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Sample records for strongly positioned nucleosomes

  1. Nucleosome Positioning and Epigenetics

    Science.gov (United States)

    Schwab, David; Bruinsma, Robijn

    2008-03-01

    The role of chromatin structure in gene regulation has recently taken center stage in the field of epigenetics, phenomena that change the phenotype without changing the DNA sequence. Recent work has also shown that nucleosomes, a complex of DNA wrapped around a histone octamer, experience a sequence dependent energy landscape due to the variation in DNA bend stiffness with sequence composition. In this talk, we consider the role nucleosome positioning might play in the formation of heterochromatin, a compact form of DNA generically responsible for gene silencing. In particular, we discuss how different patterns of nucleosome positions, periodic or random, could either facilitate or suppress heterochromatin stability and formation.

  2. A positioned +1 nucleosome enhances promoter-proximal pausing

    OpenAIRE

    Jimeno-Gonz?lez, Silvia; Ceballos-Ch?vez, Mar?a; Reyes, Jos? C.

    2015-01-01

    Chromatin distribution is not uniform along the human genome. In most genes there is a promoter-associated nucleosome free region (NFR) followed by an array of nucleosomes towards the gene body in which the first (+1) nucleosome is strongly positioned. The function of this characteristic chromatin distribution in transcription is not fully understood. Here we show in vivo that the +1 nucleosome plays a role in modulating RNA polymerase II (RNAPII) promoter-proximal pausing. When a +1 nucleoso...

  3. Weakly positioned nucleosomes enhance the transcriptional competency of chromatin.

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    Yaakov Belch

    2010-09-01

    Full Text Available Transcription is affected by nucleosomal resistance against polymerase passage. In turn, nucleosomal resistance is determined by DNA sequence, histone chaperones and remodeling enzymes. The contributions of these factors are widely debated: one recent title claims "… DNA-encoded nucleosome organization…" while another title states that "histone-DNA interactions are not the major determinant of nucleosome positions." These opposing conclusions were drawn from similar experiments analyzed by idealized methods. We attempt to resolve this controversy to reveal nucleosomal competency for transcription.To this end, we analyzed 26 in vivo, nonlinked, and in vitro genome-wide nucleosome maps/replicates by new, rigorous methods. Individual H2A nucleosomes are reconstituted inaccurately by transcription, chaperones and remodeling enzymes. At gene centers, weakly positioned nucleosome arrays facilitate rapid histone eviction and remodeling, easing polymerase passage. Fuzzy positioning is not due to artefacts. At the regional level, transcriptional competency is strongly influenced by intrinsic histone-DNA affinities. This is confirmed by reproducing the high in vivo occupancy of translated regions and the low occupancy of intergenic regions in reconstitutions from purified DNA and histones. Regional level occupancy patterns are protected from invading histones by nucleosome excluding sequences and barrier nucleosomes at gene boundaries and within genes.Dense arrays of weakly positioned nucleosomes appear to be necessary for transcription. Weak positioning at exons facilitates temporary remodeling, polymerase passage and hence the competency for transcription. At regional levels, the DNA sequence plays a major role in determining these features but positions of individual nucleosomes are typically modified by transcription, chaperones and enzymes. This competency is reduced at intergenic regions by sequence features, barrier nucleosomes, and proteins

  4. Physics behind the mechanical nucleosome positioning code

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    Zuiddam, Martijn; Everaers, Ralf; Schiessel, Helmut

    2017-11-01

    The positions along DNA molecules of nucleosomes, the most abundant DNA-protein complexes in cells, are influenced by the sequence-dependent DNA mechanics and geometry. This leads to the "nucleosome positioning code", a preference of nucleosomes for certain sequence motives. Here we introduce a simplified model of the nucleosome where a coarse-grained DNA molecule is frozen into an idealized superhelical shape. We calculate the exact sequence preferences of our nucleosome model and find it to reproduce qualitatively all the main features known to influence nucleosome positions. Moreover, using well-controlled approximations to this model allows us to come to a detailed understanding of the physics behind the sequence preferences of nucleosomes.

  5. DNA methylation, nucleosome formation and positioning.

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    Pennings, Sari; Allan, James; Davey, Colin S

    2005-02-01

    Recent mapping of nucleosome positioning on several long gene regions subject to DNA methylation has identified instances of nucleosome repositioning by this base modification. The evidence for an effect of CpG methylation on nucleosome formation and positioning in chromatin is reviewed here in the context of the complex sequence-structure requirements of DNA wrapping around the histone octamer and the role of this epigenetic mark in gene repression.

  6. Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection.

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    Oh, Jaewook; Sanders, Iryna F; Chen, Eric Z; Li, Hongzhe; Tobias, John W; Isett, R Benjamin; Penubarthi, Sindura; Sun, Hao; Baldwin, Don A; Fraser, Nigel W

    2015-01-01

    HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes). During lytic infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the lytic infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell DNA. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is in full swing (6 hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152 kb). Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (nucleosome free regions -NFR or Nucleosome depleted regions -NDR), or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during lytic infection. On average, DNA encoding Immediate Early (IE), Early (E) and Late (L) genes appear to have a similar density of nucleosomes.

  7. Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection.

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    Jaewook Oh

    Full Text Available HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes. During lytic infection, partial micrococcal nuclease (MNase digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the lytic infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell DNA. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is in full swing (6 hr PI, using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152 kb. Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (nucleosome free regions -NFR or Nucleosome depleted regions -NDR, or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during lytic infection. On average, DNA encoding Immediate Early (IE, Early (E and Late (L genes appear to have a similar density of nucleosomes.

  8. Painting a perspective on the landscape of nucleosome positioning.

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    Johnson, Steven M

    2010-06-01

    DNA sequence influences the position of nucleosomes and chromatin architecture. The extent to which underlying DNA sequence affects nucleosome positioning is currently a topic of considerable discussion and active experimentation. To contribute to the discussion, I will outline a few of the methods, data and arguments that I find compelling and believe will ultimately resolve the question of what positions nucleosomes. Basically, I will give a portrait of my current perspective on what influences the landscape of nucleosome positioning and chromatin architecture.

  9. An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo

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    Gracey Lia E

    2010-07-01

    Full Text Available Abstract Background The physiological function of eukaryotic DNA occurs in the context of nucleosomal arrays that can expose or obscure defined segments of the genome. Certain DNA sequences are capable of strongly positioning a nucleosome in vitro, suggesting the possibility that favorable intrinsic signals might reproducibly structure chromatin segments. As high-throughput sequencing analyses of nucleosome coverage in vitro and in vivo have become possible, a vigorous debate has arisen over the degree to which intrinsic DNA:nucleosome affinities orchestrate the in vivo positions of nucleosomes, thereby controlling physical accessibility of specific sequences in DNA. Results We describe here the in vivo consequences of placing a synthetic high-affinity nucleosome-positioning signal, the 601 sequence, into a DNA plasmid vector in mice. Strikingly, the 601 sequence was sufficient to position nucleosomes during an early phase after introduction of the DNA into the mice (when the plasmid vector transgene was active. This positioning capability was transient, with a loss of strong positioning at a later time point when the transgenes had become silent. Conclusions These results demonstrate an ability of DNA sequences selected solely for nucleosome affinity to organize chromatin in vivo, and the ability of other mechanisms to overcome these interactions in a dynamic nuclear environment.

  10. Statistical physics of nucleosome positioning and chromatin structure

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    Morozov, Alexandre

    2012-02-01

    Genomic DNA is packaged into chromatin in eukaryotic cells. The fundamental building block of chromatin is the nucleosome, a 147 bp-long DNA molecule wrapped around the surface of a histone octamer. Arrays of nucleosomes are positioned along DNA according to their sequence preferences and folded into higher-order chromatin fibers whose structure is poorly understood. We have developed a framework for predicting sequence-specific histone-DNA interactions and the effective two-body potential responsible for ordering nucleosomes into regular higher-order structures. Our approach is based on the analogy between nucleosomal arrays and a one-dimensional fluid of finite-size particles with nearest-neighbor interactions. We derive simple rules which allow us to predict nucleosome occupancy solely from the dinucleotide content of the underlying DNA sequences.Dinucleotide content determines the degree of stiffness of the DNA polymer and thus defines its ability to bend into the nucleosomal superhelix. As expected, the nucleosome positioning rules are universal for chromatin assembled in vitro on genomic DNA from baker's yeast and from the nematode worm C.elegans, where nucleosome placement follows intrinsic sequence preferences and steric exclusion. However, the positioning rules inferred from in vivo C.elegans chromatin are affected by global nucleosome depletion from chromosome arms relative to central domains, likely caused by the attachment of the chromosome arms to the nuclear membrane. Furthermore, intrinsic nucleosome positioning rules are overwritten in transcribed regions, indicating that chromatin organization is actively managed by the transcriptional and splicing machinery.

  11. Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

    DEFF Research Database (Denmark)

    Helbo, Alexandra Søgaard; Lay, Fides D; Jones, Peter A

    2017-01-01

    Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analy......Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high....... The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1...... the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide....

  12. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

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    Soler-López Montserrat

    2011-10-01

    Full Text Available Abstract Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site and TTS (Transcription Termination Site (at least in yeast is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression.

  13. The Effects of Nucleosome Positioning and Chromatin Architecture on Transgene Expression

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    Kempton, Colton E.

    2017-01-01

    Eukaryotes use proteins to carefully package and compact their genomes to fit into the nuclei of their individual cells. Nucleosomes are the primary level of compaction. Nucleosomes are formed when DNA wraps around an octamer of histone proteins and a nucleosome's position can limit access to genetic regulatory elements. Therefore, nucleosomes…

  14. Cracking the chromatin code: Precise rule of nucleosome positioning

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    Trifonov, Edward N.

    2011-03-01

    Various aspects of packaging DNA in eukaryotic cells are outlined in physical rather than biological terms. The informational and physical nature of packaging instructions encoded in DNA sequences is discussed with the emphasis on signal processing difficulties - very low signal-to-noise ratio and high degeneracy of the nucleosome positioning signal. As the author has been contributing to the field from its very onset in 1980, the review is mostly focused at the works of the author and his colleagues. The leading concept of the overview is the role of deformational properties of DNA in the nucleosome positioning. The target of the studies is to derive the DNA bendability matrix describing where along the DNA various dinucleotide elements should be positioned, to facilitate its bending in the nucleosome. Three different approaches are described leading to derivation of the DNA deformability sequence pattern, which is a simplified linear presentation of the bendability matrix. All three approaches converge to the same unique sequence motif CGRAAATTTYCG or, in binary form, YRRRRRYYYYYR, both representing the chromatin code.

  15. The Effects of Nucleosome Positioning and Chromatin Architecture on Transgene Expression

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    Kempton, Colton E.

    Eukaryotes use proteins to carefully package and compact their genomes to fit into the nuclei of their individual cells. Nucleosomes are the primary level of compaction. Nucleosomes are formed when DNA wraps around an octamer of histone proteins and a nucleosome's position can limit access to genetic regulatory elements. Therefore, nucleosomes represent a basic level of gene regulation. DNA and its associated proteins, called chromatin, is usually classified as euchromatin or heterochromatin. Euchromatin is transcriptionally active with loosely packed nucleosomes while heterochromatin is condensed with tightly packed nucleosomes and is transcriptionally silent. In order to become active, heterochromatin must first be remodeled. We have studied the effects of nucleosome positioning on transgene expression in vivo using Caenorhabditis elegans as a model. We show that both location and polarity of the DNA sequence can influence transgene expression. We also discuss some considerations for working with CRISPR/Cas9. A major reason for doing in vitro nucleosome reconstitutions is to determine the effects of DNA sequence on nucleosome formation and position. It has previously been implied that nucleosome reconstitutions are stochastic and not very reproducible. We show that nucleosome reconstitutions are highly reproducible under our reaction conditions. Our results also indicate that a minimum depth of 35X sequencing coverage be maintained for maximal gains in Pearson's correlation coefficients. Communicating science with others is an important skill for any researcher. The rising generation of scientists need mentors who can teach them how to be independent thinkers who can carry out scientific experiments and communicate their finding to others. With this goal in mind, we have devised a scaffolding pedagogical method to help transform undergraduates into confident independent thinkers and researchers.

  16. LeNup: Learning Nucleosome positioning from DNA sequences with improved convolutional neural networks.

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    Zhang, Juhua; Peng, Wenbo; Wang, Lei

    2018-01-10

    Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy profiles and computational tools to the analysis on these data, the complex language of eukaryotic Nucleosome positioning remains incompletely understood. Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) to understand nucleosome positioning. We combined Inception-like networks with a gating mechanism for the response of multiple patterns and long term association in DNA sequences. We developed the open-source package LeNup based on the CNN to predict nucleosome positioning in Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster as well as Saccharomyces cerevisiae genomes. We trained LeNup on four benchmark datasets. LeNup achieved greater predictive accuracy than previously published methods. LeNup is freely available as Python and Lua script source code under a BSD style license from https://github.com/biomedBit/LeNup. jhzhang@bit.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  17. Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.

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    Guillem Portella

    Full Text Available Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models. We found that methylation of CpG steps destabilizes nucleosomes, especially when these are placed in sites where the DNA minor groove faces the histone core. The larger stiffness of methylated CpG steps is a crucial factor behind the decrease in nucleosome stability. Methylation changes the positioning and phasing of the nucleosomal DNA, altering the accessibility of DNA to regulatory proteins, and accordingly gene functionality. Our theoretical calculations highlight a simple physical-based explanation on the foundations of epigenetic signaling.

  18. Replication-Coupled Nucleosome Assembly and Positioning by ATP-Dependent Chromatin-Remodeling Enzymes

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    Tejas Yadav

    2016-04-01

    Full Text Available During DNA replication, chromatin must be disassembled and faithfully reassembled on newly synthesized genomes. The mechanisms that govern the assembly of chromatin structures following DNA replication are poorly understood. Here, we exploited Okazaki fragment synthesis and other assays to study how nucleosomes are deposited and become organized in S. cerevisiae. We observe that global nucleosome positioning is quickly established on newly synthesized DNA in vivo. Importantly, we find that ATP-dependent chromatin-remodeling enzymes, Isw1 and Chd1, collaborate with histone chaperones to remodel nucleosomes as they are loaded behind a replication fork. Using a whole-genome sequencing approach, we determine that the positioning of newly deposited nucleosomes in vivo is specified by the combined actions of ATP-dependent chromatin-remodeling enzymes and select DNA-binding proteins. Altogether, our data provide in vivo evidence for coordinated “loading and remodeling” of nucleosomes behind the replication fork, allowing for rapid organization of chromatin during S phase.

  19. Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data.

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    Xuekui Zhang

    Full Text Available We describe a model-based method, PING, for predicting nucleosome positions in MNase-Seq and MNase- or sonicated-ChIP-Seq data. PING compares favorably to NPS and TemplateFilter in scalability, accuracy and robustness to low read density. To demonstrate that PING predictions from widely available sonicated data can have sufficient spatial resolution to be to be useful for biological inference, we use Illumina H3K4me1 ChIP-seq data to detect changes in nucleosome positioning around transcription factor binding sites due to tamoxifen stimulation, to discriminate functional and non-functional transcription factor binding sites more effectively than with enrichment profiles, and to confirm that the pioneer transcription factor Foxa2 associates with the accessible major groove of nucleosomal DNA.

  20. Designing nucleosomal force sensors

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    Tompitak, M.; de Bruin, L.; Eslami-Mossallam, B.; Schiessel, H.

    2017-05-01

    About three quarters of our DNA is wrapped into nucleosomes: DNA spools with a protein core. It is well known that the affinity of a given DNA stretch to be incorporated into a nucleosome depends on the geometry and elasticity of the basepair sequence involved, causing the positioning of nucleosomes. Here we show that DNA elasticity can have a much deeper effect on nucleosomes than just their positioning: it affects their "identities". Employing a recently developed computational algorithm, the mutation Monte Carlo method, we design nucleosomes with surprising physical characteristics. Unlike any other nucleosomes studied so far, these nucleosomes are short-lived when put under mechanical tension whereas other physical properties are largely unaffected. This suggests that the nucleosome, the most abundant DNA-protein complex in our cells, might more properly be considered a class of complexes with a wide array of physical properties, and raises the possibility that evolution has shaped various nucleosome species according to their genomic context.

  1. Nature of the Nucleosomal Barrier to RNA Polymerase II | Center for Cancer Research

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    In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged into nucleosomes, but in vitro encounters with the nucleosomes induce catalytic inactivation (arrest) of the pol II core enzyme. To determine potential mechanisms making nucleosomes transparent to transcription in vivo, we analyzed the nature of the nucleosome-induced arrest. We found that the arrests have been detected mostly at positions of strong intrinsic pause sites of DNA.

  2. Periodic Distribution of a Putative Nucleosome Positioning Motif in Human, Nonhuman Primates, and Archaea: Mutual Information Analysis

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    Sosa, Daniela; Miramontes, Pedro; Li, Wentian; Mireles, Víctor; Bobadilla, Juan R.; José, Marco V.

    2013-01-01

    Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats. PMID:23841049

  3. Exploring the Link between Nucleosome Occupancy and DNA Methylation

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    Cecilia Lövkvist

    2018-01-01

    Full Text Available Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and the level of CpG methylation. Several studies imply a causal link where CpG methylation might induce nucleosome formation, whereas others argue the opposite, i.e., that nucleosome occupancy might influence CpG methylation. Correlations are indeed evident between nucleosomes, CpG density and CpG methylation—at least near promoter sites. It is however less established whether there is an immediate causal relation between nucleosome occupancy and the presence of CpG sites—or if nucleosome occupancy could be influenced by other factors. In this work, we test for such causality in human genomes by analyzing the three quantities both near and away from promoter sites. For data from the human genome we compare promoter regions with given CpG densities with genomic regions without promoters but of similar CpG densities. We find the observed correlation between nucleosome occupancy and CpG density, respectively CpG methylation, to be specific to promoter regions. In other regions along the genome nucleosome occupancy is statistically independent of the positioning of CpGs or their methylation levels. Anti-correlation between CpG density and methylation level is however similarly strong in both regions. On promoters, nucleosome occupancy is more strongly affected by the level of gene expression than CpG density or CpG methylation—calling into question any direct causal relation between nucleosome occupancy and CpG organization. Rather, our results suggest that for organisms with cytosine methylation nucleosome occupancy might be primarily linked to gene expression, with no strong impact on methylation.

  4. PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

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    Woo, Sangsoon; Zhang, Xuekui; Sauteraud, Renan; Robert, François; Gottardo, Raphael

    2013-08-15

    MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase- or sonicated- ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance with nucleR and ChIPseqR. PING 2.0 is available from the Bioconductor website at http://bioconductor.org. It can run on Linux, Mac and Windows.

  5. Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans.

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    Jeffers, Tess E; Lieb, Jason D

    2017-01-01

    Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone-DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. Here, we explored the functional implications of nucleosome properties on gene expression and development in Caenorhabditis elegans embryos. We performed a time-course of micrococcal nuclease (MNase) digestion and measured the relative sensitivity or resistance of nucleosomes throughout the genome. Fragile nucleosomes were defined by nucleosomal DNA fragments that were recovered preferentially in early MNase-digestion time points. Nucleosome fragility was strongly and positively correlated with the AT content of the underlying DNA sequence. There was no correlation between promoter nucleosome fragility and the levels of histone modifications or histone variants. Genes with fragile nucleosomes in their promoters tended to be lowly expressed and expressed in a context-specific way, operating in neuronal response, the immune system, and stress response. In addition to DNA-encoded nucleosome fragility, we also found fragile nucleosomes at locations where we expected to find destabilized nucleosomes, for example, at transcription factor binding sites where nucleosomes compete with DNA-binding factors. Our data suggest that in C. elegans promoters, nucleosome fragility is in large part DNA-encoded and that it poises genes for future context-specific activation in response to environmental stress and developmental cues. © 2017 Jeffers and Lieb; Published by Cold Spring Harbor Laboratory Press.

  6. The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences.

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    Kensche, Philip Reiner; Hoeijmakers, Wieteke Anna Maria; Toenhake, Christa Geeke; Bras, Maaike; Chappell, Lia; Berriman, Matthew; Bártfai, Richárd

    2016-03-18

    In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated processes and it is central to the control of gene expression. For Plasmodium falciparum, a causative agent of human malaria, the nucleosome positioning profile of regulatory regions deserves particular attention because of their extreme AT-content. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit by demarcating landmark sites (transcription/translation start and end sites). In addition, our analysis provides strong indications for the function of positioned nucleosomes in splice site recognition. Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region, but lack the stereotypic downstream nucleosome arrays, highlighting a key difference in chromatin organization compared to model organisms. Furthermore, we observe transcription-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrate that nucleosome positioning and dynamics can be predictive for the functionality of regulatory DNA elements. Collectively, the strong nucleosome positioning over splice sites and surrounding putative transcription factor binding sites highlights the regulatory capacity of the nucleosome landscape in this deadly human pathogen. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Deposition of nucleosomal antigens (histones and DNA) in the epidermal basement membrane in human lupus nephritis.

    NARCIS (Netherlands)

    Grootscholten, C.; Bruggen, M.C.J. van; Pijl, J.W. van der; Jong, E.M.G.J. de; Ligtenberg, G.; Derksen, R.H.W.M.; Berden, J.H.M.

    2003-01-01

    OBJECTIVE: Antinuclear autoantibodies complexed to nucleosomes can bind to heparan sulfate (HS) in the glomerular basement membrane. This binding is due to the binding of the positively charged histones to the strongly anionic HS. Nucleosomes and histones have been identified in glomerular deposits

  8. Regulation of BAZ1A and nucleosome positioning in the nucleus accumbens in response to cocaine.

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    Sun, HaoSheng; Damez-Werno, Diane M; Scobie, Kimberly N; Shao, Ning-Yi; Dias, Caroline; Rabkin, Jacqui; Wright, Katherine N; Mouzon, Ezekiell; Kabbaj, Mohamed; Neve, Rachael; Turecki, Gustavo; Shen, Li; Nestler, Eric J

    2017-06-14

    Chromatin regulation, in particular ATP-dependent chromatin remodelers, have previously been shown to be important in the regulation of reward-related behaviors in animal models of mental illnesses. Here we demonstrate that BAZ1A, an accessory subunit of the ISWI family of chromatin remodeling complexes, is downregulated in the nucleus accumbens (NAc) of mice exposed repeatedly to cocaine and of cocaine-addicted humans. Viral-mediated overexpression of BAZ1A in mouse NAc reduces cocaine reward as assessed by conditioned place preference (CPP), but increases cocaine-induced locomotor activation. Furthermore, we investigate nucleosome repositioning genome-wide by conducting chromatin immunoprecipitation (ChIP)-sequencing for total H3 in NAc of control mice and after repeated cocaine administration, and find extensive nucleosome occupancy and shift changes across the genome in response to cocaine exposure. These findings implicate BAZ1A in molecular and behavioral plasticity to cocaine and offer new insight into the pathophysiology of cocaine addiction. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

  9. Nucleosome Organization in Human Embryonic Stem Cells.

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    Puya G Yazdi

    Full Text Available The fundamental repeating unit of eukaryotic chromatin is the nucleosome. Besides being involved in packaging DNA, nucleosome organization plays an important role in transcriptional regulation and cellular identity. Currently, there is much debate about the major determinants of the nucleosome architecture of a genome and its significance with little being known about its role in stem cells. To address these questions, we performed ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated our data with numerous epigenomic maps. Our analyses have revealed that the genome is a determinant of nucleosome organization with transcriptionally inactive regions characterized by a "ground state" of nucleosome profiles driven by underlying DNA sequences. DNA sequence preferences are associated with heterogeneous chromatin organization around transcription start sites. Transcription, histone modifications, and DNA methylation alter this "ground state" by having distinct effects on both nucleosome positioning and occupancy. As the transcriptional rate increases, nucleosomes become better positioned. Exons transcribed and included in the final spliced mRNA have distinct nucleosome profiles in comparison to exons not included at exon-exon junctions. Genes marked by the active modification H3K4m3 are characterized by lower nucleosome occupancy before the transcription start site compared to genes marked by the inactive modification H3K27m3, while bivalent domains, genes associated with both marks, lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin states are associated with unique nucleosome profiles. Nucleosome organization varies around transcription factor binding in enhancers versus promoters. DNA methylation is associated with increasing nucleosome occupancy and different types of methylations have distinct location preferences within the nucleosome core particle. Finally, computational

  10. Plasticity and epigenetic inheritance of centromere-specific histone H3 (CENP-A)-containing nucleosome positioning in the fission yeast.

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    Yao, Jianhui; Liu, Xingkun; Sakuno, Takeshi; Li, Wenzhu; Xi, Yuanxin; Aravamudhan, Pavithra; Joglekar, Ajit; Li, Wei; Watanabe, Yoshinori; He, Xiangwei

    2013-06-28

    Nucleosomes containing the specific histone H3 variant CENP-A mark the centromere locus on each chromatin and initiate kinetochore assembly. For the common type of regional centromeres, little is known in molecular detail of centromeric chromatin organization, its propagation through cell division, and how distinct organization patterns may facilitate kinetochore assembly. Here, we show that in the fission yeast S. pombe, a relatively small number of CENP-A/Cnp1 nucleosomes are found within the centromeric core and that their positioning relative to underlying DNA varies among genetically homogenous cells. Consistent with the flexible positioning of Cnp1 nucleosomes, a large portion of the endogenous centromere is dispensable for its essential activity in mediating chromosome segregation. We present biochemical evidence that Cnp1 occupancy directly correlates with silencing of the underlying reporter genes. Furthermore, using a newly developed pedigree analysis assay, we demonstrated the epigenetic inheritance of Cnp1 positioning and quantified the rate of occasional repositioning of Cnp1 nucleosomes throughout cell generations. Together, our results reveal the plasticity and the epigenetically inheritable nature of centromeric chromatin organization.

  11. Dynamic nucleosome organization at hox promoters during zebrafish embryogenesis.

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    Steven E Weicksel

    Full Text Available Nucleosome organization at promoter regions plays an important role in regulating gene activity. Genome-wide studies in yeast, flies, worms, mammalian embryonic stem cells and transformed cell lines have found well-positioned nucleosomes flanking a nucleosome depleted region (NDR at transcription start sites. This nucleosome arrangement depends on DNA sequence (cis-elements as well as DNA binding factors and ATP-dependent chromatin modifiers (trans-factors. However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome must undergo a broad reprogramming event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development, we map nucleosome positions at the promoter region of 37 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a progressive process that takes place over several stages. At stages immediately after fertilization, nucleosomes appear to be largely disordered at hox promoter regions. At stages after activation of the embryonic genome, nucleosomes are detectable at hox promoters, with positions becoming more uniform and more highly occupied. Since the genomic sequence is invariant during embryogenesis, this progressive change in nucleosome arrangement suggests that trans-factors play an important role in organizing nucleosomes during embryogenesis. Separating hox genes into expressed and non-expressed groups shows that expressed promoters have better positioned and occupied nucleosomes, as well as distinct NDRs, than non-expressed promoters. Finally, by blocking the retinoic acid-signaling pathway, we disrupt early hox gene transcription, but observe no effect on nucleosome positions, suggesting that active hox transcription is not a driving force behind the arrangement of nucleosomes at the promoters of hox genes during early development.

  12. Nucleosomal TATA-switch: competing orientations of TATA on the nucleosome.

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    Hapala, Jan; Trifonov, Edward N

    2013-09-15

    Transcription is known to be affected by the rotational setting of the transcription response elements within nucleosomes. We studied the rotational positioning of the TATA box, the most universal promoter motif. We applied a bioinformatic high-resolution nucleosome mapping technique to eukaryotic promoters. Our results show that the nucleosome DNA sequence harboring the TATA box encodes alternative rotational positions for the same piece of DNA. This may serve for switching the gene activity on and off. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Nucleosome dynamics: HMGB1 facilitates nucleosome restructuring and collaborates in estrogen-responsive gene expression

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    William M. Scovell

    2016-12-01

    Full Text Available The genome in the human cell is extraordinarily compacted in the nucleus. As a result, much of the DNA is inaccessible and functionally inert. Notwithstanding the highly efficient packaging, mechanisms have evolved to render DNA sites accessible that then enable a multitude of factors to carry out ongoing and vital functions. The compaction is derived from DNA complexation within nucleosomes, which can further consolidate into a higher-order chromatin structure. The nucleosome and nucleosomal DNA are not static in nature, but are dynamic, undergoing structural and functional changes as the cell responds to stresses and/or metabolic or environmental cues. We are only beginning to understand the forces and the complexes that engage the nucleosome to unearth the tightly bound and inaccessible DNA sequences and provide an opening to more accessible target sites. In many cases, current findings support a major role for the action of ATP-dependent chromatin remodeling complexes (CRCs in providing an avenue to factor accessibility that leads to the activation of transcription. The estrogen receptor α (ERα does not bind to the estrogen response element (ERE in the canonical nucleosome. However, evidence will be presented that HMGB1 restructures the nucleosome in an ATP-independent manner and also facilitates access and strong binding of ERα to ERE. The features that appear important in the mechanism of action for HMGB1 will be highlighted, in addition to the characteristic features of the restructured nucleosome. These findings, together with previous evidence, suggest a collaborative role for HMGB1 in the step-wise transcription of estrogen-responsive genes. In addition, alternate mechanistic pathways will be discussed, with consideration that “HMGB1 restructuring” of the nucleosome may generally be viewed as a perturbation of the equilibrium of an ensemble of nearly isoenergetic nucleosome states in an energy landscape that is driven by

  14. Translation efficiency in yeasts correlates with nucleosome formation in promoters.

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    Matushkin, Yu G; Levitsky, V G; Orlov, Yu L; Likhoshvai, V A; Kolchanov, N A

    2013-01-01

    Elongation efficiency index (EEI) was suggested earlier to estimate gene expression efficiency by nucleotide context of coding sequence in unicellular organisms. We have analyzed association between EEI and nucleosome formation potential (NFP) in 5' regulatory regions upstream translation initiation site (TIS) from two yeast species. Theoretical estimations of NFP based on DNA sequence were obtained by Recon method. Experimental estimation of nucleosome occupancy was obtained by high-throughput sequencing data of nucleosomal DNA in Saccharomyces cerevisiae . For the sample of all genes correlation coefficient was calculated between two vectors: vector of NFP values for fixed position relative to TIS and vector of EEI values. Profiles of correlation coefficients of NFP and EEI were counted in (-600; +600) regions relative to TIS for gene sequences extracted from GenBank. We found regions of strong negative dependence between NFP and EEI for all genes as well as for 10% highly expressed genes in Schizosaccharomyces pombe (10% of EEI-highest genes). At the same time, we found positive dependence between NFP and EEI for all genes and for low expressed genes in S. cerevisiae (10% of EEI-lowest genes). The association between NFP and EEI could be explained by evolutionary selection of context characteristics of nucleotide sequences for gene expression optimization.

  15. Baculoviruses and nucleosome management

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    Volkman, Loy E., E-mail: lvolkman@berkeley.edu

    2015-02-15

    Negatively-supercoiled-ds DNA molecules, including the genomes of baculoviruses, spontaneously wrap around cores of histones to form nucleosomes when present within eukaryotic nuclei. Hence, nucleosome management should be essential for baculovirus genome replication and temporal regulation of transcription, but this has not been documented. Nucleosome mobilization is the dominion of ATP-dependent chromatin-remodeling complexes. SWI/SNF and INO80, two of the best-studied complexes, as well as chromatin modifier TIP60, all contain actin as a subunit. Retrospective analysis of results of AcMNPV time course experiments wherein actin polymerization was blocked by cytochalasin D drug treatment implicate actin-containing chromatin modifying complexes in decatenating baculovirus genomes, shutting down host transcription, and regulating late and very late phases of viral transcription. Moreover, virus-mediated nuclear localization of actin early during infection may contribute to nucleosome management. - Highlights: • Baculoviruses have negatively-supercoiled, circular ds DNA. • Negatively-supercoiled DNA spontaneously forms nucleosomes in the nucleus. • Nucleosomes must be mobilized for replication and transcription to proceed. • Actin-containing chromatin modifiers participate in baculovirus replication.

  16. The size of the nucleosome

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    Bohr, Jakob; Olsen, Kasper

    2011-01-01

    The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We suggest that the size of the nucleosome core particle......-pairs of the linker-DNA is included the estimate of the size of an ideal nucleosome is in close agreement with the experimental numbers. Interestingly, the size of the nucleosome is shown to be a consequence of intrinsic properties of the DNA double helix....

  17. ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

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    Dann, Geoffrey P.; Liszczak, Glen P.; Bagert, John D.; Müller, Manuel M.; Nguyen, Uyen T. T.; Wojcik, Felix; Brown, Zachary Z.; Bos, Jeffrey; Panchenko, Tatyana; Pihl, Rasmus; Pollock, Samuel B.; Diehl, Katharine L.; Allis, C. David; Muir, Tom W.

    2018-01-01

    ATP-dependent chromatin remodellers regulate access to genetic information by controlling nucleosome positions in vivo1. However, the mechanism by which remodellers discriminate between different nucleosome substrates is poorly understood. Many chromatin remodelling proteins possess conserved protein domains that interact with nucleosomal features2. Here we used a quantitative high-throughput approach, based on the use of a DNA-barcoded mononucleosome library, to profile the biochemical activity of human ISWI family remodellers in response to a diverse set of nucleosome modifications. We show that accessory (non-ATPase) subunits of ISWI remodellers can distinguish between differentially modified nucleosomes, directing remodelling activity towards specific nucleosome substrates according to their modification state. Unexpectedly, we show that the nucleosome acidic patch3 is necessary for maximum activity of all ISWI remodellers evaluated. This dependence also extends to CHD and SWI/SNF family remodellers, suggesting that the acidic patch may be generally required for chromatin remodelling. Critically, remodelling activity can be regulated by modifications neighbouring the acidic patch, signifying that it may act as a tunable interaction hotspot for ATP-dependent chromatin remodellers and, by extension, many other chromatin effectors that engage this region of the nucleosome surface4–9. PMID:28767641

  18. Genomic sequence is highly predictive of local nucleosome depletion.

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    Guo-Cheng Yuan

    2008-01-01

    Full Text Available The regulation of DNA accessibility through nucleosome positioning is important for transcription control. Computational models have been developed to predict genome-wide nucleosome positions from DNA sequences, but these models consider only nucleosome sequences, which may have limited their power. We developed a statistical multi-resolution approach to identify a sequence signature, called the N-score, that distinguishes nucleosome binding DNA from non-nucleosome DNA. This new approach has significantly improved the prediction accuracy. The sequence information is highly predictive for local nucleosome enrichment or depletion, whereas predictions of the exact positions are only modestly more accurate than a null model, suggesting the importance of other regulatory factors in fine-tuning the nucleosome positions. The N-score in promoter regions is negatively correlated with gene expression levels. Regulatory elements are enriched in low N-score regions. While our model is derived from yeast data, the N-score pattern computed from this model agrees well with recent high-resolution protein-binding data in human.

  19. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.

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    Snyder, Matthew W; Kircher, Martin; Hill, Andrew J; Daza, Riza M; Shendure, Jay

    2016-01-14

    Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA (cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo nucleosome occupancy and found that short cfDNA fragments harbor footprints of transcription factors. The cfDNA nucleosome occupancies correlate well with the nuclear architecture, gene structure, and expression observed in cells, suggesting that they could inform the cell type of origin. Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how nucleosome footprints can be used to infer cell types contributing to cfDNA in pathological states such as cancer. Since this strategy does not rely on genetic differences to distinguish between contributing tissues, it may enable the noninvasive monitoring of a much broader set of clinical conditions than currently possible. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions.

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    Yanping Fan

    Full Text Available In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs. The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+, divalent (Mg(2+ or trivalent (Co(NH(3(6 (3+ cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+, to partial aggregation with Mg(2+ and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+. The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.

  1. Structural features based genome-wide characterization and prediction of nucleosome organization

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    Gan Yanglan

    2012-03-01

    Full Text Available Abstract Background Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. Results We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. Conclusions Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence

  2. The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer

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    Qiu, Yupeng; Levendosky, Robert F.; Chakravarthy, Srinivas; Patel, Ashok; Bowman, Gregory D.; Myong, Sua

    2017-10-01

    Chromatin remodelers catalyze dynamic packaging of the genome by carrying out nucleosome assembly/disassembly, histone exchange, and nucleosome repositioning. Remodeling results in evenly spaced nucleosomes, which requires probing both sides of the nucleosome, yet the way remodelers organize sliding activity to achieve this task is not understood. Here, we show that the monomeric Chd1 remodeler shifts DNA back and forth by dynamically alternating between different segments of the nucleosome. During sliding, Chd1 generates unstable remodeling intermediates that spontaneously relax to a pre-remodeled position. We demonstrate that nucleosome sliding is tightly controlled by two regulatory domains: the DNA-binding domain, which interferes with sliding when its range is limited by a truncated linking segment, and the chromodomains, which play a key role in substrate discrimination. We propose that active interplay of the ATPase motor with the regulatory domains may promote dynamic nucleosome structures uniquely suited for histone exchange and chromatin reorganization during transcription.

  3. Transcription factor binding sites prediction based on modified nucleosomes.

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    Mohammad Talebzadeh

    Full Text Available In computational methods, position weight matrices (PWMs are commonly applied for transcription factor binding site (TFBS prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data from these aligned and periodic patterns can improve the performance of binding region prediction. In this study, we propose two effective features, "modified nucleosomes neighboring" and "modified nucleosomes occupancy", to decrease FP in binding site discovery. Based on these features, we designed a logistic regression classifier which estimates the probability of a region as a TFBS. Our model learned each feature based on Sp1 binding sites on Chromosome 1 and was tested on the other chromosomes in human CD4+T cells. In this work, we investigated 21 histone modifications and found that only 8 out of 21 marks are strongly correlated with transcription factor binding regions. To prove that these features are not specific to Sp1, we combined the logistic regression classifier with the PWM, and created a new model to search TFBSs on the genome. We tested the model using transcription factors MAZ, PU.1 and ELF1 and compared the results to those using only the PWM. The results show that our model can predict Transcription factor binding regions more successfully. The relative simplicity of the model and capability of integrating other features make it a superior method

  4. Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence

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    Takizawa, Yoshimasa; Tanaka, Hiroki; Machida, Shinichi; Koyama, Masako; Maehara, Kazumitsu; Wade, Paul A.; Wolf, Matthias

    2018-01-01

    Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the ALB1 gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The ALB1 enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the ALB1 enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the ALB1 enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the ALB1 enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the ALB1 enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the ALB1 enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone–DNA contacts may be responsible for the enhanced DNA accessibility in the nucleosome with the ALB1 enhancer DNA. PMID:29563192

  5. Role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders.

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    López, Alberto J; Wood, Marcelo A

    2015-01-01

    It is becoming increasingly important to understand how epigenetic mechanisms control gene expression during neurodevelopment. Two epigenetic mechanisms that have received considerable attention are DNA methylation and histone acetylation. Human exome sequencing and genome-wide association studies have linked several neurobiological disorders to genes whose products actively regulate DNA methylation and histone acetylation. More recently, a third major epigenetic mechanism, nucleosome remodeling, has been implicated in human developmental and intellectual disability (ID) disorders. Nucleosome remodeling is driven primarily through nucleosome remodeling complexes with specialized ATP-dependent enzymes. These enzymes directly interact with DNA or chromatin structure, as well as histone subunits, to restructure the shape and organization of nucleosome positioning to ultimately regulate gene expression. Of particular interest is the neuron-specific Brg1/hBrm Associated Factor (nBAF) complex. Mutations in nBAF subunit genes have so far been linked to Coffin-Siris syndrome (CSS), Nicolaides-Baraitser syndrome (NBS), schizophrenia, and Autism Spectrum Disorder (ASD). Together, these human developmental and ID disorders are powerful examples of the impact of epigenetic modulation on gene expression. This review focuses on the new and emerging role of nucleosome remodeling in neurodevelopmental and ID disorders and whether nucleosome remodeling affects gene expression required for cognition independently of its role in regulating gene expression required for development.

  6. Role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders

    Directory of Open Access Journals (Sweden)

    Alberto J Lopez

    2015-04-01

    Full Text Available It is becoming increasingly important to understand how epigenetic mechanisms control gene expression during neurodevelopment. Two epigenetic mechanisms that have received considerable attention are DNA methylation and histone acetylation. Human exome sequencing and genome-wide association studies have linked several neurobiological disorders to genes whose products actively regulate DNA methylation and histone acetylation. More recently, a third major epigenetic mechanism, nucleosome remodeling, has been implicated in human developmental and intellectual disability disorders. Nucleosome remodeling is driven primarily through nucleosome remodeling complexes with specialized ATP-dependent enzymes. These enzymes directly interact with DNA or chromatin structure, as well as histone subunits, to restructure the shape and organization of nucleosome positioning to ultimately regulate gene expression. Of particular interest is the neuron-specific Brg1/hBrm Associated Factor (nBAF complex. Mutations in nBAF subunit genes have so far been linked to Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, schizophrenia, and Autism Spectrum Disorder. Together, these human developmental and intellectual disability disorders are powerful examples of the impact of epigenetic modulation on gene expression. This review focuses on the new and emerging role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders and whether nucleosome remodeling affects gene expression required for cognition independently of its role in regulating gene expression required for development.

  7. Dynamic and selective nucleosome repositioning during endotoxin tolerance.

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    El Gazzar, Mohamed; Liu, Tiefu; Yoza, Barbara K; McCall, Charles E

    2010-01-08

    Sepsis is encoded by a sequel of transcription activation and repression events that initiate, sustain, and resolve severe systemic inflammation. The repression/silencing phase occurs in blood leukocytes of animals and humans following the initiation of systemic inflammation due to developing endotoxin tolerance. We previously reported that NF-kappaB transcription factor RelB and histone H3 lysine methyltransferase G9a directly interact to induce facultative heterochromatin assembly and regulate epigenetic silencing during endotoxin tolerance, which is a major feature of sepsis. The general objective of this study was to assess whether dynamic temporal, structural, and positional changes of nucleosomes influence the sepsis phenotype. We used the THP-1 sepsis cell model to isolate mononucleosomes by rapid cell permeabilization and digestion of chromatin with micrococcal nuclease and then compared tumor necrosis factor alpha (TNFalpha) proximal promoter nucleosome alignment in endotoxin-responsive and -tolerant phenotypes. We found differential and dynamic repositioning of nucleosomes from permissive to repressive locations during the activation and silencing phases of transcription reprogramming and identified the following mechanisms that may participate in the process. 1) Two proximal nucleosomes repositioned to expose the primary NF-kappaB DNA binding site in endotoxin-responsive cells, and this "promoter opening" required the ATP-independent chaperone NAP1 to replace the core histone H2A with the H2A.Z variant. 2) During RelB-dependent endotoxin tolerance, the two nucleosomes repositioned and masked the primary NF-kappaB DNA binding site. 3) Small interfering RNA-mediated inhibition of RelB expression prevented repressive nucleosome repositioning and tolerance induction, but the "open" promoter required endotoxin-induced NF-kappaB p65 promoter binding to initiate transcription, supporting the known requirement of p65 posttranslational modifications for

  8. Multiple distinct stimuli increase measured nucleosome occupancy around human promoters.

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    Chuong D Pham

    Full Text Available Nucleosomes can block access to transcription factors. Thus the precise localization of nucleosomes relative to transcription start sites and other factor binding sites is expected to be a critical component of transcriptional regulation. Recently developed microarray approaches have allowed the rapid mapping of nucleosome positions over hundreds of kilobases (kb of human genomic DNA, although these approaches have not yet been widely used to measure chromatin changes associated with changes in transcription. Here, we use custom tiling microarrays to reveal changes in nucleosome positions and abundance that occur when hormone-bound glucocorticoid receptor (GR binds to sites near target gene promoters in human osteosarcoma cells. The most striking change is an increase in measured nucleosome occupancy at sites spanning ∼1 kb upstream and downstream of transcription start sites, which occurs one hour after addition of hormone, but is lost at 4 hours. Unexpectedly, this increase was seen both on GR-regulated and GR-non-regulated genes. In addition, the human SWI/SNF chromatin remodeling factor (a GR co-activator was found to be important for increased occupancy upon hormone treatment and also for low nucleosome occupancy without hormone. Most surprisingly, similar increases in nucleosome occupancy were also seen on both regulated and non-regulated promoters during differentiation of human myeloid leukemia cells and upon activation of human CD4+ T-cells. These results indicate that dramatic changes in chromatin structure over ∼2 kb of human promoters may occur genomewide and in response to a variety of stimuli, and suggest novel models for transcriptional regulation.

  9. Defensive marketing: how a strong incumbent can protect its position.

    Science.gov (United States)

    Roberts, John H

    2005-11-01

    There has been a lot of research on marketing as an offensive tactic-how it can help companies successfully launch new products, enter new markets, or gain share with existing products in their current markets. But for nearly every new product launch, market entrant, or industry upstart grabbing market share, there is an incumbent that must defend its position. And there has been little research on how these defenders can use marketing to preemptively respond to new or anticipated threats. John H. Roberts outlines four basic types of defensive marketing strategies: positive, inertial, parity, and retarding. With the first two, you establish and communicate your points of superiority relative to the new entrant; with the second two, you establish and communicate strategic points of comparability with your rival. Before choosing a strategy, you need to assess the weapons you have available to protect your market position-your brand identity, the products and services that support that identity, and your means of communicating it. Then assess your customers' value to you and their vulnerability to being poached by rivals. The author explains how Australian telecommunications company Telstra, facing deregulation, used a combination of the four strategies (plus the author's customer response model) to fend off market newcomer Optus. Telstra was prepared, for instance, to reach deep into its pockets and engage in a price war. But the customer response model indicated that a parity strategy-in which Telstra would offer lower rates on some routes and at certain times of day, even though its prices, on average, were higher than its rival's-was more likely to prevent consumers from switching. Ultimately, Telstra was able to retain several points of market share it otherwise would have lost. The strategies described here, though specific to Telstra's situation, offer lessons for any company facing new and potentially damaging competition.

  10. Theoretical analysis of epigenetic cell memory by nucleosome modification

    DEFF Research Database (Denmark)

    Dodd, Ian B; Micheelsen, Mille A; Sneppen, Kim

    2007-01-01

    Chromosomal regions can adopt stable and heritable alternative states resulting in bistable gene expression without changes to the DNA sequence. Such epigenetic control is often associated with alternative covalent modifications of histones. The stability and heritability of the states are thought...... strong bistability that is resistant both to high noise due to random gain or loss of nucleosome modifications and to random partitioning upon DNA replication. However, robust bistability required: (1) cooperativity, the activity of more than one modified nucleosome, in the modification reactions and (2...

  11. Consequences of cisplatin binding on nucleosome structure and dynamics.

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    Todd, Ryan C; Lippard, Stephen J

    2010-12-22

    The effects of cisplatin binding to DNA were explored at the nucleosome level to incorporate key features of the eukaryotic nuclear environment. An X-ray crystal structure of a site-specifically platinated nucleosome carrying a 1,3-cis-{Pt(NH₃)₂}²+-d(GpTpG) intrastrand cross-link reveals the details of how this adduct dictates the rotational positioning of DNA in the nucleosome. Results from in vitro nucleosome mobility assays indicate that a single platinum adduct interferes with ATP-independent sliding of DNA around the octamer core. Data from in vitro transcription experiments suggest that RNA polymerases can successfully navigate along cisplatin-damaged DNA templates that contain nucleosomes, but stall when the transcription elongation complex physically contacts a platinum cross-link located on the template strand. These results provide information about the effects of cisplatin binding to nuclear DNA and enhance our understanding of the mechanism of transcription inhibition by platinum anticancer compounds. Copyright © 2010 Elsevier Ltd. All rights reserved.

  12. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

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    de Dieuleveult, Maud; Yen, Kuangyu; Hmitou, Isabelle; Depaux, Arnaud; Boussouar, Fayçal; Dargham, Daria Bou; Jounier, Sylvie; Humbertclaude, Hélène; Ribierre, Florence; Baulard, Céline; Farrell, Nina P.; Park, Bongsoo; Keime, Céline; Carrière, Lucie; Berlivet, Soizick; Gut, Marta; Gut, Ivo; Werner, Michel; Deleuze, Jean-François; Olaso, Robert; Aude, Jean-Christophe; Chantalat, Sophie; Pugh, B. Franklin; Gérard, Matthieu

    2015-01-01

    Summary ATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers1–3 target specific nucleosomes to regulate transcription is unclear. Here, we present genome-wide remodeller-nucleosome interaction profiles for Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind one or both full nucleosomes that flank MNase-defined nucleosome-free promoter regions (NFRs), where they separate divergent transcription. Surprisingly, large CpG-rich NFRs that extend downstream of annotated transcriptional start sites (TSSs) are nevertheless chromatinized with non-nucleosomal or subnucleosomal histone variants (H3.3 and H2A.Z) and modifications (H3K4me3 and H3K27ac). RNA polymerase (pol) II therefore navigates hundreds of bp of altered chromatin in the sense direction before encountering an MNase-resistant nucleosome at the 3′ end of the NFR. Transcriptome analysis upon remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. Whereas at active genes individual remodellers play either positive or negative roles via altering nucleosome stability, at polycomb-enriched bivalent genes the same remodellers act in an opposite manner. These findings indicate that remodellers target specific nucleosomes at the edge of NFRs, where they regulate ES cell transcriptional programs. PMID:26814966

  13. Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate.

    Science.gov (United States)

    Girish, Taverekere S; McGinty, Robert K; Tan, Song

    2016-04-24

    Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucleosome complex. Our studies indicate that Set8 employs its i-SET and c-SET domains to engage nucleosomal DNA 1 to 1.5 turns from the nucleosomal dyad and in doing so, it positions the SET domain for catalysis with H4 Lys20. Surprisingly, we find that a basic N-terminal extension to the SET domain plays an even more prominent role in nucleosome binding, possibly by making an arginine anchor interaction with the nucleosome H2A/H2B acidic patch. We further show that proliferating cell nuclear antigen and the nucleosome compete for binding to Set8 through this basic extension, suggesting a mechanism for how nucleosome binding protects Set8 from proliferating cell nuclear antigen-dependent degradation during the cell cycle. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Positive semidefinite matrix completion, universal rigidity and the Strong Arnold Property

    NARCIS (Netherlands)

    M. Laurent (Monique); A. Varvitsiotis (Antonios)

    2014-01-01

    htmlabstractThis paper addresses the following three topics: positive semidefinite (psd) matrix completions, universal rigidity of frameworks, and the Strong Arnold Property (SAP). We show some strong connections among these topics, using semidefinite programming as unifying theme. Our main

  15. The impact of the nucleosome code on protein-coding sequence evolution in yeast.

    Directory of Open Access Journals (Sweden)

    Tobias Warnecke

    2008-11-01

    Full Text Available Coding sequence evolution was once thought to be the result of selection on optimal protein function alone. Selection can, however, also act at the RNA level, for example, to facilitate rapid translation or ensure correct splicing. Here, we ask whether the way DNA works also imposes constraints on coding sequence evolution. We identify nucleosome positioning as a likely candidate to set up such a DNA-level selective regime and use high-resolution microarray data in yeast to compare the evolution of coding sequence bound to or free from nucleosomes. Controlling for gene expression and intra-gene location, we find a nucleosome-free "linker" sequence to evolve on average 5-6% slower at synonymous sites. A reduced rate of evolution in linker is especially evident at the 5' end of genes, where the effect extends to non-synonymous substitution rates. This is consistent with regular nucleosome architecture in this region being important in the context of gene expression control. As predicted, codons likely to generate a sequence unfavourable to nucleosome formation are enriched in linker sequence. Amino acid content is likewise skewed as a function of nucleosome occupancy. We conclude that selection operating on DNA to maintain correct positioning of nucleosomes impacts codon choice, amino acid choice, and synonymous and non-synonymous rates of evolution in coding sequence. The results support the exclusion model for nucleosome positioning and provide an alternative interpretation for runs of rare codons. As the intimate association of histones and DNA is a universal characteristic of genic sequence in eukaryotes, selection on coding sequence composition imposed by nucleosome positioning should be phylogenetically widespread.

  16. Nucleosomes shape DNA polymorphism and divergence.

    Directory of Open Access Journals (Sweden)

    Sasha A Langley

    2014-07-01

    Full Text Available An estimated 80% of genomic DNA in eukaryotes is packaged as nucleosomes, which, together with the remaining interstitial linker regions, generate higher order chromatin structures [1]. Nucleosome sequences isolated from diverse organisms exhibit ∼10 bp periodic variations in AA, TT and GC dinucleotide frequencies. These sequence elements generate intrinsically curved DNA and help establish the histone-DNA interface. We investigated an important unanswered question concerning the interplay between chromatin organization and genome evolution: do the DNA sequence preferences inherent to the highly conserved histone core exert detectable natural selection on genomic divergence and polymorphism? To address this hypothesis, we isolated nucleosomal DNA sequences from Drosophila melanogaster embryos and examined the underlying genomic variation within and between species. We found that divergence along the D. melanogaster lineage is periodic across nucleosome regions with base changes following preferred nucleotides, providing new evidence for systematic evolutionary forces in the generation and maintenance of nucleosome-associated dinucleotide periodicities. Further, Single Nucleotide Polymorphism (SNP frequency spectra show striking periodicities across nucleosomal regions, paralleling divergence patterns. Preferred alleles occur at higher frequencies in natural populations, consistent with a central role for natural selection. These patterns are stronger for nucleosomes in introns than in intergenic regions, suggesting selection is stronger in transcribed regions where nucleosomes undergo more displacement, remodeling and functional modification. In addition, we observe a large-scale (∼180 bp periodic enrichment of AA/TT dinucleotides associated with nucleosome occupancy, while GC dinucleotide frequency peaks in linker regions. Divergence and polymorphism data also support a role for natural selection in the generation and maintenance of these

  17. Comparative analysis of methods for genome-wide nucleosome cartography.

    Science.gov (United States)

    Quintales, Luis; Vázquez, Enrique; Antequera, Francisco

    2015-07-01

    Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use. © The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  18. Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo.

    Science.gov (United States)

    Chen, Poshen B; Zhu, Lihua J; Hainer, Sarah J; McCannell, Kurtis N; Fazzio, Thomas G

    2014-12-15

    Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, differences in nucleosome composition or dynamics may also regulate accessibility. Methods for mapping nucleosome positions and occupancies genome-wide (MNase-seq) have uncovered the nucleosome landscapes of many different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays. Here we probe the genome-wide accessibility of multiple cell types in an unbiased manner using restriction endonuclease digestion of chromatin coupled to deep sequencing (RED-seq). Using this method, we identified differences in chromatin accessibility between populations of cells, not only in nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the majority of the genome that is packaged into nucleosome arrays. Furthermore, we identified both large differences in chromatin accessibility in distinct cell lineages and subtle but significant changes during differentiation of mouse embryonic stem cells (ESCs). Most significantly, using RED-seq, we identified differences in accessibility among nucleosomes harboring well-studied histone variants, and show that these differences depend on factors required for their deposition. Using an unbiased method to probe chromatin accessibility genome-wide, we uncover unique features of chromatin structure that are not observed using more widely-utilized methods. We demonstrate that different types of nucleosomes within mammalian cells exhibit different degrees of accessibility. These findings provide significant insight into the regulation of DNA accessibility.

  19. Positive semidefinite matrix completion, universal rigidity and the Strong Arnold Property

    NARCIS (Netherlands)

    Laurent, Monique; Varvitsiotis, A.

    This paper addresses the following three topics: positive semidefinite (psd) matrix completions, universal rigidity of frameworks, and the Strong Arnold Property (SAP). We show some strong connections among these topics, using semidefinite programming as unifying theme. Our main contribution is a

  20. Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis.

    Science.gov (United States)

    Lorzadeh, Alireza; Lopez Gutierrez, Rodrigo; Jackson, Linda; Moksa, Michelle; Hirst, Martin

    2017-12-12

    We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution based analysis methodology (nucleosome density ChIP-seq; ndChIP-seq) that enables the generation of combined measurements of micrococcal nuclease (MNase) accessibility with histone modification genome-wide. Nucleosome position and local density, and the posttranslational modification of their histone subunits, act in concert to regulate local transcription states. Combinatorial measurements of nucleosome accessibility with histone modification generated by ndChIP-seq allows for the simultaneous interrogation of these features. The ndChIP-seq methodology is applicable to small numbers of primary cells inaccessible to cross-linking based ChIP-seq protocols. Taken together, ndChIP-seq enables the measurement of histone modification in combination with local nucleosome density to obtain new insights into shared mechanisms that regulate RNA transcription within rare primary cell populations.

  1. Characterization of Dnmt1 Binding and DNA Methylation on Nucleosomes and Nucleosomal Arrays.

    Directory of Open Access Journals (Sweden)

    Anna Schrader

    Full Text Available The packaging of DNA into nucleosomes and the organisation into higher order structures of chromatin limits the access of sequence specific DNA binding factors to DNA. In cells, DNA methylation is preferentially occuring in the linker region of nucleosomes, suggesting a structural impact of chromatin on DNA methylation. These observations raise the question whether DNA methyltransferases are capable to recognize the nucleosomal substrates and to modify the packaged DNA. Here, we performed a detailed analysis of nucleosome binding and nucleosomal DNA methylation by the maintenance DNA methyltransferase Dnmt1. Our binding studies show that Dnmt1 has a DNA length sensing activity, binding cooperatively to DNA, and requiring a minimal DNA length of 20 bp. Dnmt1 needs linker DNA to bind to nucleosomes and most efficiently recognizes nucleosomes with symmetric DNA linkers. Footprinting experiments reveal that Dnmt1 binds to both DNA linkers exiting the nucleosome core. The binding pattern correlates with the efficient methylation of DNA linkers. However, the enzyme lacks the ability to methylate nucleosomal CpG sites on mononucleosomes and nucleosomal arrays, unless chromatin remodeling enzymes create a dynamic chromatin state. In addition, our results show that Dnmt1 functionally interacts with specific chromatin remodeling enzymes to enable complete methylation of hemi-methylated DNA in chromatin.

  2. Nucleosome Repositioning: A Novel Mechanism for Nicotine- and Cocaine-Induced Epigenetic Changes.

    Directory of Open Access Journals (Sweden)

    Amber N Brown

    Full Text Available Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug naïve positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse.

  3. Nucleosome Repositioning: A Novel Mechanism for Nicotine- and Cocaine-Induced Epigenetic Changes.

    Science.gov (United States)

    Brown, Amber N; Vied, Cynthia; Dennis, Jonathan H; Bhide, Pradeep G

    2015-01-01

    Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug naïve positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse.

  4. Nucleosomes in serum as a marker for cell death.

    Science.gov (United States)

    Holdenrieder, S; Stieber, P; Bodenmüller, H; Fertig, G; Fürst, H; Schmeller, N; Untch, M; Seidel, D

    2001-07-01

    The concentration of nucleosomes is elevated in blood of patients with diseases which are associated with enhanced cell death. In order to detect these circulating nucleosomes, we used the Cell Death Detection-ELISAplus (CDDE) from Roche Diagnostics (Mannheim, Germany) (details at http:\\\\biochem.roche.com). For its application in liquid materials we performed various modifications: we introduced a standard curve with nucleosome-rich material, which enabled direct quantification and improved comparability of the values within (CVintraassay:3.0-4.11%) and between several runs (CVinterassay:8.6-13.5%), and tested the analytical specificity of the ELISA. Because of the fast elimination of nucleosomes from circulation and their limited stability, we compared plasma and serum matrix and investigated in detail the pre-analytical handling of serum samples which can considerably influence the test results. Careless venipuncture producing hemolysis, delayed centrifugation and bacterial contamination of the blood samples led to false-positive results; delayed stabilization with EDTA and insufficient storage conditions resulted in false-negative values. At temperatures of -20 degrees C, serum samples which were treated with 10 mM EDTA were stable for at least 6 months. In order to avoid possible interfering factors, we recommend a schedule for the pre-analytical handling of the samples. As the first stage, the possible clinical application was investigated in the sera of 310 persons. Patients with solid tumors (n=220; mean=361 Arbitrary Units (AU)) had considerably higher values than healthy persons (n=50; mean=30 AU; p=0.0001) and patients with inflammatory diseases (n=40; mean= 296 AU; p=0.096). Within the group of patients with tumors, those in advanced stages (UICC 4) showed significantly higher values than those in early stages (UICC 1-3) (p=0.0004).

  5. Visual evoked potentials show strong positive association with intracranial pressure in patients with cryptococcal meningitis

    Directory of Open Access Journals (Sweden)

    Marcelo Adriano da Cunha Silva Vieira

    2015-04-01

    Full Text Available Objective : To verify the relationship between intracranial pressure and flash visual evoked potentials (F-VEP in patients with cryptococcal meningitis. Method The sample included adults diagnosed with cryptococcal meningitis admitted at a reference hospital for infectious diseases. The patients were subjected to F-VEP tests shortly before lumbar puncture. The Pearson’s linear correlation coefficient was calculated and the linear regression analysis was performed. Results : Eighteen individuals were subjected to a total of 69 lumbar punctures preceded by F-VEP tests. At the first lumbar puncture performed in each patient, N2 latency exhibited a strong positive correlation with intracranial pressure (r = 0.83; CI = 0.60 - 0.94; p < 0.0001. The direction of this relationship was maintained in subsequent punctures. Conclusion : The intracranial pressure measured by spinal tap manometry showed strong positive association with the N2 latency F-VEP in patients with cryptococcal meningitis.

  6. From nucleosome to chromosome: a dynamic organization of genetic information

    NARCIS (Netherlands)

    Fransz, P.F.; Jong, de J.H.S.G.M.

    2011-01-01

    Gene activity is controlled at different levels of chromatin organization, which involve genomic sequences, nucleosome structure, chromatin folding and chromosome arrangement. These levels are interconnected and influence each other. At the basic level nucleosomes generally occlude the DNA sequence

  7. From nucleosome to chromosome : a dynamic organization of genetic information

    NARCIS (Netherlands)

    Fransz, P.; de Jong, H.

    2011-01-01

    Gene activity is controlled at different levels of chromatin organization, which involve genomic sequences, nucleosome structure, chromatin folding and chromosome arrangement. These levels are interconnected and influence each other. At the basic level nucleosomes generally occlude the DNA sequence

  8. Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail-H2A Acidic Patch Interaction.

    Science.gov (United States)

    Chen, Qinming; Yang, Renliang; Korolev, Nikolay; Liu, Chuan Fa; Nordenskiöld, Lars

    2017-06-30

    Chromatin folding and dynamics are critically dependent on nucleosome-nucleosome interactions with important contributions from internucleosome binding of the histone H4 N-terminal tail K16-R23 domain to the surface of the H2A/H2B dimer. The H4 Lys16 plays a pivotal role in this regard. Using in vitro reconstituted 12-mer nucleosome arrays, we have investigated the mechanism of the H4 N-terminal tail in maintaining nucleosome-nucleosome stacking and mediating intra- and inter-array chromatin compaction, with emphasis on the role of K16 and the positive charge region, R17-R23. Analytical ultracentrifugation sedimentation velocity experiments and precipitation assays were employed to analyze effects on chromatin folding and self-association, respectively. Effects on chromatin folding caused by various mutations and modifications at position K16 in the H4 histone were studied. Additionally, using charge-quenching mutations, we characterized the importance of the interaction of the residues within the H4 positive charge region R17-R23 with the H2A acidic patch of the adjacent nucleosome. Furthermore, crosslinking experiments were conducted to establish the proximity of the basic tail region to the acidic patch. Our data indicate that the positive charge and length of the side chain of H4 K16 are important for its access to the adjacent nucleosome in the process of nucleosome-nucleosome stacking and array folding. The location and orientation of the H4 R17-R23 domain on the H2A/H2B dimer surface of the neighboring nucleosome core particle (NCP) in the compacted chromatin fiber were established. The dominance of electrostatic interactions in maintaining intra-array interaction was demonstrated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.

    Science.gov (United States)

    Bednar, Jan; Garcia-Saez, Isabel; Boopathi, Ramachandran; Cutter, Amber R; Papai, Gabor; Reymer, Anna; Syed, Sajad H; Lone, Imtiaz Nisar; Tonchev, Ognyan; Crucifix, Corinne; Menoni, Hervé; Papin, Christophe; Skoufias, Dimitrios A; Kurumizaka, Hitoshi; Lavery, Richard; Hamiche, Ali; Hayes, Jeffrey J; Schultz, Patrick; Angelov, Dimitar; Petosa, Carlo; Dimitrov, Stefan

    2017-05-04

    Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Nucleosomal DNA fragments in autoimmune diseases

    NARCIS (Netherlands)

    Holdenrieder, Stefan; Eichhorn, Peter; Beuers, Ulrich; Samtleben, Walter; Schoenermarck, Ulf; Zachoval, Reinhart; Nagel, Dorothea; Stieber, Petra

    2006-01-01

    The inadequate response of immune cells to circulating apoptotic products, such as nucleosomal DNA fragments, is assumed to be a potent stimulus for the production of autoantibodies during the pathogenesis and progression of systemic lupus erythematosus (SLE). Here, we analyzed the levels of

  11. Damping at positive frequencies in the limit J⊥-->0 in the strongly correlated Hubbard model

    Science.gov (United States)

    Mohan, Minette M.

    1992-08-01

    I show damping in the two-dimensional strongly correlated Hubbard model within the retraceable-path approximation, using an expansion around dominant poles for the self-energy. The damping half-width ~J2/3z occurs only at positive frequencies ω>5/2Jz, the excitation energy of a pure ``string'' state of length one, where Jz is the Ising part of the superexchange interaction, and occurs even in the absence of spin-flip terms ~J⊥ in contrast to other theoretical treatments. The dispersion relation for both damped and undamped peaks near the upper band edge is found and is shown to have lost the simple J2/3z dependence characteristic of the peaks near the lower band edge. The position of the first three peaks near the upper band edge agrees well with numerical simulations on the t-J model. The weight of the undamped peaks near the upper band edge is ~J4/3z, contrasting with Jz for the weight near the lower band edge.

  12. In silico evidence for sequence-dependent nucleosome sliding

    Energy Technology Data Exchange (ETDEWEB)

    Lequieu, Joshua; Schwartz, David C.; de Pablo, Juan J.

    2017-10-18

    Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nudeosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nudeosome repositioning. The mechanism of nudeosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.

  13. Interaction of influenza virus proteins with nucleosomes

    International Nuclear Information System (INIS)

    Garcia-Robles, Inmaculada; Akarsu, Hatice; Mueller, Christoph W.; Ruigrok, Rob W.H.; Baudin, Florence

    2005-01-01

    During influenza virus infection, transcription and replication of the viral RNA take place in the cell nucleus. Directly after entry in the nucleus the viral ribonucleoproteins (RNPs, the viral subunits containing vRNA, nucleoprotein and the viral polymerase) are tightly associated with the nuclear matrix. Here, we have analysed the binding of RNPs, M1 and NS2/NEP proteins to purified nucleosomes, reconstituted histone octamers and purified single histones. RNPs and M1 both bind to the chromatin components but at two different sites, RNP to the histone tails and M1 to the globular domain of the histone octamer. NS2/NEP did not bind to nucleosomes at all. The possible consequences of these findings for nuclear release of newly made RNPs and for other processes during the infection cycle are discussed

  14. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.

    Science.gov (United States)

    Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A; Lim, Wendell A; Narlikar, Geeta J; Almeida, Ricardo

    2016-04-28

    The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo.

  15. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.

    Science.gov (United States)

    Pass, Daniel Antony; Sornay, Emily; Marchbank, Angela; Crawford, Margaret R; Paszkiewicz, Konrad; Kent, Nicholas A; Murray, James A H

    2017-09-01

    All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more

  16. Staphylococcus aureus protease: a probe of exposed, non-basic histone sequences in nucleosomes

    Energy Technology Data Exchange (ETDEWEB)

    Rill, R.L.; Oosterhof, D.K.

    1980-01-01

    The digestion of histones in chicken erythrocyte nucleosome cores and chromatin by Staphylococcus aureus protease was examined. This protease cleaves specifically at acidic residues and prefers glu-X bonds under the conditions used. Only 1 of 24 glutamic and 2 of 13 aspartic acids among all four core histones are located in basic, amino-terminal tails, hence staph. protease is a highly specific probe of exposed non-basic sequences. Staph. protease readily degraded H1, H5, and H3; moderately degraded H2b, and only slightly degraded H2a and H4 in nucleosomes and nucleosome cores. Electrophoresis of core histone fragments from limited digests showed that most glutamic acids were inaccessible, but at least five sites in non-basic sequences were readily cleaved. Tentative assignments of these fragments based on comparisons with products from limited digests of pure histones suggested that most accessible sites in nucleosome cores occur in H3. The most probable sites of H3 cutting are glutamic acids at positions 51, 60, 73, 94, and 97. At least one site in H2b, probably the equivalent of glu-105 in the calf H2b sequence, was accessible. No sites in H2a and H4 appeared highly accessible. H5 was readily cleaved at a site near the amino-terminus. These data substantiate the other evidence that non-basic core histone sequences are located primarily in the nucleosome interior, but that H3 binds to the ends of core DNA and thereby is partly exposed as the upper and lower surfaces of the disk-shaped core.

  17. Nucleosome structure of the yeast CHA1 promoter

    DEFF Research Database (Denmark)

    Moreira, José Manuel Alfonso; Holmberg, S

    1998-01-01

    The Saccharomyces cerevisiae CHA1 gene encodes the catabolic L-serine (L-threonine) dehydratase. We have previously shown that the transcriptional activator protein Cha4p mediates serine/threonine induction of CHA1 expression. We used accessibility to micrococcal nuclease and DNase I to determine...... the in vivo chromatin structure of the CHA1 chromosomal locus, both in the non-induced state and upon induction. Upon activation, a precisely positioned nucleosome (nuc-1) occluding the TATA box and the transcription start site is removed. A strain devoid of Cha4p showed no chromatin alteration under inducing......, in a sir4 deletion strain, repression of CHA1 is partly lost and activator-independent remodeling of nuc-1 is observed. We propose a model for CHA1 activation based on promoter remodeling through interactions of Cha4p with chromatin components other than basal factors and associated proteins....

  18. Nucleosomal arrangement affects single-molecule transcription dynamics.

    Science.gov (United States)

    Fitz, Veronika; Shin, Jaeoh; Ehrlich, Christoph; Farnung, Lucas; Cramer, Patrick; Zaburdaev, Vasily; Grill, Stephan W

    2016-10-24

    In eukaryotes, gene expression depends on chromatin organization. However, how chromatin affects the transcription dynamics of individual RNA polymerases has remained elusive. Here, we use dual trap optical tweezers to study single yeast RNA polymerase II (Pol II) molecules transcribing along a DNA template with two nucleosomes. The slowdown and the changes in pausing behavior within the nucleosomal region allow us to determine a drift coefficient, χ, which characterizes the ability of the enzyme to recover from a nucleosomal backtrack. Notably, χ can be used to predict the probability to pass the first nucleosome. Importantly, the presence of a second nucleosome changes χ in a manner that depends on the spacing between the two nucleosomes, as well as on their rotational arrangement on the helical DNA molecule. Our results indicate that the ability of Pol II to pass the first nucleosome is increased when the next nucleosome is turned away from the first one to face the opposite side of the DNA template. These findings help to rationalize how chromatin arrangement affects Pol II transcription dynamics.

  19. Hinge and chromoshadow of HP1α participate in recognition of K9 methylated histone H3 in nucleosomes.

    Science.gov (United States)

    Mishima, Yuichi; Watanabe, Makoto; Kawakami, Toru; Jayasinghe, Chanika D; Otani, Junji; Kikugawa, Yusuke; Shirakawa, Masahiro; Kimura, Hiroshi; Nishimura, Osamu; Aimoto, Saburo; Tajima, Shoji; Suetake, Isao

    2013-01-09

    The majority of the genome in eukaryotes is packaged into transcriptionally inactive chromatin. Heterochromatin protein 1 (HP1) is a major player in the establishment and maintenance of heterochromatin. HP1 specifically recognizes a methylated lysine residue at position 9 in histone H3 through its N-terminal chromo domain (CD). To elucidate the binding properties of HP1α to nucleosomes in vitro, we reconstituted nucleosomes containing histone H3 trimethylated at lysine 9. HP1α exhibited high-affinity binding to nucleosomes containing methylated histone H3 in a nucleosome core-number-dependent manner. The hinge region (HR) connecting the CD and C-terminal chromoshadow domain (CSD), and the CSD contributed to the selective binding of HP1α to histone H3 with trimethylated lysine 9 through weak DNA binding and by suppressing the DNA binding, respectively. We propose that not only the specific recognition of lysine 9 methylation of histone H3 by the CD but also the HR and the CSD cooperatively contribute to the selective binding of HP1α to histone H3 lysine 9 methylated nucleosomes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Population genomics of the honey bee reveals strong signatures of positive selection on worker traits.

    Science.gov (United States)

    Harpur, Brock A; Kent, Clement F; Molodtsova, Daria; Lebon, Jonathan M D; Alqarni, Abdulaziz S; Owayss, Ayman A; Zayed, Amro

    2014-02-18

    Most theories used to explain the evolution of eusociality rest upon two key assumptions: mutations affecting the phenotype of sterile workers evolve by positive selection if the resulting traits benefit fertile kin, and that worker traits provide the primary mechanism allowing social insects to adapt to their environment. Despite the common view that positive selection drives phenotypic evolution of workers, we know very little about the prevalence of positive selection acting on the genomes of eusocial insects. We mapped the footprints of positive selection in Apis mellifera through analysis of 40 individual genomes, allowing us to identify thousands of genes and regulatory sequences with signatures of adaptive evolution over multiple timescales. We found Apoidea- and Apis-specific genes to be enriched for signatures of positive selection, indicating that novel genes play a disproportionately large role in adaptive evolution of eusocial insects. Worker-biased proteins have higher signatures of adaptive evolution relative to queen-biased proteins, supporting the view that worker traits are key to adaptation. We also found genes regulating worker division of labor to be enriched for signs of positive selection. Finally, genes associated with worker behavior based on analysis of brain gene expression were highly enriched for adaptive protein and cis-regulatory evolution. Our study highlights the significant contribution of worker phenotypes to adaptive evolution in social insects, and provides a wealth of knowledge on the loci that influence fitness in honey bees.

  1. Plasma levels of nucleosomes and nucleosome-autoantibody complexes in murine lupus: effects of disease progression and lipopolyssacharide administration.

    NARCIS (Netherlands)

    Licht, R.; Bruggen, M.C.J. van; Oppers-Walgreen, B.; Rijke, T.P.M.; Berden, J.H.M.

    2001-01-01

    OBJECTIVE: To evaluate the effect of disease progression and lipopolysaccharide (LPS) administration on the presence of nucleosomes, antinucleosome reactivity, and nucleosome-Ig complexes in the circulation of MRL and control mice. METHODS: Plasma samples from lupus-prone (MRL/lpr and MRL/+) and

  2. Genetic signature of strong recent positive selection at interleukin-32 gene in goat

    Directory of Open Access Journals (Sweden)

    Akhtar Rasool Asif

    2017-07-01

    Full Text Available Objective Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. Methods By using fixation index (FST based method, IL-32 (9375 gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and FST. Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8 in Codeml program of phylogenetic analysis by maximum liklihood. Results IL-32 is detected under positive selection using the FST simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%, bison (91.97%, camel (58.39%, cat (56.59%, buffalo (56.50%, human (56.13%, dog (50.97%, horse (54.04%, and rabbit (53.41% respectively. Conclusion This study provides evidence for IL-32 gene as under significant positive selection in goat.

  3. Genetic signature of strong recent positive selection at interleukin-32 gene in goat.

    Science.gov (United States)

    Asif, Akhtar Rasool; Qadri, Sumayyah; Ijaz, Nabeel; Javed, Ruheena; Ansari, Abdur Rahman; Awais, Muhammd; Younus, Muhammad; Riaz, Hasan; Du, Xiaoyong

    2017-07-01

    Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. By using fixation index ( F ST ) based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and F ST . Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8) in Codeml program of phylogenetic analysis by maximum liklihood. IL-32 is detected under positive selection using the F ST simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%), bison (91.97%), camel (58.39%), cat (56.59%), buffalo (56.50%), human (56.13%), dog (50.97%), horse (54.04%), and rabbit (53.41%) respectively. This study provides evidence for IL-32 gene as under significant positive selection in goat.

  4. Nucleosome Core Particle Disassembly and Assembly Kinetics Studied Using Single-Molecule Fluorescence.

    Science.gov (United States)

    Hazan, Noa Plavner; Tomov, Toma E; Tsukanov, Roman; Liber, Miran; Berger, Yaron; Masoud, Rula; Toth, Katalin; Langowski, Joerg; Nir, Eyal

    2015-10-20

    The stability of the nucleosome core particle (NCP) is believed to play a major role in regulation of gene expression. To understand the mechanisms that influence NCP stability, we studied stability and dissociation and association kinetics under different histone protein (NCP) and NaCl concentrations using single-pair Förster resonance energy transfer and alternating laser excitation techniques. The method enables distinction between folded, unfolded, and intermediate NCP states and enables measurements at picomolar to nanomolar NCP concentrations where dissociation and association reactions can be directly observed. We reproduced the previously observed nonmonotonic dependence of NCP stability on NaCl concentration, and we suggest that this rather unexpected behavior is a result of interplay between repulsive and attractive forces within positively charged histones and between the histones and the negatively charged DNA. Higher NaCl concentrations decrease the attractive force between the histone proteins and the DNA but also stabilize H2A/H2B histone dimers, and possibly (H3/H4)2 tetramers. An intermediate state in which one DNA arm is unwrapped, previously observed at high NaCl concentrations, is also explained by this salt-induced stabilization. The strong dependence of NCP stability on ion and histone concentrations, and possibly on other charged macromolecules, may play a role in chromosomal morphology. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. Good Health, Strong Families, and Positive Early Learning Experiences: Promoting Better Public Policies for America's Infants and Toddlers

    Science.gov (United States)

    Lally, J. Ronald; Lurie-Hurvitz, Erica; Cohen, Julie

    2006-01-01

    The ZERO TO THREE Policy Center has three areas of focus: good health, strong families, and positive early learning experiences. Effective policies must promote healthy functioning in all domains, including cognitive, physical, and social and emotional development. Comprehensive services are essential to meeting the needs of very young children…

  6. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

    Science.gov (United States)

    Fuda, Nicholas J; Guertin, Michael J; Sharma, Sumeet; Danko, Charles G; Martins, André L; Siepel, Adam; Lis, John T

    2015-03-01

    Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters.

  7. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

    Directory of Open Access Journals (Sweden)

    Nicholas J Fuda

    2015-03-01

    Full Text Available Previous studies have shown that GAGA Factor (GAF is enriched on promoters with paused RNA Polymerase II (Pol II, but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters.

  8. Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation.

    Science.gov (United States)

    Xi, Yuanxin; Yao, Jianhui; Chen, Rui; Li, Wei; He, Xiangwei

    2011-05-01

    The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity-nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed "fragile nucleosomes" throughout the yeast genome, nearly 1000 of which were at previously determined "nucleosome-free" loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation, and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.

  9. Investigation of a strong positive ionospheric storm during geomagnetic disturbances occurred in the Brazilian sector

    Science.gov (United States)

    de Abreu, A. J.; Sahai, Y.; Fagundes, P. R.; de Jesus, R.; Bittencourt, J. A.; Pillat, V. G.

    2012-12-01

    In this paper, we have investigated the responses of the ionospheric F region at equatorial and low latitude regions in the Brazilian sector during the super geomagnetic storm on 15-16 May 2005. The geomagnetic storm reached a minimum Dst of -263 nT at 0900 UT on 15 May. In this paper, we present vertical total electron content (vTEC) and phase fluctuations (in TECU/min) from Global Positioning System (GPS) observations obtained at Belém (BELE), Brasília (BRAZ), Presidente Prudente (UEPP), and Porto Alegre (POAL), Brazil, during the period 14-17 May 2005. Also, we present ionospheric parameters h'F, hpF2, and foF2, using the Canadian Advanced Digital Ionosonde (CADI) obtained at Palmas (PAL) and São José dos Campos (SJC), Brazil, for the same period. The super geomagnetic storm has fast decrease in the Dst index soon after SSC at 0239 UT on 15 May. It is a good possibility of prompt penetration of electric field of magnetospheric origin resulting in uplifting of the F region. The vTEC observations show a trough at BELE and a crest above UEPP, soon after SSC, indicating strengthening of nighttime equatorial anomaly. During the daytime on 15 and 16 May, in the recovery phase, the variations in foF2 at SJC and the vTEC observations, particularly at BRAZ, UEPP, and POAL, show large positive ionospheric storm. There is ESF on the all nights at PAL, in the post-midnight (UT) sector, and phase fluctuations only on the night of 14-15 May at BRAZ, after the SSC. No phase fluctuations are observed at the equatorial station BELE and low latitude stations (BRAZ, UEPP, and POAL) at all other times. This indicates that the plasma bubbles are generated and confined on this magnetically disturbed night only up to the low magnetic latitude and drifted possibly to west.

  10. On Strong Positive Frequency Dependencies of Quality Factors in Local-Earthquake Seismic Studies

    Science.gov (United States)

    Morozov, Igor B.; Jhajhria, Atul; Deng, Wubing

    2018-03-01

    Many observations of seismic waves from local earthquakes are interpreted in terms of the frequency-dependent quality factor Q( f ) = Q0 f^{η } , where η is often close to or exceeds one. However, such steep positive frequency dependencies of Q require careful analysis with regard to their physical consistency. In particular, the case of η = 1 corresponds to frequency-independent (elastic) amplitude decays with time and consequently requires no Q-type attenuation mechanisms. For η > 1, several problems with physical meanings of such Q-factors occur. First, contrary to the key premise of seismic attenuation, high-frequency parts of the wavefield are enhanced with increasing propagation times relative to the low-frequency ones. Second, such attenuation cannot be implemented by mechanical models of wave-propagating media. Third, with η > 1, the velocity dispersion associated with such Q(f) occurs over unrealistically short frequency range and has an unexpected oscillatory shape. Cases η = 1 and η > 1 are usually attributed to scattering; however, this scattering must exhibit fortuitous tuning into the observation frequency band, which appears unlikely. The reason for the above problems is that the inferred Q values are affected by the conventional single-station measurement procedure. Both parameters Q 0 and are apparent, i.e., dependent on the selected parameterization and inversion method, and they should not be directly attributed to the subsurface. For η ≈ 1, parameter Q 0 actually describes the frequency-independent amplitude decay in access of some assumed geometric spreading t -α , where α is usually taken equal one. The case η > 1 is not allowed physically and could serve as an indicator of problematic interpretations. Although the case 0 < η < 1 is possible, its parameters Q 0 and may also be biased by the measurement procedure. To avoid such difficulties of Q-based approaches, we recommend measuring and interpreting the amplitude-decay rates

  11. Start Position Strongly Influences Fixation Patterns during Face Processing: Difficulties with Eye Movements as a Measure of Information Use

    Science.gov (United States)

    Arizpe, Joseph; Kravitz, Dwight J.; Yovel, Galit; Baker, Chris I.

    2012-01-01

    Fixation patterns are thought to reflect cognitive processing and, thus, index the most informative stimulus features for task performance. During face recognition, initial fixations to the center of the nose have been taken to indicate this location is optimal for information extraction. However, the use of fixations as a marker for information use rests on the assumption that fixation patterns are predominantly determined by stimulus and task, despite the fact that fixations are also influenced by visuo-motor factors. Here, we tested the effect of starting position on fixation patterns during a face recognition task with upright and inverted faces. While we observed differences in fixations between upright and inverted faces, likely reflecting differences in cognitive processing, there was also a strong effect of start position. Over the first five saccades, fixation patterns across start positions were only coarsely similar, with most fixations around the eyes. Importantly, however, the precise fixation pattern was highly dependent on start position with a strong tendency toward facial features furthest from the start position. For example, the often-reported tendency toward the left over right eye was reversed for the left starting position. Further, delayed initial saccades for central versus peripheral start positions suggest greater information processing prior to the initial saccade, highlighting the experimental bias introduced by the commonly used center start position. Finally, the precise effect of face inversion on fixation patterns was also dependent on start position. These results demonstrate the importance of a non-stimulus, non-task factor in determining fixation patterns. The patterns observed likely reflect a complex combination of visuo-motor effects and simple sampling strategies as well as cognitive factors. These different factors are very difficult to tease apart and therefore great caution must be applied when interpreting absolute

  12. Multiscale modelling of nucleosome core particle aggregation

    Science.gov (United States)

    Lyubartsev, Alexander P.; Korolev, Nikolay; Fan, Yanping; Nordenskiöld, Lars

    2015-02-01

    The nucleosome core particle (NCP) is the basic building block of chromatin. Under the influence of multivalent cations, isolated mononucleosomes exhibit a rich phase behaviour forming various columnar phases with characteristic NCP-NCP stacking. NCP stacking is also a regular element of chromatin structure in vivo. Understanding the mechanism of nucleosome stacking and the conditions leading to self-assembly of NCPs is still incomplete. Due to the complexity of the system and the need to describe electrostatics properly by including the explicit mobile ions, novel modelling approaches based on coarse-grained (CG) methods at the multiscale level becomes a necessity. In this work we present a multiscale CG computer simulation approach to modelling interactions and self-assembly of solutions of NCPs induced by the presence of multivalent cations. Starting from continuum simulations including explicit three-valent cobalt(III)hexammine (CoHex3+) counterions and 20 NCPs, based on a previously developed advanced CG NCP model with one bead per amino acid and five beads per two DNA base pair unit (Fan et al 2013 PLoS One 8 e54228), we use the inverse Monte Carlo method to calculate effective interaction potentials for a ‘super-CG’ NCP model consisting of seven beads for each NCP. These interaction potentials are used in large-scale simulations of up to 5000 NCPs, modelling self-assembly induced by CoHex3+. The systems of ‘super-CG’ NCPs form a single large cluster of stacked NCPs without long-range order in agreement with experimental data for NCPs precipitated by the three-valent polyamine, spermidine3+.

  13. Spin excitations in systems with hopping electron transport and strong position disorder in a large magnetic field

    Science.gov (United States)

    Shumilin, A. V.

    2016-10-01

    We discuss the spin excitations in systems with hopping electron conduction and strong position disorder. We focus on the problem in a strong magnetic field when the spin Hamiltonian can be reduced to the effective single-particle Hamiltonian and treated with conventional numerical technics. It is shown that in a 3D system with Heisenberg exchange interaction the spin excitations have a delocalized part of the spectrum even in the limit of strong disorder, thus leading to the possibility of the coherent spin transport. The spin transport provided by the delocalized excitations can be described by a diffusion coefficient. Non-homogenous magnetic fields lead to the Anderson localization of spin excitations while anisotropy of the exchange interaction results in the Lifshitz localization of excitations. We discuss the possible effect of the additional exchange-driven spin diffusion on the organic spin-valve devices.

  14. G+C content dominates intrinsic nucleosome occupancy

    Directory of Open Access Journals (Sweden)

    Hughes Timothy R

    2009-12-01

    Full Text Available Abstract Background The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging. A wide variety of DNA sequence features are believed to influence nucleosome formation, including periodic dinucleotide signals, poly-A stretches and other short motifs, and sequence properties that influence DNA structure, including base content. It was recently shown by Kaplan et al. that a probabilistic model using composition of all 5-mers within a nucleosome-sized tiling window accurately predicts intrinsic nucleosome occupancy across an entire genome in vitro. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences. Results We find that a simple linear combination of only 14 simple DNA sequence attributes (G+C content, two transformations of dinucleotide composition, and the frequency of eleven 4-bp sequences explains nucleosome occupancy in vitro and in vivo in a manner comparable to the Kaplan model. G+C content and frequency of AAAA are the most important features. G+C content is dominant, alone explaining ~50% of the variation in nucleosome occupancy in vitro. Conclusions Our findings provide a dramatically simplified means to predict and understand intrinsic nucleosome occupancy. G+C content may dominate because it both reduces frequency of poly-A-like stretches and correlates with many other DNA structural characteristics. Since G+C content is enriched or depleted at many types of features in diverse eukaryotic genomes, our results suggest that variation in nucleotide composition may have a widespread and direct influence on chromatin structure.

  15. Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility.

    Science.gov (United States)

    Lorzadeh, Alireza; Bilenky, Misha; Hammond, Colin; Knapp, David J H F; Li, Luolan; Miller, Paul H; Carles, Annaick; Heravi-Moussavi, Alireza; Gakkhar, Sitanshu; Moksa, Michelle; Eaves, Connie J; Hirst, Martin

    2016-11-15

    Nucleosome position, density, and post-translational modification are widely accepted components of mechanisms regulating DNA transcription but still incompletely understood. We present a modified native ChIP-seq method combined with an analytical framework that allows MNase accessibility to be integrated with histone modification profiles. Application of this methodology to the primitive (CD34+) subset of normal human cord blood cells enabled genomic regions enriched in one versus two nucleosomes marked by histone 3 lysine 4 trimethylation (H3K4me3) and/or histone 3 lysine 27 trimethylation (H3K27me3) to be associated with their transcriptional and DNA methylation states. From this analysis, we defined four classes of promoter-specific profiles and demonstrated that a majority of bivalent marked promoters are heterogeneously marked at a single-cell level in this primitive cell type. Interestingly, extension of this approach to human embryonic stem cells revealed an altered relationship between chromatin modification state and nucleosome content at promoters, suggesting developmental stage-specific organization of histone methylation states. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Vaccination with L. infantum chagasi nucleosomal histones confers protection against new world cutaneous leishmaniasis caused by Leishmania braziliensis.

    Science.gov (United States)

    Carneiro, Marcia W; Santos, Diego M; Fukutani, Kiyoshi F; Clarencio, Jorge; Miranda, Jose Carlos; Brodskyn, Claudia; Barral, Aldina; Barral-Netto, Manoel; Soto, Manuel; de Oliveira, Camila I

    2012-01-01

    Nucleosomal histones are intracellular proteins that are highly conserved among Leishmania species. After parasite destruction or spontaneous lysis, exposure to these proteins elicits a strong host immune response. In the present study, we analyzed the protective capability of Leishmania infantum chagasi nucleosomal histones against L. braziliensis infection using different immunization strategies. BALB/c mice were immunized with either a plasmid DNA cocktail (DNA) containing four Leishmania nucleosomal histones or with the DNA cocktail followed by the corresponding recombinant proteins plus CpG (DNA/Protein). Mice were later challenged with L. braziliensis, in the presence of sand fly saliva. Lesion development, parasite load and the cellular immune response were analyzed five weeks after challenge. Immunization with either DNA alone or with DNA/Protein was able to inhibit lesion development. This finding was highlighted by the absence of infected macrophages in tissue sections. Further, parasite load at the infection site and in the draining lymph nodes was also significantly lower in vaccinated animals. This outcome was associated with increased expression of IFN-γ and down regulation of IL-4 at the infection site. The data presented here demonstrate the potential use of L. infantum chagasi nucleosomal histones as targets for the development of vaccines against infection with L. braziliensis, as shown by the significant inhibition of disease development following a live challenge.

  17. Probing Enhanced Double-Strand Break Formation at Abasic Sites within Clustered Lesions in Nucleosome Core Particles.

    Science.gov (United States)

    Banerjee, Samya; Chakraborty, Supratim; Jacinto, Marco Paolo; Paul, Michael D; Balster, Morgan V; Greenberg, Marc M

    2017-01-10

    DNA is rapidly cleaved under mild alkaline conditions at apyrimidinic/apurinic sites, but the half-life is several weeks in phosphate buffer (pH 7.5). However, abasic sites are ∼100-fold more reactive within nucleosome core particles (NCPs). Histone proteins catalyze the strand scission, and at superhelical location 1.5, the histone H4 tail is largely responsible for the accelerated cleavage. The rate constant for strand scission at an abasic site is enhanced further in a nucleosome core particle when it is part of a bistranded lesion containing a proximal strand break. Cleavage of this form results in a highly deleterious double-strand break. This acceleration is dependent upon the position of the abasic lesion in the NCP and its structure. The enhancement in cleavage rate at an apurinic/apyrimidinic site rapidly drops off as the distance between the strand break and abasic site increases and is negligible once the two forms of damage are separated by 7 bp. However, the enhancement of the rate of double-strand break formation increases when the size of the gap is increased from one to two nucleotides. In contrast, the cleavage rate enhancement at 2-deoxyribonolactone within bistranded lesions is more modest, and it is similar in free DNA and nucleosome core particles. We postulate that the enhanced rate of double-strand break formation at bistranded lesions containing apurinic/apyrimidinic sites within nucleosome core particles is a general phenomenon and is due to increased DNA flexibility.

  18. Nucleosome structure incorporated histone acetylation site prediction in Arabidopsis thaliana.

    Science.gov (United States)

    Zhao, Chen; Liu, Hui; Li, Jiang; Deng, Youping; Shi, Tieliu

    2010-11-02

    Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana. Concerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana are conserved and cross predictable with that of human by peptide based methods. However, the predicted specificity is overestimated, because of the existence of non-observed acetylable site. Here, by performing a complete exploration on the factors that affect the acetylability of lysines in histones, we focused on the relative position of lysine at nucleosome level, and defined a new structure feature to promote the performance in predicting the acetylability of all the histone lysines in A. thaliana. We found a new spacial correlated acetylation factor, and defined a ε-N spacial location based feature, which contains five core spacial ellipsoid wired areas. By incorporating the new feature, the performance of predicting the acetylability of all the histone lysines in A. Thaliana was promoted, in which the previous mispredicted acetylable lysines were corrected by comparing to the peptide-based prediction.

  19. Naturally occuring nucleosome positioning signals in human exons and introns

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren; Chauvin, Yves

    1996-01-01

    We describe the structural implications of a periodic pattern found in human exons and introns by hidden Markov models. We show that exons (besides the reading frame) have a specific sequential structure in the form of a pattern with triplet consensus non-T(A/T)G, and a minimal periodicity...

  20. Thermodynamics of nucleotide binding to actomyosin V and VI: a positive heat capacity change accompanies strong ADP binding.

    Science.gov (United States)

    Robblee, James P; Cao, Wenxiang; Henn, Arnon; Hannemann, Diane E; De La Cruz, Enrique M

    2005-08-02

    We have measured the energetics of ATP and ADP binding to single-headed actomyosin V and VI from the temperature dependence of the rate and equilibrium binding constants. Nucleotide binding to actomyosin V and VI can be modeled as two-step binding mechanisms involving the formation of collision complexes followed by isomerization to states with high nucleotide affinity. Formation of the actomyosin VI-ATP collision complex is much weaker and slower than for actomyosin V. A three-step binding mechanism where actomyosin VI isomerizes between two conformations, one competent to bind ATP and one not, followed by rapid ATP binding best accounts for the data. ADP binds to actomyosin V more tightly than actomyosin VI. At 25 degrees C, the strong ADP-binding equilibria are comparable for actomyosin V and VI, and the different overall ADP affinities arise from differences in the ADP collision complex affinity. The actomyosin-ADP isomerization leading to strong ADP binding is entropy driven at >15 degrees C and occurs with a large, positive change in heat capacity (DeltaC(P) degrees ) for both actomyosin V and VI. Sucrose slows ADP binding and dissociation from actomyosin V and VI but not the overall equilibrium constants for strong ADP binding, indicating that solvent viscosity dampens ADP-dependent kinetic transitions, presumably a tail swing that occurs with ADP binding and release. We favor a mechanism where strong ADP binding increases the dynamics and flexibility of the actomyosin complex. The heat capacity (DeltaC(P) degrees ) and entropy (DeltaS degrees ) changes are greater for actomyosin VI than actomyosin V, suggesting different extents of ADP-induced structural rearrangement.

  1. Structural Mechanisms of Nucleosome Recognition by Linker Histones.

    Science.gov (United States)

    Zhou, Bing-Rui; Jiang, Jiansheng; Feng, Hanqiao; Ghirlando, Rodolfo; Xiao, T Sam; Bai, Yawen

    2015-08-20

    Linker histones bind to the nucleosome and regulate the structure of chromatin and gene expression. Despite more than three decades of effort, the structural basis of nucleosome recognition by linker histones remains elusive. Here, we report the crystal structure of the globular domain of chicken linker histone H5 in complex with the nucleosome at 3.5 Å resolution, which is validated using nuclear magnetic resonance spectroscopy. The globular domain sits on the dyad of the nucleosome and interacts with both DNA linkers. Our structure integrates results from mutation analyses and previous cross-linking and fluorescence recovery after photobleach experiments, and it helps resolve the long debate on structural mechanisms of nucleosome recognition by linker histones. The on-dyad binding mode of the H5 globular domain is different from the recently reported off-dyad binding mode of Drosophila linker histone H1. We demonstrate that linker histones with different binding modes could fold chromatin to form distinct higher-order structures. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones.

    Science.gov (United States)

    Liokatis, Stamatios

    2017-03-26

    Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications (PTMs). They are newly identified species with unknown means of establishment and functional implications. Current analytical methods are inadequate to detect the copy-specific occurrence of PTMs on the nucleosomal sister histones. This protocol presents a biochemical method for the in vitro reconstitution of nucleosomes containing differentially isotope-labeled sister histones. The generated complex can be also asymmetrically modified, after including a premodified histone pool during refolding of histone subcomplexes. These asymmetric nucleosome preparations can be readily reacted with histone-modifying enzymes to study modification cross-talk mechanisms imposed by the asymmetrically pre-incorporated PTM using nuclear magnetic resonance (NMR) spectroscopy. Particularly, the modification reactions in real-time can be mapped independently on the two sister histones by performing different types of NMR correlation experiments, tailored for the respective isotope type. This methodology provides the means to study crosstalk mechanisms that contribute to the formation and propagation of asymmetric PTM patterns on nucleosomal complexes.

  3. Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes

    NARCIS (Netherlands)

    Vlijm, R.; Lee, M.; Lipfert, J.; Lusser, A.; Dekker, C.; Dekker, N.H.

    2015-01-01

    DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length

  4. Structure of the CENP-A nucleosome and its implications for centromeric chromatin architecture.

    Science.gov (United States)

    Tachiwana, Hiroaki; Kurumizaka, Hitoshi

    2011-01-01

    Centromeres are dictated by the epigenetic inheritance of the centromeric nucleosome containing the centromere-specific histone H3 variant, CENP-A. The structure of the CENP-A nucleosome has been considered to be the fundamental architecture of the centromeric chromatin. Controversy exists in the literature regarding the CENP-A nucleosome structures, with octasome, hemisome, compact octasome, hexasome, and tetrasome models being reported. Some of these CENP-A nucleosome models may correspond to transient intermediates for the assembly of the mature CENP-A nucleosome; however, their significances are still unclear. Therefore, the structure of the mature CENP-A nucleosome has been eagerly awaited. We reconstituted the human CENP-A nucleosome with its cognate centromeric DNA fragment, and determined its crystal structure. In this review, we describe the structure and the physical properties of the CENP-A nucleosome, and discuss their implications for centromeric chromatin architecture.

  5. Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

    OpenAIRE

    Xi, Yuanxin; Yao, Jianhui; Chen, Rui; Li, Wei; He, Xiangwei

    2011-01-01

    The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity—nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed “fragile nucleosomes” throughout the yeast genome, nearly 10...

  6. Lipid-rich carcinoma of the breast that is strongly positive for estrogen receptor: a case report and literature review

    Directory of Open Access Journals (Sweden)

    Oba T

    2016-03-01

    Full Text Available Takaaki Oba,1 Mayu Ono,1 Asumi Iesato,1 Toru Hanamura,1 Takayuki Watanabe,1 Tokiko Ito,1 Toshiharu Kanai,1 Kazuma Maeno,1 Ken-ichi Ito,1 Ayako Tateishi,2 Akihiko Yoshizawa,2 Fumiyoshi Takayama31Division of Breast, Endocrine and Respiratory Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 2Department of Laboratory Medicine, Shinshu University Hospital, 3Imaging Center, Ichinose Neurosurgical Hospital, Matsumoto, JapanAbstract: Lipid-rich carcinoma (LRC of the breast is a rare breast cancer variant that accounts for <1% of all breast malignancies. It has been reported that LRCs are negative for estrogen receptor. Here, we report a case of LRC of the breast that was strongly positive for estrogen receptor and treated with endocrine adjuvant therapy. A 52-year-old postmenopausal female noticed a lump in her right breast by self-examination and presented to our hospital. Physical examination revealed an elastic 30 mm ×20 mm hard mass in the upper medial part of her right breast. The findings obtained using ultrasonography, mammography, and contrast-enhanced magnetic resonance imaging suggested breast cancer. Core needle biopsy resulted in the diagnosis of invasive carcinoma. The patient underwent mastectomy and sentinel lymph node biopsy. Histopathologically, the tumor cells were abundant in foamy cytoplasm. Because the presence of marked cytoplasmic lipid droplets was confirmed by Sudan IV staining and electron microscopic examination of the tumor and the lipid droplets were negative for periodic acid–Schiff staining, the tumor was diagnosed as an LRC. Immunohistochemically, estrogen and progesterone receptors of the tumor were strongly positive, human epidermal growth factor receptor type 2 was negative, and the ratio of Ki-67-positive cells was ~30%. After surgery, the patient underwent combination chemotherapy with anthracycline, cyclophosphamide, and 5-fluorouracil, followed by docetaxel. Thereafter

  7. The StrongWomen Change Clubs: Engaging Residents to Catalyze Positive Change in Food and Physical Activity Environments

    Directory of Open Access Journals (Sweden)

    Rebecca A. Seguin

    2014-01-01

    Full Text Available Introduction. The epidemic of obesity is a multifaceted public health issue. Positive policy and environmental changes are needed to support healthier eating and increased physical activity. Methods. StrongWomen Change Clubs (SWCCs were developed through an academic-community research partnership between researchers at Cornell University and Tufts University and community partners (cooperative extension educators in rural towns in seven U.S. states. Extension educators served as the local leader and each recruited 10–15 residents to undertake a project to improve some aspect of the nutrition or physical activity environment. Most residents had limited (or no experience in civic engagement. At 6 and 12 months after implementation, the research team conducted key informant interviews with SWCC leaders to capture their perceptions of program process, benchmark achievement, and self-efficacy. Results. At 12 months, each SWCC had accomplished one benchmark; the majority had completed three or more benchmarks. They described common processes for achieving benchmarks such as building relationships and leveraging stakeholder partnerships. Barriers to benchmark achievement included busy schedules and resistance to and slow pace of change. Conclusion. Findings suggest that community change initiatives that involve stakeholders, build upon existing activities and organizational resources, and establish feasible timelines and goals can successfully catalyze environmental change.

  8. Nitrated nucleosome levels and neuropsychiatric events in systemic lupus erythematosus;

    DEFF Research Database (Denmark)

    Ferreira, Isabel; Croca, Sara; Raimondo, Maria Gabriella

    2017-01-01

    BACKGROUND: In patients with systemic lupus erythematosus (SLE) there is no serological test that will reliably distinguish neuropsychiatric (NP) events due to active SLE from those due to other causes. Previously we showed that serum levels of nitrated nucleosomes (NN) were elevated in a small n...

  9. Genome-scale identification of nucleosome organization by using 1000 porcine oocytes at different developmental stages.

    Directory of Open Access Journals (Sweden)

    Chenyu Tao

    Full Text Available The nucleosome is the basic structural unit of chromosomes, and its occupancy and distribution in promoters are crucial for the regulation of gene expression. During the growth process of porcine oocytes, the "growing" oocytes (SF have a much higher transcriptional activity than the "fully grown" oocytes (BF. However, the chromosome status of the two kinds of oocytes remains poorly understood. In this study, we profiled the nucleosome distributions of SF and BF with as few as 1000 oocytes. By comparing the altered regions, we found that SF tended toward nucleosome loss and more open chromosome architecture than BF did. BF had decreased nucleosome occupancy in the coding region and increased nucleosome occupancy in the promoter compared to SF. The nucleosome occupancy of SF was higher than that of BF in the GC-poor regions, but lower than that of BF in the GC-rich regions. The nucleosome distribution around the transcriptional start site (TSS of all the genes of the two samples was basically the same, but the nucleosome occupancy around the TSS of SF was lower than that of BF. GO functional annotation of genes with different nucleosome occupancy in promoter showed the genes were mainly involved in cell, cellular process, and metabolic process biological process. The results of this study revealed the dynamic reorganization of porcine oocytes in different developmental stages and the critical role of nucleosome arrangement during the oocyte growth process.

  10. Arginine-phosphate salt bridges between histones and DNA: Intermolecular actuators that control nucleosome architecture

    Science.gov (United States)

    Yusufaly, Tahir I.; Li, Yun; Singh, Gautam; Olson, Wilma K.

    2014-10-01

    Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.

  11. The Scc2/Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions

    Science.gov (United States)

    Lopez-Serra, Lidia; Kelly, Gavin; Patel, Harshil; Stewart, Aengus; Uhlmann, Frank

    2014-01-01

    The cohesin complex is at the heart of many chromosomal activities, including sister chromatid cohesion and transcriptional regulation1-3. Cohesin loading onto chromosomes depends on the Scc2/Scc4 cohesin loader complex4-6, but the chromatin features that form cohesin loading sites remain poorly understood. Here, we show that the RSC chromatin remodeling complex recruits budding yeast Scc2/Scc4 to broad nucleosome-free regions, that the cohesin loader itself helps to maintain. Consequently, inactivation of the cohesin loader or RSC complex have similar effects on nucleosome positioning, gene expression and sister chromatid cohesion. These results reveal an intimate link between local chromatin structure and higher order chromosome architecture. Our findings pertain to the similarities between two severe human disorders, Cornelia de Lange syndrome, caused by mutations in the human cohesin loader, and Coffin-Siris syndrome, resulting from mutations in human RSC complex components7-9. Both could arise from gene misregulation due to related changes in the nucleosome landscape. PMID:25173104

  12. The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding

    Science.gov (United States)

    Hieb, Aaron R.; Gansen, Alexander; Böhm, Vera; Langowski, Jörg

    2014-01-01

    The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is needed. Using bulk and single-molecule FRET, we find that TBP binds a minimal consensus TATA box as a two-state equilibrium process, showing no evidence for intermediate states. However, upon addition of flanking DNA sequence, we observe non-specific cooperative binding to multiple DNA sites that compete for TATA-box specificity. Thus, we conclude that TBP binding is defined by a branched pathway, wherein TBP initially binds with little sequence specificity and is thermodynamically positioned by its kinetic stability to the TATA box. Furthermore, we observed the real-time access of TBP binding to TATA box DNA located within the DNA entry–exit site of the nucleosome. From these data, we determined salt-dependent changes in the nucleosome conformation regulate TBP's access to the TATA box, where access is highly constrained under physiological conditions, but is alleviated by histone acetylation and TFIIA. PMID:24829456

  13. The conformational state of the nucleosome entry-exit site modulates TATA box-specific TBP binding.

    Science.gov (United States)

    Hieb, Aaron R; Gansen, Alexander; Böhm, Vera; Langowski, Jörg

    2014-07-01

    The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is needed. Using bulk and single-molecule FRET, we find that TBP binds a minimal consensus TATA box as a two-state equilibrium process, showing no evidence for intermediate states. However, upon addition of flanking DNA sequence, we observe non-specific cooperative binding to multiple DNA sites that compete for TATA-box specificity. Thus, we conclude that TBP binding is defined by a branched pathway, wherein TBP initially binds with little sequence specificity and is thermodynamically positioned by its kinetic stability to the TATA box. Furthermore, we observed the real-time access of TBP binding to TATA box DNA located within the DNA entry-exit site of the nucleosome. From these data, we determined salt-dependent changes in the nucleosome conformation regulate TBP's access to the TATA box, where access is highly constrained under physiological conditions, but is alleviated by histone acetylation and TFIIA. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Poly-dA:dT tracts form an in vivo nucleosomal turnstile.

    Directory of Open Access Journals (Sweden)

    Carl G de Boer

    Full Text Available Nucleosomes regulate many DNA-dependent processes by controlling the accessibility of DNA, and DNA sequences such as the poly-dA:dT element are known to affect nucleosome binding. We demonstrate that poly-dA:dT tracts form an asymmetric barrier to nucleosome movement in vivo, mediated by ATP-dependent chromatin remodelers. We theorize that nucleosome transit over poly-A elements is more energetically favourable in one direction, leading to an asymmetric arrangement of nucleosomes around these sequences. We demonstrate that different arrangements of poly-A and poly-T tracts result in very different outcomes for nucleosome occupancy in yeast, mouse, and human, and show that yeast takes advantage of this phenomenon in its promoter architecture.

  15. Linker histones: novel insights into structure-specific recognition of the nucleosome.

    Science.gov (United States)

    Cutter, Amber R; Hayes, Jeffrey J

    2017-04-01

    Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.

  16. Anti-dsDNA, anti-nucleosome and anti-C1q antibodies as disease activity markers in patients with systemic lupus erythematosus

    Directory of Open Access Journals (Sweden)

    Živković Valentina

    2014-01-01

    Full Text Available Introduction. In spite of the growing number of reports on the study of anti-nucleosome and anti-C1q antibodies, there are still controversies on their significance as disease activity markers in patients with systemic lupus erythematosus (SLE and their use in everyday clinical practice. Objective. Our aim was to assess the presence of anti-dsDNA, anti-nucleosome and anti-C1q antibodies in SLE patients, as well as to establish their sensitivity, specificity, positive and negative predictive value, and their correlation with SLE and lupus nephritis clinical activity. Methods. The study enrolled 85 patients aged 45.3±9.7 years on the average, with SLE of average duration 10.37±7.99 years, hospitalized at the Institute „Niška Banja“ during 2011, and 30 healthy individuals as controls. Disease activity was assessed using Systemic Lupus Erythematosus Disease Activity Index (SLEDAI. In all examinees the levels of anti-dsDNA, anti-nucleosome and anti-C1q antibodies were measured using the ELISA method with Alegria Test Strips Orgentec (Germany. Results. Patients with active lupus nephritis had a higher presence of anti-C1q antibodies and higher co-positivity of anti-dsDNA, anti-nucleosome, and anti-C1q antibodies compared to those with inactive lupus nephritis (77.77% vs. 21.74%; p<0.01. SLE patients with SLEDAI ≥11 had a higher presence of antinucleosome (93.75% vs. 64.15%; p<0.01 and anti-C1q antibodies (46.87% vs. 22.64%; p<0.05, as well as a higher mean level of anti-nucleosome antibodies (107.79±83.46 U/ml vs. 57.81±63.15 U/ml; p<0.05, compared to those with SLEDAI of 0-10. There was a positive correlation between the SLEDAI and the level of anti-dsDNA (r=0.290; p<0.01, anti-nucleosome (r=0.443; p<0.001, and anti-C1q antibodies (r=0.382; p<0.001. Only anti-C1q antibodies demonstrated correlation with proteinuria (r=0.445; p<0.001. Conclusion. Anti-nucleosome and anti-C1q antibodies demonstrated association with SLE and lupus nephritis

  17. Strong Purifying Selection at Synonymous Sites in D. melanogaster

    Science.gov (United States)

    Lawrie, David S.; Messer, Philipp W.; Hershberg, Ruth; Petrov, Dmitri A.

    2013-01-01

    Synonymous sites are generally assumed to be subject to weak selective constraint. For this reason, they are often neglected as a possible source of important functional variation. We use site frequency spectra from deep population sequencing data to show that, contrary to this expectation, 22% of four-fold synonymous (4D) sites in Drosophila melanogaster evolve under very strong selective constraint while few, if any, appear to be under weak constraint. Linking polymorphism with divergence data, we further find that the fraction of synonymous sites exposed to strong purifying selection is higher for those positions that show slower evolution on the Drosophila phylogeny. The function underlying the inferred strong constraint appears to be separate from splicing enhancers, nucleosome positioning, and the translational optimization generating canonical codon bias. The fraction of synonymous sites under strong constraint within a gene correlates well with gene expression, particularly in the mid-late embryo, pupae, and adult developmental stages. Genes enriched in strongly constrained synonymous sites tend to be particularly functionally important and are often involved in key developmental pathways. Given that the observed widespread constraint acting on synonymous sites is likely not limited to Drosophila, the role of synonymous sites in genetic disease and adaptation should be reevaluated. PMID:23737754

  18. The Nucleosome Assembly Activity of NAP1 Is Enhanced by Alien▿

    OpenAIRE

    Eckey, Maren; Hong, Wei; Papaioannou, Maria; Baniahmad, Aria

    2007-01-01

    The assembly of nucleosomes into chromatin is essential for the compaction of DNA and inactivation of the DNA template to modulate and repress gene expression. The nucleosome assembly protein 1, NAP1, assembles nucleosomes independent of DNA synthesis and was shown to enhance coactivator-mediated gene expression, suggesting a role for NAP1 in transcriptional regulation. Here, we show that Alien, known to harbor characteristics of a corepressor of nuclear hormone receptors such as of the vitam...

  19. Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy

    Directory of Open Access Journals (Sweden)

    Maria E. Valieva

    2017-01-01

    Full Text Available A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers. Human FACT and its version without the C-terminal domain (CTD and the high mobility group (HMG domain of the structure-specific recognition protein 1 (SSRP1 subunit did not change the structure of the nucleosomes, while FACT without the acidic C-terminal domains of the suppressor of Ty 16 (Spt16 and the SSRP1 subunits caused nucleosome aggregation. Proteolytic removal of histone tails significantly disturbed the nucleosome structure, inducing partial unwrapping of nucleosomal DNA. Human FACT reduced DNA unwrapping and stabilized the structure of tailless nucleosomes. CTD and/or HMG domains of SSRP1 are required for this FACT activity. In contrast, previously it has been shown that yeast FACT unfolds (reorganizes nucleosomes using the CTD domain of SSRP1-like Pol I-binding protein 3 subunit (Pob3. Thus, yeast and human FACT complexes likely utilize the same domains for nucleosome reorganization and stabilization, respectively, and these processes are mechanistically similar.

  20. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation

    Science.gov (United States)

    Cauchy, Pierre; Maqbool, Muhammad A.; Zacarias-Cabeza, Joaquin; Vanhille, Laurent; Koch, Frederic; Fenouil, Romain; Gut, Marta; Gut, Ivo; Santana, Maria A.; Griffon, Aurélien; Imbert, Jean; Moraes-Cabé, Carolina; Bories, Jean-Christophe; Ferrier, Pierre; Spicuglia, Salvatore; Andrau, Jean-Christophe

    2016-01-01

    Ets1 is a sequence-specific transcription factor that plays an important role during hematopoiesis, and is essential for the transition of CD4−/CD8− double negative (DN) to CD4+/CD8+ double positive (DP) thymocytes. Using genome-wide and functional approaches, we investigated the binding properties, transcriptional role and chromatin environment of Ets1 during this transition. We found that while Ets1 binding at distal sites was associated with active genes at both DN and DP stages, its enhancer activity was attained at the DP stage, as reflected by levels of the core transcriptional hallmarks H3K4me1/3, RNA Polymerase II and eRNA. This dual, stage-specific ability reflected a switch from non-T hematopoietic toward T-cell specific gene expression programs during the DN-to-DP transition, as indicated by transcriptome analyses of Ets1−/− thymic cells. Coincidentally, Ets1 associates more specifically with Runx1 in DN and with TCF1 in DP cells. We also provide evidence that Ets1 predominantly binds distal nucleosome-occupied regions in DN and nucleosome-depleted regions in DP. Finally and importantly, we demonstrate that Ets1 induces chromatin remodeling by displacing H3K4me1-marked nucleosomes. Our results thus provide an original model whereby the ability of a transcription factor to bind nucleosomal DNA changes during differentiation with consequences on its cognate enhancer activity. PMID:26673693

  1. Characterization of nonlymphoid cells in rat spleen, with special reference to strongly Ia-positive branched cells in T-cell areas

    International Nuclear Information System (INIS)

    Dijkstra, C.D.

    1982-01-01

    By use of a monoclonal antibody against Ia antigen in an immunoperoxidase method, strongly Ia-positive branched cells are found in the T-cell areas of the splenic white pulp of the rat. In order to further characterize these cells, enzyme histochemical characteristics, phagocytic capacity, and irradiation sensitivity have been studied. Evidence is presented that these strongly Ia-positive branched cells represent interdigitating cells. The influence of whole-body irradiation on interdigitating cells is discussed. Comparison with data from the literature on the in vitro dendritic cell isolated from spleen cell suspensions reveals many similarities between the described interdigitating cell in vivo and the dendritic cell in vitro

  2. Removal of histone tails from nucleosome dissects the physical mechanisms of salt-induced aggregation, linker histone H1-induced compaction, and 30-nm fiber formation of the nucleosome array

    International Nuclear Information System (INIS)

    Hizume, Kohji; Nakai, Tonau; Araki, Sumiko; Prieto, Eloise; Yoshikawa, Kenichi; Takeyasu, Kunio

    2009-01-01

    In order to reveal the roles of histone tails in the formation of higher-order chromatin structures, we employed atomic force microscopy (AFM), and an in vitro reconstitution system to examine the properties of reconstituted chromatin composed of tail-less histones and a long DNA (106-kb plasmid) template. The tail-less nucleosomes did not aggregate at high salt concentrations or with an excess amount of core histones, in contrast with the behavior of nucleosomal arrays composed of nucleosomes containing normal, N-terminal tails. Analysis of our nucleosome distributions reveals that the attractive interaction between tail-less nucleosomes is weakened. Addition of linker histone H1 into the tail-less nucleosomal array failed to promote the formation of 30 nm chromatin fibers that are usually formed in the normal nucleosomal array. These results demonstrate that the attractive interaction between nucleosomes via histone tails plays a critical role in the formation of the uniform 30-nm chromatin fiber.

  3. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

    Science.gov (United States)

    Erb, Ionas; van Nimwegen, Erik

    2011-01-01

    The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of 6 'proximal promoter motifs' (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.

  4. Strong subjective recovery as a protective factor against the effects of positive symptoms on quality of life outcomes in schizophrenia.

    Science.gov (United States)

    Kukla, Marina; Lysaker, Paul H; Roe, David

    2014-08-01

    Interest in recovery from schizophrenia has been growing steadily, with much of the focus on remission from psychotic symptoms and a return to functioning. Less is known about the experience of subjective recovery and its relationships with other important outcomes, such as quality of life and the formation and sustenance of social connections. This study sought to address this gap in knowledge by examining the links between self perceived recovery, symptoms, and the social components of quality of life. Sixty eight veterans with schizophrenia-spectrum disorders who were participating in a study of cognitive remediation and work were concurrently administered the Recovery Assessment Scale, Positive and Negative Syndrome Scale, and the Heinrichs-Carpenter Quality of Life Scale (QLS). Linear regression analyses demonstrated that subjective recovery moderated the relationship between positive symptoms and both QLS intrapsychic foundations scores and QLS instrumental role functioning after controlling for negative symptoms. Further examination of this interaction revealed that for individuals with substantial positive symptoms, higher levels of subjective recovery were associated with better instrumental role functioning and intrapsychic foundational abilities. Greater self perceived recovery is linked with stronger quality of life, both in regards to the cognitive and affective bases for socialization and active community involvement, even in the presence of substantial psychotic symptoms. Clinical implications of these findings are discussed. Published by Elsevier Inc.

  5. Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

    Directory of Open Access Journals (Sweden)

    Amy Sebeson

    Full Text Available The binding sequence for any transcription factor can be found millions of times within a genome, yet only a small fraction of these sequences encode functional transcription factor binding sites. One of the reasons for this dichotomy is that many other factors, such as nucleosomes, compete for binding. To study how the competition between nucleosomes and transcription factors helps determine a functional transcription factor site from a predicted transcription factor site, we compared experimentally-generated in vitro nucleosome occupancy with in vivo nucleosome occupancy and transcription factor binding in murine embryonic stem cells. Using a solution hybridization enrichment technique, we generated a high-resolution nucleosome map from targeted regions of the genome containing predicted sites and functional sites of Oct4/Sox2 regulation. We found that at Pax6 and Nes, which are bivalently poised in stem cells, functional Oct4 and Sox2 sites show high amounts of in vivo nucleosome displacement compared to in vitro. Oct4 and Sox2, which are active, show no significant displacement of in vivo nucleosomes at functional sites, similar to nonfunctional Oct4/Sox2 binding. This study highlights a complex interplay between Oct4 and Sox2 transcription factors and nucleosomes among different target genes, which may result in distinct patterns of stem cell gene regulation.

  6. The nucleosome assembly activity of NAP1 is enhanced by Alien.

    Science.gov (United States)

    Eckey, Maren; Hong, Wei; Papaioannou, Maria; Baniahmad, Aria

    2007-05-01

    The assembly of nucleosomes into chromatin is essential for the compaction of DNA and inactivation of the DNA template to modulate and repress gene expression. The nucleosome assembly protein 1, NAP1, assembles nucleosomes independent of DNA synthesis and was shown to enhance coactivator-mediated gene expression, suggesting a role for NAP1 in transcriptional regulation. Here, we show that Alien, known to harbor characteristics of a corepressor of nuclear hormone receptors such as of the vitamin D receptor (VDR), binds in vivo and in vitro to NAP1 and modulates its activity by enhancing NAP1-mediated nucleosome assembly on DNA. Furthermore, Alien reduces the accessibility of the histones H3 and H4 for NAP1-promoted assembly reaction. This indicates that Alien sustains and reinforces the formation of nucleosomes. Employing deletion mutants of Alien suggests that different regions of Alien are involved in enhancement of NAP1-mediated nucleosome assembly and in inhibiting the accessibility of the histones H3 and H4. In addition, we provide evidence that Alien is associated with chromatin and with micrococcus nuclease-prepared nucleosome fractions and interacts with the histones H3 and H4. Furthermore, chromatin immunoprecipitation and reimmunoprecipitation experiments suggest that NAP1 and Alien localize to the endogenous CYP24 promoter in vivo, a VDR target gene. Based on these findings, we present here a novel pathway linking corepressor function with nucleosome assembly activity.

  7. Nucleosomes and histones are present in glomerular deposits in human lupus nephritis

    NARCIS (Netherlands)

    vanBruggen, MCJ; Kramers, C; Walgreen, B; Elema, JD; Kallenberg, CGM; vandenBorn, J; Smeenk, RJT; Assmann, KJM; Muller, S; Monestier, M; Berden, JHM

    Background. Recently we showed that antinuclear autoantibodies complexed to nucleosomes can bind to heparan sulphate (HS) in the glomerular basement membrane (GEM) via the histone part of the nucleosome. Histones have been identified in glomerular deposits in human and murine lupus nephritis. In

  8. PARP-1 Interaction with and Activation by Histones and Nucleosomes.

    Science.gov (United States)

    Thomas, Colin; Kotova, Elena; Tulin, Alexei V

    2017-01-01

    Poly(ADP-ribose) Polymerase 1 (PARP-1) is an abundant chromatin associated protein, typical for most eukaryotic nuclei. The localization of PARP-1 in chromatin and its enzymatic activation involves multiple interactions of PARP-1 with nucleosomal histones, other proteins, and DNA. We report a set of methods designed to reconstitute PARP-1 regulation in vitro. These methods involve the expression of PARP-1 and PARP-1-regulating proteins using bacterial and eukaryotic systems, purification of these proteins using chromatography, testing of individual interactions in vitro, assembly of active complexes, and reconstitution of PARP-1 regulating reactions in vitro.

  9. Evaluation of DNA typing as a positive identification method for soft and hard tissues immersed in strong acids.

    Science.gov (United States)

    Robino, C; Pazzi, M; Di Vella, G; Martinelli, D; Mazzola, L; Ricci, U; Testi, R; Vincenti, M

    2015-11-01

    Identification of human remains can be hindered by several factors (e.g., traumatic mutilation, carbonization or decomposition). Moreover, in some criminal cases, offenders may purposely adopt various expedients to thwart the victim's identification, including the dissolution of body tissues by the use of corrosive reagents, as repeatedly reported in the past for Mafia-related murders. By means of an animal model, namely porcine samples, we evaluated standard DNA typing as a method for identifying soft (muscle) and hard (bone and teeth) tissues immersed in strong acids (hydrochloric, nitric and sulfuric acid) or in mixtures of acids (aqua regia). Samples were tested at different time intervals, ranging between 2 and 6h (soft tissues) and 2-28 days (hard tissues). It was shown that, in every type of acid, complete degradation of the DNA extracted from soft tissues preceded tissue dissolution and could be observed within 4h of immersion. Conversely, high molecular weight DNA amenable to STR analysis could be isolated from hard tissues as long as cortical bone fragments were still present (28 days for sulfuric acid, 7 days for nitric acid, 2 days for hydrochloric acid and aqua regia), or the integrity of the dental pulp chamber was preserved (7 days, in sulfuric acid only). The results indicate that DNA profiling of acid-treated body parts (in particular, cortical bone) is still feasible at advanced stages of corrosion, even when the morphological methods used in forensic anthropology and odontology can no longer be applied for identification purposes. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  10. Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy

    Directory of Open Access Journals (Sweden)

    Yingxue Ren

    2015-03-01

    Full Text Available In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, nucleosome dynamics during a genome response have not been well characterized [1,2]. We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the significant nucleosomal loss occurring at 4 h after stimulation. Data have been deposited to the Gene Expression Omnibus (GEO database repository with the dataset identifier GSE64507.

  11. Vegetation heterogeneity and landscape position exert strong controls on soil CO2 efflux in a moist, Appalachian watershed

    Science.gov (United States)

    Atkins, J. W.; Epstein, H. E.; Welsch, D. L.

    2014-12-01

    In topographically complex watersheds, landscape position and vegetation heterogeneity can alter the soil water regime through both lateral and vertical redistribution, respectively. These alterations of soil moisture may have significant impacts on the spatial heterogeneity of biogeochemical cycles throughout the watershed. To evaluate how landscape position and vegetation heterogeneity affect soil CO2 efflux (FSOIL) we conducted observations across the Weimer Run watershed (373 ha), located near Davis, West Virginia, for three growing seasons with varying precipitation (2010 - 1042 mm; 2011 - 1739 mm; 2012 - 1244 mm; precipitation data from BDKW2 station, MesoWest, University of Utah). An apparent soil temperature threshold of 11 °C at 12 cm depth on FSOIL was observed in our data - where FSOIL rates greatly increase in variance above this threshold. For analysis, FSOIL values above this threshold were isolated and examined. Differences in FSOIL among years were apparent by elevation (F4,633 = 3.17; p = 0.013) and by vegetation cover (F4, 633 = 2.96; p = 0.019). For the Weimer Run watershed, vegetation exerts the major control on soil CO2 efflux (FSOIL), with the plots beneath shrubs at all elevations for all years showing the greatest mean rates of FSOIL (6.07 μmol CO2 m-2 s-1) compared to plots beneath closed-forest canopy (4.69 μmol CO2 m-2 s-1) and plots located in open, forest gaps (4.09 μmol CO2 m-2 s-1) plots. During periods of high soil moisture, we find that CO2 efflux rates are constrained and that maximum efflux rates in this system occur during periods of average to below average soil water availability. These findings offer valuable insight into the processes occurring within these topographically complex, temperate and humid systems, and the interactions of abiotic and biotic factors mediating biogeochemical cycles. With possible changing rainfall patterns as predicted by climate models, it is important to understand the couplings between water

  12. Links between DNA methylation and nucleosome occupancy in the human genome.

    Science.gov (United States)

    Collings, Clayton K; Anderson, John N

    2017-01-01

    DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome. The results demonstrated that increasing methylated CpG density is correlated with nucleosome occupancy in the total genome and within nearly all subgenomic regions. Features with elevated methylated CpG density such as exons, SINE-Alu sequences, H3K36-trimethylated peaks, and methylated CpG islands are among the highest nucleosome occupied elements in the genome, while some of the lowest occupancies are displayed by unmethylated CpG islands and unmethylated transcription factor binding sites. Additionally, outside of CpG islands, the density of CpGs within nucleosomes was shown to be important for the nucleosomal location of DNA methylation with low CpG frequencies favoring linker methylation and high CpG frequencies favoring core particle methylation. Prominent exceptions to the correlations between methylated CpG density and nucleosome occupancy include CpG islands marked by H3K27me3 and CpG-poor heterochromatin marked by H3K9me3, and these modifications, along with DNA methylation, distinguish the major silencing mechanisms of the human epigenome. Thus, the relationship between DNA methylation and nucleosome occupancy is influenced by the density of methylated CpG dinucleotides and by other epigenomic components in chromatin.

  13. Strong positive effects of termites on savanna bird abundance and diversity are amplified by large herbivore exclusion.

    Science.gov (United States)

    Moe, Stein R; Eldegard, Katrine; Rannestad, Ole Tobias; Okullo, Paul; Lindtjørn, Ommund; Støen, Ole Gunnar; Dale, Svein

    2017-12-01

    Vast areas of the African savanna landscapes are characterized by tree-covered Macrotermes termite mounds embedded within a relatively open savanna matrix. In concert with termites, large herbivores are important determinants of savanna woody vegetation cover. The relative cover of woody species has considerable effects on savanna function. Despite the potentially important ecological relationships between termite mounds, woody plants, large herbivores, and birds, these associations have previously received surprisingly little attention. We experimentally studied the effects of termites and large herbivores on the avian community in Lake Mburo National Park, Uganda, where woody vegetation is essentially limited to termite mounds. Our experiment comprised of four treatments in nine replicates; unfenced termite mounds, fenced mounds (excluding large mammals), unfenced adjacent savanna, and fenced savanna. We recorded species identity, abundance, and behavior of all birds observed on these plots over a two-month period, from late dry until wet season. Birds used termite mounds almost exclusively, with only 3.5% of observations occurring in the treeless intermound savanna matrix. Mean abundance and species richness of birds doubled on fenced (large herbivores excluded) compared to unfenced mounds. Feeding behavior increased when large mammals were excluded from mounds, both in absolute number of observed individuals, and relative to other behaviors. This study documents the fundamental positive impact of Macrotermes termites on bird abundance and diversity in an African savanna. Birds play crucial functional roles in savanna ecosystems, for example, by dispersing fruits or regulating herbivorous insect populations. Thus, the role of birds in savanna dynamics depends on the distribution and abundance of termite mounds.

  14. The changing paradigm: estrogen receptor α recognition on DNA and within the dynamic nature of nucleosomes

    Directory of Open Access Journals (Sweden)

    William M. Scovell

    2015-03-01

    Full Text Available Estrogen receptor alpha (ERα plays a major role in the expression of estrogen-responsive genes. Although its conventional binding characteristics have been considered coincident with & exclusively in the class of steroid hormone receptors, increasing evidence challenges this paradigm. ERα was shown to bind to consensus estrogen response element half-sites (cHERE in DNA in the presence of the ubiquitous, abundant & conserved architectural protein, high mobility group protein 1 (HMGB1. It also binds to direct repeats with various spacers, in addition to everted repeats. These in vitro binding sites have been shown to be active in vivo, with both the binding affinity and transcriptional activity increased in the presence of HMGB1. Surprisingly, ERα does not bind to the optimally oriented cERE at the dyad in rotationally phased and translationally positioned nucleosomes. However, the presence of HMGB1 restructures the nucleosome to facilitate increased ERα accessibility, resulting in sequence-specific estrogen receptor binding. The finding that HMGB1 interacts with unbound ERα provides a unique avenue for enhanced ERα activity and possibly an increase in the extent of targeting at estrogen-responsive genes. The findings are consistent with ERα 1 targeting a much wider selection of genomic response elements (half-sites and inverted, direct and everted repeats and 2 exhibiting characteristics of both steroid and non steroid nuclear receptors. Growing evidence already shows a competition occurs at the DNA level between ERα and the non steroid nuclear hormone receptor, thyroid receptor (TR. Collectively, these reports suggest a less restrictive cataloging for estrogen receptor and a broader paradigm for understanding its role in the regulation of estrogen-responsive genes and influence on non steroid hormone receptor activities.

  15. Starting off on the right foot: strong right-footers respond faster with the right foot to positive words and with the left foot to negative words.

    Science.gov (United States)

    de la Vega, Irmgard; Graebe, Julia; Härtner, Leonie; Dudschig, Carolin; Kaup, Barbara

    2015-01-01

    Recent studies have provided evidence for an association between valence and left/right modulated by handedness, which is predicted by the body-specificity hypothesis (Casasanto, 2009) and also reflected in response times. We investigated whether such a response facilitation can also be observed with foot responses. Right-footed participants classified positive and negative words according to their valence by pressing a key with their left or right foot. A significant interaction between valence and foot only emerged in the by-items analysis. However, when dividing participants into two groups depending on the strength of their footedness, an interaction between valence and left/right was observed for strong right-footers, who responded faster with the right foot to positive words, and with the left foot to negative words. No interaction emerged for weak right-footers. The results strongly support the assumption that fluency lies at the core of the association between valence and left/right.

  16. Altered nucleosomes of active nucleolar chromatin contain accessible histone H3 in its hyperacetylated forms

    International Nuclear Information System (INIS)

    Johnson, E.M.; Sterner, R.; Allfrey, V.G.

    1987-01-01

    Chromatin of the organism Physarum polycephalum contains a class of conformationally altered nucleosomes previously localized to the transcribing regions of ribosomal genes in nucleoli. When nuclei are treated with 2-iodo[2-tritium]acetate, the histone H3 sulfhydryl group of the altered nucleosomes is derivatized while that of folded nucleosomes is not, and the labeled histones can then be identified by autoradiography of gels that separate H3 isoforms. The H3 derivatized is predominantly of tri- and tetraacetylated forms. In contrast, total free histone reacted with iodoacetate shows no preferential labeling of isoforms. Selective reaction of acetylated H3 is prevalent in both nucleolar and non-nucleolar chromatin. The results link specific patterns of H3 acetylation to changes in nucleosome conformation that occur during transcription

  17. Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

    OpenAIRE

    Teif, Vladimir B.; Mallm, Jan-Philipp; Sharma, Tanvi; Mark Welch, David B.; Rippe, Karsten; Eils, Roland; Langowski, J?rg; Olins, Ada L.; Olins, Donald E.

    2017-01-01

    ABSTRACT Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of ep...

  18. Soft skills turned into hard facts: nucleosome remodelling at developmental switches.

    Science.gov (United States)

    Chioda, M; Becker, P B

    2010-07-01

    Nucleosome remodelling factors are regulators of DNA accessibility in chromatin and lubricators of all major functions of eukaryotic genomes. Their action is transient and reversible, yet can be decisive for irreversible cell-fate decisions during development. In addition to the well-known local actions of nucleosome remodelling factors during transcription initiation, more global and fundamental roles for remodelling complexes in shaping the epigenome during development are emerging.

  19. Herpes simplex virus 1 DNA is in unstable nucleosomes throughout the lytic infection cycle, and the instability of the nucleosomes is independent of DNA replication.

    Science.gov (United States)

    Lacasse, Jonathan J; Schang, Luis M

    2012-10-01

    Herpes simplex virus 1 (HSV-1) DNA is chromatinized during latency and consequently regularly digested by micrococcal nuclease (MCN) to nucleosome-size fragments. In contrast, MCN digests HSV-1 DNA in lytically infected cells to mostly heterogeneous sizes. Yet HSV-1 DNA coimmunoprecipitates with histones during lytic infections. We have shown that at 5 h postinfection, most nuclear HSV-1 DNA is in particularly unstable nucleoprotein complexes and consequently is more accessible to MCN than DNA in cellular chromatin. HSV-1 DNA was quantitatively recovered at this time in complexes with the biophysical properties of mono- to polynucleosomes following a modified MCN digestion developed to detect potential unstable intermediates. We proposed that most HSV-1 DNA is in unstable nucleosome-like complexes during lytic infections. Physiologically, nucleosome assembly typically associates with DNA replication, although DNA replication transiently disrupts nucleosomes. It therefore remained unclear whether the instability of the HSV-1 nucleoprotein complexes was related to the ongoing viral DNA replication. Here we tested whether HSV-1 DNA is in unstable nucleosome-like complexes before, during, or after the peak of viral DNA replication or when HSV-1 DNA replication is inhibited. HSV-1 DNA was quantitatively recovered in complexes fractionating as mono- to polynucleosomes from nuclei harvested at 2, 5, 7, or 9 h after infection, even if viral DNA replication was inhibited. Therefore, most HSV-1 DNA is in unstable nucleosome-like complexes throughout the lytic replication cycle, and the instability of these complexes is surprisingly independent of HSV-1 DNA replication. The specific accessibility of nuclear HSV-1 DNA, however, varied at different times after infection.

  20. Inducible nucleosome depletion at OREBP-binding-sites by hypertonic stress.

    Directory of Open Access Journals (Sweden)

    Edith H Y Tong

    Full Text Available BACKGROUND: Osmotic Response Element-Binding Protein (OREBP, also known as TonEBP or NFAT5, is a unique transcription factor. It is hitherto the only known mammalian transcription factor that regulates hypertonic stress-induced gene transcription. In addition, unlike other monomeric members of the NFAT family, OREBP exists as a homodimer and it is the only transcription factor known to bind naked DNA targets by complete encirclement in vitro. Nevertheless, how OREBP interacts with target DNA, also known as ORE/TonE, and how it elicits gene transcription in vivo, remains unknown. METHODOLOGY: Using hypertonic induction of the aldose reductase (AR gene activation as a model, we showed that OREs contained dynamic nucleosomes. Hypertonic stress induced a rapid and reversible loss of nucleosome(s around the OREs. The loss of nucleosome(s was found to be initiated by an OREBP-independent mechanism, but was significantly potentiated in the presence of OREBP. Furthermore, hypertonic induction of AR gene was associated with an OREBP-dependent hyperacetylation of histones that spanned the 5' upstream sequences and at least some exons of the gene. Nevertheless, nucleosome loss was not regulated by the acetylation status of histone. SIGNIFICANCE: Our findings offer novel insights into the mechanism of OREBP-dependent transcriptional regulation and provide a basis for understanding how histone eviction and transcription factor recruitment are coupled.

  1. Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex.

    Science.gov (United States)

    Torrado, Mario; Low, Jason K K; Silva, Ana P G; Schmidberger, Jason W; Sana, Maryam; Sharifi Tabar, Mehdi; Isilak, Musa E; Winning, Courtney S; Kwong, Cherry; Bedward, Max J; Sperlazza, Mary J; Williams, David C; Shepherd, Nicholas E; Mackay, Joel P

    2017-12-01

    The nucleosome remodelling and deacetylase (NuRD) complex is essential for the development of complex animals. NuRD has roles in regulating gene expression and repairing damaged DNA. The complex comprises at least six proteins with two or more paralogues of each protein routinely identified when the complex is purified from cell extracts. To understand the structure and function of NuRD, a map of direct subunit interactions is needed. Dozens of published studies have attempted to define direct inter-subunit connectivities. We propose that conclusions reported in many such studies are in fact ambiguous for one of several reasons. First, the expression of many NuRD subunits in bacteria is unlikely to lead to folded, active protein. Second, interaction studies carried out in cells that contain endogenous NuRD complex can lead to false positives through bridging of target proteins by endogenous components. Combining existing information on NuRD structure with a protocol designed to minimize false positives, we report a conservative and robust interaction map for the NuRD complex. We also suggest a 3D model of the complex that brings together the existing data on the complex. The issues and strategies discussed herein are also applicable to the analysis of a wide range of multi-subunit complexes. Micrococcal nuclease (MNase), EC 3.1.31.1; histone deacetylase (HDAC), EC 3.5.1.98. © 2017 Federation of European Biochemical Societies.

  2. A randomized controlled trial of strong minds: A school-based mental health program combining acceptance and commitment therapy and positive psychology.

    Science.gov (United States)

    Burckhardt, Rowan; Manicavasagar, Vijaya; Batterham, Philip J; Hadzi-Pavlovic, Dusan

    2016-08-01

    To date, most early intervention programs have been based on emotion regulation strategies that address dysfunctional cognitive appraisals, problem-solving skills, and rumination. Another emotion regulation strategy, 'acceptance' training, has largely been overlooked. To examine the efficacy of this strategy, a school-based mental health program combining positive psychology with acceptance and commitment therapy (Strong Minds) was evaluated in a randomized controlled trial with a sample of 267 Year 10 and 11 high-school students in Sydney, Australia. Mixed models for repeated measures examined whether the program led to reductions in symptoms amongst students who commenced the program with high depression, anxiety, and stress scores, and increased wellbeing scores amongst all students. Results demonstrated that compared to controls, participants in the Strong Minds condition with elevated symptom scores (n=63) reported significant reductions in depression (p=.047), stress (p=.01), and composite depression/anxiety symptoms (p=.02) with medium to strong effect sizes (Cohen's d=0.53, 0.74, and 0.57, respectively). Increased wellbeing (p=.03) in the total sample and decreased anxiety scores (p=.048) for students with elevated symptoms were significant for Year 10 students with medium effect sizes (Cohen's d=0.43 and 0.54, respectively). This study tentatively suggests that including the emotion regulation strategy of acceptance in early intervention programs may be effective in reducing symptoms and improving wellbeing in high school students. Further research to investigate the generalizability of these findings is warranted. Copyright © 2016 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  3. Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact.

    Science.gov (United States)

    Yazdi, Puya G; Pedersen, Brian A; Taylor, Jared F; Khattab, Omar S; Chen, Yu-Han; Chen, Yumay; Jacobsen, Steven E; Wang, Ping H

    2015-01-01

    Deciphering the multitude of epigenomic and genomic factors that influence the mutation rate is an area of great interest in modern biology. Recently, chromatin has been shown to play a part in this process. To elucidate this relationship further, we integrated our own ultra-deep sequenced human nucleosomal DNA data set with a host of published human genomic and cancer genomic data sets. Our results revealed, that differences in nucleosome occupancy are associated with changes in base-specific mutation rates. Increasing nucleosome occupancy is associated with an increasing transition to transversion ratio and an increased germline mutation rate within the human genome. Additionally, cancer single nucleotide variants and microindels are enriched within nucleosomes and both the coding and non-coding cancer mutation rate increases with increasing nucleosome occupancy. There is an enrichment of cancer indels at the theoretical start (74 bp) and end (115 bp) of linker DNA between two nucleosomes. We then hypothesized that increasing nucleosome occupancy decreases access to DNA by DNA repair machinery and could account for the increasing mutation rate. Such a relationship should not exist in DNA repair knockouts, and we thus repeated our analysis in DNA repair machinery knockouts to test our hypothesis. Indeed, our results revealed no correlation between increasing nucleosome occupancy and increasing mutation rate in DNA repair knockouts. Our findings emphasize the linkage of the genome and epigenome through the nucleosome whose properties can affect genome evolution and genetic aberrations such as cancer.

  4. Strongly positive anti-CCP antibodies in patients with sacroiliitis or reactive arthritis post-E. coli infection: A mini case-series based review.

    Science.gov (United States)

    Singh Sangha, Miljyot; Wright, Matthew Liam; Ciurtin, Coziana

    2018-01-01

    We report here on four cases of patients with strongly positive anti-citrullinated cyclic peptides (anti-CCP) antibodies and clinical features of seronegative spondyloarthritis (SpA) and reactive arthritis. The four patients had various clinical presentations: one had an initial diagnosis of seropositive rheumatoid arthritis (RA) with involvement of the sacroiliac joints (similar to previous reports of the association of two diseases); one had a clinical picture of reactive arthritis following an episode of an Escherichia coli positive urinary tract infection; and two had asymmetrical sacroiliitis (SII), but no evidence of peripheral joint involvement (never reported before). In all cases, high titers of anti-CCP antibodies were found. We present a comparison of the clinical manifestations, radiographic features and treatment regimens of these cases. Our report supports previous literature data of possible overlap existing between RA and SpA, but also presents for the first time the association of high titers of anti-CCP antibodies with SII and reactive arthritis in patients with no peripheral small joint involvement. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

  5. Structure of centromere chromatin: from nucleosome to chromosomal architecture.

    Science.gov (United States)

    Schalch, Thomas; Steiner, Florian A

    2017-08-01

    The centromere is essential for the segregation of chromosomes, as it serves as attachment site for microtubules to mediate chromosome segregation during mitosis and meiosis. In most organisms, the centromere is restricted to one chromosomal region that appears as primary constriction on the condensed chromosome and is partitioned into two chromatin domains: The centromere core is characterized by the centromere-specific histone H3 variant CENP-A (also called cenH3) and is required for specifying the centromere and for building the kinetochore complex during mitosis. This core region is generally flanked by pericentric heterochromatin, characterized by nucleosomes containing H3 methylated on lysine 9 (H3K9me) that are bound by heterochromatin proteins. During mitosis, these two domains together form a three-dimensional structure that exposes CENP-A-containing chromatin to the surface for interaction with the kinetochore and microtubules. At the same time, this structure supports the tension generated during the segregation of sister chromatids to opposite poles. In this review, we discuss recent insight into the characteristics of the centromere, from the specialized chromatin structures at the centromere core and the pericentromere to the three-dimensional organization of these regions that make up the functional centromere.

  6. A T9G mutation in the prototype TATA-box TCACTATATATAG determines nucleosome formation and synergy with upstream activator sequences in plant promoters.

    Science.gov (United States)

    Ranjan, Amol; Ansari, Suraiya A; Srivastava, Rakesh; Mantri, Shrikant; Asif, Mehar H; Sawant, Samir V; Tuli, Rakesh

    2009-12-01

    We had earlier reported that mutations to G and C at the seventh and eighth positions in the prototype TATA-box TCACTATATATAG inhibited light-dependent activation of transcription from the promoter. In this study, we characterized mutations at the ninth position of the prototype TATA-box. Substitution of T at the ninth position with G or C enhanced transcription from the promoter in transgenic tobacco (Nicotiana tabacum) plants. The effect of T9G/C mutations was not light dependent, although the 9G/C TATA-box showed synergy with the light-responsive element (lre). However, the 9G/C mutants in the presence of lre failed to respond to phytochromes, sugar, and calcium signaling, in contrast to the prototype TATA-box with lre. The 9G/C mutation shifted the point of initiation of transcription, and transcription activation was dependent upon the type of activating element present upstream. The synergy in activation was noticed with lre and legumin activators but not with rbcS, Pcec, and PR-1a activators. The 9G mutation resulted in a micrococcal nuclease-sensitive region over the TATA-box, suggesting a nucleosome-free region, in contrast to the prototype promoter, which had a distinct nucleosome on the TATA-box. Thus, the transcriptional augmentation with mutation at the ninth position might be because of the loss of a repressive nucleosomal structure on the TATA-box. In agreement with our findings, the promoters containing TATAGATA as identified by genome-wide analysis of Arabidopsis (Arabidopsis thaliana) are not tightly repressed.

  7. Solution structure of variant H2A.Z.1 nucleosome investigated by small-angle X-ray and neutron scatterings.

    Science.gov (United States)

    Sugiyama, Masaaki; Horikoshi, Naoki; Suzuki, Yuya; Taguchi, Hiroyuki; Kujirai, Tomoya; Inoue, Rintaro; Oba, Yojiro; Sato, Nobuhiro; Martel, Anne; Porcar, Lionel; Kurumizaka, Hitoshi

    2015-12-01

    Solution structures of nucleosomes containing a human histone variant, H2A.Z.1, were measured by small-angle X-ray and neutron scatterings (SAXS and SANS). SAXS revealed that the outer shape, reflecting the DNA shape, of the H2A.Z.1 nucleosome is almost the same as that of the canonical H2A nucleosome. In contrast, SANS employing a contrast variation technique revealed that the histone octamer of the H2A.Z.1 nucleosome is smaller than that of the canonical nucleosome. The DNA within the H2A.Z.1 nucleosome was more susceptible to micrococcal nuclease than that within the canonical nucleosome. These results suggested that the DNA is loosely wrapped around the histone core in the H2A.Z.1 nucleosome.

  8. Chromatin Regulation of Estrogen-Mediated Transcription in Breast Cancer: Rules for Binding Sites in Nucleosomes and Modified Histones that Enhance ER Binding

    National Research Council Canada - National Science Library

    Chrivia, John C

    2005-01-01

    .... Using gel shift assays, we tested whether ER can bind these nucleosomes. We have also found that the non-histone chromatin protein HMOB2 enhances binding of ER to an ERE located at the center of the nucleosome...

  9. The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes

    NARCIS (Netherlands)

    Vlijm, R.; Kim, S.H.; De Zwart, P. L.; Dalal, Y.; Dekker, C.

    2017-01-01

    Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted

  10. Transmission of modified nucleosomes from the mouse male germline to the zygote and subsequent remodeling of paternal chromatin.

    NARCIS (Netherlands)

    Heijden, G.W. van der; Derijck, A.H.A.; Ramos, L.; Giele, M.M.; Vlag, J. van der; Boer, P. de

    2006-01-01

    Rapidly after gamete fusion, the sperm nucleus loses its specific chromatin conformation and the DNA is repopulated with maternally derived nucleosomes. We evaluated the nature of paternally derived nucleosomes and the dynamics of sperm chromatin remodeling in the zygote directly after gamete

  11. Nucleosome Binding Alters the Substrate Bonding Environment of Histone H3 Lysine 36 Methyltransferase NSD2.

    Science.gov (United States)

    Poulin, Myles B; Schneck, Jessica L; Matico, Rosalie E; Hou, Wangfang; McDevitt, Patrick J; Holbert, Marc; Schramm, Vern L

    2016-06-01

    Nuclear receptor-binding SET domain protein 2 (NSD2) is a histone H3 lysine 36 (H3K36)-specific methyltransferase enzyme that is overexpressed in a number of cancers, including multiple myeloma. NSD2 binds to S-adenosyl-l-methionine (SAM) and nucleosome substrates to catalyze the transfer of a methyl group from SAM to the ε-amino group of histone H3K36. Equilibrium binding isotope effects and density functional theory calculations indicate that the SAM methyl group is sterically constrained in complex with NSD2, and that this steric constraint is released upon nucleosome binding. Together, these results show that nucleosome binding to NSD2 induces a significant change in the chemical environment of enzyme-bound SAM.

  12. New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

    Science.gov (United States)

    Luger, Karolin; Dechassa, Mekonnen L.; Tremethick, David J.

    2012-01-01

    The compaction of genomic DNA into chromatin has profound implications for the regulation of key processes such as transcription, replication and DNA repair. Nucleosomes, the repeating building blocks of chromatin, vary in the composition of their histone protein components. This is the result of the incorporation of variant histones and post-translational modifications of histone amino acid side chains. The resulting changes in nucleosome structure, stability and dynamics affect the compaction of nucleosomal arrays into higher-order structures. It is becoming clear that chromatin structures are not nearly as uniform and regular as previously assumed. This implies that chromatin structure must also be viewed in the context of specific biological functions. PMID:22722606

  13. ATP-Dependent Chromatin Remodeling Factors and Their Roles in Affecting Nucleosome Fiber Composition

    Directory of Open Access Journals (Sweden)

    Alexandra Lusser

    2011-10-01

    Full Text Available ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.

  14. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery...

  15. NAP-1, Nucleosome assembly protein 1, a histone chaperone involved in Drosophila telomeres.

    Science.gov (United States)

    López-Panadès, Elisenda; Casacuberta, Elena

    2016-03-01

    Telomere elongation is a function that all eukaryote cells must accomplish in order to guarantee, first, the stability of the end of the chromosomes and second, to protect the genetic information from the inevitable terminal erosion. The targeted transposition of the telomere transposons HeT-A, TART and TAHRE perform this function in Drosophila, while the telomerase mechanism elongates the telomeres in most eukaryotes. In order to integrate telomere maintenance together with cell cycle and metabolism, different components of the cell interact, regulate, and control the proteins involved in telomere elongation. Different partners of the telomerase mechanism have already been described, but in contrast, very few proteins have been related with assisting the telomere transposons of Drosophila. Here, we describe for the first time, the implication of NAP-1 (Nucleosome assembly protein 1), a histone chaperone that has been involved in nuclear transport, transcription regulation, and chromatin remodeling, in telomere biology. We find that Nap-1 and HeT-A Gag, one of the major components of the Drosophila telomeres, are part of the same protein complex. We also demonstrate that their close interaction is necessary to guarantee telomere stability in dividing cells. We further show that NAP-1 regulates the transcription of the HeT-A retrotransposon, pointing to a positive regulatory role of NAP-1 in telomere expression. All these results facilitate the understanding of the transposon telomere maintenance mechanism, as well as the integration of telomere biology with the rest of the cell metabolism. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Recent insights from single-molecule studies into nucleosome structure and dynamics

    NARCIS (Netherlands)

    Ordu, O.; Lusser, A; Dekker, N.H.

    2016-01-01

    Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a short piece of DNA wrapped around a core of eight histone proteins. In addition to their role

  17. Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A

    Science.gov (United States)

    Stumme-Diers, Micah P; Banerjee, Siddhartha; Hashemi, Mohtadin; Sun, Zhiqiang

    2018-01-01

    Abstract In the absence of a functioning centromere, chromosome segregation becomes aberrant, leading to an increased rate of aneuploidy. The highly specific recognition of centromeres by kinetochores suggests that specific structural characteristics define this region, however, the structural details and mechanism underlying this recognition remains a matter of intense investigation. To address this, high-speed atomic force microscopy was used for direct visualization of the spontaneous dynamics of CENP-A nucleosomes at the sub-second time scale. We report that CENP-A nucleosomes change conformation spontaneously and reversibly, utilizing two major pathways: unwrapping, and looping of the DNA; enabling core transfer between neighboring DNA substrates. Along with these nucleosome dynamics we observed that CENP-A stabilizes the histone core against dissociating to histone subunits upon unwrapping DNA, unique from H3 cores which are only capable of such plasticity in the presence of remodeling factors. These findings have implications for the dynamics and integrity of nucleosomes at the centromere. PMID:29040671

  18. Extracellular histones, cell-free DNA, or nucleosomes: differences in immunostimulation.

    Science.gov (United States)

    Marsman, Gerben; Zeerleder, Sacha; Luken, Brenda M

    2016-12-08

    In inflammation, extensive cell death may occur, which results in the release of chromatin components into the extracellular environment. Individually, the purified chromatin components double stranded (ds)DNA and histones have been demonstrated, both in vitro and in vivo, to display various immunostimulatory effects, for example, histones induce cytotoxicity and proinflammatory signaling through toll-like receptor (TLR)2 and 4, while DNA induces signaling through TLR9 and intracellular nucleic acid sensing mechanisms. However, DNA and histones are organized in nucleosomes in the nucleus, and evidence suggests that nucleosomes are released as such in inflammation. The cytotoxicity and proinflammatory signaling induced by nucleosomes have not been studied as extensively as the separate effects brought about by histones and dsDNA, and there appear to be some marked differences. Remarkably, little distinction between the different forms in which histones circulate has been made throughout literature. This is partly due to the limitations of existing techniques to differentiate between histones in their free or DNA-bound form. Here we review the current understanding of immunostimulation induced by extracellular histones, dsDNA and nucleosomes, and discuss the importance of techniques that in their detection differentiate between these different chromatin components.

  19. Extranuclear detection of histones and nucleosomes in activated human lymphoblasts as an early event in apoptosis.

    NARCIS (Netherlands)

    Gabler, C.; Blank, N.; Hieronymus, T.; Schiller, M.; Berden, J.H.M.; Kalden, J.R.; Lorenz, H.M.

    2004-01-01

    OBJECTIVE: To evaluate the presence of histones and nucleosomes in cell lysates of freshly isolated peripheral blood mononuclear cells (PBMC), fully activated lymphoblasts, or lymphoblasts after induction of apoptosis. METHODS: Each histone class (H1, H2A, H2B, H3, and H4) was detected by western

  20. Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Howell, Steven C. [George Washington Univ., Washington, DC (United States)

    2016-01-31

    We set out to determine quantitative information regarding the dynamic conformation of nucleosome arrays in solution using experimental SAXS. Toward this end, we developed a CG simulation algorithm for dsDNA which rapidly generates ensembles of structures through Metropolis MC sampling of a Markov chain.

  1. Functional roles of the DNA-binding HMGB domain in the histone chaperone FACT in nucleosome reorganization.

    Science.gov (United States)

    McCullough, Laura L; Connell, Zaily; Xin, Hua; Studitsky, Vasily M; Feofanov, Alexey V; Valieva, Maria E; Formosa, Tim

    2018-03-07

    The essential histone chaperone FAcilitates Chromatin Transcription (FACT) promotes both nucleosome assembly and disassembly. FACT is a heterodimer of Spt16 with either SSRP1 or Pob3, differing primarily by the presence of a high-mobility group B (HMGB) DNA-binding domain furnished only by SSRP1. Yeast FACT lacks the intrinsic HMGB domain found in SSRP1-based homologs such as human FACT, but yeast FACT activity is supported by Nhp6, which is a freestanding, single HMGB domain protein. The importance of histone binding by FACT domains has been established, but the roles of DNA binding activity remain poorly understood. Here, we examined these roles by fusing single or multiple HMGB modules to Pob3 to mimic SSRP1 or to test the effects of extended DNA-binding capacity. Human FACT and a yeast mimic both required Nhp6 to support nucleosome reorganization in vitro, indicating that a single intrinsic DNA-binding HMGB module is insufficient for full FACT activity. Three fused HMGB modules supported activity without Nhp6 assistance, but this FACT variant did not efficiently release from nucleosomes and was toxic in vivo. Notably, intrinsic DNA-binding HMGB modules reduced the DNA accessibility and histone H2A-H2B dimer loss normally associated with nucleosome reorganization. We propose that DNA bending by HMGB domains promotes nucleosome destabilization and reorganization by exposing FACT's histone binding sites, but DNA bending also produces DNA curvature needed to accommodate nucleosome assembly. Intrinsic DNA bending activity therefore favors nucleosome assembly by FACT over nucleosome reorganization, but excessive activity impairs FACT release, suggesting a quality control checkpoint during nucleosome assembly. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Genome-wide analysis of H3.3 dissociation reveals high nucleosome turnover at distal regulatory regions of embryonic stem cells.

    Science.gov (United States)

    Ha, Misook; Kraushaar, Daniel C; Zhao, Keji

    2014-01-01

    The histone variant H3.3 plays a critical role in maintaining the pluripotency of embryonic stem cells (ESCs) by regulating gene expression programs important for lineage specification. H3.3 is deposited by various chaperones at regulatory sites, gene bodies, and certain heterochromatic sites such as telomeres and centromeres. Using Tet-inhibited expression of epitope-tagged H3.3 combined with ChIP-Seq we undertook genome-wide measurements of H3.3 dissociation rates across the ESC genome and examined the relationship between H3.3-nucleosome turnover and ESC-specific transcription factors, chromatin modifiers, and epigenetic marks. Our comprehensive analysis of H3.3 dissociation rates revealed distinct H3.3 dissociation dynamics at various functional chromatin domains. At transcription start sites, H3.3 dissociates rapidly with the highest rate at nucleosome-depleted regions (NDRs) just upstream of Pol II binding, followed by low H3.3 dissociation rates across gene bodies. H3.3 turnover at transcription start sites, gene bodies, and transcription end sites was positively correlated with transcriptional activity. H3.3 is found decorated with various histone modifications that regulate transcription and maintain chromatin integrity. We find greatly varying H3.3 dissociation rates across various histone modification domains: high dissociation rates at active histone marks and low dissociation rates at heterochromatic marks. Well- defined zones of high H3.3-nucleosome turnover were detected at binding sites of ESC-specific pluripotency factors and chromatin remodelers, suggesting an important role for H3.3 in facilitating protein binding. Among transcription factor binding sites we detected higher H3.3 turnover at distal cis-acting sites compared to proximal genic transcription factor binding sites. Our results imply that fast H3.3 dissociation is a hallmark of interactions between DNA and transcriptional regulators. Our study demonstrates that H3.3 turnover and

  3. Absence of Granzyme B Positive Tumour-Infiltrating Lymphocytes in Primary Melanoma Excisional Biopsies is Strongly Associated with the Presence of Sentinel Lymph Node Metastasis

    Directory of Open Access Journals (Sweden)

    I. S. van Houdt

    2009-01-01

    Full Text Available Background: Sentinel Lymph Node (SLN status is strongly related to clinical outcome in melanoma patients. In this study we investigated the possible association between the presence of activated and/or suppressive Tumour Infiltrating Lymphocytes (TILs and SLN status in clinically stage I/II melanoma patients.

  4. Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes

    Czech Academy of Sciences Publication Activity Database

    Munoz-Viana, R.; Wildhaber, T.; Trejo-Arellano, M.S.; Mozgová, Iva; Hennig, L.

    2017-01-01

    Roč. 92, č. 3 (2017), s. 363-374 ISSN 0960-7412 Institutional support: RVO:61388971 Keywords : Arabidopsis thaliana * chromatin * CAF-1 Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 5.901, year: 2016

  5. Plant 5S rDNA has multiple alternative nucleosome positions

    Czech Academy of Sciences Publication Activity Database

    Fulneček, Jaroslav; Matyášek, Roman; Kovařík, Aleš

    2006-01-01

    Roč. 49, č. 7 (2006), s. 840-850 ISSN 0831-2796 R&D Projects: GA ČR(CZ) GP204/03/P104; GA ČR(CZ) GA521/04/0775; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507 Keywords : 5S rRNA genes * chromatin * repeat length Subject RIV: BO - Biophysics Impact factor: 1.972, year: 2006

  6. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

    Czech Academy of Sciences Publication Activity Database

    Dršata, Tomáš; Špačková, Naďa; Jurečka, P.; Zgarbová, M.; Šponer, Jiří; Lankaš, Filip

    2014-01-01

    Roč. 42, č. 11 (2014), s. 7383-7394 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GA14-21893S Grant - others:GA MŠk(CZ) ED2.1.00/03.0058; GA MŠk(CZ) ED1.1.00/02.0068 Program:ED; ED Institutional support: RVO:61388963 ; RVO:68081707 Keywords : molecular dynamics simulations * sequence-directed curvature * adenine-thymine tract Subject RIV: BO - Biophysics Impact factor: 9.112, year: 2014 http://nar.oxfordjournals.org/content/42/11/7383

  7. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle.

    Science.gov (United States)

    Hergeth, Sonja P; Schneider, Robert

    2015-11-01

    The linker histone H1 family members are a key component of chromatin and bind to the nucleosomal core particle around the DNA entry and exit sites. H1 can stabilize both nucleosome structure and higher-order chromatin architecture. In general, H1 molecules consist of a central globular domain with more flexible tail regions at both their N- and C-terminal ends. The existence of multiple H1 subtypes and a large variety of posttranslational modifications brings about a considerable degree of complexity and makes studying this protein family challenging. Here, we review recent progress in understanding the function of linker histones and their subtypes beyond their role as merely structural chromatin components. We summarize current findings on the role of H1 in heterochromatin formation, transcriptional regulation and embryogenesis with a focus on H1 subtypes and their specific modifications. © 2015 The Authors.

  8. Target model of nucleosome particle for track structure calculations and DNA damage modeling

    Czech Academy of Sciences Publication Activity Database

    Michalik, Věslav; Běgusová, Marie

    1994-01-01

    Roč. 66, č. 3 (1994), s. 267-277 ISSN 0955-3002 R&D Projects: GA ČR(CZ) GA204/93/2451; GA AV ČR(CZ) IA135102; GA AV ČR(CZ) IA50405 Keywords : DNA nucleosome * ionizing radiation * theoretical modeling Subject RIV: AQ - Safety, Health Protection, Human - Machine Impact factor: 2.761, year: 1994

  9. Nucleosome–nucleosome interactions via histone tails and linker DNA regulate nuclear rigidity

    Science.gov (United States)

    Shimamoto, Yuta; Tamura, Sachiko; Masumoto, Hiroshi; Maeshima, Kazuhiro

    2017-01-01

    Cells, as well as the nuclei inside them, experience significant mechanical stress in diverse biological processes, including contraction, migration, and adhesion. The structural stability of nuclei must therefore be maintained in order to protect genome integrity. Despite extensive knowledge on nuclear architecture and components, however, the underlying physical and molecular mechanisms remain largely unknown. We address this by subjecting isolated human cell nuclei to microneedle-based quantitative micromanipulation with a series of biochemical perturbations of the chromatin. We find that the mechanical rigidity of nuclei depends on the continuity of the nucleosomal fiber and interactions between nucleosomes. Disrupting these chromatin features by varying cation concentration, acetylating histone tails, or digesting linker DNA results in loss of nuclear rigidity. In contrast, the levels of key chromatin assembly factors, including cohesin, condensin II, and CTCF, and a major nuclear envelope protein, lamin, are unaffected. Together with in situ evidence using living cells and a simple mechanical model, our findings reveal a chromatin-based regulation of the nuclear mechanical response and provide insight into the significance of local and global chromatin structures, such as those associated with interdigitated or melted nucleosomal fibers. PMID:28428255

  10. Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription.

    Science.gov (United States)

    Knight, Britta; Kubik, Slawomir; Ghosh, Bhaswar; Bruzzone, Maria Jessica; Geertz, Marcel; Martin, Victoria; Dénervaud, Nicolas; Jacquet, Philippe; Ozkan, Burak; Rougemont, Jacques; Maerkl, Sebastian J; Naef, Félix; Shore, David

    2014-08-01

    In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. We show that the regulatory properties of the two promoter types are remarkably similar, suggesting that they are determined to a large extent by Rap1 and the Fhl1/Ifh1 pair. Rapid depletion experiments allowed us to define a hierarchy of TF binding in which Rap1 acts as a pioneer factor required for binding of all other TFs. We also uncovered unexpected features underlying recruitment of Fhl1, whose forkhead DNA-binding domain is not required for binding at most promoters, and Hmo1, whose binding is supported by repeated motifs. Finally, we describe unusually micrococcal nuclease (MNase)-sensitive nucleosomes at all RPG promoters, located between the canonical +1 and -1 nucleosomes, which coincide with sites of Fhl1/Ifh1 and Hmo1 binding. We speculate that these "fragile" nucleosomes play an important role in regulating RPG transcriptional output. © 2014 Knight et al.; Published by Cold Spring Harbor Laboratory Press.

  11. Regulation of biosynthesis and intracellular localization of rice and tobacco homologues of nucleosome assembly protein 1.

    Science.gov (United States)

    Dong, Aiwu; Zhu, Yan; Yu, Yu; Cao, Kaiming; Sun, Chongrong; Shen, Wen-Hui

    2003-02-01

    The nucleosome assembly protein 1 (NAP1) is considered to be a conserved histone chaperone, facilitating the assembly of nucleosomes in all eukaryotes. However, studies in yeast and animal cells also indicated that NAP1 proteins have diverse functions likely independent of nucleosome-assembly activity. Here, we describe the isolation and characterization of cDNAs encoding NAP1-like proteins from the monocotyledon rice ( Oryza sativa L.) and the dicotyledon tobacco ( Nicotiana tabacum L.). Northern-blot analysis demonstrated that the two rice NAP1-like genes are predominantly expressed in stem tissues such as root and shoot apical meristems as well as in young flowers. During the cell cycle, all four tobacco NAP1-like genes are highly expressed, with one of them showing a slightly increased expression at the G1/S transition. These results are consistent with a role for plant NAP1-like proteins in cell division. In vitro binding assays revealed that different NAP1-like proteins bind, with distinct relative binding strengths, to different classes of histone. Intracellular localization analyses showed that some NAP1-like proteins could be targeted into the nucleus whereas others are exclusively cytoplasm-localized. It is thus likely that different plant NAP1-like proteins have distinct functions in vivo. Plant NAP1-like proteins were observed to concentrate around the metaphase plate and in the phragmoplast, suggesting a role in mitotic events and cytokinesis.

  12. Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance.

    Directory of Open Access Journals (Sweden)

    Shikhar Sharma

    2011-02-01

    Full Text Available How epigenetic information is propagated during somatic cell divisions is still unclear but is absolutely critical for preserving gene expression patterns and cellular identity. Here we show an unanticipated mechanism for inheritance of DNA methylation patterns where the epigenetic mark not only recruits the catalyzing enzyme but also regulates the protein level, i.e. the enzymatic product (5-methylcytosine determines the level of the methylase, thus forming a novel homeostatic inheritance system. Nucleosomes containing methylated DNA stabilize de novo DNA methyltransferases, DNMT3A/3B, allowing little free DNMT3A/3B enzymes to exist in the nucleus. Stabilization of DNMT3A/3B on nucleosomes in methylated regions further promotes propagation of DNA methylation. However, reduction of cellular DNA methylation levels creating more potential CpG substrates counter-intuitively results in a dramatic decrease of DNMT3A/3B proteins due to diminished nucleosome binding and subsequent degradation of the unstable free proteins. These data show an unexpected self-regulatory inheritance mechanism that not only ensures somatic propagation of methylated states by DNMT1 and DNMT3A/3B enzymes but also prevents aberrant de novo methylation by causing degradation of free DNMT3A/3B enzymes.

  13. Genomic selection strategies in breeding programs: Strong positive interaction between application of genotypic information and intensive use of young bulls on genetic gain

    DEFF Research Database (Denmark)

    Buch, Line Hjortø; Sørensen, Morten Kargo; Berg, Peer

    2012-01-01

    ) a positive interaction exists between the use of genotypic information and a short generation interval on ΔGAG and (iii) the inclusion of an indicator trait in the selection index will only result in a negligible increase in ΔGAG if genotypic information about the breeding goal trait is known. We examined......We tested the following hypotheses: (i) breeding schemes with genomic selection are superior to breeding schemes without genomic selection regarding annual genetic gain of the aggregate genotype (ΔGAG), annual genetic gain of the functional traits and rate of inbreeding per generation (ΔF), (ii...... four breeding schemes with or without genomic selection and with or without intensive use of young bulls using pseudo-genomic stochastic simulations. The breeding goal consisted of a milk production trait and a functional trait. The two breeding schemes with genomic selection resulted in higher ΔGAG...

  14. Chromatin associated mechanisms in base excision repair - nucleosome remodeling and DNA transcription, two key players.

    Science.gov (United States)

    Menoni, Hervé; Di Mascio, Paolo; Cadet, Jean; Dimitrov, Stefan; Angelov, Dimitar

    2017-06-01

    Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health. Although the enzymology of BER mechanisms has been largely elucidated using chemically defined DNA damage substrates and purified proteins, the complex interplay of BER with another vital process like transcription or when DNA is in its natural state (i.e. wrapped in nucleosome and assembled in chromatin fiber is largely unexplored. Cells use chromatin remodeling factors to overcome the general repression associated with the nucleosomal organization. It is broadly accepted that energy-dependent nucleosome remodeling factors disrupt histones-DNA interactions at the expense of ATP hydrolysis to favor transcription as well as DNA repair. Importantly, unlike transcription, BER is not part of a regulated developmental process but represents a maintenance system that should be efficient anytime and anywhere in the genome. In this review we will discuss how BER can deal with chromatin organization to maintain genetic information. Emphasis will be placed on the following challenging question: how BER is initiated within chromatin? Copyright © 2017 Elsevier Inc. All rights reserved.

  15. The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression.

    Directory of Open Access Journals (Sweden)

    Peng Cui

    Full Text Available To further understand the relationship between nucleosome-space occupancy (NO and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse tissues--cerebrum, testis, and ESCs--and found, through clustering analysis for transcriptional activation, that the NO variations among chromosomes are closely associated with distinct expression levels between house-keeping (HK genes and tissue-specific (TS genes. Both TS and HK genes form clusters albeit the obvious majority. This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types.

  16. The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression

    KAUST Repository

    Cui, Peng

    2011-08-19

    To further understand the relationship between nucleosome-space occupancy (NO) and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3)-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse tissues-cerebrum, testis, and ESCs-and found, through clustering analysis for transcriptional activation, that the NO variations among chromosomes are closely associated with distinct expression levels between house-keeping (HK) genes and tissue-specific (TS) genes. Both TS and HK genes form clusters albeit the obvious majority. This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types. © 2011 Cui et al.

  17. Analysis of the histone protein tail and DNA in nucleosome using molecular dynamics simulation

    Science.gov (United States)

    Fujimori, R.; Komatsu, Y.; Fukuda, M.; Miyakawa, T.; Morikawa, R.; Takasu, M.

    2013-02-01

    We study the effect of the tails of H3 and H4 histones in the nucleosomes, where DNA and histones are packed in the form of chromatin. We perform molecular dynamics simulations of the complex of DNA and histones and calculate the mean square displacement and the gyration radius of the complex of DNA and histones for the cases with tails intact and the cases with tails missing. Our results show that the H3 tails are important for the motion of the histones. We also find that the motion of one tail is affected by other tails, although the tails are distanced apart, suggesting the correlated motion in biological systems.

  18. The Structural Location of DNA Lesions in Nucleosome Core Particles Determines Accessibility by Base Excision Repair Enzymes*

    Science.gov (United States)

    Rodriguez, Yesenia; Smerdon, Michael J.

    2013-01-01

    Packaging of DNA into chromatin affects accessibility of DNA regulatory factors involved in transcription, replication, and repair. Evidence suggests that even in the nucleosome core particle (NCP), accessibility to damaged DNA is hindered by the presence of the histone octamer. Base excision repair is the major pathway in mammalian cells responsible for correcting a large number of chemically modified bases. We have measured the repair of site-specific uracil and single nucleotide gaps along the surface of the NCP. Our results indicate that removal of DNA lesions is greatly dependent on their rotational and translational positioning in NCPs. Significantly, the rate of uracil removal with outwardly oriented DNA backbones is 2–10-fold higher than those with inwardly oriented backbones. In general, uracils with inwardly oriented backbones farther away from the dyad center of the NCP are more accessible than those near the dyad. The translational positioning of outwardly oriented gaps is the key factor driving gap filling activity. An outwardly oriented gap near the DNA ends exhibits a 3-fold increase in gap filling activity as compared with one near the dyad with the same rotational orientation. Near the dyad, uracil DNA glycosylase/APE1 removes an outwardly oriented uracil efficiently; however, polymerase β activity is significantly inhibited at this site. These data suggest that the hindrance presented by the location of a DNA lesion is dependent on the structural requirements for enzyme catalysis. Therefore, remodeling at DNA damage sites in NCPs is critical for preventing accumulation of aborted intermediates and ensuring completion of base excision repair. PMID:23543741

  19. ATP-independent cooperative binding of yeast Isw1a to bare and nucleosomal DNA.

    Directory of Open Access Journals (Sweden)

    Anne De Cian

    Full Text Available Among chromatin remodeling factors, the ISWI family displays a nucleosome-enhanced ATPase activity coupled to DNA translocation. While these enzymes are known to bind to DNA, their activity has not been fully characterized. Here we use TEM imaging and single molecule manipulation to investigate the interaction between DNA and yeast Isw1a. We show that Isw1a displays a highly cooperative ATP-independent binding to and bridging between DNA segments. Under appropriate tension, rare single nucleation events can sometimes be observed and loop DNA with a regular step. These nucleation events are often followed by binding of successive complexes bridging between nearby DNA segments in a zipper-like fashion, as confirmed by TEM observations. On nucleosomal substrates, we show that the specific ATP-dependent remodeling activity occurs in the context of cooperative Isw1a complexes bridging extranucleosomal DNA. Our results are interpreted in the context of the recently published partial structure of Isw1a and support its acting as a "protein ruler" (with possibly more than one tick.

  20. The Cac2 subunit is essential for productive histone binding and nucleosome assembly in CAF-1

    Energy Technology Data Exchange (ETDEWEB)

    Mattiroli, Francesca; Gu, Yajie; Balsbaugh, Jeremy L.; Ahn, Natalie G.; Luger, Karolin

    2017-04-18

    Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding. The large subunit, Cac1 organizes the assembly of CAF-1. Strikingly, H3-H4 binding is mediated by a composite interface, shaped by Cac1-bound Cac2 and the Cac1 acidic region. Cac2 is indispensable for productive histone binding, while deletion of Cac3 has only moderate effects on H3-H4 binding and nucleosome assembly. These results define direct structural roles for yeast CAF-1 subunits and uncover a previously unknown critical function of the middle subunit in CAF-1.

  1. FACT, the Bur kinase pathway, and the histone co-repressor HirC have overlapping nucleosome-related roles in yeast transcription elongation.

    Directory of Open Access Journals (Sweden)

    Jennifer R Stevens

    Full Text Available Gene transcription is constrained by the nucleosomal nature of chromosomal DNA. This nucleosomal barrier is modulated by FACT, a conserved histone-binding heterodimer. FACT mediates transcription-linked nucleosome disassembly and also nucleosome reassembly in the wake of the RNA polymerase II transcription complex, and in this way maintains the repression of 'cryptic' promoters found within some genes. Here we focus on a novel mutant version of the yeast FACT subunit Spt16 that supplies essential Spt16 activities but impairs transcription-linked nucleosome reassembly in dominant fashion. This Spt16 mutant protein also has genetic effects that are recessive, which we used to show that certain Spt16 activities collaborate with histone acetylation and the activities of a Bur-kinase/Spt4-Spt5/Paf1C pathway that facilitate transcription elongation. These collaborating activities were opposed by the actions of Rpd3S, a histone deacetylase that restores a repressive chromatin environment in a transcription-linked manner. Spt16 activity paralleling that of HirC, a co-repressor of histone gene expression, was also found to be opposed by Rpd3S. Our findings suggest that Spt16, the Bur/Spt4-Spt5/Paf1C pathway, and normal histone abundance and/or stoichiometry, in mutually cooperative fashion, facilitate nucleosome disassembly during transcription elongation. The recessive nature of these effects of the mutant Spt16 protein on transcription-linked nucleosome disassembly, contrasted to its dominant negative effect on transcription-linked nucleosome reassembly, indicate that mutant FACT harbouring the mutant Spt16 protein competes poorly with normal FACT at the stage of transcription-linked nucleosome disassembly, but effectively with normal FACT for transcription-linked nucleosome reassembly. This functional difference is consistent with the idea that FACT association with the transcription elongation complex depends on nucleosome disassembly, and that the

  2. Nitrated nucleosome levels and neuropsychiatric events in systemic lupus erythematosus; a multi-center retrospective case-control study

    DEFF Research Database (Denmark)

    Ferreira, Isabel; Croca, Sara; Raimondo, Maria Gabriella

    2017-01-01

    BACKGROUND: In patients with systemic lupus erythematosus (SLE) there is no serological test that will reliably distinguish neuropsychiatric (NP) events due to active SLE from those due to other causes. Previously we showed that serum levels of nitrated nucleosomes (NN) were elevated in a small n...

  3. The incorporation of the novel histone variant H2AL2 confers unusual structural and functional properties of the nucleosome

    Czech Academy of Sciences Publication Activity Database

    Syed, S.H.; Boulard, M.; Shukla, M.S.; Gautier, T.; Travers, A.; Bednár, Jan; Faivre-Moskalenko, C.; Dimitrov, S.; Angelov, D.

    2009-01-01

    Roč. 37, č. 14 (2009), s. 4684-4695 ISSN 0305-1048 Grant - others:GA MŠk(CZ) LC535; GA ČR(CZ) GA304/05/2168 Program:LC Institutional research plan: CEZ:AV0Z50110509 Keywords : nucleosome * histone * variant Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.479, year: 2009

  4. A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex.

    Science.gov (United States)

    Ma, Honglei; Duan, Jingbo; Ke, Jiyuan; He, Yuanzheng; Gu, Xin; Xu, Ting-Hai; Yu, Hong; Wang, Yonghong; Brunzelle, Joseph S; Jiang, Yi; Rothbart, Scott B; Xu, H Eric; Li, Jiayang; Melcher, Karsten

    2017-06-01

    TOPLESS are tetrameric plant corepressors of the conserved Tup1/Groucho/TLE (transducin-like enhancer of split) family. We show that they interact through their TOPLESS domains (TPDs) with two functionally important ethylene response factor-associated amphiphilic repression (EAR) motifs of the rice strigolactone signaling repressor D53: the universally conserved EAR-3 and the monocot-specific EAR-2. We present the crystal structure of the monocot-specific EAR-2 peptide in complex with the TOPLESS-related protein 2 (TPR2) TPD, in which the EAR-2 motif binds the same TPD groove as jasmonate and auxin signaling repressors but makes additional contacts with a second TPD site to mediate TPD tetramer-tetramer interaction. We validated the functional relevance of the two TPD binding sites in reporter gene assays and in transgenic rice and demonstrate that EAR-2 binding induces TPD oligomerization. Moreover, we demonstrate that the TPD directly binds nucleosomes and the tails of histones H3 and H4. Higher-order assembly of TPD complexes induced by EAR-2 binding markedly stabilizes the nucleosome-TPD interaction. These results establish a new TPD-repressor binding mode that promotes TPD oligomerization and TPD-nucleosome interaction, thus illustrating the initial assembly of a repressor-corepressor-nucleosome complex.

  5. A cassette of basic amino acids in histone H2B regulates nucleosome dynamics and access to DNA damage.

    Science.gov (United States)

    Rodriguez, Yesenia; Duan, Mingrui; Wyrick, John J; Smerdon, Michael J

    2018-03-27

    Nucleosome dynamics, such as spontaneous DNA unwrapping, are postulated to have a critical role in regulating the access of DNA repair machinery to DNA lesions within nucleosomes. However, the specific histone domains that regulate nucleosome dynamics and their impact on DNA repair are not well understood. Previous studies have identified the histone H2B repression (or HBR) domain, a highly conserved, basic region in the N-terminal tail of histone H2B, which significantly influences gene expression, chromatin assembly, and DNA damage and repair. However, knowledge about the molecular mechanism(s) that may account for these observations is limited. Here, we characterized the stability and dynamics of ΔHBR mutant nucleosome core particles (NCPs) in vitro by restriction-enzyme accessibility, FRET, and temperature-induced sliding of histone octamers. Our results indicate that ΔHBR NCPs are more dynamic and the steady-state fraction of the ΔHBR NCP population occupying the unwrapped state is larger than that of WT NCPs. Moreover, ΔHBR-histone octamers are more susceptible to temperature-induced sliding on DNA than WT histone octamers. Notably, the activity of base-excision repair (BER) enzymes at uracil lesions and single-nucleotide gaps is enhanced in a site-specific manner in ΔHBR NCPs and correlates well with increased DNA unwrapping in these damaged regions. Finally, removal of the HBR domain is insufficient for completely alleviating the structural constraints imposed by histone octamers on the activity of BER enzymes. In summary, our findings indicate that the conserved HBR domain of histone H2B regulates the accessibility of repair factors to DNA lesions in nucleosomes. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Changes in Nucleosome Occupancy Associated with Metabolic Alterations in Aged Mammalian Liver

    Directory of Open Access Journals (Sweden)

    Irina M. Bochkis

    2014-11-01

    Full Text Available Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months and old (21 months mice. Transcriptional changes suggest that derepression of the nuclear receptors PPARα, PPARγ, and LXRα in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors and candidates associated with nuclear lamina (Hdac3 and Srf implicated to govern metabolic function of aging liver. Winged-helix transcription factor Foxa2 and nuclear receptor corepressor Hdac3 exhibit a reciprocal binding pattern at PPARα targets contributing to gene expression changes that lead to steatosis in aged liver.

  7. Towards the theoretical bases of the folding of the 100-A nucleosome filament

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1994-01-01

    We attempt to model DNA packaging at the various stages of ever increasing DNA folding from the 100-A nucleosome filament to various further stages leading up to the metaphase chromosome. We have assumed that a phase transition has induced chromatin into a condensed mode. The mean-field model allows the simultaneous discussion of chromatin with packaging ration η and DNA replication at various stages of folding. We derive a formula correlating (during the S phase of the cell cycle) the DNA polymerase velocity r f (measured in nucleotides per minute) in a relation of inverse proportionality with the degree of DNA packaging: r f = λη -1/2 , where the dimensional constant λ has been determined. This model suggests that in the heterochromatic regions of chromatin there is reduced activity of DNA polymerases. We discuss the possible relevance of our model to late replicating telomeres in yeast and several higher eukaryotes. (author). 28 refs, 3 tabs

  8. Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

    Science.gov (United States)

    Duan, Zhao-Wen; Li, Wei; Xie, Ping; Dou, Shuo-Xing; Wang, Peng-Ye

    2010-04-01

    Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking" interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

  9. Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

    International Nuclear Information System (INIS)

    Zhao-Wen, Duan; Wei, Li; Ping, Xie; Shuo-Xing, Dou; Peng-Ye, Wang

    2010-01-01

    Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking” interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon. (cross-disciplinary physics and related areas of science and technology)

  10. Thermomechanical damage of nucleosome by the shock wave initiated by ion passing through liquid water

    International Nuclear Information System (INIS)

    Yakubovich, Alexander V.; Surdutovich, Eugene; Solov’yov, Andrey V.

    2012-01-01

    We report on the results of full-atom molecular dynamics simulations of the heat spike in the water medium caused by the propagation of the heavy ion in the vicinity of its Bragg peak. High rate of energy transfer from an ion to the molecules of surrounding water environment leads to the rapid increase of the temperature of the molecules in the vicinity of ions trajectory. As a result of an abrupt increase of the temperature we observe the formation of the nanoscale shock wave propagating through the medium. We investigate the thermomechanical damage caused by the shock wave to the nucleosome located in the vicinity of heavy ion trajectory. We observe the substantial deformation of the DNA secondary structure. We show that the produced shock wave can lead to the thermomechanical breakage of the DNA backbone covalent bonds and present estimates for the number of such strand brakes per one cell nucleus.

  11. A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis.

    Science.gov (United States)

    Börner, Kenneth; Jain, Dhawal; Vazquez-Pianzola, Paula; Vengadasalam, Sandra; Steffen, Natascha; Fyodorov, Dmitry V; Tomancak, Pavel; Konev, Alexander; Suter, Beat; Becker, Peter B

    2016-03-15

    The Chromatin Accessibility Complex (CHRAC) consists of the ATPase ISWI, the large ACF1 subunit and a pair of small histone-like proteins, CHRAC-14/16. CHRAC is a prototypical nucleosome sliding factor that mobilizes nucleosomes to improve the regularity and integrity of the chromatin fiber. This may facilitate the formation of repressive chromatin. Expression of the signature subunit ACF1 is restricted during embryonic development, but remains high in primordial germ cells. Therefore, we explored roles for ACF1 during Drosophila oogenesis. ACF1 is expressed in somatic and germline cells, with notable enrichment in germline stem cells and oocytes. The asymmetrical localization of ACF1 to these cells depends on the transport of the Acf1 mRNA by the Bicaudal-D/Egalitarian complex. Loss of ACF1 function in the novel Acf1(7) allele leads to defective egg chambers and their elimination through apoptosis. In addition, we find a variety of unusual 16-cell cyst packaging phenotypes in the previously known Acf1(1) allele, with a striking prevalence of egg chambers with two functional oocytes at opposite poles. Surprisingly, we found that the Acf1(1) deletion--despite disruption of the Acf1 reading frame--expresses low levels of a PHD-bromodomain module from the C-terminus of ACF1 that becomes enriched in oocytes. Expression of this module from the Acf1 genomic locus leads to packaging defects in the absence of functional ACF1, suggesting competitive interactions with unknown target molecules. Remarkably, a two-fold overexpression of CHRAC (ACF1 and CHRAC-16) leads to increased apoptosis and packaging defects. Evidently, finely tuned CHRAC levels are required for proper oogenesis. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length.

    Directory of Open Access Journals (Sweden)

    Hua Wong

    Full Text Available In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.

  13. Chemical Synthesis of K34-Ubiquitylated H2B for Nucleosome Reconstitution and Single-Particle Cryo-Electron Microscopy Structural Analysis.

    Science.gov (United States)

    Li, Jiabin; He, Qiaoqiao; Liu, Yuntao; Liu, Sanling; Tang, Shan; Li, Chengmin; Sun, Demeng; Li, Xiaorun; Zhou, Min; Zhu, Ping; Bi, Guoqiang; Zhou, Zhenghong; Zheng, Ji-Shen; Tian, Changlin

    2017-01-17

    Post-translational modifications (e.g., ubiquitylation) of histones play important roles in dynamic regulation of chromatin. Histone ubiquitylation has been speculated to directly influence the structure and dynamics of nucleosomes. However, structural information for ubiquitylated nucleosomes is still lacking. Here we report an alternative strategy for total chemical synthesis of homogenous histone H2B-K34-ubiquitylation (H2B-K34Ub) by using acid-cleavable auxiliary-mediated ligation of peptide hydrazides for site-specific ubiquitylation. Synthetic H2B-K34Ub was efficiently incorporated into nucleosomes and further used for single-particle cryo-electron microscopy (cryo-EM) imaging. The cryo-EM structure of the nucleosome containing H2B-K34Ub suggests that two flexible ubiquitin domains protrude between the DNA chains of the nucleosomes. The DNA chains around the H2B-K34 sites shift and provide more space for ubiquitin to protrude. These analyses indicated local and slight structural influences on the nucleosome with ubiquitylation at the H2B-K34 site. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Computer Modeling Reveals that Modifications of the Histone Tail Charges Define Salt-Dependent Interaction of the Nucleosome Core Particles

    OpenAIRE

    Yang, Ye; Lyubartsev, Alexander P.; Korolev, Nikolay; Nordenskiöld, Lars

    2009-01-01

    Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were con...

  15. Variability in Chromatin Architecture and Associated DNA Repair at Genomic Positions Containing Somatic Mutations.

    Science.gov (United States)

    Lim, Byungho; Mun, Jihyeob; Kim, Yong Sung; Kim, Seon-Young

    2017-06-01

    Dynamic chromatin structures result in differential chemical reactivity to mutational processes throughout the genome. To identify chromatin features responsible for mutagenesis, we compared chromatin architecture around single-nucleotide variants (SNV), insertion/deletions (indels), and their context-matched, nonmutated positions. We found epigenetic differences between genomic regions containing missense SNVs and those containing frameshift indels across multiple cancer types. Levels of active histone marks were higher around frameshift indels than around missense SNV, whereas repressive histone marks exhibited the reverse trend. Accumulation of repressive histone marks and nucleosomes distinguished mutated positions (both SNV and indels) from the context-matched, nonmutated positions, whereas active marks were associated with substitution- and cancer type-specific mutagenesis. We also explained mutagenesis based on genome maintenance mechanisms, including nucleotide excision repair (NER), mismatch repair (MMR), and DNA polymerase epsilon (POLE). Regional NER variation correlated strongly with chromatin features; NER machineries exhibited shifted or depleted binding around SNV, resulting in decreased NER at mutation positions, especially at sites of recurrent mutations. MMR-deficient tumors selectively acquired SNV in regions with high active histone marks, especially H3K36me3, whereas POLE-deficient tumors selectively acquired indels and SNV in regions with low active histone marks. These findings demonstrate the importance of fine-scaled chromatin structures and associated DNA repair mechanisms in mutagenesis. Cancer Res; 77(11); 2822-33. ©2017 AACR . ©2017 American Association for Cancer Research.

  16. Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution studied by Molecular Dynamics Simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Roccatano, Danilo; Barthel, Andre; Zacharias, Martin W.

    2007-01-24

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Comparative explicit solvent molecular dynamics (MD) simulations have been performed on a complete nucleosome core particle with and without N-terminal histone tails for more than 20 ns. Main purpose of the simulations was to study the dynamics of mobile elements such as histone N-terminal tails and how packing and DNA-bending influences the fine structure and dynamics of DNA. Except for the tails, histone and DNA molecules stayed on average close to the crystallographic start structure supporting the quality of the current force field approach. Despite the packing strain, no increase of transitions to noncanonical nucleic acid backbone conformations compared to regular B-DNA was observed. The pattern of kinks and bends along the DNA remained close to the experiment overall. In addition to the local dynamics, the simulations allowed the analysis of the superhelical mobility indicating a limited relative mobility of DNA segments separated by one superhelical turn (mean relative displacement of approximately 60.2 nm, mainly along the superhelical axis). An even higher rigidity was found for relative motions (distance fluctuations) of segments separated by half a superhelical turn (approximately 60.1 nm). The N-terminal tails underwent dramatic conformational rearrangements on the nanosecond time scale toward partially and transiently wrapped states around the DNA. Many of the histone tail changes corresponded to coupled association and folding events from fully solvent-exposed states toward complexes with the major and minor grooves of DNA. The simulations indicate that the rapid conformational changes of the tails can modulate the DNA accessibility within a few nanoseconds

  17. Interaction of nucleosome assembly proteins abolishes nuclear localization of DGKζ by attenuating its association with importins

    International Nuclear Information System (INIS)

    Okada, Masashi; Hozumi, Yasukazu; Ichimura, Tohru; Tanaka, Toshiaki; Hasegawa, Hiroshi; Yamamoto, Masakazu; Takahashi, Nobuya; Iseki, Ken; Yagisawa, Hitoshi; Shinkawa, Takashi; Isobe, Toshiaki; Goto, Kaoru

    2011-01-01

    Diacylglycerol kinase (DGK) is involved in the regulation of lipid-mediated signal transduction through the metabolism of a second messenger diacylglycerol. Of the DGK family, DGKζ, which contains a nuclear localization signal, localizes mainly to the nucleus but translocates to the cytoplasm under pathological conditions. However, the detailed mechanism of translocation and its functional significance remain unclear. To elucidate these issues, we used a proteomic approach to search for protein targets that interact with DGKζ. Results show that nucleosome assembly protein (NAP) 1-like 1 (NAP1L1) and NAP1-like 4 (NAP1L4) are identified as novel DGKζ binding partners. NAP1Ls constitutively shuttle between the nucleus and the cytoplasm in transfected HEK293 cells. The molecular interaction of DGKζ and NAP1Ls prohibits nuclear import of DGKζ because binding of NAP1Ls to DGKζ blocks import carrier proteins, Qip1 and NPI1, to interact with DGKζ, leading to cytoplasmic tethering of DGKζ. In addition, overexpression of NAP1Ls exerts a protective effect against doxorubicin-induced cytotoxicity. These findings suggest that NAP1Ls are involved in a novel molecular basis for the regulation of nucleocytoplasmic shuttling of DGKζ and provide a clue to examine functional significance of its translocation under pathological conditions.

  18. Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution.

    Science.gov (United States)

    Zhang, Hui; Li, Feifei; Jia, Yan; Xu, Bingxiang; Zhang, Yiqun; Li, Xiaoli; Zhang, Zhihua

    2017-12-15

    High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interaction sites at kilobase resolution from MNase-seq data, termed chromatin interaction site detector (CISD), and a CISD-based chromatin loop predictor (CISD_loop) that predicts chromatin-chromatin interactions (CCIs) from low-resolution Hi-C data. We show that the predictions of CISD and CISD_loop overlap closely with chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) anchors and loops, respectively. The validity of CISD/CISD_loop was further supported by a 3C assay at about 5 kb resolution. Finally, we demonstrate that only modest amounts of MNase-seq and Hi-C data are sufficient to achieve ultrahigh resolution CCI maps. Our results suggest that CCIs may result in characteristic nucleosomes arrangement patterns flanking the interaction sites, and our algorithms may facilitate precise and systematic investigations of CCIs on a larger scale than hitherto have been possible. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Skin vaccination using microneedles coated with a plasmid DNA cocktail encoding nucleosomal histones of Leishmania spp.

    Science.gov (United States)

    Moreno, Esther; Schwartz, Juana; Calvo, Alba; Blanco, Laura; Larrea, Esther; Irache, Juan M; Sanmartín, Carmen; Coulman, Sion A; Soto, Manuel; Birchall, James C; Espuelas, Socorro

    2017-11-25

    Vaccine delivery using microneedles (MNs) represents a safe, easily disposable and painless alternative to traditional needle immunizations. The MN delivery of DNA vaccines to the dermis may result in a superior immune response and/or an equivalent immune response at a lower vaccine dose (dose-sparing). This could be of special interest for immunization programs against neglected tropical diseases such as leishmaniasis. In this work, we loaded a MN device with 60μg of a plasmid DNA cocktail encoding the Leishmania infantum nucleosomal histones H2A, H2B, H3 and H4 and compared its immunogenicity and protective capacity against conventional s.c. or i.d. injection of the plasmid. Mice immunized with MNs showed increased ratios of IFN-γ/IL-10, IFN-γ/IL-13, IFN-γ/IL-4, and IFN-γ/TGF-β in the spleens and lymph nodes compared with mice immunized by s.c. and i.d. routes. Furthermore, CCXCL9, CXCL10 and CCL2 levels were also higher. These data suggest that the nucleic acid immunization using MNs produced a better bias towards a Th1 response. However, none of the immunizations strategies were able to control Leishmania major infection in BALB/c mice, as illustrated by an increase in lesion size and parasite burden. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Dengue virus capsid protein binds core histones and inhibits nucleosome formation in human liver cells.

    Directory of Open Access Journals (Sweden)

    Tonya M Colpitts

    Full Text Available Dengue virus (DENV is a member of the Flaviviridae and a globally (reemerging pathogen that causes serious human disease. There is no specific antiviral or vaccine for dengue virus infection. Flavivirus capsid (C is a structural protein responsible for gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. Flaviviral replication is known to occur in the cytoplasm yet a large portion of capsid protein localizes to the nucleus during infection. The reasons for the nuclear presences of capsid are not completely understood. Here, we expressed mature DENV C in a tandem affinity purification assay to identify potential binding partners in human liver cells. DENV C targeted the four core histones, H2A, H2B, H3 and H4. DENV C bound recombinant histones in solution and colocalized with histones in the nucleus and cytoplasm of liver cells during DENV infection. We show that DENV C acts as a histone mimic, forming heterodimers with core histones, binding DNA and disrupting nucleosome formation. We also demonstrate that DENV infection increases the amounts of core histones in livers cells, which may be a cellular response to C binding away the histone proteins. Infection with DENV additionally alters levels of H2A phosphorylation in a time-dependent manner. The interactions of C and histones add an interesting new role for the presence of C in the nucleus during DENV infection.

  1. Dengue virus capsid protein binds core histones and inhibits nucleosome formation in human liver cells.

    Science.gov (United States)

    Colpitts, Tonya M; Barthel, Sebastian; Wang, Penghua; Fikrig, Erol

    2011-01-01

    Dengue virus (DENV) is a member of the Flaviviridae and a globally (re)emerging pathogen that causes serious human disease. There is no specific antiviral or vaccine for dengue virus infection. Flavivirus capsid (C) is a structural protein responsible for gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. Flaviviral replication is known to occur in the cytoplasm yet a large portion of capsid protein localizes to the nucleus during infection. The reasons for the nuclear presences of capsid are not completely understood. Here, we expressed mature DENV C in a tandem affinity purification assay to identify potential binding partners in human liver cells. DENV C targeted the four core histones, H2A, H2B, H3 and H4. DENV C bound recombinant histones in solution and colocalized with histones in the nucleus and cytoplasm of liver cells during DENV infection. We show that DENV C acts as a histone mimic, forming heterodimers with core histones, binding DNA and disrupting nucleosome formation. We also demonstrate that DENV infection increases the amounts of core histones in livers cells, which may be a cellular response to C binding away the histone proteins. Infection with DENV additionally alters levels of H2A phosphorylation in a time-dependent manner. The interactions of C and histones add an interesting new role for the presence of C in the nucleus during DENV infection.

  2. Dengue Virus Capsid Protein Binds Core Histones and Inhibits Nucleosome Formation in Human Liver Cells

    Science.gov (United States)

    Colpitts, Tonya M.; Barthel, Sebastian; Wang, Penghua; Fikrig, Erol

    2011-01-01

    Dengue virus (DENV) is a member of the Flaviviridae and a globally (re)emerging pathogen that causes serious human disease. There is no specific antiviral or vaccine for dengue virus infection. Flavivirus capsid (C) is a structural protein responsible for gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. Flaviviral replication is known to occur in the cytoplasm yet a large portion of capsid protein localizes to the nucleus during infection. The reasons for the nuclear presences of capsid are not completely understood. Here, we expressed mature DENV C in a tandem affinity purification assay to identify potential binding partners in human liver cells. DENV C targeted the four core histones, H2A, H2B, H3 and H4. DENV C bound recombinant histones in solution and colocalized with histones in the nucleus and cytoplasm of liver cells during DENV infection. We show that DENV C acts as a histone mimic, forming heterodimers with core histones, binding DNA and disrupting nucleosome formation. We also demonstrate that DENV infection increases the amounts of core histones in livers cells, which may be a cellular response to C binding away the histone proteins. Infection with DENV additionally alters levels of H2A phosphorylation in a time-dependent manner. The interactions of C and histones add an interesting new role for the presence of C in the nucleus during DENV infection. PMID:21909430

  3. Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI.

    Directory of Open Access Journals (Sweden)

    Giosalba Burgio

    2008-06-01

    Full Text Available Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.

  4. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling.

    Directory of Open Access Journals (Sweden)

    Justin W Leung

    2014-03-01

    Full Text Available Histone ubiquitinations are critical for the activation of the DNA damage response (DDR. In particular, RNF168 and RING1B/BMI1 function in the DDR by ubiquitinating H2A/H2AX on Lys-13/15 and Lys-118/119, respectively. However, it remains to be defined how the ubiquitin pathway engages chromatin to provide regulation of ubiquitin targeting of specific histone residues. Here we identify the nucleosome acid patch as a critical chromatin mediator of H2A/H2AX ubiquitination (ub. The acidic patch is required for RNF168- and RING1B/BMI1-dependent H2A/H2AXub in vivo. The acidic patch functions within the nucleosome as nucleosomes containing a mutated acidic patch exhibit defective H2A/H2AXub by RNF168 and RING1B/BMI1 in vitro. Furthermore, direct perturbation of the nucleosome acidic patch in vivo by the expression of an engineered acidic patch interacting viral peptide, LANA, results in defective H2AXub and RNF168-dependent DNA damage responses including 53BP1 and BRCA1 recruitment to DNA damage. The acidic patch therefore is a critical nucleosome feature that may serve as a scaffold to integrate multiple ubiquitin signals on chromatin to compose selective ubiquitinations on histones for DNA damage signaling.

  5. Efficient cleavage of single and clustered AP site lesions within mono-nucleosome templates by CHO-K1 nuclear extract contrasts with retardation of incision by purified APE1

    Science.gov (United States)

    Eccles, Laura J.; Menoni, Hervé; Angelov, Dimitar; Lomax, Martine E.; O’Neill, Peter

    2015-01-01

    Clustered DNA damage is a unique characteristic of radiation-induced DNA damage and the formation of these sites poses a serious challenge to the cell’s repair machinery. Within a cell DNA is compacted, with nucleosomes being the first order of higher level structure. However, few data are reported on the efficiency of clustered-lesion processing within nucleosomal DNA templates. Here, we show retardation of cleavage of a single AP site by purified APE1 when contained in nucleosomal DNA, compared to cleavage of an AP site in non-nucleosomal DNA. This retardation seen in nucleosomal DNA was alleviated by incubation with CHO-K1 nuclear extract. When clustered DNA damage sites containing bistranded AP sites were present in nucleosomal DNA, efficient cleavage of the AP sites was observed after treatment with nuclear extract. The resultant DSB formation led to DNA dissociating from the histone core and nucleosomal dispersion. Clustered damaged sites containing bistranded AP site/8-oxoG residues showed no retardation of cleavage of the AP site but retardation of 8-oxoG excision, compared to isolated lesions, thus DSB formation was not seen. An increased understanding of processing of clustered DNA damage in a nucleosomal environment may lead to new strategies to enhance the cytotoxic effects of radiotherapeutics. PMID:26439176

  6. Immunization strategies against visceral leishmaniosis with the nucleosomal histones of Leishmania infantum encoded in DNA vaccine or pulsed in dendritic cells.

    Science.gov (United States)

    Carrión, Javier; Folgueira, Cristina; Alonso, Carlos

    2008-05-12

    Immunization of BALB/c mice with a DNA vaccine encoding the nucleosomal histones from Leishmania infantum resulted in a complete failure of protection against visceral leishmaniosis (VL), whereas the adoptive transfer of bone marrow-derived dendritic cells pulsed with the same pathoantigens plays an essential role in controlling parasite growth in half of the cases. Reduction of the visceral parasite burden seems to be related to low persistence of regulatory T-cells in the spleen from vaccinated mice. These results provide clues for the optimization of this vaccine strategy with the four Leishmania nucleosomal histones against L. infantum infection.

  7. Testing strong interaction theories

    International Nuclear Information System (INIS)

    Ellis, J.

    1979-01-01

    The author discusses possible tests of the current theories of the strong interaction, in particular, quantum chromodynamics. High energy e + e - interactions should provide an excellent means of studying the strong force. (W.D.L.)

  8. Friend of GATA (FOG interacts with the nucleosome remodeling and deacetylase complex (NuRD to support primitive erythropoiesis in Xenopus laevis.

    Directory of Open Access Journals (Sweden)

    Mizuho S Mimoto

    Full Text Available Friend of GATA (FOG plays many diverse roles in adult and embryonic hematopoiesis, however the mechanisms by which it functions and the roles of potential interaction partners are not completely understood. Previous work has shown that overexpression of FOG in Xenopus laevis causes loss of blood suggesting that in contrast to its role in mammals, FOG might normally function to repress erythropoiesis in this species. Using loss-of-function analysis, we demonstrate that FOG is essential to support primitive red blood cell (RBC development in Xenopus. Moreover, we show that it is specifically required to prevent excess apoptosis of circulating primitive RBCs and that in the absence of FOG, the pro-apoptotic gene Bim-1 is strongly upregulated. To identify domains of FOG that are essential for blood development and, conversely, to begin to understand the mechanism by which overexpressed FOG represses primitive erythropoiesis, we asked whether FOG mutants that are unable to interact with known co-factors retain their ability to rescue blood formation in FOG morphants and whether they repress erythropoiesis when overexpressed in wild type embryos. We find that interaction of FOG with the Nucleosome Remodeling and Deacetylase complex (NuRD, but not with C-terminal Binding Protein, is essential for normal primitive RBC development. In contrast, overexpression of all mutant and wild type constructs causes a comparable repression of primitive erythropoiesis. Together, our data suggest that a requirement for FOG and its interaction with NuRD during primitive erythropoiesis are conserved in Xenopus and that loss of blood upon FOG overexpression is due to a dominant-interfering effect.

  9. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers.

    Science.gov (United States)

    Umeyama, Taichi; Ito, Takashi

    2017-10-03

    Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  10. High mobility group protein number17 cross-links primarily to histone H2A in the reconstituted HMG 17 - nucleosome core particle complex

    International Nuclear Information System (INIS)

    Cook, G.R.; Yau, P.; Yasuda, H.; Traut, R.R.; Bradbury, E.M.

    1986-01-01

    The neighbor relationship of lamb thymus High Mobility Group (HMG) protein 17 to native HeLa nucleosome core particle histones in the reconstituted complex has been studied. 125 I-labeled HMG 17 was cross-linking to core histones using the protein-protein cross-linking reagent 2-iminothiolane. Specific cross-linked products were separated on a two-dimensional Triton-acid-urea/SDS gel system, located by autoradiography, excised and quantified. Disulfide bonds in the cross links were then cleaved and the protein constituents were identified by SDS gel electrophoresis. HMG 17 cross-linked primarily to histone H2A while lower levels of cross-linking occurred between HMG 17 and the other histones. In contrast, cross-linking between two HMG 17 molecules bound on the same nucleosome was relatively rare. It is concluded that the same nucleosome was relatively rare. It is concluded that H2A comprises part of the HMG 17 binding site but that HMG 17 is sufficiently elongated and mobile to permit cross-linking to the other histones and to a second HMG 17 molecule. These results are in agreement with the current model for the structure of the nucleosome and the proposed binding sites for HMG 17

  11. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    Directory of Open Access Journals (Sweden)

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  12. Strongly Correlated Topological Insulators

    Science.gov (United States)

    2016-02-03

    Strongly Correlated Topological Insulators In the past year, the grant was used for work in the field of topological phases, with emphasis on finding...surface of topological insulators. In the past 3 years, we have started a new direction, that of fractional topological insulators. These are materials...in which a topologically nontrivial quasi-flat band is fractionally filled and then subject to strong interactions. The views, opinions and/or

  13. Strong Cosmic Censorship

    Science.gov (United States)

    Isenberg, James

    2017-01-01

    The Hawking-Penrose theorems tell us that solutions of Einstein's equations are generally singular, in the sense of the incompleteness of causal geodesics (the paths of physical observers). These singularities might be marked by the blowup of curvature and therefore crushing tidal forces, or by the breakdown of physical determinism. Penrose has conjectured (in his `Strong Cosmic Censorship Conjecture`) that it is generically unbounded curvature that causes singularities, rather than causal breakdown. The verification that ``AVTD behavior'' (marked by the domination of time derivatives over space derivatives) is generically present in a family of solutions has proven to be a useful tool for studying model versions of Strong Cosmic Censorship in that family. I discuss some of the history of Strong Cosmic Censorship, and then discuss what is known about AVTD behavior and Strong Cosmic Censorship in families of solutions defined by varying degrees of isometry, and discuss recent results which we believe will extend this knowledge and provide new support for Strong Cosmic Censorship. I also comment on some of the recent work on ``Weak Null Singularities'', and how this relates to Strong Cosmic Censorship.

  14. The nucleosome (histone-DNA complex) is the TLR9-specific immunostimulatory component of Plasmodium falciparum that activates DCs.

    Science.gov (United States)

    Gowda, Nagaraj M; Wu, Xianzhu; Gowda, D Channe

    2011-01-01

    The systemic clinical symptoms of Plasmodium falciparum infection such as fever and chills correspond to the proinflammatory cytokines produced in response to the parasite components released during the synchronized rupture of schizonts. We recently demonstrated that, among the schizont-released products, merozoites are the predominant components that activate dendritic cells (DCs) by TLR9-specific recognition to induce the maturation of cells and to produce proinflammatory cytokines. We also demonstrated that DNA is the active constituent and that formation of a DNA-protein complex is essential for the entry of parasite DNA into cells for recognition by TLR9. However, the nature of endogenous protein-DNA complex in the parasite is not known. In this study, we show that parasite nucleosome constitute the major protein-DNA complex involved in the activation of DCs by parasite nuclear material. The parasite components were fractionated into the nuclear and non-nuclear materials. The nuclear material was further fractionated into chromatin and the proteins loosely bound to chromatin. Polynucleosomes and oligonucleosomes were prepared from the chromatin. These were tested for their ability to activate DCs obtained by the FLT3 ligand differentiation of bone marrow cells from the wild type, and TLR2(-/-), TLR9(-/-) and MyD88(-/-) mice. DCs stimulated with the nuclear material and polynucleosomes as well as mono- and oligonucleosomes efficiently induced the production of proinflammatory cytokines in a TLR9-dependent manner, demonstrating that nucleosomes (histone-DNA complex) represent the major TLR9-specific DC-immunostimulatory component of the malaria parasite nuclear material. Thus, our data provide a significant insight into the activation of DCs by malaria parasites and have important implications for malaria vaccine development.

  15. The nucleosome (histone-DNA complex is the TLR9-specific immunostimulatory component of Plasmodium falciparum that activates DCs.

    Directory of Open Access Journals (Sweden)

    Nagaraj M Gowda

    Full Text Available The systemic clinical symptoms of Plasmodium falciparum infection such as fever and chills correspond to the proinflammatory cytokines produced in response to the parasite components released during the synchronized rupture of schizonts. We recently demonstrated that, among the schizont-released products, merozoites are the predominant components that activate dendritic cells (DCs by TLR9-specific recognition to induce the maturation of cells and to produce proinflammatory cytokines. We also demonstrated that DNA is the active constituent and that formation of a DNA-protein complex is essential for the entry of parasite DNA into cells for recognition by TLR9. However, the nature of endogenous protein-DNA complex in the parasite is not known. In this study, we show that parasite nucleosome constitute the major protein-DNA complex involved in the activation of DCs by parasite nuclear material. The parasite components were fractionated into the nuclear and non-nuclear materials. The nuclear material was further fractionated into chromatin and the proteins loosely bound to chromatin. Polynucleosomes and oligonucleosomes were prepared from the chromatin. These were tested for their ability to activate DCs obtained by the FLT3 ligand differentiation of bone marrow cells from the wild type, and TLR2(-/-, TLR9(-/- and MyD88(-/- mice. DCs stimulated with the nuclear material and polynucleosomes as well as mono- and oligonucleosomes efficiently induced the production of proinflammatory cytokines in a TLR9-dependent manner, demonstrating that nucleosomes (histone-DNA complex represent the major TLR9-specific DC-immunostimulatory component of the malaria parasite nuclear material. Thus, our data provide a significant insight into the activation of DCs by malaria parasites and have important implications for malaria vaccine development.

  16. The NF-κB-like factor DIF could explain some positive effects of a mild stress on longevity, behavioral aging, and resistance to strong stresses in Drosophila melanogaster.

    Science.gov (United States)

    Le Bourg, Eric; Malod, Kévin; Massou, Isabelle

    2012-08-01

    A mild cold stress can have positive effects on longevity, aging and resistance to severe stresses in flies (heat, cold, fungal infection), but the causes of these effects remain elusive. In order to know whether these effects could be explained by the DIF transcription factor (a NF-κB-like factor in the Toll innate immunity pathway), the Dif ( 1 ) mutant and its control cn bw strain were subjected to a pretreatment by cold. The DIF factor seems to be involved in the response to fungal infection after a mild cold stress and in the resistance to heat. However, DIF seems to have no role in the increased longevity of non-infected flies and resistance to a severe cold shock, because the cold pretreatment slightly increased longevity in females, mainly in Dif ( 1 ) ones, and resistance to a long cold shock in both sexes of these strains.

  17. Strong Arcwise Connectedness

    OpenAIRE

    Espinoza, Benjamin; Gartside, Paul; Kovan-Bakan, Merve; Mamatelashvili, Ana

    2012-01-01

    A space is `n-strong arc connected' (n-sac) if for any n points in the space there is an arc in the space visiting them in order. A space is omega-strong arc connected (omega-sac) if it is n-sac for all n. We study these properties in finite graphs, regular continua, and rational continua. There are no 4-sac graphs, but there are 3-sac graphs and graphs which are 2-sac but not 3-sac. For every n there is an n-sac regular continuum, but no regular continuum is omega-sac. There is an omega-sac ...

  18. Abortion: Strong's counterexamples fail

    DEFF Research Database (Denmark)

    Di Nucci, Ezio

    2009-01-01

    This paper shows that the counterexamples proposed by Strong in 2008 in the Journal of Medical Ethics to Marquis's argument against abortion fail. Strong's basic idea is that there are cases--for example, terminally ill patients--where killing an adult human being is prima facie seriously morally......'s scenarios have some valuable future or admitted that killing them is not seriously morally wrong. Finally, if "valuable future" is interpreted as referring to objective standards, one ends up with implausible and unpalatable moral claims....

  19. A strong comeback

    International Nuclear Information System (INIS)

    Marier, D.

    1992-01-01

    This article presents the results of a financial rankings survey which show a strong economic activity in the independent energy industry. The topics of the article include advisor turnover, overseas banks, and the increase in public offerings. The article identifies the top project finance investors for new projects and restructurings and rankings for lenders

  20. Strong Electroweak Symmetry Breaking

    CERN Document Server

    Grinstein, Benjamin

    2011-01-01

    Models of spontaneous breaking of electroweak symmetry by a strong interaction do not have fine tuning/hierarchy problem. They are conceptually elegant and use the only mechanism of spontaneous breaking of a gauge symmetry that is known to occur in nature. The simplest model, minimal technicolor with extended technicolor interactions, is appealing because one can calculate by scaling up from QCD. But it is ruled out on many counts: inappropriately low quark and lepton masses (or excessive FCNC), bad electroweak data fits, light scalar and vector states, etc. However, nature may not choose the minimal model and then we are stuck: except possibly through lattice simulations, we are unable to compute and test the models. In the LHC era it therefore makes sense to abandon specific models (of strong EW breaking) and concentrate on generic features that may indicate discovery. The Technicolor Straw Man is not a model but a parametrized search strategy inspired by a remarkable generic feature of walking technicolor,...

  1. Plasmons in strong superconductors

    International Nuclear Information System (INIS)

    Baldo, M.; Ducoin, C.

    2011-01-01

    We present a study of the possible plasmon excitations that can occur in systems where strong superconductivity is present. In these systems the plasmon energy is comparable to or smaller than the pairing gap. As a prototype of these systems we consider the proton component of Neutron Star matter just below the crust when electron screening is not taken into account. For the realistic case we consider in detail the different aspects of the elementary excitations when the proton, electron components are considered within the Random-Phase Approximation generalized to the superfluid case, while the influence of the neutron component is considered only at qualitative level. Electron screening plays a major role in modifying the proton spectrum and spectral function. At the same time the electron plasmon is strongly modified and damped by the indirect coupling with the superfluid proton component, even at moderately low values of the gap. The excitation spectrum shows the interplay of the different components and their relevance for each excitation modes. The results are relevant for neutrino physics and thermodynamical processes in neutron stars. If electron screening is neglected, the spectral properties of the proton component show some resemblance with the physical situation in high-T c superconductors, and we briefly discuss similarities and differences in this connection. In a general prospect, the results of the study emphasize the role of Coulomb interaction in strong superconductors.

  2. Positional games

    CERN Document Server

    Hefetz, Dan; Stojaković, Miloš; Szabó, Tibor

    2014-01-01

    This text serves as a thorough introduction to the rapidly developing field of positional games. This area constitutes an important branch of combinatorics, whose aim it is to systematically develop an extensive mathematical basis for a variety of two-player perfect information games. These range from such popular games as Tic-Tac-Toe and Hex to purely abstract games played on graphs and hypergraphs. The subject of positional games is strongly related to several other branches of combinatorics such as Ramsey theory, extremal graph and set theory, and the probabilistic method. These notes cover a variety of topics in positional games, including both classical results and recent important developments. They are presented in an accessible way and are accompanied by exercises of varying difficulty, helping the reader to better understand the theory. The text will benefit both researchers and graduate students in combinatorics and adjacent fields.

  3. Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells

    Directory of Open Access Journals (Sweden)

    Sharma Shikhar

    2012-01-01

    Full Text Available Abstract Background DNA methylation, histone modifications and nucleosome occupancy act in concert for regulation of gene expression patterns in mammalian cells. Recently, G9a, a H3K9 methyltransferase, has been shown to play a role in establishment of DNA methylation at embryonic gene targets in ES cells through recruitment of de novo DNMT3A/3B enzymes. However, whether G9a plays a similar role in maintenance of DNA methylation in somatic cells is still unclear. Results Here we show that G9a is not essential for maintenance of DNA methylation in somatic cells. Knockdown of G9a has no measurable effect on DNA methylation levels at G9a-target loci. DNMT3A/3B remain stably anchored to nucleosomes containing methylated DNA even in the absence of G9a, ensuring faithful propagation of methylated states in cooperation with DNMT1 through somatic divisions. Moreover, G9a also associates with nucleosomes in a DNMT3A/3B and DNA methylation-independent manner. However, G9a knockdown synergizes with pharmacologic inhibition of DNMTs resulting in increased hypomethylation and inhibition of cell proliferation. Conclusions Taken together, these data suggest that G9a is not involved in maintenance of DNA methylation in somatic cells but might play a role in re-initiation of de novo methylation after treatment with hypomethylating drugs, thus serving as a potential target for combinatorial treatments strategies involving DNMTs inhibitors.

  4. Strong-coupling approximations

    International Nuclear Information System (INIS)

    Abbott, R.B.

    1984-03-01

    Standard path-integral techniques such as instanton calculations give good answers for weak-coupling problems, but become unreliable for strong-coupling. Here we consider a method of replacing the original potential by a suitably chosen harmonic oscillator potential. Physically this is motivated by the fact that potential barriers below the level of the ground-state energy of a quantum-mechanical system have little effect. Numerically, results are good, both for quantum-mechanical problems and for massive phi 4 field theory in 1 + 1 dimensions. 9 references, 6 figures

  5. Strong interaction and QFD

    International Nuclear Information System (INIS)

    Ebata, T.

    1981-01-01

    With an assumed weak multiplet structure for bosonic hadrons, which is consistent with the ΔI = 1/2 rule, it is shown that the strong interaction effective hamiltonian is compatible with the weak SU(2) x U(1) gauge transformation. Especially the rho-meson transforms as a triplet under SU(2)sub(w), and this is the origin of the rho-photon analogy. It is also shown that the existence of the non-vanishing Cabibbo angle is a necessary condition for the absence of the exotic hadrons. (orig.)

  6. Strong Coupling Holography

    CERN Document Server

    Dvali, Gia

    2009-01-01

    We show that whenever a 4-dimensional theory with N particle species emerges as a consistent low energy description of a 3-brane embedded in an asymptotically-flat (4+d)-dimensional space, the holographic scale of high-dimensional gravity sets the strong coupling scale of the 4D theory. This connection persists in the limit in which gravity can be consistently decoupled. We demonstrate this effect for orbifold planes, as well as for the solitonic branes and string theoretic D-branes. In all cases the emergence of a 4D strong coupling scale from bulk holography is a persistent phenomenon. The effect turns out to be insensitive even to such extreme deformations of the brane action that seemingly shield 4D theory from the bulk gravity effects. A well understood example of such deformation is given by large 4D Einstein term in the 3-brane action, which is known to suppress the strength of 5D gravity at short distances and change the 5D Newton's law into the four-dimensional one. Nevertheless, we observe that the ...

  7. Dynamics of gene expression with positive feedback to histone modifications at bivalent domains

    Science.gov (United States)

    Huang, Rongsheng; Lei, Jinzhi

    2018-03-01

    Experiments have shown that in embryonic stem cells, the promoters of many lineage-control genes contain “bivalent domains”, within which the nucleosomes possess both active (H3K4me3) and repressive (H3K27me3) marks. Such bivalent modifications play important roles in maintaining pluripotency in embryonic stem cells. Here, to investigate gene expression dynamics when there are regulations in bivalent histone modifications and random partition in cell divisions, we study how positive feedback to histone methylation/demethylation controls the transition dynamics of the histone modification patterns along with cell cycles. We constructed a computational model that includes dynamics of histone marks, three-stage chromatin state transitions, transcription and translation, feedbacks from protein product to enzymes to regulate the addition and removal of histone marks, and the inheritance of nucleosome state between cell cycles. The model reveals how dynamics of both nucleosome state transition and gene expression are dependent on the enzyme activities and feedback regulations. Results show that the combination of stochastic histone modification at each cell division and the deterministic feedback regulation work together to adjust the dynamics of chromatin state transition in stem cell regenerations.

  8. LIGO: The strong belief

    CERN Multimedia

    Antonella Del Rosso

    2016-01-01

    Twenty years of designing, building and testing a number of innovative technologies, with the strong belief that the endeavour would lead to a historic breakthrough. The Bulletin publishes an abstract of the Courier’s interview with Barry Barish, one of the founding fathers of LIGO.   The plots show the signals of gravitational waves detected by the twin LIGO observatories at Livingston, Louisiana, and Hanford, Washington. (Image: Caltech/MIT/LIGO Lab) On 11 February, the Laser Interferometer Gravitational-Wave Observatory (LIGO) and Virgo collaborations published a historic paper in which they showed a gravitational signal emitted by the merger of two black holes. These results come after 20 years of hard work by a large collaboration of scientists operating the two LIGO observatories in the US. Barry Barish, Linde Professor of Physics, Emeritus at the California Institute of Technology and former Director of the Global Design Effort for the Internat...

  9. Interaction of nucleosome assembly proteins abolishes nuclear localization of DGK{zeta} by attenuating its association with importins

    Energy Technology Data Exchange (ETDEWEB)

    Okada, Masashi; Hozumi, Yasukazu [Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Yamagata 990-9585 (Japan); Ichimura, Tohru [Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Hachioji 192-0397 (Japan); Tanaka, Toshiaki; Hasegawa, Hiroshi; Yamamoto, Masakazu; Takahashi, Nobuya [Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Yamagata 990-9585 (Japan); Iseki, Ken [Department of Emergency and Critical Care Medicine, Yamagata University School of Medicine, Yamagata 990-9585 (Japan); Yagisawa, Hitoshi [Laboratory of Biological Signaling, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297 (Japan); Shinkawa, Takashi; Isobe, Toshiaki [Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Hachioji 192-0397 (Japan); Goto, Kaoru, E-mail: kgoto@med.id.yamagata-u.ac.jp [Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Yamagata 990-9585 (Japan)

    2011-12-10

    Diacylglycerol kinase (DGK) is involved in the regulation of lipid-mediated signal transduction through the metabolism of a second messenger diacylglycerol. Of the DGK family, DGK{zeta}, which contains a nuclear localization signal, localizes mainly to the nucleus but translocates to the cytoplasm under pathological conditions. However, the detailed mechanism of translocation and its functional significance remain unclear. To elucidate these issues, we used a proteomic approach to search for protein targets that interact with DGK{zeta}. Results show that nucleosome assembly protein (NAP) 1-like 1 (NAP1L1) and NAP1-like 4 (NAP1L4) are identified as novel DGK{zeta} binding partners. NAP1Ls constitutively shuttle between the nucleus and the cytoplasm in transfected HEK293 cells. The molecular interaction of DGK{zeta} and NAP1Ls prohibits nuclear import of DGK{zeta} because binding of NAP1Ls to DGK{zeta} blocks import carrier proteins, Qip1 and NPI1, to interact with DGK{zeta}, leading to cytoplasmic tethering of DGK{zeta}. In addition, overexpression of NAP1Ls exerts a protective effect against doxorubicin-induced cytotoxicity. These findings suggest that NAP1Ls are involved in a novel molecular basis for the regulation of nucleocytoplasmic shuttling of DGK{zeta} and provide a clue to examine functional significance of its translocation under pathological conditions.

  10. Splice variants of the SWR1-type nucleosome remodeling factor Domino have distinct functions during Drosophila melanogaster oogenesis.

    Science.gov (United States)

    Börner, Kenneth; Becker, Peter B

    2016-09-01

    SWR1-type nucleosome remodeling factors replace histone H2A by variants to endow chromatin locally with specialized functionality. In Drosophila melanogaster a single H2A variant, H2A.V, combines functions of mammalian H2A.Z and H2A.X in transcription regulation and the DNA damage response. A major role in H2A.V incorporation for the only SWR1-like enzyme in flies, Domino, is assumed but not well documented in vivo. It is also unclear whether the two alternatively spliced isoforms, DOM-A and DOM-B, have redundant or specialized functions. Loss of both DOM isoforms compromises oogenesis, causing female sterility. We systematically explored roles of the two DOM isoforms during oogenesis using a cell type-specific knockdown approach. Despite their ubiquitous expression, DOM-A and DOM-B have non-redundant functions in germline and soma for egg formation. We show that chromatin incorporation of H2A.V in germline and somatic cells depends on DOM-B, whereas global incorporation in endoreplicating germline nurse cells appears to be independent of DOM. By contrast, DOM-A promotes the removal of H2A.V from stage 5 nurse cells. Remarkably, therefore, the two DOM isoforms have distinct functions in cell type-specific development and H2A.V exchange. © 2016. Published by The Company of Biologists Ltd.

  11. Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling.

    Science.gov (United States)

    Harrer, Nadine; Schindler, Christina E M; Bruetzel, Linda K; Forné, Ignasi; Ludwigsen, Johanna; Imhof, Axel; Zacharias, Martin; Lipfert, Jan; Mueller-Planitz, Felix

    2018-02-06

    Chromatin remodeling factors assume critical roles by regulating access to nucleosomal DNA. To determine the architecture of the Drosophila ISWI remodeling enzyme, we developed an integrative structural approach that combines protein cross-linking, mass spectrometry, small-angle X-ray scattering, and computational modeling. The resulting structural model shows the ATPase module in a resting state with both ATPase lobes twisted against each other, providing support for a conformation that was recently trapped by crystallography. The autoinhibiting NegC region does not protrude from the ATPase module as suggested previously. The regulatory NTR domain is located near both ATPase lobes. The full-length enzyme is flexible and can adopt a compact structure in solution with the C-terminal HSS domain packing against the ATPase module. Our data imply a series of conformational changes upon activation of the enzyme and illustrate how the NTR, NegC, and HSS domains contribute to regulation of the ATPase module. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Dual roles of p300 in chromatin assembly and transcriptional activation in cooperation with nucleosome assembly protein 1 in vitro.

    Science.gov (United States)

    Asahara, Hiroshi; Tartare-Deckert, Sophie; Nakagawa, Takeya; Ikehara, Tsuyoshi; Hirose, Fumiko; Hunter, Tony; Ito, Takashi; Montminy, Marc

    2002-05-01

    In a yeast two-hybrid screen to identify proteins that bind to the KIX domain of the coactivator p300, we obtained cDNAs encoding nucleosome assembly protein 1 (NAP-1), a 60-kDa histone H2A-H2B shuttling protein that promotes histone deposition. p300 associates preferentially with the H2A-H2B-bound form of NAP-1 rather than with the unbound form of NAP-1. Formation of NAP-1-p300 complexes was found to increase during S phase, suggesting a potential role for p300 in chromatin assembly. In micrococcal nuclease and supercoiling assays, addition of p300 promoted efficient chromatin assembly in vitro in conjunction with NAP-1 and ATP-utilizing chromatin assembly and remodeling factor; this effect was dependent in part on the intrinsic histone acetyltransferase activity of p300. Surprisingly, NAP-1 potently inhibited acetylation of core histones by p300, suggesting that efficient assembly requires acetylation of either NAP-1 or p300 itself. As p300 acted cooperatively with NAP-1 in stimulating transcription from a chromatin template in vitro, our results suggest a dual role of NAP-1-p300 complexes in promoting chromatin assembly and transcriptional activation.

  13. Transcription factor 19 interacts with histone 3 lysine 4 trimethylation and controls gluconeogenesis via the nucleosome-remodeling-deacetylase complex.

    Science.gov (United States)

    Sen, Sabyasachi; Sanyal, Sulagna; Srivastava, Dushyant Kumar; Dasgupta, Dipak; Roy, Siddhartha; Das, Chandrima

    2017-12-15

    Transcription factor 19 (TCF19) has been reported as a type 1 diabetes-associated locus involved in maintenance of pancreatic β cells through a fine-tuned regulation of cell proliferation and apoptosis. TCF19 also exhibits genomic association with type 2 diabetes, although the precise molecular mechanism remains unknown. It harbors both a plant homeodomain and a forkhead-associated domain implicated in epigenetic recognition and gene regulation, a phenomenon that has remained unexplored. Here, we show that TCF19 selectively interacts with histone 3 lysine 4 trimethylation through its plant homeodomain finger. Knocking down TCF19 under high-glucose conditions affected many metabolic processes, including gluconeogenesis. We found that TCF19 overexpression represses de novo glucose production in HepG2 cells. The transcriptional repression of key genes, induced by TCF19, coincided with NuRD (nucleosome-remodeling-deacetylase) complex recruitment to the promoters of these genes. TCF19 interacted with CHD4 (chromodomain helicase DNA-binding protein 4), which is a part of the NuRD complex, in a glucose concentration-independent manner. In summary, our results show that TCF19 interacts with an active transcription mark and recruits a co-repressor complex to regulate gluconeogenic gene expression in HepG2 cells. Our study offers critical insights into the molecular mechanisms of transcriptional regulation of gluconeogenesis and into the roles of chromatin readers in metabolic homeostasis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. John Strong (1941 - 2006)

    CERN Multimedia

    Wickens, F

    Our friend and colleague John Strong was cruelly taken from us by a brain tumour on Monday 31st July, a few days before his 65th birthday John started his career working with a group from Westfield College, under the leadership of Ted Bellamy. He obtained his PhD and spent the early part of his career on experiments at Rutherford Appleton Laboratory (RAL), but after the early 1970s his research was focussed on experiments in CERN. Over the years he made a number of notable contributions to experiments in CERN: The Omega spectrometer adopted a system John had originally developed for experiments at RAL using vidicon cameras to record the sparks in the spark chambers; He contributed to the success of NA1 and NA7, where he became heavily involved in the electronic trigger systems; He was responsible for the second level trigger system for the ALEPH detector and spent five years leading a team that designed and built the system, which ran for twelve years with only minor interventions. Following ALEPH he tur...

  15. Stirring Strongly Coupled Plasma

    CERN Document Server

    Fadafan, Kazem Bitaghsir; Rajagopal, Krishna; Wiedemann, Urs Achim

    2009-01-01

    We determine the energy it takes to move a test quark along a circle of radius L with angular frequency w through the strongly coupled plasma of N=4 supersymmetric Yang-Mills (SYM) theory. We find that for most values of L and w the energy deposited by stirring the plasma in this way is governed either by the drag force acting on a test quark moving through the plasma in a straight line with speed v=Lw or by the energy radiated by a quark in circular motion in the absence of any plasma, whichever is larger. There is a continuous crossover from the drag-dominated regime to the radiation-dominated regime. In the crossover regime we find evidence for significant destructive interference between energy loss due to drag and that due to radiation as if in vacuum. The rotating quark thus serves as a model system in which the relative strength of, and interplay between, two different mechanisms of parton energy loss is accessible via a controlled classical gravity calculation. We close by speculating on the implicati...

  16. Strong-interaction nonuniversality

    International Nuclear Information System (INIS)

    Volkas, R.R.; Foot, R.; He, X.; Joshi, G.C.

    1989-01-01

    The universal QCD color theory is extended to an SU(3) 1 direct product SU(3) 2 direct product SU(3) 3 gauge theory, where quarks of the ith generation transform as triplets under SU(3)/sub i/ and singlets under the other two factors. The usual color group is then identified with the diagonal subgroup, which remains exact after symmetry breaking. The gauge bosons associated with the 16 broken generators then form two massive octets under ordinary color. The interactions between quarks and these heavy gluonlike particles are explicitly nonuniversal and thus an exploration of their physical implications allows us to shed light on the fundamental issue of strong-interaction universality. Nonuniversality and weak flavor mixing are shown to generate heavy-gluon-induced flavor-changing neutral currents. The phenomenology of these processes is studied, as they provide the major experimental constraint on the extended theory. Three symmetry-breaking scenarios are presented. The first has color breaking occurring at the weak scale, while the second and third divorce the two scales. The third model has the interesting feature of radiatively induced off-diagonal Kobayashi-Maskawa matrix elements

  17. Vaccination with a plasmid DNA cocktail encoding the nucleosomal histones of Leishmania confers protection against murine cutaneous leishmaniosis.

    Science.gov (United States)

    Iborra, Salvador; Soto, Manuel; Carrión, Javier; Alonso, Carlos; Requena, Jose M

    2004-09-28

    Leishmania histones are relevant immunogens for the host immune system during both Leishmania infection and disease. In the present paper we have evaluated the prophylactic value of the four Leishmania infantum histones forming the nucleosomal core in the murine model of cutaneous leishmaniasis. In a first stage, the immune response elicited by the intramuscular injection of a mixture of four plasmid DNAs, encoding the L. infantum histones H2A, H2B, H3 and H4, was determined in BALB/c mice. It was found that the immunized animals developed a specific Th1 immune response, which was associated with an antigen-specific production of interferon (IFN-gamma) and a limited humoral response against histones (dominated by antibodies of the IgG2a isotype). According to the pure Th1-type immune response elicited by the DNA vaccination with Leishmania histones, vaccinated mice showed a solid immunity that efficiently controlled the Leishmania major infection. The protection in mice vaccinated with histone-DNAs was associated with a low humoral response against leishmanial antigens, an enhanced IFN-gamma production and little, if any, IL-4 production. The relative contribution of both CD8(+) and CD4(+) T cells to the IFN-gamma production, and the IL-12 dependence were also evaluated. All these data indicated that DNA vaccination with Leishmania histones genes results in a specific Th1-like response during L. major infection, and that both CD4(+) and CD8(+) T cells contribute to the resistance of vaccinated mice to cutaneous leishmaniasis.

  18. Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails.

    Science.gov (United States)

    Stützer, Alexandra; Liokatis, Stamatios; Kiesel, Anja; Schwarzer, Dirk; Sprangers, Remco; Söding, Johannes; Selenko, Philipp; Fischle, Wolfgang

    2016-01-21

    Post-translational histone modifications and linker histone incorporation regulate chromatin structure and genome activity. How these systems interface on a molecular level is unclear. Using biochemistry and NMR spectroscopy, we deduced mechanistic insights into the modification behavior of N-terminal histone H3 tails in different nucleosomal contexts. We find that linker histones generally inhibit modifications of different H3 sites and reduce H3 tail dynamics in nucleosomes. These effects are caused by modulations of electrostatic interactions of H3 tails with linker DNA and largely depend on the C-terminal domains of linker histones. In agreement, linker histone occupancy and H3 tail modifications segregate on a genome-wide level. Charge-modulating modifications such as phosphorylation and acetylation weaken transient H3 tail-linker DNA interactions, increase H3 tail dynamics, and, concomitantly, enhance general modifiability. We propose that alterations of H3 tail-linker DNA interactions by linker histones and charge-modulating modifications execute basal control mechanisms of chromatin function. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Vaccination with Leishmania infantum acidic ribosomal P0 but not with nucleosomal histones proteins controls Leishmania infantum infection in hamsters.

    Science.gov (United States)

    Pereira, Lais; Abbehusen, Melissa; Teixeira, Clarissa; Cunha, Jurema; Nascimento, Ivan P; Fukutani, Kyioshi; dos-Santos, Washington; Barral, Aldina; de Oliveira, Camila Indiani; Barral-Netto, Manoel; Soto, Manoel; Brodskyn, Cláudia Ida

    2015-02-01

    Several intracellular Leishmania antigens have been identified in order to find a potential vaccine capable of conferring long lasting protection against Leishmania infection. Histones and Acid Ribosomal proteins are already known to induce an effective immune response and have successfully been tested in the cutaneous leishmaniasis mouse model. Here, we investigate the protective ability of L. infantum nucleosomal histones (HIS) and ribosomal acidic protein P0 (LiP0) against L. infantum infection in the hamster model of visceral leishmaniasis using two different strategies: homologous (plasmid DNA only) or heterologous immunization (plasmid DNA plus recombinant protein and adjuvant). Immunization with both antigens using the heterologous strategy presented a high antibody production level while the homologous strategy immunized group showed predominantly a cellular immune response with parasite load reduction. The pcDNA-LiP0 immunized group showed increased expression ratio of IFN-γ/IL-10 and IFN-γ/TGF-β in the lymph nodes before challenge. Two months after infection hamsters immunized with the empty plasmid presented a pro-inflammatory immune response in the early stages of infection with increased expression ratio of IFN-γ/IL-10 and IFN-γ/TGF-β, whereas hamsters immunized with pcDNA-HIS presented an increase only in the ratio IFN-γ/ TGF-β. On the other hand, hamsters immunized with LiP0 did not present any increase in the IFN-γ/TGF-β and IFN-γ/IL-10 ratio independently of the immunization strategy used. Conversely, five months after infection, hamsters immunized with HIS maintained a pro-inflammatory immune response (ratio IFN-γ/ IL-10) while pcDNA-LiP0 immunized hamsters continued showing a balanced cytokine profile of pro and anti-inflammatory cytokines. Moreover we observed a significant reduction in parasite load in the spleen, liver and lymph node in this group compared with controls. Our results suggest that vaccination with L. infantum LiP0

  20. Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles.

    Science.gov (United States)

    Yang, Ye; Lyubartsev, Alexander P; Korolev, Nikolay; Nordenskiöld, Lars

    2009-03-18

    Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were constructed to represent different extents of covalent modification on the histone tails: (nonmodified) recombinant (rNCP), acetylated (aNCP), and acetylated and phosphorylated (paNCP). The simulation cell contained 10 NCPs in a dielectric continuum with explicit mobile counterions and added salt. The NCP-NCP interaction is decisively dependent on the modification state of the histone tails and on salt conditions. Increasing the monovalent salt concentration (KCl) from salt-free to physiological concentration leads to NCP aggregation in solution for rNCP, whereas NCP associates are observed only occasionally in the system of aNCPs. In the presence of divalent salt (Mg(2+)), rNCPs form dense stable aggregates, whereas aNCPs form aggregates less frequently. Aggregates are formed via histone-tail bridging and accumulation of counterions in the regions of NCP-NCP contacts. The paNCPs do not show NCP-NCP interaction upon addition of KCl or in the presence of Mg(2+). Simulations for systems with a gradual substitution of K(+) for Mg(2+), to mimic the Mg(2+) titration of an NCP solution, were performed. The rNCP system showed stronger aggregation that occurred at lower concentrations of added Mg(2+), compared to the aNCP system. Additional molecular dynamics simulations performed with a single NCP in the simulation cell showed that detachment of the tails from the NCP core was modest under a wide range of salt concentrations. This implies that salt-induced tail dissociation of the

  1. Quantum electrodynamics of strong fields

    International Nuclear Information System (INIS)

    Greiner, W.

    1983-01-01

    Quantum Electrodynamics of Strong Fields provides a broad survey of the theoretical and experimental work accomplished, presenting papers by a group of international researchers who have made significant contributions to this developing area. Exploring the quantum theory of strong fields, the volume focuses on the phase transition to a charged vacuum in strong electric fields. The contributors also discuss such related topics as QED at short distances, precision tests of QED, nonperturbative QCD and confinement, pion condensation, and strong gravitational fields In addition, the volume features a historical paper on the roots of quantum field theory in the history of quantum physics by noted researcher Friedrich Hund

  2. Strong WW Interaction at LHC

    Energy Technology Data Exchange (ETDEWEB)

    Pelaez, Jose R

    1998-12-14

    We present a brief pedagogical introduction to the Effective Electroweak Chiral Lagrangians, which provide a model independent description of the WW interactions in the strong regime. When it is complemented with some unitarization or a dispersive approach, this formalism allows the study of the general strong scenario expected at the LHC, including resonances.

  3. Strong-back safety latch

    International Nuclear Information System (INIS)

    DeSantis, G.N.

    1995-01-01

    The calculation decides the integrity of the safety latch that will hold the strong-back to the pump during lifting. The safety latch will be welded to the strong-back and will latch to a 1.5-in. dia cantilever rod welded to the pump baseplate. The static and dynamic analysis shows that the safety latch will hold the strong-back to the pump if the friction clamps fail and the pump become free from the strong-back. Thus, the safety latch will meet the requirements of the Lifting and Rigging Manual for under the hook lifting for static loading; it can withstand shock loads from the strong-back falling 0.25 inch

  4. Strong-back safety latch

    Energy Technology Data Exchange (ETDEWEB)

    DeSantis, G.N.

    1995-03-06

    The calculation decides the integrity of the safety latch that will hold the strong-back to the pump during lifting. The safety latch will be welded to the strong-back and will latch to a 1.5-in. dia cantilever rod welded to the pump baseplate. The static and dynamic analysis shows that the safety latch will hold the strong-back to the pump if the friction clamps fail and the pump become free from the strong-back. Thus, the safety latch will meet the requirements of the Lifting and Rigging Manual for under the hook lifting for static loading; it can withstand shock loads from the strong-back falling 0.25 inch.

  5. Titanium: light, strong, and white

    Science.gov (United States)

    Woodruff, Laurel; Bedinger, George

    2013-01-01

    Titanium (Ti) is a strong silver-gray metal that is highly resistant to corrosion and is chemically inert. It is as strong as steel but 45 percent lighter, and it is twice as strong as aluminum but only 60 percent heavier. Titanium dioxide (TiO2) has a very high refractive index, which means that it has high light-scattering ability. As a result, TiO2 imparts whiteness, opacity, and brightness to many products. ...Because of the unique physical properties of titanium metal and the whiteness provided by TiO2, titanium is now used widely in modern industrial societies.

  6. The SNAP Strong Lens Survey

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, P.

    2005-01-03

    Basic considerations of lens detection and identification indicate that a wide field survey of the types planned for weak lensing and Type Ia SNe with SNAP are close to optimal for the optical detection of strong lenses. Such a ''piggy-back'' survey might be expected even pessimistically to provide a catalogue of a few thousand new strong lenses, with the numbers dominated by systems of faint blue galaxies lensed by foreground ellipticals. After sketching out our strategy for detecting and measuring these galaxy lenses using the SNAP images, we discuss some of the scientific applications of such a large sample of gravitational lenses: in particular we comment on the partition of information between lens structure, the source population properties and cosmology. Understanding this partitioning is key to assessing strong lens cosmography's value as a cosmological probe.

  7. Strong coupling phase in QED

    International Nuclear Information System (INIS)

    Aoki, Ken-ichi

    1988-01-01

    Existence of a strong coupling phase in QED has been suggested in solutions of the Schwinger-Dyson equation and in Monte Carlo simulation of lattice QED. In this article we recapitulate the previous arguments, and formulate the problem in the modern framework of the renormalization theory, Wilsonian renormalization. This scheme of renormalization gives the best understanding of the basic structure of a field theory especially when it has a multi-phase structure. We resolve some misleading arguments in the previous literature. Then we set up a strategy to attack the strong phase, if any. We describe a trial; a coupled Schwinger-Dyson equation. Possible picture of the strong coupling phase QED is presented. (author)

  8. Position Information

    Data.gov (United States)

    Social Security Administration — The Position Information Data Asset provides the ability to search for active SSA position descriptions using various search criteria. An individual may search by PD...

  9. Positioning consumption

    DEFF Research Database (Denmark)

    Halkier, Bente; Keller, Margit

    2014-01-01

    This article analyses the ways in which media discourses become a part of contested consumption activities. We apply a positioning perspective with practice theory to focus on how practitioners relate to media discourse as a symbolic resource in their everyday practices. A typology of performance...... positionings emerges based on empirical examples of research in parent–children consumption. Positionings are flexible discursive fixations of the relationship between the performances of the practitioner, other practitioners, media discourse and consumption activities. The basic positioning types...

  10. Positive Psychology

    Science.gov (United States)

    Peterson, Christopher

    2009-01-01

    Positive psychology is a deliberate correction to the focus of psychology on problems. Positive psychology does not deny the difficulties that people may experience but does suggest that sole attention to disorder leads to an incomplete view of the human condition. Positive psychologists concern themselves with four major topics: (1) positive…

  11. Strong Decomposition of Random Variables

    DEFF Research Database (Denmark)

    Hoffmann-Jørgensen, Jørgen; Kagan, Abram M.; Pitt, Loren D.

    2007-01-01

    A random variable X is stongly decomposable if X=Y+Z where Y=Φ(X) and Z=X-Φ(X) are independent non-degenerated random variables (called the components). It is shown that at least one of the components is singular, and we derive a necessary and sufficient condition for strong decomposability...

  12. Strong interaction at finite temperature

    Indian Academy of Sciences (India)

    Abstract. We review two methods discussed in the literature to determine the effective parameters of strongly interacting particles as they move through a heat bath. The first one is the general method of chiral perturbation theory, which may be readily applied to this problem. The other is the method of thermal QCD sum rules ...

  13. Strong-strong beam-beam simulation on parallel computer

    Energy Technology Data Exchange (ETDEWEB)

    Qiang, Ji

    2004-08-02

    The beam-beam interaction puts a strong limit on the luminosity of the high energy storage ring colliders. At the interaction points, the electromagnetic fields generated by one beam focus or defocus the opposite beam. This can cause beam blowup and a reduction of luminosity. An accurate simulation of the beam-beam interaction is needed to help optimize the luminosity in high energy colliders.

  14. Strong-strong beam-beam simulation on parallel computer

    International Nuclear Information System (INIS)

    Qiang, Ji

    2004-01-01

    The beam-beam interaction puts a strong limit on the luminosity of the high energy storage ring colliders. At the interaction points, the electromagnetic fields generated by one beam focus or defocus the opposite beam. This can cause beam blowup and a reduction of luminosity. An accurate simulation of the beam-beam interaction is needed to help optimize the luminosity in high energy colliders

  15. Ubiquitous positioning

    CERN Document Server

    Mannings, Robin

    2008-01-01

    This groundbreaking resource offers a practical, in-depth understanding of Ubiquitous Positioning - positioning systems that identify the location and position of people, vehicles and objects in time and space in the digitized networked economy. The future and growth of ubiquitous positioning will be fueled by the convergence of many other areas of technology, from mobile telematics, Internet technology, and location systems, to sensing systems, geographic information systems, and the semantic web. This first-of-its-kind volume explores ubiquitous positioning from a convergence perspective, of

  16. PREFACE: Strongly correlated electron systems Strongly correlated electron systems

    Science.gov (United States)

    Saxena, Siddharth S.; Littlewood, P. B.

    2012-07-01

    This special section is dedicated to the Strongly Correlated Electron Systems Conference (SCES) 2011, which was held from 29 August-3 September 2011, in Cambridge, UK. SCES'2011 is dedicated to 100 years of superconductivity and covers a range of topics in the area of strongly correlated systems. The correlated electronic and magnetic materials featured include f-electron based heavy fermion intermetallics and d-electron based transition metal compounds. The selected papers derived from invited presentations seek to deepen our understanding of the rich physical phenomena that arise from correlation effects. The focus is on quantum phase transitions, non-Fermi liquid phenomena, quantum magnetism, unconventional superconductivity and metal-insulator transitions. Both experimental and theoretical work is presented. Based on fundamental advances in the understanding of electronic materials, much of 20th century materials physics was driven by miniaturisation and integration in the electronics industry to the current generation of nanometre scale devices. The achievements of this industry have brought unprecedented advances to society and well-being, and no doubt there is much further to go—note that this progress is founded on investments and studies in the fundamentals of condensed matter physics from more than 50 years ago. Nevertheless, the defining challenges for the 21st century will lie in the discovery in science, and deployment through engineering, of technologies that can deliver the scale needed to have an impact on the sustainability agenda. Thus the big developments in nanotechnology may lie not in the pursuit of yet smaller transistors, but in the design of new structures that can revolutionise the performance of solar cells, batteries, fuel cells, light-weight structural materials, refrigeration, water purification, etc. The science presented in the papers of this special section also highlights the underlying interest in energy-dense materials, which

  17. Positioning consumption

    DEFF Research Database (Denmark)

    Halkier, Bente; Keller, Margit

    2014-01-01

    This article analyses the ways in which media discourses become a part of contested consumption activities. We apply a positioning perspective with practice theory to focus on how practitioners relate to media discourse as a symbolic resource in their everyday practices. A typology of performance...... positionings emerges based on empirical examples of research in parent–children consumption. Positionings are flexible discursive fixations of the relationship between the performances of the practitioner, other practitioners, media discourse and consumption activities. The basic positioning types...... are the practice maintenance and the practice change position, with different sorts of adapting in between. Media discourse can become a resource for a resistant position against social control or for an appropriating position in favour of space for action. Regardless of the current relation to a particular media...

  18. Strongly correlated systems experimental techniques

    CERN Document Server

    Mancini, Ferdinando

    2015-01-01

    The continuous evolution and development of experimental techniques is at the basis of any fundamental achievement in modern physics. Strongly correlated systems (SCS), more than any other, need to be investigated through the greatest variety of experimental techniques in order to unveil and crosscheck the numerous and puzzling anomalous behaviors characterizing them. The study of SCS fostered the improvement of many old experimental techniques, but also the advent of many new ones just invented in order to analyze the complex behaviors of these systems. Many novel materials, with functional properties emerging from macroscopic quantum behaviors at the frontier of modern research in physics, chemistry and materials science, belong to this class of systems. The volume presents a representative collection of the modern experimental techniques specifically tailored for the analysis of strongly correlated systems. Any technique is presented in great detail by its own inventor or by one of the world-wide recognize...

  19. Strongly Correlated Systems Theoretical Methods

    CERN Document Server

    Avella, Adolfo

    2012-01-01

    The volume presents, for the very first time, an exhaustive collection of those modern theoretical methods specifically tailored for the analysis of Strongly Correlated Systems. Many novel materials, with functional properties emerging from macroscopic quantum behaviors at the frontier of modern research in physics, chemistry and materials science, belong to this class of systems. Any technique is presented in great detail by its own inventor or by one of the world-wide recognized main contributors. The exposition has a clear pedagogical cut and fully reports on the most relevant case study where the specific technique showed to be very successful in describing and enlightening the puzzling physics of a particular strongly correlated system. The book is intended for advanced graduate students and post-docs in the field as textbook and/or main reference, but also for other researchers in the field who appreciates consulting a single, but comprehensive, source or wishes to get acquainted, in a as painless as po...

  20. Strongly correlated systems numerical methods

    CERN Document Server

    Mancini, Ferdinando

    2013-01-01

    This volume presents, for the very first time, an exhaustive collection of those modern numerical methods specifically tailored for the analysis of Strongly Correlated Systems. Many novel materials, with functional properties emerging from macroscopic quantum behaviors at the frontier of modern research in physics, chemistry and material science, belong to this class of systems. Any technique is presented in great detail by its own inventor or by one of the world-wide recognized main contributors. The exposition has a clear pedagogical cut and fully reports on the most relevant case study where the specific technique showed to be very successful in describing and enlightening the puzzling physics of a particular strongly correlated system. The book is intended for advanced graduate students and post-docs in the field as textbook and/or main reference, but also for other researchers in the field who appreciate consulting a single, but comprehensive, source or wishes to get acquainted, in a as painless as possi...

  1. Strongly nonlinear oscillators analytical solutions

    CERN Document Server

    Cveticanin, Livija

    2014-01-01

    This book provides the presentation of the motion of pure nonlinear oscillatory systems and various solution procedures which give the approximate solutions of the strong nonlinear oscillator equations. The book presents the original author’s method for the analytical solution procedure of the pure nonlinear oscillator system. After an introduction, the physical explanation of the pure nonlinearity and of the pure nonlinear oscillator is given. The analytical solution for free and forced vibrations of the one-degree-of-freedom strong nonlinear system with constant and time variable parameter is considered. Special attention is given to the one and two mass oscillatory systems with two-degrees-of-freedom. The criteria for the deterministic chaos in ideal and non-ideal pure nonlinear oscillators are derived analytically. The method for suppressing chaos is developed. Important problems are discussed in didactic exercises. The book is self-consistent and suitable as a textbook for students and also for profess...

  2. Flavour Democracy in Strong Unification

    CERN Document Server

    Abel, S A; Abel, Steven; King, Steven

    1998-01-01

    We show that the fermion mass spectrum may naturally be understood in terms of flavour democratic fixed points in supersymmetric theories which have a large domain of attraction in the presence of "strong unification". Our approach provides an alternative to the approximate Yukawa texture zeroes of the Froggatt-Nielsen mechanism. We discuss a particular model based on a broken gauged $SU(3)_L\\times SU(3)_R$ family symmetry which illustrates our approach.

  3. Positional Concerns and Institutions

    DEFF Research Database (Denmark)

    Landes, Xavier

    2013-01-01

    their implications for economics, positional concerns imply important normative dimensions. There have been presumed to be a symptom of envy, reduce people’s happiness, and create problems of social interaction or economic inefficiencies. Individuals are, for instance, prone to pick states of the world that improve...... that invoking envy or subjective well-being is not fully satisfying for regulating positional concerns. More compelling reasons seem, in complement with efficiency, to be related to considerations for equality. In other words, if institutions could have strong reasons to pay attention to and regulate positional...... concerns, it would be in virtue of their impact on the social product and individuals’ conditions of living....

  4. Atoms in strong laser fields

    International Nuclear Information System (INIS)

    L'Huillier, A.

    2002-01-01

    When a high-power laser focuses into a gas of atoms, the electromagnetic field becomes of the same magnitude as the Coulomb field which binds a 1s electron in a hydrogen atom. 3 highly non-linear phenomena can happen: 1) ATI (above threshold ionization): electrons initially in the ground state absorb a large number of photons, many more than the minimum number required for ionization; 2) multiple ionization: many electrons can be emitted one at a time, in a sequential process, or simultaneously in a mechanism called direct or non-sequential; and 3) high order harmonic generation (HHG): efficient photon emission in the extreme ultraviolet range, in the form of high-order harmonics of the fundamental laser field can occur. The theoretical problem consists in solving the time dependent Schroedinger equation (TDSE) that describes the interaction of a many-electron atom with a laser field. A number of methods have been proposed to solve this problem in the case of a hydrogen atom or a single-active electron atom in a strong laser field. A large effort is presently being devoted to go beyond the single-active approximation. The understanding of the physics of the interaction between atoms and strong laser fields has been provided by a very simple model called ''simple man's theory''. A unified view of HHG, ATI, and non-sequential ionization, originating from the simple man's model and the strong field approximation, expressed in terms of electrons trajectories or quantum paths is slowly emerging. (A.C.)

  5. Strongly Interacting Light Dark Matter

    Directory of Open Access Journals (Sweden)

    Sebastian Bruggisser, Francesco Riva, Alfredo Urbano

    2017-09-01

    Full Text Available In the presence of approximate global symmetries that forbid relevant interactions, strongly coupled light Dark Matter (DM can appear weakly coupled at small energy and generate a sizable relic abundance. Fundamental principles like unitarity restrict these symmetries to a small class, where the leading interactions are captured by effective operators up to dimension-8. Chiral symmetry, spontaneously broken global symmetries and non-linearly realized supersymmetry are examples of this. Their DM candidates (composite fermions, pseudo Nambu-Goldstone Bosons and Goldstini are interesting targets for LHC missing-energy searches.

  6. Strongly interacting light dark matter

    International Nuclear Information System (INIS)

    Bruggisser, Sebastian; Riva, Francesco; Urbano, Alfredo

    2016-07-01

    In the presence of approximate global symmetries that forbid relevant interactions, strongly coupled light Dark Matter (DM) can appear weakly coupled at small-energy and generate a sizable relic abundance. Fundamental principles like unitarity restrict these symmetries to a small class, where the leading interactions are captured by effective operators up to dimension-8. Chiral symmetry, spontaneously broken global symmetries and non-linearly realized supersymmetry are examples of this. Their DM candidates (composite fermions, pseudo-Nambu-Goldstone Bosons and Goldstini) are interesting targets for LHC missing-energy searches.

  7. Rydberg atoms in strong fields

    International Nuclear Information System (INIS)

    Kleppner, D.; Tsimmerman, M.

    1985-01-01

    Experimental and theoretical achievements in studying Rydberg atoms in external fields are considered. Only static (or quasistatic) fields and ''one-electron'' atoms, i.e. atoms that are well described by one-electron states, are discussed. Mainly behaviour of alkali metal atoms in electric field is considered. The state of theoretical investigations for hydrogen atom in magnetic field is described, but experimental data for atoms of alkali metals are presented as an illustration. Results of the latest experimental and theoretical investigations into the structure of Rydberg atoms in strong fields are presented

  8. Scalar strong interaction hadron theory

    CERN Document Server

    Hoh, Fang Chao

    2015-01-01

    The scalar strong interaction hadron theory, SSI, is a first principles' and nonlocal theory at quantum mechanical level that provides an alternative to low energy QCD and Higgs related part of the standard model. The quark-quark interaction is scalar rather than color-vectorial. A set of equations of motion for mesons and another set for baryons have been constructed. This book provides an account of the present state of a theory supposedly still at its early stage of development. This work will facilitate researchers interested in entering into this field and serve as a basis for possible future development of this theory.

  9. Strong Plate, Weak Slab Dichotomy

    Science.gov (United States)

    Petersen, R. I.; Stegman, D. R.; Tackley, P.

    2015-12-01

    Models of mantle convection on Earth produce styles of convection that are not observed on Earth.Moreover non-Earth-like modes, such as two-sided downwellings, are the de facto mode of convection in such models.To recreate Earth style subduction, i.e. one-sided asymmetric recycling of the lithosphere, proper treatment of the plates and plate interface are required. Previous work has identified several model features that promote subduction. A free surface or pseudo-free surface and a layer of material with a relatively low strength material (weak crust) allow downgoing plates to bend and slide past overriding without creating undue stress at the plate interface. (Crameri, et al. 2012, GRL)A low viscosity mantle wedge, possibly a result of slab dehydration, decouples the plates in the system. (Gerya et al. 2007, Geo)Plates must be composed of material which, in the case of the overriding plate, are is strong enough to resist bending stresses imposed by the subducting plate and yet, as in the case of the subducting plate, be weak enough to bend and subduct when pulled by the already subducted slab. (Petersen et al. 2015, PEPI) Though strong surface plates are required for subduction such plates may present a problem when they encounter the lower mantle.As the subducting slab approaches the higher viscosity, lower mantle stresses are imposed on the tip.Strong slabs transmit this stress to the surface.There the stress field at the plate interface is modified and potentially modifies the style of convection. In addition to modifying the stress at the plate interface, the strength of the slab affects the morphology of the slab at the base of the upper mantle. (Stegman, et al 2010, Tectonophysics)Slabs that maintain a sufficient portion of their strength after being bent require high stresses to unbend or otherwise change their shape.On the other hand slabs that are weakened though the bending process are more amenable to changes in morphology. We present the results of

  10. EDITORIAL: Strongly correlated electron systems Strongly correlated electron systems

    Science.gov (United States)

    Ronning, Filip; Batista, Cristian

    2011-03-01

    Strongly correlated electrons is an exciting and diverse field in condensed matter physics. This special issue aims to capture some of that excitement and recent developments in the field. Given that this issue was inspired by the 2010 International Conference on Strongly Correlated Electron Systems (SCES 2010), we briefly give some history in order to place this issue in context. The 2010 International Conference on Strongly Correlated Electron Systems was held in Santa Fe, New Mexico, a reunion of sorts from the 1989 International Conference on the Physics of Highly Correlated Electron Systems that also convened in Santa Fe. SCES 2010—co-chaired by John Sarrao and Joe Thompson—followed the tradition of earlier conferences, in this century, hosted by Buzios (2008), Houston (2007), Vienna (2005), Karlsruhe (2004), Krakow (2002) and Ann Arbor (2001). Every three years since 1997, SCES has joined the International Conference on Magnetism (ICM), held in Recife (2000), Rome (2003), Kyoto (2006) and Karlsruhe (2009). Like its predecessors, SCES 2010 topics included strongly correlated f- and d-electron systems, heavy-fermion behaviors, quantum-phase transitions, non-Fermi liquid phenomena, unconventional superconductivity, and emergent states that arise from electronic correlations. Recent developments from studies of quantum magnetism and cold atoms complemented the traditional subjects and were included in SCES 2010. 2010 celebrated the 400th anniversary of Santa Fe as well as the birth of astronomy. So what's the connection to SCES? The Dutch invention of the first practical telescope and its use by Galileo in 1610 and subsequent years overturned dogma that the sun revolved about the earth. This revolutionary, and at the time heretical, conclusion required innovative combinations of new instrumentation, observation and mathematics. These same combinations are just as important 400 years later and are the foundation of scientific discoveries that were discussed

  11. Nuclear Positioning

    Science.gov (United States)

    Gundersen, Gregg G.; Worman, Howard J.

    2013-01-01

    SUMMARY The nucleus is the largest organelle and is commonly depicted in the center of the cell. Yet during cell division, migration and differentiation, it frequently moves to an asymmetric position aligned with cell function. We consider the toolbox of proteins that move and anchor the nucleus within the cell and how forces generated by the cytoskeleton are coupled to the nucleus to move it. The significance of proper nuclear positioning is underscored by numerous diseases resulting from genetic alterations in the toolbox proteins. Finally, we discuss how nuclear position may influence cellular organization and signaling pathways. PMID:23498944

  12. Physics of Strongly Coupled Plasma

    Energy Technology Data Exchange (ETDEWEB)

    Kraeft, Wolf-Dietrich [Universitat Rostock (Germany)

    2007-07-15

    Strongly coupled plasmas (or non-ideal plasmas) are multi-component charged many-particle systems, in which the mean value of the potential energy of the system is of the same order as or even higher than the mean value of the kinetic energy. The constituents are electrons, ions, atoms and molecules. Dusty (or complex) plasmas contain still mesoscopic (multiply charged) particles. In such systems, the effects of strong coupling (non-ideality) lead to considerable deviations of physical properties from the corresponding properties of ideal plasmas, i.e., of plasmas in which the mean kinetic energy is essentially larger than the mean potential energy. For instance, bound state energies become density dependent and vanish at higher densities (Mott effect) due to the interaction of the pair with the surrounding particles. Non-ideal plasmas are of interest both for general scientific reasons (including, for example, astrophysical questions), and for technical applications such as inertially confined fusion. In spite of great efforts both experimentally and theoretically, satisfactory information on the physical properties of strongly coupled plasmas is not at hand for any temperature and density. For example, the theoretical description of non-ideal plasmas is possible only at low densities/high temperatures and at extremely high densities (high degeneracy). For intermediate degeneracy, however, numerical experiments have to fill the gap. Experiments are difficult in the region of 'warm dense matter'. The monograph tries to present the state of the art concerning both theoretical and experimental attempts. It mainly includes results of the work performed in famous Russian laboratories in recent decades. After outlining basic concepts (chapter 1), the generation of plasmas is considered (chapter 2, chapter 3). Questions of partial (chapter 4) and full ionization (chapter 5) are discussed including Mott transition and Wigner crystallization. Electrical and

  13. Pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA or histone modification H3K9Me3

    DEFF Research Database (Denmark)

    Rasmussen, Louise; Herzog, Marielle; Rømer, Eva

    2016-01-01

    Aim: To evaluate pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA (5mC) or histone modification H3K9Me3 (H3K9Me3). Materials and methods: Six studies were designed to assess the possible influence of pre-analytical variables. Study 1: influence of stas...... significantly lower levels of 5mC or H3K9Me3 compared to levels in healthy individuals. Conclusion: Levels of 5mC or H3K9Me3 appear stable in most pre-analytical settings if blood samples are stored at room temperature until centrifugation.......3K9Me3 measurements were performed using enzyme-linked immunosorbent assays. Results: Stasis, white-cell and platelet contamination, within-day variations, varying storage time before centrifugation, colonoscopy, and surgical trauma had no significant influence on levels of 5mC or H3K9Me3. Day......-to-day variations of 12.7% and 11.5% (intra-individual) and 98.1% and 60.8% (inter-individual) were shown for 5mC and H3K9Me3, respectively. Levels of 5mC or H3K9Me3 were significantly higher in samples stored at room temperature until centrifugation compared to samples stored on ice. Patients with cancer had...

  14. High-mobility group nucleosome-binding domain 2 protein inhibits the invasion of Klebsiella pneumoniae into mouse lungs in vivo.

    Science.gov (United States)

    Zheng, Shuang; Ren, Laibin; Li, Heng; Shen, Xiaofei; Yang, Xiaolong; Li, Na; Wang, Xinyuan; Guo, Xiaojuan; Wang, Xiaoying; Huang, Ning

    2015-07-01

    Since bacterial invasion into host cells is a critical step in the infection process and the predominance of multiple-antibiotic-resistant Klebsiella (K.) pneumoniae strains, using molecular agents to interfere with K. pneumoniae invasion is an attractive approach for the prevention of infection and suppress the immune inflammatory response. In previous studies by our group, high-mobility group nucleosome-binding domain 2 (HMGN2) protein was shown to exhibit anti-bacterial activity in vitro. The objective of the present study was to investigate the effects of HMGN2 protein on the invasion of K. pneumoniae 03183 in vivo. The results showed that pre-treatment with 128 µg/ml HMGN2 significantly reduced K. pneumoniae 03183 invasion into mouse lungs and increased the mRNA expression of CXCL1 and LCN2 within 2 h. Immunohistochemical staining showed that F-actin expression was significantly decreased, and fluorescence microscopy and western blot analysis further demonstrated that HMGN2 significantly blocked K. pneumoniae 03183-induced actin polymerization. These changes implied that HMGN2 may provide protection against K. pneumoniae 03183 infection in vivo.

  15. Radiographic positioning

    International Nuclear Information System (INIS)

    Eisenberg, R.L.; Dennis, C.A.; May, C.

    1989-01-01

    This book concentrates on the routine radiographic examinations commonly performed. It details the wide variety of examinations possible and their place in initial learning and in the radiology department as references for those occasions when an unusual examination is requested. This book provides information ranging from basic terminology to skeletal positioning to special procedures. Positions are discussed and supplemented with a picture of a patient, the resulting radiograph, and a labeled diagram. Immobilization and proper shielding of the patient are also shown

  16. [Positive psychiatry].

    Science.gov (United States)

    Timmerby, Nina; Austin, Stephen; Bech, Per

    2016-02-08

    Positive psychiatry (PP) is a field within psychiatry with a particular focus on promoting well-being in people who already have or are at high risk of developing mental or physical illness. PP should be considered a supplement to trad-tional psychiatry and a call for therapists in psychiatry to focus on the person as a whole rather than just as a patient. PP is in line with current national and international health policy focus on promoting positive mental health.

  17. Position encoder

    International Nuclear Information System (INIS)

    Goursky, Vsevolod

    1975-01-01

    A circuitry for deriving the quotient of signal delivered by position-sensitive detectors is described. Digital output is obtained in the form of 10- to 12-bit words. Impact position may be determined with 0.25% accuracy when the dynamic range of the energy signal is less 1:10, and 0.5% accuracy when the dynamic range is 1:20. The division requires an average time of 5μs for 10-bit words

  18. Position encoder

    International Nuclear Information System (INIS)

    Goursky, V.

    1975-05-01

    This paper describes circuitry for deriving the quotient of signals delivered by position-sensitive detectors. Digital output is obtained in the form of 10 to 12 bit words. Impact position may be determined with 0.25% accuracy when the dynamic range of the energy signal is less than 1:10, and 0.5% accuracy when the dynamic range is 1:20. The division requires an average time of 5μs for 10-bit words [fr

  19. Strongly coupled dust coulomb clusters

    International Nuclear Information System (INIS)

    Juan Wentau; Lai Yingju; Chen Mingheng; I Lin

    1999-01-01

    The structures and motions of quasi-2-dimensional strongly coupled dust Coulomb clusters with particle number N from few to hundreds in a cylindrical rf plasma trap are studied and compared with the results from the molecular dynamic simulation using more ideal models. Shell structures with periodic packing in different shells and intershell rotational motion dominated excitations are observed at small N. As N increases, the boundary has less effect, the system recovers to the triangular lattice with isotropic vortex type cooperative excitations similar to an infinite N system except the outer shell region. The above generic behaviors are mainly determined by the system symmetry and agree with the simulation results. The detailed interaction form causes minor effect such as the fine structure of packing

  20. Probability densities in strong turbulence

    Science.gov (United States)

    Yakhot, Victor

    2006-03-01

    In this work we, using Mellin’s transform combined with the Gaussian large-scale boundary condition, calculate probability densities (PDFs) of velocity increments P(δu,r), velocity derivatives P(u,r) and the PDF of the fluctuating dissipation scales Q(η,Re), where Re is the large-scale Reynolds number. The resulting expressions strongly deviate from the Log-normal PDF P(δu,r) often quoted in the literature. It is shown that the probability density of the small-scale velocity fluctuations includes information about the large (integral) scale dynamics which is responsible for the deviation of P(δu,r) from P(δu,r). An expression for the function D(h) of the multifractal theory, free from spurious logarithms recently discussed in [U. Frisch, M. Martins Afonso, A. Mazzino, V. Yakhot, J. Fluid Mech. 542 (2005) 97] is also obtained.

  1. Strong Ideal Convergence in Probabilistic Metric Spaces

    Indian Academy of Sciences (India)

    In the present paper we introduce the concepts of strongly ideal convergent sequence and strong ideal Cauchy sequence in a probabilistic metric (PM) space endowed with the strong topology, and establish some basic facts. Next, we define the strong ideal limit points and the strong ideal cluster points of a sequence in this ...

  2. Strong ideal convergence in probabilistic metric spaces

    Indian Academy of Sciences (India)

    In the present paper we introduce the concepts of strongly ideal convergent sequence and strong ideal Cauchy sequence in a probabilistic metric (PM) space endowed with the strong topology, and establish some basic facts. Next, we define the strong ideal limit points and the strong ideal cluster points of a sequence in this ...

  3. Researcher positioning

    DEFF Research Database (Denmark)

    Mørck, Line Lerche; Khawaja, Iram

    2009-01-01

    abstract  This article focuses on the complex and multi-layered process of researcher positioning, specifically in relation to the politically sensitive study of marginalised and ‘othered' groups such as Muslims living in Denmark. We discuss the impact of different ethnic, religious and racial...... backgrounds, of membership in a minoritised[i] or majoritised group, and the influence of different theoretical and methodological outlooks on our common goal of trying to transcend existing othering and objectifying representations of Muslims in Western societies. This process sometimes entails a direct...... political and personal involvement by the researcher, which challenges traditional perspectives on research and researcher positioning. A key point in this regard is the importance of constant awareness of and reflection on the multiple ways in which one's positioning as a researcher influences the research...

  4. Remnants of strong tidal interactions

    International Nuclear Information System (INIS)

    Mcglynn, T.A.

    1990-01-01

    This paper examines the properties of stellar systems that have recently undergone a strong tidal shock, i.e., a shock which removes a significant fraction of the particles in the system, and where the shocked system has a much smaller mass than the producer of the tidal field. N-body calculations of King models shocked in a variety of ways are performed, and the consequences of the shocks are investigated. The results confirm the prediction of Jaffe for shocked systems. Several models are also run where the tidal forces on the system are constant, simulating a circular orbit around a primary, and the development of tidal radii under these static conditions appears to be a mild process which does not dramatically affect material that is not stripped. The tidal radii are about twice as large as classical formulas would predict. Remnant density profiles are compared with a sample of elliptical galaxies, and the implications of the results for the development of stellar populations and galaxies are considered. 38 refs

  5. John Strong - 1941-2006

    CERN Document Server

    2006-01-01

    Our friend and colleague John Strong was cruelly taken from us by a brain tumour on 31 July, a few days before his 65th birthday. John started his career and obtained his PhD in a group from Westfield College, initially working on experiments at Rutherford Appleton Laboratory (RAL). From the early 1970s onwards, however, his research was focused on experiments in CERN, with several particularly notable contributions. The Omega spectrometer adopted a system John had originally developed for experiments at RAL using vidicon cameras (a type of television camera) to record the sparks in the spark chambers. This highly automated system allowed Omega to be used in a similar way to bubble chambers. He contributed to the success of NA1 and NA7, where he became heavily involved in the electronic trigger systems. In these experiments the Westfield group joined forces with Italian colleagues to measure the form factors of the pion and the kaon, and the lifetime of some of the newly discovered charm particles. Such h...

  6. Strong seismic ground motion propagation

    International Nuclear Information System (INIS)

    Seale, S.; Archuleta, R.; Pecker, A.; Bouchon, M.; Mohammadioun, G.; Murphy, A.; Mohammadioun, B.

    1988-10-01

    At the McGee Creek, California, site, 3-component strong-motion accelerometers are located at depths of 166 m, 35 m and 0 m. The surface material is glacial moraine, to a depth of 30.5 m, overlying homfels. Accelerations were recorded from two California earthquakes: Round Valley, M L 5.8, November 23, 1984, 18:08 UTC and Chalfant Valley, M L 6.4, July 21, 1986, 14:42 UTC. By separating out the SH components of acceleration, we were able to determine the orientations of the downhole instruments. By separating out the SV component of acceleration, we were able to determine the approximate angle of incidence of the signal at 166 m. A constant phase velocity Haskell-Thomson model was applied to generate synthetic SH seismograms at the surface using the accelerations recorded at 166 m. In the frequency band 0.0 - 10.0 Hz, we compared the filtered synthetic records to the filtered surface data. The onset of the SH pulse is clearly seen, as are the reflections from the interface at 30.5 m. The synthetic record closely matches the data in amplitude and phase. The fit between the synthetic accelerogram and the data shows that the seismic amplification at the surface is a result of the contrast of the impedances (shear stiffnesses) of the near surface materials

  7. Renormalization in theories with strong vector forces

    International Nuclear Information System (INIS)

    Kocic, A.

    1991-01-01

    There are not many field theories in four dimensions that have sensible ultraviolet and interesting (non-trivial) infrared behavior. At present, asymptotically free theories seem to have deserved their legitimacy and there is a strong prejudice that they might be the only ones to have such a distinction. This belief stems mostly from the fact that most of the knowledge of field theory in four dimensions comes from perturbation theory. However, nonperturbative studies of the lower dimensional theories reveal a host of interesting phenomena that are perturbative studies of the lower dimensional theories reveal a host of interesting phenomena that perturbatively inaccessible. The lack of asymptotic freedom implies that the coupling constant grows at short distances and perturbation theory breaks down. Thus, in such theories, ultraviolet behavior requires nonperturbative treatment. Recently, the interest in strongly coupled gauge theories has been revived. In particularly, four dimensional quantum electrodynamics has received considerable attention. This was motivated by the discovery of an ultraviolet stable fixed point at strong couplings. If this fixed point would turn out to be non-gaussian, then QED would be the first nontrivial nonasymptotically free theory in four dimensions. The importance of such a result would be twofold. First, the old question of the existence of QED could be settled. Of course, this would be the case provided that the low energy limit of the theory actually describes photons and electrons; apriori, there is no reason to assume this. Second, the discovery of a nontrivial nonasymptotically free theory would be of great paradigmatic value. The theories which quenched QED resembles the most are nonabelian gauge theories with many flavors with beta-function positive or vanishing at weak couplings. These theories are at present considered as viable candidates for technicolor unification schemes

  8. Researcher Positioning

    DEFF Research Database (Denmark)

    Khawaja, Iram; Mørck, Line Lerche

    2009-01-01

    involvement by the researcher, which challenges traditional perspectives onresearch and researcher positioning. A key point in this regard is the importance ofconstant awareness of and reflection on the multiple ways in which one's positioningas a researcher influences the research process. Studying the other...

  9. Strongly interacting photons and atoms

    International Nuclear Information System (INIS)

    Alge, W.

    1999-05-01

    This thesis contains the main results of the research topics I have pursued during the my PhD studies at the University of Innsbruck and partly in collaboration with the Institut d' Optique in Orsay, France. It is divided into three parts. The first and largest part discusses the possibility of using strong standing waves as a tool to cool and trap neutral atoms in optical cavities. This is very important in the field of nonlinear optics where several successful experiments with cold atoms in cavities have been performed recently. A discussion of the optical parametric oscillator in a regime where the nonlinearity dominates the evolution is the topic of the second part. We investigated mainly the statistical properties of the cavity output of the three interactive cavity modes. Very recently a system has been proposed which promises fantastic properties. It should exhibit a giant Kerr nonlinearity with negligible absorption thus leading to a photonic turnstile device based on cold atoms in cavity. We have shown that this model suffers from overly simplistic assumptions and developed several more comprehensive approaches to study the behavior of this system. Apart from the division into three parts of different contents the thesis is divided into publications, supplements and invisible stuff. The intention of the supplements is to reach researchers which work in related areas and provide them with more detailed information about the concepts and the numerical tools we used. It is written especially for diploma and PhD students to give them a chance to use the third part of our work which is actually the largest one. They consist of a large number of computer programs we wrote to investigate the behavior of the systems in parameter regions where no hope exists to solve the equations analytically. (author)

  10. Topics in strong Langmuir turbulence

    International Nuclear Information System (INIS)

    Skoric, M.M.

    1981-01-01

    This thesis discusses certain aspects of the turbulence of a fully ionised non-isothermal plasma dominated by the Langmuir mode. Some of the basic properties of strongly turbulent plasmas are reviewed. In particular, interest is focused on the state of Langmuir turbulence, that is the turbulence of a simple externally unmagnetized plasma. The problem of the existence and dynamics of Langmuir collapse is discussed, often met as a non-linear stage of the modulational instability in the framework of the Zakharov equations (i.e. simple time-averaged dynamical equations). Possible macroscopic consequences of such dynamical turbulent models are investigated. In order to study highly non-linear collapse dynamics in its advanced stage, a set of generalized Zakharov equations are derived. Going beyond the original approximation, the author includes the effects of higher electron non-linearities and a breakdown of slow-timescale quasi-neutrality. He investigates how these corrections may influence the collapse stabilisation. Recently, it has been realised that the modulational instability in a Langmuir plasma will be accompanied by the collisionless-generation of a slow-timescale magnetic field. Accordingly, a novel physical situation has emerged which is investigated in detail. The stability of monochromatic Langmuir waves in a self-magnetized Langmuir plasma, is discussed, and the existence of a novel magneto-modulational instability shown. The wave collapse dynamics is investigated and a physical interpretation of the basic results is given. A problem of the transient analysis of an interaction of time-dependent electromagnetic pulses with linear cold plasma media is investigated. (Auth.)

  11. Promoting Strong Written Communication Skills

    Science.gov (United States)

    Narayanan, M.

    2015-12-01

    The reason that an improvement in the quality of technical writing is still needed in the classroom is due to the fact that universities are facing challenging problems not only on the technological front but also on the socio-economic front. The universities are actively responding to the changes that are taking place in the global consumer marketplace. Obviously, there are numerous benefits of promoting strong written communication skills. They can be summarized into the following six categories. First, and perhaps the most important: The University achieves learner satisfaction. The learner has documented verbally, that the necessary knowledge has been successfully acquired. This results in learner loyalty that in turn will attract more qualified learners.Second, quality communication lowers the cost per pupil, consequently resulting in increased productivity backed by a stronger economic structure and forecast. Third, quality communications help to improve the cash flow and cash reserves of the university. Fourth, having high quality communication enables the university to justify the need for high costs of tuition and fees. Fifth, better quality in written communication skills result in attracting top-quality learners. This will lead to happier and satisfied learners, not to mention greater prosperity for the university as a whole. Sixth, quality written communication skills result in reduced complaints, thus meaning fewer hours spent on answering or correcting the situation. The University faculty and staff are thus able to devote more time on scholarly activities, meaningful research and productive community service. References Boyer, Ernest L. (1990). Scholarship reconsidered: Priorities of the Professorate.Princeton, NJ: Carnegie Foundation for the Advancement of Teaching. Hawkins, P., & Winter, J. (1997). Mastering change: Learning the lessons of the enterprise.London: Department for Education and Employment. Buzzel, Robert D., and Bradley T. Gale. (1987

  12. Demand for Neste's City products grows strongly

    International Nuclear Information System (INIS)

    Anon.

    1994-01-01

    Finland's oil, chemicals, and gas company, Neste Corporation, is well on the road to better financial performance after a very difficult year in 1992. Among the factors contributing to this optimism are Neste's pioneering low environmental impact traffic fuels. Neste Corporation's net sales in 1993 rose 9.9 % on 1992 figures to USD 11,011 million. Investments totalled USD 681 million. Profitability also improved during 1993, and the operating margin rose by 57 %, despite the recession affecting the Finnish economy and the instability of the international market. The operational loss for the year before extraordinary items, reserves, and taxes was USD 265 million, one-third less than in 1992. Neste's strategy has been to achieve a strong position in the Baltic Rim region by becoming the quality and cost leader in oil refining, and by expanding Neste's position in its key markets. A total of 3.3 million tonnes of petroleum products were exported from Finland in 1993. Neste's most important export markets were Sweden, Germany, Poland, the Baltic countries, and the St. Petersburg region. Some 20 % of exports went to customers outside Europe. In addition to Finland, Neste has concertedly developed its service station network in Poland and the Baltic countries

  13. Positioning apparatus

    Science.gov (United States)

    Vogel, Max A.; Alter, Paul

    1986-01-01

    An apparatus for precisely positioning materials test specimens within the optimum neutron flux path emerging from a neutron source located in a housing. The test specimens are retained in a holder mounted on the free end of a support pivotably mounted and suspended from a movable base plate. The support is gravity biased to urge the holder in a direction longitudinally of the flux path against the housing. Means are provided for moving the base plate in two directions to effect movement of the holder in two mutually perpendicular directions normal to the axis of the flux path.

  14. COMPANIES WITH MARKET POSITIONING BRANDS

    OpenAIRE

    Ruxandra Radoviciu; Filimon Stremtan

    2009-01-01

    Positioning a company on the market by the usage of brands is defined as the act ofdesigning the supply and its image on the market, so as to occupy a distinct place in the minds of theirtarget audience. The role of positioning in developing marketing strategy to differentiate products andservices involves the selection of attributes that are considered important for consumers. In order togain a strong position on the market the companies must perform a market analysis, an internalanalysis an...

  15. Atoms and clusters in strong laser fields

    NARCIS (Netherlands)

    Marchenko, T.

    2008-01-01

    This thesis describes experimental and theoretical studies on the interaction of strong infrared laser fields with atoms and atomic clusters. Part I provides an overview of the main strong-field phenomena in atoms, molecules and clusters and describes the state-of-the-art in strong-field science.

  16. Strong Bisimilarity of Simple Process Algebras

    DEFF Research Database (Denmark)

    Srba, Jirí

    2003-01-01

    We study bisimilarity and regularity problems of simple process algebras. In particular, we show PSPACE-hardness of the following problems: (i) strong bisimilarity of Basic Parallel Processes (BPP), (ii) strong bisimilarity of Basic Process Algebra (BPA), (iii) strong regularity of BPP, and (iv) ...

  17. 78 FR 15710 - Strong Sensitizer Guidance

    Science.gov (United States)

    2013-03-12

    ... definition of ``strong sensitizer'' found at 16 CFR 1500.3(c)(5). The Commission is proposing to revise the supplemental definition of ``strong sensitizer'' due to advancements in the science of sensitization that have... document is intended to clarify the ``strong sensitizer'' definition, assist manufacturers in understanding...

  18. WE-E-BRE-11: New Method to Simulate DNA Damage Using Ionization Cross-Sections and a Geometrical Nucleosome Model

    International Nuclear Information System (INIS)

    Pater, P; Seuntjens, J; El Naqa, I

    2014-01-01

    Purpose: To obtain probability distributions of various DNA damage types as a function of the incident electron kinetic energy. Methods: Using Geant4-DNA electron ionization cross-sections, we calculated path length distributions for electrons of energies between 10 eV and 1 MeV, defined as the length between two subsequent interactions. These path lengths were then convolved with probability distributions for the creation of same-strand damage, opposite-strand damage, clustered damage, isolated damage, and same DNA strand target damage. These probability distributions of DNA damage were obtained by a Monte Carlo routine calculating probabilities of interaction in DNA targets inside a nucleosome geometrical model. Results represent the probability of a secondary electron, initially created inside a DNA strand target, of undergoing its next interaction: (1) in the opposite strand (DSB), (2) in the same strand (SSB+), (3) in either the opposite or same-strand (clustered), (4) in the same DNA target (multiple-hit) or (5) more than 10 base pairs away (isolated). Results: Electrons with kinetic energy between 50 and 250 eV have a maximal probability of creating DSB, SSB+, clustered damage and multiple-hits in the same target The probabilities for these damage patterns have values of 2.5%, 4.3%, 6.7% and 5.4%, respectively. Isolated damage is most probable between 700 eV to 900 eV with a probability of 0.2%. Conclusion: We obtained DNA damage probability distributions as a function of electron incident energy. We showed that electrons with kinetic energies between 50 and 250 eV have the highest probability of producing complex forms of DNA damage (DSB, SSB+). We also showed that a double ionization within the same DNA target is the most frequent outcome occurring 5% of the time. It is expected that electron slowing down spectra can be convolved with our formalism to calculate source specific DNA damage patterns. Research grants from governments of Canada and Quebec. PP

  19. Application of strong phosphoric acid to radiochemistry

    International Nuclear Information System (INIS)

    Terada, Kikuo

    1977-01-01

    Not only inorganic and organic compounds but also natural substrances, such as accumulations in soil, are completely decomposed and distilled by heating with strong phosphoric acid for 30 to 50 minutes. As applications of strong phosphoric acid to radiochemistry, determination of uranium and boron by use of solubilization effect of this substance, titration of uranyl ion by use of sulfuric iron (II) contained in this substance, application to tracer experiment, and determination of radioactive ruthenium in environmental samples are reviewed. Strong phosphoric acid is also applied to activation analysis, for example, determination of N in pyrographite with iodate potassium-strong phosphoric acid method, separation of Os and Ru with sulfuric cerium (IV) - strong phosphoric acid method or potassium dechromate-strong phosphoric acid method, analysis of Se, As and Sb rocks and accumulations with ammonium bromide, sodium chloride and sodium bromide-strong phosphoric acid method. (Kanao, N.)

  20. Explicit strong stability preserving multistep Runge–Kutta methods

    KAUST Repository

    Bresten, Christopher

    2015-10-15

    High-order spatial discretizations of hyperbolic PDEs are often designed to have strong stability properties, such as monotonicity. We study explicit multistep Runge-Kutta strong stability preserving (SSP) time integration methods for use with such discretizations. We prove an upper bound on the SSP coefficient of explicit multistep Runge-Kutta methods of order two and above. Numerical optimization is used to find optimized explicit methods of up to five steps, eight stages, and tenth order. These methods are tested on the linear advection and nonlinear Buckley-Leverett equations, and the results for the observed total variation diminishing and/or positivity preserving time-step are presented.

  1. Strongly correlating liquids and their isomorphs

    OpenAIRE

    Pedersen, Ulf R.; Gnan, Nicoletta; Bailey, Nicholas P.; Schröder, Thomas B.; Dyre, Jeppe C.

    2010-01-01

    This paper summarizes the properties of strongly correlating liquids, i.e., liquids with strong correlations between virial and potential energy equilibrium fluctuations at constant volume. We proceed to focus on the experimental predictions for strongly correlating glass-forming liquids. These predictions include i) density scaling, ii) isochronal superposition, iii) that there is a single function from which all frequency-dependent viscoelastic response functions may be calculated, iv) that...

  2. Atom collisions in a strong electromagnetic field

    International Nuclear Information System (INIS)

    Smirnov, V.S.; Chaplik, A.V.

    1976-01-01

    It is shown that the long-range part of interatomic interaction is considerably altered in a strong electromagnetic field. Instead of the van der Waals law the potential asymptote can best be described by a dipole-dipole R -3 law. Impact broadening and the line shift in a strong nonresonant field are calculated. The possibility of bound states of two atoms being formed in a strong light field is discussed

  3. Strong ideal convergence in probabilistic metric spaces

    Indian Academy of Sciences (India)

    sequence and strong ideal Cauchy sequence in a probabilistic metric (PM) space endowed with the strong topology, and ... also important applications in nonlinear analysis [2]. The theory was brought to ..... for each t > 0 since each set on the right-hand side of the relation (3.1) belongs to I. Thus, by Definition 2.11 and the ...

  4. Large N baryons, strong coupling theory, quarks

    International Nuclear Information System (INIS)

    Sakita, B.

    1984-01-01

    It is shown that in QCD the large N limit is the same as the static strong coupling limit. By using the static strong coupling techniques some of the results of large N baryons are derived. The results are consistent with the large N SU(6) static quark model. (author)

  5. Optimization of strong and weak coordinates

    NARCIS (Netherlands)

    Swart, M.; Bickelhaupt, F.M.

    2006-01-01

    We present a new scheme for the geometry optimization of equilibrium and transition state structures that can be used for both strong and weak coordinates. We use a screening function that depends on atom-pair distances to differentiate strong coordinates from weak coordinates. This differentiation

  6. Strong decays of nucleon and delta resonances

    International Nuclear Information System (INIS)

    Bijker, R.; Leviatan, A.

    1996-01-01

    We study the strong couplings of the nucleon and delta resonances in a collective model. In the ensuing algebraic treatment we derive closed expressions for decay widths which are used to analyze the experimental data for strong decays into the pion and eta channels. (Author)

  7. Theoretical studies of strongly correlated fermions

    Energy Technology Data Exchange (ETDEWEB)

    Logan, D. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

    1997-04-01

    Strongly correlated fermions are investigated. An understanding of strongly correlated fermions underpins a diverse range of phenomena such as metal-insulator transitions, high-temperature superconductivity, magnetic impurity problems and the properties of heavy-fermion systems, in all of which local moments play an important role. (author).

  8. Seismic switch for strong motion measurement

    Science.gov (United States)

    Harben, P.E.; Rodgers, P.W.; Ewert, D.W.

    1995-05-30

    A seismic switching device is described that has an input signal from an existing microseismic station seismometer and a signal from a strong motion measuring instrument. The seismic switch monitors the signal level of the strong motion instrument and passes the seismometer signal to the station data telemetry and recording systems. When the strong motion instrument signal level exceeds a user set threshold level, the seismometer signal is switched out and the strong motion signal is passed to the telemetry system. The amount of time the strong motion signal is passed before switching back to the seismometer signal is user controlled between 1 and 15 seconds. If the threshold level is exceeded during a switch time period, the length of time is extended from that instant by one user set time period. 11 figs.

  9. Near-field strong coupling of single quantum dots.

    Science.gov (United States)

    Groß, Heiko; Hamm, Joachim M; Tufarelli, Tommaso; Hess, Ortwin; Hecht, Bert

    2018-03-01

    Strong coupling and the resultant mixing of light and matter states is an important asset for future quantum technologies. We demonstrate deterministic room temperature strong coupling of a mesoscopic colloidal quantum dot to a plasmonic nanoresonator at the apex of a scanning probe. Enormous Rabi splittings of up to 110 meV are accomplished by nanometer-precise positioning of the quantum dot with respect to the nanoresonator probe. We find that, in addition to a small mode volume of the nanoresonator, collective coherent coupling of quantum dot band-edge states and near-field proximity interaction are vital ingredients for the realization of near-field strong coupling of mesoscopic quantum dots. The broadband nature of the interaction paves the road toward ultrafast coherent manipulation of the coupled quantum dot-plasmon system under ambient conditions.

  10. Benign positional vertigo

    Science.gov (United States)

    Vertigo - positional; Benign paroxysmal positional vertigo; BPPV: dizziness- positional ... Benign positional vertigo is also called benign paroxysmal ... ear has fluid-filled tubes called semicircular canals. When you ...

  11. Strong and superstrong pulsed magnetic fields generation

    CERN Document Server

    Shneerson, German A; Krivosheev, Sergey I

    2014-01-01

    Strong pulsed magnetic fields are important for several fields in physics and engineering, such as power generation and accelerator facilities. Basic aspects of the generation of strong and superstrong pulsed magnetic fields technique are given, including the physics and hydrodynamics of the conductors interacting with the field as well as an account of the significant progress in generation of strong magnetic fields using the magnetic accumulation technique. Results of computer simulations as well as a survey of available field technology are completing the volume.

  12. Impurity screening in strongly coupled plasma systems

    CERN Document Server

    Kyrkos, S

    2003-01-01

    We present an overview of the problem of screening of an impurity in a strongly coupled one-component plasma within the framework of the linear response (LR) theory. We consider 3D, 2D and quasi-2D layered systems. For a strongly coupled plasma the LR can be determined by way of the known S(k) structure functions. In general, an oscillating screening potential with local overscreening and antiscreening regions emerges. In the case of the bilayer, this phenomenon becomes global, as overscreening develops in the layer of the impurity and antiscreening in the adjacent layer. We comment on the limitations of the LR theory in the strong coupling situation.

  13. The lambda sigma calculus and strong normalization

    DEFF Research Database (Denmark)

    Schack-Nielsen, Anders; Schürmann, Carsten

    Explicit substitution calculi can be classified into several dis- tinct categories depending on whether they are confluent, meta-confluent, strong normalization preserving, strongly normalizing, simulating, fully compositional, and/or local. In this paper we present a variant of the λσ-calculus......, which satisfies all seven conditions. In particular, we show how to circumvent Mellies counter-example to strong normalization by a slight restriction of the congruence rules. The calculus is implemented as the core data structure of the Celf logical framework. All meta-theoretic aspects of this work...

  14. Titanium Alloy Strong Back for IXO Mirror Segments

    Science.gov (United States)

    Byron, Glenn P.; Kai-Wang, Chan

    2011-01-01

    A titanium-alloy mirror-holding fixture called a strong back allows the temporary and permanent bonding of a 50 degree D263 glass x-ray mirror (IXO here stands for International X-ray Observatory). The strong back is used to hold and position a mirror segment so that mounting tabs may be bonded to the mirror with ultra-low distortion of the optical surface. Ti-15%Mo alloy was the material of choice for the strong back and tabs because the coefficient of thermal expansion closely matches that of the D263 glass and the material is relatively easy to machine. This invention has the ability to transfer bonded mounting points from a temporary location on the strong back to a permanent location on the strong back with minimal distortion. Secondly, it converts a single mirror segment into a rigid body with an acceptable amount of distortion of the mirror, and then maneuvers that rigid body into optical alignment such that the mirror segment can be bonded into a housing simulator or mirror module. Key problems are that the mirrors are 0.4-mm thick and have a very low coefficient of thermal expansion (CTE). Because the mirrors are so thin, they are very flexible and are easily distorted. When permanently bonding the mirror, the goal is to achieve a less than 1-micron distortion. Temperature deviations in the lab, which have been measured to be around 1 C, have caused significant distortions in the mirror segment.

  15. Strong combined gene-environment effects in anti-cyclic citrullinated peptide-positive rheumatoid arthritis

    DEFF Research Database (Denmark)

    Pedersen, Line Merete Blak; Jacobsen, Søren; Garred, Peter

    2007-01-01

    To study the role of shared epitope (SE) susceptibility genes, alone and in combination with tobacco smoking and other environmental risk factors, for risk of subtypes of rheumatoid arthritis (RA) defined by the presence or absence of serum antibodies against cyclic citrullinated peptides (CCPs)....

  16. The LACARA Vacuum Laser Accelerator Experiment: Beam Positioning and Alignment in a Strong Magnetic Field

    International Nuclear Information System (INIS)

    Shchelkunov, Sergey V.; Marshall, T. C.; Hirshfield, J. L.; Wang, Changbiao; LaPointe, M. A.

    2006-01-01

    LACARA (laser cyclotron auto-resonance accelerator) is a vacuum laser accelerator of electrons that is under construction at the Accelerator Test Facility (ATF), Brookhaven National Laboratory. It is expected that the experiment will be assembled by September 2006; this paper presents progress towards this goal. According to numerical studies, as an electron bunch moves along the LACARA solenoidal magnetic field (∼5.2 T, length ∼1 m), it will be accelerated from 50 to ∼75 MeV by interacting with a 0.8 TW Gaussian-mode circularly polarized optical pulse provided by the ATF CO2 10.6μm laser system. The LACARA laser transport optics must handle 10 J and be capable of forming a Gaussian beam inside the solenoid with a 1.4 mm waist and a Rayleigh range of 60 cm. The electron optics must transport a bunch having input emittance of 0.015 mm-mrad and 100 μm waist through the magnet. Precision alignment between the electron beam and the solenoid magnetic axis is required, and a method to achieve this is described in detail. Emittance- filtering may be necessary to yield an accelerated bunch having a narrow (∼1%) energy-spread

  17. Very Strong Binding for a Neutral Calix[4]pyrrole Receptor Displaying Positive Allosteric Binding

    DEFF Research Database (Denmark)

    Duedal, Troels; Nielsen, Kent; Olsen, Gunnar

    2017-01-01

    The dual-analyte responsive behavior of tetraTTF-calix[4]pyrrole receptor 1 has shown to complex electron-deficient planar guests in a 2:1 fashion in the so-called 1,3-alternate conformation. However, stronger 1:1 complexes have been demonstrated with tetraalkylammonium halide salts that defer...... receptor 1 to its so-called cone conformation. Herein, we report the complexation of an electron-deficient planar guest, namely 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA, 2), that champions the complexation with 1 resulting in a very high association constant Ka = 3 × 1010 M−2...

  18. Studies Of Positive-Position-Feedback Control

    Science.gov (United States)

    Fanson, James L.; Caughey, Thomas K.

    1992-01-01

    Report discusses theoretical and experimental studies of positive-position-feedback control for suppressing vibrations in large flexible structures. Positive-position-feedback control involves placement of actuators and sensors on structure; control voltages applied to actuators in response to outputs of sensors processed via compensator algorithm. Experiments demonstrate feasibility of suppressing vibrations by positive position feedback, and spillover of vibrational energy into uncontrolled modes has stabilizing effect if control gain sufficiently small.

  19. Strong Coupling Corrections in Quantum Thermodynamics

    Science.gov (United States)

    Perarnau-Llobet, M.; Wilming, H.; Riera, A.; Gallego, R.; Eisert, J.

    2018-03-01

    Quantum systems strongly coupled to many-body systems equilibrate to the reduced state of a global thermal state, deviating from the local thermal state of the system as it occurs in the weak-coupling limit. Taking this insight as a starting point, we study the thermodynamics of systems strongly coupled to thermal baths. First, we provide strong-coupling corrections to the second law applicable to general systems in three of its different readings: As a statement of maximal extractable work, on heat dissipation, and bound to the Carnot efficiency. These corrections become relevant for small quantum systems and vanish in first order in the interaction strength. We then move to the question of power of heat engines, obtaining a bound on the power enhancement due to strong coupling. Our results are exemplified on the paradigmatic non-Markovian quantum Brownian motion.

  20. Finding quantum effects in strong classical potentials

    Science.gov (United States)

    Hegelich, B. Manuel; Labun, Lance; Labun, Ou Z.

    2017-06-01

    The long-standing challenge to describing charged particle dynamics in strong classical electromagnetic fields is how to incorporate classical radiation, classical radiation reaction and quantized photon emission into a consistent unified framework. The current, semiclassical methods to describe the dynamics of quantum particles in strong classical fields also provide the theoretical framework for fundamental questions in gravity and hadron-hadron collisions, including Hawking radiation, cosmological particle production and thermalization of particles created in heavy-ion collisions. However, as we show, these methods break down for highly relativistic particles propagating in strong fields. They must therefore be improved and adapted for the description of laser-plasma experiments that typically involve the acceleration of electrons. Theory developed from quantum electrodynamics, together with dedicated experimental efforts, offer the best controllable context to establish a robust, experimentally validated foundation for the fundamental theory of quantum effects in strong classical potentials.

  1. The Charm and Beauty of Strong Interactions

    Science.gov (United States)

    El-Bennich, Bruno

    2018-01-01

    We briefly review common features and overlapping issues in hadron and flavor physics focussing on continuum QCD approaches to heavy bound states, their mass spectrum and weak decay constants in different strong interaction models.

  2. Atomica ionization by strong coherent radiation

    International Nuclear Information System (INIS)

    Brandi, H.S.; Davidovich, L.

    1979-07-01

    The relation among the three most frequently used non-perturbative methods proposed to study the ionization of atoms by strong electromagnetic fields is established. Their range of validity is also determined. (Author) [pt

  3. Perturbation of an exact strong gravity solution

    International Nuclear Information System (INIS)

    Baran, S.A.

    1982-10-01

    Perturbations of an exact strong gravity solution are investigated. It is shown, by using the new multipole expansions previously presented, that this exact and static spherically symmetric solution is stable under odd parity perturbations. (author)

  4. Strong-force theorists scoop Noble Prize

    CERN Multimedia

    Durrani, Matin

    2004-01-01

    Three US theorists have shared the 2004 Nobel Prize in Physics "for the discovery of asymptotic freedom in the theory of the strong interaction". Their theoretical work explains why quarks behave almost as free particles at high energies (½ page)

  5. Calculating hadronic properties in strong QCD

    International Nuclear Information System (INIS)

    Pennington, M.R.

    1996-01-01

    This talk gives a brief review of the progress that has been made in calculating the properties of hadrons in strong QCD. In keeping with this meeting I will concentrate on those properties that can be studied with electromagnetic probes. Though perturbative QCD is highly successful, it only applies in a limited kinematic regime, where hard scattering occur, and the quarks move in the interaction region as if they are free, pointlike objects. However, the bulk of strong interactions are governed by the long distance regime, where the strong interaction is strong. It is this regime of length scales of the order of a Fermi, that determines the spectrum of light hadrons and their properties. The calculation of these properties requires an understanding of non-perturbative QCD, of confinement and chiral symmetry breaking. (author)

  6. Building strong brands – does it matter?

    OpenAIRE

    Aure, Kristin Gaaseide; Nervik, Kristine Dybvik

    2014-01-01

    Brand equity has proven, through several decades of research, to be a primary source of competitive advantage and future earnings (Yoo & Donthu, 2001). Building strong brands has therefore become a priority for many organizations, with the presumption that building strong brands yields these advantages (Yasin et al., 2007). A quantitative survey was conducted at Sunnmøre in Norway in order to answer the two developed research questions. - Does the brand equity dimensions; brand...

  7. Algebra of strong and electroweak interactions

    International Nuclear Information System (INIS)

    Bolokhov, S.V.; Vladimirov, Yu.S.

    2004-01-01

    The algebraic approach to describing the electroweak and strong interactions is considered within the frames of the binary geometrophysics, based on the principles of the Fokker-Feynman direct interparticle interaction theories of the Kaluza-Klein multidimensional geometrical models and the physical structures theory. It is shown that in this approach the electroweak and strong elementary particles interaction through the intermediate vector bosons, are characterized by the subtypes of the algebraic classification of the complex 3 x 3-matrices [ru

  8. Manipulating light with strongly modulated photonic crystals

    International Nuclear Information System (INIS)

    Notomi, Masaya

    2010-01-01

    Recently, strongly modulated photonic crystals, fabricated by the state-of-the-art semiconductor nanofabrication process, have realized various novel optical properties. This paper describes the way in which they differ from other optical media, and clarifies what they can do. In particular, three important issues are considered: light confinement, frequency dispersion and spatial dispersion. First, I describe the latest status and impact of ultra-strong light confinement in a wavelength-cubic volume achieved in photonic crystals. Second, the extreme reduction in the speed of light is reported, which was achieved as a result of frequency dispersion management. Third, strange negative refraction in photonic crystals is introduced, which results from their unique spatial dispersion, and it is clarified how this leads to perfect imaging. The last two sections are devoted to applications of these novel properties. First, I report the fact that strong light confinement and huge light-matter interaction enhancement make strongly modulated photonic crystals promising for on-chip all-optical processing, and present several examples including all-optical switches/memories and optical logics. As a second application, it is shown that the strong light confinement and slow light in strongly modulated photonic crystals enable the adiabatic tuning of light, which leads to various novel ways of controlling light, such as adiabatic frequency conversion, efficient optomechanics systems, photon memories and photons pinning.

  9. Strong Motion Earthquake Data Values of Digitized Strong-Motion Accelerograms, 1933-1994

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Strong Motion Earthquake Data Values of Digitized Strong-Motion Accelerograms is a database of over 15,000 digitized and processed accelerograph records from...

  10. The extended reciprocity: Strong belief outperforms persistence.

    Science.gov (United States)

    Kurokawa, Shun

    2017-05-21

    The existence of cooperation is a mysterious phenomenon and demands explanation, and direct reciprocity is one key potential explanation for the evolution of cooperation. Direct reciprocity allows cooperation to evolve for cooperators who switch their behavior on the basis of information about the opponent's behavior. Here, relevant to direct reciprocity is information deficiency. When the opponent's last move is unknown, how should players behave? One possibility is to choose cooperation with some default probability without using any further information. In fact, our previous paper (Kurokawa, 2016a) examined this strategy. However, there might be beneficial information other than the opponent's last move. A subsequent study of ours (Kurokawa, 2017) examined the strategy which uses the own last move when the opponent's last move is unknown, and revealed that referring to the own move and trying to imitate it when information is absent is beneficial. Is there any other beneficial information else? How about strong belief (i.e., have infinite memory and believe that the opponent's behavior is unchanged)? Here, we examine the evolution of strategies with strong belief. Analyzing the repeated prisoner's dilemma game and using evolutionarily stable strategy (ESS) analysis against an invasion by unconditional defectors, we find the strategy with strong belief is more likely to evolve than the strategy which does not use information other than the opponent player's last move and more likely to evolve than the strategy which uses not only the opponent player's last move but also the own last move. Strong belief produces the extended reciprocity and facilitates the evolution of cooperation. Additionally, we consider the two strategies game between strategies with strong belief and any strategy, and we consider the four strategies game in which unconditional cooperators, unconditional defectors, pessimistic reciprocators with strong belief, and optimistic reciprocators with

  11. A strongly coupled quark-gluon plasma

    Energy Technology Data Exchange (ETDEWEB)

    Shuryak, Edward [Department of Physics and Astronomy, University at Stony Brook, NY 11794 (United States)

    2004-08-01

    Successful description of robust collective flow phenomena at RHIC by ideal hydrodynamics, recent observations of bound c-barc,q-barq states on the lattice, and other theoretical developments indicate that QGP produced at RHIC, and probably in a wider temperature region T{sub c} < T < 4T{sub c}, is not a weakly coupled quasiparticle gas as believed previously. We discuss how strong the interaction is and why it seems to generate hundreds of binary channels with bound states, surviving well inside the QGP phase. We in particular discuss their effect on pressure and viscosity. We conclude by reviewing the similar phenomena for other 'strongly coupled systems', such as (i) strongly coupled supersymmetric theories studied via Maldacena duality; (ii) trapped ultra-cold atoms with very large scattering length, tuned to Feschbach resonances.

  12. Strong Coupling between Plasmons and Organic Semiconductors

    Directory of Open Access Journals (Sweden)

    Joel Bellessa

    2014-05-01

    Full Text Available In this paper we describe the properties of organic material in strong coupling with plasmon, mainly based on our work in this field of research. The strong coupling modifies the optical transitions of the structure, and occurs when the interaction between molecules and plasmon prevails on the damping of the system. We describe the dispersion relation of different plasmonic systems, delocalized and localized plasmon, coupled to aggregated dyes and the typical properties of these systems in strong coupling. The modification of the dye emission is also studied. In the second part, the effect of the microscopic structure of the organics, which can be seen as a disordered film, is described. As the different molecules couple to the same plasmon mode, an extended coherent state on several microns is observed.

  13. A theory of the strong interactions

    International Nuclear Information System (INIS)

    Gross, D.J.

    1979-01-01

    The most promising candidate for a fundamental microscopic theory of the strong interactions is a gauge theory of colored quarks-Quantum Chromodynamics (QCD). There are many excellent reasons for believing in this theory. It embodies the broken symmetries, SU(3) and chiral SU(3)xSU(3), of the strong interactions and reflects the success of (albeit crude) quark models in explaining the spectrum of the observed hadrons. The hidden quantum number of color, necessary to account for the quantum numbers of the low lying hadrons, plays a fundamental role in this theory as the SU(3) color gauge vector 'gluons' are the mediators of the strong interactions. The absence of physical quark states can be 'explained' by the hypothesis of color confinement i.e. that hadrons are permanently bound in color singlet bound states. Finally this theory is unique in being asymptotically free, thus accounting for the almost free field theory behvior of quarks observed at short distances. (Auth.)

  14. Electromagnetic processes in strong crystalline fields

    CERN Multimedia

    2007-01-01

    We propose a number of new investigations on aspects of radiation from high energy electron and positron beams (10-300 GeV) in single crystals and amorphous targets. The common heading is radiation emission by electrons and positrons in strong electromagnetic fields, but as the setup is quite versatile, other related phenomena in radiation emission can be studied as well. The intent is to clarify the role of a number of important aspects of radiation in strong fields as e.g. observed in crystals. We propose to measure trident 'Klein-like' production in strong crystalline fields, 'crystalline undulator' radiation, 'sandwich' target phenomena, LPM suppression of pair production as well as axial and planar effects in contributions of spin to the radiation.

  15. Patterns of Strong Coupling for LHC Searches

    CERN Document Server

    Liu, Da; Rattazzi, Riccardo; Riva, Francesco

    2016-11-23

    Even though the Standard Model (SM) is weakly coupled at the Fermi scale, a new strong dynamics involving its degrees of freedom may conceivably lurk at slightly higher energies, in the multi TeV range. Approximate symmetries provide a structurally robust context where, within the low energy description, the dimensionless SM couplings are weak, while the new strong dynamics manifests itself exclusively through higher-derivative interactions. We present an exhaustive classification of such scenarios in the form of effective field theories, paying special attention to new classes of models where the strong dynamics involves, along with the Higgs boson, the SM gauge bosons and/or the fermions. The IR softness of the new dynamics suppresses its effects at LEP energies, but deviations are in principle detectable at the LHC, even at energies below the threshold for production of new states. Our construction provides the so far unique structurally robust context where to motivate several searches in Higgs physics, d...

  16. Electronic Structure of Strongly Correlated Materials

    CERN Document Server

    Anisimov, Vladimir

    2010-01-01

    Electronic structure and physical properties of strongly correlated materials containing elements with partially filled 3d, 4d, 4f and 5f electronic shells is analyzed by Dynamical Mean-Field Theory (DMFT). DMFT is the most universal and effective tool used for the theoretical investigation of electronic states with strong correlation effects. In the present book the basics of the method are given and its application to various material classes is shown. The book is aimed at a broad readership: theoretical physicists and experimentalists studying strongly correlated systems. It also serves as a handbook for students and all those who want to be acquainted with fast developing filed of condensed matter physics.

  17. Aperture averaging in strong oceanic turbulence

    Science.gov (United States)

    Gökçe, Muhsin Caner; Baykal, Yahya

    2018-04-01

    Receiver aperture averaging technique is employed in underwater wireless optical communication (UWOC) systems to mitigate the effects of oceanic turbulence, thus to improve the system performance. The irradiance flux variance is a measure of the intensity fluctuations on a lens of the receiver aperture. Using the modified Rytov theory which uses the small-scale and large-scale spatial filters, and our previously presented expression that shows the atmospheric structure constant in terms of oceanic turbulence parameters, we evaluate the irradiance flux variance and the aperture averaging factor of a spherical wave in strong oceanic turbulence. Irradiance flux variance variations are examined versus the oceanic turbulence parameters and the receiver aperture diameter are examined in strong oceanic turbulence. Also, the effect of the receiver aperture diameter on the aperture averaging factor is presented in strong oceanic turbulence.

  18. Electromagnetic Processes in strong Crystalline Fields

    CERN Multimedia

    2007-01-01

    We propose a number of new investigations on aspects of radiation from high energy electron and positron beams (10-300 GeV) in single crystals and amorphous targets. The common heading is radiation emission by electrons and positrons in strong electromagnetic fields, but as the setup is quite versatile, other related phenomena in radiation emission can be studied as well. The intent is to clarify the role of a number of important aspects of radiation in strong fields as e.g. observed in crystals. We propose to measure trident 'Klein-like' production in strong crystalline fields, 'crystalline undulator' radiation, 'sandwich' target phenomena, LPM suppression of pair production as well as axial and planar effects in contributions of spin to the radiation.

  19. Perceptual Sensitivity and Response to Strong Stimuli Are Related.

    Science.gov (United States)

    Bolders, Anna C; Tops, Mattie; Band, Guido P H; Stallen, Pieter Jan M

    2017-01-01

    To shed new light on the long-standing debate about the (in)dependence of sensitivity to weak stimuli and overreactivity to strong stimuli, we examined the relation between these tendencies within the neurobehavioral framework of the Predictive and Reactive Control Systems (PARCS) theory (Tops et al., 2010, 2014). Whereas previous studies only considered overreactivity in terms of the individual tendency to experience unpleasant affect (punishment reactivity) resulting from strong sensory stimulation, we also took the individual tendency to experience pleasant affect (reward reactivity) resulting from strong sensory stimulation into account. According to PARCS theory, these temperamental tendencies overlap in terms of high reactivity toward stimulation, but oppose each other in terms of the response orientation (approach or avoid). PARCS theory predicts that both types of reactivity to strong stimuli relate to sensitivity to weak stimuli, but that these relationships are suppressed due to the opposing relationship between reward and punishment reactivity. We measured punishment and reward reactivity to strong stimuli and sensitivity to weak stimuli using scales from the Adult Temperament Questionnaire (Evans and Rothbart, 2007). Sensitivity was also measured more objectively using the masked auditory threshold. We found that sensitivity to weak stimuli (both self-reported and objectively assessed) was positively associated with self-reported punishment and reward reactivity to strong stimuli, but only when these reactivity measures were controlled for each other, implicating a mutual suppression effect. These results are in line with PARCS theory and suggest that sensitivity to weak stimuli and overreactivity are dependent, but this dependency is likely to be obscured if punishment and reward reactivity are not both taken into account.

  20. Perceptual Sensitivity and Response to Strong Stimuli Are Related

    Directory of Open Access Journals (Sweden)

    Anna C. Bolders

    2017-09-01

    Full Text Available To shed new light on the long-standing debate about the (independence of sensitivity to weak stimuli and overreactivity to strong stimuli, we examined the relation between these tendencies within the neurobehavioral framework of the Predictive and Reactive Control Systems (PARCS theory (Tops et al., 2010, 2014. Whereas previous studies only considered overreactivity in terms of the individual tendency to experience unpleasant affect (punishment reactivity resulting from strong sensory stimulation, we also took the individual tendency to experience pleasant affect (reward reactivity resulting from strong sensory stimulation into account. According to PARCS theory, these temperamental tendencies overlap in terms of high reactivity toward stimulation, but oppose each other in terms of the response orientation (approach or avoid. PARCS theory predicts that both types of reactivity to strong stimuli relate to sensitivity to weak stimuli, but that these relationships are suppressed due to the opposing relationship between reward and punishment reactivity. We measured punishment and reward reactivity to strong stimuli and sensitivity to weak stimuli using scales from the Adult Temperament Questionnaire (Evans and Rothbart, 2007. Sensitivity was also measured more objectively using the masked auditory threshold. We found that sensitivity to weak stimuli (both self-reported and objectively assessed was positively associated with self-reported punishment and reward reactivity to strong stimuli, but only when these reactivity measures were controlled for each other, implicating a mutual suppression effect. These results are in line with PARCS theory and suggest that sensitivity to weak stimuli and overreactivity are dependent, but this dependency is likely to be obscured if punishment and reward reactivity are not both taken into account.

  1. Experimental investigation of strong field trident production

    CERN Document Server

    Esberg, J; Knudsen, H; Thomsen, H D; Uggerhøj, E; Uggerhøj, U I; Sona, P; Mangiarotti, A; Ketel, T J; Dizdar, A; Dalton, M M; Ballestrero, S; Connell, S H

    2010-01-01

    We show by experiment that an electron impinging on an electric field that is of critical magnitude in its rest frame, may produce an electron-positron pair. Our measurements address higher-order QED, using the strong electric fields obtainable along particular crystallographic directions in single crystals. For the amorphous material our data are in good agreement with theory, whereas a discrepancy with theory on the magnitude of the trident enhancement is found in the precisely aligned case where the strong electric field acts.

  2. Gluon scattering amplitudes at strong coupling

    Energy Technology Data Exchange (ETDEWEB)

    Alday, Luis F. [Institute for Theoretical Physics and Spinoza Institute, Utrecht University, 3508 TD Utrecht (Netherlands); Maldacena, Juan [School of Natural Sciences, Institute for Advanced Study, Princeton, NJ 08540 (United States)

    2007-06-15

    We describe how to compute planar gluon scattering amplitudes at strong coupling in N = 4 super Yang Mills by using the gauge/string duality. The computation boils down to finding a certain classical string configuration whose boundary conditions are determined by the gluon momenta. The results are infrared divergent. We introduce the gravity version of dimensional regularization to define finite quantities. The leading and subleading IR divergencies are characterized by two functions of the coupling that we compute at strong coupling. We compute also the full finite form for the four point amplitude and we find agreement with a recent ansatz by Bern, Dixon and Smirnov.

  3. Strong boundedness of analytic functions in tubes

    Directory of Open Access Journals (Sweden)

    Richard D. Carmichael

    1979-01-01

    Full Text Available Certain classes of analytic functions in tube domains TC=ℝn+iC in n-dimensional complex space, where C is an open connected cone in ℝn, are studied. We show that the functions have a boundedness property in the strong topology of the space of tempered distributions g′. We further give a direct proof that each analytic function attains the Fourier transform of its spectral function as distributional boundary value in the strong (and weak topology of g′.

  4. Including virtual photons in strong interactions

    International Nuclear Information System (INIS)

    Rusetsky, A.

    2003-01-01

    In the perturbative field-theoretical models we investigate the inclusion of the electromagnetic interactions into the purely strong theory that describes hadronic processes. In particular, we study the convention for splitting electromagnetic and strong interactions and the ambiguity of such a splitting. The issue of the interpretation of the parameters of the low-energy effective field theory in the presence of electromagnetic interactions is addressed, as well as the scale and gauge dependence of the effective theory couplings. We hope, that the results of these studies are relevant for the electromagnetic sector of ChPT. (orig.)

  5. Thermodynamical instabilities under strong magnetic fields

    Science.gov (United States)

    Chen, Y. J.

    2017-03-01

    The thermodynamical instabilities of low densities in the n p matter and n p e matter are studied within several relativistic nuclear models under some values of magnetic fields. The results are compared between each other and the effects of the symmetry energy slope at saturation density on the instability are investigated. The instability regions can exhibit bands due to the presence of Landau levels for very strong magnetic fields of the order of 1017 G, while for weaker magnetic fields, the bands are replaced by many diffused or scattered pieces. It also shows that the proton fraction in the inner crust of neutron stars may be complex under strong magnetic fields.

  6. Universal behavior of strongly correlated Fermi systems

    Energy Technology Data Exchange (ETDEWEB)

    Shaginyan, Vasilii R [B.P. Konstantinov St. Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad region, Rusian Federation (Russian Federation); Amusia, M Ya [A.F. Ioffe Physico-Technical Institute, Russian Academy of Sciences, St. Petersburg (Russian Federation); Popov, Konstantin G [Komi Scientific Center, Ural Branch of the Russian Academy of Sciences, Syktyvkar (Russian Federation)

    2007-06-30

    This review discusses the construction of a theory and the analysis of phenomena occurring in strongly correlated Fermi systems such as high-T{sub c} superconductors, heavy-fermion metals, and quasi-two-dimensional Fermi systems. It is shown that the basic properties and the universal behavior of strongly correlated Fermi systems can be described in the framework of the Fermi-condensate quantum phase transition and the well-known Landau paradigm of quasiparticles and the order parameter. The concept of fermion condensation may be fruitful in studying neutron stars, finite Fermi systems, ultra-cold gases in traps, and quark plasma. (reviews of topical problems)

  7. Universal behavior of strongly correlated Fermi systems

    International Nuclear Information System (INIS)

    Shaginyan, Vasilii R; Amusia, M Ya; Popov, Konstantin G

    2007-01-01

    This review discusses the construction of a theory and the analysis of phenomena occurring in strongly correlated Fermi systems such as high-T c superconductors, heavy-fermion metals, and quasi-two-dimensional Fermi systems. It is shown that the basic properties and the universal behavior of strongly correlated Fermi systems can be described in the framework of the Fermi-condensate quantum phase transition and the well-known Landau paradigm of quasiparticles and the order parameter. The concept of fermion condensation may be fruitful in studying neutron stars, finite Fermi systems, ultra-cold gases in traps, and quark plasma. (reviews of topical problems)

  8. Analytical solution of strongly nonlinear Duffing oscillators

    OpenAIRE

    El-Naggar, A.M.; Ismail, G.M.

    2016-01-01

    In this paper, a new perturbation technique is employed to solve strongly nonlinear Duffing oscillators, in which a new parameter α=α(ε)α=α(ε) is defined such that the value of α is always small regardless of the magnitude of the original parameter εε. Therefore, the strongly nonlinear Duffing oscillators with large parameter ε are transformed into a small parameter system with respect to αα. Approximate solution obtained by the present method is compared with the solution of energy balance m...

  9. De Sitter vacua of strongly interacting QFT

    Energy Technology Data Exchange (ETDEWEB)

    Buchel, Alex [Department of Applied Mathematics, University of Western Ontario,London, Ontario N6A 5B7 (Canada); Department of Physics and Astronomy, University of Western Ontario,London, Ontario N6A 5B7 (Canada); Perimeter Institute for Theoretical Physics,Waterloo, Ontario N2J 2W9 (Canada); Karapetyan, Aleksandr [Department of Applied Mathematics, University of Western Ontario,London, Ontario N6A 5B7 (Canada)

    2017-03-22

    We use holographic correspondence to argue that Euclidean (Bunch-Davies) vacuum is a late-time attractor of the dynamical evolution of quantum gauge theories at strong coupling. The Bunch-Davies vacuum is not an adiabatic state, if the gauge theory is non-conformal — the comoving entropy production rate is nonzero. Using the N=2{sup ∗} gauge theory holography, we explore prospects of explaining current accelerated expansion of the Universe as due to the vacuum energy of a strongly coupled QFT.

  10. Earthquake source model using strong motion displacement

    Indian Academy of Sciences (India)

    The strong motion displacement records available during an earthquake can be treated as the response of the earth as the a structural system to unknown forces acting at unknown locations. Thus, if the part of the earth participating in ground motion is modelled as a known finite elastic medium, one can attempt to model the ...

  11. Vector mesons in strongly interacting matter

    Indian Academy of Sciences (India)

    probes like photons, pions or protons or the heated and compressed hadronic matter generated in a heavy-ion collision. Leaving any nuclear medium without strong final-state interactions, dileptons are the optimum decay channel as they avoid any final-state distortion of the 4- momenta of the decay products entering eq.

  12. Vector mesons in strongly interacting matter

    Indian Academy of Sciences (India)

    Properties of hadrons in strongly interacting matter provide a link between quantum chromodynamics in the ... Top: Spectral function of the ρ-meson at normal nuclear matter density as a function of mass and ... directly but folded with the branching ratio ΓV →p1+p2 /Γtot into the specific final channel one is investigating.

  13. Strong industrial base vital for economic revival

    CERN Multimedia

    2001-01-01

    At the inauguration of a 2-day conference on nuclear technology in Islamabad, the chairman of PAEC said that Pakistan needs to develop a strong industrial base and capability to export equipment to improve the economic condition of the country. He descibed how Pakistan has already had a breakthrough with the export of equipment to CERN, Geneva (1 page).

  14. Chaos desynchronization in strongly coupled systems

    International Nuclear Information System (INIS)

    Wu Ye; Liu Weiqing; Xiao, Jinghua; Zhan Meng

    2007-01-01

    The dynamics of chaos desynchronization in strongly coupled oscillator systems is studied. We find a new bifurcation from synchronous chaotic state, chaotic short wave bifurcation, i.e. a chaotic desynchronization attractor is new born in the systems due to chaos desynchronization. In comparison with the usual periodic short wave bifurcation, very rich but distinct phenomena are observed

  15. Strong wind climatic zones in South Africa

    CSIR Research Space (South Africa)

    Kruger, AC

    2010-01-01

    Full Text Available In this paper South Africa is divided into strong wind climate zones, which indicate the main sources of annual maximum wind gusts. By the analysis of wind gust data of 94 weather stations, which had continuous climate time series of 10 years...

  16. Reducing Weak to Strong Bisimilarity in CCP

    Directory of Open Access Journals (Sweden)

    Andrés Aristizábal

    2012-12-01

    Full Text Available Concurrent constraint programming (ccp is a well-established model for concurrency that singles out the fundamental aspects of asynchronous systems whose agents (or processes evolve by posting and querying (partial information in a global medium. Bisimilarity is a standard behavioural equivalence in concurrency theory. However, only recently a well-behaved notion of bisimilarity for ccp, and a ccp partition refinement algorithm for deciding the strong version of this equivalence have been proposed. Weak bisimiliarity is a central behavioural equivalence in process calculi and it is obtained from the strong case by taking into account only the actions that are observable in the system. Typically, the standard partition refinement can also be used for deciding weak bisimilarity simply by using Milner's reduction from weak to strong bisimilarity; a technique referred to as saturation. In this paper we demonstrate that, because of its involved labeled transitions, the above-mentioned saturation technique does not work for ccp. We give an alternative reduction from weak ccp bisimilarity to the strong one that allows us to use the ccp partition refinement algorithm for deciding this equivalence.

  17. Strong motion duration and earthquake magnitude relationships

    International Nuclear Information System (INIS)

    Salmon, M.W.; Short, S.A.; Kennedy, R.P.

    1992-06-01

    Earthquake duration is the total time of ground shaking from the arrival of seismic waves until the return to ambient conditions. Much of this time is at relatively low shaking levels which have little effect on seismic structural response and on earthquake damage potential. As a result, a parameter termed ''strong motion duration'' has been defined by a number of investigators to be used for the purpose of evaluating seismic response and assessing the potential for structural damage due to earthquakes. This report presents methods for determining strong motion duration and a time history envelope function appropriate for various evaluation purposes, for earthquake magnitude and distance, and for site soil properties. There are numerous definitions of strong motion duration. For most of these definitions, empirical studies have been completed which relate duration to earthquake magnitude and distance and to site soil properties. Each of these definitions recognizes that only the portion of an earthquake record which has sufficiently high acceleration amplitude, energy content, or some other parameters significantly affects seismic response. Studies have been performed which indicate that the portion of an earthquake record in which the power (average rate of energy input) is maximum correlates most closely with potential damage to stiff nuclear power plant structures. Hence, this report will concentrate on energy based strong motion duration definitions

  18. Morphological modelling of strongly curved islands

    NARCIS (Netherlands)

    Roelvink, D.; Den Heijer, C.; Van Thiel De Vries, J.S.M.

    2013-01-01

    Land reclamations and island coasts often involve strongly curved shorelines, which are challenging to be properly modeled by numerical morphological models. Evaluation of the long term development of these types of coasts as well as their response to storm conditions requires proper representation

  19. Nonlinear Electron Waves in Strongly Magnetized Plasmas

    DEFF Research Database (Denmark)

    Pécseli, Hans; Juul Rasmussen, Jens

    1980-01-01

    Weakly nonlinear dispersive electron waves in strongly magnetized plasma are considered. A modified nonlinear Schrodinger equation is derived taking into account the effect of particles resonating with the group velocity of the waves (nonlinear Landau damping). The possibility of including the ion...

  20. Strong and Reversible Monovalent Supramolecular Protein Immobilization

    NARCIS (Netherlands)

    Young, Jacqui F.; Nguyen, Hoang D.; Yang, Lanti; Huskens, Jurriaan; Jonkheijm, Pascal; Brunsveld, Luc

    2010-01-01

    Proteins with an iron clasp: Site-selective incorporation of a ferrocene molecule into a protein allows for easy, strong, and reversible supramolecular protein immobilization through a selective monovalent interaction of the ferrocene with a cucurbit[7]uril immobilized on a gold surface. The

  1. Experimental investigation of strong field trident production

    NARCIS (Netherlands)

    Esberg, J.; Kirsebom, K.; Knudsen, H.; Thomsen, H.D.; Uggerhøj, E.; Uggerhøj, U.I.; Sona, P.; Mangiarotti, A.; Ketel, T.J.; Ditzdar, A.; Dalton, M.M.; Ballestrero, S.; Connell, S.H.

    2010-01-01

    We show by experiment that an electron impinging on an electric field that is of critical magnitude in its rest frame, may produce an electron-positron pair. Our measurements address higher-order QED, using the strong electric fields obtainable along particular crystallographic directions in single

  2. Strong-coupling diffusion in relativistic systems

    Indian Academy of Sciences (India)

    hanced values needed to interpret the data at higher energies point towards the importance of strong-coupling effects. ... when all secondary particles have been created. For short times in the initial phase ... It is decisive for a proper representation of the available data for relativistic heavy-ion collisions at and beyond SPS.

  3. Bottomonia: open bottom strong decays and spectrum

    Directory of Open Access Journals (Sweden)

    Santopinto E.

    2014-05-01

    Full Text Available We present our results for the bottomonium spectrum with self energy corrections. The bare masses used in the calculation are computed within Godfrey and Isgur’s relativized quark model. We also discuss our results for the open bottom strong decay widths of higher bottomonia in the 3P0 pair-creation model.

  4. Strong motion duration and earthquake magnitude relationships

    Energy Technology Data Exchange (ETDEWEB)

    Salmon, M.W.; Short, S.A. [EQE International, Inc., San Francisco, CA (United States); Kennedy, R.P. [RPK Structural Mechanics Consulting, Yorba Linda, CA (United States)

    1992-06-01

    Earthquake duration is the total time of ground shaking from the arrival of seismic waves until the return to ambient conditions. Much of this time is at relatively low shaking levels which have little effect on seismic structural response and on earthquake damage potential. As a result, a parameter termed ``strong motion duration`` has been defined by a number of investigators to be used for the purpose of evaluating seismic response and assessing the potential for structural damage due to earthquakes. This report presents methods for determining strong motion duration and a time history envelope function appropriate for various evaluation purposes, for earthquake magnitude and distance, and for site soil properties. There are numerous definitions of strong motion duration. For most of these definitions, empirical studies have been completed which relate duration to earthquake magnitude and distance and to site soil properties. Each of these definitions recognizes that only the portion of an earthquake record which has sufficiently high acceleration amplitude, energy content, or some other parameters significantly affects seismic response. Studies have been performed which indicate that the portion of an earthquake record in which the power (average rate of energy input) is maximum correlates most closely with potential damage to stiff nuclear power plant structures. Hence, this report will concentrate on energy based strong motion duration definitions.

  5. Controlling Josephson dynamics by strong microwave fields

    NARCIS (Netherlands)

    Chesca, B.; Savel'ev, E.; Rakhmanov, A.L.; Smilde, H.J.H.; Hilgenkamp, Johannes W.M.

    2008-01-01

    We observe several sharp changes in the slope of the current-voltage characteristics (CVCs) of thin-film ramp-edge Josephson junctions between YBa2Cu3O7−delta and Nb when applying strong microwave fields. Such behavior indicates an intriguing Josephson dynamics associated with the switching from a

  6. Strong-coupling diffusion in relativistic systems

    Indian Academy of Sciences (India)

    Different from the early universe, heavy-ion collisions at very high energies do not reach statistical equilibrium, although thermal models explain many of their features. To account for nonequilibrium strong-coupling effects, a Fokker–Planck equation with time-dependent diffusion coefficient is proposed. A schematic model ...

  7. Weak and strong nonlinearities in magnetic bearings

    Czech Academy of Sciences Publication Activity Database

    Půst, Ladislav

    2004-01-01

    Roč. 39, č. 7 (2004), s. 779-795 ISSN 0094-114X R&D Projects: GA ČR GA101/00/1471; GA AV ČR IBS2076301 Institutional research plan: CEZ:AV0Z2076919 Keywords : weak nonlinearitiy * strong nonlinearity * magnetics bearings Subject RIV: BI - Acoustics Impact factor: 0.605, year: 2004

  8. Rotating compressible fluids under strong stratification

    Czech Academy of Sciences Publication Activity Database

    Feireisl, Eduard; Lu, Y.; Novotný, A.

    2014-01-01

    Roč. 19, October (2014), s. 11-18 ISSN 1468-1218 Keywords : rotating fluid * compressible Navier-Stokes * strong stratification Subject RIV: BA - General Mathematics Impact factor: 2.519, year: 2014 http://www.sciencedirect.com/science/article/pii/S1468121814000212#

  9. Super-strong Magnetic Field in Sunspots

    Science.gov (United States)

    Okamoto, Takenori J.; Sakurai, Takashi

    2018-01-01

    Sunspots are the most notable structure on the solar surface with strong magnetic fields. The field is generally strongest in a dark area (umbra), but sometimes stronger fields are found in non-dark regions, such as a penumbra and a light bridge. The formation mechanism of such strong fields outside umbrae is still puzzling. Here we report clear evidence of the magnetic field of 6250 G, which is the strongest field among Stokes I profiles with clear Zeeman splitting ever observed on the Sun. The field was almost parallel to the solar surface and located in a bright region sandwiched by two opposite-polarity umbrae. Using a time series of spectral data sets, we discuss the formation process of the super-strong field and suggest that this strong field region was generated as a result of compression of one umbra pushed by the horizontal flow from the other umbra, such as the subduction of the Earth’s crust in plate tectonics.

  10. Strongly coupled semidirect mediation of supersymmetry breaking

    International Nuclear Information System (INIS)

    Ibe, M.; Izawa, K.-I.; Nakai, Y.

    2009-01-01

    Strongly coupled semidirect gauge mediation models of supersymmetry breaking through massive mediators with standard-model charges are investigated by means of composite degrees of freedom. Sizable mediation is realized to generate the standard-model gaugino masses for a small mediator mass without breaking the standard-model symmetries.

  11. A Note on Strongly Dense Matrices

    Czech Academy of Sciences Publication Activity Database

    Fiedler, Miroslav; Hall, F.J.

    2015-01-01

    Roč. 1, č. 4 (2015), s. 721-730 ISSN 2199-675X Institutional support: RVO:67985807 Keywords : strongly dense matrix * Boolean matrix * nonnegative matrix * idempotent matrix * intrinsic product * generalized complementary basic matrix Subject RIV: BA - General Mathematics

  12. Strongly 2-connected orientations of graphs

    DEFF Research Database (Denmark)

    Thomassen, Carsten

    2014-01-01

    We prove that a graph admits a strongly 2-connected orientation if and only if it is 4-edge-connected, and every vertex-deleted subgraph is 2-edge-connected. In particular, every 4-connected graph has such an orientation while no cubic 3-connected graph has such an orientation....

  13. The Shape of Strongly Disturbed Dayside Magnetopause

    Directory of Open Access Journals (Sweden)

    Alexei V. Dmitriev Alla V. Suvorova

    2013-01-01

    Full Text Available During strong geomagnetic disturbances, the Earth¡¦s magnetosphere exhibits unusual and nonlinear interaction with the incident flow of magnetized solar wind plasma. Global Magneto-hydro-dynamic (MHD modeling of the magnetosphere predicts that the storm-time effects at the magnetopause result from the abnormal plasma transport and/or extremely strong field aligned currents. In-situ observations of the magnetospheric boundary, magnetopause, by Geosynchronous Operational Environmental Satellite (GOES allowed us to find experimentally such effects as a saturation of the dayside reconnection, unusual bluntness and prominent duskward skewing of the nose magnetopause. The saturation and duskward skewing were attributed to the storm-time magnetopause formation under strong southward interplanetary magnetic field (IMF. The unusual bluntness was observed during both high solar wind pressure and strong southward IMF. We suggest that these phenomena are caused by a substantial contribution of the cross-tail current magnetic field and the hot magnetospheric plasma from the asymmetrical ring current into the pressure balance at the dayside magnetopause.

  14. Cognitive-Processing Bias in Chinese Student Teachers with Strong and Weak Professional Identity

    Science.gov (United States)

    Wang, Xin-qiang; Zhu, Jun-cheng; Liu, Lu; Chen, Xiang-yu

    2017-01-01

    Professional identity plays an important role in career development. Although many studies have examined professional identity, differences in cognitive-processing biases between Chinese student teachers with strong and weak professional identity are poorly understood. The current study adopted Tversky’s social-cognitive experimental paradigm to explore cognitive-processing biases in Chinese student teachers with strong and weak professional identity. Experiment 1 showed that participants with strong professional identity exhibited stronger positive-coding bias toward positive profession-related life events, relative to that observed in those with weak professional identity. Experiment 2 showed that participants with strong professional identity exhibited greater recognition bias for previously read items, relative to that observed in those with weak professional identity. Overall, the results suggested that participants with strong professional identity exhibited greater positive cognitive-processing bias relative to that observed in those with weak professional identity. PMID:28555123

  15. Position automatic determination technology

    International Nuclear Information System (INIS)

    1985-10-01

    This book tells of method of position determination and characteristic, control method of position determination and point of design, point of sensor choice for position detector, position determination of digital control system, application of clutch break in high frequency position determination, automation technique of position determination, position determination by electromagnetic clutch and break, air cylinder, cam and solenoid, stop position control of automatic guide vehicle, stacker crane and automatic transfer control.

  16. Strong transthyretin immunostaining: potential pitfall in cardiac amyloid typing.

    Science.gov (United States)

    Satoskar, Anjali A; Efebera, Yvonne; Hasan, Ayesha; Brodsky, Sergey; Nadasdy, Gyongyi; Dogan, Ahmet; Nadasdy, Tibor

    2011-11-01

    Although systemic amyloidosis commonly presents with renal disease, cardiac involvement usually determines the patient's prognosis. Cardiac involvement is seen in light chain amyloid and transthyretin amyloidosis. Distinguishing between these two is critical because prognosis and treatment differ. Our study demonstrates the unreliability of transthyretin immunostaining in subtyping cardiac amyloid. Between January 2003 and August 2010, we retrieved 229 native endomyocardial biopsies, of which 24 had amyloid. Immunohistochemistry for κ, λ, transthyretin, and serum amyloid A protein was performed on formalin-fixed, paraffin-embedded sections. Staining was graded as weak (trace to 1+) or strong (2 to 3+). Mass spectrometry (MS)-based proteomic typing of microdissected amyloid material was performed on selected cases. Fifteen patients had monoclonal gammopathy/plasma cell dyscrasia with cardiac amyloid. Eight of them (53%) showed strong transthyretin staining in the cardiac amyloid deposits. MS was performed in 5 of these 8 biopsies, and all 5 biopsies revealed light chain amyloid-type amyloid. Two of these 5 light chain amyloid biopsies did not even have concomitant strong staining for the appropriate light chain. Among the 15 cases with plasma cell dyscrasia, only 7 biopsies showed strong staining for the corresponding monoclonal light chain. Strong, false-positive immunostaining for transthyretin in cardiac amyloid is a potential pitfall, augmented by the frequent lack of staining for immunoglobulin light chains. Therefore, the presence of amyloid in the cardiac biopsy should prompt a search for plasma cell dyscrasia irrespective of transthyretin staining. Confirmation with MS should be sought, particularly if there is any discrepancy between κ/λ staining and serum immunofixation results.

  17. STRONG SOLAR WIND DYNAMIC PRESSURE PULSES: INTERPLANETARY SOURCES AND THEIR IMPACTS ON GEOSYNCHRONOUS MAGNETIC FIELDS

    International Nuclear Information System (INIS)

    Zuo, Pingbing; Feng, Xueshang; Wang, Yi; Xie, Yanqiong; Xu, Xiaojun

    2015-01-01

    In this investigation, we first present a statistical result of the interplanetary sources of very strong solar wind dynamic pressure pulses (DPPs) detected by WIND during solar cycle 23. It is found that the vast majority of strong DPPs reside within solar wind disturbances. Although the variabilities of geosynchronous magnetic fields (GMFs) due to the impact of positive DPPs have been well established, there appears to be no systematic investigations on the response of GMFs to negative DPPs. Here, we study both the decompression effects of very strong negative DPPs and the compression from strong positive DPPs on GMFs at different magnetic local time sectors. In response to the decompression of strong negative DPPs, GMFs on the dayside near dawn and near dusk on the nightside, are generally depressed. But near the midnight region, the responses of GMF are very diverse, being either positive or negative. For part of the events when GOES is located at the midnight sector, the GMF is found to abnormally increase as the result of magnetospheric decompression caused by negative DPPs. It is known that under certain conditions magnetic depression of nightside GMFs can be caused by the impact of positive DPPs. Here, we find that a stronger pressure enhancement may have a higher probability of producing the exceptional depression of GMF at the midnight region. Statistically, both the decompression effect of strong negative DPPs and the compression effect of strong positive DPPs depend on the magnetic local time, which are stronger at the noon sector

  18. Strong ground motion prediction using virtual earthquakes.

    Science.gov (United States)

    Denolle, M A; Dunham, E M; Prieto, G A; Beroza, G C

    2014-01-24

    Sedimentary basins increase the damaging effects of earthquakes by trapping and amplifying seismic waves. Simulations of seismic wave propagation in sedimentary basins capture this effect; however, there exists no method to validate these results for earthquakes that have not yet occurred. We present a new approach for ground motion prediction that uses the ambient seismic field. We apply our method to a suite of magnitude 7 scenario earthquakes on the southern San Andreas fault and compare our ground motion predictions with simulations. Both methods find strong amplification and coupling of source and structure effects, but they predict substantially different shaking patterns across the Los Angeles Basin. The virtual earthquake approach provides a new approach for predicting long-period strong ground motion.

  19. Strong negative terahertz photoconductivity in photoexcited graphene

    Science.gov (United States)

    Fu, Maixia; Wang, Xinke; Ye, Jiasheng; Feng, Shengfei; Sun, Wenfeng; Han, Peng; Zhang, Yan

    2018-01-01

    Terahertz (THz) response of a chemical vapor deposited graphene on a quartz substrate has been investigated by using an ultrafast optical-pump THz-probe spectroscopy. Without photoexcitation, the frequency-dependence optical conductivity shows a strong carrier response owing to the intrinsically doped graphene. Upon photoexcitation, an enhancement in THz transmission is observed and the transmission increases nonlinearly with the increase of pump power, which is rooted in a reduction of intrinsic conductivity arising from the strong enhancement of carrier scattering rather than THz emission occurrence. The modulation depth of 18.8% was experimentally achieved, which is more than four times greater than that of the previous reported. The photoinduced response here highlights the variety of response possible in graphene depending on the sample quality, carrier mobility and doping level. The graphene provides promising applications in high-performance THz modulators and THz photoelectric devices.

  20. Cosmological applications of strong gravitational lensing

    DEFF Research Database (Denmark)

    Paraficz, Danuta

    value of the energy density of the two above components, together with measuring the Hubble constant that determines the age of the Universe, is a major goal of modern astrophysics. An interesting method for estimating these parameters is strong gravitational lensing of quasars (QSOs). As shown...... by Refsdal (1964), H0, !m and !! can be measured based on the time delay ("t) between multiply lensed images of QSOs, because "t depends on H0 and on the distances to lens and source, hence!m and !!. Determination of cosmological parameters using gravitational lensing suffers from some degeneracies......, but it is based on well understood physics and unlike distance ladder methods there are no calibration issues. Moreover, it has an advantage over some of the leading methods (such as Type Ia SNe) in that it is a purely cosmological approach. In this thesis, the property of strong gravitational lensing - time...

  1. Gallstone ileus resulting in strong intestinal obstruction

    Directory of Open Access Journals (Sweden)

    Israel Szajnbok

    Full Text Available Mechanic intestinal obstruction, caused by the passage of biliary calculus from vesicle to intestine, through fistulization, although not frequent, deserve study due to the morbi-mortality rates. Incidence in elder people explains the association with chronic degenerative diseases, increasing complexity in terms of therapy decision. Literature discusses the need and opportunity for the one or two-phase surgical attack of the cholecystenteric fistule, in front of the resolution on the obstructive urgency and makes reference to Gallstone Ileus as an exception for strong intestinal obstruction. The more frequent intestinal obstruction observed is when it occurs a Gallstone Ileus impacting in terms of ileocecal valve. The authors submit a Gallstone Ileus manifestation as causing strong intestinal obstruction, discussing aspects regarding diagnostic and treatment.

  2. Strong gauge boson scattering at the LHC

    CERN Document Server

    Rindani, S.D.

    2009-01-01

    In the standard model with electroweak symmetry breaking through the Higgs mechanism, electroweak gauge-boson scattering amplitudes are large if the Higgs boson is heavy, and electroweak gauge interactions become strong. In theories with electroweak symmetry breaking through alternative mechanisms, there could be a strongly interacting gauge sector, possibly with resonances in an accessible energy region. In general, the scattering of longitudinally polarized massive gauge bosons can give information on the mechanism of spontaneous symmetry breaking. At energies below the symmetry breaking scale, the equivalence theorem relates the scattering amplitudes to those of the "would-be" Goldstone modes. In the absence of Higgs bosons, unitarity would be restored by some new physics which can be studied through WW scattering. Some representatives models are discussed. Isolating WW scattering at a hadron collider from other contributions involving W emission from parton lines needs a good understanding of the backgrou...

  3. Strong spin-photon coupling in silicon.

    Science.gov (United States)

    Samkharadze, N; Zheng, G; Kalhor, N; Brousse, D; Sammak, A; Mendes, U C; Blais, A; Scappucci, G; Vandersypen, L M K

    2018-03-09

    Long coherence times of single spins in silicon quantum dots make these systems highly attractive for quantum computation, but how to scale up spin qubit systems remains an open question. As a first step to address this issue, we demonstrate the strong coupling of a single electron spin and a single microwave photon. The electron spin is trapped in a silicon double quantum dot, and the microwave photon is stored in an on-chip high-impedance superconducting resonator. The electric field component of the cavity photon couples directly to the charge dipole of the electron in the double dot, and indirectly to the electron spin, through a strong local magnetic field gradient from a nearby micromagnet. Our results provide a route to realizing large networks of quantum dot-based spin qubit registers. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  4. Cosmogenic photons strongly constrain UHECR source models

    Directory of Open Access Journals (Sweden)

    van Vliet Arjen

    2017-01-01

    Full Text Available With the newest version of our Monte Carlo code for ultra-high-energy cosmic ray (UHECR propagation, CRPropa 3, the flux of neutrinos and photons due to interactions of UHECRs with extragalactic background light can be predicted. Together with the recently updated data for the isotropic diffuse gamma-ray background (IGRB by Fermi LAT, it is now possible to severely constrain UHECR source models. The evolution of the UHECR sources especially plays an important role in the determination of the expected secondary photon spectrum. Pure proton UHECR models are already strongly constrained, primarily by the highest energy bins of Fermi LAT’s IGRB, as long as their number density is not strongly peaked at recent times.

  5. Waves in strong centrifugal fields: dissipationless gas

    Science.gov (United States)

    Bogovalov, S. V.; Kislov, V. A.; Tronin, I. V.

    2015-04-01

    Linear waves are investigated in a rotating gas under the condition of strong centrifugal acceleration of the order 106 g realized in gas centrifuges for separation of uranium isotopes. Sound waves split into three families of the waves under these conditions. Dispersion equations are obtained. The characteristics of the waves strongly differ from the conventional sound waves on polarization, velocity of propagation and distribution of energy of the waves in space for two families having frequencies above and below the frequency of the conventional sound waves. The energy of these waves is localized in rarefied region of the gas. The waves of the third family were not specified before. They propagate exactly along the rotational axis with the conventional sound velocity. These waves are polarized only along the rotational axis. Radial and azimuthal motions are not excited. Energy of the waves is concentrated near the wall of the rotor where the density of the gas is largest.

  6. Quantum strongly secure ramp secret sharing

    DEFF Research Database (Denmark)

    Zhang, Paul; Matsumoto, Rytaro Yamashita

    2015-01-01

    Quantum secret sharing is a scheme for encoding a quantum state (the secret) into multiple shares and distributing them among several participants. If a sufficient number of shares are put together, then the secret can be fully reconstructed. If an insufficient number of shares are put together...... however, no information about the secret can be revealed. In quantum ramp secret sharing, partial information about the secret is allowed to leak to a set of participants, called an unqualified set, that cannot fully reconstruct the secret. By allowing this, the size of a share can be drastically reduced....... This paper introduces a quantum analog of classical strong security in ramp secret sharing schemes. While the ramp secret sharing scheme still leaks partial information about the secret to unqualified sets of participants, the strong security condition ensures that qudits with critical information can...

  7. Quantum Transport in Strongly Correlated Systems

    DEFF Research Database (Denmark)

    Bohr, Dan

    2007-01-01

    the density matrix renormalization group (DMRG) method. We present two DMRG setups for calculating the linear conductance of strongly correlated nanostructures in the infinitesimal source-drain voltage regime. The first setup describes the leads by modified real-space tight-binding chains, whereas the second...... screening plays a much less significant role than in bulk systems due to the reduced size of the objects, therefore making it necessary to consider the importance of correlations between electrons. The work presented in this thesis deals with quantum transport through strongly correlated systems using....... Thus both coherence and correlation effects are important in this model, and the methods applied should be able to handle both these effects rigorously. We present the DMRG setup for this model and benchmark against existing Greens function results for the model. Then we present initial DMRG results...

  8. Hydrogen atoms in a strong magnetic field

    International Nuclear Information System (INIS)

    Santos, R.R. dos.

    1975-07-01

    The energies and wave functions of the 14 lowest states of a Hydrogen atom in a strong magnetic field are calculated, using a variational scheme. The equivalence between the atomic problem and the problems related with excitons and impurities in semiconductors in the presence of a strong magnetic field are shown. The calculations of the energies and wave functions have been divided in two regions: the first, for the magnetic field ranging between zero and 10 9 G; in the second the magnetic field ranges between 10 9 and 10 11 G. The results have been compared with those obtained by previous authors. The computation time necessary for the calculations is small. Therefore this is a convenient scheme to obtain the energies and wave functions for the problem. Transition probabilities, wavelengths and oscillator strengths for some allowed transitions are also calculated. (Author) [pt

  9. Strong Josephson Coupling in Planar Graphene Junctions

    Science.gov (United States)

    Park, Jinho; Lee, Gil-Ho; Lee, Jae Hyeong; Takane, Yositake; Imura, Ken-Ichiro; Taniguchi, Takashi; Watanabe, Kenji; Lee, Hu-Jong

    A recent breakthrough of processing graphene, employing encapsulation by hexagonal boron nitride layers (BGB structure), allows realizing the ballistic carrier transport in graphene. Thereafter, ballistic Josephson coupling has been studied by closely edge-contacted BGB structure with two superconducting electrodes. Here, we report on the strong Josephson coupling with planar graphene junction in truly short and ballistic regime. Our device showed high transmission probability and the junction critical current (IC) oscillating for sweeping the gate voltage along with the normal conductance oscillation (Fabry-Perot oscillations), providing a direct evidence for the ballistic nature of the junction pair current. We also observed the convex-upward shape of decreasing critical currents with increasing temperature, canonical properties of the short Josephson coupling. By fitting these curves into theoretical models, we demonstrate the strong Josephson coupling in our devices, which is also supported by the exceptionally large value of ICRN ( 2 Δ / e RNis the normal resistance).

  10. Electroweak and Strong Interactions Phenomenology, Concepts, Models

    CERN Document Server

    Scheck, Florian

    2012-01-01

    Electroweak and Strong Interaction: Phenomenology, Concepts, Models, begins with relativistic quantum mechanics and some quantum field theory which lay the foundation for the rest of the text. The phenomenology and the physics of the fundamental interactions are emphasized through a detailed discussion of the empirical fundamentals of unified theories of strong, electromagnetic, and weak interactions. The principles of local gauge theories are described both in a heuristic and a geometric framework. The minimal standard model of the fundamental interactions is developed in detail and characteristic applications are worked out. Possible signals of physics beyond that model, notably in the physics of neutrinos are also discussed. Among the applications scattering on nucleons and on nuclei provide salient examples. Numerous exercises with solutions make the text suitable for advanced courses or individual study. This completely updated revised new edition contains an enlarged chapter on quantum chromodynamics an...

  11. Frictional Coulomb drag in strong magnetic fields

    DEFF Research Database (Denmark)

    Bønsager, Martin Christian; Flensberg, Karsten; Hu, Ben Yu-Kuang

    1997-01-01

    A treatment of frictional Coulomb drag between two two-dimensional electron layers in a strong perpendicular magnetic field, within the independent electron picture, is presented. Assuming fully resolved Landau levels, the linear response theory expression for the transresistivity rho(21) is eval......A treatment of frictional Coulomb drag between two two-dimensional electron layers in a strong perpendicular magnetic field, within the independent electron picture, is presented. Assuming fully resolved Landau levels, the linear response theory expression for the transresistivity rho(21......) is evaluated using diagrammatic techniques. The transresistivity is given by an integral over energy and momentum transfer weighted by the product of the screened interlayer interaction and the phase space for scattering events. We demonstrate, by a numerical analysis of the transresistivity, that for well...

  12. Orbits in weak and strong bars

    CERN Document Server

    Contopoulos, George

    1980-01-01

    The authors study the plane orbits in simple bar models embedded in an axisymmetric background when the bar density is about 1% (weak), 10% (intermediate) or 100% (strong bar) of the axisymmetric density. Most orbits follow the stable periodic orbits. The basic families of periodic orbits are described. In weak bars with two Inner Lindblad Resonances there is a family of stable orbits extending from the center up to the Outer Lindblad Resonance. This family contains the long period orbits near corotation. Other stable families appear between the Inner Lindblad Resonances, outside the Outer Lindblad Resonance, around corotation (short period orbits) and around the center (retrograde). Some families become unstable or disappear in strong bars. A comparison is made with cases having one or no Inner Lindblad Resonance. (12 refs).

  13. Strong sum distance in fuzzy graphs.

    Science.gov (United States)

    Tom, Mini; Sunitha, Muraleedharan Shetty

    2015-01-01

    In this paper the idea of strong sum distance which is a metric, in a fuzzy graph is introduced. Based on this metric the concepts of eccentricity, radius, diameter, center and self centered fuzzy graphs are studied. Some properties of eccentric nodes, peripheral nodes and central nodes are obtained. A characterisation of self centered complete fuzzy graph is obtained and conditions under which a fuzzy cycle is self centered are established. We have proved that based on this metric, an eccentric node of a fuzzy tree G is a fuzzy end node of G and a node is an eccentric node of a fuzzy tree if and only if it is a peripheral node of G and the center of a fuzzy tree consists of either one or two neighboring nodes. The concepts of boundary nodes and interior nodes in a fuzzy graph based on strong sum distance are introduced. Some properties of boundary nodes, interior nodes and complete nodes are studied.

  14. Analytical solution of strongly nonlinear Duffing oscillators

    Directory of Open Access Journals (Sweden)

    A.M. El-Naggar

    2016-06-01

    Full Text Available In this paper, a new perturbation technique is employed to solve strongly nonlinear Duffing oscillators, in which a new parameter α=α(ε is defined such that the value of α is always small regardless of the magnitude of the original parameter ε. Therefore, the strongly nonlinear Duffing oscillators with large parameter ε are transformed into a small parameter system with respect to α. Approximate solution obtained by the present method is compared with the solution of energy balance method, homotopy perturbation method, global error minimization method and lastly numerical solution. We observe from the results that this method is very simple, easy to apply, and gives a very good accuracy not only for small parameter εbut also for large values of ε.

  15. Strong interaction studies with kaonic atoms

    Directory of Open Access Journals (Sweden)

    Marton J.

    2016-01-01

    Full Text Available The strong interaction of antikaons (K− with nucleons and nuclei in the low-energy regime represents an active research field connected intrinsically with few-body physics. There are important open questions like the question of antikaon nuclear bound states - the prototype system being K−pp. A unique and rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions in low-lying states of light kaonic atoms like kaonic hydrogen isotopes. In the SIDDHARTA experiment at the electron-positron collider DAΦNE of LNF-INFN we measured the most precise values of the strong interaction observables, i.e. the strong interaction on the 1s ground state of the electromagnetically bound K−p atom leading to a hadronic shift ϵ1s and a hadronic broadening Γ1s of the 1s state. The SIDDHARTA result triggered new theoretical work which achieved major progress in the understanding of the low-energy strong interaction with strangeness. Antikaon-nucleon scattering lengths have been calculated constrained by the SIDDHARTA data on kaonic hydrogen. For the extraction of the isospin-dependent scattering lengths a measurement of the hadronic shift and width of kaonic deuterium is necessary. Therefore, new X-ray studies with the focus on kaonic deuterium are in preparation (SIDDHARTA2. Many improvements in the experimental setup will allow to measure kaonic deuterium which is challenging due to the anticipated low X-ray yield. Especially important are the data on the X-ray yields of kaonic deuterium extracted from a exploratory experiment within SIDDHARTA.

  16. SUSY strong production (leptonic) with ATLAS

    CERN Document Server

    Saito, Tomoyuki; The ATLAS collaboration

    2017-01-01

    Supersymmetry is one of the most motivated scenarios for physics beyond the Standard Model. This article summarizes recent ATLAS results on searches for supersymmetry in proton-proton collisions at a centre-of-mass energy of 13 TeV at LHC, which target supersymmetric particles produced by strong interaction in events with leptonic fi nal states. No signi ficant excess above the Standard Model expectation is observed and exclusion limits have been set on squark and gluino masses in various scenarios.

  17. Strong coupling QED with two fermionic flavors

    Energy Technology Data Exchange (ETDEWEB)

    Wang, K.C.

    1990-11-01

    We report the recent results of our simulation of strong coupling QED, with non-compact action, on lattices 10{sup 4} and 16{sup 4}. Since we are dealing with two staggered fermionic flavors, we use hybrid algorithm to do the simulation. In addition to the measurement of the chiral order parameter {l angle}{bar {psi}}{psi}{r angle}, we also measure magnetic monopole susceptibility, {chi}, throughout the region of chiral transition. 6 refs., 6 figs.

  18. Magnetic properties of strongly asymmetric nuclear matter

    International Nuclear Information System (INIS)

    Kutschera, M.; Wojcik, W.

    1988-01-01

    We investigate stability of neutron matter containing a small proton admixture with respect to spin fluctuations. We establish conditions under which strongly asymmetric nuclear matter could acquire a permanent magnetization. It is shown that if the protons are localized, the system becomes unstable to spin fluctuations for arbitrarily weak proton-neutron spin interactions. For non-localized protons there exists a threshold value of the spin interaction above which the system can develop a spontaneous polarization. 12 refs., 2 figs. (author)

  19. Strong coupling analogue of the Born series

    International Nuclear Information System (INIS)

    Dolinszky, T.

    1989-10-01

    In a given partial wave, the strength of the centrifugal term to be incorporated into the WKBA solutions in different spatial regions can be adjusted so as to make the first order wave functions everywhere smooth and, in strong coupling, exactly reproduce Quantum Mechanics throughout the space. The relevant higher order approximations supply an absolute convergent series expansion of the exact scattering state. (author) 4 refs.; 2 figs.; 2 tabs

  20. Strong-Q-sequences and small d

    Czech Academy of Sciences Publication Activity Database

    Chodounský, David

    2012-01-01

    Roč. 159, č. 3 (2012), s. 2942-2946 ISSN 0166-8641. [Prague Symposium on General Topology and its Relations to Modern Analysis and Algebra /11./. Prague, 07.08.2011-12.08.2011] Institutional support: RVO:67985840 Keywords : Katowice problem * strong-Q-sequence * dominating number Subject RIV: BA - General Mathematics Impact factor: 0.562, year: 2012 http://www.sciencedirect.com/science/article/pii/S0166864112002222

  1. Superbainite. A novel very strong bainitic microstructure

    International Nuclear Information System (INIS)

    Garcia-Mateo, C.; Caballero, E. G.; Bhadeshia, H. K. D. H.

    2005-01-01

    In this work very recent results are how that reveals the possibility of obtaining bainite by isothermal transformation at very low temperatures, of about 150 degree centigree, in high carbon high silicon steels. The microstructure thus obtained is a mixture of fine plates of bainite ferrite (20-40 nm thickness) and thin films of carbon enriched austenite. These microstructures are very hard (600 HV) and strong (2.5 GPa). (Author) 18 refs

  2. Strong decays of nonstrange q3 baryons

    International Nuclear Information System (INIS)

    Bijker, R.; Iachello, F.; Leviatan, A.

    1997-01-01

    We study strong decays of nonstrange baryons by making use of the algebraic approach to hadron structure. Within this framework we derive closed expressions for decay widths in an elementary-meson emission model and use these to analyze the experimental data for N * →N+π, N * →Δ+π, N * →N+η, Δ * →N+π, Δ * →Δ+π, and Δ * →Δ+η decays. copyright 1997 The American Physical Society

  3. Electromotive force in strongly compressible magnetohydrodynamic turbulence

    Science.gov (United States)

    Yokoi, N.

    2017-12-01

    Variable density fluid turbulence is ubiquitous in geo-fluids, not to mention in astrophysics. Depending on the source of density variation, variable density fluid turbulence may be divided into two categories: the weak compressible (entropy mode) turbulence for slow flow and the strong compressible (acoustic mode) turbulence for fast flow. In the strong compressible turbulence, the pressure fluctuation induces a strong density fluctuation ρ ', which is represented by the density variance ( denotes the ensemble average). The turbulent effect on the large-scale magnetic-field B induction is represented by the turbulent electromotive force (EMF) (u': velocity fluctuation, b': magnetic-field fluctuation). In the usual treatment in the dynamo theory, the expression for the EMF has been obtained in the framework of incompressible or weak compressible turbulence, where only the variation of the mean density , if any, is taken into account. We see from the equation of the density fluctuation ρ', the density variance is generated by the large mean density variation ∂ coupled with the turbulent mass flux . This means that in the region where the mean density steeply changes, the density variance effect becomes relevant for the magnetic field evolution. This situation is typically the case for phenomena associated with shocks and compositional discontinuities. With the aid of the analytical theory of inhomogeneous compressible magnetohydrodynamic (MHD) turbulence, the expression for the turbulent electromotive force is investigated. It is shown that, among others, an obliqueness (misalignment) between the mean density gradient ∂ and the mean magnetic field B may contribute to the EMF as ≈χ B×∂ with the turbulent transport coefficient χ proportional to the density variance (χ ). This density variance effect is expected to strongly affect the EMF near the interface, and changes the transport properties of turbulence. In the case of an interface under the MHD slow

  4. Simulation of turbulent flows containing strong shocks

    Science.gov (United States)

    Fryxell, Bruce; Menon, Suresh

    2008-12-01

    Simulation of turbulent flows with strong shocks is a computationally challenging problem. The requirements for a method to produce accurate results for turbulence are orthogonal to those needed to treat shocks properly. In order to prevent an unphysical rate of decay of turbulent structures, it is necessary to use a method with very low numerical dissipation. Because of this, central difference schemes are widely used. However, computing strong shocks with a central difference scheme can produce unphysical post-shock oscillations that corrupt the entire flow unless additional dissipation is added. This dissipation can be difficult to localize to the area near the shock and can lead to inaccurate treatment of the turbulence. Modern high-resolution shock-capturing methods usually use upwind algorithms to provide the dissipation necessary to stabilize shocks. However, this upwind dissipation can also lead to an unphysical rate of decay of the turbulence. This paper discusses a hybrid method for simulating turbulent flows with strong shocks that couples a high-order central difference scheme with a high-resolution shock-capturing method. The shock-capturing method is used only in the vicinity of discontinuities in the flow, whereas the central difference scheme is used in the remainder of the computational domain. Results of this new method will be shown for a variety of test problems. Preliminary results for a realistic application involving detonation in gas-particle flows will also be presented.

  5. Strong CP, flavor, and twisted split fermions

    International Nuclear Information System (INIS)

    Harnik, Roni; Perez, Gilad; Schwartz, Matthew D.; Shirman, Yuri

    2005-01-01

    We present a natural solution to the strong CP problem in the context of split fermions. By assuming CP is spontaneously broken in the bulk, a weak CKM phase is created in the standard model due to a twisting in flavor space of the bulk fermion wavefunctions. But the strong CP phase remains zero, being essentially protected by parity in the bulk and CP on the branes. As always in models of spontaneous CP breaking, radiative corrections to theta bar from the standard model are tiny, but even higher dimension operators are not that dangerous. The twisting phenomenon was recently shown to be generic, and not to interfere with the way that split fermions naturally weaves small numbers into the standard model. It follows that out approach to strong CP is compatible with flavor, and we sketch a comprehensive model. We also look at deconstructed version of this setup which provides a viable 4D model of spontaneous CP breaking which is not in the Nelson-Barr class. (author)

  6. Transport phenomena in strongly correlated Fermi liquids

    Energy Technology Data Exchange (ETDEWEB)

    Kontani, Hiroshi [Nagoya Univ., Aichi (Japan). Dept. of Physics

    2013-03-01

    Comprehensive overview. Written by an expert of this topic. Provides the reader with current developments in the field. In conventional metals, various transport coefficients are scaled according to the quasiparticle relaxation time, {tau}, which implies that the relaxation time approximation (RTA) holds well. However, such a simple scaling does not hold in many strongly correlated electron systems, reflecting their unique electronic states. The most famous example would be cuprate high-Tc superconductors (HTSCs), where almost all the transport coefficients exhibit a significant deviation from the RTA results. To better understand the origin of this discrepancy, we develop a method for calculating various transport coefficients beyond the RTA by employing field theoretical techniques. Near the magnetic quantum critical point, the current vertex correction (CVC), which describes the electron-electron scattering beyond the relaxation time approximation, gives rise to various anomalous transport phenomena. We explain anomalous transport phenomena in cuprate HTSCs and other metals near their magnetic or orbital quantum critical point using a uniform approach. We also discuss spin related transport phenomena in strongly correlated systems. In many d- and f-electron systems, the spin current induced by the spin Hall effect is considerably greater because of the orbital degrees of freedom. This fact attracts much attention due to its potential application in spintronics. We discuss various novel charge, spin and heat transport phenomena in strongly correlated metals.

  7. Simulation of turbulent flows containing strong shocks

    International Nuclear Information System (INIS)

    Fryxell, Bruce; Menon, Suresh

    2008-01-01

    Simulation of turbulent flows with strong shocks is a computationally challenging problem. The requirements for a method to produce accurate results for turbulence are orthogonal to those needed to treat shocks properly. In order to prevent an unphysical rate of decay of turbulent structures, it is necessary to use a method with very low numerical dissipation. Because of this, central difference schemes are widely used. However, computing strong shocks with a central difference scheme can produce unphysical post-shock oscillations that corrupt the entire flow unless additional dissipation is added. This dissipation can be difficult to localize to the area near the shock and can lead to inaccurate treatment of the turbulence. Modern high-resolution shock-capturing methods usually use upwind algorithms to provide the dissipation necessary to stabilize shocks. However, this upwind dissipation can also lead to an unphysical rate of decay of the turbulence. This paper discusses a hybrid method for simulating turbulent flows with strong shocks that couples a high-order central difference scheme with a high-resolution shock-capturing method. The shock-capturing method is used only in the vicinity of discontinuities in the flow, whereas the central difference scheme is used in the remainder of the computational domain. Results of this new method will be shown for a variety of test problems. Preliminary results for a realistic application involving detonation in gas-particle flows will also be presented.

  8. Strong semiclassical approximation of Wigner functions for the Hartree dynamics

    KAUST Repository

    Athanassoulis, Agissilaos

    2011-01-01

    We consider the Wigner equation corresponding to a nonlinear Schrödinger evolution of the Hartree type in the semiclassical limit h → 0. Under appropriate assumptions on the initial data and the interaction potential, we show that the Wigner function is close in L 2 to its weak limit, the solution of the corresponding Vlasov equation. The strong approximation allows the construction of semiclassical operator-valued observables, approximating their quantum counterparts in Hilbert-Schmidt topology. The proof makes use of a pointwise-positivity manipulation, which seems necessary in working with the L 2 norm and the precise form of the nonlinearity. We employ the Husimi function as a pivot between the classical probability density and the Wigner function, which - as it is well known - is not pointwise positive in general.

  9. The INGV Real Time Strong Motion Database

    Science.gov (United States)

    Massa, Marco; D'Alema, Ezio; Mascandola, Claudia; Lovati, Sara; Scafidi, Davide; Gomez, Antonio; Carannante, Simona; Franceschina, Gianlorenzo; Mirenna, Santi; Augliera, Paolo

    2017-04-01

    The INGV real time strong motion data sharing is assured by the INGV Strong Motion Database. ISMD (http://ismd.mi.ingv.it) was designed in the last months of 2011 in cooperation among different INGV departments, with the aim to organize the distribution of the INGV strong-motion data using standard procedures for data acquisition and processing. The first version of the web portal was published soon after the occurrence of the 2012 Emilia (Northern Italy), Mw 6.1, seismic sequence. At that time ISMD was the first European real time web portal devoted to the engineering seismology community. After four years of successfully operation, the thousands of accelerometric waveforms collected in the archive need necessary a technological improvement of the system in order to better organize the new data archiving and to make more efficient the answer to the user requests. ISMD 2.0 was based on PostgreSQL (www.postgresql.org), an open source object- relational database. The main purpose of the web portal is to distribute few minutes after the origin time the accelerometric waveforms and related metadata of the Italian earthquakes with ML≥3.0. Data are provided both in raw SAC (counts) and automatically corrected ASCII (gal) formats. The web portal also provide, for each event, a detailed description of the ground motion parameters (i.e. Peak Ground Acceleration, Velocity and Displacement, Arias and Housner Intensities) data converted in velocity and displacement, response spectra up to 10.0 s and general maps concerning the recent and the historical seismicity of the area together with information about its seismic hazard. The focal parameters of the events are provided by the INGV National Earthquake Center (CNT, http://cnt.rm.ingv.it). Moreover, the database provides a detailed site characterization section for each strong motion station, based on geological, geomorphological and geophysical information. At present (i.e. January 2017), ISMD includes 987 (121

  10. Engaging Military Fathers in a Reflective Parenting Program: Lessons from Strong Families Strong Forces

    Science.gov (United States)

    DeVoe, Ellen R.; Paris, Ruth

    2015-01-01

    Through Strong Families Strong Forces, a reflective parenting program for military families with young children, we were privileged to work with contemporary military fathers who served in the post-9/11 conflicts in Afghanistan and Iraq. Due to this work, the authors gained valuable insight into the complexity of fathering during wartime, the…

  11. 77 FR 16131 - Establishing a White House Council on Strong Cities, Strong Communities

    Science.gov (United States)

    2012-03-20

    ... Order 13602 of March 15, 2012 Establishing a White House Council on Strong Cities, Strong Communities By... enable them to develop and implement economic strategies to become more competitive, sustainable, and inclusive, it is hereby ordered as follows: Section 1. Policy. Cities, towns, and regions across our Nation...

  12. Strong coupling of collection of emitters on hyperbolic meta-material

    Science.gov (United States)

    Biehs, Svend-Age; Xu, Chenran; Agarwal, Girish S.

    2018-04-01

    Recently, considerable effort has been devoted to the realization of a strong coupling regime of the radiation matter interaction in the context of an emitter at a meta surface. The strong interaction is well realized in cavity quantum electrodynamics, which also show that strong coupling is much easier to realize using a collection of emitters. Keeping this in mind, we study if emitters on a hyperbolic meta materials can yield a strong coupling regime. We show that strong coupling can be realized for densities of emitters exceeding a critical value. A way to detect strong coupling between emitters and hyperbolic metamaterials is to use the Kretschman-Raether configuration. The strong coupling appears as the splitting of the reflectivity dip. In the weak coupling regime, the dip position shifts. The shift and splitting can be used to sense active molecules at surfaces.

  13. Bound states in a strong magnetic field

    International Nuclear Information System (INIS)

    Machado, C. S.; Navarra, F. S.; Noronha, J.; Oliveira, E. G.; Ferreira Filho, L. G.

    2013-01-01

    We expect a strong magnetic field to be produced in the perpendicular direction to the reaction plane, in a noncentral heavy-ion collision . The strength of the magnetic field is estimated to be eB∼m 2 π ∼ 0.02 GeV 2 at the RHIC and eB∼ 15m 2 π ∼ 0.3 GeV 2 at the LHC. We investigate the effects of the magnetic field on B 0 and D 0 mesons, focusing on the changes of the energy levels and of the mass of the bound states.

  14. Strong signatures of right-handed compositeness

    Energy Technology Data Exchange (ETDEWEB)

    Redi, Michele [INFN, Sesto Fiorentino, Firenze (Italy); Sanz, Veronica [York Univ., Toronto, ON (Canada). Dept. of Physics and Astronomy; Sussex Univ., Brighton (United Kingdom). Dept. of Physics and Astronomy; Vries, Maikel de; Weiler, Andreas [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2013-05-15

    Right-handed light quarks could be significantly composite, yet compatible with experimental searches at the LHC and precision tests on Standard Model couplings. In these scenarios, that are motivated by flavor physics, one expects large cross sections for the production of new resonances coupled to light quarks. We study experimental strong signatures of right-handed compositeness at the LHC, and constrain the parameter space of these models with recent results by ATLAS and CMS. We show that the LHC sensitivity could be significantly improved if dedicated searches were performed, in particular in multi-jet signals.

  15. The Dark Side of Strongly Coupled Theories

    DEFF Research Database (Denmark)

    Kouvaris, Christoforos

    2008-01-01

    We investigate the constraints of dark matter search experiments on the different candidates emerging from the minimal quasi-conformal strong coupling theory with fermions in the adjoint representation. For one candidate, the current limits of CDMS exclude a tiny window of masses around 120 GeV. We...... also investigate under what circumstances the newly proposed candidate composed of a -2 negatively charged particle and a $^4He^{+2}$ can explain the discrepancy between the results of the CDMS and DAMA experiments. We found that this type of dark matter should give negative results in CDMS, while...

  16. Fundamental Structure of Matter and Strong Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Jian-Ping Chen

    2011-11-01

    More than 99% of the visible matter in the universe are the protons and neutrons. Their internal structure is mostly governed by the strong interaction. Understanding their internal structure in terms of fundamental degrees-of-freedom is one of the most important subjects in modern physics. Worldwide efforts in the last few decades have lead to numerous surprises and discoveries, but major challenges still remain. An overview of the progress will be presented with a focus on the recent studies of the proton and neutron's electromagnetic and spin structure. Future perspectives will be discussed.

  17. Strong Interaction Studies with PANDA at FAIR

    International Nuclear Information System (INIS)

    Schönning, Karin

    2016-01-01

    The Facility for Antiproton and Ion Research (FAIR) in Darmstadt, Germany, provides unique possibilities for a new generation of nuclear-, hadron- and atomic physics experiments. The future PANDA experiment at FAIR will offer a broad physics programme with emphasis on different aspects of hadron physics. Understanding the strong interaction in the perturbative regime remains one of the greatest challenges in contemporary physics and hadrons provide several important keys. In these proceedings, PANDA will be presented along with some high-lights of the planned physics programme

  18. Hawking radiation and strong gravity black holes

    International Nuclear Information System (INIS)

    Qadir, A.; Sayed, W.A.

    1979-01-01

    It is shown that the strong gravity theory of Salam et al. places severe restrictions on black hole evaporation. Two major implications are that: mini blck holes (down to masses approximately 10 -16 kg) would be stable in the present epoch; and that some suggested mini black hole mechanisms to explain astrophysical phenomena would not work. The first result implies that f-gravity appears to make black holes much safer by removing the possibility of extremely violent black hole explosions suggested by Hawking. (Auth.)

  19. Wormhole effect in a strong topological insulator

    Science.gov (United States)

    Rosenberg, G.; Guo, H.-M.; Franz, M.

    2010-07-01

    An infinitely thin solenoid carrying magnetic flux Φ (a “Dirac string”) inserted into an ordinary band insulator has no significant effect on the spectrum of electrons. In a strong topological insulator, remarkably, such a solenoid carries protected gapless one-dimensional fermionic modes when Φ=hc/2e . These modes are spin-filtered and represent a distinct bulk manifestation of the topologically nontrivial insulator. We establish this “wormhole” effect by both general qualitative considerations and by numerical calculations within a minimal lattice model. We also discuss the possibility of experimental observation of a closely related effect in artificially engineered nanostructures.

  20. Strong piezoelectricity in bioinspired peptide nanotubes.

    Science.gov (United States)

    Kholkin, Andrei; Amdursky, Nadav; Bdikin, Igor; Gazit, Ehud; Rosenman, Gil

    2010-02-23

    We show anomalously strong shear piezoelectric activity in self-assembled diphenylalanine peptide nanotubes (PNTs), indicating electric polarization directed along the tube axis. Comparison with well-known piezoelectric LiNbO(3) and lateral signal calibration yields sufficiently high effective piezoelectric coefficient values of at least 60 pm/V (shear response for tubes of approximately 200 nm in diameter). PNTs demonstrate linear deformation without irreversible degradation in a broad range of driving voltages. The results open up a wide avenue for developing new generations of "green" piezoelectric materials and piezonanodevices based on bioactive tubular nanostructures potentially compatible with human tissue.

  1. Development of a strong electromagnet wiggler

    International Nuclear Information System (INIS)

    Burns, M.J.; Deis, G.A.; Holmes, R.H.; Van Maren, R.D.; Halbach, K.

    1987-01-01

    The Strong Electromagnet (SEM) wiggler is a permanent magnet-assisted electromagnet under development at the Lawrence Livermore National Laboratory (LLNL) as part of the Induction Linac Free-Electron-Laser (IFEL) program. This concept uses permanent magnets within the wiggler to provide a reverse bias flux in the iron and thus delay the onset of magnetic saturation. The electromagnet coils determine the wiggler field and operate at low current densities by virtue of their placement away from the midplane. We describe here the design approach used and test data from a 7-period wiggler prototype that includes curved pole tips to provide wiggle-plane focusing. 7 refs

  2. Strong Interactions Physics at BaBar

    Energy Technology Data Exchange (ETDEWEB)

    Pioppi, M.

    2005-03-14

    Recent results obtained by BABAR experiment and related to strong interactions physics are presented, with particular attention to the extraction of the first four hadronic-mass moments and the first three lepton-energy moments in semileptonic decays. From a simultaneous fit to the moments, the CKM element |V{sub cb}|, the inclusive B {yields} X{sub c}lv and other heavy quark parameters are derived. The second topic is the ambiguity-free measurement of cos(2{beta}) in B {yields} J/{Psi}K* decays. With approximately 88 million of B{bar B} pairs, negative solutions for cos(2{beta}) are excluded at 89%.

  3. Phase diagram of strongly correlated Fermi systems

    International Nuclear Information System (INIS)

    Zverev, M.V.; Khodel', V.A.; Baldo, M.

    2000-01-01

    Phase transitions in uniform Fermi systems with repulsive forces between the particles caused by restructuring of quasiparticle filling n(p) are analyzed. It is found that in terms of variables, i.e. density ρ, nondimensional binding constant η, phase diagram of a strongly correlated Fermi system for rather a wide class of interactions reminds of a puff-pastry pie. Its upper part is filled with fermion condensate, the lower one - with normal Fermi-liquid. They are separated by a narrow interlayer - the Lifshits phase, characterized by the Fermi multibound surface [ru

  4. Quantum electrodynamics in strong external fields

    International Nuclear Information System (INIS)

    Mueller, B.; Rafelski, J.; Kirsch, J.

    1981-05-01

    We review the theoretical description of quantum electrodynamics in the presence of strong and supercritical fields. In particular, the process of the spontaneous vacuum decay accompanied by the observable positron emission in heavy ion collisions is described. Emphasis is put on the proper formulation of many-body aspects in the framework of quantum field theory. The extension of the theory to the description of Bose fields and many-body effects is presented, and the Klein paradox is resolved. Some implications of the theoretical methods developed here are presented concerning non-abelian gauge theories and the quark confinement puzzle. (orig.)

  5. Strong Interaction Studies with PANDA at FAIR

    Science.gov (United States)

    Schönning, Karin

    2016-10-01

    The Facility for Antiproton and Ion Research (FAIR) in Darmstadt, Germany, provides unique possibilities for a new generation of nuclear-, hadron- and atomic physics experiments. The future PANDA experiment at FAIR will offer a broad physics programme with emphasis on different aspects of hadron physics. Understanding the strong interaction in the perturbative regime remains one of the greatest challenges in contemporary physics and hadrons provide several important keys. In these proceedings, PANDA will be presented along with some high-lights of the planned physics programme.

  6. Differentiation of 13 positive emotions by appraisals.

    Science.gov (United States)

    Tong, Eddie M W

    2015-01-01

    This research examined how strongly appraisals can differentiate positive emotions and how they differentiate positive emotions. Thirteen positive emotions were examined, namely, amusement, awe, challenge, compassion, contentment, gratitude, hope, interest, joy, pride, relief, romantic love and serenity. Participants from Singapore and the USA recalled an experience of each emotion and thereafter rated their appraisals of the experience. In general, the appraisals accurately classified the positive emotions at rates above chance levels, and the appraisal-emotion relationships conformed to predictions. Also, the appraisals were largely judged by participants as relevant to their positive emotion experiences, and the appraisal-emotion relationships were largely consistent across the two countries.

  7. Iterative solutions of nonlinear equations with strongly accretive or strongly pseudocontractive maps

    International Nuclear Information System (INIS)

    Chidume, C.E.

    1994-03-01

    Let E be a real q-uniformly smooth Banach space. Suppose T is a strongly pseudo-contractive map with open domain D(T) in E. Suppose further that T has a fixed point in D(T). Under various continuity assumptions on T it is proved that each of the Mann iteration process or the Ishikawa iteration method converges strongly to the unique fixed point of T. Related results deal with iterative solutions of nonlinear operator equations involving strongly accretive maps. Explicit error estimates are also provided. (author). 38 refs

  8. Towards TDDFT for Strongly Correlated Materials

    Directory of Open Access Journals (Sweden)

    Shree Ram Acharya

    2016-09-01

    Full Text Available We present some details of our recently-proposed Time-Dependent Density-Functional Theory (TDDFT for strongly-correlated materials in which the exchange-correlation (XC kernel is derived from the charge susceptibility obtained using Dynamical Mean-Field Theory (the TDDFT + DMFT approach. We proceed with deriving the expression for the XC kernel for the one-band Hubbard model by solving DMFT equations via two approaches, the Hirsch–Fye Quantum Monte Carlo (HF-QMC and an approximate low-cost perturbation theory approach, and demonstrate that the latter gives results that are comparable to the exact HF-QMC solution. Furthermore, through a variety of applications, we propose a simple analytical formula for the XC kernel. Additionally, we use the exact and approximate kernels to examine the nonhomogeneous ultrafast response of two systems: a one-band Hubbard model and a Mott insulator YTiO3. We show that the frequency dependence of the kernel, i.e., memory effects, is important for dynamics at the femtosecond timescale. We also conclude that strong correlations lead to the presence of beats in the time-dependent electric conductivity in YTiO3, a feature that could be tested experimentally and that could help validate the few approximations used in our formulation. We conclude by proposing an algorithm for the generalization of the theory to non-linear response.

  9. The Athens Acropolis Strong Motion Array

    Science.gov (United States)

    Kalogeras, I. S.; Evangelidis, C. P.; Melis, N. S.; Boukouras, K.

    2012-04-01

    During the last decades, extensive restoration works through a dedicated "Acropolis Restoration Service" (YSMA) take place in the Acropolis, the greatest sanctuary of ancient Athens. Since 2008, a permanent strong motion array was deployed by the Institute of Geodynamics, National Observatory of Athens (NOA-IG) in collaboration with YSMA. Free field installations were decided at sites showing various characteristics, aiming to investigate differences in geotechnical properties as well as the structure response of Parthenon itself. The installation phase is presented, with the techniques used to overcome difficulties (i.e. extreme weather conditions, power and communication limitations, restoration works and visitors) and the special care taken for the specific archaeological site. Furthermore, indicative examples of seismic events recorded by the array are analyzed and the complexity of the hill and the monument is made apparent. Among them, the long distance events of Tohoku, Japan 2010 and Van, Turkey 2011, some regional moderate earthquakes in Greece and some weak earthquakes from the vicinity. Continuous ambient noise monitoring using PQLX software gives some first indicative results, showing a variety of characteristics at installation sites. Finally, further developments and future steps are presented such as: the extension of the array, the integration of seismic data within the GIS platform of YSMA at the site and the use of strong motion records, in conjunction with data from other monitoring systems operating in Acropolis for the study of specific monuments.

  10. Relativistically strong electromagnetic radiation in a plasma

    Science.gov (United States)

    Bulanov, S. V.; Esirkepov, T. Zh.; Kando, M.; Kiriyama, H.; Kondo, K.

    2016-03-01

    Physical processes in a plasma under the action of relativistically strong electromagnetic waves generated by high-power lasers have been briefly reviewed. These processes are of interest in view of the development of new methods for acceleration of charged particles, creation of sources of bright hard electromagnetic radiation, and investigation of macroscopic quantum-electrodynamical processes. Attention is focused on nonlinear waves in a laser plasma for the creation of compact electron accelerators. The acceleration of plasma bunches by the radiation pressure of light is the most efficient regime of ion acceleration. Coherent hard electromagnetic radiation in the relativistic plasma is generated in the form of higher harmonics and/or electromagnetic pulses, which are compressed and intensified after reflection from relativistic mirrors created by nonlinear waves. In the limit of extremely strong electromagnetic waves, radiation friction, which accompanies the conversion of radiation from the optical range to the gamma range, fundamentally changes the behavior of the plasma. This process is accompanied by the production of electron-positron pairs, which is described within quantum electrodynamics theory.

  11. Strong Double Higgs Production at the LHC

    CERN Document Server

    Contino, Roberto; Moretti, Mauro; Piccinini, Fulvio; Rattazzi, Riccardo

    2010-01-01

    The hierarchy problem and the electroweak data, together, provide a plausible motivation for considering a light Higgs emerging as a pseudo-Goldstone boson from a strongly-coupled sector. In that scenario, the rates for Higgs production and decay differ significantly from those in the Standard Model. However, one genuine strong coupling signature is the growth with energy of the scattering amplitudes among the Goldstone bosons, the longitudinally polarized vector bosons as well as the Higgs boson itself. The rate for double Higgs production in vector boson fusion is thus enhanced with respect to its negligible rate in the SM. We study that reaction in pp collisions, where the production of two Higgs bosons at high pT is associated with the emission of two forward jets. We concentrate on the decay mode hh -> WW^(*)WW^(*) and study the semi-leptonic decay chains of the W's with 2, 3 or 4 leptons in the final states. While the 3 lepton final states are the most relevant and can lead to a 3 sigma signal significa...

  12. Finite temperature system of strongly interacting baryons

    Energy Technology Data Exchange (ETDEWEB)

    Bowers, R.L.; Gleeson, A.M.; Pedigo, R.D.; Wheeler, J.W.

    1976-07-01

    A fully relativistic finite temperature many body theory is constructed and used to examine the bulk properties of a system of strongly interacting baryons. The strong interactions are described by a two parameter phenomenological model fit to a simple description of nuclear matter at T = 0. The zero temperature equation of state for such a system which has already been discussed in the literature was developed to give a realistic description of nuclear matter. The model presented here is the exact finite temperature extension of that model. The effect of the inclusion of baryon pairs for T greater than or equal to 2mc/sup 2//k is discussed in detail. The phase transition identified with nuclear matter vanishes for system temperatures in excess of T/sub C/ = 1.034 x 10/sup 11/ /sup 0/K. All values of epsilon (P,T) correspond to systems that are causal in the sense that the locally determined speed of sound never exceeds the speed of light.

  13. Finite temperature system of strongly interacting baryons

    International Nuclear Information System (INIS)

    Bowers, R.L.; Gleeson, A.M.; Pedigo, R.D.; Wheeler, J.W.

    1976-07-01

    A fully relativistic finite temperature many body theory is constructed and used to examine the bulk properties of a system of strongly interacting baryons. The strong interactions are described by a two parameter phenomenological model fit to a simple description of nuclear matter at T = 0. The zero temperature equation of state for such a system which has already been discussed in the literature was developed to give a realistic description of nuclear matter. The model presented here is the exact finite temperature extension of that model. The effect of the inclusion of baryon pairs for T greater than or equal to 2mc 2 /k is discussed in detail. The phase transition identified with nuclear matter vanishes for system temperatures in excess of T/sub C/ = 1.034 x 10 11 0 K. All values of epsilon (P,T) correspond to systems that are causal in the sense that the locally determined speed of sound never exceeds the speed of light

  14. Holographic gauge mediation via strongly coupled messengers

    International Nuclear Information System (INIS)

    McGuirk, Paul; Shiu, Gary; Sumitomo, Yoske

    2010-01-01

    We consider a relative of semidirect gauge mediation where the hidden sector exists at large 't Hooft coupling. Such scenarios can be difficult to describe using perturbative field theory methods but may fall into the class of holographic gauge mediation scenarios, meaning that they are amenable to the techniques of gauge/gravity duality. We use a recently found gravity solution to examine one such case, where the hidden sector is a cascading gauge theory resulting in a confinement scale not much smaller than the messenger mass. In the original construction of holographic gauge mediation, as in other examples of semidirect gauge mediation at strong coupling, the primary contributions to visible sector soft terms come from weakly coupled messenger mesons. In contrast to these examples, we describe the dual of a gauge theory where there are significant contributions from scales in which the strongly coupled messenger quarks are the effective degrees of freedom. In this regime, the visible sector gaugino mass can be calculated entirely from holography.

  15. NMR study of strongly correlated electron systems

    Science.gov (United States)

    Kitaoka, Y.; Tou, H.; Zheng, G.-q.; Ishida, K.; Asayama, K.; Kobayashi, T. C.; Kohda, A.; Takeshita, N.; Amaya, K.; Onuki, Y.; Geibel, G.; Schank, C.; Steglich, F.

    1995-02-01

    Various types of ground states in strongly correlated electron systems have been systematically investigated by means of NMR/NQR at low temperatures under high magnetic field and pressure. We focus on two well-known heavy-electron families, CeCu 2X 2 (X = Si and Ge) (Ce(122)) and UM 2Al 3 (M = Ni and Pd) (U(123)). The Cu NQR experiments on CeCu 2X 2 under high pressure indicate that the physical property of CeCu 2Ge 2 at high pressure, i.e. above the transition at 7.6 GPa from antiferromagnetic (AF) to superconductivity, are clearly related to tha CeCu 2Si 2 at ambient pressure. In addition to the H-T phase diagram established below 7 T, NMR and specific heat experiments on polycrystal CeCu 2.05Si 2 have revealed the presence of a new phase above 7 T. In a high-quality polycrystal of UPd 2Al 3 with a record high- Tc of 2 K at ambient pressure and the narrowest Al NQR line width, the nuclear-spin lattice relaxation rate, 27(1/ T1) measured in zero field has been found to obey the T3 law down to 0.13 K, giving strong evidence that the energy gap vanishes along lines on the Fermi surface. Thus it seems that all heavy-electron superconductors exhibit lines of zero gap, regardless of their different magnetic properties.

  16. Positive Education: Positive Psychology and Classroom Interventions

    Science.gov (United States)

    Seligman, Martin E. P.; Ernst, Randal M.; Gillham, Jane; Reivich, Karen; Linkins, Mark

    2009-01-01

    Positive education is defined as education for both traditional skills and for happiness. The high prevalence worldwide of depression among young people, the small rise in life satisfaction, and the synergy between learning and positive emotion all argue that the skills for happiness should be taught in school. There is substantial evidence from…

  17. Want Positive Behavior? Use Positive Language

    Science.gov (United States)

    Wood, Chip; Freeman-Loftis, Babs

    2012-01-01

    Positive adult language is the professional use of words and tone of voice to enable students to learn in an engaged, active way. This includes learning social skills. To guide children toward choosing and maintaining positive behaviors, adults need to carefully choose the words and tone of voice used when speaking to them. Learning to use…

  18. Deposition of newly synthesized histones: new histones H2A and H2B do not deposit in the same nucleosome with new Histones H3 and H4

    International Nuclear Information System (INIS)

    Jackson, V.

    1987-01-01

    The authors have developed procedures to study histone-histone interactions during the deposition of histones in replicating cells. Cells are labeled for 60 min with dense amino acids, and subsequently, the histones within the nucleosomes are cross-linked into an octameric complex with formaldehyde. These complexes are sedimented to equilibrium in density gradients and octamer and dioctamer complexes separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With reversal of the cross-link, the distribution of the individual density-labeled histones in the octamer is determined. Newly synthesized H3 and H4 deposits as a tetramer and are associated with old H2A and H2B. Newly synthesized H2A and H2B deposit as a dimer associated with old H2A, H2B, H3, and H4. The significance of these results with respect to the dynamics of histone interactions in the nucleus is discussed. Control experiments are presented to test for artifactual formation of these complexes during preparative procedures. In addition, reconstitution experiments were performed to demonstrate that the composition of these octameric complexes can be determined from their distribution of density gradients

  19. Enhanced thermal photon and dilepton production in strongly coupled = 4 SYM plasma in strong magnetic field

    Science.gov (United States)

    Mamo, Kiminad A.

    2013-08-01

    We calculate the DC conductivity tensor of strongly coupled = 4 super-Yang-Mills (SYM) plasma in a presence of a strong external magnetic field B ≫ T 2 by using its gravity dual and employing both the RG flow approach and membrane paradigm which give the same results. We find that, since the magnetic field B induces anisotropy in the plasma, different components of the DC conductivity tensor have different magnitudes depending on whether its components are in the direction of the magnetic field B. In particular, we find that a component of the DC conductivity tensor in the direction of the magnetic field B increases linearly with B while the other components (which are not in the direction of the magnetic field B) are independent of it. These results are consistent with the lattice computations of the DC conductivity tensor of the QCD plasma in an external magnetic field B. Using the DC conductivity tensor, we calculate the soft or low-frequency thermal photon and dilepton production rates of the strongly coupled = 4 SYM plasma in the presence of the strong external magnetic field B ≫ T 2. We find that the strong magnetic field B enhances both the thermal photon and dilepton production rates of the strongly coupled = 4 SYM plasma in a qualitative agreement with the experimentally observed enhancements at the heavy-ion collision experiments.

  20. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    Science.gov (United States)

    Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

    2014-09-01

    High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

  1. Convex Modeling of Interactions with Strong Heredity.

    Science.gov (United States)

    Haris, Asad; Witten, Daniela; Simon, Noah

    2016-01-01

    We consider the task of fitting a regression model involving interactions among a potentially large set of covariates, in which we wish to enforce strong heredity. We propose FAMILY, a very general framework for this task. Our proposal is a generalization of several existing methods, such as VANISH [Radchenko and James, 2010], hierNet [Bien et al., 2013], the all-pairs lasso, and the lasso using only main effects. It can be formulated as the solution to a convex optimization problem, which we solve using an efficient alternating directions method of multipliers (ADMM) algorithm. This algorithm has guaranteed convergence to the global optimum, can be easily specialized to any convex penalty function of interest, and allows for a straightforward extension to the setting of generalized linear models. We derive an unbiased estimator of the degrees of freedom of FAMILY, and explore its performance in a simulation study and on an HIV sequence data set.

  2. Strong Turbulence in Low-beta Plasmas

    DEFF Research Database (Denmark)

    Tchen, C. M.; Pécseli, Hans; Larsen, Søren Ejling

    1980-01-01

    An investigation of the spectral structure of turbulence in a plasma confined by a strong homogeneous magnetic field was made by means of a fluid description. The turbulent spectrum is divided into subranges. Mean gradients of velocity and density excite turbulent motions, and govern the production...... subrange. The spectra of velocity and potential fluctuations interact in the coupling subrange, and the energy is transferred along the spectrum in the inertia subrange. Applying the method of cascade decomposition, the spectral laws k-3, k-3, k-2 are obtained for the velocity fluctuations, and k-3, k-5, k......-3/2 for the potential fluctuations in the production, coupling and inertia subranges, respectively. The coefficient of Bohm diffusion is reproduced, and its role in electrostatic coupling is derived. Comparison is made with measured power laws reported in the literature, from Q-devices, hot...

  3. Strong crystal size effect on deformation twinning

    DEFF Research Database (Denmark)

    Yu, Qian; Shan, Zhi-Wei; Li, Ju

    2010-01-01

    find that the stress required for deformation twinning increases drastically with decreasing sample size of a titanium alloy single crystal7, 8, until the sample size is reduced to one micrometre, below which the deformation twinning is entirely replaced by less correlated, ordinary dislocation...... plasticity. Accompanying the transition in deformation mechanism, the maximum flow stress of the submicrometre-sized pillars was observed to saturate at a value close to titanium’s ideal strength9, 10. We develop a ‘stimulated slip’ model to explain the strong size dependence of deformation twinning....... The sample size in transition is relatively large and easily accessible in experiments, making our understanding of size dependence11, 12, 13, 14, 15, 16, 17 relevant for applications....

  4. Towards Integrated Marmara Strong Motion Network

    Science.gov (United States)

    Durukal, E.; Erdik, M.; Safak, E.; Ansal, A.; Ozel, O.; Alcik, H.; Mert, A.; Kafadar, N.; Korkmaz, A.; Kurtulus, A.

    2009-04-01

    Istanbul has a 65% chance of having a magnitude 7 or above earthquake within the next 30 years. As part of the preparations for the future earthquake, strong motion networks have been installed in and around Istanbul. The Marmara Strong Motion Network, operated by the Department of Earthquake Engineering of Kandilli Observatory and Earthquake Research Institute, encompasses permanent systems outlined below. It is envisaged that the networks will be run by a single entity responsible for technical management and maintanence, as well as for data management, archiving and dissemination through dedicated web-based interfaces. • Istanbul Earthquake Rapid Response and Early Warning System - IERREWS (one hundred 18-bit accelerometers for rapid response; ten 24-bit accelerometers for early warning) • IGDAŞ Gas Shutoff Network (100 accelerometers to be installed in 2010 and integrated with IERREWS) • Structural Monitoring Arrays - Fatih Sultan Mehmet Suspension Bridge (1200m-long suspension bridge across the Bosphorus, five 3-component accelerometers + GPS sensors) - Hagia Sophia Array (1500-year-old historical edifice, 9 accelerometers) - Süleymaniye Mosque Array (450-year-old historical edifice,9 accelerometers) - Fatih Mosque Array (237-year-old historical edifice, 9 accelerometers) - Kanyon Building Array (high-rise office building, 5 accelerometers) - Isbank Tower Array (high-rise office building, 5 accelerometers) - ENRON Array (power generation facility, 4 acelerometers) - Mihrimah Sultan Mosque Array (450-year-old historical edifice,9 accelerometers + tiltmeters, to be installed in 2009) - Sultanahmet Mosque Array, (390-year-old historical edifice, 9 accelerometers + tiltmeters, to be installed in 2009) • Special Arrays - Atakoy Vertical Array (four 3-component accelerometers at 25, 50, 75, and 150 m depths) - Marmara Tube Tunnel (1400 m long submerged tunnel, 128 ch. accelerometric data, 24 ch. strain data, to be installed in 2010) - Air-Force Academy

  5. Strongly coupled band in 140Gd

    International Nuclear Information System (INIS)

    Falla-Sotelo, F.; Oliveira, J.R.B.; Rao, M.N.

    2005-01-01

    Several high-K states are known to exist in the mass 130-140 region. For the N=74 even-even isotopes, Kπ = 8 - isomers, with lifetimes ranging from ns to ms, are known in 128 Xe, 130 Ba, 132 Ce, 134 Nd, 136 Sm, and 138 Gd[. In 140 Gd, we have observed for the first time a band also based on an Iπ = 8 - state. This could be the first case of a Kπ = 8 - state observed in an N=76 even-even isotope. The systematics of the Kπ = 8 - isomeric states in N=74 isotopes has been studied by A.M. Bruce et al. These states decay towards the K = 0 ground state band, and the transitions are K-forbidden. The 140 Gd case presents strong similarities but also some significant differences with relation to the N=74 isotopes. We propose the same configuration but with larger deformation in 140 Gd

  6. Thomson scattering in strong external fields

    Science.gov (United States)

    Varró, S.; Ehlotzky, F.

    1992-09-01

    In the present paper we shall investigate relativistic Thomson scattering in two external fields. A free classical electron will be embedded in a strong, constant and homogeneous magnetic field and in a powerful electromagnetic field. Both fields will be considered in the Redmond configuration, in which case the electromagnetic wave is circularly polarized and propagates in the direction of the homogeneous magnetic field. The electron will be allowed to have arbitrary initial conditions and the electromagnetic wave will be switched on either suddenly or adiabatically. We shall present the exact solution of the Lorentz equation of motion in the above external field configuration and we shall evaluate the spectrum and cross sections of the scattered radiation. In particular, we shall consider scattering close to resonance and we shall compare our results with the findings of earlier work.

  7. Strongly Interacting Matter at High Energy Density

    International Nuclear Information System (INIS)

    McLerran, L.

    2008-01-01

    This lecture concerns the properties of strongly interacting matter (which is described by Quantum Chromodynamics) at very high energy density. I review the properties of matter at high temperature, discussing the deconfinement phase transition. At high baryon density and low temperature, large N c arguments are developed which suggest that high baryonic density matter is a third form of matter, Quarkyonic Matter, that is distinct from confined hadronic matter and deconfined matter. I finally discuss the Color Glass Condensate which controls the high energy limit of QCD, and forms the low x part of a hadron wavefunction. The Glasma is introduced as matter formed by the Color Glass Condensate which eventually thermalizes into a Quark Gluon Plasma

  8. Strong curvature effects in Neumann wave problems

    DEFF Research Database (Denmark)

    Willatzen, Morten; Pors, A.; Gravesen, Jens

    2012-01-01

    Waveguide phenomena play a major role in basic sciences and engineering. The Helmholtz equation is the governing equation for the electric field in electromagnetic wave propagation and the acoustic pressure in the study of pressure dynamics. The Schro¨dinger equation simplifies to the Helmholtz...... equation for a quantum-mechanical particle confined by infinite barriers relevant in semiconductor physics. With this in mind and the interest to tailor waveguides towards a desired spectrum and modal pattern structure in classical structures and nanostructures, it becomes increasingly important...... to understand the influence of curvature effects in waveguides. In this work, we demonstrate analytically strong curvature effects for the eigenvalue spectrum of the Helmholtz equation with Neumann boundary conditions in cases where the waveguide cross section is a circular sector. It is found that the linear...

  9. Neutrino oscillations in strong magnetic fields

    International Nuclear Information System (INIS)

    Likhachev, G.G.; Studenikin, A.I.

    1994-07-01

    Neutrino conversion processes between two neutrino species and the corresponding oscillations induced by strong magnetic fields are considered. The value of the critical strength of magnetic field B cr as a function of characteristics of neutrinos in vacuum (Δm 2 ν , mixing angle θ), effective particle density of matter n eff , neutrino (transition) magnetic moment μ-tilde and energy E is introduced. It is shown that the neutrino conversion and oscillations effects induced by magnetic fields B ≥ B cr are important and may result in the depletion of the initial type of ν's in the bunch. A possible increase of these effects in the case when neutrinos pass through a sudden decrease of density of matter (''cross-boundary effect'') and applications to neutrinos from neutron stars and supernova are discussed. (author). 25 refs

  10. Transport phenomena in strongly correlated Fermi liquids

    CERN Document Server

    Kontani, Hiroshi

    2013-01-01

    In conventional metals, various transport coefficients are scaled according to the quasiparticle relaxation time, \\tau, which implies that the relaxation time approximation (RTA) holds well. However, such a simple scaling does not hold in many strongly correlated electron systems, reflecting their unique electronic states. The most famous example would be cuprate high-Tc superconductors (HTSCs), where almost all the transport coefficients exhibit a significant deviation from the RTA results. To better understand the origin of this discrepancy, we develop a method for calculating various transport coefficients beyond the RTA by employing field theoretical techniques. Near the magnetic quantum critical point, the current vertex correction (CVC), which describes the electron-electron scattering beyond the relaxation time approximation, gives rise to various anomalous transport phenomena. We explain anomalous transport phenomena in cuprate HTSCs and other metals near their magnetic or orbital quantum critical poi...

  11. Cosmological applications of strong gravitational lensing

    DEFF Research Database (Denmark)

    Paraficz, Danuta

    value of the energy density of the two above components, together with measuring the Hubble constant that determines the age of the Universe, is a major goal of modern astrophysics. An interesting method for estimating these parameters is strong gravitational lensing of quasars (QSOs). As shown......One of the most intriguing recent results in physics is the growing evidence that an unknown energy field and an unknown kind of matter are the major components of the Universe (70% and 30%, respectively; see e.g. Riess et al. 1998, Spergel et al. 2007). Understanding and estimating the precise...... by Refsdal (1964), H0, !m and !! can be measured based on the time delay ("t) between multiply lensed images of QSOs, because "t depends on H0 and on the distances to lens and source, hence!m and !!. Determination of cosmological parameters using gravitational lensing suffers from some degeneracies...

  12. Weak and strong typicality in quantum systems.

    Science.gov (United States)

    Santos, Lea F; Polkovnikov, Anatoli; Rigol, Marcos

    2012-07-01

    We study the properties of mixed states obtained from eigenstates of many-body lattice Hamiltonians after tracing out part of the lattice. Two scenarios emerge for generic systems: (i) The diagonal entropy becomes equivalent to the thermodynamic entropy when a few sites are traced out (weak typicality); and (ii) the von Neumann (entanglement) entropy becomes equivalent to the thermodynamic entropy when a large fraction of the lattice is traced out (strong typicality). Remarkably, the results for few-body observables obtained with the reduced, diagonal, and canonical density matrices are very similar to each other, no matter which fraction of the lattice is traced out. Hence, for all physical quantities studied here, the results in the diagonal ensemble match the thermal predictions.

  13. Machine Learning Phases of Strongly Correlated Fermions

    Directory of Open Access Journals (Sweden)

    Kelvin Ch’ng

    2017-08-01

    Full Text Available Machine learning offers an unprecedented perspective for the problem of classifying phases in condensed matter physics. We employ neural-network machine learning techniques to distinguish finite-temperature phases of the strongly correlated fermions on cubic lattices. We show that a three-dimensional convolutional network trained on auxiliary field configurations produced by quantum Monte Carlo simulations of the Hubbard model can correctly predict the magnetic phase diagram of the model at the average density of one (half filling. We then use the network, trained at half filling, to explore the trend in the transition temperature as the system is doped away from half filling. This transfer learning approach predicts that the instability to the magnetic phase extends to at least 5% doping in this region. Our results pave the way for other machine learning applications in correlated quantum many-body systems.

  14. The new <Strong Italian Earthquakes>>

    Directory of Open Access Journals (Sweden)

    G. Valensise

    1995-06-01

    Full Text Available We describe a new catalogue of strong ltalian earthquakes that the Istituto Nazionale di Geofisica in collaboration with SGA, has recently made available to the international scientific community and to the general public. The new catalogue differs from previous efforts in that for each event the usual seismic parameters are complemented by a list of intensity rated localities, a complete list of relevant references, a series of synoptic comments describing different aspects of the earthquake phenomenology. and in most cases even the text of the original written sources. The printed part of the catalogue has been published as a special monograph which contains also a computer version of the full database in the form of a CD-ROM. The software package includes a computer program for retrieving, selecting and displaying the catalogue data.

  15. Strong curvature effects in Neumann wave problems

    International Nuclear Information System (INIS)

    Willatzen, M.; Pors, A.; Gravesen, J.

    2012-01-01

    Waveguide phenomena play a major role in basic sciences and engineering. The Helmholtz equation is the governing equation for the electric field in electromagnetic wave propagation and the acoustic pressure in the study of pressure dynamics. The Schrödinger equation simplifies to the Helmholtz equation for a quantum-mechanical particle confined by infinite barriers relevant in semiconductor physics. With this in mind and the interest to tailor waveguides towards a desired spectrum and modal pattern structure in classical structures and nanostructures, it becomes increasingly important to understand the influence of curvature effects in waveguides. In this work, we demonstrate analytically strong curvature effects for the eigenvalue spectrum of the Helmholtz equation with Neumann boundary conditions in cases where the waveguide cross section is a circular sector. It is found that the linear-in-curvature contribution originates from parity symmetry breaking of eigenstates in circular-sector tori and hence vanishes in a torus with a complete circular cross section. The same strong curvature effect is not present in waveguides subject to Dirichlet boundary conditions where curvature contributions contribute to second-order in the curvature only. We demonstrate this finding by considering wave propagation in a circular-sector torus corresponding to Neumann and Dirichlet boundary conditions, respectively. Results for relative eigenfrequency shifts and modes are determined and compared with three-dimensional finite element method results. Good agreement is found between the present analytical method using a combination of differential geometry with perturbation theory and finite element results for a large range of curvature ratios.

  16. Bodrum Strong Motion Network, Mugla, Turkey

    Science.gov (United States)

    Alcik, H. A.; Tanircan, G.; Korkmaz, A.

    2015-12-01

    The Gulf of Gökova is located in southwestern Turkey near the Aegean Sea and surrounded by Datça Peninsula to the south, the island of Kos to the west and Bodrum Peninsula to the north. The Bodrum peninsula with a population of one million in summer season is one of the most populated touristic centers of Turkey. This region is also surrounded by numerous active seismic entities such as Ula-Ören Fault Zone, Gökova Graben etc.. and demonstrates high seismic hazard. In the past, many destructive earthquakes have occurred in southwestern Turkey. One of the destructive historical earthquakes is 1493 Kos event (Mw=6.9) caused heavy damage in Bodrum. In the instrumental period seismic activity in the Gökova region includes the Ms>6.0 earthquakes of 23 April 1933 (Ms=6.4), 23 May 1941 (Ms=6.0), 13 December 1941 (Ms=6.5) events. Intense earthquake activity (Mw5+) occurred in Gulf of Gökova in August 2004 and January 2005. Considering the high seismicity and population of this region, a strong ground motion monitoring system stationed in dense settlements in the Bodrum Peninsula: Bodrum, Turgutreis, Yalıkavak, Çiftlik and Ortakent was deployed on June 2015. The network consists of 5 strong motion recorders, has been set up with the aim of monitoring of regional earthquakes, collecting accurate and reliable data for engineering and scientific research purposes, in particular to provide input for future earthquake rapid reporting and early warning implementation projects on urban environments in the Bodrum peninsula and the surrounding areas. In this poster presentation, we briefly introduce the Bodrum Network and discuss our future plans for further developments.

  17. Is It Possible to Predict Strong Earthquakes?

    Science.gov (United States)

    Polyakov, Y. S.; Ryabinin, G. V.; Solovyeva, A. B.; Timashev, S. F.

    2015-07-01

    The possibility of earthquake prediction is one of the key open questions in modern geophysics. We propose an approach based on the analysis of common short-term candidate precursors (2 weeks to 3 months prior to strong earthquake) with the subsequent processing of brain activity signals generated in specific types of rats (kept in laboratory settings) who reportedly sense an impending earthquake a few days prior to the event. We illustrate the identification of short-term precursors using the groundwater sodium-ion concentration data in the time frame from 2010 to 2014 (a major earthquake occurred on 28 February 2013) recorded at two different sites in the southeastern part of the Kamchatka Peninsula, Russia. The candidate precursors are observed as synchronized peaks in the nonstationarity factors, introduced within the flicker-noise spectroscopy framework for signal processing, for the high-frequency component of both time series. These peaks correspond to the local reorganizations of the underlying geophysical system that are believed to precede strong earthquakes. The rodent brain activity signals are selected as potential "immediate" (up to 2 weeks) deterministic precursors because of the recent scientific reports confirming that rodents sense imminent earthquakes and the population-genetic model of K irshvink (Soc Am 90, 312-323, 2000) showing how a reliable genetic seismic escape response system may have developed over the period of several hundred million years in certain animals. The use of brain activity signals, such as electroencephalograms, in contrast to conventional abnormal animal behavior observations, enables one to apply the standard "input-sensor-response" approach to determine what input signals trigger specific seismic escape brain activity responses.

  18. Strong Firms Lobby, Weak Firms Bribe

    DEFF Research Database (Denmark)

    Bennedsen, Morten; Feldmann, Sven E.; Lassen, David Dreyer

    We use survey responses by firms to examine the firm-level determinants and effects of political influence, their perception of corruption and prevalence of bribe paying. We find that: (a) measures of political influence and corruption/bribes are uncorrelated at the firm level; (b) firms...... that are larger, older, exporting, government-owned, are widely held and/or have fewer competitors, have more political influence, perceive corruption to be less of a problem and pay bribes less often; (c) influence increases sales and government subsidies and in general makes the firm have a more positive view...

  19. Strong Motion Seismograph Based On MEMS Accelerometer

    Science.gov (United States)

    Teng, Y.; Hu, X.

    2013-12-01

    The MEMS strong motion seismograph we developed used the modularization method to design its software and hardware.It can fit various needs in different application situation.The hardware of the instrument is composed of a MEMS accelerometer,a control processor system,a data-storage system,a wired real-time data transmission system by IP network,a wireless data transmission module by 3G broadband,a GPS calibration module and power supply system with a large-volumn lithium battery in it. Among it,the seismograph's sensor adopted a three-axis with 14-bit high resolution and digital output MEMS accelerometer.Its noise level just reach about 99μg/√Hz and ×2g to ×8g dynamically selectable full-scale.Its output data rates from 1.56Hz to 800Hz. Its maximum current consumption is merely 165μA,and the device is so small that it is available in a 3mm×3mm×1mm QFN package. Furthermore,there is access to both low pass filtered data as well as high pass filtered data,which minimizes the data analysis required for earthquake signal detection. So,the data post-processing can be simplified. Controlling process system adopts a 32-bit low power consumption embedded ARM9 processor-S3C2440 and is based on the Linux operation system.The processor's operating clock at 400MHz.The controlling system's main memory is a 64MB SDRAM with a 256MB flash-memory.Besides,an external high-capacity SD card data memory can be easily added.So the system can meet the requirements for data acquisition,data processing,data transmission,data storage,and so on. Both wired and wireless network can satisfy remote real-time monitoring, data transmission,system maintenance,status monitoring or updating software.Linux was embedded and multi-layer designed conception was used.The code, including sensor hardware driver,the data acquisition,earthquake setting out and so on,was written on medium layer.The hardware driver consist of IIC-Bus interface driver, IO driver and asynchronous notification driver. The

  20. Noise Spectroscopy in Strongly Correlated Oxides

    Science.gov (United States)

    Alsaqqa, Ali M.

    Strongly correlated materials are an interesting class of materials, thanks to the novel electronic and magnetic phenomena they exhibit as a result of the interplay of various degrees of freedom. This gives rise to an array of potential applications, from Mott-FET to magnetic storage. Many experimental probes have been used to study phase transitions in strongly correlated oxides. Among these, resistance noise spectroscopy, together with conventional transport measurements, provides a unique viewpoint to understand the microscopic dynamics near the phase transitions in these oxides. In this thesis, utilizing noise spectroscopy and transport measurements, four different strongly correlated materials were studied: (1) neodymium nickel oxide (NdNiO 3) ultrathin films, (2) vanadium dioxide (VO2) microribbons, (3) copper vanadium bronze (CuxV2O 5) microribbons and (4) niobium triselenide (NbSe3) microribbons. Ultra thin films of rare-earth nickelates exhibit several temperature-driven phase transitions. In this thesis, we studied the metal-insulator and Neel transitions in a series of NdNiO3 films with different lattice mismatches. Upon colling down, the metal-insulator phase transition is accompanied by a structural (orthorohombic to monoclinic) and magnetic (paramagnetic to antiferromagnetic) transitions as well, making the problem more interesting and complex at the same time. The noise is of the 1/f type and is Gaussian in the high temperature phase, however deviations are seen in the low temperature phases. Below the metal-insulator transition, noise magnitude increases by orders of magnitude: a sign of inhomogeneous electrical conduction as result of phase separation. This is further assured by the non-Gaussian noise signature. At very low temperatures (T thesis, we tried to answer this question by utilizing three different tuning parameters: temperature, voltage bias and strain. Our results point to an unusual noise behavior in the high-temperature metallic phase

  1. Serial position learning in honeybees.

    Directory of Open Access Journals (Sweden)

    Randolf Menzel

    Full Text Available Learning of stimulus sequences is considered as a characteristic feature of episodic memory since it contains not only a particular item but also the experience of preceding and following events. In sensorimotor tasks resembling navigational performance, the serial order of objects is intimately connected with spatial order. Mammals and birds develop episodic(-like memory in serial spatio-temporal tasks, and the honeybee learns spatio-temporal order when navigating between the nest and a food source. Here I examine the structure of the bees' memory for a combined spatio-temporal task. I ask whether discrimination and generalization are based solely on simple forms of stimulus-reward learning or whether they require sequential configurations. Animals were trained to fly either left or right in a continuous T-maze. The correct choice was signaled by the sequence of colors (blue, yellow at four positions in the access arm. If only one of the possible 4 signals is shown (either blue or yellow, the rank order of position salience is 1, 2 and 3 (numbered from T-junction. No learning is found if the signal appears at position 4. If two signals are shown, differences at positions 1 and 2 are learned best, those at position 3 at a low level, and those at position 4 not at all. If three or more signals are shown these results are corroborated. This salience rank order again appeared in transfer tests, but additional configural phenomena emerged. Most of the results can be explained with a simple model based on the assumption that the four positions are equipped with different salience scores and that these add up independently. However, deviations from the model are interpreted by assuming stimulus configuration of sequential patterns. It is concluded that, under the conditions chosen, bees rely most strongly on memories developed during simple forms of associative reward learning, but memories of configural serial patterns contribute, too.

  2. Thermal infrared anomalies of several strong earthquakes.

    Science.gov (United States)

    Wei, Congxin; Zhang, Yuansheng; Guo, Xiao; Hui, Shaoxing; Qin, Manzhong; Zhang, Ying

    2013-01-01

    In the history of earthquake thermal infrared research, it is undeniable that before and after strong earthquakes there are significant thermal infrared anomalies which have been interpreted as preseismic precursor in earthquake prediction and forecasting. In this paper, we studied the characteristics of thermal radiation observed before and after the 8 great earthquakes with magnitude up to Ms7.0 by using the satellite infrared remote sensing information. We used new types of data and method to extract the useful anomaly information. Based on the analyses of 8 earthquakes, we got the results as follows. (1) There are significant thermal radiation anomalies before and after earthquakes for all cases. The overall performance of anomalies includes two main stages: expanding first and narrowing later. We easily extracted and identified such seismic anomalies by method of "time-frequency relative power spectrum." (2) There exist evident and different characteristic periods and magnitudes of thermal abnormal radiation for each case. (3) Thermal radiation anomalies are closely related to the geological structure. (4) Thermal radiation has obvious characteristics in abnormal duration, range, and morphology. In summary, we should be sure that earthquake thermal infrared anomalies as useful earthquake precursor can be used in earthquake prediction and forecasting.

  3. Strong Correlation Physics in Aromatic Hydrocarbon Superconductors

    Science.gov (United States)

    Capone, Massimo; Giovannetti, Gianluca

    2012-02-01

    We show, by means of ab-initio calculations, that electron-electron correlations play an important role in doped aromatic hydrocarbon superconductors, including potassium doped picene with Tc= 18K [1], coronene and phenanthrene [2]. For the case of picene the inclusion of exchange interactions by means of hybrid functionals reproduces the correct gap for the undoped compound and predicts an antiferromagnetic state for x=3, where superconductivity has been observed [3]. The latter finding is compatible with a sizable value of the correlation strength. The differences between the different compounds are analyzed and results of Dynamical Mean-Field Theory including both correlation effects and electron-phonon interactions are presented. Finally we discuss the consequences of strong correlations in an organic superconductor in relation to the properties of Cs3C60, in which electron correlations drive an antiferromagnetic state [4] but also lead to an enhancement of superconductivity [5]. 1. R. Mitsuhashi et al. Nature 464, 76 (2010)2. X.F. Wang et al, Nat. Comm. 2, 507 (2011)3. G. Giovannetti and M. Capone, Phys. Rev. B 83, 134508 (2011)4. Y. Takabayashi et al., Science 323, 1585 (2009)5. M. Capone et al. Rev. Mod. Phys. 81, 943 (2009

  4. Binary Polymer Brushes of Strongly Immiscible Polymers.

    Science.gov (United States)

    Chu, Elza; Babar, Tashnia; Bruist, Michael F; Sidorenko, Alexander

    2015-06-17

    The phenomenon of microphase separation is an example of self-assembly in soft matter and has been observed in block copolymers (BCPs) and similar materials (i.e., supramolecular assemblies (SMAs) and homo/block copolymer blends (HBCs)). In this study, we use microphase separation to construct responsive polymer brushes that collapse to generate periodic surfaces. This is achieved by a chemical reaction between the minor block (10%, poly(4-vinylpyridine)) of the block copolymer and a substrate. The major block of polystyrene (PS) forms mosaic-like arrays of grafted patches that are 10-20 nm in size. Depending on the nature of the assembly (SMA, HBC, or neat BCP) and annealing method (exposure to vapors of different solvents or heating above the glass transition temperature), a range of "mosaic" brushes with different parameters can be obtained. Successive grafting of a secondary polymer (polyacrylamide, PAAm) results in the fabrication of binary polymer brushes (BPBs). Upon being exposed to specific selective solvents, BPBs may adopt different conformations. The surface tension and adhesion of the binary brush are governed by the polymer occupying the top stratum. The "mosaic" brush approach allows for a combination of strongly immiscible polymers in one brush. This facilitates substantial contrast in the surface properties upon switching, previously only possible for substrates composed of predetermined nanostructures. We also demonstrate a possible application of such PS/PAAm brushes in a tunable bioadhesion-bioadhesive (PS on top) or nonbioadhesive (PAAm on top) surface as revealed by Escherichia coli bacterial seeding.

  5. Quasinormal Modes and Strong Cosmic Censorship

    Science.gov (United States)

    Cardoso, Vitor; Costa, João L.; Destounis, Kyriakos; Hintz, Peter; Jansen, Aron

    2018-01-01

    The fate of Cauchy horizons, such as those found inside charged black holes, is intrinsically connected to the decay of small perturbations exterior to the event horizon. As such, the validity of the strong cosmic censorship (SCC) conjecture is tied to how effectively the exterior damps fluctuations. Here, we study massless scalar fields in the exterior of Reissner-Nordström-de Sitter black holes. Their decay rates are governed by quasinormal modes of the black hole. We identify three families of modes in these spacetimes: one directly linked to the photon sphere, well described by standard WKB-type tools; another family whose existence and time scale is closely related to the de Sitter horizon; finally, a third family which dominates for near-extremally charged black holes and which is also present in asymptotically flat spacetimes. The last two families of modes seem to have gone unnoticed in the literature. We give a detailed description of linear scalar perturbations of such black holes, and conjecture that SCC is violated in the near extremal regime.

  6. Strong coupling from the Hubbard model

    Science.gov (United States)

    Minahan, Joseph A.

    2006-10-01

    It was recently observed that the one-dimensional half-filled Hubbard model reproduces the known part of the perturbative spectrum of planar {\\cal N}=4 super Yang Mills in the SU(2) sector. Assuming that this identification is valid beyond perturbation theory, we investigate the behaviour of this spectrum as the 't Hooft parameter λ becomes large. We show that the full dimension Δ of the Konishi superpartner is the solution of a sixth-order polynomial while Δ for a bare dimension 5 operator is the solution of a cubic. In both cases, the equations can be solved easily as a series expansion for both small and large λ and the equations can be inverted to express λ as an explicit function of Δ. We then consider more general operators and show how Δ depends on λ in the strong coupling limit. We are also able to distinguish those states in the Hubbard model which correspond to the gauge-invariant operators for all values of λ. Finally, we compare our results with known results for strings on AdS5 × S5, where we find agreement for a range of R-charges.

  7. Strongly coupled band in {sup 140}Gd

    Energy Technology Data Exchange (ETDEWEB)

    Falla-Sotelo, F.; Oliveira, J.R.B.; Rao, M.N. [Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo (Brazil)] (and others)

    2005-07-01

    Several high-K states are known to exist in the mass 130-140 region. For the N=74 even-even isotopes, K{pi} = 8{sup -} isomers, with lifetimes ranging from ns to ms, are known in {sup 128}Xe, {sup 130}Ba, {sup 132}Ce, {sup 134}Nd, {sup 136}Sm, and {sup 138}Gd[. In {sup 140}Gd, we have observed for the first time a band also based on an I{pi} = 8{sup -} state. This could be the first case of a K{pi} = 8{sup -} state observed in an N=76 even-even isotope. The systematics of the K{pi} = 8{sup -} isomeric states in N=74 isotopes has been studied by A.M. Bruce et al. These states decay towards the K = 0 ground state band, and the transitions are K-forbidden. The {sup 140}Gd case presents strong similarities but also some significant differences with relation to the N=74 isotopes. We propose the same configuration but with larger deformation in {sup 140}Gd.

  8. Stable states in a strong IR field

    Science.gov (United States)

    Zhong, Changchun; Robicheaux, Francis

    2015-05-01

    It is found that 10% of atoms stay in the quasi-stable states after being exposed to intense laser or microwave (MW) pulses, even though the pulses' intensity is much stronger than that needed for static fields ionization. The reason why atoms survive those strong pulses has attracted growing attentions. A. Arakelyan et al. have observed the optical spectra of the surviving Lithium atoms after interaction with intense 38-GHz MW fields for more than 1000 cycles, and the spectra exhibit a periodic train of peaks 38 GHz apart. It suggests that those weakly bound Rydberg electrons seldom go back to the ionic core, where the cycle average energy exchange happens. In this study, we are interested in the electron behavior in the presence of intense infrared fields with a much shorter wavelength (1000 nm). By solving the full 3D time dependent Schrodinger equation, we calculate the spectra of the surviving atoms under intense IR fields. Our numerical calculations show atoms survive the intense field in quasi-stable states for a long time, and the optical spectra are obviously modulated by the IR frequency. Through tuning the ponderomotive energy, we see how field parameters affect the behavior of electrons. Different atoms, such as Hydrogen, Helium, Lithium, and Sodium, are tested to see how atom's energy structures influence the results.

  9. Strong reinforcing selection in a Texas wildflower.

    Science.gov (United States)

    Hopkins, Robin; Guerrero, Rafael F; Rausher, Mark D; Kirkpatrick, Mark

    2014-09-08

    Reinforcement, the process of increased reproductive isolation due to selection against hybrids, is an important mechanism by which natural selection contributes to speciation [1]. Empirical studies suggest that reinforcement has generated reproductive isolation in many taxa (reviewed in [2-4]), and theoretical work shows it can act under broad selective conditions [5-11]. However, the strength of selection driving reinforcement has never been measured in nature. Here, we quantify the strength of reinforcing selection in the Texas wildflower Phlox drummondii using a strategy that weds a population genetic model with field data. Reinforcement in this system is caused by variation in two loci that affect flower color [12]. We quantify sharp clines in flower color where this species comes into contact with its congener, Phlox cuspidata. We develop a spatially explicit population genetic model for these clines based on the known genetics of flower color. We fit our model to the data using likelihood, and we searched parameter space using Markov chain Monte Carlo methods. We find that selection on flower color genes generated by reinforcement is exceptionally strong. Our findings demonstrate that natural selection can play a decisive role in the evolution of reproductive isolation through the process of reinforcement. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Thermal Infrared Anomalies of Several Strong Earthquakes

    Directory of Open Access Journals (Sweden)

    Congxin Wei

    2013-01-01

    Full Text Available In the history of earthquake thermal infrared research, it is undeniable that before and after strong earthquakes there are significant thermal infrared anomalies which have been interpreted as preseismic precursor in earthquake prediction and forecasting. In this paper, we studied the characteristics of thermal radiation observed before and after the 8 great earthquakes with magnitude up to Ms7.0 by using the satellite infrared remote sensing information. We used new types of data and method to extract the useful anomaly information. Based on the analyses of 8 earthquakes, we got the results as follows. (1 There are significant thermal radiation anomalies before and after earthquakes for all cases. The overall performance of anomalies includes two main stages: expanding first and narrowing later. We easily extracted and identified such seismic anomalies by method of “time-frequency relative power spectrum.” (2 There exist evident and different characteristic periods and magnitudes of thermal abnormal radiation for each case. (3 Thermal radiation anomalies are closely related to the geological structure. (4 Thermal radiation has obvious characteristics in abnormal duration, range, and morphology. In summary, we should be sure that earthquake thermal infrared anomalies as useful earthquake precursor can be used in earthquake prediction and forecasting.

  11. Quantum centipedes with strong global constraint

    Science.gov (United States)

    Grange, Pascal

    2017-06-01

    A centipede made of N quantum walkers on a one-dimensional lattice is considered. The distance between two consecutive legs is either one or two lattice spacings, and a global constraint is imposed: the maximal distance between the first and last leg is N  +  1. This is the strongest global constraint compatible with walking. For an initial value of the wave function corresponding to a localized configuration at the origin, the probability law of the first leg of the centipede can be expressed in closed form in terms of Bessel functions. The dispersion relation and the group velocities are worked out exactly. Their maximal group velocity goes to zero when N goes to infinity, which is in contrast with the behaviour of group velocities of quantum centipedes without global constraint, which were recently shown by Krapivsky, Luck and Mallick to give rise to ballistic spreading of extremal wave-front at non-zero velocity in the large-N limit. The corresponding Hamiltonians are implemented numerically, based on a block structure of the space of configurations corresponding to compositions of the integer N. The growth of the maximal group velocity when the strong constraint is gradually relaxed is explored, and observed to be linear in the density of gaps allowed in the configurations. Heuristic arguments are presented to infer that the large-N limit of the globally constrained model can yield finite group velocities provided the allowed number of gaps is a finite fraction of N.

  12. Strongly correlated superconductivity and quantum criticality

    Science.gov (United States)

    Tremblay, A.-M. S.

    Doped Mott insulators and doped charge-transfer insulators describe classes of materials that can exhibit unconventional superconducting ground states. Examples include the cuprates and the layered organic superconductors of the BEDT family. I present results obtained from plaquette cellular dynamical mean-field theory. Continuous-time quantum Monte Carlo evaluation of the hybridization expansion allows one to study the models in the large interaction limit where quasiparticles can disappear. The normal state which is unstable to the superconducting state exhibits a first-order transition between a pseudogap and a correlated metal phase. That transition is the finite-doping extension of the metal-insulator transition obtained at half-filling. This transition serves as an organizing principle for the normal and superconducting states of both cuprates and doped organic superconductors. In the less strongly correlated limit, these methods also describe the more conventional case where the superconducting dome surrounds an antiferromagnetic quantum critical point. Sponsored by NSERC RGPIN-2014-04584, CIFAR, Research Chair in the Theory of Quantum Materials.

  13. Strong liquid-crystalline polymeric compositions

    Science.gov (United States)

    Dowell, F.

    1993-12-07

    Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

  14. Grassy Silica Nanoribbons and Strong Blue Luminescence

    Science.gov (United States)

    Wang, Shengping; Xie, Shuang; Huang, Guowei; Guo, Hongxuan; Cho, Yujin; Chen, Jun; Fujita, Daisuke; Xu, Mingsheng

    2016-09-01

    Silicon dioxide (SiO2) is one of the key materials in many modern technological applications such as in metal oxide semiconductor transistors, photovoltaic solar cells, pollution removal, and biomedicine. We report the accidental discovery of free-standing grassy silica nanoribbons directly grown on SiO2/Si platform which is commonly used for field-effect transistors fabrication without other precursor. We investigate the formation mechanism of this novel silica nanostructure that has not been previously documented. The silica nanoribbons are flexible and can be manipulated by electron-beam. The silica nanoribbons exhibit strong blue emission at about 467 nm, together with UV and red emissions as investigated by cathodoluminescence technique. The origins of the luminescence are attributed to various defects in the silica nanoribbons; and the intensity change of the blue emission and green emission at about 550 nm is discussed in the frame of the defect density. Our study may lead to rational design of the new silica-based materials for a wide range of applications.

  15. Toward a Strongly Interacting Scalar Higgs Particle

    International Nuclear Information System (INIS)

    Shalaby, Abouzeid M.; El-Houssieny, M.

    2008-01-01

    We calculate the vacuum energy of the non-Hermitian and PT symmetric (-gφ 4 ) 2+1 scalar field theory. Rather than the corresponding Hermitian theory and due to the asymptotic freedom property of the theory, the vacuum energy does not blow up for large energy scales which is a good sign to solve the hierarchy problem when using this model to break the U(1)xSU(2) symmetry in the standard model. The theory is strongly interacting and in fact, all the dimensionful parameters in the theory like mass and energy are finite even for very high energy scales. Moreover, relative to the vacuum energy for the Hermitian φ 4 theory, the vacuum energy of the non-Hermitian and PT symmetric (-gφ 4 ) 2+1 theory is tiny, which is a good sign toward the solution of the cosmological constant problem. Remarkably, these features of the non-Hermitian and PT symmetric (-gφ 4 ) 2+1 scalar field theory make it very plausible to be employed as a Higgs mechanism in the standard model instead of the problematic Hermitian Higgs mechanism

  16. Intense Shock Waves and Strongly Coupled Plasmas

    Science.gov (United States)

    Fortov, Vladimir

    2005-07-01

    The report presents the recent results of experimental investigations of equations of state, compositions, thermodynamical and transport properties, electrical conductivity and opacity of strongly coupled plasmas generated by intense shock and rarefaction waves. The experimental methods for generation of high energy densities in matter, drivers for shock waves and fast diagnostic tools are discussed. Application of intense shock waves to solid and porous targets generates nonideal plasmas in megabar-gigabar pressure range. Compression of plasma by a series of reverberating shock waves allows us to decrease irreversible heating effects. To increase the irreversibility effects and to generate high temperature plasma states the experiments on shock compression of porous samples (fine metal powder, aerogels) were performed. The adiabatic expansion of matter initially compressed by intense shocks up to megabars allows investigating the intermediate region between the solid and vapor phase of nonideal plasmas, including the metal-insulator transition phase and the high temperature saturation curve with critical points of metals. The shock-wave-induced non-equilibrium phenomena at fast melting, spallation and adiabatic condensation are analyzed in the framework of the interspinodal decomposition model. The spall strength of single and polycrystal metals at extremely fast deformation produced by fast shock waves is discussed. The ``pressure ionization'' phenomena in hydrogen, helium, argon, xenon, krypton, neon, iodine, silica, sulfur, fullerenes, and some metals are analyzed on the base of multiple shock compression experiments. For some simple metals (Li, Na, Ca) the effect of ``dielectrization'' as a result of multiple shock compression are discussed.

  17. Thermal Infrared Anomalies of Several Strong Earthquakes

    Science.gov (United States)

    Wei, Congxin; Guo, Xiao; Qin, Manzhong

    2013-01-01

    In the history of earthquake thermal infrared research, it is undeniable that before and after strong earthquakes there are significant thermal infrared anomalies which have been interpreted as preseismic precursor in earthquake prediction and forecasting. In this paper, we studied the characteristics of thermal radiation observed before and after the 8 great earthquakes with magnitude up to Ms7.0 by using the satellite infrared remote sensing information. We used new types of data and method to extract the useful anomaly information. Based on the analyses of 8 earthquakes, we got the results as follows. (1) There are significant thermal radiation anomalies before and after earthquakes for all cases. The overall performance of anomalies includes two main stages: expanding first and narrowing later. We easily extracted and identified such seismic anomalies by method of “time-frequency relative power spectrum.” (2) There exist evident and different characteristic periods and magnitudes of thermal abnormal radiation for each case. (3) Thermal radiation anomalies are closely related to the geological structure. (4) Thermal radiation has obvious characteristics in abnormal duration, range, and morphology. In summary, we should be sure that earthquake thermal infrared anomalies as useful earthquake precursor can be used in earthquake prediction and forecasting. PMID:24222728

  18. Positions, positionings and posture of the enunciator

    Directory of Open Access Journals (Sweden)

    Alain Rabatel

    2013-12-01

    Full Text Available This article draws connections between the notions of enunciator position, positioning and posture, which structure the dialogic, cognitive and interactional co- production of utterances. The notion of enunciative position corresponds to the fact that the (first or second enunciator refers to objects of discourse while positioning himself/herself with regard to them, by indicating from what point of view he/she considers them. In view of the dialogic nature of the discourse, two modal subjects and levels of responsibility can be discerned: the first enunciator has the role of the agent in charge of the discourse and the second enunciator fulfills internal functions of validation, assuming thus a sort of responsibility which does not necessarily commit the first enunciator. The article then analyses the dialogic strategies of positioning by enunciative reduplication and separation which account for auto- dialogic and hetero-dialogic situations. Finally it deals with the enunciative postures of co-enunciation, over-enunciation and under-enunciation, which refine the notions of enunciative reduplication or separation, by specifying the degrees of agreement, according to dialectic between discordant concordance and concordant discordance.

  19. Positive Mental Well-Being.

    Science.gov (United States)

    Houghton, Stephen; Wood, Lisa; Marais, Ida; Rosenberg, Michael; Ferguson, Renee; Pettigrew, Simone

    2017-04-01

    This study presents a Rasch-derived short form of the Warwick-Edinburgh Mental Well-Being Scale for use as a screening tool in the general population. Data from 2,005 18- to 69-year-olds revealed problematic discrimination at specific thresholds. Estimation of model fit also deviated from Rasch model expectations. Following deletion of 4 items, the 10 remaining items indicated the data fitted the model. No items showed differential item functioning, thereby making comparisons of overall positive mental well-being for the different age, gender, and income groups valid and accurate. Cronbach's alpha and Rasch Person Separation Index indicated a strong degree of reliability. Overall, the 10-item scale challenges researchers and clinicians to reconsider the assessment of positive mental well-being.

  20. Virtual detector theory for strong-field atomic ionization

    Science.gov (United States)

    Wang, Xu; Tian, Justin; Eberly, J. H.

    2018-04-01

    A virtual detector (VD) is an imaginary device located at a fixed position in space that extracts information from the wave packet passing through it. By recording the particle momentum and the corresponding probability current at each time, the VDs can accumulate and build the differential momentum distribution of the particle, in a way that resembles real experiments. A mathematical proof is given for the equivalence of the differential momentum distribution obtained by the VD method and by Fourier transforming the wave function. In addition to being a tool for reducing the computational load, VDs have also been found useful in interpreting the ultrafast strong-field ionization process, especially the controversial quantum tunneling process.

  1. Strong Turbulence in Alkali Halide Negative Ion Plasmas

    Science.gov (United States)

    Sheehan, Daniel

    1999-11-01

    Negative ion plasmas (NIPs) are charge-neutral plasmas in which the negative charge is dominated by negative ions rather than electrons. They are found in laser discharges, combustion products, semiconductor manufacturing processes, stellar atmospheres, pulsar magnetospheres, and the Earth's ionosphere, both naturally and man-made. They often display signatures of strong turbulence^1. Development of a novel, compact, unmagnetized alkali halide (MX) NIP source will be discussed, it incorporating a ohmically-heated incandescent (2500K) tantulum solenoid (3cm dia, 15 cm long) with heat shields. The solenoid ionizes the MX vapor and confines contaminant electrons, allowing a very dry (electron-free) source. Plasma densities of 10^10 cm-3 and positive to negative ion mass ratios of 1 Fusion 4, 91 (1978).

  2. Mechanics of magnetic fluid column in strong magnetic fields

    International Nuclear Information System (INIS)

    Polunin, V.M.; Ryapolov, P.A.; Platonov, V.B.

    2017-01-01

    Elastic-and magnetic properties of magnetic fluid confined by ponderomotive force in a tube fixed in horizontal position are considered. The system is placed in a strong magnetic field under the influence of external static and dynamic perturbations. An experimental setup has been developed. A theoretical basis of the processes of magnetic colloid elastic deformation has been proposed. The values of the static ponderomotive elasticity coefficient and the elasticity coefficient under dynamic action are experimentally determined. The calculations of the saturation magnetization for two magnetic fluid samples, carried out according to the equation containing the dynamic elasticity coefficient, are in good agreement with the experimental magnetization curve. The described method is of interest when studying magnetophoresis and aggregation of nanoparticles in magnetic colloids.

  3. Strong signatures of selection in the domestic pig genome

    DEFF Research Database (Denmark)

    Rubin, Carl-Johan; Megens, Hendrik-Jan; Barrio, Alvaro Martinez

    2012-01-01

    . We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white......Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci...... that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig—the elongation of the back...

  4. Strong Localization in Disordered Media: Analysis of the Backscattering Cone

    KAUST Repository

    Delgado, Edgar

    2012-06-01

    A very interesting effect in light propagation through a disordered system is Anderson localization of light, this phenomenon emerges as the result of multiple scattering of waves by electric inhomogeneities like spatial variations of index of refraction; as the amount of scattering is increased, light propagation is converted from quasi-diffusive to exponentially localized, with photons confined in a limited spatial region characterized by a fundamental quantity known as localization length. Light localization is strongly related to another interference phenomenon emerged from the multiple scattering effect: the coherent backscattering effect. In multiple scattering of waves, in fact, coherence is preserved in the backscattering direction and produces a reinforcement of the field flux originating an observable peak in the backscattered intensity, known as backscattering cone. The study of this peak provide quantitative information about the transport properties of light in the material. In this thesis we report a complete FDTD ab-initio study of light localization and coherent backscattering. In particular, we consider a supercontinuum pulse impinging on a sample composed of randomly positioned scatterers. We study coherent backscattering by averaging over several realizations of the sample properties. We study then the coherent backscattering cone properties as the relative permittivity of the sample is changed, relating the latter with the light localization inside the sample. We demonstrate important relationships between the width of the backscattering cone and the localization length, which shows a linear proportionality in the strong localization regime.

  5. Strong hydrological control on nutrient cycling of subtropical rainforests

    Science.gov (United States)

    Lin, T. C.; Chang, C. T.; Huang, J. C.; Wang, L.; Lin, N. H.

    2016-12-01

    Forest nutrient cycling is strongly controlled by both biological and hydrological factors. However, based on a close examination of earlier reports, we highlight the role of hydrological control on nutrient cycling at a global scale and is more important at humid tropical and subtropical forests. we analyzed the nutrient budget of precipitation input and stream water output from 1994 to 2013 in a subtropical forest in Taiwan and conducted a data synthesis using results from 32 forests across the globe. The results revealed that monthly input and output of ions were positively correlated with water quantity, indicating hydrological control on nutrient cycling. Hydrological control is also evident from the greater ions export via stream water during the warm and wet growing season. The synthesis also illustrates that strong hydrological control leads to lower nitrogen retention and greater net loss of base cations in humid regions, particularly in the humid tropical and subtropical forests. Our result is of great significance in an era of global climate change because climate change could directly affect ecosystem nutrient cycling particularly in the tropics through changes in patterns of precipitation regime.

  6. Measuring mixing efficiency in experiments of strongly stratified turbulence

    Science.gov (United States)

    Augier, P.; Campagne, A.; Valran, T.; Calpe Linares, M.; Mohanan, A. V.; Micard, D.; Viboud, S.; Segalini, A.; Mordant, N.; Sommeria, J.; Lindborg, E.

    2017-12-01

    Oceanic and atmospheric models need better parameterization of the mixing efficiency. Therefore, we need to measure this quantity for flows representative of geophysical flows, both in terms of types of flows (with vortices and/or waves) and of dynamical regimes. In order to reach sufficiently large Reynolds number for strongly stratified flows, experiments for which salt is used to produce the stratification have to be carried out in a large rotating platform of at least 10-meter diameter.We present new experiments done in summer 2017 to study experimentally strongly stratified turbulence and mixing efficiency in the Coriolis platform. The flow is forced by a slow periodic movement of an array of large vertical or horizontal cylinders. The velocity field is measured by 3D-2C scanned horizontal particles image velocimetry (PIV) and 2D vertical PIV. Six density-temperature probes are used to measure vertical and horizontal profiles and signals at fixed positions.We will show how we rely heavily on open-science methods for this study. Our new results on the mixing efficiency will be presented and discussed in terms of mixing parameterization.

  7. Strong Coupling Gauge Theories in LHC ERA

    Science.gov (United States)

    Fukaya, H.; Harada, M.; Tanabashi, M.; Yamawaki, K.

    2011-01-01

    Higgs, or techni-dilaton - composite Higgs near conformality / Koichi Yamawaki -- Phase diagram of strongly interacting theories / Francesco Sannino -- Resizing conformal windows / O. Antipin and K. Tuominen -- Nearly conformal gauge theories on the lattice / Zoltan Fodor ... [et al.] -- Going beyond QCD in lattice gauge theory / G. T. Fleming -- Phases of QCD from small to large N[symbol]: (some) lattice results / A. Deuzeman, E. Pallante and M. P. Lombardo -- Lattice gauge theory and (quasi)-conformal technicolor / D. K. Sinclair and J. B. Kogut -- Study of the running coupling constant in 10-flavor QCD with the Schrodinger functional method / N. Yamada ... [et al.] -- Study of the running coupling in twisted Polyakov scheme / T. Aoyama ... [et al.].Running coupling in strong gauge theories via the lattice / Zoltan Fodor ... [et al.] -- Higgsinoless supersymmetry and hidden gravity / Michael L. Graesser, Ryuichiro Kitano and Masafumi Kurachi -- The latest status of LHC and the EWSB physics / S. Asai -- Continuum superpartners from supersymmetric unparticles / Hsin-Chia Cheng -- Review of minimal flavor constraints for technicolor / Hidenori S. Fukano and Francesco Sannino -- Standard model and high energy Lorentz violation / Damiano Anselmi -- Dynamical electroweak symmetry breaking and fourth family / Michio Hashimoto -- Holmorphic supersymmetric Nambu-Jona-Lasino model and dynamical electroweak symmetry breaking / Dong-Won Jung, Otto C. W. Kong and Jae Sik Lee -- Ratchet model of Baryogenesis / Tatsu Takeuchi, Azusa Minamizaki and Akio Sugamoto -- Classical solutions of field equations in Einstein Gauss-Bonnet gravity / P. Suranyi, C. Vaz and L. C. R. Wijewardhana -- Black holes constitute all dark matter / Paul H. Frampton -- Electroweak precision test and Z [symbol] in the three site Higgsless model / Tomohiro Abe -- Chiral symmetry and BRST symmetry breaking, quaternion reality and the lattice simulation / Sadataka Furui -- Holographic techni-dilaton, or

  8. Strong ground motion spectra for layered media

    International Nuclear Information System (INIS)

    Askar, A.; Cakmak, A.S.; Engin, H.

    1977-01-01

    This article presents an analytic method and calculations of strong motion spectra for the energy, displacement, velocity and acceleration based on the physical and geometric ground properties at a site. Although earthquakes occur with large deformations and high stress intensities which necessarily lead to nonlinear phenomena, most analytical efforts to date have been based on linear analyses in engineering seismology and soil dynamics. There are, however, a wealth of problems such as the shifts in frequency, dispersion due to the amplitude, the generation of harmonics, removal of resonance infinities, which cannot be accounted for by a linear theory. In the study, the stress-strain law for soil is taken as tau=G 0 γ+G 1 γ 3 +etaγ where tau is the stress, γ is the strain, G 0 and G 1 are the elasticity coefficients and eta is the damping and are different in each layer. The above stress-strain law describes soils with hysterisis where the hysterisis loops for various amplitudes of the strain are no longer concentric ellipses as for linear relations but are oval shapes rotated with respect to each other similar to the materials with the Osgood-Ramberg law. It is observed that even slight nonlinearities may drastically alter the various response spectra from that given by linear analysis. In fact, primary waves cause resonance conditions such that secondary waves are generated. As a result, a weak energy transfer from the primary to the secondary waves takes place, thus altering the wave spectrum. The mathematical technique that is utilized for the solution of the nonlinear equation is a special perturbation method as an extension of Poincare's procedure. The method considers shifts in the frequencies which are determined by the boundedness of the energy

  9. Strong Algerian Earthquake Strikes Near Capital City

    Science.gov (United States)

    Ayadi, A.; Maouche, S.; Harbi, A.; Meghraoui, M.; Beldjoudi, H.; Oussadou, F.; Mahsas, A.; Benouar, D.; Heddar, A.; Rouchiche, Y.; Kherroubi, A.; Frogneux, M.; Lammali, K.; Benhamouda, F.; Sebaï, A.; Bourouis, S.; Alasset, P. J.; Aoudia, A.; Cakir, Z.; Merahi, M.; Nouar, O.; Yelles, A.; Bellik, A.; Briole, P.; Charade, O.; Thouvenot, F.; Semane, F.; Ferkoul, A.; Deramchi, A.; Haned, S. A.

    On 21 May 2003, a damaging earthquake of Mw 6.8 struck the region of Boumerdes 40 km east of Algiers in northern Algeria (Figure 1). The mainshock, which lasted ~ 36-40 s, had devastating effects and claimed about 2300 victims, caused more than 11,450 injuries, and left about 200,000 people homeless. It destroyed and seriously damaged around 180,000 housing units and 6000 public buildings with losses estimated at $5 billion. The mainshock was widely felt within a radius of ~ 400 km in Algeria. To the north, the earthquake was felt in southeastern Spain, including the Balearic Islands, and also in Sardinia and in southern France. The mainshock location, which was calculated at 36.91°N, 3.58°E (15 km offshore of Zemmouri; Figure 1), and the local magnitude (Md 6.4) are from seismic records of local stations. International seismological centers obtained Mw 6.8 (NEIC) with a thrust focal mechanism solution and 1.83 × 1026 dyne.cm for the seismic moment. A sequence of aftershocks affected the epicentral area with two strong shocks reaching Mw 5.8 on 27 and 29 May 2003. Field investigations allowed us to assign a maximum intensity X (European Macroseismic Scale 98) and to report rockfalls, minor surface cracks, and liquefaction phenomena. The mainshock was not associated with inland surface faulting, but one of the most striking coseismic effects is the coastal uplift and the backwash along the littoral of the Mitidja basin.

  10. Strong economic growth driving increased electricity consumption

    International Nuclear Information System (INIS)

    Tiusanen, P.

    2000-01-01

    The Finnish economy is growing faster today than anyone dared hope only a few years ago. Growth estimates for 2000 have already had to be raised. This strong level of economic growth has been reflected in electricity consumption, which has continued to increase, despite the exceptionally warm winter. A major part of this increased electricity usage has so far been met through imports. The continued growth in electricity imports has largely been a result of the fact that the good water level situation in Sweden and Norway, together with the mild winter, has kept electricity prices exceptionally low on the Nordic electricity exchange. The short period of low temperatures seen at the end of January showed, however, that this type of temperature fluctuation, combined with the restrictions that exist in regard to transfer capacity, can serve to push Nordic exchange electricity prices to record levels. This increase in price also highlights the fact that we are approaching a situation in which capacity will be insufficient to meet demand. A truly tough winter has not been seen since the Nordic region's electricity markets were deregulated. The lesson that needs to be learnt is that Finland needs sufficient capacity of her own to meet demand even during particularly cold winters. Finland used 77.9 billion kWh of electricity last year, up 1.6% or 1.3 billion kWh on 1998. This growth was relatively evenly distributed among different user groups. This year, electricity consumption is forecast to grow by 2-3%

  11. Kinetic theory for strongly coupled Coulomb systems

    Science.gov (United States)

    Dufty, James; Wrighton, Jeffrey

    2018-01-01

    The calculation of dynamical properties for matter under extreme conditions is a challenging task. The popular Kubo-Greenwood model exploits elements from equilibrium density-functional theory (DFT) that allow a detailed treatment of electron correlations, but its origin is largely phenomenological; traditional kinetic theories have a more secure foundation but are limited to weak ion-electron interactions. The objective here is to show how a combination of the two evolves naturally from the short-time limit for the generator of the effective single-electron dynamics governing time correlation functions without such limitations. This provides a theoretical context for the current DFT-related approach, the Kubo-Greenwood model, while showing the nature of its corrections. The method is to calculate the short-time dynamics in the single-electron subspace for a given configuration of the ions. This differs from the usual kinetic theory approach in which an average over the ions is performed as well. In this way the effective ion-electron interaction includes strong Coulomb coupling and is shown to be determined from DFT. The correlation functions have the form of the random-phase approximation for an inhomogeneous system but with renormalized ion-electron and electron-electron potentials. The dynamic structure function, density response function, and electrical conductivity are calculated as examples. The static local field corrections in the dielectric function are identified in this way. The current analysis is limited to semiclassical electrons (quantum statistical potentials), so important quantum conditions are excluded. However, a quantization of the kinetic theory is identified for broader application while awaiting its detailed derivation.

  12. Transport Theory for Plasmas that are Strongly Magnetized and Strongly Coupled

    Science.gov (United States)

    Baalrud, Scott; Daligault, Jerome

    2016-10-01

    Plasmas with components that are magnetized, strongly coupled, or both arise in a variety of frontier plasma physics experiments including magnetized dusty plasmas, nonneutral plasmas, magnetized ICF concepts, as well as from self-generated fields in ICF. Here, a species is considered strongly magnetized if the gyroradius is smaller than the spatial scale over which Coulomb interactions occur. A theory for transport properties is described that treats a wide range of both coupling and magnetization strengths. The approach is based on an extension of the recent effective potential transport theory to include a strong magnetic field. The underlying kinetic theory is based on an extension of the Boltzmann equation to include a strong magnetic field in the dynamics of binary scattering events. Corresponding magnetohydrodynamic equations are derived by solving the kinetic equation using a Chapman-Enskog like spectral method. Results are compared with classical molecular dynamics simulations of self-diffusion of the one component plasmas, and with simulations of parallel to perpendicular temperature equilibration of an initially anisotropic distribution. This material is based upon work supported by AFOSR Award FA9550-16-1-0221 and DOE OFES Award DE-SC0016159.

  13. ''Strong gammas''. List of strong gamma-rays emitted from radionuclides. Documentation of the PC diskette

    International Nuclear Information System (INIS)

    Ichimiya, T.; Narita, T.; Kitao, K.

    1994-01-01

    The PC diskette containing the ''List of strong gamma-rays emitted from radionuclides'' as published by T. Narita et al. in the report JAERI-M-94-059, March 1994, is described. The diskette is available from the IAEA Nuclear Data Section, costfree, upon request. (author)

  14. Strong Feller solutions to SPDEďs are strong Feller in the weak topology

    Czech Academy of Sciences Publication Activity Database

    Maslowski, Bohdan; Seidler, Jan

    2001-01-01

    Roč. 148, č. 2 (2001), s. 111-129 ISSN 0039-3223 R&D Projects: GA ČR GA201/98/1454 Keywords : strong Feller property% stochastic parabolic equations Subject RIV: BA - General Mathematics Impact factor: 0.399, year: 2001

  15. Strong-field ionization of polar molecules: Stark-shift-corrected strong-field approximation

    DEFF Research Database (Denmark)

    Dimitrovski, Darko; Martiny, Christian P. J.; Madsen, Lars Bojer

    2010-01-01

    We extend the molecular strong-field approximation for ionization, in the tunneling limit, to include systematically the linear and quadratic static Stark shifts of the ionizing molecular orbital. This approach, simple to implement, is capable of describing the essential physics of the process of...

  16. Multi-technology positioning

    CERN Document Server

    Lohan, Elena-Simona; Wymeersch, Henk; Seco-Granados, Gonzalo; Nykänen, Ossi

    2017-01-01

    This book provides an overview of positioning technologies, applications and services in a format accessible to a wide variety of readers. Readers who have always wanted to understand how satellite-based positioning, wireless network positioning, inertial navigation, and their combinations work will find great value in this book. Readers will also learn about the advantages and disadvantages of different positioning methods, their limitations and challenges. Cognitive positioning, adding the brain to determine which technologies to use at device runtime, is introduced as well. Coverage also includes the use of position information for Location Based Services (LBS), as well as context-aware positioning services, designed for better user experience. • Brings understanding of positioning technology to readers from a variety of disciplines • Reviews multiple techniques, providing insight on the pros, cons and challenges related to each • Designed to be a tutorial on basic principles, avoiding unnecessary de...

  17. Navicular bone position determined by positional MRI

    DEFF Research Database (Denmark)

    Hansen, Philip; Johannsen, Finn E; Hangaard, Stine

    2016-01-01

    -scanner). Scanning was performed in supine and standing position, respectively. Two radiologists evaluated the images in a blinded manner. Reliability and agreement were assessed by calculation of intraclass correlation coefficient (ICC) and 95 % limits of agreement as a percentage of the mean (LOA%). RESULTS...

  18. Reflection Positive Doubles

    OpenAIRE

    Jaffe, Arthur; Janssens, Bas

    2016-01-01

    Here we introduce reflection positive doubles, a general framework for reflection positivity, covering a wide variety of systems in statistical physics and quantum field theory. These systems may be bosonic, fermionic, or parafermionic in nature. Within the framework of reflection positive doubles, we give necessary and sufficient conditions for reflection positivity. We use a reflection-invariant cone to implement our construction. Our characterization allows for a direct interpretation in t...

  19. Perception of eye positions

    NARCIS (Netherlands)

    Lorteije, J.A.M.; Wezel, R.J.A. van; Lankheet, M.J.M.

    2002-01-01

    In a two-alternative forced-choice psychophysical test human subjects were tested for their ability to perceive their own viewing direction. A small red flash was presented at different horizontal positions left or right from the subjects' eye position on the screen. Eye positions were recorded with

  20. The Positivity Scale

    Science.gov (United States)

    Caprara, Gian Vittorio; Alessandri, Guido; Eisenberg, Nancy; Kupfer, A.; Steca, Patrizia; Caprara, Maria Giovanna; Yamaguchi, Susumu; Fukuzawa, Ai; Abela, John

    2012-01-01

    Five studies document the validity of a new 8-item scale designed to measure "positivity," defined as the tendency to view life and experiences with a positive outlook. In the first study (N = 372), the psychometric properties of Positivity Scale (P Scale) were examined in accordance with classical test theory using a large number of…