WorldWideScience

Sample records for ltr retrotransposons adjacent

  1. 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.

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

    African Journals Online (AJOL)

    GRACE

    2006-07-03

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

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

    Science.gov (United States)

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

    2015-05-01

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

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

    Science.gov (United States)

    Cheng, Xu-Dong; Ling, Hong-Qing

    2006-06-01

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

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

    African Journals Online (AJOL)

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

  6. 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

  7. 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

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

    Science.gov (United States)

    K.J. Garner; J.M. Slavicek

    1999-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

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

  10. 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.

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

    Science.gov (United States)

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

    2015-02-01

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

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

    Science.gov (United States)

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

    2015-10-15

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

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

    Science.gov (United States)

    Bae, Young-An

    2016-11-01

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

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

    Science.gov (United States)

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

    2015-08-14

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

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

    Science.gov (United States)

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

    2017-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Steinbiss Sascha

    2012-11-01

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

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

    Science.gov (United States)

    Steinbiss, Sascha; Kastens, Sascha; Kurtz, Stefan

    2012-11-07

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

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

    Science.gov (United States)

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

    2017-08-18

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

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

    Science.gov (United States)

    Kojima, Kenji K; Jurka, Jerzy

    2015-01-01

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

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Domingues Douglas S

    2012-04-01

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

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

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2010-01-01

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

  3. 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.

  4. 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.

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

    Science.gov (United States)

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

    2008-04-01

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

  6. 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.

  7. 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.

  8. 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.

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

    Science.gov (United States)

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

    2017-06-01

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

  10. Drosophila: Retrotransposons Making up Telomeres.

    Science.gov (United States)

    Casacuberta, Elena

    2017-07-19

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

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

    Science.gov (United States)

    Tetreault, Hannah M.; Ungerer, Mark C.

    2016-01-01

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

  12. Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

    Directory of Open Access Journals (Sweden)

    Ma Bi

    2017-10-01

    Full Text Available Copia and Gypsy play important roles in structural, functional and evolutionary dynamics of plant genomes. In this study, a total of 106 and 101, Copia and Gypsy reverse transcriptase (rt were amplified respectively in the Morus notabilis genome using degenerate primers. All sequences exhibited high levels of heterogeneity, were rich in AT and possessed higher sequence divergence of Copia rt in comparison to Gypsy rt. Two reasons are likely to account for this phenomenon: a these elements often experience deletions or fragmentation by illegitimate or unequal homologous recombination in the transposition process; b strong purifying selective pressure drives the evolution of these elements through “selective silencing” with random mutation and eventual deletion from the host genome. Interestingly, mulberry rt clustered with other rt from distantly related taxa according to the phylogenetic analysis. This phenomenon did not result from horizontal transposable element transfer. Results obtained from fluorescence in situ hybridization revealed that most of the hybridization signals were preferentially concentrated in pericentromeric and distal regions of chromosomes, and these elements may play important roles in the regions in which they are found. Results of this study support the continued pursuit of further functional studies of Copia and Gypsy in the mulberry genome.

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

    Science.gov (United States)

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

    2015-02-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2010-11-01

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

  17. 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.

  18. 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.

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

    Science.gov (United States)

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

    2007-02-01

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

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Wei Chang

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

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

    Czech Academy of Sciences Publication Activity Database

    Ganesh, Sravya; Svoboda, Petr

    2016-01-01

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

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Morales Maria E

    2005-02-01

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

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

    Science.gov (United States)

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

    2013-09-01

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

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    Alfica Sehgal

    2007-08-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Busby Jason N

    2007-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Bonnivard Eric

    2009-04-01

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

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Shunsuke Suzuki

    2007-04-01

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

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

    Science.gov (United States)

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

    2014-06-04

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

  14. A specific insertion of a solo-LTR characterizes the Y-chromosome of Bryonia dioica (Cucurbitaceae).

    Science.gov (United States)

    Oyama, Ryan K; Silber, Martina V; Renner, Susanne S

    2010-06-14

    Relatively few species of flowering plants are dioecious and even fewer are known to have sex chromosomes. Current theory posits that homomorphic sex chromosomes, such as found in Bryonia dioica (Cucurbitaceae), offer insight into the early stages in the evolution of sex chromosomes from autosomes. Little is known about these early steps, but an accumulation of transposable element sequences has been observed on the Y-chromosomes of some species with heteromorphic sex chromosomes. Recombination, by which transposable elements are removed, is suppressed on at least part of the emerging Y-chromosome, and this may explain the correlation between the emergence of sex chromosomes and transposable element enrichment. We sequenced 2321 bp of the Y-chromosome in Bryonia dioica that flank a male-linked marker, BdY1, reported previously. Within this region, which should be suppressed for recombination, we observed a solo-LTR nested in a Copia-like transposable element. We also found other, presumably paralogous, solo-LTRs in a consensus sequence of the underlying Copia-like transposable element. Given that solo-LTRs arise via recombination events, it is noteworthy that we find one in a genomic region where recombination should be suppressed. Although the solo-LTR could have arisen before recombination was suppressed, creating the male-linked marker BdY1, our previous study on B. dioica suggested that BdY1 may not lie in the recombination-suppressed region of the Y-chromosome in all populations. Presence of a solo-LTR near BdY1 therefore fits with the observed correlation between retrotransposon accumulation and the suppression of recombination early in the evolution of sex chromosomes. These findings further suggest that the homomorphic sex chromosomes of B. dioica, the first organism for which genetic XY sex-determination was inferred, are evolutionarily young and offer reference information for comparative studies of other plant sex chromosomes.

  15. 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 a standard Loop Transfer Recovery (LTR) design problem. As a consequence of the connection between LTR and FDI design, it is shown in an example how the LQG/LTR design method for full order and a proportional-integral observer can be applied with advantages in connection with FDI....

  16. 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...

  17. Retrotransposon Domestication and Control in Dictyostelium discoideum

    Directory of Open Access Journals (Sweden)

    Marek Malicki

    2017-10-01

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

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

    Science.gov (United States)

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

    2002-01-01

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

  19. 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...

  20. Retrotransposons and non-protein coding RNAs

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2009-01-01

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

  1. Citrus and Prunuscopia-like retrotransposons.

    Science.gov (United States)

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

    1999-08-01

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

  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. Alterations in HIV-1 LTR promoter activity during AIDS progression

    International Nuclear Information System (INIS)

    Hiebenthal-Millow, Kirsten; Greenough, Thomas C.; Bretttler, Doreen B.; Schindler, Michael; Wildum, Steffen; Sullivan, John L.; Kirchhoff, Frank

    2003-01-01

    HIV-1 variants evolving in AIDS patients frequently show increased replicative capacity compared to those present during early asymptomatic infection. It is known that late stage HIV-1 variants often show an expanded coreceptor tropism and altered Nef function. In the present study we investigated whether enhanced HIV-1 LTR promoter activity might also evolve during disease progression. Our results demonstrate increased LTR promoter activity after AIDS progression in 3 of 12 HIV-1-infected individuals studied. Further analysis revealed that multiple alterations in the U3 core-enhancer and in the transactivation-response (TAR) region seem to be responsible for the enhanced functional activity. Our findings show that in a subset of HIV-1-infected individuals enhanced LTR transcription contributes to the increased replicative potential of late stage virus isolates and might accelerate disease progression

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

    Directory of Open Access Journals (Sweden)

    Kong Yoon

    2008-10-01

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

  5. MASiVEdb: the Sirevirus Plant Retrotransposon Database

    Directory of Open Access Journals (Sweden)

    Bousios Alexandros

    2012-04-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Science.gov (United States)

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

    2012-07-01

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

  8. 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

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

    Directory of Open Access Journals (Sweden)

    Sophie Lanciano

    2017-02-01

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

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

    Science.gov (United States)

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

    2017-02-01

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

  11. Nuclear Matrix protein SMAR1 represses HIV-1 LTR mediated transcription through chromatin remodeling

    International Nuclear Information System (INIS)

    Sreenath, Kadreppa; Pavithra, Lakshminarasimhan; Singh, Sandeep; Sinha, Surajit; Dash, Prasanta K.; Siddappa, Nagadenahalli B.; Ranga, Udaykumar; Mitra, Debashis; Chattopadhyay, Samit

    2010-01-01

    Nuclear Matrix and MARs have been implicated in the transcriptional regulation of host as well as viral genes but their precise role in HIV-1 transcription remains unclear. Here, we show that > 98% of HIV sequences contain consensus MAR element in their promoter. We show that SMAR1 binds to the LTR MAR and reinforces transcriptional silencing by tethering the LTR MAR to nuclear matrix. SMAR1 associated HDAC1-mSin3 corepressor complex is dislodged from the LTR upon cellular activation by PMA/TNFα leading to an increase in the acetylation and a reduction in the trimethylation of histones, associated with the recruitment of RNA Polymerase II on the LTR. Overexpression of SMAR1 lead to reduction in LTR mediated transcription, both in a Tat dependent and independent manner, resulting in a decreased virion production. These results demonstrate the role of SMAR1 in regulating viral transcription by alternative compartmentalization of LTR between the nuclear matrix and chromatin.

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

    African Journals Online (AJOL)

    ONOS

    2010-03-29

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

  13. Retrotransposons as regulators of gene expression.

    Science.gov (United States)

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

    2016-02-12

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

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

    OpenAIRE

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2005-05-05

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

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

    Science.gov (United States)

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

    2000-01-01

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

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

    Science.gov (United States)

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

    2017-08-07

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

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

    Directory of Open Access Journals (Sweden)

    Wilson Leung

    2017-08-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

  1. An Analysis Of Pole/zero Cancellation In LTR-based Feedback Design

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Jannerup, Ole Erik

    1990-01-01

    The pole/zero cancellation in LTR-based feedback design will be analyzed for both full-order as well as minimal-order observers. The asymptotic behaviour of the sensitivity function from the LTR-procedure are given in explicit expressions in the case when a zero is not cancelled by an equivalent...... pole. It will be shown that the non-minimum phase case is included as a special case. The results are not based on any specific LTR-method....

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

    Science.gov (United States)

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

    2013-06-06

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

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

    Science.gov (United States)

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

    2015-05-01

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

  4. Modeling the amplification dynamics of human Alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    Dale J Hedges

    2005-09-01

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

  5. Modeling the amplification dynamics of human alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    2005-09-01

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

  6. The Microprocessor controls the activity of mammalian retrotransposons

    DEFF Research Database (Denmark)

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

    2013-01-01

    RNA biogenesis, also recognizes and binds RNAs derived from human long interspersed element 1 (LINE-1), Alu and SVA retrotransposons. Expression analyses demonstrate that cells lacking a functional Microprocessor accumulate LINE-1 mRNA and encoded proteins. Furthermore, we show that structured regions...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  8. Accurate episomal HIV 2-LTR circles quantification using optimized DNA isolation and droplet digital PCR.

    Science.gov (United States)

    Malatinkova, Eva; Kiselinova, Maja; Bonczkowski, Pawel; Trypsteen, Wim; Messiaen, Peter; Vermeire, Jolien; Verhasselt, Bruno; Vervisch, Karen; Vandekerckhove, Linos; De Spiegelaere, Ward

    2014-01-01

    In HIV-infected patients on combination antiretroviral therapy (cART), the detection of episomal HIV 2-LTR circles is a potential marker for ongoing viral replication. Quantification of 2-LTR circles is based on quantitative PCR or more recently on digital PCR assessment, but is hampered due to its low abundance. Sample pre-PCR processing is a critical step for 2-LTR circles quantification, which has not yet been sufficiently evaluated in patient derived samples. We compared two sample processing procedures to more accurately quantify 2-LTR circles using droplet digital PCR (ddPCR). Episomal HIV 2-LTR circles were either isolated by genomic DNA isolation or by a modified plasmid DNA isolation, to separate the small episomal circular DNA from chromosomal DNA. This was performed in a dilution series of HIV-infected cells and HIV-1 infected patient derived samples (n=59). Samples for the plasmid DNA isolation method were spiked with an internal control plasmid. Genomic DNA isolation enables robust 2-LTR circles quantification. However, in the lower ranges of detection, PCR inhibition caused by high genomic DNA load substantially limits the amount of sample input and this impacts sensitivity and accuracy. Moreover, total genomic DNA isolation resulted in a lower recovery of 2-LTR templates per isolate, further reducing its sensitivity. The modified plasmid DNA isolation with a spiked reference for normalization was more accurate in these low ranges compared to genomic DNA isolation. A linear correlation of both methods was observed in the dilution series (R2=0.974) and in the patient derived samples with 2-LTR numbers above 10 copies per million peripheral blood mononuclear cells (PBMCs), (R2=0.671). Furthermore, Bland-Altman analysis revealed an average agreement between the methods within the 27 samples in which 2-LTR circles were detectable with both methods (bias: 0.3875±1.2657 log10). 2-LTR circles quantification in HIV-infected patients proved to be more

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

    DEFF Research Database (Denmark)

    Fukai, Eigo; Stougaard, Jens; Hayashi, Makoto

    2013-01-01

    Long terminal repeat retrotransposons occupy a large portion of genomes in flowering plants. In spite of their abundance, the majority are silenced and rarely transpose. One of the examples of a highly active retrotransposon is Lotus Retrotransposon 1(LORE1), of the model legume Lotus japonicus...... significance of LORE1 as a member of chromovirus, a chromodomain containing clade of the Gypsy superfamily. Then we discuss possibilities and methodologies for using endogenous transposable elements as mutagens to generate gene tagging populations in plants...

  10. Plant centromeric retrotransposons: a structural and cytogenetic perspective

    Czech Academy of Sciences Publication Activity Database

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

    2011-01-01

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

  11. Stress-induced rearrangement of Fusarium retrotransposon sequences.

    Science.gov (United States)

    Anaya, N; Roncero, M I

    1996-11-27

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

  12. The effects of multiple UV exposures on HIV-LTR (long terminal repeat) expression

    International Nuclear Information System (INIS)

    Schreck, S.; Milton, J.; Panozzo, J.; Libertin, C.R.; Woloschak, G.E.; Loyola Univ., Maywood, IL

    1995-01-01

    Previous studies have shown that cellular stress agents such as UV radiation induce transcription from the long terminal repeat (LTR) of the human immunodeficiency virus (HIV). Using HeLa cells stably transfected with the HIV-LTR sequence, which transcriptionally drives the chloramphenicol acetyl transferase (CAT) reporter gene, we examined the effects of multiple exposures to UVC (254 nm) on HIV-LTR-CAT expression. Low doses (≤ 5 J m -2 ) had no effect on CAT expression, but up to 29-fold induction was observed with 10 J m -2 when cells were harvested 48 h after completion of the exposure. Little difference was noted in induction levels when cells were exposed to one 25 J m -2 dose, viable cells were harvested at 24 h, 48 h or 72 h, and cell lysates were assayed for CAT expression. Two sequential 12.5 J m -2 exposures, given 24 h apart, resulted in an additive effect on CAT expression; these two exposures produced CAT activity equivalent to that induced following a single 25 J m -2 dose. Our data suggest that HIV-LTR requires a specific threshold UV dose in order to elicit induction; a maximal induction dose is also evident; exposures higher than this maximal dose contribute no more to HIV-LTR induction in viable cells. (author)

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

    Directory of Open Access Journals (Sweden)

    Palhares Alessandra C

    2012-06-01

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

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  15. 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...

  16. Cellular specificity of HIV-1 replication can be controlled by LTR sequences

    International Nuclear Information System (INIS)

    Reed-Inderbitzin, Edward; Maury, Wendy

    2003-01-01

    Two well-established determinants of retroviral tropism are envelope sequences that regulate entry and LTR sequences that can regulate viral expression in a cell-specific manner. Studies with human immunodeficiency virus-1 (HIV-1) have demonstrated that tropism of this virus maps primarily to variable envelope sequences. Studies have demonstrated that T cell and macrophage-specific transcription factor binding motifs exist in the upstream region of the LTR U3; however, the ability of the core enhancer/promoter proximal elements (two NF-κB and three Sp1 sites) to function well in macrophages and T cells have led many to conclude that HIV LTR sequences are not primary determinants of HIV tropism. To determine if cellular specificity could be imparted to HIV by the core enhancer elements, the enhancer/promoter proximal region of the HIV LTR was substituted with motifs that control gene expression in a myeloid-specific manner. The enhancer region from equine infectious anemia virus (EIAV) when substituted for the HIV enhancer/promoter proximal region was found to drive expression in a macrophage-specific manner and was responsive to HIV Tat. The addition of a 5' methylation-dependent binding site (MDBP) and a promoter proximal Sp1 motif increased expression without altering cellular specificity. Spacing between the promoter proximal region and the TATA box was also found to influence LTR activity. Infectivity studies using chimeric LTRs within the context of a dual-tropic infectious molecular clone established that these LTRs directed HIV replication and production of infectious virions in macrophages but not primary T cells or T cell lines. This investigation demonstrates that cellular specificity can be imparted onto HIV-1 replication at the level of viral transcription and not entry

  17. Rapid turnover of 2-LTR HIV-1 DNA during early stage of highly active antiretroviral therapy.

    Directory of Open Access Journals (Sweden)

    Weijun Zhu

    Full Text Available BACKGROUND: Despite prolonged treatment with highly active antiretroviral therapy (HAART, the infectious HIV-1 continues to replicate and resides latently in the resting memory CD4+ T lymphocytes, which blocks the eradication of HIV-1. The viral persistence of HIV-1 is mainly caused by its proviral DNA being either linear nonintegrated, circular nonintegrated, or integrated. Previous reports have largely focused on the dynamics of HIV-1 DNA from the samples collected with relatively long time intervals during the process of disease and HAART treatment, which may have missed the intricate changes during the intervals in early treatment. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we investigated the dynamics of HIV-1 DNA in patients during the early phase of HARRT treatment. Using optimized real time PCR, we observed significant changes in 2-LTR during the first 12-week of treatment, while total and integrated HIV-1 DNA remained stable. The doubling time and half-life of 2-LTR were not correlated with the baseline and the rate of changes in plasma viral load and various CD4+ T-cell populations. Longitudinal analyses on 2-LTR sequences and plasma lipopolysaccharide (LPS levels did not reveal any significant changes in the same treatment period. CONCLUSIONS/SIGNIFICANCE: Our study revealed the rapid changes in 2-LTR concentration in a relatively large number of patients during the early HAART treatment. The rapid changes indicate the rapid infusion and clearance of cells bearing 2-LTR in the peripheral blood. Those changes are not expected to be caused by the blocking of viral integration, as our study did not include the integrase inhibitor raltegravir. Our study helps better understand the dynamics of HIV-DNA and its potential role as a biomarker for the diseases and for the treatment efficacy of HAART.

  18. Characterization of EIAV LTR variability and compartmentalization in various reservoir tissues of long-term inapparent carrier ponies

    International Nuclear Information System (INIS)

    Reis, Jenner K.P.; Craigo, Jodi K.; Cook, Sheila J.; Issel, Charles J.; Montelaro, Ronald C.

    2003-01-01

    Dynamic genomic variation resulting in changes in envelope antigenicity has been established as a fundamental mechanism of persistence by equine infectious anemia virus (EIAV), as observed with other lentiviruses, including HIV-1. In addition to the reported changes in envelope sequences, however, certain studies indicate the viral LTR as a second variable EIAV gene, with the enhancer region being designated as hypervariable. These observations have lead to the suggestion that LTR variation may alter viral replication properties to optimize to the microenvironment of particular tissue reservoirs. To test this hypothesis directly, we examined the population of LTR quasispecies contained in various tissues of two inapparent carrier ponies experimentally infected with a reference EIAV biological clone for 18 months. The results of these studies demonstrated that the EIAV LTR is in fact highly conserved with respect to the infecting LTR species after 1.5 years of persistent infection and regardless of the tissue reservoir. Thus, these comprehensive analyses demonstrate for the first time that the EIAV LTR is highly conserved during long-term persistent infection and that the observed variations in viral LTR are associated more with in vitro adaptation to replication in cultured cells rather than in vivo replication in natural target cells

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

    Science.gov (United States)

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

    2016-09-08

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

  20. Enhancement of Intranasal Vaccination in Mice with Deglycosylated Chain A Ricin by LTR72, a Novel Mucosal Adjuvant

    National Research Council Canada - National Science Library

    Kende, Meir; Del Giudice, Giuseppe; Rivera, Noelia; Hewetson, John

    2006-01-01

    .... However, in the presence of 4, 2, or 1 microg of the mucosal adjuvant LTR72, a mutant of the heat-labile enterotoxin of Escherichia coli, the low antibody response and protection were substantially enhanced...

  1. Enhancement of Intranasal Vaccination in Mice with Deglycosylated Chain A Ricin by LTR72, a Novel Mucosal Adjuvant

    National Research Council Canada - National Science Library

    Kende, Meir; Del Giudice, Giuseppe; Rivera, Noelia; Hewetson, John

    2006-01-01

    .... However, in the presence of 4, 2, or 1 micro-gram of the mucosal adjuvant LTR72, a mutant of the heat-labile enterotoxin of Escherichia coli, the low antibody response and protection were substantially enhanced...

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

    Science.gov (United States)

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

    2004-06-01

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

  3. Regulatory elements involved in tax-mediated transactivation of the HTLV-I LTR.

    Science.gov (United States)

    Seeler, J S; Muchardt, C; Podar, M; Gaynor, R B

    1993-10-01

    HTLV-I is the etiologic agent of adult T-cell leukemia. In this study, we investigated the regulatory elements and cellular transcription factors which function in modulating HTLV-I gene expression in response to the viral transactivator protein, tax. Transfection experiments into Jurkat cells of a variety of site-directed mutants in the HTLV-1 LTR indicated that each of the three motifs A, B, and C within the 21-bp repeats, the binding sites for the Ets family of proteins, and the TATA box all influenced the degree of tax-mediated activation. Tax is also able to activate gene expression of other viral and cellular promoters. Tax activation of the IL-2 receptor and the HIV-1 LTR is mediated through NF-kappa B motifs. Interestingly, sequences in the 21-bp repeat B and C motifs contain significant homology with NF-kappa B regulatory elements. We demonstrated that an NF-kappa B binding protein, PRDII-BF1, but not the rel protein, bound to the B and C motifs in the 21-bp repeat. PRDII-BF1 was also able to stimulate activation of HTLV-I gene expression by tax. The role of the Ets proteins on modulating tax activation was also studied. Ets 1 but not Ets 2 was capable of increasing the degree of tax activation of the HTLV-I LTR. These results suggest that tax activates gene expression by either direct or indirect interaction with several cellular transcription factors that bind to the HTLV-I LTR.

  4. FoxA1 binding to the MMTV LTR modulates chromatin structure and transcription

    International Nuclear Information System (INIS)

    Holmqvist, Per-Henrik; Belikov, Sergey; Zaret, Kenneth S.; Wrange, Oerjan

    2005-01-01

    Novel binding sites for the forkhead transcription factor family member Forkhead box A (FoxA), previously referred to as Hepatocyte Nuclear Factor 3 (HNF3), were found within the mouse mammary tumor virus long terminal repeat (MMTV LTR). The effect of FoxA1 on MMTV LTR chromatin structure, and expression was evaluated in Xenopus laevis oocytes. Mutagenesis of either of the two main FoxA binding sites showed that the distal site, -232/-221, conferred FoxA1-dependent partial inhibition of glucocorticoid receptor (GR) driven MMTV transcription. The proximal FoxA binding segment consisted of two individual FoxA sites at -57/-46 and -45/-34, respectively, that mediated an increased basal MMTV transcription. FoxA1 binding altered the chromatin structure of both the inactive- and the hormone-activated MMTV LTR. Hydroxyl radical foot printing revealed FoxA1-mediated changes in the nucleosome arrangement. Micrococcal nuclease digestion showed the hormone-dependent sub-nucleosome complex, containing ∼120 bp of DNA, to be expanded by FoxA1 binding to the proximal segment into a larger complex containing ∼200 bp. The potential function of the FoxA1-mediated expression of the MMTV provirus for maintenance of expression in different tissues is discussed

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

    Directory of Open Access Journals (Sweden)

    Kota Inoue

    2017-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Gozde Yuzbasioglu

    2016-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Erin C Macaulay

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

  8. A novel function for spumaretrovirus integrase: an early requirement for integrase-mediated cleavage of 2 LTR circles

    Directory of Open Access Journals (Sweden)

    Mouscadet Jean-François

    2005-05-01

    Full Text Available Abstract Retroviral integration is central to viral persistence and pathogenesis, cancer as well as host genome evolution. However, it is unclear why integration appears essential for retrovirus production, especially given the abundance and transcriptional potential of non-integrated viral genomes. The involvement of retroviral endonuclease, also called integrase (IN, in replication steps apart from integration has been proposed, but is usually considered to be accessory. We observe here that integration of a retrovirus from the spumavirus family depends mainly on the quantity of viral DNA produced. Moreover, we found that IN directly participates to linear DNA production from 2-LTR circles by specifically cleaving the conserved palindromic sequence found at LTR-LTR junctions. These results challenge the prevailing view that integrase essential function is to catalyze retroviral DNA integration. Integrase activity upstream of this step, by controlling linear DNA production, is sufficient to explain the absolute requirement for this enzyme. The novel role of IN over 2-LTR circle junctions accounts for the pleiotropic effects observed in cells infected with IN mutants. It may explain why 1 2-LTR circles accumulate in vivo in mutants carrying a defective IN while their linear and integrated DNA pools decrease; 2 why both LTRs are processed in a concerted manner. It also resolves the original puzzle concerning the integration of spumaretroviruses. More generally, it suggests to reassess 2-LTR circles as functional intermediates in the retrovirus cycle and to reconsider the idea that formation of the integrated provirus is an essential step of retrovirus production.

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

    Directory of Open Access Journals (Sweden)

    Lu Wang

    2017-08-01

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

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

    Science.gov (United States)

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

    2008-11-01

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

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

    Science.gov (United States)

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

    2011-05-01

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

  12. Bond graph modeling and LQG/LTR controller design of magnetically levitation systems

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Shik; Park, Jeon Soo [Busan National Univ. (Korea, Republic of)

    1991-09-01

    A logical and systematic procedure to derive a mathematical model for magnetically levitation (MAGLEV) systems with a combined lift and guidance is developed by using bond graph modeling techniques. First, bond graph is contructed for the 1{sup st}-dimensional MAGLEV system in which three subsystems (energy feeding, track and vehicle) are considered. And, the 2{sup nd}-dimensional MAGLEV system in which lift and guidance dynamics are coupled is modeled by using the concept of multi-port field in bond graph languages. Finally, the LQG/LTR control system is designed for a multivariable MAGLEV system with stagger configuration type. In this paper, it has been shown that the bond graph is an excellent effective method for modeling multi-energy domain systems such as MAGLEV systems with uncertainties such as mass variations, track irregularities and wind gusts. (Author).

  13. Bond graph modeling and LQG/LTR controller design of magnetically levitation systems

    International Nuclear Information System (INIS)

    Kim, Jong Shik; Park, Jeon Soo

    1991-01-01

    A logical and systematic procedure to derive a mathematical model for magnetically levitation (MAGLEV) systems with a combined lift and guidance is developed by using bond graph modeling techniques. First, bond graph is contructed for the 1 st -dimensional MAGLEV system in which three subsystems (energy feeding, track and vehicle) are considered. And, the 2 nd -dimensional MAGLEV system in which lift and guidance dynamics are coupled is modeled by using the concept of multi-port field in bond graph languages. Finally, the LQG/LTR control system is designed for a multivariable MAGLEV system with stagger configuration type. In this paper, it has been shown that the bond graph is an excellent effective method for modeling multi-energy domain systems such as MAGLEV systems with uncertainties such as mass variations, track irregularities and wind gusts. (Author)

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

    Directory of Open Access Journals (Sweden)

    Maria J Aristizabal

    2015-10-01

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

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

    Science.gov (United States)

    Smýkal, Petr

    2006-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Anderly C Chueh

    2009-01-01

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

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

    Science.gov (United States)

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

    2015-04-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2000-01-01

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

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

    Science.gov (United States)

    Honda, Tomoyuki

    2016-05-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ramos Kenneth

    2010-10-01

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  3. LQG/LTR optimal attitude control of small flexible spacecraft using free-free boundary conditions

    Science.gov (United States)

    Fulton, Joseph M.

    Due to the volume and power limitations of a small satellite, careful consideration must be taken while designing an attitude control system for 3-axis stabilization. Placing redundancy in the system proves difficult and utilizing power hungry, high accuracy, active actuators is not a viable option. Thus, it is customary to find dependable, passive actuators used in conjunction with small scale active control components. This document describes the application of Elastic Memory Composite materials in the construction of a flexible spacecraft appendage, such as a gravity gradient boom. Assumed modes methods are used with Finite Element Modeling information to obtain the equations of motion for the system while assuming free-free boundary conditions. A discussion is provided to illustrate how cantilever mode shapes are not always the best assumption when modeling small flexible spacecraft. A key point of interest is first resonant modes may be needed in the system design plant in spite of these modes being greater than one order of magnitude in frequency when compared to the crossover frequency of the controller. LQG/LTR optimal control techniques are implemented to compute attitude control gains while controller robustness considerations determine appropriate reduced order controllers and which flexible modes to include in the design model. Key satellite designer concerns in the areas of computer processor sizing, material uncertainty impacts on the system model, and system performance variations resulting from appendage length modifications are addressed.

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

    Directory of Open Access Journals (Sweden)

    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

  5. 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.

  6. The dual action of poly(ADP-ribose polymerase -1 (PARP-1 inhibition in HIV-1 infection: HIV-1 LTR inhibition and diminution in Rho GTPase activity

    Directory of Open Access Journals (Sweden)

    Slava eRom

    2015-08-01

    Full Text Available The transcription of HIV-1 (HIV is regulated by complex mechanisms involving various cellular factors and virus-encoded transactivators. Poly(ADP-ribose polymerase 1 (PARP-1 inhibition has emerged recently as a potent anti-inflammatory tool, since PARP-1 is involved in the regulation of some genes through its interaction with various transcription factors. We propose a novel approach to diminish HIV replication via PARP-1 inhibition using human primary monocyte-derived macrophages (MDM as an in vitro model system. PARP-1 inhibitors were able to reduce HIV replication in MDM by 60-80% after 7 days infection. Long Terminal Repeat (LTR acts as a switch in virus replication and can be triggered by several agents such as: Tat, tumor necrosis factor α (TNFα, and phorbol 12-myristate 13-acetate (PMA. Overexpression of Tat in MDM transfected with an LTR reporter plasmid led to a 4.2-fold increase in LTR activation; PARP inhibition resulted in 70% reduction of LTR activity. LTR activity, which increased 3-fold after PMA or TNFα treatment, was reduced by PARP inhibition (by 85-95%. MDM treated with PARP inhibitors showed 90% reduction in NFκB activity (known to mediate PMA- and TNFα-induced HIV LTR activation. Cytoskeleton rearrangements are important in effective HIV-1 infection. PARP inactivation reduced actin cytoskeleton rearrangements by affecting Rho GTPase machinery. These findings suggest that HIV replication in MDM could be suppressed by PARP inhibition via NFκB suppression, diminution of LTR activation and its effects on the cytoskeleton. PARP appears to be essential for HIV replication and its inhibition may provide a potent approach to treatment of HIV infection.

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

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

    1999-12-17

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

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

    Science.gov (United States)

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

    2013-05-29

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

  10. Cloning and heterologous expression of a hydrophobin gene Ltr.hyd from the tiger milk mushroom Lentinus tuber-regium in yeast-like cells of Tremella fuciformis

    Directory of Open Access Journals (Sweden)

    Dongmei Liu

    2018-03-01

    Full Text Available Background: Hydrophobins are small proteins secreted by filamentous fungi, which show a highly surface activity. Because of the signally self-assembling abilities and surface activities, hydrophobins were considered as candidates in many aspects, for example, stabilizing foams and emulsions in food products. Lentinus tuber-regium, known as tiger milk mushroom, is both an edible and medicinal sclerotium-producing mushroom. Up to now, the hydrophobins of L. tuber-regium have not been identified. Results: In this paper, a Class I hydrophobin gene, Ltr.hyd, was cloned from L. tuber-regium and expressed in the yeast-like cells of Tremella fuciformis mediated by Agrobacterium tumefaciens. The expression vector pGEH-GH was under the control of T. fuciformis glyceraldehyde-3-phosphate dehydrogenase gene (gpd promoter. The integration of Ltr.hyd into the genome of T. fuciformis was confirmed by PCR, Southern blot, fluorescence observation and quantitative real-time PCR (qRT-PCR. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE demonstrated that recombinant hydrophobin rLtr.HYD with an expected molecular mass of 13 kDa was extracted. The yield of rLtr.HYD was 0.66 mg/g dry weight. The emulsifying activity of rLtr.HYD was better than the typical food emulsifiers sodium caseinate and Tween 20. Conclusions: We evaluated the emulsifying property of hydrophobin Ltr.HYD, which can be potentially used as a food emulsifier. Keywords: Agrobacterium tumefaciens, Emulsifier, Expression vector, Filamentous fungi, Gel electrophoresis, Glyceraldehyde-3-phosphate dehydrogenase, Heterogenous expression, Hydrophobin, Quantitative real-time PCR, Southern blot, Surface activity

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

    Directory of Open Access Journals (Sweden)

    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.

  12. Selection of reliable reference genes for gene expression studies in Trichoderma afroharzianum LTR-2 under oxalic acid stress.

    Science.gov (United States)

    Lyu, Yuping; Wu, Xiaoqing; Ren, He; Zhou, Fangyuan; Zhou, Hongzi; Zhang, Xinjian; Yang, Hetong

    2017-10-01

    An appropriate reference gene is required to get reliable results from gene expression analysis by quantitative real-time reverse transcription PCR (qRT-PCR). In order to identify stable and reliable reference genes in Trichoderma afroharzianum under oxalic acid (OA) stress, six commonly used housekeeping genes, i.e., elongation factor 1, ubiquitin, ubiquitin-conjugating enzyme, glyceraldehyde-3-phosphate dehydrogenase, α-tubulin, actin, from the effective biocontrol isolate T. afroharzianum strain LTR-2 were tested for their expression during growth in liquid culture amended with OA. Four in silico programs (comparative ΔCt, NormFinder, geNorm and BestKeeper) were used to evaluate the expression stabilities of six candidate reference genes. The elongation factor 1 gene EF-1 was identified as the most stably expressed reference gene, and was used as the normalizer to quantify the expression level of the oxalate decarboxylase coding gene OXDC in T. afroharzianum strain LTR-2 under OA stress. The result showed that the expression of OXDC was significantly up-regulated as expected. This study provides an effective method to quantify expression changes of target genes in T. afroharzianum under OA stress. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Skew-adjacency matrices of graphs

    NARCIS (Netherlands)

    Cavers, M.; Cioaba, S.M.; Fallat, S.; Gregory, D.A.; Haemers, W.H.; Kirkland, S.J.; McDonald, J.J.; Tsatsomeros, M.

    2012-01-01

    The spectra of the skew-adjacency matrices of a graph are considered as a possible way to distinguish adjacency cospectral graphs. This leads to the following topics: graphs whose skew-adjacency matrices are all cospectral; relations between the matchings polynomial of a graph and the characteristic

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

    Directory of Open Access Journals (Sweden)

    Soledad Sacristán

    2009-10-01

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

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

    Science.gov (United States)

    Cho, Jungnam; Paszkowski, Jerzy

    2017-08-26

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

  16. GABBR1 has a HERV-W LTR in its regulatory region – a possible implication for schizophrenia

    Directory of Open Access Journals (Sweden)

    Hegyi Hedi

    2013-02-01

    Full Text Available Abstract Schizophrenia is a complex disease with uncertain aetiology. We suggest GABBR1, GABA receptor B1 implicated in schizophrenia based on a HERV-W LTR in the regulatory region of GABBR1. Our hypothesis is supported by: (i GABBR1 is in the 6p22 genomic region most often implicated in schizophrenia; (ii microarray studies found that only presynaptic pathway-related genes, including GABA receptors, have altered expression in schizophrenic patients and (iii it explains how HERV-W elements, expressed in schizophrenia, play a role in the disease: by altering the expression of GABBR1 via a long terminal repeat that is also a regulatory element to GABBR1. Reviewers This paper was reviewed by Sandor Pongor and Martijn Huynen.

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

    Directory of Open Access Journals (Sweden)

    William Dunker

    2017-12-01

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

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

    Science.gov (United States)

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

    2001-06-01

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

  19. Mutations in the Lactococcus lactis Ll.LtrB group II intron that retain mobility in vivo

    Directory of Open Access Journals (Sweden)

    D'Souza Lisa M

    2002-12-01

    Full Text Available Abstract Background Group II introns are mobile genetic elements that form conserved secondary and tertiary structures. In order to determine which of the conserved structural elements are required for mobility, a series of domain and sub-domain deletions were made in the Lactococcus lactis group II intron (Ll.LtrB and tested for mobility in a genetic assay. Point mutations in domains V and VI were also tested. Results The largest deletion that could be made without severely compromising mobility was 158 nucleotides in DIVb(1–2. This mutant had a mobility frequency comparable to the wild-type Ll.LtrB intron (ΔORF construct. Hence, all subsequent mutations were done in this mutant background. Deletion of DIIb reduced mobility to approximately 18% of wild-type, while another deletion in domain II (nts 404–459 was mobile to a minor extent. Only two deletions in DI and none in DIII were tolerated. Some mobility was also observed for a DIVa deletion mutant. Of the three point mutants at position G3 in DV, only G3A retained mobility. In DVI, deletion of the branch-point nucleotide abolished mobility, but the presence of any nucleotide at the branch-point position restored mobility to some extent. Conclusions The smallest intron capable of efficient retrohoming was 725 nucleotides, comprising the DIVb(1–2 and DII(iia,b deletions. The tertiary elements found to be nonessential for mobility were alpha, kappa and eta. In DV, only the G3A mutant was mobile. A branch-point residue is required for intron mobility.

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

    Hajek, Kathryn L.; Friesen, Paul D.

    1998-01-01

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

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

    Directory of Open Access Journals (Sweden)

    John Karijolich

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

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  4. Histone acetyltransferase (HAT) activity of p300 modulates human T lymphotropic virus type 1 p30II-mediated repression of LTR transcriptional activity

    International Nuclear Information System (INIS)

    Michael, Bindhu; Nair, Amrithraj M.; Datta, Antara; Hiraragi, Hajime; Ratner, Lee; Lairmore, Michael D.

    2006-01-01

    Human T-lymphotropic virus type-1 (HTLV-1) is a deltaretrovirus that causes adult T cell leukemia/lymphoma, and is implicated in a variety of lymphocyte-mediated inflammatory disorders. HTLV-1 provirus has regulatory and accessory genes in four pX open reading frames. HTLV-1 pX ORF-II encodes two proteins, p13 II and p30 II , which are incompletely defined in virus replication or pathogenesis. We have demonstrated that pX ORF-II mutations block virus replication in vivo and that ORF-II encoded p30 II , a nuclear-localizing protein that binds with CREB-binding protein (CBP)/p300, represses CREB and Tax responsive element (TRE)-mediated transcription. Herein, we have identified p30 II motifs important for p300 binding and in regulating TRE-mediated transcription in the absence and presence of HTLV-1 provirus. Within amino acids 100-179 of p30 II , a region important for repression of LTR-mediated transcription, we identified a single lysine residue at amino acid 106 (K3) that significantly modulates the ability of p30 II to repress TRE-mediated transcription. Exogenous p300, in a dose-responsive manner, reverses p30 II -dependent repression of TRE-mediated transcription, in the absence or presence of the provirus, In contrast to wild type p300, p300 HAT mutants (defective in histone acetyltransferase activity) only partially rescued p30 II -mediated LTR repression. Deacetylation by histone deacetylase-1 (HDAC-1) enhanced p30 II -mediated LTR repression, while inhibition of deacetylation by trichostatin A decreases p30 II -mediated LTR repression. Collectively, our data indicate that HTLV-1 p30 II modulates viral gene expression in a cooperative manner with p300-mediated acetylation

  5. LQG/LTR [linear quadratic Gaussian with loop transfer recovery] robust control system design for a low-pressure feedwater heater train

    International Nuclear Information System (INIS)

    Murphy, G.V.; Bailey, J.M.

    1990-01-01

    This paper uses the linear quadratic Gaussian with loop transfer recovery (LQG/LTR) control system design method to obtain a level control system for a low-pressure feedwater heater train. The control system performance and stability robustness are evaluated for a given set of system design specifications. The tools for analysis are the return ratio, return difference, and inverse return difference singular-valve plots for a loop break at the plant output. 3 refs., 7 figs., 2 tabs

  6. Intracellular high mobility group B1 protein (HMGB1) represses HIV-1 LTR-directed transcription in a promoter- and cell-specific manner

    International Nuclear Information System (INIS)

    Naghavi, Mojgan H.; Nowak, Piotr; Andersson, Jan; Soennerborg, Anders; Yang Huan; Tracey, Kevin J.; Vahlne, Anders

    2003-01-01

    We investigated whether the high mobility group B 1 (HMGB1), an abundant nuclear protein in all mammalian cells, affects HIV-1 transcription. Intracellular expression of human HMGB1 repressed HIV-1 gene expression in epithelial cells. This inhibitory effect of HMGB1 was caused by repression of long terminal repeat (LTR)-mediated transcription. Other viral promoters/enhancers, including simian virus 40 or cytomegalovirus, were not inhibited by HMGB1. In addition, HMGB1 inhibition of HIV-1 subtype C expression was dependent on the number of NFκB sites in the LTR region. The inhibitory effect of HMGB1 on viral gene expression observed in HeLa cells was confirmed by an upregulation of viral replication in the presence of antisense HMGB1 in monocytic cells. In contrast to what was found in HeLa cells and monocytic cells, endogenous HMGB1 expression did not affect HIV-1 replication in unstimulated Jurkat cells. Thus, intracellular HMGB1 affects HIV-1 LTR-directed transcription in a promoter- and cell-specific manner

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Juan-Carlos Herrera

    2013-12-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    Ilaria eSciamanna

    2016-02-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Science.gov (United States)

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

    2012-01-01

    Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes within the Mexican axolotl (Ambystoma mexicanum) that is indicative of cellular reprogramming of differentiated cells into a germline-like state. In this work, we focus on one of these genes, the long interspersed nucleotide element-1 (LINE-1) retrotransposon, which is usually active in germ cells and silent in most of the somatic tissues in other organisms. LINE-1 was found to be dramatically upregulated during regeneration. In addition, higher genomic LINE-1 content was also detected in the limb regenerate when compared to that before amputation indicating that LINE-1 retrotransposition is indeed active during regeneration. Active LINE-1 retrotransposition has been suggested to have a potentially deleterious impact on genomic integrity. Silencing of activated LINE-1 by small RNAs has been reported to be part of the machinery aiming to maintain genomic integrity. Indeed, we were able to identify putative LINE-1-related piRNAs in the limb blastema. Transposable element-related piRNAs have been identified frequently in the germline in other organisms. Thus, we present here a scenario in which a unique germline-like state is established during axolotl limb regeneration, and the re-activation of LINE-1 may serve as a marker for cellular dedifferentiation in the early-stage of limb regeneration. PMID:22913491

  14. 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

  15. Ex vivo response to histone deacetylase (HDAC inhibitors of the HIV long terminal repeat (LTR derived from HIV-infected patients on antiretroviral therapy.

    Directory of Open Access Journals (Sweden)

    Hao K Lu

    Full Text Available Histone deacetylase inhibitors (HDACi can induce human immunodeficiency virus (HIV transcription from the HIV long terminal repeat (LTR. However, ex vivo and in vivo responses to HDACi are variable and the activity of HDACi in cells other than T-cells have not been well characterised. Here, we developed a novel assay to determine the activity of HDACi on patient-derived HIV LTRs in different cell types. HIV LTRs from integrated virus were amplified using triple-nested Alu-PCR from total memory CD4+ T-cells (CD45RO+ isolated from HIV-infected patients prior to and following suppressive antiretroviral therapy. NL4-3 or patient-derived HIV LTRs were cloned into the chromatin forming episomal vector pCEP4, and the effect of HDACi investigated in the astrocyte and epithelial cell lines SVG and HeLa, respectively. There were no significant differences in the sequence of the HIV LTRs isolated from CD4+ T-cells prior to and after 18 months of combination antiretroviral therapy (cART. We found that in both cell lines, the HDACi panobinostat, trichostatin A, vorinostat and entinostat activated patient-derived HIV LTRs to similar levels seen with NL4-3 and all patient derived isolates had similar sensitivity to maximum HDACi stimulation. We observed a marked difference in the maximum fold induction of luciferase by HDACi in HeLa and SVG, suggesting that the effect of HDACi may be influenced by the cellular environment. Finally, we observed significant synergy in activation of the LTR with vorinostat and the viral protein Tat. Together, our results suggest that the LTR sequence of integrated virus is not a major determinant of a functional response to an HDACi.

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

    Directory of Open Access Journals (Sweden)

    Xueli Zhang

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

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

    Science.gov (United States)

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

    2013-01-01

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

  18. Time-constrained project scheduling with adjacent resources

    NARCIS (Netherlands)

    Hurink, Johann L.; Kok, A.L.; Paulus, J.J.; Schutten, Johannes M.J.

    We develop a decomposition method for the Time-Constrained Project Scheduling Problem (TCPSP) with adjacent resources. For adjacent resources the resource units are ordered and the units assigned to a job have to be adjacent. On top of that, adjacent resources are not required by single jobs, but by

  19. Time-constrained project scheduling with adjacent resources

    NARCIS (Netherlands)

    Hurink, Johann L.; Kok, A.L.; Paulus, J.J.; Schutten, Johannes M.J.

    2008-01-01

    We develop a decomposition method for the Time-Constrained Project Scheduling Problem (TCPSP) with Adjacent Resources. For adjacent resources the resource units are ordered and the units assigned to a job have to be adjacent. On top of that, adjacent resources are not required by single jobs, but by

  20. 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

  1. Rotavirus 2/6 Viruslike Particles Administered Intranasally with Cholera Toxin, Escherichia coli Heat-Labile Toxin (LT), and LT-R192G Induce Protection from Rotavirus Challenge

    OpenAIRE

    O’Neal, Christine M.; Clements, John D.; Estes, Mary K.; Conner, Margaret E.

    1998-01-01

    We have shown that rotavirus 2/6 viruslike particles composed of proteins VP2 and VP6 (2/6-VLPs) administered to mice intranasally with cholera toxin (CT) induced protection from rotavirus challenge, as measured by virus shedding. Since it is unclear if CT will be approved for human use, we evaluated the adjuvanticity of Escherichia coli heat-labile toxin (LT) and LT-R192G. Mice were inoculated intranasally with 10 μg of 2/6-VLPs combined with CT, LT, or LT-R192G. All three adjuvants induced ...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    Sharma, Vishakha; Nandineni, Madhusudan R

    2014-04-01

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

  4. Spondylolisthesis adjacent to a cervical disc arthroplasty does not increase the risk of adjacent level degeneration.

    Science.gov (United States)

    Kieser, David Christopher; Cawley, Derek Thomas; Roscop, Cecile; Mazas, Simon; Coudert, Pierre; Boissiere, Louis; Obeid, Ibrahim; Vital, Jean-Marc; Pointillart, Vincent; Gille, Olivier

    2018-03-31

    To understand whether a spondylolisthesis in the sub-axial spine cranial to a cervical disc arthroplasty (CDA) construes a risk of adjacent level disease (ALD). A retrospective review of 164 patients with a minimum 5-year follow-up of a cervical disc arthroplasty was performed. Multi-level surgeries, including hybrid procedures, were included. Multiple implant types were included. The two inter-vertebral discs (IVD) cranial of the CDA were monitored for evidence of radiologic degeneration using the Kettler criteria. The rate of ALD in CDA found in this series was 17.8%, with most affecting the immediately adjacent IVD (27.4 and 7.6%, respectively p = 0.000). Pre-operative mild spondylolisthesis adjacent to a planned CDA was not found to be a risk factor for ALD within 5 years. Those with a degenerative spondylolisthesis are at higher risk of ALD (33%) than those with a non-degenerative cause for their spondylolisthesis (11%). Post-operative CDA alignment, ROM or induced spondylolisthesis do not affect the rate of ALD in those with an adjacent spondylolisthesis. Patients with ALD experience significantly worse 5-year pain and functional outcomes than those unaffected by ALD. A pre-operatively identified mild spondylolisthesis in the sub-axial spine cranially adjacent to a planned CDA is not a risk factor for ALD within 5 years. These slides can be retrieved under Electronic Supplementary Material.

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

    Directory of Open Access Journals (Sweden)

    Abigail L Savage

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

  6. Rotavirus 2/6 Viruslike Particles Administered Intranasally with Cholera Toxin, Escherichia coli Heat-Labile Toxin (LT), and LT-R192G Induce Protection from Rotavirus Challenge

    Science.gov (United States)

    O’Neal, Christine M.; Clements, John D.; Estes, Mary K.; Conner, Margaret E.

    1998-01-01

    We have shown that rotavirus 2/6 viruslike particles composed of proteins VP2 and VP6 (2/6-VLPs) administered to mice intranasally with cholera toxin (CT) induced protection from rotavirus challenge, as measured by virus shedding. Since it is unclear if CT will be approved for human use, we evaluated the adjuvanticity of Escherichia coli heat-labile toxin (LT) and LT-R192G. Mice were inoculated intranasally with 10 μg of 2/6-VLPs combined with CT, LT, or LT-R192G. All three adjuvants induced equivalent geometric mean titers of rotavirus-specific serum antibody and intestinal immunoglobulin G (IgG). Mice inoculated with 2/6-VLPs with LT produced significantly higher titers of intestinal IgA than mice given CT as the adjuvant. All mice inoculated with 2/6-VLPs mixed with LT and LT-R192G were totally protected (100%) from rotavirus challenge, while mice inoculated with 2/6-VLPs mixed with CT showed a mean 91% protection from challenge. The availability of a safe, effective mucosal adjuvant such as LT-R192G will increase the practicality of administering recombinant vaccines mucosally. PMID:9525668

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

    OpenAIRE

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2014-10-01

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

  9. Neuromuscular adaptations induced by adjacent joint training.

    Science.gov (United States)

    Ema, R; Saito, I; Akagi, R

    2018-03-01

    Effects of resistance training are well known to be specific to tasks that are involved during training. However, it remains unclear whether neuromuscular adaptations are induced after adjacent joint training. This study examined the effects of hip flexion training on maximal and explosive knee extension strength and neuromuscular performance of the rectus femoris (RF, hip flexor, and knee extensor) compared with the effects of knee extension training. Thirty-seven untrained young men were randomly assigned to hip flexion training, knee extension training, or a control group. Participants in the training groups completed 4 weeks of isometric hip flexion or knee extension training. Standardized differences in the mean change between the training groups and control group were interpreted as an effect size, and the substantial effect was assumed to be ≥0.20 of the between-participant standard deviation at baseline. Both types of training resulted in substantial increases in maximal (hip flexion training group: 6.2% ± 10.1%, effect size = 0.25; knee extension training group: 20.8% ± 9.9%, effect size = 1.11) and explosive isometric knee extension torques and muscle thickness of the RF in the proximal and distal regions. Improvements in strength were accompanied by substantial enhancements in voluntary activation, which was determined using the twitch interpolation technique and RF activation. Differences in training effects on explosive torques and neural variables between the two training groups were trivial. Our findings indicate that hip flexion training results in substantial neuromuscular adaptations during knee extensions similar to those induced by knee extension training. © 2017 The Authors. Scandinavian Journal of Medicine & Science In Sports Published by John Wiley & Sons Ltd.

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

    KAUST Repository

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

    2011-01-01

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

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

    KAUST Repository

    La, Honggui

    2011-09-06

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

  12. 33 CFR 80.1395 - Puget Sound and adjacent waters.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Puget Sound and adjacent waters. 80.1395 Section 80.1395 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... waters. The 72 COLREGS shall apply on all waters of Puget Sound and adjacent waters, including Lake Union...

  13. Early Verb Constructions in French: Adjacency on the Left Edge

    Science.gov (United States)

    Veneziano, Edy; Clark, Eve V.

    2016-01-01

    Children acquiring French elaborate their early verb constructions by adding adjacent morphemes incrementally at the left edge of core verbs. This hypothesis was tested with 2657 verb uses from four children between 1;3 and 2;7. Consistent with the Adjacency Hypothesis, children added clitic subjects frst only to present tense forms (as in…

  14. Objectifying the Adjacent and Opposite Angles: A Cultural Historical Analysis

    Science.gov (United States)

    Daher, Wajeeh; Musallam, Nadera

    2018-01-01

    The angle topic is central to the development of geometric knowledge. Two of the basic concepts associated with this topic are the adjacent and opposite angles. It is the goal of the present study to analyze, based on the cultural historical semiotics framework, how high-achieving seventh grade students objectify the adjacent and opposite angles'…

  15. On Pathos Adjacency Cut Vertex Jump Graph of a Tree

    OpenAIRE

    Nagesh.H.M; R.Chandrasekhar

    2014-01-01

    In this paper the concept of pathos adjacency cut vertex jump graph PJC(T) of a tree T is introduced. We also present a characterization of graphs whose pathos adjacency cut vertex jump graphs are planar, outerplanar, minimally non-outerplanar, Eulerian and Hamiltonian.

  16. Loading effects of anterior cervical spine fusion on adjacent segments

    Directory of Open Access Journals (Sweden)

    Chien-Shiung Wang

    2012-11-01

    Full Text Available Adjacent segment degeneration typically follows anterior cervical spine fusion. However, the primary cause of adjacent segment degeneration remains unknown. Therefore, in order to identify the loading effects that cause adjacent segment degeneration, this study examined the loading effects to superior segments adjacent to fused bone following anterior cervical spine fusion. The C3–C6 cervical spine segments of 12 sheep were examined. Specimens were divided into the following groups: intact spine (group 1; and C5–C6 segments that were fused via cage-instrumented plate fixation (group 2. Specimens were cycled between 20° flexion and 15° extension with a displacement control of 1°/second. The tested parameters included the range of motion (ROM of each segment, torque and strain on both the body and inferior articular process at the superior segments (C3–C4 adjacent to the fused bone, and the position of the neutral axis of stress at under 20° flexion and 15° extension. Under flexion and Group 2, torque, ROM, and strain on both the bodies and facets of superior segments adjacent to the fused bone were higher than those of Group 1. Under extension and Group 2, ROM for the fused segment was less than that of Group 1; torque, ROM, and stress on both the bodies and facets of superior segments adjacent to the fused bone were higher than those of Group 1. These analytical results indicate that the muscles and ligaments require greater force to achieve cervical motion than the intact spine following anterior cervical spine fusion. In addition, ROM and stress on the bodies and facets of the joint segments adjacent to the fused bone were significantly increased. Under flexion, the neutral axis of the stress on the adjacent segment moved backward, and the stress on the bodies of the segments adjacent to the fused bone increased. These comparative results indicate that increased stress on the adjacent segments is caused by stress-shielding effects

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

    Science.gov (United States)

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

    2018-03-01

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

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

    Science.gov (United States)

    Boronnikova, S V; Kalendar', R N

    2010-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Kristel Kaer

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

  20. Community conservation adjacent to Ruaha National Park, Tanzania

    Science.gov (United States)

    Sue Stolberger

    2007-01-01

    In the areas adjacent to Ruaha National Park where rural communities exist, much more work and education is required to enable them to benefit directly and indirectly from tourism and managing their own natural resources.

  1. Influence of cantilevered sheet pile deflection on adjacent roadways.

    Science.gov (United States)

    2009-06-01

    Cantilevered sheet pile walls are often used adjacent roadways as temporary support during construction. Excess movement of these walls has led to excessive roadway distress causing additional repairs to be necessary. This study assessed the effects ...

  2. Suprabasalt stratigraphy within and adjacent to the reference repository location

    International Nuclear Information System (INIS)

    Bjornstad, B.N.

    1983-01-01

    This data-package contains six detailed stratigraphic correlations and structure cross sections of suprabasalt sediments in the area adjacent to and including the Reference Repository Location. 4 refs., 1 fig

  3. Sleeping sickness surveys: game reserve adjacent villages in Malawi

    African Journals Online (AJOL)

    Sleeping sickness surveys: game reserve adjacent villages in Malawi. ... Sera from 160 game ranger volunteers and from 82 suspected cases_of Rhodesian sleeping sickness were tested by use of ELISA, ... AJOL African Journals Online.

  4. Objectifying the adjacent and opposite angles: a cultural historical analysis

    Science.gov (United States)

    Daher, Wajeeh; Musallam, Nadera

    2018-02-01

    The angle topic is central to the development of geometric knowledge. Two of the basic concepts associated with this topic are the adjacent and opposite angles. It is the goal of the present study to analyze, based on the cultural historical semiotics framework, how high-achieving seventh grade students objectify the adjacent and opposite angles' concepts. We videoed the learning of a group of three high-achieving students who used technology, specifically GeoGebra, to explore geometric relations related to the adjacent and opposite angles' concepts. To analyze students' objectification of these concepts, we used the categories of objectification of knowledge (attention and awareness) and the categories of generalization (factual, contextual and symbolic), developed by Radford. The research results indicate that teacher's and students' verbal and visual signs, together with the software dynamic tools, mediated the students' objectification of the adjacent and opposite angles' concepts. Specifically, eye and gestures perceiving were part of the semiosis cycles in which the participating students were engaged and which related to the mathematical signs that signified the adjacent and the opposite angles. Moreover, the teacher's suggestions/requests/questions included/suggested semiotic signs/tools, including verbal signs that helped the students pay attention, be aware of and objectify the adjacent and opposite angles' concepts.

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

    Science.gov (United States)

    Pelsy, F.; Merdinoglu, D.

    2002-09-01

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

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

    Science.gov (United States)

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

    1999-01-01

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

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

    Science.gov (United States)

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

    1999-10-01

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

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

    Science.gov (United States)

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

    2001-11-01

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

  9. NF90 una proteína celular que se une a RNAds inhibe la transactivación del LTR del HIV-1 mediada por TAT

    Directory of Open Access Journals (Sweden)

    Silvio Urcuqui Inchima

    2001-04-01

    Full Text Available

    La transactivación del LTR de HIV-1 requiere la interacción de la proteína Tat ( trans-activation transcription con la estructura TAR ( trans-activation response, que se encuentra localizada en el extremo 5’ de todos los transcriptos virales. La interacción de la proteína Tat con TAR forma un precomplejo transcripcional indispensable para la eficiente transcripción del genoma viral.
    La interacción de diferentes factores celulares (cdk9 y ciclina T, entre otros con el precomplejo Tat-TAR, constituye un complejo estable que facilita la fosforilación de la subunidad mayor de la RNA polimerasa II, asegurando una eficiente elongación de los transcriptos virales. No se han descripto proteínas capaces de regular negativamente la función de Tat con resultados nefastos para la replicación viral. También se ha descrito otro tipo de proteínas celulares con capacidad de interactuar con TAR. El ejemplo mejor caracterizado es la proteína-kinasa dependiente de RNA (PKR, se autofosforila y mediante fosforilación del factor eIF2, inhibe la síntesis de proteínas. Con el presente trabajo se
    pretendió aislar y caracterizar otras proteínas celulares capaces de interactuar con la estructura TAR y estudiar su efecto en la función de Tat.

     

  10. The Volpe Center GPS Adjacent Band Compatibility Program Plan : GPS Adjacent Band Compatibility Workshop, Volpe Center, Cambridge MA

    Science.gov (United States)

    2014-09-18

    Approach to DOT GPS Adjacent Band Compatibility Assessment. Identify forums and provide public outreach to make sure the progress and work are as open and transparent as possible. Develop an implementation plan that incorporates aspects from the DOT ...

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

    Science.gov (United States)

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

    2018-05-09

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

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

    Science.gov (United States)

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

    2018-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Daniil Nikitin

    2018-01-01

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

  14. Emission of pesticides during drilling and deposition in adjacent areas

    Directory of Open Access Journals (Sweden)

    Heimbach, Udo

    2014-02-01

    Full Text Available In seven experiments seeds of maize, oil seed rape and barley, treated with neonicotinoids, were sown using pneumatic drilling equipment with deflectors attached in case of pneumatic suction systems. Directly adjacent to the drilled area of usually about 50 m width were replicated areas with bare soil as well as with crops. During maize (Zea mays drilling flowering oil seed rape (Brassica napus and during drilling of barley (Hordeum vulgare and oil seed rape flowering white mustard (Sinapis alba was adjacent. The amount of residues in the adjacent non crop areas in Petri dishes being distributed on the bare soil declined only slowly from 1 to 20 m distance from the area drilled. Seed batches with more abrasion and higher content of active substances in the dust resulted in higher residues off crop. After drilling of maize in four experiments in Petri dishes in adjacent non crop areas in 1-5 m distance between 0.02 and 0.40 g a.s./ha of neonicotinoids and in the adjacent oil seed rape a total of 0.05–0.80 g a.s./ha were detected. After drilling oil seed rape or barley these values were only 0.02–0.06 g a.s./ha in Petri dishes in non crop areas and 0.03-0.08 g a.s./ha in total in adjacent white mustard. In gauze net samplers installed vertically in 3 m distance in non crop areas up to seven times higher values were detected compared to Petri dishes.

  15. Fulltext PDF

    Indian Academy of Sciences (India)

    2012-01-24

    Jan 24, 2012 ... Based on this, we constructed periodic consensus sequences of these three kinds of ... T is the period of P. To determine the value of the parameter par, we ..... Mager DL 2007 Repeated recruitment of LTR retrotransposons.

  16. Modeling fires in adjacent ship compartments with computational fluid dynamics

    International Nuclear Information System (INIS)

    Wix, S.D.; Cole, J.K.; Koski, J.A.

    1998-01-01

    This paper presents an analysis of the thermal effects on radioactive (RAM) transportation pack ages with a fire in an adjacent compartment. An assumption for this analysis is that the adjacent hold fire is some sort of engine room fire. Computational fluid dynamics (CFD) analysis tools were used to perform the analysis in order to include convective heat transfer effects. The analysis results were compared to experimental data gathered in a series of tests on the United States Coast Guard ship Mayo Lykes located at Mobile, Alabama. (authors)

  17. Nonlinear spin wave coupling in adjacent magnonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sadovnikov, A. V., E-mail: sadovnikovav@gmail.com; Nikitov, S. A. [Laboratory “Metamaterials,” Saratov State University, Saratov 410012 (Russian Federation); Kotel' nikov Institute of Radioengineering and Electronics, Russian Academy of Sciences, Moscow 125009 (Russian Federation); Beginin, E. N.; Morozova, M. A.; Sharaevskii, Yu. P.; Grishin, S. V.; Sheshukova, S. E. [Laboratory “Metamaterials,” Saratov State University, Saratov 410012 (Russian Federation)

    2016-07-25

    We have experimentally studied the coupling of spin waves in the adjacent magnonic crystals. Space- and time-resolved Brillouin light-scattering spectroscopy is used to demonstrate the frequency and intensity dependent spin-wave energy exchange between the side-coupled magnonic crystals. The experiments and the numerical simulation of spin wave propagation in the coupled periodic structures show that the nonlinear phase shift of spin wave in the adjacent magnonic crystals leads to the nonlinear switching regime at the frequencies near the forbidden magnonic gap. The proposed side-coupled magnonic crystals represent a significant advance towards the all-magnonic signal processing in the integrated magnonic circuits.

  18. Nonlinear spin wave coupling in adjacent magnonic crystals

    International Nuclear Information System (INIS)

    Sadovnikov, A. V.; Nikitov, S. A.; Beginin, E. N.; Morozova, M. A.; Sharaevskii, Yu. P.; Grishin, S. V.; Sheshukova, S. E.

    2016-01-01

    We have experimentally studied the coupling of spin waves in the adjacent magnonic crystals. Space- and time-resolved Brillouin light-scattering spectroscopy is used to demonstrate the frequency and intensity dependent spin-wave energy exchange between the side-coupled magnonic crystals. The experiments and the numerical simulation of spin wave propagation in the coupled periodic structures show that the nonlinear phase shift of spin wave in the adjacent magnonic crystals leads to the nonlinear switching regime at the frequencies near the forbidden magnonic gap. The proposed side-coupled magnonic crystals represent a significant advance towards the all-magnonic signal processing in the integrated magnonic circuits.

  19. Herpetology of the American Madrean Archipelago and adjacent valleys

    Science.gov (United States)

    Lawrence L. C. Jones

    2005-01-01

    Approximately 110 species of amphibians (18 frogs and toads, and 1 salamander) and reptiles (47 snakes, 39 lizards, and 5 turtles) are known from the American Madrean Archipelago and adjacent valleys. The high diversity of the herpetofauna comes from a variety of factors, including a convergence of biotic communities representing deserts, grasslands, and mountains....

  20. Developmental tumors and adjacent cortical dysplasia: single or dual pathology?

    Science.gov (United States)

    Palmini, André; Paglioli, Eliseu; Silva, Vinicius Duval

    2013-12-01

    Developmental tumors often lead to refractory partial seizures and constitute a well-defined, surgically remediable epilepsy syndrome. Dysplastic features are often associated with these tumors, and their significance carries both practical and conceptual relevance. If associated focal cortical dysplasia (FCD) relates to the extent of the epileptogenic tissue, then presurgical evaluation and surgical strategies should target both the tumor and the surrounding dyslaminated cortex. Furthermore, the association has been included in the recently revised classification of FCD and the epileptogenicity of this associated dysplastic tissue is crucial to validate such revision. In addition to the possibility of representing dual pathology, the association of developmental tumors and adjacent dysplasia may instead represent a single developmental lesion with distinct parts distributed along a histopathologic continuum. Moreover, the possibility that this adjacent dyslamination is of minor epileptogenic relevance should also be entertained. Surgical data show that complete resection of the solid tumors and immediately adjacent tissue harboring satellites may disrupt epileptogenic networks and lead to high rates of seizure freedom, challenging the epileptogenic relevance of more extensive adjacent dyslaminated cortex. Whether the latter is a primary or secondary abnormality and whether dyslaminated cortex in the context of a second lesion may produce seizures after complete resection of the main lesion is still to be proven. Wiley Periodicals, Inc. © 2013 International League Against Epilepsy.

  1. The dynamics of microtidal lagoons and adjacent coasts

    NARCIS (Netherlands)

    Stive, M.J.F.; Capobianco, M.; Wang, Z.B.; Ruol, P.

    1996-01-01

    We have formulated an aggregated-scale behaviour-model for the interaction between a tidal basin and its adjacent coastal environment, without adopting a priory assumptions about their independent dynamic equilibrium behaviour. Necessarily so, the model combines observations and findings resuhing

  2. Do Mangroves Subsidize Carbon to Adjacent Mudflat Fish Communities?

    Science.gov (United States)

    Henkel, S.; Kasten, S.; Hartmann, J.; Staubwasser, M.; Hernandez, M. F.; West, L.; Midway, S. R.; Polito, M. J.

    2017-12-01

    Mangroves are often implicated as energetic sources for fisheries productivity. However, the validity of this connection still remains in contention. Stable isotopes may provide answers by tracking the use of specific basal carbon sources in fish and invertebrates living in mangrove-mudflat habitat mosaics. We analyzed 307 consumer samples representing n=44 fish and invertebrate species collected from mangrove forest creeks and adjacent mudflats in coastal Tanzania using bulk carbon and nitrogen stable isotope analysis. Given the proposed high productivity of mangrove habitats, we hypothesize that mudflat communities will have carbon stable isotope values similar to mangrove communities either through the flux of mangrove carbon into adjacent mudflats and/or via the movement of mudflat fish communities into and out of mangrove habitats. Alternatively, mangrove carbon is often refractory, which may result in mudflat communities with isotopic values that differ from those found in adjacent mangrove communities. This scenario would suggest limited carbon flow between mudflat and mangrove food webs and that the movement of fish into and out of mangrove habitats is related to shelter from predation more than feeding. Data analysis is ongoing to test these competing hypotheses. By understanding the contribution of mangrove carbon to adjacent habitats, managers in Tanzania can make better informed decisions regarding the protection of mangroves and the local fisheries, which are a crucial source of income and food.

  3. Measurement Methods to Determine Air Leakage Between Adjacent Zones

    Energy Technology Data Exchange (ETDEWEB)

    Hult, Erin L. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Dickerhoff, Darryl J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Price, Phillip N. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2012-09-01

    Air leakage between adjacent zones of a building can lead to indoor air quality and energy efficiency concerns, however there is no existing standard for measuring inter-zonal leakage. In this study, synthesized data and field measurements are analyzed in order to explore the uncertainty associated with different methods for collecting and analyzing fan pressurization measurements to calculate interzone leakage.

  4. Optimal induced universal graphs and adjacency labeling for trees

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Dahlgaard, Søren; Knudsen, Mathias Bæk Tejs

    2015-01-01

    bound. The lower bound and previously best upper bounds were presented in Alstrup and Rauhe (FOCS'02). Our upper bounds are obtained through a log2 n + O(1) labeling scheme for adjacency queries in forests. We hereby solve an open problem being raised repeatedly over decades, e.g. in Kannan, Naor...

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

    Directory of Open Access Journals (Sweden)

    Piñeyro David

    2011-11-01

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

  6. LTR Control Methodologies for Microvibrations

    DEFF Research Database (Denmark)

    Aglietti, G.S.; Stoustrup, Jakob; Rogers, E.

    1998-01-01

    Microvibrations at frequencies between 1 and 1000 Hz generated by on-board equipment can propagate through a satellite's structure and hence significantly reduce the performance of sensitive payloads. This paper describes a Lagrange-Rayleigh-Ritz method for developing models suitable for the desi...... of active control schemes. Here Loop Transfer Recovery based controller design methods are employed with this modeling strategy...

  7. Cryopreserved embryo transfer: adjacent or non-adjacent to failed fresh long GnRH-agonist protocol IVF cycle.

    Science.gov (United States)

    Volodarsky-Perel, Alexander; Eldar-Geva, Talia; Holzer, Hananel E G; Schonberger, Oshrat; Reichman, Orna; Gal, Michael

    2017-03-01

    The optimal time to perform cryopreserved embryo transfer (CET) after a failed oocyte retrieval-embryo transfer (OR-ET) cycle is unknown. Similar clinical pregnancy rates were recently reported in immediate and delayed CET, performed after failed fresh OR-ET, in cycles with the gonadotrophin-releasing hormone (GnRH) antagonist protocol. This study compared outcomes of CET performed adjacently (<50 days, n = 67) and non-adjacently (≥50 to 120 days, n = 62) to the last OR-day of cycles with the GnRH agonist down-regulation protocol. Additional inclusion criteria were patients' age 20-38 years, the transfer of only 1-2 cryopreserved embryos, one treatment cycle per patient and artificial preparation for CET. Significantly higher implantation, clinical pregnancy and live birth rates were found in the non-adjacent group than in the adjacent group: 30.5% versus 11.3% (P = 0.001), 41.9% versus 17.9% (P = 0.003) and 32.3% versus 13.4% (P = 0.01), respectively. These results support the postponement of CET after a failed OR-ET for at least one menstrual cycle, when a preceding long GnRH-agonist protocol is used. Copyright © 2016 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  8. 33 CFR 148.217 - How can a State be designated as an adjacent coastal State?

    Science.gov (United States)

    2010-07-01

    ... an adjacent coastal State? 148.217 Section 148.217 Navigation and Navigable Waters COAST GUARD... General § 148.217 How can a State be designated as an adjacent coastal State? (a) Adjacent coastal States... as an adjacent coastal State in the notice may request to be designated as one if the environmental...

  9. Extraosseous Gaucher cell deposition without adjacent bone involvement.

    Science.gov (United States)

    Meyer, Brendan J; Mills, Anne M; Gaskin, Cree M

    2014-10-01

    Extraosseous Gaucher cell deposits are a rare complication of Gaucher disease that can mimic malignancy. We describe a case of Gaucher cell deposition in the subcutaneous soft tissues overlying the lower thoracic spine in an 18-year-old woman with known type III Gaucher disease. This case is unique in the literature because this subcutaneous Gaucher mass was not associated with extension from underlying bone involvement or clear lymph node origin. It demonstrated no discernible continuity with the adjacent thoracic spinous processes, the cortices of which appeared intact. Although patients with Gaucher disease are at increased risk of malignancy, Gaucher cell deposition should remain a differential consideration for soft tissue masses with or without adjacent bone involvement in patients with known Gaucher disease.

  10. A new nuclear safety programme for areas adjacent to Finland

    International Nuclear Information System (INIS)

    Varjoranta, T.

    1997-01-01

    The projects aimed at improving nuclear and radiation safety in areas adjacent to Finland have been compiled into one programme. The purpose of the programme is to promote activities that minimise accident risks at nuclear power plants and that improve preparedness for situations involving a risk. Nuclear materials are also to be kept under strict control. In the last few years, nuclear and radiation safety has clearly improved in areas adjacent to Finland. But work is still needed to reduce the remaining risks. The Finnish support programme comprises two very definite functions. On one hand, the programme acts as a catalyst for projects launched by the Russians themselves or by the Western partners together, and strives to pave the way for international financing projects. On the other hand, assistance is given as direct support for certain hand-picked projects. (orig.)

  11. Fish species diversity and conservation in Beijing and adjacent areas

    OpenAIRE

    Chunguang Zhang; Yahui Zhao; Yingchun Xing; Ruilu Guo; Qing Zhang; Yun Feng; Enyuan Fan

    2011-01-01

    Based on field surveys between 2002 and 2010, and fish collections in the National Zoological Museum, Institute of Zoology, Chinese Academy of Sciences, a total of 93 wild fish species including 12 in-troduced species had been recorded in Beijing and adjacent areas. Eighty five of these species, including some migratory and estuarine fishes, are native to the region. Only 43 native wild species were collected in our field work from 2002 to 2010. Compared with the historical records, nearly 50...

  12. Plutonium in soil adjacent to Rocky Flats plant

    International Nuclear Information System (INIS)

    Hume, M.W.; Illsley, C.T.

    1979-01-01

    In 1975, lawsuits were filed claiming contaminated lands adjacent to the plant. Five remote as well as 89 sites on lands under litigation were sampled using four sampling techniques at each site. An additional 71 sites were sampled using the Rockwell International technique. No results approached the EPA proposed guideline screening level of 200 mCi/km 2 , although numerous sites to the last of the plant exceed 2 d/m/g (10 mCi/km 2 )

  13. The Benguela upwelling ecosystem lies adjacent to the south ...

    African Journals Online (AJOL)

    denise

    The Benguela upwelling ecosystem lies adjacent to the south-western coast of Africa, from southern Angola. (15°S) to Cape Agulhas (35°S; Fig. 1). Ecologically, it is split into separate northern and southern sub- systems by a zone of intense perennial upwelling near. Lüderitz (26–27.5°S; Shannon 1985). As is charac-.

  14. Symmetry breaking of adjacent tracks in perpendicular recording system

    International Nuclear Information System (INIS)

    Xie Huang; Wei Dan

    2007-01-01

    The track density increase in a perpendicular magnetic recording system is limited by the adjacent-track interference (ATI). In this work, a composite micromagnetic simulation model of the read/write process is developed to analyse ATI by the symmetry of signal and noise in two adjacent W = 60 nm tracks with the track pitch of the order of 100 nm. Based on the two-dimensional medium noise distribution of dibit recording, it is found that the noise in the first and later recorded tracks start to be asymmetric when the track pitch is lower than 2 W; if the read width is limited within 2/3 of the write width, the asymmetry of noise appears when the track pitch is less than 1.5 W. At higher recording densities, the signal-to-noise ratio degradation is mainly due to the noise caused by the interference from the signal of the adjacent track. Side writing can be effectively eliminated by the use of a guard band whose width is at least half the track width

  15. Using BRDFs for accurate albedo calculations and adjacency effect corrections

    Energy Technology Data Exchange (ETDEWEB)

    Borel, C.C.; Gerstl, S.A.W.

    1996-09-01

    In this paper the authors discuss two uses of BRDFs in remote sensing: (1) in determining the clear sky top of the atmosphere (TOA) albedo, (2) in quantifying the effect of the BRDF on the adjacency point-spread function and on atmospheric corrections. The TOA spectral albedo is an important parameter retrieved by the Multi-angle Imaging Spectro-Radiometer (MISR). Its accuracy depends mainly on how well one can model the surface BRDF for many different situations. The authors present results from an algorithm which matches several semi-empirical functions to the nine MISR measured BRFs that are then numerically integrated to yield the clear sky TOA spectral albedo in four spectral channels. They show that absolute accuracies in the albedo of better than 1% are possible for the visible and better than 2% in the near infrared channels. Using a simplified extensive radiosity model, the authors show that the shape of the adjacency point-spread function (PSF) depends on the underlying surface BRDFs. The adjacency point-spread function at a given offset (x,y) from the center pixel is given by the integral of transmission-weighted products of BRDF and scattering phase function along the line of sight.

  16. Smarandachely Adjacent-Vertex-Distinguishing Proper Edge Chromatic Number of Cm∨Kn

    OpenAIRE

    Shunqin Liu

    2016-01-01

    According to different conditions, researchers have defined a great deal of coloring problems and the corresponding chromatic numbers. Such as, adjacent-vertex-distinguishing total chromatic number, adjacent-vertex-distinguishing proper edge chromatic number, smarandachely-adjacent-vertex-distinguishing proper edge chromatic number, smarandachely-adjacent-vertex-distinguishing proper total chromatic number. And we focus on the smarandachely adjacent-vertex-distinguishing proper edge chromatic...

  17. Adjacent segment disease and C-ADR: promises fulfilled?

    Science.gov (United States)

    Riew, K Daniel; Schenk-Kisser, Jeannette M.; Skelly, Andrea C.

    2012-01-01

    Study design: Systematic review. Clinical question: Do the rates and timing of adjacent segment disease (ASD) differ between cervical total disc arthroplasty (C-ADR) and anterior cervical discectomy and fusion (ACDF) in patients treated for cervical degenerative disc disease? Methods: A systematic search of MEDLINE/PubMed and bibliographies of key articles was done to identify studies with long-term follow-up for symptomatic and/or radiographic ASD comparing C-ADR with fusion for degenerative disc disease of the cervical spine. The focus was on studies with longer follow-up (48–60 months) of primary US Food and Drug Administration trials of Prestige ST, Prodisc-C, and Bryan devices as available. Trials of other discs with a minimum of 24 months follow-up were considered for inclusion. Studies evaluating lordosis/angle changes at adjacent segments and case series were excluded. Results: From 14 citations identified, four reports from three randomized controlled trials and four nonrandomized studies are summarized. Risk differences between C-ADR and ACF for symptomatic ASD were 1.5%–2.3% and were not significant across RCT reports. Time to development of ASD did not significantly differ between treatments. Rates of radiographic ASD were variable. No meaningful comparison of ASD rates based on disc design was possible. No statistical differences in adjacent segment range of motion were noted between treatment groups. Conclusion: Our analysis reveals that, to date, there is no evidence that arthroplasty decreases ASD compared with ACDF; the promise of arthroplasty decreasing ASD has not been fulfilled. PMID:23236312

  18. Microwave treatment of renal cell carcinoma adjacent to renal sinus.

    Science.gov (United States)

    Gao, Yongyan; Liang, Ping; Yu, Xiaoling; Yu, Jie; Cheng, Zhigang; Han, Zhiyu; Duan, Shaobo; Huang, Hui

    2016-11-01

    To evaluate the efficacy and safety of ultrasound (US)-guided percutaneous microwave ablation (MWA) for renal cell carcinoma (RCC) adjacent to renal sinus. This retrospective study included 41 patients who underwent US-guided percutaneous MWA of 41 RCCs adjacent to the renal sinus from April 2006 to December 2015. Contrast-enhanced images of US and computed tomography (CT) or magnetic resonance (MR) imaging were performed at pre-ablation and 1day, 1 month, 3 months, and every 6 months after ablation. Initial ablation success (IAS), disease-free survival (DFS), RCC-related survival (RRS), and overall survival (OS) were recorded at the follow-up visits. IAS was achieved in 92.7% (38/41) of the study subjects. The IAS significantly differed between patients with RCCs ≤4cm (100%, 29/29) and RCCs >4cm (75%, 9/12, p=0.021). During the median follow-up of 37.6 (range, 3.0-97.3) months, the estimated 1-, 3-, and 5-year DFS of patients with an initial tumor of ≤4cm were 100%, 89.7%, and 81.5%, respectively. The 1-, 3-, and 5-year RRS were 100%, 93.3%, and 93.3%, respectively. The 1-, 3-, and 5-year OS were 97.1%, 87.8%, and 83.6%, respectively. The multivariate analysis using the Cox proportional hazard model revealed no independent predictor of recurrence among all the variables. There were no MWA-related deaths among the study subjects. One patient developed a retroperitoneal abscess after ablation. US-guided percutaneous MWA appears to be a promising method for RCCs adjacent to renal sinus, especially for tumors ≤4cm. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Cystic adventitial degeneration: ectopic ganglia from adjacent joint capsules.

    Science.gov (United States)

    Ortmann, J; Widmer, M K; Gretener, S; Do, D D; Willenberg, T; Daliri, A; Baumgartner, I

    2009-11-01

    Cystic adventitial degeneration is a rare non-atherosclerotic cause of peripheral arterial occlusive disease, mainly seen in young men without other evidence of vascular disease. Diagnosis will be established by clinical findings and by ultrasound or angiography and can be treated by excision or enucleation of the affected arterial segment or by percutaneous ultrasound-guided aspiration. However, the etiology of adventitial cysts remains unknown. We report a case of cystic adventitial degeneration showing a connection between the joint capsule and the adventitial cyst, supporting the theory that cystic adventitial degeneration may represent ectopic ganglia from adjacent joint capsules.

  20. Adjacent Lumbar Disc Herniation after Lumbar Short Spinal Fusion

    OpenAIRE

    Ninomiya, Koshi; Iwatsuki, Koichi; Ohnishi, Yu-ichiro; Ohkawa, Toshika; Yoshimine, Toshiki

    2014-01-01

    A 70-year-old outpatient presented with a chief complaint of sudden left leg motor weakness and sensory disturbance. He had undergone L4/5 posterior interbody fusion with L3–5 posterior fusions for spondylolisthesis 3 years prior, and the screws were removed 1 year later. He has been followed up for 3 years, and there had been no adjacent segment problems before this presentation. Lumbar magnetic resonance imaging (MRI) showed a large L2/3 disc hernia descending to the L3/4 level. Compared to...

  1. Osteoid Osteoma of Cervical Spine in two adjacent Vertebrae

    Directory of Open Access Journals (Sweden)

    MR Etemadifar

    2005-09-01

    Full Text Available Osteoid osteoma is a benign bone tumor, mainly seen in 10-30 years male. Spine is a relatively common site and almost always, posterior elements are involved. Plain X-Ray-, CT scan and Isotope scan help to identify and localize spine lesions. We described one 18 years old boy with 3 years low neck pain. Isotope scan, MRI and CT scan showed two lesions in C7 and T1. Gross inspection and histopathology examination confirmed osteoid osteoma in two adjacent vertebrae which has not been reported elsewhere in the literature. Key words: Osteoid Osteoma, Spine, Multifocal

  2. Microwave treatment of renal cell carcinoma adjacent to renal sinus

    International Nuclear Information System (INIS)

    Gao, Yongyan; Liang, Ping; Yu, Xiaoling; Yu, Jie; Cheng, Zhigang; Han, Zhiyu; Duan, Shaobo; Huang, Hui

    2016-01-01

    Highlights: • This study shows US-guided microwave ablation appears to be a promising method to treat renal cell carcinoma adjacent to renal sinus. • The estimated 1-, 3- and 5-year RCC-related survival were 100%, 93.3% and 93.3%, respectively. • The estimated 1-, 3- and 5-year overall survival were 97.1%, 87.8%, 83.6%, respectively. • For patients with RCC ≤4 cm, initial ablation success was 100% (29/29) and the estimated 5-year disease-free survival were 81.5%. - Abstract: Purpose: To evaluate the efficacy and safety of ultrasound (US)-guided percutaneous microwave ablation (MWA) for renal cell carcinoma (RCC) adjacent to renal sinus. Materials and methods: This retrospective study included 41 patients who underwent US-guided percutaneous MWA of 41 RCCs adjacent to the renal sinus from April 2006 to December 2015. Contrast-enhanced images of US and computed tomography (CT) or magnetic resonance (MR) imaging were performed at pre-ablation and 1 day, 1 month, 3 months, and every 6 months after ablation. Initial ablation success (IAS), disease-free survival (DFS), RCC-related survival (RRS), and overall survival (OS) were recorded at the follow-up visits. Results: IAS was achieved in 92.7% (38/41) of the study subjects. The IAS significantly differed between patients with RCCs ≤4 cm (100%, 29/29) and RCCs >4 cm (75%, 9/12, p = 0.021). During the median follow-up of 37.6 (range, 3.0–97.3) months, the estimated 1-, 3-, and 5-year DFS of patients with an initial tumor of ≤4 cm were 100%, 89.7%, and 81.5%, respectively. The 1-, 3-, and 5-year RRS were 100%, 93.3%, and 93.3%, respectively. The 1-, 3-, and 5-year OS were 97.1%, 87.8%, and 83.6%, respectively. The multivariate analysis using the Cox proportional hazard model revealed no independent predictor of recurrence among all the variables. There were no MWA-related deaths among the study subjects. One patient developed a retroperitoneal abscess after ablation. Conclusion: US-guided percutaneous MWA

  3. Microwave treatment of renal cell carcinoma adjacent to renal sinus

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yongyan, E-mail: gaoyongyan7@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Department of Ultrasound, The General Hospital of Chinese People’s Armed Police Forces, 69 Yongding Road, Beijing, 100039 (China); Liang, Ping, E-mail: liangping301@hotmail.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Yu, Xiaoling, E-mail: 784107477@qq.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Yu, Jie, E-mail: 1411495161@qq.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Cheng, Zhigang, E-mail: 13691367317@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Han, Zhiyu, E-mail: hanzhiyu122@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Duan, Shaobo, E-mail: Dustin2662@163.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China); Huang, Hui, E-mail: 309hh@sina.com [Department of Interventional Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853 (China)

    2016-11-15

    Highlights: • This study shows US-guided microwave ablation appears to be a promising method to treat renal cell carcinoma adjacent to renal sinus. • The estimated 1-, 3- and 5-year RCC-related survival were 100%, 93.3% and 93.3%, respectively. • The estimated 1-, 3- and 5-year overall survival were 97.1%, 87.8%, 83.6%, respectively. • For patients with RCC ≤4 cm, initial ablation success was 100% (29/29) and the estimated 5-year disease-free survival were 81.5%. - Abstract: Purpose: To evaluate the efficacy and safety of ultrasound (US)-guided percutaneous microwave ablation (MWA) for renal cell carcinoma (RCC) adjacent to renal sinus. Materials and methods: This retrospective study included 41 patients who underwent US-guided percutaneous MWA of 41 RCCs adjacent to the renal sinus from April 2006 to December 2015. Contrast-enhanced images of US and computed tomography (CT) or magnetic resonance (MR) imaging were performed at pre-ablation and 1 day, 1 month, 3 months, and every 6 months after ablation. Initial ablation success (IAS), disease-free survival (DFS), RCC-related survival (RRS), and overall survival (OS) were recorded at the follow-up visits. Results: IAS was achieved in 92.7% (38/41) of the study subjects. The IAS significantly differed between patients with RCCs ≤4 cm (100%, 29/29) and RCCs >4 cm (75%, 9/12, p = 0.021). During the median follow-up of 37.6 (range, 3.0–97.3) months, the estimated 1-, 3-, and 5-year DFS of patients with an initial tumor of ≤4 cm were 100%, 89.7%, and 81.5%, respectively. The 1-, 3-, and 5-year RRS were 100%, 93.3%, and 93.3%, respectively. The 1-, 3-, and 5-year OS were 97.1%, 87.8%, and 83.6%, respectively. The multivariate analysis using the Cox proportional hazard model revealed no independent predictor of recurrence among all the variables. There were no MWA-related deaths among the study subjects. One patient developed a retroperitoneal abscess after ablation. Conclusion: US-guided percutaneous MWA

  4. 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

    International Nuclear Information System (INIS)

    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-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

  5. 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.

  6. Adjacent segment disease in degenerative pathologies with posterior instrumentation

    Directory of Open Access Journals (Sweden)

    Ana Guadalupe Ramírez Olvera

    2015-03-01

    Full Text Available OBJECTIVE: To establish the real incidence of adjacent segment disease after fusion, and to identify the levels and predisposing factors for the pathology, as well as the functional results. METHODS: a retrospective case series study with level of evidence IIB, in a sample of 179 patients diagnosed with stenosis of the lumbar spine, spondylolisthesis and degenerative scoliosis, submitted to surgery in the period 2005 to December 2013, with posterior instrumentation and posterolateral fusion, with follow-up from 2007 until May 2014, in which the symptomology and radiographic findings were evaluated, to establish the diagnosis and treatment. RESULTS: the study included 179 patients diagnosed with stenosis of the lumbar spine (n=116, isthmic and degenerative spondylolisthesis (n=50 and degenerative scoliosis (n=13; during the study, 20 cases of adjacent level segment were identified, 80% of which were treated surgically with extension of the instrumentation, while 20% were treated conservatively with NSAIDs and therapeutic blocks. CONCLUSION: An incidence of 11% was found, with an average of 3.25 years in diagnosis and treatment, a prevalence of females and diagnosis of stenosis of the lumbar canal on posterior instrumentation, a predominance of levels L4-L5; 80% were treated with extension of the instrumentation. The complications were persistent radiculopathy, infection of the surgical wound, and one death due to causes not related to the lumbar pathology.

  7. ORNAMENTAL PLANTS OF CHECHNYA AND ITS ADJACENT AREAS

    Directory of Open Access Journals (Sweden)

    Musa A. Taysumov

    2018-01-01

    Full Text Available Abstract. The aim of the research is to summarize the scattered information about the types of decorative flora of the Chechen Republic and adjacent territories; to identify highly resistant ornamental plants for cities and settlements of the North Caucasus and other territories of Russia. Discussion. Currently, in a variety of botanical gardens of the North Caucasus grows a large number of decorative plant species, widely used in green construction. However, not all species posses the quality to sufficient resist unfavorable conditions of the changed abiotic and biotic environment. Among the studied, the most valuable and promising for widespread introduction are the species of more than 122 taxa, the decorative effect of which is preserved throughout the year with no signs of aging. Many examples of the targeted use of herbs, tree species, lianas, bulbous plants were cited in the research. We give a large list of Caucasian species for growing on lawns, flowerbeds, flower gardens, alpine and stony mountains, roadsides and parks, urban parks, squares and alleys as a type of gardening. Their decorative properties, vitality, durability, life form and other bio-ecological features, attitude to abiotic factors (soil conditions, illumination, temperature, soil and atmospheric humidification conditions, etc. were taken into account. Conclusion. We give a large list of ornamental species and various planting techniques of specific species are introduced in conditions of Chechnya and its adjacent territories as well as the methods of implementing in the landscaping practice in other (middle and northern regions of Russia.

  8. Absorbed dose distribution analyses in irradiation with adjacent fields

    International Nuclear Information System (INIS)

    Cudalbu, C.; Onuc, C.; Andrada, S.

    2002-01-01

    Because the special irradiation technique with adjacent fields is the most used in the case of medulloblastoma treatment, we consider very important to specify some general information about medulloblastoma. This malignant disease has a large incidence in children with age between 5-7 years. This tumor usually originates in the cerebellum and is referred to as primitive undifferentiated tumor. It may spread contiguously to the cerebellar peduncle, floor of the fourth ventricle, into the cervical spine. In addition, it may spread via the cerebrospinal fluid intracranially and/or to the spinal cord. For this purpose it is necessary to perform a treatment technique with cranial tangential fields combined with adjacent fields for the entire spinal cord to achieve a perfect coverage of the zones with malignant cells. The treatment in this case is an association between surgery-radio-chemotherapy, where the radiotherapy has a very important roll and a curative purpose. This is due to the fact that the migration of malignant cells in the body can't be controlled by surgery. Because of this special irradiation technique used in medulloblastoma treatment, we chase to describe in this paper this complex type of irradiation where the implications of the beams divergence in doses distribution are essentials

  9. Calculations of the electrostatic potential adjacent to model phospholipid bilayers.

    Science.gov (United States)

    Peitzsch, R M; Eisenberg, M; Sharp, K A; McLaughlin, S

    1995-03-01

    We used the nonlinear Poisson-Boltzmann equation to calculate electrostatic potentials in the aqueous phase adjacent to model phospholipid bilayers containing mixtures of zwitterionic lipids (phosphatidylcholine) and acidic lipids (phosphatidylserine or phosphatidylglycerol). The aqueous phase (relative permittivity, epsilon r = 80) contains 0.1 M monovalent salt. When the bilayers contain equipotential surfaces are discrete domes centered over the negatively charged lipids and are approximately twice the value calculated using Debye-Hückel theory. When the bilayers contain > 25% acidic lipid, the -25 mV equipotential profiles are essentially flat and agree well with the values calculated using Gouy-Chapman theory. When the bilayers contain 100% acidic lipid, all of the equipotential surfaces are flat and agree with Gouy-Chapman predictions (including the -100 mV surface, which is located only 1 A from the outermost atoms). Even our model bilayers are not simple systems: the charge on each lipid is distributed over several atoms, these partial charges are non-coplanar, there is a 2 A ion-exclusion region (epsilon r = 80) adjacent to the polar headgroups, and the molecular surface is rough. We investigated the effect of these four factors using smooth (or bumpy) epsilon r = 2 slabs with embedded point charges: these factors had only minor effects on the potential in the aqueous phase.

  10. UNITED STATES DEPARTMENT OF TRANSPORTATION GLOBAL POSITIONING SYSTEM (GPS) ADJACENT BAND COMPATIBILITY ASSESSMENT

    Science.gov (United States)

    2018-04-01

    The goal of the U.S. Department of Transportation (DOT) Global Positioning System (GPS) Adjacent Band Compatibility Assessment is to evaluate the maximum transmitted power levels of adjacent band radiofrequency (RF) systems that can be tolerated by G...

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

    Directory of Open Access Journals (Sweden)

    Shunri Jiang

    2017-01-01

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

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

    Science.gov (United States)

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

    2015-10-25

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

  13. Tritium in the Savannah River Estuary and adjacent marine waters

    International Nuclear Information System (INIS)

    Hayes, D.W.

    1978-01-01

    The tritium distribution in the Savannah River estuary and adjacent marine waters was measured to provide information on the dilution, mixing, and movement of Savannah River water in this region. The Savannah River marine region was chosen because the average tritium concentration in this river is 5 pCi/ml, whereas other rivers in the southeastern United States average less than 0.5 pCi/ml. The increased tritium concentration in the Savannah River is due to releases from the Savannah River Plant of the Department of Energy. Tritium measurements have proved particularly effective in estimating the flushing time of the Savannah River estuary (2.4 days) and in delineating the relative contribution to the water masses in Ossabaw and Port Royal Sounds from the River and from sea water. Ossabaw and Port Royal Sounds are located approximately 20 km south and north of the Savannah River estuary, respectively

  14. Tritium in the Savannah River estuary and adjacent marine waters

    International Nuclear Information System (INIS)

    Hayes, D.W.

    1979-01-01

    The tritium distribution in the Savannah River estuary and adjacent marine waters was measured to provide information on the dilution, mixing and movement of Savannah River water in this region. The Savannah River marine region was chosen because the average tritium concentration in this river is approximately 5 pCi/ml, whereas other rivers in the southeastern United States of America average less than 0.5 pCi/ml. The increased tritium concentration in the Savannah River is due to releases from the Savannah River Plant of the Department of Energy. Tritium measurements have proved particularly effective in estimating the flushing time of the Savannah River estuary (2.4 days) and in delineating the relative contribution to the water masses in Ossabaw and Port Royal Sounds from the river and from sea-water. Ossabaw and Port Royal Sounds are located approximately 20 km south and north of the Savannah River estuary respectively. (author)

  15. Adjacent Lumbar Disc Herniation after Lumbar Short Spinal Fusion

    Directory of Open Access Journals (Sweden)

    Koshi Ninomiya

    2014-01-01

    Full Text Available A 70-year-old outpatient presented with a chief complaint of sudden left leg motor weakness and sensory disturbance. He had undergone L4/5 posterior interbody fusion with L3–5 posterior fusions for spondylolisthesis 3 years prior, and the screws were removed 1 year later. He has been followed up for 3 years, and there had been no adjacent segment problems before this presentation. Lumbar magnetic resonance imaging (MRI showed a large L2/3 disc hernia descending to the L3/4 level. Compared to the initial MRI, this hernia occurred in an “intact” disc among multilevel severely degenerated discs. Right leg paresis and bladder dysfunction appeared a few days after admission. Microscopic lumbar disc herniotomy was performed. The right leg motor weakness improved just after the operation, but the moderate left leg motor weakness and difficulty in urination persisted.

  16. Edge scour in current adjacent to stone covers

    DEFF Research Database (Denmark)

    Petersen, Thor Ugelvig; Sumer, B. Mutlu; Meyer, Knud Erik

    The present paper reports some early results of an experimental investigation of edge scour in currents. Two kinds of measurements are made (1) Particle Image Velocimetry (PIV) measurements of secondary currents that take place near a junction between the stone cover and the sand bed in a clear......-water experiment; and (2) scour measurements in actual scour experiment in the live-bed regime. The early results indicate that edge scour in a steady current propagating in-line with a stone layer is caused by the combined action of two effects; (1) Primary flow and (2) Secondary flow. The primary flow stirs up...... the sediment and puts into suspension, and the secondary flow carries it away from the junction between the stone layer and the sand bed, resulting in a scour hole forming adjacent to the toe of the stone layer....

  17. GOAT ROCKS WILDERNESS AND ADJACENT ROADLESS AREAS, WASHINGTON.

    Science.gov (United States)

    Church, S.E.; Close, T.J.

    1984-01-01

    The Goat Rocks Wilderness and adjacent roadless areas are a rugged, highly forested, scenic area located on the crest of the Cascade Range in south-central Washington. Several mineral claims have been staked in the area. Mineral surveys were conducted. Geochemical, geophysical, and geologic investigations indicate that three areas have probable mineral-resource potential for base metals in porphyry-type deposits. Available data are not adequate to permit definition of the potential for oil and gas. There is little likelihood for the occurrence of other kinds of energy resources in the area. Evaluation of resource potential in the three areas identified as having probable mineral-resource potential could be improved by more detailed geochemical studies and geologic mapping.

  18. Adjacent segment infection after surgical treatment of spondylodiscitis.

    Science.gov (United States)

    Siam, Ahmed Ezzat; El Saghir, Hesham; Boehm, Heinrich

    2016-03-01

    This is the first case series to describe adjacent segment infection (ASI) after surgical treatment of spondylodiscitis (SD). Patients with SD, spondylitis who were surgically treated between 1994 and 2012 were included. Out of 1187 cases, 23 (1.94 %) returned to our institution (Zentralklinik Bad Berka) with ASI: 10 males, 13 females, with a mean age of 65.1 years and a mean follow-up of 69 months. ASI most commonly involved L3-4 (seven patients), T12-L1 (five) and L2-3 (four). The mean interval between operations of primary infection and ASI was 36.9 months. All cases needed surgical intervention, debridement, reconstruction and fusion with longer instrumentation, with culture and sensitivity-based postoperative antimicrobial therapy. At last follow-up, six patients (26.1 %) were mobilized in a wheelchair with a varying degree of paraplegia (three had pre-existing paralysis). Three patients died within 2 months after the ASI operation (13 %). Excellent outcomes were achieved in five patients, and good in eight. Adjacent segment infection after surgical treatment of spondylodiscitis is a rare complication (1.94 %). It is associated with multimorbidity and shows a high mortality rate and a high neurological affection rate. Possible explanations are: haematomas of repeated micro-fractures around screw loosening, haematogenous spread, direct inoculation or a combination of these factors. ASI may also lead to proximal junctional kyphosis, as found in this series. We suggest early surgical intervention with anterior debridement, reconstruction and fusion with posterior instrumentation, followed by antimicrobial therapy for 12 weeks. Level IV retrospective uncontrolled case series.

  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. On Mathematical Optimization for the Visualization of Frequencies and Adjacencies as Rectangular Maps

    DEFF Research Database (Denmark)

    Carrizosa, Emilio; Guerrero, Vanesa; Morales, Dolores Romero

    2018-01-01

    individuals as adjacent rectangular portions as possible and adding as few false adjacencies, i.e., adjacencies between rectangular portions corresponding to non-adjacent individuals, as possible. We formulate this visualization problem as a Mixed Integer Linear Programming (MILP) model. We propose......In this paper we address the problem of visualizing a frequency distribution and an adjacency relation attached to a set of individuals. We represent this information using a rectangular map, i.e., a subdivision of a rectangle into rectangular portions so that each portion is associated with one...

  1. Methodology for the systematic reviews on an adjacent segment pathology.

    Science.gov (United States)

    Norvell, Daniel C; Dettori, Joseph R; Skelly, Andrea C; Riew, K Daniel; Chapman, Jens R; Anderson, Paul A

    2012-10-15

    A systematic review. To provide a detailed description of the methods undertaken in the systematic search and analytical summary of adjacent segment pathology (ASP) issues and to describe the process used to develop consensus statements and clinical recommendations regarding factors associated with the prevention and treatment of ASP. We present methods used in conducting the systematic, evidence-based reviews and development of expert panel consensus statements and clinical recommendations on the classification, natural history, risk factors, and treatment of radiographical and clinical ASP. Our intent is that clinicians will combine the information from these reviews with an understanding of their own capacities and experience to better manage patients at risk of ASP and consider future research for the prevention and treatment of ASP. A systematic search and critical review of the English-language literature was undertaken for articles published on the classification, risk, risk factors, and treatment of radiographical and clinical ASP. Articles were screened for relevance using a priori criteria, and relevant articles were critically reviewed. Whether an article was included for review depended on whether the study question was descriptive, one of therapy, or one of prognosis. The strength of evidence for the overall body of literature in each topic area was determined by 2 independent reviewers considering risk of bias, consistency, directness, and precision of results using a modification of the Grades of Recommendation Assessment, Development and Evaluation (GRADE) criteria. Disagreements were resolved by consensus. Findings from articles meeting inclusion criteria were summarized. From these summaries, consensus statements or clinical recommendations were formulated among subject experts through a modified Delphi process using the GRADE approach. A total of 3382 articles were identified and screened on 14 topics relating to the classification, risks, risk

  2. Characterization of adjacent breast tumors using oligonucleotide microarrays

    International Nuclear Information System (INIS)

    Unger, Meredith A; Rishi, Mazhar; Clemmer, Virginia B; Hartman, Jennifer L; Keiper, Elizabeth A; Greshock, Joel D; Chodosh, Lewis A; Liebman, Michael N; Weber, Barbara L

    2001-01-01

    Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles. Total RNA was extracted from two tumors with no apparent physical connection that were located in the right breast of an 87-year-old woman diagnosed with invasive ductal carcinoma (IDC). The RNA was hybridized to the Affymetrix Human Genome U95A Gene Chip ® (12,500 known human genes) and analyzed using the Gene Chip Analysis Suite ® 3.3 (Affymetrix, Inc, Santa Clara, CA, USA) and JMPIN ® 3.2.6 (SAS Institute, Inc, Cary, NC, USA). Gene expression profiles of tumors from five additional patients were compared in order to evaluate the heterogeneity in gene expression between tumors with similar clinical characteristics. The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis. Analysis of gene expression profiles from different individuals, however, generated a pairwise correlation coefficient of 0.710. Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making

  3. A deterministic seismic hazard map of India and adjacent areas

    International Nuclear Information System (INIS)

    Parvez, Imtiyaz A.; Vaccari, Franco; Panza, Giuliano

    2001-09-01

    A seismic hazard map of the territory of India and adjacent areas has been prepared using a deterministic approach based on the computation of synthetic seismograms complete of all main phases. The input data set consists of structural models, seismogenic zones, focal mechanisms and earthquake catalogue. The synthetic seismograms have been generated by the modal summation technique. The seismic hazard, expressed in terms of maximum displacement (DMAX), maximum velocity (VMAX), and design ground acceleration (DGA), has been extracted from the synthetic signals and mapped on a regular grid of 0.2 deg. x 0.2 deg. over the studied territory. The estimated values of the peak ground acceleration are compared with the observed data available for the Himalayan region and found in good agreement. Many parts of the Himalayan region have the DGA values exceeding 0.6 g. The epicentral areas of the great Assam earthquakes of 1897 and 1950 represent the maximum hazard with DGA values reaching 1.2-1.3 g. (author)

  4. Earthquake response of adjacent structures with viscoelastic and friction dampers

    Directory of Open Access Journals (Sweden)

    Žigić Miodrag

    2015-01-01

    Full Text Available We study the seismic response of two adjacent structures connected with a dry friction damper. Each of them consists of a viscoelastic rod and a rigid block, which can slide without friction along the moving base. A simplified earthquake model is used for modeling the horizontal ground motion. Energy dissipation is taken by the presence of the friction damper, which is modeled by the set-valued Coulomb friction law. Deformation of viscoelastic rods during the relative motion of the blocks represents another way of energy dissipation. The constitutive equation of a viscoelastic body is described by the fractional Zener model, which includes fractional derivatives of stress and strain. The problem merges fractional derivatives as non-local operators and theory of set-valued functions as the non-smooth ones. Dynamical behaviour of the problem is governed by a pair of coupled multi-valued differential equations. The posed Cauchy problem is solved by use of the Grünwald-Letnikov numerical scheme. The behaviour of the system is analyzed for different values of system parameters.

  5. Repeated adjacent-segment degeneration after posterior lumbar interbody fusion.

    Science.gov (United States)

    Okuda, Shinya; Oda, Takenori; Yamasaki, Ryoji; Maeno, Takafumi; Iwasaki, Motoki

    2014-05-01

    One of the most important sequelae affecting long-term results is adjacent-segment degeneration (ASD) after posterior lumbar interbody fusion (PLIF). Although several reports have described the incidence rate, there have been no reports of repeated ASD. The purpose of this report was to describe 1 case of repeated ASD after PLIF. A 62-year-old woman with L-4 degenerative spondylolisthesis underwent PLIF at L4-5. At the second operation, L3-4 PLIF was performed for L-3 degenerative spondylolisthesis 6 years after the primary operation. At the third operation, L2-3 PLIF was performed for L-2 degenerative spondylolisthesis 1.5 years after the primary operation. Vertebral collapse of L-1 was detected 1 year after the third operation, and the collapse had progressed. At the fourth operation, 3 years after the third operation, vertebral column resection of L-1 and replacement of titanium mesh cages with pedicle screw fixation between T-4 and L-5 was performed. Although the patient's symptoms resolved after each operation, the time between surgeries shortened. The sacral slope decreased gradually although each PLIF achieved local lordosis at the fused segment.

  6. DNA sequence responsible for the amplification of adjacent genes.

    Science.gov (United States)

    Pasion, S G; Hartigan, J A; Kumar, V; Biswas, D K

    1987-10-01

    A 10.3-kb DNA fragment in the 5'-flanking region of the rat prolactin (rPRL) gene was isolated from F1BGH(1)2C1, a strain of rat pituitary tumor cells (GH cells) that produces prolactin in response to 5-bromodeoxyuridine (BrdU). Following transfection and integration into genomic DNA of recipient mouse L cells, this DNA induced amplification of the adjacent thymidine kinase gene from Herpes simplex virus type 1 (HSV1TK). We confirmed the ability of this "Amplicon" sequence to induce amplification of other linked or unlinked genes in DNA-mediated gene transfer studies. When transferred into the mouse L cells with the 10.3-5'rPRL gene sequence of BrdU-responsive cells, both the human growth hormone and the HSV1TK genes are amplified in response to 5-bromodeoxyuridine. This observation is substantiated by BrdU-induced amplification of the cotransferred bacterial Neo gene. Cotransfection studies reveal that the BrdU-induced amplification capability is associated with a 4-kb DNA sequence in the 5'-flanking region of the rPRL gene of BrdU-responsive cells. These results demonstrate that genes of heterologous origin, linked or unlinked, and selected or unselected, can be coamplified when located within the amplification boundary of the Amplicon sequence.

  7. Modern sedimentary processes along the Doce river adjacent continental shelf

    Directory of Open Access Journals (Sweden)

    Valéria da Silva Quaresma

    Full Text Available In areas of the continental shelf where sediment supply is greater than the sediment dispersion capacity, an extensive terrigenous deposits and consequently submerged deltas can be formed. The Eastern Brazilian shelf is characterized by the occurrence of river feed deltas in between starving coasts. Herein, modern sedimentary processes acting along the Doce river adjacent continental shelf are investigated. The main objective was to understand the shelf sediment distribution, recognizing distinct sedimentary patterns and the major influence of river sediment discharge in the formation of shelf deposits. The study used 98 surficial samples that were analyzed for grain size, composition and bulk density. Results revealed 3 distinct sectors: south - dominated by mud fraction with a recent deposition from riverine input until 30 m deep and from this depth bioclastic sands dominate; central north - sand mud dominated, been recognized as a bypass zone of resuspended sediment during high energy events; and north - relict sands with high carbonate content. The modern sedimentation processes along the Doce river continental shelf is dominated by distinct sedimentary regimes, showing a strong fluvial influence associated with wave/wind induced sediment dispersion and a carbonate regime along the outer shelf. These regimes seem to be controlled by the distance from the river mouth and bathymetric gradients.

  8. Oligocene paleogeography of the northern Great Plains and adjacent mountains

    International Nuclear Information System (INIS)

    Seeland, D.

    1985-01-01

    Early Oligocene paleogeography of the northern Great Plains and adjacent mountains is inferred in part from published surface and subsurface studies of the pre-Oligocene surface. These studies are combined with published and unpublished information on clast provenance, crossbedding orientation, and Eocene paleogeography. The Oligocene Arctic Ocean-Gulf of Mexico continental divide extended from the southern Absaroka Mountains east along the Owl Creek Mountains, across the southern Powder River Basin, through the northern Black Hills, and eastward across South Dakota. Streams north of the divide flowed northeastward. The Olligocene White River Group contains 50 to 90 percent airfall pyroclastic debris from a northern Great Basin source. Most of the uranium deposits of the region in pre-Oligocene rocks can be related to a uranium source in the volcanic ash of the White River; in many places the pre-Oligocene deposits can be related to specific Oligocene channels. Uranium deposits in sandstones of major Oligocene rivers are an important new type of deposit. The Oligocene channel sandstones also contain small quantities of gold, molybdenum, gas, and oil

  9. Mechanical interactions between adjacent airways in the lung.

    Science.gov (United States)

    Ma, Baoshun; Bates, Jason H T

    2014-03-15

    The forces of mechanical interdependence between the airways and the parenchyma in the lung are powerful modulators of airways responsiveness. Little is known, however, about the extent to which adjacent airways affect each other's ability to narrow due to distortional forces generated within the intervening parenchyma. We developed a two-dimensional computational model of two airways embedded in parenchyma. The parenchyma itself was modeled in three ways: 1) as a network of hexagonally arranged springs, 2) as a network of triangularly arranged springs, and 3) as an elastic continuum. In all cases, we determined how the narrowing of one airway was affected when the other airway was relaxed vs. when it narrowed to the same extent as the first airway. For the continuum and triangular network models, interactions between airways were negligible unless the airways lay within about two relaxed diameters of each other, but even at this distance the interactions were small. By contrast, the hexagonal spring network model predicted that airway-airway interactions mediated by the parenchyma can be substantial for any degree of airway separation at intermediate values of airway contraction forces. Evidence to date suggests that the parenchyma may be better represented by the continuum model, which suggests that the parenchyma does not mediate significant interactions between narrowing airways.

  10. Cryogun cryotherapy for oral leukoplakia and adjacent melanosis lesions.

    Science.gov (United States)

    Chen, Hsin-Ming; Cheng, Shih-Jung; Lin, Hung-Pin; Yu, Chuan-Hang; Wu, Yang-Che; Chiang, Chun-Pin

    2015-09-01

    Our previous study has shown that cryogun cryotherapy is a good and effective treatment modality for oral leukoplakia. In this study, we used cryogun cryotherapy to treat 72 oral leukoplakia and adjacent smoking-induced melanosis (OLM) lesions on the buccal mucosae. Of 72 OLM lesions, 14 had epithelial hyperplasia with parakeratosis, 24 had epithelial hyperplasia with hyperkeratosis, 26 had mild dysplasia, seven had moderate dysplasia, and one had severe dysplasia. Complete regression was achieved in all 72 OLM lesions after a mean of 3.3 ± 1.3 cryogun cryotherapy treatments. We found that OLM lesions in patients without smoking habit, with the greatest diameter cryotherapy treatment to achieve complete regression than those OLM lesions in patients with smoking habit, with the greatest diameter ≥ 2.8 cm, without epithelial dysplasia, or with a surface keratin thickness > 50 μm (all P-values cryotherapy treatment number (all P-values cryotherapy treatment required to achieve complete regression of the OLM lesion by multivariate logistic regression analyses. Cryogun cryotherapy is an effective treatment modality for OLM lesions. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Flow and edge scour in current adjacent to stone covers

    DEFF Research Database (Denmark)

    Petersen, Thor U.; Sumer, B. Mutlu; Bøgelund, Jon

    2015-01-01

    This paper presents the results of an experimental investigation on edge scour adjacent to a stone cover laid on a sandy bed. The three-dimensional flow over the edge of the stone layer has been investigated by the use of particle image velocimetry. The flow measurements show a significant amount...... of turbulence in the primary flow near the junction between the stone layer and the sand bed and the formation of complex secondary-flow structures. The results show that the flow and the edge scour process in a steady current are governed by the size of the roughness elements and to some extent the side slope...... of the berm. The edge scour is caused by the combined action of the primary flow and the secondary flow. The primary flow stirs up the sediment and puts it into suspension, and the secondary flow carries it away from the junction between the stone layer and the sand bed, resulting in a scour hole forming...

  12. Review of vibration effect during piling installation to adjacent structure

    Science.gov (United States)

    Rahman, Nurul Aishah Abd; Musir, Adhilla Ainun; Dahalan, Nurol Huda; Ghani, Abdul Naser Abdul; Khalil, Muhamad Kasimi Abd

    2017-12-01

    Basically, many major structures across the world such as towers, high rise building, houses and bridges utilize pile as a support material. The use of pile is important to strengthen the structures. However, this has led to another problem to the nearest surrounding structures resulted from pile driving. As part of a construction work, unavoidable pile driving activity generates a vibration towards the surrounding structures if uncontrolled may cause damage to the adjacent structure. As the current construction works are frequently located in urban areas where the distance between the nearest building structures is not far, vibration may cause damage to nearby structures. Knowing which part of the building that is mostly affected by various vibration patterns from the impact of pile driving is crucial. Thus, it is very important to predict the impact of vibration during piling installation work. This paper reviews the vibrations generated by piling activity toward surrounding structures in terms sources of vibration, impact of piling installation, pile-soil interaction, and factors affecting the vibration impact of building as well as to study the parameters involved in vibration generation during piling works.

  13. Concentric network symmetry grasps authors' styles in word adjacency networks

    Science.gov (United States)

    Amancio, Diego R.; Silva, Filipi N.; Costa, Luciano da F.

    2015-06-01

    Several characteristics of written texts have been inferred from statistical analysis derived from networked models. Even though many network measurements have been adapted to study textual properties at several levels of complexity, some textual aspects have been disregarded. In this paper, we study the symmetry of word adjacency networks, a well-known representation of text as a graph. A statistical analysis of the symmetry distribution performed in several novels showed that most of the words do not display symmetric patterns of connectivity. More specifically, the merged symmetry displayed a distribution similar to the ubiquitous power-law distribution. Our experiments also revealed that the studied metrics do not correlate with other traditional network measurements, such as the degree or the betweenness centrality. The discriminability power of the symmetry measurements was verified in the authorship attribution task. Interestingly, we found that specific authors prefer particular types of symmetric motifs. As a consequence, the authorship of books could be accurately identified in 82.5% of the cases, in a dataset comprising books written by 8 authors. Because the proposed measurements for text analysis are complementary to the traditional approach, they can be used to improve the characterization of text networks, which might be useful for applications based on stylistic classification.

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

    Science.gov (United States)

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Francesca Lugani

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

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

    Science.gov (United States)

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

    2018-02-01

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

  17. A systematic review of definitions and classification systems of adjacent segment pathology.

    Science.gov (United States)

    Kraemer, Paul; Fehlings, Michael G; Hashimoto, Robin; Lee, Michael J; Anderson, Paul A; Chapman, Jens R; Raich, Annie; Norvell, Daniel C

    2012-10-15

    Systematic review. To undertake a systematic review to determine how "adjacent segment degeneration," "adjacent segment disease," or clinical pathological processes that serve as surrogates for adjacent segment pathology are classified and defined in the peer-reviewed literature. Adjacent segment degeneration and adjacent segment disease are terms referring to degenerative changes known to occur after reconstructive spine surgery, most commonly at an immediately adjacent functional spinal unit. These can include disc degeneration, instability, spinal stenosis, facet degeneration, and deformity. The true incidence and clinical impact of degenerative changes at the adjacent segment is unclear because there is lack of a universally accepted classification system that rigorously addresses clinical and radiological issues. A systematic review of the English language literature was undertaken and articles were classified using the Grades of Recommendation Assessment, Development, and Evaluation criteria. RESULTS.: Seven classification systems of spinal degeneration, including degeneration at the adjacent segment, were identified. None have been evaluated for reliability or validity specific to patients with degeneration at the adjacent segment. The ways in which terms related to adjacent segment "degeneration" or "disease" are defined in the peer-reviewed literature are highly variable. On the basis of the systematic review presented in this article, no formal classification system for either cervical or thoracolumbar adjacent segment disorders currently exists. No recommendations regarding the use of current classification of degeneration at any segments can be made based on the available literature. A new comprehensive definition for adjacent segment pathology (ASP, the now preferred terminology) has been proposed in this Focus Issue, which reflects the diverse pathology observed at functional spinal units adjacent to previous spinal reconstruction and balances

  18. Adjacent-segment disease after thoracic pedicle screw fixation.

    Science.gov (United States)

    Agarwal, Nitin; Heary, Robert F; Agarwal, Prateek

    2018-03-01

    OBJECTIVE Pedicle screw fixation is a technique widely used to treat conditions ranging from spine deformity to fracture stabilization. Pedicle screws have been used traditionally in the lumbar spine; however, they are now being used with increasing frequency in the thoracic spine as a more favorable alternative to hooks, wires, or cables. Although safety concerns, such as the incidence of adjacent-segment disease (ASD) after cervical and lumbar fusions, have been reported, such issues in the thoracic spine have yet to be addressed thoroughly. Here, the authors review the literature on ASD after thoracic pedicle screw fixation and report their own experience specifically involving the use of pedicle screws in the thoracic spine. METHODS Select references from online databases, such as PubMed (provided by the US National Library of Medicine at the National Institutes of Health), were used to survey the literature concerning ASD after thoracic pedicle screw fixation. To include the authors' experience at Rutgers New Jersey Medical School, a retrospective review of a prospectively maintained database was performed to determine the incidence of complications over a 13-year period in 123 consecutive adult patients who underwent thoracic pedicle screw fixation. Children, pregnant or lactating women, and prisoners were excluded from the review. By comparing preoperative and postoperative radiographic images, the occurrence of thoracic ASD and disease within the surgical construct was determined. RESULTS Definitive radiographic fusion was detected in 115 (93.5%) patients. Seven incidences of instrumentation failure and 8 lucencies surrounding the screws were observed. One patient was observed to have ASD of the thoracic spine. The mean follow-up duration was 50 months. CONCLUSIONS This long-term radiographic evaluation revealed the use of pedicle screws for thoracic fixation to be an effective stabilization modality. In particular, ASD seems to be less of a problem in the

  19. Tidally influenced alongshore circulation at an inlet-adjacent shoreline

    Science.gov (United States)

    Hansen, Jeff E.; Elias, Edwin P.L.; List, Jeffrey H.; Erikson, Li H.; Barnard, Patrick L.

    2013-01-01

    The contribution of tidal forcing to alongshore circulation inside the surfzone is investigated at a 7 km long sandy beach adjacent to a large tidal inlet. Ocean Beach in San Francisco, CA (USA) is onshore of a ∼150 km2 ebb-tidal delta and directly south of the Golden Gate, the sole entrance to San Francisco Bay. Using a coupled flow-wave numerical model, we find that the tides modulate, and in some cases can reverse the direction of, surfzone alongshore flows through two separate mechanisms. First, tidal flow through the inlet results in a barotropic tidal pressure gradient that, when integrated across the surfzone, represents an important contribution to the surfzone alongshore force balance. Even during energetic wave conditions, the tidal pressure gradient can account for more than 30% of the total alongshore pressure gradient (wave and tidal components) and up to 55% during small waves. The wave driven component of the alongshore pressure gradient results from alongshore wave height and corresponding setup gradients induced by refraction over the ebb-tidal delta. Second, wave refraction patterns over the inner shelf are tidally modulated as a result of both tidal water depth changes and strong tidal flows (∼1 m/s), with the effect from currents being larger. These tidally induced changes in wave refraction result in corresponding variability of the alongshore radiation stress and pressure gradients within the surfzone. Our results indicate that tidal contributions to the surfzone force balance can be significant and important in determining the direction and magnitude of alongshore flow.

  20. FSH: fast spaced seed hashing exploiting adjacent hashes.

    Science.gov (United States)

    Girotto, Samuele; Comin, Matteo; Pizzi, Cinzia

    2018-01-01

    Patterns with wildcards in specified positions, namely spaced seeds , are increasingly used instead of k -mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as they can provide better sensitivity. Many of these applications require to compute the hashing of each position in the input sequences with respect to the given spaced seed, or to multiple spaced seeds. While the hashing of k -mers can be rapidly computed by exploiting the large overlap between consecutive k -mers, spaced seeds hashing is usually computed from scratch for each position in the input sequence, thus resulting in slower processing. The method proposed in this paper, fast spaced-seed hashing (FSH), exploits the similarity of the hash values of spaced seeds computed at adjacent positions in the input sequence. In our experiments we compute the hash for each positions of metagenomics reads from several datasets, with respect to different spaced seeds. We also propose a generalized version of the algorithm for the simultaneous computation of multiple spaced seeds hashing. In the experiments, our algorithm can compute the hashing values of spaced seeds with a speedup, with respect to the traditional approach, between 1.6[Formula: see text] to 5.3[Formula: see text], depending on the structure of the spaced seed. Spaced seed hashing is a routine task for several bioinformatics application. FSH allows to perform this task efficiently and raise the question of whether other hashing can be exploited to further improve the speed up. This has the potential of major impact in the field, making spaced seed applications not only accurate, but also faster and more efficient. The software FSH is freely available for academic use at: https://bitbucket.org/samu661/fsh/overview.

  1. 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

  2. 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.

  3. Folding and fracturing of rock adjacent to salt diapirs

    Science.gov (United States)

    Rowan, Mark G.

    2017-04-01

    When John Ramsay wrote his groundbreaking book in 1967, deformation around salt diapirs was not something he covered. At the time, most geologists considered diapirs to form due to density inversion, rising through thick overlying strata due to buoyancy. In doing so, salt was thought to shove aside the younger rocks, shearing and fracturing them in drag folds and supposedly producing "salt gouge". Even after it was realized that the majority of diapirs spend most of their history growing at or just beneath the surface, the relative rise of salt and sinking of minibasins were (and are) still thought by many to be accommodated in part by shear and fracturing of rocks in a collar zone around the salt. There are two arguments against this model. The first is mechanical: whereas halite behaves as a viscous fluid, even young sediment deforms as a brittle material with layer anisotropy. Thus, the salt-sediment interface is the outer margin of an intrasalt shear zone caused by viscous drag against the diapir margin. The velocity of salt flow decreases dramatically toward the edge of the diapir, so that the outermost salt effectively doesn't move. Hence, no shear or fracturing is expected in surrounding strata. The second and more important argument is that empirical field data do not support the idea of drag folds and associated deformation. Certainly, strata are typically folded and thinned adjacent to diapirs. However, stratal upturn is generated by monoclinal drape folding of the diapir roof over the edge of the rising salt, and thinning is caused by deposition onto the bathymetric highs formed by the diapirs, often supplemented by roof erosion and slumping. Halokinetic sequences observed in numerous salt basins (e.g., Paradox Basin, La Popa Basin, Spanish Pyrenees, Sivas Basin, Zagros Mountains, Kuqa Basin) contain no diapir-parallel shear zones and minimal thinning and fracturing caused by diapir rise. Even megaflaps, in which strata extend for kilometers up the sides

  4. Impact of body mass index on adjacent segment disease after lumbar fusion for degenerative spine disease.

    Science.gov (United States)

    Ou, Chien-Yu; Lee, Tao-Chen; Lee, Tsung-Han; Huang, Yu-Hua

    2015-04-01

    Adjacent segment disease is an important complication after fusion of degenerative lumbar spines. However, the role of body mass index (BMI) in adjacent segment disease has been addressed less. To examine the relationship between BMI and adjacent segment disease after lumbar fusion for degenerative spine diseases. For this retrospective study, we enrolled 190 patients undergoing lumbar fusion surgery for degeneration. BMI at admission was documented. Adjacent segment disease was defined by integration of the clinical presentations and radiographic criteria based on the morphology of the dural sac on magnetic resonance images. Adjacent segment disease was identified in 13 of the 190 patients, accounting for 6.8%. The interval between surgery and diagnosis as adjacent segment disease ranged from 21 to 66 months. Five of the 13 patients required subsequent surgical intervention for clinically relevant adjacent segment disease. In the logistic regression model, BMI was a risk factor for adjacent segment disease after lumbar fusion for degenerative spine diseases (odds ratio, 1.68; 95% confidence interval, 1.27-2.21; P disease rate by 67.6%. The patients were subdivided into 2 groups based on BMI, and up to 11.9% of patients with BMI ≥ 25 kg/m were diagnosed as having adjacent segment disease at the last follow-up. BMI is a risk factor for adjacent segment disease in patients undergoing lumbar fusion for degenerative spine diseases. Because BMI is clinically objective and modifiable, controlling body weight before or after surgery may provide opportunities to reduce the rate of adjacent segment disease and to improve the outcome of fusion surgery.

  5. Magnetotelluric Investigation in the Jiyang Depression and its Adjacent Areas

    Science.gov (United States)

    Zhang, L.; Hao, T.; Duan, Q.

    2008-12-01

    The Jiyang Depression is a secondary tectonic unit of the Bohai Bay Basin, and is a Mesozoic-Cenozoic continental-facie depositional depression. The Jiyang Depression consists of the Dongying, Zanhua, Chezhen, and Huimin sags, and the Yihezhuang, Chenjiazhuang, Qingcheng, Binxian, Guangrao, Shouguang, and heaves. In order to delineate shallow and deep structures of the depression, we conduct a magnetotelluric (MT) investigation in the Jiyang Depression and its adjacent areas. We use a remote reference setup to reduce noise disturbance, when several magnetotelluric sounding stations are measuring synchronously at different sites. The acquired MT data are to be processed and interpreted. We execute time series processing with the remote reference technique. The surveyed area is seriously interfered by noise. To improve quality of the data, we perform noise identification and manual selection of the time series segments. Identification of polarization modes is an important task for MT data qualitative interpretation. We apply for a PCA (principal component analysis) based method to automatically identify apparent polarized resistivity curves of TE and TM modes. The method recognizes the distortion and major variation of TE and TM curves and distinguishes the two kinds of curves with principal component analysis. From the apparent resistivity-frequency profile result, we can see that the Chenning Uplift and the Chenjiazhuang Heave reveal a 3-layered structure of medium-low-high, from the shallow to the deep. The structure is especially distinct for the Chenning Uplift, where there is a laterally steady-spreading high- resistivity zone corresponding to the frequency band lower than 1 Hz. The Dongying Sag is characteristic of high-low-medium from the shallow to the deep, and has a low-resistivity anomaly zone with obvious and wide lateral extending in the medium frequency band, which reflects that the deposition thickness of the basin is relatively big. The Guangrao

  6. Treatment Outcome and Patient Satisfaction with Two Adjacent Implant-Supported Restorations in the Esthetic Zone

    NARCIS (Netherlands)

    Tymstra, Nynke; Meijer, Henny J. A.; Stellingsma, Kees; Raghoebar, Gerry M.; Vissink, Arjan

    2010-01-01

    The purpose of this study was to evaluate the clinical and radiographic parameters as well as the esthetic outcome of two adjacent implant-supported restorations and the surrounding peri-implant mucosa in the maxillary esthetic zone. Ten patients were treated with two adjacent implants in the

  7. Variable length adjacent partitioning for PTS based PAPR reduction of OFDM signal

    International Nuclear Information System (INIS)

    Ibraheem, Zeyid T.; Rahman, Md. Mijanur; Yaakob, S. N.; Razalli, Mohammad Shahrazel; Kadhim, Rasim A.

    2015-01-01

    Peak-to-Average power ratio (PAPR) is a major drawback in OFDM communication. It leads the power amplifier into nonlinear region operation resulting into loss of data integrity. As such, there is a strong motivation to find techniques to reduce PAPR. Partial Transmit Sequence (PTS) is an attractive scheme for this purpose. Judicious partitioning the OFDM data frame into disjoint subsets is a pivotal component of any PTS scheme. Out of the existing partitioning techniques, adjacent partitioning is characterized by an attractive trade-off between cost and performance. With an aim of determining effects of length variability of adjacent partitions, we performed an investigation into the performances of a variable length adjacent partitioning (VL-AP) and fixed length adjacent partitioning in comparison with other partitioning schemes such as pseudorandom partitioning. Simulation results with different modulation and partitioning scenarios showed that fixed length adjacent partition had better performance compared to variable length adjacent partitioning. As expected, simulation results showed a slightly better performance of pseudorandom partitioning technique compared to fixed and variable adjacent partitioning schemes. However, as the pseudorandom technique incurs high computational complexities, adjacent partitioning schemes were still seen as favorable candidates for PAPR reduction

  8. Variable length adjacent partitioning for PTS based PAPR reduction of OFDM signal

    Energy Technology Data Exchange (ETDEWEB)

    Ibraheem, Zeyid T.; Rahman, Md. Mijanur; Yaakob, S. N.; Razalli, Mohammad Shahrazel; Kadhim, Rasim A. [School of Computer and Communication Engineering, Universiti Malaysia Perlis, 02600 Arau, Perlis (Malaysia)

    2015-05-15

    Peak-to-Average power ratio (PAPR) is a major drawback in OFDM communication. It leads the power amplifier into nonlinear region operation resulting into loss of data integrity. As such, there is a strong motivation to find techniques to reduce PAPR. Partial Transmit Sequence (PTS) is an attractive scheme for this purpose. Judicious partitioning the OFDM data frame into disjoint subsets is a pivotal component of any PTS scheme. Out of the existing partitioning techniques, adjacent partitioning is characterized by an attractive trade-off between cost and performance. With an aim of determining effects of length variability of adjacent partitions, we performed an investigation into the performances of a variable length adjacent partitioning (VL-AP) and fixed length adjacent partitioning in comparison with other partitioning schemes such as pseudorandom partitioning. Simulation results with different modulation and partitioning scenarios showed that fixed length adjacent partition had better performance compared to variable length adjacent partitioning. As expected, simulation results showed a slightly better performance of pseudorandom partitioning technique compared to fixed and variable adjacent partitioning schemes. However, as the pseudorandom technique incurs high computational complexities, adjacent partitioning schemes were still seen as favorable candidates for PAPR reduction.

  9. 33 CFR 110.168 - Hampton Roads, Virginia and adjacent waters (Datum: NAD 83).

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Hampton Roads, Virginia and adjacent waters (Datum: NAD 83). 110.168 Section 110.168 Navigation and Navigable Waters COAST GUARD..., Virginia and adjacent waters (Datum: NAD 83). (a) Anchorage Grounds—(1) Anchorage A [Naval Anchorage]. The...

  10. ''Dural tail'' adjacent to acoustic neuroma on MRI: a case report

    International Nuclear Information System (INIS)

    Lunardi, P.; Mastronardi, L.; Nardacci, B.; Acqui, M.; Fortuna, A.

    1993-01-01

    A 'dural tail' on Gd-DTPA-enhanced MRI has been often observed adjacent to meningiomas and considered to be useful in distinguishing meningioma of the cerebellopontine angle from acoustic neuroma. However, demonstration of a dural tail adjacent to an acoustic neuroma indicates that this sign is not specific. (orig.)

  11. Fluorides leaching from restorative materials and the effect on adjacent teeth

    DEFF Research Database (Denmark)

    Qvist, Vibeke; Poulsen, Agneta; Teglers, Poul Thorpen

    2010-01-01

    Placing a Class II restoration in a tooth changes the local environment, including that for the adjacent tooth. Apart from the change to a less- or non-cariogenic environment for the restored tooth, the effect of leachable components from a restoration in the adjacent tooth should be taken into c...

  12. Constructing an optimal facility layout to maximize adjacency as a function of common boundary length

    Science.gov (United States)

    Ghassemi Tari, Farhad; Neghabi, Hossein

    2018-03-01

    An effective facility layout implies that departments with high flow are laid adjacent. However, in the case of a very narrow boundary length between the neighbouring departments, the adjacency would actually be useless. In traditional layout design methods, a score is generally assigned independent of the department's boundary length. This may result in a layout design with a restricted material flow. This article proposes a new concept of adjacency in which the department pairs are laid adjacent with a wider path. To apply this concept, a shop with unequal rectangular departments is contemplated and a mathematical programming model with the objective of maximizing the sum of the adjacency degrees is proposed. A computational experiment is conducted to demonstrate the efficiency of the layout design. It is demonstrated that the new concept provides a more efficient and a more realistic layout design.

  13. Retrotransposon Targeting of Tumor Cells

    National Research Council Canada - National Science Library

    Wu, Dongdong; DeVaux, George

    2005-01-01

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

  14. Adjacent field separations for homogenous dose distribution at particular depth and associated hot and cold spots

    International Nuclear Information System (INIS)

    Supe, S.S.; Deka, A.C.; Deka, B.C.; Sathiyanaranyanan, V.K.

    1991-01-01

    In radiotherapy treatment planning we come across many situations when treatment is given by using two adjacent fields, for e.g. for treatment of Hodgkin's disease. A pair of adjacent field have been used regularly for the treatment of ovarian tumours. A small separation is given at the skin level, otherwise hot spots are observed at the depth of interest. The separation depend upon tumour depths, and source to skin distance (SSD). Formulae have been derived for the separation as well as for hot and cold spots. The case of adjacent field becomes more complicated when anterior as well as posterior adjacent fields are used. It is not completely possible to avoid the hot and cold spots in such cases. This is partially avoided by shifting the gap on the skin surface during the course of treatment. (author). 2 refs., 2 tabs

  15. Incidence of root canal treatment of second molars following adjacent impacted third molar extraction

    Directory of Open Access Journals (Sweden)

    Yener Oguz

    2016-03-01

    Conclusion: Although the incidence is minimal, iatrogenic subluxation injuries occurring during the surgical removal of impacted third molars can lead to pulpal complications and a requirement for root canal treatment of adjacent second molars.

  16. 76 FR 74585 - Railroad Workplace Safety; Adjacent-Track On-Track Safety for Roadway Workers

    Science.gov (United States)

    2011-11-30

    ... impression that adjacent-track on-track safety was in effect, but it was not, due to a miscommunication. Of... the solution to the problem.'' And while the RWP Working Group did in fact draft this language, and...

  17. 31. Introduction with adjacent production of foundry and rolling department of electrolysis shop

    International Nuclear Information System (INIS)

    Ivanov, A.V.

    1993-01-01

    The introduction with adjacent production of foundry and rolling department of electrolysis shop was conducted. The foundry machine was described. The chemical properties of aluminium for ferrous alloy production were defined.

  18. Numerical Simulation of Salinity and Dissolved Oxygen at Perdido Bay and Adjacent Coastal Ocean

    Science.gov (United States)

    Environmental Fluid Dynamic Code (EFDC), a numerical estuarine and coastal ocean circulation hydrodynamic model, was used to simulate the distribution of the salinity, temperature, nutrients and dissolved oxygen (DO) in Perdido Bay and adjacent Gulf of Mexico. External forcing fa...

  19. An implant periapical lesion associated with an endodontic-periodontic lesion of an adjacent molar

    OpenAIRE

    Chou, Ting-An; Chang, Yu-Liang; Yu, Ling-Min; Pan, Whei-Ling; Ju, Yuh-Ren; Chan, Chiu-Po

    2010-01-01

    Adjacent natural teeth with untreated pulpal or periodontal pathology may be a potential risk for implant infection. We report a rare case of an implant periapical lesion (IPL) possibly caused by direct extension of a periradicular lesion of an adjacent tooth. A 40-year-old female patient, who had previously received three implants on the edentulous areas of teeth 16, 36 and 46, had a recurrent infection over the lower left second molar area for 2 years. A periapical radiograph revealed incom...

  20. Local adjacency metric dimension of sun graph and stacked book graph

    Science.gov (United States)

    Yulisda Badri, Alifiah; Darmaji

    2018-03-01

    A graph is a mathematical system consisting of a non-empty set of nodes and a set of empty sides. One of the topics to be studied in graph theory is the metric dimension. Application in the metric dimension is the navigation robot system on a path. Robot moves from one vertex to another vertex in the field by minimizing the errors that occur in translating the instructions (code) obtained from the vertices of that location. To move the robot must give different instructions (code). In order for the robot to move efficiently, the robot must be fast to translate the code of the nodes of the location it passes. so that the location vertex has a minimum distance. However, if the robot must move with the vertex location on a very large field, so the robot can not detect because the distance is too far.[6] In this case, the robot can determine its position by utilizing location vertices based on adjacency. The problem is to find the minimum cardinality of the required location vertex, and where to put, so that the robot can determine its location. The solution to this problem is the dimension of adjacency metric and adjacency metric bases. Rodrguez-Velzquez and Fernau combine the adjacency metric dimensions with local metric dimensions, thus becoming the local adjacency metric dimension. In the local adjacency metric dimension each vertex in the graph may have the same adjacency representation as the terms of the vertices. To obtain the local metric dimension of values in the graph of the Sun and the stacked book graph is used the construction method by considering the representation of each adjacent vertex of the graph.

  1. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.

    Directory of Open Access Journals (Sweden)

    Regina S Baucom

    2009-11-01

    Full Text Available Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75% of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR retrotransposon class of retroelements, with >400 families (>350 newly discovered contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families and LINEs (at least 30 families, were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to

  2. Analysis of CD83 antigen expression in human breast fibroadenoma and adjacent tissue

    Directory of Open Access Journals (Sweden)

    Marcus Nascimento Borges

    Full Text Available CONTEXT AND OBJECTIVE: Dendritic cell maturation is considered essential for starting an immune response. The CD83 antigen is an important marker of dendritic cell maturation. The objectives here were to analyze CD83 antigen expression in human breast fibroadenoma and breast tissue adjacent to the lesion and to identify clinical factors that might influence this expression. DESIGN AND SETTING: This was a retrospective study at a public university hospital, in which 29 histopathological samples of breast fibroadenoma and adjacent breast tissue, from 28 women of reproductive age, were analyzed. METHODS: The immunohistochemistry method was used to analyze the cell expression of the antigen. The antigen expression in the cells was evaluated by means of random manual counting using an optical microscope. RESULTS: Positive expression of the CD83 antigen in the epithelial cells of the fibroadenoma (365.52; standard deviation ± 133.13 in relation to the adjacent breast tissue cells (189.59; standard deviation ± 140.75 was statistically larger (P < 0.001. Several clinical features were analyzed, but only parity was shown to influence CD83 antigen expression in the adjacent breast tissue, such that positive expression was more evident in nulliparous women (P = 0.042. CONCLUSIONS: The expression of the CD83 antigen in the fibroadenoma was positive and greater than in the adjacent breast tissue. Positive expression of the antigen in the adjacent breast tissue was influenced by parity, and was significantly more evident in nulliparous women.

  3. Risk Factors for the Development of Adjacent Segment Disease Following Anterior Cervical Arthrodesis

    Directory of Open Access Journals (Sweden)

    Ezgi Akar

    2015-06-01

    Full Text Available Aim: The aim of this study was to clinically and radiologically evaluate the efficacy of anterior cervical discectomy and fusion (ACDF in the treatment of adjacent level degeneration. Methods: We retrospectively evaluated 89 patients (55 females, 34 males who underwent ACDF. Adjacent segment degeneration findings were evaluated by investigating new osteophyte formation, growth of existing osteophytes, ossification of the anterior longitudinal ligament, presence of intervertebral disc space narrowing, sagittal alignment and range of motion (ROM using serial radiographs and magnetic resonance imaging. Results: The mean age of the 89 patients was 41.3 (24-76 years. The mean follow-up duration was 34.3 (12-64 months. Radiographic evidence of adjacent segment degeneration was observed in 12 patients (13.4%. Nine (75% patients had new complaints. Of the patients who had degenerative changes, 7 were (58% were male, 5 (42% were female; the mean age was 46 (30- 62 years. It was observed that the level of fusion and the number of fusion did not increase the adjacent segment degeneration. All of 12 patients were observed to have a non lordotic cervical spine and increased ROM. Conclusion: Development of degeneration at the level adjacent to region anterior cervical discectomy and fusion performed is higher compared to non-adjacent levels. The level of fusion and the number of fusion levels have no effect on the development of degeneration. (The Medical Bulletin of Haseki 2015; 53:120-3

  4. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

    Science.gov (United States)

    Evgen'ev, M B; Corces, V G; Lankenau, D H

    1992-06-05

    We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

  5. Diffusion-Weighted MRI Assessment of Adjacent Disc Degeneration After Thoracolumbar Vertebral Fractures

    Energy Technology Data Exchange (ETDEWEB)

    Noriega, David C., E-mail: dcnoriega1970@gmail.com [Valladolid University Hospital, Spine Department (Spain); Marcia, Stefano, E-mail: stemarcia@gmail.com [SS. Trinità Hospital ASL 8 Cagliari, Department of Radiology (Italy); Ardura, Francisco, E-mail: fardura@ono.com [Valladolid University Hospital, Spine Department (Spain); Lite, Israel Sanchez, E-mail: israelslite@hotmail.com [Valladolid University Hospital, Radiology Department (Spain); Marras, Mariangela, E-mail: mariangela.marrasmd@gmail.com [Azienda Ospedaliero Brotzu (A.O.B.), Department of Radiology (Italy); Saba, Luca, E-mail: lucasaba@tiscali.it [Azienda Ospedaliero Universitaria (A.O.U.), Department of Radiology (Italy)

    2016-09-15

    ObjectiveThe purpose of this study was to assess, by the mean apparent diffusion coefficient (ADC), if a relationship exists between disc ADC and MR findings of adjacent disc degeneration after thoracolumbar fractures treated by anatomic reduction using vertebral augmentation (VAP).Materials and MethodsTwenty non-consecutive patients (mean age 50.7 years; range 45–56) treated because of vertebral fractures, were included in this study. There were 10 A3.1 and 10 A1.2 fractures (AO classification). Surgical treatment using VAP was applied in 14 cases, and conservative in 6 patients. MRI T2-weighted images and mapping of apparent diffusion coefficient (ADC) of the intervertebral disc adjacent to the fractured segment were performed after a mean follow-up of 32 months. A total of 60 discs, 3 per patient, were analysed: infra-adjacent, supra-adjacent and a control disc one level above the supra-adjacent.ResultsNo differences between patients surgically treated and those following a conservative protocol regarding the average ADC values obtained in the 20 control discs analysed were found. Considering all discs, average ADC in the supra-adjacent level was lower than in the infra-adjacent (1.35 ± 0.12 vs. 1.53 ± 0.06; p < 0.001). Average ADC values of the discs used as a control were similar to those of the infra-adjacent level (1.54 ± 0.06). Compared to surgically treated patients, discs at the supra-adjacent fracture level showed statistically significant lower values in cases treated conservatively (p < 0.001). The variation in the delay of surgery had no influence on the average values of ADC at any of the measured levels.ConclusionsADC measurements of the supra-adjacent discs after a mean follow-up of 32 months following thoracolumbar fractures, showed that restoration of the vertebral collapse by minimally invasive VAP prevents posttraumatic disc degeneration.

  6. 33 CFR 148.510 - What happens when a petition for exemption involves the interests of an adjacent coastal State?

    Science.gov (United States)

    2010-07-01

    ... exemption involves the interests of an adjacent coastal State? 148.510 Section 148.510 Navigation and... petition for exemption involves the interests of an adjacent coastal State? If the petition for exemption concerns an adjacent coastal State, the Commandant (CG-5) forwards the petition to the Governor of the...

  7. Sacroiliac Joint Fusion Minimally Affects Adjacent Lumbar Segment Motion: A Finite Element Study.

    Science.gov (United States)

    Lindsey, Derek P; Kiapour, Ali; Yerby, Scott A; Goel, Vijay K

    2015-01-01

    Adjacent segment disease is a recognized consequence of fusion in the spinal column. Fusion of the sacroiliac joint is an effective method of pain reduction. Although effective, the consequences of sacroiliac joint fusion and the potential for adjacent segment disease for the adjacent lumbar spinal levels is unknown. The objective of this study was to quantify the change in range of motion of the sacroiliac joint and the adjacent lumbar spinal motion segments due to sacroiliac joint fusion and compare these changes to previous literature to assess the potential for adjacent segment disease in the lumbar spine. An experimentally validated finite element model of the lumbar spine and pelvis was used to simulate a fusion of the sacroiliac joint using three laterally placed triangular implants (iFuse Implant System, SI-BONE, Inc., San Jose, CA). The range of motion of the sacroiliac joint and the adjacent lumbar spinal motion segments were calculated using a hybrid loading protocol and compared with the intact range of motion in flexion, extension, lateral bending, and axial rotation. The range of motions of the treated sacroiliac joints were reduced in flexion, extension, lateral bending, and axial rotation, by 56.6%, 59.5%, 27.8%, and 53.3%, respectively when compared with the intact condition. The stiffening of the sacroiliac joint resulted in increases at the adjacent lumbar motion segment (L5-S1) for flexion, extension, lateral bending, and axial rotation, of 3.0%, 3.7%, 1.1%, and 4.6%, respectively. Fusion of the sacroiliac joint resulted in substantial (> 50%) reductions in flexion, extension, and axial rotation of the sacroiliac joint with minimal (sacroiliac joint fusion, the long-term clinical results remain to be investigated.

  8. Uplink scheduling and adjacent-channel coupling loss analysis for TD-LTE deployment.

    Science.gov (United States)

    Yeo, Woon-Young; Moon, Sung Ho; Kim, Jae-Hoon

    2014-01-01

    TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI.

  9. The relative influence of road characteristics and habitat on adjacent lizard populations in arid shrublands

    Science.gov (United States)

    Hubbard, Kaylan A.; Chalfoun, Anna D.; Gerow, Kenneth G.

    2016-01-01

    As road networks continue to expand globally, indirect impacts to adjacent wildlife populations remain largely unknown. Simultaneously, reptile populations are declining worldwide and anthropogenic habitat loss and fragmentation are frequently cited causes. We evaluated the relative influence of three different road characteristics (surface treatment, width, and traffic volume) and habitat features on adjacent populations of Northern Sagebrush Lizards (Sceloporus graciosus graciosus), Plateau Fence Lizards (S. tristichus), and Greater Short-Horned Lizards (Phrynosoma hernandesi) in mixed arid shrubland habitats in southwest Wyoming. Neither odds of lizard presence nor relative abundance was significantly related to any of the assessed road characteristics, although there was a trend for higher Sceloporus spp. abundance adjacent to paved roads. Sceloporus spp. relative abundance did not vary systematically with distance to the nearest road. Rather, both Sceloporus spp. and Greater Short-Horned Lizards were associated strongly with particular habitat characteristics adjacent to roads. Sceloporus spp. presence and relative abundance increased with rock cover, relative abundance was associated positively with shrub cover, and presence was associated negatively with grass cover. Greater Short-Horned Lizard presence increased with bare ground and decreased marginally with shrub cover. Our results suggest that habitat attributes are stronger correlates of lizard presence and relative abundance than individual characteristics of adjacent roads, at least in our system. Therefore, an effective conservation approach for these species may be to consider the landscape through which new roads and their associated development would occur, and the impact that placement could have on fragment size and key habitat elements.

  10. Non-target adjacent stimuli classification improves performance of classical ERP-based brain computer interface

    Science.gov (United States)

    Ceballos, G. A.; Hernández, L. F.

    2015-04-01

    Objective. The classical ERP-based speller, or P300 Speller, is one of the most commonly used paradigms in the field of Brain Computer Interfaces (BCI). Several alterations to the visual stimuli presentation system have been developed to avoid unfavorable effects elicited by adjacent stimuli. However, there has been little, if any, regard to useful information contained in responses to adjacent stimuli about spatial location of target symbols. This paper aims to demonstrate that combining the classification of non-target adjacent stimuli with standard classification (target versus non-target) significantly improves classical ERP-based speller efficiency. Approach. Four SWLDA classifiers were trained and combined with the standard classifier: the lower row, upper row, right column and left column classifiers. This new feature extraction procedure and the classification method were carried out on three open databases: the UAM P300 database (Universidad Autonoma Metropolitana, Mexico), BCI competition II (dataset IIb) and BCI competition III (dataset II). Main results. The inclusion of the classification of non-target adjacent stimuli improves target classification in the classical row/column paradigm. A gain in mean single trial classification of 9.6% and an overall improvement of 25% in simulated spelling speed was achieved. Significance. We have provided further evidence that the ERPs produced by adjacent stimuli present discriminable features, which could provide additional information about the spatial location of intended symbols. This work promotes the searching of information on the peripheral stimulation responses to improve the performance of emerging visual ERP-based spellers.

  11. Analysis of CD83 antigen expression in human breast fibroadenoma and adjacent tissue.

    Science.gov (United States)

    Borges, Marcus Nascimento; Facina, Gil; Silva, Ismael Dale Cotrin Guerreiro; Waitzberg, Angela Flávia Logullo; Nazario, Afonso Celso Pinto

    2011-12-01

    Dendritic cell maturation is considered essential for starting an immune response. The CD83 antigen is an important marker of dendritic cell maturation. The objectives here were to analyze CD83 antigen expression in human breast fibroadenoma and breast tissue adjacent to the lesion and to identify clinical factors that might influence this expression. This was a retrospective study at a public university hospital, in which 29 histopathological samples of breast fibroadenoma and adjacent breast tissue, from 28 women of reproductive age, were analyzed. The immunohistochemistry method was used to analyze the cell expression of the antigen. The antigen expression in the cells was evaluated by means of random manual counting using an optical microscope. Positive expression of the CD83 antigen in the epithelial cells of the fibroadenoma (365.52; standard deviation ± 133.13) in relation to the adjacent breast tissue cells (189.59; standard deviation ± 140.75) was statistically larger (P fibroadenoma was positive and greater than in the adjacent breast tissue. Positive expression of the antigen in the adjacent breast tissue was influenced by parity, and was significantly more evident in nulliparous women.

  12. Gas explosion in a room with a window and passage to an adjacent room

    Directory of Open Access Journals (Sweden)

    Polandov Yuri

    2016-01-01

    Full Text Available Some publications describe an effect, produced during a physical model experiment, when an adjacent gas-free room influences the gas explosion pressure in a room with a window. The explosion pressure in this case significantly exceeds (2.5 times the explosion pressure in a room without an adjacent room. This result has been confirmed by our studies. Based on other available information about the influence of the ignition point location on the explosion pressure in one room, it was suggested that this could be true for an explosion in two rooms. In our studies we used a test unit with two connected chambers, each having a volume of 1.125 m3. It turned out that this influence of the adjacent volume was not so unambiguous as it was described in those publications. It was found out that the maximum effect of explosion pressure amplification by the adjacent room is achieved, when the igniter is located in the chamber filled with a gas-air mixture in the area between the center of the chamber and the window (maximum amplification by more than 3 times. This effect is lower directly by the window (1.8 times and is practically absent in case of ignition within the area near the passage connecting the chamber with the adjacent room. This suggests that the effect discovered earlier is a special case of the general dependence of the gas explosion pressure in two chambers on the igniter location.

  13. Benign Lesions in Mucosa Adjacent to Intestinal-Type Sinonasal Adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Blanca Vivanco

    2011-01-01

    Full Text Available Occupational exposure to wood dust is a strong risk factor for the development of intestinal-type sinonasal adenocarcinoma (ITAC; however, knowledge on possible precursor lesions or biomarkers is limited. Fifty-one samples of tumor-adjacent mucosa and 19 control samples of mucosa from the unaffected fossa of ITAC patients were evaluated for histological changes and p53 protein expression. Mild dysplasia was observed in 14%, cuboidal metaplasia in 57%, intestinal metaplasia in 8%, squamous metaplasia in 24%, and cylindrocellular hyperplasia in 53% of cases. P53 immunopositivity was generally weak occurring most frequently in squamous metaplasia. Wood dust etiology did not appear of influence on the histological changes, but p53 showed a tendency for higher positivity. Dysplasia adjacent to tumor was indicative of subsequent development of recurrence. In conclusion, precursor lesions do occur in mucosa adjacent to ITAC. This is clinically important, because it may justify the screening of high-risk individuals such as woodworkers.

  14. Sound insulation property of membrane-type acoustic metamaterials carrying different masses at adjacent cells

    Science.gov (United States)

    Zhang, Yuguang; Wen, Jihong; Zhao, Honggang; Yu, Dianlong; Cai, Li; Wen, Xisen

    2013-08-01

    We present the experimental realization and theoretical understanding of membrane-type acoustic metamaterials embedded with different masses at adjacent cells, capable of increasing the transmission loss at low frequency. Owing to the reverse vibration of adjacent cells, Transmission loss (TL) peaks appear, and the magnitudes of the TL peaks exceed the predicted results of the composite wall. Compared with commonly used configuration, i.e., all cells carrying with identical mass, the nonuniformity of attaching masses causes another much low TL peak. Finite element analysis was employed to validate and provide insights into the TL behavior of the structure.

  15. TP53 mutations in clinically normal mucosa adjacent to oral carcinomas

    DEFF Research Database (Denmark)

    Thode, Christenze; Bilde, Anders; von Buchwald, Christian

    2010-01-01

    BACKGROUND: The tumour-suppressor protein p53 often accumulates in histologically normal epithelium adjacent to oral squamous cell carcinomas (OSCC). We investigated whether this was associated with mutations in TP53, the gene for p53, and might implicate impending malignancy. METHODS: Specimens...... products were separated by denatured gradient gel electrophoresis. Fragments with a deviant DGEE pattern were sequenced. RESULTS: TP53 mutations were found in six of 18 tumours. Fourteen specimens contained histologically normal mucosa adjacent to the tumour; 13 of these showed small clusters of p53...

  16. Tabu search approaches for the multi-level warehouse layout problem with adjacency constraints

    Science.gov (United States)

    Zhang, G. Q.; Lai, K. K.

    2010-08-01

    A new multi-level warehouse layout problem, the multi-level warehouse layout problem with adjacency constraints (MLWLPAC), is investigated. The same item type is required to be located in adjacent cells, and horizontal and vertical unit travel costs are product dependent. An integer programming model is proposed to formulate the problem, which is NP hard. Along with a cube-per-order index policy based heuristic, the standard tabu search (TS), greedy TS, and dynamic neighbourhood based TS are presented to solve the problem. The computational results show that the proposed approaches can reduce the transportation cost significantly.

  17. Intranasal Administration of 2/6-Rotavirus-Like Particles with Mutant Escherichia coli Heat-Labile Toxin (LT-R192G) Induces Antibody-Secreting Cell Responses but Not Protective Immunity in Gnotobiotic Pigs

    Science.gov (United States)

    Yuan, Lijuan; Geyer, Annelise; Hodgins, Douglas C.; Fan, Zhiqian; Qian, Yuan; Chang, Kyeong-Ok; Crawford, Sue E.; Parreño, Viviana; Ward, Lucy A.; Estes, Mary K.; Conner, Margaret E.; Saif, Linda J.

    2000-01-01

    We investigated the immunogenicity of recombinant double-layered rotavirus-like particle (2/6-VLPs) vaccines derived from simian SA11 or human (VP6) Wa and bovine RF (VP2) rotavirus strains. The 2/6-VLPs were administered to gnotobiotic pigs intranasally (i.n.) with a mutant Escherichia coli heat-labile toxin, LT-R192G (mLT), as mucosal adjuvant. Pigs were challenged with virulent Wa (P1A[8],G1) human rotavirus at postinoculation day (PID) 21 (two-dose VLP regimen) or 28 (three-dose VLP regimen). In vivo antigen-activated antibody-secreting cells (ASC) (effector B cells) and in vitro antigen-reactivated ASC (derived from memory B cells) from intestinal and systemic lymphoid tissues (duodenum, ileum, mesenteric lymph nodes [MLN], spleen, peripheral blood lymphocytes [PBL], and bone marrow lymphocytes) collected at selected times were quantitated by enzyme-linked immunospot assays. Rotavirus-specific immunoglobulin M (IgM), IgA, and IgG ASC and memory B-cell responses were detected by PID 21 or 28 in intestinal and systemic lymphoid tissues after i.n. inoculation with two or three doses of 2/6-VLPs with or without mLT. Greater mean numbers of virus-specific ASC and memory B cells in all tissues prechallenge were induced in pigs inoculated with two doses of SA11 2/6-VLPs plus mLT compared to SA11 2/6-VLPs without mLT. After challenge, anamnestic IgA and IgG ASC and memory B-cell responses were detected in intestinal lymphoid tissues of all VLP-inoculated groups, but serum virus-neutralizing antibody titers were not significantly enhanced compared to the challenged controls. Pigs inoculated with Wa-RF 2/6-VLPs (with or without mLT) developed higher anamnestic IgA and IgG ASC responses in ileum after challenge compared to pigs inoculated with SA11 2/6-VLPs (with or without mLT). Three doses of SA 11 2/6-VLP plus mLT induced the highest mean numbers of IgG memory B cells in MLN, spleen, and PBL among all groups postchallenge. However, no significant protection against

  18. Spatiotemporal evolution of Calophaca (Fabaceae) reveals multiple dispersals in the Central Asian mountains and adjacent regions

    Science.gov (United States)

    Ming-Li Zhang; Zhi-Bin Wen; Peter W. Fritsch; Stewart C. Sanderson

    2015-01-01

    The Central Asian flora plays a significant role in Eurasia and the Northern Hemisphere. Calophaca, a member of this flora, includes eight currently recognized species, and is centered in Central Asia, with some taxa extending into adjacent areas. A phylogenetic analysis of the genus utilizing nuclear ribosomal ITS and plastid trnS-trnG and rbcL sequences was carried...

  19. Long-term soil accumulation of chromium, copper, and arsenic adjacent to preservative-treated wood.

    Science.gov (United States)

    S. Lebow; D. Foster; J. Evans

    2004-01-01

    Chromated copper arsenate (CCA) treated wood has been used extensively in outdoor applications. The Environmental Protection Agency (EPA) and CCA producers recently reached an agreement to limit future use of CCA for some types of applications. One area of concern is the long-term accumulation of leached CCA in soil adjacent to treated wood structures. Interpreting...

  20. Testing EGM2008 on Leveling Data from Scandinavia, Adjacent Baltic Areas, and Greenland

    DEFF Research Database (Denmark)

    Strykowski, Gabriel; Forsberg, René

    2010-01-01

    We tested EGM2008 on GPS/leveling data from Scandinavia and adjacent areas. EGM2008 performs at the same level as the best regional geoid model, NKG2004. However, the direct evaluation of EGM2008 is difficult in Greenland because no leveling data are available. Nevertheless, we show on 78 GPS-MSS...

  1. Preliminary assessment of illegal hunting by communities adjacent to the northern Gonarezhou National Park, Zimbabwe

    NARCIS (Netherlands)

    Gandiwa, E.

    2011-01-01

    Illegal hunting of wildlife is a major issue in today’s society, particularly in tropical ecosystems. In this study, a total of 114 local residents from eight villages located in four wards adjacent to the northern Gonarezhou National Park, south-eastern Zimbabwe were interviewed in 2009, using

  2. Regional Spectral Model simulations of the summertime regional climate over Taiwan and adjacent areas

    Science.gov (United States)

    Ching-Teng Lee; Ming-Chin Wu; Shyh-Chin Chen

    2005-01-01

    The National Centers for Environmental Prediction (NCEP) regional spectral model (RSM) version 97 was used to investigate the regional summertime climate over Taiwan and adjacent areas for June-July-August of 1990 through 2000. The simulated sea-level-pressure and wind fields of RSM1 with 50-km grid space are similar to the reanalysis, but the strength of the...

  3. Resonance properties of tidal channels with multiple retention basisn: role of adjacent sea

    NARCIS (Netherlands)

    Roos, Pieter C.; Schuttelaars, H.M.

    2015-01-01

    We present an idealised model of the tidal response in a main channel with multiple secondary basins, co-oscillating with an adjacent sea. The sea is represented as a semi-infinite strip of finite width, anywhere between the limits of a channel extension (narrow) and a half-plane (wide). The sea

  4. Ten-year survival rates of teeth adjacent to treated and untreated posterior bounded edentulous spaces.

    Science.gov (United States)

    Aquilino, S A; Shugars, D A; Bader, J D; White, B A

    2001-05-01

    Failure to replace a single missing posterior tooth may lead to a variety of dental problems, which may ultimately result in tooth loss. However, little is known about the fate of the adjacent teeth if a missing posterior tooth is not replaced. This retrospective study evaluated the survival of teeth adjacent to treated and untreated posterior bounded edentulous spaces. Data were obtained from electronic treatment records from the Kaiser Permanente Dental Care Program, Portland, Ore. A final sample of 317 patients who met the study inclusion criteria was identified. Each bounded edentulous space was placed in 1 of 3 treatment categories: untreated, restored with a fixed partial denture, or restored with a removable partial denture. Subsequent treatment and the status of the teeth adjacent to the bounded edentulous space were followed through December 1999. Ten-year Kaplan-Meier survival estimates were generated for each treatment group, and differences in survival were evaluated with the log-rank chi-square test (alpha=.05). There was a significant difference in survival among the 3 treatment categories (P=.005). Spaces restored with a fixed partial denture had longer 10-year survival estimates (92%) than those that remained untreated (81%). Spaces restored with a removable partial denture had the poorest 10-year survival rate (56%). Under the conditions and selection bias associated with this retrospective study, the survival of teeth adjacent to a single posterior edentulous space was negatively associated with removable partial denture placement compared with no treatment or the use of a fixed partial denture.

  5. Status of fisher in the northern Idaho panhandle and adjacent mountain ranges

    Science.gov (United States)

    Michael Lucid; L. Robinson; S. Cushman; L. Allen; M. Schwartz; K. Pilgrim

    2013-01-01

    The Multi-species Baseline Initiative (MBI) is a collaborative of organizations which is conducting a comprehensive inventory for fisher (Martes pennanti) and other wildlife species across the Idaho Panhandle and adjacent mountain ranges. From 2010-2012, MBI partners established 112 forest carnivore bait stations to collect photographs and DNA from 22 wildlife species...

  6. International comparison calculations for a BWR lattice with adjacent gadolinium pins

    International Nuclear Information System (INIS)

    Maeder, C.; Wydler, P.

    1984-09-01

    The results of burnup calculations for a simplified BWR fuel element with two adjacent gadolinium rods are presented and discussed. Ten complete solutions were contributed by Denmark, France, Italy (3), Japan (3), Switzerland and the UK. Partial results obtained from Poland and the USA are included in an Appendix. (Auth.)

  7. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue.

    Science.gov (United States)

    Geybels, Milan S; Zhao, Shanshan; Wong, Chao-Jen; Bibikova, Marina; Klotzle, Brandy; Wu, Michael; Ostrander, Elaine A; Fan, Jian-Bing; Feng, Ziding; Stanford, Janet L

    2015-12-01

    Aberrant DNA methylation may promote prostate carcinogenesis. We investigated epigenome-wide DNA methylation profiles in prostate cancer (PCa) compared to adjacent benign tissue to identify differentially methylated CpG sites. The study included paired PCa and adjacent benign tissue samples from 20 radical prostatectomy patients. Epigenetic profiling was done using the Infinium HumanMethylation450 BeadChip. Linear models that accounted for the paired study design and False Discovery Rate Q-values were used to evaluate differential CpG methylation. mRNA expression levels of the genes with the most differentially methylated CpG sites were analyzed. In total, 2,040 differentially methylated CpG sites were identified in PCa versus adjacent benign tissue (Q-value Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. This study of PCa versus adjacent benign tissue showed many differentially methylated CpGs and regions in and outside gene promoter regions, which may potentially be used for the development of future epigenetic-based diagnostic tests or as therapeutic targets. © 2015 Wiley Periodicals, Inc.

  8. Headwater fish population responses to planting grass filter strips adjacent to channelized agricultural headwater streams

    Science.gov (United States)

    Grass filter strips are a widely used conservation practice in the Midwestern United States for reducing nutrient, pesticide, and sediment inputs into agricultural streams. Only a limited amount of information is available on the ecological effects of planting grass filter strips adjacent to channe...

  9. An assessment of transport timescales and return coefficient in adjacent tropical estuaries

    NARCIS (Netherlands)

    Andutta, Fernando P.; Helfer, Fernanda; de Miranda, Luiz Bruner; Deleersnijder, E.L.C.; Thomas, C.J.; Lemckert, Charles

    2016-01-01

    Transport timescales (TTS), namely residence time and exposure time, were computed for adjacent shallow meso-tidal tropical estuarines system using the Lagrangian model D-Waq Part coupled with the hydrodynamic model Delft3D-Flow, and the Constituent-oriented Age and Residence time Theory, CART.

  10. Effects of ecological compensation meadows on arthropod diversity in adjacent intensively managed grassland

    NARCIS (Netherlands)

    Albrecht, M.; Duelli, P.; Obrist, M.K.; Müller, C.; Schüpbach, B.; Kleijn, D.; Schmid, B.

    2010-01-01

    An important goal of ecological compensation areas (ECAs) is to increase biodiversity in adjacent intensively managed farmland and the agricultural landscape at large. We tested whether this goal can be achieved in the case of the agri-environmental restoration scheme implemented for Swiss grassland

  11. Antibacterial Activity of Orthodontic Cement Containing Quaternary Ammonium Polyethylenimine Nanoparticles Adjacent to Orthodontic Brackets

    OpenAIRE

    Eldad Sharon; Revital Sharabi; Adi Eden; Asher Zabrovsky; Gilad Ben-Gal; Esi Sharon; Yoav Pietrokovski; Yael Houri-Haddad; Nurit Beyth

    2018-01-01

    Enamel demineralization is a common problem found in patients using orthodontic devices, such as orthodontic braces. It was found that Streptoccocus mutans growth increases adjacent to orthodontic devices, which may result in caries development. Incorporated antibacterial quaternary ammonium polyethylenimine (QPEI) nanoparticles were previously shown to be highly efficacious against various bacteria. Combining antibacterial materials in orthodontic cement may be advantageous to prevent bacter...

  12. Low-loss hollow-core silica fibers with adjacent nested anti-resonant tubes

    DEFF Research Database (Denmark)

    Habib, Selim; Bang, Ole; Bache, Morten

    2015-01-01

    We report on numerical design optimization of hollow-core antiresonant fibers with the aim of reducing transmission losses. We show that re-arranging the nested anti-resonant tubes in the cladding to be adjacent has the effect of significantly reducing leakage as well as bending losses, and for r...

  13. Edge effects of stink bugs in corn, cotton, peanut and soybean fields adjacent to woodland.

    Science.gov (United States)

    Producers face significant crop losses from stink bug species in the southeastern USA, but the high mobility and polyphagy of the bugs make predictions of their presence in crops difficult. While there is some evidence that they colonize crops from adjacent crops, there are no studies of their colo...

  14. Post-frontier forest change adjacent to Braulio Carrillo National Park, Costa Rica

    Science.gov (United States)

    John Schelhas; G. Arturo Sanchez-Azofeifa

    2006-01-01

    Effective biodiversity conservation in national parks depends to a large extent on adjacent forest cover. While deforestation and forest fragmentation as a result of colonization and agriculture have been widespread in neotropical countries over the past few decades, in some places agricultural intensification, wage labor, and rural to urban migration are becoming the...

  15. Histological and histomorphometrical evaluation of tissue reactions adjacent to endosteal implants in monkeys

    DEFF Research Database (Denmark)

    Gotfredsen, K; Rostrup, E; Hjörting-Hansen, E

    1992-01-01

    A qualitative and quantitative histological study of the initial healing response adjacent to 24 submerged and non-submerged implants placed in the lower jaws of 6 monkeys is presented. The histomorphometric analysis showed no significant differences in mineralized bone-implant contact length...

  16. Examining incentives for adjacent non-industrial private forest landowners to cooperate

    Science.gov (United States)

    Melinda Vokoun; Gregory S Amacher; Jay Sullivan; Dave Wear

    2010-01-01

    Individual landowners may capture non-timber benefits from both their own forested parcels and adjacent parcels owned by different landowners. These benefits may affect incentives for landowners to cooperate in their forest management decisions. Landowner survey data is used to examine incentives to cooperate concerning joint forest management and coordination of...

  17. Deformations and damage to buildings adjacent to deep excavations in soft soils

    NARCIS (Netherlands)

    Korff, M.

    2009-01-01

    The objective of this study is to gain insight into mechanisms of soil-structure interaction for buildings adjacent to deep excavations and to find a reliable method to design and monitor deep excavations in urban areas with soft soil conditions. The research focuses on typical Dutch conditions. The

  18. Non-Adjacent Dependency Learning in Infants at Familial Risk of Dyslexia

    Science.gov (United States)

    Kerkhoff, Annemarie; de Bree, Elise; de Klerk, Maartje; Wijnen, Frank

    2013-01-01

    This study tests the hypothesis that developmental dyslexia is (partly) caused by a deficit in implicit sequential learning, by investigating whether infants at familial risk of dyslexia can track non-adjacent dependencies in an artificial language. An implicit learning deficit would hinder detection of such dependencies, which mark grammatical…

  19. Adjacency-blurring-effect of scenes modeled by the radiosity method

    Energy Technology Data Exchange (ETDEWEB)

    Borel, C.C.; Gerstl, S.A.W.

    1992-05-01

    In this paper we describe a method to simulate images through a scattering atmosphere. We compute the scattering of light from adjacent surfaces into the field-of-view (FOV) with the extended radiosity method. Our simulation takes aerosol scattering phase functions and ground bidirectional reflectance distributions (BRDF) into account. 10 refs.

  20. Tourist preferences for ecotourism in rural communities adjacent to Kruger National Park: A choice experiment approach

    NARCIS (Netherlands)

    Chaminuka, P.; Groeneveld, R.A.; Selomane, A.O.; Ierland, van E.C.

    2012-01-01

    This paper analyses the potential for development of ecotourism in rural communities adjacent to Kruger National Park (KNP) in South Africa. We determine preferences of tourists, according to origin and income levels, for ecotourism and their marginal willingness to pay (MWTP) for three ecotourism

  1. 77 FR 53164 - Railroad Workplace Safety; Adjacent-Track On-Track Safety for Roadway Workers

    Science.gov (United States)

    2012-08-31

    ...-0059, Notice No. 6] RIN 2130-AC37 Railroad Workplace Safety; Adjacent-Track On-Track Safety for Roadway... complex issues raised in both the petitions for reconsideration of the final rule published November 30... issues. One of the Petitions included a request for a delay in the effective date of the final rule until...

  2. 78 FR 33754 - Railroad Workplace Safety; Adjacent-Track On-Track Safety for Roadway Workers

    Science.gov (United States)

    2013-06-05

    ...-0059, Notice No. 7] RIN 2130-AC37 Railroad Workplace Safety; Adjacent-Track On-Track Safety for Roadway... and comments raised a number of substantive issues requiring a detailed response. As FRA's response to... INFORMATION: On November 30, 2011, FRA published a final rule amending its regulations on railroad workplace...

  3. 77 FR 13978 - Railroad Workplace Safety; Adjacent-Track On-Track Safety for Roadway Workers

    Science.gov (United States)

    2012-03-08

    ...-0059, Notice No. 5] RIN 2130-AB96 Railroad Workplace Safety; Adjacent-Track On-Track Safety for Roadway... that raise a number of substantive issues requiring a detailed response. Accordingly, in order to...: On November 30, 2011, FRA published a final rule amending its regulations on railroad workplace...

  4. 27 CFR 19.241 - Operations bond-distilled spirits plant and adjacent bonded wine cellar.

    Science.gov (United States)

    2010-04-01

    ... spirits plant and adjacent bonded wine cellar. 19.241 Section 19.241 Alcohol, Tobacco Products and... wine cellar. (a) General. A wine cellar under the provisions of 27 CFR part 24 shall be treated as... subpart G for the production of distilled spirits; and (2) Such wine cellar and distilled spirits plant...

  5. Impacted maxillary canines and root resorption of adjacent teeth: A retrospective observational study.

    Science.gov (United States)

    Guarnieri, R; Cavallini, C; Vernucci, R; Vichi, M; Leonardi, R; Barbato, E

    2016-11-01

    The prevalence of impacted maxillary canine is reported to be between 1% and 3%. The lack of monitoring and the delay in the treatment of the impacted canine can cause different complications such as: displacement of adjacent teeth, loss of vitality of neighbouring teeth, shortening of the dental arch, follicular cysts, canine ankylosis, recurrent infections, recurrent pain, internal resorption of the canine and the adjacent teeth, external resorption of the canine and the adjacent teeth, combination of these factors. An appropriate diagnosis, accurate predictive analysis and early intervention are likely to prevent such undesirable effects. The objective is to evaluate, by means of a retrospective observational study, the possibility of carrying out a predictive analysis of root resorption adjacent to the impacted canines by means of orthopantomographs, so as to limit the prescription of additional 3D radiography. 120 subjects with unilateral or bilateral maxillary impacted canine were examined and 50 patients with 69 impacted maxillary canine (22 male, 28 female; mean age: 11.7 years) satisfied the inclusion criteria of the study. These patients were subjected to a basic clinical and radiographic investigation (orthopantomographs and computerized tomography). All panoramic films were viewed under standardized conditions for the evaluation of two main variables: maxillary canine angulations (a, b, g angles) and the overlapping between the impacted teeth and the lateral incisor (Analysis of Lindauer). Binary logistic regression was used to estimate the likelihood of resorbed lateral incisors depending on sector location and angle measurements. Results indicated that b angle has the greatest influence on the prediction of root resorption (predictive value of b angle = 76%). If β angle <18° and Lindauer = I, the probability of resorption is 0.06. Evaluation of b angle and superimposition lateral incisor/impacted canine analysed on orthopantomographs could be one of

  6. On the Adjacent Strong Equitable Edge Coloring of Pn ∨ Pn, Pn ∨ Cn and Cn ∨ Cn

    OpenAIRE

    Liu Jun; Zhao Chuan Cheng; Yao Shu Xia; Guo Ren Zhi; Yue Qiu Ju

    2016-01-01

    A proper edge coloring of graph G is called equitable adjacent strong edge coloring if colored sets from every two adjacent vertices incident edge are different,and the number of edges in any two color classes differ by at most one,which the required minimum number of colors is called the adjacent strong equitable edge chromatic number. In this paper, we discuss the adjacent strong equitable edge coloring of join-graphs about Pn ∨ Pn, Pn ∨ Cn and Cn ∨ Cn.

  7. Pelvic incidence-lumbar lordosis mismatch predisposes to adjacent segment disease after lumbar spinal fusion.

    Science.gov (United States)

    Rothenfluh, Dominique A; Mueller, Daniel A; Rothenfluh, Esin; Min, Kan

    2015-06-01

    Several risk factors and causes of adjacent segment disease have been debated; however, no quantitative relationship to spino-pelvic parameters has been established so far. A retrospective case-control study was carried out to investigate spino-pelvic alignment in patients with adjacent segment disease compared to a control group. 45 patients (ASDis) were identified that underwent revision surgery for adjacent segment disease after on average 49 months (7-125), 39 patients were selected as control group (CTRL) similar in the distribution of the matching variables, such as age, gender, preoperative degenerative changes, and numbers of segments fused with a mean follow-up of 84 months (61-142) (total n = 84). Several radiographic parameters were measured on pre- and postoperative radiographs, including lumbar lordosis measured (LL), sacral slope, pelvic incidence (PI), and tilt. Significant differences between ASDis and CTRL groups on preoperative radiographs were seen for PI (60.9 ± 10.0° vs. 51.7 ± 10.4°, p = 0.001) and LL (48.1 ± 12.5° vs. 53.8 ± 10.8°, p = 0.012). Pelvic incidence was put into relation to lumbar lordosis by calculating the difference between pelvic incidence and lumbar lordosis (∆PILL = PI-LL, ASDis 12.5 ± 16.7° vs. CTRL 3.4 ± 12.1°, p = 0.001). A cutoff value of 9.8° was determined by logistic regression and ROC analysis and patients classified into a type A (∆PILL lordosis mismatch. In type A spino-pelvic alignment, 25.5 % of patients underwent revision surgery for adjacent segment disease, whereas 78.3 % of patients classified as type B alignment had revision surgery. Classification of patients into type A and B alignments yields a sensitivity for predicting adjacent segment disease of 71 %, a specificity of 81 % and an odds ratio of 10.6. In degenerative disease of the lumbar spine a high pelvic incidence with diminished lumbar lordosis seems to predispose to adjacent segment disease. Patients with such pelvic incidence

  8. Treatment of Osteomyelitis: A Case for Disruption of the Affected Adjacent Periosteum.

    Science.gov (United States)

    Hudson, John W; Daly, Austin P; Foster, Michael

    2017-10-01

    To evaluate the response of mandibular osteomyelitis treated by surgical decortication with disruption of the affected adjacent periosteum in concert with long-term targeted antibiotic therapy. The hypothesis is that, by removing the buccal cortical plate and disrupting the hypertrophically inflamed adjacent periosteum, the medullary bone will be brought in contact with bleeding tissue and circulating immunologic factors and antibiotics, which will promote definitive resolution. A retrospective review was conducted of 7 patient charts with associated radiographs from November 2010 to August 2016 treated by the first author at the University of Tennessee Medical Center (Knoxville, TN). Patients with chronic suppurative or nonsuppurative osteomyelitis of the mandible without condylar involvement or pathologic fracture were selected and treated with decortication with periosteal disruption in combination with long-term targeted antibiotic therapy. Seven patients (3 women and 4 men; mean age, 60 yr) underwent decortication with periosteal disruption of the affected area and received at least 6 weeks of targeted intravenous antibiotics. Computed tomography was performed preoperatively and a repeat study was performed after completion of antibiotics. In each case, post-treatment imaging showed definitive resolution after treatment with decortication in concert with disruption of the inflamed hypertrophic periosteum and intravenous antibiotics. Debridement of the infected cortical bone with restoration of the blood supply through disruption of the adjacent periosteum provided definitive resolution of mandibular osteomyelitis in the 7 patients treated. The hypothesis is that disruption of the affected adjacent periosteum reintroduces an immune-mediated response in concert with improved antibiotic delivery to and penetrance of the diseased mandible, aiding in definitive resolution. Decortication with periosteal disruption allows for preservation of the inferior alveolar

  9. A Voronoi interior adjacency-based approach for generating a contour tree

    Science.gov (United States)

    Chen, Jun; Qiao, Chaofei; Zhao, Renliang

    2004-05-01

    A contour tree is a good graphical tool for representing the spatial relations of contour lines and has found many applications in map generalization, map annotation, terrain analysis, etc. A new approach for generating contour trees by introducing a Voronoi-based interior adjacency set concept is proposed in this paper. The immediate interior adjacency set is employed to identify all of the children contours of each contour without contour elevations. It has advantages over existing methods such as the point-in-polygon method and the region growing-based method. This new approach can be used for spatial data mining and knowledge discovering, such as the automatic extraction of terrain features and construction of multi-resolution digital elevation model.

  10. Maxillary second molar impaction in the adjacent ectopic third molar: Report of five rare cases

    Science.gov (United States)

    Souki, Bernardo Q.; Cheib, Paula L.; de Brito, Gabriela M.; Pinto, Larissa S. M. C.

    2015-01-01

    Maxillary second molar impaction in the adjacent ectopic third molar is a rare condition that practitioners might face in the field of pediatric dentistry and orthodontics. The early diagnosis and extraction of the adjacent ectopic third molar have been advocated, and prior research has reported a high rate of spontaneous eruption following third molar removal. However, some challenges in the daily practice are that the early diagnosis of this type of tooth impaction is difficult with conventional radiographic examination, and sometimes the early surgical removal of the maxillary third molar must be postponed because of the risks of damaging the second molar. The objective of this study is to report a case series of five young patients with maxillary second molar impaction and to discuss the difficulty of early diagnosis with the conventional radiographic examination, and unpredictability of self-correction. PMID:26321848

  11. Flexible Connection Elastomeric Rubber as a Pounding Resisting Element between Two Adjacent Buildings

    Directory of Open Access Journals (Sweden)

    Yuskar Lase

    2013-03-01

    Full Text Available To solve pounding problem of two adjacent buildings, structural designer usually employs a dilatation between the structures or make the two structures as a monolith structure. Other alternative is by using an elastomeric rubber as a pounding resisting element between the two structures. Effectiveness in applying elastomeric rubber component as flexible connection of two adjacent structures is the main focus of this paper. Various simulations such as structure models, earthquake excitations and openings in gap element are studied. Observation of maximum structural responses will be performed for structure model with elastomeric rubber in comparison with (1 monolith structure model and (2 structure model with rigid element (steel element. Simulation results show that application of elastomeric rubber component to prevent structures from pounding problem provides advantages especially in reducing internal forces in the shorter building. However, it slightly increases displacement of both structures.

  12. Maxillary second molar impaction in the adjacent ectopic third molar: Report of five rare cases

    Directory of Open Access Journals (Sweden)

    Bernardo Q Souki

    2015-01-01

    Full Text Available Maxillary second molar impaction in the adjacent ectopic third molar is a rare condition that practitioners might face in the field of pediatric dentistry and orthodontics. The early diagnosis and extraction of the adjacent ectopic third molar have been advocated, and prior research has reported a high rate of spontaneous eruption following third molar removal. However, some challenges in the daily practice are that the early diagnosis of this type of tooth impaction is difficult with conventional radiographic examination, and sometimes the early surgical removal of the maxillary third molar must be postponed because of the risks of damaging the second molar. The objective of this study is to report a case series of five young patients with maxillary second molar impaction and to discuss the difficulty of early diagnosis with the conventional radiographic examination, and unpredictability of self-correction.

  13. The dynamics of innovation through the expansion in the adjacent possible

    International Nuclear Information System (INIS)

    Tria, F.

    2016-01-01

    The experience of something new is part of our daily life. At different scales, innovation is also a crucial feature of many biological, technological and social systems. Recently, large databases witnessing human activities allowed the observation that novelties —such as the individual process of listening a song for the first time— and innovation processes —such as the fixation of new genes in a population of bacteria— share striking statistical regularities. We here indicate the expansion into the adjacent possible as a very general and powerful mechanism able to explain such regularities. Further, we will identify statistical signatures of the presence of the expansion into the adjacent possible in the analyzed datasets, and we will show that our modeling scheme is able to predict remarkably well these observations.

  14. A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads.

    Science.gov (United States)

    Iwaki, M; Wickham, S F; Ikezaki, K; Yanagida, T; Shih, W M

    2016-12-12

    Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes.

  15. Microemulsions as model fluids for enhanced oil recovery: dynamics adjacent to planar hydrophilic walls

    Directory of Open Access Journals (Sweden)

    Mattauch S.

    2012-10-01

    Full Text Available After the dynamics of microemulsions adjacent to a planar hydrophilic wall have been characterized using grazing incidence neutron spin echo spectroscopy, the model of Seifert was employed to explain the discovered acceleration for the surface near lamellar ordered membranes. Reflections of hydrodynamic waves by the wall – or the volume conservation between the membrane and the wall – explain faster relaxations and, therefore, a lubrication effect that is important for flow fields in narrow pores. The whole scenery is now spectated by using different scenarios of a bicontinuous microemulsion exposed to clay particles and of a lamellar microemulsion adjacent to a planar wall. The Seifert concept could successfully be transferred to the new problems.

  16. Genetic organization of the unc-22 IV gene and the adjacent region in Caenorhabditis elegans.

    Science.gov (United States)

    Rogalski, T M; Baillie, D L

    1985-01-01

    The genetic organization of the region immediately adjacent to the unc-22 IV gene in Caenorhabditis elegans has been studied. We have identified twenty essential genes in this interval of approximately 1.5-map units on Linkage Group IV. The mutations that define these genes were positioned by recombination mapping and complementation with several deficiencies. With few exceptions, the positions obtained by these two methods agreed. Eight of the twenty essential genes identified are represented by more than one allele. Three possible internal deletions of the unc-22 gene have been located by intra-genic mapping. In addition, the right end point of a deficiency or an inversion affecting the adjacent genes let-56 and unc-22 has been positioned inside the unc-22 gene.

  17. The Impact of a Shopping Centre on the Value of Adjacent Residential Properties

    OpenAIRE

    M. C. Sale

    2015-01-01

    One of the most significant changes in the South African retail landscape over the past few decades is the increase in the number and size of retail shopping centres situated in, or close to, residential areas. These shopping centres have the potential to generate both positive and negative externalities which may, in turn, be capitalised into adjacent residential property prices. However, policy makers are still unsure as to the effect of commercial land uses such as shopping centres on surr...

  18. Core-adjacent instrumentation systems for pebble bed reactors for process heat application - state of planning

    International Nuclear Information System (INIS)

    Benninghofen, G.; Serafin, N.; Spillekothen, H.G.; Hecker, R.; Brixy, H.; Serpekian, T.

    1982-06-01

    Planning and theoretical/experimental development work for core surveillance instrumentation systems is being performed to meet requirements of pebble bed reactors for process heat application. Detailed and proved instrumentation concepts are now available for the core-adjacent instrumentation systems. The current work and the results of neutron flux measurements at high temperatures are described. Operation devices for long-term accurate gas outlet temperature measurements up to approximately 1423 deg. K will also be discussed. (author)

  19. An implant periapical lesion associated with an endodontic-periodontic lesion of an adjacent molar

    Directory of Open Access Journals (Sweden)

    Ting-An Chou

    2010-09-01

    Full Text Available Adjacent natural teeth with untreated pulpal or periodontal pathology may be a potential risk for implant infection. We report a rare case of an implant periapical lesion (IPL possibly caused by direct extension of a periradicular lesion of an adjacent tooth. A 40-year-old female patient, who had previously received three implants on the edentulous areas of teeth 16, 36 and 46, had a recurrent infection over the lower left second molar area for 2 years. A periapical radiograph revealed incomplete root canal treatment and an infrabony defect on the mesial side of the lower left second molar; the defect extended to the apical third of the adjacent implant on tooth 36. Open flap debridement was performed 1 year after implant placement, but pain and swelling persisted for another year. Therefore, the second molar was extracted at the patient's request. The patient was unable to seek earlier and prompt treatment as she was abroad; therefore, we were able to observe the progression of severity in the IPL. One year after the extraction, the symptoms had subsided, and a periapical radiograph showed that the radiolucent lesion had decreased in size. She was followed for another 1.5 years and showed marked improvement. In this case, the IPL probably originated from the endodontic-periodontic problem of the adjacent molar, and the infected implant was saved by removing the infection source. We also discuss the treatment and prognosis of IPLs. To prevent the occurrence of an IPL, it is important to evaluate the pulpal and periodontal status of the teeth near the implant site when making a comprehensive treatment plan for an implant.

  20. World cup soccer players tend to be born with sun and moon in adjacent zodiacal signs

    Science.gov (United States)

    Verhulst, J

    2000-01-01

    The ecliptic elongation of the moon with respect to the sun does not show uniform distribution on the birth dates of the 704 soccer players selected for the 1998 World Cup. However, a uniform distribution is expected on astronomical grounds. The World Cup players show a very pronounced tendency (p = 0.00001) to be born on days when the sun and moon are in adjacent zodiacal signs. Key Words: soccer; World Cup; astrology; moon PMID:11131239

  1. Risk factors for adjacent segment degeneration after surgical correction of degenerative lumbar scoliosis

    Directory of Open Access Journals (Sweden)

    Kee-yong Ha

    2013-01-01

    Full Text Available Background: Degenerative lumbar scoliosis surgery can lead to development of adjacent segment degeneration (ASD after lumbar or thoracolumbar fusion. Its incidence, risk factors, morbidity and correlation between radiological and clinical symptoms of ASD have no consensus. We evaluated the correlation between the occurrence of radiologic adjacent segment disease and certain imperative parameters. Materials and Methods: 98 patients who had undergone surgical correction and lumbar/thoracolumbar fusion with pedicle screw instrumentation for degenerative lumbar scoliosis with a minimum 5 year followup were included in the study. We evaluated the correlation between the occurrence of radiologic adjacent segment disease and imperative patient parameters like age at operation, sex, body mass index (BMI, medical comorbidities and bone mineral density (BMD. The radiological parameters taken into consideration were Cobb′s angle, angle type, lumbar lordosis, pelvic incidence, intercristal line, preoperative existence of an ASD on plain radiograph and magnetic resonance imaging (MRI and surgical parameters were number of the fusion level, decompression level, floating OP (interlumbar fusion excluding L5-S1 level and posterolateral lumbar interbody fusion (PLIF. Clinical outcomes were assessed with the Visual Analogue Score (VAS and Oswestry Disability Index (ODI. Results: ASD was present in 44 (44.9% patients at an average period of 48.0 months (range 6-98 months. Factors related to occurrence of ASD were preoperative existence of disc degeneration (as revealed by MRI and age at operation ( P = 0.0001, 0.0364. There were no statistically significant differences between radiological adjacent segment degeneration and clinical results (VAS, P = 0.446; ODI, P = 0.531. Conclusions: Patients over the age of 65 years and with preoperative disc degeneration (as revealed by plain radiograph and MRI were at a higher risk of developing ASD.

  2. Finite element analysis of skirted foundation adjacent to sand slope under earthquake loading

    OpenAIRE

    Azzam, W.R.

    2015-01-01

    This paper reports the application of using a skirted foundation system to study the behavior of foundations with structural skirts adjacent to a sand slope and subjected to earthquake loading. The effect of the adopted skirts to safeguard foundation and slope from collapse is studied. The skirts effect on controlling horizontal soil movement and decreasing pore water pressure beneath foundations and beside the slopes during earthquake is investigated. This technique is investigated numerical...

  3. IMMEDIATE RECIPROCAL CHANGES AT ADJACENT LEVEL FOLLOWING SINGLE-LEVEL ALIF

    OpenAIRE

    Uribe, Enrique Vargas; Amaral, Rodrigo; Marchi, Luis; Jensen, Rubens; Oliveira, Leonardo; Fortti, Fernanda; Coutinho, Etevaldo; Pimenta, Luiz

    2015-01-01

    Objective : To assess the segmental sagittal parameters and the adjacent mobile segment after interbody fusion by anterior approach in single-level L5-S1. Methods : Retrospective study. Inclusion: Interbody fusion by anterior approach (10°/15° angle), due to DDD, low-grade spondylolisthesis and/or stenosis without prior lumbar fusion. Thirty-five cases were included (25 women; mean age 47±15 years). Analysis of lumbar radiographs were performed preoperatively and 3 months after surgery. The ...

  4. Environmental Settings and Harmful Algal Blooms in the Sea Area Adjacent to the Changjiang River Estuary

    OpenAIRE

    Zhou, Mingjiang

    2010-01-01

    The characteristics of the environmental settings of the sea area adjacent to the Changjiang River estuary include complex currents and water masses, the diluted water plume and its redirection, upwelling, front, and nutrients and their sources. The Changjiang River estuary characteristics also include the phytoplankton community, which can affect the growth, migration, assembling, resting and competition of algae to form red tides in this area.. The features of red tide events recorded in th...

  5. Experimental study on brain injury in Beagle dogs caused by adjacent cabin explosion in warship

    Directory of Open Access Journals (Sweden)

    Yan-teng LI

    2017-04-01

    Full Text Available Objective  Through the establishment of adjacent cabin blast injury model of Beagle dog, to investigate the pathophysiological changes in the experimental animals in this scenario, then speculate on the mechanisms of injury. Methods  Several adjacent cabins were built in the same size with the real warship. Seven Beagle dogs were subjected to injuries from the explosion, from whom one was selected randomly to implant intracranial pressure transducers before blast, the others were tested on the pathophysiological changes after blast. The dogs were mounted on the platform of a cabinet in the adjacent cabin, subjected to injury from 650g bare TNT explosive blast. The transducers recorded the value of space and intracranial shock wave pressure. Following blast treatment, the serum levels of IL -6, IL -8, neuron specific enolase (NSE, brain and chest CT and pathological changes of the brain tissue were observed. Results  Serum levels of IL-6, IL-8 and NSE were elevated to varying degrees after blast. All of them increased significantly at different time points after blast (P<0.05. Brain and chest CT examinations did not show any significant positive results. Pathological results showed that there was a little necrosis in the brain, some neurons had karyopycnosis, karyolysis or disappearance of the nucleoli, and the cell boundaries were blurred. The blast wave was blocked greatly by the scalp and skull (about 90%, but could still penetrate them and cause brain injuries. Conclusions  Explosion in the adjacent cabin causes mainly mild traumatic brain injuries. Blast wave can be blocked by the scalp and skull greatly. DOI: 10.11855/j.issn.0577-7402.2017.03.11

  6. Ground-water resources in the tri-state region adjacent to the Lower Delaware River

    Science.gov (United States)

    Barksdale, Henry C.; Greenman, David W.; Lang, Solomon Max; Hilton, George Stockbridge; Outlaw, Donald E.

    1958-01-01

    The purpose of this report is to appraise and evaluate the groundwater resources of a tri-state region adjacent to the lower Delaware River that is centered around Philadelphia, Pa., and Camden, N. J., and includes Wilmington, Del., and Trenton, N.J. Specifically, the region includes New Castle County, Del.; Burlington, Camden, Gloucester, Mercer, and Salem Counties in New Jersey; and Bucks, Chester, Delaware, Montgomery, and Philadelphia Counties in Pennsylvania.

  7. Ossificans myositis: inflammatory changes and contrast enhancement of adjacent bone shown by MR imaging

    International Nuclear Information System (INIS)

    David, H.; Jolles, E.; Le Friant, G.; Silvestre, A.; Sarrazin, J.L.; Gordoliani, Y.S.

    1995-01-01

    The authors report a case of ossificans myositis, in which magnetic resonance imaging (MRI) showed inflammatory changes of the adjacent bone. T 1 weighted fat saturation sequence with gadolinium injection showed enhancement of medullary and cortical bone. This potentially mistaking pattern must be known, to avoid mis diagnosing with malignant osseous tumor, specially before achievement of the characteristic pattern of zonal maturation and its calcified rim. (authors). 15 refs., 6 figs

  8. Deer use of riparian zones and adjacent pine plantations in Texas

    Science.gov (United States)

    Micah L. Poteet; Ronald E. Thill; R. Montague Whiting; R. Lee Rayburn

    1996-01-01

    The authors monitored white-tailed deer (Odocoileus virginianus) use of riparian zones (RZ’s) and adjacent pine plantations of 3 age classes (young, 1 to 3 years old; intermediate, 5 to 7 years old; and older, 9 to 13 years old) using radio telemetry for 2 years on a 1,300 ha study area near Alto, TX. Riparian zones comprised 22.0 percent of the area; young,...

  9. Relevance of adjacent joint imaging in the evaluation of ankle fractures.

    Science.gov (United States)

    Antoci, Valentin; Patel, Shaun P; Weaver, Michael J; Kwon, John Y

    2016-10-01

    Routinely obtaining adjacent joint radiographs when evaluating patients with ankle fractures may be of limited clinical utility and an unnecessary burden, particularly in the absence of clinical suspicion for concomitant injuries. One thousand, three hundred and seventy patients who sustained ankle fractures over a 5-year period presenting to two level 1 trauma centers were identified. Medical records were retrospectively reviewed for demographics, physical examination findings, and radiographic information. Analyses included descriptive statistics along with sensitivity and predictive value calculations for the presence of adjacent joint fracture. Adjacent joint imaging (n=1045 radiographs) of either the knee or foot was obtained in 873 patients (63.7%). Of those, 75/761 patients (9.9%) demonstrated additional fractures proximal to the ankle joint, most commonly of the proximal fibula. Twenty-two of 284 (7.7%) demonstrated additional fractures distal to the ankle joint, most commonly of the metatarsals. Tenderness to palpation demonstrated sensitivities of 0.92 and 0.77 and positive predictive values of 0.94 and 0.89 for the presence of proximal and distal fractures, respectively. Additionally, 19/22 (86.4%) of patients sustaining foot fractures had their injury detectable on initial ankle X-rays. Overall, only 5.5% (75/1370) of patients sustained fractures proximal to the ankle and only 0.2% (3/1370) of patients had additional foot fractures not evident on initial ankle X-rays. The addition of adjacent joint imaging for the evaluation of patients sustaining ankle fractures is low yield. As such, patient history, physical examination, and clinical suspicion should direct the need for additional X-rays. Level IV. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Zhanjun; Liu, Yu; Shen, Yuandeng [Yunnan Observatories, Chinese Academy of Sciences, Kunming, 650216 (China); Elmhamdi, Abouazza; Kordi, Ayman S. [Department of Physics and Astronomy, King Saud University, P.O. Box 2455, 11451 (Saudi Arabia); Su, Jiangtao [University of Chinese Academy of Sciences, Beijing 100049 (China); Liu, Ying D., E-mail: ydshen@ynao.ac.cn [State Key Laboratory of Space Weather, Chinese Academy of Sciences, Beijing 100190 (China)

    2017-08-20

    We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory . The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observed at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s{sup −1}. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.

  11. Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification.

    Science.gov (United States)

    O'Neill, B; Grossman, J; Tsai, M T; Gomes, J E; Lehmann, J; Peterson, J; Neves, E; Thies, J E

    2009-07-01

    Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.

  12. PROSPECTIVE STUDY OF HISTOLOGICAL PROLIFERATIVE CHANGES IN ADJACENT AREAS OF BREAST CANCER

    Directory of Open Access Journals (Sweden)

    Rema Nair Sarkar

    2016-11-01

    Full Text Available BACKGROUND Breast cancer remains a global health problem with an increasing incidence. Proliferative breast diseases are recognised as one of the risk factors in the development of carcinoma. This study was undertaken to know the frequency of proliferative lesions and other lesions in association with breast carcinomas in mastectomy specimens. MATERIALS AND METHODS 100 cases of excised carcinoma breast sent to the Department of Pathology for a three-year period at tertiary care centre was thoroughly examined and changes adjacent to the tumour was recorded and tissue was subjected for histopathological examination and results tabulated. RESULTS Infiltrating duct cell carcinoma, Not Otherwise Specified (NOS type was present in 89% of cases. Among the associated lesions, nonproliferative lesions constituted 16%, proliferative breast disease without atypia 29%, proliferative breast disease with atypia 10% and others 45%. Fibrocystic disease constituted 14% of cases, epithelial hyperplasia 15%, sclerosing adenosis 12% and atypical ductal hyperplasia in 10% of cases. Other types of associated lesions were duct carcinoma in situ in 4 cases. CONCLUSION Proliferative lesions adjacent to carcinoma breast were seen in 39% of cases. Fibrocystic disease, epithelial hyperplasia, sclerosing adenosis and atypical ductal hyperplasia being the commonest lesions adjacent to carcinoma breast in the present study.

  13. Interaction between two adjacent grounded sources in frequency domain semi-airborne electromagnetic survey.

    Science.gov (United States)

    Zhou, Haigen; Lin, Jun; Liu, Changsheng; Kang, Lili; Li, Gang; Zeng, Xinsen

    2016-03-01

    Multi-source and multi-frequency emission method can make full use of the valuable and short flight time in frequency domain semi-airborne electromagnetic (FSAEM) exploration, which has potential to investigate the deep earth structure in complex terrain region. Because several sources are adjacent in multi-source emission method, the interaction of different sources should be considered carefully. An equivalent circuit model of dual-source is established in this paper to assess the interaction between two individual sources, where the parameters are given with the typical values based on the practical instrument system and its application. By simulating the output current of two sources in different cases, the influence from the adjacent source is observed clearly. The current waveforms show that the mutual resistance causes the fluctuation and drift in another source and that the mutual inductance causes transient peaks. A field test with dual-source was conducted to certify the existence of interaction between adjacent sources. The simulation of output current also shows that current errors at low frequency are mainly caused by the mutual resistance while those at high frequency are mainly due to the mutual inductance. Increasing the distance between neighboring sources is a proposed measure to reduce the emission signal errors with designed ones. The feasible distance is discussed in the end. This study gives a useful guidance to lay multi sources to meet the requirement of measurement accuracy in FSAEM survey.

  14. Late Permian to Triassic intraplate orogeny of the southern Tianshan and adjacent regions, NW China

    Directory of Open Access Journals (Sweden)

    Wei Ju

    2014-01-01

    Based on previous studies and recent geochronogical data, we suggest that the final collision between the Tarim Craton and the North Asian continent occurred during the late Carboniferous. Therefore, the Permian was a period of intracontinental environment in the southern Tianshan and adjacent regions. We propose that an earlier, small-scale intraplate orogenic stage occurred in late Permian to Triassic time, which was the first intraplate process in the South Tianshan Orogen and adjacent regions. The later large-scale and well-known Neogene to Quaternary intraplate orogeny was induced by the collision between the India subcontinent and the Eurasian plate. The paper presents a new evolutionary model for the South Tianshan Orogen and adjacent regions, which includes seven stages: (I late Ordovician–early Silurian opening of the South Tianshan Ocean; (II middle Silurian–middle Devonian subduction of the South Tianshan Ocean beneath an active margin of the North Asian continent; (III late Devonian–late Carboniferous closure of the South Tianshan Ocean and collision between the Kazakhstan-Yili and Tarim continental blocks; (IV early Permian post-collisional magmatism and rifting; (V late Permian–Triassic the first intraplate orogeny; (VI Jurassic–Palaeogene tectonic stagnation and (VII Neocene–Quaternary intraplate orogeny.

  15. Correction of thickness measurement errors for two adjacent sheet structures in MR images

    International Nuclear Information System (INIS)

    Cheng Yuanzhi; Wang Shuguo; Sato, Yoshinobu; Nishii, Takashi; Tamura, Shinichi

    2007-01-01

    We present a new method for measuring the thickness of two adjacent sheet structures in MR images. In the hip joint, in which the femoral and acetabular cartilages are adjacent to each other, a conventional measurement technique based on the second derivative zero crossings (called the zero-crossings method) can introduce large underestimation errors in measurements of cartilage thickness. In this study, we have developed a model-based approach for accurate thickness measurement. We model the imaging process for two adjacent sheet structures, which simulate the two articular cartilages in the hip joint. This model can be used to predict the shape of the intensity profile along the sheet normal orientation. Using an optimization technique, the model parameters are adjusted to minimize the differences between the predicted intensity profile and the actual intensity profiles observed in the MR data. The set of model parameters that minimize the difference between the model and the MR data yield the thickness estimation. Using three phantoms and one normal cadaveric specimen, the usefulness of the new model-based method is demonstrated by comparing the model-based results with the results generated using the zero-crossings method. (author)

  16. Differential transcriptional profiling of damaged and intact adjacent dorsal root ganglia neurons in neuropathic pain.

    Directory of Open Access Journals (Sweden)

    A K Reinhold

    Full Text Available Neuropathic pain, caused by a lesion in the somatosensory system, is a severely impairing mostly chronic disease. While its underlying molecular mechanisms are not thoroughly understood, neuroimmune interactions as well as changes in the pain pathway such as sensitization of nociceptors have been implicated. It has been shown that not only are different cell types involved in generation and maintenance of neuropathic pain, like neurons, immune and glial cells, but, also, intact adjacent neurons are relevant to the process. Here, we describe an experimental approach to discriminate damaged from intact adjacent neurons in the same dorsal root ganglion (DRG using differential fluorescent neuronal labelling and fluorescence-activated cell sorting (FACS. Two fluorescent tracers, Fluoroemerald (FE and 1-dioctadecyl-3,3,3,3-tetramethylindocarbocyanine perchlorate (DiI, were used, whose properties allow us to distinguish between damaged and intact neurons. Subsequent sorting permitted transcriptional analysis of both groups. Results and qPCR validation show a strong regulation in damaged neurons versus contralateral controls as well as a moderate regulation in adjacent neurons. Data for damaged neurons reveal an mRNA expression pattern consistent with established upregulated genes like galanin, which supports our approach. Moreover, novel genes were found strongly regulated such as corticotropin-releasing hormone (CRH, providing novel targets for further research. Differential fluorescent neuronal labelling and sorting allows for a clear distinction between primarily damaged neuropathic neurons and "bystanders," thereby facilitating a more detailed understanding of their respective roles in neuropathic processes in the DRG.

  17. fMRI Evidence of Acupoints Specificity in Two Adjacent Acupoints

    Directory of Open Access Journals (Sweden)

    Hua Liu

    2013-01-01

    Full Text Available Objectives. Acupoint specificity is the foundation of acupuncture treatment. The aim of this study is to investigate whether the acupoint specificity exists in two adjacent acupoints. Design and Setting. Two adjacent real acupoints, LR3 (Taichong and ST44 (Neiting, and a nearby nonacupoint were selected. Thirty-three health volunteers were divided into three groups in random order, and each group only received acupuncture at one of the three points. While they received acupuncture, fMRI scan was performed. Results. The common cerebral activated areas responding to LR3 and ST44 included the contralateral primary somatosensory area (SI and ipsilateral cerebellum. Acupuncture at LR3 specifically activated contralateral middle occipital gyrus, ipsilateral medial frontal gyrus, superior parietal lobe, middle temporal gyrus, rostral anterior cingulate cortex (rACC, lentiform nucleus, insula, and contralateral thalamus. Stimulation at ST44 selectively activated ipsilateral secondary somatosensory area (SII, contralateral middle frontal gyrus, inferior frontal gyrus, lingual gyrus, lentiform nucleus, and bilateral posterior cingulate cortex (PCC. Conclusions. Acupuncture at adjacent acupoints elicits distinct cerebral activation patterns, and those specific patterns might be involved in the mechanism of the specific therapeutic effects of different acupoints.

  18. Matrix intensification alters avian functional group composition in adjacent rainforest fragments.

    Directory of Open Access Journals (Sweden)

    Justus P Deikumah

    Full Text Available Conversion of farmland land-use matrices to surface mining is an increasing threat to the habitat quality of forest remnants and their constituent biota, with consequences for ecosystem functionality. We evaluated the effects of matrix type on bird community composition and the abundance and evenness within avian functional groups in south-west Ghana. We hypothesized that surface mining near remnants may result in a shift in functional composition of avifaunal communities, potentially disrupting ecological processes within tropical forest ecosystems. Matrix intensification and proximity to the remnant edge strongly influenced the abundance of members of several functional guilds. Obligate frugivores, strict terrestrial insectivores, lower and upper strata birds, and insect gleaners were most negatively affected by adjacent mining matrices, suggesting certain ecosystem processes such as seed dispersal may be disrupted by landscape change in this region. Evenness of these functional guilds was also lower in remnants adjacent to surface mining, regardless of the distance from remnant edge, with the exception of strict terrestrial insectivores. These shifts suggest matrix intensification can influence avian functional group composition and related ecosystem-level processes in adjacent forest remnants. The management of matrix habitat quality near and within mine concessions is important for improving efforts to preserveavian biodiversity in landscapes undergoing intensification such as through increased surface mining.

  19. Antibacterial Activity of Orthodontic Cement Containing Quaternary Ammonium Polyethylenimine Nanoparticles Adjacent to Orthodontic Brackets.

    Science.gov (United States)

    Sharon, Eldad; Sharabi, Revital; Eden, Adi; Zabrovsky, Asher; Ben-Gal, Gilad; Sharon, Esi; Pietrokovski, Yoav; Houri-Haddad, Yael; Beyth, Nurit

    2018-03-27

    Enamel demineralization is a common problem found in patients using orthodontic devices, such as orthodontic braces. It was found that Streptoccocus mutans growth increases adjacent to orthodontic devices, which may result in caries development. Incorporated antibacterial quaternary ammonium polyethylenimine (QPEI) nanoparticles were previously shown to be highly efficacious against various bacteria. Combining antibacterial materials in orthodontic cement may be advantageous to prevent bacterial outgrowth adjacent to orthodontic brackets. The aim was to evaluate the efficiency of orthodontic cement containing QPEI nanoparticles in reducing S. mutans and Lactobacillus casei outgrowth adjacent to orthodontic brackets. Orthodontic brackets were bonded to the buccal surfaces of extracted lower incisors. The antibacterial effect on S. mutans and L. casei outgrowth of Neobond bracket adhesive orthodontic cement with and without QPEI nanoparticles was compared. The antibacterial effect was evaluated using crystal violet staining and bacterial count (CFU/mL). The teeth in the experimental group, with the QPEI nanoparticles cement, showed significantly lower optical density (OD) values and CFU counts of S. mutans and L. casei than the teeth in the control group ( p brackets.

  20. Dlx proteins position the neural plate border and determine adjacent cell fates.

    Science.gov (United States)

    Woda, Juliana M; Pastagia, Julie; Mercola, Mark; Artinger, Kristin Bruk

    2003-01-01

    The lateral border of the neural plate is a major source of signals that induce primary neurons, neural crest cells and cranial placodes as well as provide patterning cues to mesodermal structures such as somites and heart. Whereas secreted BMP, FGF and Wnt proteins influence the differentiation of neural and non-neural ectoderm, we show here that members of the Dlx family of transcription factors position the border between neural and non-neural ectoderm and are required for the specification of adjacent cell fates. Inhibition of endogenous Dlx activity in Xenopus embryos with an EnR-Dlx homeodomain fusion protein expands the neural plate into non-neural ectoderm tissue whereas ectopic activation of Dlx target genes inhibits neural plate differentiation. Importantly, the stereotypic pattern of border cell fates in the adjacent ectoderm is re-established only under conditions where the expanded neural plate abuts Dlx-positive non-neural ectoderm. Experiments in which presumptive neural plate was grafted to ventral ectoderm reiterate induction of neural crest and placodal lineages and also demonstrate that Dlx activity is required in non-neural ectoderm for the production of signals needed for induction of these cells. We propose that Dlx proteins regulate intercellular signaling across the interface between neural and non-neural ectoderm that is critical for inducing and patterning adjacent cell fates.

  1. Growth and decline of shoreline industry in Sydney estuary (Australia) and influence on adjacent estuarine sediments.

    Science.gov (United States)

    Birch, G F; Lean, J; Gunns, T

    2015-06-01

    Sydney estuary (Australia), like many urbanised waterways, is degraded due to an extended history of anthropogenic activity. Two major sources of contamination to this estuary are discharge by former shoreline industries and historic and contemporary catchment stormwater. The objectives of the present study were to document changes in shoreline land use from European settlement to the present day and determine the influence of this trend on the metal content of adjacent estuarine sediments. Temporal analysis of land use for seven time horizons between 1788 and 2010 showed rapid expansion of industry along much of the Sydney estuary foreshore soon after European settlement due to the benefits of easy and inexpensive access and readily available water for cooling and power. Shoreline industry attained maximum development in 1978 (32-km length) and declined rapidly to the present-day (9-km length) through redevelopment of industrial sites into medium- to high-density, high-value residential housing. Cores taken adjacent to 11 long-term industrial sites showed that past industrial practices contributed significantly to contamination of estuarine sediment. Subsurface metal concentrations were up to 35 times that of present-day surface sediment and over 100 times greater than natural background concentrations. Sedimentation rates for areas adjacent to shoreline industry were between 0.6 and 2.5 cm/year, and relaxation times were estimated at 50 to 100 years. Natural relaxation and non-disturbance of sediments may be the best management practice in most locations.

  2. 33 CFR 334.85 - New York Harbor, adjacent to the Stapleton Naval Station, Staten Island, New York; restricted area.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false New York Harbor, adjacent to the Stapleton Naval Station, Staten Island, New York; restricted area. 334.85 Section 334.85 Navigation and... RESTRICTED AREA REGULATIONS § 334.85 New York Harbor, adjacent to the Stapleton Naval Station, Staten Island...

  3. 30 CFR 785.19 - Surface coal mining and reclamation operations on areas or adjacent to areas including alluvial...

    Science.gov (United States)

    2010-07-01

    ... alluvial valley floor exists if it finds that— (i) Unconsolidated streamlaid deposits holding streams are... on areas or adjacent to areas including alluvial valley floors in the arid and semiarid areas west of....19 Surface coal mining and reclamation operations on areas or adjacent to areas including alluvial...

  4. 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

  5. Transposable elements and G-quadruplexes

    Czech Academy of Sciences Publication Activity Database

    Kejnovský, Eduard; Tokan, Viktor; Lexa, M.

    2015-01-01

    Roč. 23, č. 3 (2015), s. 615-623 ISSN 0967-3849 R&D Projects: GA ČR(CZ) GA15-02891S Institutional support: RVO:68081707 Keywords : TRINUCLEOTIDE REPEAT DNA * LTR RETROTRANSPOSONS * BINDING PROTEIN Subject RIV: BO - Biophysics Impact factor: 2.590, year: 2015

  6. Expression of protein-coding genes embedded in ribosomal DNA

    DEFF Research Database (Denmark)

    Johansen, Steinar D; Haugen, Peik; Nielsen, Henrik

    2007-01-01

    Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that e...... in the nucleolus....

  7. MR imaging of lumbar spondylolysis: signal intensity change in the pars interarticularis and adjacent structures

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Suk Whan; Lee, Ghi Jai; Shim, Jae Chan; Kim, Ho Kyun [Inje Univ. College of Medicine, Kimhae (Korea, Republic of)

    2001-05-01

    To assess changes in MR signal intensity in the pars interarticularis and adjacent structures in patients with lumbar spondylolysis. The MR images of 36 patients with lumbar spondylolysis, confirmed by plain radiographs, were retrospectively analyzed. Using a 1.0T unit, we evaluated the signal intensity of a total of 216 parts interarticulares and adjacent structures from L3 to L5, as seen on sagittal images, and differences between areas with and without spondylolysis. The signal intensity of T1-and T2-weighted images was graded 0(more hypointense than spinal body), 1(as isointense as spinal body), 2(more hyperintense than spinal body and more hypointense than epidural fat), or 3(as isointense as epidural fat). Signal intensity change in endplates and degree of spondylolisthesis were analyzed, and the relationship between these factors was determined. Spondylolysis was noted at L5 in 61 cases, at L4 in 22, and of L3 in no case. In three cases spondylolysis was unilateral, and in the remainder it was bilateral. The degree of signal intensity was the same on T1-and T2-weighted images, and no case was grade 0. Eighty-six of 133 areas without spondylolysis were grade 1, 43 were grade 2, and four were grade 3. In 42 of 47 cases, signal intensity change was localized at pedicles. Among 83 areas with spondylolysis,on the other hand, nine were grade 1, 48 were grade 2, and 26 were grade 3. Signal intensity change was most commonly observed at the pars interarticularis, pedicle, and lamina(50/74)({rho}<0.001). Signal intensity change at the pars interarticularis and adjacent structures was accompanied in most cases by degenerative endplate change(10/11) and spondylolisthesis(11/13)({rho}<0.001). In patients with spondylolysis, signal intensity was frequently higher at the pars interarticularis and adjacent structures, and is thought to have a close relationship with degenerative endplate change and spondylolisthesis. Increases in signal intensity at the pars

  8. MR imaging of lumbar spondylolysis: signal intensity change in the pars interarticularis and adjacent structures

    International Nuclear Information System (INIS)

    Jang, Suk Whan; Lee, Ghi Jai; Shim, Jae Chan; Kim, Ho Kyun

    2001-01-01

    To assess changes in MR signal intensity in the pars interarticularis and adjacent structures in patients with lumbar spondylolysis. The MR images of 36 patients with lumbar spondylolysis, confirmed by plain radiographs, were retrospectively analyzed. Using a 1.0T unit, we evaluated the signal intensity of a total of 216 parts interarticulares and adjacent structures from L3 to L5, as seen on sagittal images, and differences between areas with and without spondylolysis. The signal intensity of T1-and T2-weighted images was graded 0(more hypointense than spinal body), 1(as isointense as spinal body), 2(more hyperintense than spinal body and more hypointense than epidural fat), or 3(as isointense as epidural fat). Signal intensity change in endplates and degree of spondylolisthesis were analyzed, and the relationship between these factors was determined. Spondylolysis was noted at L5 in 61 cases, at L4 in 22, and of L3 in no case. In three cases spondylolysis was unilateral, and in the remainder it was bilateral. The degree of signal intensity was the same on T1-and T2-weighted images, and no case was grade 0. Eighty-six of 133 areas without spondylolysis were grade 1, 43 were grade 2, and four were grade 3. In 42 of 47 cases, signal intensity change was localized at pedicles. Among 83 areas with spondylolysis,on the other hand, nine were grade 1, 48 were grade 2, and 26 were grade 3. Signal intensity change was most commonly observed at the pars interarticularis, pedicle, and lamina(50/74)(ρ<0.001). Signal intensity change at the pars interarticularis and adjacent structures was accompanied in most cases by degenerative endplate change(10/11) and spondylolisthesis(11/13)(ρ<0.001). In patients with spondylolysis, signal intensity was frequently higher at the pars interarticularis and adjacent structures, and is thought to have a close relationship with degenerative endplate change and spondylolisthesis. Increases in signal intensity at the pars interarticularis and

  9. Sagittal Alignment As a Predictor of Clinical Adjacent Segment Pathology requiring Surgery after Anterior Cervical Arthrodesis

    Science.gov (United States)

    Park, Moon Soo; Kelly, Michael P.; Lee, Dong-Ho; Min, Woo-Kie; Rahman, Ra’Kerry K.; Riew, K. Daniel

    2014-01-01

    BACKGROUND CONTEXT Postoperative malalignment of the cervical spine may alter cervical spine mechanics, and put patients at risk for clinical adjacent segment pathology requiring surgery. PURPOSE To investigate whether a relationship exists between cervical spine sagittal alignment and clinical adjacent segment pathology requiring surgery (CASP-S) following anterior cervical fusion (ACF). STUDY DESIGN Retrospective matched study. PATIENT SAMPLE One hundred twenty two patients undergoing ACF from 1996 to 2008 were identified, with a minimum of 2 year follow-up. OUTCOME MEASURES Radiographs were reviewed to measure the sagittal alignment using C2 and C7 sagittal plumb lines, distance from the fusion mass plumb line to the C2 and C7 plumb lines, the alignment of the fusion mass, caudally adjacent disc angle, the sagittal slope angle of the superior endplate of the vertebra caudally adjacent to the fusion mass, T1 sagittal angle, overall cervical sagittal alignment, and curve patterns by Katsuura classification. METHODS One hundred twenty two patients undergoing ACF from 1996 to 2008 were identified, with a minimum of 1 year follow-up. Patients were divided into groups according to the development of CASP requiring surgery (Control / CASP-S) and by number/location of levels fused. Radiographs were reviewed to measure the sagittal alignment using C2 and C7 sagittal plumb lines, distance from the fusion mass plumb line to the C2 and C7 plumb lines, the alignment of the fusion mass, caudally adjacent disc angle, the sagittal slope angle of the superior endplate of the vertebra caudally adjacent to the fusion mass, T1 sagittal angle, overall cervical sagittal alignment, and curve patterns by Katsuura classification. Appropriate statistical tests were performed to calculate relationships between the variables and the development of CASP-S. No funds were received in support of this work. No benefits in any form have been or will be received from a commercial party related

  10. Hybrid dynamic stabilization: a biomechanical assessment of adjacent and supraadjacent levels of the lumbar spine.

    Science.gov (United States)

    Mageswaran, Prasath; Techy, Fernando; Colbrunn, Robb W; Bonner, Tara F; McLain, Robert F

    2012-09-01

    The object of this study was to evaluate the effect of hybrid dynamic stabilization on adjacent levels of the lumbar spine. Seven human spine specimens from T-12 to the sacrum were used. The following conditions were implemented: 1) intact spine; 2) fusion of L4-5 with bilateral pedicle screws and titanium rods; and 3) supplementation of the L4-5 fusion with pedicle screw dynamic stabilization constructs at L3-4, with the purpose of protecting the L3-4 level from excessive range of motion (ROM) and to create a smoother motion transition to the rest of the lumbar spine. An industrial robot was used to apply continuous pure moment (± 2 Nm) in flexion-extension with and without a follower load, lateral bending, and axial rotation. Intersegmental rotations of the fused, dynamically stabilized, and adjacent levels were measured and compared. In flexion-extension only, the rigid instrumentation at L4-5 caused a 78% decrease in the segment's ROM when compared with the intact specimen. To compensate, it caused an increase in motion at adjacent levels L1-2 (45.6%) and L2-3 (23.2%) only. The placement of the dynamic construct at L3-4 decreased the operated level's ROM by 80.4% (similar stability as the fusion at L4-5), when compared with the intact specimen, and caused a significant increase in motion at all tested adjacent levels. In flexion-extension with a follower load, instrumentation at L4-5 affected only a subadjacent level, L5-sacrum (52.0%), while causing a reduction in motion at the operated level (L4-5, -76.4%). The dynamic construct caused a significant increase in motion at the adjacent levels T12-L1 (44.9%), L1-2 (57.3%), and L5-sacrum (83.9%), while motion at the operated level (L3-4) was reduced by 76.7%. In lateral bending, instrumentation at L4-5 increased motion at only T12-L1 (22.8%). The dynamic construct at L3-4 caused an increase in motion at T12-L1 (69.9%), L1-2 (59.4%), L2-3 (44.7%), and L5-sacrum (43.7%). In axial rotation, only the placement of

  11. Association of endogenous retroviruses and long terminal repeats with human disorders

    Directory of Open Access Journals (Sweden)

    Iyoko eKatoh

    2013-09-01

    Full Text Available Since the human genome sequences became available in 2001, our knowledge about the human transposable elements which comprise ~40% of the total nucleotides has been expanding. Non- LTR (long terminal repeat retrotransposons are actively transposing in the present-day human genome, and have been found to cause ~100 identified clinical cases of varied disorders. In contrast, almost all of the human endogenous retroviruses (HERVs originating from ancient infectious retroviruses lost their infectivity and transposing activity at various times before the human-chimpanzee speciation (~6 million years ago, and no known HERV is presently infectious. Insertion of HERVs and mammalian apparent LTR retrotransposons (MaLRs into the chromosomal DNA influenced a number of host genes in various modes during human evolution. Apart from the aspect of genome evolution, HERVs and solitary LTRs being suppressed in normal biological processes can potentially act as extra transcriptional apparatuses of cellular genes by re-activation in individuals. There has been a reasonable prediction that aberrant LTR activation could trigger malignant disorders and autoimmune responses if epigenetic changes including DNA hypomethylation occur in somatic cells. Evidence supporting this hypothesis has begun to emerge only recently: a MaLR family LTR activation in the pathogenesis of Hodgkin’s lymphoma and a HERV-E antigen expression in an anti-renal cell carcinoma immune response. This mini review addresses the impacts of the remnant-form LTR retrotransposons on human pathogenesis.

  12. Circummandibular Wires for Treatment of Dentoalveolar Fractures Adjacent to Edentulous Areas: A Report of Two Cases.

    Science.gov (United States)

    Maloney, Karl

    2015-09-01

    In general, dentoalveolar fractures are a common injury seen in emergency departments, dental offices, and oral and maxillofacial surgery practices. These injuries can be the result of direct trauma or indirect trauma. Direct trauma more often causes trauma to the maxillary dentition due to the exposure of the maxillary anterior teeth. Indirect trauma is usually the result of forced occlusion secondary to a blow to the chin or from a whiplash injury. Falls are the most common mechanism of injury seen in the pediatric group. In adolescents, many of these fractures are sustained during sporting activities. However, the use of mouth guards and other protective equipment has decreased this number. Most adult injuries are caused by motor vehicle accidents, contact sports, falls, bicycles, interpersonal violence, medical/dental mishaps, and industrial accidents. Early intervention to reduce and stabilize the fracture is required to establish a bony union and ensure correct function. Most dentoalveolar fractures have bilateral stable adjacent dentition and are treated with a closed technique utilizing an acid-etch/resin splint followed by splint removal at 4 weeks. Other inferior stabilization treatments used are arch bars and other wiring techniques. It is widely accepted that semirigid stabilization techniques, such as an acid-etch/resin splint or wiring procedures, are adequate to treat dentoalveolar fractures. This is in contrast to the treatment of mandible fractures where AO principles of rigid fixation are often followed. Fractures that are unable to be reduced sometimes necessitate an open reduction followed by internal fixation, sometimes using a secondary splint for mobile teeth. In those rare cases when there are not stable adjacent teeth bilaterally other modalities must be considered. In the present report, two cases are presented where circummandibular wires were used to treat fractured mandibular dentoalveolar segments adjacent to edentulous areas.

  13. Agricultural intensification exacerbates spillover effects on soil biogeochemistry in adjacent forest remnants.

    Directory of Open Access Journals (Sweden)

    Raphael K Didham

    Full Text Available Land-use intensification is a central element in proposed strategies to address global food security. One rationale for accepting the negative consequences of land-use intensification for farmland biodiversity is that it could 'spare' further expansion of agriculture into remaining natural habitats. However, in many regions of the world the only natural habitats that can be spared are fragments within landscapes dominated by agriculture. Therefore, land-sparing arguments hinge on land-use intensification having low spillover effects into adjacent protected areas, otherwise net conservation gains will diminish with increasing intensification. We test, for the first time, whether the degree of spillover from farmland into adjacent natural habitats scales in magnitude with increasing land-use intensity. We identified a continuous land-use intensity gradient across pastoral farming systems in New Zealand (based on 13 components of farmer input and soil biogeochemistry variables, and measured cumulative off-site spillover effects of fertilisers and livestock on soil biogeochemistry in 21 adjacent forest remnants. Ten of 11 measured soil properties differed significantly between remnants and intact-forest reference sites, for both fenced and unfenced remnants, at both edge and interior. For seven variables, the magnitude of effects scaled significantly with magnitude of surrounding land-use intensity, through complex interactions with fencing and edge effects. In particular, total C, total N, δ15N, total P and heavy-metal contaminants of phosphate fertilizers (Cd and U increased significantly within remnants in response to increasing land-use intensity, and these effects were exacerbated in unfenced relative to fenced remnants. This suggests movement of livestock into surrounding natural habitats is a significant component of agricultural spillover, but pervasive changes in soil biogeochemistry still occur through nutrient spillover channels alone

  14. Effects of Bt-transgenic rice cultivation on planktonic communities in paddy fields and adjacent ditches

    International Nuclear Information System (INIS)

    Liu, Yongbo; Liu, Fang; Wang, Chao; Quan, Zhanjun; Li, Junsheng

    2016-01-01

    The non-target effects of transgenic plants are issues of concern; however, their impacts in cultivated agricultural fields and adjacent natural aquatic ecosystems are poorly understood. We conducted field experiments during two growing seasons to determine the effects of cultivating Bacillus thuringiensis (Bt)-transgenic rice on the phytoplankton and zooplankton communities in a paddy field and an adjacent ditch. Bt toxin was detected in soil but not in water. Water quality was not significantly different between non-Bt and Bt rice fields, but varied among up-, mid- and downstream locations in the ditch. Cultivation of Bt-transgenic rice had no effects on zooplankton communities. Phytoplankton abundance and biodiversity were not significantly different between transgenic and non-transgenic rice fields in 2013; however, phytoplankton were more abundant in the transgenic rice field than in the non-transgenic rice field in 2014. Water quality and rice type explained 65.9% and 12.8% of this difference in 2014, respectively. Phytoplankton and zooplankton were more abundant in mid- and downstream, than upstream, locations in the ditch, an effect that we attribute to water quality differences. Thus, the release of Bt toxins into field water during the cultivation of transgenic crops had no direct negative effects on plankton community composition, but indirect effects that alter environmental conditions should be taken into account during the processes of management planning and policymaking. - Highlights: • We detect fusion Cry1Ab/1Ac proteins from Bt rice entering into aquatic ecosystems. • Bt-transgenic rice cultivation have no significant effect on zooplankton community. • Bt-transgenic rice cultivation have indirect effect on phytoplankton community. • Water quality explains the difference of plankton communities in adjacent ditches.

  15. Acceptable Toxicity After Stereotactic Body Radiation Therapy for Liver Tumors Adjacent to the Central Biliary System

    Energy Technology Data Exchange (ETDEWEB)

    Eriguchi, Takahisa; Takeda, Atsuya; Sanuki, Naoko; Oku, Yohei; Aoki, Yousuke [Radiation Oncology Center, Ofuna Chuo Hospital, Kanagawa (Japan); Shigematsu, Naoyuki [Department of Radiology, Keio University School of Medicine, Tokyo (Japan); Kunieda, Etsuo, E-mail: kunieda-mi@umin.ac.jp [Department of Radiation Oncology, Tokai University, Kanagawa (Japan)

    2013-03-15

    Purpose: To evaluate biliary toxicity after stereotactic body radiation therapy (SBRT) for liver tumors. Methods and Materials: Among 297 consecutive patients with liver tumors treated with SBRT of 35 to 50 Gy in 5 fractions, patients who were irradiated with >20 Gy to the central biliary system (CBS), including the gallbladder, and had follow-up times >6 months were retrospectively analyzed. Toxicity profiles, such as clinical symptoms and laboratory and radiologic data especially for obstructive jaundice and biliary infection, were investigated in relation to the dose volume and length relationship for each biliary organ. Results: Fifty patients with 55 tumors were irradiated with >20 Gy to the CBS. The median follow-up period was 18.2 months (range, 6.0-80.5 months). In the dose length analysis, 39, 34, 14, and 2 patients were irradiated with >20 Gy, >30 Gy, >40 Gy, and >50 Gy, respectively, to >1 cm of the biliary tract. Seven patients were irradiated with >20 Gy to >20% of the gallbladder. Only 2 patients experienced asymptomatic bile duct stenosis. One patient, metachronously treated twice with SBRT for tumors adjacent to each other, had a transient increase in hepatic and biliary enzymes 12 months after the second treatment. The high-dose area >80 Gy corresponded to the biliary stenosis region. The other patient experienced biliary stenosis 5 months after SBRT and had no laboratory changes. The biliary tract irradiated with >20 Gy was 7 mm and did not correspond to the bile duct stenosis region. No obstructive jaundice or biliary infection was found in any patient. Conclusions: SBRT for liver tumors adjacent to the CBS was feasible with minimal biliary toxicity. Only 1 patient had exceptional radiation-induced bile duct stenosis. For liver tumors adjacent to the CBS without other effective treatment options, SBRT at a dose of 40 Gy in 5 fractions is a safe treatment with regard to biliary toxicity.

  16. Malaria vectors in Lake Victoria and adjacent habitats in western Kenya.

    Directory of Open Access Journals (Sweden)

    Noboru Minakawa

    Full Text Available The prevalence of malaria among the residents of the Lake Victoria basin remains high. The environment associated with the lake may maintain a high number of malaria vectors. Lake habitats including water hyacinths have been suspected to be the source of vectors. This study investigated whether malaria vectors breed in the lake habitats and adjacent backwater pools. Anopheline larvae were collected within the littoral zone of the lake and adjacent pools located along approximately 24.3 km of the lakeshore in western Kenya, and their breeding sites characterized. Three primary vector species, Anopheles arabiensis, Anopheles gambiae s.s. and Anopheles funestus s.s., and three potential vectors, were found in the lake habitats. Unexpectedly, An. arabiensis was the most dominant vector species in the lake sampling sites. Its habitats were uncovered or covered with short grass. A potential secondary malaria vector, Anopheles rivulorum, dominated the water hyacinths in the lake. Most breeding sites in the lake were limited to areas that were surrounded by tall emergent plants, including trees, and those not exposed to waves. Nearly half of adjacent habitats were lagoons that were separated from the lake by sand bars. Lagoons contained a variety of microhabitats. Anopheles arabiensis dominated open habitats, whereas An. funestus s.s. was found mainly in vegetated habitats in lagoons. The current study confirmed that several breeding sites are associated with Lake Victoria. Given that Lake Victoria is the second largest lake in the world, the lake related habitats must be extensive; therefore, making targeted vector control difficult. Further exploration is necessary to estimate the effects of lake associated habitats on malaria transmission so as to inform a rational decision-making process for vector control.

  17. Effects of Bt-transgenic rice cultivation on planktonic communities in paddy fields and adjacent ditches

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yongbo, E-mail: liuyb@craes.org.cn [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Liu, Fang [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Wang, Chao [Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380 (China); Quan, Zhanjun [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Li, Junsheng, E-mail: lijsh@creas.org.cn [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China)

    2016-09-15

    The non-target effects of transgenic plants are issues of concern; however, their impacts in cultivated agricultural fields and adjacent natural aquatic ecosystems are poorly understood. We conducted field experiments during two growing seasons to determine the effects of cultivating Bacillus thuringiensis (Bt)-transgenic rice on the phytoplankton and zooplankton communities in a paddy field and an adjacent ditch. Bt toxin was detected in soil but not in water. Water quality was not significantly different between non-Bt and Bt rice fields, but varied among up-, mid- and downstream locations in the ditch. Cultivation of Bt-transgenic rice had no effects on zooplankton communities. Phytoplankton abundance and biodiversity were not significantly different between transgenic and non-transgenic rice fields in 2013; however, phytoplankton were more abundant in the transgenic rice field than in the non-transgenic rice field in 2014. Water quality and rice type explained 65.9% and 12.8% of this difference in 2014, respectively. Phytoplankton and zooplankton were more abundant in mid- and downstream, than upstream, locations in the ditch, an effect that we attribute to water quality differences. Thus, the release of Bt toxins into field water during the cultivation of transgenic crops had no direct negative effects on plankton community composition, but indirect effects that alter environmental conditions should be taken into account during the processes of management planning and policymaking. - Highlights: • We detect fusion Cry1Ab/1Ac proteins from Bt rice entering into aquatic ecosystems. • Bt-transgenic rice cultivation have no significant effect on zooplankton community. • Bt-transgenic rice cultivation have indirect effect on phytoplankton community. • Water quality explains the difference of plankton communities in adjacent ditches.

  18. Sucrose-Metabolizing Enzymes in Transport Tissues and Adjacent Sink Structures in Developing Citrus Fruit 1

    Science.gov (United States)

    Lowell, Cadance A.; Tomlinson, Patricia T.; Koch, Karen E.

    1989-01-01

    Juice tissues of citrus lack phloem; therefore, photosynthates enroute to juice sacs exit the vascular system on the surface of each segment. Areas of extensive phloem unloading and transport (vascular bundles + segment epidermis) can thus be separated from those of assimilate storage (juice sacs) and adjacent tissues where both processes occur (peel). Sugar composition, dry weight accumulation, and activities of four sucrose-metabolizing enzymes (soluble and cell-wall-bound acid invertase, alkaline invertase, sucrose synthase, and sucrose phosphate synthase) were measured in these transport and sink tissues of grapefruit (Citrus paradisi Macf.) to determine more clearly whether a given enzyme appeared to be more directly associated with assimilate transport versus deposition or utilization. Results were compared at three developmental stages. Activity of sucrose (per gram fresh weight and per milligram protein) extracted from zones of extensive phloem unloading and transport was significantly greater than from adjacent sink tissues during the stages (II and III) when juice sacs grow most rapidly. In stage II fruit, activity of sucrose synthase also significantly surpassed that of all other sucrose-metabolizing enzymes in extracts from the transport tissues (vascular bundles + segment epidermis). In contrast, sucrose phosphate synthase and alkaline invertase at this stage of growth were the most active enzymes from adjacent, rapidly growing, phloem-free sink tissues (juice sacs). Activity of these two enzymes in extracts from juice sacs was significantly greater than that form the transport tissues (vascular bundles + segment epidermis). Soluble acid invertase was the most active enzyme in extracts from all tissues of very young fruit (stage I), including nonvascular regions, but nearly disappeared prior to the onset of juice sac sugar accumulation. The physiological function of high sucrose synthase activity in the transport tissues during rapid sucrose import

  19. Analysis of MRI signal changes in the adjacent pedicle of adolescent patients with fresh lumbar spondylolysis.

    Science.gov (United States)

    Goda, Yuichiro; Sakai, Toshinori; Sakamaki, Tadanori; Takata, Yoichiro; Higashino, Kosaku; Sairyo, Koichi

    2014-09-01

    The purpose of this study is to investigate a discrepancy between MRI and computed tomography (CT) findings in the spinal level distribution of spondylolysis. Recent advances in MRI have led to the early diagnosis of spondylolysis. Therefore, bony healing can be expected before the condition has a chance to worsen. In this study, we used MRI to examine the changes in spinal level signals in the pedicles adjacent to the pars interarticularis in adolescents with fresh lumbar spondylolysis. We then compared spinal level distribution of spondylolysis with that of previous results obtained by multidetector CT. The study included 98 adolescent patients (31 women and 67 men; mean age, 13.6 years; age range, 9-18 years) with fresh lumbar spondylolysis who showed MRI signal changes in the adjacent pedicle. An MRI signal change was defined as a high signal change on fat-suppressed imaging. MRI signal changes were detected in 150 adjacent pedicles of 101 vertebrae. Of these vertebrae, MRI signal changes in only 67 (66.3%) corresponded to L5, while changes in 34 (33.7%) corresponded to L3 or L4. In our follow-up study, the bone-healing rate with no vertebral defect was 100% at L3, 97.1% at L4, and 84.4% at L5. In addition, 11 of 34 (32.4%) vertebrae with signal changes at L3 or L4 occurred with L5 terminal-stage spondylolysis (no MRI signal change). MRI revealed a higher prevalence of L3 or L4 spondylolysis than observed with CT.

  20. An Adaptive Model for Calculating the Correlation Degree of Multiple Adjacent Signalized Intersections

    Directory of Open Access Journals (Sweden)

    Linhong Wang

    2013-01-01

    Full Text Available As an important component of the urban adaptive traffic control system, subarea partition algorithm divides the road network into some small subareas and then determines the optimal signal control mode for each signalized intersection. Correlation model is the core of subarea partition algorithm because it can quantify the correlation degree of adjacent signalized intersections and decides whether these intersections can be grouped into one subarea. In most cases, there are more than two intersections in one subarea. However, current researches only focus on the correlation model for two adjacent intersections. The objective of this study is to develop a model which can calculate the correlation degree of multiple intersections adaptively. The cycle lengths, link lengths, number of intersections, and path flow between upstream and downstream coordinated phases were selected as the contributing factors of the correlation model. Their jointly impacts on the performance of the coordinated control mode relative to the isolated control mode were further studied using numerical experiments. The paper then proposed a correlation index (CI as an alternative to relative performance. The relationship between CI and the four contributing factors was established in order to predict the correlation, which determined whether adjacent intersections could be partitioned into one subarea. A value of 0 was set as the threshold of CI. If CI was larger than 0, multiple intersections could be partitioned into one subarea; otherwise, they should be separated. Finally, case studies were conducted in a real-life signalized network to evaluate the performance of the model. The results show that the CI simulates the relative performance well and could be a reliable index for subarea partition.

  1. The genus Alphitobius Stephens (Coleoptera, Tenebrionidae, Alphitobiini in Africa and adjacent islands

    Directory of Open Access Journals (Sweden)

    Wolfgang Schawaller

    2014-06-01

    Full Text Available All species of the genus Alphitobius Stephens, 1829 (Alphitobiini Reitter, 1917, subfamily Tenebrioninae Latreille, 1802 from Africa and adjacent islands are revised. New species: Alphitobius capitaneus sp. n. from Kenya. New synonyms: Cryptops ulomoides Solier, 1851, syn. n. of Alphitobius diaperinus (Panzer, 1796; Alphitobius rufus Ardoin, 1976, syn. n. of Alphitobius hobohmi Koch, 1953; Peltoides (Micropeltoides crypticoides Pic, 1916, syn. n. of Peltoides (Micropeltoides opacus (Gerstaecker, 1871, comb. n. Homonym: Alphitobius ulomoides Koch, 1953 = Alphitobius arnoldi nom. n. New combinations from Alphitobius: Ulomoides basilewskyi (Ardoin, 1969, comb. n.; Peltoides (Micropeltoides opacus (Gerstaecker, 1871, comb. n. Figures of all examined species are added and a species key is compiled.

  2. A review of the natural history of adult Cetoniinae (Coleoptera: Scarabaeidae) from Argentina and adjacent countries.

    Science.gov (United States)

    Di Iorio, Osvaldo

    2014-04-17

    A compilation of the known natural history of adult Cetoniinae (Coleoptera: Scarabaeidae) from Argentina and adjacent countries is provided. Food items of adult Cetoniinae include pollen and/or nectar (flower visitors), sap and/or slime flux, ripened fruits on plants, green tissues and leaves, and honey. Of the 36 species of Cetoniinae from Argentina, food items are known only for 11 species (30.5%). Attraction to light and bait-traps, adult activity periods, vertebrate predators, and the occurrence in bird nests are presented and discussed. Other insects that share the same food sources and bait-traps with Cetoniinae are mentioned.

  3. Target migration from re-inflation of adjacent atelectasis during lung stereotactic body radiotherapy.

    Science.gov (United States)

    Mao, Bijing; Verma, Vivek; Zheng, Dandan; Zhu, Xiaofeng; Bennion, Nathan R; Bhirud, Abhijeet R; Poole, Maria A; Zhen, Weining

    2017-06-10

    Stereotactic body radiotherapy (SBRT) is a widely accepted option for the treatment of medically inoperable early-stage non-small cell lung cancer (NSCLC). Herein, we highlight the importance of interfraction image guidance during SBRT. We describe a case of early-stage NSCLC associated with segmental atelectasis that translocated 15 mm anteroinferiorly due to re-expansion of the adjacent segmental atelectasis following the first fraction. The case exemplifies the importance of cross-sectional image-guided radiotherapy that shows the intended target, as opposed to aligning based on rigid anatomy alone, especially in cases associated with potentially "volatile" anatomic areas.

  4. Literature and data review for the surface-water pathway: Columbia River and adjacent coastal areas

    International Nuclear Information System (INIS)

    Walters, W.H.; Dirkes, R.L.; Napier, B.A.

    1992-11-01

    As part of the Hanford Environmental Dose Reconstruction (HEDR) Project, Battelle, Pacific Northwest Laboratories reviewed literature and data on radionuclide concentrations and distribution in the water, sediment, and biota of the Columbia River and adjacent coastal areas. Over 600 documents were reviewed including Hanford reports, reports by offsite agencies, journal articles, and graduate theses. Radionuclide concentration data were used in preliminary estimates of individual dose for the period 1964 through 1966. This report summarizes the literature and database reviews and the results of the preliminary dose estimates

  5. Pollution parameters determination in water coast dispersion adjacent Carretas Point sub aquatic emissary

    International Nuclear Information System (INIS)

    Suarez Antola, R.; Malek, A.; Odino, R.; Souto, B.; Artucio, G.; Baraibar, J.

    1996-01-01

    It describes some results about transport processes, tracer techniques in Carretas Point sub aquatic emissary, discharge plume and emissary adjacent water coast in summer season. An overtaking and stability plume was verified. A contaminant unexpected and effusion localized was simulated. Scale effect near one coefficient was obtain Longitudinal dispersion coefficients and 1m2/seg and 0,02m2/seg transversal was estimated. The possibility to obtain information from first stages of transport analyzing fluorescence trace stain videos through geometric tools is discussed

  6. Histopathological effects of intraoperative radiotherapy on pancreas and adjacent tissues: a postmortem analysis

    International Nuclear Information System (INIS)

    Hoekstra, H.J.; Restrepo, C.; Kinsella, T.J.; Sindelar, W.F.

    1988-01-01

    Intraoperative radiotherapy (IORT) has been utilized in the treatment of resectable and unresectable pancreatic carcinoma at the National Cancer Institute. Detailed autopsy analyses of the radiation effects on the pancreas and adjacent tissues were performed on 13 patients dying at various times following therapy. IORT can induce a progressive retroperitoneal fibrosis and fibrosis of the porta hepatis in patients with resectable pancreatic carcinoma. In unresectable pancreatic carcinoma, the major expression of intraoperative irradiation with external beam irradiation is a progressive fibrosis of the pancreas with vascular sclerosis, nerve degeneration, atrophy of acinar cells, and atypical changes in the ducts of the pancreas, as well as degenerative changes of the pancreatic tumor

  7. On optical spectra of the NGC 6677 galaxy and the adjacent bright compact object

    International Nuclear Information System (INIS)

    Chuvaev, K.K.

    1987-01-01

    Spectral observations of NGC 6677 galaxy and the adjacent object carried out during six nights on the spectrograph with the image tube of 2.6-m Shain telescope showed, that the bright compact object is a star belonging to our galaxy but not an active galaxy. The NGC 6677 galaxy has sufficiently rich emission spectrum. On the basis of measured values of red shift Z, the inclination and the extent of emission lines, the mass of the galaxy has been estimated (M=7x10 9 M Sun )

  8. Literature and data review for the surface-water pathway: Columbia River and adjacent coastal areas

    Energy Technology Data Exchange (ETDEWEB)

    Walters, W.H.; Dirkes, R.L.; Napier, B.A.

    1992-11-01

    As part of the Hanford Environmental Dose Reconstruction (HEDR) Project, Battelle, Pacific Northwest Laboratories reviewed literature and data on radionuclide concentrations and distribution in the water, sediment, and biota of the Columbia River and adjacent coastal areas. Over 600 documents were reviewed including Hanford reports, reports by offsite agencies, journal articles, and graduate theses. Radionuclide concentration data were used in preliminary estimates of individual dose for the period 1964 through 1966. This report summarizes the literature and database reviews and the results of the preliminary dose estimates.

  9. Literature and data review for the surface-water pathway: Columbia River and adjacent coastal areas

    International Nuclear Information System (INIS)

    Walters, W.H.; Dirkes, R.L.; Napier, B.A.

    1992-04-01

    As part of the Hanford Environmental Dose Reconstruction Project, Pacific Northwest Laboratory reviewed literature and data on radionuclide concentrations and distribution in the water, sediment, and biota of the Columbia River and adjacent coastal areas. Over 600 documents were reviewed including Hanford reports, reports by offsite agencies, journal articles, and graduate theses. Certain radionuclide concentration data were used in preliminary estimates of individual dose for the 1964--1966 time period. This report summarizes the literature and database review and the results of the preliminary dose estimates

  10. Health and function assessments in two adjacent Danish birth cohorts of centenarians

    DEFF Research Database (Denmark)

    Vestergaard, Sonja; Andersen-Ranberg, Karen; Skytthe, Axel

    2016-01-01

    Using the results from measures of functional ability, cognitive and physical performance from two adjacent birth cohorts of 100-year-old adults, we aimed to elucidate the possible impact of difference in participation rates, design, and interviewer mode. Participants were birth cohort members born...... proportions of DK-1911 independently performed all activities of daily living (ADL) compared to DK-1910, but only significantly for toileting, bathing, and feeding (all p examination (MMSE) score was higher in DK-1911 than in DK-1910 (23.5 vs. 21.0; p

  11. Odonata (Insecta diversity of Salim Ali Bird Sanctuary and its adjacent areas in Thattekkad, Kerala, India

    Directory of Open Access Journals (Sweden)

    A.P. Varghese

    2014-06-01

    Full Text Available Odonata diversity of Salim Ali Bird Sanctuary and its adjacent areas in Thattekkad, Kerala, India were documented from 2010 to 2012. Opportunistic observations were carried out to record species diversity. Eighty-two species of Odonata, which included 51 species of Anisoptera (dragonflies and 31 species of Zygoptera (damselflies, were recorded during the study. Of this 21 species are endemic to the Western Ghats. The presence of the IUCN categorized nearly threatened species like Megalogomphus hannyngtoni and vulnerable species like Platysticta deccanensis and Protosticta sanguinostigma is remarkable.

  12. Experimental study of natural convection adjacent to an isothermal vertical ice cylinder in cold pure water

    International Nuclear Information System (INIS)

    Riu, Kap Jong; Yea, Yong Taeg; Park, Sang Hee

    1991-01-01

    A natural convection adjacent to an isothermal vertical ice cylinder is studied experimentally in cold pure water. The experiments are carried out as changing the temperature of the ambient water and then the flow and heat transfer characteristics is visualized and observed. It is shown that flow patterns are steady state upflow, unsteady state flow, steady state dual flow, and steady state downflow. There is also obtained a heat transfer coefficient and mean Nusselt number at various ambient temperature. These results are in good agreement with the theoretical ones. (Author)

  13. Variabilidade espacial e disponibilidade de cobre e zinco em solos de vinhedos e adjacências

    OpenAIRE

    Valladares,Gustavo Souza; Azevedo,Emílio Carlos de; Camargo,Otávio Antônio de; Grego,Célia Regina; Rastoldo,Alessandra Maria Cia Silva

    2009-01-01

    Com o tempo, o uso agrícola pode levar à contaminação do solo por metais pesados, principalmente por se servir de insumos e agroquímicos que possuem cobre e zinco em sua composição. O objetivo deste trabalho foi determinar os teores de cobre e zinco disponíveis no solo extraídos com DTPA e avaliar sua distribuição espacial empregando a geoestatística em áreas de vinhedos comerciais e experimentais e sob outros usos e coberturas nas adjacências das plantações. Foram coletadas amostras de terra...

  14. Effect of fluoridated milk on enamel demineralization adjacent to fixed orthodontic appliances

    DEFF Research Database (Denmark)

    Sköld-Larsson, Kerstin; Sollenius, Ola; Karlsson, Lena

    2012-01-01

    Abstract Objective. To investigate the effect of daily intake of fluoridated milk on enamel demineralization adjacent to fixed orthodontic brackets assessed with quantitative light-induced fluorescence (QLF). Materials and methods. Sixty-four healthy adolescents (13-18 years) undergoing orthodontic...... amount of milk without fluoride. The intervention period was 12 weeks and the end-point was mineral gain or loss in enamel, assessed by QLF on two selected sites from each individual. The attrition rate was 12.5% and 112 sites were included in the final evaluation. Results. There was no statistically...

  15. Adjacent-cell Preconditioners for solving optically thick neutron transport problems

    International Nuclear Information System (INIS)

    Azmy, Y.Y.

    1994-01-01

    We develop, analyze, and test a new acceleration scheme for neutron transport methods, the Adjacent-cell Preconditioner (AP) that is particularly suited for solving optically thick problems. Our method goes beyond Diffusion Synthetic Acceleration (DSA) methods in that it's spectral radius vanishes with increasing cell thickness. In particular, for the ID case the AP method converges immediately, i.e. in one iteration, to 10 -4 pointwise relative criterion in problems with dominant cell size of 10 mfp or thicker. Also the AP has a simple formalism and is cell-centered hence, multidimensional and high order extensions are easier to develop, and more efficient to implement

  16. Punching shear in reinforced concrete flat slabs with hole adjacent to the column and moment transfer

    Directory of Open Access Journals (Sweden)

    D. C. Oliveira

    Full Text Available The structural behavior and the ultimate punching shear resistance of internal reinforced concrete flat slab-column connections, with one hole adjacent to the column, with or without flexural moment transfer of the slab to the column was investigated. Main variables were: the existence whether or not hole, flexural reinforcement layout and ratio, the direction and sense of the moment transferred and the eccentricity of the load (M (moment transferred to column / V (shear ratio at the connection - 0,50 m or 0,25 m. Seven internal slab-column joining were tested and ultimate loads, cracking, deflections, concrete and reinforcement strains were analyzed. The existence of hole adjacent to the smaller column dimension, the hole dimension, flexural reinforcement rate and placing, the variation of relation Mu/Vu in function of the load, and, than, of eccentricity of the load, influenced the slabs behavior and rupture load. Test results were compared with the estimations from CEB-FIP/MC1990 [7], EC2/2004 [12], ACI-318:2011 [1] and NBR 6118:2007 [5]. ACI [1] and EC2 [12] presented most conservative estimates, although have presented some non conservative estimates. Brazilian NBR [5], even though being partly based in EC2 [12], presented smaller conservative estimates and more non conservative estimates. A modification on all codes is proposed for taking in account the moment caused by the eccentricity at the critical perimeter for slabs with holes.

  17. Hybrid NiCoOx adjacent to Pd nanoparticles as a synergistic electrocatalyst for ethanol oxidation

    Science.gov (United States)

    Wang, Wei; Yang, Yan; Liu, Yanqin; Zhang, Zhe; Dong, Wenkui; Lei, Ziqiang

    2015-01-01

    To improve the electrocatalytic activity of Pd for ethanol oxidation, hybrid NiCoOx adjacent to Pd catalyst (Pd-NiCoOx/C) is successfully synthesized. Physical characterization shows NiCoOx is closely adjacent to Pd nanoparticles in Pd-NiCoOx/C catalyst, which leads to Strong Metal-Support Interactions (SMSI) between the NiCoOx and Pd nanoparticles, in favor of the electrocatalytic properties. The Pd-NiCoOx/C catalyst is estimated to own larger electrochemically active surface area than Pd/C and Pd-NiO/C catalysts. Moreover, compared to Pd/C catalyst, the onset potential of Pd-NiCoOx/C catalyst is negative 40 mV for ethanol oxidation. Noticeably, the current density of Pd-NiCoOx/C catalyst is 2.05 and 1.43 times higher contrasted to Pd/C and Pd-NiO/C catalysts accordingly. Importantly, the Pd-NiCoOx/C catalyst exhibits better stability during ethanol oxidation, which is a promising electrocatalyst for application in direct alkaline alcohol fuel cells.

  18. Measuring Crowdedness between Adjacent Stations in an Urban Metro System: a Chinese Case Study

    Directory of Open Access Journals (Sweden)

    Liudan Jiao

    2017-12-01

    Full Text Available The urban metro system has been widely appreciated as the most important component in urban infrastructures. It plays a critical role in promoting urban social and economic development, and particularly in reducing the urban traffic congestion. However, there are various inherent problems with operating metro systems, which typically involve the crowdedness both at stations and inside vehicles. Both policymakers and academic researchers in China have paid little attention to the crowdedness between metro stations. In order to solve the problem of crowdedness, it is necessary to develop a method to evaluate the level of crowdedness. This work establishes a model to measure the crowdedness between adjacent stations in a metro system based on the load factor principle, passenger standing density, and other factors such as the metro operation schedule and estimations of passenger flows. The Chongqing Metro Line 3 in China is used as a case study to demonstrate the application of the evaluation model. The case study reveals that the model introduced in this study can assist with assessing the crowdedness level between adjacent stations in a metro line. The model is an effective tool for helping the metro management and administration understand the level of crowdedness, apply proper methods to mitigate the crowdedness, and thus improve the quality of the service for those utilizing the metro system.

  19. Activation gating kinetics of GIRK channels are mediated by cytoplasmic residues adjacent to transmembrane domains.

    Science.gov (United States)

    Sadja, Rona; Reuveny, Eitan

    2009-01-01

    G-protein-coupled inwardly rectifying potassium channels (GIRK/Kir3.x) are involved in neurotransmission-mediated reduction of excitability. The gating mechanism following G protein activation of these channels likely proceeds from movement of inner transmembrane helices to allow K(+) ions movement through the pore of the channel. There is limited understanding of how the binding of G-protein betagamma subunits to cytoplasmic regions of the channel transduces the signal to the transmembrane regions. In this study, we examined the molecular basis that governs the activation kinetics of these channels, using a chimeric approach. We identified two regions as being important in determining the kinetics of activation. One region is the bottom of the outer transmembrane helix (TM1) and the cytoplasmic domain immediately adjacent (the slide helix); and the second region is the bottom of the inner transmembrane helix (TM2) and the cytoplasmic domain immediately adjacent. Interestingly, both of these regions are sufficient in mediating the kinetics of fast activation gating. This result suggests that there is a cooperative movement of either one of these domains to allow fast and efficient activation gating of GIRK channels.

  20. Generation of Chimeric RNAs by cis-splicing of adjacent genes (cis-SAGe) in mammals.

    Science.gov (United States)

    Zhuo, Jian-Shu; Jing, Xiao-Yan; Du, Xin; Yang, Xiu-Qin

    2018-02-20

    Chimeric RNA molecules, possessing exons from two or more independent genes, are traditionally believed to be produced by chromosome rearrangement. However, recent studies revealed that cis-splicing of adjacent genes (cis- SAGe) is one of the major mechanisms underlying the formation of chimeric RNAs. cis-SAGe refers to intergenic splicing of directly adjacent genes with the same transcriptional orientation, resulting in read-through transcripts, termed chimeric RNAs, which contain sequences from two or more parental genes. cis-SAGe was first identified in tumor cells, since then its potential in carcinogenesis has attracted extensive attention. More and more scientists are focusing on it. With the development of research, cis-SAGe was found to be ubiquitous in various normal tissues, and might make a crucial contribution to the formation of novel genes in the evolution of genomes. In this review, we summarize the splicing pattern, expression characteristics, possible mechanisms, and significance of cis-SAGe in mammals. This review will be helpful for general understanding of the current status and development tendency of cis-SAGe.

  1. The tiger beetles (Coleoptera, Carabidae, Cicindelinae) of Israel and adjacent lands.

    Science.gov (United States)

    Matalin, Andrey V; Chikatunov, Vladimir I

    2016-01-01

    Based on field studies, museums collections and literature sources, the current knowledge of the tiger beetle fauna of Israel and adjacent lands is presented. In Israel eight species occur, one of them with two subspecies, while in the Sinai Peninsula nine species of tiger beetles are now known. In the combined regions seven genera from two tribes were found. The Rift Valley with six cicindelids species is the most specious region of Israel. Cylindera contorta valdenbergi and Cicindela javeti azari have localized distributions and should be considered regional endemics. A similarity analysis of the tiger beetles faunas of different regions of Israel and the Sinai Peninsula reveal two clusters of species. The first includes the Great Rift Valley and most parts of the Sinai Peninsula, and the second incorporates most regions of Israel together with Central Sinai Foothills. Five distinct adult phenological groups of tiger beetles can be distinguished in these two clusters: active all-year (three species), spring-fall (five species), summer (two species), spring-summer (one species) and spring (one species). The likely origins of the tiger beetle fauna of this area are presented. An annotated list and illustrated identification key of the Cicindelinae of Israel and adjacent lands are provided.

  2. Dating recent sediments from the subaqueous Yangtze Delta and adjacent continental shelf, China

    Directory of Open Access Journals (Sweden)

    Zhang-Hua Wang

    2014-04-01

    Full Text Available In this study we analyzed sediment lithology, fallout of 210Pb and 137Cs, and spheroidal carbonaceous particles (SCPs for two short cores, YZE and CX38, obtained by gravity corer from the Yangtze River mouth offshore and adjacent continental shelf, to compare geochronological methods on the recent sediments of this area. Lithology and grain size changes in YZE suggested the re-discharging of the North Channel of the Yangtze River mouth by flood events during 1949–1954 and associated accretion in the offshore area. This event was validated by a remarkable zone of declination in both 137Cs and 210Pb activities and the absolute ages derived from the 137Cs and SCPs. In contrast, 210Pb results show obvious disturbance of grain size by sediment mixing and cannot be interpreted above 100 cm. In CX38, absolute ages for the early- and mid-1950s were derived by the 137Cs and the SCP profile respectively, which occurred in a reasonable sequence. The excess 210Pb distribution shows exponentially decreasing activities with depth, and the mean sedimentation rate agrees roughly with the one inferred from the SCP profile. We suggest that the limitation of the 210Pb method needs consideration while the SCP profile has the potential to provide a useful and independent dating method for recent Yangtze offshore and adjacent shelf sediments.

  3. Local government units initiatives on coastal resource management in adjacent municipalities in Camarines Sur, Philippines

    Science.gov (United States)

    Faustino, A. Z.; Madela, H. L.

    2018-03-01

    This research was conducted to determine the local government units (LGUs) initiatives on coastal resource management (CRM) in adjacent municipalities in Camarines Sur, Philippines. The respondents of this study are 100 fisherfolk leaders in the municipalities of Calabanga, Tinambac and Siruma. Descriptive, comparative and evaluative methods of research were employed and a survey questionnaire was used as the primary tool in data gathering. On the test of difference, the computed F-value of 12.038 and p-value of .001 revealed a very high difference in the implementation of CRM initiatives in the adjacent municipalities. The respondents in this study live below the poverty threshold. The intrusion of commercial fishers and the use of active fishing gears inside the 15-km municipal waters significantly affect the marine habitat while fishpond conversion kills the natural cycle in the mangrove forests. However, the FOs membership in the Municipal Fisheries and Aquatic Resources Management Council empower them to engage in governance which can be a venue for them to recommend policies related to CRM. As a result of this study, a CRM monitoring and evaluation model was crafted to guide the LGUs in the review, revision and crafting of CRM programs.

  4. Screening of the residual normal ovarian tissue adjacent to orthotopic epithelial ovarian carcinomas in nude mice.

    Science.gov (United States)

    Zhu, G H; Wang, S T; Yao, M Z; Cai, J H; Chen, C Y; Yang, Z X; Hong, L; Yang, S Y

    2014-04-16

    The objective of this study was to explore the feasibility and methods of screening the residual normal ovarian tissue adjacent to orthotopic ovarian carcinomas in nude mice. Human epithelial ovarian cancer cells (OVCAR3) were subcutaneously implanted for a tumor source and ovarian orthotopic transplantation. The cancer tissue, proximal paraneoplastic tissue, middle paraneoplastic tissue, remote paraneoplastic tissue, and normal ovarian tissue were removed. CK-7, CA125, p53, survivin, MMP-2, and TIMP-2 expression was detected by reverse transcription polymerase chain reaction. We obtained 35 paraneoplastic residual ovarian tissues with normal biopsies from 40 cases of an orthotopic epithelial ovarian carcinoma model (87.5%). CK-7, CA125, p53, survivin, MMP-2, and TIMP-2 expression was lower in proximal paraneoplastic tissue than in cancer tissue (P tissue (P tissue as well as among residual normal ovarian tissues with different severity (P > 0.05). In ovarian tissues of 20 normal nude mice, the expression of CK- 7, CA125, p53, survivin, MMP-2, and TIMP-2 was negative. Overall, the expression levels of CK-7, CA125, p53, survivin, MMP-2, TIMP-2, and other molecular markers showed a decreasing trend in the non-cancer tissue direction. The expression levels can be used as standards to screen residual normal ovarian tissue. We can obtain relatively safe normal ovarian tissues adjacent to epithelial ovarian cancer.

  5. Spatial distribution of heavy metals in solid adjacent to the Naples-Salerno motor way

    International Nuclear Information System (INIS)

    Imperato, M.; Monetti, V.; Naimo, D.; Stanzione, D.

    1999-01-01

    This work analyses the distribution of heavy metal in soil adjacent to the Naples-Salerno motor way, an area which typically contains volcanic products from Somma-Vesuvio. The various concentrations of Pb, Cd, Zn, Mn, Cu and Cr found in different portions of the motor way (embankment, road cut, field level) are reported. The data obtained indicate high level of pollution in soil adjacent to the motor way fencing, with maximum concentrations of 1220 ppm Pb, 1.9 ppm Cd and 341 ppm Zn. Gradients of decreasing pollution with distance from the fencing and with altitude from the road surface are highest for Zn followed by Pb and Cd. The presence of these three materials in depth follows an averagely constant falling gradient, with minimum detected values at 50 cm depth. The spatial distribution of Cr does not reveal any significant differences. Relatively big levels are due to the presence in the soil of Chromium-rich minerals such as augite and olivine. Mn and Cu are found, due to local contribution, probably as a consequence of the use of copper compounds in agriculture [it

  6. Contralateral breast cancer adjacent to a fibroadenoma: report of a case.

    Science.gov (United States)

    Iwamoto, Miki; Takei, Hiroyuki; Iida, Shinya; Yamashita, Kouji; Yanagihara, Keiko; Kurita, Tomoko; Tsuchiya, Shinichi; Kanazawa, Yoshikazu; Uchida, Eiji

    2014-01-01

    A 64-year-old woman noticed a lump of the right breast and consulted our outpatient clinic. She had undergone multiple excisional biopsies of fibroadenomas in both breasts and mastectomy for invasive ductal carcinoma (IDC) of the left breast. After completing 5 years of treatment with adjuvant tamoxifen, she had undergone screening with annual physical examinations and occasional computed tomography. She was declared recurrence-free 13 years after breast cancer surgery, although lumps were detected in the right breast, probably due to fibroadenomas. Mammography, ultrasonography, and magnetic resonance imaging revealed that the lump was irregularly shaped, 2 cm in diameter, and adjacent to a fibroadenoma with macrocalcification. Two axillary lymph nodes were enlarged and suggestive of metastasis. A core needle biopsy revealed IDC of the right breast. She underwent a right partial mastectomy with axillary lymph node dissection. The IDC was 2 cm in diameter, of nuclear grade 2, and adjacent to a 0.7-cm fibroadenoma with a macrocalcification. The margins of the IDC close to the fibroadenoma were clearly demarcated by the fibrous capsule of the fibroadenoma. Four axillary lymph nodes were positive for metastasis. In the present case the presence of fibroadenoma might have interfered with the early detection of the contralateral IDC. The history of multiple excisions of fibroadenomas and mastectomy for breast cancer suggests an increased risk of contralateral breast cancer for the patient's entire life; therefore, regular annual follow-up, such as physical examinations and mammography, is recommended.

  7. Breast Cancer Arising Adjacent to an Involuting Fibroadenoma: Serial Changes in Radiologic Features

    Science.gov (United States)

    Park, Chae Jung; Kim, Eun-Kyung; Woo, Ha Young; Moon, Hee Jung; Yoon, Jung Hyun

    2015-01-01

    Fibroadenoma is a common benign breast lesion and its malignant transformation is rare. There have been several case reports and studies that retrospectively reviewed breast cancers that arose within fibroadenomas; however, none of these studies reported serial changes in radiologic features of the cancer, including findings from mammography and ultrasound (US). We report a case of breast cancer arising adjacent to an involuting fibro adenoma in a 39-year-old woman who was undergoing serial follow-up after her fibroadenoma was diagnosed. Seven years after her diagnosis, the lesion showed evidence of coarse calcifications, a typical sign of involution. Four years later, US revealed a newly developed hypoechoic lesion with irregular margins and peripherally located calcifications adjacent to the fibroadenoma. A core biopsy was performed, and histopathological examination resulted in a diagnosis of invasive ductal carcinoma. When new suspicious features are observed in a fibroadenoma, radiologists should raise the concern for breast cancer and proceed with diagnosis and treatment accordingly. PMID:26472981

  8. Regional Jurassic geologic framework of Alabama coastal waters area and adjacent Federal waters area

    Science.gov (United States)

    Mink, R.M.; Bearden, B.L.; Mancini, E.A.

    1989-01-01

    To date, numerous Jurassic hydrocarbon fields and pools have been discovered in the Cotton Valley Group, Haynesville Formation, Smackover Formation and Norphlet Formation in the tri-state area of Mississippi, Alabama and Florida, and in Alabama State coastal waters and adjacent Federal waters area. Petroleum traps are basement highs, salt anticlines, faulted salt anticlines and extensional faults associated with salt movement. Reservoirs include continental and marine sandstones, limestones and dolostones. Hydrocarbon types are oil, condensate and natural gas. The onshore stratigraphic and structural information can be used to establish a regional geologic framework for the Jurassic for the State coastal waters and adjacent Federal waters areas. Evaluation of the geologic information along with the hydrocarbon data from the tri-state area indicates that at least three Jurassic hydrocarbon trends (oil, oil and gas condensate, and deep natural gas) can be identified onshore. These onshore hydrocarbon trends can be projected into the Mobile area in the Central Gulf of Mexico and into the Pensacola, Destin Dome and Apalachicola areas in the Eastern Gulf of Mexico. Substantial reserves of natural gas are expected to be present in Alabama State waters and the northern portion of the Mobile area. Significant accumulations of oil and gas condensate may be encountered in the Pensacola, Destin Dome, and Apalachicola areas. ?? 1989.

  9. Optimal technique of linear accelerator-based stereotactic radiosurgery for tumors adjacent to brainstem.

    Science.gov (United States)

    Chang, Chiou-Shiung; Hwang, Jing-Min; Tai, Po-An; Chang, You-Kang; Wang, Yu-Nong; Shih, Rompin; Chuang, Keh-Shih

    2016-01-01

    Stereotactic radiosurgery (SRS) is a well-established technique that is replacing whole-brain irradiation in the treatment of intracranial lesions, which leads to better preservation of brain functions, and therefore a better quality of life for the patient. There are several available forms of linear accelerator (LINAC)-based SRS, and the goal of the present study is to identify which of these techniques is best (as evaluated by dosimetric outcomes statistically) when the target is located adjacent to brainstem. We collected the records of 17 patients with lesions close to the brainstem who had previously been treated with single-fraction radiosurgery. In all, 5 different lesion catalogs were collected, and the patients were divided into 2 distance groups-1 consisting of 7 patients with a target-to-brainstem distance of less than 0.5cm, and the other of 10 patients with a target-to-brainstem distance of ≥ 0.5 and linear accelerator is only 1 modality can to establish for SRS treatment. Based on statistical evidence retrospectively, we recommend VMAT as the optimal technique for delivering treatment to tumors adjacent to brainstem. Copyright © 2016 American Association of Medical Dosimetrists. All rights reserved.

  10. Node-pair reliability of network systems with small distances between adjacent nodes

    International Nuclear Information System (INIS)

    Malinowski, Jacek

    2007-01-01

    A new method for computing the node-pair reliability of network systems modeled by random graphs with nodes arranged in sequence is presented. It is based on a recursive algorithm using the 'sliding window' technique, the window being composed of several consecutive nodes. In a single step, the connectivity probabilities for all nodes included in the window are found. Subsequently, the window is moved one node forward. This process is repeated until, in the last step, the window reaches the terminal node. The connectivity probabilities found at that point are used to compute the node-pair reliability of the network system considered. The algorithm is designed especially for graphs with small distances between adjacent nodes, where the distance between two nodes is defined as the absolute value of the difference between the nodes' numbers. The maximal distance between any two adjacent nodes is denoted by Γ(G), where G symbolizes a random graph. If Γ(G)=2 then the method can be applied for directed as well as undirected graphs whose nodes and edges are subject to failure. This is important in view of the fact that many algorithms computing network reliability are designed for graphs with failure-prone edges and reliable nodes. If Γ(G)=3 then the method's applicability is limited to undirected graphs with reliable nodes. The main asset of the presented algorithms is their low numerical complexity-O(n), where n denotes the number of nodes

  11. Detection process of defects in a tube close to an adjacent element, especially in a heat exchanger

    International Nuclear Information System (INIS)

    Holt, A.E.; Wehrmeister, A.E.; Whaley, H.L.

    1978-01-01

    On-site process for obtaining, by Foucault currents, the indication of a defect in a tube close to an adjacent element masking the indication of the defect. It is characterized by the course of a reference tube with an eddy current sensor near a similar adjacent element in order to obtain an indication of reference eddy currents of the adjacent element first mentioned, the completion of a joint crossover of the above first mentioned tube so as to obtain a composite indication of eddy currents of the defect and of the adjacent element, and the generation of the indication by eddy currents of the defect by comparing the composite indication with the reference indication [fr

  12. Discovery and analysis of an active long terminal repeat-retrotransposable element in Aspergillus oryzae.

    Science.gov (United States)

    Jie Jin, Feng; Hara, Seiichi; Sato, Atsushi; Koyama, Yasuji

    2014-01-01

    Wild-type Aspergillus oryzae RIB40 contains two copies of the AO090005001597 gene. We previously constructed A. oryzae RIB40 strain, RKuAF8B, with multiple chromosomal deletions, in which the AO090005001597 copy number was found to be increased significantly. Sequence analysis indicated that AO090005001597 is part of a putative 6,000-bp retrotransposable element, flanked by two long terminal repeats (LTRs) of 669 bp, with characteristics of retroviruses and retrotransposons, and thus designated AoLTR (A. oryzae LTR-retrotransposable element). AoLTR comprised putative reverse transcriptase, RNase H, and integrase domains. The deduced amino acid sequence alignment of AoLTR showed 94% overall identity with AFLAV, an A. flavus Tf1/sushi retrotransposon. Quantitative real-time RT-PCR showed that AoLTR gene expression was significantly increased in the RKuAF8B, in accordance with the increased copy number. Inverse PCR indicated that the full-length retrotransposable element was randomly integrated into multiple genomic locations. However, no obvious phenotypic changes were associated with the increased AoLTR gene copy number.

  13. Correlation between diagnostic capability of MR-mammography and histology of tissue adjacent to tumor

    Energy Technology Data Exchange (ETDEWEB)

    Takahara, Taro [St. Marianna Univ., Kawasaki, Kanagawa (Japan)

    1996-12-01

    The purpose of this paper is to evaluate correlation between the capability in the diagnosis of tumor extent and histology of adjacent tissue. MR-mammography (MRM) was obtained in twenty-one patients with surgically resected breast cancer by 0.5 T superconducting magnet (PHILIPS GY-ROSCAN T5-II, release 3.1). Pre and postcontrast 3D-spoiled gradient echo sequence were employed for MRM with spectral presaturation with inversion recovery (SPIR) and on-resonance MTC. The contrast determination time, the passing time of the center of k-space, was 1 min 50 s in 14 cases with key-hole imaging, and 2 min 46 s in 7 cases without key-hole imaging. Early enhancing area was considered as a tumor and an accuracy of tumor extent was evaluated by two radiologists. Accurate interpretation was obtained in 9 of 9 cases with atrophic mammary gland with fatty replacement and 3 of 3 cases with severe fibrosis in mammary gland. Seven cases were unclear in tumor margin due to intense enhancement of the adjacent tissue. One of 3 cases with normal mammary gland showed unclear margin of the tumor, which corresponded to the area of rich population of lobules in a young patient. Two of 2 cases of fibrocystic change with nonproliferative lesions in one case and proliferative lesions without atypia in another, showed unclear margin of tumor. Two cases of 2 intraductal spreading and 2 of 2 cases of massive interstitial invasion also showed unclear margin. The accuracy of tumor extent was found to have no correlation with either histology or enhancing ratio of the tumor. In conclusion, it is warranted to say that histology of adjacent tissue is an important factor to determine diagnostic capability of tumor extent by MRM. Fat replacement and fibrosis of the surrounding tissue are main causes of clear visualization of tumor, while normal mammary gland in young patients, fibrocystic change, intraductal spreading and invasion lead to the unclearness of tumor margin. (author)

  14. Correlation between diagnostic capability of MR-mammography and histology of tissue adjacent to tumor

    International Nuclear Information System (INIS)

    Takahara, Taro

    1996-01-01

    The purpose of this paper is to evaluate correlation between the capability in the diagnosis of tumor extent and histology of adjacent tissue. MR-mammography (MRM) was obtained in twenty-one patients with surgically resected breast cancer by 0.5 T superconducting magnet (PHILIPS GY-ROSCAN T5-II, release 3.1). Pre and postcontrast 3D-spoiled gradient echo sequence were employed for MRM with spectral presaturation with inversion recovery (SPIR) and on-resonance MTC. The contrast determination time, the passing time of the center of k-space, was 1 min 50 s in 14 cases with key-hole imaging, and 2 min 46 s in 7 cases without key-hole imaging. Early enhancing area was considered as a tumor and an accuracy of tumor extent was evaluated by two radiologists. Accurate interpretation was obtained in 9 of 9 cases with atrophic mammary gland with fatty replacement and 3 of 3 cases with severe fibrosis in mammary gland. Seven cases were unclear in tumor margin due to intense enhancement of the adjacent tissue. One of 3 cases with normal mammary gland showed unclear margin of the tumor, which corresponded to the area of rich population of lobules in a young patient. Two of 2 cases of fibrocystic change with nonproliferative lesions in one case and proliferative lesions without atypia in another, showed unclear margin of tumor. Two cases of 2 intraductal spreading and 2 of 2 cases of massive interstitial invasion also showed unclear margin. The accuracy of tumor extent was found to have no correlation with either histology or enhancing ratio of the tumor. In conclusion, it is warranted to say that histology of adjacent tissue is an important factor to determine diagnostic capability of tumor extent by MRM. Fat replacement and fibrosis of the surrounding tissue are main causes of clear visualization of tumor, while normal mammary gland in young patients, fibrocystic change, intraductal spreading and invasion lead to the unclearness of tumor margin. (author)

  15. Quantitative evaluation in enhancement of pancreas and adjacent vessels during spiral CT

    International Nuclear Information System (INIS)

    Kim, Hyoung Seuk; Shin, Kue Hee; Park, Cheol Min; Cha, Sang Hoon; Chung, Kyoo Byung

    1997-01-01

    To determine by quantitative evaluation of pancreatic and adjacent vascular enhancement during spiral CT, the ideal scan delay for examination of the pancreas. Dual(n=3D90) and triple(n=3D90) phase spiral CT scans of patients whose pancreas showed no pathologic condition were retrospectively evaluated. Dual-phase scans were performed at 43 seconds(early), and 5-6 minutes(delayed) after the injection of 120ml of contrast material at an injection rate of 3ml/sec;triple-phase scans were performed at 25 seconds(arterial),60-65 seconds (portal) and 5-6 minutes (delayed) after the injection of 120-140ml of contrast material at an injection rate of 2-4ml/sec, and ten patients also underwent precontrast scanning. CT attenuation values(HU) were measured in the head, body and tail of the pancreas, aorta, and main portal vein during each phase of all scans. Triple-phase protocol was used to measure the effect of different total volumes and injection rates on enhancement of the pancreas and adjacent vessels. There was no significant difference in the degree of enhancement of the pancreas head, body and tail during each phase(p>0.05). The pancreas was maximally enhanced on 43 second delayed scan(132±20HU)(p 0.05). The main portal vein showed maximum enhancement on 43-second delayed scan(207±44HU)(p<0.05). Different total volume of contrast material did not change the enhancement of the pancreas and adjacent vessels. At an injection rate of 2ml/sec, peak enhancement of the pancreas, aorta and portal vein was obtained on 60-65 second delayed scan, and at 4ml/sec, peak enhancement was obtained on 25 second delayed scan(p<0.05). Observing the usual protocols for abdominal spiral CT scanning, the pancreas was most effectively evaluated using a 43-second delayed scan. An increased injection rate resulted in earlier enhancement of the pancreas, aorta and portal vein

  16. Interaction of the nucleation phenomena at adjacent sites in nucleate boiling

    International Nuclear Information System (INIS)

    Sultan, M.; Judd, R.L.

    1983-01-01

    The present investigation is an original study in nucleate pool boiling heat transfer combining theory and experiment in which water boiling at atmospheric pressure on a single copper surface at two different levels of heat and different levels of subcooling was studied. Cross spectral analysis of the signals generated by the emission of bubbles at adjacent nucleation sites was used to determine the relationship of the time elapsed between the start of bubble growth at the two neighbouring active sites with the distance separating them. The experimental results obtained indicated that for the lower level of heat flux at three different levels of subcooling, the elapsed time and distance were directly related. Theoretical predictions of a temperature disturbance propagating through the heating surface in the radial direction gave good agreement with the experimental findings, suggesting that this is the mechanism responsible for the activation of the surrounding nucleation sites

  17. Influence of road salting on the adjacent Norway spruce (Picea abies) forest

    International Nuclear Information System (INIS)

    Forczek, S.T.; Benada, O.; Kofronova, O.; Sigler, K.; Matucha, M.

    2011-01-01

    Winter deicing and traffic spreads salt to road-adjacent Norway spruce trees in the form of spraying and salt slops. Our use of Na36Cl revealed roots as the main pathway of salt uptake. One-shot application of a concentrated Na36Cl solution to spruce saplings by both irrigation and spraying causes macroscopic damage to the needles and affects the needle phyllosphere. Irrigation affects the trees more than spraying because Cl uptake through roots is faster and eventually leads to higher chloride content in the plant. Along with the root-needle route, spray-deposited chloride from the needles is re-transported back into the soil and again taken up by roots to needles

  18. The dynamics of spiral tip adjacent to inhomogeneity in cardiac tissue

    Science.gov (United States)

    Zhang, Juan; Tang, Jun; Ma, Jun; Luo, Jin Ming; Yang, Xian Qing

    2018-02-01

    Rotating spiral waves in cardiac tissue are implicated in life threatening cardiac arrhythmias. Experimental and theoretical evidences suggest the inhomogeneities in cardiac tissue play a significant role in the dynamics of spiral waves. Based on a modified 2D cardiac tissue model, the interaction of inhomogeneity on the nearby rigidly rotating spiral wave is numerically studied. The adjacent area of the inhomogeneity is divided to two areas, when the initial rotating center of the spiral tip is located in the two areas, the spiral tip will be attracted and anchor on the inhomogeneity finally, or be repulsed away. The width of the area is significantly dependent on the intensity and size of the inhomogeneity. Our numerical study sheds some light on the mechanism of the interaction of inhomogeneity on the spiral wave in cardiac tissue.

  19. Internal calibration on adjacent samples (InCAS) with Fourier transform mass spectrometry.

    Science.gov (United States)

    O'Connor, P B; Costello, C E

    2000-12-15

    Using matrix-assisted laser desorption/ionization (MAL DI) on a trapped ion mass spectrometer such as a Fourier transform mass spectrometer (FTMS) allows accumulation of ions in the cell from multiple laser shots prior to detection. If ions from separate MALDI samples are accumulated simultaneously in the cell, ions from one sample can be used to calibrate ions from the other sample. Since the ions are detected simultaneously in the cell, this is, in effect, internal calibration, but there are no selective desorption effects in the MALDI source. This method of internal calibration with adjacent samples is demonstrated here on cesium iodide clusters, peptides, oligosaccharides, poly(propylene glycol), and fullerenes and provides typical FTMS internal calibration mass accuracy of < 1 ppm.

  20. Hydrothermal manganese oxide deposits from the Izu-Ogasawara (Bonin)-Mariana Arc and adjacent areas

    Energy Technology Data Exchange (ETDEWEB)

    Usui, A.; Nishimura, A. (Geological Survey of Japan, Tsukuba (Japan))

    1992-04-27

    Modern and fossil hydrothermal manganese oxide deposits were discovered from a number of locations in the Izu-Ogasawara(Bonin)-Mariana Arc and adjacent areas during the Hakurei-Maru cruises from 1984 to 1989. This paper describes the occurrence and characteristics of these manganese deposits and their geological significance. It was found that the mineralogical and chemical composition and microstructure of the deposits are typically different from manganese nodules and crusts of hydrogenetic or diagenetic origin. Hardpans, veinlets, sheets, and irregular mass of the hydrothermal manganese deposits often cover a large area of sea bed, which suggests possible high-temperature hydrothermal sulfide deposits in their vicinity. On the other hand, the manganese minerals sometimes occur as substrate of younger hydrogenetic crusts and as nucleus of hydrogenetic nodules, which can provide a geological history of low-temperature hydrothermal activity on the past island arcs. 45 refs., 19 figs., 3 tabs.

  1. Transport of mecoprop from agricultural soils to an adjacent salt marsh

    International Nuclear Information System (INIS)

    Fletcher, Caroline A.; Scrimshaw, Mark D.; Lester, John N.

    2004-01-01

    Salt marshes are important ecological areas and play a significant role in coastal flood defence schemes. In many areas of the UK they are adjacent to agricultural areas utilised for the growth of cereal crops, for which mecoprop is used as a selective herbicide in the control of broad-leafed weeds. This study measured concentrations of mecoprop in soils, drainage ditch waters and sediments and salt marsh sediments over a period of 138 days following spring application. Soil concentrations of up to 1827 μg/g were recorded after application, which demonstrated a half life for mecoprop of from 9 to 12 days, with first order kinetics. However, a major rainfall event 9 days after application resulted in significant transport of herbicide to the salt marsh via subsurface field drains, drainage ditches and discharge sluice. Mecoprop concentrations of up to 386 μg/l observed in water samples were above UK guidelines

  2. Norway and adjacent sedimentary basins during Cenozoic times - sediment fluxes, accumulation rates and mass balance

    DEFF Research Database (Denmark)

    Gołędowski, Bartosz; Nielsen, S.B.; Clausen, O.R.

    2011-01-01

    use offshore data from adjacent sedimentary basins (the North Sea and the Norwegian shelf) to calculate the amount of erosion. We have used a broad dataset of seismic 2D lines to map depositional units and a well dataset for the stratigraphic control and the velocity distribution in the sediments. We...... have therefore obtained accumulation rates in meters per million years for 5 depositional units in three areas - Southern North Sea, Central and Northern North Sea and the Norwegian shelf. Furthermore, taking into account the decay of porosity in sediments with burial depth, we have estimated...... the sediment volumes at the time of their deposition. Such calculation gives minimum values of erosion rates onshore and a mass balance can be approximated, when considering uncertainties like deposition of sediments outside study area, post-depositional sediment removal and loss of mass due to chemical...

  3. SOIL AND “CERRADO” TREES NUTRIENTS AND METALS IN ADJACENT SANITARY LANDFILL AREA

    Directory of Open Access Journals (Sweden)

    Otacílio Antunes Santana

    2008-09-01

    Full Text Available This research verified the influence of a Sanitary Landfill located at the Jockey Club of the Brasilia City (JCB on the chemical contents in the tree species of “Cerrado”. Six 25 x 500 m blocks were established in the PNB to sample the soil and the trees to chemical analysis. Three blocks were established near the landfill area and three in the control area. Nitrogen, phosphorus, potassium, calcium, lead, chromium, copper and mercury were analyzed. The highest nutrients and metals concentrations in soil were sampled in landfill adjacent area. The significant, crescent and directly proportional relationship (R2 > 0.80; p < 0.001 were observed between the elements concentration analyzed in soil with the leaves tissues. Therefore, the studied landfill presences increased nutrients and metals concentrations in soil and leaf tissue, fact that did not occur in the control area.

  4. Species richness and distribution of chondrichthyan fishes in the Arctic Ocean and adjacent seas

    DEFF Research Database (Denmark)

    Lynghammar, A.; Christiansen, J. S.; Mecklenburg, C. W.

    2013-01-01

    The sea ice cover decreases and human activity increases in Arctic waters. Fisheries and bycatch issues, shipping and petroleum exploitation (pollution issues) make it imperative to establish biological baselines for the marine fishes inhabiting the Arctic Ocean and adjacent seas (AOAS). Species...... richness, zoogeographic affiliations and Red List statuses among chondrichthyan fishes (Chondrichthyes) were examined across 16 AOAS regions as a first step towards credible conservation actions. Published literature and museum vouchers were consulted for presence/absence data. Although many regions...... are poorly sampled, 49 chondrichthyan species have been reported from the AOAS. Skates and rays are the most species-rich taxon, represented by 27 species in family Rajidae and one species in family Dasyatidae. The sharks comprise 20 species in 13 families and the chimaeras one species in family Chimaeridae...

  5. Thermal non-equilibrium in porous medium adjacent to vertical plate: ANN approach

    Science.gov (United States)

    Ahmed, N. J. Salman; Ahamed, K. S. Nazim; Al-Rashed, Abdullah A. A. A.; Kamangar, Sarfaraz; Athani, Abdulgaphur

    2018-05-01

    Thermal non-equilibrium in porous medium is a condition that refers to temperature discrepancy in solid matrix and fluid of porous medium. This type of flow is complex flow requiring complex set of partial differential equations that govern the flow behavior. The current work is undertaken to predict the thermal non-equilibrium behavior of porous medium adjacent to vertical plate using artificial neural network. A set of neurons in 3 layers are trained to predict the heat transfer characteristics. It is found that the thermal non-equilibrium heat transfer behavior in terms of Nusselt number of fluid as well as solid phase can be predicted accurately by using well-trained neural network.

  6. A method for opening a mine field which is adjacent to a pit

    Energy Technology Data Exchange (ETDEWEB)

    Onishchenko, V.I.; Grebenyuk, V.K.; Kukharev, V.N.; Martynenko, V.P.; Omelnitskiy, A.G.; Sallin, V.I.; Sidorov, A.S.

    1982-01-01

    The method for opening a mine field adjacent to a pit includes the construction of the main and auxiliary opening drifts in the pit and the surface complex of the mine through assembling a support with subsequent filling of them by tailings of the covering rock. In order to increase the productive capacity of the mine, to reduce capital expenditures and to increase the safety of underground operations, a base is first formed from the tailing rock along the front of the open mining operations, from the bottom of the pit at the level of the stratum being opened to the surface with simultaneous layer by layer packing of the cited base, after which the opening drifts are built on this base. The mouth of the main opening drifts and the surface complex of the mine are positioned in the region of the pit.

  7. Influence of a Brazilian sewage outfall on the toxicity and contamination of adjacent sediments

    Science.gov (United States)

    Abessa, D.M.S.; Carr, R.S.; Rachid, B.R.F.; Sousa, E.C.P.M.; Hortelani, M.A.; Sarkis, J.E.

    2005-01-01

    The submarine sewage outfall of Santos (SSOS) is situated in the Santos Bay (São Paulo, Brazil) and is potentially a significant source of contaminants to the adjacent marine ecosystem. The present study aimed to assess the influence of SSOS on the sediment toxicity and contamination at Santos Bay. At the disposal site, sediments tended to be finer, organically richer and exhibited higher levels of surfactants and metals, sometimes exceeding the “Threshold Effect Level” values. The SSOS influence was more evident toward the East, where the sediments exhibited higher levels of TOC, total S and metals during the summer 2000 sampling campaign. Sediment toxicity to amphipods was consistently detected in four of the five stations studied. Amphipod survival tended to correlate negatively to Hg, total N and % mud. This work provides evidence that the SSOS discharge affects the quality of sediments from Santos Bay, and that control procedures are warranted.

  8. Estuarine Human Activities Modulate the Fate of Changjiang-derived Materials in Adjacent Seas

    Science.gov (United States)

    WU, H.

    2017-12-01

    Mega constructions have been built in many river estuaries, but their environmental consequences in the adjacent coastal oceans were often overlooked. This issue was addressed with an example of the Changjiang River Estuary, which was recently built with massive navigation and reclamation constructions in recent years. Based on the model validations against cruises data and the numerical scenario experiments, it is shown that the estuarine constructions profoundly affected the fates of riverine materials in an indeed large offshore area. This is because estuarine dynamics are highly sensitive to their bathymetries. Previously, the Three Gorges Dam (TGD) was thought to be responsible for some offshore environmental changes through modulating the river plume extension, but here we show that its influences are secondary. Since the TGD and the mega estuarine constructions were built during the similar period, their influences might be confused.

  9. Bibliography of geologic studies: Columbia Plateau (Columbia River Basalt) and adjacent areas in Idaho

    International Nuclear Information System (INIS)

    Strowd, W.

    1978-11-01

    The objective of this compilation is to present a comprehensive listing of published, unpublished, and open-file references pertaining to the geology of the Columbia Plateau and adjacent areas in the State of Idaho. The bibliography was compiled in support of Rockwell's Basalt Waste Isolation Program that is evaluating the feasibility of nuclear waste storage in the Columbia River Basalt Group. The emphasis is on stratigraphy, structural geology, seismicity, and tectonics, although the nature of Columbia River Basalt distribution in Idaho has necessitated the inclusion of a sizeable collection of references on geology marginal to the Columbia Plateau and associated mineral resources. The bibliography is divided into two major sections, the alphabetical listing of all references and the subject index. The subject index is divided into 19 categories to facilitate locating a specific reference in the user's field of interest

  10. Energy Deposition in Adjacent LHC Superconducting Magnets from Beam Loss at LHC Transfer Line Collimators

    CERN Document Server

    Beavan, S; Kain, V

    2006-01-01

    Injection intensities for the LHC are over an order of magnitude above the damage threshold. The collimation system in the two transfer lines is designed to dilute the beam sufficiently to avoid damage in case of accidental beam loss or mis-steered beam. To maximise the protection for the LHC most of the collimators are located in the last 300 m upstream of the injection point where the transfer lines approach the LHC machine. To study the issue of possible quenches following beam loss at the collimators part of the collimation section in one of the lines, TI 8, together with the adjacent part of the LHC has been modeled in FLUKA. The simulated energy deposition in the LHC for worst-case accidental losses and as well as for losses expected during a normal filling is presented.

  11. Florisitic summary of 'Manual of Vascular Plants of Northeastern United States and Adjacent Canada', second edition

    Science.gov (United States)

    Bennett, J.P.

    1996-01-01

    The second edition of the Manual of Vascular Plants of Northeastern United States and Adjacent Canada by Gleason and Cronquist (1991) is the most recent and up-to-date taxonomic treatment of the flora of that region. Since no floristic summary of the Manual was included in the publication, a computer analysis of the taxonomic data of the Manual was performed in order to generate a floristic summary. Totals of 4285 species, 1091 genera, and 191 families were tabulated. The largest genus was Carex, with 230 species; the largest family was the Asteraceae, with 528 species. Comparisons made with earlier floras of the same region indicated small declines on the order of 10% for these taxonomic groups.

  12. Bone reactions adjacent to titanium implants subjected to static load. A study in the dog (I)

    DEFF Research Database (Denmark)

    Gotfredsen, K; Berglundh, T; Lindhe, J

    2001-01-01

    The aim of the study was to evaluate the effect of lateral static load induced by an expansion force on the bone/implant interface and adjacent peri-implant bone. In 3 beagle dogs, the 2nd, 3rd and 4th mandibular premolars were extracted bilaterally. Twelve weeks later 8 implants of the ITI Dental...... Implant System were placed in each dog. Crowns connected in pairs were screwed on the implants 12 weeks after implant installation. The connected crowns contained an orthodontic expansion screw yielding 4 loading units in each dog. Clinical registrations, standardized radiographs and fluorochrome labeling...... were carried out during the 24-week loading period. Biopsies were harvested and processed for ground sectioning. The sections were subjected to histological examination. No evident marginal bone loss was observed at either test or control sites. The bone density and the mineralized bone-to-implant...

  13. Economic importance of oleoresin (Dipterocarpus alatus) to forest-adjacent households in Cambodia

    DEFF Research Database (Denmark)

    Dyrmose, Anne-Mette Hüls; Turreira Garcia, Nerea; Theilade, Ida

    2017-01-01

    interviewed and 100 resin trees were measured to examine factors affecting resin productivity. Forest-adjacent households were highly dependent on resin extraction for cash income. Households spent an average of 105 days annually on resin extraction. The mean annual household gross-income derived from liquid...... resin was USD 3,236. Solid resin contributed only a small part of household incomes except for the most remote and isolated village, Spong, in which solid resin contributed significantly to the gross-income. Resin trees yielded an average of 18 liters of oleoresin per year according to interview......The genus Dipterocarpus is the main source of marketable liquid oleoresin, which is important as a source of income for forest communities in Southeast Asia. However, deforestation and illegal as well as legal logging pose a threat to resin yielding species (Dipterocarpus spp.). There is still more...

  14. Gibbs Energy Modeling of Digenite and Adjacent Solid-State Phases

    Science.gov (United States)

    Waldner, Peter

    2017-08-01

    All sulfur potential and phase diagram data available in the literature for solid-state equilibria related to digenite have been assessed. Thorough thermodynamic analysis at 1 bar total pressure has been performed. A three-sublattice approach has been developed to model the Gibbs energy of digenite as a function of composition and temperature using the compound energy formalism. The Gibbs energies of the adjacent solid-state phases covelitte and high-temperature chalcocite are also modeled treating both sulfides as stoichiometric compounds. The novel model for digenite offers new interpretation of experimental data, may contribute from a thermodynamic point of view to the elucidation of the role of copper species within the crystal structure and allows extrapolation to composition regimes richer in copper than stoichiometric digenite Cu2S. Preliminary predictions into the ternary Cu-Fe-S system at 1273 K (1000 °C) using the Gibbs energy model of digenite for calculating its iron solubility are promising.

  15. [Characteristics of ichthyoplankton assemblages in Yangtze Estuary and adjacent waters in spring].

    Science.gov (United States)

    Liu, Shu-De; Xian, Wei-Wei; Liu, Dong

    2008-10-01

    Based on the investigation data of ichthyoplankton assemblages and environmental factors in Yangtze Estuary and adjacent waters in May 1999 and 2001, the characteristics of ichthyoplankton assemblages in these areas in spring were studied by using TWINSPAN (two-way indicator species analysis) and CCA (canonical correspondence analysis). A total of 11 540 ichthyoplankton individuals were taxonomically identified, belonging to 11 orders, 18 families and 32 species, of which, Coilia mystus, Engraulis japonicus, Chaeturichthys hexanema, Allanetta bleekeri, and Trachidermis fasciatus were the dominant species. The ichthyoplankton communities were classified into three assemblages by using TWINSPAN, i.e., estuarine assemblage dominated by C. mystus, coastal assemblage dominated by A. bleekeri and T. fasciatus; and shelf assemblage featured by E. japonicus and C. hexanema. The CCA ordination of the interrelations among the three assemblages and their correlations to the environmental variables revealed that salinity, depth, dissolved oxygen, and total suspended particulate matter were the major factors affecting the ichthyoplankton assemblages in the study areas.

  16. Metal speciation in agricultural soils adjacent to the Irankuh Pb-Zn mining area, central Iran

    Science.gov (United States)

    Mokhtari, Ahmad Reza; Roshani Rodsari, Parisa; Cohen, David R.; Emami, Adel; Dehghanzadeh Bafghi, Ali Akbar; Khodaian Ghegeni, Ziba

    2015-01-01

    Mining activities are a significant potential source of metal contamination of soils in surrounding areas, with particular concern for metals dispersed into agricultural area in forms that are bioavailable and which may affect human health. Soils in agricultural land adjacent to Pb-Zn mining operations in the southern part of the Irankuh Mountains contain elevated concentrations for a range of metals associated with the mineralization (including Pb, Zn and As). Total and partial geochemical extraction data from a suite of 137 soil samples is used to establish mineralogical controls on ore-related trace elements and help differentiate spatial patterns that can be related to the effects of mining on the agricultural land soils from general geological and environmental controls. Whereas the patterns for Pb, Zn and As are spatially related to the mining operations they display little correlation with the distribution of secondary Fe + Mn oxyhydroxides or carbonates, suggesting dispersion as dust and in forms with limited bioavailability.

  17. Stock structure of Atlantic herring Clupea harengus in the Norwegian Sea and adjacent waters

    DEFF Research Database (Denmark)

    Pampoulie, Christophe; Slotte, Aril; Oskarsson, Guomundur J.

    2015-01-01

    The genetic structure of Atlantic herring Clupea harengus L. was investigated in its north-easterly distribution in the Norwegian Sea and adjacent waters, using 23 neutral and one non-neutral (Cpa111) microsatellite loci. Fish from the suspected 2 main populations-the Norwegian spring......-spawning herring (NSSH) and the Icelandic summer-spawning herring (ISSH)-were collected at spawning locations in their respective spawning seasons from 2009 to 2012. Samples were also collected from Norwegian autumn spawning locations, from different local Norwegian fjords such as the inner part...... of Trondheimsfjorden, Lindas pollene, Landvikvannet and Lusterfjorden, as well as from suspected Faroese spawning components. The observed level of genetic differentiation was significant but low (F-ST = 0.007) and mostly attributable to the differentiation of the local Norwegian fjord populations. The locus Cpa111...

  18. [Clinics adjacent to private pharmacies in Mexico: infrastructure and characteristics of the physicians and their remuneration].

    Science.gov (United States)

    Díaz-Portillo, Sandra P; Idrovo, Álvaro J; Dreser, Anahí; Bonilla, Federico R; Matías-Juan, Bonifacia; Wirtz, Veronika J

    2015-01-01

    To analyze and compare the physicians' characteristics, their remuneration, the compliance with regulation and the services offered between clinics adjacent to pharmacies (CAF) and independent medical clinics (CMI). Questionnaire applied to 239 physicians in 18 states including the Federal District, in Mexico in 2012. Physicians in CAF had less professional experience (5 versus 12 years), less postgraduate studies (61.2 versus 81.8%) and lower average monthly salaries (USD 418 versus USD 672) than their peers in CMI. In CAF there was less compliance in relation to medical record keeping and prescribing. The employment situation of physicians in CAF is more precarious than in CMI. It is necessary to strengthen the enforcement of existing regulations and develop policies according to the monitoring of its performance, particularly, but not exclusively, in CAF.

  19. Filler-depletion layer adjacent to interface impacts performance of thermal interface material

    Directory of Open Access Journals (Sweden)

    Susumu Yada

    2016-01-01

    Full Text Available When installing thermal interface material (TIM between heat source and sink to reduce contact thermal resistance, the interfacial thermal resistance (ITR between the TIM and heat source/sink may become important, especially when the TIM thickness becomes smaller in the next-generation device integration. To this end, we have investigated ITR between TIM and aluminum surface by using the time-domain thermoreflectance method. The measurements reveal large ITR attributed to the depletion of filler particles in TIM adjacent to the aluminum surface. The thickness of the depletion layer is estimated to be about 100 nm. As a consequence, the fraction of ITR to the total contact thermal resistance becomes about 20% when the TIM thickness is about 50 μm (current thickness, and it exceeds 50% when the thickness is smaller than 10 μm (next-generation thickness.

  20. Aerial surveys of seals at Rødsand seal sanctuary and adjacent haul-out sites

    DEFF Research Database (Denmark)

    Teilmann, J.; Dietz, R.; Edren, Susi M.C.

    This report describes the preliminary results of aerial surveys at Rødsand seal sanctuary, southeast Denmark and adjacent seal haul-out sites in southwestern Baltic. The work was carried out in connection with studies of potential effects of the Nysted offshore wind farm. Rødsand seal sanctuary...... is a part of seal management area 4, and the area is believed to hold a more or less closed population with little exchange to other areas. Although the harbour seal is relatively stationary there may be movements between the haul-out sites in the area. A possible reaction to disturbance from...... the construction and operation of the wind farm may be that the seals use other haul-out sites to a higher extend....

  1. Seasonality of pathogenic fungi in mites of rubber tree plantations adjacent to fragments of Cerrado

    Directory of Open Access Journals (Sweden)

    PR. Demite

    Full Text Available Fungi are the most frequently observed pathogens of mite populations, helping to control them on different crops. Twenty-five samples of leaves were collected from rubber tree plantations adjacent to two fragments of Cerrado vegetation. Each rubber tree plantation had 25 plants selected for sampling and seven leaves from around each tree top were collected up to seven to eight meters above ground. Approximately 250 individuals of Calacarus heveae Feres, Phyllocoptruta seringueirae Feres, and Tenuipalpus heveae Baker, collected randomly, were mounted from each plantation. Hirsutella thompsoni Fisher was observed on all three mites and T. heveae was the most infected species. The highest infestation levels occurred from November to February (rainy season. In the dry season, infestation levels were below 5%. Hirsutella thompsonii has potential to be used as mycoacaricide during the rainy season.

  2. Ambiguities in the elastic scattering of 8 MeV neutrons from adjacent nuclei

    International Nuclear Information System (INIS)

    Smith, A.B.; Lawson, R.D.; Guenther, P.T.

    1989-10-01

    Ratios of the cross sections for elastic scattering of 8 MeV neutrons from adjacent nuclei are measured over the angular range ∼20 degree - 160 degree for the target pairs 51 V/Cr, 59 Co/ 58 Ni, Cu/Zn, 89 Y/ 93 Nb, 89 Y/Zr, 93 Nb/Zr, In/Cd and 209 Bi/Pb. The observed ratios vary from unity by as much as a factor of ∼2 at some angles for the lighter target pairs. Approximately half the measured ratios are reasonably explained by a simple spherical optical model, including size and isospin contributions. In all cases, the geometry of the real optical--model potential is essentially the same for neighboring nuclei, and the real--potential strengths are consistent with the Lane model. In contrast, it is found that the imaginary potential may be quite different for adjacent nuclei, and the nature of this difference is examined. It is shown that the spin--spin interaction has a negligible effect on the calculation of the elastic--scattering ratios, but that channel coupling, leading to a large reorientation of the target ground state, can be a consideration, particularly in the 59 Co/ 58 Ni case. In the A ∼ 50--60 region the calculated ratios are sensitive to spin--orbit effects, but the exact nature of this interaction must await more definitive polarization measurements. The measured and calculated results suggest that the concept of a conventional ''global'' or even ''regional'' optical potential provides no more than a qualitative representation of the physical reality for a number of cases. 48 refs., 14 figs., 3 tabs

  3. Ambiguities in the elastic scattering of 8 MeV neutrons from adjacent nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Smith, A.B.; Lawson, R.D.; Guenther, P.T.

    1989-10-01

    Ratios of the cross sections for elastic scattering of 8 MeV neutrons from adjacent nuclei are measured over the angular range {approx}20{degree} {minus} 160{degree} for the target pairs {sup 51}V/Cr, {sup 59}Co/{sup 58}Ni, Cu/Zn, {sup 89}Y/{sup 93}Nb, {sup 89}Y/Zr, {sup 93}Nb/Zr, In/Cd and {sup 209}Bi/Pb. The observed ratios vary from unity by as much as a factor of {approx}2 at some angles for the lighter target pairs. Approximately half the measured ratios are reasonably explained by a simple spherical optical model, including size and isospin contributions. In all cases, the geometry of the real optical--model potential is essentially the same for neighboring nuclei, and the real--potential strengths are consistent with the Lane model. In contrast, it is found that the imaginary potential may be quite different for adjacent nuclei, and the nature of this difference is examined. It is shown that the spin--spin interaction has a negligible effect on the calculation of the elastic--scattering ratios, but that channel coupling, leading to a large reorientation of the target ground state, can be a consideration, particularly in the {sup 59}Co/{sup 58}Ni case. In the A {approx} 50--60 region the calculated ratios are sensitive to spin--orbit effects, but the exact nature of this interaction must await more definitive polarization measurements. The measured and calculated results suggest that the concept of a conventional global'' or even regional'' optical potential provides no more than a qualitative representation of the physical reality for a number of cases. 48 refs., 14 figs., 3 tabs.

  4. Distribution of chromium in vegetation and small mammals adjacent to cooling towers

    International Nuclear Information System (INIS)

    Taylor, F.G. Jr.; Parr, P.D.; Dahlman, R.C.

    1975-01-01

    Surface contamination of vegetation by aerosol pollutants and subsequent ingestion by grazing vertebrates is a pathway for incorporation of toxic elements into food chains. Small mammals (herbivores) were live-trapped in a fescue-dominated field adjacent to large, mechanical draft cooling towers comparable to those utilized by power generation facilities. Cooling waters of the towers contain a chromate, zinc-phosphate compound to inhibit corrosion and fouling within the cooling system. A fraction of the cooling water becomes entrained within the exit air flow and is deposited as drift on the landscape. Resident mammals are chronically subjected to increased chromium exposures through both ingestion and inhalation pathways. Concentrations in vegetation ranged from 342 to 15 ppM at 15 and 130 meters down wind. Concentration levels in litter exceeded those of live plant materials by a factor of 5. Chromium distribution in mammals adjacent to the cooling towers is compared by organ analyses to corresponding organs and tissues of mammals collected remote from drift. Concentrations of chromium in pelt, hair, and bone of animals trapped near the cooling towers were significantly higher (P is less than 0.01) than tissues from control animals. Air concentrations ranged from 15 to 8 μg/m 3 at 15 and 100 meters, and thus provided a potential pathway for increased chromium levels through inhalation. Biological accumulation and retention following ingestion are discussed in a subsequent paper in this symposium (Van Hook et al.). Elevated levels of hexavalent chromium in air have been identified as a potential health hazard. Pathological studies of lung tissues were performed and were negative for lesions. (U.S.)

  5. Compensatory immigration depends on adjacent population size and habitat quality but not on landscape connectivity.

    Science.gov (United States)

    Turgeon, Katrine; Kramer, Donald L

    2012-11-01

    1. Populations experiencing localized mortality can recover in the short term by net movement of individuals from adjacent areas, a process called compensatory immigration or spillover. Little is known about the factors influencing the magnitude of compensatory immigration or its impact on source populations. Such information is important for understanding metapopulation dynamics, the use of protected areas for conservation, management of exploited populations and pest control. 2. Using two small, territorial damselfish species (Stegastes diencaeus and S. adustus) in their naturally fragmented habitat, we quantified compensatory immigration in response to localized mortality, assessed its impact on adjacent source populations and examined the importance of potential immigrants, habitat quality and landscape connectivity as limiting factors. On seven experimental sites, we repeatedly removed 15% of the initial population size until none remained and immigration ceased. 3. Immigrants replaced 16-72% of original residents in S. diencaeus and 0-69% in S. adustus. The proportion of the source population that immigrated into depleted areas varied from 9% to 61% in S. diencaeus and from 3% to 21% in S. adustus. In S. diencaeus, compensatory immigration was strongly affected by habitat quality, to a lesser extent by the abundance of potential immigrants and not by landscape connectivity. In S. adustus, immigration was strongly affected by the density of potential migrants and not by habitat quality and landscape connectivity. On two control sites, immigration in the absence of creation of vacancies was extremely rare. 4. Immigration occurred in response to localized mortality and was therefore compensatory. It was highly variable, sometimes producing substantial impacts on both depleted and source populations. The magnitude of compensatory immigration was influenced primarily by the availability of immigrants and by the potential improvement in territory quality that they

  6. Coronal MRI in the diagnosis of corona radiata infarcts adjacent to the lateral ventricles

    Energy Technology Data Exchange (ETDEWEB)

    Iwamoto, Toshihiko; Abe, Shin-e; Kanaya, Kiyoshi; Kubo, Hideki; Takasaki, Masaru (Tokyo Medical Coll. (Japan))

    1992-04-01

    To clarify pathophysiology of vascular lesions in corona radiata infarcts adjacent to the body of the lateral ventricle (CRILV), 17 patients with CRILV were studied by using magnetic resonance (MR) imaging. Based on the coronal MR images obtained between the anterior and posterior commissures, the patients were divided into two groups: (I) the group having infarcts below a line extending from the upper edge of the insular cistern to the external angle of the lateral ventricle adjacent to the corpus callosum (n=11); and (II) the group having lesions above the line towards the centrum semiovale (n=6). Most of the patients in both groups were male and had hypertension. Symptoms were gradually deteriorated and stroke in the morning was frequent in both groups, althrough the time from onset to completion was longer in Group II than Group I. In comparing clinical manifestations in Groups I and II, pure motor hemiparesis was found in 5 and 3 patients, and sensorimotor stroke in 2 and one patients, respectively. Drowsiness was found in 2 for Group I, while aphasia occurred in 2 for Group II. In addition, pseudobular and asymptomatic palsy occurred in each one patient for Group I. Prognosis was favorable in both groups, except for 2 who died of aspiration pneumonia. In Group I, 11 infarcts were well-defined, less than 15 mm in diameter on CT scans and were sclerotic in the main arteries without obstruction on angiograms. In contrast, Group II had ill-defined, larger low-density areas on CT scans and trunk obstruction of the internal carotid or middle cerebral arteries on angiograms. SPECT scans showed diffuse defect in Group II, in contrast to normal to diffuse or multiple defects in Group I. In Group I, lacunar lesions seemed to be caused by ischemia of the perforators, and in Group II, terminal zone infarcts in the territory of the cortical branches or watershed infarcts seemd to be caused by main trunk obstruction. (N.K.).

  7. MRI of lesser metatarsophalangeal joint plantar plate tears and associated adjacent interspace lesions

    Energy Technology Data Exchange (ETDEWEB)

    Umans, Hilary [Albert Einstein College of Medicine and Lenox Hill Radiology Imaging and Associates, Bronx, NY (United States); Srinivasan, Ramya; Elsinger, Elisabeth [Albert Einstein College of Medicine, Bronx, NY (United States); Wilde, Gregory E. [Lenox Hill Radiology Imaging and Associates, Bronx, NY (United States)

    2014-10-15

    To identify the variety of second and third intermetatarsal space (IS) lesions that may coexist with and without adjacent metatarsophalangeal joint (MTP) plantar plate (PP) tears. One hundred forefoot MRIs in 96 patients with metatarsalgia obtained between 30 September 2011 and 21 July 2012 using 1.5- or 3-T MRI were retrospectively reviewed in consensus by two MSK radiologists and one podiatrist (DPM). MRI was evaluated for second and third MTP PP tear and the presence/nature of second and third IS lesions. Second and third IS neuromas were measured in transverse (trans) dimension. A total of 40 PP tears were identified: 36 at the second and 4 at the third MTP. Second MTP PP tear was identified in 33 % of females and 40.5 % of males. In the 63 female feet there were 21 second MTP PP tears, all of which also had second IS lesions: pericapsular fibrosis (16), bursitis (4), and ganglion (1). In the 37 male feet there were 15 second MTP PP tears, 14 of which had second IS lesions: pericapsular fibrosis (8), bursitis (5), and ganglion (1). There was no definite second IS neuroma adjacent to any second MTP PP tear. In females without PP tear, there were 24 second (3 mm trans average) and 43 third IS neuromas (4.1 mm trans average). In males without PP tear, there were 9 second (3.4 mm trans average) and 16 third IS neuromas (4.1 mm trans average). MTP PP tears occurred in 40 % of our cases, 90 % of which occurred at the second MTP. Almost all coexisted with non-neuromatous second IS lesions. (orig.)

  8. Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

    Science.gov (United States)

    Peng, Tao; Xue, Chenghai; Bi, Jianning; Li, Tingting; Wang, Xiaowo; Zhang, Xuegong; Li, Yanda

    2008-04-26

    Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments indicate that multiple cassette exons within a gene may interact with each other. This interaction can increase the potential to generate various transcripts and adds an extra layer of complexity to gene regulation. Several cases of exon interaction have been discovered. However, the extent to which the cassette exons coordinate with each other remains unknown. Based on EST data, we employed a metric of correlation coefficients to describe the interaction between two adjacent cassette exons and then categorized these exon pairs into three different groups by their interaction (correlation) patterns. Sequence analysis demonstrates that strongly-correlated groups are more conserved and contain a higher proportion of pairs with reading frame preservation in a combinatorial manner. Multiple genome comparison further indicates that different groups of correlated pairs have different evolutionary courses: (1) The vast majority of positively-correlated pairs are old, (2) most of the weakly-correlated pairs are relatively young, and (3) negatively-correlated pairs are a mixture of old and young events. We performed a large-scale analysis of interactions between adjacent cassette exons. Compared with weakly-correlated pairs, the strongly-correlated pairs, including both the positively and negatively correlated ones, show more evidence that they are under delicate splicing control and tend to be functionally important. Additionally, the positively-correlated pairs bear strong resemblance to constitutive exons, which suggests that they may evolve from ancient constitutive exons, while negatively and weakly correlated pairs are more likely to contain newly emerging exons.

  9. IMMEDIATE RECIPROCAL CHANGES AT ADJACENT LEVEL FOLLOWING SINGLE-LEVEL ALIF

    Directory of Open Access Journals (Sweden)

    Enrique Vargas Uribe

    2015-12-01

    Full Text Available Objective : To assess the segmental sagittal parameters and the adjacent mobile segment after interbody fusion by anterior approach in single-level L5-S1. Methods : Retrospective study. Inclusion: Interbody fusion by anterior approach (10°/15° angle, due to DDD, low-grade spondylolisthesis and/or stenosis without prior lumbar fusion. Thirty-five cases were included (25 women; mean age 47±15 years. Analysis of lumbar radiographs were performed preoperatively and 3 months after surgery. The following parameters were evaluated: lumbar lordosis; segmental lordosis L4-L5 and L5-S1; sacral and L5 slope. Two independent evaluators made the measurements. Student's t test was used. Results : There was correction of lordosis at the L5-S1 level, from an average of 19° prior to surgery to 28° three months after surgery (p<0.001. It was observed reduction of the L4-L5 angle from 17° to 14° (p <0.001. Moreover, there was a small, but statistically significant, reduction of L5 inclination from 17 ° to 13 ° (p=0.007 and increase in the sacral slope from 37° to 40° (p=0.002. The change of total lumbar lordosis was not significant: 52° versus 53° (p=0.461. Before surgical correction, lordosis of the L5-S1 level contributed, on average, 37% of lumbar lordosis, and after, 54% (p<0.001. The L4-L5 level accounted for 34% and decreased to 24% (p<0.001. Conclusion : In the group studied, it was observed a decrease in lordosis of the adjacent mobile level following the treatment of the degenerate level by anterior interbody fusion and concomitant increase in lordosis.

  10. Seedling Regeneration in the Alpine Treeline Ecotone: Comparison of Wood Microsites and Adjacent Soil Substrates

    Directory of Open Access Journals (Sweden)

    Adelaide Chapman Johnson

    2016-11-01

    Full Text Available Although climate warming is generally expected to facilitate upward advance of forests, conifer seedling regeneration and survival may be hindered by low substrate moisture, high radiation, and both low and high snow accumulation. To better understand substrate-related factors promoting regeneration in the alpine treeline ecotone, this study compared 2 substrates supporting conifer seedlings: rotten downed wood and adjacent soil. Study locations, each with 3 levels of incoming radiation, were randomly selected at forest line–alpine meadow borders in Pacific Northwest wilderness areas extending along an east–west precipitation gradient. Associations among substrate type, seedling density, radiation, site moisture, site temperature, plant water potential, and plant stomatal conductance were assessed. Wood microsites, flush with the ground and supporting Abies spp conifer seedlings, extended up to 20 m into alpine meadows from the forest line. Although wood microsites thawed later in the spring and froze earlier in the fall, they had warmer summer temperatures, greater volumetric water content, and more growing degree hours, and seedlings growing on wood had higher water potentials than seedlings growing on adjacent soil. At drier eastern sites, there was a positive relationship between seedling density and volumetric water content. Further, there was a positive relationship between seedling stomatal conductance and volumetric water content. Our study indicates that in the Pacific Northwest. and likely elsewhere, seedlings benefit from wood microsites, which provide greater water content. Given predictions of increased summer drought in some locations globally, wood microsites at forest line–alpine meadows and forest line–grasslands borders may become increasingly important for successful conifer regeneration.

  11. MRI of lesser metatarsophalangeal joint plantar plate tears and associated adjacent interspace lesions

    International Nuclear Information System (INIS)

    Umans, Hilary; Srinivasan, Ramya; Elsinger, Elisabeth; Wilde, Gregory E.

    2014-01-01

    To identify the variety of second and third intermetatarsal space (IS) lesions that may coexist with and without adjacent metatarsophalangeal joint (MTP) plantar plate (PP) tears. One hundred forefoot MRIs in 96 patients with metatarsalgia obtained between 30 September 2011 and 21 July 2012 using 1.5- or 3-T MRI were retrospectively reviewed in consensus by two MSK radiologists and one podiatrist (DPM). MRI was evaluated for second and third MTP PP tear and the presence/nature of second and third IS lesions. Second and third IS neuromas were measured in transverse (trans) dimension. A total of 40 PP tears were identified: 36 at the second and 4 at the third MTP. Second MTP PP tear was identified in 33 % of females and 40.5 % of males. In the 63 female feet there were 21 second MTP PP tears, all of which also had second IS lesions: pericapsular fibrosis (16), bursitis (4), and ganglion (1). In the 37 male feet there were 15 second MTP PP tears, 14 of which had second IS lesions: pericapsular fibrosis (8), bursitis (5), and ganglion (1). There was no definite second IS neuroma adjacent to any second MTP PP tear. In females without PP tear, there were 24 second (3 mm trans average) and 43 third IS neuromas (4.1 mm trans average). In males without PP tear, there were 9 second (3.4 mm trans average) and 16 third IS neuromas (4.1 mm trans average). MTP PP tears occurred in 40 % of our cases, 90 % of which occurred at the second MTP. Almost all coexisted with non-neuromatous second IS lesions. (orig.)

  12. The ground beetles (Coleoptera: Carabidae) of the Strandzha Mountain and adjacent coastal territories (Bulgaria and Turkey).

    Science.gov (United States)

    Kostova, Rumyana; Guéorguiev, Borislav

    2016-01-01

    The knowledge of the ground-beetle fauna of Strandzha is currently incomplete, and is largely based on data from the Bulgarian part of the region and on records resulting from casual collecting. This study represents a critical revision of the available literature, museum collections and a three years field study of the carabid beetles of the Bulgarian and Turkish parts of Strandzha Mountain and the adjacent Black Sea Coast territories. A total of 328 species and subspecies of Carabidae, belonging to 327 species from the region of Strandzha Mountain and adjacent seacoast area, have been listed. Of these, 77 taxa represent new records for the Bulgarian part of the region, and 110 taxa new records for Turkish part of the studied region. Two taxa, one subgenus (Haptotapinus Reitter, 1886) and one species (Pterostichus crassiusculus), are new to the fauna of Bulgaria. Based on a misidentification, the species Apotomus testaceus is excluded from the list of the Bulgarian fauna. Seven species (Carabus violaceus azurescens, Apotomus rufus, Platynus proximus, Molops alpestris kalofericus, M. dilatatus angulicollis, Pterostichus merklii, and Calathus metallicus) are treated as doubtful for the regional fauna, and one (Apotomus rufus) also for the Bulgarian fauna. Altogether, 43 taxa collected in the Turkish part of the region are new for European Turkey. New taxa for Turkey are the genera Myas and Oxypselaphus, the subgenus Feronidius, and nine species and subspecies (Carabus granulatus granulatus, Dyschirius tristis, Bembidion normannum apfelbecki, B. subcostatum vau, Acupalpus exiguus, Myas chalybaeus, Oxypselaphus obscurus, Pterostichus leonisi, Pt. melas). In addition, there are a further seven species that are here confirmed for Turkey.

  13. A novel biomimetic orthodontic bonding agent helps prevent white spot lesions adjacent to brackets.

    Science.gov (United States)

    Manfred, Lauren; Covell, David A; Crowe, Jennifer J; Tufekci, Eser; Mitchell, John C

    2013-01-01

    To compare changes in enamel microhardness adjacent to orthodontic brackets after using bonding agents containing various compositions of bioactive glass compared to a traditional resin adhesive following a simulated caries challenge. Extracted human third molars (n  =  10 per group) had orthodontic brackets bonded using one of four novel bioactive glass (BAG)-containing orthodontic bonding agents (BAG-Bonds) or commercially available Transbond-XT. The four new adhesives contained BAG in varying percentages incorporated into a traditional resin monomer mixture. Teeth were cycled through low-pH demineralizing and physiologic-pH remineralizing solutions once each day over 14 days. Microhardness was measured on longitudinal sections of the teeth 100, 200, and 300 µm from the bracket edge and beneath the brackets, at depths of 25 to 200 µm from the enamel surface. Normalized hardness values were compared using three-way analysis of variance. Significantly less reduction in enamel microhardness was found with the experimental adhesives at depths of 25 and 50 µm at all distances from the bracket edge. In all groups, there were no significant changes in enamel microhardness past 125-µm depth. Results varied with the different BAG-Bonds, with 81BAG-Bond showing the smallest decrease in enamel microhardness. The BAG-Bonds tested in this study showed a reduction in the amount of superficial enamel softening surrounding orthodontic brackets compared to a traditional bonding agent. The results indicate that clinically, BAG-Bonds may aid in maintaining enamel surface hardness, therefore helping prevent white spot lesions adjacent to orthodontic brackets.

  14. Determining the influence of Itaipu Lake on thermal conditions for soybean development in adjacent lands

    Science.gov (United States)

    Wagner-Riddle, C.; Werner, S. S.; Caramori, P.; Ricce, W. S.; Nitsche, P.; von Bertoldi, P.; de Souza, E. F.

    2015-10-01

    Previous numerical simulations have suggested that the area adjacent to Itaipu Lake in Southern Brazil is significantly affecting the local thermal regime through development of a lake breeze. This has led to concerns that soybean growth and development, and consequently yield, has been affected by the creation of the artificial lake in this important agricultural region, but a systematic climatological study of the thermal effects of Itaipu Lake has not been conducted. The objectives of this study were to assess the spatial pattern of minimum and maximum air temperatures in a 10-km-wide area adjacent to Itaipu Lake as affected by distance from the water. Measurements were conducted over 3 years in seven transects along the shore of Itaipu Lake, with five weather stations placed in each transect. Phenological observations in soybean fields surrounding the weather stations were also conducted. Generalized additive models for location, scale, and shape (GAMLSS) analysis indicated no difference in the temperature time series as distance from water increased. Semivariograms showed that the random components in the air temperature were predominant and that there was no spatial structure to the signal. Wind direction measured over the three growing seasons demonstrated that, on average, the development of a lake breeze is limited to a few locations and a few hours of the day, supporting the temporal and spatial analysis. Phenological observations did not show differences in the timing of critical soybean stages. We suggest that the concerns that soybean development is potentially affected by the presence of Itaipu Lake are not supported by the thermal environment observed.

  15. Human papilloma viruses and cervical tumours: mapping of integration sites and analysis of adjacent cellular sequences

    International Nuclear Information System (INIS)

    Klimov, Eugene; Vinokourova, Svetlana; Moisjak, Elena; Rakhmanaliev, Elian; Kobseva, Vera; Laimins, Laimonis; Kisseljov, Fjodor; Sulimova, Galina

    2002-01-01

    In cervical tumours the integration of human papilloma viruses (HPV) transcripts often results in the generation of transcripts that consist of hybrids of viral and cellular sequences. Mapping data using a variety of techniques has demonstrated that HPV integration occurred without obvious specificity into human genome. However, these techniques could not demonstrate whether integration resulted in the generation of transcripts encoding viral or viral-cellular sequences. The aim of this work was to map the integration sites of HPV DNA and to analyse the adjacent cellular sequences. Amplification of the INTs was done by the APOT technique. The APOT products were sequenced according to standard protocols. The analysis of the sequences was performed using BLASTN program and public databases. To localise the INTs PCR-based screening of GeneBridge4-RH-panel was used. Twelve cellular sequences adjacent to integrated HPV16 (INT markers) expressed in squamous cell cervical carcinomas were isolated. For 11 INT markers homologous human genomic sequences were readily identified and 9 of these showed significant homologies to known genes/ESTs. Using the known locations of homologous cDNAs and the RH-mapping techniques, mapping studies showed that the INTs are distributed among different human chromosomes for each tumour sample and are located in regions with the high levels of expression. Integration of HPV genomes occurs into the different human chromosomes but into regions that contain highly transcribed genes. One interpretation of these studies is that integration of HPV occurs into decondensed regions, which are more accessible for integration of foreign DNA

  16. Correlation of data on strain accumulation adjacent to the San Andreas Fault with available models

    Science.gov (United States)

    Turcotte, Donald L.

    1986-01-01

    Theoretical and numerical studies of deformation on strike slip faults were performed and the results applied to geodetic observations performed in the vicinity of the San Andreas Fault in California. The initial efforts were devoted to an extensive series of finite element calculations of the deformation associated with cyclic displacements on a strike-slip fault. Measurements of strain accumulation adjacent to the San Andreas Fault indicate that the zone of strain accumulation extends only a few tens of kilometers away from the fault. There is a concern about the tendency to make geodetic observations along the line to the source. This technique has serious problems for strike slip faults since the vector velocity is also along the fault. Use of a series of stations lying perpendicular to the fault whose positions are measured relative to a reference station are suggested to correct the problem. The complexity of faulting adjacent to the San Andreas Fault indicated that the homogeneous elastic and viscoelastic approach to deformation had serious limitations. These limitation led to the proposal of an approach that assumes a fault is composed of a distribution of asperities and barriers on all scales. Thus, an earthquake on a fault is treated as a failure of a fractal tree. Work continued on the development of a fractal based model for deformation in the western United States. In order to better understand the distribution of seismicity on the San Andreas Fault system a fractal analog was developed. The fractal concept also provides a means of testing whether clustering in time or space is a scale-invariant process.

  17. Pathological interstitial vascular proliferation adjacent to glomeruli in immunoglobulin a nephropathy

    Directory of Open Access Journals (Sweden)

    Honami Mori

    2016-01-01

    Full Text Available We detected an increase in small arterioles around glomeruli, particularly adjacent to tuft adhesive lesions in immunoglobulin A nephropathy (IgAN, for the 1 st time, as far as we know. We labeled these as periglomerular microarterioles (PGMAs. This study aimed to clarify the pathological significance of PGMAs. Sixty-two patients with IgAN and 19 controls with minor glomerular abnormalities without proteinuria were evaluated in this study. The number of PGMAs located between the Bowman′s capsule and the adjoining tubules was counted for each glomerulus. The mean number of PGMAs per glomerulus in cases of IgAN was significantly higher than those of the controls (0.530 ± 0.477 vs. 0.240 ± 0.182, P <0.05. Serial sections showed that most of the PGMAs were in contact with adjacent glomeruli (71.8%, through tuft adhesive lesions (52.1%, or the vascular pole (19.7%. By single regression analysis, the number of PGMAs was found to be positively correlated with the incidence of glomerular tuft adhesion, glomerular sclerosis, or the area of interstitial fibrosis in IgAN. By multiple regression analysis, the incidence of glomerular tuft adhesion was found to be the only independent pathological feature to correlate with the number of PGMAs (P = 0.0006. We have noticed the existence of PGMAs around glomeruli as a pathological finding of IgAN. Furthermore, the number of PGMAs was associated with the incidence of tuft adhesive lesion in glomeruli of IgAN although there was no relationship between the presence of PGMAs and clinical parameters including urinary protein excretion or creatinine clearance in the present study.

  18. MRI-guided percutaneous cryoablation of renal tumors: Use of external manual displacement of adjacent bowel loops

    International Nuclear Information System (INIS)

    Tuncali, Kemal; Morrison, Paul R.; Tatli, Servet; Silverman, Stuart G.

    2006-01-01

    Purpose: We sought to investigate retrospectively the safety and effectiveness of using external hand compression to displace adjacent bowel loops during MRI-guided percutaneous cryoablation of renal tumors. Materials and methods: Fourteen patients (six women, eight men; mean age: 72 years) with 15 renal tumors (mean diameter: 2.4 cm; range: 1.4-4.6 cm) adjacent to bowel were treated with MRI-guided percutaneous cryoablation during which bowel was displaced manually. Bowel loop of concern was ascending colon (n 5), descending colon (n = 8), descending colon and small bowel (n = 1), ascending colon and small bowel (n = 1). To analyze effectiveness of the maneuver, mean distance between tumor margin and bowel before and after the maneuver were compared and analyzed using paired Student's t-test. Minimum distance between iceball edge and adjacent bowel with external manual displacement during freezing was also measured. Safety was assessed by analyzing post-procedural MR imaging for adjacent bowel wall thickening and focal fluid collections as well as patients' clinical and imaging follow-up. Results: Mean distance between tumor margin and closest adjacent bowel increased from 0.8 cm (range: 0-2 cm) before external manual compression to 2.6 cm (range: 1.6-4.1 cm) with manual displacement (p < 0.01). Mean minimum distance between iceball edge and closest adjacent bowel during the procedures was 1.6 cm (range: 0.5-3.5 cm). No evidence of bowel injury was encountered. Twelve of 15 tumors had follow-up (mean: 10 months) that showed no tumor recurrence. Conclusion: MRI-guided percutaneous cryoablation of renal tumors adjacent to bowel can be done safely and effectively using external hand compression to displace bowel loops

  19. Adjacent segment pathology following anterior decompression and fusion using cage and plate for the treatment of degenerative cervical spinal diseases.

    Science.gov (United States)

    Song, Kyung-Jin; Choi, Byung-Wan; Kim, Jong-Kil

    2014-12-01

    Retrospective study. To analyze the incidence and prevalence of clinical adjacent segment pathology (CASP) following anterior decompression and fusion with cage and plate augmentation for degenerative cervical diseases. No long-term data on the use of cage and plate augmentation have been reported. The study population consisted of 231 patients who underwent anterior cervical discectomy and fusion (ACDF) with cage and plate for degenerative cervical spinal disease. The incidence and prevalence of CASP was determined by using the Kaplan-Meier survival analysis. To analyze the factors that influence CASP, data on preoperative and postoperative sagittal alignment, spinal canal diameter, the distance between the plate and adjacent disc, extent of fusion level, and the presence or absence of adjacent segment degenerative changes by imaging studies were evaluated. CASP occurred in 15 of the cases, of which 9 required additional surgery. At 8-year follow-up, the average yearly incidence was 1.1%. The rate of disease-free survival based on Kaplan-Meier survival analysis was 93.6% at 5 years and 90.2% at 8 years. No statistically significant differences in CASP incidence based on radiological analysis were observed. Significantly high incidence of CASP was observed in the presence of increased adjacent segment degenerative changes (pdegenerative cervical disease is associated with a lower incidence in CSAP by 1.1% per year, and the extent of preoperative adjacent segment degenerative changes has been shown as a risk factor for CASP.

  20. Isotopic study of mercury sources and transfer between a freshwater lake and adjacent forest food web

    International Nuclear Information System (INIS)

    Kwon, Sae Yun; Blum, Joel D.; Nadelhoffer, Knute J.; Timothy Dvonch, J.; Tsui, Martin Tsz-Ki

    2015-01-01

    Studies of monomethylmercury (MMHg) sources and biogeochemical pathways have been extensive in aquatic ecosystems, but limited in forest ecosystems. Increasing evidence suggests that there is significant mercury (Hg) exchange between aquatic and forest ecosystems. We use Hg stable isotope ratios (δ 202 Hg and Δ 199 Hg) to investigate the relative importance of MMHg sources and assess Hg transfer pathways between Douglas Lake and adjacent forests located at the University of Michigan Biological Station, USA. We characterize Hg isotopic compositions of basal resources and use linear regression of % MMHg versus δ 202 Hg and Δ 199 Hg to estimate Hg isotope values for inorganic mercury (IHg) and MMHg in the aquatic and adjacent forest food webs. In the aquatic ecosystem, we found that lake sediment represents a mixture of IHg pools deposited via watershed runoff and precipitation. The δ 202 Hg and Δ 199 Hg values estimated for IHg are consistent with other studies that measured forest floor in temperate forests. The Δ 199 Hg value estimated for MMHg in the aquatic food web indicates that MMHg is subjected to ~ 20% photochemical degradation prior to bioaccumulation. In the forest ecosystem, we found a significant negative relationship between total Hg and δ 202 Hg and Δ 199 Hg of soil collected at multiple distances from the lakeshore and lake sediment. This suggests that IHg input from watershed runoff provides an important Hg transfer pathway between the forest and aquatic ecosystems. We measured Δ 199 Hg values for high trophic level insects and compared these insects at multiple distances perpendicular to the lake shoreline. The Δ 199 Hg values correspond to the % canopy cover suggesting that forest MMHg is subjected to varying extents of photochemical degradation and the extent may be controlled by sunlight. Our study demonstrates that the use of Hg isotopes adds important new insight into the relative importance of MMHg sources and complex Hg transfer

  1. Complex Approach to Thyroid Screening In Regions Adjacent to the Semipalatinsk Test Site Area

    International Nuclear Information System (INIS)

    Zhumadilov, Zh.Sh.; Musinov, D.R.; Vasikovsky, G.G.; Bobokhidze, D.A.; Zhigitaev, T.K.; Abisheva, G.N.

    1998-01-01

    It has been well documented that the thyroid gland is one of the most radiosensitive of organs, especially when exposure occurs during childhood. It is known as well that childhood exposure to radioactive iodine increases thyroid cancer risk. Conducting thyroid screening in regions adjacent to the Semipalatinsk Test Site (STS) area is very important for medical examination, data management and thyroid dose reconstruction. Our experience of thyroid screening based on our screening projects in Kurchatov and several regions adjacent to STS (more than 4,000 screened patients) allowed to work out the most appropriate screening protocol. A retrospective analysis of the results of surgical treatment of the 7,271 patients with thyroid abnormalities in the Semipalatinsk, Pavlodar and Ust-Kamenogorsk regions of Kazakstan and study the histological staging of 7,271 surgically removed thyroid glands was preceded by our thyroid screening projects. Ours is the first study in the Semipalatinsk region that covers the period 1966-1998.Taking into account the onset of population effective doses during 1962, it was decided to distinguish 6 periods of observation. It is known that basic effective equivalent doses for the majority of the region's population were established by radioactive events in the period 1949-1962. This explains our focus on the year 1962, but thyroid dose reconstruction matter as well as other radiation related problems are still in the progress. We need to get the accurate dosimetry data. Selection of study subjects based on the appropriate criteria needed to be adjusted and clarified in accordance with the main goal of the project and radiation related information. All specialists involved in the thyroid screening project, data management, data analyses and interpretation of the results must be trained and must be highly qualified specialists in this field of science and practice. The experiences in Nagasaki, Hiroshima and Chernobyl, and discussions with

  2. Dynamic factor analysis of groundwater quality trends in an agricultural area adjacent to Everglades National Park

    Science.gov (United States)

    Muñoz-Carpena, R.; Ritter, A.; Li, Y. C.

    2005-11-01

    The extensive eastern boundary of Everglades National Park (ENP) in south Florida (USA) is subject to one of the most expensive and ambitious environmental restoration projects in history. Understanding and predicting the water quality interactions between the shallow aquifer and surface water is a key component in meeting current environmental regulations and fine-tuning ENP wetland restoration while still maintaining flood protection for the adjacent developed areas. Dynamic factor analysis (DFA), a recent technique for the study of multivariate non-stationary time-series, was applied to study fluctuations in groundwater quality in the area. More than two years of hydrological and water quality time series (rainfall; water table depth; and soil, ground and surface water concentrations of N-NO 3-, N-NH 4+, P-PO 43-, Total P, F -and Cl -) from a small agricultural watershed adjacent to the ENP were selected for the study. The unexplained variability required for determining the concentration of each chemical in the 16 wells was greatly reduced by including in the analysis some of the observed time series as explanatory variables (rainfall, water table depth, and soil and canal water chemical concentration). DFA results showed that groundwater concentration of three of the agrochemical species studied (N-NO 3-, P-PO 43-and Total P) were affected by the same explanatory variables (water table depth, enriched topsoil, and occurrence of a leaching rainfall event, in order of decreasing relative importance). This indicates that leaching by rainfall is the main mechanism explaining concentration peaks in groundwater. In the case of N-NH 4+, in addition to leaching, groundwater concentration is governed by lateral exchange with canals. F -and Cl - are mainly affected by periods of dilution by rainfall recharge, and by exchange with the canals. The unstructured nature of the common trends found suggests that these are related to the complex spatially and temporally varying

  3. Isotopic study of mercury sources and transfer between a freshwater lake and adjacent forest food web

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Sae Yun, E-mail: saeyunk@umich.edu [Department of Earth and Environmental Sciences, University of Michigan, 1100 N. University Ave, Ann Arbor, MI 48109 (United States); Blum, Joel D. [Department of Earth and Environmental Sciences, University of Michigan, 1100 N. University Ave, Ann Arbor, MI 48109 (United States); Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University Ave, Ann Arbor, MI 48109 (United States); Nadelhoffer, Knute J. [Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University Ave, Ann Arbor, MI 48109 (United States); Timothy Dvonch, J. [Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109 (United States); Tsui, Martin Tsz-Ki [Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC 27402 (United States)

    2015-11-01

    Studies of monomethylmercury (MMHg) sources and biogeochemical pathways have been extensive in aquatic ecosystems, but limited in forest ecosystems. Increasing evidence suggests that there is significant mercury (Hg) exchange between aquatic and forest ecosystems. We use Hg stable isotope ratios (δ{sup 202}Hg and Δ{sup 199}Hg) to investigate the relative importance of MMHg sources and assess Hg transfer pathways between Douglas Lake and adjacent forests located at the University of Michigan Biological Station, USA. We characterize Hg isotopic compositions of basal resources and use linear regression of % MMHg versus δ{sup 202}Hg and Δ{sup 199}Hg to estimate Hg isotope values for inorganic mercury (IHg) and MMHg in the aquatic and adjacent forest food webs. In the aquatic ecosystem, we found that lake sediment represents a mixture of IHg pools deposited via watershed runoff and precipitation. The δ{sup 202}Hg and Δ{sup 199}Hg values estimated for IHg are consistent with other studies that measured forest floor in temperate forests. The Δ{sup 199}Hg value estimated for MMHg in the aquatic food web indicates that MMHg is subjected to ~ 20% photochemical degradation prior to bioaccumulation. In the forest ecosystem, we found a significant negative relationship between total Hg and δ{sup 202}Hg and Δ{sup 199}Hg of soil collected at multiple distances from the lakeshore and lake sediment. This suggests that IHg input from watershed runoff provides an important Hg transfer pathway between the forest and aquatic ecosystems. We measured Δ{sup 199}Hg values for high trophic level insects and compared these insects at multiple distances perpendicular to the lake shoreline. The Δ{sup 199}Hg values correspond to the % canopy cover suggesting that forest MMHg is subjected to varying extents of photochemical degradation and the extent may be controlled by sunlight. Our study demonstrates that the use of Hg isotopes adds important new insight into the relative

  4. Assessing Methane Fluxes in a Small Run-of-River Reservoir: The Importance of Adjacent Marshland

    Science.gov (United States)

    McGinnis, D. F.; Flury, S.; Fietzek, P.; Bilsley, N. A.; Bodmer, P.; Premke, K.; Maeck, A.; Lorke, A.; Schmidt, M.

    2013-12-01

    We investigate methane (CH4) emissions from a small run-of-river impoundment, the Schwentine River in Kiel, Germany. Small dammed rivers, while important regions for carbon transformation, are presently not considered in the terrestrial carbon budget and are under-represented in CH4 emission studies. Using state-of-the-art monitoring techniques, we determine that 1) the CH4 emissions well-exceed those reported for temperate reservoirs and 2) the hydrodynamic linkage to bordering marshland (consisting of reed belts, sidebays and creeks) is an important CH4 source for Schwentine River CH4. During our study, the Schwentine River discharged into the Kieler Fjord at 3 - 12 m3/s. CH4 measurements included 1) a moored sensor near the dam discharge, 2) discrete water sampling, and 3) real time surface flux measurements with floating chambers. We observed that the CH4 concentration increased nearly linearly from 2.5 km upstream towards the dam. The CH4 concentration near the dam discharge was logged and reported every 30 minutes nearly continuously from 11 July - 28 Sept 2011, and varied from 500 μmol/L to 2,200 μmol/L. Surprisingly, the CH4 mass discharge from the dam - ranging from 4 to 20 kg/day - increased with both temperature and flowrate, suggesting a flow-dependent CH4 source. We found that the bordering and numerous inundated reed belts, sidebays and small creeks, had significantly elevated CH4 concentrations. These marshland regions are relatively productive and quiescent compared to the main river, and trap organic and particulate matter, leading to enhanced CH4 production. As the river flowrate increases, the lateral exchange with these adjacent areas also increases. Using the CH4 concentration time series, measured surface diffusive and ebullition fluxes, and sediment CH4 porewater profiles, we estimate the relative contributions of CH4 in the main branch due to 1) sediment diffusion, 2) dissolution from sediment CH4 bubble release, and 3) lateral fluxes from

  5. Optimal technique of linear accelerator–based stereotactic radiosurgery for tumors adjacent to brainstem

    International Nuclear Information System (INIS)

    Chang, Chiou-Shiung; Hwang, Jing-Min; Tai, Po-An; Chang, You-Kang; Wang, Yu-Nong; Shih, Rompin; Chuang, Keh-Shih

    2016-01-01

    Stereotactic radiosurgery (SRS) is a well-established technique that is replacing whole-brain irradiation in the treatment of intracranial lesions, which leads to better preservation of brain functions, and therefore a better quality of life for the patient. There are several available forms of linear accelerator (LINAC)–based SRS, and the goal of the present study is to identify which of these techniques is best (as evaluated by dosimetric outcomes statistically) when the target is located adjacent to brainstem. We collected the records of 17 patients with lesions close to the brainstem who had previously been treated with single-fraction radiosurgery. In all, 5 different lesion catalogs were collected, and the patients were divided into 2 distance groups—1 consisting of 7 patients with a target-to-brainstem distance of less than 0.5 cm, and the other of 10 patients with a target-to-brainstem distance of ≥ 0.5 and < 1 cm. Comparison was then made among the following 3 types of LINAC-based radiosurgery: dynamic conformal arcs (DCA), intensity-modulated radiosurgery (IMRS), and volumetric modulated arc radiotherapy (VMAT). All techniques included multiple noncoplanar beams or arcs with or without intensity-modulated delivery. The volume of gross tumor volume (GTV) ranged from 0.2 cm 3 to 21.9 cm 3 . Regarding the dose homogeneity index (HI ICRU ) and conformity index (CI ICRU ) were without significant difference between techniques statistically. However, the average CI ICRU = 1.09 ± 0.56 achieved by VMAT was the best of the 3 techniques. Moreover, notable improvement in gradient index (GI) was observed when VMAT was used (0.74 ± 0.13), and this result was significantly better than those achieved by the 2 other techniques (p < 0.05). For V 4 Gy of brainstem, both VMAT (2.5%) and IMRS (2.7%) were significantly lower than DCA (4.9%), both at the p < 0.05 level. Regarding V 2 Gy of normal brain, VMAT plans had attained 6.4 ± 5%; this was significantly better

  6. Thermokarst in pingos and adjacent collapse scar bogs in interior Alaska

    Science.gov (United States)

    Douglas, T. A.; Turetsky, M. R.

    2017-12-01

    A region of discontinuous permafrost 50 kilometers southeast of Fairbanks, Alaska exhibits rapid thermokarst and landscape change. The area contains a dozen pingos (hydrolaccoliths), mounds of ice covered by earth material typically 100 meters across and 20 meters above the surrounding ground surface. The pingos have sunken craters in their centers formed through melting and collapse of an inner ice lens core. Adjacent to the pingos are collapse scar bogs in various states of formation and ice wedge terrain undergoing thaw subsidence to polygons and thermokarst mounds (baydzherakhs). With a mean annual temperature of -1 degree C the area contains warm ecosystem-protected permafrost vulnerable to thaw. We analyzed historical imagery to the 1970s to track water features in a subset of pingos. The craters have expanded over the past few decades suggesting melting and collapse of the ice cored center and potential permafrost degradation along pingo margins. Collapse scar bogs in adjacent low-elevation terrain are roughly the same size as the pingos but have little vertical elevation gradient compared to the surrounding terrain. Electrical resistivity tomography (ERT) measurements, high resolution GPS surveys, SIPRE coring, and thaw depth probing were focused along nine 400 meter transects across three of the pingos to identify relationships between geophysical properties, permafrost composition, seasonal thaw, and ecological state. A large ( 40 meters across and 20 meters thick) lens shaped region of thawed permafrost is evident in the ERT results about 10 meters below the ground surface in the center of one pingo we surveyed in detail. This is believed to be the original ice cored region of the pingo that has melted. A thin (1-5 meters thick) layer of permafrost is present above this thawed region while the rampart margins surrounding the pingo are underlain by thick (10-30 m) permafrost. The pingo and thermokarst features reside in a location where rapid permafrost

  7. Biomechanics of Artificial Disc Replacements Adjacent to a 2-Level Fusion in 4-Level Hybrid Constructs: An In Vitro Investigation

    Science.gov (United States)

    Liao, Zhenhua; Fogel, Guy R.; Wei, Na; Gu, Hongsheng; Liu, Weiqiang

    2015-01-01

    Background The ideal procedure for multilevel cervical degenerative disc diseases remains controversial. Recent studies on hybrid surgery combining anterior cervical discectomy and fusion (ACDF) and artificial cervical disc replacement (ACDR) for 2-level and 3-level constructs have been reported in the literature. The purpose of this study was to estimate the biomechanics of 3 kinds of 4-level hybrid constructs, which are more likely to be used clinically compared to 4-level arthrodesis. Material/Methods Eighteen human cadaveric spines (C2–T1) were evaluated in different testing conditions: intact, with 3 kinds of 4-level hybrid constructs (hybrid C3–4 ACDR+C4–6 ACDF+C6–7ACDR; hybrid C3–5ACDF+C5–6ACDR+C6–7ACDR; hybrid C3–4ACDR+C4–5ACDR+C5–7ACDF); and 4-level fusion. Results Four-level fusion resulted in significant decrease in the C3–C7 ROM compared with the intact spine. The 3 different 4-level hybrid treatment groups caused only slight change at the instrumented levels compared to intact except for flexion. At the adjacent levels, 4-level fusion resulted in significant increase of contribution of both upper and lower adjacent levels. However, for the 3 hybrid constructs, significant changes of motion increase far lower than 4P at adjacent levels were only noted in partial loading conditions. No destabilizing effect or hypermobility were observed in any 4-level hybrid construct. Conclusions Four-level fusion significantly eliminated motion within the construct and increased motion at the adjacent segments. For all 3 different 4-level hybrid constructs, ACDR normalized motion of the index segment and adjacent segments with no significant hypermobility. Compared with the 4-level ACDF condition, the artificial discs in 4-level hybrid constructs had biomechanical advantages compared to fusion in normalizing adjacent level motion. PMID:26694835

  8. Reproductive outcomes in an area adjacent to a petrochemical plant in southern Brazil

    Directory of Open Access Journals (Sweden)

    Oliveira Lenice Minussi

    2002-01-01

    Full Text Available OBJECTIVE: To evaluate possible adverse reproductive outcomes in an area adjacent to a petrochemical plant in southern Brazil. METHODS: A review of 17,113 birth records of the main hospital of the municipality of Montenegro, southern Brazil, from 1983 to 1998 was carried out. Three groups of cases were selected: (1 newborns with major congenital malformations; (2 newborns with low birth weight (500 g. A control was assigned to each case. Controls were the first newborns weighing > or = 2,500 g without malformations and of case-matching sex. Mother's residence during pregnancy was used as an exposure parameter. Statistical analyses were performed using Chi-square test or Fisher test, odds ratio, 0.05 significance level, and 95% confidence interval. RESULTS: For unadjusted analysis, it was found a correlation between low birth weight and geographical proximity of mother's residence to the petrochemical plant (OR = 1.66; 95% CI = 1.01--2.72 or residence on the way of preferential wind direction (OR = 1.62; 95% CI = 1.03--2.56. When other covariates were added in the conditional logistic regression (maternal smoking habits, chronic disease and age, there was no association. CONCLUSIONS: Despite final results were negative, low birth weight could be a good parameter of environmental contamination and should be closely monitored in the studied area.

  9. [Working conditions in outpatient clinics adjacent to private pharmacies in Mexico City: perspective of physicians].

    Science.gov (United States)

    Díaz-Portillo, Sandra P; Reyes-Morales, Hortensia; Cuadra-Hernández, Silvia Magali; Idrovo, Álvaro J; Nigenda, Gustavo; Dreser, Anahí

    To analyse the working conditions of physicians in outpatient clinics adjacent to pharmacies (CAFs) and their organizational elements from their own perspective. We carried out an exploratory qualitative study. Semi-structured interviews were conducted with 32 CAF physicians in Mexico City. A directed content analysis technique was used based on previously built and emerging codes which were related to the experience of the subjects in their work. Respondents perceive that work in CAFs does not meet professional expectations due to low pay, informality in the recruitment process and the absence of minimum labour guarantees. This prevents them from enjoying the benefits associated with formal employment, and sustains their desire to work in CAF only temporarily. They believe that economic incentives related to number of consultations, procedures and sales attained by the pharmacy allow them to increase their income without influencing their prescriptive behaviour. They express that the monitoring systems and pressure exerted on CAFs seek to affect their autonomy, pushing them to enhance the sales of medicines in the pharmacy. Physicians working in CAFs face a difficult employment situation. The managerial elements used to induce prescription and enhance pharmacy sales create a work environment that generates challenges for regulation and underlines the need to monitor the services provided at these clinics and the possible risk for users. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

  10. Bone marrow changes adjacent to the sacroiliac joints after pelvic radiotherapy mimicking metastases on MRI

    Energy Technology Data Exchange (ETDEWEB)

    Kanberoglu, K.; Mihmanli, I.; Kurugoglu, S.; Ogut, G.; Kantarci, F. [Dept. of Radiology, Istanbul Univ. (Turkey)

    2001-09-01

    Radiation-induced changes in the sacroiliac joints mimicking metastases on MR images were evaluated. Twelve patients who received radiotherapy to the pelvic region due to pelvic malignancy were included in the study. All patients had undergone external beam radiation therapy to the pelvic region, and 2 patients received supplementary internal radiation. The changes in the sacroiliac joints were evaluated. Computed-tomography-guided core bone biopsy from the bone marrow was taken from their corresponding MR sections in 5 of the patients. T1 hypointense and T2 hyperintense areas with ill-defined margins in the bone marrow adjacent to the sacroiliac joints were observed in all patients. On bone scintigraphy all the lesions demonstrated increased activity. Other radiological modalities excluded fracture, soft tissue mass, and osseous destruction. Bone biopsies demonstrated peritrabecular fibrosis and inflammatory cell infiltration. Patients receiving radiotherapy to the pelvis may demonstrate T1 hypointense/T2 hyperintense, ill-defined postradiotherapeutic benign changes in the sacroiliac joints. In the absence of any other signs of disease progression and when the imaging pattern is typical, close radiological follow-up should be sufficient to rule out metastases. (orig.)

  11. A database for the monitoring of thermal anomalies over the Amazon forest and adjacent intertropical oceans.

    Science.gov (United States)

    Jiménez-Muñoz, Juan C; Mattar, Cristian; Sobrino, José A; Malhi, Yadvinder

    2015-01-01

    Advances in information technologies and accessibility to climate and satellite data in recent years have favored the development of web-based tools with user-friendly interfaces in order to facilitate the dissemination of geo/biophysical products. These products are useful for the analysis of the impact of global warming over different biomes. In particular, the study of the Amazon forest responses to drought have recently received attention by the scientific community due to the occurrence of two extreme droughts and sustained warming over the last decade. Thermal Amazoni@ is a web-based platform for the visualization and download of surface thermal anomalies products over the Amazon forest and adjacent intertropical oceans using Google Earth as a baseline graphical interface (http://ipl.uv.es/thamazon/web). This platform is currently operational at the servers of the University of Valencia (Spain), and it includes both satellite (MODIS) and climatic (ERA-Interim) datasets. Thermal Amazoni@ is composed of the viewer system and the web and ftp sites with ancillary information and access to product download.

  12. Simulating pesticide transport from a sloped tropical soil to an adjacent stream.

    Science.gov (United States)

    Kahl, G; Ingwersen, J; Totrakool, S; Pansombat, K; Thavornyutikarn, P; Streck, T

    2010-01-01

    Preferential flow from stream banks is an important component of pesticide transport in the mountainous areas of northern Thailand. Models can help evaluate and interpret field data and help identify the most important transport processes. We developed a simple model to simulate the loss of pesticides from a sloped litchi (Litchi chinensis Sonn.) orchard to an adjacent stream. The water regime was modeled with a two-domain reservoir model, which accounts for rapid preferential flow simultaneously with slow flow processes in the soil matrix. Preferential flow is triggered when the topsoil matrix is saturated or the infiltration capacity exceeded. In addition, close to matrix saturation, rainfall events induce water release to the fractures and lead to desorption of pesticides from fracture walls and outflow to the stream. Pesticides undergo first order degradation and equilibrium sorption to soil matrix and fracture walls. The model was able to reproduce the dynamics of the discharge reasonably well (model efficiency [EF] = 0.56). The cumulative pesticide mass (EF = 0.91) and the pesticide concentration in the stream were slightly underestimated, but the deviation from measurement data is acceptable. Shape and timing of the simulated concentration peaks occurred in the same pattern as observed data. While the effect of surface runoff and preferential interflow on pesticide mass transport could not be absolutely clarified, according to our simulations, most concentration peaks in the stream are caused by preferential interflow pointing to the important role of this flow path in the hilly areas of northern Thailand.

  13. An isotopic investigation of mercury accumulation in terrestrial food webs adjacent to an Arctic seabird colony

    International Nuclear Information System (INIS)

    Choy, Emily S.; Gauthier, Martine; Mallory, Mark L.; Smol, John P.; Douglas, Marianne S.V.; Lean, David; Blais, Jules M.

    2010-01-01

    At Cape Vera (Devon Island, Nunavut, Canada), a seabird colony of northern fulmars (Fulmarus glacialis) congregates and releases nutrients through the deposition of guano to the coastal terrestrial environment, thus creating nutrient-fertilized habitats important to insects, birds, and mammals. Here we determined whether mercury was similarly enriched in various terrestrial food web components in this High Arctic coastal ecosystem due to seabird inputs. Stable isotopes (δ 15 N, δ 13 C) were used to identify trophic linkages and possible routes of contaminant transfer in the food web. Values of δ 15 N were significantly higher in lichens and certain plants collected closer to the bird colony, demonstrating a gradient of seabird influence, and were higher at Cape Vera than our reference site at Cape Herschel, on eastern Ellesmere Island, an area relatively unaffected by seabirds. In contrast, δ 13 C showed little variation among terrestrial species, suggesting minimal influence by seabirds. Concentrations of total mercury (THg) in primary producers and phyto/zooplankton were not significantly correlated with distance from the seabird colony or δ 15 N values, and were similar to other taxa from the High Arctic. Our results provide novel data on THg in several Arctic taxa where concentrations have not been reported previously. Moreover, the analyses indicate that δ 15 N is significantly enriched in the adjacent environment by guano fertilization, but our study was unable to show an enrichment of THg and δ 13 C in the terrestrial food web near the seabird colony.

  14. Investigation of scour adjacent to submerged geotextiles used for shore protection

    Energy Technology Data Exchange (ETDEWEB)

    Gorton, Alicia M.; Herrington, Thomas O.; Smith, Ernest R.

    2018-01-03

    This study presents the results of an experimental investigation of morphology change in the vicinity of submerged geotextiles placed within the surf zone. The study was motivated by the emerging use of submerged geotextile tubes for shore protection, shoreline stabilization, and surf amenity enhancement and the need to understand the mechanisms responsible for scour in the vicinity of these structures to preserve their structural integrity and reduce their structural failure. A movable bed physical model experiment was conducted at the U.S. Army Engineer Research and Development Center’s Large-scale Sediment Transport Facility (LSTF) to develop empirical formulations to predict the mean scour depth adjacent to geotextiles under oblique wave-breaking conditions as a function of the maximum Keulegan-Carpenter, Shields, and Reynolds numbers. The observed scour in the vicinity of the geotextiles was also compared to a previous study of scour in the vicinity of submerged cylinders. Formulations developed by Cataño-Lopera and García (2006) relating the Keulegan-Carpenter, Shields, and Reynolds numbers to the scour depth were used to predict the scour observed during the LSTF experiment. Results show that the formulations of Cataño-Lopera and García (2006) over-predict the observed scour when calculated using the maximum Keulegan-Carpenter, Shields, and Reynolds numbers. New, modified expressions of Cataño-Lopera and García (2006) were developed for use in oblique random wave fields.

  15. Impact of offshore nuclear generating stations on recreational behavior at adjacent coastal sites. Technical report

    International Nuclear Information System (INIS)

    Baker, E.J.; Moss, D.J.; West, S.G.; Weyant, J.K.

    1977-12-01

    A multi-faceted investigation was undertaken to project the impact of offshore nuclear power plants on beach visitation at adjacent beaches. 1. Related literature was reviewed concerning human adjustment to natural hazards, risk-taking behavior, and public attitudes toward nuclear power. 2. Approximately 2400 people were interviewed at beaches in three states with respect to: (a) intended avoidance of beaches near a hypothetical floating nuclear plant (FNP), (b) relative importance of proximity to a FNP, when compared to other beach attributes, (c) onshore-offshore preference for coastal nuclear plant location, (d) behavioral impact of NRC licensing of FNP's, (e) relative tourism impact of coastal nuclear plant compared to coastal coal-fired plant, (f) public concerns about nuclear safety, (g) public attitudes toward alternative energy sources, (h) public confidence in sources of information about nuclear power, (i) visual impact of a FNP, and (j) knowledge about nuclear power. 3. Four beach areas near currently operating coastal nuclear power plants were studied to assess impacts on tourism resulting from plant construction. Data suggest that proximity of a FNP is less important than other beach attributes in determining beach attractiveness, probably no more than (and perhaps less than) 5% to 10% of current beach patrons would avoid a beach after FNP siting three miles directly offshore, and impact of a FNP would decrease exponentially as distance away increased

  16. Outcomes of preoperative chemoradiotherapy for rectal cancer with invasion to the adjacent organs

    International Nuclear Information System (INIS)

    Sato, Harunobu; Koide, Yoshikazu; Shiota, Miho; Endo, Tomoyoshi; Matsuoka, Shinji; Hatta, Kouhei; Mizuno, Masahiro; Maeda, Koutarou; Toyama, Kunihiro

    2013-01-01

    We reviewed the clinical records of 13 patients who received preoperative chemoradiotherapy (CRT) to evaluate the clinical effectiveness of CRT for T4b rectal cancer. Preoperative radiotherapy consisted of 40-50 Gy delivered in fractions of 1.8-2.0 Gy per day, 5 days per week. Treatment with intravenous 5-fluorouracil, oral tegafur-uracil (UFT-E) with l-leucovorin, oral S-1, or intravenous irinotecan (CPT-11) with oral S-1 was administered during radiotherapy. At 63 days after CRT, 1 patient died because of pelvic abscess. Complete response (CR) or partial response (PR) was observed in 7 patients, 1 month after CRT. Curative surgery was performed in 9 patients. Among 10 patients who underwent surgery 70 days after CRT, 5 who showed PR 1 month after CRT underwent curative surgery; both urinary and anal function were preserved in 4 of these patients. Histological invasion to the adjacent organs was not observed in 6 patients, and 1 patient achieved histological CR. Of the 9 patients who underwent curative surgery, recurrence was observed in 2; however, the other patients survived without recurrence. Preoperative CRT was considered to be effective in improving the resection rate and prognosis in patients with T4b rectal cancer. However, careful attention should be paid to the severe toxicities associated with CRT, such as pelvic abscess. (author)

  17. Resonance properties of tidal channels with multiple retention basins: role of adjacent sea

    Science.gov (United States)

    Roos, Pieter C.; Schuttelaars, Henk M.

    2015-03-01

    We present an idealised model of the tidal response in a main channel with multiple secondary basins, co-oscillating with an adjacent sea. The sea is represented as a semi-infinite strip of finite width, anywhere between the limits of a channel extension (narrow) and a half-plane (wide). The sea geometry controls the extent to which radiative damping takes place and hence the type of conditions that effectively apply at the channel mouth. These conditions range between the two extremes of prescribing elevation (deep sea limit) and prescribing the incoming wave (sea as channel extension of the same depth, as done in an earlier study). The closer to this first extreme, the stronger the oscillations in the secondary basins may feed back onto the channel mouth and thus produce an amplified or weakened response in the system as a whole. The possibly resonant response is explained by analysing the additional waves that emerge on either side of the entrance of the secondary basin. Finally, we show that the simultaneous presence of two secondary basins may amplify or weaken the accumulated responses to these basins individually.

  18. Spatial Arrangement of Coastal Sama-Bajau Houses Based on Adjacency Diagram

    Directory of Open Access Journals (Sweden)

    Iziq Eafifi Ismail

    2015-11-01

    Full Text Available This research studies the diversification of space distribution in selected Sama-Bajau dwellings along the north coast of Sabah: Kudat and Pitas; and east coast of Sabah: Mabul Island. This study investigates the frequency of spatial arrangements in Sama-Bajau coastal houses as a preliminary step in understanding their ideal home based on the existing socio-culture and economic practice. Adjacency Distribution Diagram by Mushtaha et al (2011 is used for simpler and compact visual diagram that explains the space distribution in each house attended. This paper is exploratory and applies a qualitative method. This study suggests that the spatial distribution amongst coastal Sama-Bajau consists of Dynamic interconnectivity (Type A, linear configuration (Type B, Anarchy configuration (Type C and D and Modernist influence (Type E. The frequency of given types is found to weighs more on Type B, which is a linear configuration from the entrance towards guest area and ending up to the living area.

  19. Evaluation of the Reduction of Seismic Response of Adjacent Structures Using Viscous Damper Joint

    Directory of Open Access Journals (Sweden)

    Hamed Karbalay Malek

    2017-09-01

    Full Text Available This study examines the effect of common viscose damper on the behavior of adjacent reinforced concrete structures. For this purpose, three reinforced concrete 3, 5 and 7 floors buildings with a regular plan were selected and were compared in two cases without and with viscous dampers at the seams. They are designed based on discussions of Buildings Regulations 2800 and the 6 and 9 issues of Iranian National Building Regulations. Those buildings face under accelerograms of Bam, Mangil and El Centro, and then they are analyzed with nonlinear modal time history. This Accelerograms before applying to the structures, they are scaled based on the 2800 Regulations. Those buildings were modeled by SAP2000 finite element modeling software. Linear behavior of structural components of the structure and the non-linear behavior viscous damper were modeled. Finally, the seismic response of buildings includes the base shear force, up to a maximum lateral acceleration of seismic classes and classes for both with and without the viscous damper have been extracted and compared. The results showed the reduction in relative lateral displacement, maximum acceleration and base cut applied to structure in the presence of viscous dampers between two structures. This decline is not even in the direction that the viscous damper is viewed as significant.

  20. A numerical study of the plume in Cape Fear River Estuary and adjacent coastal ocean

    Science.gov (United States)

    Xia, M.; Xia, L.; Pietrafesa, L. J.

    2006-12-01

    Cape Fear River Estuary (CFRE), located in southeast North Carolina, is the only river estuary system in the state which is directly connected to the Atlantic Ocean. It is also an important nursery for economically and ecologically important juvenile fish, crabs, shrimp, and other species because of the tidal influence and saline waters. In this study, Environmental Fluid Dynamic Code (EFDC) is used to simulate the salinity plume and trajectory distribution at the mouth of the CFRE and adjacent coastal ocean. Prescribed with the climatological freshwater discharge rates in the rivers, the modeling system was used to simulate the salinity plume and trajectory distribution distribution in the mouth of the CFRE under the influence of climatological wind conditions and tidal effect. We analyzed the plume formation processes and the strong relationship between the various plume distributions with respect to the wind and river discharge in the region. The simulations also indicate that strong winds tend to reduce the surface CFRE plume size and distorting the bulge region near the estuary mouth due to enhanced wind induced surface mixing. Even moderate wind speeds could fully reverse the buoyancy-driven plume structure in CFRE under normal river discharge conditions. Tide and the river discharge also are important factors to influence the plume structure. The comparions between the distribution of salinity plume and trajectory also are discussed in the study.

  1. Distribution and diversity of fungal species in and adjacent to the Los Alamos National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Balice, R.G.; Jarmie, N.; Rogers, F.J.

    1997-12-01

    Fungi have demonstrated their ability to diversify and specialize to take advantage of new environments (Murphy 1996). These species are essential to the normal functioning of ecosystems and the impacts of human activities may be harmful to fungi. There is a need to inventory fungi throughout the range of their environments. Previously archived information representing 43 sample locations was used to perform a preliminary evaluation of the distributions and diversity of fungal species at the Los Alamos National Laboratory and in adjacent environments. Presence-absence data for 71 species of fungi in five habitats, pinon-juniper, canyon-bottom ponderosa pine, ponderosa pine, canyon-bottom mixed conifer, and mixed conifer were analyzed. The results indicate that even though fungi occur in each of the habitats, fungal species are not distributed evenly among these habitats. The richness of fungal species is greater in the canyon-bottom mixed conifer and mixed conifer habitats than in the pinon-juniper, canyon-bottom ponderosa pine or ponderosa pine habitats. All but three of the fungal species were recorded in either the canyon-bottom mixed conifer or the mixed conifer habitats, and all but seven of the fungal species were found in the mixed conifer habitat.

  2. Stress-induced martensitic transformation and ferroelastic deformation adjacent microhardness indents in tetragonal zirconia single crystals

    International Nuclear Information System (INIS)

    Chien, F.R.; Ubic, F.J.; Prakash, V.; Heuer, A.H.

    1998-01-01

    The stress-induced tetragonal to monoclinic (t → m) martensitic transformation, stress-induced ferroelastic domain switching, and dislocation slip were induced by Vickers microindentation at elevated temperatures in polydomain single crystals of 3 mol%-Y 2 O 3 -stabilized tetragonal ZrO 2 single crystals (3Y-TZS). Chemical etching revealed traces along t directions adjacent to indentations, and Raman spectroscopy and TEM have shown that these traces are caused by products of the martensitic transformation, i.e. the monoclinic product phase forms primarily as thin, long plates with a habit plane approximately on (bar 301) m . This habit plane and the associated shear strain arising from the transformation, visible in TEM micrographs at the intersection of crystallographically equivalent martensite plates, were successfully predicted using the observed lattice correspondence and the phenomenological invariant plane strain theory of martensitic transformations. The extent of the martensitic transformation increased with increasing temperature from room temperature up to 300 C, but then decreased at higher temperatures. Ferroelastic deformation of tetragonal ZrO 2 has been observed at all temperatures up to 1,000 C. At the highest temperature, only ferroelastic domain switching and dislocation slip occurred during indentation-induced deformation

  3. Evaluation of the maxillary sinus and adjacent structures on the orthopantomograph to the head positions

    International Nuclear Information System (INIS)

    Lee, Jin Kyung; Kim, Jae Duck

    1992-01-01

    The purpose of this study was to evaluate the utilization of the orthopantomogrph as a diagnostic aid to observe maxillary sinus and adjacent structures. For achieving this goal, the lead plates were attached to the five walls of the maxillary sinus of a human dry skull. The dry skull was placed in fourteen different positions ; standard, 20 mm forward, 20 mm backward, 10 degree upward, 10 degree downward, 20 mm lateral, forward and upward, forward and lateral, backward and upward, backward and downward, backward and lateral, upward and lateral, downward and lateral position. The obtained results were as follows: 1. The image of the medial wall was observed very differently according to the head positions. 2. The image of the anterior wall was observed at medial third to half of the maxillary sinus in each head position. 3. The image of the posterior wall was always observed at lateral third of the maxillary sinus in all head positions and more obviously in the downward-lateral position. 4. The image of the superior wall was observed at the inferior third to half of the orbit in each head position. 5. The image of the inferior wall was always observed at the inferior third of maxillary sinus in all head positions and observed more obviously in the standard and downward-lateral positions. 6. The image of the zygomatic process, zygomatic arch and zygomaticotemporal suture were observed very well in the downward-lateral position.

  4. Electron transfer in silicon-bridged adjacent chromophores: the source for blue-green emission.

    Science.gov (United States)

    Bayda, Malgorzata; Angulo, Gonzalo; Hug, Gordon L; Ludwiczak, Monika; Karolczak, Jerzy; Koput, Jacek; Dobkowski, Jacek; Marciniak, Bronislaw

    2017-05-10

    Si-Bridged chromophores have been proposed as sources for blue-green emission in several technological applications. The origin of this dual emission is to be found in an internal charge transfer reaction. The current work is an attempt to describe the details of these processes in these kinds of substances, and to design a molecular architecture to improve their performance. Nuclear motions essential for intramolecular charge transfer (ICT) can involve processes from twisted internal moieties to dielectric relaxation of the solvent. To address these issues, we studied ICT between adjacent chromophores in a molecular compound containing N-isopropylcarbazole (CBL) and 1,4-divinylbenzene (DVB) linked by a dimethylsilylene bridge. In nonpolar solvents emission arises from the local excited state (LE) of carbazole whereas in solvents of higher polarity dual emission was detected (LE + ICT). The CT character of the additional emission band was concluded from the linear dependence of the fluorescence maxima on solvent polarity. Electron transfer from CBL to DVB resulted in a large excited-state dipole moment (37.3 D) as determined from a solvatochromic plot and DFT calculations. Steady-state and picosecond time-resolved fluorescence experiments in butyronitrile (293-173 K) showed that the ICT excited state arises from the LE state of carbazole. These results were analyzed and found to be in accordance with an adiabatic version of Marcus theory including solvent relaxation.

  5. Characterization of phosphorus sorption on the sediments of Yangtze River Estuary and its adjacent areas

    International Nuclear Information System (INIS)

    Cao, Xiaoyan; Liu, Xiaoyue; Zhu, Jiamei; Wang, Lisha; Liu, Sumei; Yang, Guipeng

    2017-01-01

    This paper studied the kinetics, isotherm and thermodynamics of phosphorus sorption onto the sediments of the Yangtze River estuary and its adjacent waters, as well as the sediments' compositions and physicochemical properties. The process could be described well by a two-compartment first order equation. The sorbed phosphorus mainly consisted of Ex-P and Fe-P, with Ex-P being the dominant. The equilibrium isotherms could be fitted well with a modified Langmuir equation. The calculations of the thermodynamic parameters indicated that the process was spontaneous and exothermic. The CEC and the fractions of clay, calcite and organic matter were correlated with the sorption parameters, while the surface proton charge of the sediments was significantly negatively correlated with them. Considering the kinetics and phosphorus forms changes during the process, the sorption in our study could be considered that the physical process plays an important role. - Highlights: • The kinetic curves and phosphorus fractions changes during sorption were studied. • The sorbed phosphorus mainly consisted of Ex − P and Fe-P, with Ex − P being dominant. • The equilibrium isotherms and thermodynamic parameters were investigated. • Sediment composition and surface characteristics influenced phosphorus sorption parameters.

  6. Dinitrogen Fixation Within and Adjacent to Oxygen Deficient Waters of the Eastern Tropical South Pacific Ocean

    Science.gov (United States)

    Widner, B.; Mulholland, M. R.; Bernhardt, P. W.; Chang, B. X.; Jayakumar, A.

    2016-02-01

    Recent work suggests that planktonic diazotrophs are geographically more widely distributed than previously thought including relatively warm (14-23oC) aphotic oxygenated pelagic waters and in aphotic waters within oxygen deficient zones. Because the volume of aphotic water in the ocean is large and may increase in the future, if dinitrogen (N2) fixation is widely occurring at sub-euphotic depths, this could result in a dramatic upward revision of global nitrogen (N) inputs via this process. N2 fixation rates were measured during a cruise in the Eastern Tropical South Pacific using stable isotope tracer techniques that account for slow gas dissolution. Results are compared with light, nutrient, and oxygen gradients (and necessarily temperature gradients). In addition, rates of N2 fixation made in vertical profiles within and above oxygen deficient waters are compared with those measured in vertical profiles adjacent to oxygen deficient waters. Results suggest that while rates of N2 fixation were measurable in deeper anoxic waters, volumetric N2 fixation rates were higher in surface waters.

  7. Midlatitude Plasma Bubbles Over China and Adjacent Areas During a Magnetic Storm on 8 September 2017

    Science.gov (United States)

    Aa, Ercha; Huang, Wengeng; Liu, Siqing; Ridley, Aaron; Zou, Shasha; Shi, Liqin; Chen, Yanhong; Shen, Hua; Yuan, Tianjiao; Li, Jianyong; Wang, Tan

    2018-03-01

    This paper presents observations of postsunset super plasma bubbles over China and adjacent areas during the second main phase of a storm on 8 September 2017. The signatures of the plasma bubbles can be seen or deduced from (1) deep field-aligned total electron content depletions embedded in regional ionospheric maps derived from dense Global Navigation Satellite System networks, (2) significant equatorial and midlatitudinal plasma bite-outs in electron density measurements on board Swarm satellites, and (3) enhancements of ionosonde virtual height and scintillation in local evening associated with strong southward interplanetary magnetic field. The bubbles/depletions covered a broad area mainly within 20°-45°N and 80°-110°E with bifurcated structures and persisted for nearly 5 hr (˜13-18 UT). One prominent feature is that the bubbles extended remarkably along the magnetic field lines in the form of depleted flux tubes, reaching up to midlatitude of around 50°N (magnetic latitude: 45.5°N) that maps to an altitude of 6,600 km over the magnetic equator. The maximum upward drift speed of the bubbles over the magnetic equator was about 700 m/s and gradually decreased with altitude and time. The possible triggering mechanism of the plasma bubbles was estimated to be storm time eastward prompt penetration electric field, while the traveling ionospheric disturbance could play a role in facilitating the latitudinal extension of the depletions.

  8. Aquatic systems in and adjacent to Agulhas National Park with particular reference to the fish fauna

    Directory of Open Access Journals (Sweden)

    I.A. Russell

    2006-12-01

    Full Text Available The study aimed to determine the distribution and relative abundance of freshwater fishes in and adjacent to Agulhas National Park. Fourteen fish species were collected during surveys carried out in the Heuningnes and Ratel river systems and a variety of endorheic pans from 2003 to 2005. Seven of the species are marine fishes tolerant of low salinity (Mugil cephalus, Liza richardsonii, Monodactylus falciformis, Caffrogobius gilchristi, Rhabdosargus holubi, Solea bleekeri, Gilchristella aestuaria with the remaining seven species being primary freshwater fishes. Three are indigenous, including Pseudobarbus burchelli, Sandelia capensis, and Galaxias zebratus of which two morphological forms were recorded within Agulhas National Park. The remaining four species are invasive aliens (Cyprinus carpio, Lepomis macrochirus, Micropterus salmoides, Micropterus punctulatus. Classification using physico-chemical variables indicated four major wetland groups, with fishes occurring predominantly in the group comprising palustrine, lacustrine and riverine wetlands, and in one instance in a brackish endorheic pan. Management actions which should facilitate conservation of indigenous fishes in the Agulhas region are suggested.

  9. Distribution and diversity of fungal species in and adjacent to the Los Alamos National Laboratory

    International Nuclear Information System (INIS)

    Balice, R.G.; Jarmie, N.; Rogers, F.J.

    1997-12-01

    Fungi have demonstrated their ability to diversify and specialize to take advantage of new environments (Murphy 1996). These species are essential to the normal functioning of ecosystems and the impacts of human activities may be harmful to fungi. There is a need to inventory fungi throughout the range of their environments. Previously archived information representing 43 sample locations was used to perform a preliminary evaluation of the distributions and diversity of fungal species at the Los Alamos National Laboratory and in adjacent environments. Presence-absence data for 71 species of fungi in five habitats, pinon-juniper, canyon-bottom ponderosa pine, ponderosa pine, canyon-bottom mixed conifer, and mixed conifer were analyzed. The results indicate that even though fungi occur in each of the habitats, fungal species are not distributed evenly among these habitats. The richness of fungal species is greater in the canyon-bottom mixed conifer and mixed conifer habitats than in the pinon-juniper, canyon-bottom ponderosa pine or ponderosa pine habitats. All but three of the fungal species were recorded in either the canyon-bottom mixed conifer or the mixed conifer habitats, and all but seven of the fungal species were found in the mixed conifer habitat

  10. Metals in soils adjacent to avenues of highly dense traffic of Sao Paulo city, Brazil

    International Nuclear Information System (INIS)

    Ticianelli, Regina B.; Ribeiro, Andreza P.; Figueiredo, Ana M.G.; Nammoura-Neto, Georges M.; Silva, Nathalia C.

    2009-01-01

    Sao Paulo is the largest city in Brazil with about 19 millions of inhabitants in the metropolitan area, more than 8 million motor vehicles and strong industrial activity at the metropolitan region, which are responsible for increasing pollution in the region. Nevertheless, there is little information on metal contents in the metropolitan region soils, which would be very useful as a fingerprint of the environmental pollution. The present study aimed to determine As, Ba, Co, Cr, Sb and Zn concentrations in soils adjacent to avenues of highly dense traffic downtown Sao Paulo city: Consolacao/Reboucas Avenues; 23 de Maio Avenue and Tiradentes Avenue, to assess their possible sources and potential environmental impact. The analytical technique employed was Instrumental Neutron Activation Analysis (INAA). The results show metal concentration levels higher than the values reference values for soils of Sao Paulo, according to the Environmental Protection Agency of the State Sao Paulo (CETESB) guidelines. As, Ba and Zn showed concentration levels above the Intervention Values in some points, indicating direct or indirect potential risks to human health. The traffic related element Ba, Sb and Zn presented concentrations above the Prevention Values in points with high density traffic and may be associated to vehicular emissions. (author)

  11. Carry-over of thermophilic Campylobacter spp. between sequential and adjacent poultry flocks.

    Science.gov (United States)

    Alter, Thomas; Weber, Rita Margarete; Hamedy, Ahmad; Glünder, Gerhard

    2011-01-10

    Nineteen flocks of four poultry species were monitored at a veterinary field station to investigate the distribution and spread of Campylobacter genotypes between sequential and adjacent flocks. Caecal and liver samples were obtained at frequent intervals from birds of all flocks and examined for Campylobacter. Amplified fragment length polymorphism (AFLP) analysis was performed to genotype Campylobacter isolates. Of the 1643 caecal and liver samples investigated, 452 (27.5%) caecal samples and 11 (0.7%) liver samples contained Campylobacter. Of the caecal isolates 76.3% were identified as Campylobacter jejuni and 23.7% were identified as Campylobacter coli. Poultry flocks were largely colonized by more than one AFLP type and an intense exchange of Campylobacter genotypes between different poultry flocks occurred. These findings indicate that multiple genotypes can constitute the Campylobacter population within single poultry flocks, hinting to different sources of exposure and/or genetic drifts within the Campylobacter population. Nevertheless, in most flocks single Campylobacter genotypes predominated. Some strains superseded others resulting in colonization by successive Campylobacter genotypes during the observation period. In conclusion, the data demonstrate that the large genetic diversity of Campylobacter must be considered in epidemiological evaluations and microbial risk assessments of Campylobacter in poultry. Copyright © 2010 Elsevier B.V. All rights reserved.

  12. Microclimate and Modeled Fire Behavior Differ Between Adjacent Forest Types in Northern Portugal

    Directory of Open Access Journals (Sweden)

    Anita Pinto

    2014-10-01

    Full Text Available Fire severity varies with forest composition and structure, reflecting micrometeorology and the fuel complex, but their respective influences are difficult to untangle from observation alone. We quantify the differences in fire weather between different forest types and the resulting differences in modeled fire behavior. Collection of in-stand weather data proceeded during two summer periods in three adjacent stands in northern Portugal, respectively Pinus pinaster (PP, Betula alba (BA, and Chamaecyparis lawsoniana (CL. Air temperature, relative humidity and wind speed varied respectively as CL < PP < BA, PP < CL < BA, and CL < BA < PP. Differences between PP and the other types were greatest during the warmest and driest hours of the day in a sequence of 10 days with high fire danger. Estimates of daytime moisture content of fine dead fuels and fire behavior characteristics for this period, respectively, from Behave and BehavePlus, indicate a CL < BA < PP gradient in fire potential. High stand density in CL and BA ensured lower wind speed and higher fuel moisture content than in PP, limiting the likelihood of an extreme fire environment. However, regression tree analysis revealed that the fire behavior distinction between the three forest types was primarily a function of the surface fuel complex, and more so during extreme fire weather conditions.

  13. Differing opinions about natural gas drilling in two adjacent counties with different levels of drilling activity

    International Nuclear Information System (INIS)

    Kriesky, J.; Goldstein, B.D.; Zell, K.; Beach, S.

    2013-01-01

    The pace of development of shale gas plays varies greatly among US states and globally. Through analysis of telephone survey responses, we explore support for natural gas drilling in residents of Washington County (WC), PA (n=502) vs. residents of Allegheny County (AC), PA (n=799). WC has had intense Marcellus Shale (MS) drilling activity, in comparison to adjacent AC, which has had little drilling activity. WC residents are marginally more supportive of MS drilling than are AC residents (p=0.0768). Residents of WC are more likely to perceive MS as an economic opportunity than are AC residents (p=0.0015); to be in a family that has signed a MS lease (p<0.0001); to follow the MS issue closely (p=0.0003); to get MS information from neighbors, friends, and relatives (p<0.0001); and are marginally less likely to perceive MS as an environmental threat (p=0.1090). WC leaseholders are significantly more supportive of MS drilling than WC non-leaseholders and AC non-leaseholders (p=0.0024). Mediation analyses show that county-based differences in support of MS drilling are due to WC residents seeing more of an economic opportunity in the MS and their greater likelihood of having a family-held lease. - Highlights: • Telephone survey analysis of sources of support for Marcellus Shale drilling. • Perceived positive economic impact of drilling drives support among respondents. • Mineral rights leaseholders are significantly more supportive than non-leaseholders

  14. Motion of a cylinder adjacent to a free-surface: flow patterns and loading

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Q.; Lin, J.C. [Lehigh Univ., Bethlehem, PA (United States). Dept. of Mechanical Engineering and Mechanics; Unal, M.F.; Rockwell, D.

    2000-06-01

    The flow structure and loading due to combined translatory and sinusoidal motion of a cylinder adjacent to a free-surface are characterized using a cinema technique of high-image-density particle image velocimetry and simultaneous force measurements. The instantaneous patterns of vorticity and streamline topology are interpreted as a function of degree of submergence beneath the free-surface. The relative magnitudes of the peak vorticity and the circulation of vortices formed from the upper and lower surfaces of the cylinder, as well as vortex formation from the free-surface, are remarkably affected by the nominal submergence. The corresponding streamline topology, interpreted in terms of foci, saddle points, and multiple separation and reattachment points also exhibit substantial changes with submergence. All of these features affect the instantaneous loading of the cylinder. Calculation of instantaneous moments of vorticity and the incremental changes in these moments during the cylinder motion allow identification of those vortices that contribute most substantially to the instantaneous lift and drag. Furthermore, the calculated moments are in general accord with the time integrals of the measured lift and drag acting on the cylinder for sufficiently large submergence. (orig.)

  15. ECONOMICAL DESIGN OF CIRCULAR FOOTINGS ADJACENT TO SLOPES ON SANDY SOILS

    Directory of Open Access Journals (Sweden)

    Adnan Jayed Zedan

    2013-05-01

    Full Text Available The analysis presented here introduces three optimization techniques namely, Hooke and Jeeves, Fletcher-Reeves and Davidon-Fletcher-Powell as applied to design of the circular footing adjacent to slopes. A computer program was developed to solve this design problem using the conventional structural design approach   in conjunction with these methods, A simple study was performed to detect the sensitivity of the objective function to its design variables. A further parametric study was performed regarding the geometric configurations of the footing and loading conditions in order to provide the geotechnical engineer with some useful design curves. Hooke and Jeeves method has been proved to be very instructive in exposing the effect of the other methods.It has been proved that the minimum cost of the circular footing increases with the increase of the load whereas it decreases as the angle of internal friction increases and the Dcl/B ratio (column diameter/diameter of footing.

  16. Carbon and Nitrogen Pools and Fluxes in Adjacent Mature Norway Spruce and European Beech Forests

    Directory of Open Access Journals (Sweden)

    Filip Oulehle

    2016-11-01

    Full Text Available We compared two adjacent mature forest ecosystem types (spruce vs. beech to unravel the fate of assimilated carbon (C and the cycling of organic and inorganic nitrogen (N without the risk of the confounding influences of climatic and site differences when comparing different sites. The stock of C in biomass was higher (258 t·ha−1 in the older (150 years beech stand compared to the younger (80 years planted spruce stand (192 t·ha−1, whereas N biomass pools were comparable (1450 kg·ha−1. Significantly higher C and N soil pools were measured in the beech stand, both in forest floor and mineral soil. Cumulative annual CO2 soil efflux was similar among stands, i.e., 9.87 t·ha−1·year−1 of C in the spruce stand and 9.01 t·ha−1·year−1 in the beech stand. Soil temperature explained 78% (Q10 = 3.7 and 72% (Q10 = 4.2 of variability in CO2 soil efflux in the spruce and beech stand, respectively. However, the rather tight N cycle in the spruce stand prevented inorganic N losses, whereas losses were higher in the beech stand and were dominated by nitrate in the mineral soil. Our results highlighted the long-term consequences of forest management on C and N cycling.

  17. A review of sediment quantity issues: examples from the River Ebro and adjacent basins (Northeastern Spain).

    Science.gov (United States)

    Batalla, Ramon J; Vericat, Damià

    2011-04-01

    Sediment flows naturally through the drainage network, from source areas to deposition zones. Sedimentary disequilibrium in rivers and coastlines is related to the imbalance within the fluvial system caused mostly by dams, instream mining, and changes in land use. This phenomenon is also responsible for ecological perturbations in rivers and streams. A broad need exists to establish comprehensive management strategies (soft measures) that would go beyond site-specific engineering practices (technical measures) typically taken to solve particular problems. Long-term programs are also required to monitor sediment transport in river basins, in order to assess the magnitude and variability of sediment transfer and potential deficits. This paper shows examples of rivers with important sediment disequilibrium in the Ebro and adjacent basins. These basins, like most in the Iberian Peninsula, experience sediment discontinuity in the catchment-river-coast system. Reservoir siltation is the main quantitative issue. Land use change and especially gravel mining downstream from dams accentuate the process. We also present and discuss recent developments on water and sediment management undertaken to improve the morphosedimentary dynamics of rivers. Copyright © 2010 SETAC.

  18. Distribution of polychlorinated biphenyls in the Housatonic River and adjacent aquifer, Massachusetts

    Science.gov (United States)

    Gay, Frederick B.; Frimpter, Michael H.

    1985-01-01

    Polychlorinated biphenyls (PCB's) are sorbed to the fine-grained stream-bottom sediments along the Housatonic River from Pittsfield, Massachusetts, southward to the Massachusetts-Connecticut boundary. The highest PCB concentrations, up to 140,000 micrograms per kilogram, were found in samples of bottom material from a reach of the river between Pittsfield and Woods Pond Dam in Lee, Massachusetts. Sediments in Woods Pond have been estimated to contain about 11,000 pounds of PCB's. Approximately 490 pounds per year of PCB's have also been estimated to move past the Housatonic River gaging station at Great Barrington. The distribution of hydraulic heads, water temperatures, and concentrations of dissolved oxygen, ammonia, nitrate, iron, and manganese in ground water shows that industrial water-supply wells in a sand and gravel aquifer adjacent to a stretch of the river called Woods Pond have been inducing ground-water recharge through the PCB-contaminated bottom sediments of the pond since late 1956. These data indicate that, at one location along the shore of the pond, the upper 40 feet of the aquifer contains water derived from induced infiltration. However, this induced recharge has not moved PCB's from the bottom sediments into a vertical section of the aquifer located 5 feet downgradient from the edge of Woods Pond. Samples taken at selected intervals in this section showed that no PCB's sorbed to the aquifer material or dissolved in the ground water within the detection limits of the chemical analyses.

  19. Analysis and performance of adjacent-cell preconditioners for accelerating multidimensional transport calculations

    International Nuclear Information System (INIS)

    Azmy, Y.Y.

    1996-01-01

    The formal development of the Adjacent-cell Preconditioner (AP) and its implementation in the TORT code are briefly reviewed. Based on earlier experience with diffusion type acceleration, and excellent results in slab geometry the reciprocal averaging formula is used to mix the preconditioner elements across material and mesh discontinuities. Numerical testing of the method employing the Burre Suite of Test Problems (BSTeP), a collection of 144 cases covering a wide range in parameter space, using AP, Partial Current Rebalance (PCR), and TWODANT's Diffusion Synthetic Acceleration (DSA) is presented. While AP outperforms the other two methods for the majority of the cases included in BSTeP it consumes many more iterations than can be explained by spectral analysis of the homogeneous model problem in cases with sharp material discontinuity. In order to verify this undesirable behavior and explore potential remedies a model problem, the Periodic Horizontal Interface (PHI), is developed that permits discontinuity of nuclear properties and cell height across the interface. Fourier mode decomposition is applied to AP with the reciprocal averaging mixing formula for the PHI configuration and shown to possess a spectral radius that approaches unity as the material discontinuity gets larger. The question of whether an unconditionally stable AP exists for PHI is tackled and preliminary indications are negative. Novel preconditioners that have nontraditional cell-coupling schemes that remain stable in these regimes may have to be sought

  20. Ecohydrology of adjacent sagebrush and lodgepole pine ecosystems: the consequences of climate change and disturbance

    Science.gov (United States)

    Bradford, John B.; Schlaepfer, Daniel R.; Lauenroth, William K.

    2014-01-01

    Sagebrush steppe and lodgepole pine forests are two of the most widespread vegetation types in the western United States and they play crucial roles in the hydrologic cycle of these water-limited regions. We used a process-based ecosystem water model to characterize the potential impact of climate change and disturbance (wildfire and beetle mortality) on water cycling in adjacent sagebrush and lodgepole pine ecosystems. Despite similar climatic and topographic conditions between these ecosystems at the sites examined, lodgepole pine, and sagebrush exhibited consistent differences in water balance, notably more evaporation and drier summer soils in the sagebrush and greater transpiration and less water yield in lodgepole pine. Canopy disturbances (either fire or beetle) have dramatic impacts on water balance and availability: reducing transpiration while increasing evaporation and water yield. Results suggest that climate change may reduce snowpack, increase evaporation and transpiration, and lengthen the duration of dry soil conditions in the summer, but may have uncertain effects on drainage. Changes in the distribution of sagebrush and lodgepole pine ecosystems as a consequence of climate change and/or altered disturbance regimes will likely alter ecosystem water balance.