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Sample records for sasanda ltr copia

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

    Science.gov (United States)

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

    2017-10-01

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

  2. LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements

    Science.gov (United States)

    Esnault, Caroline; Graça, Paula; Higuet, Dominique; Bonnivard, Eric

    2013-01-01

    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. PMID:23469217

  3. 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.

  4. LTR retrotransposons in fungi.

    Directory of Open Access Journals (Sweden)

    Anna Muszewska

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

  5. LTR retroelements in the genome of Daphnia pulex.

    Science.gov (United States)

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

    2010-07-09

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

  6. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

    Science.gov (United States)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2009-11-02

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

  8. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Bernad Lucia

    2009-11-01

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

  9. LTR retroelements in the genome of Daphnia pulex

    Directory of Open Access Journals (Sweden)

    Kim Sun

    2010-07-01

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

  10. Copia is transcriptionally responsive to environmental stress.

    OpenAIRE

    Strand, D J; McDonald, J F

    1985-01-01

    Adult Drosophila subjected to a variety of environmental stresses that induce classic Drosophila heat shock response simultaneously exhibit a rapid and significant rise in copia homologous transcripts. Levels of Drosophila Adh (alcohol dehydrogenase gene) and 18s ribosomal RNA were unaffected by environmental stress. Copia's ability to be induced by stress is correlated with the presence of sequences homologous to the heat shock promoter consensus sequence which appear to be appropriately pos...

  11. Molecular characterization of a transcriptionally active Ty1/copia-like retrotransposon in Gossypium.

    Science.gov (United States)

    Cao, Yuefen; Jiang, Yurong; Ding, Mingquan; He, Shae; Zhang, Hua; Lin, Lifeng; Rong, Junkang

    2015-06-01

    A transcriptionally active Ty1/copia -like retrotransposon was identified in the genome of Gossypium barbadense. The different heat activation of this element was observed in two tetraploid cotton species. Most retrotransposons from plants are transcriptionally silent, or activated under certain conditions. Only a small portion of elements are transcriptionally active under regular condition. A long terminal repeat (LTR) retrotransposon was isolated from the cultivated Sea Island cotton (H7124) genome during the investigation of the function of a homeodomain leucine zipper gene (HD1) in trichome growth. Insertion of this element in HD1 gene of At sub-genome was related to the trichomeless stem in Gossypium barbadense. The element, named as GBRE-1, had all features of a typical Ty1/copia retrotransposon and possessed high similarity to the members of ONSEN retrotransposon family. It was 4997 bp long, comprising a single 4110 bp open reading frame, which encoded 1369 amino acids including the conserved domains of gag and pol. The expression of GBRE-1 was detected under regular condition in G. barbadense and G. hirsutum, and its expression level was increased under heat-stress condition in G. hirsutum. Besides, its expression pattern was similar to that of the ONSEN retrotransposon. Abundant cis-regulatory motifs related to stress-response and transcriptional regulation were found in the LTR sequence. These results suggested that GBRE-1 was a transcriptionally active retrotransposon in Gossypium. To our knowledge, this is the first report of the isolation of a complete Ty1/copia-type retrotransposon with present-day transcriptional activity in cotton.

  12. 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

  13. Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons.

    Science.gov (United States)

    Dupeyron, Mathilde; de Souza, Rogerio Fernandes; Hamon, Perla; de Kochko, Alexandre; Crouzillat, Dominique; Couturon, Emmanuel; Domingues, Douglas Silva; Guyot, Romain

    2017-08-01

    Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains. Reverse Trancriptase (RT) domain-based phylogeny demonstrated that Divo is a new and well-supported family in the Bianca lineage, but strictly restricted to dicotyledonous species. In C. canephora, Divo is expressed and showed a genomic distribution along gene rich and gene poor regions. The copy number, the molecular estimation of insertion time and the analysis at orthologous locations of insertions in diploid and allotetraploid coffee genomes suggest that Divo underwent a different and recent transposition activity in C. arabica and C. canephora when compared to C. eugenioides. The analysis of this novel LTR-RT family represents an important step toward uncovering the genome structure and evolution of C. arabica allotetraploid genome.

  14. 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.

  15. Phylogenetic and molecular evolutionary analyses of Ty1-copia ...

    African Journals Online (AJOL)

    The Ty1-copia group retrotransposons have been characterized in cultivated Egyptian cotton, G.barbadense L., using degenerate PCR primers for their reverse transcriptase (RT) domains. Comparative nucleotide and amino acid sequences analyses showed that G. barbadense Ty1-copia RT sequences are heterogeneous ...

  16. Isolation, characterization, and phylogenetic analysis of copia-like ...

    African Journals Online (AJOL)

    We have used the polymerase chain reaction to analyze copia-like retrotransposons in the Egyptian cotton and its progenitors. All three cotton species studied contain reverse transcriptase fragments from copia-like retrotransposons. Sequence analysis of these reverse transcriptase fragments reveals that each is different ...

  17. Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae).

    Science.gov (United States)

    Hamon, Perla; Duroy, Pierre-Olivier; Dubreuil-Tranchant, Christine; Mafra D'Almeida Costa, Paulo; Duret, Caroline; Razafinarivo, Norosoa J; Couturon, Emmanuel; Hamon, Serge; de Kochko, Alexandre; Poncet, Valérie; Guyot, Romain

    2011-06-01

    In the study, we developed new markers for phylogenetic relationships and intraspecies differentiation in Coffea. Nana and Divo, two novel Ty1-copia LTR-retrotransposon families, were isolated through C. canephora BAC clone sequencing. Nana- and Divo-based markers were used to test their: (1) ability to resolve recent phylogenetic relationships; (2) efficiency in detecting intra-species differentiation. Sequence-specific amplification polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and retrotransposon-based insertion polymorphism (RBIP) approaches were applied to 182 accessions (31 Coffea species and one Psilanthus accession). Nana- and Divo-based markers revealed contrasted transpositional histories. At the BAC clone locus, RBIP results on C. canephora demonstrated that Nana insertion took place prior to C. canephora differentiation, while Divo insertion occurred after differentiation. Combined SSAP and REMAP data showed that Nana could resolve Coffea lineages, while Divo was efficient at a lower taxonomic level. The combined results indicated that the retrotransposon-based markers were useful in highlighting Coffea genetic diversity and the chronological pattern of speciation/differentiation events. Ongoing complete sequencing of the C. canephora genome will soon enable exhaustive identification of LTR-RTN families, as well as more precise in-depth analyses on contributions to genome size variation and Coffea evolution.

  18. Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species.

    Science.gov (United States)

    Zhang, Qun-Jie; Gao, Li-Zhi

    2017-06-07

    The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice. Copyright © 2017 Zhang and Gao.

  19. Registro de información de copia

    OpenAIRE

    Biblioteca Universitaria. Unidad de Proceso Técnico

    2012-01-01

    Establecer los pasos a seguir para completar la catalogación de todos los fondos que forman parte de la colección de la Biblioteca de la Universidad de Alicante, asignando los datos de información de copia del asiento catalográfico: signatura, localización, disponibilidad de préstamo, y demás detalles de circulación.

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

    Science.gov (United States)

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

    2015-10-15

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

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

    Science.gov (United States)

    2009-01-01

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

  2. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.

    Science.gov (United States)

    Dias, Elaine Silva; Hatt, Clémence; Hamon, Serge; Hamon, Perla; Rigoreau, Michel; Crouzillat, Dominique; Carareto, Claudia Marcia Aparecida; de Kochko, Alexandre; Guyot, Romain

    2015-09-01

    Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer.

  3. LTR Design of propertional integral observers

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Stoustrup, Jakob; Shafai, B.

    1995-01-01

    This paper applies the proportional-integral (PI) observer in connection with loop transfer recovery (LTR) design for continuous-time systems. We show that a PI observer makes it possible to obtain time recovery, i.e., exact recovery for t -+ -, under mild conditions. Based on an extension...

  4. Retroviral hybrid LTR vector strategy: functional analysis of LTR elements and generation of endothelial cell specificity.

    Science.gov (United States)

    Richardson, T B; Kaspers, J; Porter, C D

    2004-05-01

    Transcriptional targeting is an important aspect of developing gene therapy vectors in order to restrict transgene expression to selected target cells. One approach, when using retroviral vectors, is to replace viral transcriptional control elements within the long terminal repeat (LTR) with sequences imparting the desired specificity. We have developed such hybrid LTR retroviruses, incorporating sequences from each of the human promoters for flt-1, ICAM-2 and KDR, as part of our antivascular cancer gene therapy strategy targeting tumour endothelial cells. The chosen fragments were used to replace the enhancer or combined enhancer and proximal promoter regions of the viral LTR. All showed activity in primary human breast microvascular endothelial cells, with viruses incorporating ICAM-2 sequences exhibiting the greatest specificity versus nonendothelial cells in vitro and a marked alteration of specificity towards endothelial cells in a subcutaneous xenograft model in vivo. Moreover, our study documents the effect of enhancer and/or proximal promoter deletion on LTR activity and reports that differential dependence in different cell lines can give the false impression of specificity if experiments are not adequately controlled. This finding also has implications for other retroviral vector designs seeking to provide transcriptional specificity and for their safety with respect to prevention of gene activation at sites of proviral integration.

  5. Detection of MMTV-like LTR and LTR-env gene sequences in human breast cancer.

    Science.gov (United States)

    Wang, Y; Pelisson, I; Melana, S M; Holland, J F; Pogo, B G

    2001-05-01

    We have previously reported, using the polymerase chain reaction (PCR), the presence of a 660 bp sequence homologous to the env gene of MMTV in 38% of the human breast cancers studied, but not in normal breasts nor in other tumors or tissues. We have now investigated the presence of MMTV-like LTR sequences in human breast cancer and normal breast tissue. Primers were selected to amplify a 630 bp sequence homologous to MMTV, but not to the endogenous retrovirus HERV-K10. This sequence was detected in 41.5% of the breast cancers and none of the normal breasts. A larger 1.2 kb LTR fragment was also amplified with high homology to MMTV. Finally, a 1.6 kb fragment containing env and LTR sequences was amplified, cloned and sequenced from breast cancer DNA. The human LTRs were highly homologous to MMTV contain enhancer and promoter elements, the glucocorticoid responsive element (GRE) and the superantigen (Sag) sequences. Presence of functional sequences implies involvement in transcriptional regulation, whereas presence of an env-LTR sequence indicates contiguity within the genome of a potential provirus. Their presence in breast cancer DNA, but not in normal tissue, suggest an exogenous origin.

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

    African Journals Online (AJOL)

    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 closely related species and populations.

  7. A parametric LTR solution for discrete-time systems

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Jannerup, Ole Erik

    1989-01-01

    A parametric LTR (loop transfer recovery) solution for discrete-time compensators incorporating filtering observers which achieve exact recovery is presented for both minimum- and non-minimum-phase systems. First the recovery error, which defines the difference between the target loop transfer...... and the full loop transfer function, is manipulated into a general form involving the target loop transfer matrix and the fundamental recovery matrix. A parametric LTR solution based on the recovery matrix is developed. It is shown that the LQR/LTR (linear quadratic Gaussian/loop transfer recovery) solution...... is included in this new parametric solution as a special case...

  8. 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.

  9. A Theory of LTR Junk-food Consumption

    OpenAIRE

    Levy, Amnon

    2003-01-01

    LTR junk-food consumption balances the marginal satisfaction with the marginal deterioration of health. An LTR person discounts the instantaneous marginal satisfaction from junk-food consumption by its implications for his survival probability. His change rate of health evaluation is increased (decreased) by junk-food consumption when health is better (worse) than a critical level. The moderating direct effects of age and relative price on junk-food consumption may be amplified, or dimmed, by...

  10. Exonization of the LTR transposable elements in human genome

    Directory of Open Access Journals (Sweden)

    Borodovsky Mark

    2007-08-01

    Full Text Available Abstract Background Retrotransposons have been shown to contribute to evolution of both structure and regulation of protein coding genes. It has been postulated that the primary mechanism by which retrotransposons contribute to structural gene evolution is through insertion into an intron or a gene flanking region, and subsequent incorporation into an exon. Results We found that Long Terminal Repeat (LTR retrotransposons are associated with 1,057 human genes (5.8%. In 256 cases LTR retrotransposons were observed in protein-coding regions, while 50 distinct protein coding exons in 45 genes were comprised exclusively of LTR RetroTransposon Sequence (LRTS. We go on to reconstruct the evolutionary history of an alternatively spliced exon of the Interleukin 22 receptor, alpha 2 gene (IL22RA2 derived from a sequence of retrotransposon of the Mammalian apparent LTR retrotransposons (MaLR family. Sequencing and analysis of the homologous regions of genomes of several primates indicate that the LTR retrotransposon was inserted into the IL22RA2 gene at least prior to the divergence of Apes and Old World monkeys from a common ancestor (~25 MYA. We hypothesize that the recruitment of the part of LTR as a novel exon in great ape species occurred prior to the divergence of orangutans and humans from a common ancestor (~14 MYA as a result of a single mutation in the proto-splice site. Conclusion Our analysis of LRTS exonization events has shown that the patterns of LRTS distribution in human exons support the hypothesis that LRTS played a significant role in human gene evolution by providing cis-regulatory sequences; direct incorporation of LTR sequences into protein coding regions was observed less frequently. Combination of computational and experimental approaches used for tracing the history of the LTR exonization process of IL22RA2 gene presents a promising strategy that could facilitate further studies of transposon initiated gene evolution.

  11. LTR: Linear Cross-Platform Integration of Microarray Data

    Science.gov (United States)

    Boutros, Paul C.

    2010-01-01

    The size and scope of microarray experiments continue to increase. However, datasets generated on different platforms or at different centres contain biases. Improved techniques are needed to remove platform- and batch-specific biases. One experimental control is the replicate hybridization of a subset of samples at each site or on each platform to learn the relationship between the two platforms. To date, no algorithm exists to specifically use this type of control. LTR is a linear-modelling-based algorithm that learns the relationship between different microarray batches from replicate hybridizations. LTR was tested on a new benchmark dataset of 20 samples hybridized to different Affymetrix microarray platforms. Before LTR, the two platforms were significantly different; application of LTR removed this bias. LTR was tested with six separate data pre-processing algorithms, and its effectiveness was independent of the pre-processing algorithm. Sample-size experiments indicate that just three replicate hybridizations can significantly reduce bias. An R library implementing LTR is available. PMID:20838609

  12. LTR: Linear Cross-Platform Integration of Microarray Data

    Directory of Open Access Journals (Sweden)

    Paul C. Boutros

    2010-08-01

    Full Text Available The size and scope of microarray experiments continue to increase. However, datasets generated on different platforms or at different centres contain biases. Improved techniques are needed to remove platform- and batch-specific biases. One experimental control is the replicate hybridization of a subset of samples at each site or on each platform to learn the relationship between the two platforms. To date, no algorithm exists to specifically use this type of control. LTR is a linear-modelling-based algorithm that learns the relationship between different microarray batches from replicate hybridizations. LTR was tested on a new benchmark dataset of 20 samples hybridized to different Affymetrix microarray platforms. Before LTR, the two platforms were significantly different; application of LTR removed this bias. LTR was tested with six separate data pre-processing algorithms, and its effectiveness was independent of the pre-processing algorithm. Sample-size experiments indicate that just three replicate hybridizations can significantly reduce bias. An R library implementing LTR is available.

  13. LTR: Linear Cross-Platform Integration of Microarray Data.

    Science.gov (United States)

    Boutros, Paul C

    2010-08-27

    The size and scope of microarray experiments continue to increase. However, datasets generated on different platforms or at different centres contain biases. Improved techniques are needed to remove platform- and batch-specific biases. One experimental control is the replicate hybridization of a subset of samples at each site or on each platform to learn the relationship between the two platforms. To date, no algorithm exists to specifically use this type of control. LTR is a linear-modelling-based algorithm that learns the relationship between different microarray batches from replicate hybridizations. LTR was tested on a new benchmark dataset of 20 samples hybridized to different Affymetrix microarray platforms. Before LTR, the two platforms were significantly different; application of LTR removed this bias. LTR was tested with six separate data pre-processing algorithms, and its effectiveness was independent of the pre-processing algorithm. Sample-size experiments indicate that just three replicate hybridizations can significantly reduce bias. An R library implementing LTR is available.

  14. Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers.

    Science.gov (United States)

    Friesen, N; Brandes, A; Heslop-Harrison, J S

    2001-07-01

    We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of

  15. The LTR promoter of the rat oncomodulin gene is regulated by cell-line specific accessibility in the LTR U3 region

    DEFF Research Database (Denmark)

    Rentsch, J. M.; Hergersberg, M.; Banville, D.

    2006-01-01

    mechanisms of LTR directed OM gene expression we tested promoter activity of this LTR by transient transfection of transformed rat fibroblasts with this sequence placed 5' of the human growth hormone hGH reporter gene. The OM LTR is a strong promoter but does not follow an expression pattern similar...... located within the U3 region of the LTR element. Several cis-elements in the OM LTR promoter exhibiting cell-line specific occupancy were identified by in vivo DMS-footprinting. Detailed analysis of protein interactions with two such sequence elements in vitro revealed binding of ubiquitously expressed...

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

    Science.gov (United States)

    Nefedova, Lidia; Kim, Alexander

    2017-04-16

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

  17. 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

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

    Science.gov (United States)

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

    1997-01-01

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

  19. LTR retrotransposons in rice (Oryza sativa, L.: recent burst amplifications followed by rapid DNA loss

    Directory of Open Access Journals (Sweden)

    Panaud Olivier

    2007-07-01

    Full Text Available Abstract Background LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice. Results Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal. Conclusion Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome.

  20. Evidence for mobility of a new family of mouse middle repetitive DNA elements (LTR-IS).

    Science.gov (United States)

    Wirth, T; Schmidt, M; Baumruker, T; Horak, I

    1984-04-25

    Locus variation and sequence conservation of mouse LTR-IS elements, a new family of middle repetitive DNA sequences was studied. It is shown that LTR-IS sequences are present in all the inbred strains and subspecies of M. musculus tested and in M. cooki and M. caroli. Their arrangement in mouse genomes is polymorphic. Southern blot analysis and DNA sequencing revealed the existence of homologous DNA sequences with and without LTR-IS element insertion. LTR-IS sequences therefore appear to have arisen in early mouse ancestors and have, at least at some point, been mobile.

  1. State-space solutions to the h_inf/ltr design problem

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik

    1993-01-01

    The LTR design problem using an JC optimality criterion is presented for two types of recovery errors, the sensitivity recovery error and the input-output recovery error. For both errors two different approaches are presented. First, following the classical LTR design philosophy, a Luenberger obs...

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

    Science.gov (United States)

    2013-01-01

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

  3. Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.

    Science.gov (United States)

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

    2016-12-07

    Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant

  4. LQG/LTR Optimal Attitude Control of Small Flexible Spacecraft Using Free-Free Boundary Conditions

    Science.gov (United States)

    2006-08-03

    quite successfully to join various types of pipes, from hydraulic pipes in F-14 fighter planes[73] and naval ships, to transport pipes in the...Gaussian/loop transfer recovery (LQG/LTR). Stein and Athans[213] provide a tutorial overview of the LQG/LTR procedure for linear multivariable feedback...to describe the orientation of the spacecraft places the 1st axis along the orbit direction (velocity or ram direction), the 2nd axis perpendicular to

  5. 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

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

    Science.gov (United States)

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

    2013-10-01

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

  7. Genetic effect of CysLTR2 polymorphisms on its mRNA synthesis and stabilization

    Directory of Open Access Journals (Sweden)

    Chung Il

    2009-10-01

    Full Text Available Abstract Background We previously demonstrated that single nucleotide polymorphism (SNP and haplotypes were associated with aspirin hypersensitivity in asthmatics. We investigated the genetic effects of the SNPs and haplotypes on the expression of the CysLTR2 gene. Methods We measured CysLTR2 protein and mRNA expression in EB virus-infected B cell lines from asthmatics having ht1+/+ and ht2+/+. A gel retardation assay was used to identify nuclear protein binding to the c.-819 promoter site. The function of promoter and 3'-UTR were assessed using pGL3 luciferase and pEGFP reporter system, respectively. Results We found that the expression of CysLTR2 protein was higher in B cell lines of asthmatics having ht2+/+ than in those having ht1+/+. PMA/ionomycin induced higher mRNA expression of CysLTR2 in B cell lines from ht2+/+ asthmatics than those from ht1+/+ asthmatics. A nuclear protein from the B cell lines showed stronger DNA binding affinity with a probe containing c.-819T than one containing c.-819G. The luciferase activity of the c.-819T type of CysLTR2 promoter was higher than that of the c.-819G type. EGFP expression was higher in the EGFP-c.2078T 3'-UTR fusion construct than in the c.2078C construct. Conclusion The sequence variants of CysLTR2 may affect its transcription and the stability of its mRNA, resulting in altered expression of CysLTR2 protein, which in turn causes some asthmatics to be susceptible to aspirin hypersensitivity.

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

    Directory of Open Access Journals (Sweden)

    Willerslev Eske

    2010-03-01

    Full Text Available Abstract 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 the elements. Less is known about the ongoing dynamics of retrotransposons, as analysis of genome sequences will only reveal insertions of retrotransposons that are fixed - or near fixation - in the population or strain from which genetic material has been extracted for sequencing. One pre-requisite for retrotransposition is transcription of the elements. Given their intrinsic sequence redundancy, transcriptome-level analyses of transposable elements are scarce. We have used recently published transcriptome data from the fission yeast Schizosaccharomyces pombe to assess the ability to detect and describe 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 was analysed for both full-length LTR retrotransposons and solitary LTRs. Results Two independent sets of transcriptome data reveal the presence of full-length, polyadenylated transcripts from LTR retrotransposons in S. pombe during growth phase in rich medium. The redundancy of retrotransposon sequences makes it difficult to assess which elements are transcriptionally active, but data strongly indicates that only a subset of the LTR retrotransposons contribute significantly to the detected transcription. A considerable level of reverse strand transcription is also detected. Equal levels of transcriptional activity are observed from both strands of solitary LTR sequences. Transcriptome data collected during meiosis suggests that transcription

  9. Akv murine leukemia virus enhances bone tumorigenesis in hMT-c-fos-LTR transgenic mice

    DEFF Research Database (Denmark)

    Schmidt, Jörg; Krump-Konvalinkova, Vera; Luz, Arne

    1995-01-01

    hMt-c-fos-LTR transgenic mice (U. Rüther, D. Komitowski, F. R. Schubert, and E. F. Wagner. Oncogene 4, 861–865, 1989) developed bone sarcomas in 20% (3/15) of females at 448 ± 25 days and in 8% (1/12) of males at 523 days. After infection of newborns with Akv, an infectious retrovirus derived from...... the ecotropic provirus of the AKR mouse, 69% (20/28) of female animals and 83% (24/29) of males developed malignant fibrous-osseous tumors. The tumors in infected transgenics developed with higher frequency and a 200-days shorter mean tumor latency period. The hMt-c-fos-LTR transgene was expressed in all...... that Akv exerts distinct pathogenic effects on the skeleton. In hMt-c-fos-LTR transgenic mice, predisposed to bone sarcomagenesis, Akv acts synergistically with the fos transgene, resulting in the development of fibrous-osseous tumors...

  10. 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...... was analysed for both full-length LTR retrotransposons and solitary LTRs. RESULTS: Two independent sets of transcriptome data reveal the presence of full-length, polyadenylated transcripts from LTR retrotransposons in S. pombe during growth phase in rich medium. The redundancy of retrotransposon sequences...... 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...

  11. Isolation and characterization of Ty1-copia group of LTRs in genome of three species of Datura: D. innoxia, D. stramonium and D. metel.

    Science.gov (United States)

    Singh, Alka; Nirala, N K; Narula, Alka; Das, Sandip; Srivastava, Prem S

    2011-07-01

    Retrotransposons (RT) constitute a major fraction of plant genome. They are implicated in evolution and sequence organization. These elements have been proposed to have major role in evolution and variation in genome size. The sequence information of these RT regions in terms of divergence and conservation could be utilized for determining the interrelationship among various copia retrotransposons within the genome. In order to assess the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequence was amplified from genomes of three medicinally important Datura species: D. innoxia, D. stramonium and D. metel using the primers derived from two conserved domains of RT region. A total of twenty one independent amplicons from RT regions were cloned, sequenced and compared. The intra-family divergence at amino acid level ranged from 4 to 52 %. Though intra-family RT sequences are conserved, no two sequences are identical. Southern blot hybridization suggested that Ty1-copia-like retrotransposons are dispersed throughout the Datura genome. The results indicate a high degree of heterogeneity among the Ty1-copia group of retroelements in Datura species.

  12. Impact of the DNA extraction method on 2-LTR DNA circle recovery from HIV-1 infected cells.

    Science.gov (United States)

    Badralmaa, Yunden; Natarajan, Ven

    2013-10-01

    Detection of episomal 2-LTR DNA circles is used as a marker for the ongoing virus replication in patients infected with HIV-1, and efficient extraction of episomal DNA is critical for accurate estimation of the 2-LTR circles. The impact of different methods of DNA extraction on the recovery of 2-LTR circles was compared using mitochondrial DNA extracted as an internal control. The bacterial plasmid DNA isolation method extracted less than 10% of cellular DNA, 40% of mitochondrial DNA and 12-20% of the input 2-LTR DNA. The total DNA isolation method recovered about 70% of mitochondrial DNA and 45% of the input 2-LTR DNA. The total nucleic acid isolation method recovered 90% of mitochondrial DNA and 60% of the input 2-LTR DNA. Similar results were obtained when the DNA was extracted from HIV-1 infected cells. Plasmid DNA isolation could not distinguish between 12 and 25 copies of 2-LTR DNA per million cells, whereas the total nucleic acid isolation showed a consistent and statistically significant difference between 12 and 25 copies. In conclusion, the total nucleic acid isolation method is more efficient than the plasmid DNA isolation method in recovering mitochondrial DNA and 2-LTR DNA circles from HIV-1 infected cells. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Divergent non-LTR retrotransposon lineages from the genomes of scorpions (Arachnida: Scorpiones).

    Science.gov (United States)

    Glushkov, Sergei; Novikova, Olga; Blinov, Alexander; Fet, Victor

    2006-03-01

    We screened across the taxonomic diversity of order Scorpiones (22 species belonging to 21 genera and 10 families) for the presence of seven different clades of non-LTR retrotransposons in their genomes using PCR with newly designed clade-specific consensus-degenerate hybrid oligonucleotide primers. Scorpion genomes were found to contain four known non-LTR retrotransposon clades: R1, I, Jockey, and CR1. In total, 35 fragments of reverse transcriptase genes of new elements from 22 scorpion species were obtained and analyzed for three clades, Jockey, I, and CR1. Phylogenies of different clades of elements were built using amino acid sequences inferred from 33 non-LTR retrotransposon clones. Distinct evolutionary lineages, with several major groups of the non-LTR retroelements were identified, showing significant variation. Four lineages were revealed in Jockey clade. The phylogeny of I clade showed strong support for the monophyletic origin of such group of elements in scorpions. Three separate lineages can be distinguished in the phylogenetic tree of CR1 clade. The large fraction of the isolated elements appeared to be defective.

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

    Science.gov (United States)

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

    2017-04-11

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

  15. Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback

    Science.gov (United States)

    Blass, Eryn; Bell, Michael; Boissinot, Stéphane

    2012-01-01

    The diversity and abundance of non–long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is littered with hundreds of thousands of copies resulting from the activity of a single clade of nLTR-RT, the L1 clade. In contrast, fish genomes contain a much more diverse repertoire of nLTR-RT, represented by numerous active clades and families. Yet, the number of nLTR-RT copies in teleostean fish is two orders of magnitude smaller than in mammals. The vast majority of insertions appear to be very recent, suggesting that nLTR-RT do not accumulate in fish genomes. This pattern had previously been explained by a high rate of turnover, in which the insertion of new elements is offset by the selective loss of deleterious inserts. The turnover model was proposed because of the similarity between fish and Drosophila genomes with regard to their nLTR-RT profile. However, it is unclear if this model applies to fish. In fact, a previous study performed on the puffer fish suggested that transposable element insertions behave as neutral alleles. Here we examined the dynamics of amplification of nLTR-RT in the three-spine stickleback (Gasterosteus aculeatus). In this species, the vast majority of nLTR-RT insertions are relatively young, as suggested by their low level of divergence. Contrary to expectations, a majority of these insertions are fixed in lake and oceanic populations; thus, nLTR-RT do indeed accumulate in the genome of their fish host. This is not to say that nLTR-RTs are fully neutral, as the lack of fixed long elements in this genome suggests a deleterious effect related to their length. This analysis does not support the turnover model and strongly suggests that a much higher rate of DNA loss in fish than in mammals is responsible for the relatively small number of nLTR-RT copies and for the scarcity of ancient elements in fish genomes. We further demonstrate that nLTR

  16. 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

  17. El derecho de copia. Análisis y construcción del derecho humano a copiar y disponer de la cultura común

    Directory of Open Access Journals (Sweden)

    Ariel Vercelli

    2013-09-01

    Full Text Available El derecho de autor ya no es lo que era. En la era digital, la copia es ubicua, pervasiva, cotidiana, silenciosa, vital. Se ha vuelto una parte sustancial de la cultura contemporánea. Aquello que hasta hace pocos años recibía el nombre de “derecho de autor” (en la tradición jurídico-política continental comienza ahora a ser ampliado hacia un “derecho de autor y derecho de copia”. En el artículo, se analiza, más allá de las limitaciones y excepciones al derecho de autor, el derecho de copia (a copiar como un derecho humano pleno a disponer de las riquezas intelectuales comunes.

  18. Copias o similitudes en las carteras de inversión de los fondos privados de pensiones en Perú

    Directory of Open Access Journals (Sweden)

    Roberto Urrunaga

    2002-09-01

    Full Text Available El objetivo es evaluar la existencia de copias entre los fondos de pensiones con relación a sus carteras de inversión en acciones. La hipótesis a descartar es que las copias sean consecuencia de la frecuencia de publicación del detalle de dichas carteras, con la intención de mostrar el error de quienes proponen medidas en contra de la competencia, como restringir la información pública mediante una menor periodicidad en tales publicaciones. El estudio muestra que solo se habrían dado copias esporádicas en algunos títulos, y que las similitudes entre los portafolios de acciones se debería precisamente a la restricción de la competencia, mediante normas como la excesiva regulación sobre los límites de inversión y la exigencia de una rentabilidad mínima.

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

    National Research Council Canada - National Science Library

    Salina, Elena A; Sergeeva, Ekaterina M; Adonina, Irina G; Shcherban, Andrey B; Belcram, Harry; Huneau, Cecile; Chalhoub, Boulos

    2011-01-01

    .... 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...

  20. 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.

  1. Crystal Structure of NFAT Bound to the HIV-1 LTR Tandem κB Enhancer Element

    Energy Technology Data Exchange (ETDEWEB)

    Bates, Darren L.; Barthel, Kristen K.B.; Wu, Yongqing; Kalhor, Reza; Stroud, James C.; Giffin, Michael J.; Chen, Lin (UCLA); (Colorado)

    2008-05-27

    Here, we have determined the crystal structure of the DNA binding domain of NFAT bound to the HIV-1 long terminal repeat (LTR) tandem {kappa}B enhancer element of 3.05 {angstrom} resolution. NFAT binds as a dimer to the upstream {kappa}B site (Core II), but as a monomer to the 3' end of the downstream {kappa}B site (Core I). The DNA shows a significant bend near the 5' end of Core I, where a lysine residue from NFAT bound to the 3' end of Core II inserts into the minor groove and seems to cause DNA bases to flip out. Consistent with this structural feature, the 5' end of Core I become hypersensitive to dimethylsulfate in the in vivo footprinting upon transcriptional activation of the HIV-1 LTR. Our studies provide a basis for futher investigating the functional mechanism of NFAT in HIV-1 transcription and replication.

  2. 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.

  3. The Ty1 LTR-retrotransposon of budding yeast, Saccharomyces cerevisiae

    Science.gov (United States)

    Curcio, M. Joan; Lutz, Sheila; Lesage, Pascale

    2015-01-01

    Summary Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses [1]. The Ty1 element of the budding yeast Saccharomyces cerevisiae was the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in the S. cerevisiae genome but also the ease and breadth of genomic, biochemical and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host co-factors known to influence retrotransposition and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology. PMID:25893143

  4. Transcriptional Dynamics of LTR Retrotransposons in Early Generation and Ancient Sunflower Hybrids

    Science.gov (United States)

    Ungerer, Mark C.; Kawakami, Takeshi

    2013-01-01

    Hybridization and abiotic stress are natural agents hypothesized to influence activation and proliferation of transposable elements in wild populations. In this report, we examine the effects of these agents on expression dynamics of both quiescent and transcriptionally active sublineages of long terminal repeat (LTR) retrotransposons in wild sunflower species with a notable history of transposable element proliferation. For annual sunflower species Helianthus annuus and H. petiolaris, neither early generation hybridization nor abiotic stress, alone or in combination, induced transcriptional activation of quiescent sublineages of LTR retrotransposons. These treatments also failed to further induce expression of sublineages that are transcriptionally active; instead, expression of active sublineages in F1 and backcross hybrids was nondistinguishable from, or intermediate relative to, parental lines, and abiotic stress generally decreased normalized expression relative to controls. In contrast to findings for early generation hybridization between H. annuus and H. petiolaris, ancient sunflower hybrid species derived from these same two species and which have undergone massive proliferation events of LTR retrotransposons display 2× to 6× higher expression levels of transcriptionally active sublineages relative to parental sunflower species H. annuus and H. petiolaris. Implications and possible explanations for these findings are discussed. PMID:23335122

  5. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae: evidence for recent horizontal transmission

    Directory of Open Access Journals (Sweden)

    Blinov Alexander

    2007-06-01

    Full Text Available Abstract Background Non-long terminal repeat (non-LTR retrotransposons are mobile genetic elements that propagate themselves by reverse transcription of an RNA intermediate. Non-LTR retrotransposons are known to evolve mainly via vertical transmission and random loss. Horizontal transmission is believed to be a very rare event in non-LTR retrotransposons. Our knowledge of distribution and diversity of insect non-LTR retrotransposons is limited to a few species – mainly model organisms such as dipteran genera Drosophila, Anopheles, and Aedes. However, diversity of non-LTR retroelements in arthropods seems to be much richer. The present study extends the analysis of non-LTR retroelements to CR1 clade from four butterfly species of genus Maculinea (Lepidoptera: Lycaenidae. The lycaenid genus Maculinea, the object of interest for evolutionary biologists and also a model group for European biodiversity studies, possesses a unique, specialized myrmecophilous lifestyle at larval stage. Their caterpillars, after three weeks of phytophagous life on specific food plants drop to the ground where they are adopted to the ant nest by Myrmica foraging workers. Results We found that the genome of Maculinea butterflies contains multiple CR1 lineages of non-LTR retrotransposons, including those from MacCR1A, MacCR1B and T1Q families. A comparative analysis of RT nucleotide sequences demonstrated an extremely high similarity among elements both in interspecific and intraspecific comparisons. CR1A-like elements were found only in family Lycaenidae. In contrast, MacCR1B lineage clones were extremely similar to CR1B non-LTR retrotransposons from Bombycidae moths: silkworm Bombyx mori and Oberthueria caeca. Conclusion The degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa. The only

  6. Utilidad de los conceptos y estrategias comunitarias en el marketing online para la prevención de la copia ilegal en el mercado musical

    OpenAIRE

    Jaimes Rangel, Anderson Alexi; Luna Mendez, Jairo Andres

    2014-01-01

    Esta investigación se dirige a determinar cuál es la utilidad de los conceptos y estrategias comunitarias en el marketing online para la prevención de la copia ilegal en el mercado musical. Con este proyecto se desea que por medio de una nueva disquera enfocada en el comercio online, y usando los conceptos del mercadeo comunitario y el mercadeo relacional, se pueda desarrollar nuevas estrategias de mercadeo en donde se logre incentivar y promover la compra de música origin...

  7. Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes

    NARCIS (Netherlands)

    van der Sluis, Renée M.; Derking, Ronald; Breidel, Seyguerney; Speijer, Dave; Berkhout, Ben; Jeeninga, Rienk E.

    2014-01-01

    HIV-1 transcription depends on cellular transcription factors that bind to sequences in the long-terminal repeat (LTR) promoter. Each HIV-1 subtype has a specific LTR promoter configuration, and minor sequence changes in transcription factor binding sites (TFBSs) or their arrangement can influence

  8. Rapamycin-induced inhibition of HTLV-I LTR activity is rescued by c-Myb

    Directory of Open Access Journals (Sweden)

    Lever Andrew ML

    2007-04-01

    Full Text Available Abstract Background Rapamycin is an immunosuppressive which represses translation of transcripts harbouring a polypyrimidine motif downstream of the mRNA cap site through the mammalian target of rapamycin complex. It inhibits the abnormal autologous proliferation of T-cell clones containing a transcriptionally active human T-lymphotropic virus, type I (HTLV-I provirus, generated from infected subjects. We showed previously that this effect is independent of the polypyrimidine motifs in the viral long terminal repeat (LTR R region suggesting that HTLV-I transcription, and not translation, is being affected. Here we studied whether rapamycin is having an effect on a specific transcription factor pathway. Further, we investigated whether mRNAs encoding transcription factors involved in HTLV-I transcriptional activation, specifically CREB, Ets and c-Myb, are implicated in the rapamycin-sensitivity of the HTLV-I LTR. Results An in vitro analysis of the role of SRE- and NF-κB-mediated transcription highlighted the latter as rapamycin sensitive. Over-expression of c-Myb reversed the rapamycin effect. Conclusion The sensitivity of HTLV-I transcription to rapamycin may be effected through an NF-κB-pathway associated with the rapamycin-sensitive mTORC1 cellular signalling network.

  9. Individual effects of the copia and gypsy enhancer and insulator on chromatin marks, eRNA synthesis, and binding of insulator proteins in transfected genetic constructs.

    Science.gov (United States)

    Fedoseeva, Daria M; Kretova, Olga V; Gorbacheva, Maria A; Tchurikov, Nickolai A

    2018-01-30

    Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer. Insertion of the insulator between the enhancer and the promoter reduced these effects. We also observed the binding of dCTCF to the enhancer and to gypsy insulator. Our data indicate that a single gypsy insulator interacts with both the enhancer and the promoter, while two copies of the gypsy insulator preferentially interact with each other. Our results suggest the formation of chromatin loops that are shaped by the enhancer and the insulator. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2017-11-15

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

  11. HIV-1 Subtypes and 5'LTR-Leader Sequence Variants Correlate with Seroconversion Status in Pumwani Sex Worker Cohort.

    Science.gov (United States)

    Sampathkumar, Raghavan; Scott-Herridge, Joel; Liang, Binhua; Kimani, Joshua; Plummer, Francis A; Luo, Ma

    2017-12-23

    Within the Pumwani sex worker cohort, a subgroup remains seronegative, despite frequent exposure to HIV-1; some of them seroconverted several years later. This study attempts to identify viral variations in 5'LTR-leader sequences (5'LTR-LS) that might contribute to the late seroconversion. The 5'LTR-LS contains sites essential for replication and genome packaging, viz, primer binding site (PBS), major splice donor (SD), and major packaging signal (PS). The 5'LTR-LS of 20 late seroconverters (LSC) and 122 early seroconverters (EC) were amplified, cloned, and sequenced. HelixTree 6.4.3 was employed to classify HIV subtypes and sequence variants based on seroconversion status. We find that HIV-1 subtypes A1.UG and D.UG were overrepresented in the viruses infecting the LSC (P < 0.0001). Specific variants of PBS (Pc < 0.0001), SD1 (Pc < 0.0001), and PS (Pc < 0.0001) were present only in the viral population from EC or LSC. Combinations of PBS [PBS-2 (Pc < 0.0001) and PBS-3 (Pc < 0.0001)] variants with specific SD sequences were only seen in LSC or EC. Combinations of A1.KE or D with specific PBS and SD variants were only present in LSC or EC (Pc < 0.0001). Furthermore, PBS variants only present in LSC co-clustered with PBS references utilizing tRNAArg; whereas, the PBS variants identified only in EC co-clustered with PBS references using tRNALys3 and its variants. This is the first report that specific PBS, SD1, and PS sequence variants within 5'LTR-LS are associated with HIV-1 seroconversion, and it could aid designing effective anti-HIV strategies.

  12. Horizontal transfer of non-LTR retrotransposons from arthropods to flowering plants.

    Science.gov (United States)

    Gao, Dongying; Chu, Ye; Xia, Han; Xu, Chunming; Heyduk, Karolina; Abernathy, Brian; Ozias-Akins, Peggy; Leebens-Mack, James H; Jackson, Scott A

    2017-10-23

    Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses indicated that AdLINE3 is a member of the RTE clade, originally identified in a nematode and rarely reported in plants. We identified RTE elements in 82 plants, spanning angiosperms to algae, including recently active elements in some flowering plants. RTE elements in flowering plants were likely derived from a single family we refer to as An-RTE. Interestingly, An-RTEs show significant DNA sequence identity with non-LTR retroelements from 42 animals belonging to four phyla. Moreover, the sequence identity of RTEs between two arthropods and two plants was higher than that of homologous genes. Phylogenetic and evolutionary analyses of RTEs from both animals and plants suggest that the An-RTE family was likely transferred horizontally into angiosperms from an ancient aphid(s) or ancestral arthropod(s). Notably, some An-RTEs were recruited as coding sequences of functional genes participating in metabolic or other biochemical processes in plants. This is the first potential example of horizontal transfer of transposons between animals and flowering plants. Our findings help to understand exchanges of genetic material between the kingdom Animalia and Plantae and suggest arthropods likely impacted on plant genome evolution. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

  13. Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia.

    Science.gov (United States)

    Lovsin, N; Gubensek, F; Kordi, D

    2001-12-01

    The evolution of the novel L2 clade of non-long terminal repeat (LTR) retrotransposons and their evolutionary dynamics in Deuterostomia has been examined. The short-term evolution of long interspersed nuclear element 2s (LINE2s) has been studied in 18 reptilian species by analysis of a PCR amplified 0.7-kb fragment encoding the palm/fingers subdomain of reverse transcriptase (RT). Most of the reptilian LINE2s examined are inactive since they contain multiple stop codons, indels, or frameshift mutations that disrupt the RT. Analysis of reptilian LINE2s has shown a high degree of sequence divergence and an unexpectedly large number of deletions. The evolutionary dynamics of LINE2s in reptiles has been found to be complex. LINE2s are shown to form a novel clade of non-LTR retrotransposons that is well separated from the CR1 clade. This novel L2 clade is more widely distributed than previously thought, and new representatives have been discovered in echinoderms, insects, teleost fishes, Xenopus, Squamata, and marsupials. There is an apparent absence of LINE2s from different vertebrate classes, such as cartilaginous fishes, Archosauria (birds and crocodiles), and turtles. Whereas the LINE2s are present in echinoderms and teleost fishes in a conserved form, in most tetrapods only highly degenerated pseudogenes can be found. The predominance of inactive LINE2s in Tetrapoda indicates that, in the host genomes, only inactive copies are still present. The present data indicate that the vertical inactivation of LINE2s might have begun at the time of Tetrapoda origin, 400 MYA. The evolutionary dynamics of the L2 clade in Deuterostomia can be described as a gradual vertical inactivation in Tetrapoda, stochastic loss in Archosauria and turtles, and strict vertical transmission in echinoderms and teleost fishes.

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

    Science.gov (United States)

    Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2015-01-01

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

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

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    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.

  16. 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

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

    Science.gov (United States)

    Wells, D J

    1999-06-01

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

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

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    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.

  19. Regulation of FeLV-945 by c-Myb binding and CBP recruitment to the LTR

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    Finstad Samantha L

    2004-09-01

    Full Text Available Abstract Background Feline leukemia virus (FeLV induces degenerative, proliferative and malignant hematologic disorders in its natural host, the domestic cat. FeLV-945 is a viral variant identified as predominant in a cohort of naturally infected animals. FeLV-945 contains a unique sequence motif in the long terminal repeat (LTR comprised of a single copy of transcriptional enhancer followed by a 21-bp sequence triplicated in tandem. The LTR is precisely conserved among independent cases of multicentric lymphoma, myeloproliferative disease and anemia in animals from the cohort. The 21-bp triplication was previously shown to act as a transcriptional enhancer preferentially in hematopoietic cells and to confer a replicative advantage. The objective of the present study was to examine the molecular mechanism by which the 21-bp triplication exerts its influence and the selective advantage responsible for its precise conservation. Results Potential binding sites for the transcription factor, c-Myb, were identified across the repeat junctions of the 21-bp triplication. Such sites would not occur in the absence of the repeat; thus, a requirement for c-Myb binding to the repeat junctions of the triplication would exert a selective pressure to conserve its sequence precisely. Electrophoretic mobility shift assays demonstrated specific binding of c-Myb to the 21-bp triplication. Reporter gene assays showed that the triplication-containing LTR is responsive to c-Myb, and that responsiveness requires the presence of both c-Myb binding sites. Results further indicated that c-Myb in complex with the 21-bp triplication recruits the transcriptional co-activator, CBP, a regulator of normal hematopoiesis. FeLV-945 replication was shown to be positively regulated by CBP in a manner dependent on the presence of the 21-bp triplication. Conclusion Binding sites for c-Myb across the repeat junctions of the 21-bp triplication may account for its precise conservation in

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

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    Shunri Jiang

    2017-01-01

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

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

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    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.

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

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    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.

  3. Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products

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    Hsiao Chiu-Bin

    2006-11-01

    Full Text Available Abstract Background While viruses have long been shown to capitalize on their limited genomic size by utilizing both strands of DNA or complementary DNA/RNA intermediates to code for viral proteins, it has been assumed that human retroviruses have all their major proteins translated only from the plus or sense strand of RNA, despite their requirement for a dsDNA proviral intermediate. Several studies, however, have suggested the presence of antisense transcription for both HIV-1 and HTLV-1. More recently an antisense transcript responsible for the HTLV-1 bZIP factor (HBZ protein has been described. In this study we investigated the possibility of an antisense gene contained within the human immunodeficiency virus type 1 (HIV-1 long terminal repeat (LTR. Results Inspection of published sequences revealed a potential transcription initiator element (INR situated downstream of, and in reverse orientation to, the usual HIV-1 promoter and transcription start site. This antisense initiator (HIVaINR suggested the possibility of an antisense gene responsible for RNA and protein production. We show that antisense transcripts are generated, in vitro and in vivo, originating from the TAR DNA of the HIV-1 LTR. To test the possibility that protein(s could be translated from this novel HIV-1 antisense RNA, recombinant HIV antisense gene-FLAG vectors were designed. Recombinant protein(s were produced and isolated utilizing carboxy-terminal FLAG epitope (DYKDDDDK sequences. In addition, affinity-purified antisera to an internal peptide derived from the HIV antisense protein (HAP sequences identified HAPs from HIV+ human peripheral blood lymphocytes. Conclusion HIV-1 contains an antisense gene in the U3-R regions of the LTR responsible for both an antisense RNA transcript and proteins. This antisense transcript has tremendous potential for intrinsic RNA regulation because of its overlap with the beginning of all HIV-1 sense RNA transcripts by 25 nucleotides. The

  4. Unexpected Modulation of Recall B and T Cell Responses after Immunization with Rotavirus-like Particles in the Presence of LT-R192G

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    Christelle Basset

    2010-08-01

    Full Text Available LT-R192G, a mutant of the thermolabile enterotoxin of E. coli, is a potent adjuvant of immunization. Immune responses are generally analyzed at the end of protocols including at least 2 administrations, but rarely after a prime. To investigate this point, we compared B and T cell responses in mice after one and two intrarectal immunizations with 2/6 rotavirus-like particles (2/6-VLP and LT-R192G. After a boost, we found, an unexpected lower B cell expansion measured by flow cytometry, despite a secondary antibody response. We then analyzed CD4+CD25+Foxp3+ regulatory T cells (Tregs and CD4+CD25+Foxp3− helper T cells after in vitro (restimulation of mesenteric lymph node cells with the antigen (2/6-VLP, the adjuvant (LT-R192G or both. 2/6-VLP did not activate CD4+CD25+Foxp3− nor Foxp3+ T cells from non-immunized and 2/6-VLP immunized mice, whereas they did activate both subsets from mice immunized with 2/6-VLP in the presence of adjuvant. LT-R192G dramatically decreased CD4+CD25+Foxp3+ T cells from non-immunized and 2/6-VLP immunized mice but not from mice immunized with 2/6-VLP and adjuvant. Moreover, in this case, LT-R192G increased Foxp3 expression on CD4+CD25+Foxp3+ cells, suggesting specific Treg activation during the recall. Finally, when both 2/6-VLP and LT-R192G were used for restimulation, LT-R192G clearly suppressed both 2/6-VLP-specific CD4+CD25+Foxp3− and Foxp3+ T cells. All together, these results suggest that LT-R192G exerts different effects on CD4+CD25+Foxp3+ T cells, depending on a first or a second contact. The unexpected immunomodulation observed during the recall should be considered in designing vaccination protocols.

  5. Unexpected Modulation of Recall B and T Cell Responses after Immunization with Rotavirus-like Particles in the Presence of LT-R192G

    Science.gov (United States)

    Thiam, Fatou; Martino, Cyrille Di; Bon, Fabienne; Charpilienne, Annie; Cachia, Claire; Poncet, Didier; Clements, John D.; Basset, Christelle; Kohli, Evelyne

    2010-01-01

    LT-R192G, a mutant of the thermolabile enterotoxin of E. coli, is a potent adjuvant of immunization. Immune responses are generally analyzed at the end of protocols including at least 2 administrations, but rarely after a prime. To investigate this point, we compared B and T cell responses in mice after one and two intrarectal immunizations with 2/6 rotavirus-like particles (2/6-VLP) and LT-R192G. After a boost, we found, an unexpected lower B cell expansion measured by flow cytometry, despite a secondary antibody response. We then analyzed CD4+CD25+Foxp3+ regulatory T cells (Tregs) and CD4+CD25+Foxp3− helper T cells after in vitro (re)stimulation of mesenteric lymph node cells with the antigen (2/6-VLP), the adjuvant (LT-R192G) or both. 2/6-VLP did not activate CD4+CD25+Foxp3− nor Foxp3+ T cells from non-immunized and 2/6-VLP immunized mice, whereas they did activate both subsets from mice immunized with 2/6-VLP in the presence of adjuvant. LT-R192G dramatically decreased CD4+CD25+Foxp3+ T cells from non-immunized and 2/6-VLP immunized mice but not from mice immunized with 2/6-VLP and adjuvant. Moreover, in this case, LT-R192G increased Foxp3 expression on CD4+CD25+Foxp3+ cells, suggesting specific Treg activation during the recall. Finally, when both 2/6-VLP and LT-R192G were used for restimulation, LT-R192G clearly suppressed both 2/6-VLP-specific CD4+CD25+Foxp3− and Foxp3+ T cells. All together, these results suggest that LT-R192G exerts different effects on CD4+CD25+Foxp3+ T cells, depending on a first or a second contact. The unexpected immunomodulation observed during the recall should be considered in designing vaccination protocols. PMID:22069670

  6. Unexpected modulation of recall B and T cell responses after immunization with rotavirus-like particles in the presence of LT-R192G.

    Science.gov (United States)

    Thiam, Fatou; Martino, Cyrille Di; Bon, Fabienne; Charpilienne, Annie; Cachia, Claire; Poncet, Didier; Clements, John D; Basset, Christelle; Kohli, Evelyne

    2010-08-01

    LT-R192G, a mutant of the thermolabile enterotoxin of E. coli, is a potent adjuvant of immunization. Immune responses are generally analyzed at the end of protocols including at least 2 administrations, but rarely after a prime. To investigate this point, we compared B and T cell responses in mice after one and two intrarectal immunizations with 2/6 rotavirus-like particles (2/6-VLP) and LT-R192G. After a boost, we found, an unexpected lower B cell expansion measured by flow cytometry, despite a secondary antibody response. We then analyzed CD4(+)CD25(+)Foxp3(+) regulatory T cells (Tregs) and CD4(+)CD25(+)Foxp3(-) helper T cells after in vitro (re)stimulation of mesenteric lymph node cells with the antigen (2/6-VLP), the adjuvant (LT-R192G) or both. 2/6-VLP did not activate CD4(+)CD25(+)Foxp3(-) nor Foxp3(+) T cells from non-immunized and 2/6-VLP immunized mice, whereas they did activate both subsets from mice immunized with 2/6-VLP in the presence of adjuvant. LT-R192G dramatically decreased CD4(+)CD25(+)Foxp3(+) T cells from non-immunized and 2/6-VLP immunized mice but not from mice immunized with 2/6-VLP and adjuvant. Moreover, in this case, LT-R192G increased Foxp3 expression on CD4(+)CD25(+)Foxp3(+) cells, suggesting specific Treg activation during the recall. Finally, when both 2/6-VLP and LT-R192G were used for restimulation, LT-R192G clearly suppressed both 2/6-VLP-specific CD4(+)CD25(+)Foxp3(-) and Foxp3(+) T cells. All together, these results suggest that LT-R192G exerts different effects on CD4(+)CD25(+)Foxp3(+) T cells, depending on a first or a second contact. The unexpected immunomodulation observed during the recall should be considered in designing vaccination protocols.

  7. Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes.

    Science.gov (United States)

    van der Sluis, Renée M; Derking, Ronald; Breidel, Seyguerney; Speijer, Dave; Berkhout, Ben; Jeeninga, Rienk E

    2014-04-01

    HIV-1 transcription depends on cellular transcription factors that bind to sequences in the long-terminal repeat (LTR) promoter. Each HIV-1 subtype has a specific LTR promoter configuration, and minor sequence changes in transcription factor binding sites (TFBSs) or their arrangement can influence transcriptional activity, virus replication and latency properties. Previously, we investigated the proviral latency properties of different HIV-1 subtypes in the SupT1 T cell line. Here, subtype-specific latency and replication properties were studied in primary PHA-activated T lymphocytes. No major differences in latency and replication capacity were measured among the HIV-1 subtypes. Subtype B and AE LTRs were studied in more detail with regard to a putative AP-1 binding site using luciferase reporter constructs. c-Jun, a member of the AP-1 transcription factor family, can activate both subtype B and AE LTRs, but the latter showed a stronger response, reflecting a closer match with the consensus AP-1 binding site. c-Jun overexpression enhanced Tat-mediated transcription of the viral LTR, but in the absence of Tat inhibited basal promoter activity. Thus, c-Jun can exert a positive or negative effect via the AP-1 binding site in the HIV-1 LTR promoter, depending on the presence or absence of Tat.

  8. Prólogo arameo y anotaciones hebreas de Alfonso de Zamora para una copia manuscrita del Targum a los Profetas encargada por la Universidad de Salamanca

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    Fontela, Carlos Alonso

    2009-12-01

    Full Text Available University Library Ms. Or. 645, f. 110r (ol. Warner 65 F contains, besides a draft for an Aramaic prologue to the work on Targum written by Alonso de Zamora ca. 1532, additional notes written by himself dealing with the comission he received to copying Targumic texts. The present article improves the edition of the Aramaic prologue, previously published by Neubauer (1895, offering a Spanish translation and the edition of the marginal notes, that contain a draft of the prayers (תפלותופיהספדים for the partial colophons of the books of Ezekiel, Hosea and Joel’s Targums. These pa - tial colophons in the Leiden Ms. coincide with the clean drafts by Zamora preserved in an autograph manuscript, Salamanca University Library Ms. M-3 (Est.-1, Cajón I-Núm. 2. An explanation concerning additional annotations (the incipit of Isaiah 57, that spoiled the folio, and led it to its being re-used by Alonso de Zamora as a draft.

    El ms. Or. 645, f.º 110r (ol. Warner 65 F de la Leiden University Library, además del borrador de un prólogo arameo a la obra de Targum escrito por Alfonso de Zamora hacia el año 1532 por encargo de la Universidad de Salamanca, contiene otras anotaciones del mismo autor que aquí se publican por primera vez y que también formaban parte del mismo encargo de copia de textos targúmicos. En el presente artículo, además de mejorar el texto arameo del prólogo ya publicado por Neubauer en 1895, se ofrece su traducción española por primera vez. Asimismo, se publica y traduce una anotación marginal que consiste en un borrador de las jaculatorias o doxologías (תפלותופיהספדים para los colofones parciales de los libros del Targum de Ezequiel, Oseas y Joel. Estos colofones parciales del ms. de Leiden coinciden con los pasados a limpio que se conservan en el manuscrito autógrafo de Alfonso de Zamora ms. M-3 (Est.-1, Cajón I-Núm. 2 de la Biblioteca Universitaria de Salamanca. Se

  9. LAS REPRODUCCIONES PROVISIONALES Y LA COPIA PRIVADA DIGITAL COMO LÍMITES AL DERECHO DE REPRODUCCIÓN* –LA TRANSPOSICIÓN DE LA DIRECTIVA 2001/29/CE AL DERECHO ESPAÑOL

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    Juan Carlos Martínez Salcedo

    2013-11-01

    Full Text Available La Directiva 2001/29/CE de la Unión Europea puso a la vanguardia jurídica el régimen aplicable a las reproducciones provisionales y la copia privada como excepciones al derecho de reproducción. Dado que España, como Estado miembro de la Unión Europea, debía transponer al derecho nacional la directiva en mención, es necesario definir el alcance de su incorporación, para identificar los criterios aplicables al caso concreto, para determinar la licitud de las copias privadas y de las reproducciones provisionales de las obras protegidas, los efectos de estas frente al titular de los derechos de autor o conexos y las posibles afectaciones al usuario por las medidas anticopia. Con este propósito, se contrastará el enunciado normativo comunitario frente al adoptado en el derecho interno, coadyuvados de algunas decisiones jurisprudenciales y desarrollos doctrinales recientes.

  10. The Salmonella enterica serovar Typhi ltrR-ompR-ompC-ompF genes are involved in resistance to the bile salt sodium deoxycholate and in bacterial transformation.

    Science.gov (United States)

    Villarreal, J M; Becerra-Lobato, N; Rebollar-Flores, J E; Medina-Aparicio, L; Carbajal-Gómez, E; Zavala-García, M L; Vázquez, A; Gutiérrez-Ríos, R M; Olvera, L; Encarnación, S; Martínez-Batallar, A G; Calva, E; Hernández-Lucas, I

    2014-06-01

    A characterization of the LtrR regulator, an S. Typhi protein belonging to the LysR family is presented. Proteomics, outer membrane protein profiles and transcriptional analyses demonstrated that LtrR is required for the synthesis of OmpR, OmpC and OmpF. DNA-protein interaction analysis showed that LtrR binds to the regulatory region of ompR and then OmpR interacts with the ompC and ompF promoters inducing porin synthesis. LtrR-dependent and independent ompR promoters were identified, and both promoters are involved in the synthesis of OmpR for OmpC and OmpF production. To define the functional role of the ltrR-ompR-ompC-ompF genetic network, mutants in each gene were obtained. We found that ltrR, ompR, ompC and ompF were involved in the control of bacterial transformation, while the two regulators and ompC are necessary for the optimal growth of S. Typhi in the presence of one of the major bile salts found in the gut, sodium deoxycholate. The data presented establish the pivotal role of LtrR in the regulatory network of porin synthesis and reveal new genetic strategies of survival and cellular adaptation to the environment used by Salmonella. © 2014 John Wiley & Sons Ltd.

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

    Science.gov (United States)

    Petit, Julie; Bourgeois, Emmanuelle; Stenger, Wilfried; Bès, Martine; Droc, Gaétan; Meynard, Donaldo; Courtois, Brigitte; Ghesquière, Alain; Sabot, François; Panaud, Olivier; Guiderdoni, Emmanuel

    2009-12-01

    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 element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O

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

    Science.gov (United States)

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

    2017-02-06

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

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

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    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.

  14. Characterization of non-LTR retrotransposable TRAS elements in the aphids Acyrthosiphon pisum and Myzus persicae (Aphididae, Hemiptera).

    Science.gov (United States)

    Monti, Valentina; Serafini, Chiara; Manicardi, Gian Carlo; Mandrioli, Mauro

    2013-01-01

    A non-LTR TRAS retrotransposon (identified as TRASAp1) has been amplified in the pea aphid Acyrthosiphon pisum and its presence has been assessed also in the peach potato aphid Myzus persicae. This TRAS element possesses 2 overlapping ORFs (a gag-ORF1 and a pol-ORF2 containing the reverse transcriptase and the endonuclease domains) that show a similarity ranging from 40% to 48% to proteins coded by other TRAS elements identified in insects (including the beetle Tribolium castaneum and the moth Bombyx mori). The study of the TRAS chromosomal insertion sites, performed by standard fluorescent in situ hybridization (FISH) and fiber FISH, showed that TRAS elements were located in a subtelomeric position, just before the telomeric (TTAGG) n repeats. In both the aphid species, TRAS elements were present at all termini of autosomes, but the 2 X chromosome telomeres show a clear-cut structural difference. Indeed, cromomycin A3 staining, together with FISH using a TRAS probe, revealed that TRAS signals only occur at the telomere opposite to the NOR-bearing one. Lastly, the analysis of the distribution of TRAS retrotransposons in a M. persicae strain possessing spontaneous fragmentations of the X chromosomes assessed that TRAS elements were not involved in the healing of de novo telomeres.

  15. Mycobacterial and HIV infections up-regulated human zinc finger protein 134, a novel positive regulator of HIV-1 LTR activity and viral propagation.

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    Ronald Benjamin

    Full Text Available BACKGROUND: Concurrent occurrence of HIV and Tuberculosis (TB infections influence the cellular environment of the host for synergistic existence. An elementary approach to understand such coalition at the molecular level is to understand the interactions of the host and the viral factors that subsequently effect viral replication. Long terminal repeats (LTR of HIV genome serve as a template for binding trans-acting viral and cellular factors that regulate its transcriptional activity, thereby, deciding the fate of HIV pathogenesis, making it an ideal system to explore the interplay between HIV and the host. METHODOLOGY/PRINCIPAL FINDINGS: In this study, using biotinylated full length HIV-1 LTR sequence as bait followed by MALDI analyses, we identified and further characterized human-Zinc-finger-protein-134 (hZNF-134 as a novel positive regulator of HIV-1 that promoted LTR-driven transcription and viral production. Over-expression of hZNF-134 promoted LTR driven luciferase activity and viral transcripts, resulting in increased virus production while siRNA mediated knockdown reduced both the viral transcripts and the viral titers, establishing hZNF-134 as a positive effector of HIV-1. HIV, Mycobacteria and HIV-TB co-infections increased hZNF-134 expressions in PBMCs, the impact being highest by mycobacteria. Corroborating these observations, primary TB patients (n = 22 recorded extraordinarily high transcript levels of hZNF-134 as compared to healthy controls (n = 16. CONCLUSIONS/SIGNIFICANCE: With these observations, it was concluded that hZNF-134, which promoted HIV-1 LTR activity acted as a positive regulator of HIV propagation in human host. High titers of hZNF-134 transcripts in TB patients suggest that up-regulation of such positive effectors of HIV-1 upon mycobacterial infection can be yet another mechanism by which mycobacteria assists HIV-1 propagation during HIV-TB co-infections. hZNF-134, an uncharacterized host protein, thus

  16. The HIV-1 Integrase α4-Helix Involved in LTR-DNA Recognition Is also a Highly Antigenic Peptide Element

    Science.gov (United States)

    Azzi, Sandy; Parissi, Vincent; Maroun, Richard G.; Eid, Pierre; Mauffret, Olivier; Fermandjian, Serge

    2010-01-01

    Monoclonal antibodies (MAbas) constitute remarkable tools to analyze the relationship between the structure and the function of a protein. By immunizing a mouse with a 29mer peptide (K159) formed by residues 147 to 175 of the HIV-1 integrase (IN), we obtained a monoclonal antibody (MAba4) recognizing an epitope lying in the N-terminal portion of K159 (residues 147–166 of IN). The boundaries of the epitope were determined in ELISA assays using peptide truncation and amino acid substitutions. The epitope in K159 or as a free peptide (pep-a4) was mostly a random coil in solution, while in the CCD (catalytic core domain) crystal, the homologous segment displayed an amphipathic helix structure (α4-helix) at the protein surface. Despite this conformational difference, a strong antigenic crossreactivity was observed between pep-a4 and the protein segment, as well as K156, a stabilized analogue of pep-a4 constrained into helix by seven helicogenic mutations, most of them involving hydrophobic residues. We concluded that the epitope is freely accessible to the antibody inside the protein and that its recognition by the antibody is not influenced by the conformation of its backbone and the chemistry of amino acids submitted to helicogenic mutations. In contrast, the AA →Glu mutations of the hydrophilic residues Gln148, Lys156 and Lys159, known for their interactions with LTRs (long terminal repeats) and inhibitors (5 CITEP, for instance), significantly impaired the binding of K156 to the antibody. Moreover, we found that in competition ELISAs, the processed and unprocessed LTR oligonucleotides interfered with the binding of MAba4 to IN and K156, confirming that the IN α4-helix uses common residues to interact with the DNA target and the MAba4 antibody. This also explains why, in our standard in vitro concerted integration assays, MAba4 strongly impaired the IN enzymatic activity. PMID:21209864

  17. The HIV-1 integrase α4-helix involved in LTR-DNA recognition is also a highly antigenic peptide element.

    Directory of Open Access Journals (Sweden)

    Sandy Azzi

    Full Text Available Monoclonal antibodies (MAbas constitute remarkable tools to analyze the relationship between the structure and the function of a protein. By immunizing a mouse with a 29mer peptide (K159 formed by residues 147 to 175 of the HIV-1 integrase (IN, we obtained a monoclonal antibody (MAba4 recognizing an epitope lying in the N-terminal portion of K159 (residues 147-166 of IN. The boundaries of the epitope were determined in ELISA assays using peptide truncation and amino acid substitutions. The epitope in K159 or as a free peptide (pep-a4 was mostly a random coil in solution, while in the CCD (catalytic core domain crystal, the homologous segment displayed an amphipathic helix structure (α4-helix at the protein surface. Despite this conformational difference, a strong antigenic crossreactivity was observed between pep-a4 and the protein segment, as well as K156, a stabilized analogue of pep-a4 constrained into helix by seven helicogenic mutations, most of them involving hydrophobic residues. We concluded that the epitope is freely accessible to the antibody inside the protein and that its recognition by the antibody is not influenced by the conformation of its backbone and the chemistry of amino acids submitted to helicogenic mutations. In contrast, the AA →Glu mutations of the hydrophilic residues Gln148, Lys156 and Lys159, known for their interactions with LTRs (long terminal repeats and inhibitors (5CITEP, for instance, significantly impaired the binding of K156 to the antibody. Moreover, we found that in competition ELISAs, the processed and unprocessed LTR oligonucleotides interfered with the binding of MAba4 to IN and K156, confirming that the IN α4-helix uses common residues to interact with the DNA target and the MAba4 antibody. This also explains why, in our standard in vitro concerted integration assays, MAba4 strongly impaired the IN enzymatic activity.

  18. Marcadores virológicos no convencionales en pacientes infectados con el virus de la inmunodeficiencia humana: ADN HIV-T, ADN HIV- 2LTR y ARN de HIV Non conventional virological markers in HIV-infected patients: T-HIV DNA, 2LTR-HIV DNA and HIV RNA

    Directory of Open Access Journals (Sweden)

    Rosana Gariglio

    2004-10-01

    Full Text Available La terapia antirretroviral de alta eficacia (TAAE induce una reducción marcada y persistente de la viremia plasmática, contribuyendo a disminuir la mortalidad y morbilidad de los pacientes HIV-positivos. Así, la carga viral (CV es el método de referencia para evaluar la eficacia terapéutica. Sin embargo, aun en presencia de una TAAE eficiente no se ha logrado la erradicación viral. En este estudio analizamos la presencia del ADN total de HIV (ADN HIV-T, del ADN no integrado con 2LTR (ADN HIV-2LTR y del ARN de HIV, en un grupo de 55 pacientes HIV-positivos en distintos estadios clínicos, con y sin TAAE, mediante ensayos de PCR con revelado colorimétrico en microplaca, optimizados en nuestro laboratorio. La sensibilidad clínica del ARN del HIV fue evaluada con el bDNA, resultando del 74% y del 64%, respectivamente, con una concordancia del 85%. Este ensayo podría ser utilizado en el seguimiento de pacientes bajo TAAE. El ADN HIV-2LTR resultó positivo en el 54% aunque estuvo ausente en pacientes con elevada CV. Este marcador se consideraba un producto lábil y su presencia se asociaba a infección reciente. Sin embargo, actuales evidencias ponen en discusión su estabilidad por lo que su significado clínico debe ser reconsiderado. La ausencia del ADN HIV-2LTR en pacientes con CV detectable puede relacionarse con la heterogeneidad de la secuencia utilizada para su detección. El ADN HIV-T estuvo presente en el 100% de las muestras y resultaría relevante como marcador de remisión cuando se dispongan de terapias que efectivamente erradiquen la infección.Highly active antiretroviral therapy (HAART induces a persistent reduction of the plasmatic viremia, contributing to decrease mortality and morbidity of infected people with human immunodeficiency virus (HIV. Thus, viral load (VL is the reference method to evaluate therapy effectiveness. However, even in the presence of efficient HAART viral eradication was yet not achieved. In this

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

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    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

  20. Deletion of the LTR enhancer/promoter has no impact on the integration profile of MLV vectors in human hematopoietic progenitors.

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    Arianna Moiani

    Full Text Available Moloney murine leukemia virus (MLV-derived gamma-retroviral vectors integrate preferentially near transcriptional regulatory regions in the human genome, and are associated with a significant risk of insertional gene deregulation. Self-inactivating (SIN vectors carry a deletion of the U3 enhancer and promoter in the long terminal repeat (LTR, and show reduced genotoxicity in pre-clinical assays. We report a high-definition analysis of the integration preferences of a SIN MLV vector compared to a wild-type-LTR MLV vector in the genome of CD34(+ human hematopoietic stem/progenitor cells (HSPCs. We sequenced 13,011 unique SIN-MLV integration sites and compared them to 32,574 previously generated MLV sites in human HSPCs. The SIN-MLV vector recapitulates the integration pattern observed for MLV, with the characteristic clustering of integrations around enhancer and promoter regions associated to H3K4me3 and H3K4me1 histone modifications, specialized chromatin configurations (presence of the H2A.Z histone variant and binding of RNA Pol II. SIN-MLV and MLV integration clusters and hot spots overlap in most cases and are generated at a comparable frequency, indicating that the reduced genotoxicity of SIN-MLV vectors in hematopoietic cells is not due to a modified integration profile.

  1. Characterization of interactions between transcription factors and a regulatory region spanning nt-320 to-281 of the HIV-1 LTR in T-lymphoid and non-T-lymphoid cells

    NARCIS (Netherlands)

    Pereira, LA; Churchill, MJ; Elefanty, AG; Gouskos, T; Lambert, PF; Ramsay, RG; Deacon, NJ

    2002-01-01

    HIV-1 gene expression is regulated by the interplay of transcription factors with multiple binding motifs present within the U3, R and U5 regions of the long terminal repeat (LTR). Here we report novel DNA binding complexes (termed 9a, 9b and 9c) between nuclear proteins from T-lymphoid and

  2. A new sensitive indicator cell line reveals cross-transactivation of the viral LTR by gorilla and chimpanzee simian foamy viruses.

    Science.gov (United States)

    Lambert, Caroline; Rua, Réjane; Gessain, Antoine; Buseyne, Florence

    2016-09-01

    The majority of currently identified simian foamy virus (SFV)-infected Cameroonian and Gabonese individuals harbor SFV from the gorilla lineage. We constructed an indicator cell line for the quantification of gorilla SFVs, in which the U3 sequence of a gorilla SFV directs the expression of the β-galactosidase protein. The gorilla foamy virus activated β-galactosidase (GFAB) cells efficiently quantified two zoonotic primary gorilla isolates and SFVs from three chimpanzee subspecies. Primary gorilla SFVs replicated more slowly and at lower levels than primary chimpanzee SFVs. Analysis of previously described motifs of Tas proteins and U3 LTRs involved in viral gene synthesis revealed conservation of such motifs in Tas proteins from gorilla and chimpanzee SFVs, but little sequence homology in the LTR regions previously shown to interact with viral and cellular factors. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Dual role of novel ingenol derivatives from Euphorbia tirucalli in HIV replication: inhibition of de novo infection and activation of viral LTR.

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    Celina M Abreu

    Full Text Available HIV infection is not cleared by antiretroviral drugs due to the presence of latently infected cells that are not eliminated with current therapies and persist in the blood and organs of infected patients. New compounds to activate these latent reservoirs have been evaluated so that, along with HAART, they can be used to activate latent virus and eliminate the latently infected cells resulting in eradication of viral infection. Here we describe three novel diterpenes isolated from the sap of Euphorbia tirucalli, a tropical shrub. These molecules, identified as ingenols, were modified at carbon 3 and termed ingenol synthetic derivatives (ISD. They activated the HIV-LTR in reporter cell lines and human PBMCs with latent virus in concentrations as low as 10 nM. ISDs were also able to inhibit the replication of HIV-1 subtype B and C in MT-4 cells and human PBMCs at concentrations of EC50 0.02 and 0.09 µM respectively, which are comparable to the EC50 of some antiretroviral currently used in AIDS treatment. Control of viral replication may be caused by downregulation of surface CD4, CCR5 and CXCR4 observed after ISD treatment in vitro. These compounds appear to be less cytotoxic than other diterpenes such as PMA and prostratin, with effective dose versus toxic dose TI>400. Although the mechanisms of action of the three ISDs are primarily attributed to the PKC pathway, downregulation of surface receptors and stimulation of the viral LTR might be differentially modulated by different PKC isoforms.

  4. Mice Develop Effective but Delayed Protective Immune Responses When Immunized as Neonates either Intranasally with Nonliving VP6/LT(R192G) or Orally with Live Rhesus Rotavirus Vaccine Candidates

    OpenAIRE

    VanCott, John L.; Prada, Anne E.; McNeal, Monica M.; Stone, Susan C.; Basu, Mitali; Huffer, Bert; Smiley, Kristi L.; Shao, Mingyuan; Bean, Judy A.; Clements, John D.; Choi, Anthony H.-C.; Ward, Richard L.

    2006-01-01

    Rotavirus vaccines are delivered early in life, when the immune system is immature. To determine the effects of immaturity on responses to candidate vaccines, neonatal (7 days old) and adult mice were immunized with single doses of either Escherichia coli-expressed rotavirus VP6 protein and the adjuvant LT(R192G) or live rhesus rotavirus (RRV), and protection against fecal rotavirus shedding following challenge with the murine rotavirus strain EDIM was determined. Neonatal mice immunized intr...

  5. 28S junctions and chimeric elements of the rDNA targeting non-LTR retrotransposon R2 in crustacean living fossils (Branchiopoda, Notostraca).

    Science.gov (United States)

    Luchetti, Andrea; Mingazzini, Valentina; Mantovani, Barbara

    2012-07-01

    The 28S rRNA genes of several metazoans are interrupted by site-specific targeting non-LTR retrotransposons, such as R2. R2 elements have been deeply analyzed but aspects of their retrotransposition mechanism and the origin of the wide diversity observed are still debated. We characterized six new R2 lineages in four tadpole shrimp species (Notostraca), samples deriving from a parthenogenetic population of Triops cancriformis (R2Tc_it) and from bisexual Lepidurus populations of L. lubbocki (R2Ll), L. couesii (R2LcA, R2LcB, R2LcC) and L. arcticus (R2La). All elements fit the canonical R2 structure but R2Ll which turned out to be a chimera with an additional ORF originating from another R2. Consistently with data on LINEs, R2Ll could be the result of recombination due to reverse transcriptase template jump. The analysis of 28S/R2 5' end junctions further suggests aberrant homologous recombination, as observed in RNA viruses. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. High-Resolution NMR Analysis of the Conformations of Native and Base Analog Substituted Retroviral and LTR-Retrotransposon PPT Primers

    Science.gov (United States)

    Yi-Brunozzi, Hye Young; Brinson, Robert G.; Brabazon, Danielle M.; Lener, Daniela; Le Grice, Stuart F.J.; Marino, John P.

    2009-01-01

    Summary A purine-rich region of the plus-strand RNA genome of retroviruses and long terminal repeat (LTR)-containing retrotransposons, known as the polypurine tract (PPT), is resistant to hydrolysis by the RNase H domain of reverse transcriptase (RT) and ultimately serves as a primer for plus-strand DNA synthesis. The mechanisms underlying PPT resistance and selective processing remain largely unknown. Here, two RNA/DNA hybrids derived from the PPTs of HIV-1 and Ty3 were probed using high-resolution NMR for preexisting structural distortions in the absence of RT. The PPTs were selectively modified through base-pair changes or by incorporation of the thymine isostere, 2,4-difluoro-5-methyl-benzene (dF), into the DNA strand. Although both wild-type (WT) and mutated hybrids adopted global A-form-like helical geometries, observed structural perturbations in the base-pair and dF-modified hybrids suggested that the PPT hybrids may function as structurally coupled domains. PMID:18355725

  7. Cytosine DNA methylation at promoter of non LTR retrotransposon and heat shock protein gene (HSP70) of Entamoeba histolytica and lack of correlation with transcription status.

    Science.gov (United States)

    Agrahari, Mridula; Gaurav, Amit Kumar; Bhattacharya, Alok; Bhattacharya, Sudha

    2017-03-01

    Non LTR retrotransposons (EhLINEs and EhSINEs) occupy 11% of the Entamoeba histolytica genome. Since promoter DNA methylation at cytosines has been correlated with transcriptional silencing of transposable elements in model organisms we checked whether this was the case in EhLINE1. We located promoter activity in a 841bp fragment at 5'-end of this element by luciferase reporter assay. From RNAseq and RT-PCR analyses we selected a transcriptionally active and silent copy to study cytosine DNA methylation of the promoter region by bisulfite sequencing. None of the cytosines were methylated in either copy. Further, we looked at methylation status of a few selected cytosines in all 5'-intact EhLINE1 copies by single nucleotide incorporation opposite cytosine in bisulfite-treated DNA, where dGTP would be incorporated if the cytosine was methylated. Again we did not find evidence of cytosine methylation, indicating that expression status of this element was not correlated with promoter DNA methylation. To test for any role of cytosine methylation in transcriptional regulation of the E. histolytica Hsp70 gene in which the promoter is fully methylated under normal growth conditions, we checked methylation status and found that the promoter remained fully methylated during heat-shock as well, although transcription was greatly enhanced by heat-shock, showing that cytosine methylation is not a repressive mark for EhHsp70. Our data present direct evidence that promoter methylation, a common mode of transposon silencing, is unlikely to be involved in transcriptional regulation of EhLINE1, and reinforce the conclusion that promoter DNA methylation may not be a major contributor to transcriptional regulation in E. histolytica. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Mice develop effective but delayed protective immune responses when immunized as neonates either intranasally with nonliving VP6/LT(R192G) or orally with live rhesus rotavirus vaccine candidates.

    Science.gov (United States)

    VanCott, John L; Prada, Anne E; McNeal, Monica M; Stone, Susan C; Basu, Mitali; Huffer, Bert; Smiley, Kristi L; Shao, Mingyuan; Bean, Judy A; Clements, John D; Choi, Anthony H-C; Ward, Richard L

    2006-05-01

    Rotavirus vaccines are delivered early in life, when the immune system is immature. To determine the effects of immaturity on responses to candidate vaccines, neonatal (7 days old) and adult mice were immunized with single doses of either Escherichia coli-expressed rotavirus VP6 protein and the adjuvant LT(R192G) or live rhesus rotavirus (RRV), and protection against fecal rotavirus shedding following challenge with the murine rotavirus strain EDIM was determined. Neonatal mice immunized intranasally with VP6/LT(R192G) were unprotected at 10 days postimmunization (dpi) and had no detectable rotavirus B-cell (antibody) or CD4(+) CD8(+) T-cell (rotavirus-inducible, Th1 [gamma interferon and interleukin-2 {IL-2}]-, Th2 [IL-5 and IL-4]-, or ThIL-17 [IL-17]-producing spleen cells) responses. However, by 28 and 42 dpi, these mice were significantly (P >or= 0.003) protected and contained memory rotavirus-specific T cells but produced no rotavirus antibody. In contrast, adult mice were nearly fully protected by 10 dpi and contained both rotavirus immunoglobulin G and memory T cells. Neonates immunized orally with RRV were also less protected (P=0.01) than adult mice by 10 dpi and produced correspondingly less rotavirus antibody. Both groups contained few rotavirus-specific memory T cells. Protection levels by 28 dpi for neonates or adults were equal, as were rotavirus antibody levels. This report introduces a neonatal mouse model for active protection studies with rotavirus vaccines. It indicates that, with time, neonatal mice develop full protection after intranasal immunization with VP6/LT(R192G) or oral immunization with a live heterologous rotavirus and supports reports that protection depends on CD4(+) T cells or antibody, respectively.

  9. Discovery and partial characterization of a non-LTR retrotransposon that may be associated with abdominal segment deformity disease (ASDD) in the whiteleg shrimp Penaeus (Litopenaeus) vannamei

    Science.gov (United States)

    2013-01-01

    Background Abdominal segment deformity disease (ASDD) of cultivated whiteleg shrimp Penaeus (Litopenaeus) vannamei causes economic loss of approximately 10% in affected specimens because of the unsightliness of distorted abdominal muscles. It is associated with the presence of viral-like particles seen by electron microscopy in the ventral nerve cords of affected shrimp. Thus, shotgun cloning was carried out to seek viral-like sequences in affected shrimp. Results A new retrovirus-like element of 5052 bp (named abdominal segment deformity element or ASDE) was compiled by shotgun cloning and 3′ and 5′ RACE using RNA and DNA extracted from ventral nerve cords of ASDD shrimp. ASDE contained 7 putative open reading frames (ORF). One ORF (called the PENS sub-domain), had a deduced amino acid (aa) sequence homologous to the GIY-YIG endonuclease domain of penelope-like retrotransposons while two others were homologous to the reverse transcriptase (RT) and RNaseH domains of the pol gene of non-long terminal repeat (non-LTR) retrotransposons (called the NLRS sub-domain). No single amplicon of 5 kb containing both these elements was obtained by PCR or RT-PCR from ASDD shrimp. Subsequent analysis indicated that PENS and NLRS were not contiguous and that NLRS was a host genetic element. In situ hybridization using a dioxygenin-labeled NLRS probe revealed that NLRS gave positive reactions in abdominal-ganglion neurons of ASDD shrimp but not normal shrimp. Preliminary analysis indicated that long-term use of female broodstock after eyestalk ablation in the hatchery increased the intensity of RT-PCR amplicons for NLRS and also the prevalence of ASDD in mysis 3 offspring of the broodstock. The deformities persist upon further cultivation until shrimp harvest but do not increase in prevalence and do not affect growth or survival. Conclusions Our results suggested that NLRS is a shrimp genetic element associated with ASDD and that immediate preventative measures could include

  10. Functionally conserved RNA-binding and protein-protein interaction properties of LINE-ORF1p in an ancient clade of non-LTR retrotransposons of Entamoeba histolytica.

    Science.gov (United States)

    Gaurav, Amit Kumar; Kumar, Jitender; Agrahari, Mridula; Bhattacharya, Alok; Yadav, Vijay Pal; Bhattacharya, Sudha

    2017-01-01

    Retrotransposons are mobile genetic elements found in most organisms. Their origin and evolution is not very well understood. Retrotransposons that lack long terminal repeats (non-LTR) have been classified based on their reverse transcriptase (RT) and endonuclease sequences into groups, of which R2 is the most ancient. Its members contain a single open reading frame (ORF) while there are two ORFs in the other groups, of which ORF2 contains the RT and endonuclease sequences. It is thought that ORF1 was added later to the single-ORF-containing elements, and codes for a protein with nucleic acid binding activity. We have examined the non-LTR retrotransposons in Entamoeba histolytica, an early-branching parasitic protist, which belongs to the R2 group. However, unlike other members of R2, E. histolytica contains two ORFs. Here we show that EhLINE1-ORF1p is functionally related to the ORF1p found in the non-R2 groups. Its N-terminal region has RNA-binding activity and its C-terminal has a coiled coil domain which participates in protein-protein interaction. It lacks sequence-specificity of RNA-binding and binds to EhLINE1-RNA fragment and ribosomal RNA with comparable affinities. Our study suggests that ORF1p could have evolved independently to maintain functional conservation. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Cocaine promotes both initiation and elongation phase of HIV-1 transcription by activating NF-κB and MSK1 and inducing selective epigenetic modifications at HIV-1 LTR

    Energy Technology Data Exchange (ETDEWEB)

    Sahu, Geetaram; Farley, Kalamo [Division of Infectious Diseases, Department of Medicine, George Washington University, Washington, DC (United States); El-Hage, Nazira [Virginia Commonwealth University, Richmond, VA (United States); Aiamkitsumrit, Benjamas; Fassnacht, Ryan [Division of Infectious Diseases, Department of Medicine, George Washington University, Washington, DC (United States); Kashanchi, Fatah [George Mason University, Manassas, VA (United States); Ochem, Alex [ICGEB, Wernher and Beit Building, Anzio Road, Observatory, 7925 Cape Town (South Africa); Simon, Gary L. [Division of Infectious Diseases, Department of Medicine, George Washington University, Washington, DC (United States); Karn, Jonathan [Case Western Reserve University, Cleveland, OH (United States); Hauser, Kurt F. [Virginia Commonwealth University, Richmond, VA (United States); Tyagi, Mudit, E-mail: tmudit@email.gwu.edu [Division of Infectious Diseases, Department of Medicine, George Washington University, Washington, DC (United States); Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC 20037 (United States)

    2015-09-15

    Cocaine accelerates human immunodeficiency virus (HIV-1) replication by altering specific cell-signaling and epigenetic pathways. We have elucidated the underlying molecular mechanisms through which cocaine exerts its effect in myeloid cells, a major target of HIV-1 in central nervous system (CNS). We demonstrate that cocaine treatment promotes HIV-1 gene expression by activating both nuclear factor-kappa B (NF-ĸB) and mitogen- and stress-activated kinase 1 (MSK1). MSK1 subsequently catalyzes the phosphorylation of histone H3 at serine 10, and p65 subunit of NF-ĸB at 276th serine residue. These modifications enhance the interaction of NF-ĸB with P300 and promote the recruitment of the positive transcription elongation factor b (P-TEFb) to the HIV-1 LTR, supporting the development of an open/relaxed chromatin configuration, and facilitating the initiation and elongation phases of HIV-1 transcription. Results are also confirmed in primary monocyte derived macrophages (MDM). Overall, our study provides detailed insights into cocaine-driven HIV-1 transcription and replication. - Highlights: • Cocaine induces the initiation phase of HIV transcription by activating NF-ĸB. • Cocaine induced NF-ĸB phosphorylation promotes its interaction with P300. • Cocaine enhances the elongation phase of HIV transcription by stimulating MSK1. • Cocaine activated MSK1 catalyzes the phosphorylation of histone H3 at its Ser10. • Cocaine induced H3S10 phosphorylation facilitates the recruitment of P-TEFb at LTR.

  12. Cocaine promotes both initiation and elongation phase of HIV-1 transcription by activating NF-κB and MSK1 and inducing selective epigenetic modifications at HIV-1 LTR

    Science.gov (United States)

    Sahu, Geetaram; Farley, Kalamo; El-Hage, Nazira; Aiamkitsumrit, Benjamas; Fassnacht, Ryan; Kashanchi, Fatah; Ochem, Alex; Simon, Gary L.; Karn, Jonathan; Hauser, Kurt F.; Tyagi, Mudit

    2015-01-01

    Cocaine accelerates human immunodeficiency virus (HIV-1) replication by altering specific cell-signaling and epigenetic pathways. We have elucidated the underlying molecular mechanisms through which cocaine exerts its effect in myeloid cells, a major target of HIV-1 in central nervous system (CNS). We demonstrate that cocaine treatment promotes HIV-1 gene expression by activating both nuclear factor-kappa B (NF-κB) and mitogen- and stress-activated kinase 1 (MSK1). MSK1 subsequently catalyzes the phosphorylation of histone H3 at serine 10, and p65 subunit of NF-κB at 276th serine residue. These modifications enhance the interaction of NF-κB with P300 and promote the recruitment of the positive transcription elongation factor b (P-TEFb) to the HIV-1 LTR, supporting the development of an open/relaxed chromatin configuration, and facilitating the initiation and elongation phases of HIV-1 transcription. Results are also confirmed in primary monocyte derived macrophages (MDM). Overall, our study provides detailed insights into cocaine-driven HIV-1 transcription and replication. PMID:25980739

  13. LTR real-time PCR for HIV-1 DNA quantitation in blood cells for early diagnosis in infants born to seropositive mothers treated in HAART area (ANRS CO 01).

    Science.gov (United States)

    Avettand-Fènoël, Véronique; Chaix, Marie-Laure; Blanche, Stéphane; Burgard, Marianne; Floch, Corinne; Toure, Kadidia; Allemon, Marie-Christine; Warszawski, Josiane; Rouzioux, Christine

    2009-02-01

    HIV-1 diagnosis in babies born to seropositive mothers is one of the challenges of HIV epidemics in children. A simple, rapid protocol was developed for quantifying HIV-1 DNA in whole blood samples and was used in the ANRS French pediatric cohort in conditions of prevention of mother-to-child transmission. A quantitative HIV-1 DNA protocol (LTR real-time PCR) requiring small blood volumes was developed. First, analytical reproducibility was evaluated on 172 samples. Results obtained on blood cell pellets and Ficoll-Hypaque separated mononuclear cells were compared in 48 adult HIV-1 samples. Second, the protocol was applied to HIV-1 diagnosis in infants in parallel with plasma HIV-RNA quantitation. This prospective study was performed in children born between May 2005 and April 2007 included in the ANRS cohort. The assay showed good reproducibility. The 95% detection cut-off value was 6 copies/PCR, that is, 40 copies/10(6) leukocytes. HIV-DNA levels in whole blood were highly correlated with those obtained after Ficoll-Hypaque separation (r = 0.900, P mothers have received HAART. (c) 2008 Wiley-Liss, Inc.

  14. Controller reconfiguration based on LTR design

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Stoustrup, J.

    2003-01-01

    Design of controller reconfiguration (CR) for systems with sensor faults are considered in this paper. One way to accommodate a failing sensor, is by replacing it by an observer based on the remaining outputs. A similar approach can be applied for a faulty actuator by duality. By including observ...

  15. Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile.

    Science.gov (United States)

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

    2015-12-01

    Posidonia oceanica is a monocotyledonous marine plant that plays a crucial role in maintaining the Mediterranean environment. Despite its ecological importance, basic knowledge of the functional and structural genomics of this species is still limited, as it is for the other seagrasses. Here, for the first time, we report data on the repetitive component of the genome of this seagrass using a low coverage of Illumina sequences and different assembly approaches. A dataset of 19,760 assembled sequences, mostly belonging to the repetitive fraction of the genome, was produced and annotated. Based on mapping Illumina reads onto this dataset, the genome structure of P. oceanica and its repetitive component was inferred. A very large proportion of the genome is represented by long-terminal-repeat (LTR) retrotransposons of both the Copia and Gypsy superfamilies. Posidonia LTR-retrotransposons were classified and their sequences analysed. Gypsy elements belong to three main lineages, while Copia ones belong to seven lineages. Gypsy elements were more represented than Copia ones in the set of assembled sequences and in the genome. Analysis of sequence variability indicated that Gypsy lineages have experienced amplification in more recent times compared to Copia ones. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.).

    Science.gov (United States)

    Rey-Baños, Rita; Sáenz de Miera, Luis E; García, Pedro; Pérez de la Vega, Marcelino

    2017-01-01

    Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic

  17. Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik..

    Directory of Open Access Journals (Sweden)

    Rita Rey-Baños

    Full Text Available Retrotransposons with long terminal repeats (LTR-RTs are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry

  18. An application of LTR design in fault detection

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik

    1998-01-01

    The fault detection and isolation (FDI) problem is considered in this paper. The FDI problem is formulated as a filter design problem, where the faults in the system is estimated and the disturbance acting on the system is rejected. It turns out that the filter design problem can be considered as...

  19. Genome-wide detection of Ty1-copia and Ty3-gypsy group ...

    African Journals Online (AJOL)

    Jane

    Zhang1*. 1College of Horticulture, Nanjing Agricultural University, 1 Tongwei Road, Nanjing 210095, People's Republic of China. ... xyacetic acid; PCR, polymerase chain reaction; RT, reverse ..... and 200 ng, and PCR product of the Ty3-gypsy RT domain, corresponding to 250, 400, 500 and 800 pg, were fixed to the filter.

  20. Del grabado como estrategia. Mediaciones entre el original y la copia.

    Directory of Open Access Journals (Sweden)

    Patricia Zalamea.

    2008-08-01

    Full Text Available By tracing the origins of printmaking in Europe between the ffteenth and seventeenth centuries, this article explores the self-refexive possibilities of the médium, whose reproductive abilities redefne Western art in a number of ways. It establishes a comparison between the phenomenon of replication in both prints and paintings, in connection to the Renaissance notion of artistic identity and signatures, which may be understood as an extensión of the artist’s persona. Similarly, it analyzes the ways in which prints question the relationship between origináis and copies, both historically and in terms of our current understanding of reproductions, while probing concepts such as invention and imitation, as well as the artist’s hand. Using this background information, an interpretation of a specifc engraving, the Nymph of Fontainebleau, is proposed. Attributed to Pierre Milán and René Boyvin, this work may be read as an artistic declaration about print’s ability to recréate other visual media, and to extend itself both in space and time.

  1. Copia y simulacro en el Sofista de Platón

    Directory of Open Access Journals (Sweden)

    Carlos Másmela

    2013-11-01

    Full Text Available Within the Sophist, Plato establishes a clear distinction between two types of mimetic art: the copy and the simulacrum. Such a distinction avoids reducing the image to the faithful reproduction of a sensitive model. The present article aims at making visible the fact that the phantasma (simulacrum, and not the copy, constitutes the starting point of artistic creation.

  2. Borradores, originales, copias y recopilaciones: Los Libros de Estatutos del cabildo catedralicio sevillano

    Directory of Open Access Journals (Sweden)

    Diego Belmonte Fernández

    2014-12-01

    Full Text Available In this study we will decipher the process by which the canonry of the Cathedral of Seville created a series of codices, generically called Statute Books, in which were written the rules that governed the see until the fall of the Old Regime. We aim to understand how they became the unordered group of rules and laws that finally were. Also we will clarify how and when these manuscripts, sometimes recipients of unpublished information, were used, were born and died. In addition, we will show another scriptural practice of the canonry used to publicize their statutes which had not attracted attention until now.

  3. Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome.

    Science.gov (United States)

    González, Leonardo Galindo; Deyholos, Michael K

    2012-11-21

    Flax (Linum usitatissimum L.) is an important crop for the production of bioproducts derived from its seed and stem fiber. Transposable elements (TEs) are widespread in plant genomes and are a key component of their evolution. The availability of a genome assembly of flax (Linum usitatissimum) affords new opportunities to explore the diversity of TEs and their relationship to genes and gene expression. Four de novo repeat identification algorithms (PILER, RepeatScout, LTR_finder and LTR_STRUC) were applied to the flax genome assembly. The resulting library of flax repeats was combined with the RepBase Viridiplantae division and used with RepeatMasker to identify TEs coverage in the genome. LTR retrotransposons were the most abundant TEs (17.2% genome coverage), followed by Long Interspersed Nuclear Element (LINE) retrotransposons (2.10%) and Mutator DNA transposons (1.99%). Comparison of putative flax TEs to flax transcript databases indicated that TEs are not highly expressed in flax. However, the presence of recent insertions, defined by 100% intra-element LTR similarity, provided evidence for recent TE activity. Spatial analysis showed TE-rich regions, gene-rich regions as well as regions with similar genes and TE density. Monte Carlo simulations for the 71 largest scaffolds (≥ 1 Mb each) did not show any regional differences in the frequency of TE overlap with gene coding sequences. However, differences between TE superfamilies were found in their proximity to genes. Genes within TE-rich regions also appeared to have lower transcript expression, based on EST abundance. When LTR elements were compared, Copia showed more diversity, recent insertions and conserved domains than the Gypsy, demonstrating their importance in genome evolution. The calculated 23.06% TE coverage of the flax WGS assembly is at the low end of the range of TE coverages reported in other eudicots, although this estimate does not include TEs likely found in unassembled repetitive regions of

  4. Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L. genome

    Directory of Open Access Journals (Sweden)

    González Leonardo Galindo

    2012-11-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. is an important crop for the production of bioproducts derived from its seed and stem fiber. Transposable elements (TEs are widespread in plant genomes and are a key component of their evolution. The availability of a genome assembly of flax (Linum usitatissimum affords new opportunities to explore the diversity of TEs and their relationship to genes and gene expression. Results Four de novo repeat identification algorithms (PILER, RepeatScout, LTR_finder and LTR_STRUC were applied to the flax genome assembly. The resulting library of flax repeats was combined with the RepBase Viridiplantae division and used with RepeatMasker to identify TEs coverage in the genome. LTR retrotransposons were the most abundant TEs (17.2% genome coverage, followed by Long Interspersed Nuclear Element (LINE retrotransposons (2.10% and Mutator DNA transposons (1.99%. Comparison of putative flax TEs to flax transcript databases indicated that TEs are not highly expressed in flax. However, the presence of recent insertions, defined by 100% intra-element LTR similarity, provided evidence for recent TE activity. Spatial analysis showed TE-rich regions, gene-rich regions as well as regions with similar genes and TE density. Monte Carlo simulations for the 71 largest scaffolds (≥ 1 Mb each did not show any regional differences in the frequency of TE overlap with gene coding sequences. However, differences between TE superfamilies were found in their proximity to genes. Genes within TE-rich regions also appeared to have lower transcript expression, based on EST abundance. When LTR elements were compared, Copia showed more diversity, recent insertions and conserved domains than the Gypsy, demonstrating their importance in genome evolution. Conclusions The calculated 23.06% TE coverage of the flax WGS assembly is at the low end of the range of TE coverages reported in other eudicots, although this estimate does not include

  5. Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.).

    Science.gov (United States)

    Kim, Sunggil; Park, Jee Young; Yang, Tae-Jin

    2015-06-01

    Intact retrotransposon and DNA transposons inserted in a single gene were characterized in onions (Allium cepa) and their transcription and copy numbers were estimated in this study. While analyzing diverse onion germplasm, large insertions in the DFR-A gene encoding dihydroflavonol 4-reductase (DFR) involved in the anthocyanin biosynthesis pathway were found in two accessions. A 5,070-bp long terminal repeat (LTR) retrotransposon inserted in the active DFR-A (R4) allele was identified from one of the large insertions and designated AcCOPIA1. An intact ORF encoded typical domains of copia-like LTR retrotransposons. However, AcCOPIA1 contained atypical 'TG' and 'TA' dinucleotides at the ends of the LTRs. A 4,615-bp DNA transposon was identified in the other large insertion. This DNA transposon, designated AcCACTA1, contained an ORF coding for a transposase showing homology with the CACTA superfamily transposable elements (TEs). Another 5,073-bp DNA transposon was identified from the DFR-A (TRN) allele. This DNA transposon, designated AchAT1, belonged to the hAT superfamily with short 4-bp terminal inverted repeats (TIRs). Finally, a 6,258-bp non-autonomous DNA transposon, designated AcPINK, was identified in the ANS-p allele encoding anthocyanidin synthase, the next downstream enzyme to DFR in the anthocyanin biosynthesis pathway. AcPINK also possessed very short 3-bp TIRs. Active transcription of AcCOPIA1, AcCACTA1, and AchAT1 was observed through RNA-Seq analysis and RT-PCR. The copy numbers of AcPINK estimated by mapping the genomic DNA reads produced by NextSeq 500 were predominantly high compared with the other TEs. A series of evidence indicated that these TEs might have transposed in these onion genes very recently, providing a stepping stone for elucidation of enormously large-sized onion genome structure.

  6. Genome-wide analysis of salinity-stress induced DNA methylation alterations in cotton (Gossypium hirsutum L.) using the Me-DIP sequencing technology.

    Science.gov (United States)

    Lu, X K; Shu, N; Wang, J J; Chen, X G; Wang, D L; Wang, S; Fan, W L; Guo, X N; Guo, L X; Ye, W W

    2017-06-29

    Cytosine DNA methylation is a significant form of DNA modification closely associated with gene expression in eukaryotes, fungi, animals, and plants. Although the reference genomes of cotton (Gossypium hirsutum L.) have been publically available, the salinity-stress-induced DNA methylome alterations in cotton are not well understood. Here, we constructed a map of genome-wide DNA methylation characteristics of cotton leaves under salt stress using the methylated DNA immunoprecipitation sequencing method. The results showed that the methylation reads on chromosome 9 were most comparable with those on the other chromosomes, but the greatest changes occurred on chromosome 8 under salt stress. The DNA methylation pattern analysis indicated that a relatively higher methylation density was found in the upstream2k and downstream2k elements of the CDS region and CG-islands. Almost 94% of the reads belonged to LTR-gspsy and LTR-copia, and the number of methylation reads in LTR-gypsy was four times greater than that in LTR-copia in both control and stressed samples. The analysis of differentially methylated regions (DMRs) showed that the gene elements upstream2k, intron, and downstream2k were hypomethylated, but the CDS regions were hypermethylated. The GO (Gene Ontology) analysis suggested that the methylated genes were most enriched in cellular processes, metabolic processes, cell parts and catalytic activities, which might be closely correlated with response to NaCl stress. In this study, we completed a genomic DNA methylation profile and conducted a DMR analysis under salt stress, which provided valuable information for the better understanding of epigenetics in response to salt stress in cotton.

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

    Science.gov (United States)

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

    2014-05-04

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

  8. ESTUDIO TÉCNICO Y PROCESO DE INTERVENCIÓN EN UNA "PIEDAD" SOBRE LIENZO, COPIA DE WILLEM KEY

    OpenAIRE

    OLCINA LÓPEZ, MARÍA CARMEN

    2016-01-01

    [EN] The subject of this Final Degree Project is a XIXth century’s painting, under the theme of Pieta, technically painted in oil on canvas. The artistic features of this artwork drove us to think, from the beginning, that it probably was a copy of a Flemish painting. After a systematic search for references, the original was found at the Alte Pinakothek in Munich. This finding allowed us to delve into the origins and the technical, artistic and iconic study of this painting. Related to the i...

  9. Representando la "Copia feliz de Edén". Rugendas: paisaje e identidad nacional en Chile, siglo XIX.

    Directory of Open Access Journals (Sweden)

    Gabriel Cid Rodríguez Jacinta Vergara Brunet

    2012-07-01

    Full Text Available El presente artículo aborda el proceso de construcción de la identidad nacional chilena en el siglo XIX a través de la pintura de paisajes del artista Johann Moritz Rugendas. En este se evalúa la reformulación del territorio chileno en paisaje nacional por medio de la obra del artista viajero, y su recepción en la sociedad chilena decimonónica. La representación del paisaje chileno en Rugendas se articula con un proyecto político de nación que intenta hacer de Chile una excepción en el concierto latinoamericano, para lo cual las nociones del aislamiento geográfico del país se tornarán relevantes. Asimismo, se desarrollarán las vinculaciones entre Rugendas ylas orientaciones teóricas del naturalista Alexander von Humboldt, claves para comprender la formulación del paisaje desde la perspectiva del romanticismo. En este sentido, se estudiarán los mecanismos de representación del “otro” que subyacen en la pintura de paisajes en Rugendas.

  10. Retrotranspositions in orthologous regions of closely related grass species

    Directory of Open Access Journals (Sweden)

    Swigoňová Zuzana

    2006-08-01

    Full Text Available Abstract Background Retrotransposons are commonly occurring eukaryotic transposable elements (TEs. Among these, long terminal repeat (LTR retrotransposons are the most abundant TEs and can comprise 50–90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail. Results Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative sequence in each species, LTR retrotransposons occupy 45.1% of the maize, 21.1% of the rice, and 3.7% of the sorghum regions. The most common elements in the maize retrotransposon-rich regions are the copia-like retrotransposons with 39% and the gypsy-like retrotransposons with 37%. Using the contiguous sequence of the orthologous regions, we detected 108 retrotransposons with intact target duplication sites and both LTR termini. Here, we show that 74% of these elements inserted into their host genome less than 1 million years ago and that many retroelements expanded in size by the insertion of other sequences. These inserts were predominantly other retroelements, however, several of them were also fragmented genes. Unforeseen was the finding of intact genes embedded within LTR retrotransposons. Conclusion Although the abundance of retroelements between maize and rice is consistent with their different genome sizes of 2,364 and 389 Mb respectively, the content of retrotransposons in sorghum (790 Mb is surprisingly low. In all three species, retrotransposition is a very recent activity relative to their speciation. While it was known that genes re-insert into non-orthologous positions of plant genomes, they appear to re-insert also within retrotransposons, potentially

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

    Directory of Open Access Journals (Sweden)

    Feng Jiang

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

  12. Evaluation of the Effectiveness of LTR Training versus Simulation Training and Stress Inoculation

    Science.gov (United States)

    2016-10-01

    live animal model for many emergency procedures in the complex educational training system of the military to prepare medical personnel for deployment... education training objectives. The integration of simulation technology has augmented but not replaced the live animal model for many emergency...translation of the Department of Defense’s medical education training objectives. The integration of simulation technology has augmented but not replaced the

  13. 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.

  14. Evaluation of the Effectiveness of LTR Training versus Simulation Training and Stress Inoculation

    Science.gov (United States)

    2015-10-01

    processes and purposeful actions. System dynamics modeling relies on both quantitative and qualitative data and allows us to run simulations on...Live tissue training Stress Inoculation Combat medic readiness Combat casualty care Military preparedness System Dynamics Modeling Return on...body (simulator). 4. Ride Along Supplement: one day of trainee ride-along as a paramedic’s shadow, with the Emergency Medical Service ( EMS ) agency

  15. Evidence for RNA synthesis in the intergenic region between enhancer and promoter and its inhibition by insulators in Drosophila melanogaster

    Science.gov (United States)

    Tchurikov, Nickolai A.; Kretova, Olga V.; Moiseeva, Evgenia D.; Sosin, Dmitri V.

    2009-01-01

    Uncovering the nature of communication between enhancers, promoters and insulators is important for understanding the fundamental mechanisms that ensure appropriate gene expression levels. Here we describe an approach employing transient expression of genetic luciferase reporter gene constructs with quantitative RT–PCR analysis of transcription between an enhancer and Hsp70 promoter. We tested genetic constructs containing gypsy and/or Fab7 insulators in different orientations, and an enhancer from copia LTR-retroelement [(enh)copia]. A single gypsy or Fab7 insulator inserted between the promoter and enhancer in any polarity reduced enhancer action. A pair of insulators flanking the gene in any orientation exhibited increased insulation activity. We detected promoter-independent synthesis of non-coding RNA in the intergenic region of the constructs, which was induced by the enhancer in both directions and repressed by a single insulator or a pair of insulators. These results highlight the involvement of RNA-tracking mechanisms in the communications between enhancers and promoters, which are inhibited by insulators. PMID:19022852

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

    Science.gov (United States)

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

    2017-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Rossi Magdalena

    2001-01-01

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

  18. DESARROLLO E IMPLEMENTACION DE UNA HERRAMIENTA COMPUTAICONAL PARA LA DETECCION DE COPIAS EN DOCUMENTOS DIGITALES EN LA EDUCACION: DOCUMENT COPY DETECTOR (DOCODE)

    OpenAIRE

    VELASQUEZ SILVA, JUAN DOMINGO

    2012-01-01

    Actualmente, la sociedad enfrenta una transformación importante en la manera en que gestiona el conocimiento. El acceso a las redes digitales y la disponibilidad de enormes cantidades de información han adquirido una centralidad nunca antes vista. En este contexto, la masificación de Internet no solo ha cambiado considerablemente la forma en que los estudiantes acceden a la información para el desarrollo de sus experiencias educativas, sino que también ha impactado en las prácticas de los ...

  19. The Hairless Stem Phenotype of Cotton (Gossypium barbadense) Is Linked to a Copia-Like Retrotransposon Insertion in a Homeodomain-Leucine Zipper Gene (HD1).

    Science.gov (United States)

    Ding, Mingquan; Ye, Wuwei; Lin, Lifeng; He, Shae; Du, Xiongming; Chen, Aiqun; Cao, Yuefen; Qin, Yuan; Yang, Fen; Jiang, Yurong; Zhang, Hua; Wang, Xiyin; Paterson, Andrew H; Rong, Junkang

    2015-09-01

    Cotton (Gossypium) stem trichomes are mostly single cells that arise from stem epidermal cells. In this study, a homeodomain-leucine zipper gene (HD1) was found to cosegregate with the dominant trichome locus previously designated as T1 and mapped to chromosome 6. Characterization of HD1 orthologs revealed that the absence of stem trichomes in modern Gossypium barbadense varieties is linked to a large retrotransposon insertion in the ninth exon, 2565 bp downstream from the initial codon in the At subgenome HD1 gene (At-GbHD1). In both the At and Dt subgenomes, reduced transcription of GbHD1 genes is caused by this insertion. The disruption of At-HD1 further affects the expression of downstream GbMYB25 and GbHOX3 genes. Analyses of primitive cultivated accessions identified another retrotransposon insertion event in the sixth exon of At-GbHD1 that might predate the previously identified retrotransposon in modern varieties. Although both retrotransposon insertions results in similar phenotypic changes, the timing of these two retrotransposon insertion events fits well with our current understanding of the history of cotton speciation and dispersal. Taken together, the results of genetics mapping, gene expression and association analyses suggest that GbHD1 is an important component that controls stem trichome development and is a promising candidate gene for the T1 locus. The interspecific phenotypic difference in stem trichome traits also may be attributable to HD1 inactivation associated with retrotransposon insertion. Copyright © 2015 by the Genetics Society of America.

  20. The Hairless Stem Phenotype of Cotton (Gossypium barbadense) Is Linked to a Copia-Like Retrotransposon Insertion in a Homeodomain-Leucine Zipper Gene (HD1)

    OpenAIRE

    Ding, Mingquan; Ye, Wuwei; Lin, Lifeng; He, Shae; Du, Xiongming; Chen, Aiqun; Cao, Yuefen; Qin, Yuan; Yang, Fen; Jiang, Yurong; Zhang, Hua; Wang, Xiyin; Paterson, Andrew H.; Rong, Junkang

    2015-01-01

    Cotton (Gossypium) stem trichomes are mostly single cells that arise from stem epidermal cells. In this study, a homeodomain-leucine zipper gene (HD1) was found to cosegregate with the dominant trichome locus previously designated as T1 and mapped to chromosome 6. Characterization of HD1 orthologs revealed that the absence of stem trichomes in modern Gossypium barbadense varieties is linked to a large retrotransposon insertion in the ninth exon, 2565 bp downstream from the initial codon in th...

  1. 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.

  2. 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,

  3. Costruzione di chimere molecolari dell'enzima Integrasi di HIV con attività idrolizzante delle LTR virali.

    OpenAIRE

    Muthusamy, Regina

    2014-01-01

    La Sindrome da Immunodeficienza Acquisita (AIDS o SIDA) causata da HIV-1 (Virus dell'Immunodeficienza umana) è caratterizzata dalla graduale compromissione del sistema immunitario del soggetto colpito. Le attuali terapie farmacologiche, purtroppo, non riescono a eliminare l'infezione a causa della comparsa di continui ceppi resistenti ai farmaci, e inoltre questi trattamenti non sono in grado di eliminare i reservoir virali latenti e permettere l'eradicazione definitiva del virus dall’orga...

  4. Using LQG/LTR Optimal Control Method to Improve Stability and Performance of Industrial Gas Turbine System

    OpenAIRE

    Fereidoon Shabaninia; Kazem Jafari

    2012-01-01

    The gas turbine is a power plant, which produces a great amount of energy for its size and weight. Its compactness, low weigh, and multiple fuels make it a natural power plant for various industries such as power generation or oil and gas process plants. In any of these applications, the performance and stability of the gas turbines are the end products that strongly influence the profitability of the business that employs them. Control and analyses of gas turbines for achieving stability and...

  5. 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.

  6. Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction

    Directory of Open Access Journals (Sweden)

    Larance Ronsard

    2017-04-01

    Full Text Available HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat, a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR RNA. In this study, HIV-1 infected patients (n = 120 from North India revealed Ser46Phe (20% and Ser61Arg (2% mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities. Molecular dynamics simulation data verified that the variants with this mutation had a higher binding affinity for TAR than both the wild-type Tat and other variants that lacked Ser46Phe and Ser61Arg. Other mutations in Tat conferred varying affinities for TAR interaction leading to differential transactivation abilities. This is the first report from North India with a clinical validation of CD4 counts to demonstrate the influence of Tat genetic variations affecting the stability of Tat and its interaction with TAR. This study highlights the co-evolution pattern of Tat and predominant nucleotides for Tat activity, facilitating the identification of genetic determinants for the attenuation of viral gene expression.

  7. Transcriptomic analysis of genes and LTR retrotransposons in rice (Oryza sativa ssp. japonica) in response to iron toxicity

    OpenAIRE

    Finatto, Taciane

    2012-01-01

    A toxidez por ferro em plantas está associada com a presença de grandes concentrações de ferro (Fe) reduzido (Fe2+) na solução do solo, esta condição pode ocorrer em solos irrigados por inundação. Os sintomas de toxidez por ferro incluem estresse oxidativo nas folhas como resultado do excesso de Fe2+ absorvido pelas raízes, resultando em perdas na produtividade. As respostas das plantas às condições de estresse envolvem a percepção dos estímulos, transdução de sinais e ativação da transcrição...

  8. SIRE1 RETROTRANSPOSONS IN BARLEY (Hordeum vulgare L.).

    Science.gov (United States)

    Cakmak, B; Marakli, S; Gozukirmizi, N

    2015-07-01

    Sireviruses are genera of copia LTR retrotransposons with a unique genome structure among retrotransposons. Barley (Hordeum vulgare L.) is an economically important plant. In this study, we used mature barley embryos, 10-day-old roots and 10-day-old leaves derived from the same barley plant to investigate SIRE) retrotransposon movements by Inter-Retrotransposon Amplified Polymorphism (IRAP) technique. We found polymorphism rates between 0-64% among embryos, roots and leaves. Polymorphism rates were detected to be 0-27% among embryos, 8-60% among roots, and 11-50% among leaves. Polymorphisms were observed not only among the parts of different individuals, but also on the parts of the same plant (23-64%). The internal domains of SIRE1 (GAG, ENV and RT) were also analyzed in the embryos, roots and leaves. Analysis of band profiles showed no polymorphism for GAG, however, different band patterns were observed among samples for RT and ENV. The sequencing of SIRE1 GAG, ENV and RT domains revealed 79% similarity for GAG, 96% for ENV and 83% for RT to copia retrotransposons. Comparison between barley retrotransposons and SIRE1 in barley indicated that SIRE1-GAG, ENV and RT might be diverge earlier from barley retrotransposons. SIRE1 sequences were compared with SIRE1 in barley, results showed the closest homologues were SIRE1-ENVand SIRE1-RTsequences, and SIRE1-GAG sequences was a sister group to sequences of Glycine max. This study is the first detailed investigation of SIRE1 in barley genome. The obtained findings are expected to contribute to the comprehension of SIRE1 retrotransposon and its role in barley genome.

  9. Cloning and characterization of dispersed repetitive DNA derived from microdissected sex chromosomes of Rumex acetosa.

    Science.gov (United States)

    Mariotti, Beatrice; Navajas-Pérez, Rafael; Lozano, Rafael; Parker, John S; de la Herrán, Roberto; Rejón, Carmelo Ruiz; Rejón, Manuel Ruiz; Garrido-Ramos, Manuel; Jamilena, Manuel

    2006-02-01

    Rumex acetosa is characterized by a multiple chromosome system (2n = 12 + XX for females, and 2n = 12 + XY1Y2 for males), in which sex is determined by the ratio between the number of X chromosomes and autosome sets. For a better understanding of the molecular structure and evolution of plant sex chromosomes, we have generated a sex chromosome specific library of R. acetosa by microdissection. The screening of this library has allowed us to identify 5 repetitive DNA families that have been characterized in detail. One of these families, DOP-20, has shown no homology with other sequences in databases. Nevertheless, the putative proteins encoded by the other 4 families, DOP-8, DOP-47, DOP-60, and DOP-61, show homology with proteins from different plant retroelements, including poly proteins from Ty3-gypsy- and Ty1-copia-like long terminal repeat (LTR) retroelements, and reverse transcriptase from non-LTR retro elements. Results indicate that sequences from these 5 families are dispersed throughout the genome of both males and females, but no appreciable accumulation or differentiation of these types of sequences have been found in the Y chromosomes. These repetitive DNA sequences are more conserved in the genome of other dioecious species such as Rumex papillaris, Rumex intermedius, Rumex thyrsoides, Rumex hastatulus, and Rumex suffruticosus, than in the polygamous, gynodioecious, or hermaphrodite species Rumex induratus, Rumex lunaria, Rumex con glom er atus, Rumex crispus, and Rumex bucephalo phorus, which supports a single origin of dioecious species in this genus. The implication of these transposable elements in the origin and evolution of the heteromorphic sex chromosomes of R. acetosa is discussed.

  10. Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.

    Science.gov (United States)

    Cavallini, Andrea; Natali, Lucia; Zuccolo, Andrea; Giordani, Tommaso; Jurman, Irena; Ferrillo, Veronica; Vitacolonna, Nicola; Sarri, Vania; Cattonaro, Federica; Ceccarelli, Marilena; Cionini, Pier Giorgio; Morgante, Michele

    2010-02-01

    A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

  11. CG gene body DNA methylation changes and evolution of duplicated genes in cassava

    Science.gov (United States)

    Wang, Haifeng; Beyene, Getu; Zhai, Jixian; Feng, Suhua; Fahlgren, Noah; Taylor, Nigel J.; Bart, Rebecca; Carrington, James C.; Jacobsen, Steven E.; Ausin, Israel

    2015-01-01

    DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits. PMID:26483493

  12. 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.

  13. Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence.

    Science.gov (United States)

    Iquebal, M A; Tomar, Rukam S; Parakhia, M V; Singla, Deepak; Jaiswal, Sarika; Rathod, V M; Padhiyar, S M; Kumar, Neeraj; Rai, Anil; Kumar, Dinesh

    2017-07-13

    Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25-80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.

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

    Science.gov (United States)

    Cavrak, Vladimir V; Lettner, Nicole; Jamge, Suraj; Kosarewicz, Agata; Bayer, Laura Maria; Mittelsten Scheid, Ortrun

    2014-01-01

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

    KAUST Repository

    Chen, Jit Ern

    2017-10-20

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

  16. 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.

  17. CG gene body DNA methylation changes and evolution of duplicated genes in cassava.

    Science.gov (United States)

    Wang, Haifeng; Beyene, Getu; Zhai, Jixian; Feng, Suhua; Fahlgren, Noah; Taylor, Nigel J; Bart, Rebecca; Carrington, James C; Jacobsen, Steven E; Ausin, Israel

    2015-11-03

    DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.

  18. Impacto de la variación en el número de copias y del estado de metilación de genes supresores de tumor en las vías de progresión del meningioma

    OpenAIRE

    San Miguel Díez, Teresa

    2015-01-01

    El meningioma es el tumor del sistema nervioso central más frecuente en la edad adulta, con una incidencia superior al 30% y una evidente predominancia femenina. La sintomatología deriva fundamentalmente de la localización del tumor, que crece desde las células de la cubierta aracnoidea. El tratamiento es principalmente quirúrgico, y su radicalidad se relaciona clásicamente con la aparición de recidivas tumorales, que es la principal complicación que sufren los afectados. Macroscópicamente, s...

  19. Bases genéticas de la discapacidad intelectual y los trastornos del espectro autista: aplicación de las nuevas tecnologías al análisis de variantes del número de copias (CNVs)

    OpenAIRE

    Quintela García, Inés

    2017-01-01

    La discapacidad intelectual (DI) es un trastorno del neurodesarrollo complejo y fenotípicamente heterogéneo caracterizado por deficiencias significativas en el funcionamiento intelectual y en las habilidades adaptativas de inicio en el período del desarrollo. El trastorno del espectro autista (TEA) es un trastorno del neurodesarrollo caracterizado por deficiencias en las habilidades para la comunicación, en la interacción social y en el desarrollo del lenguaje y por la presencia de intereses ...

  20. HIIT och dess effekt på löpekonomi hos vältränade löpare och triatleter

    OpenAIRE

    Kalenius, Richard

    2015-01-01

    Background: Running economy is one of the key factors to achieve top performance in endurance events. Little evidence exists for improving running economy using high-intensity interval training while running.   Objectives: The purpose of this study was to examine how HIIT affects running economy and VO2max.   Method: 14 well-trained athletes (age 35 ± 8,9 years, height 175 ± 11,7 cm and weight 69 ± 12,2 kg) were divided into two separate groups (HIIT and Control). HIIT group performed 3 HIIT ...

  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 RNA.

  2. Primitive Genepools of Asian Pears and Their Complex Hybrid Origins Inferred from Fluorescent Sequence-Specific Amplification Polymorphism (SSAP Markers Based on LTR Retrotransposons.

    Directory of Open Access Journals (Sweden)

    Shuang Jiang

    Full Text Available Recent evidence indicated that interspecific hybridization was the major mode of evolution in Pyrus. The genetic relationships and origins of the Asian pear are still unclear because of frequent hybrid events, fast radial evolution, and lack of informative data. Here, we developed fluorescent sequence-specific amplification polymorphism (SSAP markers with lots of informative sites and high polymorphism to analyze the population structure among 93 pear accessions, including nearly all species native to Asia. Results of a population structure analysis indicated that nearly all Asian pear species experienced hybridization, and originated from five primitive genepools. Four genepools corresponded to four primary Asian species: P. betulaefolia, P. pashia, P. pyrifolia, and P. ussuriensis. However, cultivars of P. ussuriensis were not monophyletic and introgression occurred from P. pyrifolia. The specific genepool detected in putative hybrids between occidental and oriental pears might be from occidental pears. The remaining species, including P. calleryana, P. xerophila, P. sinkiangensis, P. phaeocarpa, P. hondoensis, and P. hopeiensis in Asia, were inferred to be of hybrid origins and their possible genepools were identified. This study will be of great help for understanding the origin and evolution of Asian pears.

  3. Primitive Genepools of Asian Pears and Their Complex Hybrid Origins Inferred from Fluorescent Sequence-Specific Amplification Polymorphism (SSAP) Markers Based on LTR Retrotransposons.

    Science.gov (United States)

    Jiang, Shuang; Zheng, Xiaoyan; Yu, Peiyuan; Yue, Xiaoyan; Ahmed, Maqsood; Cai, Danying; Teng, Yuanwen

    2016-01-01

    Recent evidence indicated that interspecific hybridization was the major mode of evolution in Pyrus. The genetic relationships and origins of the Asian pear are still unclear because of frequent hybrid events, fast radial evolution, and lack of informative data. Here, we developed fluorescent sequence-specific amplification polymorphism (SSAP) markers with lots of informative sites and high polymorphism to analyze the population structure among 93 pear accessions, including nearly all species native to Asia. Results of a population structure analysis indicated that nearly all Asian pear species experienced hybridization, and originated from five primitive genepools. Four genepools corresponded to four primary Asian species: P. betulaefolia, P. pashia, P. pyrifolia, and P. ussuriensis. However, cultivars of P. ussuriensis were not monophyletic and introgression occurred from P. pyrifolia. The specific genepool detected in putative hybrids between occidental and oriental pears might be from occidental pears. The remaining species, including P. calleryana, P. xerophila, P. sinkiangensis, P. phaeocarpa, P. hondoensis, and P. hopeiensis in Asia, were inferred to be of hybrid origins and their possible genepools were identified. This study will be of great help for understanding the origin and evolution of Asian pears.

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

    Science.gov (United States)

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

    2015-11-24

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

  5. DOE/NV/26383-LTR2008-01 Letter Report Yucca Mountain Environmental Monitoring Systems Initiative - Air Quality Scoping Study for Caliente, Lincoln County, Nevada

    Energy Technology Data Exchange (ETDEWEB)

    J. Engelbrecht; I. Kavouras; D. Campbell; S. Campbell; S. Kohl; D. Shafer

    2009-04-02

    The Desert Research Institute (DRI) is performing a scoping study as part of the U.S. Department of Energy's Yucca Mountain Environmental Monitoring Systems Initiative (EMSI). The main objective is to obtain baseline air quality information for Yucca Mountain and an area surrounding the Nevada Test Site (NTS). Air quality and meteorological monitoring and sampling equipment housed in a mobile trailer (shelter) is collecting data at eight sites outside the NTS, including Ash Meadows National Wildlife Refuge (NWR), Beatty, Sarcobatus Flats, Rachel, Caliente, Pahranagat NWR, Crater Flat, and Tonopah Airport, and at four sites on the NTS (Engelbrecht et al., 2007a-d). The trailer is stationed at any one site for approximately eight weeks at a time. This letter report provides a summary of air quality and meteorological data, on completion of the site's sampling program.

  6. Development of 5' LTR DNA methylation of latent HIV-1 provirus in cell line models and in long-term-infected individuals

    Czech Academy of Sciences Publication Activity Database

    Trejbalová, K.; Kovářová, D.; Blažková, J.; Machala, L.; Jilich, D.; Weber, Jan; Kučerová, D.; Vencálek, O.; Hirsch, Ivan; Hejnar, J.

    2016-01-01

    Roč. 8, Feb 19 (2016), č. článku 19. ISSN 1868-7083 Institutional support: RVO:61388963 Keywords : HIV -1 * latent reservoir * DNA methylation * chromatin conformation * latent HIV -1 provirus reactivation * HIV -1-infected individuals Subject RIV: EE - Microbiology, Virology Impact factor: 4.987, year: 2016 http://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-016-0185-6

  7. Development of 5 ' LTR DNA methylation of latent HIV-1 provirus in cell line models and in long-term-infected individuals

    Czech Academy of Sciences Publication Activity Database

    Trejbalová, Kateřina; Kovářová, Denisa; Blažková, Jana; Machala, L.; Jilich, D.; Weber, J.; Kučerová, Dana; Vencálek, O.; Hirsch, Ivan; Hejnar, Jiří

    2016-01-01

    Roč. 8, zima (2016), č. článku 19. ISSN 1868-7083 R&D Projects: GA ČR GAP304/12/1736 Institutional support: RVO:68378050 Keywords : HIV -1 * latent reservoir * DNA methylation * chromatin conformation * latent HIV -1 provirus reactivation * HIV -1-infected individuals Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.987, year: 2016

  8. MASiVEdb: the Sirevirus Plant Retrotransposon Database

    Directory of Open Access Journals (Sweden)

    Bousios Alexandros

    2012-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Petr Novák

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

  10. Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea).

    Science.gov (United States)

    Yu, Qingyi; Guyot, Romain; de Kochko, Alexandre; Byers, Anne; Navajas-Pérez, Rafael; Langston, Brennick J; Dubreuil-Tranchant, Christine; Paterson, Andrew H; Poncet, Valérie; Nagai, Chifumi; Ming, Ray

    2011-07-01

    Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  11. Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements

    Directory of Open Access Journals (Sweden)

    Fellers John P

    2013-01-01

    Full Text Available Abstract Background Wheat leaf rust (Puccinia triticina Eriks; Pt and stem rust fungi (P. graminis f.sp. tritici; Pgt are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The Pt genome, currently estimated at 135 Mb, is significantly larger than Pgt, at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of Pt conserved proteins were characterized to gain insight into gene content, genome complexity and expansion. Results A bacterial artificial chromosome (BAC library was made from P. triticina race 1, BBBD and probed with Pt homologs of genes encoding two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in Pgt. Conclusions The three Pt loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes between Pt and Pgt is extended to the more distant poplar rust, Melampsora larici-populina. The loci also reveal that genome expansion in Pt is in part due to higher occurrence of repeat-elements in this species.

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

    Directory of Open Access Journals (Sweden)

    Scott eJackson

    2014-07-01

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

  13. A Tat-conjugated Peptide Nucleic Acid Tat-PNA-DR Inhibits Hepatitis B Virus Replication In Vitro and In Vivo by Targeting LTR Direct Repeats of HBV RNA

    Science.gov (United States)

    Zeng, Zhengyang; Han, Shisong; Hong, Wei; Lang, Yange; Li, Fangfang; Liu, Yongxiang; Li, Zeyong; Wu, Yingliang; Li, Wenxin; Zhang, Xianzheng; Cao, Zhijian

    2016-01-01

    Hepatitis B virus (HBV) infection is a major cause of chronic active hepatitis, cirrhosis, and primary hepatocellular carcinoma, all of which are severe threats to human health. However, current clinical therapies for HBV are limited by potential side effects, toxicity, and drug-resistance. In this study, a cell-penetrating peptide-conjugated peptide nucleic acid (PNA), Tat-PNA-DR, was designed to target the direct repeat (DR) sequences of HBV. Tat-PNA-DR effectively inhibited HBV replication in HepG2.2.15 cells. Its anti-HBV effect relied on the binding of Tat-PNA-DR to the DR, whereby it suppressed the translation of hepatitis B e antigen (HBeAg), HBsAg, HBV core, hepatitis B virus x protein, and HBV reverse transcriptase (RT) and the reverse transcription of the HBV genome. Furthermore, Tat-PNA-DR administered by intravenous injection efficiently cleared HBeAg and HBsAg in an acute hepatitis B mouse model. Importantly, it induced an 80% decline in HBV DNA in mouse serum, which was similar to the effect of the widely used clinical drug Lamivudine (3TC). Additionally, a long-term hydrodynamics HBV mouse model also demonstrated Tat-PNA-DR's antiviral effect. Interestingly, Tat-PNA-DR displayed low cytotoxicity, low mouse acute toxicity, low immunogenicity, and high serum stability. These data indicate that Tat-PNA-DR is a unique PNA and a promising drug candidate against HBV. PMID:26978579

  14. Residues R{sup 199}H{sup 200} of prototype foamy virus transactivator Bel1 contribute to its binding with LTR and IP promoters but not its nuclear localization

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Qinglin; Tan, Juan [Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071 (China); Cui, Xiaoxu [Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071 (China); Centre Laboratory, TianJin 4th Centre Hospital, Tianjin 300140 (China); Luo, Di; Yu, Miao [Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071 (China); Liang, Chen [Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada H3T 1E2 (Canada); Departments of Medicine McGill University, Montreal, QC (Canada); Microbiology and Immunology, McGill University, Montreal, QC (Canada); Qiao, Wentao, E-mail: wentaoqiao@nankai.edu.cn [Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin 300071 (China)

    2014-01-20

    Prototype foamy virus encodes a transactivator called Bel1 that enhances viral gene transcription and is essential for PFV replication. Nuclear localization of Bel1 has been reported to rely on two proximal basic motifs R{sup 199}H{sup 200} and R{sup 221}R{sup 222}R{sup 223} that likely function together as a bipartite nuclear localization signal. In this study, we report that mutating R{sup 221}R{sup 222}R{sup 223}, but not R{sup 199}H{sup 200}, relocates Bel1 from the nucleus to the cytoplasm, suggesting an essential role for R{sup 221}R{sup 222}R{sup 223} in the nuclear localization of Bel1. Although not affecting the nuclear localization of Bel1, mutating R{sup 199}H{sup 200} disables Bel1 from transactivating PFV promoters. Results of EMSA reveal that the R{sup 199}H{sup 200} residues are vital for the binding of Bel1 to viral promoter DNA. Moreover, mutating R{sup 199}H{sup 200} in Bel1 impairs PFV replication to a much greater extent than mutating R{sup 221}R{sup 222}R{sup 223}. Collectively, our findings suggest that R{sup 199}H{sup 200} directly participate in Bel1 binding to viral promoter DNA and are indispensible for Bel1 transactivation activity. - Highlights: • The R{sup 221}R{sup 222}R{sup 223} residues are essential for the nuclear localization of Bel1. • Although not affecting the nuclear localization of Bel1, mutating R{sup 199}H{sup 200} disables Bel1 from transactivating PFV promoters. • The R{sup 199}H{sup 200} residues directly participate in Bel1 binding to viral promoter DNA. • Mutating R{sup 199}H{sup 200} in Bel1 impairs PFV replication to a much greater extent than mutating R{sup 221}R{sup 222}R{sup 223}.

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

    Directory of Open Access Journals (Sweden)

    Bridier-Nahmias Antoine

    2012-12-01

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

  16. Repetitive DNA in the pea (Pisum sativum L. genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Navrátilová Alice

    2007-11-01

    Full Text Available Abstract Background Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum. Results Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. Conclusion We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-06-10

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

  18. El plagio en las examinaciones matemáticas

    National Research Council Canada - National Science Library

    Omar Mejía Pérez

    2014-01-01

    ... información, es el plagio, copia o trampa. Este fenómeno ocurre por diversos motivos, pero presenta varias consistencias en la conducta de los alumnos al atender un examen, como se evidenció...

  19. AcEST: DK957356 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 7.8 sp|Q5SSZ5|TENS3_MOUSE Tensin-3 OS=Mus musculus GN=Tns3 PE=1 SV=1 30 7.9 >sp|P04146|COPIA_DROME Copia pro...EQELREQVHNLEDRLKRYEKNACAATV 2162 >sp|Q5SSZ5|TENS3_MOUSE Tensin-3 OS=Mus musculus GN=Tns3 PE=1 SV=1 Length =

  20. The dynamic effect of reading direction habit on spatial asymmetry of image perception.

    Science.gov (United States)

    Afsari, Zaeinab; Ossandón, José P; König, Peter

    2016-09-01

    Exploration of images after stimulus onset is initially biased to the left. Here, we studied the causes of such an asymmetry and investigated effects of reading habits, text primes, and priming by systematically biased eye movements on this spatial bias in visual exploration. Bilinguals first read text primes with right-to-left (RTL) or left-to-right (LTR) reading directions and subsequently explored natural images. In Experiment 1, native RTL speakers showed a leftward free-viewing shift after reading LTR primes but a weaker rightward bias after reading RTL primes. This demonstrates that reading direction dynamically influences the spatial bias. However, native LTR speakers who learned an RTL language late in life showed a leftward bias after reading either LTR or RTL primes, which suggests the role of habit formation in the production of the spatial bias. In Experiment 2, LTR bilinguals showed a slightly enhanced leftward bias after reading LTR text primes in their second language. This might contribute to the differences of native RTL and LTR speakers observed in Experiment 1. In Experiment 3, LTR bilinguals read normal (LTR, habitual reading) and mirrored left-to-right (mLTR, nonhabitual reading) texts. We observed a strong leftward bias in both cases, indicating that the bias direction is influenced by habitual reading direction and is not secondary to the actual reading direction. This is confirmed in Experiment 4, in which LTR participants were asked to follow RTL and LTR moving dots in prior image presentation and showed no change in the normal spatial bias. In conclusion, the horizontal bias is a dynamic property and is modulated by habitual reading direction.

  1. The Prevalence of Latent Trigger Points in Lower Limb Muscles in Asymptomatic Subjects.

    Science.gov (United States)

    Zuil-Escobar, Juan Carlos; Martínez-Cepa, Carmen Belén; Martín-Urrialde, Jose Antonio; Gómez-Conesa, Antonia

    2016-11-01

    Latent trigger points (LTrPs) are prevalent in persons with musculoskeletal pain. Because they could be present in healthy persons, it is necessary to evaluate the prevalence of LTrPs in asymptomatic subjects. To assess the prevalence of LTrPs in lower limb muscles, to evaluate the relationship between LTrP prevalence, gender, and leg dominance, and to determine intra-rater reliability for the diagnosis of LTrPs. Cross-sectional study. University community. A total of 206 asymptomatic subjects (113 women and 93 men, aged 23.2 ± 5.2 years). Not applicable. The prevalence of the LTrPs located in the gastrocnemius, soleus, peroneus longus, peroneus brevis, tibialis anterior, extensor digitorum longus, flexor digitorum longus, rectus femoris, vastus medialis, and vastus lateralis was studied, using the diagnosis criteria recommended by Simons, Travell, and Simons. The pressure pain threshold was also evaluated. Of the 206 subjects evaluated, 166 (77.7%; 95% confidence interval [CI], 72-83.4) were found to have at least one LTrP in the lower limb muscles. The average number of LTrPs found per individual was 7.5 ± 7.7. The prevalence in each muscle group ranged from 19.9% (95% CI, 14.4-25.4) to 37.4% (95% CI, 30.8-44), with gastrocnemius LTrPs being the most prevalent. Women had more LTrPs (9.6 ± 7.8) than did men (4.9 ± 6.6) (P .05). The most prevalent diagnosis criteria were the presence of a taut band and a tender spot (98%-100%); the local twitch response was the least prevalent diagnosis criteria (0%-3.5%). Intra-rater reliability was excellent for all the diagnosis criteria in all the muscles evaluated (κ = 0.762-1), except for the jump sign and the referred pain in several LTrPs. LTrPs were prevalent in the lower limb muscles of asymptomatic subjects. Women have more LTrPs than do men. No differences in LTrP prevalence were found between sides. The presence of the taut band and the tender spot were the most prevalent and reliable diagnosis criteria. It is

  2. EL ESQUIZOFRÉNICO CASO DEL DR JUAN L. Y MR...(O LA FÁBULA DEL AUTOR QUE SE MUERDE SU PROPIA COLA

    Directory of Open Access Journals (Sweden)

    Juan Nicolás Leguizamón

    2011-04-01

    Full Text Available Fernández-Fischer, bajo el seudónimo de Juan Nicolás leguizamón,  elabora en su artículo un tratamiento de la idea de autoría que habita el texto La Biología de una idea. ¿A quién se le debería designar artista, cuando el autor le pertenece a la obra de arte y no lo contrario?: la pregunta que plantea quien escribe el artículo y su intento por desarrollarla tallan hondo en el alma vanidosa del creador quien se siente expuesto en su propósito de hacer algo, ¡por fin!, que le sea absolutamente propio. Luego, queda la incómoda sensación de distancia hacia lo que podría constituir un oasis: la copia (la cual implica lectura y esta, a su vez, cuotas de infidelidad a la copia anterior. El encargo del artículo es, en sí mismo, una copia que activa la obra a la que alude y su escritura, copia de la copia.

  3. Efficient human immunodeficiency virus replication requires a fine-tuned level of transcription

    NARCIS (Netherlands)

    Marzio, Giuseppe; Vink, Monique; Verhoef, Koen; de Ronde, Anthony; Berkhout, Ben

    2002-01-01

    Transcription represents a crucial step in the life cycle of human immunodeficiency virus (HIV) and is highly regulated. Here we show that the strength of the viral long terminal repeat (LTR) promoter is optimized for efficient replication. Artificially increasing the rate of LTR-driven

  4. NCBI nr-aa BLAST: CBRC-TTRU-01-1000 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TTRU-01-1000 ref|ZP_06018941.1| low temperature requirement protein LtrA [Lact...obacillus crispatus MV-3A-US] gb|EEX30492.1| low temperature requirement protein LtrA [Lactobacillus crispatus MV-3A-US] ZP_06018941.1 0.001 23% ...

  5. Dicty_cDB: VSK419 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available quence. 38 1.8 5 AL845481 |AL845481.5 Zebrafish DNA sequence from clone DKEY-46N18 in linkage group 17. 36 2.1 6 X15345 |X15345.1 Ham...ster H-19 proviral DNA (LTR- v-src -LTR). 34 2.2 2 dna u

  6. Acoustic Propagation in the Labrador Sea

    Science.gov (United States)

    1977-03-08

    referred to Director , Naval Research Laboratory, Washington, DC 20375. AUTHORITY ONR ltr, 31 Jan 2006; ONR ltr, 31 Jan 2006 THIS PAGE IS UNCLASSIFIED AD...hnmmo•,0ssfro. tac IC toteHa. SOUND) SPEA at 11 SOUN SPIED w.1t SOUNO $il 0ID ill 4 m 80 x Onem 56 nm 21 f• 3 (C) Figl. Al -- Traunimoiiose• trm

  7. Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean

    Science.gov (United States)

    Preferential accumulation of transposable elements (TEs), particularly LTR-retrotransposons (LTR-RTs) in recombination-suppressed pericentromeric regions, seems to be a general pattern of TE distribution in many flowering plants. However, whether such a pattern occurs primarily by preferential inser...

  8. High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes

    DEFF Research Database (Denmark)

    Wang, Wen; Zheng, Hongkung; Fan, Chuanzhu

    2006-01-01

    and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons...

  9. Cardiorespiratory response to exercise on a large therapeutic roll.

    Science.gov (United States)

    Gappmaier, Eduard; Tavazoie, Sima F; Jacketta, Michael G

    2013-09-01

    Large therapeutic rolls (LTR) and balls are popular rehabilitation tools and have also been advertised as cardiovascular training devices. The aim of this study was to determine if individuals of varying fitness levels would reach aerobic training levels by evidence-based standards as described in American College of Sports Medicine (ACSM) publications. Fourteen volunteers performed a maximal exercise test and on subsequent days, two submaximal exercise tests on the LTR (LTR-A and -B). LTR-A consisted of four 5-minute stages of exercise at progressive intensity levels. LTR-B included 20 minutes of continuous exercise. Oxygen consumption (VO2) and heart rate (HR) during exercise on the LTR were compared with ACSM recommended standards. The average (range) peak intensity achieved during LTR-A was 66.8% (51.7-82.7%) of maximal VO2 reserve (VO2R) and 82.9% (70.7%-91.2%) of maximal heart rate (HRmax). During LTR-B, HR and VO2 of all participants was maintained at moderate exercise intensity and averaged 56% of VO2R and 78% of HRmax during the 20 minute exercise period. These findings suggest that individuals with a wide range of aerobic fitness are able to reach and maintain aerobic training levels with appropriate exercise on a large therapeutic roll or ball.

  10. The impact of latent trigger points on regional muscle function.

    Science.gov (United States)

    Lucas, Karen R

    2008-10-01

    To date, most investigation of latent myofascial trigger points (LTrPs) has occurred in pain populations. Many have thought that LTrPs are clinically relevant as -potential precursors to developing active myofascial trigger points and spontaneous pain. Nociceptive substances have been found in greater concentrations at LTrP sites compared with non-TrP sites, indicating the potential for group III and IV afferent fibers to provide input to the central nervous system from affected peripheral sites. Fatigue and neurophysiologic studies provide evidence as to the pathways via which group III and IV afferents can alter activity of the motoneuron pool and therefore affect muscle activation and performance. This article offers suggestions as to the mechanisms via which LTrP-related pathophysiology may explain the clinical examination findings associated with LTrP-containing and functionally related muscles.

  11. ‘Copiar y pegar’ en investigaciones en el pregrado: haciendo mal uso del Internet

    Directory of Open Access Journals (Sweden)

    Charles Huamaní

    2008-06-01

    Full Text Available Introducción: La ética en el proceso de investigación es un tema poco abordado durante el pregrado, por lo que debe ser analizada para prevenir infracciones que podrían afectar el desarrollo de todo investigador en formación. Objetivo: Determinar las características de copia en los trabajos de investigación realizados durante el pregrado, por estudiantes de Medicina Humana de segundo año. Diseño: Estudio observacional retrospectivo. Lugar: Facultad de Medicina, Universidad Nacional Mayor de San Marcos. Población: la sección de la ‘introducción’ de trabajos de investigación realizados el año 2004 en un curso curricular. Intervenciones: se revisó manualmente las oraciones de la ‘introducción’ de los trabajos, se describen el tipo de copia, el número de trabajos, autores, asesores, párrafos copiados, y el tipo de fuentes de información y de copia. Principales medidas de resultados: frecuencias y porcentajes de oraciones copiadas y tipo de copia. Resultados: Se revisó un total de 24 trabajos de investigación, con un promedio de 6 autores y 2 asesores por trabajo, 23 tenían alguna evidencia de copia electrónica, 8 sólo tenían copia literal; del total de oraciones evaluadas, el 64% corresponde a copia total de oraciones; sólo el 30% de las fuentes copiadas eran publicaciones científicas en línea, el resto son fuentes de acceso público no especializadas. Conclusiones: se describe una alta frecuencia de copia en investigaciones durante el pregrado provenientes de fuentes electrónicas, por lo que es necesario prevenir que se repita en futuras investigaciones al implementar sistemas de búsqueda sistemática de plagio.

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

    Directory of Open Access Journals (Sweden)

    Ning eCui

    2016-04-01

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

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

    DEFF Research Database (Denmark)

    Østergaard, Mette; Pedersen, Lene; Schmidt, Jörg

    1997-01-01

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

  14. PANAL DE ABEJAS [Material gráfico

    OpenAIRE

    Anonymous

    1990-01-01

    ENTRE LOS PRODUCTOS APÍCOLAS DESTACAN: LA MIEL, EL POLEN, LA CERA, LOS PROPÓLEOS, LA APITOXINA Y LA JALEA REAL. RETRATO DE SERAFÍN TALAVERA MOLINA ENSEÑANDO UN PANAL EN CORRALILLOS. Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  15. Entrega de título de 'Cartero Honorario' : Comida en 'El Ulises'

    OpenAIRE

    Foto Fe-mir

    1982-01-01

    Nota al verso de la foto 3: De izquierda a derecha. Miguel Ángel Eced, Manuel de Bustos, Manuel Tomás, Antonio Díaz-Miguel. Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  16. Entrega uniforme de Cartero Honorario

    OpenAIRE

    Anonymous

    1985-01-01

    Nota al verso de la foto 1: Santiago Bartolomé Sobrino. Manuel de bustos Navarro. El día en que me entregó el uniforme de cartero. Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  17. Comparative genomic in situ hybridization analysis on the ...

    African Journals Online (AJOL)

    AJL

    2012-04-10

    Apr 10, 2012 ... 125: 1198-1205. Kumar A, Pearce S R, McLean K, Harrison G, Heslop-Harrison JS. (1997). The Ty1-copia group of retrotransposons in plants: genomic organization, evolution, and use as molecular markers. Genetica,. 100: 205-217. Langdon T (2000). Retrotransposon evolution in diverse plant genomes.

  18. La cartografía histórica marítima en la Biblioteca Luis Ángel Arango

    Directory of Open Access Journals (Sweden)

    Boletín Cultural y Bibliográfico Banco de la República

    2016-08-01

    Casi todos estos facsímiles fueron publicados en España en la segunda mitad del siglo XX, inicialmente por Carlos Sanz, y luego como publicaciones conmemorativas del Quinto Centenario del Descubrimiento de América, con ediciones numeradas de gran calidad que son copias fieles del documento original certificadas por notario.

  19. Veneno en la red

    OpenAIRE

    Christian Ferrer

    2015-01-01

    Refiere a más de seis mil virus que han parasitado la industria de la computación y sus redes. La tipología de los delitos informáticos cubre desde la copia ilegal del software, al sabotaje informático; del acceso sin autorización, al espionaje.

  20. L’esperienza ebraica transnazionale nel bacino del Mediterraneo: oltre l’Olocausto

    Directory of Open Access Journals (Sweden)

    Philip Balma

    2013-12-01

    Full Text Available Recensione di: Raniero Speelman, Monica Jansen & Silvia Gaiga, Ebrei migranti. Le voci della diaspora / Jewish Migration. Voices of the Diaspora, Italianistica Ultraiectina 7, Utrecht, Igitur, 2012, 389 p.,ISBN: 9789067010320, open access, € 21,88 (copia cartacea.

  1. II. Cuestionario para probar la pertenencia a casta de mulatos o mestizos en pleito por

    Directory of Open Access Journals (Sweden)

    Historia Social y de la Cultura Anuario Colombiano de

    1965-01-01

    Full Text Available Es copia de los documentos originales que se encuentran a folios números 42 recto a 43 y vuelto del tomo 1° del fondo de "Genealogías", que se guarda en el Archivo Histórico Nacional. Bogotá.

  2. Aaron Swartz (1986–2013). Una vita per la cultura libera e la giustizia sociale

    OpenAIRE

    Maria Chiara Pievatolo

    2014-01-01

    Naturally, doing things like changing the university are much harder than simply becoming yet another professor. Chi fosse interessato a leggere il tributo ad Aaron Swartz curato da Bernardo Parrella e Andrea Zanni può prelevarne una copia anche dall’archivio Marini,...

  3. Aaron Swartz (1986–2013. Una vita per la cultura libera e la giustizia sociale

    Directory of Open Access Journals (Sweden)

    Maria Chiara Pievatolo

    2014-01-01

    Full Text Available Naturally, doing things like changing the university are much harder than simply becoming yet another professor. Chi fosse interessato a leggere il tributo ad Aaron Swartz curato da Bernardo Parrella e Andrea Zanni può prelevarne una copia anche dall’archivio Marini,...

  4. GenBank blastx search result: AK063533 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK063533 001-117-B08 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  5. GenBank blastx search result: AK119477 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK119477 001-134-B09 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  6. GenBank blastx search result: AK060772 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060772 001-033-B05 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  7. GenBank blastx search result: AK119569 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK119569 002-117-A08 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  8. GenBank blastn search result: AK109423 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK109423 006-305-G05 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  9. GenBank blastn search result: AK100132 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK100132 J023010C03 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  10. GenBank blastn search result: AK069187 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK069187 J023009G22 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  11. GenBank blastx search result: AK058605 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK058605 001-018-A02 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  12. GenBank blastn search result: AK109722 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK109722 002-146-B04 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  13. GenBank blastx search result: AK059048 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK059048 001-021-D12 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  14. GenBank blastn search result: AK060205 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060205 001-002-A05 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  15. GenBank blastn search result: AK106843 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK106843 002-116-H10 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  16. GenBank blastx search result: AK060340 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060340 001-008-D02 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  17. GenBank blastx search result: AK064276 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK064276 002-105-F03 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  18. GenBank blastn search result: AK120398 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK120398 J013087C11 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  19. GenBank blastx search result: AK059681 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK059681 001-031-H08 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  20. GenBank blastx search result: AK059987 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK059987 006-212-H01 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  1. HIV transcription is induced in dying cells

    Energy Technology Data Exchange (ETDEWEB)

    Woloschak, G.E.; Chang-Liu, Chin-Mei [Argonne National Lab., IL (United States); Schreck, S. [Argonne National Lab., IL (United States)]|[Univ. of South Carolina, Columbia, SC (United States). Dept. of Chemistry; Panozzo, J. [Loyola Univ. Medical Center, Maywood, IL (United States); Libertin, C.R. [Loyola Univ. Medical Center, Maywood, IL (United States)

    1996-02-01

    Using HeLa cells stably transfected with an HIV-LTR-CAT construct, we demonstrated a peak in CAT induction that occurs in viable (but not necessarily cell-division-competent) cells 24 h following exposure to some cell-killing agents. {gamma} rays were the only cell-killing agent which did not induce HIV transcription; this can be attributed to the fact that {gamma}-ray-induced apoptotic death requires functional p53, which is not present in HeLa cells. For all other agents, HIV-LTR induction was dose-dependent and correlated with the amount of cell killing that occurred in the culture. Doses which caused over 99% cell killing induced HIV-LTR transcription maximally, demonstrating that cells that will go on to die by 14 days are the cells expressing HIV-LTR-CAT.

  2. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection

    National Research Council Canada - National Science Library

    Wenhui Hu; Rafal Kaminski; Fan Yang; Yonggang Zhang; Laura Cosentino; Fang Li; Biao Luo; David Alvarez-Carbonell; Yoelvis Garcia-Mesa; Jonathan Karn; Xianming Mo; Kamel Khalili

    2014-01-01

    .... We identified highly specific targets within the HIV-1 LTR U3 region that were efficiently edited by Cas9/gRNA, inactivating viral gene expression and replication in latently infected microglial...

  3. GenBank blastn search result: AK063493 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK063493 001-116-C12 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  4. GenBank blastn search result: AK064276 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK064276 002-105-F03 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  5. GenBank blastx search result: AK106752 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK106752 002-115-D01 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  6. GenBank blastn search result: AK111471 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK111471 002-183-E12 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  7. GenBank blastn search result: AK070880 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK070880 J023064I03 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  8. GenBank blastn search result: AK109912 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK109912 002-149-H11 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  9. GenBank blastn search result: AK071961 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK071961 J013077G18 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  10. GenBank blastn search result: AK120496 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK120496 J013120I03 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  11. GenBank blastx search result: AK109716 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK109716 002-145-H10 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  12. GenBank blastn search result: AK072535 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK072535 J023133G14 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  13. GenBank blastx search result: AK062180 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK062180 001-046-D08 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  14. GenBank blastx search result: AK058710 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK058710 001-019-D05 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  15. GenBank blastx search result: AK059271 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK059271 001-025-B11 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  16. GenBank blastx search result: AK062235 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK062235 001-047-D12 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  17. GenBank blastx search result: AK060277 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060277 001-005-H07 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  18. GenBank blastx search result: AK104337 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK104337 001-033-D06 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  19. GenBank blastx search result: AK106843 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK106843 002-116-H10 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  20. GenBank blastn search result: AK100455 [KOME

    Lifescience Database Archive (English)

    Full Text Available tilization-independent endosperm proteins, hypothetical protein, putative non-LTR r...AK100455 J023091E18 AF466200.2 Sorghum bicolor putative protein kinase gene, partial cds; putative Cf-2, fer

  1. GenBank blastx search result: AK058204 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK058204 001-010-A06 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  2. GenBank blastx search result: AK119480 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK119480 001-134-B12 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  3. GenBank blastx search result: AK059302 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK059302 001-025-F07 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  4. GenBank blastx search result: AK061866 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK061866 001-040-H09 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  5. GenBank blastx search result: AK060458 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060458 001-012-A11 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  6. GenBank blastx search result: AK060385 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060385 001-009-F05 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  7. GenBank blastx search result: AK060739 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060739 001-032-C11 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  8. GenBank blastx search result: AK104005 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK104005 001-002-F05 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  9. GenBank blastx search result: AK111471 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK111471 002-183-E12 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  10. GenBank blastx search result: AK060922 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK060922 001-035-H05 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  11. GenBank blastx search result: AK059605 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK059605 001-030-E11 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  12. GenBank blastx search result: AK103954 [KOME

    Lifescience Database Archive (English)

    Full Text Available al cds; putative Cf-2, fertilization-independent endosperm proteins, hypothetical protein, putative non-LTR ...AK103954 001-014-H03 AF466200.2 Sorghum bicolor putative protein kinase gene, parti

  13. Novel 3′-Processing Integrase Activity Assay by Real-Time PCR for Screening and Identification of HIV-1 Integrase Inhibitors

    National Research Council Canada - National Science Library

    Sakkhachornphop, Supachai; Thongkum, Weeraya; Tayapiwatana, Chatchai

    2015-01-01

    .... Recently, we have developed a novel real-time PCR based assay for the detection of 3[variant prime]P activity in vitro. The methodology usually involves biotinylated HIV-1 LTR, HIV-1 integrase...

  14. Outbreak of Pneumocystis Pneumonia in Renal and Liver Transplant Patients Caused by Genotypically Distinct Strains of Pneumocystis jirovecii

    DEFF Research Database (Denmark)

    Rostved, Andreas A; Sassi, Monica; Kurtzhals, Jørgen A L

    2013-01-01

    An outbreak of 29 cases of Pneumocystis jirovecii pneumonia (PCP) occurred among renal and liver transplant recipients (RTR and LTR) in the largest Danish transplantation centre between 2007 and 2010, when routine PCP prophylaxis was not used.......An outbreak of 29 cases of Pneumocystis jirovecii pneumonia (PCP) occurred among renal and liver transplant recipients (RTR and LTR) in the largest Danish transplantation centre between 2007 and 2010, when routine PCP prophylaxis was not used....

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

    Science.gov (United States)

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

    2016-07-27

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

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

    Directory of Open Access Journals (Sweden)

    Iyoko Katoh

    2011-11-01

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

  17. Kajian Potensi Air Rawa dan Kearifan Lokal sebagai Dasar Pengelolaan Air Rawa Yomoth sebagai Sumber Air Bersih di Distrik Agats Kabupaten Asmat Provinsi Papua

    Directory of Open Access Journals (Sweden)

    Yoseph Kamun

    2016-10-01

    Tujuanpenelitianiniadalah (1 mengkajikebutuhanairbersihpenduduk dansumber- sumber air bersih di daerah penelitian, (2 mengkaji  karasteristik  potensi  air  rawa Yomoth sebagaisumberairbersihdan(3menyusun  kerangkadasarpengelolaan airrawaYomoth sebagaisumberair bersihyangberbasiskearifanlokal. Metode penelian adalah survey, dengan data diperoleh dan wawancara terhadap koresponden  yangditentukan  secarapurposive  sampling.  Datadianalisis  secara  deskriptip kuantitatif untuk mendapatkan gambaran tentang jumlah angka dan   pembahasan  objek kesimpulansecarakeruangan(spasial.Hasilpenelitianmenunjukkanbahwa:(1KebutuhanairbersihdiKotaAgatsKabupaten Asmatberdasarkansampel30KKyangdiperolehadalahsebesarrata-rata60ltr/harimakatotal kebutuhanair92.46ltr3/haridenganjumlah pendudukKotaAgats1541orang.Makakebutuhan airbersihpada5tahunmendatangadalah14736ltr3dengantingkatpenduduk1615orang,pada 10tahunmendatang  adalah31171ltr3  dengantingkatpenduduk1708orang,pada15tahun mendatangadalah49411ltr3  dengantingkatpenduduk1805orang,pada20tahunmendatang adalah69058ltr3dengantinkatpenduduk1892orangdanpada25tahunmedatangadalah88147 ltr3   dengan  tingkat  penduduk  1932  orang.  (2  Air  rawa  Yomoth  sebagai  sumber  air  bersih mempunyaikapasitasdayadukung2.302.140m3 dengankualitasbaikuntukdikelolasebagai sumbercadanganairbersih,walaupunterdapatpembatasberupasifatfisikairrawa,kandungan unsurkimiadanbiologisnya.(3UpayapengelolaanairrawaYomothdilakukandengancara perlindungan,penyelamatandanpelestarianterhadaphutandansumberdayaairrawa,dengan melakukan  tindakan  perlindungan  kearifan  lokal  dan  peraturan  daerah  sebagai  suatu  dasar hukum dalam pengambilan kebijakan dan keputusan.Mengingat secara ariftelah  melalui

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

    Directory of Open Access Journals (Sweden)

    James M Fox

    2016-03-01

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

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

    Science.gov (United States)

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

    2012-10-01

    Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  20. Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses.

    Directory of Open Access Journals (Sweden)

    Jumpei Ito

    2017-07-01

    Full Text Available Human endogenous retroviruses (HERVs and other long terminal repeat (LTR-type retrotransposons (HERV/LTRs have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs. Overall, 794,972 HERV-TFBSs were identified. Subsequently, we identified "HERV/LTR-shared regulatory element (HSRE," defined as a TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type. HSREs could be an indication that the regulatory elements of HERV/LTRs are present before their insertions. We identified 2,201 HSREs, comprising specific associations of 354 HERV/LTRs and 84 TFs. Clustering analysis showed that HERV/LTRs can be grouped according to the TF binding patterns; HERV/LTR groups bounded to pluripotent TFs (e.g., SOX2, POU5F1, and NANOG, embryonic endoderm/mesendoderm TFs (e.g., GATA4/6, SOX17, and FOXA1/2, hematopoietic TFs (e.g., SPI1 (PU1, GATA1/2, and TAL1, and CTCF were identified. Regulatory elements of HERV/LTRs tended to locate nearby and/or interact three-dimensionally with the genes involved in immune responses, indicating that the regulatory elements play an important role in controlling the immune regulatory network. Further, we demonstrated subgroup-specific TF binding within LTR7, LTR5B, and LTR5_Hs, indicating that gains or losses of the regulatory elements occurred during genomic invasions of the HERV/LTRs. Finally, we constructed dbHERV-REs, an interactive database of HERV/LTR regulatory elements (http://herv-tfbs.com/. This study provides fundamental information in understanding the impact of HERV/LTRs on host transcription, and offers insights into

  1. HCV非结构蛋白5A对HIV长末端重复序列影响的初步探讨

    Directory of Open Access Journals (Sweden)

    PENG Milin

    2014-02-01

    Full Text Available ObjectiveTo investigate the effect of nonstructural protein 5A (NS5A encoded by the human hepatitis C virus (HCV RNA genome on human immunodeficiency virus (HIV long terminal repeat (LTR and to provide an experimental basis for the study on the effect of HCV on HIV. MethodsHepatocellular carcinoma Huh7 cells were divided into blank group, control group, and experimental group to be transfected with plasmid pGL3-LTR-Luc (containing luciferase reporter gene driven by the LTR promoter, plasmid pRc/CMV plus plasmid pGL3-LTR-Luc, and plasmid pCNS5A (containing HCV NS5A gene plus plasmid pGL3-LTR-Luc, respectively; Huh7 cells were collected 48 h later. The protein and mRNA expression levels of HCV NS5A were measured by immunocytochemistry, Western blot, and RT-PCR. The relative luciferase activity was measured to evaluate the HIV LTR activity and the effect of HCV NS5A on HIV LTR. The activity values were expressed as mean±SD, and Levene′s test of homogeneity of variance was used; comparison between all groups was made by one-way analysis of variance (ANOVA, and comparison between two groups was made by least significant difference (LSD test. ResultsThe mRNA and protein expression of HCV NS5A was detected in the cytoplasm of Huh7 cells in experimental group. The one-way ANOVA showed that there were significant differences in LTR luciferase activity between the three groups (F=7.876, P=0002. The LSD test showed that the experimental group had a significantly higher relative luciferase activity than the blank group and control group (22476±4471 vs 15887±3039, P=0.002; 22476±4471 vs 16321±4162, P=0.008. ConclusionHuh7 cells can be transfected with the HCV NS5A expression plasmid (pCNS5A. HCV NS5A can activate HIV LTR, which suggests that HCV NS5A may be one of the molecular mechanisms of HCV promoting HIV replication.

  2. En los umbrales del archivo : Distancias y olvidos en la teoría de Walter Benjamin

    OpenAIRE

    Cappannini, Cecilia Beatriz

    2010-01-01

    El presente trabajo realizado en el marco del Proyecto de investigación de la Adscripción a la Cátedra Fundamentos de Estética- Estética, se propone analizar cómo Benjamin a través de la noción de imagen dialéctica, pone en el centro del debate la antigua ambigüedad platónica respecto del arte. Considerado por un lado como copia de copia que corrompe el alma al alejarla de la verdad y por otro lado, como vehículo sensible a la contemplación de la Idea de Belleza. Entonces, si la representa...

  3. Role of p16ink4a and bmi-1 in oxidative stress-induced premature senescence in human dental pulp stem cells

    OpenAIRE

    Mas Bargues, Cristina

    2017-01-01

    Las células madre son aquellas células que se dividen asimétricamente para producir una copia de sí mismas y una segunda célula que seguirá su camino hasta convertirse en una célula diferenciada y especializada. Así pues, las células madre que podemos encontrar en el organismo adulto comparten al menos dos características. En primer lugar, se pueden hacer copias idénticas de sí mismas durante largos períodos de tiempo; esta capacidad de proliferar se refiere como auto-renovación a largo pl...

  4. Low doses of neutrons induce changes in gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Woloschak, G.E.; Chang-Liu, C.M. (Argonne National Lab., IL (United States)); Panozzo, J.; Libertin, C.R. (Loyola Univ., Maywood, IL (United States))

    1993-01-01

    Studies were designed to identify genes induced following low-dose neutron but not following [gamma]-ray exposure in fibroblasts. Our past work had shown differences in the expression of [beta]-protein kinase C and c-fos genes, both being induced following [gamma]-ray but not neutron exposure. We have identified two genes that are induced following neutron, but not [gamma]-ray, exposure: Rp-8 (a gene induced by apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency (HIV). Rp-8 mRNA induction was demonstrated in Syrian hamster embryo fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.5 cGy/min) and at high dose rate (12 cGy/min). The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measures of CAT activity and CAT transcripts following irradiation demonstrated an unresponsiveness to [gamma] rays over a broad range of doses. Twofold induction of the HIV-LTR was detected following neutron exposure (48 cGy) administered at low (0.5 cGy/min) but not high (12 cGy/min) dose rates. Ultraviolet-mediated HIV-LTR induction was inhibited by low-dose-rate neutron exposure.

  5. Low doses of neutrons induce changes in gene expression

    Energy Technology Data Exchange (ETDEWEB)

    Woloschak, G.E.; Chang-Liu, C.M. [Argonne National Lab., IL (United States); Panozzo, J.; Libertin, C.R. [Loyola Univ., Maywood, IL (United States)

    1993-06-01

    Studies were designed to identify genes induced following low-dose neutron but not following {gamma}-ray exposure in fibroblasts. Our past work had shown differences in the expression of {beta}-protein kinase C and c-fos genes, both being induced following {gamma}-ray but not neutron exposure. We have identified two genes that are induced following neutron, but not {gamma}-ray, exposure: Rp-8 (a gene induced by apoptosis) and the long terminal repeat (LTR) of the human immunodeficiency (HIV). Rp-8 mRNA induction was demonstrated in Syrian hamster embryo fibroblasts and was found to be induced in cells exposed to neutrons administered at low (0.5 cGy/min) and at high dose rate (12 cGy/min). The induction of transcription from the LTR of HIV was demonstrated in HeLa cells bearing a transfected construct of the chloramphenicol acetyl transferase (CAT) gene driven by the HIV-LTR promoter. Measures of CAT activity and CAT transcripts following irradiation demonstrated an unresponsiveness to {gamma} rays over a broad range of doses. Twofold induction of the HIV-LTR was detected following neutron exposure (48 cGy) administered at low (0.5 cGy/min) but not high (12 cGy/min) dose rates. Ultraviolet-mediated HIV-LTR induction was inhibited by low-dose-rate neutron exposure.

  6. Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii.

    Science.gov (United States)

    Najnin, T; Siddiqui, K S; Taha, T; Elkaid, N; Kornfeld, G; Curmi, P M G; Cavicchioli, R

    2016-04-07

    Cold environments dominate the Earth's biosphere and the resident microorganisms play critical roles in fulfilling global biogeochemical cycles. However, only few studies have examined the molecular basis of thermosensing; an ability that microorganisms must possess in order to respond to environmental temperature and regulate cellular processes. Two component regulatory systems have been inferred to function in thermal regulation of gene expression, but biochemical studies assessing these systems in Bacteria are rare, and none have been performed in Archaea or psychrophiles. Here we examined the LtrK/LtrR two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii, assessing kinase and phosphatase activities of wild-type and mutant proteins. LtrK was thermally unstable and had optimal phosphorylation activity at 10 °C (the lowest optimum activity for any psychrophilic enzyme), high activity at 0 °C and was rapidly thermally inactivated at 30 °C. These biochemical properties match well with normal environmental temperatures of M. burtonii (0-4 °C) and the temperature this psychrophile is capable of growing at in the laboratory (-2 to 28 °C). Our findings are consistent with a role for LtrK in performing phosphotransfer reactions with LtrR that could lead to temperature-dependent gene regulation.

  7. Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution.

    Science.gov (United States)

    El Baidouri, Moaine; Panaud, Olivier

    2013-01-01

    Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants.

  8. Human endogenous retrovirus K106 (HERV-K106 was infectious after the emergence of anatomically modern humans.

    Directory of Open Access Journals (Sweden)

    Aashish R Jha

    Full Text Available HERV-K113 and HERV-K115 have been considered to be among the youngest HERVs because they are the only known full-length proviruses that are insertionally polymorphic and maintain the open reading frames of their coding genes. However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older. A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking. Therefore, we sought to determine how recently HERVs were exogenous and infectious by examining sequence variation in the long terminal repeat (LTR regions of all full-length HERV-K loci. We used the traditional method of inter-LTR comparison to analyze all full length HERV-Ks and determined that two insertions, HERV-K106 and HERV-K116 have no differences between their 5' and 3' LTR sequences, suggesting that these insertions were endogenized in the recent evolutionary past. Among these insertions with no sequence differences between their LTR regions, HERV-K106 had the most intact viral sequence structure. Coalescent analysis of HERV-K106 3' LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans.

  9. Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories.

    Science.gov (United States)

    Guyot, Romain; Darré, Thibaud; Dupeyron, Mathilde; de Kochko, Alexandre; Hamon, Serge; Couturon, Emmanuel; Crouzillat, Dominique; Rigoreau, Michel; Rakotomalala, Jean-Jacques; Raharimalala, Nathalie E; Akaffou, Sélastique Doffou; Hamon, Perla

    2016-10-01

    The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.

  10. Correlation between lung to thorax transverse area ratio and observed/expected lung area to head circumference ratio in fetuses with left-sided diaphragmatic hernia.

    Science.gov (United States)

    Hidaka, Nobuhiro; Murata, Masaharu; Sasahara, Jun; Ishii, Keisuke; Mitsuda, Nobuaki

    2015-05-01

    Observed/expected lung area to head circumference ratio (o/e LHR) and lung to thorax transverse area ratio (LTR) are the sonographic indicators of postnatal outcome in fetuses with congenital diaphragmatic hernia (CDH), and they are not influenced by gestational age. We aimed to evaluate the relationship between these two parameters in the same subjects with fetal left-sided CDH. Fetuses with left-sided CDH managed between 2005 and 2012 were included. Data of LTR and o/e LHR values measured on the same day prior to 33 weeks' gestation in target fetuses were retrospectively collected. The correlation between the two parameters was estimated using the Spearman's rank-correlation coefficient, and linear regression analysis was used to assess the relationship between them. Data on 61 measurements from 36 CDH fetuses were analyzed to obtain a Spearman's rank-correlation coefficient of 0.74 with the following linear equation: LTR = 0.002 × (o/e LHR) + 0.005. The determination coefficient of this linear equation was sufficiently high at 0.712, and the prediction accuracy obtained with this regression formula was considered satisfactory. A good linear correlation between the LTR and the o/e LHR was obtained, suggesting that we can translate the predictive parameters for each other. This information is expected to be useful to improve our understanding of different investigations focusing on LTR or o/e LHR as a predictor of postnatal outcome in CDH. © 2014 Japanese Teratology Society.

  11. Selective histonedeacetylase inhibitor M344 intervenes in HIV-1 latency through increasing histone acetylation and activation of NF-kappaB.

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    Hao Ying

    Full Text Available BACKGROUND: Histone deacetylase (HDAC inhibitors present an exciting new approach to activate HIV production from latently infected cells to potentially enhance elimination of these cells and achieve a cure. M344, a novel HDAC inhibitor, shows robust activity in a variety of cancer cells and relatively low toxicity compared to trichostatin A (TSA. However, little is known about the effects and action mechanism of M344 in inducing HIV expression in latently infected cells. METHODOLOGY/PRINCIPAL FINDINGS: Using the Jurkat T cell model of HIV latency, we demonstrate that M344 effectively reactivates HIV-1 gene expression in latently infected cells. Moreover, M344-mediated activation of the latent HIV LTR can be strongly inhibited by a NF-κB inhibitor aspirin. We further show that M344 acts by increasing the acetylation of histone H3 and histone H4 at the nucleosome 1 (nuc-1 site of the HIV-1 long terminal repeat (LTR and by inducing NF-κB p65 nuclear translocation and direct RelA DNA binding at the nuc-1 region of the HIV-1 LTR. We also found that M344 synergized with prostratin to activate the HIV-1 LTR promoter in latently infected cells. CONCLUSIONS/SIGNIFICANCE: These results suggest the potential of M344 in anti-latency therapies and an important role for histone modifications and NF-κB transcription factors in regulating HIV-1 LTR gene expression.

  12. La flora de la Real Expedición Botánica, primera escuela de arte en el Nuevo Reino de Granada

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    Marta Fajardo de Rueda

    1986-01-01

    Full Text Available Describe los trabajos realizados por los colaboradores, pintores, de Mutis en la representación de la rica flora neogranadina y afirma como a través de esta obra de carácter esencialmente científico se fueron sentando las bases para el surgimiento de pintores criollos que abandonaron las copias de grabados europeos y se dedicaron más a la realidad americana.

  13. Algunas reflexiones desde la acuarela de Mario Conde

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    Pamela Romano

    2012-11-01

    Full Text Available This brief reflection on the work of Mario Conde starts paying attention to the special relationship the artist has with the watercolor technique, deploying from that relationship a copy-based ethics. From that materiality Conde builds his response to the postmodern moment in which art in general, and particularly Bolivian art, is been developed given its current social conditions. The ethics of the copy is explored especially in two of his works: "Exterminator Angel" where  copying addresses colonial issues that return to question and challenge the very notion of homeland, and "Drunk with power (Géricault in Los Andes" where the copy,  adapted to Andean latitudes, exudes a desire to restore the sacred and  auratic character of artwork as well as of the Andean imagery.Esta breve reflexión sobre la obra de Mario Conde se inicia poniendo atención en la relación particular que tiene el pintor con la técnica de la acuarela, desplegando desde esa relación una ética basada en la copia. Desde esa materialidad Conde concretiza su respuesta al momento posmoderno en que se desarrolla el arte en general, y el boliviano en particular dadas sus condiciones sociales actuales. La ética de la copia es explorada especialmente en dos de sus obras: “Ángel exterminador” donde la copia aborda temáticas coloniales que retornan para poner en cuestión y entredicho la noción de patria, y “Ebrios de poder (Géricault en Los Andes” donde la copia adaptada a latitudes andinas destila un deseo de restablecer el carácter sagrado y aurático de la obra de arte como del imaginario andino.

  14. Informe del Visitador Real Don Andrés Berdugo y Oquendo sobre el estado social y Económico de la población indígena, blanca y mestiza de las Provincias de Tunja y Vélez a mediados del siglo XVIII

    Directory of Open Access Journals (Sweden)

    Andrés Berdugo

    1963-01-01

    Full Text Available El documento original se halla en el Archivo Nacional de Colombia, fondo Visitas, Boyacá, T. VII, ff. 1 a 85.  Hemos conservado la ortografía original. Los títulos del margen son nuestros. El arreglo para la publicación estuvo a cargo del Prof. Jaime Jaramillo Uribe. La copia de los originales fue hecha por Josefina Chaves de Bonilla.

  15. Detection, quantification and genetic variability of Mycoplasma hyopneumoniae from apparently healthy and pneumonic swine

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    Yaima Burgher Pulgarón

    2015-12-01

    Full Text Available As diferenças moleculares entre as estirpes de Mycoplasma hyopneumoniae presentes em pulmões de suínos com pneumonia tem sido estudadas. Porém, estudos comparativos relativos as estirpes presentes nos suínos aparentemente saudáveis não foram levados a cabo. O objetivo do estudo foi a detecção, quantificação e analise molecular de M. hyopneumoniae nos pulmões suínos com e sem lesões pneumônicas. Para a detecção de M. hyopneumoniae usaramse o PCR Multiplo (YAMAGUTI, 2008, o PCR a Tempo Real (STRAIT et al., 2008 e a amplificação de múltiplo VNTR (VRANCKX et al., 2011. A caracterização molecular das estirpes foi realizada mediante a análise do número de copias de VNTR em P97R1, P146R3, H2R1 e H4. O M. hyopneumoniae foi detectado em amostras de suínos saudáveis e pneumônicos e a quantidade de M. hyopneumoniae nas amostras positivas variou com o tipo de ensaio. O maior número de amostras positivas foi identificado pela amplificação de múltiplas VNTR combinado com a eletroforese de capilares. Usando o PCR a Tempo Real, 4.9*104 copias de genoma/mL de M. hyopneumoniae foram detectadas em pulmões aparentemente saudáveis. Uma quantidade média de 3.9*106 copias de genoma/mL de M. hyopneumoniae foi detectada em pulmões pneumônicos. A análise do número de copias de VNTR demonstrou uma elevada variabilidade.

  16. Difusión en abierto de la producción documental EEAD-CSIC e identificadores y perfiles públicos de investigador: vías actuales

    OpenAIRE

    Martínez Giménez, José Carlos

    2015-01-01

    4 copias .pdf de 1) Cartel de difusión. 2) Ficha de recogida de datos personales relacionados con identificadores y perfiles públicos de investigador. 3) Presentación-introducción expuesta en las sesiones grupales. 4) Póster-Directorio de Perfiles públicos de investigadores y técnicos EEAD-CSIC en Google Scholar (a fecha 28 feb. 2015).

  17. Curso sobre la gestión de los procesos técnicos a través del puesto de trabajo

    OpenAIRE

    Mangiaterra, Norma Ethel; Martínez Tamayo, Ana María

    2002-01-01

    Contenidos del curso: - La Biblioteca como sistema de gestión integrado. Factores que la afectan. - El puesto de trabajo en las organizaciones modernas. - La gestión de los procesos técnicos y TSW (Technical Services Workstation) - TSW: definición, caracterización y funciones. - TSW del catalogador, del indizador/clasificador - TSW y conexión de bases de datos. - TSW y registros por copia. - TSW e Internet Dep...

  18. GenBank blastn search result: AK318517 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK318517 J043004B20 EF560592.1 EF560592 Triticum turgidum subsp. durum retrotransposon... Copia WIS-1, complete sequence; transposon Caspar-1, partial sequence; transposon Hades-1, retrotransposon Veju-1, and transposon... Caspar-2, complete sequence; transposon Hades-2, partial sequence; transposon Orph...eus-1 and Pm3-3 pseudogene, complete sequence; and transposon Isaac-3, partial sequence. PLN 2e-40 1 -1 ...

  19. 180 tesis de grado extranjeras sobre política colombiana

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    Rodrigo Losada Lora

    1979-06-01

    Full Text Available La Fundación para la Educación Superior y el Desarrollo (FEDESARROLLO entregó a la Biblioteca Luis-Ángel Arango 180 copias de tesis de grado presentadas en universidades extranjeras. Las tesis tratan, en su totalidad o en parte sustancial, sobre temas de política colombiana, entendiendo esta en un sentido amplio (Gobierno, partidos, elecciones, militares, grupos de presión, etc..

  20. Camilo José Cela con niños

    OpenAIRE

    Anonymous

    1986-01-01

    En el verso: dedicatorias de los niños de la foto: "A mi amigo Camilo José Cela. Álvaro", "Al mejor escritor del mundo, camilo José Cela. Con mucho cariño. Covadonga" Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  1. Laryngotracheal reconstruction and cricotracheal resection in children: recent experience at Great Ormond Street Hospital.

    Science.gov (United States)

    Bajaj, Y; Cochrane, L A; Jephson, C G; Wyatt, M E; Bailey, C M; Albert, D M; Hartley, B E J

    2012-04-01

    Surgery for paediatric airway stenosis is constantly evolving. Surgery is the primary treatment modality via either an open or endoscopic approach. The objective of this study was to review the results of laryngotracheal reconstruction (LTR) and cricotracheal resection (CTR) procedures performed at Great Ormond Street Hospital over the past 10 years. All patients who underwent open airway reconstruction surgery from January 2000 to December 2010 were included in this study. Patients treated entirely endoscopically were excluded. The data was collected using the electronic operating theatre database and the discharge summary database. Complete data was available for 199 patients who underwent open airway reconstruction from January 2000 to December 2010. The procedures included single stage LTR (57, 28.6%), two stage LTR (115, 57.7%), single-stage stomal reconstruction (14), single-stage CTR (8) and two-stage CTR (5). The diagnoses at the initial airway endoscopy were laryngeal web (22), subglottic stenosis (151), posterior glottic stenosis (9), suprastomal collapse (15), supraglottic stenosis (1) and tracheal stenosis (1). For those with subglottic stenosis, the stenosis was grade 1 in 1 patient, grade 2 in 26 patients, grade 3 in 117 patients and grade 4 in 6 patients. At the completion of intervention 175/199 (87.9%) patients reported improvement in their symptoms. Amongst the subglottic stenosis group, post LTR success was achieved in 100% with grade 1 stenosis, 92.3% with grade 2 stenosis, 88.1% in grade 3 stenosis and 83.3% in grade 4 stenosis. Of the two-stage LTR procedures, 100/115 (86.9%) had their tracheostomy removed and 15/115 (13.1%) have failed decannulation. Of the single-stage LTR group, 50/57 (87.7%) patients were better both on airway examination and symptomatically postoperatively. Of the single-stage stomal reconstruction group, 13/14 (92.8%) were better symptomatically and on airway examination. Patients who underwent single-stage CTR had a

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1989-08-01

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

  3. Patient histories, retention, and outcome models for younger and older adults in DATOS.

    Science.gov (United States)

    Grella, C E; Hser, Y I; Joshi, V; Anglin, M D

    1999-12-01

    Structural equation modeling with multiple groups was used to examine relationships among pretreatment patient characteristics, treatment retention, and treatment outcomes among younger and older adults in the Drug Abuse Treatment Outcome Studies. Separate models were tested for 551 patients treated in long-term residential (LTR) programs and 571 patients treated in outpatient drug-free (ODF) programs. There was a stronger positive relationship between treatment retention and abstinence at follow-up for younger adults in both treatment modalities. Prior treatment history had a negative effect on self-efficacy to resist drug use for older adults in LTR. Negative reference group influence was reduced for all groups following treatment, however, it was more strongly related to abstinence for younger adults in LTR and for older adults in ODF. Clinical implications of age-related differences in these relationships are discussed.

  4. Antibiosis functions during interactions of Trichoderma afroharzianum and Trichoderma gamsii with plant pathogenic Rhizoctonia and Pythium.

    Science.gov (United States)

    Zhang, Xinjian; Harvey, Paul R; Stummer, Belinda E; Warren, Rosemary A; Zhang, Guangzhi; Guo, Kai; Li, Jishun; Yang, Hetong

    2015-09-01

    Trichoderma afroharzianum is one of the best characterized Trichoderma species, and strains have been utilized as plant disease suppressive inoculants. In contrast, Trichoderma gamsii has only recently been described, and there is limited knowledge of its disease suppressive efficacies. Comparative studies of changes in gene expression during interactions of these species with their target plant pathogens will provide fundamental information on pathogen antibiosis functions. In the present study, we used complementary DNA amplified fragment length polymorphism (cDNA-AFLP) analysis to investigate changes in transcript profiling of T. afroharzianum strain LTR-2 and T. gamsii strain Tk7a during in vitro interactions with plant pathogenic Rhizoctonia solani and Pythium irregulare. Considerable differences were resolved in the overall expression profiles of strains LTR-2 and Tk7a when challenged with either plant pathogen. In strain LTR-2, previously reported mycoparasitism-related genes such as chitinase, polyketide synthase, and non-ribosomal peptide synthetase were found to be differentially expressed. This was not so for strain Tk7a, with the only previously reported antibiosis-associated genes being small secreted cysteine-rich proteins. Although only one differentially expressed gene was common to both strains LTR-2 and Tk7a, numerous genes reportedly associated with pathogen antibiosis processes were differentially expressed in both strains, including degradative enzymes and membrane transport proteins. A number of novel potential antibiosis-related transcripts were found from strains LTR-2 and Tk7a and remain to be identified. The expression kinetics of 20 Trichoderma (10 from strain LTR-2, 10 from strain Tk7a) transcript-derived fragments (TDFs) were quantified by quantitative reverse transcription PCR (RT-qPCR) at pre- and post-mycelia contact stages of Trichoderma-prey interactions, thereby confirming differential gene expression. Collectively, this research

  5. A Lentiviral Vector Expressing Desired Gene Only in Transduced Cells: An Approach for Suicide Gene Therapy.

    Science.gov (United States)

    Mohammadi, Zahra; Shariati, Laleh; Khanahmad, Hossein; Kolahdouz, Mahsa; Kianpoor, Fariborz; Ghanbari, Jahan Afrooz; Hejazi, Zahra; Salehi, Mansoor; Nikpour, Parvaneh; Tabatabaiefar, Mohammad Amin

    2015-09-01

    Suicide gene therapy is a therapeutic strategy, in which cell suicide inducing transgenes are introduced into target cells. Inserting a toxin-encoding gene into a lentiviral vector leads to decreased efficiency of virus production due to lethal effect of toxin on packaging cells. In this study, we designed and constructed a transfer vector to express the toxin in transduced cells but not in packaging cells. Plasmid pLenti-F/GFP was constructed by cutting out R 5'LTR-R 3'LTR fragment with the AflII restriction endonuclease from a plasmid pLenti4-GW/H1/TO-laminshRNA, followed by ligating R 5'LTR-R 3'LTR fragment, constructed by three PCR stages. The promoter and GFP CDS were inserted in opposite strand. For lentiviral production, the HEK293T cell line was co-transfected with the PMD2G, psPAX2, and pLenti-F/GFP plasmids (envelope, packaging, and transfer plasmids).Viral vector titers were assayed. The HEK293T cell line was transduced with this virus. PCR was performed to confirm the presence of the promoter fragment between the R and U5 in 3'LTR. The lentivirus titers were approximately 2 × 10(5). The GFP expression was seen in 51 % of the HEK293T cells transduced with lentivirus. The PCR product size was 1440 bp confirming the promoter fragment position between the R and U5 in 3'LTR. The strategy enables us to use a broad spectrum of toxin genes in gene therapy and helps avoid the death of the packaging cells with lentiviral vectors carrying a toxin-encoding gene, thereby increasing the efficiency of viral production in packaging cells.

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

    Science.gov (United States)

    Shimizu, Takashi; Kida, Yutaka; Kuwano, Koichi

    2004-09-01

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

  7. Laryngotracheal reconstruction outcomes in hypotonic children.

    Science.gov (United States)

    Virbalas, Jordan M; Bent, John P; Cohen, Hillel W; Parikh, Sanjay R

    2013-12-01

    Children with poor muscle tone may demonstrate upper airway obstruction due to several mechanisms including obstructive sleep apnea, laryngopharyngeal reflux, and laryngomalacia. Though hypotonia has been shown to compromise the pediatric airway, and some authors suggest that neurologic deficits can compromise the success of laryngotracheal reconstruction (LTR), to our knowledge no studies have evaluated the effect of neurologic diagnoses or hypotonia on outcomes in LTR. To determine whether hypotonic children with subglottic stenosis have lower rates of successful decannulation after LTR compared with children without neurologic deficit. A retrospective medical chart review was conducted for 27 children aged 0 to 6 years, who underwent LTR for subglottic stenosis between December 2007 and December 2012 at a tertiary care children's hospital. Children were classified based on documented neurologic findings. Group 1 comprised those children without neurologic impairment (n = 16). Group 2 included those children with a documented neurocognitive or neuromuscular diagnosis but without evidence of hypotonia (n = 7). Group 3 comprised hypotonic children (n = 4). INTERVENTIONS Laryngotracheal reconstruction. The number of procedures performed after LTR to optimize the airway and whether the child was successfully decannulated. All 16 of the neurologically intact patients (100%) were decannulated. Among children with a neurologic deficit, 5 of 7 (71%) were ultimately decannulated. No hypotonic children 0 of 4 were decannulated. The difference in rates of decannulation between unaffected and normotonic children with a neurologic deficit was not statistically significant (P = .08). However, the difference in outcomes between hypotonic children and neurologically intact patients was statistically significant (P hypotonic children may experience poorer rates of post-LTR decannulation compared with children without neurologic deficit. Dynamic upper airway

  8. Silencing of human T-cell leukemia virus type I gene transcription by epigenetic mechanisms

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    Mueller Nancy

    2005-10-01

    Full Text Available Abstract Background Human T-cell leukemia virus type I (HTLV-I causes adult T-cell leukemia (ATL after a long latent period. Among accessory genes encoded by HTLV-I, the tax gene is thought to play a central role in oncogenesis. However, Tax expression is disrupted by several mechanims including genetic changes of the tax gene, deletion/hypermethylation of 5'-LTR. To clarify the role of epigenetic changes, we analyzed DNA methylation and histone modification in the whole HTLV-I provirus genome. Results The gag, pol and env genes of HTLV-I provirus were more methylated than pX region, whereas methylation of 5'-LTR was variable and 3'-LTR was not methylated at all. In ATL cell lines, complete DNA methylation of 5'-LTR was associated with transcriptional silencing of viral genes. HTLV-I provirus was more methylated in primary ATL cells than in carrier state, indicating the association with disease progression. In seroconvertors, DNA methylation was already observed in internal sequences of provirus just after seroconversion. Taken together, it is speculated that DNA methylation first occurs in the gag, pol and env regions and then extends in the 5' and 3' directions in vivo, and when 5'-LTR becomes methylated, viral transcription is silenced. Analysis of histone modification in the HTLV-I provirus showed that the methylated provirus was associated with hypoacetylation. However, the tax gene transcript could not be detected in fresh ATL cells regardless of hyperacetylated histone H3 in 5'-LTR. The transcription rapidly recovered after in vitro culture in such ATL cells. Conclusion These results showed that epigenetic changes of provirus facilitated ATL cells to evade host immune system by suppressing viral gene transcription. In addition, this study shows the presence of another reversible mechanism that suppresses the tax gene transcription without DNA methylation and hypoacetylated histone.

  9. The local twitch response during trigger point dry needling: Is it necessary for successful outcomes?

    Science.gov (United States)

    Perreault, Thomas; Dunning, James; Butts, Raymond

    2017-10-01

    Myofascial trigger point (MTrP) injection and trigger point dry needling (TrPDN) are widely accepted therapies for myofascial pain syndrome (MPS). Empirical evidence suggests eliciting a local twitch response (LTR) during needling is essential. This is the first review exploring the available literature, regardless of study design, on the neurophysiological effects and clinical significance of the LTR as it relates to reductions in pain and disability secondary to MTrP needling. PubMed, MEDLINE, Science Direct and Google Scholar were searched up until October 2016 using terms related to trigger point needling and the LTR. and Discussion: Several studies show that eliciting a LTR does not correlate with changes in pain and disability, and multiple systematic reviews have failed to conclude whether the LTR is relevant to the outcome of TrPDN. Post needling soreness is consistently reported in studies using repeated in and out needling to elicit LTRs and increases in proportion to the number of needle insertions. In contrast, needle winding without LTRs to MTrPs and connective tissue is well supported in the literature, as it is linked to anti-nociception and factors related to tissue repair and remodeling. Additionally, the positive biochemical changes in the MTrP after needling may simply be a wash out effect related to local vasodilation. While the LTR during TrPDN appears unnecessary for managing myofascial pain and unrelated to many of the positive effects of TrPDN, further investigation is required. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

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

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    Amyotte Stefan G

    2012-07-01

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

  11. DETERMINATION OF THE DISTRIBUTION AND INVENTORY OF RADIONUCLIDES WITHIN A SAVANNAH RIVER SITE WATERWAY

    Energy Technology Data Exchange (ETDEWEB)

    Hiergesell, R.; Phifer, M.

    2012-11-09

    An investigation was conducted to evaluate the radionuclide inventory within the Lower Three Runs (LTR) Integrator Operable Unit (IOU) at the U.S. Department of Energy’s (DOE’s) Savannah River Site (SRS). The scope of this effort included the analysis of previously existing sampling and analysis data as well as additional streambed and floodplain sampling and analysis data acquired to delineate horizontal and vertical distributions of the radionuclide as part of the ongoing SRS environmental restoration program, and specifically for the LTR IOU program. While cesium-137 (Cs-137) is the most significant and abundant radionuclide associated with the LTR IOU it is not the only radionuclide, hence the scope included evaluating all radionuclides present and includes an evaluation of inventory uncertainty for use in sensitivity and uncertainty analyses. The scope involved evaluation of the radionuclide inventory in the P-Reactor and RReactor cooling water effluent canal systems, PAR Pond (including Pond C) and the floodplain and stream sediment sections of LTR between the PAR Pond Dam and the Savannah River. The approach taken was to examine all of the available Sediment and Sediment/Soil analysis data available along the P- and R-Reactor cooling water re-circulation canal system, the ponds situated along those canal reaches and along the length of LTR below Par Pond dam. By breaking the IOU into a series of sub-components and sub-sections, the mass of contaminated material was estimated and a representative central concentration of each radionuclide was computed for each compartment. The radionuclide inventory associated with each sub-compartment was then aggregated to determine the total radionuclide inventory that represented the full LTR IOU. Of special interest was the inventory of Cs-137 due to its role in contributing to the potential dose to an offsite member of the public. The overall LTR IOU inventory of Cs-137 was determined to be 75.5 Ci, which is similar

  12. HIV transcription is induced with some forms of cell killing

    Energy Technology Data Exchange (ETDEWEB)

    Woloschak, G.E. [Argonne National Lab., IL (United States); Schreck, S. [Argonne National Lab., IL (United States)][South Carolina Univ., Columbia, SC (United States). Dept. of Chemistry; Panozzo, J. [Loyola Univ. Medical Center, Maywood, IL (United States); Chang-Liu, C.-M. [Argonne National Lab., IL (United States); Libertin, C.R. [Loyola Univ. Medical Center, Maywood, IL (United States)

    1996-11-01

    Using HeLa cells stably transfected with an HIV-LTR-CAT construct`, we demonstrated a peak in CAT induction that occurs in viable (but not necessarily cell-division-competent) cells 24 h following exposure to some cell-killing agents. {Gamma} rays were the only cell-killing agent which did not induce HIV transcription; this can be attributed to the fact that {gamma}-ray-induced apoptotic death requires function p53, which is missing in HeLa cells. For all other agents, HIV-LTR induction was dose-dependent and correlated with the amount of cell killing that occurred in the culture.

  13. High Energy Halogen Chemistry.

    Science.gov (United States)

    1978-01-01

    ion 10 wa c app lied to (3- n itro - gave tri methyLsi lylr nethy l 2-fluoro-2.2-dinitroeth I ether. This propy l)tr imethy lsilane , (4-n itr ohuty...Polymer Intermediate Department Wilmington, Delaware 19898 Attn: Dr. Bergman IITRI 1 10 W. 35th Street Chicago, IL 60616 Attn : Dr. A. Tuff is Cordova

  14. Construction of a novel lentiviral vector carrying human B-domain ...

    African Journals Online (AJOL)

    USER

    2010-03-29

    Mar 29, 2010 ... MSCs, mesenchymal stem cells; FCM, flow cytometry; RT-. PCR, reverse transcription polymerase chain reaction; mRNA, messager ribonucleic acid; RCLs, replication competent lentiviruses; LTR, long terminal repeat. prophylactically (Hilgartner, 2002). Purified FVIII concentrates concentrated from human ...

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

    NARCIS (Netherlands)

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

    1988-01-01

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

  16. Use of inactivated E.Coli enterotoxins to enhance respiratory mucosal adjuvanticity during vaccination in swine

    Science.gov (United States)

    In order to augment responses to respiratory vaccines in swine, various adjuvants were intranasally co-administered with an antigen to pigs. Detoxified E. coli enterotoxins LTK63 and LTR72 enhanced mucosal and systemic immunity to the model peptide, exhibiting their efficacy as mucosal adjuvants for...

  17. Cambio Climatico: Indicadores, estrategias de vida y eficiencia en su prediccion en las comunidades de Santa Maria y Apopata, Puno.

    OpenAIRE

    Fernández-Baca, Edith

    2008-01-01

    This brief presentation reports the results of SANREM CRSP LTR-4 project work in communities of Apopata and Santa Maria in Peru to study the presence of climate change and adaptive strategies made by local people. The results are shown in terms of indicators measured, livelihood strategies, and forecast efficiency. LTRA-4 (Practices and Strategies for Vulnerable Agro-Ecosystems)

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

    NARCIS (Netherlands)

    Jeang, K. T.; Berkhout, B.

    1992-01-01

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

  19. 76 FR 3150 - Office of Biotechnology Activities; Recombinant DNA Research: Action Under the NIH Guidelines for...

    Science.gov (United States)

    2011-01-19

    ... repeat (LTR), in order to address the small risk of recombination with endogenous retroviruses which.... As the risk of recombination and possible transmission to humans is more likely with gammaretroviral... containment; and (2) Neither parental transgenic rodent contains the following genetic modifications: (a...

  20. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

    NARCIS (Netherlands)

    Syed, H.; Sorensen, A.P.; Antonise, R.; van de Wiel, C.; van der Linden, C.G.; van 't Westende, W.; Hooftman, D.A.P.; den Nijs, J.C.M.; Flavell, A.J.

    2006-01-01

    Abstract Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187

  1. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

    NARCIS (Netherlands)

    Syed, N.; Sorensen, A.P.; Antonise, R.; Wiel, van de C.C.M.; Linden, van der C.G.; Westende, van 't W.P.C.; Hooftman, D.A.P.; Nijs, den H.C.M.; Flavell, A.

    2006-01-01

    Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187

  2. Clinical implication of latent myofascial trigger point.

    Science.gov (United States)

    Celik, Derya; Mutlu, Ebru Kaya

    2013-08-01

    Myofascial trigger points (MTrPs) are hyperirritable points located within a taut band of skeletal muscle or fascia, which cause referred pain, local tenderness and autonomic changes when compressed. There are fundamental differences between the effects produced by the two basic types of MTrPs (active and latent). Active trigger points (ATrPs) usually produce referred pain and tenderness. In contrast, latent trigger points (LTrPs) are foci of hyperirritability in a taut band of muscle, which are clinically associated with a local twitch response, tenderness and/or referred pain upon manual examination. LTrPs may be found in many pain-free skeletal muscles and may be "activated" and converted to ATrPs by continuous detrimental stimuli. ATrPs can be inactivated by different treatment strategies; however, they never fully disappear but rather convert to the latent form. Therefore, the diagnosis and treatment of LTrPs is important. This review highlights the clinical implication of LTrPs.

  3. Functional Analysis of the Proto-oncogenes Septin9 and Nras

    DEFF Research Database (Denmark)

    Lassen, Louise Berkhoudt

    regardless of genotype indicating an oncogenic role of SEPT9. Nras is a potent proto-oncogene involved in signaling through a number of proliferative pathways. Earlier detected retroviral integration sites resulting in B-cell lymphomas were used to create Nras knock in models harboring the LTR from...

  4. Mutated N-ras does not induce p19 in CO25 cell line

    African Journals Online (AJOL)

    kamel

    2012-06-28

    Jun 28, 2012 ... The mouse cell line (CO25) used in this study was transfected with a glucocorticoid inducible mutated human N-ras oncogene under transcriptional control of the steroid-sensitive promoter of the mouse mammary tumors virus long terminal repeat MMTV-LTR. This study was aimed to investigate the.

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

    Science.gov (United States)

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

    2010-05-01

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

  6. Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices.

    Science.gov (United States)

    Roulin, Anne; Chaparro, Cristian; Piégu, Benoit; Jackson, Scott; Panaud, Olivier

    2010-02-11

    Rice is one of the most important crops, feeding more than half of the world population. There are two cultivated species, the African rice Oryza glaberrima and the Asian rice O. sativa. Although the African species is gradually replaced by O. sativa in most of African rice agrosystems, this species represents an important reservoir of genes of agronomical interest. Their exploitation for the development of modern African rice varieties requires a good understanding of the genetic relationships between the two cultivated species. We took advantage of the recent availability of the sequence of the chromosome 3 short arm of O. glaberrima to estimate the date of radiation between O. glaberrima and O. sativa lineages, using all the long terminal repeat (LTR)-retrotransposons as paleogenomic markers. We first demonstrated that in two distinct lineages, LTR-retrotransposons mutate at the same rate. Based on LTR-retrotransposons shared by both species in orthologous position, we then estimated that O. glaberrima and O. sativa progenitors diverged 1.2 Ma. This constitutes one of the first studies using such a large sample of transposable elements to reconstruct the phylogeny of species. Given the number of genome sequencing projects, there is no doubt that such approach will allow to resolve phylogenetic incongruities. The application of this method to other plant genomes will also facilitate further understanding of evolution of LTR-retrotransposons and eventually of the whole genome in divergent plant lineages.

  7. polyvinylchloride and poly(methyl methacrylate) polyblends

    Indian Academy of Sciences (India)

    TECS

    mechanism governing the conduction, the activation energies in low temperature (LTR) and high temperature. (HTR) regions have been calculated ... The physical mixing or blending of two polymers produces an alloy with quite different ... mainly to its high electrical and chemical resistance and its unique ability to be mixed ...

  8. Novel 3′-Processing Integrase Activity Assay by Real-Time PCR for Screening and Identification of HIV-1 Integrase Inhibitors

    Directory of Open Access Journals (Sweden)

    Supachai Sakkhachornphop

    2015-01-01

    Full Text Available The 3′-end processing (3′P of each viral long terminal repeat (LTR during human immunodeficiency virus type-1 (HIV-1 integration is a vital step in the HIV life cycle. Blocking the 3′P using 3′P inhibitor has recently become an attractive strategy for HIV-1 therapeutic intervention. Recently, we have developed a novel real-time PCR based assay for the detection of 3′P activity in vitro. The methodology usually involves biotinylated HIV-1 LTR, HIV-1 integrase (IN, and specific primers and probe. In this novel assay, we designed the HIV-1 LTR substrate based on a sequence with a homology to HIV-1 LTR labeled at its 3′ end with biotin on the sense strand. Two nucleotides at the 3′ end were subsequently removed by IN activity. Only two nucleotides labeled biotin were captured on an avidin-coated tube; therefore, inhibiting the binding of primers and probe results in late signals in the real-time PCR. This novel assay has successfully detected both the 3′P activity of HIV-1 IN and the anti-IN activity by Raltegravir and sodium azide agent. This real-time PCR assay has been shown to be effective and inexpensive for a high-throughput screening of novel IN inhibitors.

  9. Plastid-bearing sea slugs fix CO2 in the light but do not require photosynthesis to survive

    NARCIS (Netherlands)

    G. Christa (Gregor); V. Zimorski (Verena); C. Woehle (Christian); A.G.M. Tielens (Aloysius); H. Wägele (Heike); W. Martin (William); D.B. Gould (Douglas )

    2013-01-01

    textabstractSeveral sacoglossan sea slugs (Plakobranchoidea) feed upon plastids of large unicellular algae. Four species-called long-term retention (LtR) species-are known to sequester ingested plastids within specialized cells of the digestive gland. There, the stolen plastids (kleptoplasts) remain

  10. Plastid-bearing sea slugs fix CO2 in the light but do not require photosynthesis to survive

    NARCIS (Netherlands)

    Christa, Gregor; Zimorski, Verena; Woehle, Christian; Tielens, Aloysius G M; Wägele, Heike; Martin, William F; Gould, Sven B

    2014-01-01

    Several sacoglossan sea slugs (Plakobranchoidea) feed upon plastids of large unicellular algae. Four species--called long-term retention (LtR) species--are known to sequester ingested plastids within specialized cells of the digestive gland. There, the stolen plastids (kleptoplasts) remain

  11. Sequence heterogeneity of the envelope -like domain in the ...

    African Journals Online (AJOL)

    Abbreviations; LTR: long terminal repeat, ORF: open-reading frame, PCR: polymerase chain reaction, RT: reverse transcriptase gene. The current study aimed to investigate the evolution of env-like sequences in the Egyptian cotton Gossypium barbadense. DNA sequence determination and analysis of env -like sequences ...

  12. The impact of education, cultural background, and lifestyle on symptoms of the menopausal transition: the Women's Health at Midlife Study.

    Science.gov (United States)

    Lerner-Geva, Liat; Boyko, Valentina; Blumstein, Tzvia; Benyamini, Yael

    2010-05-01

    This study aimed to examine differences in symptom clusters among women in midlife from different cultural origins and to identify sociodemographic, lifestyle, and health characteristics that could account for the differences between the cultural groups in symptom reporting. Israeli women aged 45-64 were randomly selected according to age and population strata of three groups: long-term Jewish residents (LTR), Jewish immigrants from the former Soviet Union, and Arab women (mostly Israeli-born). Interviews were conducted with 540 LTR, 151 immigrants, and 123 Arab women. The survey instrument included the occurrence and rating of how bothersome to everyday function were 16 symptoms. Three outcome variables included hot flashes and two scales for mental and somatic symptoms extracted from exploratory factor analysis. Multivariate logistic regressions showed that immigrants and Arab women (compared to LTR) had a significantly lower risk of reporting hot flashes and mental and somatic symptoms. Menopausal status was related only to hot flashes. Low education and depression were associated with the three symptom scales, whereas nonhealthy lifestyle was related only to somatic symptoms. Our main finding is that cultural group is an independent predictor of each of the three menopausal symptom scales. A possible explanation for the lower reporting of symptoms among Arab and immigrant groups is that they differ from the LTR in level of acculturation and attitudes toward menopause. These findings support the proposition of a cultural factor in menopausal symptomatology that needs to be addressed by clinicians caring for women at midlife.

  13. Tri-LORE-gy

    DEFF Research Database (Denmark)

    Mun, Terry

    Lotus japonicus is a model legume widely used in the study of plant development, physiology, and host-microbe interactions. The provision of genomic and transcriptomic data, the availability of a large mutant collection generated from saturation mutagenesis by an activated endogenous LTR retrotra...

  14. Modeling and Simulation of Avionics Systems and Command, Control and Communications Systems

    Science.gov (United States)

    1980-01-01

    produit compatible LTR it Aossmbleur 84. BSa fonctions sont. 1 Is ga stion do. tiches *I& gestion des Svdnements Is &aoption des nessources *la gection...between actual ominml tracks for approncli profile 7, showing the effect of the wind on the tracking accuracy on the curved segment HUMANA of THE

  15. Connecting with Teachers: The Case for Language Teaching Research in the Social Sciences

    Science.gov (United States)

    Kiely, Richard

    2014-01-01

    Paul Stapleton's assessment of the current state of language teaching research (LTR) raises important issues. However, his proposal that social science research approaches in ELT have failed, and that that they should be replaced by approaches from the biological sciences, is unlikely to connect with the knowledge-building needs of ELT…

  16. A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria

    Science.gov (United States)

    Quiles-Puchalt, Nuria; Tormo-Más, María Ángeles; Campoy, Susana; Toledo-Arana, Alejandro; Monedero, Vicente; Lasa, Íñigo; Novick, Richard P.; Christie, Gail E.; Penadés, José R.

    2013-01-01

    The propagation of bacteriophages and other mobile genetic elements requires exploitation of the phage mechanisms involved in virion assembly and DNA packaging. Here, we identified and characterized four different families of phage-encoded proteins that function as activators required for transcription of the late operons (morphogenetic and lysis genes) in a large group of phages infecting Gram-positive bacteria. These regulators constitute a super-family of proteins, here named late transcriptional regulators (Ltr), which share common structural, biochemical and functional characteristics and are unique to this group of phages. They are all small basic proteins, encoded by genes present at the end of the early gene cluster in their respective phage genomes and expressed under cI repressor control. To control expression of the late operon, the Ltr proteins bind to a DNA repeat region situated upstream of the terS gene, activating its transcription. This involves the C-terminal part of the Ltr proteins, which control specificity for the DNA repeat region. Finally, we show that the Ltr proteins are the only phage-encoded proteins required for the activation of the packaging and lysis modules. In summary, we provide evidence that phage packaging and lysis is a conserved mechanism in Siphoviridae infecting a wide variety of Gram-positive bacteria. PMID:23771138

  17. Mutated N-ras does not induce p19 arf in CO25 cell line | Saleh ...

    African Journals Online (AJOL)

    The mouse cell line (CO25) used in this study was transfected with a glucocorticoid inducible mutated human N-ras oncogene under transcriptional control of the steroid-sensitive promoter of the mouse mammary tumors virus long terminal repeat MMTV-LTR. This study was aimed to investigate the expression of p19arf and ...

  18. Glucocorticoid regulation of transcription at an amplified, episomal promoter

    Energy Technology Data Exchange (ETDEWEB)

    Ostrowski, M.C.; Richard-Foy, H.; Wolford, R.G.; Berard, D.S.; Hager, G.L.

    1983-11-01

    The mouse mammary tumor virus long terminal repeat (MMTV LTR) has been introduced into cultured murine cells, using the 69% transforming fragment of bovine papiloma virus type 1 (BVP). Transformed cells contain up to 200 copies of the chimeric molecules per diploid genome. The restriction endonuclease map of the acquired recombinants, as well as the physical structure of the DNA, indicates that the LTR-BVP molecules present in these cells occur exclusively as unintegrated, extrachromosomal episome. When a 72-base pair direct repeat ''enhancer'' element (derived from the Harvey sarcoma retrovirus) was included in the MMTV LTR-BPV chimeric plasmids, DNA acquired through transfection, with a single exception, was integrated or rearranged or both. Two approaches showed that the MMTV LTR present in the episomal state was capable of supporting glucocorticoid hormone-regulated transcription. The authors have therefore demonstrated the hormone response for the first time in a totally defined primary sequence environment. Significant differences both in the basal level of MMTV-initiated transcription and in the extend of glucocorticoid induction were observed in individual cell lines with similar episomal copy numbers. These phenotypic variations suggest that epigenetic structure is an important component of the mechanism of regulation.

  19. HTLV-1 Tax Effects on Cellular Mitotic Regulation

    Science.gov (United States)

    2007-04-12

    8217LTR are alternatively spliced and polyadenylated. Retrovirology 3:15. 19. Cavrois, M., I. Leclercq, O. Gout , A. Gessain, S. Wain-Hobson, and E...leukemia/lymphoma and approaches to therapy . Oncogene 24:6047-57. 183. Tinker-Kulberg, R. L., and D. O. Morgan. 1999. Pds1 and Esp1 control both

  20. Molecular distribution of gypsy-like retrotransposons in cotton ...

    African Journals Online (AJOL)

    PCR primers specific for conserved domains of the reverse transcriptase (RT) genes of gypsy-like retrotransposons amplified their corresponding gene in two Gossypium barbadense cultivars. Analysis with the FASTA software showed a high DNA sequence homology to pine, gypsy LTR-retrotransposon. Using the PCR ...

  1. Brief communication

    Indian Academy of Sciences (India)

    2012-01-24

    Jan 24, 2012 ... Mager DL 2007 Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet. 3 e10. Ryan FP 2011 Human endogenous retroviruses in multiple sclerosis: Potential for Novel neuro-pharmacological research. Curr. Neuropharmacol.

  2. The impact of p53 on the early stage replication of retrovirus.

    Science.gov (United States)

    Kinnetz, Michaela; Alghamdi, Faris; Racz, Michael; Hu, Wenwei; Shi, Binshan

    2017-08-09

    The function of p53 in cancer biology has been studied extensively, but its role in anti-retrovirus infection has been elusive for many years. The restriction of retrovirus early stage replication by p53 was investigated in this study. VSV-G pseudotyped retrovirus with GFP reporter gene was used to infect both HCT116 p53(+/+) cells and its isogenic p53 knockout HCT116 p53(-/-) cells. The infection was detected by flow cytometry. Reverse transcription products were quantified by real time PCR. Mutation analysis was performed after 1-LTR cycle and 2-LTR cycle DNA were amplified and PCR products were sequenced. Transcription and translation of cyclin-dependent kinase inhibitor 1 (p21(Cip1)) and SAM domain and HD domain-containing protein 1 (SAMHD1) were analyzed by TaqMan PCR and Western blot experiments. siRNA experiment was applied to study the role of p53 downstream gene p21(Cip1) in the restriction of retrovirus infection. It was found that the block of retrovirus infection in non-cycling cells was significantly attenuated in HCT116 p53(-/-) cells when compared to HCT116 p53(+/+) cells. It was found that both late reverse transcription products and viral 2-LTR cycle DNA were significantly increased in infected non-cycling HCT116 p53(-/-) cells. Furthermore, the mutation frequency detected in 1-LTR DNA from HCT116 p53(+/+) cells were significantly decreased in comparison to HCT116 p53(-/-) cells. A higher number of insertion and deletion mutations were detected in the joint region of 2-LTR cycle DNA in infected p53(+/+) cells. Cell cycle analysis showed retrovirus infection promoted host cell replication. Higher levels of mRNA and protein of p21(Cip1) were found in HCT116 p53(+/+) cells in comparison to the HCT116 p53(-/-) cells. Furthermore, knockdown of p21(Cip1) in non-cycling HCT116 p53(+/+) cells significantly increased the infection. The results of this study showed that p53 is an important restriction factor that interferes with retrovirus infection in its

  3. Using mobile health technology to deliver decision support for self-monitoring after lung transplantation.

    Science.gov (United States)

    Jiang, Yun; Sereika, Susan M; DeVito Dabbs, Annette; Handler, Steven M; Schlenk, Elizabeth A

    2016-10-01

    Lung transplant recipients (LTR) experience problems recognizing and reporting critical condition changes during their daily health self-monitoring. Pocket PATH(®), a mobile health application, was designed to provide automatic feedback messages to LTR to guide decisions for detecting and reporting critical values of health indicators. To examine the degree to which LTR followed decision support messages to report recorded critical values, and to explore predictors of appropriately following technology decision support by reporting critical values during the first year after transplantation. A cross-sectional correlational study was conducted to analyze existing data from 96 LTR who used the Pocket PATH for daily health self-monitoring. When a critical value is entered, the device automatically generated a feedback message to guide LTR about when and what to report to their transplant coordinators. Their socio-demographics and clinical characteristics were obtained before discharge. Their use of Pocket PATH for health self-monitoring during 12 months was categorized as low (≤25% of days), moderate (>25% to ≤75% of days), and high (>75% of days) use. Following technology decision support was defined by the total number of critical feedback messages appropriately handled divided by the total number of critical feedback messages generated. This variable was dichotomized by whether or not all (100%) feedback messages were appropriately followed. Binary logistic regression was used to explore predictors of appropriately following decision support. Of the 96 participants, 53 had at least 1 critical feedback message generated during 12 months. Of these 53 participants, the average message response rate was 90% and 33 (62%) followed 100% decision support. LTR who moderately used Pocket PATH (n=23) were less likely to follow technology decision support than the high (odds ratio [OR]=0.11, p=0.02) and low (OR=0.04, p=0.02) use groups. The odds of following decision

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

    Directory of Open Access Journals (Sweden)

    Sudhir Kumar Rai

    2017-12-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  6. Kinase-inducible domain-like region of HTLV type 1 tax is important for NF-kappaB activation.

    Science.gov (United States)

    Kuo, Y L; Tang, Y; Harrod, R; Cai, P; Giam, C Z

    2000-11-01

    Partial proteolysis of HTLV-1 Tax protein has revealed the region surrounding amino acid residues (88)KVL(90) to be highly exposed. The protein sequence surrounding this region ((81)QRTSKTLKVLTPPIT(95)) bears resemblance to the kinase-inducible domain (KID, (129)SRRPSYRKILNE(140)) of CREB and is involved in recruiting transcriptional coactivators, p300 and CBP, for trans-activating the viral long terminal repeat (LTR). Data have also revealed the KID-like region to be important for Tax binding to DNA. Here we report that single (K88A, V89A, L90A) and double alanine substitutions (V89A-L90A) in the (88)KVL(90) motif attenuate the ability of Tax to activate NF-kappaB. Deletions near or spanning this motif also had the same effect. The alanine substitutions affect HTLV-1 LTR activation and NF-kappaB activation differently, with K88A and V89A mutants showing much reduced activities for HTLV LTR activation while retaining attenuated but significant NF-kappaB-activating function. In contrast, although the L90A mutant is similarly attenuated for NF-kappaB activation, it showed significant activity in LTR trans-activation. Incorporation of both V89A and L90A substitutions in a V89A-L90A double mutant further reduced NF-kappaB activation and completely abrogated LTR trans-activation. In aggregate, these results demonstrate the importance of the KID-like domain of Tax and implicate its interaction with cellular factors other than p300/CBP in NF-kappaB activation.

  7. A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase - Structural and modeling insight into its functions

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hui-Guang [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States); Huang, Philip L. [American Biosciences, Boston, MA 02114 (United States); Zhang, Dawei; Sun, Yongtao [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States); Chen, Hao-Chia [Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892 (United States); Zhang, John [Department of Chemistry, New York University, New York, NY 10003 (United States); Huang, Paul L. [Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114 (United States); Kong, Xiang-Peng, E-mail: xiangpeng.kong@med.nyu.edu [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States); Lee-Huang, Sylvia, E-mail: sylvia.lee-huang@med.nyu.edu [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States)

    2010-01-01

    We report here the high-resolution atomic structures of GAP31 crystallized in the presence of HIV-LTR DNA oligonucleotides systematically designed to examine the adenosine glycosidase activity of this anti-HIV and anti-tumor plant protein. Structural analysis and molecular modeling lead to several novel findings. First, adenine is bound at the active site in the crystal structures of GAP31 to HIV-LTR duplex DNA with 5' overhanging adenosine ends, such as the 3'-processed HIV-LTR DNA but not to DNA duplex with blunt ends. Second, the active site pocket of GAP31 is ideally suited to accommodate the 5' overhanging adenosine of the 3'-processed HIV-LTR DNA and the active site residues are positioned to perform the adenosine glycosidase activity. Third, GAP31 also removes the 5'-end adenine from single-stranded HIV-LTR DNA oligonucleotide as well as any exposed adenosine, including that of single nucleotide dAMP but not from AMP. Fourth, GAP31 does not de-purinate guanosine from di-nucleotide GT. These results suggest that GAP31 has DNA adenosine glycosidase activity against accessible adenosine. This activity is distinct from the generally known RNA N-glycosidase activity toward the 28S rRNA. It may be an alternative function that contributes to the antiviral and anti-tumor activities of GAP31. These results provide molecular insights consistent with the anti-HIV mechanisms of GAP31 in its inhibition on the integration of viral DNA into the host genome by HIV-integrase as well as irreversible topological relaxation of the supercoiled viral DNA.

  8. A New Activity of Anti-HIV and Anti-tumor Protein GAP31: DNA Adenosine Glycosidase – Structural and Modeling Insight into its Functions

    Energy Technology Data Exchange (ETDEWEB)

    Li, H.; Huang, P; Zhang, D; Sun, Y; Chen, H; Zhang, J; Huang, P; Kong, X; Lee-Huang, S

    2010-01-01

    We report here the high-resolution atomic structures of GAP31 crystallized in the presence of HIV-LTR DNA oligonucleotides systematically designed to examine the adenosine glycosidase activity of this anti-HIV and anti-tumor plant protein. Structural analysis and molecular modeling lead to several novel findings. First, adenine is bound at the active site in the crystal structures of GAP31 to HIV-LTR duplex DNA with 5' overhanging adenosine ends, such as the 3'-processed HIV-LTR DNA but not to DNA duplex with blunt ends. Second, the active site pocket of GAP31 is ideally suited to accommodate the 5' overhanging adenosine of the 3'-processed HIV-LTR DNA and the active site residues are positioned to perform the adenosine glycosidase activity. Third, GAP31 also removes the 5'-end adenine from single-stranded HIV-LTR DNA oligonucleotide as well as any exposed adenosine, including that of single nucleotide dAMP but not from AMP. Fourth, GAP31 does not de-purinate guanosine from di-nucleotide GT. These results suggest that GAP31 has DNA adenosine glycosidase activity against accessible adenosine. This activity is distinct from the generally known RNA N-glycosidase activity toward the 28S rRNA. It may be an alternative function that contributes to the antiviral and anti-tumor activities of GAP31. These results provide molecular insights consistent with the anti-HIV mechanisms of GAP31 in its inhibition on the integration of viral DNA into the host genome by HIV-integrase as well as irreversible topological relaxation of the supercoiled viral DNA.

  9. Clonal isolation of different strains of mouse mammary tumor virus-like DNA sequences from both the breast tumors and non-Hodgkin's lymphomas of individual patients diagnosed with both malignancies.

    Science.gov (United States)

    Etkind, Polly R; Stewart, Alexandre F R; Dorai, Thambi; Purcell, Daniel J; Wiernik, Peter H

    2004-09-01

    In a previous study, we had detected the presence of mouse mammary tumor virus (MMTV)-like envelope (ENV) gene sequences in both the breast tumors and non-Hodgkin's lymphoma tissue of two of our breast tumor patients who had been diagnosed simultaneously with both malignancies. The aim of this study was to determine if MMTV-like DNA sequences are present in the breast tumors and non-Hodgkin's lymphomas of additional patients suffering from both malignancies and if so to characterize these sequences in detail. DNA was extracted from formalin-fixed, paraffin-embedded tissue sample blocks of breast tumors and non-Hodgkin's lymphomas from patients suffering from both malignancies. A 250-bp region of the MMTV ENV gene and a 630-bp region of the MMTV long terminal repeat (LTR) open reading frame (ORF) that encodes the MMTV superantigen (sag) gene were amplified by PCR from the isolated DNA. Amplified products were analyzed by Southern blotting, cloned, and sequenced. MMTV-like ENV and LTR sequences were detected in both the breast tumors and non-Hodgkin's lymphomas of 6 of 12 patients suffering from both malignancies. A novel mutant of the MMTV ENV gene was identified in these patients. Characterization of the MMTV-like LTR highly variable sag sequences revealed total or nearly total identity to three distinct MMTV proviruses from two different branches of the MMTV phylogenetic tree. The presence of MMTV-like ENV and LTR sequences in both the breast tumors and non-Hodgkin's lymphomas of 6 additional patients suggests a possible involvement of these sequences in these two malignancies. MMTV-like LTR sequence homology to different MMTV proviruses revealed the presence of more than one strain of MMTV-like sequences in each individual suggesting the possibility of multiple infections in these patients.

  10. Identificación de mutaciones en pacientes diagnosticados con MELAS y/o MERRF

    OpenAIRE

    Andrés Ruiz; Gabriel Bedoya Berrío; José William Cornejo Ochoa; Victoria Parra; Luis Carlos Burgos Herrera

    2001-01-01

    Además de los 3.000 millones de pares de bases del DNA nuclear, cada célula contiene múltiples copias de un genoma de 16.569 pb contenido en la mitocondria, denominado DNA mitocondrial (mtDNA). Esta organela es de vital importancia, ya que en ella se produce más del 80% de la energía celular
    a través de la cadena respiratoria y LA fosforilación oxidativa; cualquier disfunción en estos procesos puede generar una citopatía mitocondrial (1), como: encefalomiopatía mitocondria...

  11. CON LOS CALADOS [Material gráfico

    OpenAIRE

    Anonymous

    1980-01-01

    LA CONFECCIÓN DE LOS CALADOS SE REALIZÓ DENTRO DE LA UNIDAD DE PRODUCCIÓN FAMILIAR, AL MENOS HASTA 1891. YA EN 1901, EL ÉXITO PRODUCTOR Y EL AUGE EN LA DEMANDA EXTERNA, BENEFICIAN LA APERTURA DE LA PRIMERA CASA EXPORTADORA DE CALADOS INSULAR. RETRATO DE YOLANDA VALDIVIA CABRERA JUNTO A SUS CALADOS Y BORDADOS CANARIOS. Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  12. La digital library “SHOAH” dell’ Archivio Centrale dello Stato : Un progetto di recupero e di digital preservation di documenti audiovisivi di storia orale

    OpenAIRE

    Davide Merlitti; Micaela Procaccia; Umberto Parrini; Maria Emilia Masci

    2012-01-01

    ItLa digital library “Ti Racconto la Storia : Voci dalla Shoah” (sito web: http://www.shoah.acs.beniculturali.it/) è il risultato di un progetto durato diversi anni, nato con l’obiettivo di preservare e diffondere un considerevole patrimonio documentario audiovisivo che il Ministero per i Beni e le Attività Culturali ha ricevuto in copia dalla Survivors of the Shoah Visual History Foundation nell’ambito di un accordo di collaborazione. La trasformazione di un sistema software proprietario per...

  13. TELAR MANUAL HORIZONTAL. CAIDEROS [Material gráfico

    OpenAIRE

    Anonymous

    1980-01-01

    MARÍA DE LAS NIEVES TRABAJA EN EL TELAR. CONOCIÓ EL OFICIO DE LA MANO DE SU ABUELA DE LA QUE HEREDÓ SU TELAR Y HERRAMIENTAS NECESARIAS PARA EL TRABAJO DE LA LANA OFICIO EXCLUSIVAMENTE FEMENINO QUE SE PRACTICABA COMO COMPLEMENTO A LOS ESCASOS INGRESOS DE LAS ACTIVIDADES AGRÍCOLAS Y PASTOREO. ES COMÚN EL TRASPASO DE LA ABUELA A LA NIETA, PUES ÉSTA CUENTA CON LA EDAD PARA ENCARGARSE DEL TELAR CUANDO LA ABUELA COMIENZA A SER DEMASIADO MAYOR. Copia digital. Madrid : Ministerio de Educación,...

  14. Decreto de libros prohibidos del Papa Alejandro VII

    OpenAIRE

    2012-01-01

    "Alexander Papa Septimus ad perpetuam furor an Rei memoriam [...]" Manuscrito. -- 2 hs. [P.V. 3 - ff. 241-242v.] [f. 243-243v. en bl.] : Papel; 200x295mm. -- Conservación regular, manchas de oxidación Texto en Latín. -- Copia de obra impresa en la Imprenta Apostólica de Roma. Vivas Moreno, Agustín. "Fondos documentales del Archivo Histórico de la Universidad de Salamanca. La colección de Papeles Varios: análisis descriptivo, tesauro y gestión documental automatizada". Tesis doctoral,...

  15. Arte y síndrome de Down

    OpenAIRE

    Pachajoa Londoño, Harry Mauricio

    2011-01-01

    El síndrome de Down es la alteración cromosómica más frecuente y se presenta en 1 de cada 700 nacimientos vivos, es la primera causa de retardo mental de origen genético, caracterizado por retardo mental y características físicas típicas como braquicefalia, occipucio plano, fisuras palpebrales inclinadas hacia arriba, pliegues epicanticos y orejas de implantación baja entre otras, causadas por una copia extra del cromosoma

  16. Manuscritos americanos de la Biblioteca Histórica: Relaciones Históricas de Fernando de Alva Ixtlilxóchitl. American manuscripts at the Biblioteca Historica: Fernando de Alva Ixtlilxóchitl´s Historical Works

    OpenAIRE

    Ysern de la Calle, Javier

    2014-01-01

    Fernando de Alva Ixtlilxóchitl (1578-1648) fue uno de los primeros mestizos en investigar acerca de la historia de sus antepasados. Presentadas tradicionalmente de forma conjunta bajo el título de Obras o Relaciones Históricas, Alva Ixtlilxóchitl escribió diversas relaciones que pasaron de mano en mano durante décadas hasta perderse. Debido a su valor documental, a lo largo de los siglos se realizaron numerosas copias que a su vez se han reproducido nuevamente otras tantas veces. En este artí...

  17. Los manuscritos americanos de la Biblioteca Histórica "Marqués de Valdecilla" UCM

    OpenAIRE

    Cabello Martín, Mercedes; Diez Baños, Aurora; Torres Santo Domingo, Marta

    2013-01-01

    La Biblioteca Histórica de la Universidad Complutense de Madrid posee un pequeño conjunto de diecisiete manuscritos americanos, bien copiados en América o de tema americano. Entre ellos destacan algunas piezas excepcionales, como una copia de la Materia Medicinal de Francisco Hernández del siglo XVI, una crónica del noble indígena Fernando Alva Ixtlilxochitl del siglo XVII, o el conjunto de papeles relativos a la conspiración de La Guaira, de finales del siglo XVIII. Entre los manuscritos del...

  18. Manuscritos americanos de la Biblioteca Histórica: Relaciones Históricas de Fernando de Alva Ixtlilxóchitl

    OpenAIRE

    Ysern de la Calle, Javier

    2014-01-01

    Fernando de Alva Ixtlilxóchitl (1578-1648) fue uno de los primeros mestizos en investigar acerca de la historia de sus antepasados. Presentadas tradicionalmente de forma conjunta bajo el título de Obras o Relaciones Históricas, Alva Ixtlilxóchitl escribió diversas relaciones que pasaron de mano en mano durante décadas hasta perderse. Debido a su valor documental, a lo largo de los siglos se realizaron numerosas copias que a su vez se han reproducido nuevamente otras tantas veces. En este artí...

  19. Lyonización desfavorable: A propósito de una familia con retinosis pigmentaria Unfavorable lyonization: Apropos of a family with retinitis pigmentosa

    OpenAIRE

    Rubén Rangel Fleites; Noel Taboada Lugo; Carlos Lima León; Gladys Membrides Pérez

    2005-01-01

    Durante muchos años la expresión de los genes ligados al cromosoma x representó una incógnita para los genetistas. Si bien los varones poseen sólo una copia de cada gen ligado al x, en tanto que las mujeres tienen dos, la cantidad de producto formado por un solo alelo en el varón o por un par de alelos en la mujer era equivalente. Finalmente esto fue explicado con la formulación del principio de inactivación del cromosoma x, que conlleva a tres consecuencias importantes: compensación de dosis...

  20. Genetic background of hereditary cutaneous hyaluronosis and familial shar pei fever

    OpenAIRE

    Martínez Díaz, Verónica Lucía

    2015-01-01

    Los perros de raza Shar Pei tienen dos características fenotípicas propias de la raza que son las arrugas de la piel (ahora conocido como Hialuronosis Cutánea Hereditaria-HCH) y un desorden genético llamado Fiebre Familiar del Shar Pei (FSF) que se cree que es causada por un exceso de Ácido Hialurónico (HA). El origen genético se describe como una mutación reguladora (Variación Número de Copias- CNV) localizada upstream del gen que sintetiza HA (HAS2) en el cromosoma 13. Se construyó un model...

  1. Entre o plágio e a autoria: qual o papel da universidade?

    OpenAIRE

    Silva,Obdália Santana Ferraz

    2008-01-01

    Este estudio tiene como finalidad discutir sobre el plagio en el contexto académico, entretanto, hecho que viene afirmándose significativamente a partir de los hipertextos digitales, y considerando que, a medida que textos de todos los tipos, se refieren a las varias áreas del conocimiento, circulan velozmente por la red, se van ampliando entre los graduados las facilidades de hacerse copias, en detrimento de la construcción de la autoría. En la intención de c...

  2. Plano Oficial de Urbanización de Algarrobo, 1950: urbanismo saludable y visión de futuro para un balneario de la antigua Provincia de Santiago (Chile / Official Plan of Private Algarrobo, 1950: healthy urban planning and vision for a resort of the old Province of Santiago (Chile.

    Directory of Open Access Journals (Sweden)

    Pavez Reyes, María Isabel

    2006-11-01

    Full Text Available Se analiza el proyecto urbano para la comuna de Algarrobo (Chile, aprobado en 1950, a partir de copia matriz de plano en Archivo Histórico del departamento de Urbanismo FAU. U. de Chile. A cargo de esta planificación estuvo la Sección de Urbanismo del Departamento de Arquitectura de la D.G.O.P., dirigida por el Arqto. Luis Muñoz Maluschka./This article analyzes the project for Algarrobo approved in 1950 when Luis Muñoz M. was in charge of the plan management.

  3. DETALLE DEL TALLER DE RAFAEL TORRES OSORIO [Material gráfico

    OpenAIRE

    Anonymous

    1988-01-01

    EL TALLER RAFAEL TORRES E HIJO ESTÁ DIVIDIDO EN DOS ESTANCIAS. EN UNA DE ELLAS SE LOCALIZAN LAS HERRAMIENTAS NECESARIAS PARA LA ELABORACIÓN DE LA HOJA DEL CUCHILLO CANARIO, EN LA OTRA SE ENCUENTRAN LAS HERRAMIENTAS DESTINADAS A LA ELABORACIÓN D LOS CABOS. EL TALLER SE ENCUENTRA EN LA CALLE JOSÉ SAMSO HENRÍQUEZ, Nº 42, SANTA MARÍA DE GUÍA Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  4. Los manuscritos de El yo y el ello : Una relectura del Icc

    OpenAIRE

    Cosentino, Juan Carlos

    2012-01-01

    Indagamos, a partir de los manuscritos inéditos de Das Ich und das Es, los puntos eminentes instaurados por la lectura de sus tres versiones: borrador, copia en limpio y texto publicado, en el momento en que surge una disimetría entre lo reprimido-icc y un Icc no-todo reprimido. Estos documentos revelan una transcripción 'casi' directa de las formulaciones freudianas en un estado naciente que llevan la marca de pensamientos urgidos por lo real del psicoanálisis, cuando todavía no está present...

  5. Los manuscritos de El yo y el ello: una relectura del Icc

    OpenAIRE

    Cosentino, Juan Carlos

    2012-01-01

    Indagamos, a partir de los manuscritos inéditos de Das Ich und das Es, los puntos eminentes instaurados por la lectura de sus tres versiones: borrador, copia en limpio y texto publicado, en el momento en que surge una disimetría entre lo reprimido-icc y un Icc no-todo reprimido. Estos documentos revelan una transcripción 'casi' directa de las formulaciones freudianas en un estado naciente que llevan la marca de pensamientos urgidos por lo real del psicoanálisis, cuando todavía no está present...

  6. SIMÓN TALAVERA SUÁREZ [Material gráfico

    OpenAIRE

    Anonymous

    2002-01-01

    RETRATO DE SIMÓN TALAVERA SUÁREZ CON UN ENJAMBRE DE ABEJAS, EN CORRALILLOS. SIMÓN TALAVERA SUÁREZ LLEVA DESDE LOS 7 AÑOS EN EL OFICIO DE APICULTOR, SE TRATA DE UNA TRADICIÓN FAMILIAR. LA APICULTURA O EL CULTIVO DE ABEJAS ES UNA ACTIVIDAD AGROPECUARIA ORIENTADA A LA CRIANZA ABEJAS Y A PRESTARLES LOS CUIDADOS NECESARIOS CON EL OBJETO DE OBTENER LOS PRODUCTOS QUE SON CAPACES DE ELABORAR Y RECOLECTAR. Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección Gener...

  7. Caracterización de variantes genómicas. Aplicación de nuevas tecnologías al estudio del retraso mental.

    OpenAIRE

    Madrigal Bajo, Irene

    2008-01-01

    Estudios recientes han permitido estimar que aproximadamente un 5% del genoma consiste en duplicaciones segmentarias (DS), secuencias de entre 1-100 kb con un nivel de similitud de más del 95% (Eichler, 2001). Las regiones flanqueadas por duplicaciones segmentarias son susceptibles de sufrir reordenamientos mediante recombinación homóloga no alélica y se ha hipotetizado que estas regiones representan puntos calientes de inestabilidad genómica propensos a variación en número de copia (CNVs). E...

  8. El “núcleo duro” de los fascismos periféricos en América Latina

    OpenAIRE

    López de la Torre, Carlos Fernando

    2017-01-01

    El presente trabajo analiza la estructura ideológica y la praxis política de las experiencias fascistas que se desarrollaron en América Latina en la primera mitad del siglo XX, desde el periodo de entreguerras hasta los primeros años de la Guerra Fría. Al retomar los componentes que los conforman, el “núcleo duro” que dirige sus ideales y acciones, se muestra que los fascismos latinoamericanos no fueron simples copias de los europeos. Por el contrario, fueron resultado de una realidad local c...

  9. HÁBITO DE LAS MARÍAS [Material gráfico

    OpenAIRE

    Anonymous

    2005-01-01

    EL HÁBITO ES UNA PIEZA VESTIDA POR UNA PROMESA O AGRADECIMIENTO A LOS FAVORES CONCEDIDOS POR LOS SANTOS O VIRGEN A LOS QUE SE TIENE DEVOCIÓN. EL MODELO IMITA EL TRAJE QUE LLEVA LA IMAGEN VENERADA. LA DIVULGACIÓN DE INFORMACIÓN SOBRE LA VESTIMENTA TRADICIONAL HA REPERCUTIDO EN LA CALIDAD Y VARIEDAD DE LOS TRAJES TRADICIONALES CANARIOS Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  10. Fragmentos de paisaje y arquitectura. El pabellón de Ciudad Real en la II F.I.C. Madrid, 1953

    OpenAIRE

    Coca Leicher, José de

    2010-01-01

    RESUMEN Miguel Fisac, dispone un conjunto de piezas que recrean la esencia del paisaje manchego superando la simple copia de los arquetipos populares. El hueco entre dos tapias encaladas y una señal de carretera invitan al visitante del pabellón a iniciar un recorrido hacia la abstracción que nos sumergirá en un nuevo paisaje físico y mental. Mediante texto y dibujos propios, se reconstituye el desconocido pabellón, necesario eslabón en su obra del "periodo experimental" hoy lamentablemente ...

  11. RELACIONES ENTRE EL APARATO DE GOLGI Y LA MITOSIS: PAPEL DE LA GOLGINA P115 EN LA ACTIVACION DE CDK1 Y EL PUNTO DE CONTROL G2/M D ELA MITOSIS EN DROSOPHILA

    OpenAIRE

    Ibar ValenZuela, MARÍA CONSUELO

    2013-01-01

    Las células eucariontes tienen organelos derivados de membrana dentro de los cuales se encuentra el retículo endoplasmático y el aparato de Golgi, los cuales les permiten separar y organizar las distintas funciones celulares. Estos organelos tienen que ser mantenidos en las células hijas durante la división celular, generando las preguntas: ¿qué ocurre cuando las células se dividen? ¿se dividen los organelos existentes o nuevas copias son generadas? ¿cómo esto se encuentra acop...

  12. Dai fondi privati di Modena agli archivi di Addis Abeba. Un progetto per censire, condividere e restituire un passato comune

    Directory of Open Access Journals (Sweden)

    Marzia Maccaferri

    2013-06-01

    Full Text Available Return and Sharing memories è un progetto pilota che intende restituire al popolo etiope la memoria storica dell’effimero impero italiano nel Corno d'Africa (1935-1941. Punto di partenza del progetto è duplicare le testimonianze fotografiche raccolte a Modena e donarne copia all’Università di Addis Abeba, mettendole a disposizione di ricercatori e studenti. L’obbiettivo è affrontare gli studi coloniali da una prospettiva diversa, attraverso la condivisione della memoria storica con gli ex-nemici, favorendo lo studio congiunto del passato che accomuna Etiopia e Italia.

  13. Marie Darrieussecq, Rapporto di polizia. Le accuse di plagio e altri metodi di controllo della scrittura

    Directory of Open Access Journals (Sweden)

    Niccolò Scaffai

    2012-04-01

    Full Text Available A Marie Darrieussecq è successo qualcosa di strano. Non è il fatto di essere nata in Francia, a Bayonne, nel 1969. Né di essere una scrittrice (oltre che una studiosa di letteratura e una psicanalista, che ha pubblicato fiction, racconti autobiografici, saggi letterari. Questo non è così strano. Lo è invece il fatto che metà dei suoi romanzi siano stati considerati, da lettori diversi e soprattutto da altri scrittori, prodotti di «imitazione», «copia», «plagio psichico», o addirittura di «sottrazione di manoscritto»

  14. Herramienta para la generación aleatoria de enunciados de examen de tipo test

    OpenAIRE

    Lima Díez, Sandra

    2016-01-01

    Las pruebas de evaluación de algunas asignaturas en la Escuela Técnica Superior de Ingenieros Informáticos de la Universidad Politécnica de Madrid se realizan mediante exámenes de tipo test que contienen diferentes ejercicios relacionados con el temario impartido. Es habitual generar diferentes versiones del mismo examen que se reparten en un orden determinado entre todos alumnos con el fin de evitar la copia de resultados y por ello se requiere que el mismo contenido de la pru...

  15. Expresión de la procedencia en lenguas indoeuropeas antiguas: latín, griego e hitita

    OpenAIRE

    González Saavedra, Berta

    2016-01-01

    La tesis doctoral tiene como objetivo mostrar la dispersión semántica de tres marcas relacionadas con el ámbito de la Procedencia. Corresponden a tres lenguas indoeuropeas antiguas y no están relacionadas etimológicamente entre sí. Las marcas estudiadas son el ablativo latino en las comedias de Plauto (salvo la Vidularia), el sufijo griego ¿then en la Ilíada y la Odisea y el ablativo hitita en textos de hitita antiguo y copias manuscritas de hitita antiguo realizadas en épocas posteriores. Pa...

  16. Expresión de la procedencia en lenguas indoeuropeas antiguas: latín, griego e hitita

    OpenAIRE

    González Saavedra, Berta

    2015-01-01

    La tesis doctoral tiene como objetivo mostrar la dispersión semántica de tres marcas relacionadas con el ámbito de la Procedencia. Corresponden a tres lenguas indoeuropeas antiguas y no están relacionadas etimológicamente entre sí. Las marcas estudiadas son el ablativo latino en las comedias de Plauto (salvo la Vidularia), el sufijo griego ¿then en la Ilíada y la Odisea y el ablativo hitita en textos de hitita antiguo y copias manuscritas de hitita antiguo realizadas en épocas posteriores. Pa...

  17. Conciencia agente: cómo sabemos lo que hacemos

    Directory of Open Access Journals (Sweden)

    Antoni Gomila

    2008-02-01

    Full Text Available ¿Cómo distinguimos qué movimientos son voluntarios y cuáles no? Gracias al trabajo de Sato y Yasuda (2005 sobre los factores determinantes de nuestra experiencia agente, parece que la clave está en que anticipamos de manera automática la estimulación sensorial propioceptiva que debe seguir a determinada intención motora, en una escala temporal muy precisa. Sus resultados avalan el modelo cibernético de control motor denominado "del modelo interno y la copia de eferencia".

  18. Difusión y reproducción digital de obras de arte por medio de bibliotecas virtuales y consecuencias de una nueva revolución cultural

    OpenAIRE

    Galán, Ilia

    2009-01-01

    Ponencias de la Segunda Conferencia internacional sobre brecha digital e inclusión social, celebrada del 28 al 30 de octubre de 2009 en la Universidad Carlos III de Madrid La clonación de obras de arte que permite reproducirlas indefinidamente por medios digitales sin que puedan distinguirse originales y copias es algo posible desde hace muy poco por medio de algunas empresas, como FACTUM ARTE. La indistinción hace que una obra antes exclusiva de unos pocos pueda ser ahora patrimonio de to...

  19. PATIO DE LA CASA DEL CAPITÁN QUESADA [Material gráfico

    OpenAIRE

    Anonymous

    1980-01-01

    LA CONSTRUCCIÓN DE LA CASA DATA DEL SIGLO XVIII. CONSTA DE DOS PLANTAS CON PUERTAS Y VENTANAS DE MADERA. ES UNO DE LOS EJEMPLOS DE LA ARQUITECTURA DOMÉSTICA DEL MUNICIPIO, POR ELLO FUE DECLARADA BIEN DE INTERÉS CULTURAL. RUIZ DE QUESADA FUE UN IMPORTANTE CAPITÁN DE LAS MILICIAS, ADEMÁS EJERCIÓ COMO MECENAS DEL TEMPLO DE SANTIAGO DE LOS CABALLEROS. ANEXO SELLO DE LA COMISIÓN DEL PATRIMONIO HISTÓRICO ARTÍSTICO DE GÁLDAR. Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte...

  20. CASA DEL CAPITÁN DON ESTEBAN RUIZ DE QUESADA [Material gráfico

    OpenAIRE

    Anonymous

    1980-01-01

    ESTEBAN RUIZ DE QUESADA FUE BENEFACTOR DE SU CIUDAD Y PRINCIPAL PROMOTOR DEL ACTUAL TEMPLO DE SANTIAGO DE LOS CABALLEROS. ANEXO SELLO DE LA COMISIÓN DEL PATRIMONIO HISTÓRICO ARTÍSTICO DE GÁLDAR. PATRIMONIO GALDENSE DEL SIGLO XVIII, ES UNO DE LOS EJEMPLOS DE LA ARQUITECTURA DOMÉSTICA DEL MUNICIPIO. CONSTA DE DOS PLANTAS CON PUERTAS Y VENTANAS DE MADERA. Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 2015

  1. SGSI : Cotecom

    OpenAIRE

    Grassot Roselló, Esteve

    2014-01-01

    Implantació d'un sistema de gestió de la seguretat informàtica que cobreixi el personal, equips informàtics, el CPD, la sala de comunicacions, còpies de seguretat, armaris de xarxa, electrònica de xarxa, servidors, serveis i dades de Cotecom. Implantación de un sistema de gestión de la seguridad informática que cubra al personal, equipos informáticos, el CPD, la sala de comunicaciones, copias de seguridad, armarios de red, electrónica de red, servidores, servicios y datos de Cotecom. Ma...

  2. Cuba, nuestra revolución

    Directory of Open Access Journals (Sweden)

    Sebastián Salazar Bondy

    2011-05-01

    Full Text Available Texto de un folleto publicado en 1962 por Ediciones de la Patria Libre, dirigidas porManuel Scorza. Redactado en forma de carta, se trata de un texto revelador de la actitudde la intelectualidad peruana (y latinoamericana ante la entonces reciente revolucióncubana. Cuarenta años después, los lectores elaborarán sus propias reflexiones. Lapublicación del texto fue sugerida por el doctor Raymundo Prado, quien ademásproporcionó copia del mismo. Agradecemos a la señora Irma Lostanau por su gentilezaal autorizarnos a publicarlo.

  3. EVALUATION OF FRINGE PROJECTION AND LASER SCANNING FOR 3D RECONSTRUCTION OF DENTAL PIECES

    OpenAIRE

    NATALIA MÚNERA; GABRIEL J. LORA; JORGE GARCIA-SUCERQUIA

    2012-01-01

    La generación rápida de prototipos y la copia de objetos 3D reales desempeñan un papel clave en algunas industrias. Ambas aplicaciones se basan en la producción de archivos apropiados de fabricación asistida por computadora (CAM). Estos archivos representan un conjunto de coordenadas del objeto y que pueden ser entendidos por máquinas de control numérico (CNC). Técnicas de no contacto, como el escaneo láser y la proyección de franjas, se cuentan entre las posibilidades de generar los archivos...

  4. Una marca de agua inteligente aplicada al dinero electrónico

    OpenAIRE

    Jaimes, Patricia; Hermosillo, Gabriel; Roberto, Gomez

    2009-01-01

    International audience; El uso de las marcas de agua se ha incrementado, principalmente por la necesidad de proteger los derechos de autor, detener copias ilegales o medir la integridad de los datos de ciertos archivos. Es bien sabido que se puede insertar código ejecutable en imágenes, pero hasta ahora solamente se ha estudiado como una amenaza de seguridad para el usuario. Nosotros proponemos utilizar esta característica de manera segura para expandir las aplicaciones actuales de las marcas...

  5. Veterinaria.org y REDVET se podrá acceder desde cualquier idioma ademas del español.

    OpenAIRE

    Veterinaria.org

    2009-01-01

    ResumenVeterinaria.org se conoce como la Primera Comunidad VeterinariaLatinoamericana y como el Primer portal vertical en español para el sector veterinario; igualmente creó como medio de expresión oficial la Revista Electrónica de Veterinaria REDVET que es la primera revista científica en formato digital y en español dirigida a veterinarios siendo además de libre acceso pues se edita bajo la licencia «Creative Commons», que permite el uso y copia de sus contenidos con la única condición de c...

  6. Bellezas prestadas: La colección nacional de reproducciones artísticas

    Directory of Open Access Journals (Sweden)

    Bolaños, María

    2013-12-01

    Full Text Available The role of the copy in the history of art; museums of art reproductions and the Spanish collection at the end of the 19th century; the phenomenon of the copy in ancient Rome and in the successive rebirths and recoveries of the classic in the Western tradition; historical and conceptual paradoxes that encloses the reproduction of sculptures; the incorporation of the national collection of casts to he National Museum of Sculpture.Del papel de la copia en la historia del arte; de los museos de reproducciones artísticas en Europa y de la colección española fundada a fines del siglo XIX; del fenómeno de la copia en la antigua Roma y en los sucesivos renacimientos y recuperaciones de lo antiguo que han pautado la tradición occidental; de las paradojas históricas y conceptuales que encierra la reproducción de esculturas; de la incorporación de la colección nacional de vaciados a los fondos del Museo Nacional de Escultura.

  7. Más allá del blanco y negro. Estudio histórico de fotografías coloreadas y su conservación

    Directory of Open Access Journals (Sweden)

    Enara Artetxe Sánchez

    2010-08-01

    Full Text Available La gran mayoría de las colecciones fotográficas antiguas poseen copias coloreadas a mano. El estudio de dichas imágenes y su intervención han sido objeto de estudio en dos proyectos de investigación avalados por el MEC y la UPV/EHU que han sido llevados a cabo por investigadores y profesores de la Universidad del País Vasco. Dichos proyectos han evaluado el efecto de los tratamientos más comunes de conservación-restauración de papel tanto sobre los procedimientos pictóricos seleccionados (acuarelas y óleos como sobre los componentes de la imagen fotográfica en papeles salados, albúminas y copias a la gelatina de revelado químico. Además, este trabajo ha dado como resultado una tesis doctoral presentada en el Departamento de Pintura de la UPV/EHU en el 2009.

  8. Molecular cytogenetic analysis of Podocarpus and comparison with other gymnosperm species.

    Science.gov (United States)

    Murray, Brian G; Friesen, Nikolai; Heslop-Harrison, J S Pat

    2002-04-01

    DNA sequences have been mapped to the chromosomes of Podocarpus species from New Zealand and Australia by fluorescent in situ hybridization. Unlike other conifers, these species show only one pair of major sites of 45S rDNA genes, and two additional minor sites were seen in the Australian P. lawrencei. Unusually, 45S sequences collocalize to the same chromosomal region as the 5S rDNA. The telomere probe (TTTAGGG)n hybridizes to the ends of all chromosomes as well as to a large number of small sites distributed along the length of all chromosomes. Two other simple sequence repeats, (AAC)5 and (GATA)4, show a diffuse pattern of hybridization sites distributed along chromosomes. Southern blots using a variety of probes obtained from the reverse transcriptase of retroelements (gypsy, copia and LINE) from P. totara, P. nivalis and Dacrycarpus dacrydioides show that these retroelements are abundant and widespread in Podocarpaceae and also in others conifers. Some retroelements such as copia pPonty3 and gypsy pPot1li are more abundant in the genome of Picea abies and Ginkgo biloba than in the species from which they were amplified.

  9. Un nuevo Van Dyck en la Casa Consistorial de Palma de Mallorca: El martirio de San Sebastián del Conde de Monterrey

    Directory of Open Access Journals (Sweden)

    Díaz Padrón, Matías

    2012-09-01

    Full Text Available The author identifies the large canvas of the Martyrdom of Saint Sebastian in the town hall of Palma de Mallorca, considered to be a copy for the past 300 years. Neither the quality of this work nor its prestigious origin were known. Now it is possible to trace it to the collection of the count of Monterrey, contemporary with the artist. The devotion to this saint on both the island and Peninsula explains the considerable number of versions, replicas and copies in Spain. Documentary and formal sources and the preparatory drawings for this successful composition are also discussed.El autor identifica el Martirio de San Sebastián, lienzo de gran tamaño, que consta como copia desde hace tres siglos en la Casa Consistorial de Palma de Mallorca. No se tenía conciencia de su calidad ni del prestigioso origen que hoy localizamos en la colección del conde de Monterrey, contemporáneo del pintor. Estudia la devoción al santo en la isla y en España que explica el gran número de versiones, réplicas y copias vinculadas con el ambiente hispano. También trata las fuentes documentales y formales y los dibujos preparatorios de esta afortunada composición en la producción del maestro.

  10. Sensibilidad del equipo Cobas AmpliScreenTM HIV-1 Test, v1.5, para la detección de HIV-1

    Directory of Open Access Journals (Sweden)

    Lucía P Gomez

    Full Text Available Las técnicas de amplificación de ácidos nucleicos (NAT se incorporaron en los bancos de sangre para reducir el riesgo residual de transmisión de infecciones por vía transfusional. La cocirculación de distintas variantes del HIV-1 en Argentina indica la necesidad de evaluar la sensibilidad de los ensayos serológicos y moleculares disponibles para su detección. En este trabajo se evaluó la sensibilidad del equipo COBAS AmpliScreenTM HIV-1 Test, versión 1.5 (Roche, para detectar ARN viral en plasmas de individuos infectados con HIV-1 de Argentina. Los resultados demuestran que esta técnica tiene una alta sensibilidad para detectar ARN de HIV-1 en las condiciones ensayadas: para ensayo de mini-pooles (pooles = 50 copias de ARN/ml, la sensibilidad fue = 92 %, y para procedimiento estándar (plasmas = 207 copias de ARN/ml, la sensibilidad fue 100 %. Además, la técnica COBAS AmpliScreenTM HIV-1 Test, versión 1.5 (Roche, es adecuada para la detección de las variantes de HIV-1 prevalentes.

  11. 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.

  12. Laboratory Technology Research: Abstracts of FY 1996 projects

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    The Laboratory Technology Research (LTR) program supports high-risk, multidisciplinary research partnerships to investigate challenging scientific problems whose solutions have promising commercial potential. These partnerships capitalize on two great strengths of this country: the world-class basic research capability of the DOE Energy Research (ER) multi-program national laboratories and the unparalleled entrepreneurial spirit of American industry. Projects supported by the LTR program are conducted by the five ER multi-program laboratories: Argonne, Brookhaven, Lawrence Berkeley, Oak Ridge, and Pacific Northwest National Laboratories. These projects explore the applications of basic research advances relevant to Department of Energy`s (DOE) mission over a full range of scientific disciplines. The program presently emphasizes three critical areas of mission-related research: advanced materials, intelligent processing/manufacturing research, and sustainable environments.

  13. Laboratory technology research: Abstracts of FY 1998 projects

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-11-01

    The Laboratory Technology Research (LTR) program supports high-risk, multidisciplinary research partnerships to investigate challenging scientific problems whose solutions have promising commercial potential. These partnerships capitalize on two great strengths of the country: the world-class basic research capability of the DOE Office of Science (SC) national laboratories and the unparalleled entrepreneurial spirit of American industry. Projects supported by the LTR program in FY 1998 explore the applications of basic research advances relevant to DOE`s mission over a full range of scientific disciplines. The program presently emphasizes three critical areas of mission-related research: advanced materials, intelligent processing and manufacturing research, and environmental and biomedical research. Abstracts for 85 projects are contained in this report.

  14. Loop transfer recovery for general observer architecture

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Søgaard-Andersen, Per; Stoustrup, Jakob

    1991-01-01

    A general and concise formulation is given of the loop transfer recovery (LTR) design problem based on recovery errors. Three types of recovery errors are treated: open loop recovery, sensitivity recovery and input-output recovery errors. The three corresponding versions of the asymptotic recovery...... recovery cases. This general recovery formulation covers all known observer based compensator types as special cases. The conditions given in this setting are effectively the aim of all known LTR design methods. The recovery formulation is interpreted in terms of a modelmatching problem as well, which...... is examined by means of the Q-parametrization. It is shown how the general controller obtained by the Q-parametrization can be written as a Luenberger observer based controller. In all cases, n controller states suffice to achieve recovery. The compensators are characterized for errors both on the input...

  15. Natural history of the ERVWE1 endogenous retroviral locus

    Directory of Open Access Journals (Sweden)

    Duret Laurent

    2005-09-01

    Full Text Available Abstract Background The human HERV-W multicopy family includes a unique proviral locus, termed ERVWE1, whose full-length envelope ORF was preserved through evolution by the action of a selective pressure. The encoded Env protein (Syncytin is involved in hominoid placental physiology. Results In order to infer the natural history of this domestication process, a comparative genomic analysis of the human 7q21.2 syntenic regions in eutherians was performed. In primates, this region was progressively colonized by LTR-elements, leading to two different evolutionary pathways in Cercopithecidae and Hominidae, a genetic drift versus a domestication, respectively. Conclusion The preservation in Hominoids of a genomic structure consisting in the juxtaposition of a retrotransposon-derived MaLR LTR and the ERVWE1 provirus suggests a functional link between both elements.

  16. Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

    DEFF Research Database (Denmark)

    Gresham, D.; Usaite, Renata; Germann, S.M.

    2010-01-01

    To study adaptive evolution in defined environments, we performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications and delet......To study adaptive evolution in defined environments, we performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications....... Extrachromosomal DNA circles (GAP1(circle)) contain GAP1, the replication origin ARS1116, and a single hybrid LTR derived from recombination between the two flanking LTRs. Formation of the GAP1(circle) is associated with deletion of chromosomal GAP1 (gap1 Delta) and production of a single hybrid LTR at the GAP1...

  17. In vitro cow uterine response to Escherichia coli, leukotrienes and cytokines.

    Science.gov (United States)

    Korzekwa, A J; Łupicka, M; Socha, B M-; Szczepańska, A A; Piotrowicz, E; Barański, W

    2016-12-01

    The aim was to determine the dynamic profile of interactions between Escherichia coli (E. coli) and the actions of leukotrienes (LTs) and TNF and INFγ (cytokines) in the uterus in vitro. Uterine explants (N=6) were incubated for 2, 12 and 24h either as E. coli-treated (10 6 CFU) or non-treated and/or with: LTB 4 and C 4 (10 -6 M, for both LTs), LTs receptors antagonists (aLTR; 10 -6 M) and/or cytokines (each 10ng/ml). Toll Like Receptor 4 (TLR4) mRNA expression increased in explants incubated with E. coli, cytokines and LTs after 2 and 12h and aLTR inhibited the effect of LTs in explants incubated with E. coli (Pcytokines after 2h and cytokines with LTs after 12h (Pcytokines, with LTs (Pcytokines participate in this process. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Retention and patient engagement models for different treatment modalities in DATOS.

    Science.gov (United States)

    Joe, G W; Simpson, D D; Broome, K M

    1999-12-01

    A model to explain treatment retention in terms of process components--therapeutic involvement and session attributes for the 1st month--and patient background factors were tested in long-term residential (LTR), outpatient drug free (ODF), and outpatient methadone (OMT) treatments. The data was collected in the national Drug Abuse Treatment Outcome Studies (DATOS), and included 1362 patients in LTR, 866 in ODF, and 981 in OMT programs. Structural equation models showed there were positive reciprocal effects between therapeutic involvement and session attributes in all three modalities, and these variables had direct positive effects on treatment retention. Motivation at intake was a strong determinant of therapeutic involvement. Other patient background factors were significantly related to retention, including pretreatment depression, alcohol dependence, legal pressure, and frequency of cocaine use.

  19. HIV transcription is induced in dying cells

    Energy Technology Data Exchange (ETDEWEB)

    Woloschak, G.E.; Chang-Liu, Chin-Mei [Argonne National Lab., IL (United States); Schreck, S. [Argonne National Lab., IL (United States)]|[Univ. of South Carolina, Columbia, SC (United States). Dept. of Chemistry

    1995-06-01

    Using HeLa cells stably transfected with an HIV-LTR-CAT construct, we demonstrated a peak in CAT induction that occurs in viable (but not necessarily cell-division-competent) cells 24 h following exposure to some cell-killing agents. {gamma} rays were the only cell-killing agent which did not induce HIV transcription; this can be attributed to the fact that {gamma}-ray-induced apoptotic death requires functional p53, which is not present in HeLa cells. For all other agents, HIV-LTR induction was dose-dependent and correlated with the amount of cell killing that occurred in the culture. 14 refs., 4 figs., 1 tab.

  20. GADD45 proteins inhibit HIV-1 replication through specific suppression of HIV-1 transcription.

    Science.gov (United States)

    Liang, Zhibin; Liu, Ruikang; Zhang, Hui; Zhang, Suzhen; Hu, Xiaomei; Tan, Juan; Liang, Chen; Qiao, Wentao

    2016-06-01

    GADD45 proteins are a group of stress-induced proteins and participate in various cellular pathways including cell cycle regulation, cell survival and death, DNA repair and demethylation. It was recently shown that HIV-1 infection induces the expression of GADD45 proteins. However, the effect of GADD45 on HIV-1 replication has not been studied. Here, we report that overexpression of GADD45 proteins reduces HIV-1 production through suppressing transcription from the HIV-1 LTR promoter. This inhibitory effect is specific to HIV-1, since GADD45 proteins neither inhibit the LTR promoters from other retroviruses nor reduce the production of these viruses. Knockdown of endogenous GADD45 modestly activates HIV-1 in the J-Lat A72 latency cell line, which suggests GADD45 proteins might play a role in maintaining HIV-1 latency. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Impact of late-to-refill reminder calls on medication adherence in the Medicare Part D population: evaluation of a randomized controlled study

    Directory of Open Access Journals (Sweden)

    Taitel MS

    2017-02-01

    Full Text Available Michael S Taitel, Ying Mu, Angshuman Gooptu, Youbei Lou Health Analytics, Research & Reporting, Walgreen Co., Deerfield, IL, USA Objectives: This study evaluates a nationwide pharmacy chain’s late-to-refill (LTR reminder program that entails local pharmacists placing reminder calls to Medicare Part D patients. Methods: We conducted a randomized controlled study among 735,218 patients who exhibited nonadherent behavior by not refilling a maintenance medication 3 days from an expected refill date. Patients were randomly assigned to an intervention group who received LTR reminder calls or to a control group. We used Walgreens pharmaceutical claims data from 2015 to estimate the impact of LTR calls on short-term and annual adherence. Results: The initial refill rate within the first 14 days of the expected refill date significantly increased in the intervention group by 22.8% (6.09 percentage points compared to the control group (P<0.001. The proportion of days covered (PDC in the intervention group increased significantly by 1.5% (0.856 percentage points relative to the control group (P<0.001 over 365 days. Patients in the intervention group were significantly more adherent (PDC ≥80% by 3% (0.97 percentage points compared to the control group (P<0.001. Over a 270-day follow-up period, persistence significantly increased by 2.15 days in the intervention group (P<0.001. Conclusion: Results from this study suggest that LTR reminder calls increased adherence for Medicare Part D patients who are late in refilling their medications and therefore have the potential to reduce their risk for hospitalization and health care costs. Additionally, the intervention increased the number of patients with PDC ≥80% by ~3%, positively impacting Medicare Part D plan quality rating. Keywords: reminder system, tailored intervention, Medicare Part D, adherence, persistence

  2. HIV dynamics linked to memory CD4+ T cell homeostasis.

    Science.gov (United States)

    Murray, John M; Zaunders, John; Emery, Sean; Cooper, David A; Hey-Nguyen, William J; Koelsch, Kersten K; Kelleher, Anthony D

    2017-01-01

    The dynamics of latent HIV is linked to infection and clearance of resting memory CD4+ T cells. Infection also resides within activated, non-dividing memory cells and can be impacted by antigen-driven and homeostatic proliferation despite suppressive antiretroviral therapy (ART). We investigated whether plasma viral level (pVL) and HIV DNA dynamics could be explained by HIV's impact on memory CD4+ T cell homeostasis. Median total, 2-LTR and integrated HIV DNA levels per μL of peripheral blood, for 8 primary (PHI) and 8 chronic HIV infected (CHI) individuals enrolled on a raltegravir (RAL) based regimen, exhibited greatest changes over the 1st year of ART. Dynamics slowed over the following 2 years so that total HIV DNA levels were equivalent to reported values for individuals after 10 years of ART. The mathematical model reproduced the multiphasic dynamics of pVL, and levels of total, 2-LTR and integrated HIV DNA in both PHI and CHI over 3 years of ART. Under these simulations, residual viremia originated from reactivated latently infected cells where most of these cells arose from clonal expansion within the resting phenotype. Since virion production from clonally expanded cells will not be affected by antiretroviral drugs, simulations of ART intensification had little impact on pVL. HIV DNA decay over the first year of ART followed the loss of activated memory cells (120 day half-life) while the 5.9 year half-life of total HIV DNA after this point mirrored the slower decay of resting memory cells. Simulations had difficulty reproducing the fast early HIV DNA dynamics, including 2-LTR levels peaking at week 12, and the later slow loss of total and 2-LTR HIV DNA, suggesting some ongoing infection. In summary, our modelling indicates that much of the dynamical behavior of HIV can be explained by its impact on memory CD4+ T cell homeostasis.

  3. Clonidine prophylaxis for narcotic and sedative withdrawal syndrome following laryngotracheal reconstruction.

    Science.gov (United States)

    Deutsch, E S; Nadkarni, V M

    1996-11-01

    To determine the efficacy of transdermal clonidine hydrochloride for prophylaxis of withdrawal syndromes that are common following more than 7 days of deep sedation after single-stage laryngotracheal reconstruction (LTR) surgery. Consecutive case series. Pediatric intensive care unit at tertiary care referral center, university-affiliated children's hospital. Ten consecutive patients who had undergone single-stage LTR and received sedation with a combination of narcotics and benzodiazepines. A sustained release transdermal clonidine hydrochloride patch (50-100 micrograms/d; mean, 5.8 micrograms/kg per day; range, 4.2-8.5 micrograms/kg per day) was applied to 8 consecutive patients before discontinuation of sedative infusions and elective extubation. Physicians continued to treat patients for withdrawal symptoms, if seen, at their discretion. Seventeen characteristic narcotic and sedative withdrawal symptoms recorded at baseline and serially for at least 48 hours following discontinuation of deep sedation. No severe symptoms of narcotic or sedative withdrawal (seizure, choreoathetosis, tremors, or dehydration) were seen in any patient during treatment with clonidine. Not more than 2 minor withdrawal symptoms (lethargy and respiratory rate > 40 breaths/min) occurred simultaneously during treatment with clonidine in any patient. Two of 8 patients had clonidine patches removed prematurely. Both patients experienced withdrawal symptoms within hours, and these symptoms subsided in the 1 patient whose clonidine patch was reinstituted. No significant sustained side effects, bradycardia, or dysrhythmia necessitated discontinuation of clonidine therapy, and no rebound withdrawal was seen with routine discontinuation of clonidine after 7 days of therapy. Transdermal clonidine prophylaxis may be a safe and efficacious adjunct to prevent withdrawal symptoms in pediatric patients who have undergone single-stage LTR. Use of a validated withdrawal symptom scoring tool is indicated

  4. Durable Flap-Valve Mitigation of Duodenogastric Reflux,  Remnant Gastritis and Dumping Syndrome Following Billroth I Reconstruction.

    Science.gov (United States)

    Hoya, Yoshiyuki; Taki, Tetsuya; Watanabe, Atsushi; Nakayoshi, Tomoko; Okamoto, Tomoyoshi; Mitsumori, Norio; Yanaga, Katsuhiko

    2016-04-01

    We have reported the short-term results of pylorus reconstruction gastrectomy (PRG) that prevents duodenogastric reflux (DGR) and remnant gastritis after distal gastrectomy. We herein report the long-term results of the PRG. PRG was performed in 37 patients (age 31 to 86 [mean 67.8 ± 12.3] years, male:female = 22:15) with gastric cancer from June 2006 through December 2013. We examined the long-term outcome in 28 patients (age 41 to 86 [mean 67.0 ± 10.7] years, male:female = 18:10) that passed over 3 years after surgery (LTR 44.1 ± 11.7 months), and compared with their short-term result after the operation (STR 13.1 ± 6.9 months). The adverse events of gastric surgery evaluated in this study consisted of the degree of remnant gastritis, the presence of dumping syndrome, and degree of weight loss (%). There was no difference in the degree of DGR and remnant gastritis by gastroscopic finding between LTR and STR after PRG (P = 0.21). Statistically, there was no difference in the bile acid concentration of remnant gastric juice between LTR and STR (108.4 ± 254.1 vs. 94.0 ± 208.6 μmol/L, P = 0.33), and weight loss of LTR was the same as that of STR (5.67 ± 7.08 vs. 4.59 ± 5.63%, P = 0.34). There were few morphological changes in the reconstructed pylorus by the long-term course, but 2 patients showed mild atrophy. The form of reconstructed pylorus and the effect that reduces side effects of Billroth I seem to last for a long time.

  5. Discrimination between Fatigue Cracking and Mechanical Damage in Aircraft Fastener Holes by Eddy-Current Phase Rotation

    Science.gov (United States)

    2016-08-01

    Mandache, C., Yanishevsky, M., and Brothers , M., Generic bolt hole eddy current testing probability of detection, LTR-SMPL-2007-0138, National...procedures and phase-analysis based interpretation to reduce false calls,United States Air Force, Wright -Patterson AFB, OH, USA [4] Brausch, J. C...flight structures, AFRL-RX-WP-TR-2008-4373, United States Air Force, Wright -Patterson Air Force Base, OH, USA (2008). [5] Hagemaier, D. J. “Eddy

  6. Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved.

    Directory of Open Access Journals (Sweden)

    Patrick Gemmell

    2016-06-01

    Full Text Available About 8% of the human genome is made up of endogenous retroviruses (ERVs. Though most human endogenous retroviruses (HERVs are thought to be irrelevant to our biology notable exceptions include members of the HERV-H family that are necessary for the correct functioning of stem cells. ERVs are commonly found in two forms, the full-length proviral form, and the more numerous solo-LTR form, thought to result from homologous recombination events. Here we introduce a phylogenetic framework to study ERV insertion and solo-LTR formation. We then apply the framework to site patterns sampled from a set of long alignments covering six primate genomes. Studying six categories of ERVs we quantitatively recapitulate patterns of insertional activity that are usually described in qualitative terms in the literature. A slowdown in most ERV groups is observed but we suggest that HERV-K activity may have increased in humans since they diverged from chimpanzees. We find that the rate of solo-LTR formation decreases rapidly as a function of ERV age and that an age dependent model of solo-LTR formation describes the history of ERVs more accurately than the commonly used exponential decay model. We also demonstrate that HERV-H loci are markedly less likely to form solo-LTRs than ERVs from other families. We conclude that the slower dynamics of HERV-H suggest a host role for the internal regions of these exapted elements and posit that in future it will be possible to use the relationship between full-length proviruses and solo-LTRs to help identify large scale co-options in distant vertebrate genomes.

  7. Myocyte enhancer factor (MEF)-2 plays essential roles in T-cell transformation associated with HTLV-1 infection by stabilizing complex between Tax and CREB.

    Science.gov (United States)

    Jain, Pooja; Lavorgna, Alfonso; Sehgal, Mohit; Gao, Linlin; Ginwala, Rashida; Sagar, Divya; Harhaj, Edward W; Khan, Zafar K

    2015-02-27

    The exact molecular mechanisms regarding HTLV-1 Tax-mediated viral gene expression and CD4 T-cell transformation have yet to be fully delineated. Herein, utilizing virus-infected primary CD4+ T cells and the virus-producing cell line, MT-2, we describe the involvement and regulation of Myocyte enhancer factor-2 (specifically MEF-2A) during the course of HTLV-1 infection and associated disease syndrome. Inhibition of MEF-2 expression by shRNA and its activity by HDAC9 led to reduced viral replication and T-cell transformation in correlation with a heightened expression of MEF-2 in ATL patients. Mechanistically, MEF-2 was recruited to the viral promoter (LTR, long terminal repeat) in the context of chromatin, and constituted Tax/CREB transcriptional complex via direct binding to the HTLV-1 LTR. Furthermore, an increase in MEF-2 expression was observed upon infection in an extent similar to CREB (known Tax-interacting transcription factor), and HATs (p300, CBP, and p/CAF). Confocal imaging confirmed MEF-2 co-localization with Tax and these proteins were also shown to interact by co-immunoprecipitation. MEF-2 stabilization of Tax/CREB complex was confirmed by a novel promoter-binding assay that highlighted the involvement of NFAT (nuclear factor of activated T cells) in this process via Tax-mediated activation of calcineurin (a calcium-dependent serine-threonine phosphatase). MEF-2-integrated signaling pathways (PI3K/Akt, NF-κB, MAPK, JAK/STAT, and TGF-β) were also activated during HTLV-1 infection of primary CD4+ T cells, possibly regulating MEF-2 activity. We demonstrate the involvement of MEF-2 in Tax-mediated LTR activation, viral replication, and T-cell transformation in correlation with its heightened expression in ATL patients through direct binding to DNA within the HTLV-1 LTR.

  8. A comparison of the effect of the active release and muscle energy techniques on the latent trigger points of the upper trapezius.

    Science.gov (United States)

    Sadria, Golnaz; Hosseini, Majid; Rezasoltani, Asghar; Akbarzadeh Bagheban, Alireza; Davari, Ahmadreza; Seifolahi, Afsaneh

    2017-10-01

    The increasing use of computer in daily life has brought about numerous musculoskeletal problems. Impairments in the head, neck and shoulders are more common compared with the other parts of the body. The aim of this study was to compare the effect of two manual treatments in two separate groups, i.e., active release technique (ART) and muscle energy technique (MET) on the latent trigger points (LTrPs) in the upper trapezius muscle. The set criteria in the study included the active range of cervical lateral flexion, pain intensity on the visual analog scale (VAS), and the upper trapezius muscle thickness. This clinical trial study assessed the outcome measures within and between groups before and after the intervention. The target population were 64 (32 males, 32 females) participants who had been selected from among the staff members and the students of a rehabilitation school, and the employees of an engineering company who had LTrPs in their upper trapezius muscle and were from 18 to 50 years old. The immediate effects of MET and ART on the patients of each groups with LTrPs in their upper trapezius muscle were increased active range of cervical lateral flexion (P < 0.001), decreased pain intensity on VAS (P < 0.05) and decreased thickness of the upper trapezius muscle (P < 0.01). Both manual techniques of ART and MET reduced the symptoms of LTrPs in the upper trapezius in the two groups equally, neither technique being superior to the other. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Mechanisms of Cytotoxicity of the Aids Virus

    Science.gov (United States)

    1992-10-10

    the above experiments was a significant pcoblem in data interpretation. To mare clearly define the cellular localizaticn of vpr by imarflurrescence, we...Department of Pathology , George Washington University, Washington D.C. 200372; and Henry M. Jackson Foundation for the Advancement of Military Medicine and the...cellular transcriptional factors. (mouse mammary tumour virus) LTR-linked nef Specific targets of PKC, PKA, cAMP-dependent transgenic lines expressed Nef

  10. Derepression of the plant Chromovirus LORE1 induces germline transposition in regenerated plants.

    Directory of Open Access Journals (Sweden)

    Eigo Fukai

    2010-03-01

    Full Text Available Transposable elements represent a large proportion of the eukaryotic genomes. Long Terminal Repeat (LTR retrotransposons are very abundant and constitute the predominant family of transposable elements in plants. Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements. These elements contain chromodomains in their integrases, which suggests a preference for insertion into heterochromatin. In turn, this preference might have contributed to the patterning of heterochromatin observed in host genomes. Despite their potential importance for our understanding of plant genome dynamics and evolution, the regulatory mechanisms governing the behavior of chromoviruses and their activities remain largely uncharacterized. Here, we report a detailed analysis of the spatio-temporal activity of a plant chromovirus in the endogenous host. We examined LORE1a, a member of the endogenous chromovirus LORE1 family from the model legume Lotus japonicus. We found that this chromovirus is stochastically de-repressed in plant populations regenerated from de-differentiated cells and that LORE1a transposes in the male germline. Bisulfite sequencing of the 5' LTR and its surrounding region suggests that tissue culture induces a loss of epigenetic silencing of LORE1a. Since LTR promoter activity is pollen specific, as shown by the analysis of transgenic plants containing an LTR::GUS fusion, we conclude that male germline-specific LORE1a transposition in pollen grains is controlled transcriptionally by its own cis-elements. New insertion sites of LORE1a copies were frequently found in genic regions and show no strong insertional preferences. These distinctive novel features of LORE1 indicate that this chromovirus has considerable potential for generating genetic and epigenetic diversity in the host plant population. Our results also define conditions for the use of LORE1a as a genetic tool.

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

    Science.gov (United States)

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

    2016-03-01

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

  12. Agroforestry and sustainable vegetable production case study: Nghia Trung Village, Bu Dang District, Binh Phuoc Province, Vietnam

    OpenAIRE

    Du, L.V.

    2007-01-01

    This presentation describes soil conservation studies to be conducted in Vietnam, LTR-5 site. It discusses a baseline study that covered issues on no-tillage vegetable systems and soil and water conservation. It gives a profile of the study area in Vietnam, and outlines the structure of cashew production including farmer perception, intercropping and the potential for future research. LTRA-5 (Agroforestry and Sustainable Vegetable Production)

  13. Genetic Mechanisms in Aspirin-Exacerbated Respiratory Disease

    OpenAIRE

    Shrestha Palikhe, Nami; Kim, Seung-Hyun; Jin, Hyun Jung; Hwang, Eui-Kyung; Nam, Young Hee; Park, Hae-Sim

    2012-01-01

    Aspirin-exacerbated respiratory disease (AERD) refers to the development of bronchoconstriction in asthmatics following the exposure to aspirin or other nonsteroidal anti-inflammatory drugs. The key pathogenic mechanisms associated with AERD are the overproduction of cysteinyl leukotrienes (CysLTs) and increased CysLTR1 expression in the airway mucosa and decreased lipoxin and PGE2 synthesis. Genetic studies have suggested a role for variability of genes in disease susceptibility and the resp...

  14. Photosynthetic acclimation responses of maize seedlings grown under artificial laboratory light gradients mimicking natural canopy conditions

    Directory of Open Access Journals (Sweden)

    Matthias eHirth

    2013-09-01

    Full Text Available In this study we assessed the ability of the C4 plant maize to perform long-term photosynthetic acclimation in an artificial light quality system previously used for analysing short-term and long-term acclimation responses (LTR in C3 plants. We aimed to test if this light system could be used as a tool for analysing redox-regulated acclimation processes in maize seedlings. Photosynthetic parameters obtained from maize samples harvested in the field were used as control. The results indicated that field grown maize performed a pronounced LTR with significant differences between the top and the bottom levels of the plant stand corresponding to the strong light gradients occurring in it. We compared these data to results obtained from maize seedlings grown under artificial light sources preferentially exciting either photosystem II or photosystem I. In C3 plants, this light system induces redox signals within the photosynthetic electron transport chain which trigger state transitions and differential phosphorylation of light harvesting complexes of photosystem II (LHCII. The LTR to these redox signals induces changes in the accumulation of plastid psaA transcripts, in chlorophyll (Chl fluorescence values Fs/Fm, in Chl a/b ratios and in transient starch accumulation in C3 plants. Maize seedlings grown in this light system exhibited a pronounced ability to perform both short-term and long-term acclimation at the level of psaA transcripts, Chl fluorescence values Fs/Fm and Chl a/b ratios. Interestingly, maize seedlings did not exhibit redox-controlled variations of starch accumulation probably because of its specific differences in energy metabolism. In summary, the artificial laboratory light system was found to be well-suited to mimic field light conditions and provides a physiological tool for studying the molecular regulation of the LTR of maize in more detail.

  15. Thin Film Composite Materials, Phase 2

    Science.gov (United States)

    1987-01-01

    L FR RE TTRA C TON F ,, oAT . 0O M,,,,.L .,O "igure 7.NO w, 24 4 3 2 LTR-87-DC-006 5. Tapered Rotating Cylinder With Liquid Return Channel. As shown in...nucleus, such as dust, pollen or ice crystals, which are thought to be important in initiating rain. We have conflicting requirements in this respect

  16. Selection of Human Antibody Fragments Which Bind Novel Breast Tumor Antigens

    Science.gov (United States)

    1998-09-01

    Gov’t. agencies only; Proprietary Info; Sep 98 Other requests shall be referred to USARMC, Fort Detrick, MD 21702-5012 AUTHORITY USAMRMC ltr, 1 Jun 2001 ...growth. (1991). Growth Regulation. 1: 72-82. 51. Tagliabue, E., Centis, F., Campiglio, M., Mastroianni, A., Martignone, S., Pellegrini , R., Casalini, P...SHEETS*#:, PETER AMERSDORFER§, RICARDA FINNERN§, PETER SARGENT¶, ERICKA LINDQVIST!I, ROBERT SCHIER§, GRETE HEMINGSEN§, CINDY WONG§, JOHN C. GERHART

  17. Clinical Investigation Program Report Control Symbol MED 300.

    Science.gov (United States)

    1983-10-01

    Hannan CJ Jr, Garcia AR. Thyrotropin-releasing hormone (TRH) increases mor- bidity and mortality in the gerbil stroke model. Neurosci Ltr 1982; 33:299...residency seminar. Accepted by Psychiatric Education. Jensen PS, Case report of conversion catatonia, Indication for hypnosis . (Abst) Accepted by Hospital and...inhibition in the gerbil. Presented at Soc Neurosci , 12th Annual Meeting, Minneapolis, MN, 31 Oct - 5 Nov 1982. (C) Hannan CJ. COMT in the gerbil brain

  18. A chromosome conformation capture ordered sequence of the barley genome

    Czech Academy of Sciences Publication Activity Database

    Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S. O.; Wicker, T.; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, S.; Munoz-Amatrian, M.; Houben, A.; Doležel, Jaroslav; Ayling, S.; Lonardi, S.; Mayer, K.F.X.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh, R.; Stein, N.

    2017-01-01

    Roč. 544, č. 7651 (2017), s. 427-433 ISSN 0028-0836 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : bacterial artificial chromosomes * inverted-repeat elements * complex-plant genomes * hi-c * environmental adaptation * ltr retrotransposons * structural variation * maize genome * software * database Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 40.137, year: 2016

  19. First molecular characterization of visna/maedi viruses from naturally infected sheep in Turkey.

    Science.gov (United States)

    Muz, Dilek; Oğuzoğlu, Tuba Ciğdem; Rosati, Sergio; Reina, Ramses; Bertolotti, Luigi; Burgu, Ibrahim

    2013-03-01

    Recent worldwide serological and genetic studies of small ruminant lentiviruses (SRLV) have led to the description of new genotypes and the development of new diagnostic tests. This study investigated the detection and molecular characterization of visna/maedi virus (VMV) infection in serum and blood samples from pure and mixed sheep breeds acquired from different regions in Turkey using ELISA and PCR techniques. The prevalence of VMV was 67.8 % by ELISA and/or LTR-PCR with both assays showing a medium level of agreement (kappa: 0.26; ± 0.038 CI). Positivity of VMV in sheep increased according to the age of the animal, although PCR positivity was higher than ELISA in young individuals. Phylogenetic analysis of 33 LTR sequences identified two distinct clades that were closely related to American and Greek LTR sequences. Phylogenetic analysis of 10 partial gag gene sequences identified A2, A3, A5, A9, A11 subtypes of genotype A SRLVs. In vitro culture of all isolates in fetal sheep lung cells (FSLC) showed a slow/low phenotype causing less or no lytic infection compared with infection with the WLC-1 American strain characterized by a rapid/highly lytic phenotype. Phylogenetic analysis revealed that Turkish VMV sequences preceded the establishment of American or Greek strains that were associated with the migration of sheep from the Middle East to Western Europe several centuries ago. This is the first study that describes Turkish VMV sequences with the molecular characterization of LTR and gag genes, and it strongly suggests that SRLV-genotype A originated in Turkey.

  20. A Different Road to Implementation of the Total Force Policy

    Science.gov (United States)

    2013-03-01

    Army General Eric K. Shinseki, “Beret Wear Policy,” HQDA LTR 670- 01-1, Washington, DC, June 14, 2001 . 20 Kotter , Leading Change, 21. 21 Kotter ... Kotter , this stage is the one most familiar to military leadership. All leaders learn about the importance of a clear vision and strategy at all...John P. Kotter , Leading Change (Boston, Massachusetts: Harvard Business Review Press, 1996), 21. 11 Ibid., 26. 12 Ibid., 21-22. 13 Ibid., 20. 14

  1. Geothermal Energy in the Pacific Region. Appendix A: Exploration for a Geothermal System in the Lualualei Valley, Oahu, Hawaii. Appendix B: Exploration on Adak Island Alaska

    Science.gov (United States)

    1975-05-01

    VA 22203. AUTHORITY ONR ltr, 11 Dec 1975 THIS PAGE IS UNCLASSIFIED ..-*~* .-- . .... ’NJ Geothermal Energy in the Pacific Region ; I L. T. Grose and...Appendix A accompanies a report entitled " Geothermal Energy in the Pacific Region" by L. T. Grose and G. V. Keller, May, 1975. This project has been...Islands comprise an area of active to recently active volcanism which should be favorable for the occurrence of geothermal energy . Adak Naval Base is an

  2. Laboratory technology research - abstracts of FY 1997 projects

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    The Laboratory Technology Research (LTR) program supports high-risk, multidisciplinary research partnerships to investigate challenging scientific problems whose solutions have promising commercial potential. These partnerships capitalize on two great strengths of this country: the world-class basic research capability of the DOE Energy Research (ER) multi-program national laboratories and the unparalleled entrepreneurial spirit of American industry. A distinguishing feature of the ER multi-program national laboratories is their ability to integrate broad areas of science and engineering in support of national research and development goals. The LTR program leverages this strength for the Nation`s benefit by fostering partnerships with US industry. The partners jointly bring technology research to a point where industry or the Department`s technology development programs can pursue final development and commercialization. Projects supported by the LTR program are conducted by the five ER multi-program laboratories. These projects explore the applications of basic research advances relevant to DOE`s mission over a full range of scientific disciplines. The program presently emphasizes three critical areas of mission-related research: advanced materials; intelligent processing/manufacturing research; and sustainable environments.

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

    Science.gov (United States)

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

    2014-06-01

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

  4. Tyl6, a novel Ty3/gypsy-like retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica.

    Science.gov (United States)

    Kovalchuk, Andriy; Senam, Senam; Mauersberger, Stephan; Barth, Gerold

    2005-09-01

    The novel LTR retrotransposon Tyl6 was detected in the genome of the dimorphic fungus Yarrowia lipolytica. Sequence analysis revealed that this element is related to the well-known Ty3 element of Saccharomyces cerevisiae and, especially, to the recently described Tse3 retrotransposon of Saccharomyces exiguus and to the del1-like plant retrotransposons. Tyl6 is 5108 bp long, is flanked by two identical long terminal repeats (LTR), each of 276 bp, and its ORFs are separated by a -1 frameshift. Both ORFs are intact and deduced translation products display a significant similarity with those of previously described Ty3/gypsy retrotransposons. Distribution of Tyl6 among Y. lipolytica strains of different origins was also analysed. A single copy of the novel retrotransposon is present in some commonly used laboratory strains, which are derivatives of the wild-type isolate YB423-12, whereas other strains of independent origin are devoid of Ty16. No solo LTR of Tyl6 was detected in the analysed strains. Copyright 2005 John Wiley & Sons, Ltd.

  5. 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.

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

    Science.gov (United States)

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

    2015-12-24

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

  7. I-mfa domain proteins specifically interact with HTLV-1 Tax and repress its transactivating functions

    Energy Technology Data Exchange (ETDEWEB)

    Kusano, Shuichi, E-mail: skusano@m2.kufm.kagoshima-u.ac.jp [Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Yoshimitsu, Makoto; Hachiman, Miho [Division of Hematology and Immunology, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Ikeda, Masanori [Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan)

    2015-12-15

    The I-mfa domain proteins HIC (also known as MDFIC) and I-mfa (also known as MDFI) are candidate tumor suppressor genes that are involved in cellular and viral transcriptional regulation. Here, we show that HIC and I-mfa directly interact with human T-cell leukemia virus type-1 (HTLV-1) Tax protein in vitro. In addition, HIC and I-mfa repress Tax-dependent transactivation of an HTLV-1 long terminal repeat (LTR) reporter construct in COS-1, Jurkat and high-Tax-producing HTLV-1-infected T cells. HIC also interacts with Tax through its I-mfa domain in vivo and represses Tax-dependent transactivation of HTLV-1 LTR and NF-κB reporter constructs in an interaction-dependent manner. Furthermore, we show that HIC decreases the nuclear distribution and stimulates the proteasomal degradation of Tax. These data reveal that HIC specifically interacts with HTLV-1 Tax and negatively regulates Tax transactivational activity by altering its subcellular distribution and stability. - Highlights: • I-mfa domain proteins, HIC and I-mfa, specifically interact with HTLV-1 Tax. • HIC and I-mfa repress the Tax-dependent transactivation of HTLV-1 LTR. • HIC represses the Tax-dependent transactivation of NF-κΒ. • HIC decreases the nuclear distribution of Tax. • HIC stimulates the proteasomal degradation of Tax.

  8. Short- and long-term racing performance of Standardbred pacers and trotters after early surgical intervention for tarsal osteochondrosis.

    Science.gov (United States)

    McCoy, A M; Ralston, S L; McCue, M E

    2015-07-01

    Osteochondrosis (OC) is commonly diagnosed in young Standardbred racehorses but its effect on performance when surgically treated at a young age is still incompletely understood. This is especially true for Standardbred pacers, which are underrepresented in the existing literature. To characterise the short- (2-year-old) and long-term (through 5-year-old) racing performance in Standardbred pacers and trotters after early surgical intervention (race records for each horse included starts, wins, finishes in the top 3 (win, place or show), earnings and fastest time. Comparisons between OC-affected and unaffected horses were made for the entire population and within gaits. A smaller related population (n = 94) had these performance measures evaluated for their 2-5-year-old racing seasons. Osteochondrosis status was associated with few performance measures. Trotters were at higher risk for lesions of the medial malleolus but lower risk for lesions of the distal intermediate ridge of the tibia than were pacers. Horses with bilateral OC lesions and lateral trochlear ridge (LTR) lesions started fewer races at 2 years of age than those with unilateral lesions or without LTR lesions. Osteochondrosis seemed to have minimal effect on racing performance in this cohort, although horses with bilateral and LTR lesions started fewer races at 2 years. There was evidence for different distribution of OC lesions among pacers and trotters, which should be explored further. Standardbreds undergoing early removal of tarsal OC lesions can be expected to perform equivalently to their unaffected counterparts. © 2014 EVJ Ltd.

  9. Cysteinyl Leukotriene Receptor-1 Antagonists as Modulators of Innate Immune Cell Function

    Directory of Open Access Journals (Sweden)

    A. J. Theron

    2014-01-01

    Full Text Available Cysteinyl leukotrienes (cysLTs are produced predominantly by cells of the innate immune system, especially basophils, eosinophils, mast cells, and monocytes/macrophages. Notwithstanding potent bronchoconstrictor activity, cysLTs are also proinflammatory consequent to their autocrine and paracrine interactions with G-protein-coupled receptors expressed not only on the aforementioned cell types, but also on Th2 lymphocytes, as well as structural cells, and to a lesser extent neutrophils and CD8+ cells. Recognition of the involvement of cysLTs in the immunopathogenesis of various types of acute and chronic inflammatory disorders, especially bronchial asthma, prompted the development of selective cysLT receptor-1 (cysLTR1 antagonists, specifically montelukast, pranlukast, and zafirlukast. More recently these agents have also been reported to possess secondary anti-inflammatory activities, distinct from cysLTR1 antagonism, which appear to be particularly effective in targeting neutrophils and monocytes/macrophages. Underlying mechanisms include interference with cyclic nucleotide phosphodiesterases, 5′-lipoxygenase, and the proinflammatory transcription factor, nuclear factor kappa B. These and other secondary anti-inflammatory mechanisms of the commonly used cysLTR1 antagonists are the major focus of the current review, which also includes a comparison of the anti-inflammatory effects of montelukast, pranlukast, and zafirlukast on human neutrophils in vitro, as well as an overview of both the current clinical applications of these agents and potential future applications based on preclinical and early clinical studies.

  10. Characterizing the functions of Ty1 Gag and the Gag-derived restriction factor p22/p18.

    Science.gov (United States)

    Pachulska-Wieczorek, Katarzyna; Błaszczyk, Leszek; Gumna, Julita; Nishida, Yuri; Saha, Agniva; Biesiada, Marcin; Garfinkel, David J; Purzycka, Katarzyna J

    2016-01-01

    The long terminal repeat (LTR) and non-LTR retrotransposons comprise approximately half of the human genome, and we are only beginning to understand their influence on genome function and evolution. The LTR retrotransposon Ty1 is the most abundant mobile genetic element in the S. cerevisiae reference genome. Ty1 replicates via an RNA intermediate and shares several important structural and functional characteristics with retroviruses. However, unlike retroviruses Ty1 retrotransposition is not infectious. Retrotransposons integrations can cause mutations and genome instability. Despite the fact that S. cerevisiae lacks eukaryotic defense mechanisms such as RNAi, they maintain a relatively low copy number of the Ty1 retrotransposon in their genomes. A novel restriction factor derived from the C-terminal half of Gag (p22/p18) and encoded by internally initiated transcript inhibits retrotransposition in a dose-dependent manner. Therefore, Ty1 evolved a specific GAG organization and expression strategy to produce products both essential and antagonistic for retrotransposon movement. In this commentary we discuss our recent research aimed at defining steps of Ty1 replication influenced by p22/p18 with particular emphasis on the nucleic acid chaperone functions carried out by Gag and the restriction factor.

  11. Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse.

    Directory of Open Access Journals (Sweden)

    Rebecca R Bellone

    Full Text Available Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP where homozygotes (LP/LP are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1 as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ(2=1022.00, p<<0.0005, and CSNB, testing 43 horses (χ(2=43, p<<0.0005. The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.

  12. Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse

    Science.gov (United States)

    Bellone, Rebecca R.; Holl, Heather; Setaluri, Vijayasaradhi; Devi, Sulochana; Maddodi, Nityanand; Archer, Sheila; Sandmeyer, Lynne; Ludwig, Arne; Foerster, Daniel; Pruvost, Melanie; Reissmann, Monika; Bortfeldt, Ralf; Adelson, David L.; Lim, Sim Lin; Nelson, Janelle; Haase, Bianca; Engensteiner, Martina; Leeb, Tosso; Forsyth, George; Mienaltowski, Michael J.; Mahadevan, Padmanabhan; Hofreiter, Michael; Paijmans, Johanna L. A.; Gonzalez-Fortes, Gloria; Grahn, Bruce; Brooks, Samantha A.

    2013-01-01

    Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ2=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ2=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder. PMID:24167615

  13. Integrase and integration: biochemical activities of HIV-1 integrase

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    Deprez Eric

    2008-12-01

    Full Text Available Abstract Integration of retroviral DNA is an obligatory step of retrovirus replication because proviral DNA is the template for productive infection. Integrase, a retroviral enzyme, catalyses integration. The process of integration can be divided into two sequential reactions. The first one, named 3'-processing, corresponds to a specific endonucleolytic reaction which prepares the viral DNA extremities to be competent for the subsequent covalent insertion, named strand transfer, into the host cell genome by a trans-esterification reaction. Recently, a novel specific activity of the full length integrase was reported, in vitro, by our group for two retroviral integrases (HIV-1 and PFV-1. This activity of internal cleavage occurs at a specific palindromic sequence mimicking the LTR-LTR junction described into the 2-LTR circles which are peculiar viral DNA forms found during viral infection. Moreover, recent studies demonstrated the existence of a weak palindromic consensus found at the integration sites. Taken together, these data underline the propensity of retroviral integrases for binding symmetrical sequences and give perspectives for targeting specific sequences used for gene therapy.

  14. Characterization of Three nef-Defective Human Immunodeficiency Virus Type 1 Strains Associated with Long-Term Nonprogression

    Science.gov (United States)

    Rhodes, David I.; Ashton, Lesley; Solomon, Ajantha; Carr, Andrew; Cooper, David; Kaldor, John; Deacon, Nicholas

    2000-01-01

    Long-term survivors (LTS) of human immunodeficiency virus type 1 (HIV-1) infection provide an opportunity to investigate both viral and host factors that influence the rate of disease progression. We have identified three HIV-1-infected individuals in Australia who have been infected for over 11 years with viruses that contain deletions in the nef and nef-long terminal repeat (nef/LTR) overlap regions. These viruses differ from each other and from other nef-defective strains of HIV-1 previously identified in Australia. One individual, LTS 3, is infected with a virus containing a nef gene with a deletion of 29 bp from the nef/LTR overlap region, resulting in a truncated Nef open reading frame. In addition to the Nef defect, only viruses containing truncated Vif open reading frames of 37 or 69 amino acids could be detected in peripheral blood mononuclear cells isolated from this patient. LTS 3 had a viral load of less than 20 copies of RNA/ml of plasma. The other two long-term survivors, LTS 9 and LTS 11, had loads of less than 200 copies of RNA/ml of plasma and are infected with viruses with larger deletions in both the nef alone and nef/LTR overlap regions. These viruses contain wild-type vif, vpu, and vpr accessory genes. All three strains of virus had envelope sequences characteristic of macrophagetropic viruses. These findings further indicate the reduced pathogenic potential of nef-defective viruses. PMID:11044102

  15. MGEScan: a Galaxy-based system for identifying retrotransposons in genomes.

    Science.gov (United States)

    Lee, Hyungro; Lee, Minsu; Mohammed Ismail, Wazim; Rho, Mina; Fox, Geoffrey C; Oh, Sangyoon; Tang, Haixu

    2016-08-15

    : MGEScan-long terminal repeat (LTR) and MGEScan-non-LTR are successfully used programs for identifying LTRs and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not supported by easy-to-use interfaces nor well suited for data visualization in general data formats. Here, we present MGEScan, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters. MGEScan and Galaxy empower researchers to identify transposable elements in a graphical user interface with ready-to-use workflows. MGEScan also visualizes the custom annotation tracks for mobile genetic elements in public genome browsers. A maximum speed-up of 3.26× is attained for execution time using concurrent processing and MPI on four virtual cores. MGEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-based web server, and on a virtual cluster on the Amazon cloud. MGEScan tutorials and source code are available at http://mgescan.readthedocs.org/ hatang@indiana.edu or syoh@ajou.ac.kr Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Efficient transfer of HTLV-1 tax gene in various primary and immortalized cells using a flap lentiviral vector.

    Science.gov (United States)

    Royer-Leveau, Christelle; Mordelet, Elodie; Delebecque, Frédéric; Gessain, Antoine; Charneau, Pierre; Ozden, Simona

    2002-08-01

    Human T cell leukemia virus type 1 (HTLV-1) causes two major diseases: adult T-cell leukemia-lymphoma and tropical spastic paraparesis/HTLV-1 associated myelopathy (TSP/HAM). In order to understand the involvement of Tax protein in HTLV-1 pathogenesis, we constructed a HIV-1 based lentiviral vector containing the central DNA flap sequence and either the green fluorescent protein (GFP) or the HTLV-1 tax genes. Using these vectors, GFP and tax genes were introduced in several primary and immortalized cells of endothelial, lymphoid, astrocytic or macrophagic origin. As assessed by GFP expression, up to 100% efficiency of transduction was obtained for all cell types tested. Tax expression was detected by Western blot and immuno-fluorescence in the transduced cells. After transduction, the Tax transcriptional activity was confirmed by the transactivation of HTLV-1 LTR-lacZ or HTLV-1 LTR-GFP reporter genes. Increased CD25 and HLA DR expression was observed in human peripheral blood lymphocytes transduced with the Tax vector. These results indicate that both pathways of Tax transactivation, CREB (viral LTR) and NF-kappa B (CD25 and HLA DR), are functional after transduction by TRIP Tax vector. Therefore, this vector provides a useful tool for investigating the role of the Tax viral protein in the pathogenesis of diseases linked to HTLV-1 infection.

  17. FACE RECOGNITION BASED ON LOCAL DERIVATIVE TETRA PATTERN

    Directory of Open Access Journals (Sweden)

    A Geetha

    2017-02-01

    Full Text Available This paper proposes a new face recognition algorithm called local derivative tetra pattern (LDTrP. The new technique LDTrP is used to alleviate the face recognition rate under real-time challenges. Local derivative pattern (LDP is a directional feature extraction method to encode directional pattern features based on local derivative variations. The nth -order LDP is proposed to encode the first (n-1th order local derivative direction variations. The LDP templates extract high-order local information by encoding various distinctive spatial relationships contained in a given local region. The local tetra pattern (LTrP encodes the relationship between the reference pixel and its neighbours by using the first-order derivatives in vertical and horizontal directions. LTrP extracts values which are based on the distribution of edges which are coded using four directions. The LDTrP combines the higher order directional feature from both LDP and LTrP. Experimental results on ORL and JAFFE database show that the performance of LDTrP is consistently better than LBP, LTP and LDP for face identification under various conditions. The performance of the proposed method is measured in terms of recognition rate.

  18. Production and processing of siRNA precursor transcripts from the highly repetitive maize genome.

    Directory of Open Access Journals (Sweden)

    Christopher J Hale

    2009-08-01

    Full Text Available Mutations affecting the maintenance of heritable epigenetic states in maize identify multiple RNA-directed DNA methylation (RdDM factors including RMR1, a novel member of a plant-specific clade of Snf2-related proteins. Here we show that RMR1 is necessary for the accumulation of a majority of 24 nt small RNAs, including those derived from Long-Terminal Repeat (LTR retrotransposons, the most common repetitive feature in the maize genome. A genetic analysis of DNA transposon repression indicates that RMR1 acts upstream of the RNA-dependent RNA polymerase, RDR2 (MOP1. Surprisingly, we show that non-polyadenylated transcripts from a sampling of LTR retrotransposons are lost in both rmr1 and rdr2 mutants. In contrast, plants deficient for RNA Polymerase IV (Pol IV function show an increase in polyadenylated LTR RNA transcripts. These findings support a model in which Pol IV functions independently of the small RNA accumulation facilitated by RMR1 and RDR2 and support that a loss of Pol IV leads to RNA Polymerase II-based transcription. Additionally, the lack of changes in general genome homeostasis in rmr1 mutants, despite the global loss of 24 nt small RNAs, challenges the perceived roles of siRNAs in maintaining functional heterochromatin in the genomes of outcrossing grass species.

  19. Perioperative care following complex laryngotracheal reconstruction in infants and children

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    Gupta Punkaj

    2010-01-01

    Full Text Available Laryngotracheal reconstruction (LTR involves surgical correction of a stenotic airway with cartilage interpositional grafting, followed by either placement of a tracheostomy and an intraluminal stent (two-stage LTR or placement of an endotracheal tube with postoperative sedation and mechanical ventilation for an extended period of time (single-stage LTR. With single-stage repair, there may be several perioperative challenges including the provision of adequate sedation, avoidance of the development of tolerance to sedative and analgesia agents, the need to use neuromuscular blocking agents, the maintenance of adequate pulmonary toilet to avoid perioperative nosocomial infections, and optimization of postoperative respiratory function to facilitate successful tracheal extubation. We review the perioperative management of these patients, discuss the challenges during the postoperative period, and propose recommendations for the prevention of reversible causes of extubation failure in this article. Optimization to ensure a timely tracheal extubation and successful weaning of mechanical ventilator, remains the primary key to success in these surgeries as extubation failure or the need for prolonged postoperative mechanical ventilation can lead to failure of the graft site, the need for prolonged Pediatric Intensive Care Unit care, and in some cases, the need for a tracheostomy to maintain an adequate airway.

  20. Human-specific HERV-K insertion causes genomic variations in the human genome.

    Directory of Open Access Journals (Sweden)

    Wonseok Shin

    Full Text Available Human endogenous retroviruses (HERV sequences account for about 8% of the human genome. Through comparative genomics and literature mining, we identified a total of 29 human-specific HERV-K insertions. We characterized them focusing on their structure and flanking sequence. The results showed that four of the human-specific HERV-K insertions deleted human genomic sequences via non-classical insertion mechanisms. Interestingly, two of the human-specific HERV-K insertion loci contained two HERV-K internals and three LTR elements, a pattern which could be explained by LTR-LTR ectopic recombination or template switching. In addition, we conducted a polymorphic test and observed that twelve out of the 29 elements are polymorphic in the human population. In conclusion, human-specific HERV-K elements have inserted into human genome since the divergence of human and chimpanzee, causing human genomic changes. Thus, we believe that human-specific HERV-K activity has contributed to the genomic divergence between humans and chimpanzees, as well as within the human population.

  1. Costs and benefits of treatment for cocaine addiction in DATOS.

    Science.gov (United States)

    Flynn, P M; Kristiansen, P L; Porto, J V; Hubbard, R L

    1999-12-01

    Our objective was to examine the cost of long-term residential (LTR) and outpatient drug-free (ODF) treatments for cocaine-dependent patients participating in the Drug Abuse Treatment Outcome Studies (DATOS), calculate the tangible cost of crime to society, and determine treatment benefits. Subjects were 502 cocaine-dependent patients selected from a national and naturalistic nonexperimental evaluation of community-based treatment. Financial data were available for programs from 10 US cities where the subjects received treatment between 1991 and 1993. Treatment costs were estimated from the 1992 National Drug Abuse Treatment Unit Survey (NDATUS), and tangible costs of crime were estimated from reports of illegal acts committed before, during, and after treatment. Sensitivity analyses examined results for three methods of estimating the costs of crime and cost-benefit ratios. Results showed that cocaine-dependent patients treated in both LTR and ODF programs had reductions in costs of crime from before to after treatment. LTR patients had the highest levels and costs of crime before treatment, had the greatest amount of crime cost reductions in the year after treatment, and yielded the greatest net benefits. Cost-benefit ratios for both treatment modalities provided evidence of significant returns on treatment investments for cocaine addiction.

  2. Interaction of the phospholipid scramblase 1 with HIV-1 Tat results in the repression of Tat-dependent transcription

    Energy Technology Data Exchange (ETDEWEB)

    Kusano, Shuichi, E-mail: skusano@m2.kufm.kagoshima-u.ac.jp; Eizuru, Yoshito

    2013-04-19

    Highlights: •PLSCR1 specifically interacted with HIV-1 Tat in vitro and in vivo. •PLSCR1 repressed Tat-dependent transactivation of the HIV-1 LTR. •Suppression of PLSCR1 expression enhanced the levels of HIV-1 transcripts. •PLSCR1 reduced the nuclear localization of Tat. -- Abstract: Human phospholipid scramblase 1 (PLSCR1) is an interferon (IFN)-stimulated gene and possesses an IFN-mediated antiviral function. We show here that PLSCR1 directly interacts with human immunodeficiency virus type-1 (HIV-1) Tat. This interaction occurs both in vitro and in vivo through amino acids 160–250 of PLSCR1. Overexpression of PLSCR1 efficiently represses the Tat-dependent transactivation of the HIV-1 long terminal repeat (LTR) and reduces the nuclear translocation of Tat. In addition, shRNA-mediated suppression of endogenous PLSCR1 expression enhances the levels of gag mRNA in an HIV-1-infected T-cell line. These findings indicate that PLSCR1 negatively regulates the Tat-dependent transactivation of the HIV-1 LTR during HIV-1 infection.

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

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    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

  4. Hijacking of the O-GlcNAcZYME complex by the HTLV-1 Tax oncoprotein facilitates viral transcription.

    Science.gov (United States)

    Groussaud, Damien; Khair, Mostafa; Tollenaere, Armelle I; Waast, Laetitia; Kuo, Mei-Shiue; Mangeney, Marianne; Martella, Christophe; Fardini, Yann; Coste, Solène; Souidi, Mouloud; Benit, Laurence; Pique, Claudine; Issad, Tarik

    2017-07-01

    The viral Tax oncoprotein plays a key role in both Human T-cell lymphotropic virus type 1 (HTLV-1)-replication and HTLV-1-associated pathologies, notably adult T-cell leukemia. Tax governs the transcription from the viral 5'LTR, enhancing thereby its own expression, via the recruitment of dimers of phosphorylated CREB to cAMP-response elements located within the U3 region (vCRE). In addition to phosphorylation, CREB is also the target of O-GlcNAcylation, another reversible post-translational modification involved in a wide range of diseases, including cancers. O-GlcNAcylation consists in the addition of O-linked-N-acetylglucosamine (O-GlcNAc) on Serine or Threonine residues, a process controlled by two enzymes: O-GlcNAc transferase (OGT), which transfers O-GlcNAc on proteins, and O-GlcNAcase (OGA), which removes it. In this study, we investigated the status of O-GlcNAcylation enzymes in HTLV-1-transformed T cells. We found that OGA mRNA and protein expression levels are increased in HTLV-1-transformed T cells as compared to control T cell lines while OGT expression is unchanged. However, higher OGA production coincides with a reduction in OGA specific activity, showing that HTLV-1-transformed T cells produce high level of a less active form of OGA. Introducing Tax into HEK-293T cells or Tax-negative HTLV-1-transformed TL-om1 T cells is sufficient to inhibit OGA activity and increase total O-GlcNAcylation, without any change in OGT activity. Furthermore, Tax interacts with the OGT/OGA complex and inhibits the activity of OGT-bound OGA. Pharmacological inhibition of OGA increases CREB O-GlcNAcylation as well as HTLV-1-LTR transactivation by Tax and CREB recruitment to the LTR. Moreover, overexpression of wild-type CREB but not a CREB protein mutated on a previously described O-GlcNAcylation site enhances Tax-mediated LTR transactivation. Finally, both OGT and OGA are recruited to the LTR. These findings reveal the interplay between Tax and the O-GlcNAcylation pathway

  5. Molecular epidemiology of endemic human T-lymphotropic virus type 1 in a rural community in Guinea-Bissau.

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    Carla van Tienen

    Full Text Available Human T-Lymphotropic Virus Type 1 (HTLV-1 infection causes lethal adult T-cell leukemia (ATL and severely debilitating HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP in up to 5% of infected adults. HTLV-1 is endemic in parts of Africa and the highest prevalence in West Africa (5% has been reported in Caio, a rural area in the North-West of Guinea-Bissau. It is not known which HTLV-1 variants are present in this community. Sequence data can provide insights in the molecular epidemiology and help to understand the origin and spread of HTLV-1.To gain insight into the molecular diversity of HTLV-1 in West Africa.HTLV-1 infected individuals were identified in community surveys between 1990-2007. The complete Long Terminal Repeat (LTR and p24 coding region of HTLV-1 was sequenced from infected subjects. Socio-demographic data were obtained from community census and from interviews performed by fieldworkers. Phylogenetic analyses were performed to characterize the relationship between the Caio HTLV-1 and HTLV-1 from other parts of the world.LTR and p24 sequences were obtained from 72 individuals (36 LTR, 24 p24 only and 12 both. Consistent with the low evolutionary change of HTLV-1, many of the sequences from unrelated individuals showed 100% nucleotide identity. Most (45 of 46 of the LTR sequences clustered with the Cosmopolitan HTLV-1 subtype 1a, subgroup D (1aD. LTR and p24 sequences from two subjects were divergent and formed a significant cluster with HTLV-1 subtype 1g, and with the most divergent African Simian T-cell Lymphotropic Virus, Tan90.The Cosmopolitan HTLV-1 1aD predominates in this rural West African community. However, HTLV-1 subtype 1g is also present. This subtype has not been described before in West Africa and may be more widespread than previously thought. These data are in line with the hypothesis that multiple monkey-to-man zoonotic events are contributing to HTLV-1 diversity.

  6. El retrato de Carlos I de Van Dyck del palacio de Summerset identificado en los fondos del Museo del Prado

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    Díaz Padrón, Matías

    2007-06-01

    Full Text Available The Equestrian Portrait of Charles I of England, coming from the Spanish royal collections and in the Prado Museum since the 19th century, has always been considered to be a copy of Van Dyck. It is now possible to demonstrate the authenticity of this work, the dimensions, quality and technique of which are identical to the Van Dyck in the National Gallery. The author studies the Madrid autograph replica stylistically and through the use of documentary materials ranging in date from 1650 to 1727. In 1654, when it was in Summerset Palace, the Prado version was considered to be “the best by Van Dyck,” and through this study the work is returned to his hand.

    El retrato ecuestre de Carlos I de Inglaterra del museo del Prado, fue tenido siempre por copia de Van Dyck y en los depósitos desde el legado de Fernando VII. Hoy es posible probar su autenticidad y restitución a Van Dyck de dimensiones, calidad y técnica idéntica al conocido en la National Gallery. Al estudio estilístico unimos el hallazgo documental en lista de obras que proponen a Cárdenas para la colección del rey de España el 25 de mayo de 1654. La otra réplica la adquirió B. Gerbier el 21 de junio de 1650, cuatro años antes de la memoria de la almoneda del rey inglés citada. De aquí que son dos originales, no uno. El del museo del Prado que hoy restituimos a van Dyck cubre el espacio de la documentación hasta ahora conocida en la colección de Felipe V en la Granja en 1727, con localización en 1680 en las colecciones del marques de Mejorada, y Ensenada a continuación. Sigue un análisis de las fuentes de inspiración copias localizadas y su historia externa en los inventarios y testamentarías en España. Esta réplica (como copia hasta ahora en el museo del Prado constaba en la memoria de 1654 así: “Este cuadro es lo mejor que hizo Van Dyck”. Un alto precio y localización en el palacio de Summerset.

  7. Historia de la Cirugía de Columna y Médula

    OpenAIRE

    Germán Peña Quiñones; Enrique Jiménez Hakim

    2004-01-01

    ANTIGÜEDAD La evidencia más antigua de lesiones de columna se encuentra en el Papiro de Edwin Smith que de acuerdo con el Profesor JH Breasted, egiptólogo que lo estudió, fue escrito 1700 años A.C. y es copia de un manuscrito original que data de 3000 años A.C. y nos da información de la medicina de Egipto; en él se describen 6 casos de lesiones traumáticas de la columna, dos de ellas con lesión neurológica consistente en cuadriplejía y lesión de esfínteres y se hace diferenc...

  8. DINÁMICA DEL COMPLEJO DEL PORO NUCLEAR

    Directory of Open Access Journals (Sweden)

    TD GEYDAN

    2010-01-01

    Full Text Available El complejo del poro nuclear (CPN es un conjunto supra-molecular compuesto de múltiples copias de 30 familias de proteínas diferentes, siendo 456 nucleoporinas (Nups en total, que atraviesan la envoltura nuclear de todos los organismos pertenecientes al dominio Eukaria. El CPN es la compuerta del núcleo; por lo tanto, todas las macromo- léculas deben atravesarla para transitar del núcleo al citoplasma y viceversa. Durante los últimos años, se han propuesto varios modelos para explicar la regulación y el transporte de macromoléculas a través del CPN. En esta nota se describe la estructura, los meca- nismos y procesos involucrados durante el transporte a través del CPN, y cómo estos procesos son regulados por interacciones macromoleculares altamente dinámicas.

  9. Atlas humano. - radiografías normales del adulto, en bajo relieve

    OpenAIRE

    Otero Silva, José

    2011-01-01

    Tiene por objeto la presente poner en su conocimiento una obra de medicina, la cual, sin duda, puede ser de gran importancia como libro de consulta y de enseñanza. La forman cuatro lujosos álbumes de copias radiográficas en negativo, tal como se ven las películas en los negatoscopios. Cada album consta de cien radiografías  patantadas que están explicadas con sus historias clínicas y diagnósticos radiológicos correspondientes. El album número 1 contiene radiografías óseas. El album número 2 r...

  10. A Model System in S2 Cells to Test the Functional Activities of Drosophila Insulators.

    Science.gov (United States)

    Tikhonov, M; Gasanov, N B; Georgiev, P; Maksimenko, O

    2015-01-01

    Insulators are a special class of regulatory elements that can regulate interactions between enhancers and promoters in the genome of high eukaryotes. To date, the mechanisms of insulator action remain unknown, which is primarily related to the lack of convenient model systems. We suggested studying a model system which is based on transient expression of a plasmid with an enhancer of the copia transposable element, in Drosophila embryonic cell lines. We demonstrated that during transient transfection of circle plasmids with a well-known Drosophila insulator from the gypsy retrotransposon, the insulator exhibits in an enhancer-blocking assay the same properties as in Drosophila stable transgenic lines. Therefore, the Drosophila cell line is suitable for studying the main activities of insulators, which provides additional opportunities for investigating the functional role of certain insulator proteins.

  11. El Instituto Oceanográfico en la provincia de Málaga

    OpenAIRE

    Baro Domínguez, Jorge

    2014-01-01

    El Centro Oceanográfico de Málaga desde los años setenta hasta la actualidad. Introducción y contexto “El obispo de Málaga bendice la primera piedra del Instituto Internacional de Oceanografía”. Así aparecía en las Efemérides del diario Sur de Málaga refiriéndose a la colocación en 1929 de la primera piedra de lo que posteriormente sería el Laboratorio Oceanográfico, Acuario y Museo de Málaga. Hay una copia en los archivos del Centro Oceanográfico de la fotografía de prensa que rememor...

  12. Resúmenes anuales termopluviométricos de la Estación Experimental de Aula Dei (EEAD-CSIC): 1990-2012

    OpenAIRE

    Estación Experimental de Aula Dei; Gracia Ballarín, Ricardo

    2013-01-01

    [ES] 1 fichero .xls (ResAnTermPluvio(1990-2012).xls) con datos meteorológicos promedio. El fichero contiene 12 hojas de cálculo diferenciadas con los datos de medias calculadas año a año. Se han incorporado, además los ficheros copia en formato .pdf de cada una de esas hojas de cálculo, año a año. [EN] 1 File .xls (ResAnTermPluvio(1990-2012).xls) with meteorological data. The file groups 12 spreadsheets with the mean data differentiated annually. We have also incorporated files copies in a...

  13. La contaminación en la Commedia

    OpenAIRE

    Tonello, Elisabetta

    2016-01-01

    El fenómeno de la contaminación en un tradición tan nutrida como la de la Comedia de Dante se presenta de las más variadas formas, en virtud de los contextos de copia de los manuscritos, de las tipologías de los copistas y del estado de conservación de los testimonios. Mediante una reseña de las distintas categorías de la contaminación individuadas por la crítica (contaminación y contaminación extraestemática, contaminación de lecciones y de ejemplares, contaminacio...

  14. Papeles del Marqués del Risco referentes al Perú [Manuscrito

    OpenAIRE

    López Martínez, Juan Luis, , Marqués del Risco, (1644-1703

    2016-01-01

    Contenido:1. (h.1)5 hojas conteniendo dibujos a pluma, el 1 es una portada que representa un Templete, el 2&xBA una escena de la vida de Moisés, el 3 y el 4&xBA escudos de armas y el 5 retrato de un personaje ricamente vestido, que el autor el índice cree ser el Marqués del Risco.En el fol. 9 descripción de cómo ha de ser una lámina.2. (h.11) -Copia de comunicación de S.M. al Consejo de la Corona de Aragón para que le propongan al Marqués del Risco si hubiere alguna vacante correspondiente a ...

  15. Los hurtos del ingenio y la paternidad literaria en Miguel de Cervantes

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    Aurora Egido

    2013-12-01

    Full Text Available Starting from the semantic differences between hurtar (to filch and robar (to steal, this article analyses the ingenious craft through which, in all his works, Cervantes stole other people's words and quotes, making them his own through a double process of intertextuality and orality. Rather than in the copia verborum, the author of Don Quixote was interested in transforming other authors' concepts and ideas by means of an exercise of ruminatio and compound imitation that went well beyond the rhetorical practices and normative precepts of his age. Without neglecting the requirements of dispositio and elocutio, as an authentic pioneer in every field, Cervantes concentrated his endeavours particularly on inventio, which paved the way to modern fiction. This explains his emphatic claims in his prologues to indisputable fatherhood of the books generated by his intellect, as legitimate sons.

  16. Comparative analysis of DNA methylation polymorphism in drought sensitive (HPKC2) and tolerant (HPK4) genotypes of horse Gram (Macrotyloma uniflorum).

    Science.gov (United States)

    Bhardwaj, Jyoti; Mahajan, Monika; Yadav, Sudesh Kumar

    2013-08-01

    DNA methylation is known as an epigenetic modification that affects gene expression in plants. Variation in CpG methylation behavior was studied in two natural horse gram (Macrotyloma uniflorum [Lam.] Verdc.) genotypes, HPKC2 (drought-sensitive) and HPK4 (drought-tolerant). The methylation pattern in both genotypes was studied through methylation-sensitive amplified polymorphism. The results revealed that methylation was higher in HPKC2 (10.1%) than in HPK4 (8.6%). Sequencing demonstrated sequence homology with the DRE binding factor (cbf1), the POZ/BTB protein, and the Ty1-copia retrotransposon among some of the polymorphic fragments showing alteration in methylation behavior. Differences in DNA methylation patterns could explain the differential drought tolerance and the epigenetic signature of these two horse gram genotypes.

  17. Estudio de variantes estructurales del genoma humano asociadas a trastornos del neurodesarrollo

    OpenAIRE

    Villatoro Gómez, Sergio

    2016-01-01

    Bibliografia El síndrome de Angelman (SA) y el de Prader Wili (SPW) son trastornos del neurodesarrollo cuya principal etiología molecular es la deleción de la región 15q11.2-q13. Esta deleción está promovida por la Recombinación Homóloga No Alélica (NAHR) y mediada por secuencias altamente repetitivas de bajo número de copias (LCRs) que la flanquean. La orientación de estas LCRs predispone al reordenamiento final que se obtendrá por NAHR. Las LCRs en orientación directa generan deleciones ...

  18. Modelos romanos en la arquitectura monumental de Colonia Patricia Corduba

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    Márquez, Carlos

    1998-12-01

    Full Text Available Examination of a number of Roman architectural fragments from Colonia Patricia makes possible the identification of the buildings to which they belong. This prompts a revision not only of the date and function of these buildings, but also of their placement within the urban landscape. In the choice of materials and scale of its buildings Patricia closely follows models from Rome itself.Este trabajo analiza de forma detallada algunos elementos arquitectónicos romanos de Colonia Patricia para poder adscribirlos a edificios urbanos. De esta forma se pueden plantear nuevas hipótesis sobre cronología, función e inserción de los mismos en el marco urbanístico, concluyendo la absoluta dependencia de la capital de la provincia Baetica de modelos procedentes de Roma a los que copia en material y dimensiones.

  19. El resurgir de la mujer fatal en publicidad: La reinvención de un mito

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    Tatiana Hidalgo-Marí

    2015-06-01

    Full Text Available La representación de la  “mujer fatal” es una imagen muy utilizada a la hora de poner en escena a la mujer en publicidad.  El carácter seductor y persuasivo de este estereotipo femenino encaja perfectamente en la idiosincrasia publicitaria que pretende persuadir y/o seducir al receptor para motivarle la predisposición a la pieza. No obstante, la forma en que se representa la mujer fatal en publicidad se aleja, en muchos casos, de la esencia clásica que sustentó al arquetipo tradicional. Este artículo pretende dejar constancia de cómo se representa la mujer fatal en publicidad, cómo se distorsiona el carácter formal de dicho arquetipo y se exponen nuevos reflejos de mujeres fatales, siendo éstas copias inexactas del arquetipo tradicional que las sustenta.

  20. ¿Quién teme al periódico digital?

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    Dra. Lucía Martínez Odriozola

    1999-01-01

    Full Text Available En un momento en que hablar de los diarios en Internet está de moda y en el que se hacen cábalas constantemente con el futuro de la prensa tradicional y su sustitución por los denominados periódicos digitales, el presente trabajo, basado en un estudio realizado en el País Vasco (UPV-EHU, pone en cuestión que en realidad estos últimos sean, de momento, una amenaza real para los diarios convencionales.Ni empresarialmente, ya que ambas versiones, papel y digital, pertenecen a la misma empresa editora; ni periodísticamente, porque las ediciones digitales son un mero volcado o copia de las de papel, que no aprovechan las prácticamente infinitas posibilidades que les otorga el soporte electrónico ni han creado un lenguaje propio para el nuevo medio.

  1. Diagnóstico molecular del Cáncer de mama por el oncogén HER-2/NEU mediante la técnica de Fish para el Departamento del Cauca (Colombia

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    M. Osorio

    2001-07-01

    Full Text Available Se evaluó la presencia del gen Her2-/neu en una muestra de 28 pacientes con diagnóstico decáncer de mama a quienes se les realizaron biopsias o mastectomías desde enero de 2000 afebrero de 2002. Las láminas embebidas en parafina fueron suministradas por la Compañía dePatólogos del Cauca y el Departamento de Patología del Hospital Universitario San Joséde Popayán; Cauca. Se utilizó la técnica de Hibridización in situpor Fluorescencia (FISH paravisualizar copias del gen Her-2/neu.

  2. Bellezas de porcelana: El japonismo y la representación de la mujer japonesa y su influencia en la occidental a través de las artes (Último tercio del siglo XIX-Primer cuarto del siglo XX)

    OpenAIRE

    Diez Galindo, David

    2016-01-01

    En este proyecto de fin de máster se va a poder observar una evolución en la representación de la mujer occidental, la cual imitó los canones de belleza y las características de una de las figuras más representativas de toda la historia de Japón, la geisha. Se copia su iconografía y los elementos del mundo que la rodeaban para mostrar un tipo de mujer diferente a la que se había representado en la pintura occidental hasta la época. Un tipo de mujer con una carga sensual y elegante basada en c...

  3. 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

  4. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges.

    Science.gov (United States)

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

    2012-03-01

    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.

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

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    Debbie Laudencia-Chingcuanco

    2012-01-01

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

  6. El análisis molecular y el inmunogénico sugieren la ausencia de las proteínas hidrofílicas de superficie en Leishmania (Viannia panamensis

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    Marcel Marín

    2008-09-01

    Full Text Available Introducción. Los dos subgéneros en los cuales se divide el género Leishmania: Viannia y Leishmania, presentan diferencias significativas en las manifestaciones clínicas que causan, en su comportamiento de crecimiento en cultivos in vitro, en sus características genéticas y en la expresión de varias proteínas, entre ellas las de la familia hidrofílica de superficie superficie. Objetivo. Caracterizar las proteínas hidrofílicas de superficie en Leishmania (Viannia panamensis. Materiales y métodos. Se amplificaron los genes hasp en L. (V. panamensis usando cebadores específicos para la especie Leishmania (Leishmania major. Los productos de la amplificación fueron clonados, secuenciados y analizados con herramientas bioinformáticas. Posteriormente, se realizó un análisis serológico por medio de ensayo inmunoabsorbente ligado a enzimas y Western blot para detectar la presencia de anticuerpos específicos contra las proteínas hidrofílicas recombinantes de superficie de L. (L. major en sueros de pacientes con leishmaniasis de zonas endémicas de Colombia. Resultados. Se encontró una copia de un pseudogen en L. (V. panamensis, el cual presentó una identidad del 60% con el gen haspa de L. (L. major. Sólo se encontraron anticuerpos contra las proteínas recombinantes de superficie hidrofílicas en sueros de pacientes con leishmaniasis visceral. Conclusión. Estos resultados sugieren que no existe ninguna copia de un gen funcional hasp en L. (V. panamensis, lo que indica una pérdida de la familia de genes en esta especie de Leishmania perteneciente al subgénero Viannia.

  7. El manuscrito jerezano de La Mojigata, comedia de Leandro Fernández de Moratín

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    López Romero, José

    2003-12-01

    Full Text Available The volume found in the Public Library of Jerez containing three Spanish Comedies by Leandro Fernández de Moratín, has the enormous importance of including first editions of both The new comedy (1792 and The old man and the little girl (1790, and especially a manuscript copy of The prude, a work which circulated in literary circles of Madrid during the early 1790s, and being even performed in some of them without Moratin's permission. This article tries to compare the Jerez manuscript copy with others already known, and with final edition of de work, and at the same time to shed some light on the identity of the owner of the volume where The prude is included.El volumen encontrado en la Biblioteca Municipal de Jerez de la Frontera con tres Comedias españolas de Leandro Fernández de Moratín, tiene el enorme valor de incluir primeras ediciones de La comedia nueva (1792 y de El viejo y la niña (1790 y, sobre todo, una copia manuscrita de La mojigata, obra que en los primeros años de la década de 1790 circuló de esa forma por tertulias madrileñas, en algunas de las cuales hasta se representó sin el consentimiento de Moratín. Este trabajo intenta cotejar la copia manuscrita jerezana con otras ya conocidas y con la edición definitiva de la obra, así como arrojar alguna luz sobre la identidad del propietario del volumen en el que aquélla se incluye.

  8. Un nuevo dibujo de Francisco Pacheco para su Libro de retratos: la efigie de Pablo de Céspedes en los Uffizi

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    Navarrete Prieto, Benito

    2016-03-01

    Full Text Available The author presents an original drawing by Francisco Pacheco, a portrait of the painter Pablo de Céspedes, related to Pacheco’s famous Libro de retratos. The drawing is the original of five copies by different hands kept at The Hispanic Society of America (Nueva York, the Royal Library of the Escorial, and the Amunátegui Collection; two copies are in the National Library of Spain, one of which is by Francisco de Goya. The drawing under consideration was formerly attributed to Barocci and comes from the prestigious collection donated by Santarelli to the Uffizi Gallery in the 19th century. This discovery highlights the importance of the copies conserved at The Hispanic Society and suggests there may be more unidentified portraits by Pacheco.Se da a conocer aquí un dibujo autógrafo de Francisco Pacheco, retrato del pintor Pablo de Céspedes y relacionado con el Libro de retratos de aquél. Este dibujo es la fuente original que siguieron las cinco copias conservadas en la Hispanic Society of America de Nueva York, en el manuscrito de la Real Biblioteca de El Escorial, en la colección Anmunátegui, y dos en la Biblioteca Nacional de España, una de mano de Francisco de Goya. El dibujo, atribuido hasta ahora a Barocci en el Gabinete de Dibujos y Estampas de los Uffizi, procede de la prestigiosa donación Santarelli. El hallazgo supone la constatación de la importancia de las copias de la Hispanic Society, que abren la posibilidad de que existan otros originales de Pacheco aún no identificados.

  9. Una defensa ética de lo teatral. Rousseau o el sobrino de Rameau

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    de Eugenio Pérez, Guillermo

    2013-06-01

    Full Text Available In this paper there are two opposite models for identity to be discussed, departing from the comparison made by philosopher Bernard Williams between the figures of Rousseau and Rameau’s nephew. Against the representational conception of an identity as the copy or proyection of an inner self, we propose a more performative notion of personality, conceived in terms of spontaneity and multiplicity as sources of the contemporary subject. In the background of this reflection there is the hypothesis that both methods of producing personal identity respond to aesthetic conceptions that are deeply rooted. One of them is closer to the pictorial model of a copy from an original, and the other, theatrical, is based in the importance of performance on creative processes.En este trabajo se discuten dos modelos opuestos de construcción de la identidad a partir de la contraposición que hace el filósofo Bernard Williams de las figuras de Rousseau y el sobrino de Rameau de Diderot. Frente a la concepción representacional de la identidad como copia o proyección de un ser interior, se propone una noción performativa de la personalidad basada en la espontaneidad y la multiplicidad como fuentes del sujeto contemporáneo. En el trasfondo de esta reflexión se encuentra la hipótesis de que ambos métodos de producción ética de la identidad personal responden a concepciones estéticas profundamente enraizadas, una más próxima al modelo pictórico de copia de un original y la otra, teatral, basada en la importancia de la interpretación en los procesos de creación.

  10. HER2-Overexpressing Breast Cancers Amplify FGFR Signaling upon Acquisition of Resistance to Dual Therapeutic Blockade of HER2.

    Science.gov (United States)

    Hanker, Ariella B; Garrett, Joan T; Estrada, Mónica Valeria; Moore, Preston D; Ericsson, Paula González; Koch, James P; Langley, Emma; Singh, Sharat; Kim, Phillip S; Frampton, Garrett M; Sanford, Eric; Owens, Philip; Becker, Jennifer; Groseclose, M Reid; Castellino, Stephen; Joensuu, Heikki; Huober, Jens; Brase, Jan C; Majjaj, Samira; Brohée, Sylvain; Venet, David; Brown, David; Baselga, José; Piccart, Martine; Sotiriou, Christos; Arteaga, Carlos L

    2017-08-01

    Purpose: Dual blockade of HER2 with trastuzumab and lapatinib or pertuzumab has been shown to be superior to single-agent trastuzumab. However, a significant fraction of HER2-overexpressing (HER2+) breast cancers escape from these drug combinations. In this study, we sought to discover the mechanisms of acquired resistance to the combination of lapatinib + trastuzumab.Experimental Design: HER2+ BT474 xenografts were treated with lapatinib + trastuzumab long-term until resistance developed. Potential mechanisms of acquired resistance were evaluated in lapatinib + trastuzumab-resistant (LTR) tumors by targeted capture next-generation sequencing. In vitro experiments were performed to corroborate these findings, and a novel drug combination was tested against LTR xenografts. Gene expression and copy-number analyses were performed to corroborate our findings in clinical samples.Results: LTR tumors exhibited an increase in FGF3/4/19 copy number, together with an increase in FGFR phosphorylation, marked stromal changes in the tumor microenvironment, and reduced tumor uptake of lapatinib. Stimulation of BT474 cells with FGF4 promoted resistance to lapatinib + trastuzumab in vitro Treatment with FGFR tyrosine kinase inhibitors reversed these changes and overcame resistance to lapatinib + trastuzumab. High expression of FGFR1 correlated with a statistically shorter progression-free survival in patients with HER2+ early breast cancer treated with adjuvant trastuzumab. Finally, FGFR1 and/or FGF3 gene amplification correlated with a lower pathologic complete response in patients with HER2+ early breast cancer treated with neoadjuvant anti-HER2 therapy.Conclusions: Amplification of FGFR signaling promotes resistance to HER2 inhibition, which can be diminished by the combination of HER2 and FGFR inhibitors. Clin Cancer Res; 23(15); 4323-34. ©2017 AACR. ©2017 American Association for Cancer Research.

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

    Science.gov (United States)

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

    2013-01-01

    Background and Aims Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots. Methods To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. Key Results The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4–5 % (asparagus) or 3–4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. Conclusions Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae. PMID:23887091

  12. Inducible expression of IkappaBalpha repressor mutants interferes with NF-kappaB activity and HIV-1 replication in Jurkat T cells.

    Science.gov (United States)

    Kwon, H; Pelletier, N; DeLuca, C; Genin, P; Cisternas, S; Lin, R; Wainberg, M A; Hiscott, J

    1998-03-27

    Human immunodeficiency virus (HIV-1) utilizes the NF-kappaB/Rel proteins to regulate transcription through NF-kappaB binding sites in the HIV-1 long terminal repeat (LTR). Normally, NF-kappaB is retained in the cytoplasm by inhibitory IkappaB proteins; after stimulation by multiple activators including viruses, IkappaBalpha is phosphorylated and degraded, resulting in NF-kappaB release. In the present study, we examined the effect of tetracycline-inducible expression of transdominant repressors of IkappaBalpha (TD-IkappaBalpha) on HIV-1 multiplication using stably selected Jurkat T cells. TD-IkappaBalpha was inducibly expressed as early as 3 h after doxycycline addition and dramatically reduced both NF-kappaB DNA binding activity and LTR-directed gene activity. Interestingly, induced TD-IkappaBalpha expression also decreased endogenous IkappaBalpha expression to undetectable levels by 24 h after induction, demonstrating that TD-IkappaBalpha repressed endogenous NF-kappaB-dependent gene transcription. TD-IkappaBalpha expression also sensitized Jurkat cells to tumor necrosis factor-induced apoptosis. De novo HIV-1 infection of Jurkat cells was dramatically altered by TD-IkappaBalpha induction, resulting in inhibition of HIV-1 multiplication, as measured by p24 antigen, reverse transcriptase, and viral RNA. Given the multiple functions of the NF-kappaB/IkappaB pathway, TD-IkappaBalpha expression may interfere with HIV-1 multiplication at several levels: LTR-mediated transcription, Rev-mediated export of viral RNA, inhibition of HIV-1-induced pro-inflammatory cytokines, and increased sensitivity of HIV-1-infected cells to apoptosis.

  13. Molecular characteristics of the complete genome of a J-subgroup avian leukosis virus strain isolated from Eurasian teal in China.

    Science.gov (United States)

    Zeng, Xiangwei; Gao, Yulong; Li, Delong; Hao, Ruijun; Liu, Wansi; Han, Chunyan; Gao, Honglei; Qi, Xiaole; Wang, Yongqiang; Liu, Lanlan; Wang, Xiaomei

    2014-10-01

    The J-subgroup avian leukosis virus (ALV-J) strain WB11098J was isolated from a wild Eurasian teal, and its proviral genomic sequences were determined. The complete proviral sequence of WB11098J was 7868 nt long. WB11098J was 95.3.9 % identical to the prototype strain HPRS-103, 94.2 % identical to the American strain ADOL-7501, 94.5-94.7 % identical to Chinese broiler isolates, 94.8-97.5 % identical to layer chicken isolates, and 94.4-95.0 % identical to Chinese local chicken isolates at the nucleotide level. Phylogenetic analysis showed that the WB11098J isolate shared the greatest homology with the layer strain SD09DP03 and was included in the same cluster. Interestingly, two 19-bp insertions in the U3 regions of the 5'LTR and 5'UTR that were most likely derived from other retroviruses were found in the WB11098J isolate. These insertions separately introduced one E2BP-binding site in the U3 region of the 5'LTR and a RNA polymerase II transcription factor IIB and core promoter motif of ten elements in the 5'UTR. A 5-bp deletion was identified in the U3 region of the 5'LTR. No nucleotides were deleted in the rTM or DR-1 regions in the 3'UTR. A 1-bp deletion was detected in the E element and introduced a specific and distinct binding site for c-Ets-1. Our study is the first to report the molecular characteristics of the complete genome of an ALV-J that was isolated from a wild bird and will provide necessary information for further understanding of the evolution of ALV-J.

  14. Exposure to hypomethylating agent, 5-azacytidine, may improve iCasp9 suicide gene therapy for treating GvHD in allografts.

    Science.gov (United States)

    Bôle-Richard, E; Gamonet, C; Certoux, J-M; Idirene, I; Larosa, F; Deconinck, E; Mosseley, A-M; Tiberghien, P; Borg, C; Ferrand, C; Deschamps, M

    2016-08-01

    Anti-tumor cellular immunotherapies that implement a suicide gene system can limit potential undesirable effects. In a haplo-identical bone marrow transplant clinical trial, over 90% of iCaspase-9-expressing cells were eradicated after AP1903 exposure, and signs of graft-versus-host disease disappeared. Nevertheless, low numbers of genetically modified T cells survived this treatment. We studied genetically modified cell lines (GMCL) that carried a dual iCaspase-9/ΔCD19 DNA construct (ΔCD19=truncated CD19). With AP1903 exposure, a low percentage of cells (1.47±0.67%; n=5 replications) persisted in vitro. Repeated exposures to increasing AP1903 doses generated low (GMCLLR) and high AP1903-responders (GMCLHR), which expressed different levels of surface ΔCD19 and intracellular iCaspase-9. Compared with GMCLHR, GMCLLR exhibited higher methylation of 5'-long-terminal repeat (LTR) promoters, both in the number of sequences with at least one methylated CpG (16 vs 51.5%, respectively) and in the number of CpG islands (1.2 vs 8.9%, respectively). Four days of 5-azacytidine exposure reduced methylation and increased ΔCD19 and iCaspase-9 expression. Interestingly, LTR demethylation restored GMCLLR sensitivity to AP1903 by 24.3-fold (1.8 vs 43.8%) without affecting GMCLHR. We showed that 5'-LTR-methylation inhibited transgene expression and caused AP1903 hypo-responsiveness. Treating with a hypomethylating agent restored AP1903 sensitivity. This approach can be applied in further clinical trials to improve iCaspase-9 response if low response is detected.

  15. Polarized expression of the membrane ASP protein derived from HIV-1 antisense transcription in T cells

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    Gay Bernard

    2011-09-01

    Full Text Available Abstract Background Retroviral gene expression generally depends on a full-length transcript that initiates in the 5' LTR, which is either left unspliced or alternatively spliced. We and others have demonstrated the existence of antisense transcription initiating in the 3' LTR in human lymphotropic retroviruses, including HTLV-1, HTLV-2, and HIV-1. Such transcripts have been postulated to encode antisense proteins important for the establishment of viral infections. The antisense strand of the HIV-1 proviral DNA contains an ORF termed asp, coding for a highly hydrophobic protein. However, although anti-ASP antibodies have been described to be present in HIV-1-infected patients, its in vivo expression requires further support. The objective of this present study was to clearly demonstrate that ASP is effectively expressed in infected T cells and to provide a better characterization of its subcellular localization. Results We first investigated the subcellular localization of ASP by transfecting Jurkat T cells with vectors expressing ASP tagged with the Flag epitope to its N-terminus. Using immunofluorescence microscopy, we found that ASP localized to the plasma membrane in transfected Jurkat T cells, but with different staining patterns. In addition to an entire distribution to the plasma membrane, ASP showed an asymmetric localization and could also be detected in membrane connections between two cells. We then infected Jurkat T cells with NL4.3 virus coding for ASP tagged with the Flag epitope at its C-terminal end. By this approach, we were capable of showing that ASP is effectively expressed from the HIV-1 3' LTR in infected T cells, with an asymmetric localization of the viral protein at the plasma membrane. Conclusion These results demonstrate for the first time that ASP can be detected when expressed from full-length HIV-1 proviral DNA and that its localization is consistent with Jurkat T cells overexpressing ASP.

  16. Molecular characteristics of Polish field strains of Marek's disease herpesvirus isolated from vaccinated chickens

    Directory of Open Access Journals (Sweden)

    Kozdruń Wojciech

    2011-02-01

    Full Text Available Abstract Background Twenty-nine Marek's disease virus (MDV strains were isolated during a 3 year period (2007-2010 from vaccinated and infected chicken flocks in Poland. These strains had caused severe clinical symptoms and lesions. In spite of proper vaccination with mono- or bivalent vaccines against Marek's disease (MD, the chickens developed symptoms of MD with paralysis. Because of this we decided to investigate possible changes and mutations in the field strains that could potentially increase their virulence. We supposed that such mutations may have been caused by recombination with retroviruses of poultry - especially reticuloendotheliosis virus (REV. Methods In order to detect the possible reasons of recent changes in virulence of MDV strains, polymerase chain reaction (PCR analyses for meq oncogene and for long-terminal repeat (LTR region of REV were conducted. The obtained PCR products were sequenced and compared with other MDV and REV strains isolated worldwide and accessible in the GeneBank database. Results Sequencing of the meq oncogene showed a 68 basepair insertion and frame shift within 12 of 24 field strains. Interestingly, the analyses also showed 0.78, 0.8, 0.82, 1.6 kb and other random LTR-REV insertions into the MDV genome in 28 of 29 of strains. These genetic inserts were present after passage in chicken embryo kidney cells suggesting LTR integration into a non-functional region of the MDV genome. Conclusion The results indicate the presence of a recombination between MDV and REV under field conditions in Polish chicken farms. The genetic changes within the MDV genome may influence the virus replication and its features in vivo. However, there is no evidence that meq alteration and REV insertions are related to the strains' virulence.

  17. Dynamics of viral replication in blood and lymphoid tissues during SIVmac251 infection of macaques

    Directory of Open Access Journals (Sweden)

    Mannioui Abdelkrim

    2009-01-01

    Full Text Available Abstract Background Extensive studies of primary infection are crucial to our understanding of the course of HIV disease. In SIV-infected macaques, a model closely mimicking HIV pathogenesis, we used a combination of three markers -- viral RNA, 2LTR circles and viral DNA -- to evaluate viral replication and dissemination simultaneously in blood, secondary lymphoid tissues, and the gut during primary and chronic infections. Subsequent viral compartmentalization in the main target cells of the virus in peripheral blood during the chronic phase of infection was evaluated by cell sorting and viral quantification with the three markers studied. Results The evolutions of viral RNA, 2LTR circles and DNA levels were correlated in a given tissue during primary and early chronic infection. The decrease in plasma viral load principally reflects a large decrease in viral replication in gut-associated lymphoid tissue (GALT, with viral RNA and DNA levels remaining stable in the spleen and peripheral lymph nodes. Later, during chronic infection, a progressive depletion of central memory CD4+ T cells from the peripheral blood was observed, accompanied by high levels of viral replication in the cells of this subtype. The virus was also found to replicate at this point in the infection in naive CD4+ T cells. Viral RNA was frequently detected in monocytes, but no SIV replication appeared to occur in these cells, as no viral DNA or 2LTR circles were detected. Conclusion We demonstrated the persistence of viral replication and dissemination, mostly in secondary lymphoid tissues, during primary and early chronic infection. During chronic infection, the central memory CD4+ T cells were the major site of viral replication in peripheral blood, but viral replication also occurred in naive CD4+ T cells. The role of monocytes seemed to be limited to carrying the virus as a cargo because there was an observed lack of replication in these cells. These data may have important

  18. Draft genome of the living fossil Ginkgo biloba.

    Science.gov (United States)

    Guan, Rui; Zhao, Yunpeng; Zhang, He; Fan, Guangyi; Liu, Xin; Zhou, Wenbin; Shi, Chengcheng; Wang, Jiahao; Liu, Weiqing; Liang, Xinming; Fu, Yuanyuan; Ma, Kailong; Zhao, Lijun; Zhang, Fumin; Lu, Zuhong; Lee, Simon Ming-Yuen; Xu, Xun; Wang, Jian; Yang, Huanming; Fu, Chengxin; Ge, Song; Chen, Wenbin

    2016-11-21

    Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways. The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.

  19. Proliferation of endogenous retroviruses in the early stages of a host germ line invasion.

    Science.gov (United States)

    Ishida, Yasuko; Zhao, Kai; Greenwood, Alex D; Roca, Alfred L

    2015-01-01

    Endogenous retroviruses (ERVs) comprise 8% of the human genome and are common in all vertebrate genomes. The only retrovirus known to be currently transitioning from exogenous to endogenous form is the koala retrovirus (KoRV), making koalas (Phascolarctos cinereus) ideal for examining the early stages of retroviral endogenization. To distinguish endogenous from exogenous KoRV proviruses, we isolated koala genomic regions flanking KoRV integration sites. In three wild southern Australian koalas, there were fewer KoRV loci than in three captive Queensland koalas, consistent with reports that southern Australian koalas carry fewer KoRVs. Of 39 distinct KoRV proviral loci examined in a sire-dam-progeny triad, all proved to be vertically transmitted and endogenous; none was exogenous. Of the 39 endogenous KoRVs (enKoRVs), only one was present in the genomes of both the sire and the dam, suggesting that, at this early stage in the retroviral invasion of a host germ line, very large numbers of ERVs have proliferated at very low frequencies in the koala population. Sequence divergence between the 5'- and 3'-long terminal repeats (LTRs) of a provirus can be used as a molecular clock. Within each of ten enKoRVs, the 5'-LTR sequence was identical to the 3'-LTR sequence, suggesting a maximum age for enKoRV invasion of the koala germ line of approximately 22,200-49,900 years ago, although a much younger age is possible. Across the ten proviruses, seven LTR haplotypes were detected, indicating that at least seven different retroviral sequences had entered the koala germ line. © 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.

  20. ONSL and OSKM cocktails act synergistically in reprogramming human somatic cells into induced pluripotent stem cells.

    Science.gov (United States)

    Jung, Laura; Tropel, Philippe; Moal, Yohann; Teletin, Marius; Jeandidier, Eric; Gayon, Régis; Himmelspach, Christian; Bello, Fiona; André, Cécile; Tosch, Adeline; Mansouri, Ahmed; Bruant-Rodier, Catherine; Bouillé, Pascale; Viville, Stéphane

    2014-06-01

    The advent of human induced pluripotent stem cells (hiPSC) is revolutionizing many research fields including cell-replacement therapy, drug screening, physiopathology of specific diseases and more basic research such as embryonic development or diseases modeling. Despite the large number of reports on reprogramming methods, techniques in use remain globally inefficient. We present here a new optimized approach to improve this efficiency. After having tested different monocistronic vectors with poor results, we adopted a polycistronic cassette encoding Thomson's cocktail OCT4, NANOG, SOX2 and LIN28 (ONSL) separated by 2A peptides. This cassette was tested in various vector backbones, based on lentivirus or retrovirus under a LTR or EF1 alpha promoter. This allowed us to show that ONSL-carrier retrovectors reprogrammed adult fibroblast cells with a much higher efficiency (up to 0.6%) than any other tested. We then compared the reprogramming efficiencies of two different polycistronic genes, ONSL and OCT4, SOX2, KLF4 and cMYC (OSKM) placed in the same retrovector backbone. Interestingly, in this context ONSL gene reprograms more efficiently than OSKM but OSKM reprograms faster suggesting that the two cocktails may reprogram through distinct pathways. By equally mixing RV-LTR-ONSL and RV-LTR-OSKM, we indeed observed a remarkable synergy, yielding a reprogramming efficiency of >2%. We present here a drastic improvement of the reprogramming efficiency, which opens doors to the development of automated and high throughput strategies of hiPSC production. Furthermore, non-integrative reprogramming protocols (i.e. mRNA) may take advantage of this synergy to boost their efficiency. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Long-distance effects of insertional mutagenesis.

    Directory of Open Access Journals (Sweden)

    Ruchi Singhal

    2011-01-01

    Full Text Available Most common systems of genetic engineering of mammalian cells are associated with insertional mutagenesis of the modified cells. Insertional mutagenesis is also a popular approach to generate random alterations for gene discovery projects. A better understanding of the interaction of the structural elements within an insertional mutagen and the ability of such elements to influence host genes at various distances away from the insertion site is a matter of considerable practical importance.We observed that, in the context of a lentiviral construct, a transcript, which is initiated at an internal CMV promoter/enhancer region and incorporates a splice donor site, is able to extend past a collinear viral LTR and trap exons of host genes, while the polyadenylation signal, which is naturally present in the LTR, is spliced out. Unexpectedly, when a vector, which utilizes this phenomenon, was used to produce mutants with elevated activity of NF-κB, we found mutants, which owed their phenotype to the effect of the insert on a gene located tens or even hundreds of kilobases away from the insertion site. This effect did not result from a CMV-driven transcript, but was sensitive to functional suppression of the insert. Interestingly, despite the long-distance effect, expression of loci most closely positioned to the insert appeared unaffected.We concluded that a polyadenylation signal in a retroviral LTR, when occurring within an intron, is an inefficient barrier against the formation of a hybrid transcript, and that a vector containing a strong enhancer may selectively affect the function of genes far away from its insertion site. These phenomena have to be considered when experimental or therapeutic transduction is performed. In particular, the long-distance effects of insertional mutagenesis bring into question the relevance of the lists of disease-associated retroviral integration targets, which did not undergo functional validation.

  2. The new 1.8 I DI turbo-jet gasoline engine from Fiat Powertrain Technologies

    Energy Technology Data Exchange (ETDEWEB)

    Andriesse, Dirk; Comignaghi, Emilio; Lucignano, Gennaro; Oreggioni, Aldo; Quinto, Stefano; Sacco, Dario [Fiat Powertrain Technologies, Arese-Turin (Italy)

    2008-07-01

    The newly developed 1.8 ltr gasoline DI Turbo-Jet engine extends the gasoline product portfolio of Fiat Powertrain Technologies after the successful launch of the 1.4 ltr T-jet engine family in 2007. FPT retains the turbo downsizing concept the most efficient measure to meet the required reduction of CO2 emissions enhancing in the meantime the fun to drive characteristics of the gasoline engine, with the aim to equal at least those of DI turbo diesel units. The adoption of the turbocharger permits as well to differentiate the engines by tuning according to the brand requirements of the various Fiat Group car platforms. The common mechanical base is ideal to provide both the best thermodynamic efficiency and the cost advantages given by the production volumes. Thanks to the direct injection, the double continuously variable cam phasing and turbo charging the new 1.8 ltr DI Turbo-Jet engine develops high specific maximum torque and power values: the HP variant reaches nearly 200 Nm/l and 100 kW/l. The excellent low end torque and fast turbo response are obtained by newly developed advanced EMS scavenging strategies. The final result is highlighted by the 23.1 bar BMEP value at 1400 rpm for the Soft version which is the benchmark today for all gasoline turbocharged engines on the market. Emission levels meet the new Euro 5 standards with a large margin thanks to multiple injection and high pressure stratified charge start strategies even using a packaging friendly low volume close coupled catalytic system. To reach the stringent NVH requirements the engine is mechanically optimised by adopting a slightly over square bore/stroke ratio, a long conrod, a moderate rated engine speed and low alternating masses. Excellent results are obtained which equal those of competitor engines without the use of secondary order balancing shafts. (orig.)

  3. Effects of Mutations in the G Tract of the Human Immunodeficiency Virus Type 1 Polypurine Tract on Virus Replication and RNase H Cleavage

    Science.gov (United States)

    Julias, John G.; McWilliams, Mary Jane; Sarafianos, Stefan G.; Alvord, W. Gregory; Arnold, Eddy; Hughes, Stephen H.

    2004-01-01

    The RNase H cleavages that generate and remove the polypurine tract (PPT) primer during retroviral reverse transcription must be specific in order to create a linear viral DNA that is suitable for integration. Lentiviruses contain a highly conserved sequence consisting of six guanine residues at the 3′ end of the PPT (hereafter referred to as the G tract). We introduced mutations into the G tract of a human immunodeficiency virus type 1-based vector and determined the effects on the virus titer and RNase H cleavage specificity. Most mutations in the G tract had little or no effect on the virus titer. Mutations at the second and fifth positions of the G tract increased the proportion of two-long-terminal-repeat (2-LTR) circle junctions with one or two nucleotide insertions. The second and fifth positions of the G tract make specific contacts with amino acids in the RNase H domain that are important for RNase H cleavage specificity. These complementary data define protein-nucleic acid interactions that help control the specificity of RNase H cleavage. When the G-tract mutants were analyzed in a viral background that was deficient in integrase, in most cases the proportion of consensus 2-LTR circle junctions increased. However, in the case of a mutant with Ts at the second and fifth positions of the G tract, the proportion of 2-LTR circle junctions containing the one-nucleotide insertion increased, suggesting that linear viral DNAs containing an extra base are substrates for integration. This result is consistent with the idea that the 3′ end-processing reactions of retroviral integrases may help to generate defined ends from a heterogenous population of linear viral DNAs. PMID:15542682

  4. Alternate Polypurine Tracts (PPTs) Affect the Rous Sarcoma Virus RNase H Cleavage Specificity and Reveal a Preferential Cleavage following a GA Dinucleotide Sequence at the PPT-U3 Junction

    Science.gov (United States)

    Chang, Kevin W.; Julias, John G.; Alvord, W. Gregory; Oh, Jangsuk; Hughes, Stephen H.

    2005-01-01

    Retroviral polypurine tracts (PPTs) serve as primers for plus-strand DNA synthesis during reverse transcription. The generation and removal of the PPT primer requires specific cleavages by the RNase H activity of reverse transcriptases; removal of the PPT primer defines the left end of the linear viral DNA. We replaced the endogenous PPT from RSVP(A)Z, a replication-competent shuttle vector based on Rous sarcoma virus (RSV), with alternate retroviral PPTs and the duck hepatitis B virus “PPT.” Viruses in which the endogenous RSV PPT was replaced with alternate PPTs had lower relative titers than the wild-type virus. 2-LTR circle junction analysis showed that the alternate PPTs caused significant decreases in the fraction of viral DNAs with complete (consensus) ends and significant increases in the insertion of part or all of the PPT at the 2-LTR circle junctions. The last two nucleotides in the 3′ end of the RSV PPT are GA. Examination of the (mis)cleavages of the alternate PPTs revealed preferential cleavages after GA dinucleotide sequences. Replacement of the terminal 3′ A of the RSV PPT with G caused a preferential miscleavage at a GA sequence spanning the PPT-U3 boundary, resulting in the deletion of the terminal adenine normally present at the 5′ end of the U3. A reciprocal G-to-A substitution at the 3′ end of the murine leukemia virus PPT increased the relative titer of the chimeric RSV-based virus and the fraction of consensus 2-LTR circle junctions. PMID:16227289

  5. Isolation and characterization of functional tripartite group II introns using a Tn5-based genetic screen.

    Directory of Open Access Journals (Sweden)

    Christine Ritlop

    Full Text Available BACKGROUND: Group II introns are RNA enzymes that splice themselves from pre-mRNA transcripts. Most bacterial group II introns harbour an open reading frame (ORF, coding for a protein with reverse transcriptase, maturase and occasionally DNA binding and endonuclease activities. Some ORF-containing group II introns were shown to be mobile retroelements that invade new DNA target sites. From an evolutionary perspective, group II introns are hypothesized to be the ancestors of the spliceosome-dependent nuclear introns and the small nuclear RNAs (snRNAs--U1, U2, U4, U5 and U6 that are important functional elements of the spliceosome machinery. The ability of some group II introns fragmented in two or three pieces to assemble and undergo splicing in trans supports the theory that spliceosomal snRNAs evolved from portions of group II introns. METHODOLOGY/PRINCIPAL FINDINGS: We used a transposon-based genetic screen to explore the ability of the Ll.LtrB group II intron from the Gram-positive bacterium Lactococcus lactis to be fragmented into three pieces in vivo. Trans-splicing tripartite variants of Ll.LtrB were selected using a highly efficient and sensitive trans-splicing/conjugation screen. We report that numerous fragmentation sites located throughout Ll.LtrB support tripartite trans-splicing, showing that this intron is remarkably tolerant to fragmentation. CONCLUSIONS/SIGNIFICANCE: This work unveils the great versatility of group II intron fragments to assemble and accurately trans-splice their flanking exons in vivo. The selected introns represent the first evidence of functional tripartite group II introns in bacteria and provide experimental support for the proposed evolutionary relationship between group II introns and snRNAs.

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

    Science.gov (United States)

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

    2004-06-15

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

  7. CSIR Annual report 2000

    CSIR Research Space (South Africa)

    CSIR

    2000-01-01

    Full Text Available on its way to seek- ing the sporting goal of a lifetime by providing vital input to and assistance for the 2006 Football World Cup Bid. � Ltr: Thys du Plooy, Hendrik Theron, Francois le Roux, Jean-Jacques Juame, Pierre Barlow, JP Delport, Michelle... of quality and business excellence. � Marten Grundlingh and Louise Watt received the William T Pecora Award, jointly sponsored by the US Department of the Interior and the National Aeronautics and Space Administration (NASA), for outstanding contributions...

  8. Study of Nilsson Potential at different nuclear deformations

    Directory of Open Access Journals (Sweden)

    Azam Kardan

    2017-11-01

    Full Text Available p { margin-bottom: 0.1in; direction: ltr; color: rgb(0, 0, 0; line-height: 120%; }p.western { }p.ctl { } We have studied the Nilsson potential energies at different deformation parameters using a code based on the perturbative treatment. Special attention is given to the projection of a proton state at different deformations on the asymptotic basis functions. Our calculations show that the spin-orbit and the orbital angular momentum terms couple different asymptotic eigenstates, Nilsson Hamiltonian being hence not diagonal in these basis functions. Therefore, at least at deformations 0.4, the asymptotic quantum numbers are not good quantum numbers.

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

    DEFF Research Database (Denmark)

    Fort, Alexandre; Hashimoto, Kosuke; Yamada, Daisuke

    2014-01-01

    The importance of microRNAs and long noncoding RNAs in the regulation of pluripotency has been documented; however, the noncoding components of stem cell gene networks remain largely unknown. Here we investigate the role of noncoding RNAs in the pluripotent state, with particular emphasis...... on nuclear and retrotransposon-derived transcripts. We have performed deep profiling of the nuclear and cytoplasmic transcriptomes of human and mouse stem cells, identifying a class of previously undetected stem cell-specific transcripts. We show that long terminal repeat (LTR)-derived transcripts contribute...

  10. The repetitive component of the sunflower genome

    Directory of Open Access Journals (Sweden)

    T. Giordani

    2014-08-01

    Full Text Available The sunflower (Helianthus annuus and species belonging to the genus Helianthus are emerging as a model species and genus for a number of studies on genome evolution. In this review, we report on the repetitive component of the H. annuus genome at the biochemical, molecular, cytological, and genomic levels. Recent work on sunflower genome composition is described, with emphasis on different types of repeat sequences, especially LTR-retrotransposons, of which we report on isolation, characterisation, cytological localisation, transcription, dynamics of proliferation, and comparative analyses within the genus Helianthus.

  11. Ocurrencia de micorrizas en plantas de maíz, soja y trigo en sistemas de siembra directa

    OpenAIRE

    García de Salamone, Inés Eugenia; Michelena, Roberto Oscar; Rodríguez, Analía; Montemitoli, Ivana; Gatti, S.; Rorig, Marcela

    2006-01-01

    p.67-72 La longitud total (LTR), micorrizada (LRM) y el porcentaje de micorrización natural (PM) de raíces de maíz y soja cultivados sobre un Argiudol vértico (Ramírez, Entre Ríos) y de trigo sobre un Hapustol éntico (Bengolea, Córdoba) se determinaron en floración a tres profundidades. Parcelas de 50x50 m correspondientes a lotes manejados durante mas de 10 años con siembra directa (SD) fueron subdivididas en tres bloques. Adicionalmente dos experimentos factoriales analizaron en invernác...

  12. Strategic Floodplain Reconnection Along the Lower Tisza and Lower Illinois Rivers: Identifying Opportunities, Tradeoffs, and Limitations

    Science.gov (United States)

    Guida, R.; Remo, J. W.; Secchi, S.; Swanson, T.; Kiss, T.

    2015-12-01

    During the late 19th and into the 20th Centuries, the Tisza and Illinois Rivers were highly altered through the construction of levees and dams to reclaim their floodplain-wetland systems for agriculture and to facilitate navigation. In recent decades, flood levels have continued to rise due to aggradation on the confined floodplains reducing flood-conveyance capacity. As a result, "Room for the River" proposals have gained more prominence. Our overarching hypothesis is that strategically reconnecting these rivers to their floodplains will reduce flood levels and increase ecological habitat while limiting socioeconomic impacts. In this study, we assessed several reconnection scenarios, including levee setbacks and removals, for the Lower Tisza River (LTR; Hungary) and the Lower Illinois River (LIR; Illinois, USA). To model water-surface elevations (WSELs) for the 5- through 500-year flood events, we employed HEC-RAS (1D) and SOBEK (1D/2D) hydraulic models. To determine socioeconomic tradeoffs using these modeled WSELs, we developed a corresponding suite of expected annual damages (EADs) using FEMA's Hazus-MH flood-loss modeling software for buildings and integrated geospatial and soil productivity indices to estimate agricultural losses. To assess ecosystem benefits of reconnection along the LTR, we used historic wetland extent as a proxy for increasing needed floodplain habitats. For the LIR, we performed habitat screening using Land Capability Potential Index and other assessment tools to estimate potential ecosystem benefits. Results indicate that levee removal and/or setbacks may reduce flood heights up to 1.6 m along the LTR and over 1.0 m along the LIR. While urban areas have the highest EADs, several lower-production agricultural areas show potential for reducing flood heights while minimizing damages. Strategic-floodplain reconnection benefits along the LTR and LIR include over half of historically-significant wetlands being reconnected and the creation of

  13. Does plasminogen activator inhibitor-1 drive lymphangiogenesis?

    DEFF Research Database (Denmark)

    Bruyère, Françoise; Melen-Lamalle, Laurence; Blacher, Silvia

    2010-01-01

    The purpose of this study is to explore the function of plasminogen activator inhibitor-1 (PAI-1) during pathological lymphangiogenesis. PAI-1, the main physiological inhibitor of plasminogen activators is involved in pathological angiogenesis at least by controlling extracellular proteolysis...... by mammary carcinoma cell injection or spontaneously appearing in transgenic mice expressing the polyomavirus middle T antigen (PymT) under the control of a mouse mammary tumor virus long-terminal repeat promoter (MMTV-LTR). We also investigated inflammation-related lymphatic vessel recruitment by using two...... as a potential therapeutic target to counteract pathological lymphangiogenesis....

  14. Characterization of Three nef-Defective Human Immunodeficiency Virus Type 1 Strains Associated with Long-Term Nonprogression

    OpenAIRE

    David I. Rhodes; Ashton, Lesley; Solomon, Ajantha; Carr, Andrew; Cooper, David; Kaldor, John; Deacon, Nicholas

    2000-01-01

    Long-term survivors (LTS) of human immunodeficiency virus type 1 (HIV-1) infection provide an opportunity to investigate both viral and host factors that influence the rate of disease progression. We have identified three HIV-1-infected individuals in Australia who have been infected for over 11 years with viruses that contain deletions in the nef and nef-long terminal repeat (nef/LTR) overlap regions. These viruses differ from each other and from other nef-defective strains of HIV-1 previous...

  15. U.S. Army Chemical Corps Historical Studies, Gas Warfare in World War I: The 92nd Division in the Marbache Sector, October 1918

    Science.gov (United States)

    1959-12-01

    material that was available at 4 That the French thought highly of them is evident in Cable P-1335, Pershing to CofS Washington, D.C., 19 Jun, and Ltr...LirceJ they fear gas more than ’Boche Germans’." 8 On 21 August advance infantry elements of the 92nd arrived in the St. Die sector, high in the Vosges ...Civil Authority in order to free ground for agricul- ture," and begin the training programs that had been planned earlier that month.135 The thought

  16. Efficient replication and expression of murine leukemia virus with major deletions in the enhancer region of U3

    DEFF Research Database (Denmark)

    Pedersen, K.; Lovmand, S.; Bonefeld-Jørgensen, Eva Cecilie

    1992-01-01

    The effect of deletions within the enhancer region in the U3 part of the LTR derived from the murine retrovirus Akv was studied. The deletions were stably transmitted through normal virus replication as shown by sequence analysis of cloned polymerase chain reaction product of the cDNA copy...... of the viral RNA. Genetic tagging of the retrovirus with lacO facilitated the analysis. Among the individual mutated LTRs an over 100-fold difference in a transient expression assay was previously detected. This difference was not revealed in studies of viral replication in cell culture, where the expression...

  17. History of the Army Ground Forces. Study Number 11. Training in the Ground Army 1942-1945

    Science.gov (United States)

    1948-01-01

    Casablanca Conf. 11-26 Jan 43. See AGF Chrnolog under date 26 Jan 43. 107. Interviews by AGF Hist Off of bd staff offs, Jan 44. 108. AGF ltr to OG’S, 7...Activities considered ap- propriate for this -hour included War Department orientation films , forums based on "Army Talks" and discussions of current... films were shown. 4. Units should keep up-to-date situation maps and use them as a basis for orientation discussions. 5. A daily news bulletin should

  18. Transposable elements and circular DNAs

    KAUST Repository

    Mourier, Tobias

    2016-09-26

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

  19. Remote Data Transfer (RDT): An Interprocess Data Transfer Method for Distributed Environments

    Science.gov (United States)

    1992-05-01

    D’L-TR-3339 AD-A250 859 TECHNICAL REPORT BRL-TR-3339 r iAY2 0 I992i 51BR L 2 REMOTE DATA TRANSFER (RDT): AN INTERPROCESS DATA TRANSFER METHOD FOR...30 Sep 91 4. TITLE AND SUBTITLE S. FUNDING NUMBERS Remote Data Transfer (RdT): An Interprocess Data Transfer Method C-AHPCRC for Distributed...NUMBER OF PAGES 57 RPC: Remote Procedure Call; RdT: Remote Data Transfer ; 16. PRICE CODE XDR: External Data Representation, computer programs, software

  20. Targeting the Prometastatic Microenvironment of the Involuting Mammary Gland

    Science.gov (United States)

    2015-09-01

    the cloning of two LTBP1 hairpins (sh1 within the coding region, sh2 in the 3’UTR) and scrambled controls into pLKO-GFP and pLKO-RFP vectors... cloning the MMTV-LTR, rabbit beta-globin gene, and polyA sequence into pGEM5z. We have encountered problems in cloning human LTBP1 into pHIV-ZsGreen prior...training and professional development has the project provided. 1. Dr. Gann has taken a course in “Scientific Ethics ”. 2. Dr. Gann has acquired

  1. Estimating implementation and operational costs of an integrated tiered CD4 service including laboratory and point of care testing in a remote health district in South Africa.

    Directory of Open Access Journals (Sweden)

    Naseem Cassim

    Full Text Available An integrated tiered service delivery model (ITSDM has been proposed to provide 'full-coverage' of CD4 services throughout South Africa. Five tiers are described, defined by testing volumes and number of referring health-facilities. These include: (1 Tier-1/decentralized point-of-care service (POC in a single site; Tier-2/POC-hub servicing processing 600 samples/day and serving > 100 or > 200 health-clinics, respectively. The objective of this study was to establish costs of existing and ITSDM-tiers 1, 2 and 3 in a remote, under-serviced district in South Africa.Historical health-facility workload volumes from the Pixley-ka-Seme district, and the total volumes of CD4 tests performed by the adjacent district referral CD4 laboratories, linked to locations of all referring clinics and related laboratory-to-result turn-around time (LTR-TAT data, were extracted from the NHLS Corporate-Data-Warehouse for the period April-2012 to March-2013. Tiers were costed separately (as a cost-per-result including equipment, staffing, reagents and test consumable costs. A one-way sensitivity analyses provided for changes in reagent price, test volumes and personnel time.The lowest cost-per-result was noted for the existing laboratory-based Tiers- 4 and 5 ($6.24 and $5.37 respectively, but with related increased LTR-TAT of > 24-48 hours. Full service coverage with TAT < 6-hours could be achieved with placement of twenty-seven Tier-1/POC or eight Tier-2/POC-hubs, at a cost-per-result of $32.32 and $15.88 respectively. A single district Tier-3 laboratory also ensured 'full service coverage' and < 24 hour LTR-TAT for the district at $7.42 per-test.Implementing a single Tier-3/community laboratory to extend and improve delivery of services in Pixley-ka-Seme, with an estimated local ∼ 12-24-hour LTR-TAT, is ∼ $2 more than existing referred services per-test, but 2-4 fold cheaper than implementing eight Tier-2/POC-hubs or providing twenty-seven Tier-1/POCT CD4

  2. Preferential Occupancy of R2 Retroelements on the B Chromosomes of the Grasshopper Eyprepocnemis plorans

    OpenAIRE

    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...

  3. Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers

    DEFF Research Database (Denmark)

    Kaczkowski, Bogumil; Tanaka, Yuji; Kawaji, Hideya

    2016-01-01

    Genes that are commonly deregulated in cancer are clinically attractive as candidate pan-diagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression (CAGE) profiles from 225 different cancer cell lines and 339 corresponding primary cell...... RNAs which are upregulated in cancer, defining promoters which overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall...

  4. Random DNA libraries from three species of the stick insect genus Bacillus (Insecta: Phasmida): repetitive DNA characterization and first observation of polyneopteran MITEs.

    Science.gov (United States)

    Ricci, Marco; Luchetti, Andrea; Bonandin, Livia; Mantovani, Barbara

    2013-12-01

    The repetitive DNA content of the stick insect species Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric), and Bacillus atticus (obligate parthenogenetic) was analyzed through the survey of random genomic libraries roughly corresponding to 0.006% of the genome. By repeat masking, 19 families of transposable elements were identified (two LTR and six non-LTR retrotransposons; 11 DNA transposons). Moreover, a de novo analysis revealed, among the three libraries, the first MITE family observed in polyneopteran genomes. On the whole, transposable element abundance represented 23.3% of the genome in B. rossius, 22.9% in B. atticus, and 18% in B. grandii. Tandem repeat content in the three libraries is much lower: 1.32%, 0.64%, and 1.86% in B. rossius, B. grandii, and B. atticus, respectively. Microsatellites are the most abundant in all species. Minisatellites were only found in B. rossius and B. atticus, and five monomers belonging to the Bag320 satellite family were detected in B. atticus. Assuming the survey provides adequate representation of the relative genome, the obligate parthenogenetic species (B. atticus), compared with the other two species analyzed, does not show a lower transposable element content, as expected from some theoretical and empirical studies.

  5. No Evidence of XMRV or MuLV Sequences in Prostate Cancer, Diffuse Large B-Cell Lymphoma, or the UK Blood Donor Population

    Directory of Open Access Journals (Sweden)

    Mark James Robinson

    2011-01-01

    Full Text Available Xenotropic murine leukaemia virus-related virus (XMRV is a recently described retrovirus which has been claimed to infect humans and cause associated pathology. Initially identified in the US in patients with prostate cancer and subsequently in patients with chronic fatigue syndrome, doubt now exists that XMRV is a human pathogen. We studied the prevalence of genetic sequences of XMRV and related MuLV sequences in human prostate cancer, from B cell lymphoma patients and from UK blood donors. Nucleic acid was extracted from fresh prostate tissue biopsies, formalin-fixed paraffin-embedded (FFPE prostate tissue and FFPE B-cell lymphoma. The presence of XMRV-specific LTR or MuLV generic gag-like sequences was investigated by nested PCR. To control for mouse DNA contamination, a PCR that detected intracisternal A-type particle (IAP sequences was included. In addition, DNA and RNA were extracted from whole blood taken from UK blood donors and screened for XMRV sequences by real-time PCR. XMRV or MuLV-like sequences were not amplified from tissue samples. Occasionally MuLV gag and XMRV-LTR sequences were amplified from Indian prostate cancer samples, but were always detected in conjunction with contaminating murine genomic DNA. We found no evidence of XMRV or MuLV infection in the UK blood donors.

  6. Transcutaneous immunization with cross-reacting material CRM(197) of diphtheria toxin boosts functional antibody levels in mice primed parenterally with adsorbed diphtheria toxoid vaccine.

    Science.gov (United States)

    Stickings, Paul; Peyre, Marisa; Coombes, Laura; Muller, Sylviane; Rappuoli, Rino; Del Giudice, Giuseppe; Partidos, Charalambos D; Sesardic, Dorothea

    2008-04-01

    Transcutaneous immunization (TCI) capitalizes on the accessibility and immunocompetence of the skin, elicits protective immunity, simplifies vaccine delivery, and may be particularly advantageous when frequent boosting is required. In this study we examined the potential of TCI to boost preexisting immune responses to diphtheria in mice. The cross-reacting material (CRM(197)) of diphtheria toxin was used as the boosting antigen and was administered alone or together with either one of two commonly used mucosal adjuvants, cholera toxin (CT) and a partially detoxified mutant of heat-labile enterotoxin of Escherichia coli (LTR72). We report that TCI with CRM(197) significantly boosted preexisting immune responses elicited after parenteral priming with aluminum hydroxide-adsorbed diphtheria toxoid (DTxd) vaccine. In the presence of LTR72 as an adjuvant, toxin-neutralizing antibody titers were significantly higher than those elicited by CRM(197) alone and were comparable to the functional antibody levels induced after parenteral booster immunization with the adsorbed DTxd vaccine. Time course study showed that high levels of toxin-neutralizing antibodies persisted for at least 14 weeks after the transcutaneous boost. In addition, TCI resulted in a vigorous antigen-specific proliferative response in all groups of mice boosted with the CRM(197) protein. These findings highlight the promising prospect of using booster administrations of CRM(197) via the transcutaneous route to establish good herd immunity against diphtheria.

  7. Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies.

    Science.gov (United States)

    Macfarlane, Catriona M; Badge, Richard M

    2015-04-28

    To date, the human population census of proviruses of the Betaretrovirus-like human endogenous retroviral (HERV-K) (HML-2) family has been compiled from a limited number of complete genomes, making it certain that rare polymorphic loci are under-represented and are yet to be described. Here we describe a suppression PCR-based method called genome-wide amplification of proviral sequences (GAPS) that selectively amplifies DNA fragments containing the termini of HERV-K(HML-2) proviral sequences and their flanking genomic sequences. We analysed the HERV-K(HML-2) proviral content of 101 unrelated humans, 4 common chimpanzees and three centre d'etude du polymorphisme humain (CEPH) pedigrees (44 individuals). The technique isolated HERV-K(HML-2) proviruses that had integrated in the genomes of the great apes throughout their divergence and included evolutionarily young elements still unfixed for presence/absence. By examining the HERV-K(HML-2) proviral content of 145 humans we detected a new insertionally polymorphic Type I HERV-K(HML-2) provirus. We also observed provirus versus solo long terminal repeat (LTR) polymorphism within humans at a previously unreported, but ancient, locus. Finally, we report two novel chimpanzee specific proviruses, one of which is dimorphic for a provirus versus solo LTR. Thus GAPS enables the isolation of uncharacterised HERV-K(HML-2) proviral sequences and provides a direct means to assess inter-individual genetic variation associated with HERV-K(HML-2) proviruses.

  8. Fetal Hypotrophy Is an Important Marker in Diagnosis of Preeclampsia in Pregnant Patients After Solid Organ Transplantation.

    Science.gov (United States)

    Cyganek, Anna; Pietrzak, Bronisława; Dąbrowski, Filip A; Jabiry-Zieniewicz, Zoulikha; Chlebus, Marcin; Wielgos, Mirosław; Grzechocińska, Barbara

    2017-06-20

    BACKGROUND The purpose of this study was to use a multidisciplinary approach to define the importance of fetal growth disturbances in pregnant patients after renal or liver transplantation in diagnosis and treatment of preeclampsia. MATERIAL AND METHODS We assessed 108 pregnancies in patients with renal or liver transplants. Statistical analysis included Pearson's chi-square test and Fisher's exact test. RESULTS In the renal transplant (RTR) group, preeclampsia was diagnosed in 40% according to ISSHP. In the liver transplant (LTR) group, ISSHP guidelines allow this diagnose in 14.6% of patients. Intrauterine fetal hypotrophy occurred in 53.3% of RTR patients with clinical symptoms of preeclampsia and in none of stabile patients. Premature delivery rate was 40% in patients with hypotrophy and only in 15.5% without. For LTR patients, hypotrophy was diagnosed in 16.4% patients with clinical symptoms of preeclampsia and in 12.7% of stabile patients. Premature delivery rate was 14.5% in patients with hypotrophy and in 14.5% without. CONCLUSIONS Fetal hypotrophy is strongly associated with premature delivery and risk of preeclampsia in pregnancies after renal transplantation. There is a need for including ultrasound findings in diagnostic criteria of preeclampsia. Fetal growth monitoring may help in prediction of premature delivery in these group.

  9. An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data.

    Science.gov (United States)

    Tsangaras, Kyriakos; Mayer, Jens; Alquezar-Planas, David E; Greenwood, Alex D

    2015-11-24

    Transcriptome analysis of polar bear (Ursus maritimus) tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV). Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs) of a newly described endogenous retrovirus were characterized from the polar bear draft genome sequence. Closely related sequences were identified by PCR analysis of brown bear (Ursus arctos) and black bear (Ursus americanus) but were absent in non-Ursinae bear species. The virus was therefore designated UrsusERV. Two distinct groups of LTRs were observed including a recombinant ERV that contained one LTR belonging to each group indicating that genomic invasions by at least two UrsusERV variants have recently occurred. Age estimates based on proviral LTR divergence and conservation of integration sites among ursids suggest the viral group is only a few million years old. The youngest provirus was polar bear specific, had intact open reading frames (ORFs) and could potentially encode functional proteins. Phylogenetic analyses of UrsusERV consensus protein sequences suggest that it is part of a pig, gibbon and koala retrovirus clade. The young age estimates and lineage specificity of the virus suggests UrsusERV is a recent cross species transmission from an unknown reservoir and places the viral group among the youngest of ERVs identified in mammals.

  10. An Evolutionarily Young Polar Bear (Ursus maritimus Endogenous Retrovirus Identified from Next Generation Sequence Data

    Directory of Open Access Journals (Sweden)

    Kyriakos Tsangaras

    2015-11-01

    Full Text Available Transcriptome analysis of polar bear (Ursus maritimus tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV. Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs of a newly described endogenous retrovirus were characterized from the polar bear draft genome sequence. Closely related sequences were identified by PCR analysis of brown bear (Ursus arctos and black bear (Ursus americanus but were absent in non-Ursinae bear species. The virus was therefore designated UrsusERV. Two distinct groups of LTRs were observed including a recombinant ERV that contained one LTR belonging to each group indicating that genomic invasions by at least two UrsusERV variants have recently occurred. Age estimates based on proviral LTR divergence and conservation of integration sites among ursids suggest the viral group is only a few million years old. The youngest provirus was polar bear specific, had intact open reading frames (ORFs and could potentially encode functional proteins. Phylogenetic analyses of UrsusERV consensus protein sequences suggest that it is part of a pig, gibbon and koala retrovirus clade. The young age estimates and lineage specificity of the virus suggests UrsusERV is a recent cross species transmission from an unknown reservoir and places the viral group among the youngest of ERVs identified in mammals.

  11. p27(SJ), a novel protein in St John's Wort, that suppresses expression of HIV-1 genome.

    Science.gov (United States)

    Darbinian-Sarkissian, N; Darbinyan, A; Otte, J; Radhakrishnan, S; Sawaya, B E; Arzumanyan, A; Chipitsyna, G; Popov, Y; Rappaport, J; Amini, S; Khalili, K

    2006-02-01

    Transcription of the HIV-1 genome is controlled by the cooperation of viral regulatory proteins and several host factors which bind to specific DNA sequences within the viral promoter spanning the long terminal repeat, (LTR). Here, we describe the identification of a novel protein, p27(SJ), present in a laboratory callus culture of Hypericum perforatum (St John's Wort) that suppresses transcription of the HIV-1 genome in several human cell types including primary culture of microglia and astrocytes. p27(SJ) associates with C/EBPbeta, a transcription factor that regulates expression of the HIV-1 genome in macrophages and monocytic cells, and the viral transactivator, Tat. The association of p27(SJ) with C/EBPbeta and Tat alters their subcellular localization, causing their accumulation in the perinuclear cytoplasmic compartment of the cells. Fusion of a nuclear localization signal to p27(SJ) forces its entry into the nucleus and diminishes the capacity of p27(SJ) to suppress Tat activity, but does not alter its ability to suppress C/EBPbeta activation of the LTR. Results from binding assays showed the inhibitory effect of p27(SJ) on C/EBPbeta interaction with DNA. Finally, our results demonstrate that expression of p27(SJ) decreases the level of viral replication in HIV-1-infected cells. These observations suggest the potential for the development of a therapeutic advance based on p27(SJ) protein to control HIV-1 transcription and replication in cells associated with HIV-1 infection in the brain.

  12. Effect of the linkers between the zinc fingers in zinc finger protein 809 on gene silencing and nuclear localization

    Energy Technology Data Exchange (ETDEWEB)

    Ichida, Yu, E-mail: ichida-y@ncchd.go.jp; Utsunomiya, Yuko; Onodera, Masafumi

    2016-03-18

    Zinc finger protein 809 (ZFP809) belongs to the Kruppel-associated box-containing zinc finger protein (KRAB-ZFP) family and functions in repressing the expression of Moloney murine leukemia virus (MoMLV). ZFP809 binds to the primer-binding site (PBS)located downstream of the MoMLV-long terminal repeat (LTR) and induces epigenetic modifications at integration sites, such as repressive histone modifications and de novo DNA methylation. KRAB-ZFPs contain consensus TGEKP linkers between C2H2 zinc fingers. The phosphorylation of threonine residues within linkers leads to the inactivation of zinc finger binding to target sequences. ZFP809 also contains consensus linkers between zinc fingers. However, the function of ZFP809 linkers remains unknown. In the present study, we constructed ZFP809 proteins containing mutated linkers and examined their ability to silence transgene expression driven by MLV, binding ability to MLV PBS, and cellular localization. The results of the present study revealed that the linkers affected the ability of ZFP809 to silence transgene expression. Furthermore, this effect could be partly attributed to changes in the localization of ZFP809 proteins containing mutated linkers. Further characterization of ZFP809 linkers is required for understanding the functions and features of KRAB-ZFP-containing linkers. - Highlights: • ZFP809 has three consensus linkers between the zinc fingers. • Linkers are required for ZFP809 to silence transgene expression driven by MLV-LTR. • Linkers affect the precise nuclear localization of ZFP809.

  13. Targeted HIV-1 Latency Reversal Using CRISPR/Cas9-Derived Transcriptional Activator Systems.

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    Julia K Bialek

    Full Text Available CRISPR/Cas9 technology is currently considered the most advanced tool for targeted genome engineering. Its sequence-dependent specificity has been explored for locus-directed transcriptional modulation. Such modulation, in particular transcriptional activation, has been proposed as key approach to overcome silencing of dormant HIV provirus in latently infected cellular reservoirs. Currently available agents for provirus activation, so-called latency reversing agents (LRAs, act indirectly through cellular pathways to induce viral transcription. However, their clinical performance remains suboptimal, possibly because reservoirs have diverse cellular identities and/or proviral DNA is intractable to the induced pathways. We have explored two CRISPR/Cas9-derived activator systems as targeted approaches to induce dormant HIV-1 proviral DNA. These systems recruit multiple transcriptional activation domains to the HIV 5' long terminal repeat (LTR, for which we have identified an optimal target region within the LTR U3 sequence. Using this target region, we demonstrate transcriptional activation of proviral genomes via the synergistic activation mediator complex in various in culture model systems for HIV latency. Observed levels of induction are comparable or indeed higher than treatment with established LRAs. Importantly, activation is complete, leading to production of infective viral particles. Our data demonstrate that CRISPR/Cas9-derived technologies can be applied to counteract HIV latency and may therefore represent promising novel approaches in the quest for HIV elimination.

  14. Genetic Mechanisms in Aspirin-Exacerbated Respiratory Disease

    Directory of Open Access Journals (Sweden)

    Nami Shrestha Palikhe

    2012-01-01

    Full Text Available Aspirin-exacerbated respiratory disease (AERD refers to the development of bronchoconstriction in asthmatics following the exposure to aspirin or other nonsteroidal anti-inflammatory drugs. The key pathogenic mechanisms associated with AERD are the overproduction of cysteinyl leukotrienes (CysLTs and increased CysLTR1 expression in the airway mucosa and decreased lipoxin and PGE2 synthesis. Genetic studies have suggested a role for variability of genes in disease susceptibility and the response to medication. Potential genetic biomarkers contributing to the AERD phenotype include HLA-DPB1, LTC4S, ALOX5, CYSLT, PGE2, TBXA2R, TBX21, MS4A2, IL10, ACE, IL13, KIF3A, SLC22A2, CEP68, PTGER, and CRTH2 and a four-locus SNP set composed of B2ADR, CCR3, CysLTR1, and FCER1B. Future areas of investigation need to focus on comprehensive approaches to identifying biomarkers for early diagnosis.

  15. Quantitatively increased somatic transposition of transposable elements in Drosophila strains compromised for RNAi.

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    Weiwu Xie

    Full Text Available In Drosophila melanogaster, small RNAs homologous to transposable elements (TEs are of two types: piRNA (piwi-interacting RNA with size 23-29nt and siRNA (small interfering RNA with size 19-22nt. The siRNA pathway is suggested to silence TE activities in somatic tissues based on TE expression profiles, but direct evidence of transposition is lacking. Here we developed an efficient FISH (fluorescence in Situ hybridization based method for polytene chromosomes from larval salivary glands to reveal new TE insertions. Analysis of the LTR-retrotransposon 297 and the non-LTR retroposon DOC shows that in the argonaut 2 (Ago2 and Dicer 2 (Dcr2 mutant strains, new transposition events are much more frequent than in heterozygous strains or wild type strains. The data demonstrate that the siRNA pathway represses TE transposition in somatic cells. Nevertheless, we found that loss of one functional copy of Ago2 or Dcr2 increases somatic transpositions of the elements at a lower level depending on the genetic background, suggesting a quantitative role for RNAi core components on mutation frequency.

  16. The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery.

    Science.gov (United States)

    Raiz, Julija; Damert, Annette; Chira, Sergiu; Held, Ulrike; Klawitter, Sabine; Hamdorf, Matthias; Löwer, Johannes; Strätling, Wolf H; Löwer, Roswitha; Schumann, Gerald G

    2012-02-01

    SINE-VNTR-Alu (SVA) elements are non-autonomous, hominid-specific non-LTR retrotransposons and distinguished by their organization as composite mobile elements. They represent the evolutionarily youngest, currently active family of human non-LTR retrotransposons, and sporadically generate disease-causing insertions. Since preexisting, genomic SVA sequences are characterized by structural hallmarks of Long Interspersed Elements 1 (LINE-1, L1)-mediated retrotransposition, it has been hypothesized for several years that SVA elements are mobilized by the L1 protein machinery in trans. To test this hypothesis, we developed an SVA retrotransposition reporter assay in cell culture using three different human-specific SVA reporter elements. We demonstrate that SVA elements are mobilized in HeLa cells only in the presence of both L1-encoded proteins, ORF1p and ORF2p. SVA trans-mobilization rates exceeded pseudogene formation frequencies by 12- to 300-fold in HeLa-HA cells, indicating that SVA elements represent a preferred substrate for L1 proteins. Acquisition of an AluSp element increased the trans-mobilization frequency of the SVA reporter element by ~25-fold. Deletion of (CCCTCT)(n) repeats and Alu-like region of a canonical SVA reporter element caused significant attenuation of the SVA trans-mobilization rate. SVA de novo insertions were predominantly full-length, occurred preferentially in G+C-rich regions, and displayed all features of L1-mediated retrotransposition which are also observed in preexisting genomic SVA insertions.

  17. HTLV-1 Tax mediated downregulation of miRNAs associated with chromatin remodeling factors in T cells with stably integrated viral promoter.

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    Saifur Rahman

    Full Text Available RNA interference (RNAi is a natural cellular mechanism to silence gene expression and is predominantly mediated by microRNAs (miRNAs that target messenger RNA. Viruses can manipulate the cellular processes necessary for their replication by targeting the host RNAi machinery. This study explores the effect of human T-cell leukemia virus type 1 (HTLV-1 transactivating protein Tax on the RNAi pathway in the context of a chromosomally integrated viral long terminal repeat (LTR using a CD4(+ T-cell line, Jurkat. Transcription factor profiling of the HTLV-1 LTR stably integrated T-cell clone transfected with Tax demonstrates increased activation of substrates and factors associated with chromatin remodeling complexes. Using a miRNA microarray and bioinformatics experimental approach, Tax was also shown to downregulate the expression of miRNAs associated with the translational regulation of factors required for chromatin remodeling. These observations were validated with selected miRNAs and an HTLV-1 infected T cells line, MT-2. miR-149 and miR-873 were found to be capable of directly targeting p300 and p/CAF, chromatin remodeling factors known to play critical role in HTLV-1 pathogenesis. Overall, these results are first in line establishing HTLV-1/Tax-miRNA-chromatin concept and open new avenues toward understanding retroviral latency and/or replication in a given cell type.

  18. A suicide gene approach using the human pro-apoptotic protein tBid inhibits HIV-1 replication

    Directory of Open Access Journals (Sweden)

    Gueckel Eva

    2011-01-01

    Full Text Available Abstract Background Regulated expression of suicide genes is a powerful tool to eliminate specific subsets of cells and will find widespread usage in both basic and applied science. A promising example is the specific elimination of human immunodeficiency virus type 1 (HIV-1 infected cells by LTR-driven suicide genes. The success of this approach, however, depends on a fast and effective suicide gene, which is expressed exclusively in HIV-1 infected cells. These preconditions have not yet been completely fulfilled and, thus, success of suicide approaches has been limited so far. We tested truncated Bid (tBid, a human pro-apoptotic protein that induces apoptosis very rapidly and efficiently, as suicide gene for gene therapy against HIV-1 infection. Results When tBid was introduced into the HIV-1 LTR-based, Tat- and Rev-dependent transgene expression vector pLRed(INS2R, very efficient induction of apoptosis was observed within 24 hours, but only in the presence of both HIV-1 regulatory proteins Tat and Rev. Induction of apoptosis was not observed in their absence. Cells containing this vector rapidly died when transfected with plasmids containing full-length viral genomic DNA, completely eliminating the chance for HIV-1 replication. Viral replication was also strongly reduced when cells were infected with HIV-1 particles. Conclusions This suicide vector has the potential to establish a safe and effective gene therapy approach to exclusively eliminate HIV-1 infected cells before infectious virus particles are released.

  19. Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

    Directory of Open Access Journals (Sweden)

    Ahn Jong Hwa

    2011-01-01

    Full Text Available Abstract Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

  20. Voriconazole increases the risk for cutaneous squamous cell carcinoma after lung transplantation.

    Science.gov (United States)

    Kolaitis, Nicholas A; Duffy, Erin; Zhang, Alice; Lo, Michelle; Barba, David T; Chen, Meng; Soriano, Teresa; Hu, Jenny; Nabili, Vishad; Saggar, Rajeev; Sayah, David M; DerHovanessian, Ariss; Shino, Michael Y; Lynch, Joseph P; Kubak, Bernie M; Ardehali, Abbas; Ross, David J; Belperio, John A; Elashoff, David; Saggar, Rajan; Weigt, S Samuel

    2017-01-01

    Lung transplant recipients (LTR) are at high risk of cutaneous squamous cell carcinoma (SCC). Voriconazole exposure after lung transplant has recently been reported as a risk factor for SCC. We sought to study the relationship between fungal prophylaxis with voriconazole and the risk of SCC in sequential cohorts from a single center. We evaluated 400 adult LTR at UCLA between 7/1/2005 and 12/22/2012. On 7/1/2009, our center instituted a protocol switch from targeted to universal antifungal prophylaxis for at least 6 months post-transplant. Using Cox proportional hazards models, time to SCC was compared between targeted (N = 199) and universal (N = 201) prophylaxis cohorts. Cox models were also used to assess SCC risk as a function of time-dependent cumulative exposure to voriconazole and other antifungal agents. The risk of SCC was greater in the universal prophylaxis cohort (HR 2.02, P Voriconazole exposure was greater in the universal prophylaxis cohort, and the cumulative exposure to voriconazole was associated with SCC (HR 1.75, P Voriconazole did not increase the risk of advanced tumors. Exposure to other antifungal agents was not associated with SCC. Voriconazole should be used cautiously in this population. © 2016 The Authors. Transplant International published by John Wiley & Sons Ltd on behalf of Steunstichting ESOT.