that UV radiation plays an important role in the molecular chemistry of this region. We detected the typical PDR molecules CN, HCN, HCO, C2H, and c-C3H2. While the IF and the MP1 have a chemis...

  9. The Reactivation of Main-Belt Comet 324P/La Sagra (P/2010 R2)

    CERN Document Server

    Hsieh, Henry H

    2015-01-01

    We present observations using the Baade Magellan and Canada-France-Hawaii telescopes showing that main-belt comet 324P/La Sagra, formerly known as P/2010 R2, has become active again for the first time since originally observed to be active in 2010-2011. The object appears point-source-like in March and April 2015 as it approached perihelion (true anomaly of ~300 deg), but was ~1 mag brighter than expected if inactive, suggesting the presence of unresolved dust emission. Activity was confirmed by observations of a cometary dust tail in May and June 2015. We find an apparent net dust production rate of <0.1 kg/s during these observations. 324P is now the fourth main-belt comet confirmed to be recurrently active, a strong indication that its activity is driven by sublimation. It now has the largest confirmed active range of all likely main-belt comets, and also the most distant confirmed inbound activation point at R~2.8 AU. Further observations during the current active period will allow direct comparisons o...

  10. Apoptosis Induction by Targeting Interferon Gamma Receptor 2 (IFNgammaR2) in Prostate Cancer: Ligand (IFNgamma) Independent Novel Function of IFNgammaR2 as a Bax Inhibitor

    Science.gov (United States)

    2016-10-01

    Accomplished experiments 10 NFkB inhibitor ( Parthenolide ) suppressed IFNγR2 expression To develop technologies targeting IFNγR2, we proposed...inhibitor. Parthenolide is a plant-derived compound which is known to inhibit NFkB activity[9, 10]. In our preliminary study, we found that parthenolide ...line (Fig.12. We found that IFNγR2 expression was suppressed by parthenolide (from 5 uM) within 1 day after the treatment (Fig. 12 shows the result of

  11. Expanding the Chemistry of Actinide Metallocene Bromides. Synthesis, Properties and Molecular Structures of the Tetravalent and Trivalent Uranium Bromide Complexes: (C5Me4R2UBr2, (C5Me4R2U(O-2,6-iPr2C6H3(Br, and [K(THF][(C5Me4R2UBr2] (R = Me, Et

    Directory of Open Access Journals (Sweden)

    Alejandro G. Lichtscheidl

    2016-01-01

    Full Text Available The organometallic uranium species (C5Me4R2UBr2 (R = Me, Et were obtained by treating their chloride analogues (C5Me4R2UCl2 (R = Me, Et with Me3SiBr. Treatment of (C5Me4R2UCl2 and (C5Me4R2UBr2 (R = Me, Et with K(O-2,6-iPr2C6H3 afforded the halide aryloxide mixed-ligand complexes (C5Me4R2U(O-2,6-iPr2C6H3(X (R = Me, Et; X = Cl, Br. Complexes (C5Me4R2U(O-2,6-iPr2C6H3(Br (R = Me, Et can also be synthesized by treating (C5Me4R2U(O-2,6-iPr2C6H3(Cl (R = Me, Et with Me3SiBr, respectively. Reduction of (C5Me4R2UCl2 and (C5Me4R2UBr2 (R = Me, Et with KC8 led to isolation of uranium(III “ate” species [K(THF][(C5Me52UX2] (X = Cl, Br and [K(THF0.5][(C5Me4Et2UX2] (X = Cl, Br, which can be converted to the neutral complexes (C5Me4R2U[N(SiMe32] (R = Me, Et. Analyses by nuclear magnetic resonance spectroscopy, X-ray crystallography, and elemental analysis are also presented.

  12. Abnormal Ca2+ homeostasis, atrial arrhythmogenesis and sinus node dysfunction in murine hearts modelling RyR2 modification

    Directory of Open Access Journals (Sweden)

    Yanmin eZhang

    2013-06-01

    Full Text Available RyR2 mutations are implicated in catecholaminergic polymorphic ventricular tachycardia thought to result from altered myocyte Ca2+ homeostasis reflecting inappropriate ‘leakiness’ of RyR2-Ca2+ release channels arising from increases in their basal activity, alterations in their phosphorylation, or defective interactions with other molecules or ions. The latter include calstabin, calsequestrin-2, Mg2+, and extraluminal or intraluminal Ca2+. Recent clinical studies additionally associate RyR2 abnormalities with atrial arrhythmias including atrial tachycardia, fibrillation and standstill, and sinus node dysfunction. Some RyR2 mutations associated with CPVT in mouse models also show such arrhythmias that similarly correlate with altered Ca2+ homeostasis. Some examples show evidence for increased Ca2+/calmodulin-dependent protein kinase II phosphorylation of RyR2. A homozygotic RyR2-P2328S variant demonstrates potential arrhythmic substrate resulting from reduced conduction velocity in addition to delayed afterdepolarizations and ectopic action potential firing. Finally, one model with an increased RyR2 activity in the sino-atrial node shows decreased automaticity in the presence of Ca2+-dependent decreases in ICa,L and diastolic sarcoplasmic reticular Ca2+ depletion.

  13. Facilitating Semantic Interoperability Among Ocean Data Systems: ODIP-R2R Student Outcomes

    Science.gov (United States)

    Stocks, K. I.; Chen, Y.; Shepherd, A.; Chandler, C. L.; Dockery, N.; Elya, J. L.; Smith, S. R.; Ferreira, R.; Fu, L.; Arko, R. A.

    2014-12-01

    With informatics providing an increasingly important set of tools for geoscientists, it is critical to train the next generation of scientists in information and data techniques. The NSF-supported Rolling Deck to Repository (R2R) Program works with the academic fleet community to routinely document, assess, and preserve the underway sensor data from U.S. research vessels. The Ocean Data Interoperability Platform (ODIP) is an EU-US-Australian collaboration fostering interoperability among regional e-infrastructures through workshops and joint prototype development. The need to align terminology between systems is a common challenge across all of the ODIP prototypes. Five R2R students were supported to address aspects of semantic interoperability within ODIP. Developing a vocabulary matching service that links terms from different vocabularies with similar concept. The service implements Google Refine reconciliation service interface such that users can leverage Google Refine application as a friendly user interface while linking different vocabulary terms. Developing Resource Description Framework (RDF) resources that map Shipboard Automated Meteorological Oceanographic System (SAMOS) vocabularies to internationally served vocabularies. Each SAMOS vocabulary term (data parameter and quality control flag) will be described as an RDF resource page. These RDF resources allow for enhanced discoverability and retrieval of SAMOS data by enabling data searches based on parameter. Improving data retrieval and interoperability by exposing data and mapped vocabularies using Semantic Web technologies. We have collaborated with ODIP participating organizations in order to build a generalized data model that will be used to populate a SPARQL endpoint in order to provide expressive querying over our data files. Mapping local and regional vocabularies used by R2R to those used by ODIP partners. This work is described more fully in a companion poster. Making published Linked Data

  14. Identification of R2TP complex of Leishmania donovani and Plasmodium falciparum using genome wide in-silico analysis.

    Science.gov (United States)

    Ahmad, Moaz; Afrin, Farhat; Tuteja, Renu

    2013-11-01

    Recently discovered R2TP complex is an important multiprotein complex involved in multiple cellular process like snoRNP biogenesis, PIKK signaling, RNA polymerase II assembly and apoptosis. Within R2TP complex, Pih1 tightly interacts with Rvb1/Rvb2 and with Tah1 to form R2TP macromolecular complex. R2TP complex further interacts with Hsp90 to form R2TP-Hsp90 complex, which has been found critical in many cellular process. The genome wide screening of Leishmania donovani and Plasmodium falciparum led to the identification of RuvB like1, RuvB like 2, Pih1, and Tah1. Therefore, we speculate that this complex is also important for these parasites as in the yeast. The detailed analysis of crucial components of R2TP complex, Ld-RuvB like 1, and Ld-RuvB like 2, revealed the presence of characteristic motifs like DNA binding motif and ATPase motifs. Hsp90 is also reported from Leishmania donovani and Plasmodium falciparum suggesting that the R2TP complex further interacts with Hsp90 to form R2TP-Hsp90 complex. Recently it has been discovered that RuvB like proteins are overexpressed in many cancers and their ATPase activity is crucial for cancer cell proliferation and the human RuvBs have been proposed as suitable drug target for cancer. Similarly one of the Plasmodium falciparum RuvB like protein (PfRuvB3) has been found to be specific to the stage where nuclear division led multiplication of parasite take place. Considering all these it seems that the R2TP complex may be playing some critical role both in the cancer cell proliferation in human and rapid multiplication of the parasites Leishmania donovani and Plasmodium falciparum.

  15. The essential role of AMPA receptor GluR2 subunit RNA editing in the normal and diseased brain

    Directory of Open Access Journals (Sweden)

    Amanda Lorraine Wright

    2012-04-01

    Full Text Available AMPA receptors are comprised of different combinations of GluR1-GluR4 (also known as GluA1-GluA4 and GluR-A to GluR-D subunits. The GluR2 subunit is subject to Q/R site RNA editing by the ADAR2 enzyme, which converts a codon for glutamine (Q, present in the GluR2 gene, to a codon for arginine (R found in the mRNA. AMPA receptors are calcium (Ca2+-permeable if they contain the unedited GluR2(Q subunit or if they lack the GluR2 subunit. While most AMPA receptors in the brain contain the edited GluR2(R subunit and are therefore Ca2+-impermeable, recent evidence suggests that Ca2+-permeable GluR2-lacking AMPA receptors are important in synaptic plasticity and learning. However, the presence of Ca2+-permeable AMPA receptors containing unedited GluR2 leads to excitotoxic cell loss. Recent studies have indicated that RNA editing of GluR2 is deregulated in diseases, such as amyotrophic lateral sclerosis (ALS, as well in acute neurodegenerative conditions, such as ischemia. More recently, studies have investigated the regulation of RNA editing and possible causes for its deregulation during disease. In this review, we will explore the role of GluR2 RNA editing in the healthy and diseased brain and outline new insights into the mechanisms that control this process.

  16. Engineered Serratia marcescens for efficient (3R)-acetoin and (2R,3R)-2,3-butanediol production.

    Science.gov (United States)

    Bai, Fangmin; Dai, Lu; Fan, Jiying; Truong, Ngoctu; Rao, Ben; Zhang, Liaoyuan; Shen, Yaling

    2015-05-01

    (3R)-Acetoin and (2R,3R)-2,3-butanediol are important pharmaceutical intermediates. However, until now, the quantity of natural microorganisms with the ability to produce single configuration of optically pure (3R)-acetoin and (2R,3R)-2,3-butanediol is rare. In this study, a meso-2,3-butanediol dehydrogenase encoded by the slaC gene from Serratia marcescens MG1 was identified for meso-2,3-butanediol and (2S,3S)-2,3-butanediol biosynthesis. Inactivation of the slaC gene could significantly decrease meso-2,3-butanediol and (2S,3S)-2,3-butanediol and result in a large quantity of (3R)-acetoin accumulation. Furthermore, a (2R,3R)-2,3-butanediol dehydrogenase encoded by the bdhA gene from Bacillus subtilis 168 was introduced into the slaC mutant strain of Serratia marcescens MG1. Excess (2R,3R)-2,3-butanediol dehydrogenase could accelerate the reaction from (3R)-acetoin to (2R,3R)-2,3-butanediol and lead to (2R,3R)-2,3-butanediol accumulation. In fed-batch fermentation, the excess (2R,3R)-2,3-butanediol dehydrogenase expression strain could produce 89.81 g/l (2R,3R)-2,3-butanediol with a productivity of 1.91 g/l/h at 48 h. These results provided potential applications for (3R)-acetoin and (2R,3R)-2,3-butanediol production.

  17. Crystalline structure of N-(S)-2-heptyl (1R,2R)-2-(2,3-anthracenedicarboximido)cyclohexanecarboxamide that differs from its preferred conformation in the solvent used for crystallization.

    Science.gov (United States)

    Akasaka, Kazuaki; Ohtaki, Takashi; Kabuto, Chizuko; Kitahara, Takeshi; Ohrui, Hiroshi

    2005-10-01

    The crystalline structure of N-(S)-2-heptyl (1R,2R)-2-(2,3-anthracenedicarboximido)cyclohexamide (1), which was crystallized from methanol, was determined by an X-ray analysis and had a different conformation from its preferred one in CD3OD by a 1H-NMR analysis. Inter- and intra-molecular CH-pi interaction in a crystal plays a very important role in crystal packing. The preferred conformation of the amide derivative in a solution allows us to exploit (1R,2R)-2-(2,3-anthracenedicarboximido)cyclohexanecarbonyl chloride as a conversion reagent to determine the absolute configuration of chiral amines by 1H-NMR.

  18. 一套仿ProAc R2.5的Hi-End级DIY音箱

    Institute of Scientific and Technical Information of China (English)

    谈耀明

    2005-01-01

    近20年来,最成功的英国音箱莫过于B&W和ProAc等少数几个品牌的产品,尤其是ProAc(中文译为“贵族”)。它的中档Tablette系列历久不衰,受到许多发烧友追捧,是ProAc最畅销的产品,但代表ProAc最高水平的却是Response系列音箱。该系列音箱面世以来反应热烈,最成功的设计要算Response 2.5(以下简称“R2.5”)中小型落地箱。

  19. The ICH S5(R2) guideline for the testing of medicinal agents.

    Science.gov (United States)

    Wise, L David

    2013-01-01

    Relying on previous regulatory guidelines from multiple countries, the ICH S5(R2) guideline outlines the preclinical safety studies needed for registration of new medicinal products in the member countries (European Union, Japan, and the United States). The primary purpose of the guideline is to provide a testing strategy to detect and reveal toxicity to the reproductive system including development of the embryo. There are basically three study designs outlined by the guidance, assessment of fertility in adults, pre- and postnatal development of exposed offspring, and morphological evaluation following exposure during major organogenesis. This chapter discusses the major points addressed in the guidance for each study type, and points to additional references that discuss the practical details for conducting such studies.

  20. Spectral line survey of the ultracompact HII region Monoceros R2

    Science.gov (United States)

    Ginard, D.; González-García, M.; Fuente, A.; Cernicharo, J.; Alonso-Albi, T.; Pilleri, P.; Gerin, M.; García-Burillo, S.; Ossenkopf, V.; Rizzo, J. R.; Kramer, C.; Goicoechea, J. R.; Pety, J.; Berné, O.; Joblin, C.

    2012-07-01

    Context. Ultracompact (UC) Hii regions constitute one of the earliest phases in the formation of a massive star and are characterized by extreme physical conditions (G0 > 105 Habing field and n > 106 cm-3). The UC Hii Mon R2 is the closest example and an excellent target to study the chemistry in these complex regions. Aims: Our goal is to investigate the chemistry of the molecular gas around UC Hii Mon R2 and the variations caused by the different local physical conditions. Methods: We carried out 3 mm and 1 mm spectral surveys using the IRAM 30-m telescope towards three positions that represent different physical environments in Mon R2: (i) the ionization front (IF) at (0″, 0″), and two peaks in the molecular cloud; (ii) molecular Peak 1 (hereafter MP1) at the offset (+15″, -15″); and (iii) molecular Peak 2 (hereafter MP2) at the farther offset (0″, 40″). In addition, we carried out extensive modeling to explain the chemical differences between the three observed regions. Results: We detected more than 30 different species (including isotopologues and deuterated compounds). In particular, we detected SO+ and C4H confirming that ultraviolet (UV) radiation plays an important role in the molecular chemistry of this region. In agreement with this interpretation, we detected the typical photo-dissociation region (PDR) molecules CN, HCN, HCO, C2H, and c-C3H2. There are chemical differences between the observed positions. While the IF and the MP1 have a chemistry similar to that found in high UV field and dense PDRs such as the Orion Bar, the MP2 is similar to lower UV/density PDRs such as the Horsehead nebula. Our chemical modeling supports this interpretation. In addition to the PDR-like species, we detected complex molecules such as CH3CN, H2CO, HC3N, CH3OH, and CH3C2H that are not usually found in PDRs. The sulfur compounds CS, HCS+, C2S, H2CS, SO, and SO2 and the deuterated species DCN and C2D were also identified. The origin of these complex species

  1. Problems with change in R2 as applied to theory of reasoned action research.

    Science.gov (United States)

    Trafimow, David

    2004-12-01

    The paradigm of choice for theory of reasoned action research seems to depend largely on the notion of change in variance accounted for (DeltaR2) as new independent variables are added to a multiple regression equation. If adding a particular independent variable of interest increases the variance in the dependent variable that can be accounted for by the list of independent variables, then the research is deemed to be 'successful', and the researcher is considered to have made a convincing argument about the importance of the new variable. In contrast to this trend, I present arguments that suggest serious problems with the paradigm, and conclude that studies on attitude-behaviour relations would advance the field of psychology to a far greater extent if researchers abandoned it.

  2. Geometric Flows and Perelman's Thermodynamics for Black Ellipsoids in $R^2$ and Einstein Gravity Theories

    CERN Document Server

    Gheorghiu, Tamara; Vacaru, Olivia; Vacaru, Sergiu I

    2016-01-01

    We study geometric relativistic flow and Ricci soliton equations which (for respective nonholonomic constraints and self-similarity conditions) are equivalent to the gravitational field equations of $R^2$ gravity and/or to the Einstein equations with scalar field in general relativity, GR. Perelman's functionals are generalized for modified gravity theories, MGTs, which allows to formulate an analogous statistical thermodynamics for geometric flows and Ricci solitons. There are constructed and analyzed generic off-diagonal black ellipsoid, black hole and solitonic exact solutions in MGTs and GR encoding geometric flow evolution scenarios and nonlinear parametric interactions. Such new classes of solutions in MGTs can be with polarized and/or running constants, nonholonomically deformed horizons and/or imbedded self-consistently into solitonic backgrounds. They exist also in GR as generic off-diagonal vacuum configurations with effective cosmological constant and/or mimicking effective scalar field interaction...

  3. Enzymatic Enantioselective Synthesis of (R)-2-Trimethylsilyl-2-hydroxyl-propionitrile by Defatted Apple Seed Meal

    Institute of Scientific and Technical Information of China (English)

    LI, Ning; ZONG,Min-Hua; WANG, Ju-Fang; LIU, Chen; WU, Hong

    2003-01-01

    The enantioselective synthesis of (R)-2-trimethylsilyl-2-hydroxyl-propionitrile by ( R )-oxynitrilase contained in defatted apple seed meal in a biphasic system was successfully performed. The influences of some factors on the reaction were investigated systematically. Diisopropyl ether was found to be the best for this reaction among all the organic solvents examined. The optimal concentration of defatted apple seed meal, aqueous phase content, concentrations of acetyltrimethylsilane and acetone cyanohydrin, buffer pH, reaction temperature were 4% (W/V),23% (V/V), 20 mmol.L-1, 40 mmol.L-1, pH=5.0 and 40 ℃, respectively, under which the initial reaction rate, substrate conversion and product enantiomeric excess were 9.4mmol.L-1·h-1, 99% and > 99%, respectively.

  4. Biped 4R2C six-bar mechanism with inner and outer feet

    Science.gov (United States)

    Liu, Chao; Wang, Hao; Yao, Yan-an

    2016-01-01

    Most current biped robots are equipped with two feet arranged in the right and left which inspired by the human body system. Different from the existing configurations, a novel biped robot with inner and outer feet based on a spatial six-bar 4R2C(R and C denote revolute and cylindric joints, respectively) mechanism is proposed. It can move along a line or a curve by three walking modes that are dwell adjustment mode, limit position adjustment mode and any position adjustment mode. Kinematic, gait planning and stability analyses are performed respectively, and a prototype is developed. Lastly, a potential application is considered and two manipulating modes(sphere and cylinder manipulating modes) are carried out. This interesting mechanism feathering its single closed-chain structure and unique work performance is expected to motivate the configuration creation of biped robots.

  5. Orbital and epicyclic frequencies around neutron and strange stars in $R^2$ gravity

    CERN Document Server

    Staykov, Kalin V; Yazadjiev, Stoytcho S

    2015-01-01

    According to various models, orbital and epicyclic frequencies or some of them are related to the quasi-periodic oscillations observed in the X-ray flux of some pulsars. It is expected that they origin from the inner edge of the accretion discs, deep into the gravitational field of the compact objects. Considering the planed new generation X-ray timing observatories with large collective areas, the quasi-periodic oscillations might be excellent instrument for testing gravity in strong field regime and respectively alternative gravitational theories. We examined these frequencies for a particle on a circular orbit around neutron or strange stars in $R^2$ gravity. The case of slow rotation is considered too. All results are compared to the General Relativistic case and the deviations are commented, as well as the deviations due to the rotations in both theories.

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

    Directory of Open Access Journals (Sweden)

    Kong Yoon

    2008-10-01

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

  7. The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story.

    Science.gov (United States)

    Bousios, Alexandros; Kourmpetis, Yiannis A I; Pavlidis, Pavlos; Minga, Evangelia; Tsaftaris, Athanasios; Darzentas, Nikos

    2012-02-01

    Sireviruses are one of the three genera of Copia long terminal repeat (LTR) retrotransposons, exclusive to and highly abundant in plants, and with a unique, among retrotransposons, genome structure. Yet, perhaps due to the few references to the Sirevirus origin of some families, compounded by the difficulty in correctly assigning retrotransposon families into genera, Sireviruses have hardly featured in recent research. As a result, analysis at this key level of classification and details of their colonization and impact on plant genomes are currently lacking. Recently, however, it became possible to accurately assign elements from diverse families to this genus in one step, based on highly conserved sequence motifs. Hence, Sirevirus dynamics in the relatively obese maize genome can now be comprehensively studied. Overall, we identified >10 600 intact and approximately 28 000 degenerate Sirevirus elements from a plethora of families, some brought into the genus for the first time. Sireviruses make up approximately 90% of the Copia population and it is the only genus that has successfully infiltrated the genome, possibly by experiencing intense amplification during the last 600 000 years, while being constantly recycled by host mechanisms. They accumulate in chromosome-distal gene-rich areas, where they insert in between gene islands, mainly in preferred zones within their own genomes. Sirevirus LTRs are heavily methylated, while there is evidence for a palindromic consensus target sequence. This work brings Sireviruses in the spotlight, elucidating their lifestyle and history, and suggesting their crucial role in the current genomic make-up of maize, and possibly other plant hosts.

  8. An R2R3-MYB Transcription Factor Regulates Eugenol Production in Ripe Strawberry Fruit Receptacles.

    Science.gov (United States)

    Medina-Puche, Laura; Molina-Hidalgo, Francisco Javier; Boersma, Maaike; Schuurink, Robert C; López-Vidriero, Irene; Solano, Roberto; Franco-Zorrilla, José-Manuel; Caballero, José Luis; Blanco-Portales, Rosario; Muñoz-Blanco, Juan

    2015-06-01

    Eugenol is a volatile phenylpropanoid that contributes to flower and ripe fruit scent. In ripe strawberry (Fragaria × ananassa) fruit receptacles, eugenol is biosynthesized by eugenol synthase (FaEGS2). However, the transcriptional regulation of this process is still unknown. We have identified and functionally characterized an R2R3 MYB transcription factor (emission of benzenoid II [FaEOBII]) that seems to be the orthologous gene of PhEOBII from Petunia hybrida, which contributes to the regulation of eugenol biosynthesis in petals. The expression of FaEOBII was ripening related and fruit receptacle specific, although high expression values were also found in petals. This expression pattern of FaEOBII correlated with eugenol content in both fruit receptacle and petals. The expression of FaEOBII was repressed by auxins and activated by abscisic acid, in parallel to the ripening process. In ripe strawberry receptacles, where the expression of FaEOBII was silenced, the expression of cinnamyl alcohol dehydrogenase1 and FaEGS2, two structural genes involved in eugenol production, was down-regulated. A subsequent decrease in eugenol content in ripe receptacles was also observed, confirming the involvement of FaEOBII in eugenol metabolism. Additionally, the expression of FaEOBII was under the control of FaMYB10, another R2R3 MYB transcription factor that regulates the early and late biosynthetic genes from the flavonoid/phenylpropanoid pathway. In parallel, the amount of eugenol in FaMYB10-silenced receptacles was also diminished. Taken together, these data indicate that FaEOBII plays a regulating role in the volatile phenylpropanoid pathway gene expression that gives rise to eugenol production in ripe strawberry receptacles.

  9. EXPOSE-R2: The Astrobiological ESA Mission on Board of the International Space Station.

    Science.gov (United States)

    Rabbow, Elke; Rettberg, Petra; Parpart, Andre; Panitz, Corinna; Schulte, Wolfgang; Molter, Ferdinand; Jaramillo, Esther; Demets, René; Weiß, Peter; Willnecker, Rainer

    2017-01-01

    On July 23, 2014, the Progress cargo spacecraft 56P was launched from Baikonur to the International Space Station (ISS), carrying EXPOSE-R2, the third ESA (European Space Agency) EXPOSE facility, the second EXPOSE on the outside platform of the Russian Zvezda module, with four international astrobiological experiments into space. More than 600 biological samples of archaea, bacteria (as biofilms and in planktonic form), lichens, fungi, plant seeds, triops eggs, mosses and 150 samples of organic compounds were exposed to the harsh space environment and to parameters similar to those on the Mars surface. Radiation dosimeters distributed over the whole facility complemented the scientific payload. Three extravehicular activities later the chemical samples were returned to Earth on March 2, 2016, with Soyuz 44S, having spent 588 days in space. The biological samples arrived back later, on June 18, 2016, with 45S, after a total duration in space of 531 days. The exposure of the samples to Low Earth Orbit vacuum lasted for 531 days and was divided in two parts: protected against solar irradiation during the first 62 days, followed by exposure to solar radiation during the subsequent 469 days. In parallel to the space mission, a Mission Ground Reference (MGR) experiment with a flight identical Hardware and a complete flight identical set of samples was performed at the premises of DLR (German Aerospace Center) in Cologne by MUSC (Microgravity User Support Center), according to the mission data either downloaded from the ISS (temperature data, facility status, inner pressure status) or provided by RedShift Design and Engineering BVBA, Belgium (calculated ultra violet radiation fluence data). In this paper, the EXPOSE-R2 facility, the experimental samples, mission parameters, environmental parameters, and the overall mission and MGR sequences are described, building the background for the research papers of the individual experiments, their analysis and results.

  10. EXPOSE-R2: The Astrobiological ESA Mission on Board of the International Space Station

    Directory of Open Access Journals (Sweden)

    Elke Rabbow

    2017-08-01

    Full Text Available On July 23, 2014, the Progress cargo spacecraft 56P was launched from Baikonur to the International Space Station (ISS, carrying EXPOSE-R2, the third ESA (European Space Agency EXPOSE facility, the second EXPOSE on the outside platform of the Russian Zvezda module, with four international astrobiological experiments into space. More than 600 biological samples of archaea, bacteria (as biofilms and in planktonic form, lichens, fungi, plant seeds, triops eggs, mosses and 150 samples of organic compounds were exposed to the harsh space environment and to parameters similar to those on the Mars surface. Radiation dosimeters distributed over the whole facility complemented the scientific payload. Three extravehicular activities later the chemical samples were returned to Earth on March 2, 2016, with Soyuz 44S, having spent 588 days in space. The biological samples arrived back later, on June 18, 2016, with 45S, after a total duration in space of 531 days. The exposure of the samples to Low Earth Orbit vacuum lasted for 531 days and was divided in two parts: protected against solar irradiation during the first 62 days, followed by exposure to solar radiation during the subsequent 469 days. In parallel to the space mission, a Mission Ground Reference (MGR experiment with a flight identical Hardware and a complete flight identical set of samples was performed at the premises of DLR (German Aerospace Center in Cologne by MUSC (Microgravity User Support Center, according to the mission data either downloaded from the ISS (temperature data, facility status, inner pressure status or provided by RedShift Design and Engineering BVBA, Belgium (calculated ultra violet radiation fluence data. In this paper, the EXPOSE-R2 facility, the experimental samples, mission parameters, environmental parameters, and the overall mission and MGR sequences are described, building the background for the research papers of the individual experiments, their analysis and results.

  11. On supersymmetric geometric flows and R2 inflation from scale invariant supergravity

    Science.gov (United States)

    Rajpoot, Subhash; Vacaru, Sergiu I.

    2017-09-01

    Models of geometric flows pertaining to R2 scale invariant (super) gravity theories coupled to conformally invariant matter fields are investigated. Related to this work are supersymmetric scalar manifolds that are isomorphic to the Kählerian spaces Mn = SU(1 , 1 + k) / U(1) × SU(1 + k) as generalizations of the non-supersymmetric analogs with SO(1 , 1 + k) / SO(1 + k) manifolds. For curved superspaces with geometric evolution of physical objects, a complete supersymmetric theory has to be elaborated on nonholonomic (super) manifolds and bundles determined by non-integrable superdistributions with additional constraints on (super) field dynamics and geometric evolution equations. We also consider generalizations of Perelman's functionals using such nonholonomic variables which result in the decoupling of geometric flow equations and Ricci soliton equations with supergravity modifications of the R2 gravity theory. As such, it is possible to construct exact non-homogeneous and locally anisotropic cosmological solutions for various types of (super) gravity theories modeled as modified Ricci soliton configurations. Such solutions are defined by employing the general ansatz encompassing coefficients of generic off-diagonal metrics and generalized connections that depend generically on all spacetime coordinates. We consider nonholonomic constraints resulting in diagonal homogeneous configurations encoding contributions from possible nonlinear parametric geometric evolution scenarios, off-diagonal interactions and anisotropic polarization/modification of physical constants. In particular, we analyze small parametric deformations when the underlying scale symmetry is preserved and the nontrivial anisotropic vacuum corresponds to generalized de Sitter spaces. Such configurations may mimic quantum effects whenever transitions to flat space are possible. Our approach allows us to generate solutions with scale violating terms induced by geometric flows, off

  12. An R2R3-MYB Transcription Factor Regulates Capsaicinoid Biosynthesis.

    Science.gov (United States)

    Arce-Rodríguez, Magda L; Ochoa-Alejo, Neftalí

    2017-07-01

    Capsaicinoids are responsible for the hot taste of chili peppers. They are restricted to the genus Capsicum and are synthesized by the acylation of the aromatic compound vanillylamine (derived from the phenylpropanoid pathway) with a branched-chain fatty acid by the catalysis of the putative enzyme capsaicinoid synthase. R2R3-MYB transcription factors have been reported in different species of plants as regulators of structural genes of the phenylpropanoid pathway; therefore, we hypothesized that MYB genes might be involved in the regulation of the biosynthesis of pungent compounds. In this study, an R2R3-MYB transcription factor gene, designated CaMYB31, was isolated and characterized in Capsicum annuum 'Tampiqueño 74'. Bioinformatic analysis suggested that CaMYB31 could be involved in secondary metabolism, stress and plant hormone responses, and development. CaMYB31 expression analysis from placental tissue of pungent and nonpungent chili pepper fruits showed a positive correlation with the structural genes Ca4H, Comt, Kas, pAmt, and AT3 expression and also with the content of capsaicin and dihydrocapsacin during fruit development. However, CaMYB31 also was expressed in vegetative tissues (leaves, roots, and stems). Moreover, CaMYB31 silencing significantly reduced the expression of capsaicinoid biosynthetic genes and the capsaicinoid content. Additionally, CaMYB31 expression was affected by the plant hormones indoleacetic acid, jasmonic acid, salicylic acid, and gibberellic acid or by wounding, temperature, and light, factors known to affect the production of capsaicinoids. These findings indicate that CaMYB31 is indeed involved in the regulation of structural genes of the capsaicinoid biosynthetic pathway. © 2017 American Society of Plant Biologists. All Rights Reserved.

  13. An R2R3-MYB Transcription Factor Regulates Capsaicinoid Biosynthesis1[OPEN

    Science.gov (United States)

    Arce-Rodríguez, Magda L.

    2017-01-01

    Capsaicinoids are responsible for the hot taste of chili peppers. They are restricted to the genus Capsicum and are synthesized by the acylation of the aromatic compound vanillylamine (derived from the phenylpropanoid pathway) with a branched-chain fatty acid by the catalysis of the putative enzyme capsaicinoid synthase. R2R3-MYB transcription factors have been reported in different species of plants as regulators of structural genes of the phenylpropanoid pathway; therefore, we hypothesized that MYB genes might be involved in the regulation of the biosynthesis of pungent compounds. In this study, an R2R3-MYB transcription factor gene, designated CaMYB31, was isolated and characterized in Capsicum annuum ‘Tampiqueño 74’. Bioinformatic analysis suggested that CaMYB31 could be involved in secondary metabolism, stress and plant hormone responses, and development. CaMYB31 expression analysis from placental tissue of pungent and nonpungent chili pepper fruits showed a positive correlation with the structural genes Ca4H, Comt, Kas, pAmt, and AT3 expression and also with the content of capsaicin and dihydrocapsacin during fruit development. However, CaMYB31 also was expressed in vegetative tissues (leaves, roots, and stems). Moreover, CaMYB31 silencing significantly reduced the expression of capsaicinoid biosynthetic genes and the capsaicinoid content. Additionally, CaMYB31 expression was affected by the plant hormones indoleacetic acid, jasmonic acid, salicylic acid, and gibberellic acid or by wounding, temperature, and light, factors known to affect the production of capsaicinoids. These findings indicate that CaMYB31 is indeed involved in the regulation of structural genes of the capsaicinoid biosynthetic pathway. PMID:28483879

  14. Apoptosis Induction by Targeting Interferon Gamma Receptor 2 (IFNgammaR2) in Prostate Cancer: Ligand (IFNgamma)-Independent Novel Function of IFNgammaR2 as a Bax Inhibitor

    Science.gov (United States)

    2015-08-01

    AWARD NUMBER: W81XWH-12-1-0331 TITLE: Apoptosis Induction by Targeting Interferon Gamma Receptor 2 (IFNgammaR2) in Prostate Cancer: Ligand...DATE August 2015 2. REPORT TYPE Annual 3. DATES COVERED 1Aug2014 - 31Jul2015 4. TITLE AND SUBTITLE Apoptosis Induction by Targeting Interferon ...Introduction In our preliminary study, we identified interferon γ receptor 2 (IFNγR2) as a Bax suppressor using yeast-based functional screening of Bax

  15. 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 BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

  16. Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons

    Directory of Open Access Journals (Sweden)

    Brookfield John FY

    2007-07-01

    Full Text Available Abstract Background Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods. Results 380 elements belonging to the young AluYg6 subfamily were identified in the human genome, a number significantly exceeding prior expectations. An AluYg6 element was also identified in the chimpanzee genome, indicating that the subfamily is older than previously estimated, and appears to have undergone a period of dormancy before its expansion. The relative contributions of back mutation and gene conversion to variation at the six diagnostic positions are examined, and cases of complete forward gene conversion events are reported. Two small subfamilies derived from AluYg6 have been identified, named AluYg6a2 and AluYg5b3, which contain 40 and 27 members, respectively. These small subfamilies are used to illustrate the ambiguity regarding Alu subfamily definition, and to assess the contribution of secondary source genes to the AluYg6 subfamily. Conclusion The number of elements in the AluYg6 subfamily greatly exceeds prior expectations, indicating that the current knowledge of young Alu subfamilies is incomplete, and that prior analyses that have been carried out using these data may have generated inaccurate results. A definition of primary and secondary source genes has been provided, and it has been shown that several source genes have contributed to the proliferation of the AluYg6 subfamily. Access to the sequence data for the complete AluYg6 subfamily will be invaluable in future computational analyses investigating

  17. Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

    Directory of Open Access Journals (Sweden)

    de la Chaux Nicole

    2009-08-01

    Full Text Available Abstract Background Roo is the most abundant retrotransposon in the fruit fly Drosophila melanogaster. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of Drosophila genome organization. We here study the phylogenetic distribution and evolution of roo, and its highly diverged relative rooA in 12 completely sequenced genomes of the genus Drosophila. Results We identify a total of 164 roo copies, 57 of which were previously unidentified copies that occur in 9 of the 12 genomes. Additionally we find 66 rooA copies in four genomes and remnants of this element in two additional genomes. We further increased the number of elements by searching for individual roo/rooA sequence domains. Most of our roo and rooA elements have been recently inserted. Most elements within a genome are highly similar. A comparison of the phylogenetic tree of our roo and rooA elements shows that the split between roo and rooA took place early in Drosophila evolution. Furthermore there is one incongruency between the species tree and the phylogenetic tree of the roo element. This incongruency regards the placement of elements from D. mojavensis, which are more closely related to D. melanogaster than elements from D. willistoni. Conclusion Within genomes, the evolutionary dynamics of roo and rooA range from recent transpositional activity to slow decay and extinction. Among genomes, the balance of phylogenetic evidence, sequence divergence distribution, and the occurrence of solo-LTR elements suggests an origin of roo/rooA within the Drosophila clade. We discuss the possibility of a horizontal gene transfer of roo within this clade.

  18. Achilles, a New Family of Transcriptionally Active Retrotransposons from the Olive Fruit Fly, with Y Chromosome Preferential Distribution.

    Directory of Open Access Journals (Sweden)

    Konstantina T Tsoumani

    Full Text Available Sex chromosomes have many unusual features relative to autosomes. The in depth exploration of their structure will improve our understanding of their origin and divergence (degeneration as well as the evolution of genetic sex determination pathways which, most often are attributed to them. In Tephritids, the structure of Y chromosome, where the male-determining factor M is localized, is largely unexplored and limited data concerning its sequence content and evolution are available. In order to get insight into the structure and organization of the Y chromosome of the major olive insect pest, the olive fly Bactrocera oleae, we characterized sequences from a Pulse Field Gel Electrophoresis (PFGE-isolated Y chromosome. Here, we report the discovery of the first olive fly LTR retrotransposon with increased presence on the Y chromosome. The element belongs to the BEL-Pao superfamily, however, its sequence comparison with the other members of the superfamily suggests that it constitutes a new family that we termed Achilles. Its ~7.5 kb sequence consists of the 5'LTR, the 5'non-coding sequence and the open reading frame (ORF, which encodes the polyprotein Gag-Pol. In situ hybridization to the B. oleae polytene chromosomes showed that Achilles is distributed in discrete bands dispersed on all five autosomes, in all centromeric regions and in the granular heterochromatic network corresponding to the mitotic sex chromosomes. The between sexes comparison revealed a variation in Achilles copy number, with male flies possessing 5-10 copies more than female (CI range: 18-38 and 12-33 copies respectively per genome. The examination of its transcriptional activity demonstrated the presence of at least one intact active copy in the genome, showing a differential level of expression between sexes as well as during embryonic development. The higher expression was detected in male germline tissues (testes. Moreover, the presence of Achilles-like elements in

  19. 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.

  20. Histone H3R2 Symmetric Dimethylation and Histone H3K4 Trimethylation Are Tightly Correlated in Eukaryotic Genomes

    OpenAIRE

    Chih-Chi Yuan; Adam G.W. Matthews; Yi Jin; Chang Feng Chen; Brad A. Chapman; Toshiro K. Ohsumi; Karen C. Glass; Tatiana G. Kutateladze; Mark L. Borowsky; Kevin Struhl; Marjorie A. Oettinger

    2012-01-01

    The preferential in vitro interaction of the PHD finger of RAG2, a subunit of the V(D)J recombinase, with histone H3 tails simultaneously trimethylated at lysine 4 and symmetrically dimethylated at arginine 2 (H3R2me2sK4me3) predicted the existence of the previously unknown histone modification H3R2me2s. Here, we report the in vivo identification of H3R2me2s . Consistent with the binding specificity of the RAG2 PHD finger, high levels of H3R2me2sK4me3 are found at antigen receptor gene segmen...

  1. Synthesis of protected (2S,4R)-2-amino-4-methyldecanoic acid, a proposed component of culicinins

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Tian Tian Sun; Duo Mei; Jun Fei Wang; Ying Xia Li

    2008-01-01

    The protected (2S,4R)-2-amino-4-methyldecanoic acid, a proposed component of culicinins has been synthesized over 10 steps and in total 28% yields using Wittig reaction and Schollkopf amino acid synthesis as key steps.

  2. Exploring the GluR2 ligand-binding core in complex with the bicyclical AMPA analogue (S)-4-AHCP

    DEFF Research Database (Denmark)

    Nielsen, Bettina B; Pickering, Darryl S; Greenwood, Jeremy R;

    2005-01-01

    The X-ray structure of the ionotropic GluR2 ligand-binding core (GluR2-S1S2J) in complex with the bicyclical AMPA analogue (S)-2-amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]-4-isoxazolyl)propionic acid [(S)-4-AHCP] has been determined, as well as the binding pharmacology of this construct...

  3. Mycobacterium simiae infection in two unrelated patients with different forms of inherited IFN-γR2 deficiency.

    Science.gov (United States)

    Martínez-Barricarte, Rubén; Megged, Orli; Stepensky, Polina; Casimir, Pierre; Moncada-Velez, Marcela; Averbuch, Diana; Assous, Marc Victor; Abuzaitoun, Omar; Kong, Xiao-Fei; Pedergnana, Vincent; Deswarte, Caroline; Migaud, Mélanie; Rose-John, Stefan; Itan, Yuval; Boisson, Bertrand; Belkadi, Aziz; Conti, Francesca; Abel, Laurent; Vogt, Guillaume; Boisson-Dupuis, Stephanie; Casanova, Jean-Laurent; Bustamante, Jacinta

    2014-11-01

    Interferon-γ receptor 2 (IFN-γR2) deficiency is a rare primary immunodeficiency characterized by predisposition to infections with weakly virulent mycobacteria, such as environmental mycobacteria and BCG vaccines. We describe here two children with IFN-γR2 deficiency, from unrelated, consanguineous kindreds of Arab and Israeli descent. The first patient was a boy who died at the age of 4.5 years, from recurrent, disseminated disease caused by Mycobacterium simiae. His IFN-γR2 defect was autosomal recessive and complete. The second patient was a girl with multiple disseminated mycobacterial infections, including infection with M. simiae. She died at the age of 5 years, a short time after the transplantation of umbilical cord blood cells from an unrelated donor. Her IFN-γR2 defect was autosomal recessive and partial. Autosomal recessive IFN-γR2 deficiency is life-threatening, even in its partial form, and genetic diagnosis and familial counseling are therefore particularly important for this condition. These two cases are the first of IFN-γR2 deficiency associated with M. simiae infection to be described.

  4. Life beyond MSE and R2 — improving validation of predictive models with observations

    Science.gov (United States)

    Papritz, Andreas; Nussbaum, Madlene

    2017-04-01

    Machine learning and statistical predictive methods are evaluated by the closeness of predictions to observations of a test dataset. Common criteria for rating predictive methods are bias and mean square error (MSE), characterizing systematic and random prediction errors. Many studies also report R2-values, but their meaning is not always clear (correlation between observations and predictions or MSE skill score; Wilks, 2011). The same criteria are also used for choosing tuning parameters of predictive procedures by cross-validation and bagging (e.g. Hastie et al., 2009). For evident reasons, atmospheric sciences have developed a rich box of tools for forecast verification. Specific criteria have been proposed for evaluating deterministic and probabilistic predictions of binary, multinomial, ordinal and continuous responses (see reviews by Wilks, 2011, Jollie and Stephenson, 2012 and Gneiting et al., 2007). It appears that these techniques are not very well-known in the geosciences community interested in machine learning. In our presentation we review techniques that offer more insight into proximity of data and predictions than bias, MSE and R2 alone. We mention here only examples: (i) Graphing observations vs. predictions is usually more appropriate than the reverse (Piñeiro et al., 2008). (ii) The decomposition of the Brier score score (= MSE for probabilistic predictions of binary yes/no data) into reliability and resolution reveals (conditional) bias and capability of discriminating yes/no observations by the predictions. We illustrate the approaches by applications from digital soil mapping studies. Gneiting, T., Balabdaoui, F., and Raftery, A. E. (2007). Probabilistic forecasts, calibration and sharpness. Journal of the Royal Statistical Society Series B, 69, 243-268. Hastie, T., Tibshirani, R., and Friedman, J. (2009). The Elements of Statistical Learning; Data Mining, Inference and Prediction. Springer, New York, second edition. Jolliffe, I. T. and

  5. mGluR2/3 mechanisms in primate dorsolateral prefrontal cortex: Evidence for both presynaptic and postsynaptic actions

    Science.gov (United States)

    Jin, Lu E.; Wang, Min; Yang, Sheng-Tao; Yang, Yang; Galvin, Veronica C.; Lightbourne, Taber C.; Ottenheimer, David; Zhong, Qiaonan; Stein, Josh; Raja, Anusha; Paspalas, Constantinos D.; Arnsten, Amy F.T.

    2016-01-01

    Cognitive deficits in psychiatric and age-related disorders generally involve dysfunction of the dorsolateral prefrontal cortex (dlPFC), but there are few treatments for these debilitating symptoms. Group II metabotropic glutamate receptors (mGluR2/3), which couple to Gi/Go, have been a focus of therapeutics based on rodent research, where mGluR2/3 have been shown to reduce axonal glutamate release and increase glial glutamate uptake. However, this strategy has had mixed results in patients, and understanding mGluR2/3 mechanisms in primates will help guide therapeutic interventions. The current study examined mGluR2/3 localization and actions in the primate dlPFC layer III circuits underlying working memory, where the persistent firing of “Delay cells” is mediated by NMDA receptors and weakened by cAMP-PKA-potassium channel signaling in dendritic spines. Immunoelectron microscopy identified postsynaptic mGluR2/3 in the spines, in addition to the traditional presynaptic and astrocytic locations. In vivo iontophoretic application of the mGluR2/3 agonists (2R, 4R)-APDC or LY379268 onto dlPFC Delay cells produced an inverted-U effect on working memory representation, with enhanced neuronal firing following low doses of mGluR2/3 agonists. The enhancing effects were reversed by an mGluR2/3 antagonist or by activating cAMP signaling, consistent with mGluR2/3 inhibiting postsynaptic cAMP signaling in spines. Systemic administration of these agonists to monkeys performing a working memory task also produced an inverted-U dose-response, where low doses improved performance but higher doses, similar to clinical trials, had mixed effects. Our data suggest that low dose mGluR2/3 stimulation may have therapeutic effects through unexpected postsynaptic actions in dlPFC, strengthening synaptic connections and improving cognitive function. PMID:27502475

  6. Characterization and expression analysis of SOLD1, a novel member of the retrotransposon-derived Ly-6 superfamily, in bovine placental villi.

    Directory of Open Access Journals (Sweden)

    Koichi Ushizawa

    Full Text Available BACKGROUND: Ly-6 superfamily members have a conserved Ly-6 domain that is defined by a distinct disulfide bonding pattern between eight or ten cysteine residues. These members are divided into membrane-type and secretory-type proteins. In the present study, we report the identification of a novel Ly-6 domain protein, secreted protein of Ly-6 domain 1 (SOLD1, from bovine placenta. PRINCIPAL FINDINGS: SOLD1 mRNA was expressed in trophoblast mononucleate cells and the protein was secreted into and localized in the extracellular matrix of the mesenchyme in cotyledonary villi. SOLD1 bound mainly with type I collagen telopeptide. We confirmed secretion of SOLD1 from the basolateral surface of a bovine trophoblast cell line (BT-1. It may be related to the organization of the extra-cellular matrix in the mesenchyme of fetal villi. Since trophoblast mononucleate cells are epithelial cells, their polar organization is expected to have a crucial role in the SOLD1 secretion system. We established that SOLD1 is an intronless bovine gene containing the Alu retrotransposon, which was integrated via cytoplasmic reverse transcription. CONCLUSION: We identified a novel retrotransposon-like Ly-6 domain protein in bovine placenta. SOLD1 is a crucial secreted protein that is involved in the organization of the mesenchyme of the cotyledonary villi. Furthermore, the gene encoding SOLD1 has an interesting genomic structure.

  7. Differential Expression of Retrotransposon WIS 2-1A Response to Vacuum,Low-Energy N+ Implantation and 60Coγ-ray Irradiation in Wheat

    Institute of Scientific and Technical Information of China (English)

    ZHAO Huiru; GU Yunhong; YA Huiyuan; JIAO Zhen; QIN Guangyong

    2009-01-01

    Mutagenesis and retrotransposons have a close relationship,but little attention has been paid yet to the activity of rtrotransposons produced by physical mutagens. The variation of retrotransposon WIS 2-1A activity in wheat(Triticum aestivum L.)embryos at three different growth times(30 h,45 h and 60 h)was investigated after they had been treated with N+ implantation in a vacuum of 5x10-2 Pa and irradiation by 60Coγ-ray respectively.For each of the three growth times the expression of WIS 2-1A showed almost entirely a same trend of downregulation,upregulation,then downregulation,and upregulation again with the increase in dose of N+ implantation,but the expression appeared irregular with the increase in irradiation of 60Coγ-ray.In conclusion,the acutely activating effect of WIS 2-1A stimulated by vacuum and high dose N+ implantation within a shorter incubation time may provide a convenient tool to advance the research on mutagenic breeding and function genes.

  8. Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae

    Directory of Open Access Journals (Sweden)

    Manicacci Domenica

    2009-03-01

    Full Text Available Abstract Background Horizontal transfers (HTs refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum, as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae. Results We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers. Conclusion This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.

  9. Expression of the Idefix retrotransposon in early follicle cells in the germarium of Drosophila melanogaster is determined by its LTR sequences and a specific genomic context.

    Science.gov (United States)

    Tcheressiz, S; Calco, V; Arnaud, F; Arthaud, L; Dastugue, B; Vaury, C

    2002-04-01

    Retrotransposons are transcriptionally activated in different tissues and cell types by a variety of genomic and environmental factors. Transcription of LTR retrotransposons is controlled by cis-acting regulatory sequences in the 5' LTR. Mobilization of two LTR retroelements, Idefix and ZAM, occurs in the unstable RevI line of Drosophila melanogaster, in which their copy numbers are high, while they are low in all other stocks tested. Here we show that both a full-length and a subgenomic Idefix transcript that are necessary for its mobilization are present in the Rev1 line, but not in the other lines. Studies on transgenic strains demonstrate that the 5' LTR of Idefix contains sequences that direct the tissue-specific expression of the retroelement in testes and ovaries of adult flies. In ovaries, expression occurs in the early follicle and in other somatic cells of the germarium, and is strictly associated with the unstable genetic context conferred by the RevI line. Control of tissue-specific Idefix expression by interactions between cis-acting sequences of its LTR and trans-acting genomic factors provides an opportunity to use this retroelement as a tool for the study of the early follicle cell lineage in the germarium.

  10. Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes.

    Science.gov (United States)

    Ono, Ryuichi; Ishii, Masayuki; Fujihara, Yoshitaka; Kitazawa, Moe; Usami, Takako; Kaneko-Ishino, Tomoko; Kanno, Jun; Ikawa, Masahito; Ishino, Fumitoshi

    2015-07-28

    The CRISPR/Cas system efficiently introduces double strand breaks (DSBs) at a genomic locus specified by a single guide RNA (sgRNA). The DSBs are subsequently repaired through non-homologous end joining (NHEJ) or homologous recombination (HR). Here, we demonstrate that DSBs introduced into mouse zygotes by the CRISPR/Cas system are repaired by the capture of DNA sequences deriving from retrotransposons, genomic DNA, mRNA and sgRNA. Among 93 mice analysed, 57 carried mutant alleles and 22 of them had long de novo insertion(s) at DSB-introduced sites; two were spliced mRNAs of Pcnt and Inadl without introns, indicating the involvement of reverse transcription (RT). Fifteen alleles included retrotransposons, mRNAs, and other sequences without evidence of RT. Two others were sgRNAs with one containing T7 promoter-derived sequence suggestive of a PCR product as its origin. In conclusion, RT-product-mediated DSB repair (RMDR) and non-RMDR repair were identified in the mouse zygote. We also confirmed that both RMDR and non-RMDR take place in CRISPR/Cas transfected NIH-3T3 cells. Finally, as two de novo MuERV-L insertions in C57BL/6 mice were shown to have characteristic features of RMDR in natural conditions, we hypothesize that RMDR contributes to the emergence of novel DNA sequences in the course of evolution.

  11. Microstructural Analysis of Peripheral Lung Tissue through CPMG Inter-Echo Time R2 Dispersion.

    Directory of Open Access Journals (Sweden)

    Felix T Kurz

    Full Text Available Since changes in lung microstructure are important indicators for (early stage lung pathology, there is a need for quantifiable information of diagnostically challenging cases in a clinical setting, e.g. to evaluate early emphysematous changes in peripheral lung tissue. Considering alveoli as spherical air-spaces surrounded by a thin film of lung tissue allows deriving an expression for Carr-Purcell-Meiboom-Gill transverse relaxation rates R2 with a dependence on inter-echo time, local air-tissue volume fraction, diffusion coefficient and alveolar diameter, within a weak field approximation. The model relaxation rate exhibits the same hyperbolic tangent dependency as seen in the Luz-Meiboom model and limiting cases agree with Brooks et al. and Jensen et al. In addition, the model is tested against experimental data for passively deflated rat lungs: the resulting mean alveolar radius of RA = 31.46 ± 13.15 μm is very close to the literature value (∼34 μm. Also, modeled radii obtained from relaxometer measurements of ageing hydrogel foam (that mimics peripheral lung tissue are in good agreement with those obtained from μCT images of the same foam (mean relative error: 0.06 ± 0.01. The model's ability to determine the alveolar radius and/or air volume fraction will be useful in quantifying peripheral lung microstructure.

  12. Electric hyperscaling violating solutions in Einstein-Maxwell-dilaton gravity with R^2 corrections

    CERN Document Server

    O'Keeffe, Daniel K

    2013-01-01

    In the context of holography applied to condensed matter physics, we study Einstein-Maxwell-dilaton theory with curvature squared corrections. This theory has three couplings eta_i for the three R^2 invariants and two theory functions: a dilaton potential V(phi) and a dilaton-dependent gauge coupling f(phi). We find hyperscaling violating solutions of this theory, parametrized by dynamical critical exponent z and HSV parameter theta. We obtain restrictions on the form of the theory functions required to support HSV-type solutions using three physical inputs: the null energy condition, causality z $\\leq$ 1, and d_eff = d - theta lying in the range 0 < d_eff $\\leq$ d. The NEC constraints are linear in the eta_i and (quartic) polynomial in d,z,theta. The allowed ranges of z,theta change depending on the signs of eta_i. For the case of Einstein-Weyl gravity, we further narrow down the theory functions and solution parameters required for crossover solutions interpolating between HSV, AdS_d+2 near the boundary,...

  13. An R2R3-MYB transcription factor regulates carotenoid pigmentation in Mimulus lewisii flowers.

    Science.gov (United States)

    Sagawa, Janelle M; Stanley, Lauren E; LaFountain, Amy M; Frank, Harry A; Liu, Chang; Yuan, Yao-Wu

    2016-02-01

    Carotenoids are yellow, orange, and red pigments that contribute to the beautiful colors and nutritive value of many flowers and fruits. The structural genes in the highly conserved carotenoid biosynthetic pathway have been well characterized in multiple plant systems, but little is known about the transcription factors that control the expression of these structural genes. By analyzing a chemically induced mutant of Mimulus lewisii through bulk segregant analysis and transgenic experiments, we have identified an R2R3-MYB, Reduced Carotenoid Pigmentation 1 (RCP1), as the first transcription factor that positively regulates carotenoid biosynthesis during flower development. Loss-of-function mutations in RCP1 lead to down-regulation of all carotenoid biosynthetic genes and reduced carotenoid content in M. lewisii flowers, a phenotype recapitulated by RNA interference in the wild-type background. Overexpression of this gene in the rcp1 mutant background restores carotenoid production and, unexpectedly, results in simultaneous decrease of anthocyanin production in some transgenic lines by down-regulating the expression of an activator of anthocyanin biosynthesis. Identification of transcriptional regulators of carotenoid biosynthesis provides the 'toolbox' genes for understanding the molecular basis of flower color diversification in nature and for potential enhancement of carotenoid production in crop plants via genetic engineering. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  14. Dyadic Bivariate Fourier Multipliers for Multi-Wavelets in L2(R2)

    Institute of Scientific and Technical Information of China (English)

    Zhongyan Li∗; Xiaodi Xu

    2015-01-01

    The single 2 dilation orthogonal wavelet multipliers in one dimensional case and single A-dilation (where A is any expansive matrix with integer entries and|detA|=2) wavelet multipliers in high dimensional case were completely characterized by the Wutam Consortium (1998) and Z. Y. Li, et al. (2010). But there exist no more results on orthogonal multivariate wavelet matrix multipliers corresponding integer expansive dilation matrix with the absolute value of determinant not 2 in L2(R2). In this paper, we choose as the dilation matrix and consider the 2I2-dilation orthogonal multivariate wavelet Y={y1,y2,y3}, (which is called a dyadic bivariate wavelet) multipliers. We call the 3×3 matrix-valued function A(s)=[ fi,j(s)]3×3, where fi,j are measurable functions, a dyadic bivariate matrix Fourier wavelet multiplier if the inverse Fourier transform of A(s)(cy1(s),cy2(s),cy3(s))⊤ = ( b g1(s), b g2(s), b g3(s))⊤ is a dyadic bivariate wavelet whenever (y1,y2,y3) is any dyadic bivariate wavelet. We give some conditions for dyadic matrix bivariate wavelet multipliers. The results extended that of Z. Y. Li and X. L. Shi (2011). As an application, we construct some useful dyadic bivariate wavelets by using dyadic Fourier matrix wavelet multipliers and use them to image denoising.

  15. Observational and Dynamical Characterization of Main-Belt Comet P/2010 R2 (La Sagra)

    CERN Document Server

    Hsieh, Henry H; Haghighipour, Nader; Novakovic, Bojan; Jedicke, Robert; Wainscoat, Richard J; Denneau, Larry; Abe, Shinsuke; Chen, Wen-Ping; Fitzsimmons, Alan; Granvik, Mikael; Grav, Tommy; Ip, Wing; Kaluna, Heather M; Kinoshita, Daisuke; Kleyna, Jan; Knight, Matthew M; Lacerda, Pedro; Lisse, Carey M; Maclennan, Eric; Meech, Karen J; Micheli, Marco; Milani, Andrea; Pittichova, Jana; Schunova, Eva; Tholen, David J; Wasserman, Lawrence H; Burgett, William S; Chambers, K C; Heasley, Jim N; Kaiser, N; Magnier, Eugene A; Morgan, Jeffrey S; Price, Paul A; Jorgensen, Uffe G; Dominik, Martin; Hinse, Tobias; Sahu, Kailash; Snodgrass, Colin

    2011-01-01

    We present observations of the recently discovered comet-like main-belt object P/2010 R2 (La Sagra) obtained by Pan-STARRS 1 and the Faulkes Telescope-North on Haleakala in Hawaii, the University of Hawaii 2.2 m, Gemini-North, and Keck I telescopes on Mauna Kea, the Danish 1.54 m telescope (operated by the MINDSTEp consortium) at La Silla, and the Isaac Newton Telescope on La Palma. An antisolar dust tail is observed to be present from August 2010 through February 2011, while a dust trail aligned with the object's orbit plane is also observed from December 2010 through August 2011. Assuming typical phase darkening behavior, P/La Sagra is seen to increase in brightness by >1 mag between August 2010 and December 2010, suggesting that dust production is ongoing over this period. These results strongly suggest that the observed activity is cometary in nature (i.e., driven by the sublimation of volatile material), and that P/La Sagra is therefore the most recent main-belt comet to be discovered. We find an approxi...

  16. Cloning and characterisation of genes for tetrapyrrole biosynthesis from the cyanobacterium Anacystis nidulans R2.

    Science.gov (United States)

    Jones, M C; Jenkins, J M; Smith, A G; Howe, C J

    1994-02-01

    The genes for 5-aminolevulinic acid dehydratase (ALAD) and uroporphyrinogen III synthase (UROS), two enzymes in the biosynthetic pathway for tetrapyrroles, were independently isolated from a plasmid-based genomic library of Anacystis nidulans R2 (also called Synechococcus sp. PCC7942), by their ability to complement Escherichia coli strains carrying mutations in the equivalent genes (hemB and hemD respectively). The identity of the genes was confirmed by comparing the appropriate enzyme activities in complemented and mutant strains. Subclones of the original plasmids that were also capable of complementing the mutants were sequenced. The inferred amino acid sequence of the cyanobacterial HemB protein indicates a significant difference in the metal cofactor requirement from the higher-plant enzymes, which was confirmed by overexpression and biochemical analysis. The organisation of the cyanobacterial hemD locus differs markedly from other prokaryotes. Two open reading frames were found immediately upstream of hemD. The product of one shows considerable similarity to published sequences from other organisms for uroporphyrinogen III methylase (UROM), an enzyme involved in the production of sirohaem and cobalamins (including vitamin B-12). The product of the other shows motifs which are similar to those found in proteins responsible for metabolic regulation in yeast and indicates that this family of transcription control proteins, which has previously been reported only from eukaryotes, is also represented in prokaryotes.

  17. On the Jeans Theorem and the “Tolman–Oppenheimer–Volkoff Equation” in R2 Gravity

    Directory of Open Access Journals (Sweden)

    Rishabh Jain

    2016-01-01

    Full Text Available Corda, Mosquera Cuesta, and Lorduy Gòmez have shown that spherically symmetric stationary states can be used as a model for galaxies in the framework of the linearized R2 gravity. Those states could represent a partial solution to the Dark Matter Problem. Here, we discuss an improvement of this work. In fact, as the star density is a functional of the invariants of the associated Vlasov equation, we show that any of these invariants is in its turn a functional of the local energy and the angular momentum. As a consequence, the star density depends only on these two integrals of the Vlasov system. This result is known as the “Jeans theorem.” In addition, we find an analogy of the historical Tolman–Oppenheimer–Volkoff equation for the system considered in this paper. For the sake of completeness, in the final section of the paper, we consider two additional models which argue that Dark Matter could not be an essential element.

  18. Characterization and Application of Biosurfactant Produced by Bacillus licheniformis R2.

    Science.gov (United States)

    Joshi, Sanket J; Geetha, S J; Desai, Anjana J

    2015-09-01

    The biosurfactant produced by Bacillus licheniformis R2 was characterized and studied for enhancing the heavy crude oil recovery at 80 °C in coreflood experiments. The strain was found to be nonpathogenic and produced biosurfactant, reducing the surface tension of medium from 70 to 28 mN/m with 1.1 g/l yield. The biosurfactant was quite stable during exposure to elevated temperatures (85 °C for 90 days), high salinity (10 % NaCl), and a wide range of pH (5-12) for 10 days. It was characterized as lipopeptide similar to lichenysin-A, with a critical micelle concentration of about 19.4 mg/l. The efficiency of crude biosurfactant for enhanced oil recovery by core flood studies revealed it to recovering additional 37.1 % oil from Berea sandstone cores at 80 °C. The results are indicative of the potential for the development of lipopeptide biosurfactant-based ex situ microbial enhanced heavy oil recovery from depleting oil fields with extreme temperatures.

  19. Effect of High-level Copper Diet on Expression of TrxR2 mRNA and Reduction Activity of TrxR2 of Liver in Broiler%高铜日粮对肉鸡肝脏TrxR2基因mRNA表达和还原活性的影响

    Institute of Scientific and Technical Information of China (English)

    刘好朋; 唐兆新; 苏荣胜; 胡京京; 韩前彪; 胡锴; 刘传敦; 万婷

    2011-01-01

    In order to examine the effect of high dietary copper on expression of TrxR2 mRNA in liver,and the reduction activity of TrxR2, the experiment was conducted with two hundred healthy 1 day-old Cobb broilers which were randomly divided into four groups based on diets as follows: control group (Cu 11 mg · kg-1 as the group Ⅰ ) and high copper groups (Cu content 110, 330, 550 mg · kg-1 , named group Ⅱ 、Ⅲ and Ⅳ ). The liver was taken from broiler in each group at the lOth , 30th and 50th days, respectively, reduction activity of the liver TrxR2 was detefmined by the method of DTNB, and the testing material was liver mitochondria which has been extraction from the liver, and the expression of the liver TrxR2 was determined by the method of semi-quantification and reverse transcription polymerase chain reaction (RT-PCR). The results showed that the reduction activity of liver TrxR2 decreased (P<0. 05) and the expression of TrxR2 mRNA was reduced (P<0. 05)at 50 d of Group Ⅳ , the reduction activity of liver TrxR2 was mcreased(P<0. 05) at 30 d and reduced (P>0. 05)at 50 d of Group Ⅲ , The experiental results indicated that fed high copper diets (330-550 mg · kg-1) could decrease TrxR2 mRNA expression in the liver and increase the reduction activity of TrxR2 first, and decrease it on 50 days.%本文旨在了解高铜日粮对肉鸡肝脏TrxR2基因mRNA表达和还原活性的影响.200羽1日龄Cobb商品代肉鸡随机分为4组,各组日粮中铜含量分别为:对照组(Ⅰ组)11 mg·kg-1、试验Ⅱ组110 mg·kg1、试验Ⅲ组330mg·kg-1和试验Ⅳ组550 mg·kg-1.饲养至10、30、50 d时每组各取5只鸡用于采集肝脏样品,提取肝脏线粒体用DTNB法测定肝脏TrxR2的还原活性,提取肝脏总RNA用RT-PCR法测定TrxR2 mRNA在肝脏中的表达量.结果显示,饲喂铜含量为550 mg·kg-1日粮50 d时还原活性降低(P<0.05)、TrxR2基因mRNA的表达量降低(P<0.05),饲喂铜含量为330 mg·kg-1日粮30 d时TrxR2

  20. BOLD-MRI of breast invasive ductal carcinoma: correlation of R2* value and the expression of HIF-1{alpha}

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Min; Guo, Xiaojuan; Wang, Shuangkun [Capital Medical University, Department of Radiology, Beijing Chao Yang Hospital, Beijing (China); Jin, Mulan; Wang, Ying [Capital Medical University Beijing, Department of Pathology, Beijing Chaoyang Hospital, Beijing (China); Li, Jie; Liu, Jun [Capital Medical University Beijing, Department of Breast Surgery, Beijing Chaoyang Hospital, Beijing (China)

    2013-12-15

    To explore the reliability and feasibility of blood oxygenation level-dependent-based functional magnetic resonance imaging (BOLD-fMRI) to depict hypoxia in breast invasive ductal carcinoma. A total of 103 women with 104 invasive ductal carcinomas (IDCs) underwent breast BOLD-fMRI at 3.0 T. Histological specimens were analysed for tumour size, grade, axillary lymph nodes and expression of oestrogen receptors, progesterone receptors, human epidermal growth factor receptor 2, p53, Ki-67 and hypoxia inducible factor 1{alpha} (HIF-1{alpha}). The distribution and reliability of R2* were analysed. Correlations of the R2* value with the prognostic factors and HIF-1{alpha} were respectively analysed. The R2* map of IDC demonstrated a relatively heterogeneous signal. The mean R2* value was (53.4 {+-} 18.2) Hz. The Shapiro-Wilk test (W = 0.971, P = 0.020) suggested that the sample did not follow a normal distribution. The inter-rater and intrarater correlation coefficient was 0.967 and 0.959, respectively. The R2* values of IDCs were significantly lower in patients without axillary lymph nodes metastasis. The R2* value had a weak correlation with Ki67 expression (r = 0.208, P = 0.038). The mean R2* value correlated moderately with the level of HIF-1{alpha} (r = 0.516, P = 0.000). BOLD-fMRI is a simple and non-invasive technique that yields hypoxia information on breast invasive ductal carcinomas. (orig.)

  1. Rolling Deck to Repository (R2R): Products and Services for the U.S. Research Fleet Community

    Science.gov (United States)

    Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Smith, S. R.; Stocks, K. I.

    2016-02-01

    The Rolling Deck to Repository (R2R) program is working to ensure open access to environmental sensor data routinely acquired by the U.S. academic research fleet. Currently 25 vessels deliver 7 TB/year of data to R2R from a suite of geophysical, oceanographic, meteorological, and navigational sensors on over 400 cruises worldwide. R2R ensures these data are preserved in trusted repositories, discoverable via standard protocols, and adequately documented for reuse. R2R has recently expanded to include the vessels Sikuliaq, operated by the University of Alaska; Falkor, operated by the Schmidt Ocean Institute; and Ronald H. Brown and Okeanos Explorer, operated by NOAA. R2R maintains a master catalog of U.S. research cruises, currently holding over 4,670 expeditions including vessel and cruise identifiers, start/end dates and ports, project titles and funding awards, science parties, dataset inventories with instrument types and file formats, data quality assessments, and links to related content at other repositories. Standard post-field cruise products are published including shiptrack navigation, near-real-time MET/TSG data, underway geophysical profiles, and CTD profiles. Software tools available to users include the R2R Event Logger and the R2R Nav Manager. A Digital Object Identifier (DOI) is published for each cruise, original field sensor dataset, standard post-field product, and document (e.g. cruise report) submitted by the science party. Scientists are linked to personal identifiers such as ORCIDs where available. Using standard identifiers such as DOIs and ORCIDs facilitates linking with journal publications and generation of citation metrics. R2R collaborates in the Ocean Data Interoperability Platform (ODIP) to strengthen links among regional and national data systems, populates U.S. cruises in the POGO global catalog, and is working toward membership in the DataONE alliance. It is a lead partner in the EarthCube GeoLink project, developing Semantic Web

  2. Characterization of Fe17R2 phases (R=Pr and Sm) oxidized at 200 °C

    Science.gov (United States)

    Gama, S.; Ribeiro, C. A.; Cabral, F. A. O.; Colucci, C. C.; de Morais, E.; Sanjurjo, N. L.; Campos, C.; Ardisson, J. D.; Persiano, A. I. C.

    1996-04-01

    The results of oxygen absorption in temperatures ranging from 200 to 500 °C are reported for the phases Fe17R2, R=Pr and Sm. It was observed that the oxygen saturation limit is temperature dependent, being of 3 at/fu at 200 °C, 12.8 at/fu at 300 °C, 20.3 at/fu at 400 °C, and 28.5 at/fu at 500 °C. This implies that above 200 °C the phase is deeply altered by oxygen absorption. Samples with absorption at 200 °C were studied as prepared and heat treated at 500 °C/40 h. The results show that the heat-treated samples consist of Fe17R2, Fe, and R2O3. Metallographic examination, susceptibility, and Mössbauer spectroscopy data support the hypothesis that the as-prepared samples consist of a mixture of Fe17R2 and ordered interstitial Fe17R2Ox.

  3. Decreased Adiponectin-Mediated Signaling Through the AdipoR2 Pathway Is Associated With Carotid Plaque Instability.

    Science.gov (United States)

    Gasbarrino, Karina; Zheng, Huaien; Hafiane, Anouar; Veinot, John P; Lai, Chi; Daskalopoulou, Stella S

    2017-04-01

    Adiponectin, the most abundantly secreted anti-inflammatory adipokine, protects against all stages of atherosclerotic plaque formation by acting on its receptors, AdipoR1 (adiponectin receptor 1) and AdipoR2 (adiponectin receptor 2). Through binding of AdipoR1, adiponectin leads to the activation of the AMPK (adenosine monophosphate-activated protein kinase) pathway, whereas stimulation of PPAR-α (peroxisome proliferator-activated receptor-α) is attributed to the binding of AdipoR2. However, the role of adiponectin and its receptors in plaque instability remains to be characterized. Thus, we aimed to investigate whether the adiponectin-AdipoR pathway is associated with carotid atherosclerotic plaque instability. The instability of plaque specimens obtained from patients who underwent a carotid endarterectomy (n=143) was assessed using gold standard histological classifications. Using immunohistochemistry, we showed that adiponectin and AdipoR1/AdipoR2 are expressed in human carotid plaques and that their expression was localized most abundantly in areas of macrophage and foam cell accumulation. Unstable plaques expressed more adiponectin protein (Western blot, Padiponectin with a decrease in AdipoR2 expression and activity was observed in unstable plaques, suggesting that reduced signaling through the AdipoR2 pathway, and not through AdipoR1, may contribute to plaque instability. © 2017 American Heart Association, Inc.

  4. Gene Expression Profiling Identifies Important Genes Affected by R2 Compound Disrupting FAK and P53 Complex

    Directory of Open Access Journals (Sweden)

    Vita M. Golubovskaya

    2014-01-01

    Full Text Available Focal Adhesion Kinase (FAK is a non-receptor kinase that plays an important role in many cellular processes: adhesion, proliferation, invasion, angiogenesis, metastasis and survival. Recently, we have shown that Roslin 2 or R2 (1-benzyl-15,3,5,7-tetraazatricyclo[3.3.1.1~3,7~]decane compound disrupts FAK and p53 proteins, activates p53 transcriptional activity, and blocks tumor growth. In this report we performed a microarray gene expression analysis of R2-treated HCT116 p53+/+ and p53−/− cells and detected 1484 genes that were significantly up- or down-regulated (p < 0.05 in HCT116 p53+/+ cells but not in p53−/− cells. Among up-regulated genes in HCT p53+/+ cells we detected critical p53 targets: Mdm-2, Noxa-1, and RIP1. Among down-regulated genes, Met, PLK2, KIF14, BIRC2 and other genes were identified. In addition, a combination of R2 compound with M13 compound that disrupts FAK and Mmd-2 complex or R2 and Nutlin-1 that disrupts Mdm-2 and p53 decreased clonogenicity of HCT116 p53+/+ colon cancer cells more significantly than each agent alone in a p53-dependent manner. Thus, the report detects gene expression profile in response to R2 treatment and demonstrates that the combination of drugs targeting FAK, Mdm-2, and p53 can be a novel therapy approach.

  5. The role of miR-2∼13∼71 cluster in resistance to deltamethrin in Culex pipiens pallens.

    Science.gov (United States)

    Guo, Qin; Huang, Yun; Zou, Feifei; Liu, Bingqian; Tian, Mengmeng; Ye, Wenyun; Guo, Juxin; Sun, Xueli; Zhou, Dan; Sun, Yan; Ma, Lei; Shen, Bo; Zhu, Changliang

    2017-05-01

    Excessive and continuous application of deltamethrin has resulted in the development of deltamethrin resistance among mosquitoes, which becomes a major obstacle for mosquito control. In a previous study, differentially expressed miRNAs between deltamethrin-susceptible (DS) strain and deltamethrin-resistant (DR) strain using illumina sequencing in Culex pipiens pallens were identified. In this study, we applied RNAi and the Centers for Disease Control and Prevention (CDC) bottle bioassay to investigate the relationship between miR-2∼13∼71 cluster (miR-2, miR-13 and miR-71) and deltamethrin resistance. We used quantitative real-time PCR (qRT-PCR) to measure expression levels of miR-2∼13∼71 clusters. MiR-2∼13∼71 cluster was down regulated in adult female mosquitoes from the DR strain and played important roles in deltamethrin resistance through regulating target genes, CYP9J35 and CYP325BG3. Knocking down CYP9J35 and CYP325BG3 resulted in decreased mortality of DR mosquitoes. This study provides the first evidence that miRNA clusters are associated with deltamethrin resistance in mosquitoes. Moreover, we investigated the regulatory networks formed between miR-2∼13∼71 cluster and its target genes, which provide a better understanding of the mechanism involved in deltamethrin resistance. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. The genetic diversity and evolution of field pea (Pisum studied by high throughput retrotransposon based insertion polymorphism (RBIP marker analysis

    Directory of Open Access Journals (Sweden)

    Smýkal Petr

    2010-02-01

    Full Text Available Abstract Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP markers by the Tagged Array Marker (TAM method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3 corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture

  7. An LTR Retrotransposon-Derived Gene Displays Lineage-Specific Structural and Putative Species-Specific Functional Variations in Eutherians

    Science.gov (United States)

    Irie, Masahito; Koga, Akihiko; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2016-01-01

    Amongst the 11 eutherian-specific genes acquired from a sushi-ichi retrotransposon is the CCHC type zinc-finger protein-encoding gene SIRH11/ZCCHC16. Its contribution to eutherian brain evolution is implied because of its involvement in cognitive function in mice, possibly via the noradrenergic system. Although, the possibility that Sirh11/Zcchc16 functions as a non-coding RNA still remains, dN/dS ratios in pairwise comparisons between its orthologs have provided supportive evidence that it acts as a protein. It became a pseudogene in armadillos (Cingulata) and sloths (Pilosa), the only two extant orders of xenarthra, which prompted us to examine the lineage-specific variations of SIRH11/ZCCHC16 in eutherians. We examined the predicted SIRH11/ZCCHC16 open reading frame (ORF) in 95 eutherian species based on the genomic DNA information in GenBank. A large variation in the SIRH11/ZCCHC16 ORF was detected in several lineages. These include a lack of a CCHC RNA-binding domain in its C-terminus, observed in gibbons (Hylobatidae: Primates) and megabats (Megachiroptera: Chiroptera). A lack of the N-terminal half, on the other hand, was observed in New World monkeys (Platyrrhini: Primates) and species belonging to New World and African Hystricognaths (Caviomorpha and Bathyergidae: Rodents) along with Cetacea and Ruminantia (Cetartiodactyla). Among the hominoids, interestingly, three out of four genera of gibbons have lost normal SIRH11/ZCCHC16 function by deletion or the lack of the CCHC RNA-binding domain. Our extensive dN/dS analysis suggests that such truncated SIRH11/ZCCHC16 ORFs are functionally diversified even within lineages. Combined, our results show that SIRH11/ZCCHC16 may contribute to the diversification of eutherians by lineage-specific structural changes after its domestication in the common eutherian ancestor, followed by putative species-specific functional changes that enhanced fitness and occurred as a consequence of complex natural selection events

  8. Production, extraction and characterization of exopolysaccharides produced by the native Leuconostoc pseudomesenteroides R2 strain

    Directory of Open Access Journals (Sweden)

    Elinalva M. Paulo

    2012-06-01

    Full Text Available The genus Leuconostoc belongs to a group of lactic acid bacteria usually isolated from fermented vegetables, which includes species involved in the production of exopolysaccharides (EPS. These biopolymers possess considerable commercial potential. Because of the wide variety of industrial applications of EPS, this study aimed to produce and characterize the native exopolysaccharide strain Leuconostoc pseudomesenteroides R2, which was isolated from cabbage collected in a semi-arid region of Bahia. We employed the following conditions for the production of EPS: 10.7% sucrose, pH 8.2, without agitation and incubation at 28ºC for 30 hours. The fermentation broth was treated with ethanol and generated two types of polysaccharide substances (EPS I and EPS II. The identification of EPS I and EPS II was conducted using FT-IR, ¹H, 13C and DEPT-135 NMR spectra. The two substances were identified as linear dextran α polysaccharides (1 → 6 which indicated different characteristics with respect to thermal analysis and density of free packaging, viscosity and time of solubilization. Both dextrans are of low density, possess high thermal stability and exhibited the behavior characteristic of pseudoplastic polymers.O gênero Leuconostoc pertence a um grupo de bactérias lácticas normalmente isoladas de vegetais fermentados, que inclui espécies envolvidas na produção de exopolissacarídeos (EPS. Esses biopolímeros possuem potencial comercial considerável. Devido à grande variedade de aplicações industriais, de EPS, o presente estudo teve como objetivo produzir e caracterizar o nativo exopolissacarídeo cepa Leuconostoc pseudomesenteroides R2, que foi isolado de repolho coletado em uma região semi-árida da Bahia. Utilizamos as seguintes condições para a produção de EPS: 10,7% de sacarose, pH 8,2, sem agitação e incubação a 28º C por 30 horas. O caldo fermentado foi tratado com etanol, gerando dois tipos de substâncias de polissacar

  9. Isolation and characterization of a fipronil-degrading strain R-2 and its degrading characteristics%锐劲特降解菌株R-2的分离、鉴定及降解特性

    Institute of Scientific and Technical Information of China (English)

    宋瑶; 李荣; 王融; 张曼曼; 杨洪杏; 李顺鹏; 蒋建东

    2011-01-01

    A bacterial strain R-2, capable of degrading fipronil, was isolated from a long-term fipronil-polluted activated sludge in a fipronil manufacture factory. Strain R-2 was preliminarily identified as Paracoccus sp. based on its physiological and biochemical properties, as well as the 16S rRNA gene sequence analysis. Strain R-2 could utilize fipronil as the sole carbon source for growth, and degrade 85% of 50 mg/L fipronil within 3 d in mineral salts medium. The optimal pH value and temperature for fipronil degradation by strain R-2 were 6.0-7.0 and 30 ℃, respectively. The degrading rate showed a negative correlation with the initial concentration of fipronil. The addition of 0.1 mmol/L Zn2+or Fe3+ to the culture medium could significantly increase the degradation of fipronil. In both sterile and non-sterile soils, strain could remove 63.4%-71.2% of 100 μg/g fipronil within 10 d.%从长期受锐劲特污染的农药厂活性污泥中分离到一株锐劲特降解菌株R-2,根据其生理生化特征和16S rRNA基因序列同源性分析.将该菌株鉴定为Paracoccus sp..菌株R-2能以锐劲特为唯一碳源生长,在含有50 mg/L的锐劲特的基础盐培养基中,3 d的降解率达到85%.菌株R-2降解锐劲特的最适温度为30℃,最适pH值为6.0-7.0,其降解锐劲特的效率与锐劲特初始浓度呈负相关.添加0.1 mmol/L的Zn或Fe能够显著促进菌株对锐劲特的降解.灭菌与非灭菌土壤降解试验表明,菌株R-2均可以在10 d内降解63.4%-71.2%的100 μg/g的锐劲特.

  10. 基于螺旋理论的2R2T四自由度并联机器人机构综合%Type Synthesis of 2R2T 4-DOF Parallel Manipulators Based on Screw Theory

    Institute of Scientific and Technical Information of China (English)

    林玲; 刘辉

    2006-01-01

    基于螺旋理论,提出了2R2T四自由度并联机器人对称结构的一种设计方法;通过给定动平台的约束系统,采用螺旋理论和零空间方法,得到支链上所提供的基螺旋系;再经基螺旋系的组合,2R2T四自由度的一种新型的对称结构;分析了该机构的运动学性质.

  11. Detection of reactive ions in the ultracompact HII regions Mon R2 and G29.96-0.02

    CERN Document Server

    Rizzo, J R; Rodríguez-Franco, A; García-Burillo, S

    2003-01-01

    We report the first detection of the reactive ions CO+ and HOC+ towards ultracompact (UC) HII regions, particularly in Mon R2 and G29.96-0.02. We have observed two positions in Mon R2, namely the peak of the UC HII region and a position in the high density molecular cloud which bounds it. CO+ and HOC+ were detected at the UC HII region but not at the molecular cloud, as expected if the CO$^+$ and HOC$^+$ emissions arise in the PDR surrounding the \\uch. The measured CO$^+$ and HOC$^+$ column densities are of the order of 10$^{11}$ cm$^{-2}$ in both sources, which yields a strikingly low [HCO$^+$]/[HOC$^+$] abundance ratio of 460 in Mon R2. These values are similar to those found in some other well-known PDRs, like NGC 7023 and the Orion Bar. We briefly discuss the chemical implications of these results.

  12. Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris).

    Science.gov (United States)

    Stracke, Ralf; Holtgräwe, Daniela; Schneider, Jessica; Pucker, Boas; Sörensen, Thomas Rosleff; Weisshaar, Bernd

    2014-09-25

    The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Although genome-wide analysis of this gene family has been carried out in some species, the R2R3-MYB genes in Beta vulgaris ssp. vulgaris (sugar beet) as the first sequenced member of the order Caryophyllales, have not been analysed heretofore. We present a comprehensive, genome-wide analysis of the MYB genes from Beta vulgaris ssp. vulgaris (sugar beet) which is the first species of the order Caryophyllales with a sequenced genome. A total of 70 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Also, organ specific expression patterns were determined from RNA-seq data. The R2R3-MYB genes were functionally categorised which led to the identification of a sugar beet-specific clade with an atypical amino acid composition in the R3 domain, putatively encoding betalain regulators. The functional classification was verified by experimental confirmation of the prediction that the R2R3-MYB gene Bv_iogq encodes a flavonol regulator. This study provides the first step towards cloning and functional dissection of the role of MYB transcription factor genes in the nutritionally and evolutionarily interesting species B. vulgaris. In addition, it describes the flavonol regulator BvMYB12, being the first sugar beet R2R3-MYB with an experimentally proven function.

  13. Structural insights into the human RyR2 N-terminal region involved in cardiac arrhythmias

    Energy Technology Data Exchange (ETDEWEB)

    Borko, Ľubomír; Bauerová-Hlinková, Vladena, E-mail: vladena.bauerova@savba.sk; Hostinová, Eva; Gašperík, Juraj [Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava (Slovakia); Beck, Konrad [Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY Wales (United Kingdom); Lai, F. Anthony [Cardiff University School of Medicine, Cardiff CF14 4XN Wales (United Kingdom); Zahradníková, Alexandra, E-mail: vladena.bauerova@savba.sk [Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava (Slovakia); Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlárska 5, 833 34 Bratislava (Slovakia); Ševčík, Jozef, E-mail: vladena.bauerova@savba.sk [Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava (Slovakia)

    2014-11-01

    X-ray and solution structures of the human RyR2 N-terminal region were obtained under near-physiological conditions. The structure exhibits a unique network of interactions between its three domains, revealing an important stabilizing role of the central helix. Human ryanodine receptor 2 (hRyR2) mediates calcium release from the sarcoplasmic reticulum, enabling cardiomyocyte contraction. The N-terminal region of hRyR2 (amino acids 1–606) is the target of >30 arrhythmogenic mutations and contains a binding site for phosphoprotein phosphatase 1. Here, the solution and crystal structures determined under near-physiological conditions, as well as a homology model of the hRyR2 N-terminal region, are presented. The N-terminus is held together by a unique network of interactions among its three domains, A, B and C, in which the central helix (amino acids 410–437) plays a prominent stabilizing role. Importantly, the anion-binding site reported for the mouse RyR2 N-terminal region is notably absent from the human RyR2. The structure concurs with the differential stability of arrhythmogenic mutations in the central helix (R420W, I419F and I419F/R420W) which are owing to disparities in the propensity of mutated residues to form energetically favourable or unfavourable contacts. In solution, the N-terminus adopts a globular shape with a prominent tail that is likely to involve residues 545–606, which are unresolved in the crystal structure. Docking the N-terminal domains into cryo-electron microscopy maps of the closed and open RyR1 conformations reveals C{sup α} atom movements of up to 8 Å upon channel gating, and predicts the location of the leucine–isoleucine zipper segment and the interaction site for spinophilin and phosphoprotein phosphatase 1 on the RyR surface.

  14. p53R2 overexpression in cervical cancer promotes AKT signaling and EMT, and is correlated with tumor progression, metastasis and poor prognosis.

    Science.gov (United States)

    Jiang, Chao; Xu, Rui; Li, Xiao-Xing; Wang, Yan-Yan; Liang, Wen-Qian; Zeng, Ju-Deng; Zhang, Shan-Shan; Xu, Xiao-Yi; Yang, Yang; Zhang, Mei-Yin; Wang, Hui-Yun; Zheng, X F Steven

    2017-08-25

    p53R2 is a p53-inducible ribonucleotide reductase subunit involved in deoxyribonucleotide biosynthesis and DNA repair. Although p53R2 has been linked to human cancer, its role in cervical cancer remains unknown. In this study, we investigated the expression and clinical significance of p53R2 in early-stage cervical cancer. p53R2 expression is significantly upregulated at both mRNA and protein levels in cervical cancer cells and tissues, compared with that in matched normal cervical cells and tissues, respectively. p53R2 overexpression is associated with increased risk of pelvic lymph node metastasis (PLNM, p = 0.001) and cancer relapse (p = 0.009). Patients with high p53R2 expression have a shorter overall survival (OS) and disease-free survival (DFS). p53R2 is an independent factor for predicting OS and DFS of cervical cancer patients. We further show that p53R2 is important for oncogenic growth, migration and invasion in cervical cancer cells. Mechanistically, p53R2 promotes Akt signaling and epithelial-mesenchymal transition (EMT). In conclusion, our study demonstrates for the first time that p53R2 protein is overexpressed in early-stage cervical cancer and unravels some unconventional oncogenic functions of p53R2. p53R2 may be a useful prognostic biomarker and therapeutic target for cervical cancer.

  15. The Microsoft Data Warehouse Toolkit With SQL Server 2008 R2 and the Microsoft Business Intelligence Toolset

    CERN Document Server

    Mundy, Joy; Kimball, Ralph

    2011-01-01

    Best practices and invaluable advice from world-renowned data warehouse expertsIn this book, leading data warehouse experts from the Kimball Group share best practices for using the upcoming "Business Intelligence release" of SQL Server, referred to as SQL Server 2008 R2. In this new edition, the authors explain how SQL Server 2008 R2 provides a collection of powerful new tools that extend the power of its BI toolset to Excel and SharePoint users and they show how to use SQL Server to build a successful data warehouse that supports the business intelligence requirements that are common to most

  16. Synthesis, conformational preferences and antimicrobial evaluation of N-piperazinoacetyl-r-2,c-6-diphenylpiperidin-4-ones

    Science.gov (United States)

    Akila, A.; Jeganathan, P.; Ponnuswamy, S.

    2016-09-01

    Five new N-piperazinoacetyl-r-2,c-6-diphenylpiperidin-4-ones 11-15 have been synthesized and characterized using IR, 1H, 13C, DEPT & 2D NMR and mass spectral studies. The NMR spectral data indicate that the N-piperazinoacetyl-r-2,c-6-diphenylpiperidin-4-ones 11-15 prefer to exist in an equilibrium between B1 and B2 conformations. Furthermore, the antibacterial and antifungal studies were carried out. The results show that the piperazinoacetyl piperidin-4-ones 11-15 exhibit good activity against the selected bacterial and fungal strains.

  17. Spectroscopic studies of the iron and manganese reconstituted tyrosyl radical in Bacillus cereus ribonucleotide reductase R2 protein.

    Directory of Open Access Journals (Sweden)

    Ane B Tomter

    Full Text Available Ribonucleotide reductase (RNR catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g(1-value of 2.0090 for the tyrosyl radical was extracted. This g(1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν(7a = 1500 cm(-1 was found to be insensitive to deuterium-oxide exchange. Additionally, the (18O-sensitive Fe-O-Fe symmetric stretching (483 cm(-1 of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g(1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011 J Biol Chem 286: 33053-33060 indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8

  18. 8-THP-DHI analogs as potent Type I dual TIE-2/VEGF-R2 receptor tyrosine kinase inhibitors.

    Science.gov (United States)

    Hudkins, Robert L; Zulli, Allison L; Underiner, Ted L; Angeles, Thelma S; Aimone, Lisa D; Meyer, Sheryl L; Pauletti, Daniel; Chang, Hong; Fedorov, Elena V; Almo, Steven C; Fedorov, Alexander A; Ruggeri, Bruce A

    2010-06-01

    A novel series of 8-(2-tetrahydropyranyl)-12,13-dihydroindazolo[5,4-a]pyrrolo[3,4-c]carbazoles (THP-DHI) was synthesized and evaluated as dual TIE-2 and VEGF-R2 receptor tyrosine kinase inhibitors. Development of the structure-activity relationships (SAR) with the support of X-ray crystallography led to identification of 7f and 7g as potent, selective dual TIE-2/VEGF-R2 inhibitors with excellent cellular potency and acceptable pharmacokinetic properties. Compounds 7f and 7g were orally active in tumor models with no observed toxicity.

  19. Molecular cloning and evolutionary analysis of hog badger bitter taste receptor T2R2 gene%猪獾苦味受体T2R2基因的分子克隆与进化分析

    Institute of Scientific and Technical Information of China (English)

    徐怀亮; 姚永芳; 朱庆

    2009-01-01

    Recognition of natural bitter toxins through taste is one of the most effective mechanisms of self-safety. An approximate 1 169 bp sequence of the bitter taste receptor T2R2 gene was obtained by PCR and cloning technique from hog badger genomic DNA(GenBank accession number: FJ812727). This sequence contains a complete single exon (without intron) 915 bp in size, which encodes 304 amino acid residues. The isoelectric point (pi) of the protein is 9.76 and its mo-lecular weight is 34.74 kDa. Topology prediction showed that the T2R2 protein contained one N-glycosylation site, one N-myristoylation site, and two potential protein kinase C phosphorylation sites. Additionally, the whole peptide chain was comprised of seven transmembrane helix regions, four extracellular regions, and four intracellular regions. The T2R2 is a hydrophobic protein with a few hydrophilic components. Homology analysis of the T2R2 gene sequences by Clustal Windicated that the cDNA sequence homology of T2R2 gene in hog badger with dog, cat, cattle, horse, chimpanzee, and mouse is 91.4%, 90.6%, 84.4%, 85.4%, 83.8%and 72.1%, respectively, and the homology of amino acid sequence is 85.5%, 85.8%, 74.0%, 77.6%, 75.3% and 61.5%, respectively. The results of nucleotide acid substitution computation and selective test showed that strong purifying selection (functional constraint) occurred between hog badger and the six species, respec-tively, which mainly existed in the transmembrane regions of T2R2. In addition, the Neighbour-Joining tree of T2R2 gene exons from these seven species is consistent with their species tree, indicating that the T2R2 gene is suitable for constructing molecular phylogenetic tree among different species likewise.%苦味的感知是机体有效的自我保护机制之一,文章采用PCR和克隆测序方法首次从猪獾基因组中获得一全长为1 169 bp的苦味受体T2R2基因DNA序列(GenBank登录号:FJ812727).该序列含有完整的1个外

  20. NMR studies of the R2 repeat and related peptide fragments of the DNA binding domain of c-Myb. New light on the structure and folding of R2.

    Science.gov (United States)

    Ségalas, I.; Desjardins, S.; Oulyadi, H.; Prigent, Y.; Tribouillard, S.; Bernardi, E.; Schoofs, A. R.; Davoust1, D.; Toma, F.

    1999-10-01

    The solution structure of the R2 repeat of the DNA binding domain of the protooncogene c-Myb contains a N-terminal structural motif comprising two antiparallel helices. The motif is stabilized by interactions involving conserved residues. The recognition region in C-terminal position is flexible. This structure differs from that of R2 of another c-Myb protein. La structure en solution de la répétition R2 du domaine de liaison à l'ADN du protooncogène c-Myb possède un motif à deux hélices antiparallèles dans la moitié N-terminale, stabilisé par des interactions entre résidus conservés. La région de reconnaissance à l'ADN en position C-terminale est flexible. Cette structure diffère de celle montrée pour la répétition R2 d'une autre protéine c-Myb.

  1. Analysis of LINE-1 expression in human pluripotent cells.

    Science.gov (United States)

    Muñoz-Lopez, Martin; Garcia-Cañadas, Marta; Macia, Angela; Morell, Santiago; Garcia-Perez, Jose L

    2012-01-01

    Half of the human genome is composed of repeated DNA, and some types are mobile within our genome (transposons and retrotransposons). Despite their abundance, only a small fraction of them are currently active in our genome (Long Interspersed Element-1 (LINE-1), Alu, and SVA elements). LINE-1 or L1 elements are a family of active non-LTR retrotransposons, the ongoing mobilization of which still impacts our genome. As selfish DNA elements, L1 activity is more prominent in early human development, where new insertions would be transmitted to the progeny. Here, we describe the conventional methods aimed to determine the expression level of LINE-1 elements in pluripotent human cells.

  2. The mGluR2 positive allosteric modulator, SAR218645, improves memory and attention deficits in translational models of cognitive symptoms associated with schizophrenia

    OpenAIRE

    Guy Griebel; Philippe Pichat; Denis Boulay; Vanessa Naimoli; Lisa Potestio; Robert Featherstone; Sukhveen Sahni; Henry Defex; Christophe Desvignes; Franck Slowinski; Xavier Vigé; Bergis, Olivier E.; Rosy Sher; Raymond Kosley; Sathapana Kongsamut

    2016-01-01

    Normalization of altered glutamate neurotransmission through activation of the mGluR2 has emerged as a new approach to treat schizophrenia. These studies describe a potent brain penetrant mGluR2 positive allosteric modulator (PAM), SAR218645. The compound behaves as a selective PAM of mGluR2 in recombinant and native receptor expression systems, increasing the affinity of glutamate at mGluR2 as inferred by competition and GTPγ35S binding assays. SAR218645 augmented the mGluR2-mediated respons...

  3. Characterization of a citrus R2R3-MYB transcription factor that regulates the flavonol and hydroxycinnamic acid biosynthesis

    Science.gov (United States)

    Flavonols and hydroxycinnamic acids are important phenylpropanoid metabolites in plants. In this study, we isolated and characterized a citrus R2R3-MYB transcription factor CsMYBF1, encoding a protein belonging to the flavonol-specific MYB subgroup. Ectopic expression of CsMYBF1 in tomato led to an ...

  4. Synthesis of Novel Nucleoside Analog (3R)-2,3-Dideoxy-3- (N-hydroxy-N-methylamino)-L-arabinofuranosyl Uracil

    Institute of Scientific and Technical Information of China (English)

    Ji Cheng CHU; Hong Sheng GUO; Jun Biao CHANG; Kang ZHAO

    2004-01-01

    The synthesis of novel nucleoside analog (3R)-2,3-dideoxy-3-(N-hydroxy-N- methylamino)-L-arabinofuranosyl uracil was studied. A twelve-step synthetic route, started from L-ascorbic acid, was designed, and the final product was obtained in 20.8% yield.

  5. Improving the specificity of R2' to the deoxyhaemoglobin content of brain tissue: Prospective correction of macroscopic magnetic field gradients.

    Science.gov (United States)

    Blockley, Nicholas P; Stone, Alan J

    2016-07-15

    The reversible transverse relaxation rate, R2', is sensitive to the deoxyhaemoglobin content of brain tissue, enabling information about the oxygen extraction fraction to be obtained. However, R2' is also sensitive to macroscopic magnetic field gradients, particularly at air-tissue interfaces where a large susceptibility difference is present. It is important that this latter effect is minimised in order to produce meaningful estimates of blood oxygenation. Therefore, the aim of this study was to implement a technique to prospectively correct for the effect of susceptibility induced magnetic field gradients on R2' weighted data. This was achieved by combining the Gradient-Echo Slice Excitation Profile Imaging (GESEPI) technique with an Asymmetric Spin Echo (ASE) pulse sequence. The main advantages of this approach are (i) shorter acquisition times, since a separately acquired magnetic field map is not required and (ii) simpler analysis, since retrospective correction for the effects of magnetic field gradients in postprocessing is not required. In these experiments we show that with this newly developed technique it is possible to correct the majority of grey matter voxels for the expected distribution of through-slice magnetic field gradients to produce maps of R2' in a short scan duration.

  6. PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression

    Energy Technology Data Exchange (ETDEWEB)

    Rajakumara, Eerappa; Wang, Zhentian; Ma, Honghui; Hu, Lulu; Chen, Hao; Lin, Yan; Guo, Rui; Wu, Feizhen; Li, Haitao; Lan, Fei; Shi, Yujiang Geno; Xu, Yanhui; Patel, Dinshaw J.; Shi, Yang (MSKCC); (Constellation); (Fudan); (Tsinghua)

    2011-08-29

    Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHD{sub UHRF1}), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD{sub UHRF1} bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD{sub UHRF1} binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.

  7. R2P’s “Ulterior Motive Exemption” and the Failure to Protect in Libya

    Directory of Open Access Journals (Sweden)

    Jeffrey Bachman

    2015-11-01

    Full Text Available Mass atrocity prevention has been controversial, both when members of the international community have taken action as well as when they have failed to do so. In 1999, then UN Secretary-General Kofi Annan challenged the international community to reconcile the need to respect state sovereignty with the need to protect populations from egregious human rights violations. R2P’s emergence offered an opportunity to move past the discourse and practice associated with its predecessor—“humanitarian intervention.” However, while R2P has succeeded in changing the discourse, it has failed to make a change in practice. A source of this failure is R2P’s “ulterior motive exemption.” Using the R2P intervention in Libya as a case study, this article concludes that because ulterior motives existed: (1 NATO’s primary intent of civilian protection quickly evolved into the intent to overthrow Muammar Qaddafi; (2 in exceeding its mandate, NATO committed an act of aggression; (3 NATO continued to militarily support the rebels while they were committing war crimes and severe human rights violations; (4 NATO’s actions resulted in civilian casualties, which NATO has refused to investigate; and (5 NATO abdicated its responsibility to protect Libyans from the human suffering that continued subsequent to Qaddafi’s execution.

  8. Stability of R2* and quantitative susceptibility mapping of the brain tissue in a large scale multi-center study

    Science.gov (United States)

    Wang, Rongpin; Xie, Guangyou; Zhai, Maoxiong; Zhang, Zhongping; Wu, Bing; Zheng, Dandan; Hong, Nan; Jiang, Tao; Wen, Baohong; Cheng, Jingliang

    2017-01-01

    Multi-center studies are advantageous for enrolling participants of varying pathological and demographical conditions, and especially in neurological studies. Hence stability of the obtained quantitative R2* and susceptibility in multicenter studies is a key issue for their widespread applications. In this work, the stabilities of simultaneously obtained R2* and susceptibility are investigated and compared across 10 sites that are equipped with the same scanner and receiver coil, the same post-processing process was used to achieve consistent experiment setup. Two healthy adult volunteers (one male and female) participated in this study. High intraclass correlation coefficient was obtained for both susceptibility (0.94) and R2* (0.96). The coefficients of variance for all measurements obtained were smaller than 0.1, the largest variations of measurements in all the chosen ROIs fall within ±20% from the median value. Higher level of stability was obtained in R2* as compared to susceptibility at 1 mm resolution (P < 0.05) and at 1.5 mm (P < 0.01). PMID:28349957

  9. An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae (on linr)

    NARCIS (Netherlands)

    Wang, Kui-Lin; Bolitho, Karen; Grafton, Karryn; Kortstee, A.J.; Karunairetnam, Sakuntala; McGhie, T.K.; Espley, R.V.; Hellens, R.P.; Allan, A.C.

    2010-01-01

    Background - The control of plant anthocyanin accumulation is via transcriptional regulation of the genes encoding the biosynthetic enzymes. A key activator appears to be an R2R3 MYB transcription factor. In apple fruit, skin anthocyanin levels are controlled by a gene called MYBA or MYB1, while the

  10. Phosphorylation-Dependent PIH1D1 Interactions Define Substrate Specificity of the R2TP Cochaperone Complex

    Directory of Open Access Journals (Sweden)

    Zuzana Hořejší

    2014-04-01

    Full Text Available The R2TP cochaperone complex plays a critical role in the assembly of multisubunit machines, including small nucleolar ribonucleoproteins (snoRNPs, RNA polymerase II, and the mTORC1 and SMG1 kinase complexes, but the molecular basis of substrate recognition remains unclear. Here, we describe a phosphopeptide binding domain (PIH-N in the PIH1D1 subunit of the R2TP complex that preferentially binds to highly acidic phosphorylated proteins. A cocrystal structure of a PIH-N domain/TEL2 phosphopeptide complex reveals a highly specific phosphopeptide recognition mechanism in which Lys57 and 64 in PIH1D1, along with a conserved DpSDD phosphopeptide motif within TEL2, are essential and sufficient for binding. Proteomic analysis of PIH1D1 interactors identified R2TP complex substrates that are recruited by the PIH-N domain in a sequence-specific and phosphorylation-dependent manner suggestive of a common mechanism of substrate recognition. We propose that protein complexes assembled by the R2TP complex are defined by phosphorylation of a specific motif and recognition by the PIH1D1 subunit.

  11. R2P’s “Ulterior Motive Exemption” and the Failure to Protect in Libya

    Directory of Open Access Journals (Sweden)

    Jeffrey Bachman

    2015-11-01

    Full Text Available Mass atrocity prevention has been controversial, both when members of the international community have taken action as well as when they have failed to do so. In 1999, then UN Secretary-General Kofi Annan challenged the international community to reconcile the need to respect state sovereignty with the need to protect populations from egregious human rights violations. R2P’s emergence offered an opportunity to move past the discourse and practice associated with its predecessor—“humanitarian intervention.” However, while R2P has succeeded in changing the discourse, it has failed to make a change in practice. A source of this failure is R2P’s “ulterior motive exemption.” Using the R2P intervention in Libya as a case study, this article concludes that because ulterior motives existed: (1 NATO’s primary intent of civilian protection quickly evolved into the intent to overthrow Muammar Qaddafi; (2 in exceeding its mandate, NATO committed an act of aggression; (3 NATO continued to militarily support the rebels while they were committing war crimes and severe human rights violations; (4 NATO’s actions resulted in civilian casualties, which NATO has refused to investigate; and (5 NATO abdicated its responsibility to protect Libyans from the human suffering that continued subsequent to Qaddafi’s execution.

  12. Cloning of a third nitrate reductase gene from the cyanobacterium Anacystis nidulans R2 using a shuttle cosmid library

    NARCIS (Netherlands)

    Kuhlemeier, C.J.; Teeuwsen, V.J.P.; Janssen, M.J.T.; Arkel, G.A. van

    1984-01-01

    A strategy for gene cloning in the cyanobacterium Anacystis nidulans R2 was developed which made use of a gene library constructed in a shuttle cosmid vector. The method involved phenotypic complementation of mutants with pooled cosmid DNA. The development of the procedure and its application to the

  13. Mutation E169K in junctophilin-2 causes atrial fibrillation due to impaired RyR2 stabilization

    Science.gov (United States)

    Voigt, Niels; Garbino, Alejandro; Dixit, Sayali S.; Landstrom, Andrew P.; Li, Na; Wang, Qiongling; Olivotto, Iacopo; Dobrev, Dobromir; Ackerman, Michael J.; Wehrens, Xander H.T.

    2013-01-01

    Objectives To study the role of junctophilin 2 (JPH2) in atrial fibrillation (AF). Background JPH2 is believed to have an important role in sarcoplasmic reticulum (SR) Ca2+ handling and modulation of ryanodine receptor Ca2+ channels (RyR2). Whereas defective RyR2-mediated Ca2+ release contributes to the pathogenesis of AF, nothing is known about the potential role of JPH2 in atrial arrhythmias. Methods Screening 203 unrelated hypertrophic cardiomyopathy patients uncovered a novel JPH2 missense mutation (E169K) in 2 patients with juvenile-onset paroxysmal AF (pAF). Pseudo-knockin (PKI) mouse models were generated to determine the molecular defects underlying the development of AF caused by this JPH2 mutation. Results PKI mice expressing E169K mutant JPH2 exhibited a higher incidence of inducible AF compared with wildtype (WT)-PKI mice, while A399S-PKI mice expressing a HCM-linked JPH2 mutation not associated with atrial arrhythmias were not significantly different from WT-PKI. E169K-PKI but not A399A-PKI atrial cardiomyocytes showed an increased incidence of abnormal SR Ca2+ release events. These changes were attributed to reduced binding of E169KJPH2 to RyR2. Atrial JPH2 levels in WT-JPH2 transgenic, nontransgenic, and JPH2 knockdown mice correlated negatively with the incidence of pacing-induced AF. Ca2+ spark frequency in atrial myocytes and the open probability of single RyR2 channels from JPH2 knockdown mice was significantly reduced by a small JPH2-mimicking oligopeptide. Moreover, patients with pAF had reduced atrial JPH2 levels per RyR2 channel compared to sinus rhythm patients, and an increased frequency of spontaneous Ca2+ release events. Conclusions Our data suggest a novel mechanism by which reduced JPH2-mediated stabilization of RyR2 due to loss-of-function mutation or reduced JPH2:RyR2 ratios can promote SR Ca2+ leak and atrial arrhythmias, representing a potential novel therapeutic target for AF. PMID:23973696

  14. 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

    retrotransposon 1 (LORE1) for generating a virtually unlimited supply of insertion mutants simply by cultivating progeny from a single founder line. Novel insertions were then systematically annotated by combining an accurate and efficient amplification protocol with two-dimensional pooling and next......-generation sequencing. Automatic assignment of insertions to individuals within the pools was done using an in-house developed bioinformatics pipeline. Analysis of the 8935 novel LORE1 insertions obtained in this study showed LORE1 to be an efficient mutagen with strong exon-specific insertional preference....... 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...

  15. OBSERVATIONAL AND DYNAMICAL CHARACTERIZATION OF MAIN-BELT COMET P/2010 R2 (La Sagra)

    Energy Technology Data Exchange (ETDEWEB)

    Hsieh, Henry H.; Yang Bin; Haghighipour, Nader; Jedicke, Robert; Wainscoat, Richard J.; Denneau, Larry; Kaluna, Heather M.; Kleyna, Jan [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu HI 96822 (United States); Novakovic, Bojan [Department of Astronomy, Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade (Serbia); Abe, Shinsuke; Chen Wenping; Ip, Wing; Kinoshita, Daisuke [Institute of Astronomy, National Central University, 300 Jhongda Rd, Jhongli 32001, Taiwan (China); Fitzsimmons, Alan; Lacerda, Pedro [Astronomy Research Centre, Queens University Belfast, Belfast BT7 1NN (United Kingdom); Granvik, Mikael [Department of Physics, P.O. Box 64, 00014 University of Helsinki (Finland); Grav, Tommy [Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Knight, Matthew M. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Lisse, Carey M. [Planetary Exploration Group, Space Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723 (United States); Maclennan, Eric, E-mail: hsieh@ifa.hawaii.edu [Department of Physics and Astronomy, Northern Arizona University, 602 South Humphreys Street, Flagstaff, AZ 86011 (United States); and others

    2012-05-15

    We present observations of the recently discovered comet-like main-belt object P/2010 R2 (La Sagra) obtained by Pan-STARRS1 and the Faulkes Telescope-North on Haleakala in Hawaii, the University of Hawaii 2.2 m, Gemini-North, and Keck I telescopes on Mauna Kea, the Danish 1.54 m telescope (operated by the MiNDSTEp consortium) at La Silla, and the Isaac Newton Telescope on La Palma. An antisolar dust tail is observed to be present from 2010 August through 2011 February, while a dust trail aligned with the object's orbit plane is also observed from 2010 December through 2011 August. Assuming typical phase darkening behavior, P/La Sagra is seen to increase in brightness by >1 mag between 2010 August and December, suggesting that dust production is ongoing over this period. These results strongly suggest that the observed activity is cometary in nature (i.e., driven by the sublimation of volatile material), and that P/La Sagra is therefore the most recent main-belt comet to be discovered. We find an approximate absolute magnitude for the nucleus of H{sub R} = 17.9 {+-} 0.2 mag, corresponding to a nucleus radius of {approx}0.7 km, assuming an albedo of p = 0.05. Comparing the observed scattering surface areas of the dust coma to that of the nucleus when P/La Sagra was active, we find dust-to-nucleus area ratios of A{sub d} /A{sub N} = 30-60, comparable to those computed for fellow main-belt comets 238P/Read and P/2008 R1 (Garradd), and one to two orders of magnitude larger than for two other main-belt comets (133P/Elst-Pizarro and 176P/LINEAR). Using optical spectroscopy to search for CN emission, we do not detect any conclusive evidence of sublimation products (i.e., gas emission), finding an upper limit CN production rate of Q{sub CN} < 6 Multiplication-Sign 10{sup 23} mol s{sup -1}, from which we infer an H{sub 2}O production rate of Q{sub H{sub 2O}} < 10{sup 26} mol s{sup -1}. Numerical simulations indicate that P/La Sagra is dynamically stable for >100 Myr

  16. Gene Expression Profiling Identifies Important Genes Affected by R2 Compound Disrupting FAK and P53 Complex

    Energy Technology Data Exchange (ETDEWEB)

    Golubovskaya, Vita M., E-mail: Vita.Golubovskaya@roswellpark.org; Ho, Baotran [Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263 (United States); Conroy, Jeffrey [Genomics Shared Resource, Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY 14263 (United States); Liu, Song; Wang, Dan [Bioinformatics Core Facility, Biostatistics, Roswell Park Cancer Institute, Buffalo, NY 14263 (United States); Cance, William G. [Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263 (United States)

    2014-01-21

    Focal Adhesion Kinase (FAK) is a non-receptor kinase that plays an important role in many cellular processes: adhesion, proliferation, invasion, angiogenesis, metastasis and survival. Recently, we have shown that Roslin 2 or R2 (1-benzyl-15,3,5,7-tetraazatricyclo[3.3.1.1~3,7~]decane) compound disrupts FAK and p53 proteins, activates p53 transcriptional activity, and blocks tumor growth. In this report we performed a microarray gene expression analysis of R2-treated HCT116 p53{sup +/+} and p53{sup −/−} cells and detected 1484 genes that were significantly up- or down-regulated (p < 0.05) in HCT116 p53{sup +/+} cells but not in p53{sup −/−} cells. Among up-regulated genes in HCT p53{sup +/+} cells we detected critical p53 targets: Mdm-2, Noxa-1, and RIP1. Among down-regulated genes, Met, PLK2, KIF14, BIRC2 and other genes were identified. In addition, a combination of R2 compound with M13 compound that disrupts FAK and Mmd-2 complex or R2 and Nutlin-1 that disrupts Mdm-2 and p53 decreased clonogenicity of HCT116 p53{sup +/+} colon cancer cells more significantly than each agent alone in a p53-dependent manner. Thus, the report detects gene expression profile in response to R2 treatment and demonstrates that the combination of drugs targeting FAK, Mdm-2, and p53 can be a novel therapy approach.

  17. Bone quantitative susceptibility mapping using a chemical species-specific R2* signal model with ultrashort and conventional echo data.

    Science.gov (United States)

    Dimov, Alexey V; Liu, Zhe; Spincemaille, Pascal; Prince, Martin R; Du, Jiang; Wang, Yi

    2017-03-05

    To develop quantitative susceptibility mapping (QSM) of bone using an ultrashort echo time (UTE) gradient echo (GRE) sequence for signal acquisition and a bone-specific effective transverse relaxation rate ( R2*) to model water-fat MR signals for field mapping. Three-dimensional radial UTE data (echo times ≥ 40 μs) was acquired on a 3 Tesla scanner and fitted with a bone-specific signal model to map the chemical species and susceptibility field. Experiments were performed ex vivo on a porcine hoof and in vivo on healthy human subjects (n = 7). For water-fat separation, a bone-specific model assigning R2* decay mostly to water was compared with the standard models that assigned the same decay for both fat and water. In the ex vivo experiment, bone QSM was correlated with CT. Compared with standard models, the bone-specific R2* method significantly reduced errors in the fat fraction within the cortical bone in all tested data sets, leading to reduced artifacts in QSM. Good correlation was found between bone CT and QSM values in the porcine hoof (R(2)  = 0.77). Bone QSM was successfully generated in all subjects. The QSM of bone is feasible using UTE with a conventional echo time GRE acquisition and a bone-specific R2* signal model. Magn Reson Med 000:000-000, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  18. Casein-Coated Fe5C2 Nanoparticles with Superior r2 Relaxivity for Liver-Specific Magnetic Resonance Imaging.

    Science.gov (United States)

    Cowger, Taku A; Tang, Wei; Zhen, Zipeng; Hu, Kai; Rink, David E; Todd, Trever J; Wang, Geoffrey D; Zhang, Weizhong; Chen, Hongmin; Xie, Jin

    2015-01-01

    Iron oxide nanoparticles have been extensively used as T2 contrast agents for liver-specific magnetic resonance imaging (MRI). The applications, however, have been limited by their mediocre magnetism and r2 relaxivity. Recent studies show that Fe5C2 nanoparticles can be prepared by high temperature thermal decomposition. The resulting nanoparticles possess strong and air stable magnetism, suggesting their potential as a novel type of T2 contrast agent. To this end, we improve the synthetic and surface modification methods of Fe5C2 nanoparticles, and investigated the impact of size and coating on their performances for liver MRI. Specifically, we prepared 5, 14, and 22 nm Fe5C2 nanoparticles and engineered their surface by: 1) ligand addition with phospholipids, 2) ligand exchange with zwitterion-dopamine-sulfonate (ZDS), and 3) protein adsorption with casein. It was found that the size and surface coating have varied levels of impact on the particles' hydrodynamic size, viability, uptake by macrophages, and r2 relaxivity. Interestingly, while phospholipid- and ZDS-coated Fe5C2 nanoparticles showed comparable r2, the casein coating led to an r2 enhancement by more than 2 fold. In particular, casein coated 22 nm Fe5C2 nanoparticle show a striking r2 of 973 mM(-1)s(-1), which is one of the highest among all of the T2 contrast agents reported to date. Small animal studies confirmed the advantage of Fe5C2 nanoparticles over iron oxide nanoparticles in inducing hypointensities on T2-weighted MR images, and the particles caused little toxicity to the host. The improvements are important for transforming Fe5C2 nanoparticles into a new class of MRI contrast agents. The observations also shed light on protein-based surface modification as a means to modulate contrast ability of magnetic nanoparticles.

  19. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.

    Directory of Open Access Journals (Sweden)

    Ivana Nemčovičová

    2013-03-01

    Full Text Available The TRAIL (TNF-related apoptosis inducing ligand death receptors (DRs of the tumor necrosis factor receptor superfamily (TNFRSF can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways.

  20. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.

    Science.gov (United States)

    Nemčovičová, Ivana; Benedict, Chris A; Zajonc, Dirk M

    2013-03-01

    The TRAIL (TNF-related apoptosis inducing ligand) death receptors (DRs) of the tumor necrosis factor receptor superfamily (TNFRSF) can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV) expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER) and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways.

  1. Co-translational localization of an LTR-retrotransposon RNA to the endoplasmic reticulum nucleates virus-like particle assembly sites.

    Directory of Open Access Journals (Sweden)

    Jung H Doh

    2014-03-01

    Full Text Available The transcript of retrovirus-like transposons functions as an mRNA for synthesis of capsid and replication proteins and as the genomic RNA of virus-like particles (VLPs, wherein the genome is replicated. Retrotransposon RNA and proteins coalesce in a cytoplasmic focus, or retrosome, to initiate VLP assembly, but it is not known how the retrosome is nucleated. We determined how the RNA and Gag protein of the Saccharomyces cerevisiae Ty1 retrotransposon are directed to the retrosome. We found that Ty1 RNA is translated in association with signal recognition particle (SRP, a universally conserved chaperone that binds specific ribosome-nascent chain (RNC complexes and targets the nascent peptide to the endoplasmic reticulum (ER. Gag is translocated to the ER lumen; yet, it is also found in the cytoplasm, associated with SRP-RNC complexes. In the absence of ER translocation, Gag is synthesized but rapidly degraded, and Ty1 RNA does not coalesce in retrosomes. These findings suggest that Gag adopts a stable conformation in the ER lumen, is retrotranslocated to the cytoplasm, binds to Ty1 RNA on SRP-RNC complexes and multimerizes to nucleate retrosomes. Consistent with this model, we show that slowing the rate of co-translational ER translocation by limiting SRP increases the prevalence of retrosomes, while suppressing the translocation defect of srp hypomorphs by slowing translational elongation rapidly decreases retrosome formation. Thus, retrosomes are dynamic foci of Ty1 RNA-RNC complexes whose formation is modulated by the rate of co-translational ER translocation. Together, these findings suggest that translating Ty1 mRNA and the genomic RNA of VLPs originate in a single pool and moreover, that co-translational localization of Ty1 RNA nucleates the presumptive VLP assembly site. The separation of nascent Gag from its RNA template by transit through the ER allows Gag to bind translating Ty1 RNA without displaying a cis-preference for its encoding

  2. 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.

  3. A Novel Retrotransposon Inserted in the Dominant Vrn-B1 Allele Confers Spring Growth Habit in Tetraploid Wheat (Triticum turgidum L.).

    Science.gov (United States)

    Chu, C-G; Tan, C T; Yu, G-T; Zhong, S; Xu, S S; Yan, L

    2011-12-01

    Vernalization genes determine winter/spring growth habit in temperate cereals and play important roles in plant development and environmental adaptation. In wheat (Triticum L. sp.), it was previously shown that allelic variation in the vernalization gene VRN1 was due to deletions or insertions either in the promoter or in the first intron. Here, we report a novel Vrn-B1 allele that has a retrotransposon in its promoter conferring spring growth habit. The VRN-B1 gene was mapped in a doubled haploid population that segregated for winter-spring growth habit but was derived from two spring tetraploid wheat genotypes, the durum wheat (T. turgidum subsp. durum) variety 'Lebsock' and T. turgidum subsp. carthlicum accession PI 94749. Genetic analysis revealed that Lebsock carried the dominant Vrn-A1 and recessive vrn-B1 alleles, whereas PI 94749 had the recessive vrn-A1 and dominant Vrn-B1 alleles. The Vrn-A1 allele in Lebsock was the same as the Vrn-A1c allele previously reported in hexaploid wheat. No differences existed between the vrn-B1 and Vrn-B1 alleles, except that a 5463-bp insertion was detected in the 5'-UTR region of the Vrn-B1 allele. This insertion was a novel retrotransposon (designated as retrotrans_VRN), which was flanked by a 5-bp target site duplication and contained primer binding site and polypurine tract motifs, a 325-bp long terminal repeat, and an open reading frame encoding 1231 amino acids. The insertion of retrotrans_VRN resulted in expression of Vrn-B1 without vernalization. Retrotrans_VRN is prevalent among T. turgidum subsp. carthlicum accessions, less prevalent among T. turgidum subsp. dicoccum accessions, and rarely found in other tetraploid wheat subspecies.

  4. Rolling Deck to Repository (R2R): Supporting Global Data Access Through the Ocean Data Interoperability Platform (ODIP)

    Science.gov (United States)

    Arko, R. A.; Stocks, K.; Chandler, C. L.; Smith, S. R.; Miller, S. P.; Maffei, A. R.; Glaves, H. M.; Carbotte, S. M.

    2013-12-01

    The U.S. National Science Foundation supports a fleet of academic research vessels operating throughout the world's oceans. In addition to supporting the mission-specific goals of each expedition, these vessels routinely deploy a suite of underway environmental sensors, operating like mobile observatories. Recognizing that the data from these instruments have value beyond each cruise, NSF funded R2R in 2009 to ensure that these data are routinely captured, cataloged and described, and submitted to the appropriate national repository for long-term public access. In 2013, R2R joined the Ocean Data Interoperability Platform (ODIP; http://odip.org/). The goal of ODIP is to remove barriers to the effective sharing of data across scientific domains and international boundaries, by providing a forum to harmonize diverse regional systems. To advance this goal, ODIP organizes international workshops to foster the development of common standards and develop prototypes to evaluate and test potential standards and interoperability solutions. ODIP includes major organizations engaged in ocean data stewardship in the EU, US, and Australia, supported by the International Oceanographic Data and Information Exchange (IODE). Within the broad scope of ODIP, R2R focuses on contributions in 4 key areas: ● Implement a 'Linked Open Data' approach to disseminate data and documentation, using existing World Wide Web Consortium (W3C) specifications and machine-readable formats. Exposing content as Linked Open Data will provide a simple mechanism for ODIP collaborators to browse and compare data sets among repositories. ● Map key vocabularies used by R2R to their European and Australian counterparts. The existing heterogeneity among terms inhibits data discoverability, as a user searching on the term with which s/he is familiar may not find all data of interest. Mapping key terms across the different ODIP partners, relying on the backbone thesaurus provided by the NERC Vocabulary Server

  5. 圈4C 的(r1,r2,r3,r4)−冠的优美性%The gracefulness of the (r1, r2, r3, r4)−corona of the cycle 4C

    Institute of Scientific and Technical Information of China (English)

    吴跃生

    2012-01-01

      讨论了圈4C 的( r r 21,,, r r 43)−冠的优美性,用构造性的方法给出了圈4C 的( r r 21,,, r r 43)−冠的优美标号。证明了圈4C 的( r r 21,,, r r 43)−冠都是交错图。%  Discussed the gracefulness of the( r r 2 1 , , , r r 4 3 )−corona of the cycle 4C .The graceful labeling was given.Proved that the( r r 2 1 , , , r r 4 3 )−corona of the cycle 4C are graceful graph.

  6. Identificación de Genes R1 y R2 que confieren resistencia a Phytophthora infestans en genotipos colombianos de papa Identification of R1 and R2 Genes conferring resistance to Phytophthora infestans in Colombian potato genotypes

    Directory of Open Access Journals (Sweden)

    Núñez Víctor M.

    2003-12-01

    Full Text Available En Colombia, actualmente existen genotipos de papa con excelente calidad industrial pero muy susceptibles a P. infestans. La mejor manera de combatir este problema es mediante resistencia genética, puesto que la inversión para controlar esta enfermedad por medios químicos es muy costosa, sin olvidar la contaminación ambiental que producen. El objetivo de este trabajo fue la identificación de genes R1 y R2 en los diferenciales de papa respectivos (Solanum tuberosum ssp. tuberosum mediante evaluación de resistencia a P. infestans y la detección molecular por medio de PCR (alelo R1 y AFLP (alelo R2. Para la detección del alelo R1 fueron empleados los primers GP179, GP21, 76-2SF2/76-2SR, SPUD237 y Sol 2749-2770F / Sol 3246-3267R. Los primers GP179, GP21 y SPUD237 fueron inespecíficos para Rl, ya que se generó un producto de amplificación en los diferenciales 1 y 2, así como también en Solanum phureja. Los primers 76-2SF2/76-2SR, y Sol 2749-2770F / Sol 3246-3267R generaron un producto de amplificación en los diferenciales 1 y 2; por el contrario, el fragmento estuvo ausente en el material susceptible. Para la detección del alelo R2, fueron implementados cinco marca­dores AFLP, de los cuales sólo dos fueron reconocidos visualmente en el diferencial 2. Los resultados mostra­ron una evidente correspondencia fenotípica y genotípica con respecto a la presencia de los genes Rl y R2. La identificación molecular de genes de resistencia a P. infestans permitirá desarrollar programas de mejoramiento genético que beneficien directamente los rendimientos de los cultivos de papa, sobre todo los de mayor interés industrial para nuestro país.Excellent industrial quality potato genotypes are currently available in Colombia; however, they are very sus­ceptible to P. infestans. The best way of fighting this problem is by genetic resistance, given that the expense of controlling this disease through chemicals is high, plus the environmental

  7. The Construction and Optimization of Moodle Platform on Windows Server 2012 R2 and Wamp Server%基于Windows Server 2012 R2、WampServer环境的Moodle平台搭建及优化扩展

    Institute of Scientific and Technical Information of China (English)

    马东宇

    2014-01-01

    研究了以WampServer集成环境为Web服务器,在Windows Server 2012 R2系统下搭建Moodle平台的过程,经比较试验得出了基于 Windows 8界面操作系统的平台架设环境,并从功能扩展和性能优化等方面给出了解决方案。%A process of Moodle platform construction is researched,using WampServer integrating environment as Web server under a system of Windows Server 2012 R2.After comparable experiments,a platform construction environment on Windows 8 surface operating system is got.And a solution is given from functional expansion,performance optimization and other aspects.

  8. A Classification of Quadratic Harmonic Morphisms Between Semi-Euclidean Spaces R3r→R2s%二次调和同态φ:R3r→R2s的分类

    Institute of Scientific and Technical Information of China (English)

    卢卫君; 方丽菁

    2005-01-01

    在给出半定欧氏空间之间二次调和同态的结构方程之后,通过对结构方程的系数矩阵的分析及特殊坐标系的运用,推广Ou-Wood关于欧氏空间之间二次调和同态的结果,获得二次调和同态R3r→R2s的分类.%In this paper,we study quadratic harmonic morphisms between semi-Euclidean spaces.We give a structure equation of such morphisms using their coefficient matrices analysis and special coordinates generalizing the results of Ou-Wood on quadratic harmonic morphisms between Euclidean spaces.As an application,we obtain a classification of quadratic harmonic morphisms R3r→R2s.

  9. Muscle-specific overexpression of AdipoR1 or AdipoR2 gives rise to common and discrete local effects whilst AdipoR2 promotes additional systemic effects

    Science.gov (United States)

    Keshvari, Sahar; Henstridge, Darren C.; Ng, Choaping; Febbraio, Mark A.; Whitehead, Jonathan P.

    2017-01-01

    Hypoadiponectinemia and adiponectin resistance are implicated in the aetiology of obesity-related cardiometabolic disorders, hence represent a potential therapeutic axis. Here we characterised the effects of in vivo electrotransfer-mediated overexpression of the adiponectin receptors, AdipoR1 or AdipoR2, into tibialis anterior muscle (TAM) of lean or obese mice. In lean mice, TAM-specific overexpression of AdipoR1 (TAMR1) or AdipoR2 (TAMR2) increased phosphorylation of AMPK, AKT and ERK and expression of the insulin responsive glucose transporter glut4. In contrast, only TAMR2 increased pparα and a target gene acox1. These effects were decreased in obese mice despite no reduction in circulating adiponectin levels. TAMR2 also increased expression of adipoQ in TAM of lean and obese mice. Furthermore, in obese mice TAMR2 promoted systemic effects including; decreased weight gain; reduced epididymal fat mass and inflammation; increased epididymal adipoQ expression; increased circulating adiponectin. Collectively, these results demonstrate that AdipoR1 and AdipoR2 exhibit overlapping and distinct effects in skeletal muscle consistent with enhanced adiponectin sensitivity but these appear insufficient to ameliorate established obesity-induced adiponectin resistance. We also identify systemic effects upon TAMR2 in obese mice and postulate these are mediated by altered myokine production. Further studies are warranted to investigate this possibility which may reveal novel therapeutic approaches. PMID:28145500

  10. Web-based health care agents; the case of reminders and todos, too (R2Do2).

    Science.gov (United States)

    Silverman, B G; Andonyadis, C; Morales, A

    1998-11-01

    This paper describes efforts to develop and field an agent-based, healthcare middleware framework that securely connects practice rule sets to patient records to anticipate health todo items and to remind and alert users about these items over the web. Reminders and todos, too (R2Do2) is an example of merging data- and document-centric architectures, and of integrating agents into patient-provider collaboration environments. A test of this capability verifies that R2Do2 is progressing toward its two goals: (1) an open standards framework for middleware in the healthcare field; and (2) an implementation of the 'principle of optimality' to derive the best possible health plans for each user. This paper concludes with lessons learned to date.

  11. 2MASS wide field extinction maps: IV. The Orion, Mon R2, Rosette, and Canis Major star forming regions

    CERN Document Server

    Lombardi, Marco; lada, Charles

    2011-01-01

    We present a near-infrared extinction map of a large region (approximately 2200 deg^2) covering the Orion, the Monoceros R2, the Rosette, and the Canis Major molecular clouds. We used robust and optimal methods to map the dust column density in the near-infrared (NICER and NICEST) towards ~19 million stars of the Two Micron All Sky Survey (2MASS) point source catalog. Over the relevant regions of the field, we reached a 1-sigma error of 0.03 mag in the K-band extinction with a resolution of 3 arcmin. We measured the cloud distances by comparing the observed density of foreground stars with the prediction of galactic models, thus obtaining d_{Orion A} = (371 +/- 10) pc, d_{Orion B} = (398 +/- 12) pc, $d_{Mon R2} = (905 +/- 37) pc, $d_{Rosette} = (1330 +/- 48) pc, and $d_{CMa} = (1150 +/- 64) pc, values that compare very well with independent estimates.

  12. Rolling Deck to Repository (R2R): Organizing Datasets from Heterogeneous Shipboard Data into an Integrated Catalog

    Science.gov (United States)

    Clark, P. D.; Arko, R. A.; Sweeney, A.; Fischman, D.; Miller, S. P.; Stocks, K.

    2010-12-01

    The goal of the Rolling Deck to Repository (R2R; rvdata.us) program is to develop and implement a fleet-wide information management system to preserve and provide access to routine underway data collected by U.S. academic research vessels. One of the program’s primary challenges is to develop a workflow for routinely gathering data from a fleet with heterogeneous instrumentation and file systems, breaking out the data into discrete data sets, and transferring the data to the appropriate National Data Center. Because R2R expects to receive 300-400 cruises per year from a wide range of vessel classes and at least two dozen major device types, this workflow must be highly automated. R2R has developed and implemented a workflow for processing underway data: - Collection: data are provided at the end of a cruise as a cruise distribution using the mechanism preferred by the vessel operator. - Inventory: a complete inventory of each cruise distribution is created, listing the filename, date, size, and checksum. This inventory is published online by R2R. - Raw Archive: the entire original cruise distribution is transmitted securely to the National Geophysical Data Center for deep archive. - Data Breakout: data from each device are extracted from the cruise distribution according to a vessel profile yielding a discrete data set. Once a data set is broken out and any proprietary holds are cleared, it is delivered to the appropriate National Data Center for archiving and dissemination. It may also be processed further for quality assessment/quality control and/or publication of standard products. Data sets sent to a National Data Center will have unique and persistent R2R identifiers, which link to parent cruise information on the R2R site. The site will include the URL link to each data set at the National Data Center, allowing a user browsing the R2R cruise catalog to download it. Because each vessel operator typically has a customized system for naming and organizing

  13. Role of GluR2 expression in AMPA-induced toxicity in cultured murine cerebral cortical neurons

    DEFF Research Database (Denmark)

    Jensen, Jette Bisgaard; Lund, Trine Meldgaard; Timmermann, Daniel B.

    2001-01-01

    alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPA-R)-mediated neurotoxicity was studied in relation to subunit expression and the presence of Ca(2+)-permeable receptor channels. AMPA-mediated toxicity had two components: 1) a direct AMPA-R-mediated component, which was not due...... of the Mg(2+) block of the NMDA receptor on AMPA-R stimulation. The involvement of Ca(2+) influx through AMPA-R was also examined. The number of neurons possessing Ca(2+)-permeable AMPA-R increased during culture development, concurrently with an increasing susceptibility for AMPA-induced toxicity during...... development. GluR2(R) levels also increased during development, and channel blockers of Ca(2+)-permeable AMPA-R lacking the GluR2(R) subunit (spermine and philanthotoxin) failed to prevent neurotoxicity or increases in [Ca(2+)](i). Thus, the direct AMPA-R-mediated toxicity may be explained by initiation...

  14. Ab initio study of metastable layered perovskites R2Ti2O7 (R = Sm and Gd)

    Science.gov (United States)

    Sayede, Adlane; Bruyer, Emilie; Springborg, Michael

    2012-09-01

    The structural, electronic, and ferroelectric properties of metastable R2Ti2O7(R= Sm and Gd) layered perovskites materials are investigated by first-principles density functional theory calculations. The computed structural parameters are found to be in good agreement with experimental findings. The calculated spontaneous polarizations of the studied titanates are found to be larger than the spontaneous polarization of the usual R2Ti2O7 layered perovskites materials. GGA+U electronic structures predict a good photocatalytic activity for the studied compounds, in particular for Gd2Ti2O7, which lacks electron-carriers trapping in the conduction band. From the results of the total energy and the polarization as functions of structure we estimate the responses of the materials to external electrostatic fields.

  15. Comparing consistency of R2* and T2*-weighted BOLD analysis of resting state fetal fMRI

    Science.gov (United States)

    Seshamani, Sharmishtaa; Blazejewska, Anna I.; Gatenby, Christopher; Mckown, Susan; Caucutt, Jason; Dighe, Manjiri; Studholme, Colin

    2015-03-01

    Understanding when and how resting state brain functional activity begins in the human brain is an increasing area of interest in both basic neuroscience and in the clinical evaluation of the brain during pregnancy and after premature birth. Although fMRI studies have been carried out on pregnant women since the 1990's, reliable mapping of brain function in utero is an extremely challenging problem due to the unconstrained fetal head motion. Recent studies have employed scrubbing to exclude parts of the time series and whole subjects from studies in order to control the confounds of motion. Fundamentally, even after correction of the location of signals due to motion, signal intensity variations are a fundamental limitation, due to coil sensitivity and spin history effects. An alternative technique is to use a more parametric MRI signal derived from multiple echoes that provides a level of independence from basic MRI signal variation. Here we examine the use of R2* mapping combined with slice based multi echo geometric distortion correction for in-utero studies. The challenges for R2* mapping arise from the relatively low signal strength of in-utero data. In this paper we focus on comparing activation detection in-utero using T2W and R2* approaches. We make use a subset of studies with relatively limited motion to compare the activation patterns without the additional confound of significant motion. Results at different gestational ages indicate comparable agreement in many activation patterns when limited motion is present, and the detection of some additional networks in the R2* data, not seen in the T2W results.

  16. Modulation of sweet taste by umami compounds via sweet taste receptor subunit hT1R2.

    Directory of Open Access Journals (Sweden)

    Jaewon Shim

    Full Text Available Although the five basic taste qualities-sweet, sour, bitter, salty and umami-can be recognized by the respective gustatory system, interactions between these taste qualities are often experienced when food is consumed. Specifically, the umami taste has been investigated in terms of whether it enhances or reduces the other taste modalities. These studies, however, are based on individual perception and not on a molecular level. In this study we investigated umami-sweet taste interactions using umami compounds including monosodium glutamate (MSG, 5'-mononucleotides and glutamyl-dipeptides, glutamate-glutamate (Glu-Glu and glutamate-aspartic acid (Glu-Asp, in human sweet taste receptor hT1R2/hT1R3-expressing cells. The sensitivity of sucrose to hT1R2/hT1R3 was significantly attenuated by MSG and umami active peptides but not by umami active nucleotides. Inhibition of sweet receptor activation by MSG and glutamyl peptides is obvious when sweet receptors are activated by sweeteners that target the extracellular domain (ECD of T1R2, such as sucrose and acesulfame K, but not by cyclamate, which interact with the T1R3 transmembrane domain (TMD. Application of umami compounds with lactisole, inhibitory drugs that target T1R3, exerted a more severe inhibitory effect. The inhibition was also observed with F778A sweet receptor mutant, which have the defect in function of T1R3 TMD. These results suggest that umami peptides affect sweet taste receptors and this interaction prevents sweet receptor agonists from binding to the T1R2 ECD in an allosteric manner, not to the T1R3. This is the first report to define the interaction between umami and sweet taste receptors.

  17. Magnetic phase diagrams of R2RhIn8 (R = Tb, Dy, Ho, Er and Tm) compounds.

    Science.gov (United States)

    Cermák, P; Kratochvílová, M; Pajskr, K; Javorský, P

    2012-05-23

    We have grown and characterized single crystals of R(2)RhIn(8) (R=Tb, Dy, Ho, Er and Tm) compounds crystallizing in the tetragonal Ho(2)CoGa(8)-type crystal structure. Their magnetic properties were studied by specific heat and magnetization measurements. All the investigated compounds order antiferromagnetically with Néel temperatures of 43.6, 25.1, 10.9, 3.8 and 4.1 K, respectively. Magnetic phase diagrams were constructed.

  18. ERp46 binds to AdipoR1, but not AdipoR2, and modulates adiponectin signalling

    Energy Technology Data Exchange (ETDEWEB)

    Charlton, Hayley K.; Webster, Julie; Kruger, Sarah; Simpson, Fiona; Richards, Ayanthi A. [Diamantina Institute for Cancer, Immunology and Metabolic Medicine, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD 4102 (Australia); Whitehead, Jonathan P., E-mail: j.whitehead1@uq.edu.au [Diamantina Institute for Cancer, Immunology and Metabolic Medicine, University of Queensland, Princess Alexandra Hospital, Brisbane, QLD 4102 (Australia)

    2010-02-05

    The pleiotropic effects of the insulin-sensitizing adipokine adiponectin are mediated, at least in part, by two seven-transmembrane domain receptors AdipoR1 and AdipoR2. Recent reports indicate a role for AdipoR-binding proteins, namely APPL1, RACK1 and CK2{beta}, in proximal signal transduction events. Here we demonstrate that endoplasmic reticulum protein 46 (ERp46) interacts specifically with AdipoR1 and provide evidence that ERp46 modulates adiponectin signalling. Co-immunoprecipitation followed by mass spectrometry identified ERp46 as an AdipoR1-, but not AdipoR2-, interacting protein. Analysis of truncated constructs and GST-fusion proteins revealed the interaction was mediated by the cytoplasmic, N-terminal residues (1-70) of AdipoR1. Indirect immunofluorescence microscopy and subcellular fractionation studies demonstrated that ERp46 was present in the ER and the plasma membrane (PM). Transient knockdown of ERp46 increased the levels of AdipoR1, and AdipoR2, at the PM and this correlated with increased adiponectin-stimulated phosphorylation of AMPK. In contrast, adiponectin-stimulated phosphorylation of p38MAPK was reduced following ERp46 knockdown. Collectively these results establish ERp46 as the first AdipoR1-specific interacting protein and suggest a role for ERp46 in adiponectin receptor biology and adiponectin signalling.

  19. R2E-related MD: slow controlled losses for RadMon/BLM cross-checks

    CERN Document Server

    Calviani, M; Spiezia, G; Sapinski, M; Priebe, A; Nordt, A; Pojer, M; CERN. Geneva. ATS Department

    2011-01-01

    The purpose of the dedicated R2E MD has been to evaluate the R factor (i.e. the ratio between the thermal neutron fluence and the high energy hadron fluence (>20MeV) for various tunnel locations, to measure the HEH radiation level gradient along the MBC dipole and on the MQ, to check the ratio the BLM measured dose and RadMon SEU counts and to study the dose gradient between the standard BLM beam axis location and at the level of the equipment location. Within the R2E Mitigation Project, these accurate measurement and cross-check of the mentioned parameters are of great importance for the evaluation and interpretation of the R2E-related radiation levels, as well as for the evaluation of the failure cross-section of specific equipment (i.e. QPS ISO150). In addition, a short part of the MD has been devoted to the comparison of BLM signals generated by loss directed inwards and outwards with respect to the LHC ring.

  20. Using the Nonverbal Test SON-R2 ½ - 7 [a] to Assess Children with Autism Spectrum Disorders

    Directory of Open Access Journals (Sweden)

    Elizeu Coutinho de Macedo

    2013-11-01

    Full Text Available The relevance of cognitive assessment in Autism Spectrum Disorders is due to the association between cognitive deficits and severity of symptoms, adaptive functioning, prognosis and planning of more effective interventions.Thus, the aim of this study was to verify the non-verbal test of intelligence SON-R 2 ½ - 7 [a] adequacy in ASD group of children. The participants were 18 boys aged 4 and 7 years old, diagnosed based on the DSM-IV-TR and scored on screening instruments. The nonverbal intelligence test SON-R 2 ½ - 7 [a], the Autism Behavior Checklist (ABC, the Autism Screening Questionnaire (ASQ and the Vineland Adaptive Behavior Scales (VABS were used. The results showed that 55.6% of the group had IQs below average, and there was significant difference between the performance of TEA group and normative sample in the four subtests that compose the instrument. Intra-group analysis showed statistically significant differences between subtests, although these showed significant positive correlations with each other. Negative and significant correlations were observed between IQ Total in SON-R 2 ½ - 7 [a] the ABC and ASQ, as well as positive and significant correlations were observed between Total IQ and VABS. The results corroborate previous findings that indicate moderate relationships between intelligence, severityof symptoms and functionality, as well as the presence of specific profile of nonverbal performance in ASD group.

  1. From forced collapse to H ii region expansion in Mon R2: Envelope density structure and age determination with Herschel

    CERN Document Server

    Didelon, P; Tremblin, P; Hill, T; Hony, S; Hennemann, M; Hennebelle, P; Anderson, L D; Galliano, F; Schneider, N; Rayner, T; Rygl, K; Louvet, F; Zavagno, A; Konyves, V; Sauvage, M; Andre, Ph; Bontemps, S; Peretto, N; Griffin, M; Gonzalez, M; Lebouteiller, V; Arzoumanian, D; Benedettini, M; Di Francesco, J; Menshchikov, A; Minier, V; Luong, Q