WorldWideScience

Sample records for multiple chromatin insulators

  1. A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber

    DEFF Research Database (Denmark)

    Comet, Itys; Schuettengruber, Bernd; Sexton, Tom

    2011-01-01

    to insulate genes from regulatory elements or to take part in long-distance interactions. Using a high-resolution chromatin conformation capture (H3C) method, we show that the Drosophila gypsy insulator behaves as a conformational chromatin border that is able to prohibit contacts between a Polycomb response...... element (PRE) and a distal promoter. On the other hand, two spaced gypsy elements form a chromatin loop that is able to bring an upstream PRE in contact with a downstream gene to mediate its repression. Chromatin immunoprecipitation (ChIP) profiles of the Polycomb protein and its associated H3K27me3...... histone mark reflect this insulator-dependent chromatin conformation, suggesting that Polycomb action at a distance can be organized by local chromatin topology....

  2. Incorporating double copies of a chromatin insulator into lentiviral vectors results in less viral integrants

    DEFF Research Database (Denmark)

    Nielsen, Troels T; Jakobsson, Johan; Rosenqvist, Nina

    2009-01-01

    BACKGROUND: Lentiviral vectors hold great promise as gene transfer vectors in gene therapeutic settings. However, problems related to the risk of insertional mutagenesis, transgene silencing and positional effects have stalled the use of such vectors in the clinic. Chromatin insulators are boundary...

  3. 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.

  4. The Compass-like locus, exclusive to the Ambulacrarians, encodes a chromatin insulator binding protein in the sea urchin embryo.

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    Vincenzo Cavalieri

    Full Text Available Chromatin insulators are eukaryotic genome elements that upon binding of specific proteins display barrier and/or enhancer-blocking activity. Although several insulators have been described throughout various metazoans, much less is known about proteins that mediate their functions. This article deals with the identification and functional characterization in Paracentrotus lividus of COMPASS-like (CMPl, a novel echinoderm insulator binding protein. Phylogenetic analysis shows that the CMPl factor, encoded by the alternative spliced Cmp/Cmpl transcript, is the founder of a novel ambulacrarian-specific family of Homeodomain proteins containing the Compass domain. Specific association of CMPl with the boxB cis-element of the sns5 chromatin insulator is demonstrated by using a yeast one-hybrid system, and further corroborated by ChIP-qPCR and trans-activation assays in developing sea urchin embryos. The sns5 insulator lies within the early histone gene cluster, basically between the H2A enhancer and H1 promoter. To assess the functional role of CMPl within this locus, we challenged the activity of CMPl by two distinct experimental strategies. First we expressed in the developing embryo a chimeric protein, containing the DNA-binding domain of CMPl, which efficiently compete with the endogenous CMPl for the binding to the boxB sequence. Second, to titrate the embryonic CMPl protein, we microinjected an affinity-purified CMPl antibody. In both the experimental assays we congruently observed the loss of the enhancer-blocking function of sns5, as indicated by the specific increase of the H1 expression level. Furthermore, microinjection of the CMPl antiserum in combination with a synthetic mRNA encoding a forced repressor of the H2A enhancer-bound MBF1 factor restores the normal H1 mRNA abundance. Altogether, these results strongly support the conclusion that the recruitment of CMPl on sns5 is required for buffering the H1 promoter from the H2A enhancer

  5. Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver.

    Science.gov (United States)

    Matthews, Bryan J; Waxman, David J

    2018-05-14

    CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity. © 2018, Matthews et al.

  6. Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk.

    Science.gov (United States)

    Waller, Rosalie G; Darlington, Todd M; Wei, Xiaomu; Madsen, Michael J; Thomas, Alun; Curtin, Karen; Coon, Hilary; Rajamanickam, Venkatesh; Musinsky, Justin; Jayabalan, David; Atanackovic, Djordje; Rajkumar, S Vincent; Kumar, Shaji; Slager, Susan; Middha, Mridu; Galia, Perrine; Demangel, Delphine; Salama, Mohamed; Joseph, Vijai; McKay, James; Offit, Kenneth; Klein, Robert J; Lipkin, Steven M; Dumontet, Charles; Vachon, Celine M; Camp, Nicola J

    2018-02-01

    The high-risk pedigree (HRP) design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS) method in 11 extended, Utah, multiple myeloma (MM) HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM) cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu), a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val), a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.

  7. Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk.

    Directory of Open Access Journals (Sweden)

    Rosalie G Waller

    2018-02-01

    Full Text Available The high-risk pedigree (HRP design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS method in 11 extended, Utah, multiple myeloma (MM HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu, a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val, a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.

  8. Multiple-Nozzle Spray Head Applies Foam Insulation

    Science.gov (United States)

    Walls, Joe T.

    1993-01-01

    Spray head equipped with four-nozzle turret mixes two reactive components of polyurethane and polyisocyanurate foam insulating material and sprays reacting mixture onto surface to be insulated. If nozzle in use becomes clogged, fresh one automatically rotated into position, with minimal interruption of spraying process. Incorporates features recirculating and controlling pressures of reactive components to maintain quality of foam by ensuring proper blend at outset. Also used to spray protective coats on or in ships, aircraft, and pipelines. Sprays such reactive adhesives as epoxy/polyurethane mixtures. Components of spray contain solid-particle fillers for strength, fire retardance, toughness, resistance to abrasion, or radar absorption.

  9. Formation of multiple levels of porous silicon for buried insulators and conductors in silicon device technologies

    Science.gov (United States)

    Blewer, Robert S.; Gullinger, Terry R.; Kelly, Michael J.; Tsao, Sylvia S.

    1991-01-01

    A method of forming a multiple level porous silicon substrate for semiconductor integrated circuits including anodizing non-porous silicon layers of a multi-layer silicon substrate to form multiple levels of porous silicon. At least one porous silicon layer is then oxidized to form an insulating layer and at least one other layer of porous silicon beneath the insulating layer is metallized to form a buried conductive layer. Preferably the insulating layer and conductive layer are separated by an anodization barrier formed of non-porous silicon. By etching through the anodization barrier and subsequently forming a metallized conductive layer, a fully or partially insulated buried conductor may be fabricated under single crystal silicon.

  10. Reprogramming chromatin

    DEFF Research Database (Denmark)

    Ehrensberger, Andreas Hasso; Svejstrup, Jesper Qualmann

    2012-01-01

    attributed to high kinetic barriers that affect all cells equally and can only be overcome by rare stochastic events. The barriers to reprogramming are likely to involve transformations of chromatin state because (i) inhibitors of chromatin-modifying enzymes can enhance the efficiency of reprogramming...... and (ii) knockdown or knock-out of chromatin-modifying enzymes can lower the efficiency of reprogramming. Here, we review the relationship between chromatin state transformations (chromatin reprogramming) and cellular reprogramming, with an emphasis on transcription factors, chromatin remodeling factors...

  11. Investigating the effect of multiple layers of insulation with a bubble wrap experiment

    Science.gov (United States)

    Eggers, Dolores; Ruiz, Michael J.

    2018-03-01

    We provide a fun, inexpensive laboratory experiment for students to investigate the effects of multiple layers of insulation and observe diminishing values for additional layers using bubble wrap. This experiment provides an opportunity for students to learn about heat transfer through conduction using readily available materials. A water-ice pack is placed on top of five layers of bubble wrap. The temperature is taken between each layer periodically for at least 15 min. Students determine asymptotic temperatures for varying layers. This experiment also suggests a real world application.

  12. Chromatin Hydrodynamics

    Science.gov (United States)

    Bruinsma, Robijn; Grosberg, Alexander Y.; Rabin, Yitzhak; Zidovska, Alexandra

    2014-01-01

    Following recent observations of large scale correlated motion of chromatin inside the nuclei of live differentiated cells, we present a hydrodynamic theory—the two-fluid model—in which the content of a nucleus is described as a chromatin solution with the nucleoplasm playing the role of the solvent and the chromatin fiber that of a solute. This system is subject to both passive thermal fluctuations and active scalar and vector events that are associated with free energy consumption, such as ATP hydrolysis. Scalar events drive the longitudinal viscoelastic modes (where the chromatin fiber moves relative to the solvent) while vector events generate the transverse modes (where the chromatin fiber moves together with the solvent). Using linear response methods, we derive explicit expressions for the response functions that connect the chromatin density and velocity correlation functions to the corresponding correlation functions of the active sources and the complex viscoelastic moduli of the chromatin solution. We then derive general expressions for the flow spectral density of the chromatin velocity field. We use the theory to analyze experimental results recently obtained by one of the present authors and her co-workers. We find that the time dependence of the experimental data for both native and ATP-depleted chromatin can be well-fitted using a simple model—the Maxwell fluid—for the complex modulus, although there is some discrepancy in terms of the wavevector dependence. Thermal fluctuations of ATP-depleted cells are predominantly longitudinal. ATP-active cells exhibit intense transverse long wavelength velocity fluctuations driven by force dipoles. Fluctuations with wavenumbers larger than a few inverse microns are dominated by concentration fluctuations with the same spectrum as thermal fluctuations but with increased intensity. PMID:24806919

  13. Low-frequency and multiple-bands sound insulation using hollow boxes with membrane-type faces

    Science.gov (United States)

    Yu, Wei-wei; Fan, Li; Ma, Ren-hao; Zhang, Hui; Zhang, Shu-yi

    2018-04-01

    Hollow boxes with their faces made up of elastic membranes are used to block acoustic waves. It is demonstrated that placing a cuboid membrane-type box inside a pipe can effectively insulate acoustic waves even if the box is smaller than the cross-section of the pipe. The sound insulation is achieved within multiple frequency-bands below 500 Hz based on different mechanisms, which originate from the coaction of the cavity, membrane-type faces, and the intervals between the box and pipe walls. Furthermore, by adjusting the structural parameters and establishing an array of boxes, we can achieve better sound insulation at more frequency-bands.

  14. Chromatin dynamics in genome stability

    DEFF Research Database (Denmark)

    Nair, Nidhi; Shoaib, Muhammad; Sørensen, Claus Storgaard

    2017-01-01

    Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote...... access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance...... of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage....

  15. Growth and characterization of semi-insulating carbon-doped/undoped GaN multiple-layer buffer

    International Nuclear Information System (INIS)

    Kim, Dong-Seok; Won, Chul-Ho; Kang, Hee-Sung; Kim, Young-Jo; Kang, In Man; Lee, Jung-Hee; Kim, Yong Tae

    2015-01-01

    We have proposed a new semi-insulating GaN buffer layer, which consists of multiple carbon-doped and undoped GaN layer. The buffer layer showed sufficiently good semi-insulating characteristics, attributed to the depletion effect between the carbon-doped GaN and the undoped GaN layers, even though the thickness of the carbon-doped GaN layer in the periodic structure was designed to be very thin to minimize the total carbon incorporation into the buffer layer. The AlGaN/AlN/GaN heterostructure grown on the proposed buffer exhibited much better electrical and structural properties than that grown on the conventional thick carbon-doped semi-insulating GaN buffer layer, confirmed by Hall measurement, x-ray diffraction, and secondary ion mass spectrometry. The fabricated device also showed excellent buffer breakdown characteristics. (paper)

  16. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    Adipocyte differentiation is tightly controlled by a transcriptional cascade, which directs the extensive reprogramming of gene expression required to convert fibroblast-like precursor cells into mature lipid-laden adipocytes. Recent global analyses of transcription factor binding and chromatin...... remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications....... Such transcription factor hotspots are likely to represent key signaling nodes which integrate multiple adipogenic signals at specific chromatin sites, thereby facilitating coordinated action on gene expression....

  17. The Influence of the Presence of Multiple Voids on the Discharge Patterns in Solid Epoxy Insulation

    DEFF Research Database (Denmark)

    Holbøll, Joachim T.; Henriksen, Mogens; Larsen, Esben

    1996-01-01

    In this paper, partial discharge test results from initial long term testing on samples which contain more voids, when exposed to a high electric stress will be presented. The influence on the discharge patterns, phase- and height-analyses, of such parameter as the number of voids and the void...... diameters will be given. A first evaluation/opinion of the impact this could have on the estimation of the insulation condition of electrical equipment, based on the identification of PD-patterns, will also be given....

  18. Chromatin is wonderful stuff.

    NARCIS (Netherlands)

    van Driel, R.

    2007-01-01

    Chromatin molecules have properties that set them aside from all other biomacromolecules in the cell. (i) Chromosomes, which are single chromatin molecules, are the largest macromolecules in eukaryotic cells. (ii) Chromatin molecules carry the cell's genetic and epigenetic information and all

  19. CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells.

    Directory of Open Access Journals (Sweden)

    Laurie A Steiner

    Full Text Available CTCF and cohesinSA-1 are regulatory proteins involved in a number of critical cellular processes including transcription, maintenance of chromatin domain architecture, and insulator function. To assess changes in the CTCF and cohesinSA-1 interactomes during erythropoiesis, chromatin immunoprecipitation coupled with high throughput sequencing and mRNA transcriptome analyses via RNA-seq were performed in primary human hematopoietic stem and progenitor cells (HSPC and primary human erythroid cells from single donors.Sites of CTCF and cohesinSA-1 co-occupancy were enriched in gene promoters in HSPC and erythroid cells compared to single CTCF or cohesin sites. Cell type-specific CTCF sites in erythroid cells were linked to highly expressed genes, with the opposite pattern observed in HSPCs. Chromatin domains were identified by ChIP-seq with antibodies against trimethylated lysine 27 histone H3, a modification associated with repressive chromatin. Repressive chromatin domains increased in both number and size during hematopoiesis, with many more repressive domains in erythroid cells than HSPCs. CTCF and cohesinSA-1 marked the boundaries of these repressive chromatin domains in a cell-type specific manner.These genome wide data, changes in sites of protein occupancy, chromatin architecture, and related gene expression, support the hypothesis that CTCF and cohesinSA-1 have multiple roles in the regulation of gene expression during erythropoiesis including transcriptional regulation at gene promoters and maintenance of chromatin architecture. These data from primary human erythroid cells provide a resource for studies of normal and perturbed erythropoiesis.

  20. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

    The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active

  1. A high incidence of meiotic silencing of unsynapsed chromatin is not associated with substantial pachytene loss in heterozygous male mice carrying multiple simple robertsonian translocations.

    Directory of Open Access Journals (Sweden)

    Marcia Manterola

    2009-08-01

    Full Text Available Meiosis is a complex type of cell division that involves homologous chromosome pairing, synapsis, recombination, and segregation. When any of these processes is altered, cellular checkpoints arrest meiosis progression and induce cell elimination. Meiotic impairment is particularly frequent in organisms bearing chromosomal translocations. When chromosomal translocations appear in heterozygosis, the chromosomes involved may not correctly complete synapsis, recombination, and/or segregation, thus promoting the activation of checkpoints that lead to the death of the meiocytes. In mammals and other organisms, the unsynapsed chromosomal regions are subject to a process called meiotic silencing of unsynapsed chromatin (MSUC. Different degrees of asynapsis could contribute to disturb the normal loading of MSUC proteins, interfering with autosome and sex chromosome gene expression and triggering a massive pachytene cell death. We report that in mice that are heterozygous for eight multiple simple Robertsonian translocations, most pachytene spermatocytes bear trivalents with unsynapsed regions that incorporate, in a stage-dependent manner, proteins involved in MSUC (e.g., gammaH2AX, ATR, ubiquitinated-H2A, SUMO-1, and XMR. These spermatocytes have a correct MSUC response and are not eliminated during pachytene and most of them proceed into diplotene. However, we found a high incidence of apoptotic spermatocytes at the metaphase stage. These results suggest that in Robertsonian heterozygous mice synapsis defects on most pachytene cells do not trigger a prophase-I checkpoint. Instead, meiotic impairment seems to mainly rely on the action of a checkpoint acting at the metaphase stage. We propose that a low stringency of the pachytene checkpoint could help to increase the chances that spermatocytes with synaptic defects will complete meiotic divisions and differentiate into viable gametes. This scenario, despite a reduction of fertility, allows the spreading

  2. Radiation Effects in Advanced Multiple Gate and Silicon-on-Insulator Transistors

    Science.gov (United States)

    Simoen, Eddy; Gaillardin, Marc; Paillet, Philippe; Reed, Robert A.; Schrimpf, Ron D.; Alles, Michael L.; El-Mamouni, Farah; Fleetwood, Daniel M.; Griffoni, Alessio; Claeys, Cor

    2013-06-01

    The aim of this review paper is to describe in a comprehensive manner the current understanding of the radiation response of state-of-the-art Silicon-on-Insulator (SOI) and FinFET CMOS technologies. Total Ionizing Dose (TID) response, heavy-ion microdose effects and single-event effects (SEEs) will be discussed. It is shown that a very high TID tolerance can be achieved by narrow-fin SOI FinFET architectures, while bulk FinFETs may exhibit similar TID response to the planar devices. Due to the vertical nature of FinFETs, a specific heavy-ion response can be obtained, whereby the angle of incidence becomes highly important with respect to the vertical sidewall gates. With respect to SEE, the buried oxide in the SOI FinFETs suppresses the diffusion tails from the charge collection in the substrate compared to the planar bulk FinFET devices. Channel lengths and fin widths are now comparable to, or smaller than the dimensions of the region affected by the single ionizing ions or lasers used in testing. This gives rise to a high degree of sensitivity to individual device parameters and source-drain shunting during ion-beam or laser-beam SEE testing. Simulations are used to illuminate the mechanisms observed in radiation testing and the progress and needs for the numerical modeling/simulation of the radiation response of advanced SOI and FinFET transistors are highlighted.

  3. Overvoltage and Insulation Coordination of Overhead Lines in Multiple-Terminal MMC-HVDC Link for Wind Power Delivery

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    Huiwen He

    2017-01-01

    Full Text Available The voltage-sourced converter-based HVDC link, including the modular multilevel converter (MMC configuration, is suitable for wind power, photovoltaic energy, and other kinds of new energy delivery and grid-connection. Current studies are focused on the MMC principles and controls and few studies have been done on the overvoltage of transmission line for the MMC-HVDC link. The main reason is that environmental factors have little effect on DC cables and the single-phase/pole fault rate is low. But if the cables were replaced by the overhead lines, although the construction cost of the project would be greatly reduced, the single-pole ground fault rate would be much higher. This paper analyzed the main overvoltage types in multiple-terminal MMC-HVDC network which transmit electric power by overhead lines. Based on ±500 kV multiple-terminal MMC-HVDC for wind power delivery project, the transient simulation model was built and the overvoltage types mentioned above were studied. The results showed that the most serious overvoltage was on the healthy adjacent line of the faulty line caused by the fault clearing of DC breaker. Then the insulation coordination for overhead lines was conducted according to the overvoltage level. The recommended clearance values were given.

  4. Structured illumination to spatially map chromatin motions.

    Science.gov (United States)

    Bonin, Keith; Smelser, Amanda; Moreno, Naike Salvador; Holzwarth, George; Wang, Kevin; Levy, Preston; Vidi, Pierre-Alexandre

    2018-05-01

    We describe a simple optical method that creates structured illumination of a photoactivatable probe and apply this method to characterize chromatin motions in nuclei of live cells. A laser beam coupled to a diffractive optical element at the back focal plane of an excitation objective generates an array of near diffraction-limited beamlets with FWHM of 340  ±  30  nm, which simultaneously photoactivate a 7  ×  7 matrix pattern of GFP-labeled histones, with spots 1.70  μm apart. From the movements of the photoactivated spots, we map chromatin diffusion coefficients at multiple microdomains of the cell nucleus. The results show correlated motions of nearest chromatin microdomain neighbors, whereas chromatin movements are uncorrelated at the global scale of the nucleus. The method also reveals a DNA damage-dependent decrease in chromatin diffusion. The diffractive optical element instrumentation can be easily and cheaply implemented on commercial inverted fluorescence microscopes to analyze adherent cell culture models. A protocol to measure chromatin motions in nonadherent human hematopoietic stem and progenitor cells is also described. We anticipate that the method will contribute to the identification of the mechanisms regulating chromatin mobility, which influences most genomic processes and may underlie the biogenesis of genomic translocations associated with hematologic malignancies. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  5. Chromatin meets its organizers.

    Science.gov (United States)

    Bodnar, Megan S; Spector, David L

    2013-06-06

    Chromatin organization and gene-gene interactions are critical components of carrying out developmental programs. Phillips-Cremins et al. identify a series of unexpected architectural proteins that work in a combinatorial manner to functionally organize chromatin in a cell-type-specific manner at the submegabase-length scale. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Heterogeneous chromatin target model

    International Nuclear Information System (INIS)

    Watanabe, Makoto

    1996-01-01

    The higher order structure of the entangled chromatin fibers in a chromosome plays a key role in molecular control mechanism involved in chromosome mutation due to ionizing radiations or chemical mutagens. The condensed superstructure of chromatin is not so rigid and regular as has been postulated in general. We have proposed a rheological explanation for the flexible network system ('chromatin network') that consists of the fluctuating assembly of nucleosome clusters linked with supertwisting DNA in a chromatin fiber ('Supertwisting Particulate Model'). We have proposed a 'Heterosensitive Target Model' for cellular radiosensitivity that is a modification of 'Heterogeneous Target Model'. The heterogeneity of chromatin target is derived from the highly condensed organization of chromatin segments consist of unstable and fragile sites in the fluctuating assembly of nucleosome clusters, namely 'supranucleosomal particles' or 'superbeads'. The models have been principally supported by our electron microscopic experiments employing 'surface - spreading whole - mount technique' since 1967. However, some deformation and artifacts in the chromatin structure are inevitable with these electron microscopic procedures. On the contrary, the 'atomic force microscope (AFM)' can be operated in liquid as well as in the air. A living specimen can be examined without any preparative procedures. Micromanipulation of the isolated chromosome is also possible by the precise positional control of a cantilever on the nanometer scale. The living human chromosomes were submerged in a solution of culture medium and observed by AFM using a liquid immersion cell. The surface - spreading whole - mount technique was applicable for this observation. The particulate chromatin segments of nucleosome clusters were clearly observed within mitotic human chromosomes in a living hydrated condition. These findings support the heterogeneity of chromatin target in a living cell. (J.P.N.)

  7. EBV Latency Types Adopt Alternative Chromatin Conformations

    Science.gov (United States)

    Tempera, Italo; Klichinsky, Michael; Lieberman, Paul M.

    2011-01-01

    Epstein-Barr Virus (EBV) can establish latent infections with distinct gene expression patterns referred to as latency types. These different latency types are epigenetically stable and correspond to different promoter utilization. Here we explore the three-dimensional conformations of the EBV genome in different latency types. We employed Chromosome Conformation Capture (3C) assay to investigate chromatin loop formation between the OriP enhancer and the promoters that determine type I (Qp) or type III (Cp) gene expression. We show that OriP is in close physical proximity to Qp in type I latency, and to Cp in type III latency. The cellular chromatin insulator and boundary factor CTCF was implicated in EBV chromatin loop formation. Combining 3C and ChIP assays we found that CTCF is physically associated with OriP-Qp loop formation in type I and OriP-Cp loop formation in type III latency. Mutations in the CTCF binding site located at Qp disrupt loop formation between Qp and OriP, and lead to the activation of Cp transcription. Mutation of the CTCF binding site at Cp, as well as siRNA depletion of CTCF eliminates both OriP-associated loops, indicating that CTCF plays an integral role in loop formation. These data indicate that epigenetically stable EBV latency types adopt distinct chromatin architectures that depend on CTCF and mediate alternative promoter targeting by the OriP enhancer. PMID:21829357

  8. EBV latency types adopt alternative chromatin conformations.

    Directory of Open Access Journals (Sweden)

    Italo Tempera

    2011-07-01

    Full Text Available Epstein-Barr Virus (EBV can establish latent infections with distinct gene expression patterns referred to as latency types. These different latency types are epigenetically stable and correspond to different promoter utilization. Here we explore the three-dimensional conformations of the EBV genome in different latency types. We employed Chromosome Conformation Capture (3C assay to investigate chromatin loop formation between the OriP enhancer and the promoters that determine type I (Qp or type III (Cp gene expression. We show that OriP is in close physical proximity to Qp in type I latency, and to Cp in type III latency. The cellular chromatin insulator and boundary factor CTCF was implicated in EBV chromatin loop formation. Combining 3C and ChIP assays we found that CTCF is physically associated with OriP-Qp loop formation in type I and OriP-Cp loop formation in type III latency. Mutations in the CTCF binding site located at Qp disrupt loop formation between Qp and OriP, and lead to the activation of Cp transcription. Mutation of the CTCF binding site at Cp, as well as siRNA depletion of CTCF eliminates both OriP-associated loops, indicating that CTCF plays an integral role in loop formation. These data indicate that epigenetically stable EBV latency types adopt distinct chromatin architectures that depend on CTCF and mediate alternative promoter targeting by the OriP enhancer.

  9. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  10. Self-Healing Wire Insulation

    Science.gov (United States)

    Parrish, Clyde F. (Inventor)

    2012-01-01

    A self-healing system for an insulation material initiates a self-repair process by rupturing a plurality of microcapsules disposed on the insulation material. When the plurality of microcapsules are ruptured, reactants within the plurality of microcapsules react to form a replacement polymer in a break of the insulation material. This self-healing system has the ability to repair multiple breaks in a length of insulation material without exhausting the repair properties of the material.

  11. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-06-01

    Activities of DNA are to a great extent controlled epigenetically through the internal struc- ture of chromatin. This structure is dynamic and is influenced by different modifications of histone proteins. Various combinations of epigenetic modification of histones pinpoint to different functional regions of the DNA determining the so-called chromatin states. How- ever, the characterization of chromatin states by the DNA sequence properties remains largely unknown. In this study we aim to explore whether DNA sequence patterns in the human genome can characterize different chromatin states. Using DNA sequence motifs we built binary classifiers for each chromatic state to eval- uate whether a given genomic sequence is a good candidate for belonging to a particular chromatin state. Of four classification algorithms (C4.5, Naive Bayes, Random Forest, and SVM) used for this purpose, the decision tree based classifiers (C4.5 and Random Forest) yielded best results among those we evaluated. Our results suggest that in general these models lack sufficient predictive power, although for four chromatin states (insulators, het- erochromatin, and two types of copy number variation) we found that presence of certain motifs in DNA sequences does imply an increased probability that such a sequence is one of these chromatin states.

  12. Reprogramming the chromatin landscape

    DEFF Research Database (Denmark)

    Miranda, Tina B; Voss, Ty C; Sung, Myong-Hee

    2013-01-01

    , mechanistic details defining the cellular interactions between ER and GR are poorly understood. We investigated genome-wide binding profiles for ER and GR upon coactivation and characterized the status of the chromatin landscape. We describe a novel mechanism dictating the molecular interplay between ER...... and GR. Upon induction, GR modulates access of ER to specific sites in the genome by reorganization of the chromatin configuration for these elements. Binding to these newly accessible sites occurs either by direct recognition of ER response elements or indirectly through interactions with other factors...

  13. Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization

    Directory of Open Access Journals (Sweden)

    Vuthy Ea

    2015-07-01

    Full Text Available Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. This review presents the most recent advances in topological domains’ organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce functional interactions by contact stabilization.

  14. Proteomic interrogation of human chromatin.

    Directory of Open Access Journals (Sweden)

    Mariana P Torrente

    Full Text Available Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome" is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.

  15. Effects of fast neutrons on chromatin: dependence on chromatin structure

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [Dept. of Molecular Genetics, V. Babes National Inst., Bd. Timisoara, Bucharest (Romania); Constantinescu, B. [Dept. of Cyclotron, H. Hulubei National Inst., Bucharest (Romania); Gazdaru, D. [Dept. of Biophysics, Physics Faculty, Univ. of Bucharest (Romania)

    2002-07-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  16. Effects of fast neutrons on chromatin: dependence on chromatin structure

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.

    2002-01-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  17. Insulators form gene loops by interacting with promoters in Drosophila.

    Science.gov (United States)

    Erokhin, Maksim; Davydova, Anna; Kyrchanova, Olga; Parshikov, Alexander; Georgiev, Pavel; Chetverina, Darya

    2011-09-01

    Chromatin insulators are regulatory elements involved in the modulation of enhancer-promoter communication. The 1A2 and Wari insulators are located immediately downstream of the Drosophila yellow and white genes, respectively. Using an assay based on the yeast GAL4 activator, we have found that both insulators are able to interact with their target promoters in transgenic lines, forming gene loops. The existence of an insulator-promoter loop is confirmed by the fact that insulator proteins could be detected on the promoter only in the presence of an insulator in the transgene. The upstream promoter regions, which are required for long-distance stimulation by enhancers, are not essential for promoter-insulator interactions. Both insulators support basal activity of the yellow and white promoters in eyes. Thus, the ability of insulators to interact with promoters might play an important role in the regulation of basal gene transcription.

  18. Thermal insulation

    International Nuclear Information System (INIS)

    Aspden, G.J.; Howard, R.S.

    1988-01-01

    The patent concerns high temperature thermal insulation of large vessels, such as the primary vessel of a liquid metal cooled nuclear reactor. The thermal insulation consists of multilayered thermal insulation modules, and each module comprises a number of metal sheet layers sandwiched between a back and front plate. The layers are linked together by straps and clips to control the thickness of the module. (U.K.)

  19. Cellulose Insulation

    Science.gov (United States)

    1980-01-01

    Fire retardant cellulose insulation is produced by shredding old newspapers and treating them with a combination of chemicals. Insulating material is blown into walls and attics to form a fiber layer which blocks the flow of air. All-Weather Insulation's founders asked NASA/UK-TAP to help. They wanted to know what chemicals added to newspaper would produce an insulating material capable of meeting federal specifications. TAP researched the query and furnished extensive information. The information contributed to successful development of the product and helped launch a small business enterprise which is now growing rapidly.

  20. Thermal insulation

    International Nuclear Information System (INIS)

    Pinsky, G.P.

    1977-01-01

    Thermal insulation for vessels and piping within the reactor containment area of nuclear power plants is disclosed. The thermal insulation of this invention can be readily removed and replaced from the vessels and piping for inservice inspection, can withstand repeated wettings and dryings, and can resist high temperatures for long periods of time. 4 claims, 3 figures

  1. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

    Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate...... choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper...... organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure...

  2. Chromatin Flavors: Chromatin composition and domain organization in Drosophila melanogaster

    NARCIS (Netherlands)

    J.G. van Bemmel (Joke)

    2012-01-01

    textabstractChromatin was originally identified by W. Flemming in 1882 as not much more than the stainable substance of the cell nucleus. Flemming named this substance according to the Greek word “chroma”, meaning color. In 1911 chromatin was characterized as proteins, named histones, that

  3. Optical tweezers stretching of chromatin

    NARCIS (Netherlands)

    Pope, L.H.; Bennink, Martin L.; Greve, Jan

    2003-01-01

    Recently significant success has emerged from exciting research involving chromatin stretching using optical tweezers. These experiments, in which a single chromatin fibre is attached by one end to a micron-sized bead held in an optical trap and to a solid surface or second bead via the other end,

  4. Analysis of DNA replication associated chromatin decondensation: in vivo assay for understanding chromatin remodeling mechanisms of selected proteins.

    Science.gov (United States)

    Borysov, Sergiy; Bryant, Victoria L; Alexandrow, Mark G

    2015-01-01

    Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the initiation of DNA replication, as well as the ability of the replication machinery to proceed during elongation through the multiple levels of chromatin condensation that are likely to be encountered, is known to involve the creation of chromatin accessibility. In the latter case, chromatin access will likely need to be a transient event so as to prevent total genomic unraveling of the chromatin that would be deleterious to cells. While there are many molecular and biochemical approaches in use to study histone changes and their relationship to transcription and chromatin accessibility, few techniques exist that allow a molecular dissection of the events underlying DNA replication control as it pertains to chromatin changes and accessibility. Here, we outline a novel experimental strategy for addressing the ability of specific proteins to induce large-scale chromatin unfolding (decondensation) in vivo upon site-specific targeting to an engineered locus. Our laboratory has used this powerful system in novel ways to directly address the ability of DNA replication proteins to create chromatin accessibility, and have incorporated modifications to the basic approach that allow for a molecular genetic analysis of the mechanisms and associated factors involved in causing chromatin decondensation by a protein of interest. Alternative approaches involving co-expression of other proteins (competitors or stimulators), concurrent drug treatments, and analysis of co-localizing histone modifications are also addressed, all of which are illustrative of the utility of this experimental system for extending basic findings to physiologically relevant mechanisms. Although used by our group to analyze

  5. Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes.

    Directory of Open Access Journals (Sweden)

    Varvara A Khoroshko

    Full Text Available Late-replicating domains (intercalary heterochromatin in the Drosophila genome display a number of features suggesting their organization is quite unique. Typically, they are quite large and encompass clusters of functionally unrelated tissue-specific genes. They correspond to the topologically associating domains and conserved microsynteny blocks. Our study aims at exploring further details of molecular organization of intercalary heterochromatin and has uncovered surprising heterogeneity of chromatin composition in these regions. Using the 4HMM model developed in our group earlier, intercalary heterochromatin regions were found to host chromatin fragments with a particular epigenetic profile. Aquamarine chromatin fragments (spanning 0.67% of late-replicating regions are characterized as a class of sequences that appear heterogeneous in terms of their decompactization. These fragments are enriched with enhancer sequences and binding sites for insulator proteins. They likely mark the chromatin state that is related to the binding of cis-regulatory proteins. Malachite chromatin fragments (11% of late-replicating regions appear to function as universal transitional regions between two contrasting chromatin states. Namely, they invariably delimit intercalary heterochromatin regions from the adjacent active chromatin of interbands. Malachite fragments also flank aquamarine fragments embedded in the repressed chromatin of late-replicating regions. Significant enrichment of insulator proteins CP190, SU(HW, and MOD2.2 was observed in malachite chromatin. Neither aquamarine nor malachite chromatin types appear to correlate with the positions of highly conserved non-coding elements (HCNE that are typically replete in intercalary heterochromatin. Malachite chromatin found on the flanks of intercalary heterochromatin regions tends to replicate earlier than the malachite chromatin embedded in intercalary heterochromatin. In other words, there exists a

  6. Thermal insulation

    International Nuclear Information System (INIS)

    Durston, J.G.; Birch, W.; Facer, R.I.; Stuart, R.A.

    1977-01-01

    Reference is made to liquid metal cooled nuclear reactors. In the arrangement described the reactor vessel is clad with thermal insulation comprising a layer of insulating blocks spaced from the wall and from each other; each block is rigidly secured to the wall, and the interspaces are substantially closed against convectional flow of liquid by resilient closure members. A membrane covering is provided for the layer of blocks, with venting means to allow liquid from the reactor vessel to penetrate between the covering and the layer of blocks. The membrane covering may comprise a stainless steel sheet ribbed in orthogonal pattern to give flexibility for the accommodation of thermal strain. The insulating blocks may be comprised of stainless steel or cellular or porous material and may be hollow shells containing ceramic material or gas fillings. (U.K.)

  7. Topological insulators

    CERN Document Server

    Franz, Marcel

    2013-01-01

    Topological Insulators, volume six in the Contemporary Concepts of Condensed Matter Series, describes the recent revolution in condensed matter physics that occurred in our understanding of crystalline solids. The book chronicles the work done worldwide that led to these discoveries and provides the reader with a comprehensive overview of the field. Starting in 2004, theorists began to explore the effect of topology on the physics of band insulators, a field previously considered well understood. However, the inclusion of topology brings key new elements into this old field. Whereas it was

  8. Regulation of chromatin structure by poly(ADP-ribosylation

    Directory of Open Access Journals (Sweden)

    Sascha eBeneke

    2012-09-01

    Full Text Available The interaction of DNA with proteins in the context of chromatin has to be tightly regulated to achieve so different tasks as packaging, transcription, replication and repair. The very rapid and transient post-translational modification of proteins by poly(ADP-ribose has been shown to take part in all four. Originally identified as immediate cellular answer to a variety of genotoxic stresses, already early data indicated the ability of this highly charged nucleic acid-like polymer to modulate nucleosome structure, the basic unit of chromatin. At the same time the enzyme responsible for synthesizing poly(ADP-ribose, the zinc-finger protein poly(ADP-ribose polymerase-1 (PARP1, was shown to control transcription initiation as basic factor TFIIC within the RNA-polymerase II machinery. Later research focused more on PARP-mediated regulation of DNA repair and cell death, but in the last few years, transcription as well as chromatin modulation has re-appeared on the scene. This review will discuss the impact of PARP1 on transcription and transcription factors, its implication in chromatin remodeling for DNA repair and probably also replication, and its role in controlling epigenetic events such as DNA methylation and the functionality of the insulator protein CCCTC-binding factor.

  9. Epigenetic regulation of open chromatin in pluripotent stem cells

    Science.gov (United States)

    Kobayashi, Hiroshi; Kikyo, Nobuaki

    2014-01-01

    The recent progress in pluripotent stem cell research has opened new avenues of disease modeling, drug screening, and transplantation of patient-specific tissues that had been unimaginable until a decade ago. The central mechanism underlying pluripotency is epigenetic gene regulation; the majority of cell signaling pathways, both extracellular and cytoplasmic, eventually alter the epigenetic status of their target genes during the process of activating or suppressing the genes to acquire or maintain pluripotency. It has long been thought that the chromatin of pluripotent stem cells is globally open to enable the timely activation of essentially all genes in the genome during differentiation into multiple lineages. The current article reviews descriptive observations and the epigenetic machinery relevant to what is supposed to be globally open chromatin in pluripotent stem cells. This includes microscopic appearance, permissive gene transcription, chromatin remodeling complexes, histone modifications, DNA methylation, noncoding RNAs, dynamic movement of chromatin proteins, nucleosome accessibility and positioning, and long-range chromosomal interactions. Detailed analyses of each element, however, have revealed that the globally open chromatin hypothesis is not necessarily supported by some of the critical experimental evidence, such as genome-wide nucleosome accessibility and nucleosome positioning. Further understanding of the epigenetic gene regulation is expected to determine the true nature of the so-called globally open chromatin in pluripotent stem. PMID:24695097

  10. Radiation response and chromatin dynamics

    International Nuclear Information System (INIS)

    Ikura, Tsuyoshi

    2009-01-01

    Described is a recent progress in studies of chromatin structural alterations induced by DNA damage by radiation. DNA in eukaryotes exists in the chromatin structure and different mechanisms of response to damage and repair of DNA from those in prokaryotes have been recognized. Chromatin is composed from its unit structure of mono-nucleosome, which is formed from DNA and an octamer of core histones of H2A, H2B, H3 and H4. When DNA is damaged, histone structural alterations are required for repair factors and checkpoint proteins to access the damaged site. At the actual genome damage, chemical modification of histone to work as a code occurs dependently on the damage where chromatin remodeling factors and histone chaperone participate for structural alteration and remodeling. As well, the exchange of histone variants and fluidization of histones are recently reported. Known chemical modification involves phosphorylation, acetylation and ubiquitination of H2AX (a variant of H2A), and acetylation and methylation of H3. Each complex of TIP60, NuA4 and INO80 is known to be included in the regulation of chromatin with damaged/repaired DNA for remodeling, but little is known about recruitment of the factors concerned at the damage site. Regulatory mechanisms in above chromatin dynamics with consideration of quality and timing of radiation should be further elucidated for understanding the precise response to DNA damage. (K.T.)

  11. Chromatin remodeling, development and disease

    International Nuclear Information System (INIS)

    Ko, Myunggon; Sohn, Dong H.; Chung, Heekyoung; Seong, Rho H.

    2008-01-01

    Development is a stepwise process in which multi-potent progenitor cells undergo lineage commitment, differentiation, proliferation and maturation to produce mature cells with restricted developmental potentials. This process is directed by spatiotemporally distinct gene expression programs that allow cells to stringently orchestrate intricate transcriptional activation or silencing events. In eukaryotes, chromatin structure contributes to developmental progression as a blueprint for coordinated gene expression by actively participating in the regulation of gene expression. Changes in higher order chromatin structure or covalent modification of its components are considered to be critical events in dictating lineage-specific gene expression during development. Mammalian cells utilize multi-subunit nuclear complexes to alter chromatin structure. Histone-modifying complex catalyzes covalent modifications of histone tails including acetylation, methylation, phosphorylation and ubiquitination. ATP-dependent chromatin remodeling complex, which disrupts histone-DNA contacts and induces nucleosome mobilization, requires energy from ATP hydrolysis for its catalytic activity. Here, we discuss the diverse functions of ATP-dependent chromatin remodeling complexes during mammalian development. In particular, the roles of these complexes during embryonic and hematopoietic development are reviewed in depth. In addition, pathological conditions such as tumor development that are induced by mutation of several key subunits of the chromatin remodeling complex are discussed, together with possible mechanisms that underlie tumor suppression by the complex

  12. TAD-free analysis of architectural proteins and insulators.

    Science.gov (United States)

    Mourad, Raphaël; Cuvier, Olivier

    2018-03-16

    The three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression and DNA replication regulations. The mechanisms by which molecular drivers functionally organize the 3D genome, such as topologically associating domains (TADs), remain to be explored. Current approaches consist in assessing the enrichments or influences of proteins at TAD borders. Here, we propose a TAD-free model to directly estimate the blocking effects of architectural proteins, insulators and DNA motifs on long-range contacts, making the model intuitive and biologically meaningful. In addition, the model allows analyzing the whole Hi-C information content (2D information) instead of only focusing on TAD borders (1D information). The model outperforms multiple logistic regression at TAD borders in terms of parameter estimation accuracy and is validated by enhancer-blocking assays. In Drosophila, the results support the insulating role of simple sequence repeats and suggest that the blocking effects depend on the number of repeats. Motif analysis uncovered the roles of the transcriptional factors pannier and tramtrack in blocking long-range contacts. In human, the results suggest that the blocking effects of the well-known architectural proteins CTCF, cohesin and ZNF143 depend on the distance between loci, where each protein may participate at different scales of the 3D chromatin organization.

  13. RNA is an integral component of chromatin that contributes to its structural organization.

    Directory of Open Access Journals (Sweden)

    Antonio Rodríguez-Campos

    Full Text Available Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA(- and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with alpha-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.

  14. Absorbed Dose Distributions in Small Copper Wire Insulation due to Multiple-Sided Irradiations by 0.4 MeV Electrons

    DEFF Research Database (Denmark)

    Miller, Arne; McLaughlin, W. L.; Pedersen, Walther Batsberg

    1979-01-01

    When scanned electron beams are used to crosslink polymeric insulation of wire and cable, an important goal is to achieve optimum uniformity of absorbed dose distributions. Accurate measurements of dose distributions in a plastic dosimeter simulating a typical insulating material (polyethylene......) surrounding a copper wire core show that equal irradiations from as few as four sides give approximately isotropy and satisfactorily uniform energy depositions around the wire circumference. Electron beams of 0.4 MeV maximum energy were used to irradiate wires having a copper core of 1.0 mm dia....... and insulation thicknesses between 0.4 and 0.8 mm. The plastic dosimeter simulating polyethylene insulations was a thin radiochromic polyvinyl butyral film wrapped several times around the copper wire, such that when unwrapped and analyzed optically on a scanning microspectrophotometer, high-resolution radial...

  15. [Effects of functional interactions between nonhomologous insulators Wari and Su(Hw)].

    Science.gov (United States)

    Erokhin, M M; Georgiev, P G; Chetverina, D A

    2010-01-01

    Insulators are regulatory DNA elements restricting gene activation by enhancers. Interactions between insulators can lead to both insulation and activation of promoters by enhancers. In this work, we analyzed the effects of interaction of two Drosophila insulators, Wari and Su(Hw). The functional interaction between these insulators was found to enhance the activity of the Su(Hw) insulator only, but not of the Wari insulator. This suggests that the formation of a chromatin loop between interacting insulators is not a key factor for enhancement of insulation, which is in disagreement with the main idea of structural models. In addition, the effect of interaction between Wari and Su(Hw) depends on a distance between them and on the position in the system relative to other regulatory elements.

  16. SAGA, TFIID and regulation of transcription through chromatin

    NARCIS (Netherlands)

    Schram, A.W.

    2013-01-01

    Chromatin has an important role in eukaryotic transcription. Research into this role is ongoing and genome-wide analysis has correlated various histone modifications to multiple elements in active and silent genes, such as enhancers, promoters and coding regions. Modifications often serve to recruit

  17. Chromatin Remodeling and Plant Immunity.

    Science.gov (United States)

    Chen, W; Zhu, Q; Liu, Y; Zhang, Q

    Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense. So what are the links between Snf2-mediated ATP-dependent chromosome remodeling and plant immunity, and what mechanisms might support its involvement in disease resistance? © 2017 Elsevier Inc. All rights reserved.

  18. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

    Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet...... the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic...... landscape may be stably maintained even in the face of dramatic changes in chromatin structure....

  19. Chromatin Structure of Epstein-Barr Virus Latent Episomes.

    Science.gov (United States)

    Lieberman, Paul M

    2015-01-01

    EBV latent infection is characterized by a highly restricted pattern of viral gene expression. EBV can establish latent infections in multiple different tissue types with remarkable variation and plasticity in viral transcription and replication. During latency, the viral genome persists as a multi-copy episome, a non-integrated-closed circular DNA with nucleosome structure similar to cellular chromosomes. Chromatin assembly and histone modifications contribute to the regulation of viral gene expression, DNA replication, and episome persistence during latency. This review focuses on how EBV latency is regulated by chromatin and its associated processes.

  20. Circadian expression profiles of chromatin remodeling factor genes in Arabidopsis.

    Science.gov (United States)

    Lee, Hong Gil; Lee, Kyounghee; Jang, Kiyoung; Seo, Pil Joon

    2015-01-01

    The circadian clock is a biological time keeper mechanism that regulates biological rhythms to a period of approximately 24 h. The circadian clock enables organisms to anticipate environmental cycles and coordinates internal cellular physiology with external environmental cues. In plants, correct matching of the clock with the environment confers fitness advantages to plant survival and reproduction. Therefore, circadian clock components are regulated at multiple layers to fine-tune the circadian oscillation. Epigenetic regulation provides an additional layer of circadian control. However, little is known about which chromatin remodeling factors are responsible for circadian control. In this work, we analyzed circadian expression of 109 chromatin remodeling factor genes and identified 17 genes that display circadian oscillation. In addition, we also found that a candidate interacts with a core clock component, supporting that clock activity is regulated in part by chromatin modification. As an initial attempt to elucidate the relationship between chromatin modification and circadian oscillation, we identified novel regulatory candidates that provide a platform for future investigations of chromatin regulation of the circadian clock.

  1. A Long-Distance Chromatin Affair

    NARCIS (Netherlands)

    Denker, Annette; de Laat, Wouter

    2015-01-01

    Changes in transcription factor binding sequences result in correlated changes in chromatin composition locally and at sites hundreds of kilobases away. New studies demonstrate that this concordance is mediated via spatial chromatin interactions that constitute regulatory modules of the human

  2. Guarding against Collateral Damage during Chromatin Transactions

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Lukas, Jiri

    2013-01-01

    Signal amplifications are vital for chromatin function, yet they also bear the risk of transforming into unrestrained, self-escalating, and potentially harmful responses. Examples of inbuilt limitations are emerging, revealing how chromatin transactions are confined within physiological boundaries....

  3. Tank Insulation

    Science.gov (United States)

    1979-01-01

    For NASA's Apollo program, McDonnell Douglas Astronautics Company, Huntington Beach, California, developed and built the S-IVB, uppermost stage of the three-stage Saturn V moonbooster. An important part of the development task was fabrication of a tank to contain liquid hydrogen fuel for the stage's rocket engine. The liquid hydrogen had to be contained at the supercold temperature of 423 degrees below zero Fahrenheit. The tank had to be perfectly insulated to keep engine or solar heat from reaching the fuel; if the hydrogen were permitted to warm up, it would have boiled off, or converted to gaseous form, reducing the amount of fuel available to the engine. McDonnell Douglas' answer was a supereffective insulation called 3D, which consisted of a one-inch thickness of polyurethane foam reinforced in three dimensions with fiberglass threads. Over a 13-year development and construction period, the company built 30 tanks and never experienced a failure. Now, after years of additional development, an advanced version of 3D is finding application as part of a containment system for transporting Liquefied Natural Gas (LNG) by ship.

  4. Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells.

    Science.gov (United States)

    Forn, Marta; Muñoz, Mar; Tauriello, Daniele V F; Merlos-Suárez, Anna; Rodilla, Verónica; Bigas, Anna; Batlle, Eduard; Jordà, Mireia; Peinado, Miguel A

    2013-12-01

    DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All

  5. Chromatin in embryonic stem cell neuronal differentiation.

    Science.gov (United States)

    Meshorer, E

    2007-03-01

    Chromatin, the basic regulatory unit of the eukaryotic genetic material, is controlled by epigenetic mechanisms including histone modifications, histone variants, DNA methylation and chromatin remodeling. Cellular differentiation involves large changes in gene expression concomitant with alterations in genome organization and chromatin structure. Such changes are particularly evident in self-renewing pluripotent embryonic stem cells, which begin, in terms of cell fate, as a tabula rasa, and through the process of differentiation, acquire distinct identities. Here I describe the changes in chromatin that accompany neuronal differentiation, particularly of embryonic stem cells, and discuss how chromatin serves as the master regulator of cellular destiny.

  6. Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin

    Directory of Open Access Journals (Sweden)

    Mora Xavier

    2007-05-01

    Full Text Available Abstract Background Histone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes in physiological salt (0.14 M NaCl at constant stoichiometry. Results The H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin. Conclusion H1 subtypes freely exchange in vitro between chromatin binding sites in physiological salt (0.14 M NaCl. The large differences in relative affinity of the H1 subtypes for

  7. Chromatin Controls DNA Replication Origin Selection, Lagging-Strand Synthesis, and Replication Fork Rates.

    Science.gov (United States)

    Kurat, Christoph F; Yeeles, Joseph T P; Patel, Harshil; Early, Anne; Diffley, John F X

    2017-01-05

    The integrity of eukaryotic genomes requires rapid and regulated chromatin replication. How this is accomplished is still poorly understood. Using purified yeast replication proteins and fully chromatinized templates, we have reconstituted this process in vitro. We show that chromatin enforces DNA replication origin specificity by preventing non-specific MCM helicase loading. Helicase activation occurs efficiently in the context of chromatin, but subsequent replisome progression requires the histone chaperone FACT (facilitates chromatin transcription). The FACT-associated Nhp6 protein, the nucleosome remodelers INO80 or ISW1A, and the lysine acetyltransferases Gcn5 and Esa1 each contribute separately to maximum DNA synthesis rates. Chromatin promotes the regular priming of lagging-strand DNA synthesis by facilitating DNA polymerase α function at replication forks. Finally, nucleosomes disrupted during replication are efficiently re-assembled into regular arrays on nascent DNA. Our work defines the minimum requirements for chromatin replication in vitro and shows how multiple chromatin factors might modulate replication fork rates in vivo. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Quality labels for retrofit cavity wall insulation : a comparative analysis

    NARCIS (Netherlands)

    Rovers, Twan Johannes Hendrikus; Entrop, Alexis Gerardus; Halman, Johannes I.M.

    2017-01-01

    Retrofit cavity wall insulation can be exerted to reduce the energy use for space heating and cooling of existing buildings. In multiple countries, quality labels have emerged for this insulation service. In this research project, an evaluation framework for cavity wall insulation is developed by

  9. Retroviruses Hijack Chromatin Loops to Drive Oncogene Expression and Highlight the Chromatin Architecture around Proto-Oncogenic Loci

    Science.gov (United States)

    Pattison, Jillian M.; Wright, Jason B.; Cole, Michael D.

    2015-01-01

    The majority of the genome consists of intergenic and non-coding DNA sequences shown to play a major role in different gene regulatory networks. However, the specific potency of these distal elements as well as how these regions exert function across large genomic distances remains unclear. To address these unresolved issues, we closely examined the chromatin architecture around proto-oncogenic loci in the mouse and human genomes to demonstrate a functional role for chromatin looping in distal gene regulation. Using cell culture models, we show that tumorigenic retroviral integration sites within the mouse genome occur near existing large chromatin loops and that this chromatin architecture is maintained within the human genome as well. Significantly, as mutagenesis screens are not feasible in humans, we demonstrate a way to leverage existing screens in mice to identify disease relevant human enhancers and expose novel disease mechanisms. For instance, we characterize the epigenetic landscape upstream of the human Cyclin D1 locus to find multiple distal interactions that contribute to the complex cis-regulation of this cell cycle gene. Furthermore, we characterize a novel distal interaction upstream of the Cyclin D1 gene which provides mechanistic evidence for the abundant overexpression of Cyclin D1 occurring in multiple myeloma cells harboring a pathogenic translocation event. Through use of mapped retroviral integrations and translocation breakpoints, our studies highlight the importance of chromatin looping in oncogene expression, elucidate the epigenetic mechanisms crucial for distal cis-regulation, and in one particular instance, explain how a translocation event drives tumorigenesis through upregulation of a proto-oncogene. PMID:25799187

  10. UV-induced structural changes in chromatin

    International Nuclear Information System (INIS)

    Lang, H.; Zimmer, C.; Vengerov, Yu.Yu.

    1985-01-01

    UV-induced structural alterations of chromatin were studied by means of CD, electron microscopic, and gel electrophoretic measurements. The results indicate that chromatin undergoes serious structural changes after irradiation even at very low fluences. In the low fluence range the structural transitions from the higher ordered chromatin structure to the unfolded state occur without detectable changes in the content of histone H1 and of the core histones. Histone H1 disappears only at fluences above 10 kJ/m 2 . Furthermore, DNA in chromatin is much more sensitive against UV-irradiation and shows a higher degree of strand scission relative to free DNA. While fragmentation in free DNA occurs at fluences above 15 kJ/m 2 , it occurs even at 5.5 kJ/m 2 in the case of chromatin. The biological meaning of the observed UV-induced structural alterations of chromatin is discussed. (author)

  11. Circular chromatin complexes in human lymphocytes high-resolution autoradiography

    International Nuclear Information System (INIS)

    Becak, M.L.; Fukuda-Pizzocaro, K.; Santos, R. de C.S. dos; Brunner, O.

    1985-01-01

    Transcriptionally active chromatin fibers were observed in chromosomes presenting the loops/scaffold configuration. The active fibers showed altered nucleosomes and presented multiforked aspects which led to the formation of ring complexes. The ribonucleoprotein transcripts (RNP) appeared as networks of 0.1 μm or multiples tandemly disposed along the fiber. It is suggested that the ring complexes belong to the human genome. The possibility that these circular structures come from a prokaryote is also considered. (author) [pt

  12. Chromatin dynamics during DSB repair

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Gabrielová, Barbora; Ondřej, Vladan; Kozubek, Stanislav

    2007-01-01

    Roč. 1773, č. 10 (2007), s. 1534-1545 ISSN 0167-4889 R&D Projects: GA ČR(CZ) GP204/06/P349; GA ČR(CZ) 1QS500040508; GA AV ČR(CZ) IAA1065203; GA MŠk(CZ) 1P05OC084 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : chromatin structure * double- strand breaks (DSB) * DNA repair Subject RIV: BO - Biophysics Impact factor: 4.374, year: 2007

  13. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

    DEFF Research Database (Denmark)

    Sarusi Portuguez, Avital; Schwartz, Michal; Siersbaek, Rasmus

    2017-01-01

    The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains...... by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis...

  14. The architects of crenarchaeal chromatin : A biophysical characterization of chromatin proteins from Sulfolobus solfataricus

    NARCIS (Netherlands)

    Driessen, Rosalie Paula Catharina

    2014-01-01

    Understanding of chromatin organization and compaction in Archaea is currently limited. The genome of several megabasepairs long is folded by a set of small chromatin proteins to fit into the micron-sized cell. A first step in understanding archaeal chromatin organization is to study the action of

  15. Dietary polyphenols and chromatin remodeling.

    Science.gov (United States)

    Russo, Gian Luigi; Vastolo, Viviana; Ciccarelli, Marco; Albano, Luigi; Macchia, Paolo Emidio; Ungaro, Paola

    2017-08-13

    Polyphenols are the most abundant phytochemicals in fruits, vegetables, and plant-derived beverages. Recent findings suggest that polyphenols display the ability to reverse adverse epigenetic regulation involved in pathological conditions, such as obesity, metabolic disorder, cardiovascular and neurodegenerative diseases, and various forms of cancer. Epigenetics, defined as heritable changes to the transcriptome, independent from those occurring in the genome, includes DNA methylation, histone modifications, and posttranscriptional gene regulation by noncoding RNAs. Sinergistically and cooperatively, these processes regulate gene expression by changing chromatin organization and DNA accessibility. Such induced epigenetic changes can be inherited during cell division, resulting in permanent maintenance of the acquired phenotype, but they may also occur throughout an individual life-course and may ultimately influence phenotypic outcomes (health and disease risk). In the last decade, a number of studies have shown that nutrients can affect metabolic traits by altering the structure of chromatin and directly regulate both transcription and translational processes. In this context, dietary polyphenol-targeted epigenetics becomes an attractive approach for disease prevention and intervention. Here, we will review how polyphenols, including flavonoids, curcuminoids, and stilbenes, modulate the establishment and maintenance of key epigenetic marks, thereby influencing gene expression and, hence, disease risk and health.

  16. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

    Fog, Cathrine K; Jensen, Klaus T; Lund, Anders Henrik

    2007-01-01

    -despite the fact that all cells in the organism contain the same genetic information. A large amount of data gathered over the last decades has demonstrated that deregulation of chromatin-modifying proteins is etiologically involved in the development and progression of cancer. Here we discuss how epigenetic...... alterations influence cancer development and review known cancer-associated alterations in chromatin-modifying proteins....

  17. A microscopic analysis of Arabidopsis chromatin

    NARCIS (Netherlands)

    Willemse, J.J.

    2007-01-01

    Genetic information of eukaryotic organisms is stored as DNA in the nuclei of their cells. Nuclear DNA is associated with several proteins, which together form chromatin. The most abundant chromatin proteins arehistones,they arrange the initial packaging step of the DNA. DNA

  18. Chromatin dynamics resolved with force spectroscopy

    NARCIS (Netherlands)

    Chien, Fan-Tso

    2011-01-01

    In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases

  19. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    different proteins involved in the synthesis of mRNA from the. DNA template. ... CBP - CREB Binding Protein. CHRAC. Chromatin .... nucleosomal interactions, and thereby change the chromatin structure, as per the ..... methyltransferases in gene regulation is yet to be elucidated. .... Molecular Biology and. Genetics Unit.

  20. Chromatin Remodelers: From Function to Dysfunction

    Directory of Open Access Journals (Sweden)

    Gernot Längst

    2015-06-01

    Full Text Available Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development.

  1. Encounter times of chromatin loci influenced by polymer decondensation

    Science.gov (United States)

    Amitai, A.; Holcman, D.

    2018-03-01

    The time for a DNA sequence to find its homologous counterpart depends on a long random search inside the cell nucleus. Using polymer models, we compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined locally by potential wells. We find that reducing tethering forces acting on the polymers results in local decondensation, and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude. We derive here new asymptotic formula for the MFET, confirmed by Brownian simulations. We conclude from the present modeling approach that the fast search for homology is mediated by a local chromatin decondensation due to the release of multiple chromatin tethering forces. The present scenario could explain how the homologous recombination pathway for double-stranded DNA repair is controlled by its random search step.

  2. Economically optimal thermal insulation

    Energy Technology Data Exchange (ETDEWEB)

    Berber, J.

    1978-10-01

    Exemplary calculations to show that exact adherence to the demands of the thermal insulation ordinance does not lead to an optimal solution with regard to economics. This is independent of the mode of financing. Optimal thermal insulation exceeds the values given in the thermal insulation ordinance.

  3. To spread or not to spread - chromatin modifications in response to DNA damage

    DEFF Research Database (Denmark)

    Altmeyer, M.; Lukas, J.

    2013-01-01

    Chromatin modifications in response to DNA damage are vital for genome integrity. Multiple proteins and pathways required to generate specialized chromatin domains around DNA lesions have been identified and the increasing amount of information calls for unifying concepts that would allow us...... to grasp the ever-increasing complexity. This review aims at contributing to this trend by focusing on feed-forward and feedback mechanisms, which in mammalian cells determine the extent of chromatin modifications after DNA damage. We highlight the emerging notion that the nodal points of these highly...... dynamic pathways operate in a rate-limiting mode, whose deregulation can disrupt physiological boundaries between damaged and undamaged chromatin, dictate repair pathway choice, and determine the fate of cells exposed to genotoxic stress....

  4. Thermal insulating panel

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, J.T.

    1985-09-11

    A panel of thermal insulation material has at least one main portion which comprises a dry particulate insulation material compressed within a porous envelope so that it is rigid or substantially rigid and at least one auxiliary portion which is secured to and extends along at least one of the edges of the main portions. The auxiliary portions comprise a substantially uncompressed dry particulate insulation material contained within an envelope. The insulation material of the auxiliary portion may be the same as or may be different from the insulation material of the main portion. The envelope of the auxiliary portion may be made of a porous or a non-porous material. (author).

  5. From the chromatin interaction network to the organization of the human genome into replication N/U-domains

    International Nuclear Information System (INIS)

    Boulos, Rasha E; Julienne, Hanna; Baker, Antoine; Jensen, Pablo; Arneodo, Alain; Audit, Benjamin; Chen, Chun-Long; D'Aubenton-Carafa, Yves; Thermes, Claude; Petryk, Nataliya; Kahli, Malik; Hyrien, Olivier; Goldar, Arach

    2014-01-01

    The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome. (paper)

  6. Effect of hyperthermia on replicating chromatin

    International Nuclear Information System (INIS)

    Warters, R.L.; Roti Roti, J.L.

    1981-01-01

    The extent of heat-induced structural alterations in chromatin containing nascent (pulse-labeled) DNA was assayed using the enzyme micrococcal nuclease. The basic nucleosome structure in nascent and mature chromatin of S-phase cells appeared unaltered for up to 16 hr after exposure to hyperthermic temperatures as high as 48 0 C for 15 min. However, the rate of nuclease digestion of DNA in both nascent and mature chromatin is inhibited following exposure to hyperthermic temperatures. In unheated cells, pulse-labeled nascent DNA matured into mature chromatin structure with a half-time of 2.5 min. The half-time for the maturation of pulse-labeled DNA from nascent into mature chromatin increased in a linear manner as a function of increasing temperature of exposure with constant heating time at temperatures above 43 0 C. Both the reduced nuclease digestibility of nascent DNA and the increased time for chromatin structural changes could be due to the increased protein mass of chromatin following hyperthermia

  7. Interaction between a pair of gypsy insulators or between heterologous gypsy and Wari insulators modulates Flp site-specific recombination in Drosophila melanogaster.

    Science.gov (United States)

    Krivega, Margarita; Savitskaya, Ekaterina; Krivega, Ivan; Karakozova, Marina; Parshikov, Aleksander; Golovnin, Anton; Georgiev, Pavel

    2010-08-01

    Chromatin insulators block the action of transcriptional enhancers when interposed between an enhancer and a promoter. An Flp technology was used to examine interactions between Drosophila gypsy and Wari insulators in somatic and germ cells. The gypsy insulator consists of 12 binding sites for the Su(Hw) protein, while the endogenous Wari insulator, located on the 3' side of the white gene, is independent from the Su(Hw) protein. Insertion of the gypsy but not Wari insulator between FRT sites strongly blocks recombination between Flp dimers bound to FRT sites located on the same chromatid (recombination in cis) or in sister chromatids (unequal recombination in trans). At the same time, the interaction between Wari and gypsy insulators regulates the efficiency of Flp-mediated recombination. Thus, insulators may have a role in controlling interactions between distantly located protein complexes (not only those involved in transcriptional gene regulation) on the same chromosome or on sister chromatids in somatic and germ cells. We have also found that the frequency of Flp-mediated recombination between FRT sites is strongly dependent on the relative orientation of gypsy insulators. Taken together, our results indicate that the interactions between insulators can be visualized by Flp technology and that insulators may be involved in blocking undesirable interactions between proteins at the two-chromatid phase of the cell cycle.

  8. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.

    2013-10-17

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  9. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.; Kyriazopoulou-Panagiotopoulou, S.; Grubert, F.; Zaugg, J. B.; Kundaje, A.; Liu, Y.; Boyle, A. P.; Zhang, Q. C.; Zakharia, F.; Spacek, D. V.; Li, J.; Xie, D.; Olarerin-George, A.; Steinmetz, L. M.; Hogenesch, J. B.; Kellis, M.; Batzoglou, S.; Snyder, M.

    2013-01-01

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  10. Analysis of Myc-induced histone modifications on target chromatin.

    Directory of Open Access Journals (Sweden)

    Francesca Martinato

    Full Text Available The c-myc proto-oncogene is induced by mitogens and is a central regulator of cell growth and differentiation. The c-myc product, Myc, is a transcription factor that binds a multitude of genomic sites, estimated to be over 10-15% of all promoter regions. Target promoters generally pre-exist in an active or poised chromatin state that is further modified by Myc, contributing to fine transcriptional regulation (activation or repression of the afferent gene. Among other mechanisms, Myc recruits histone acetyl-transferases to target chromatin and locally promotes hyper-acetylation of multiple lysines on histones H3 and H4, although the identity and combination of the modified lysines is unknown. Whether Myc dynamically regulates other histone modifications (or marks at its binding sites also remains to be addressed. Here, we used quantitative chromatin immunoprecipitation (qChIP to profile a total of 24 lysine-acetylation and -methylation marks modulated by Myc at target promoters in a human B-cell line with a regulatable c-myc transgene. Myc binding promoted acetylation of multiple lysines, primarily of H3K9, H3K14, H3K18, H4K5 and H4K12, but significantly also of H4K8, H4K91 and H2AK5. Dimethylation of H3K79 was also selectively induced at target promoters. A majority of target promoters showed co-induction of multiple marks - in various combinations - correlating with recruitment of the two HATs tested (Tip60 and HBO1, incorporation of the histone variant H2A.Z and transcriptional activation. Based on this and previous findings, we surmise that Myc recruits the Tip60/p400 complex to achieve a coordinated histone acetylation/exchange reaction at activated promoters. Our data are also consistent with the additive and redundant role of multiple acetylation events in transcriptional activation.

  11. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins

    KAUST Repository

    Bigeard, Jean; Rayapuram, Naganand; Pflieger, Delphine; Hirt, Heribert

    2014-01-01

    In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.

  12. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins

    KAUST Repository

    Bigeard, Jean

    2014-07-10

    In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.

  13. Chromatin Pioneers | Center for Cancer Research

    Science.gov (United States)

    Taking advantage of their ability to explore provocative ideas, NCI investigators pioneered the study of chromatin to demonstrate its functional importance and lay the groundwork for understanding its role in cancer and other diseases.

  14. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...

  15. Panels of microporous insulation

    Energy Technology Data Exchange (ETDEWEB)

    McWilliams, J.A.; Morgan, D.E.; Jackson, J.D.J.

    1990-08-07

    Microporous thermal insulation materials have a lattice structure in which the average interstitial dimension is less than the mean free path of the molecules of air or other gas in which the material is arranged. This results in a heat flow which is less than that attributable to the molecular heat diffusion of the gas. According to this invention, a method is provided for manufacturing panels of microporous thermal insulation, in particular such panels in which the insulation material is bonded to a substrate. The method comprises the steps of applying a film of polyvinyl acetate emulsion to a non-porous substrate, and compacting powdery microporous thermal insulation material against the film so as to cause the consolidated insulation material to bond to the substrate and form a panel. The polyvinyl acetate may be applied by brushing or spraying, and is preferably allowed to dry prior to compacting the insulation material. 1 fig.

  16. Wall insulation system

    Energy Technology Data Exchange (ETDEWEB)

    Kostek, P.T.

    1987-08-11

    In a channel specially designed to fasten semi-rigid mineral fibre insulation to masonry walls, it is known to be constructed from 20 gauge galvanized steel or other suitable material. The channel is designed to have pre-punched holes along its length for fastening of the channel to the drywall screw. The unique feature of the channel is the teeth running along its length which are pressed into the surface of the butted together sections of the insulation providing a strong grip between the two adjacent pieces of insulation. Of prime importance to the success of this system is the recent technological advancements of the mineral fibre itself which allow the teeth of the channel to engage the insulation fully and hold without mechanical support, rather than be repelled or pushed back by the inherent nature of the insulation material. After the insulation is secured to the masonry wall by concrete nail fastening systems, the drywall is screwed to the channel.

  17. A new and improved algorithm for the quantification of chromatin condensation from microscopic data shows decreased chromatin condensation in regenerating axolotl limb cells.

    Directory of Open Access Journals (Sweden)

    Julian Sosnik

    Full Text Available The nuclear landscape plays an important role in the regulation of tissue and positional specific genes in embryonic and developing cells. Changes in this landscape can be dynamic, and are associated with the differentiation of cells during embryogenesis, and the de-differentiation of cells during induced pluripotent stem cell (iPSC formation and in many cancers. However, tools to quantitatively characterize these changes are limited, especially in the in vivo context, where numerous tissue types are present and cells are arranged in multiple layers. Previous tools have been optimized for the monolayer nature of cultured cells. Therefore, we present a new algorithm to quantify the condensation of chromatin in two in vivo systems. We first developed this algorithm to quantify changes in chromatin compaction and validated it in differentiating spermatids in zebrafish testes. Our algorithm successfully detected the typical increase in chromatin compaction as these cells differentiate. We then employed the algorithm to quantify the changes that occur in amphibian limb cells as they participate in a regenerative response. We observed that the chromatin in the limb cells de-compacts as they contribute to the regenerating organ. We present this new tool as an open sourced software that can be readily accessed and optimized to quantify chromatin compaction in complex multi-layered samples.

  18. Keeping it quiet: chromatin control of gammaherpesvirus latency.

    Science.gov (United States)

    Lieberman, Paul M

    2013-12-01

    The human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) establish long-term latent infections associated with diverse human cancers. Viral oncogenesis depends on the ability of the latent viral genome to persist in host nuclei as episomes that express a restricted yet dynamic pattern of viral genes. Multiple epigenetic events control viral episome generation and maintenance. This Review highlights some of the recent findings on the role of chromatin assembly, histone and DNA modifications, and higher-order chromosome structures that enable gammaherpesviruses to establish stable latent infections that mediate viral pathogenesis.

  19. ATP-dependent chromatin remodeling in the DNA-damage response

    Directory of Open Access Journals (Sweden)

    Lans Hannes

    2012-01-01

    Full Text Available Abstract The integrity of DNA is continuously challenged by metabolism-derived and environmental genotoxic agents that cause a variety of DNA lesions, including base alterations and breaks. DNA damage interferes with vital processes such as transcription and replication, and if not repaired properly, can ultimately lead to premature aging and cancer. Multiple DNA pathways signaling for DNA repair and DNA damage collectively safeguard the integrity of DNA. Chromatin plays a pivotal role in regulating DNA-associated processes, and is itself subject to regulation by the DNA-damage response. Chromatin influences access to DNA, and often serves as a docking or signaling site for repair and signaling proteins. Its structure can be adapted by post-translational histone modifications and nucleosome remodeling, catalyzed by the activity of ATP-dependent chromatin-remodeling complexes. In recent years, accumulating evidence has suggested that ATP-dependent chromatin-remodeling complexes play important, although poorly characterized, roles in facilitating the effectiveness of the DNA-damage response. In this review, we summarize the current knowledge on the involvement of ATP-dependent chromatin remodeling in three major DNA repair pathways: nucleotide excision repair, homologous recombination, and non-homologous end-joining. This shows that a surprisingly large number of different remodeling complexes display pleiotropic functions during different stages of the DNA-damage response. Moreover, several complexes seem to have multiple functions, and are implicated in various mechanistically distinct repair pathways.

  20. Translucent insulating building envelope

    DEFF Research Database (Denmark)

    Rahbek, Jens Eg

    1997-01-01

    A new type of translucent insulating material has been tested. This material is made of Celulose-Acetat and have a honey-comb structure. The material has a high solar transmittance and is highly insulating. The material is relatively cheap to produce. Danish Title: Translucent isolerende klimaskærm....

  1. Sound Insulation between Dwellings

    DEFF Research Database (Denmark)

    Rasmussen, Birgit

    2011-01-01

    Regulatory sound insulation requirements for dwellings exist in more than 30 countries in Europe. In some countries, requirements have existed since the 1950s. Findings from comparative studies show that sound insulation descriptors and requirements represent a high degree of diversity...... and initiate – where needed – improvement of sound insulation of new and existing dwellings in Europe to the benefit of the inhabitants and the society. A European COST Action TU0901 "Integrating and Harmonizing Sound Insulation Aspects in Sustainable Urban Housing Constructions", has been established and runs...... 2009-2013. The main objectives of TU0901 are to prepare proposals for harmonized sound insulation descriptors and for a European sound classification scheme with a number of quality classes for dwellings. Findings from the studies provide input for the discussions in COST TU0901. Data collected from 24...

  2. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

    Bradbury, E.M.; Baldwin, J.P.; Carpenter, B.G.; Hjelm, R.P.; Hancock, R.; Ibel, K.

    1976-01-01

    It is clear that a knowledge of the basic molecular structure of chromatin is a prerequisite for any progress toward an understanding of chromosome organization. With a two-component system, protein and nucleic acid, neutrons have a particularly powerful application to studies of the spatial arrangements of these components because of the ability, by contrast matching with H 2 O-D 2 O mixtures, to obtain neutron-scattering data on the individual components. With this approach it has been shown that the neutron diffraction of chromatin is consistent with a ''beads on a string'' model in which the bead consists of a protein core with DNA coiled on the outside. However, because chromatin is a gel and gives limited structural data, confirmation of such a model requires extension of the neutron studies by deuteration of specific chromatin components and the isolation of chromatin subunits. Although these studies are not complete, the neutron results so far obtained support the subunit model described above

  3. New mitotic regulators released from chromatin

    Directory of Open Access Journals (Sweden)

    Hideki eYokoyama

    2013-12-01

    Full Text Available Faithful action of the mitotic spindle segregates duplicated chromosomes into daughter cells. Perturbations of this process result in chromosome mis-segregation, leading to chromosomal instability and cancer development. Chromosomes are not simply passengers segregated by spindle microtubules but rather play a major active role in spindle assembly. The GTP bound form of the Ran GTPase (RanGTP, produced around chromosomes, locally activates spindle assembly factors. Recent studies have uncovered that chromosomes organize mitosis beyond spindle formation. They distinctly regulate other mitotic events, such as spindle maintenance in anaphase, which is essential for chromosome segregation. Furthermore, the direct function of chromosomes is not only to produce RanGTP but, in addition, to release key mitotic regulators from chromatin. Chromatin-remodeling factors and nuclear pore complex proteins, which have established functions on chromatin in interphase, dissociate from mitotic chromatin and function in spindle assembly or maintenance. Thus, chromosomes actively organize their own segregation using chromatin-releasing mitotic regulators as well as RanGTP.

  4. Map of open and closed chromatin domains in Drosophila genome.

    Science.gov (United States)

    Milon, Beatrice; Sun, Yezhou; Chang, Weizhong; Creasy, Todd; Mahurkar, Anup; Shetty, Amol; Nurminsky, Dmitry; Nurminskaya, Maria

    2014-11-18

    Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genome-wide patterns of open and closed chromatin have been understudied, and are at present largely predicted from chromatin modification and gene expression data. However the universal applicability of such predictions is not self-evident, and requires experimental verification. We developed and implemented a high-throughput analysis for general chromatin sensitivity to DNase I which provides a comprehensive epigenomic assessment in a single assay. Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin "states", individual chromatin modifications, nuclear lamina interactions, and gene expression. While showing that the widely trusted predictions of chromatin structure are correct in the majority of cases, we detected diverse "exceptions" from the conventional rules. We found a profound paucity of chromatin modifications in a major fraction of closed chromatin, and identified a number of loci where chromatin configuration is opposite to that expected from modification and gene expression patterns. Further, we observed that chromatin of large introns tends to be closed even when the genes are expressed, and that a significant proportion of active genes including their promoters are located in closed chromatin. These findings reveal limitations of the existing predictive models, indicate novel mechanisms of epigenetic regulation, and provide important insights into genome organization and function.

  5. Autism genes keep turning up chromatin.

    Science.gov (United States)

    Lasalle, Janine M

    2013-06-19

    Autism-spectrum disorders (ASD) are complex genetic disorders collectively characterized by impaired social interactions and language as well as repetitive and restrictive behaviors. Of the hundreds of genes implicated in ASD, those encoding proteins acting at neuronal synapses have been most characterized by candidate gene studies. However, recent unbiased genome-wide analyses have turned up a multitude of novel candidate genes encoding nuclear factors implicated in chromatin remodeling, histone demethylation, histone variants, and the recognition of DNA methylation. Furthermore, the chromatin landscape of the human genome has been shown to influence the location of de novo mutations observed in ASD as well as the landscape of DNA methylation underlying neurodevelopmental and synaptic processes. Understanding the interactions of nuclear chromatin proteins and DNA with signal transduction pathways and environmental influences in the developing brain will be critical to understanding the relevance of these ASD candidate genes and continued uncovering of the "roots" of autism etiology.

  6. Heat insulation support device

    International Nuclear Information System (INIS)

    Takahashi, Hiroyuki; Koda, Tomokazu; Motojima, Osamu; Yamamoto, Junya.

    1994-01-01

    The device of the present invention comprises a plurality of heat insulation legs disposed in a circumferential direction. Each of the heat insulative support legs has a hollow shape, and comprises an outer column and an inner column as support structures having a heat insulative property (heat insulative structure), and a thermal anchor which absorbs compulsory displacement by a thin flat plate (displacement absorber). The outer column, the thermal anchor and the inner column are connected by a support so as to offset the positional change of objects to be supported due to shrinkage when they are shrunk. In addition, the portion between the superconductive coils as the objects to be supported and the inner column is connected by the support. The superconductive thermonuclear device is entirely contained in a heat insulative vacuum vessel, and the heat insulative support legs are disposed on a lower lid of the heat insulative vacuum vessel. With such a constitution, they are strengthened against lateral load and buckling, thereby enabling to reduce the amount of heat intrusion while keeping the compulsory displacement easy to be absorbed. (I.N.)

  7. Systematic dissection of roles for chromatin regulators in a yeast stress response.

    Directory of Open Access Journals (Sweden)

    Assaf Weiner

    Full Text Available Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 gene deletion mutants, on induction/repression dynamics of 170 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants and enzymes (chromatin modifier deletions we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We followed up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during multiple stresses, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and identify a significant role for the "activating" mark H3K4me3 in gene repression.

  8. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

    DEFF Research Database (Denmark)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Po

    2014-01-01

    To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during...... replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors...... such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment...

  9. CHD chromatin remodelers and the transcription cycle

    Science.gov (United States)

    Murawska, Magdalena

    2011-01-01

    It is well established that ATP-dependent chromatin remodelers modulate DNA access of transcription factors and RNA polymerases by “opening” or “closing” chromatin structure. However, this view is far too simplistic. Recent findings have demonstrated that these enzymes not only set the stage for the transcription machinery to act but also are actively involved at every step of the transcription process. As a consequence, they affect initiation, elongation, termination and RNA processing. In this review we will use the CHD family as a paradigm to illustrate the progress that has been made in revealing these new concepts. PMID:22223048

  10. Chromatin proteins and modifications as drug targets

    DEFF Research Database (Denmark)

    Helin, Kristian; Dhanak, Dashyant

    2013-01-01

    A plethora of groundbreaking studies have demonstrated the importance of chromatin-associated proteins and post-translational modifications of histones, proteins and DNA (so-called epigenetic modifications) for transcriptional control and normal development. Disruption of epigenetic control...... is a frequent event in disease, and the first epigenetic-based therapies for cancer treatment have been approved. A generation of new classes of potent and specific inhibitors for several chromatin-associated proteins have shown promise in preclinical trials. Although the biology of epigenetic regulation...

  11. Modulation of chromatin access during adipocyte differentiation

    DEFF Research Database (Denmark)

    Mandrup, Susanne; Hager, Gordon L

    2012-01-01

    identified; however, it is not until recently that we have begun to understand how these factors act at a genome-wide scale. In a recent publication we have mapped the genome-wide changes in chromatin structure during differentiation of 3T3-L1 preadipocytes and shown that a major reorganization...... of the chromatin landscape occurs within few hours following the addition of the adipogenic cocktail. In addition, we have mapped the genome-wide profiles of several of the early adipogenic transcription factors and shown that they act in a highly cooperative manner to drive this dramatic remodeling process....

  12. Dynamics of Histone Tails within Chromatin

    Science.gov (United States)

    Bernier, Morgan; North, Justin; Page, Michael; Jaroniec, Christopher; Hammel, Christopher; Poirier, Michael

    2012-02-01

    Genetic information in humans is encoded within DNA molecules that is wrapped around histone octamer proteins and compacted into a highly conserved structural polymer, chromatin. The physical and material properties of chromatin appear to influence gene expression by altering the accessibility of proteins to the DNA. The tails of the histones are flexible domains that are thought to play a role in regulating DNA accessibility and compaction; however the molecular mechanisms for these phenomena are not understood. I will present CW-EPR studies on site directed spin labeled nucleosomes that probe the structure and dynamics of these histone tails within nucleosomes.

  13. Vacuum foil insulation system

    International Nuclear Information System (INIS)

    Hanson, J.P.; Sabolcik, R.E.; Svedberg, R.C.

    1976-01-01

    In a multifoil thermal insulation package having a plurality of concentric cylindrical cups, means are provided for reducing heat loss from the penetration region which extends through the cups. At least one cup includes an integral skirt extending from one end of the cup to intersection with the penetration means. Assembly of the insulation package with the skirted cup is facilitated by splitting the cup to allow it to be opened up and fitted around the other cups during assembly. The insulation is for an implantable nuclear powered artificial heart

  14. Chromatin organisation and cancer prognosis: a pan-cancer study.

    Science.gov (United States)

    Kleppe, Andreas; Albregtsen, Fritz; Vlatkovic, Ljiljana; Pradhan, Manohar; Nielsen, Birgitte; Hveem, Tarjei S; Askautrud, Hanne A; Kristensen, Gunnar B; Nesbakken, Arild; Trovik, Jone; Wæhre, Håkon; Tomlinson, Ian; Shepherd, Neil A; Novelli, Marco; Kerr, David J; Danielsen, Håvard E

    2018-03-01

    cohort (HR 1·7, 95% CI 1·1-2·5, in the discovery cohort; 1·9, 1·1-3·2, in the Gloucester validation cohort; 2·6, 1·2-5·6, in the QUASAR 2 cohort; 1·8, 1·1-3·0, for ovarian carcinoma; 1·6, 1·0-2·4, for uterine sarcoma; 1·43, 0·68-2·99, for prostate carcinoma; and 1·9, 1·1-3·1, for endometrial carcinoma). Chromatin heterogeneity was a significant predictor of cancer-specific survival in microsatellite unstable (HR 2·9, 95% CI 1·0-8·4) and microsatellite stable (1·8, 1·2-2·7) stage II colorectal cancer, but microsatellite instability was not a significant predictor of outcome in chromatin homogeneous (1·3, 0·7-2·4) or chromatin heterogeneous (0·8, 0·3-2·0) stage II colorectal cancer. The consistent prognostic prediction of Nucleotyping in different biological and technical circumstances suggests that the marker of chromatin heterogeneity can be reliably assessed in routine clinical practice and could be used to objectively assist decision making in a range of clinical settings. An immediate application would be to identify high-risk patients with stage II colorectal cancer who might have greater absolute benefit from adjuvant chemotherapy. Clinical trials are warranted to evaluate the survival benefit and cost-effectiveness of using Nucleotyping to guide treatment decisions in multiple clinical settings. The Research Council of Norway, the South-Eastern Norway Regional Health Authority, the National Institute for Health Research, and the Wellcome Trust. Copyright © 2018 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC-BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.

  15. E(y)2/Sus1 is required for blocking PRE silencing by the Wari insulator in Drosophila melanogaster.

    Science.gov (United States)

    Erokhin, Maksim; Parshikov, Alexander; Georgiev, Pavel; Chetverina, Darya

    2010-06-01

    Chromatin insulators affect interactions between promoters and enhancers/silencers and function as barriers to the spread of repressive chromatin. Recently, we have found an insulator, named Wari, located on the 3' side of the white gene. Here, we show that the previously identified 368-bp core of this insulator is sufficient for blocking Polycomb response element-mediated silencing. Although Wari does not contain binding sites for known insulator proteins, the E(y)2 and CP190 proteins bind to Wari as well as to the Su(Hw)-containing insulators in vivo. It may well be that these proteins are recruited to the insulator by as yet unidentified DNA-binding protein. Partial inactivation of E(y)2 in a weak e(y)2 ( u1 ) mutation impairs only the anti-silencing but not the enhancer-blocking activity of the Wari insulator. Thus, the E(y)2 protein in different Drosophila insulators serves to protect gene expression from silencing.

  16. Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains.

    Science.gov (United States)

    Van Bortle, Kevin; Ramos, Edward; Takenaka, Naomi; Yang, Jingping; Wahi, Jessica E; Corces, Victor G

    2012-11-01

    Several multiprotein DNA complexes capable of insulator activity have been identified in Drosophila melanogaster, yet only CTCF, a highly conserved zinc finger protein, and the transcription factor TFIIIC have been shown to function in mammals. CTCF is involved in diverse nuclear activities, and recent studies suggest that the proteins with which it associates and the DNA sequences that it targets may underlie these various roles. Here we show that the Drosophila homolog of CTCF (dCTCF) aligns in the genome with other Drosophila insulator proteins such as Suppressor of Hairy wing [SU(HW)] and Boundary Element Associated Factor of 32 kDa (BEAF-32) at the borders of H3K27me3 domains, which are also enriched for associated insulator proteins and additional cofactors. RNAi depletion of dCTCF and combinatorial knockdown of gene expression for other Drosophila insulator proteins leads to a reduction in H3K27me3 levels within repressed domains, suggesting that insulators are important for the maintenance of appropriate repressive chromatin structure in Polycomb (Pc) domains. These results shed new insights into the roles of insulators in chromatin domain organization and support recent models suggesting that insulators underlie interactions important for Pc-mediated repression. We reveal an important relationship between dCTCF and other Drosophila insulator proteins and speculate that vertebrate CTCF may also align with other nuclear proteins to accomplish similar functions.

  17. Fragmentation of chromatin DNA in mouse thymus cells after whole body γ-irradiation

    International Nuclear Information System (INIS)

    Wei Kang; Liu Xueying; Zhu Xuefen

    1984-01-01

    The characteristics of soluble chromatin in mouse thymus nuclei after whole body γ-irradiation were investigated by means of polyacrylamide gel electrophoresis. After deproteinization and electrophoresis eight regular DNA bands were revealed. The molecular weights of these bands were estimated by comparing their migration rates with those of the standard fragments obtained from PBR 322 digested completely by restrictive endonuclease Hae III. The molecular weight of the first band was calculated to be 186 base pairs corresponding approximately to the size of DNA fragment from a single nucleosome, and those of other bands appeared to be its multiples. The results suggested that the disintegration of chromatin DNA after γ-irradiation might have occurred at the linkage regions of chromatin. The autolysis product of normal thymus chromatin under sterile condition were also analyzed and its electrophoretic pattern was found to be just the same as that of the postirradiation product. It seems, therefore, that the endonuclease existing in normal tissues might be responsible for the postirradiation chromatin degradation. The mechanism of this kind of enzymatic digestion remains to be elucidated in further investigation. (author)

  18. Cooper Pairs in Insulators?

    International Nuclear Information System (INIS)

    Valles, James

    2008-01-01

    Nearly 50 years elapsed between the discovery of superconductivity and the emergence of the microscopic theory describing this zero resistance state. The explanation required a novel phase of matter in which conduction electrons joined in weakly bound pairs and condensed with other pairs into a single quantum state. Surprisingly, this Cooper pair formation has also been invoked to account for recently uncovered high-resistance or insulating phases of matter. To address this possibility, we have used nanotechnology to create an insulating system that we can probe directly for Cooper pairs. I will present the evidence that Cooper pairs exist and dominate the electrical transport in these insulators and I will discuss how these findings provide new insight into superconductor to insulator quantum phase transitions.

  19. Gas insulated substations

    CERN Document Server

    2014-01-01

    This book provides an overview on the particular development steps of gas insulated high-voltage switchgear, and is based on the information given with the editor's tutorial. The theory is kept low only as much as it is needed to understand gas insulated technology, with the main focus of the book being on delivering practical application knowledge. It discusses some introductory and advanced aspects in the meaning of applications. The start of the book presents the theory of Gas Insulated Technology, and outlines reliability, design, safety, grounding and bonding, and factors for choosing GIS. The third chapter presents the technology, covering the following in detail: manufacturing, specification, instrument transformers, Gas Insulated Bus, and the assembly process. Next, the book goes into control and monitoring, which covers local control cabinet, bay controller, control schemes, and digital communication. Testing is explained in the middle of the book before installation and energization. Importantly, ...

  20. Chromatin damage induced by fast neutrons or UV laser radiation

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I

    2002-07-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m{sup -2}. The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  1. Classical and Nonclassical Estrogen Receptor Action on Chromatin Templates

    National Research Council Canada - National Science Library

    Nordeen, Steven

    2000-01-01

    .... Using newly-developed approaches, I investigated mechanisms of estrogen/estrogen receptor action on chromatin templates in vitro in order to better understand the role of chromatin in steroid-regulated gene expression...

  2. Classical and Nonclassical Estrogen Receptor Action on Chromatin Templaces

    National Research Council Canada - National Science Library

    Nordeen, Steve

    2001-01-01

    .... Using newly-developed approaches, I investigated mechanisms of estrogen/estrogen receptor action on chromatin templates in vitro in order to better understand the role of chromatin in steroid-regulated gene expression...

  3. Chromatin Repressive Complexes in Stem Cells, Development, and Cancer

    DEFF Research Database (Denmark)

    Laugesen, Anne; Helin, Kristian

    2014-01-01

    The chromatin environment is essential for the correct specification and preservation of cell identity through modulation and maintenance of transcription patterns. Many chromatin regulators are required for development, stem cell maintenance, and differentiation. Here, we review the roles...

  4. Chromatin damage induced by fast neutrons or UV laser radiation

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I.

    2002-01-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m -2 . The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  5. Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells

    Directory of Open Access Journals (Sweden)

    Saera Hihara

    2012-12-01

    Full Text Available Genome information, which is three-dimensionally organized within cells as chromatin, is searched and read by various proteins for diverse cell functions. Although how the protein factors find their targets remains unclear, the dynamic and flexible nature of chromatin is likely crucial. Using a combined approach of fluorescence correlation spectroscopy, single-nucleosome imaging, and Monte Carlo computer simulations, we demonstrate local chromatin dynamics in living mammalian cells. We show that similar to interphase chromatin, dense mitotic chromosomes also have considerable chromatin accessibility. For both interphase and mitotic chromatin, we observed local fluctuation of individual nucleosomes (∼50 nm movement/30 ms, which is caused by confined Brownian motion. Inhibition of these local dynamics by crosslinking impaired accessibility in the dense chromatin regions. Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information.

  6. Wrapped Multilayer Insulation

    Science.gov (United States)

    Dye, Scott A.

    2015-01-01

    New NASA vehicles, such as Earth Departure Stage (EDS), Orion, landers, and orbiting fuel depots, need improved cryogenic propellant transfer and storage for long-duration missions. Current cryogen feed line multilayer insulation (MLI) performance is 10 times worse per area than tank MLI insulation. During each launch, cryogenic piping loses approximately 150,000 gallons (equivalent to $300,000) in boil-off during transfer, chill down, and ground hold. Quest Product Development Corp., teaming with Ball Aerospace, developed an innovative advanced insulation system, Wrapped MLI (wMLI), to provide improved thermal insulation for cryogenic feed lines. wMLI is high-performance multilayer insulation designed for cryogenic piping. It uses Quest's innovative discrete-spacer technology to control layer spacing/ density and reduce heat leak. The Phase I project successfully designed, built, and tested a wMLI prototype with a measured heat leak 3.6X lower than spiral-wrapped conventional MLI widely used for piping insulation. A wMLI prototype had a heat leak of 7.3 W/m2, or 27 percent of the heat leak of conventional MLI (26.7 W/m2). The Phase II project is further developing wMLI technology with custom, molded polymer spacers and advancing the product toward commercialization via a rigorous testing program, including developing advanced vacuuminsulated pipe for ground support equipment.

  7. Deoxyribonuclease probing of sea urchin embryo chromatin

    International Nuclear Information System (INIS)

    Landsman, D.

    1983-01-01

    The role that the sea urchin, Parechinus angulosus, embryo and sperm histone variants plays in chromatin structure has been investigated. Chromatin structure has been determined at different levels of resolution in sperm and in developing embryos using micrococcal nuclease, pancreatic deoxyribonuclease (DNase I) and restriction endonucleases. Micrococcal nuclease and restriction endonuclease digestions of sea urchin gastrula chromatin have been analysed and it is shown that it is not possible to isolate large polynucleosomal chromatin complexes which are soluble in low ionic strength buffers. The repeat length for sperm is significantly larger than blastula and gastrula repeat lengths whereas blastula and gastrula repeat lengths are not significantly different. Nucleosomal core particles have been isolated from early blastula, gastrula and sperm of sea urchins. After DNase I digestion of 5'-labelled core particles the rate constants of cutting of the DNA at the susceptible sites on these core particles have been determined. The DNase I digestion kinetics of blastula and gastrula core particles are similar whereas sperm core particles are digested at a slower rate, mainly at the sites which are closest to the ends of the core particle DNA

  8. Chromatin conformation capture strategies in molecular diagnostics

    NARCIS (Netherlands)

    de Vree, Pauline J.P.

    2015-01-01

    In this thesis I have explored the clinical potential of the 4C-technology and worked on development of a novel chromatin conformation capture based technology, called TLA. In chapter 2 I describe how the 4C-technology can be applied as a targeted strategy to identify putative fusion-genes or

  9. Chromatin organisation during Arabidopsis root development

    NARCIS (Netherlands)

    Lorvellec, M.

    2007-01-01

    The genetic information is stored in a highly compact manner in every nucleus. About 150 bp of DNA is packed around a histone octamer constituting a nucleosome. Nucleosomes are linked together by histone H1 and further compaction of this "beads on a string" form higher-order chromatin structures.

  10. Keystone Symposia on Epigenomics and Chromatin Dynamics

    DEFF Research Database (Denmark)

    Ravnskjær, Kim

    2012-01-01

    Keystone Symposia kicked off the start of 2012 with two joint meetings on Epigenomics and Chromatin Dynamics and a star-studded list of speakers. Held in Keystone, CO, January 17-22, and organized by Steven Jacobsen and Steven Henikoff and by Bradley Cairns and Geneviève Almouzni, respectively...

  11. The Latest Twists in Chromatin Remodeling.

    Science.gov (United States)

    Blossey, Ralf; Schiessel, Helmut

    2018-01-05

    In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the intrinsic sequence preference of the histone octamer, which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA; the recognition or selection of nucleosomal substrates by remodeling complexes; and, finally, the motor action on the nucleosome exerted by the chromatin remodeler. Recent work has been able to provide crucial insights at each of these three levels that add new twists to this exciting and unfinished story, which we highlight in this perspective. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. The Chromatin Scaffold Protein SAFB1 Renders Chromatin Permissive for DNA Damage Signaling

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Toledo Lazaro, Luis Ignacio; Gudjonsson, Thorkell

    2013-01-01

    Although the general relevance of chromatin modifications for genotoxic stress signaling, cell-cycle checkpoint activation, and DNA repair is well established, how these modifications reach initial thresholds in order to trigger robust responses remains largely unexplored. Here, we identify...... the chromatin-associated scaffold attachment factor SAFB1 as a component of the DNA damage response and show that SAFB1 cooperates with histone acetylation to allow for efficient γH2AX spreading and genotoxic stress signaling. SAFB1 undergoes a highly dynamic exchange at damaged chromatin in a poly......(ADP-ribose)-polymerase 1- and poly(ADP-ribose)-dependent manner and is required for unperturbed cell-cycle checkpoint activation and guarding cells against replicative stress. Altogether, our data reveal that transient recruitment of an architectural chromatin component is required in order to overcome physiological...

  13. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors.

    Science.gov (United States)

    Izhar, Lior; Adamson, Britt; Ciccia, Alberto; Lewis, Jedd; Pontano-Vaites, Laura; Leng, Yumei; Liang, Anthony C; Westbrook, Thomas F; Harper, J Wade; Elledge, Stephen J

    2015-06-09

    Localization to sites of DNA damage is a hallmark of DNA damage response (DDR) proteins. To identify DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the amyotrophic lateral sclerosis (ALS) candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a poly-(ADP-ribose) polymerase (PARP)-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors; > 70% of randomly tested transcription factors localized to sites of DNA damage, and of these, ∼90% were PARP dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding-domain dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  14. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors

    Directory of Open Access Journals (Sweden)

    Lior Izhar

    2015-06-01

    Full Text Available Localization to sites of DNA damage is a hallmark of DNA damage response (DDR proteins. To identify DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the amyotrophic lateral sclerosis (ALS candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a poly-(ADP-ribose polymerase (PARP-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors; > 70% of randomly tested transcription factors localized to sites of DNA damage, and of these, ∼90% were PARP dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding-domain dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins.

  15. Survey of thermal insulation systems

    International Nuclear Information System (INIS)

    Kinoshita, Izumi

    1983-01-01

    Better thermal insulations have been developed to meet the growing demands of industry, and studies on thermal insulation at both high temperature and low temperature have been widely performed. The purpose of this survey is to summarize data on the performances and characteristics of thermal insulation materials and thermal insulation structures (for instance, gas cooled reactors, space vehicles and LNG storage tanks), and to discuss ravious problems regarding the design of thermal insulation structures of pool-type LMFBRs. (author)

  16. Chromatin organization and cellular sensitivity to ionizing radiation

    International Nuclear Information System (INIS)

    Szumiel, I.; Walicka, M.

    1987-01-01

    The paper briefly describes chromatin organization in mammalian cells and reviews experimental work concerning relations between chromatin structure and accesibility of damaged DNA to repair enzymes. The ''contact effect'', the size of super-coiled DNA domains and ADP-ribosylation of chromatin proteins are discussed in relation to cellular radiosensitivity. 88 refs. (author)

  17. Chromatin Dynamics of the mouse β-globin locus

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); E. de Boer (Ernie); T.A. Knoch (Tobias); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractLately it has become more clear that (subtle) changes in 3D organization of chromatin can either trigger transcription or silence genes or gene clusters. It has also been postulated that due to changes in chromatin structure, a change in chromatin accessibility of transcription factors

  18. Structural chromatin organization as a factor determining the rate of chromatin endonucleolysis in irradiated and intact thymocytes

    International Nuclear Information System (INIS)

    Ryabchenko, N.I.; Ivannik, B.P.

    1987-01-01

    A study was made of chromatin endonucleolysis in hypotonized thymocytes incubating in digestive buffers containing different concentrations of potassium, magnesium, calcium, and mercaptoethanol. Inhibition of endonucleolysis by univalent cation during the first 20 min of incubation was followed by intensive chromatin degradation. A decrease in free potassium content retarded chromatin degradation and enhanced the inhibiting effect of the univalent cations. The regularities of changes in the rate of chromatin endonucleolysis in different digestive buffers were similar with both exposed and intact thymocytes

  19. Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries.

    Science.gov (United States)

    Gong, Yixiao; Lazaris, Charalampos; Sakellaropoulos, Theodore; Lozano, Aurelie; Kambadur, Prabhanjan; Ntziachristos, Panagiotis; Aifantis, Iannis; Tsirigos, Aristotelis

    2018-02-07

    The metazoan genome is compartmentalized in areas of highly interacting chromatin known as topologically associating domains (TADs). TADs are demarcated by boundaries mostly conserved across cell types and even across species. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. In this study, we first use fused two-dimensional lasso as a machine learning method to improve Hi-C contact matrix reproducibility, and, subsequently, we categorize TAD boundaries based on their insulation score. We demonstrate that higher TAD boundary insulation scores are associated with elevated CTCF levels and that they may differ across cell types. Intriguingly, we observe that super-enhancers are preferentially insulated by strong boundaries. Furthermore, we demonstrate that strong TAD boundaries and super-enhancer elements are frequently co-duplicated in cancer patients. Taken together, our findings suggest that super-enhancers insulated by strong TAD boundaries may be exploited, as a functional unit, by cancer cells to promote oncogenesis.

  20. Repression of germline RNAi pathways in somatic cells by retinoblastoma pathway chromatin complexes.

    Directory of Open Access Journals (Sweden)

    Xiaoyun Wu

    Full Text Available The retinoblastoma (Rb tumor suppressor acts with a number of chromatin cofactors in a wide range of species to suppress cell proliferation. The Caenorhabditis elegans retinoblastoma gene and many of these cofactors, called synMuv B genes, were identified in genetic screens for cell lineage defects caused by growth factor misexpression. Mutations in many synMuv B genes, including lin-35/Rb, also cause somatic misexpression of the germline RNA processing P granules and enhanced RNAi. We show here that multiple small RNA components, including a set of germline-specific Argonaute genes, are misexpressed in the soma of many synMuv B mutant animals, revealing one node for enhanced RNAi. Distinct classes of synMuv B mutants differ in the subcellular architecture of their misexpressed P granules, their profile of misexpressed small RNA and P granule genes, as well as their enhancement of RNAi and the related silencing of transgenes. These differences define three classes of synMuv B genes, representing three chromatin complexes: a LIN-35/Rb-containing DRM core complex, a SUMO-recruited Mec complex, and a synMuv B heterochromatin complex, suggesting that intersecting chromatin pathways regulate the repression of small RNA and P granule genes in the soma and the potency of RNAi. Consistent with this, the DRM complex and the synMuv B heterochromatin complex were genetically additive and displayed distinct antagonistic interactions with the MES-4 histone methyltransferase and the MRG-1 chromodomain protein, two germline chromatin regulators required for the synMuv phenotype and the somatic misexpression of P granule components. Thus intersecting synMuv B chromatin pathways conspire with synMuv B suppressor chromatin factors to regulate the expression of small RNA pathway genes, which enables heightened RNAi response. Regulation of small RNA pathway genes by human retinoblastoma may also underlie its role as a tumor suppressor gene.

  1. Reusable Surface Insulation

    Science.gov (United States)

    1997-01-01

    Advanced Flexible Reusable Surface Insulation, developed by Ames Research Center, protects the Space Shuttle from the searing heat that engulfs it on reentry into the Earth's atmosphere. Initially integrated into the Space Shuttle by Rockwell International, production was transferred to Hi-Temp Insulation Inc. in 1974. Over the years, Hi-Temp has created many new technologies to meet the requirements of the Space Shuttle program. This expertise is also used commercially, including insulation blankets to cover aircrafts parts, fire barrier material to protect aircraft engine cowlings and aircraft rescue fire fighter suits. A Fire Protection Division has also been established, offering the first suit designed exclusively by and for aircraft rescue fire fighters. Hi-Temp is a supplier to the Los Angeles City Fire Department as well as other major U.S. civil and military fire departments.

  2. Insulators for fusion applications

    International Nuclear Information System (INIS)

    1987-04-01

    Design studies for fusion devices and reactors have become more detailed in recent years and with this has come a better understanding of requirements and operating conditions for insulators in these machines. Ceramic and organic insulators are widely used for many components of fusion devices and reactors namely: radio frequency (RF) energy injection systems (BeO, Al 2 O 3 , Mg Al 2 O 4 , Si 3 N 4 ); electrical insulation for the torus structure (SiC, Al 2 O 3 , MgO, Mg Al 2 O 4 , Si 4 Al 2 O 2 N 6 , Si 3 N 4 , Y 2 O 3 ); lightly-shielded magnetic coils (MgO, MgAl 2 O 4 ); the toroidal field coil (epoxies, polyimides), neutron shield (B 4 C, TiH 2 ); high efficiency electrical generation; as well as the generation of very high temperatures for high efficiency hydrogen production processes (ZrO 2 and Al 2 O 3 - mat, graphite and carbon - felt). Timely development of insulators for fusion applications is clearly necessary. Those materials to be used in fusion machines should show high resistance to radiation damage and maintain their structural integrity. Now the need is urgent for a variety of radiation resistant materials, but much effort in these areas is required for insulators to be considered seriously by the design community. This document contains 14 papers from an IAEA meeting. It was the objective of this meeting to identify existing problems in analysing various situations of applications and requirements of electrical insulators and ceramics in fusion and to recommend strategies and different stages of implementation. This meeting was endorsed by the International Fusion Research Council

  3. Chromatin Regulation of Neuronal Maturation and Plasticity.

    Science.gov (United States)

    Gallegos, David A; Chan, Urann; Chen, Liang-Fu; West, Anne E

    2018-05-01

    Neurons are dynamic cells that respond and adapt to stimuli throughout their long postmitotic lives. The structural and functional plasticity of neurons requires the regulated transcription of new gene products, and dysregulation of transcription in either the developing or adult brain impairs cognition. We discuss how mechanisms of chromatin regulation help to orchestrate the transcriptional programs that underlie the maturation of developing neurons and the plasticity of adult neurons. We review how chromatin regulation acts locally to modulate the expression of specific genes and more broadly to coordinate gene expression programs during transitions between cellular states. These data highlight the importance of epigenetic transcriptional mechanisms in postmitotic neurons. We suggest areas where emerging methods may advance understanding in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. A transient ischemic environment induces reversible compaction of chromatin.

    Science.gov (United States)

    Kirmes, Ina; Szczurek, Aleksander; Prakash, Kirti; Charapitsa, Iryna; Heiser, Christina; Musheev, Michael; Schock, Florian; Fornalczyk, Karolina; Ma, Dongyu; Birk, Udo; Cremer, Christoph; Reid, George

    2015-11-05

    Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40-700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells.

  5. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling.

    Directory of Open Access Journals (Sweden)

    Kristofer Davie

    2015-02-01

    Full Text Available Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs. When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling

  6. Histone chaperone networks shaping chromatin function

    DEFF Research Database (Denmark)

    Hammond, Colin; Strømme, Caroline Bianchi; Huang, Hongda

    2017-01-01

    and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone...... chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin....

  7. Probing chromatin structure with nuclease sensitivity assays.

    Science.gov (United States)

    Gregory, R I; Khosla, S; Feil, R

    2001-01-01

    To further our understanding of genomic imprinting it will be essential to identify key control elements, and to investigate their regulation by both epigenetic modifications (such as DNA methylation) and trans-acting factors. So far, sequence elements that regulate parental allele-specific gene expression have been identified in a number of imprinted loci, either because of their differential DNA methylation or through functional studies in transgenic mice (1,2). A systematic search for allele-specific chromatin features constitutes an alternative strategy to identify elements that regulate imprinting. The validity of such an in vivo chromatin approach derives from the fact that in several known imprinting control-elements, a specialized organization of chromatin characterized by nuclease hypersensitivity is present on only one of the two parental chromosome (3). For example, the differentially methylated 5 -portion of the human SNRPN gene-a sequence element that controls imprinting in the Prader-Willi and Angelman syndromes' domain on chromosome 15q11- q13-has strong DNase-I hypersensitive sites on the unmethylated paternal chromosome (4). A differentially methylated region that regulates the imprinting of H19 and that of the neighboring insulin-like growth factor-2 gene on mouse chromosome 7 was also found to have parental chromosome-specific hypersensitive sites (5,6). The precise nature of the allelic nuclease hypersensitivity in these and other imprinted loci remains to be determined in more detail, for example, by applying complementary chromatin methodologies (7,8). However, it is commonly observed that a nuclease hypersensitive site corresponds to a small region where nucleosomes are absent or partially disrupted.

  8. [The biological aspects of chromatin diminution].

    Science.gov (United States)

    Akif'ev, A P; Grishanin, A K

    1993-01-01

    The chromatine diminution (CD), first discovered by Boveri (1887) in ascarids, represents programmed elimination of a part of genetic material in the nuclei of the somatic cells in cyclops and ascarids, and in the protist macronuclei. The CD can be considered as a macromutation sharply changing chromosomal structure, though minimally effecting the phenotype. The analysis of CD is of significance for discussing mechanisms of origin of chromosomal organization, transformation of genome molecular structure in eucaryote evolution, role of the extra DNA.

  9. Default assembly of early adenovirus chromatin

    International Nuclear Information System (INIS)

    Spector, David J.

    2007-01-01

    In adenovirus particles, the viral nucleoprotein is organized into a highly compacted core structure. Upon delivery to the nucleus, the viral nucleoprotein is very likely to be remodeled to a form accessible to the transcription and replication machinery. Viral protein VII binds to intra-nuclear viral DNA, as do at least two cellular proteins, SET/TAF-Iβ and pp32, components of a chromatin assembly complex that is implicated in template remodeling. We showed previously that viral DNA-protein complexes released from infecting particles were sensitive to shearing after cross-linking with formaldehyde, presumably after transport of the genome into the nucleus. We report here the application of equilibrium-density gradient centrifugation to the analysis of the fate of these complexes. Most of the incoming protein VII was recovered in a form that was not cross-linked to viral DNA. This release of protein VII, as well as the binding of SET/TAF-Iβ and cellular transcription factors to the viral chromatin, did not require de novo viral gene expression. The distinct density profiles of viral DNA complexes containing protein VII, compared to those containing SET/TAF-Iβ or transcription factors, were consistent with the notion that the assembly of early viral chromatin requires both the association of SET/TAF-1β and the release of protein VII

  10. Titration and hysteresis in epigenetic chromatin silencing

    International Nuclear Information System (INIS)

    Dayarian, Adel; Sengupta, Anirvan M

    2013-01-01

    Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of this paper is to examine how the perturbations altering the activity of histone modifying enzymes affect the epigenetic states. We analyze the implications of having the total number of silencing proteins, given by the sum of proteins bound to the nucleosomes and the ones available in the ambient, to be constant. This constraint couples different regions of chromatin through the shared reservoir of ambient silencing proteins. We show that the response of the system to perturbations depends dramatically on the titration effect caused by the above constraint. In particular, for a certain range of overall abundance of silencing proteins, the hysteresis loop changes qualitatively with certain jump replaced by continuous merger of different states. In addition, we find a nonmonotonic dependence of gene expression on the rate of histone deacetylation activity of Sir2. We discuss how these qualitative predictions of our model could be compared with experimental studies of the yeast system under anti-silencing drugs. (paper)

  11. Capturing Structural Heterogeneity in Chromatin Fibers.

    Science.gov (United States)

    Ekundayo, Babatunde; Richmond, Timothy J; Schalch, Thomas

    2017-10-13

    Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Higher order chromatin organization in cancer

    Science.gov (United States)

    Reddy, Karen L.; Feinberg, Andrew P.

    2013-01-01

    In spite of our increased understanding of how genomes are dysregulated in cancer and a plethora of molecular diagnostic tools, the front line and ‘gold standard’ detection of cancer remains the pathologist’s detection of gross changes in cellular and tissue structure, most strikingly nuclear dis-organization. In fact, for over 140 years it has been noted that nuclear morphology is often disrupted in cancer. Even today, nuclear morphology measures include nuclear size, shape, DNA content (ploidy) and ‘chromatin organization’. Given the importance of nuclear shape to diagnoses of cancer phenotypes, it is surprising and frustrating that we currently lack a detailed understanding to explain these changes and how they might arise and relate to molecular events in the cell. It is an implicit hypothesis that perturbation of chromatin and epigenetic signatures may lead to alterations in nuclear structure (or vice versa) and that these perturbations lie at the heart of cancer genesis. In this review, we attempt to synthesize research leading to our current understanding on how chromatin interactions at the nuclear lamina, epigenetic modulation and gene regulation may intersect in cancer and offer a perspective on critical experiments that would help clarify how nuclear architecture may contribute to the cancerous phenotype. We also discuss the historical understanding of nuclear structure in normal cells and as a diagnostic in cancer. PMID:23266653

  13. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture

    KAUST Repository

    Jé gu, Teddy; Domenichini, Sé verine; Blein, Thomas; Ariel, Federico; Christ, Auré lie; Kim, SoonKap; Crespi, Martin; Boutet-Mercey, Sté phanie; Mouille, Gré gory; Bourge, Mickaë l; Hirt, Heribert; Bergounioux, Catherine; Raynaud, Cé cile; Benhamed, Moussa

    2015-01-01

    Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.

  14. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture

    KAUST Repository

    Jégu, Teddy

    2015-10-12

    Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.

  15. Insulation Reformulation Development

    Science.gov (United States)

    Chapman, Cynthia; Bray, Mark

    2015-01-01

    The current Space Launch System (SLS) internal solid rocket motor insulation, polybenzimidazole acrylonitrile butadiene rubber (PBI-NBR), is a new insulation that replaced asbestos-based insulations found in Space Shuttle heritage solid rocket boosters. PBI-NBR has some outstanding characteristics such as an excellent thermal erosion resistance, low thermal conductivity, and low density. PBI-NBR also has some significant challenges associated with its use: Air entrainment/entrapment during manufacture and lay-up/cure and low mechanical properties such as tensile strength, modulus, and fracture toughness. This technology development attempted to overcome these challenges by testing various reformulated versions of booster insulation. The results suggest the SLS program should continue to investigate material alternatives for potential block upgrades or use an entirely new, more advanced booster. The experimental design was composed of a logic path that performs iterative formulation and testing in order to maximize the effort. A lab mixing baseline was developed and documented for the Rubber Laboratory in Bldg. 4602/Room 1178.

  16. Beyond insulation and isolation

    DEFF Research Database (Denmark)

    Højlund, Marie Koldkjær

    2016-01-01

    are insulation and isolation strategies to reduce measurable and perceptual noise levels. However, these strategies do not actively support the need to feel like an integral part of the shared hospital environment, which is a key element in creating healing environments, according to the paradigm of Evidence-Based...

  17. Spectroscopic study of fast-neutron-irradiated chromatin

    International Nuclear Information System (INIS)

    Radu, L.; Gazdaru, D.; Constantinescu, B.

    2004-01-01

    The effects produced by fast neutrons (0-100 Gy) on chromatin structure were analyzed by (i) [ 1 H]-NMR spectroscopy, (ii) time resolved spectroscopy, and (iii) fluorescence resonance energy transfer (FRET). Two types of chromatin were tested: (i) a chromatin from a normal tissue (liver of Wistar rats) and (ii) a chromatin from a tumoral tissue (Guerin limphotrope epithelioma, a rat solid tumor). The fast-neutron action on chromatin determines greater values of the [ 1 H]-NMR transverse relaxation time, indicating a more injured structure. Time-resolved fluorescence measurements show that the relative contribution of the excited state lifetime of bound ethidium bromide to chromatin DNA diminishes with increasing irradiation doses. This reflects the damage that occurs in DNA structure: production of single- and double-strand breaks due to sugar and base modifications. By the FRET method, the distance between dansyl chloride and acridine orange coupled at chromatin was determined. This distance increases upon fast-neutron action. The radiosensitivity of the tumor tissue chromatin seems higher than that of the normal tissue chromatin, probably because of its higher (loose) euchromatin/(compact) heterochromatin ratio. As the values of the physical parameters analyzed are specific for a determined dose, the establishment of these parameters may constitute a criterion for the microdosimetry of chromatin radiolesions produced by fast neutrons. (author)

  18. Spectroscopic study of fast-neutron-irradiated chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [V. Babes National Inst., Dept. of Molecular Genetics, Bucharest (Romania)]. E-mail: serbanradu@pcnet.ro; Gazdaru, D. [Bucharest Univ., Dept. of Biophysics, Physics Faculty, Bucharest (Romania); Constantinescu, B. [H. Hulubei National Inst., Dept. of Cyclotron, Bucharest (Romania)

    2004-02-01

    The effects produced by fast neutrons (0-100 Gy) on chromatin structure were analyzed by (i) [{sup 1}H]-NMR spectroscopy, (ii) time resolved spectroscopy, and (iii) fluorescence resonance energy transfer (FRET). Two types of chromatin were tested: (i) a chromatin from a normal tissue (liver of Wistar rats) and (ii) a chromatin from a tumoral tissue (Guerin limphotrope epithelioma, a rat solid tumor). The fast-neutron action on chromatin determines greater values of the [{sup 1}H]-NMR transverse relaxation time, indicating a more injured structure. Time-resolved fluorescence measurements show that the relative contribution of the excited state lifetime of bound ethidium bromide to chromatin DNA diminishes with increasing irradiation doses. This reflects the damage that occurs in DNA structure: production of single- and double-strand breaks due to sugar and base modifications. By the FRET method, the distance between dansyl chloride and acridine orange coupled at chromatin was determined. This distance increases upon fast-neutron action. The radiosensitivity of the tumor tissue chromatin seems higher than that of the normal tissue chromatin, probably because of its higher (loose) euchromatin/(compact) heterochromatin ratio. As the values of the physical parameters analyzed are specific for a determined dose, the establishment of these parameters may constitute a criterion for the microdosimetry of chromatin radiolesions produced by fast neutrons. (author)

  19. The chromatin remodeler SPLAYED regulates specific stress signaling pathways.

    Directory of Open Access Journals (Sweden)

    Justin W Walley

    2008-12-01

    Full Text Available Organisms are continuously exposed to a myriad of environmental stresses. Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress. An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure. Alterations in chromatin structure are brought about by a number of different mechanisms, including chromatin modifications, which covalently modify histone proteins; incorporation of histone variants; and chromatin remodeling, which utilizes ATP hydrolysis to alter histone-DNA contacts. While considerable insight into the mechanisms of chromatin remodeling has been gained, the biological role of chromatin remodeling complexes beyond their function as regulators of cellular differentiation and development has remained poorly understood. Here, we provide genetic, biochemical, and biological evidence for the critical role of chromatin remodeling in mediating plant defense against specific biotic stresses. We found that the Arabidopsis SWI/SNF class chromatin remodeling ATPase SPLAYED (SYD is required for the expression of selected genes downstream of the jasmonate (JA and ethylene (ET signaling pathways. SYD is also directly recruited to the promoters of several of these genes. Furthermore, we show that SYD is required for resistance against the necrotrophic pathogen Botrytis cinerea but not the biotrophic pathogen Pseudomonas syringae. These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks.

  20. Chromosome aberration model combining radiation tracks, chromatin structure, DSB repair and chromatin mobility

    International Nuclear Information System (INIS)

    Friedland, W.; Kundrat, P.

    2015-01-01

    The module that simulates the kinetics and yields of radiation-induced chromosome aberrations within the biophysical code PARTRAC is described. Radiation track structures simulated by Monte Carlo methods are overlapped with multi-scale models of DNA and chromatin to assess the resulting DNA damage. Spatial mobility of individual DNA ends from double-strand breaks is modelled simultaneously with their processing by the non-homologous end-joining enzymes. To score diverse types of chromosome aberrations, the joined ends are classified regarding their original chromosomal location, orientation and the involvement of centromeres. A comparison with experimental data on dicentrics induced by gamma and alpha particles shows that their relative dose dependence is predicted correctly, although the absolute yields are overestimated. The critical model assumptions on chromatin mobility and on the initial damage recognition and chromatin remodelling steps and their future refinements to solve this issue are discussed. (authors)

  1. Integrated Multilayer Insulation

    Science.gov (United States)

    Dye, Scott

    2009-01-01

    Integrated multilayer insulation (IMLI) is being developed as an improved alternative to conventional multilayer insulation (MLI), which is more than 50 years old. A typical conventional MLI blanket comprises between 10 and 120 metallized polymer films separated by polyester nets. MLI is the best thermal- insulation material for use in a vacuum, and is the insulation material of choice for spacecraft and cryogenic systems. However, conventional MLI has several disadvantages: It is difficult or impossible to maintain the desired value of gap distance between the film layers (and consequently, it is difficult or impossible to ensure consistent performance), and fabrication and installation are labor-intensive and difficult. The development of IMLI is intended to overcome these disadvantages to some extent and to offer some additional advantages over conventional MLI. The main difference between IMLI and conventional MLI lies in the method of maintaining the gaps between the film layers. In IMLI, the film layers are separated by what its developers call a micro-molded discrete matrix, which can be loosely characterized as consisting of arrays of highly engineered, small, lightweight, polymer (typically, thermoplastic) frames attached to, and placed between, the film layers. The term "micro-molded" refers to both the smallness of the frames and the fact that they are fabricated in a process that forms precise small features, described below, that are essential to attainment of the desired properties. The term "discrete" refers to the nature of the matrix as consisting of separate frames, in contradistinction to a unitary frame spanning entire volume of an insulation blanket.

  2. Topological Field Theory of Time-Reversal Invariant Insulators

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Xiao-Liang; Hughes, Taylor; Zhang, Shou-Cheng; /Stanford U., Phys. Dept.

    2010-03-19

    We show that the fundamental time reversal invariant (TRI) insulator exists in 4 + 1 dimensions, where the effective field theory is described by the 4 + 1 dimensional Chern-Simons theory and the topological properties of the electronic structure is classified by the second Chern number. These topological properties are the natural generalizations of the time reversal breaking (TRB) quantum Hall insulator in 2 + 1 dimensions. The TRI quantum spin Hall insulator in 2 + 1 dimensions and the topological insulator in 3 + 1 dimension can be obtained as descendants from the fundamental TRI insulator in 4 + 1 dimensions through a dimensional reduction procedure. The effective topological field theory, and the Z{sub 2} topological classification for the TRI insulators in 2+1 and 3+1 dimensions are naturally obtained from this procedure. All physically measurable topological response functions of the TRI insulators are completely described by the effective topological field theory. Our effective topological field theory predicts a number of novel and measurable phenomena, the most striking of which is the topological magneto-electric effect, where an electric field generates a magnetic field in the same direction, with an universal constant of proportionality quantized in odd multiples of the fine structure constant {alpha} = e{sup 2}/hc. Finally, we present a general classification of all topological insulators in various dimensions, and describe them in terms of a unified topological Chern-Simons field theory in phase space.

  3. Flightless I (Drosophila) homolog facilitates chromatin accessibility of the estrogen receptor α target genes in MCF-7 breast cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kwang Won, E-mail: kwjeong@gachon.ac.kr

    2014-04-04

    Highlights: • H3K4me3 and Pol II binding at TFF1 promoter were reduced in FLII-depleted MCF-7 cells. • FLII is required for chromatin accessibility of the enhancer of ERalpha target genes. • Depletion of FLII causes inhibition of proliferation of MCF-7 cells. - Abstract: The coordinated activities of multiple protein complexes are essential to the remodeling of chromatin structure and for the recruitment of RNA polymerase II (Pol II) to the promoter in order to facilitate the initiation of transcription in nuclear receptor-mediated gene expression. Flightless I (Drosophila) homolog (FLII), a nuclear receptor coactivator, is associated with the SWI/SNF-chromatin remodeling complex during estrogen receptor (ER)α-mediated transcription. However, the function of FLII in estrogen-induced chromatin opening has not been fully explored. Here, we show that FLII plays a critical role in establishing active histone modification marks and generating the open chromatin structure of ERα target genes. We observed that the enhancer regions of ERα target genes are heavily occupied by FLII, and histone H3K4me3 and Pol II binding induced by estrogen are decreased in FLII-depleted MCF-7 cells. Furthermore, formaldehyde-assisted isolation of regulatory elements (FAIRE)-quantitative polymerase chain reaction (qPCR) experiments showed that depletion of FLII resulted in reduced chromatin accessibility of multiple ERα target genes. These data suggest FLII as a key regulator of ERα-mediated transcription through its role in regulating chromatin accessibility for the binding of RNA Polymerase II and possibly other transcriptional coactivators.

  4. Flightless I (Drosophila) homolog facilitates chromatin accessibility of the estrogen receptor α target genes in MCF-7 breast cancer cells

    International Nuclear Information System (INIS)

    Jeong, Kwang Won

    2014-01-01

    Highlights: • H3K4me3 and Pol II binding at TFF1 promoter were reduced in FLII-depleted MCF-7 cells. • FLII is required for chromatin accessibility of the enhancer of ERalpha target genes. • Depletion of FLII causes inhibition of proliferation of MCF-7 cells. - Abstract: The coordinated activities of multiple protein complexes are essential to the remodeling of chromatin structure and for the recruitment of RNA polymerase II (Pol II) to the promoter in order to facilitate the initiation of transcription in nuclear receptor-mediated gene expression. Flightless I (Drosophila) homolog (FLII), a nuclear receptor coactivator, is associated with the SWI/SNF-chromatin remodeling complex during estrogen receptor (ER)α-mediated transcription. However, the function of FLII in estrogen-induced chromatin opening has not been fully explored. Here, we show that FLII plays a critical role in establishing active histone modification marks and generating the open chromatin structure of ERα target genes. We observed that the enhancer regions of ERα target genes are heavily occupied by FLII, and histone H3K4me3 and Pol II binding induced by estrogen are decreased in FLII-depleted MCF-7 cells. Furthermore, formaldehyde-assisted isolation of regulatory elements (FAIRE)-quantitative polymerase chain reaction (qPCR) experiments showed that depletion of FLII resulted in reduced chromatin accessibility of multiple ERα target genes. These data suggest FLII as a key regulator of ERα-mediated transcription through its role in regulating chromatin accessibility for the binding of RNA Polymerase II and possibly other transcriptional coactivators

  5. A role for chromatin topology in imprinted domain regulation.

    Science.gov (United States)

    MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

    2016-02-01

    Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

  6. Vacuum ultraviolet (VUV) absorption spectra of chromatin and its components

    International Nuclear Information System (INIS)

    Dodonova, N.Y.; Kiseleva, M.N.; Petrov, M.Y.; Tsyganenko, N.M.; Bubyakina, V.V.; Chikhirzhina, G.I.

    1984-01-01

    The electron absorption spectra of thin films of chromatin and chromatin components in the ultraviolet region (140-280 nm) were investigated. The absorption coefficients μ(lambda) of chromatin, nucleosomes with and without histone H1, total histones (TH), and DNA were compared. The spectra of nucleosomes differ from the sum-spectrum of DNA plus TH. The chromatin and nucleosome spectra are not similar in the spectral region of 190-160 nm. The lack of additivity of absorption coefficients at different wavelengths may be explained by different conformational changes of DNA, TH in nucleosomes and chromatin during the process of drying aqueous solutions for the preparation of thin films. The μ(lambda) values are useful for an estimate of the DNA and TH absorption in chromatin and nucleosomes in discussing UV and VUV irradiation damages. (Auth.)

  7. The ISWI chromatin remodeler organizes the hsrω ncRNA-containing omega speckle nuclear compartments.

    Directory of Open Access Journals (Sweden)

    Maria C Onorati

    2011-05-01

    Full Text Available The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA essential, among other functions, for the assembly and organization of the omega speckles. The nucleoplasmic omega speckles play important functions in RNA metabolism, in normal and stressed cells, by regulating availability of hnRNPs and some other RNA processing proteins. Chromatin remodelers, as well as nuclear speckles and their associated ncRNAs, are emerging as important components of gene regulatory networks, although their functional connections have remained poorly defined. Here we provide multiple lines of evidence showing that the hsrω ncRNA interacts in vivo and in vitro with ISWI, regulating its ATPase activity. Remarkably, we found that the organization of nucleoplasmic omega speckles depends on ISWI function. Our findings highlight a novel role for chromatin remodelers in organization of nucleoplasmic compartments, providing the first example of interaction between an ATP-dependent chromatin remodeler and a large ncRNA.

  8. Metal-insulator transitions

    Science.gov (United States)

    Imada, Masatoshi; Fujimori, Atsushi; Tokura, Yoshinori

    1998-10-01

    Metal-insulator transitions are accompanied by huge resistivity changes, even over tens of orders of magnitude, and are widely observed in condensed-matter systems. This article presents the observations and current understanding of the metal-insulator transition with a pedagogical introduction to the subject. Especially important are the transitions driven by correlation effects associated with the electron-electron interaction. The insulating phase caused by the correlation effects is categorized as the Mott Insulator. Near the transition point the metallic state shows fluctuations and orderings in the spin, charge, and orbital degrees of freedom. The properties of these metals are frequently quite different from those of ordinary metals, as measured by transport, optical, and magnetic probes. The review first describes theoretical approaches to the unusual metallic states and to the metal-insulator transition. The Fermi-liquid theory treats the correlations that can be adiabatically connected with the noninteracting picture. Strong-coupling models that do not require Fermi-liquid behavior have also been developed. Much work has also been done on the scaling theory of the transition. A central issue for this review is the evaluation of these approaches in simple theoretical systems such as the Hubbard model and t-J models. Another key issue is strong competition among various orderings as in the interplay of spin and orbital fluctuations. Experimentally, the unusual properties of the metallic state near the insulating transition have been most extensively studied in d-electron systems. In particular, there is revived interest in transition-metal oxides, motivated by the epoch-making findings of high-temperature superconductivity in cuprates and colossal magnetoresistance in manganites. The article reviews the rich phenomena of anomalous metallicity, taking as examples Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Ru compounds. The diverse phenomena include strong spin and

  9. Organisation de la chromatine et signalisation par les oestrogènes

    OpenAIRE

    Quintin , Justine

    2013-01-01

    A given cell has to be able to adapt its fate and homeostasis in response to endogenous and exogenous signals. This adaptation occurs through finely tuned regulations of genes' expressions leading to the variation of their transcriptomes. Multiple parameters have to be integrated in order to provide such mechanisms of regulation. First, the primary sequence of the genome and its organization into chromatin are major regulatory components that harbor genetic, structural and epigenetic informat...

  10. Vibrational energy relaxation: proposed pathway of fast local chromatin denaturation

    International Nuclear Information System (INIS)

    Harder, D.; Greinert, R.

    2002-01-01

    The molecular mechanism responsible for the a component of exchange-type chromosome aberrations, of chromosome fragmentation and of reproductive cell death is one of the unsolved issues of radiation biology. Under review is whether vibrational energy relaxation in the constitutive biopolymers of chromatin, induced by inelastic energy deposition events and mediated via highly excited vibrational states, may provide a pathway of fast local chromatin denaturation, thereby producing the severe DNA lesion able to interact chemically with other, non-damaged chromatin. (author)

  11. The Ubx Polycomb response element bypasses an unpaired Fab-8 insulator via cis transvection in Drosophila.

    Science.gov (United States)

    Lu, Danfeng; Li, Zhuoran; Li, Lingling; Yang, Liping; Chen, Guijun; Yang, Deying; Zhang, Yue; Singh, Vikrant; Smith, Sheryl; Xiao, Yu; Wang, Erlin; Ye, Yunshuang; Zhang, Wei; Zhou, Lei; Rong, Yikang; Zhou, Jumin

    2018-01-01

    Chromatin insulators or boundary elements protect genes from regulatory activities from neighboring genes or chromatin domains. In the Drosophila Abdominal-B (Abd-B) locus, the deletion of such elements, such as Frontabdominal-7 (Fab-7) or Fab-8 led to dominant gain of function phenotypes, presumably due to the loss of chromatin barriers. Homologous chromosomes are paired in Drosophila, creating a number of pairing dependent phenomena including transvection, and whether transvection may affect the function of Polycomb response elements (PREs) and thus contribute to the phenotypes are not known. Here, we studied the chromatin barrier activity of Fab-8 and how it is affected by the zygosity of the transgene, and found that Fab-8 is able to block the silencing effect of the Ubx PRE on the DsRed reporter gene in a CTCF binding sites dependent manner. However, the blocking also depends on the zygosity of the transgene in that the barrier activity is present when the transgene is homozygous, but absent when the transgene is heterozygous. To analyze this effect, we performed chromatin immunoprecipitation and quantitative PCR (ChIP-qPCR) experiments on homozygous transgenic embryos, and found that H3K27me3 and H3K9me3 marks are restricted by Fab-8, but they spread beyond Fab-8 into the DsRed gene when the two CTCF binding sites within Fab-8 were mutated. Consistent with this, the mutation reduced H3K4me3 and RNA Pol II binding to the DsRed gene, and consequently, DsRed expression. Importantly, in heterozygous embryos, Fab-8 is unable to prevent the spread of H3K27me3 and H3K9me3 marks from crossing Fab-8 into DsRed, suggesting an insulator bypass. These results suggest that in the Abd-B locus, deletion of the insulator in one copy of the chromosome could lead to the loss of insulator activity on the homologous chromosome, and in other loci where chromosomal deletion created hemizygous regions of the genome, the chromatin barrier could be compromised. This study highlights

  12. Chromatin maturation depends on continued DNA-replication

    International Nuclear Information System (INIS)

    Schlaeger, E.J.; Puelm, W.; Knippers, R.

    1983-01-01

    The structure of [ 3 H]thymidine pulse-labeled chromatin in lymphocytes differs from that of non-replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. These structural features of replicating chromatin rapidly disappear when the [ 3 H]thymidine pulse is followed by a chase in the presence of an excess of non-radioactive thymidine. However, when the rate of DNA replication is reduced, as in cycloheximide-treated lymphocytes, chromatin maturation is retarded. No chromatin maturation is observed when nuclei from pulse-labeled lymphocytes are incubated in vitro in the absence of DNA precursors. In contrast, when these nuclei are incubated under conditions known to be optimal for DNA replication, the structure of replicating chromatin is efficiently converted to that of 'mature', non-replicating chromatin. The authors conclude that the properties of nascent DNA and/or the distance from the replication fork are important factors in chromatin maturation. (Auth.)

  13. The Role of Chromatin-Associated Proteins in Cancer

    DEFF Research Database (Denmark)

    Helin, Kristian; Minucci, Saverio

    2017-01-01

    The organization of the chromatin structure is essential for maintaining cell-type-specific gene expression and therefore for cell identity. This structure is highly dynamic and is regulated by a large number of chromatin-associated proteins that are required for normal development...... and differentiation. Recurrent somatic mutations have been found with high frequency in genes coding for chromatin-associated proteins in cancer, and several of these are required for cancer maintenance. In this review, we discuss recent advances in understanding the role of chromatin-associated proteins...

  14. Heat insulating plates

    Energy Technology Data Exchange (ETDEWEB)

    Allan, J.A.F.

    1976-10-28

    Micro-porous insulation plates are dealt with, for example, how they are used in the insulation of heat storage devices. Since one side of such plates is exposed to a temperature of over 700/sup 0/C, a shrinkage of the glass texture of the covering can occur, which can exceed the shrinkage of the inner micro-porous material, so that cracks and splits in the high temperature side of the covering can come about. The task of the invention is to design the plate in such a way as to prevent this from happening. For this purpose the plate is provided, according to invention specifications, with flutes, waves, ribs, waffle or grid patterns and the covering is set into the recesses originating from this.

  15. Green insulation: hemp fibers

    Energy Technology Data Exchange (ETDEWEB)

    Anon,

    2011-09-15

    Indian hemp (Cannabis indica) is known for its psychotropic values and it is banned in most countries. However, industrial hemp (Cannabis sativa) is known for its tough fibers. Several manufactures in Europe including, small niche players, have been marketing hemp insulation products for several years. Hemp is a low environmental impact material. Neither herbicide nor pesticide is used during the growth of hemp. The fibers are extracted in a waste-free and chemical-free mechanical process. Hemp can consume CO2 during its growth. In addition, hemp fiber can be disposed of harmlessly by composting or incineration at the end of its life. Hemp fibers are processed and treated only minimally to resist rot and fungal activity. There is little health risk when producing and installing the insulation, thanks to the absence of toxic additive. Its thermal resistance is comparable to mineral wool. But the development and marketing of hemp fibers may be restricted in North America.

  16. Super-insulation

    International Nuclear Information System (INIS)

    Gerold, J.

    1985-01-01

    The invention concerns super-insulation, which also acts as spacing between two pressurized surfaces, where the crossing bars in at least two layers are provided, with interposed foil. The super-insulation is designed so that it can take compression forces and limits thermal radiation and thermal conduction sufficiently, where the total density of heat flow is usually limited to a few watts per m 2 . The solution to the problem is characterized by the fact that the bars per layer are parallel and from layer to layer they are at an angle to each other and the crossover positions of the bars of different layers are at fixed places and so form contact columns. The basic idea is that bars crossing over each other to support compression forces are used so that contact columns are formed, which are compressed to a certain extent by the load. (orig./PW) [de

  17. Compact vacuum insulation embodiments

    Science.gov (United States)

    Benson, D.K.; Potter, T.F.

    1992-04-28

    An ultra-thin compact vacuum insulation panel is comprised of two hard, but bendable metal wall sheets closely spaced apart from each other and welded around the edges to enclose a vacuum chamber. Glass or ceramic spacers hold the wall sheets apart. The spacers can be discrete spherical beads or monolithic sheets of glass or ceramic webs with nodules protruding therefrom to form essentially point' or line' contacts with the metal wall sheets. In the case of monolithic spacers that form line' contacts, two such spacers with the line contacts running perpendicular to each other form effectively point' contacts at the intersections. Corrugations accommodate bending and expansion, tubular insulated pipes and conduits, and preferred applications are also included. 26 figs.

  18. Compact vacuum insulation

    Science.gov (United States)

    Benson, D.K.; Potter, T.F.

    1993-01-05

    An ultra-thin compact vacuum insulation panel is comprised of two hard, but bendable metal wall sheets closely spaced apart from each other and welded around the edges to enclose a vacuum chamber. Glass or ceramic spacers hold the wall sheets apart. The spacers can be discrete spherical beads or monolithic sheets of glass or ceramic webs with nodules protruding therefrom to form essentially point'' or line'' contacts with the metal wall sheets. In the case of monolithic spacers that form line'' contacts, two such spacers with the line contacts running perpendicular to each other form effectively point'' contacts at the intersections. Corrugations accommodate bending and expansion, tubular insulated pipes and conduits, and preferred applications are also included.

  19. Insulating materials for optoelectronics

    International Nuclear Information System (INIS)

    Agullo-Lopez, F.

    1990-01-01

    Optoelectronics is an interdisciplinary field. Basic functions of an optoelectronic system include the generator of the optical signal, its transmission and handling and, finally, its detection, storage and display. A large variety of semiconductor and insulating materials are used or are being considered to perform those functions. The authors focus on insulating materials, mostly oxides. For signal generation, tunable solid state lasers, either vibronic or those based oon colour centres are briefly described, and their main operating parameters summarized. Reference is made to some developments on fiber and waveguide lasers. Relevant physical features of the silica fibres used for low-loss, long-band, optical transmission are reviewed, as well as present efforts to further reduce attenuation in the mid-infrared range. Particular attention is paid to photorefractive materials (LiNbO 3 , BGO, BSO, etc.), which are being investigated

  20. Super insulating aerogel glazing

    DEFF Research Database (Denmark)

    Schultz, Jørgen Munthe; Jensen, Karsten Ingerslev; Kristiansen, Finn Harken

    2004-01-01

    form the weakest part of the thermal envelope with respect to heat loss coefficient, but on the other hand also play an important role for passive solar energy utilisation. For window orientations other than south, the net energy balance will be close to or below zero. However, the properties......Monolithic silica aerogel offers the possibility of combining super insulation and high solar energy transmittance, which has been the background for a previous and a current EU project on research and development of monolithic silica aerogel as transparent insulation in windows. Generally, windows...... of aerogel glazing will allow for a positive net energy gain even for north facing vertical windows in a Danish climate during the heating season. This means that high quality daylight can be obtained even with additional energy gain. On behalf of the partners of the two EU projects, results related...

  1. Insulated pipe clamp design

    International Nuclear Information System (INIS)

    Anderson, M.J.; Hyde, L.L.; Wagner, S.E.; Severud, L.K.

    1980-01-01

    Thin wall large diameter piping for breeder reactor plants can be subjected to significant thermal shocks during reactor scrams and other upset events. On the Fast Flux Test Facility, the addition of thick clamps directly on the piping was undesired because the differential metal temperatures between the pipe wall and the clamp could have significantly reduced the pipe thermal fatigue life cycle capabilities. Accordingly, an insulated pipe clamp design concept was developed. The design considerations and methods along with the development tests are presented. Special considerations to guard against adverse cracking of the insulation material, to maintain the clamp-pipe stiffness desired during a seismic event, to minimize clamp restraint on the pipe during normal pipe heatup, and to resist clamp rotation or spinning on the pipe are emphasized

  2. Insulated pipe clamp design

    International Nuclear Information System (INIS)

    Anderson, M.J.; Hyde, L.L.; Wagner, S.E.; Severud, L.K.

    1980-01-01

    Thin wall large diameter piping for breeder reactor plants can be subjected to significant thermal shocks during reactor scrams and other upset events. On the Fast Flux Test Facility, the addition of thick clamps directly on the piping was undesired because the differential metal temperatures between the pipe wall and the clamp could have significantly reduced the pipe thermal fatigue life cycle capabilities. Accordingly, an insulated pipe clamp design concept was developed. 5 refs

  3. Pourable Foam Insulation

    Science.gov (United States)

    Harvey, James A.; Butler, John M.; Chartoff, Richard P.

    1989-01-01

    Report describes search for polyisocyanurate/polyurethane foam insulation with superior characteristics. Discusses chemistry of current formulations. Tests of formulations, of individual ingredients and or alternative new formulations described. Search revealed commercially available formulations exhibiting increased thermal stability at temperatures up to 600 degree C, pours readily before curing, presents good appearance after curing, and remains securely bonded to aluminum at cryogenic temperatures. Total of 42 different formulations investigated, 10 found to meet requirements.

  4. CTCF-dependent chromatin bias constitutes transient epigenetic memory of the mother at the H19-Igf2 imprinting control region in prospermatogonia.

    Directory of Open Access Journals (Sweden)

    Dong-Hoon Lee

    2010-11-01

    Full Text Available Genomic imprints-parental allele-specific DNA methylation marks at the differentially methylated regions (DMRs of imprinted genes-are erased and reestablished in germ cells according to the individual's sex. Imprint establishment at paternally methylated germ line DMRs occurs in fetal male germ cells. In prospermatogonia, the two unmethylated alleles exhibit different rates of de novo methylation at the H19/Igf2 imprinting control region (ICR depending on parental origin. We investigated the nature of this epigenetic memory using bisulfite sequencing and allele-specific ChIP-SNuPE assays. We found that the chromatin composition in fetal germ cells was biased at the ICR between the two alleles with the maternally inherited allele exhibiting more H3K4me3 and less H3K9me3 than the paternally inherited allele. We determined genetically that the chromatin bias, and also the delayed methylation establishment in the maternal allele, depended on functional CTCF insulator binding sites in the ICR. Our data suggest that, in primordial germ cells, maternally inherited allele-specific CTCF binding sets up allele-specific chromatin differences at the ICR. The erasure of these allele-specific chromatin marks is not complete before the process of de novo methylation imprint establishment begins. CTCF-dependent allele-specific chromatin composition imposes a maternal allele-specific delay on de novo methylation imprint establishment at the H19/Igf2 ICR in prospermatogonia.

  5. Histone modifications influence mediator interactions with chromatin

    Science.gov (United States)

    Zhu, Xuefeng; Zhang, Yongqiang; Bjornsdottir, Gudrun; Liu, Zhongle; Quan, Amy; Costanzo, Michael; Dávila López, Marcela; Westholm, Jakub Orzechowski; Ronne, Hans; Boone, Charles; Gustafsson, Claes M.; Myers, Lawrence C.

    2011-01-01

    The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator—histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. PMID:21742760

  6. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.

    Science.gov (United States)

    Liu, Sheng; Zibetti, Cristina; Wan, Jun; Wang, Guohua; Blackshaw, Seth; Qian, Jiang

    2017-07-27

    Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in various cellular and developmental contexts. The chromatin accessibility profiles provide useful information in prediction of TF binding events in various physiological conditions. Furthermore, ChIP-Seq analysis was used to determine genome-wide binding sites for a range of different TFs in multiple cell types. Integration of these two types of genomic information can improve the prediction of TF binding events. We assessed to what extent a model built upon on other TFs and/or other cell types could be used to predict the binding sites of TFs of interest. A random forest model was built using a set of cell type-independent features such as specific sequences recognized by the TFs and evolutionary conservation, as well as cell type-specific features derived from chromatin accessibility data. Our analysis suggested that the models learned from other TFs and/or cell lines performed almost as well as the model learned from the target TF in the cell type of interest. Interestingly, models based on multiple TFs performed better than single-TF models. Finally, we proposed a universal model, BPAC, which was generated using ChIP-Seq data from multiple TFs in various cell types. Integrating chromatin accessibility information with sequence information improves prediction of TF binding.The prediction of TF binding is transferable across TFs and/or cell lines suggesting there are a set of universal "rules". A computational tool was developed to predict TF binding sites based on the universal "rules".

  7. Global chromatin fibre compaction in response to DNA damage

    International Nuclear Information System (INIS)

    Hamilton, Charlotte; Hayward, Richard L.; Gilbert, Nick

    2011-01-01

    Highlights: ► Robust KAP1 phosphorylation in response to DNA damage in HCT116 cells. ► DNA repair foci are found in soluble chromatin. ► Biophysical analysis reveals global chromatin fibre compaction after DNA damage. ► DNA damage is accompanied by rapid linker histone dephosphorylation. -- Abstract: DNA is protected by packaging it into higher order chromatin fibres, but this can impede nuclear processes like DNA repair. Despite considerable research into the factors required for signalling and repairing DNA damage, it is unclear if there are concomitant changes in global chromatin fibre structure. In human cells DNA double strand break (DSB) formation triggers a signalling cascade resulting in H2AX phosphorylation (γH2AX), the rapid recruitment of chromatin associated proteins and the subsequent repair of damaged sites. KAP1 is a transcriptional corepressor and in HCT116 cells we found that after DSB formation by chemicals or ionising radiation there was a wave of, predominantly ATM dependent, KAP1 phosphorylation. Both KAP1 and phosphorylated KAP1 were readily extracted from cells indicating they do not have a structural role and γH2AX was extracted in soluble chromatin indicating that sites of damage are not attached to an underlying structural matrix. After DSB formation we did not find a concomitant change in the sensitivity of chromatin fibres to micrococcal nuclease digestion. Therefore to directly investigate higher order chromatin fibre structures we used a biophysical sedimentation technique based on sucrose gradient centrifugation to compare the conformation of chromatin fibres isolated from cells before and after DNA DSB formation. After damage we found global chromatin fibre compaction, accompanied by rapid linker histone dephosphorylation, consistent with fibres being more regularly folded or fibre deformation being stabilized by linker histones. We suggest that following DSB formation, although there is localised chromatin unfolding to

  8. Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

    Science.gov (United States)

    Chabbert, Christophe D; Adjalley, Sophie H; Steinmetz, Lars M; Pelechano, Vicent

    2018-01-01

    Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation.

  9. Reduction of heat insulation upon soaking of the insulation layer

    Science.gov (United States)

    Achtliger, J.

    1983-09-01

    Improved thermal protection of hollow masonry by introduction of a core insulation between the inner and outer shell is discussed. The thermal conductivity of insulation materials was determined in dry state and after soaking by water with different volume-related moisture contents. The interpolated thermal conductivity values from three measured values at 10 C average temperature are presented as a function of the pertinent moisture content. Fills of expanded polystyrene, perlite and granulated mineral fibers, insulating boards made of mineral fibers and in situ cellular plastics produced from urea-formaldehyde resin were investigated. Test results show a confirmation of thermal conductivity values for insulating materials in hollow masonry.

  10. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level.

    Directory of Open Access Journals (Sweden)

    Elizabeth A Rach

    2011-01-01

    Full Text Available The application of deep sequencing to map 5' capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: "focused" promoters with transcription start sites (TSSs that occur in a narrowly defined genomic span and "dispersed" promoters with TSSs that are spread over a larger window. Previous studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, but virtually no studies have directly investigated the relationship with chromatin features. Here, we show that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Dispersed promoters display higher associations with well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone variants (H2A.Z and marks (H3K4 methylation, as well as insulator binding (such as CTCF, independent of the expression levels of affected genes. Notably, differences are conserved across mammals and flies, and they provide for a clearer separation of promoter architectures than the presence and absence of CpG islands or the occurrence of stalled RNA polymerase. Computational models support the stronger contribution of chromatin features to the definition of dispersed promoters compared to focused start sites. Our results show that promoter classes defined from 5' capped transcripts not only reflect differences in the initiation process at the core promoter but also are indicative of divergent transcriptional programs established within gene-proximal nucleosome organization.

  11. Correlation analysis between ceramic insulator pollution and acoustic emissions

    Directory of Open Access Journals (Sweden)

    Benjamín Álvarez-Nasrallah

    2015-01-01

    Full Text Available Most of the studies related to insulator pollution are normally performed based on individual analysis among leakage current, relative humidity and equivalent salt deposit density (ESDD. This paper presents a correlation analysis between the leakage current and the acoustic emissions measured in a 230 kV electrical substations in the city of Barranquilla, Colombia. Furthermore, atmospheric variables were considered to develop a characterization model of the insulator contamination process. This model was used to demonstrate that noise emission levels are a reliable indicator to detect and characterize pollution on high voltage insulators. The correlation found amount the atmospheric, electrical and sound variables allowed to determine the relations for the maintenance of ceramic insulators in high-polluted areas. In this article, the results on the behavior of the leakage current in ceramic insulators and the sound produced with different atmospheric conditions are shown, which allow evaluating the best time to clean the insulator at the substation. Furthermore, by experimentation on site and using statistical models, the correlation between ambient variables and the leakage current of insulators in an electrical substation was obtained. Some of the problems that bring the external noise were overcome using multiple microphones and specialized software that enabled properly filter the sound and better measure the variables.

  12. Electrical insulating liquid: A review

    Directory of Open Access Journals (Sweden)

    Deba Kumar Mahanta

    2017-08-01

    Full Text Available Insulating liquid plays an important role for the life span of the transformer. Petroleum-based mineral oil has become dominant insulating liquid of transformer for more than a century for its excellent dielectric and cooling properties. However, the usage of petroleum-based mineral oil, derived from a nonrenewable energy source, has affected the environment for its nonbiodegradability property. Therefore, researchers direct their attention to renewable and biodegradable alternatives. Palm fatty acid ester, coconut oil, sunflower oil, etc. are considered as alternatives to replace mineral oil as transformer insulation liquid. This paper gives an extensive review of different liquid insulating materials used in a transformer. Characterization of different liquids as an insulating material has been discussed. An attempt has been made to classify different insulating liquids-based on different properties.

  13. Homoeologous chromatin exchange in a radiation-induced gene transfer

    International Nuclear Information System (INIS)

    Dvorak, J.; Knott, D.R.

    1977-01-01

    Some of the ionizing-radiation-induced translocations between alien and wheat chromosomes show no deleterious effects and are transmitted normally through the pollen. Translocations of this type will be called ''compensating''. In one such compensating translocation, designated T4, it was found that chromatin in the long arm of wheat chromosome 7D was replaced with homoeologous chromatin of the Agropyron chromosome

  14. Chromatin Immunoprecipitation (ChIP) using Drosophila tissue

    OpenAIRE

    Tran, Vuong; Gan, Qiang; Chen, Xin

    2012-01-01

    Epigenetics remains a rapidly developing field that studies how the chromatin state contributes to differential gene expression in distinct cell types at different developmental stages. Epigenetic regulation contributes to a broad spectrum of biological processes, including cellular differentiation during embryonic development and homeostasis in adulthood. A critical strategy in epigenetic studies is to examine how various histone modifications and chromatin factors regulate gene expression. ...

  15. Homoeologous chromatin exchange in a radiation-induced gene transfer

    Energy Technology Data Exchange (ETDEWEB)

    Dvorak, J; Knott, D R [Department of Crop Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

    1977-03-01

    Some of the ionizing-radiation-induced translocations between alien and wheat chromosomes show no deleterious effects and are transmitted normally through the pollen. Translocations of this type will be called ''compensating''. In one such compensating translocation, designated T4, it was found that chromatin in the long arm of wheat chromosome 7D was replaced with homologous chromatin of the Agropyron chromosome.

  16. The nucleosome: orchestrating DNA damage signaling and repair within chromatin.

    Science.gov (United States)

    Agarwal, Poonam; Miller, Kyle M

    2016-10-01

    DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.

  17. Chromatin architecture and gene expression in Escherichia coli

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Ussery, David

    2004-01-01

    Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli.......Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli....

  18. Nuclear visions enhanced: chromatin structure, organization and dynamics

    OpenAIRE

    Meshorer, Eran; Herrmann, Harald; Raška, Ivan

    2011-01-01

    The EMBO Workshop on ‘Chromatin Structure, Organization and Dynamics' took place in April 2011 in Prague, Czech Republic. Participants presented data on the generation of models of the genome, working to correlate changes in the organization of chromatin with the functional state of the genome.

  19. HAMLET interacts with histones and chromatin in tumor cell nuclei.

    Science.gov (United States)

    Düringer, Caroline; Hamiche, Ali; Gustafsson, Lotta; Kimura, Hiroshi; Svanborg, Catharina

    2003-10-24

    HAMLET is a folding variant of human alpha-lactalbumin in an active complex with oleic acid. HAMLET selectively enters tumor cells, accumulates in their nuclei and induces apoptosis-like cell death. This study examined the interactions of HAMLET with nuclear constituents and identified histones as targets. HAMLET was found to bind histone H3 strongly and to lesser extent histones H4 and H2B. The specificity of these interactions was confirmed using BIAcore technology and chromatin assembly assays. In vivo in tumor cells, HAMLET co-localized with histones and perturbed the chromatin structure; HAMLET was found associated with chromatin in an insoluble nuclear fraction resistant to salt extraction. In vitro, HAMLET bound strongly to histones and impaired their deposition on DNA. We conclude that HAMLET interacts with histones and chromatin in tumor cell nuclei and propose that this interaction locks the cells into the death pathway by irreversibly disrupting chromatin organization.

  20. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

    Chemical modifications to the DNA and histone protein components of chromatin can modulate gene expression and genome stability. Understanding the physiological impact of changes in chromatin structure remains an important question in biology. As one example, in order to generate antibody diversity...... with somatic hypermutation and class switch recombination, chromatin must be made accessible for activation-induced cytidine deaminase (AID)-mediated deamination of cytosines in DNA. These lesions are recognized and removed by various DNA repair pathways but, if not handled properly, can lead to formation...... of oncogenic chromosomal translocations. In this review, we focus the discussion on how chromatin-modifying activities and -binding proteins contribute to the native chromatin environment in which AID-induced DNA damage is targeted and repaired. Outstanding questions remain regarding the direct roles...

  1. Fast neutron irradiation effects on liver chromatin structure

    International Nuclear Information System (INIS)

    Constantinescu, B.; Radu, L.

    1996-01-01

    The growing interest in neutron therapy requires complex studies on the mechanisms of neutron action on biological systems, especially on chromatin. The chromatin was extracted from a normal tissue-livers of Wistar rats - and from a tumoral tissue - Walker tumour maintained on Wistar rats. Irradiation doses from 5 Gy to 100 Gy by fast neutron intense beams produced via d(13.5 MeV) +Be (thick target) reaction at Bucharest U-120 Classical Cyclotron were used. To study the post-irradiation effects, various methods were employed. So, the variation in the 260 nm absorbency in chromatin thermal transition was pursuit. The chromatin-ethidium bromide complexes fluorescence with λ ex =480 nm and λ em =600 nm was analyzed. To determine chromatin DNA strand breaks a fluorimetric method, with cells' suspensions as starting material was used. This method requires a partial treatment with alkali producing three components: T-estimating the total fluorescence of DNA double helix, P-assigning the untwisting rate and B-the blank, where DNA is completely unfolded The percentsge of DNA double strand,-D-, remaining after this treatment, is: %D=100x(P-B)/(T-B). The intrinsic chromatin fluorescence was determined for tyrosine (λ ex =280 nm, λ em =305 nm), specific for badic chromatin prooteins, and for tryptophane (λ ex =290 nm, λ em =345 nm) specific for acid chromatin proteins. Polyacrylamide gel electrophoresis was performed: The double fluorescent labelling of chromatin was realized with acridine orange for DNA and with dansyl chloride for chromatin proteins. Fluorescence intensity determinations were done with λ ex =505 nm, λ em =530 nm for acridine orange and with λ ex =323 nm, λ em =505 nm for dansyl chloride. A Pye Unicam SP 1800 spectrophotometer and a Aminco SPF 500 spectrofluorimeter were employed. (author)

  2. Magnetically insulated H- diodes

    International Nuclear Information System (INIS)

    Fisher, A.; Bystritskii, V.; Garate, E.; Prohaska, R.; Rostoker, N.

    1993-01-01

    At the Univ. of California, Irvine, the authors have been studying the production of intense H - beams using pulse power techniques for the past 7 years. Previously, current densities of H - ions for various diode designs at UCI have been a few A/cm 2 . Recently, they have developed diodes similar to the coaxial design of the Lebedev Physical Institute, Moscow, USSR, where current densities of up to 200 A/cm 2 were reported using nuclear activation of a carbon target. In experiments at UCI employing the coaxial diode, current densities of up to 35 A/cm 2 from a passive polyethylene cathode loaded with TiH 2 have been measured using a pinhole camera and CR-39 track recording plastic. The authors have also been working on a self-insulating, annular diode which can generate a directed beam of H - ions. In the annular diode experiments a plasma opening switch was used to provide a prepulse and a current path which self-insulated the diode. These experiments were done on the machine APEX, a 1 MV, 50 ns, 7 Ω pulseline with a unipolar negative prepulse of ∼ 100 kV and 400 ns duration. Currently, the authors are modifying the pulseline to include an external LC circuit which can generate a bipolar, 150 kV, 1 μs duration prepulse (similar prepulse characteristic as in the Lebedev Institute experiments cited above)

  3. RNA polymerase III transcription - regulated by chromatin structure and regulator of nuclear chromatin organization.

    Science.gov (United States)

    Pascali, Chiara; Teichmann, Martin

    2013-01-01

    RNA polymerase III (Pol III) transcription is regulated by modifications of the chromatin. DNA methylation and post-translational modifications of histones, such as acetylation, phosphorylation and methylation have been linked to Pol III transcriptional activity. In addition to being regulated by modifications of DNA and histones, Pol III genes and its transcription factors have been implicated in the organization of nuclear chromatin in several organisms. In yeast, the ability of the Pol III transcription system to contribute to nuclear organization seems to be dependent on direct interactions of Pol III genes and/or its transcription factors TFIIIC and TFIIIB with the structural maintenance of chromatin (SMC) protein-containing complexes cohesin and condensin. In human cells, Pol III genes and transcription factors have also been shown to colocalize with cohesin and the transcription regulator and genome organizer CCCTC-binding factor (CTCF). Furthermore, chromosomal sites have been identified in yeast and humans that are bound by partial Pol III machineries (extra TFIIIC sites - ETC; chromosome organizing clamps - COC). These ETCs/COC as well as Pol III genes possess the ability to act as boundary elements that restrict spreading of heterochromatin.

  4. Processing of DNA double strand breaks by alternative non-homologous end-joining in hyperacetylated chromatin.

    Science.gov (United States)

    Manova, Vasilissa; Singh, Satyendra K; Iliakis, George

    2012-08-22

    Mammalian cells employ at least two subpathways of non-homologous end-joining for the repair of ionizing radiation induced DNA double strand breaks: The canonical DNA-PK-dependent form of non-homologous end-joining (D-NHEJ) and an alternative, slowly operating, error-prone backup pathway (B-NHEJ). In contrast to D-NHEJ, which operates with similar efficiency throughout the cell cycle, B-NHEJ operates more efficiently in G2-phase. Notably, B-NHEJ also shows strong and as of yet unexplained dependency on growth activity and is markedly compromised in serum-deprived cells, or in cells that enter the plateau-phase of growth. The molecular mechanisms underpinning this response remain unknown. Since chromatin structure or changes in chromatin structure are prime candidate-B-NHEJ-modulators, we study here the role of chromatin hyperacetylation, either by HDAC2 knockdown or treatment with the HDAC inhibitor TSA, on the repair by B-NHEJ of IR-induced DSBs. siRNA-mediated knockdown of HDAC2 fails to provoke histone hyperacetylation in Lig4-/- MEFs and has no detectable effect on B-NHEJ function. Treatment with TSA that inhibits multiple HDACs causes efficient, reversible chromatin hyperacetylation in Lig4-/- MEFs, as well as in human HCT116 Lig4-/- cells and the human glioma cell line M059K. The IR yield of DSBs in TSA-treated cells remains similar to that of untreated cells despite the expected chromatin relaxation. In addition, chromatin hyperacetylation leaves unchanged repair of DSBs by B-NHEJ in irradiated exponentially growing, or plateau-phase cells. Notably, under the experimental conditions employed here, chromatin hyperacetylation fails to detectably modulate B-NHEJ in M059K cells as well. In summary, the results show that chromatin acetylation or deacetylation does not affect the kinetics of alternative NHEJ in all types of cells examined both in exponentially growing and serum deprived cultures. We conclude that parameters beyond chromatin acetylation determine B

  5. Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state.

    Directory of Open Access Journals (Sweden)

    Bartek Wilczynski

    Full Text Available Precise patterns of spatial and temporal gene expression are central to metazoan complexity and act as a driving force for embryonic development. While there has been substantial progress in dissecting and predicting cis-regulatory activity, our understanding of how information from multiple enhancer elements converge to regulate a gene's expression remains elusive. This is in large part due to the number of different biological processes involved in mediating regulation as well as limited availability of experimental measurements for many of them. Here, we used a Bayesian approach to model diverse experimental regulatory data, leading to accurate predictions of both spatial and temporal aspects of gene expression. We integrated whole-embryo information on transcription factor recruitment to multiple cis-regulatory modules, insulator binding and histone modification status in the vicinity of individual gene loci, at a genome-wide scale during Drosophila development. The model uses Bayesian networks to represent the relation between transcription factor occupancy and enhancer activity in specific tissues and stages. All parameters are optimized in an Expectation Maximization procedure providing a model capable of predicting tissue- and stage-specific activity of new, previously unassayed genes. Performing the optimization with subsets of input data demonstrated that neither enhancer occupancy nor chromatin state alone can explain all gene expression patterns, but taken together allow for accurate predictions of spatio-temporal activity. Model predictions were validated using the expression patterns of more than 600 genes recently made available by the BDGP consortium, demonstrating an average 15-fold enrichment of genes expressed in the predicted tissue over a naïve model. We further validated the model by experimentally testing the expression of 20 predicted target genes of unknown expression, resulting in an accuracy of 95% for temporal

  6. Insulation structure of thermonuclear device

    International Nuclear Information System (INIS)

    Suzuki, Takayuki; Usami, Saburo; Tsukamoto, Hideo; Kikuchi, Mitsuru

    1998-01-01

    The present invention provides an insulating structure of a thermonuclear device, in which insulation materials between toroidal coils are not broken even if superconductive toroidal coils are used. Namely, a tokamak type thermonuclear device of an insulating structure type comprises superconductive toroidal coils for confining plasmas arranged in a circular shape directing the center each at a predetermined angle, and the toroidal coils are insulated from each other. The insulation materials are formed by using a biaxially oriented fiber reinforced plastics. The contact surface of the toroidal coils and the insulating materials are arranged so that they are contact at a woven surface of the fiber reinforced plastics. Either or both of the contact surfaces of the fiber reinforced plastics and the toroidal coils are coated with a high molecular compound having a low friction coefficient. With such a constitution, since the interlayer shearing strength of the biaxially oriented fiber reinforced plastics is about 1/10 of the compression strength, the shearing stress exerted on the insulation material is reduced. Since a static friction coefficient on the contact surface is reduced to provide a structure causing slipping, shearing stress does not exceeds a predetermined limit. As a result, breakage of the insulation materials between the toroidal coils can be prevented. (I.S.)

  7. Plastic Materials for Insulating Applications.

    Science.gov (United States)

    Wang, S. F.; Grossman, S. J.

    1987-01-01

    Discusses the production and use of polymer materials as thermal insulators. Lists several materials that provide varying degrees of insulation. Describes the production of polymer foam and focuses on the major applications of polystyrene foam, polyurethane foam, and polyisocyanurate foam. (TW)

  8. Rapid and reversible epigenome editing by endogenous chromatin regulators.

    Science.gov (United States)

    Braun, Simon M G; Kirkland, Jacob G; Chory, Emma J; Husmann, Dylan; Calarco, Joseph P; Crabtree, Gerald R

    2017-09-15

    Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells. Furthermore, Hp1/Suv39h1 heterochromatin complex recruitment to active promoters deposits H3K9me3 domains, resulting in gene silencing that can be reversed upon washout of the chemical dimerizer. This inducible recruitment strategy provides precise kinetic information to model epigenetic memory and plasticity. It is broadly applicable to mechanistic studies of chromatin in mammalian cells and is particularly suited to the analysis of endogenous multi-subunit chromatin regulator complexes.Understanding the link between epigenetic marks and gene regulation requires the development of new tools to directly manipulate chromatin. Here the authors demonstrate a Cas9-based system to recruit chromatin remodelers to loci of interest, allowing rapid, reversible manipulation of epigenetic states.

  9. Chromatinization of the KSHV Genome During the KSHV Life Cycle

    Energy Technology Data Exchange (ETDEWEB)

    Uppal, Timsy [Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N Virginia Street, MS 320, Reno, NV 89557 (United States); Jha, Hem C. [Department of Microbiology and the Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104 (United States); Verma, Subhash C. [Department of Microbiology and Immunology, School of Medicine, University of Nevada, 1664 N Virginia Street, MS 320, Reno, NV 89557 (United States); Robertson, Erle S., E-mail: erle@mail.med.upenn.edu [Department of Microbiology and the Tumor Virology Program of the Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104 (United States)

    2015-01-14

    Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family and is the causative agent of various lymphoproliferative diseases in humans. KSHV, like other herpesviruses, establishes life-long latent infection with the expression of a limited number of viral genes. Expression of these genes is tightly regulated by both the viral and cellular factors. Recent advancements in identifying the expression profiles of viral transcripts, using tilling arrays and next generation sequencing have identified additional coding and non-coding transcripts in the KSHV genome. Determining the functions of these transcripts will provide a better understanding of the mechanisms utilized by KSHV in altering cellular pathways involved in promoting cell growth and tumorigenesis. Replication of the viral genome is critical in maintaining the existing copies of the viral episomes during both latent and lytic phases of the viral life cycle. The replication of the viral episome is facilitated by viral components responsible for recruiting chromatin modifying enzymes and replication factors for altering the chromatin complexity and replication initiation functions, respectively. Importantly, chromatin modification of the viral genome plays a crucial role in determining whether the viral genome will persist as latent episome or undergo lytic reactivation. Additionally, chromatinization of the incoming virion DNA, which lacks chromatin structure, in the target cells during primary infection, helps in establishing latent infection. Here, we discuss the recent advancements on our understating of KSHV genome chromatinization and the consequences of chromatin modifications on viral life cycle.

  10. Chromatinization of the KSHV Genome During the KSHV Life Cycle

    International Nuclear Information System (INIS)

    Uppal, Timsy; Jha, Hem C.; Verma, Subhash C.; Robertson, Erle S.

    2015-01-01

    Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family and is the causative agent of various lymphoproliferative diseases in humans. KSHV, like other herpesviruses, establishes life-long latent infection with the expression of a limited number of viral genes. Expression of these genes is tightly regulated by both the viral and cellular factors. Recent advancements in identifying the expression profiles of viral transcripts, using tilling arrays and next generation sequencing have identified additional coding and non-coding transcripts in the KSHV genome. Determining the functions of these transcripts will provide a better understanding of the mechanisms utilized by KSHV in altering cellular pathways involved in promoting cell growth and tumorigenesis. Replication of the viral genome is critical in maintaining the existing copies of the viral episomes during both latent and lytic phases of the viral life cycle. The replication of the viral episome is facilitated by viral components responsible for recruiting chromatin modifying enzymes and replication factors for altering the chromatin complexity and replication initiation functions, respectively. Importantly, chromatin modification of the viral genome plays a crucial role in determining whether the viral genome will persist as latent episome or undergo lytic reactivation. Additionally, chromatinization of the incoming virion DNA, which lacks chromatin structure, in the target cells during primary infection, helps in establishing latent infection. Here, we discuss the recent advancements on our understating of KSHV genome chromatinization and the consequences of chromatin modifications on viral life cycle

  11. Chromatin decondensed by acetylation shows an elevated radiation response

    International Nuclear Information System (INIS)

    Nackerdien, Z.; Michie, J.; Boehm, L.

    1989-01-01

    V-79 Chinese hamster lung fibroblasts exposed to 5 mM n-sodium butyrate were irradiated with 60Co gamma rays and cell survival was determined by the cell colony assay. In a separate set of experiments the acetylated chromatin obtained from these cells was irradiated and the change of molecular weight of the DNA was evaluated by alkaline sucrose density centrifugation. At a survival level of 10(-2) to 10(-4) cells exposed to butyrate were found to be 1.3-1.4 times more radiosensitive than control cells. Exposure of isolated chromatin to 100 Gy of 60Co gamma irradiation generated 0.9 +/- 0.03 single-strand breaks (ssb) per 10 Gy per 10(8) Da and 2.0 +/- 0.3 ssb/10 Gy/10(8) Da for control and acetylated chromatin, respectively. The elevated radiation sensitivity of chromatin relaxed by acetylation is in good agreement with previous results on chromatin expanded by histone H1 depletion. Packing and accessibility of DNA in chromatin appear to be major factors which influence the radiation sensitivity. The intrinsic radiation sensitivity of chromatin in various packing states is discussed in light of the variation of radiation sensitivity of whole cells in the cell cycle which incorporates repair

  12. Tracking the mechanical dynamics of human embryonic stem cell chromatin

    Directory of Open Access Journals (Sweden)

    Hinde Elizabeth

    2012-12-01

    Full Text Available Abstract Background A plastic chromatin structure has emerged as fundamental to the self-renewal and pluripotent capacity of embryonic stem (ES cells. Direct measurement of chromatin dynamics in vivo is, however, challenging as high spatiotemporal resolution is required. Here, we present a new tracking-based method which can detect high frequency chromatin movement and quantify the mechanical dynamics of chromatin in live cells. Results We use this method to study how the mechanical properties of chromatin movement in human embryonic stem cells (hESCs are modulated spatiotemporally during differentiation into cardiomyocytes (CM. Notably, we find that pluripotency is associated with a highly discrete, energy-dependent frequency of chromatin movement that we refer to as a ‘breathing’ state. We find that this ‘breathing’ state is strictly dependent on the metabolic state of the cell and is progressively silenced during differentiation. Conclusions We thus propose that the measured chromatin high frequency movements in hESCs may represent a hallmark of pluripotency and serve as a mechanism to maintain the genome in a transcriptionally accessible state. This is a result that could not have been observed without the high spatial and temporal resolution provided by this novel tracking method.

  13. Anti-chromatin antibodies in juvenile rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    V. Gerloni

    2011-09-01

    Full Text Available Objective: to evaluate the prevalence and clinical significance of anti-chromatin antibodies (Abs in juvenile rheumatoid arthritis (JRA. Methods: IgG anti-chromatin Abs were detected by an enzyme-linked immunosorbent assay (ELISA, in sera of 94 children with JRA (10 children with systemic, 38 with polyarticular and 46 with oligoarticular disease onset. As control group, 33 age- and-sex-matched healthy children (HC were also examined. Results: Abs to chromatin were detected in 24/94 (25,5% of children suffering from JRA. Particularly, the higher prevalence of anti-chromatin Abs has been found in children with oligoarticular (30,4% and polyarticular (23,7% onset JRA. In these groups Abs titers were significantly higher compared to systemic JRA and HC (p=0.003. Anti-chromatin Abs were observed more frequently in patients with oligoarticular disease and chronic uveitis (21,7%. Furthermore, higher levels of anti-chromatin Abs has been found in all the patients treated with anti-TNFα therapy (p<0.0001. Conclusions: our results confirm previous data about the prevalence of anti-chromatin Abs in JRA. These Abs were significantly higher in the group of patients with oligoarticular onset with past or present hystory of ocular involvement and in the group with polyarticular JRA treated with biologic therapy. A long-term follow-up study could be useful to evaluate the potential utility of these autoantibodies.

  14. Magnetically self-insulated transformers

    International Nuclear Information System (INIS)

    Novac, B.M.; Smith, I.R.; Brown, J.

    2002-01-01

    Magnetic insulation is the only practicable form of insulation for much equipment used in ultrahigh pulsed-power work, including transmission lines and plasma opening switches. It has not however so far been successfully exploited in the transformers that are necessarily involved, and the first proposed design that appeared more than 30 years ago raised apparently insuperable problems. The two novel arrangements for a magnetically insulated transformer described in this paper overcome the problems faced by the earlier designs and also offer considerable scope for development in a number of important areas. Theoretical justification is given for their insulating properties, and this is confirmed by proof-of-principle results obtained from a small-scale experimental prototype in which magnetic insulation was demonstrated at up to 100 kV. (author)

  15. Research on vacuum insulation for cryocables

    International Nuclear Information System (INIS)

    Graneau, P.

    1974-01-01

    Vacuum insulation, as compared with solid insulation, simplifies the construction of both resistive or superconducting cryogenic cables. The common vacuum space in the cable can furnish thermal insulation between the environment and the cryogenic coolant, provide electrical insulation between conductors, and establish thermal isolation between go- and return-coolant streams. The differences between solid and vacuum high voltage insulation are discussed, and research on the design, materials selection, and testing of vacuum insulated cryogenic cables is described

  16. Excitons in insulators

    International Nuclear Information System (INIS)

    Grasser, R.; Scharmann, A.

    1983-01-01

    This chapter investigates absorption, reflectivity, and intrinsic luminescence spectra of free and/or self-trapped (localized) excitons in alkali halides and rare gas solids. Introduces the concepts underlying the Wannier-Mott and Frenkel exciton models, two extreme pictures of an exciton in crystalline materials. Discusses the theoretical and experimental background; excitons in alkali halides; and excitons in rare gas solids. Shows that the intrinsic optical behavior of wide gap insulators in the range of the fundamental absorption edge is controlled by modified Wannier-Mott excitons. Finds that while that alkali halides only show free and relaxed molecular-like exciton emission, in rare gas crystals luminescence due to free, single and double centered localized excitons is observed. Indicates that the simultaneous existence of free and self-trapped excitons in these solid requires an energy barrier for self-trapping

  17. Chromatin regulation at the frontier of synthetic biology

    Science.gov (United States)

    Keung, Albert J.; Joung, J. Keith; Khalil, Ahmad S.; Collins, James J.

    2016-01-01

    As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including `epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication. PMID:25668787

  18. SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Treffers, Louise W; Verlaan-de Vries, Matty

    2015-01-01

    dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors, and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1, and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the SUMO......-targeted ubiquitin ligase RNF4 and degraded by the proteasome in response to DNA damage, JARID1C was SUMOylated and recruited to the chromatin to demethylate histone H3K4....

  19. DNA packing in chromatine, a manifestation of the Bonnet transformation.

    Science.gov (United States)

    Blum, Z; Lidin, S

    1988-08-01

    The packing of DNA is described using the formalism of differential geometry. Winding of the DNA double helix around the histone 2-5 octamer forming a nucleosome and the condensation of the so-formed bead-on-a-string chromatine aided by histone 1 is interpreted as two consecutive isometric, i.e. Bonnet, transformations. The DNA double helix can be approximated to a helicoid which can be transformed isometrically to a catenoid, an approximation of the nucleosome. Owing to the organization of the histone octamer the extended chromatine takes a helicoidal shape allowing a second Bonnet transformation to consummate the condensation into a chromatine fibre.

  20. Mechanism of chromatin degradation in thymocytes of irradiated rats

    International Nuclear Information System (INIS)

    Zotova, R.N.; Umanskij, S.R.; Tokarskaya, V.I.

    1983-01-01

    A biphase change in poly (ADP-ribose) polymerase activity of the thymocyte chromatin was observed after 10 Gy irradiation of rats: during the first minutes the incorporation of 14 C-NAD increased by 40% then started decreasing to make 110, 60 and 35% after 1, 2 and 3 h, respectively. Irradiation of rat thymus chromatin in vitro sharply decreased poly (ADP-ribose) polymerase activity. The possible role of changes in the poly (ADP-ribose) synthesis in the activation of nuclear Ca/Mg-dependent endonuclease and in the postirradiation degradation of the thymocyte chromatin is discussed

  1. Dysregulation of chromatin remodelling complexes in amyotrophic lateral sclerosis.

    Science.gov (United States)

    Tibshirani, Michael; Zhao, Beibei; Gentil, Benoit J; Minotti, Sandra; Marques, Christine; Keith, Julia; Rogaeva, Ekaterina; Zinman, Lorne; Rouaux, Caroline; Robertson, Janice; Durham, Heather D

    2017-11-01

    Amyotrophic lateral sclerosis is a fatal neurodegenerative disease with paralysis resulting from dysfunction and loss of motor neurons. A common neuropathological finding is attrition of motor neuron dendrites, which make central connections vital to motor control. The chromatin remodelling complex, neuronal Brahma-related gene 1 (Brg1)-associated factor complex (nBAF), is critical for neuronal differentiation, dendritic extension and synaptic function. We have identified loss of the crucial nBAF subunits Brg1, Brg1-associated factor 53b and calcium responsive transactivator in cultured motor neurons expressing FUS or TAR-DNA Binding Protein 43 (TDP-43) mutants linked to familial ALS. When plasmids encoding wild-type or mutant human FUS or TDP-43 were expressed in motor neurons of dissociated spinal cord cultures prepared from E13 mice, mutant proteins in particular accumulated in the cytoplasm. Immunolabelling of nBAF subunits was reduced in proportion to loss of nuclear FUS or TDP-43 and depletion of Brg1 was associated with nuclear retention of Brg1 mRNA. Dendritic attrition (loss of intermediate and terminal dendritic branches) occurred in motor neurons expressing mutant, but not wild-type, FUS or TDP-43. This attrition was delayed by ectopic over-expression of Brg1 and was reproduced by inhibiting Brg1 activity either through genetic manipulation or treatment with the chemical inhibitor, (E)-1-(2-Hydroxyphenyl)-3-((1R, 4R)-5-(pyridin-2-yl)-2, 5-diazabicyclo[2.2.1]heptan-2-yl)prop-2-en-1-one, demonstrating the importance of Brg1 to maintenance of dendritic architecture. Loss of nBAF subunits was also documented in spinal motor neurons in autopsy tissue from familial amyotrophic sclerosis (chromosome 9 open reading frame 72 with G4C2 nucleotide expansion) and from sporadic cases with no identified mutation, pointing to dysfunction of nBAF chromatin remodelling in multiple forms of ALS. © The Author 2017. Published by Oxford University Press. All rights reserved

  2. Replicating centromeric chromatin: Spatial and temporal control of CENP-A assembly

    International Nuclear Information System (INIS)

    Nechemia-Arbely, Yael; Fachinetti, Daniele; Cleveland, Don W.

    2012-01-01

    The centromere is the fundamental unit for insuring chromosome inheritance. This complex region has a distinct type of chromatin in which histone H3 is replaced by a structurally different homologue identified in humans as CENP-A. In metazoans, specific DNA sequences are neither required nor sufficient for centromere identity. Rather, an epigenetic mark comprised of CENP-A containing chromatin is thought to be the major determinant of centromere identity. In this view, CENP-A deposition and chromatin assembly are fundamental processes for the maintenance of centromeric identity across mitotic and meiotic divisions. Several lines of evidence support CENP-A deposition in metazoans occurring at only one time in the cell cycle. Such cell cycle-dependent loading of CENP-A is found in divergent species from human to fission yeast, albeit with differences in the cell cycle point at which CENP-A is assembled. Cell cycle dependent CENP-A deposition requires multiple assembly factors for its deposition and maintenance. This review discusses the regulation of new CENP-A deposition and its relevance to centromere identity and inheritance.

  3. Insights into Chromatin Structure and Dynamics in Plants

    Directory of Open Access Journals (Sweden)

    Stefanie Rosa

    2013-11-01

    Full Text Available The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.

  4. Probing Chromatin-modifying Enzymes with Chemical Tools

    KAUST Repository

    Fischle, Wolfgang

    2016-02-04

    Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.

  5. HACking the centromere chromatin code: insights from human artificial chromosomes.

    Science.gov (United States)

    Bergmann, Jan H; Martins, Nuno M C; Larionov, Vladimir; Masumoto, Hiroshi; Earnshaw, William C

    2012-07-01

    The centromere is a specialized chromosomal region that serves as the assembly site of the kinetochore. At the centromere, CENP-A nucleosomes form part of a chromatin landscape termed centrochromatin. This chromatin environment conveys epigenetic marks regulating kinetochore formation. Recent work sheds light on the intricate relationship between centrochromatin state, the CENP-A assembly pathway and the maintenance of centromere function. Here, we review the emerging picture of how chromatin affects mammalian kinetochore formation. We place particular emphasis on data obtained from Human Artificial Chromosome (HAC) biology and the targeted engineering of centrochromatin using synthetic HACs. We discuss implications of these findings, which indicate that a delicate balance of histone modifications and chromatin state dictates both de novo centromere formation and the maintenance of centromere identity in dividing cell populations.

  6. histone H3 predominantly mark the pericentromeric chromatin

    Indian Academy of Sciences (India)

    SANTOSH KUMAR SHARMA

    pericentromeric chromatin during mitosis in monokinetic plants. J. Genet. .... bigger), cytological preparations (easy to difficult) as well as their habitat ... Poaceae. Monocot. Land. 14. Triticum aestivum. Common wheat. Poaceae. Monocot. Land.

  7. Neutron scattering studies on chromatin higher-order structure

    Energy Technology Data Exchange (ETDEWEB)

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V. [Brookhaven National Laboratory, Upton, NY (United States)

    1994-12-31

    We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.

  8. Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin

    Science.gov (United States)

    Bandaria, Jigar N.; Qin, Peiwu; Berk, Veysel; Chu, Steven; Yildiz, Ahmet

    2016-01-01

    SUMMARY Telomeres, repetitive DNA sequences at chromosome ends, are shielded against the DNA damage response (DDR) by the shelterin complex. To understand how shelterin protects telomere ends, we investigated the structural organization of telomeric chromatin in human cells using super-resolution microscopy. We found that telomeres form compact globular structures through a complex network of interactions between shelterin subunits and telomeric DNA, and not by DNA methylation, histone deacetylation or histone trimethylation at telomeres and subtelomeric regions. Mutations that abrogate shelterin assembly or removal of individual subunits from telomeres cause up to a 10-fold increase in telomere volume. Decompacted telomeres become more accessible to telomere-associated proteins and accumulate DDR signals. Recompaction of telomeric chromatin using an orthogonal method displaces DDR signals from telomeres. These results reveal the chromatin remodeling activity of shelterin and demonstrate that shelterin-mediated compaction of telomeric chromatin provides robust protection of chromosome ends against the DDR machinery. PMID:26871633

  9. Determination of local chromatin composition by CasID.

    Science.gov (United States)

    Schmidtmann, Elisabeth; Anton, Tobias; Rombaut, Pascaline; Herzog, Franz; Leonhardt, Heinrich

    2016-09-02

    Chromatin structure and function are determined by a plethora of proteins whose genome-wide distribution is typically assessed by immunoprecipitation (ChIP). Here, we developed a novel tool to investigate the local chromatin environment at specific DNA sequences. We combined the programmable DNA binding of dCas9 with the promiscuous biotin ligase BirA* (CasID) to biotinylate proteins in the direct vicinity of specific loci. Subsequent streptavidin-mediated precipitation and mass spectrometry identified both known and previously unknown chromatin factors associated with repetitive telomeric, major satellite and minor satellite DNA. With super-resolution microscopy, we confirmed the localization of the putative transcription factor ZNF512 at chromocenters. The versatility of CasID facilitates the systematic elucidation of functional protein complexes and locus-specific chromatin composition.

  10. Aberrant Chromatin Modification as a Mechanism of Prostate Cancer Progression

    National Research Council Canada - National Science Library

    Chen, Hongwu

    2004-01-01

    .... However, the underlying mechanism is still unclear. The purpose of this study is to test the hypothesis that aberrant chromatin modification plays a critical role in prostate cancer progression...

  11. Probing Chromatin-modifying Enzymes with Chemical Tools

    KAUST Repository

    Fischle, Wolfgang; Schwarzer, Dirk

    2016-01-01

    and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites

  12. FACT facilitates chromatin transcription by RNA polymerases I and III

    DEFF Research Database (Denmark)

    Birch, Joanna L; Tan, Bertrand C-M; Panov, Kostya I

    2009-01-01

    Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle....... The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results...... in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III...

  13. Neutron scattering studies on chromatin higher-order structure

    International Nuclear Information System (INIS)

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V.

    1994-01-01

    We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist

  14. Citrullination regulates pluripotency and histone H1 binding to chromatin

    DEFF Research Database (Denmark)

    Christophorou, Maria A; Castelo-Branco, Gonçalo; Halley-Stott, Richard P

    2014-01-01

    citrullination of core histones has been linked to transcriptional regulation and the DNA damage response. PADI4 (also called PAD4 or PADV), the only PADI with a nuclear localization signal, was previously shown to act in myeloid cells where it mediates profound chromatin decondensation during the innate immune...... and activating their expression. Its inhibition lowers the percentage of pluripotent cells in the early mouse embryo and significantly reduces reprogramming efficiency. Using an unbiased proteomic approach we identify linker histone H1 variants, which are involved in the generation of compact chromatin, as novel...... PADI4 substrates. Citrullination of a single arginine residue within the DNA-binding site of H1 results in its displacement from chromatin and global chromatin decondensation. Together, these results uncover a role for citrullination in the regulation of pluripotency and provide new mechanistic...

  15. histone H3 predominantly mark the pericentromeric chromatin

    Indian Academy of Sciences (India)

    SANTOSH KUMAR SHARMA

    packaging of eukaryotic DNA in nucleoprotein complex known as .... The plant material used in the present study has ... materials (root tips/flower buds) were fixed in PHEMES ..... fications that mark active chromatin, while there are no data.

  16. Cytogenetic abnormality in man, wider implications of theories of sex chromatin origin.

    Science.gov (United States)

    MILES, C P

    1962-01-01

    Female nuclei may be identified by means of sex chromatin. In general the number of sex chromatin bodies is one less than the number of X chromosomes. An exception to this rule is a case of sex chromatin-positive XO Turner's syndrome. This case suggests the possibility of sex chromatin-positive XY males, and it may be evidence for chromosomal differentiation.

  17. Lightweight, Thermally Insulating Structural Panels

    Science.gov (United States)

    Eisen, Howard J.; Hickey, Gregory; Wen, Liang-Chi; Layman, William E.; Rainen, Richard A.; Birur, Gajanana C.

    1996-01-01

    Lightweight, thermally insulating panels that also serve as structural members developed. Honeycomb-core panel filled with low-thermal-conductivity, opacified silica aerogel preventing convection and minimizes internal radiation. Copper coating on face sheets reduces radiation. Overall thermal conductivities of panels smaller than state-of-art commercial non-structurally-supporting foam and fibrous insulations. On Earth, panels suitable for use in low-air-pressure environments in which lightweight, compact, structurally supporting insulation needed; for example, aboard high-altitude aircraft or in partially evacuated panels in refrigerators.

  18. Reflecting variable opening insulating panel

    International Nuclear Information System (INIS)

    Nungesser, W.T.

    1976-01-01

    A description is given of a reflecting variable opening insulating panel assembly, comprising a static panel assembly of reflecting insulation sheets forming a cavity along one side of the panel and a movable panel opening out by sliding from the cavity of the static panel, and a locking device for holding the movable panel in a position extending from the cavity of the static panel. This can apply to a nuclear reactor of which the base might require maintenance and periodical checking and for which it is desirable to have available certain processes for the partial dismantling of the insulation [fr

  19. Mechanism of chromatin degradation in thymocytes of irradiated rats

    International Nuclear Information System (INIS)

    Nikonova, L.V.; Nelipovich, P.A.; Umanskij, S.R.

    1983-01-01

    Chromatin digestion in isolated thymocyte nuclei with DNAase I, micrococcal nuclease and nuclease from Serratia marcescens was studied. It was shown that 3 h after irradiation (10 Gy), the kinetics of accumulation of acid soluble and salt soluble products of DNA degradation, caused by exogenous nucleases, remains unchanged. The administration of cycloheximide does not influence the sensitivity of chromatin to DNAase I and somewhat increases the rate of salt soluble products formation upon the nuclease from S, marcescens treatment

  20. 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.

  1. Fragmentation of chromatin with 125I radioactive disintegrations

    International Nuclear Information System (INIS)

    Turner, G.N.; Nobis, P.; Dewey, W.C.

    1976-01-01

    The DNA in Chinese hamster cells was labeled first for 3 h with [ 3 H]TdR and then for 3 h with [ 125 I]UdR. Chromatin was extracted, frozen, and stored at -30 0 C until 1.0 x 10 17 and 1.25 x 10 17 disintegrations/g of labeled DNA occurred for 125 I and 3 H, respectively. Velocity sedimentation of chromatin (DNA with associated chromosomal proteins) in neutral sucrose gradients indicated that the localized energy from the 125 I disintegrations, which gave about 1 double-strand break/disintegration plus an additional 1.3 single strand breaks, selectively fragmented the [ 125 I] chromatin into pieces smaller than the [ 3 H] chromatin. In other words, 125 I disintegrations caused much more localized damage in the chromatin labeled with 125 I than in the chromatin labeled with 3 H, and fragments induced in DNA by 125 I disintegrations were not held together by the associated chromosomal proteins. Use of this 125 I technique for studying chromosomal proteins associated with different regions in the cellular DNA is discussed. For these studies, the number of disintegrations required for fragmenting DNA molecules of different sizes is illustrated

  2. Cytoplasmic chromatin triggers inflammation in senescence and cancer.

    Science.gov (United States)

    Dou, Zhixun; Ghosh, Kanad; Vizioli, Maria Grazia; Zhu, Jiajun; Sen, Payel; Wangensteen, Kirk J; Simithy, Johayra; Lan, Yemin; Lin, Yanping; Zhou, Zhuo; Capell, Brian C; Xu, Caiyue; Xu, Mingang; Kieckhaefer, Julia E; Jiang, Tianying; Shoshkes-Carmel, Michal; Tanim, K M Ahasan Al; Barber, Glen N; Seykora, John T; Millar, Sarah E; Kaestner, Klaus H; Garcia, Benjamin A; Adams, Peter D; Berger, Shelley L

    2017-10-19

    Chromatin is traditionally viewed as a nuclear entity that regulates gene expression and silencing. However, we recently discovered the presence of cytoplasmic chromatin fragments that pinch off from intact nuclei of primary cells during senescence, a form of terminal cell-cycle arrest associated with pro-inflammatory responses. The functional significance of chromatin in the cytoplasm is unclear. Here we show that cytoplasmic chromatin activates the innate immunity cytosolic DNA-sensing cGAS-STING (cyclic GMP-AMP synthase linked to stimulator of interferon genes) pathway, leading both to short-term inflammation to restrain activated oncogenes and to chronic inflammation that associates with tissue destruction and cancer. The cytoplasmic chromatin-cGAS-STING pathway promotes the senescence-associated secretory phenotype in primary human cells and in mice. Mice deficient in STING show impaired immuno-surveillance of oncogenic RAS and reduced tissue inflammation upon ionizing radiation. Furthermore, this pathway is activated in cancer cells, and correlates with pro-inflammatory gene expression in human cancers. Overall, our findings indicate that genomic DNA serves as a reservoir to initiate a pro-inflammatory pathway in the cytoplasm in senescence and cancer. Targeting the cytoplasmic chromatin-mediated pathway may hold promise in treating inflammation-related disorders.

  3. Chromatin modifications and the DNA damage response to ionizing radiation

    International Nuclear Information System (INIS)

    Kumar, Rakesh; Horikoshi, Nobuo; Singh, Mayank; Gupta, Arun; Misra, Hari S.; Albuquerque, Kevin; Hunt, Clayton R.; Pandita, Tej K.

    2013-01-01

    In order to survive, cells have evolved highly effective repair mechanisms to deal with the potentially lethal DNA damage produced by exposure to endogenous as well as exogenous agents. Ionizing radiation exposure induces highly lethal DNA damage, especially DNA double-strand breaks (DSBs), that is sensed by the cellular machinery and then subsequently repaired by either of two different DSB repair mechanisms: (1) non-homologous end joining, which re-ligates the broken ends of the DNA and (2) homologous recombination, that employs an undamaged identical DNA sequence as a template, to maintain the fidelity of DNA repair. Repair of DSBs must occur within the natural context of the cellular DNA which, along with specific proteins, is organized to form chromatin, the overall structure of which can impede DNA damage site access by repair proteins. The chromatin complex is a dynamic structure and is known to change as required for ongoing cellular processes such as gene transcription or DNA replication. Similarly, during the process of DNA damage sensing and repair, chromatin needs to undergo several changes in order to facilitate accessibility of the repair machinery. Cells utilize several factors to modify the chromatin in order to locally open up the structure to reveal the underlying DNA sequence but post-translational modification of the histone components is one of the primary mechanisms. In this review, we will summarize chromatin modifications by the respective chromatin modifying factors that occur during the DNA damage response.

  4. Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of Origin Recognition Complex-binding sites in the Drosophila genome

    Science.gov (United States)

    Vorobyeva, Nadezhda E.; Mazina, Marina U.; Golovnin, Anton K.; Kopytova, Daria V.; Gurskiy, Dmitriy Y.; Nabirochkina, Elena N.; Georgieva, Sofia G.; Georgiev, Pavel G.; Krasnov, Aleksey N.

    2013-01-01

    Despite increasing data on the properties of replication origins, molecular mechanisms underlying origin recognition complex (ORC) positioning in the genome are still poorly understood. The Su(Hw) protein accounts for the activity of best-studied Drosophila insulators. Here, we show that Su(Hw) recruits the histone acetyltransferase complex SAGA and chromatin remodeler Brahma to Su(Hw)-dependent insulators, which gives rise to regions with low nucleosome density and creates conditions for ORC binding. Depletion in Su(Hw) leads to a dramatic drop in the levels of SAGA, Brahma and ORC subunits and a significant increase in nucleosome density on Su(Hw)-dependent insulators, whereas artificial Su(Hw) recruitment itself is sufficient for subsequent SAGA, Brahma and ORC binding. In contrast to the majority of replication origins that associate with promoters of active genes, Su(Hw)-binding sites constitute a small proportion (6%) of ORC-binding sites that are localized preferentially in transcriptionally inactive chromatin regions termed BLACK and BLUE chromatin. We suggest that the key determinants of ORC positioning in the genome are DNA-binding proteins that constitute different DNA regulatory elements, including insulators, promoters and enhancers. Su(Hw) is the first example of such a protein. PMID:23609538

  5. Molecular dewetting on insulators

    International Nuclear Information System (INIS)

    Burke, S A; Topple, J M; Gruetter, P

    2009-01-01

    Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C 60 on alkali halides, and the technologically important system of pentacene on SiO 2 . These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure. (topical review)

  6. Molecular dewetting on insulators.

    Science.gov (United States)

    Burke, S A; Topple, J M; Grütter, P

    2009-10-21

    Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C(60) on alkali halides, and the technologically important system of pentacene on SiO(2). These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure.

  7. Insulating fcc YH

    International Nuclear Information System (INIS)

    Molen, S. J. van der; Nagengast, D. G.; Gogh, A. T. M. van; Kalkman, J.; Kooij, E. S.; Rector, J. H.; Griessen, R.

    2001-01-01

    We study the structural, optical, and electrical properties of Mg z Y 1-z switchable mirrors upon hydrogenation. It is found that the alloys disproportionate into essentially pure YH 3-δ and MgH 2 with the crystal structure of YH 3-δ dependent on the Mg concentration z. For 0 3-δ are observed, whereas for z≥0.1 only cubic YH 3-δ is present. Interestingly, cubic YH 3-δ is expanded compared to YH 2 , in disagreement with theoretical predictions. From optical and electrical measurements we conclude that cubic YH 3-δ is a transparent insulator with properties similar to hexagonal YH 3-δ . Our results are inconsistent with calculations predicting fcc YH 3-δ to be metallic, but they are in good agreement with recent GW calculations on both hcp and fcc YH 3 . Finally, we find an increase in the effective band gap of the hydrided Mg z Y 1-z alloys with increasing z. Possibly this is due to quantum confinement effects in the small YH 3 clusters

  8. Topological Insulator Nanowires and Nanoribbons

    KAUST Repository

    Kong, Desheng; Randel, Jason C.; Peng, Hailin; Cha, Judy J.; Meister, Stefan; Lai, Keji; Chen, Yulin; Shen, Zhi-Xun; Manoharan, Hari C.; Cui, Yi

    2010-01-01

    Recent theoretical calculations and photoemission spectroscopy measurements on the bulk Bi2Se3 material show that it is a three-dimensional topological insulator possessing conductive surface states with nondegenerate spins, attractive

  9. Measure Guideline: Basement Insulation Basics

    Energy Technology Data Exchange (ETDEWEB)

    Aldrich, R.; Mantha, P.; Puttagunta, S.

    2012-10-01

    This guideline is intended to describe good practices for insulating basements in new and existing homes, and is intended to be a practical resources for building contractors, designers, and also to homeowners.

  10. Metal-insulator-semiconductor photodetectors.

    Science.gov (United States)

    Lin, Chu-Hsuan; Liu, Chee Wee

    2010-01-01

    The major radiation of the sun can be roughly divided into three regions: ultraviolet, visible, and infrared light. Detection in these three regions is important to human beings. The metal-insulator-semiconductor photodetector, with a simpler process than the pn-junction photodetector and a lower dark current than the MSM photodetector, has been developed for light detection in these three regions. Ideal UV photodetectors with high UV-to-visible rejection ratio could be demonstrated with III-V metal-insulator-semiconductor UV photodetectors. The visible-light detection and near-infrared optical communications have been implemented with Si and Ge metal-insulator-semiconductor photodetectors. For mid- and long-wavelength infrared detection, metal-insulator-semiconductor SiGe/Si quantum dot infrared photodetectors have been developed, and the detection spectrum covers atmospheric transmission windows.

  11. Metal-Insulator-Semiconductor Photodetectors

    Directory of Open Access Journals (Sweden)

    Chu-Hsuan Lin

    2010-09-01

    Full Text Available The major radiation of the Sun can be roughly divided into three regions: ultraviolet, visible, and infrared light. Detection in these three regions is important to human beings. The metal-insulator-semiconductor photodetector, with a simpler process than the pn-junction photodetector and a lower dark current than the MSM photodetector, has been developed for light detection in these three regions. Ideal UV photodetectors with high UV-to-visible rejection ratio could be demonstrated with III-V metal-insulator-semiconductor UV photodetectors. The visible-light detection and near-infrared optical communications have been implemented with Si and Ge metal-insulator-semiconductor photodetectors. For mid- and long-wavelength infrared detection, metal-insulator-semiconductor SiGe/Si quantum dot infrared photodetectors have been developed, and the detection spectrum covers atmospheric transmission windows.

  12. Interphase Chromosome Conformation and Chromatin-Chromatin Interactions in Human Epithelial Cells Cultured Under Different Gravity Conditions

    Science.gov (United States)

    Zhang, Ye; Wong, Michael; Hada, Megumi; Wu, Honglu

    2015-01-01

    Microgravity has been shown to alter global gene expression patterns and protein levels both in cultured cells and animal models. It has been suggested that the packaging of chromatin fibers in the interphase nucleus is closely related to genome function, and the changes in transcriptional activity are tightly correlated with changes in chromatin folding. This study explores the changes of chromatin conformation and chromatin-chromatin interactions in the simulated microgravity environment, and investigates their correlation to the expression of genes located at different regions of the chromosome. To investigate the folding of chromatin in interphase under various culture conditions, human epithelial cells, fibroblasts, and lymphocytes were fixed in the G1 phase. Interphase chromosomes were hybridized with a multicolor banding in situ hybridization (mBAND) probe for chromosome 3 which distinguishes six regions of the chromosome as separate colors. After images were captured with a laser scanning confocal microscope, the 3-dimensional structure of interphase chromosome 3 was reconstructed at multi-mega base pair scale. In order to determine the effects of microgravity on chromosome conformation and orientation, measures such as distance between homologous pairs, relative orientation of chromosome arms about a shared midpoint, and orientation of arms within individual chromosomes were all considered as potentially impacted by simulated microgravity conditions. The studies revealed non-random folding of chromatin in interphase, and suggested an association of interphase chromatin folding with radiation-induced chromosome aberration hotspots. Interestingly, the distributions of genes with expression changes over chromosome 3 in cells cultured under microgravity environment are apparently clustered on specific loci and chromosomes. This data provides important insights into how mammalian cells respond to microgravity at molecular level.

  13. 16 CFR 460.18 - Insulation ads.

    Science.gov (United States)

    2010-01-01

    ... Commercial Practices FEDERAL TRADE COMMISSION TRADE REGULATION RULES LABELING AND ADVERTISING OF HOME INSULATION § 460.18 Insulation ads. (a) If your ad gives an R-value, you must give the type of insulation and... your ad gives a price, you must give the type of insulation, the R-value at a specific thickness, the...

  14. Cryogenic foam insulation: Abstracted publications

    Science.gov (United States)

    Williamson, F. R.

    1977-01-01

    A group of documents were chosen and abstracted which contain information on the properties of foam materials and on the use of foams as thermal insulation at cryogenic temperatures. The properties include thermal properties, mechanical properties, and compatibility properties with oxygen and other cryogenic fluids. Uses of foams include applications as thermal insulation for spacecraft propellant tanks, and for liquefied natural gas storage tanks and pipelines.

  15. Quantum magnetotransport properties of ultrathin topological insulator films

    KAUST Repository

    Tahir, M.

    2013-01-30

    We study the quantum magnetotransport in ultrathin topological insulator films in an external magnetic field considering hybridization between the upper and lower surfaces of the film. We investigate the two possible mechanisms for splitting of Landau levels, Zeeman and hybridization effects, and show that their interplay leads to minima in the collisional and Hall conductivities with a metal-to-insulator phase transition at the charge neutrality point. Hall plateaus arise at unusual multiples of e2/h . Evidence of a quantum phase transition for the zeroth and splitting of the higher Landau levels is found from the temperature and magnetic field dependences of the transport.

  16. Quantum magnetotransport properties of ultrathin topological insulator films

    KAUST Repository

    Tahir, M.; Sabeeh, K.; Schwingenschlö gl, Udo

    2013-01-01

    We study the quantum magnetotransport in ultrathin topological insulator films in an external magnetic field considering hybridization between the upper and lower surfaces of the film. We investigate the two possible mechanisms for splitting of Landau levels, Zeeman and hybridization effects, and show that their interplay leads to minima in the collisional and Hall conductivities with a metal-to-insulator phase transition at the charge neutrality point. Hall plateaus arise at unusual multiples of e2/h . Evidence of a quantum phase transition for the zeroth and splitting of the higher Landau levels is found from the temperature and magnetic field dependences of the transport.

  17. Avalanches in insulating gases

    International Nuclear Information System (INIS)

    Verhaart, H.F.A.

    1982-01-01

    Avalanches of charged particles in gases are often studied with the ''electrical method'', the measurement of the waveform of the current in the external circuit. In this thesis a substantial improvement of the time resolution of the measuring setup, to be used for the electrical method, is reported. The avalanche is started by an N 2 -laser with a pulse duration of only 0.6 ns. With this laser it is possible to release a high number of primary electrons (some 10 8 ) which makes it possible to obtain sizeable signals, even at low E/p values. With the setup it is possible to analyze current waveforms with a time resolution down to 1.4 ns, determined by both the laser and the measuring system. Furthermore it is possible to distinguish between the current caused by the electrons and the current caused by the ions in the avalanche and to monitor these currents simultaneously. Avalanche currents are measured in N 2 , CO 2 , O 2 , H 2 O, air of varying humidity, SF 6 and SF 6 /N 2 mixtures. Depending on the nature of the gas and the experimental conditions, processes as diffusion, ionization, attachment, detachment, conversion and secondary emission are observed. Values of parameters with which these processes can be described, are derived from an analysis of the current waveforms. For this analysis already published theories and new theories described in this thesis are used. The drift velocity of both the electrons and the ions could be easily determined from measured avalanche currents. Special attention is paid to avalanches in air becasue of the practical importance of air insulation. (Auth.)

  18. In Vivo Chromatin Targets of the Transcription Factor Yin Yang 2 in Trophoblast Stem Cells

    Science.gov (United States)

    Pérez-Palacios, Raquel; Macías-Redondo, Sofía; Climent, María; Contreras-Moreira, Bruno; Muniesa, Pedro; Schoorlemmer, Jon

    2016-01-01

    Background Yin Yang 2 (YY2) is a zinc finger protein closely related to the well-characterized Yin Yang 1 (YY1). YY1 is a DNA-binding transcription factor, with defined functions in multiple developmental processes, such as implantation, cell differentiation, X inactivation, imprinting and organogenesis. Yy2 has been treated as a largely immaterial duplication of Yy1, as they share high homology in the Zinc Finger-region and similar if not identical in vitro binding sites. In contrast to these similarities, gene expression alterations in HeLa cells with attenuated levels of either Yy1 or Yy2 were to some extent gene-specific. Moreover, the chromatin binding sites for YY2, except for its association with transposable retroviral elements (RE) and Endogenous Retroviral Elements (ERVs), remain to be identified. As a first step towards defining potential Yy2 functions matching or complementary to Yy1, we considered in vivo DNA binding sites of YY2 in trophoblast stem (TS) cells. Results We report the presence of YY2 protein in mouse-derived embryonic stem (ES) and TS cell lines. Following up on our previous report on ERV binding by YY2 in TS cells, we investigated the tissue-specificity of REX1 and YY2 binding and confirm binding to RE/ERV targets in both ES cells and TS cells. Because of the higher levels of expression, we chose TS cells to understand the role of Yy2 in gene and chromatin regulation. We used in vivo YY2 association as a measure to identify potential target genes. Sequencing of chromatin obtained in chromatin-immunoprecipitation (ChIP) assays carried out with αYY2 serum allowed us to identify a limited number of chromatin targets for YY2. Some putative binding sites were validated in regular ChIP assays and gene expression of genes nearby was altered in the absence of Yy2. Conclusions YY2 binding to ERVs is not confined to TS cells. In vivo binding sites share the presence of a consensus binding motif. Selected sites were uniquely bound by YY2 as

  19. Electrical insulators for the theta-pinch fusion reactor

    International Nuclear Information System (INIS)

    Clinard, F.W. Jr.

    1976-01-01

    The five major applications for electrical insulators in the Reference Theta Pinch Reactor are as follows: (1) first-wall insulator, (2) blanket intersegment insulator, (3) graphite encapsulating insulator, (4) implosion coil insulator, and (5) compression coil insulator. Insulator design proposals and some preliminary test results are given for each application

  20. Passive Collecting of Solar Radiation Energy using Transparent Thermal Insulators, Energetic Efficiency of Transparent Thermal Insulators

    Directory of Open Access Journals (Sweden)

    Smajo Sulejmanovic

    2014-11-01

    Full Text Available This paper explains passive collection of solar radiation energy using transparent thermal insulators. Transparent thermal insulators are transparent for sunlight, at the same time those are very good thermal insulators. Transparent thermal insulators can be placed instead of standard conventional thermal insulators and additionally transparent insulators can capture solar radiation, transform it into heat and save heat just as standard insulators. Using transparent insulators would lead to reduce in usage of fossil fuels and would help protection of an environment and reduce effects of global warming, etc.

  1. Oxidative stress signaling to chromatin in health and disease

    KAUST Repository

    Kreuz, Sarah

    2016-06-20

    Oxidative stress has a significant impact on the development and progression of common human pathologies, including cancer, diabetes, hypertension and neurodegenerative diseases. Increasing evidence suggests that oxidative stress globally influences chromatin structure, DNA methylation, enzymatic and non-enzymatic post-translational modifications of histones and DNA-binding proteins. The effects of oxidative stress on these chromatin alterations mediate a number of cellular changes, including modulation of gene expression, cell death, cell survival and mutagenesis, which are disease-driving mechanisms in human pathologies. Targeting oxidative stress-dependent pathways is thus a promising strategy for the prevention and treatment of these diseases. We summarize recent research developments connecting oxidative stress and chromatin regulation.

  2. Higher-order structure of Saccharomyces cerevisiae chromatin

    International Nuclear Information System (INIS)

    Lowary, P.T.; Widom, J.

    1989-01-01

    We have developed a method for partially purifying chromatin from Saccharomyces cerevisiae (baker's yeast) to a level suitable for studies of its higher-order folding. This has required the use of yeast strains that are free of the ubiquitous yeast killer virus. Results from dynamic light scattering, electron microscopy, and x-ray diffraction show that the yeast chromatin undergoes a cation-dependent folding into 30-nm filaments that resemble those characteristic of higher-cell chromatin; moreover, the packing of nucleosomes within the yeast 30-nm filaments is similar to that of higher cells. These results imply that yeast has a protein or protein domain that serves the role of the histone H 1 found in higher cells; physical and genetic studies of the yeast activity could help elucidate the structure and function of H 1. Images of the yeast 30-nm filaments can be used to test crossed-linker models for 30-nm filament structure

  3. Chromatin Regulation and the Histone Code in HIV Latency
.

    Science.gov (United States)

    Turner, Anne-Marie W; Margolis, David M

    2017-06-01

    The formation of a latent reservoir of Human Immunodeficiency Virus (HIV) infection hidden from immune clearance remains a significant obstacle to approaches to eradicate HIV infection. Towards an understanding of the mechanisms of HIV persistence, there is a growing body of work implicating epigenetic regulation of chromatin in establishment and maintenance of this latent reservoir. Here we discuss recent advances in the field of chromatin regulation, specifically in our understanding of the histone code, and how these discoveries relate to our current knowledge of the chromatin mechanisms linked to HIV transcriptional repression and the reversal of latency. We also examine mechanisms unexplored in the context of HIV latency and briefly discuss current therapies aimed at the induction of proviral expression within latently infected cells. We aim to emphasize that a greater understanding of the epigenetic mechanisms which govern HIV latency could lead to new therapeutic targets for latency reversal and clearance cure strategies.

  4. Fast neutron biological effects on normal and tumor chromatin

    International Nuclear Information System (INIS)

    Constantinescu, B.; Bugoi, Roxana; Paunica, Tatiana; Radu, Liliana

    1997-01-01

    Growing interest in neutron therapy and radioprotection requires complex studies on the mechanisms of neutron action on biological systems, especially on chromatin (the complex of deoxyribonucleic acid-DNA- with proteins in eukaryotic cells). Our study aims to investigate the fast neutrons induced damages in normal and tumor chromatin, studying thermal transition, intrinsic fluorescence and fluorescence of chromatin-ethidium bromide complexes behavior versus irradiation dose. The Bucharest U-120 variable energy Cyclotron was employed as an intense source of fast neutrons produced by 13.5 MeV deuterons on a thick beryllium target (166.5 mg/cm 2 ) placed at 20 angle against the incident beam. The average energy is 5.24 MeV. The total yield at 0 angle is 6.7 x 10 16 n/sr·C·MeV. To determine neutron and gamma irradiation doses, home made thermoluminescent detectors-TLD(γ) and TLD (γ + n) were used: for gamma MgF 2 : Mn mixed with Teflon pellets (φ 12.5 mm, 0.6±0.1 mm thick) and for gamma plus neutrons MgF 2 :Mn mixed with 6 LiF and Teflon pellets (same dimensions). Using a 8.022 x 10 -2 albedo factor value and the equivalence 1Gy (n)=2·10 10 fast neutron/cm 2 , the dose for the irradiation of 1.2 x 10 2 Gy/μC, with an estimated precision of 15% C for neutrons and 7.8 x 10 -4 Gy/μC for gamma, at 10 cm behind Be target, was found, respectively. A diminution of the negative fluorescence intensity for chromatin-ethidium bromide complexes with the increasing of neutron dose (from 0.98 at 5 Gy to 0.85 at 100 Gy) was observed for normal chromatin. This fact reflects chromatin DNA injuries, with the decrease of double helix DNA proportion. To study the influence of gyrostan, thyroxine and D3 vitamin treatments on fast neutron radiolysis in tumor chromatin,10 mg/kg of anticancer drug gyrostan, 40μg/kg of hormonal compound thyroxine and 30,000 IU/kg of D3 vitamin were administrated, separately or associated, to Wistar rats bearing Walker carcinosarcoma. Representing

  5. Radiation-induced cell death by chromatin loss

    International Nuclear Information System (INIS)

    Campbell, I.R.; Warenius, H.M.

    1989-01-01

    A model is proposed which relates reproductive death of cells caused by radiation to loss of chromatin at cell division. This loss of chromatin can occur through chromosomal deletions or through the formation of asymmetrical chromosomal exchanges. It is proposed that smaller doses of radiation produce fewer chromatin breaks, which are more likely to be accurately repaired, compared with larger doses. Consequently, smaller doses of radiation are less efficient in causing cell death, leading to a shoulder on the cell survival curve. Experimental evidence supports this model, and the fit between the derived formula and experimental cell survival curves is good. The derived formula approximates to the linear-quadratic equation at low doses of radiation. (author)

  6. INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division

    Directory of Open Access Journals (Sweden)

    Graeme J. Gowans

    2018-01-01

    Full Text Available Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the yeast metabolic cycle (YMC. Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here, we demonstrate that the INO80 chromatin-remodeling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC1-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin to restrict proliferation to metabolically optimal states.

  7. Positron Annihilation in Insulating Materials

    International Nuclear Information System (INIS)

    Asoka-Kumar, P; Sterne, PA

    2002-01-01

    We describe positron results from a wide range of insulating materials. We have completed positron experiments on a range of zeolite-y samples, KDP crystals, alkali halides and laser damaged SiO 2 . Present theoretical understanding of positron behavior in insulators is incomplete and our combined theoretical and experimental approach is aimed at developing a predictive understanding of positrons and positronium annihilation characteristics in insulators. Results from alkali halides and alkaline-earth halides show that positrons annihilate with only the halide ions, with no apparent contribution from the alkali or alkaline-earth cations. This contradicts the results of our existing theory for metals, which predicts roughly equal annihilation contributions from cation and anion. We also present result obtained using Munich positron microprobe on laser damaged SiO 2 samples

  8. Floquet topological insulators for sound

    Science.gov (United States)

    Fleury, Romain; Khanikaev, Alexander B.; Alù, Andrea

    2016-06-01

    The unique conduction properties of condensed matter systems with topological order have recently inspired a quest for the similar effects in classical wave phenomena. Acoustic topological insulators, in particular, hold the promise to revolutionize our ability to control sound, allowing for large isolation in the bulk and broadband one-way transport along their edges, with topological immunity against structural defects and disorder. So far, these fascinating properties have been obtained relying on moving media, which may introduce noise and absorption losses, hindering the practical potential of topological acoustics. Here we overcome these limitations by modulating in time the acoustic properties of a lattice of resonators, introducing the concept of acoustic Floquet topological insulators. We show that acoustic waves provide a fertile ground to apply the anomalous physics of Floquet topological insulators, and demonstrate their relevance for a wide range of acoustic applications, including broadband acoustic isolation and topologically protected, nonreciprocal acoustic emitters.

  9. Fermi surfaces in Kondo insulators

    Science.gov (United States)

    Liu, Hsu; Hartstein, Máté; Wallace, Gregory J.; Davies, Alexander J.; Ciomaga Hatnean, Monica; Johannes, Michelle D.; Shitsevalova, Natalya; Balakrishnan, Geetha; Sebastian, Suchitra E.

    2018-04-01

    We report magnetic quantum oscillations measured using torque magnetisation in the Kondo insulator YbB12 and discuss the potential origin of the underlying Fermi surface. Observed quantum oscillations as well as complementary quantities such as a finite linear specific heat capacity in YbB12 exhibit similarities with the Kondo insulator SmB6, yet also crucial differences. Small heavy Fermi sections are observed in YbB12 with similarities to the neighbouring heavy fermion semimetallic Fermi surface, in contrast to large light Fermi surface sections in SmB6 which are more similar to the conduction electron Fermi surface. A rich spectrum of theoretical models is suggested to explain the origin across different Kondo insulating families of a bulk Fermi surface potentially from novel itinerant quasiparticles that couple to magnetic fields, yet do not couple to weak DC electric fields.

  10. Topological insulators and topological superconductors

    CERN Document Server

    Bernevig, Andrei B

    2013-01-01

    This graduate-level textbook is the first pedagogical synthesis of the field of topological insulators and superconductors, one of the most exciting areas of research in condensed matter physics. Presenting the latest developments, while providing all the calculations necessary for a self-contained and complete description of the discipline, it is ideal for graduate students and researchers preparing to work in this area, and it will be an essential reference both within and outside the classroom. The book begins with simple concepts such as Berry phases, Dirac fermions, Hall conductance and its link to topology, and the Hofstadter problem of lattice electrons in a magnetic field. It moves on to explain topological phases of matter such as Chern insulators, two- and three-dimensional topological insulators, and Majorana p-wave wires. Additionally, the book covers zero modes on vortices in topological superconductors, time-reversal topological superconductors, and topological responses/field theory and topolo...

  11. N-Butyrate alters chromatin accessibility to DNA repair enzymes

    International Nuclear Information System (INIS)

    Smith, P.J.

    1986-01-01

    Current evidence suggests that the complex nature of mammalian chromatin can result in the concealment of DNA damage from repair enzymes and their co-factors. Recently it has been proposed that the acetylation of histone proteins in chromatin may provide a surveillance system whereby damaged regions of DNA become exposed due to changes in chromatin accessibility. This hypothesis has been tested by: (i) using n-butyrate to induce hyperacetylation in human adenocarcinoma (HT29) cells; (ii) monitoring the enzymatic accessibility of chromatin in permeabilised cells; (iii) measuring u.v. repair-associated nicking of DNA in intact cells and (iv) determining the effects of n-butyrate on cellular sensitivity to DNA damaging agents. The results indicate that the accessibility of chromatin to Micrococcus luteus u.v. endonuclease is enhanced by greater than 2-fold in n-butyrate-treated cells and that there is a corresponding increase in u.v. repair incision rates in intact cells exposed to the drug. Non-toxic levels of n-butyrate induce a block to G1 phase transit and there is a significant growth delay on removal of the drug. Resistance of HT29 cells to u.v.-radiation and adriamycin is enhanced in n-butyrate-treated cells whereas X-ray sensitivity is increased. Although changes in the responses of cells to DNA damaging agents must be considered in relation to the effects of n-butyrate on growth rate and cell-cycle distribution, the results are not inconsistent with the proposal that increased enzymatic-accessibility/repair is biologically favourable for the resistance of cells to u.v.-radiation damage. Overall the results support the suggested operation of a histone acetylation-based chromatin surveillance system in human cells

  12. Heavy ion-induced lesions in DNA: A theoretical model for the initial induction of DNA strand breaks and chromatin breaks

    International Nuclear Information System (INIS)

    Schmidt, J.B.

    1993-01-01

    A theoretical model has been developed and used to calculate yields and spatial distributions of DNA strand breaks resulting from the interactions of heavy ions with chromatin in aqueous systems. The three dimensional spatial distribution of ionizing events has been modeled for charged particles as a function of charge and velocity. Chromatin has been modeled as a 30 nm diameter solenoid of nucleosomal DNA. The Monte Carlo methods used by Chatterjee et al. have been applied to DNA in a chromatin conformation. Refinements to their methods include: a combined treatment of primary and low energy (<2 keV) secondary electron interactions, an improved low energy delta ray model, and the combined simulation of direct energy deposition on the DNA and attack by diffusing hydroxyl radicals. Individual particle tracks are treated independently, which is assumed to be applicable to low fluence irradiations in which multiple particle effects are negligible. Single strand break cross section open-quotes hooksclose quotes seen in experiments at very high LET appear to be due to the collapsing radial extent of the track, as predicted in the open-quotes deep sieveclose quotes hypothesis proposed by Tobias et al. Spatial distributions of lesions produced by particles have been found to depend on chromatin structure. In the future, heavy ions may be used as a tool to probe the organization of DNA in chromatin. A Neyman A-binomial variation of the open-quotes cluster modelclose quotes for the distribution of chromatin breaks per irradiated cell has been theoretically tested. The model includes a treatment of the chromatin fragment detection technique's resolution, which places a limitation on the minimum size of fragments which can be detected. The model appears to fit some of the experimental data reasonably well. However, further experimental and theoretical refinements are desirable

  13. Chromatin structure and evolution in the human genome

    Directory of Open Access Journals (Sweden)

    Dunlop Malcolm G

    2007-05-01

    Full Text Available Abstract Background Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time. Results In this study we have shown that, paradoxically, synonymous site divergence (dS at non-CpG sites is highest in regions of open chromatin, primarily as a result of an increased number of transitions, while the rates of other traditional measures of mutation (intergenic, intronic and ancient repeat divergence as well as SNP density are highest in closed regions of the genome. Analysis of human-chimpanzee divergence across intron-exon boundaries indicates that although genes in relatively open chromatin generally display little selection at their synonymous sites, those in closed regions show markedly lower divergence at their fourfold degenerate sites than in neighbouring introns and intergenic regions. Exclusion of known Exonic Splice Enhancer hexamers has little affect on the divergence observed at fourfold degenerate sites across chromatin categories; however, we show that closed chromatin is enriched with certain classes of ncRNA genes whose RNA secondary structure may be particularly important. Conclusion We conclude that, overall, non-CpG mutation rates are lowest in open regions of the genome and that regions of the genome with a closed chromatin structure have the highest background mutation rate. This might reflect lower rates of DNA damage or enhanced DNA repair processes in regions of open chromatin. Our results also indicate that dS is a poor

  14. Model for the structure of the active nucleolar chromatin

    International Nuclear Information System (INIS)

    Labhart, P.; Ness, P.; Banz, E.; Parish, R.; Koller, T.; Universitaet Zurich, Switzerland)

    1983-01-01

    Transcribed ribosomal genes of Xenopus laevis oocytes and of Dictyostelium discoideum were studied electron microscopically using step gradients at different ionic strengths. Under these conditions the fiber of the active chromatin appears smooth and is indistinguishable from free DNA. The accessibility of the coding region and of a nontranscribed spacer region to restriction enzymes and micrococcal nuclease were investigated. All of the results obtained are consistent with a model in which active nucleolar chromatin is mostly composed of free DNA and the components required for transcription. 50 references, 7 figures

  15. Chromatin versus pathogens: the function of epigenetics in plant immunity

    Science.gov (United States)

    Ding, Bo; Wang, Guo-Liang

    2015-01-01

    To defend against pathogens, plants have developed a sophisticated innate immunity that includes effector recognition, signal transduction, and rapid defense responses. Recent evidence has demonstrated that plants utilize the epigenetic control of gene expression to fine-tune their defense when challenged by pathogens. In this review, we highlight the current understanding of the molecular mechanisms of histone modifications (i.e., methylation, acetylation, and ubiquitination) and chromatin remodeling that contribute to plant immunity against pathogens. Functions of key histone-modifying and chromatin remodeling enzymes are discussed. PMID:26388882

  16. A Method to Identify Nucleolus-Associated Chromatin Domains (NADs).

    Science.gov (United States)

    Carpentier, Marie-Christine; Picart-Picolo, Ariadna; Pontvianne, Frédéric

    2018-01-01

    The nuclear context needs to be taken into consideration to better understand the mechanisms shaping the epigenome and its organization, and therefore its impact on gene expression. For example, in Arabidopsis, heterochromatin is preferentially localized at the nuclear and the nucleolar periphery. Although chromatin domains associating with the nuclear periphery remain to be identified in plant cells, Nucleolus Associated chromatin Domains (NADs) can be identified thanks to a protocol allowing the isolation of pure nucleoli. We describe here the protocol enabling the identification of NADs in Arabidopsis. Providing the transfer of a nucleolus marker as described here in other crop species, this protocol is broadly applicable.

  17. The importance of topoisomerases for chromatin regulated genes

    DEFF Research Database (Denmark)

    Fredsøe, Jacob Christian; Pedersen, Jakob Madsen; Rødgaard, Morten Terpager

    2013-01-01

    DNA topoisomerases are enzymes, which function to relieve torsional stress in the DNA helix by introducing transient breaks into the DNA molecule. By use of Saccharomyces cerevisiae and microarray technology we have previously shown that topoisomerases are required for the activation of chromatin...... topoisomerases for optimal activation, but in contrast to the PHO5 gene, topoisomerases are not required for chromatin remodeling of the GAL1/10 promoter region, indicating a different role of the enzymes. We are currently performing a detailed investigation of the GAL genes to elucidate the precise role...

  18. Retention of the Native Epigenome in Purified Mammalian Chromatin.

    Directory of Open Access Journals (Sweden)

    Andreas H Ehrensberger

    Full Text Available A protocol is presented for the isolation of native mammalian chromatin as fibers of 25-250 nucleosomes under conditions that preserve the natural epigenetic signature. The material is composed almost exclusively of histones and DNA and conforms to the structure expected by electron microscopy. All sequences probed for were retained, indicating that the material is representative of the majority of the genome. DNA methylation marks and histone marks resembled the patterns observed in vivo. Importantly, nucleosome positions also remained largely unchanged, except on CpG islands, where nucleosomes were found to be unstable. The technical challenges of reconstituting biochemical reactions with native mammalian chromatin are discussed.

  19. Chromatin remodelling: the industrial revolution of DNA around histones.

    Science.gov (United States)

    Saha, Anjanabha; Wittmeyer, Jacqueline; Cairns, Bradley R

    2006-06-01

    Chromatin remodellers are specialized multi-protein machines that enable access to nucleosomal DNA by altering the structure, composition and positioning of nucleosomes. All remodellers have a catalytic ATPase subunit that is similar to known DNA-translocating motor proteins, suggesting DNA translocation as a unifying aspect of their mechanism. Here, we explore the diversity and specialization of chromatin remodellers, discuss how nucleosome modifications regulate remodeller activity and consider a model for the exposure of nucleosomal DNA that involves the use of directional DNA translocation to pump 'DNA waves' around the nucleosome.

  20. Topological insulators fundamentals and perspectives

    CERN Document Server

    Ortmann, Frank; Valenzuela, Sergio O

    2015-01-01

    There are only few discoveries and new technologies in physical sciences that have the potential to dramatically alter and revolutionize our electronic world. Topological insulators are one of them. The present book for the first time provides a full overview and in-depth knowledge about this hot topic in materials science and condensed matter physics. Techniques such as angle-resolved photoemission spectrometry (ARPES), advanced solid-state Nuclear Magnetic Resonance (NMR) or scanning-tunnel microscopy (STM) together with key principles of topological insulators such as spin-locked electronic

  1. Electric fields and electrical insulation

    DEFF Research Database (Denmark)

    McAllister, Iain Wilson

    2002-01-01

    The adoption of a field-theoretical approach to problems arising in the framework of electrical insulation is discussed with reference to six main topics, which have been addressed over the last 30 years. These include uniform field electrodes, Green's differential equation, electrode surface...... roughness, induced charge, electrostatic probes, and partial discharge transients, together with several follow-on aspects. Each topic is introduced and thereafter the progress achieved through the use of a field-theoretical approach is reviewed. Because the topics cover a wide spectrum of conditions......, it is amply demonstrated that such an approach can lead to significant progress in many areas of electrical insulation....

  2. Do chromatin changes around a nascent double strand DNA break spread spherically into linearly non-adjacent chromatin?

    Science.gov (United States)

    Savic, Velibor

    2013-01-01

    In the last decade, a lot has been done in elucidating the sequence of events that occur at the nascent double strand DNA break. Nevertheless, the overall structure formed by the DNA damage response (DDR) factors around the break site, the repair focus, remains poorly understood. Although most of the data presented so far only address events that occur in chromatin in cis around the break, there are strong indications that in mammalian systems it may also occur in trans, analogous to the recent findings showing this if budding yeast. There have been attempts to address the issue but the final proof is still missing due to lack of a proper experimental system. If found to be true, the spatial distribution of DDR factors would have a major impact on the neighboring chromatin both in cis and in trans, significantly affecting local chromatin function; gene transcription and potentially other functions.

  3. Propagation Characteristics of Multilayer Hybrid Insulator-Metal-Insulator and Metal-Insulator-Metal Plasmonic Waveguides

    Directory of Open Access Journals (Sweden)

    M. Talafi Noghani

    2014-02-01

    Full Text Available Propagation characteristics of symmetrical and asymmetrical multilayer hybrid insulator-metal-insulator (HIMI and metal-insulator-metal (HMIM plasmonic slab waveguides are investigated using the transfer matrix method. Propagation length (Lp and spatial length (Ls are used as two figures of merit to qualitate the plasmonic waveguides. Symmetrical structures are shown to be more performant (having higher Lp and lower Ls, nevertheless it is shown that usage of asymmetrical geometry could compensate for the performance degradation in practically realized HIMI waveguides with different substrate materials. It is found that HMIM slab waveguide could support almost long-range subdiffraction plasmonic modes at dimensions lower than the spatial length of the HIMI slab waveguide.

  4. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin

    2015-01-01

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  5. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  6. Status of epigenetic chromatin modification enzymes and esophageal squamous cell carcinoma risk in northeast Indian population.

    Science.gov (United States)

    Singh, Virendra; Singh, Laishram C; Singh, Avninder P; Sharma, Jagannath; Borthakur, Bibhuti B; Debnath, Arundhati; Rai, Avdhesh K; Phukan, Rup K; Mahanta, Jagadish; Kataki, Amal C; Kapur, Sujala; Saxena, Sunita

    2015-01-01

    Esophageal cancer incidence is reported in high frequency in northeast India. The etiology is different from other population at India due to wide variations in dietary habits or nutritional factors, tobacco/betel quid chewing and alcohol habits. Since DNA methylation, histone modification and miRNA-mediated epigenetic processes alter the gene expression, the involvement of these processes might be useful to find out epigenetic markers of esophageal cancer risk in northeast Indian population. The present investigation was aimed to carryout differential expression profiling of chromatin modification enzymes in tumor and normal tissue collected from esophageal squamous cell carcinoma (ESCC) patients. Differential mRNA expression profiling and their validation was done by quantitative real time PCR and tissue microarray respectively. Univariate and multiple logistic regression analysis were used to analyze the epidemiological data. mRNA expression data was analyzed by Student t-test. Fisher exact test was used for tissue microarray data analysis. Higher expression of enzymes regulating methylation (DOT1L and PRMT1) and acetylation (KAT7, KAT8, KAT2A and KAT6A) of histone was found associated with ESCC risk. Tissue microarray done in independent cohort of 75 patients revealed higher nuclear protein expression of KAT8 and PRMT1 in tumor similar to mRNA expression. Expression status of PRMT1 and KAT8 was found declined as we move from low grade to high grade tumor. Betel nut chewing, alcohol drinking and dried fish intake were significantly associated with increased risk of esophageal cancer among the study subject. Study suggests the association of PRMT1 and KAT8 with esophageal cancer risk and its involvement in the transition process of low to high grade tumor formation. The study exposes the differential status of chromatin modification enzymes between tumor and normal tissue and points out that relaxed state of chromatin facilitates more transcriptionally active

  7. Electrical insulation for large multiaxis superconducting magnets

    International Nuclear Information System (INIS)

    Harvey, A.R.; Rinde, J.A.

    1975-01-01

    The selection of interturn and interlayer insulation for superconducting magnets is discussed. The magnet problems of the Baseball II device are described. Manufacture of the insulation and radiation damage are mentioned. A planned experimental program is outlined

  8. Emerging Trends in Topological Insulators and Topological ...

    Indian Academy of Sciences (India)

    /fulltext/reso/022/08/0787-0800. Keywords. Superconductor, quantum Hall effect, topological insulator, Majorana fermions. Abstract. Topological insulators are new class of materials which arecharacterized by a bulk band gap like ordinary ...

  9. Igf2/H19 Imprinting Control Region (ICR: An Insulator or a Position-Dependent Silencer?

    Directory of Open Access Journals (Sweden)

    Subhasis Banerjee

    2001-01-01

    Full Text Available The imprinting control region (ICR located far upstream of the H19 gene, in conjunction with enhancers, modulates the transcription of Igf2 and H19 genes in an allele-specific manner. On paternal inheritance, the methylated ICR silences the H19 gene and indirectly facilitates transcription from the distant Igf2 promoter, whereas on the maternal chromosome the unmethylated ICR, together with enhancers, activates transcription of the H19 gene and thereby contributes to the repression of Igf2. This repression of maternal Igf2 has recently been postulated to be due to a chromatin boundary or insulator function of the unmethylated ICR. Central to the insulator model is the site-specific binding of a ubiquitous nuclear factor CTCF which exhibits remarkable flexibility in functioning as transcriptional activator or silencer. We suggest that the ICR positioned close to the enhancers in an episomal context might function as a transcriptional silencer by virtue of interaction of CTCF with its modifiers such as SIN3A and histone deacetylases. Furthermore, a localised folded chromatin structure resulting from juxtaposition of two disparate regulatory sequences (enhancer ICR could be the mechanistic basis of ICR-mediated position-dependent (ICR-promoter transcriptional repression in transgenic Drosophila.

  10. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-01-01

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome

  11. Testing Whether Defective Chromatin Assembly in S-Phase Contributes to Breast Cancer

    National Research Council Canada - National Science Library

    Adams, Peter

    2003-01-01

    .... We used a dominant negative mutant of (chromatin assembly factor-I) CAF1, a complex that assembles newly synthesized DNA into nucleosomes, to inhibit S-phase chromatin assembly and found that this induced S-phase arrest...

  12. Testing Whether Defective Chromatin Assembly in S-Phase Contributes to Breast Cancer

    National Research Council Canada - National Science Library

    Adams, Peter

    2004-01-01

    .... We used a dominant negative mutant of (chromatin assembly factor-I) CAF1, a complex that assembles newly synthesized DNA into nucleosomes, to inhibit S-phase chromatin assembly and found that this induced S-phase arrest...

  13. Relationship between chromatin structure and sensitivity to molecularly targeted auger electron radiation therapy.

    NARCIS (Netherlands)

    Terry, S.Y.A.; Vallis, K.A.

    2012-01-01

    PURPOSE: The open structure of euchromatin renders it susceptible to DNA damage by ionizing radiation (IR) compared with compact heterochromatin. The effect of chromatin configuration on the efficacy of Auger electron radiotherapy was investigated. METHODS AND MATERIALS: Chromatin structure was

  14. Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells.

    Science.gov (United States)

    Delvaux, Elaine; Mastroeni, Diego; Nolz, Jennifer; Coleman, Paul D

    2016-06-01

    We describe a novel method for assessing the "open" or "closed" state of chromatin at selected locations within the genome. This method combines the use of Benzonase, which can digest DNA in the presence of actin, with qPCR to define digested regions. We demonstrate the application of this method in brain homogenates and laser captured cells. We also demonstrate application to selected sites within more than one gene and multiple sites within one gene. We demonstrate the validity of the method by treating cells with valproate, known to render chromatin more permissive, and by comparison with classical digestion with DNase I in an in vitro preparation. Although we demonstrate the use of this method in brain tissue we also recognize its applicability to other tissue types.

  15. Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells

    Directory of Open Access Journals (Sweden)

    Elaine Delvaux

    2016-06-01

    Full Text Available We describe a novel method for assessing the “open” or “closed” state of chromatin at selected locations within the genome. This method combines the use of Benzonase, which can digest DNA in the presence of actin, with quantitative polymerase chain reaction to define digested regions. We demonstrate the application of this method in brain homogenates and laser captured cells. We also demonstrate application to selected sites within more than 1 gene and multiple sites within 1 gene. We demonstrate the validity of the method by treating cells with valproate, known to render chromatin more permissive, and by comparison with classical digestion with DNase I in an in vitro preparation. Although we demonstrate the use of this method in brain tissue, we also recognize its applicability to other tissue types.

  16. Vacuum-insulated catalytic converter

    Science.gov (United States)

    Benson, David K.

    2001-01-01

    A catalytic converter has an inner canister that contains catalyst-coated substrates and an outer canister that encloses an annular, variable vacuum insulation chamber surrounding the inner canister. An annular tank containing phase-change material for heat storage and release is positioned in the variable vacuum insulation chamber a distance spaced part from the inner canister. A reversible hydrogen getter in the variable vacuum insulation chamber, preferably on a surface of the heat storage tank, releases hydrogen into the variable vacuum insulation chamber to conduct heat when the phase-change material is hot and absorbs the hydrogen to limit heat transfer to radiation when the phase-change material is cool. A porous zeolite trap in the inner canister absorbs and retains hydrocarbons from the exhaust gases when the catalyst-coated substrates and zeolite trap are cold and releases the hydrocarbons for reaction on the catalyst-coated substrate when the zeolite trap and catalyst-coated substrate get hot.

  17. On effective holographic Mott insulators

    Energy Technology Data Exchange (ETDEWEB)

    Baggioli, Matteo; Pujolàs, Oriol [Institut de Física d’Altes Energies (IFAE), Universitat Autònoma de Barcelona,The Barcelona Institute of Science and Technology,Campus UAB, 08193 Bellaterra (Barcelona) (Spain)

    2016-12-20

    We present a class of holographic models that behave effectively as prototypes of Mott insulators — materials where electron-electron interactions dominate transport phenomena. The main ingredient in the gravity dual is that the gauge-field dynamics contains self-interactions by way of a particular type of non-linear electrodynamics. The electrical response in these models exhibits typical features of Mott-like states: i) the low-temperature DC conductivity is unboundedly low; ii) metal-insulator transitions appear by varying various parameters; iii) for large enough self-interaction strength, the conductivity can even decrease with increasing doping (density of carriers) — which appears as a sharp manifestation of ‘traffic-jam’-like behaviour; iv) the insulating state becomes very unstable towards superconductivity at large enough doping. We exhibit some of the properties of the resulting insulator-superconductor transition, which is sensitive to the momentum dissipation rate in a specific way. These models imply a clear and generic correlation between Mott behaviour and significant effects in the nonlinear electrical response. We compute the nonlinear current-voltage curve in our model and find that indeed at large voltage the conductivity is largely reduced.

  18. Improved DC Gun Insulator Assembly

    International Nuclear Information System (INIS)

    Neubauer, M.L.; Dudas, A.; Sah, R.; Poelker, M.; Surles-Law, K.E.L.

    2010-01-01

    Many user facilities such as synchrotron radiation light sources and free electron lasers require accelerating structures that support electric fields of 10-100 MV/m, especially at the start of the accelerator chain where ceramic insulators are used for very high gradient DC guns. These insulators are difficult to manufacture, require long commissioning times, and often exhibit poor reliability. Two technical approaches to solving this problem will be investigated. Firstly, inverted ceramics offer solutions for reduced gradients between the electrodes and ground. An inverted design will be presented for 350 kV, with maximum gradients in the range of 5-10 MV/m. Secondly, novel ceramic manufacturing processes will be studied, in order to protect triple junction locations from emission, by applying a coating with a bulk resistivity. The processes for creating this coating will be optimized to provide protection as well as be used to coat a ceramic with an appropriate gradient in bulk resistivity from the vacuum side to the air side of an HV standoff ceramic cylinder. Example insulator designs are being computer modelled, and insulator samples are being manufactured and tested

  19. On effective holographic Mott insulators

    International Nuclear Information System (INIS)

    Baggioli, Matteo; Pujolàs, Oriol

    2016-01-01

    We present a class of holographic models that behave effectively as prototypes of Mott insulators — materials where electron-electron interactions dominate transport phenomena. The main ingredient in the gravity dual is that the gauge-field dynamics contains self-interactions by way of a particular type of non-linear electrodynamics. The electrical response in these models exhibits typical features of Mott-like states: i) the low-temperature DC conductivity is unboundedly low; ii) metal-insulator transitions appear by varying various parameters; iii) for large enough self-interaction strength, the conductivity can even decrease with increasing doping (density of carriers) — which appears as a sharp manifestation of ‘traffic-jam’-like behaviour; iv) the insulating state becomes very unstable towards superconductivity at large enough doping. We exhibit some of the properties of the resulting insulator-superconductor transition, which is sensitive to the momentum dissipation rate in a specific way. These models imply a clear and generic correlation between Mott behaviour and significant effects in the nonlinear electrical response. We compute the nonlinear current-voltage curve in our model and find that indeed at large voltage the conductivity is largely reduced.

  20. Thermal insulation of fuel elements

    International Nuclear Information System (INIS)

    Dubrovcak, P.; Pec, V.; Pitonak, J.

    1978-01-01

    The claim of the invention concerns thermal insulation of fuel elements heated for measurement of uranium fuel physical properties. For this, layers of aluminium film and of glass fibre are wound onto the inner tube of the element cladding. The space between the inner and the outer tubes is evacuated and the tubes are spaced using spacer wires. (M.S.)

  1. Forming Refractory Insulation On Copper Wire

    Science.gov (United States)

    Setlock, J.; Roberts, G.

    1995-01-01

    Alternative insulating process forms flexible coat of uncured refractory insulating material on copper wire. Coated wire formed into coil or other complex shape. Wire-coating apparatus forms "green" coat on copper wire. After wire coiled, heating converts "green" coat to refractory electrical insulator. When cured to final brittle form, insulating material withstands temperatures above melting temperature of wire. Process used to make coils for motors, solenoids, and other electrical devices to be operated at high temperatures.

  2. Optimization design for SST-1 Tokamak insulators

    International Nuclear Information System (INIS)

    Zhang Yuanbin; Pan Wanjiang

    2012-01-01

    With the help of ANSYS FEA technique, high voltage and cryogenic proper- ties of the SST-1 Tokamak insulators were obtained, and the structure of the insulators was designed and modified by taking into account the simulation results. The simulation results indicate that the optimization structure has better high voltage insulating property and cryogenic mechanics property, and also can fulfill the qualification criteria of the SST-1 Tokamak insulators. (authors)

  3. Chromatin-bound MDM2, a new player in metabolism.

    Science.gov (United States)

    Riscal, Romain; Le Cam, Laurent; Linares, Laetitia K

    2016-01-01

    The oncoprotein MDM2 is recognized as a major negative regulator of the p53 tumor suppressor but growing evidence indicates that its oncogenic activities extend beyond p53. We show that MDM2 is recruited to chromatin independently of p53 to regulate a transcriptional program implicated in amino acid metabolism and redox homeostasis.

  4. Chromatin-bound RNA and the neurobiology of psychiatric disease.

    Science.gov (United States)

    Tushir, J S; Akbarian, S

    2014-04-04

    A large, and still rapidly expanding literature on epigenetic regulation in the nervous system has provided fundamental insights into the dynamic regulation of DNA methylation and post-translational histone modifications in the context of neuronal plasticity in health and disease. Remarkably, however, very little is known about the potential role of chromatin-bound RNAs, including many long non-coding transcripts and various types of small RNAs. Here, we provide an overview on RNA-mediated regulation of chromatin structure and function, with focus on histone lysine methylation and psychiatric disease. Examples of recently discovered chromatin-bound long non-coding RNAs important for neuronal health and function include the brain-derived neurotrophic factor antisense transcript (Bdnf-AS) which regulates expression of the corresponding sense transcript, and LOC389023 which is associated with human-specific histone methylation signatures at the chromosome 2q14.1 neurodevelopmental risk locus by regulating expression of DPP10, an auxillary subunit for voltage-gated K(+) channels. We predict that the exploration of chromatin-bound RNA will significantly advance our current knowledge base in neuroepigenetics and biological psychiatry. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  5. Interaction of maize chromatin-associated HMG proteins with mononucleosomes

    DEFF Research Database (Denmark)

    Lichota, J.; Grasser, Klaus D.

    2003-01-01

    maize HMGA and five different HMGB proteins with mononucleosomes (containing approx. 165 bp of DNA) purified from micrococcal nuclease-digested maize chromatin. The HMGB proteins interacted with the nucleosomes independent of the presence of the linker histone H1, while the binding of HMGA...

  6. Role of chromatin factors in Arabidopsis root stem cell maintenance

    NARCIS (Netherlands)

    Kornet, N.G.

    2008-01-01

    Stem cells replenish the cells present in an organism throughout its lifetime and sustain growth. They have unique characteristics: the capability to self-renew and the potential to differentiate into several cell types. Recently, it has become clear that chromatin factors support these unique

  7. Control of trichome branching by Chromatin Assembly Factor-1

    Directory of Open Access Journals (Sweden)

    Hennig Lars

    2008-05-01

    Full Text Available Abstract Background Chromatin dynamics and stability are both required to control normal development of multicellular organisms. Chromatin assembly factor CAF-1 is a histone chaperone that facilitates chromatin formation and the maintenance of specific chromatin states. In plants and animals CAF-1 is essential for normal development, but it is poorly understood which developmental pathways require CAF-1 function. Results Mutations in all three CAF-1 subunits affect Arabidopsis trichome morphology and lack of CAF-1 function results in formation of trichomes with supernumerary branches. This phenotype can be partially alleviated by external sucrose. In contrast, other aspects of the CAF-1 mutant phenotype, such as defective meristem function and organ formation, are aggravated by external sucrose. Double mutant analyses revealed epistatic interactions between CAF-1 mutants and stichel, but non-epistatic interactions between CAF-1 mutants and glabra3 and kaktus. In addition, mutations in CAF-1 could partly suppress the strong overbranching and polyploidization phenotype of kaktus mutants. Conclusion CAF-1 is required for cell differentiation and regulates trichome development together with STICHEL in an endoreduplication-independent pathway. This function of CAF-1 can be partially substituted by application of exogenous sucrose. Finally, CAF-1 is also needed for the high degree of endoreduplication in kaktus mutants and thus for the realization of kaktus' extreme overbranching phenotype.

  8. Trichostatin A induced histone acetylation causes decondensation of interphase chromatin.

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Wachsmuth (Malte); M. Frank-Stöhr (Monika); M. Stöhr (Michael); C.P. Bacher (Christian); K. Rippe (Karsten)

    2004-01-01

    textabstractThe effect of trichostatin A (TSA)-induced histone acetylation on the interphase chromatin structure was visualized in vivo with a HeLa cell line stably expressing histone H2A, which was fused to enhanced yellow fluorescent protein. The globally increased histone acetylation caused a

  9. Epigenetic regulation and chromatin remodeling in learning and memory.

    Science.gov (United States)

    Kim, Somi; Kaang, Bong-Kiun

    2017-01-13

    Understanding the underlying mechanisms of memory formation and maintenance has been a major goal in the field of neuroscience. Memory formation and maintenance are tightly controlled complex processes. Among the various processes occurring at different levels, gene expression regulation is especially crucial for proper memory processing, as some genes need to be activated while some genes must be suppressed. Epigenetic regulation of the genome involves processes such as DNA methylation and histone post-translational modifications. These processes edit genomic properties or the interactions between the genome and histone cores. They then induce structural changes in the chromatin and lead to transcriptional changes of different genes. Recent studies have focused on the concept of chromatin remodeling, which consists of 3D structural changes in chromatin in relation to gene regulation, and is an important process in learning and memory. In this review, we will introduce three major epigenetic processes involved in memory regulation: DNA methylation, histone methylation and histone acetylation. We will also discuss general mechanisms of long-term memory storage and relate the epigenetic control of learning and memory to chromatin remodeling. Finally, we will discuss how epigenetic mechanisms can contribute to the pathologies of neurological disorders and cause memory-related symptoms.

  10. Effect of triiodothyronine on rat liver chromatin protein kinase

    International Nuclear Information System (INIS)

    Kruh, J.; Tichonicky, L.

    1976-01-01

    1) Injection of triiodothyronine to rats stimulates protein kinase activity in liver chromatin nonhistone proteins. A significant increase was found after two daily injections. A 4-fold increase was observed with the purified enzyme after eight daily injections of the hormone. No variations were observed in cytosol protein kinase activity. Electrophoretic pattern, effect of heat denaturation, effect of p-hydroxymercuribenzoate seem to indicate that the enzyme present in treated rats is not identical to the enzyme in control animals, which suggests that thyroid hormone has induced nuclear protein kinase. Diiodothyronine, 3, 3', 5'-triiodothyronine have no effect on protein kinase. 2) Chromatin non-histone proteins isolated from rats injected with triiodothyronine incorporated more 32 P when incubated with [γ- 32 P]ATP than the chromatin proteins from untreated rats. Thyroidectomy reduced the in vitro 32 P incorporation. It is suggested that some of the biological activity of thyroid hormone could be mediated through its effect on chromatin non-histone proteins. (orig.) [de

  11. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-01-01

    to a particular chromatin state. Of four classification algorithms (C4.5, Naive Bayes, Random Forest, and SVM) used for this purpose, the decision tree based classifiers (C4.5 and Random Forest) yielded best results among those we evaluated. Our results

  12. Chromatin-regulating proteins as targets for cancer therapy

    International Nuclear Information System (INIS)

    Oike, Takahiro; Ogiwara, Hideaki; Kohno, Takashi; Amornwichet, Napapat; Nakano, Takashi

    2014-01-01

    Chromatin-regulating proteins represent a large class of novel targets for cancer therapy. In the context of radiotherapy, acetylation and deacetylation of histones by histone acetyltransferases (HATs) and histone deacetylases (HDACs) play important roles in the repair of DNA double-strand breaks generated by ionizing irradiation, and are therefore attractive targets for radiosensitization. Small-molecule inhibitors of HATs (garcinol, anacardic acid and curcumin) and HDACs (vorinostat, sodium butyrate and valproic acid) have been shown to sensitize cancer cells to ionizing irradiation in preclinical models, and some of these molecules are being tested in clinical trials, either alone or in combination with radiotherapy. Meanwhile, recent large-scale genome analyses have identified frequent mutations in genes encoding chromatin-regulating proteins, especially in those encoding subunits of the SWI/SNF chromatin-remodeling complex, in various human cancers. These observations have driven researchers toward development of targeted therapies against cancers carrying these mutations. DOT1L inhibition in MLL-rearranged leukemia, EZH2 inhibition in EZH2-mutant or MLL-rearranged hematologic malignancies and SNF5-deficient tumors, BRD4 inhibition in various hematologic malignancies, and BRM inhibition in BRG1-deficient tumors have demonstrated promising anti-tumor effects in preclinical models, and these strategies are currently awaiting clinical application. Overall, the data collected so far suggest that targeting chromatin-regulating proteins is a promising strategy for tomorrow's cancer therapy, including radiotherapy and molecularly targeted chemotherapy. (author)

  13. Connecting the dots: chromatin and alternative splicing in EMT.

    Science.gov (United States)

    Warns, Jessica A; Davie, James R; Dhasarathy, Archana

    2016-02-01

    Nature has devised sophisticated cellular machinery to process mRNA transcripts produced by RNA Polymerase II, removing intronic regions and connecting exons together, to produce mature RNAs. This process, known as splicing, is very closely linked to transcription. Alternative splicing, or the ability to produce different combinations of exons that are spliced together from the same genomic template, is a fundamental means of regulating protein complexity. Similar to transcription, both constitutive and alternative splicing can be regulated by chromatin and its associated factors in response to various signal transduction pathways activated by external stimuli. This regulation can vary between different cell types, and interference with these pathways can lead to changes in splicing, often resulting in aberrant cellular states and disease. The epithelial to mesenchymal transition (EMT), which leads to cancer metastasis, is influenced by alternative splicing events of chromatin remodelers and epigenetic factors such as DNA methylation and non-coding RNAs. In this review, we will discuss the role of epigenetic factors including chromatin, chromatin remodelers, DNA methyltransferases, and microRNAs in the context of alternative splicing, and discuss their potential involvement in alternative splicing during the EMT process.

  14. Modulation of the Chromatin Phosphoproteome by the Haspin Protein Kinase

    DEFF Research Database (Denmark)

    Maiolica, Alessio; de Medina-Redondo, Maria; Schoof, Erwin

    2014-01-01

    , histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin- associated proteins and identified a Haspin...

  15. Chromatin Structure in Cell Differentiation, Aging and Cancer

    NARCIS (Netherlands)

    S. Kheradmand Kia (Sima)

    2009-01-01

    textabstractChromatin is the structure that the eukaryotic genome is packaged into, allowing over a metre of DNA to fit into the small volume of the nucleus. It is composed of DNA and proteins, most of which are histones. This DNA-protein complex is the template for a number of essential cell

  16. The Structural Heat Intercept-Insulation-Vibration Evaluation Rig (SHIVER)

    Science.gov (United States)

    Johnson, W. L.; Zoeckler, J. G.; Best-Ameen, L. M.

    2015-01-01

    NASA is currently investigating methods to reduce the boil-off rate on large cryogenic upper stages. Two such methods to reduce the total heat load on existing upper stages are vapor cooling of the cryogenic tank support structure and integration of thick multilayer insulation systems to the upper stage of a launch vehicle. Previous efforts have flown a 2-layer MLI blanket and shown an improved thermal performance, and other efforts have ground-tested blankets up to 70 layers thick on tanks with diameters between 2 3 meters. However, thick multilayer insulation installation and testing in both thermal and structural modes has not been completed on a large scale tank. Similarly, multiple vapor cooled shields are common place on science payload helium dewars; however, minimal effort has gone into intercepting heat on large structural surfaces associated with rocket stages. A majority of the vapor cooling effort focuses on metallic cylinders called skirts, which are the most common structural components for launch vehicles. In order to provide test data for comparison with analytical models, a representative test tank is currently being designed to include skirt structural systems with integral vapor cooling. The tank is 4 m in diameter and 6.8 m tall to contain 5000 kg of liquid hydrogen. A multilayer insulation system will be designed to insulate the tank and structure while being installed in a representative manner that can be extended to tanks up to 10 meters in diameter. In order to prove that the insulation system and vapor cooling attachment methods are structurally sound, acoustic testing will also be performed on the system. The test tank with insulation and vapor cooled shield installed will be tested thermally in the B2 test facility at NASAs Plumbrook Station both before and after being vibration tested at Plumbrooks Space Power Facility.

  17. Polyimide Foams Offer Superior Insulation

    Science.gov (United States)

    2012-01-01

    At Langley Research Center, Erik Weiser and his colleagues in the Advanced Materials and Processing Branch were working with a new substance for fabricating composites for use in supersonic aircraft. The team, however, was experiencing some frustration. Every time they tried to create a solid composite from the polyimide (an advanced polymer) material, it bubbled and foamed. It seemed like the team had reached a dead end in their research - until they had another idea. "We said, This isn t going to work for composites, but maybe we could make a foam out of it," Weiser says. "That was kind of our eureka moment, to see if we could go in a whole other direction. And it worked." Weiser and his colleagues invented a new kind of polyimide foam insulation they named TEEK. The innovation displayed a host of advantages over existing insulation options. Compared to other commercial foams, Weiser explains, polyimide foams perform well across a broad range of temperatures, noting that the NASA TEEK foams provide effective structural insulation up to 600 F and down to cryogenic temperatures. The foam does not burn or off-gas toxic fumes, and even at -423 F - the temperature of liquid hydrogen - the material stays flexible. The inventors could produce the TEEK foam at a range of densities, from 0.5 pounds per cubic foot up to 20 pounds per cubic foot, making the foam ideal for a range of applications, including as insulation for reusable launch vehicles and for cryogenic tanks and lines. They also developed a unique, friable balloon format for manufacturing the foam, producing it as hollow microspheres that allowed the foam to be molded and then cured into any desired shape - perfect for insulating pipes of different sizes and configurations. The team s originally unplanned invention won an "R&D 100" award, and a later form of the foam, called LaRC FPF-44 (Spinoff 2009), was named "NASA Invention of the Year" in 2007.

  18. Insulator applications in a Tokamak reactor

    International Nuclear Information System (INIS)

    Leger, D.

    1986-06-01

    Insulators, among which insulators ceramics, have great potential applications in fusion reactors. They will be used for all plasma-facing components as protection and, magnetic fusion devices being subject to large electrical currents flowing in any parts of the device, for their electrical insulating properties

  19. The experiment study of the thermal insulation of the roof-slab of the main vessel of a LMFBR

    International Nuclear Information System (INIS)

    Wang Zhifeng; Wang Zhou; Yang Xianyong

    1995-01-01

    The effects of composition of insulation, i.e., reflective multi-plate thermal insulator, protecting the roof-slab of the vessel of the LMFBR on the heat transfer performance has been studied experimentally for CEFR. A economical form of the thermal insulation is suggested for CEFR. In addition, the scheme without reflective thermal insulator which has only a forced convection cooling system has been studied experimentally and a formula to calculate the average Nusselt number of the flow channel, which is valuable for CEFR design, has been raised

  20. The Chromatin Regulator Brpf1 Regulates Embryo Development and Cell Proliferation*

    Science.gov (United States)

    You, Linya; Yan, Kezhi; Zou, Jinfeng; Zhao, Hong; Bertos, Nicholas R.; Park, Morag; Wang, Edwin; Yang, Xiang-Jiao

    2015-01-01

    With hundreds of chromatin regulators identified in mammals, an emerging issue is how they modulate biological and pathological processes. BRPF1 (bromodomain- and PHD finger-containing protein 1) is a unique chromatin regulator possessing two PHD fingers, one bromodomain and a PWWP domain for recognizing multiple histone modifications. In addition, it binds to the acetyltransferases MOZ, MORF, and HBO1 (also known as KAT6A, KAT6B, and KAT7, respectively) to promote complex formation, restrict substrate specificity, and enhance enzymatic activity. We have recently showed that ablation of the mouse Brpf1 gene causes embryonic lethality at E9.5. Here we present systematic analyses of the mutant animals and demonstrate that the ablation leads to vascular defects in the placenta, yolk sac, and embryo proper, as well as abnormal neural tube closure. At the cellular level, Brpf1 loss inhibits proliferation of embryonic fibroblasts and hematopoietic progenitors. Molecularly, the loss reduces transcription of a ribosomal protein L10 (Rpl10)-like gene and the cell cycle inhibitor p27, and increases expression of the cell-cycle inhibitor p16 and a novel protein homologous to Scp3, a synaptonemal complex protein critical for chromosome association and embryo survival. These results uncover a crucial role of Brpf1 in controlling mouse embryo development and regulating cellular and gene expression programs. PMID:25773539

  1. Phospho switch triggers Brd4 chromatin binding and activator recruitment for gene-specific targeting.

    Science.gov (United States)

    Wu, Shwu-Yuan; Lee, A-Young; Lai, Hsien-Tsung; Zhang, Hong; Chiang, Cheng-Ming

    2013-03-07

    Bromodomain-containing protein 4 (Brd4) is an epigenetic reader and transcriptional regulator recently identified as a cancer therapeutic target for acute myeloid leukemia, multiple myeloma, and Burkitt's lymphoma. Although chromatin targeting is a crucial function of Brd4, there is little understanding of how bromodomains that bind acetylated histones are regulated, nor how the gene-specific activity of Brd4 is determined. Via interaction screen and domain mapping, we identified p53 as a functional partner of Brd4. Interestingly, Brd4 association with p53 is modulated by casein kinase II (CK2)-mediated phosphorylation of a conserved acidic region in Brd4 that selectively contacts either a juxtaposed bromodomain or an adjacent basic region to dictate the ability of Brd4 binding to chromatin and also the recruitment of p53 to regulated promoters. The unmasking of bromodomains and activator recruitment, concurrently triggered by the CK2 phospho switch, provide an intriguing mechanism for gene-specific targeting by a universal epigenetic reader. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Dielectric and Insulating Technology 2005 : Reviews & Forecasts

    Science.gov (United States)

    Okamoto, Tatsuki

    This article reports the state-of-art of TC-DEI ( Technical Committee of Dielectrics and Electrical Insulation of IEEJ) activites. The activiteis are basically based on the activites of 8-10 investigation committees under TC-DEI. Recent activites were categorized into three functions in this article and remarkable activity or trend for each category is mentioned as was done in the article of 2003. Thoese are activities on asset management (AI application and insulation diagnosis), activities on new insulating and functional materials (Nano composite) and activities on new insulation technology for power tansmission (high Tc superconducting cable insulation).

  3. Dielectric and Insulating Technology 2006 : Review & Forecast

    Science.gov (United States)

    Okamoto, Tatsuki

    This article reports the state-of-art of TC-DEI ( Technical Committee of Dielectrics and Electrical Insulation of IEEJ) activites. The activiteis are basically based on the activites of 8-10 investigation committees under TC-DEI. Recent activites were categorized into three functions in this article and remarkable activity or trend for each category is mentioned as was seen in the articles of 2005. Those are activities on asset management (AI application and insulation diagnosis), activities on new insulating and functional materials (Nano composite) and activities on new insulation technology for power tansmission (high Tc superconducting cable insulation).

  4. CTCF Binding Sites in the Herpes Simplex Virus 1 Genome Display Site-Specific CTCF Occupation, Protein Recruitment, and Insulator Function.

    Science.gov (United States)

    Washington, Shannan D; Musarrat, Farhana; Ertel, Monica K; Backes, Gregory L; Neumann, Donna M

    2018-04-15

    There are seven conserved CTCF binding domains in the herpes simplex virus 1 (HSV-1) genome. These binding sites individually flank the latency-associated transcript (LAT) and the immediate early (IE) gene regions, suggesting that CTCF insulators differentially control transcriptional domains in HSV-1 latency. In this work, we show that two CTCF binding motifs in HSV-1 display enhancer blocking in a cell-type-specific manner. We found that CTCF binding to the latent HSV-1 genome was LAT dependent and that the quantity of bound CTCF was site specific. Following reactivation, CTCF eviction was dynamic, suggesting that each CTCF site was independently regulated. We explored whether CTCF sites recruit the polycomb-repressive complex 2 (PRC2) to establish repressive domains through a CTCF-Suz12 interaction and found that Suz12 colocalized to the CTCF insulators flanking the ICP0 and ICP4 regions and, conversely, was removed at early times postreactivation. Collectively, these data support the idea that CTCF sites in HSV-1 are independently regulated and may contribute to lytic-latent HSV-1 control in a site-specific manner. IMPORTANCE The role of chromatin insulators in DNA viruses is an area of interest. It has been shown in several beta- and gammaherpesviruses that insulators likely control the lytic transcriptional profile through protein recruitment and through the formation of three-dimensional (3D) chromatin loops. The ability of insulators to regulate alphaherpesviruses has been understudied to date. The alphaherpesvirus HSV-1 has seven conserved insulator binding motifs that flank regions of the genome known to contribute to the establishment of latency. Our work presented here contributes to the understanding of how insulators control transcription of HSV-1. Copyright © 2018 American Society for Microbiology.

  5. Impact Verification of Aerogel Insulation Paint on Historic Brick Facades

    Science.gov (United States)

    Ganobjak, Michal; Kralova, Eva

    2017-10-01

    application, which, on the other hand may be unacceptable on the heritage conservation because of number of applications, time demand and financial costs. The effects of multiple layers on heritage attributes were not researched. Extrapolating the measured results, it can be expected that application of more than three layers of paint can significantly affect the aesthetic characteristics of the monument such as gloss and colours of historic brick facades. Due to specific material consistence of historic architecture and new insulation paint materials on the market, it is recommended to provide independent laboratory testing and on-site tests on facades of historic buildings in cooperation with the Monument Protection Board.

  6. Development of advanced materials composites for use as insulations for LH2 tanks

    Science.gov (United States)

    Lemons, C. R.; Salmassy, O. K.

    1973-01-01

    A study of thread-reinforced polyurethane foam and glass fabric liner, serving as internally bonded insulation for space shuttle LH2 tanks, is reported. Emphasis was placed on an insulation system capable of reentry and multiple reuse in the shuttle environment. The optimized manufacturing parameters associated with each element of the composite are established and the results, showing successful completion of subscale system evaluation tests using the shuttle flight environmental requirements, are given.

  7. SAP-like domain in nucleolar spindle associated protein mediates mitotic chromosome loading as well as interphase chromatin interaction

    Energy Technology Data Exchange (ETDEWEB)

    Verbakel, Werner, E-mail: werner.verbakel@chem.kuleuven.be [Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Celestijnenlaan 200G, Bus 2403, 3001 Heverlee (Belgium); Carmeliet, Geert, E-mail: geert.carmeliet@med.kuleuven.be [Laboratory of Experimental Medicine and Endocrinology, Katholieke Universiteit Leuven, Herestraat 49, Bus 902, 3000 Leuven (Belgium); Engelborghs, Yves, E-mail: yves.engelborghs@fys.kuleuven.be [Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Celestijnenlaan 200G, Bus 2403, 3001 Heverlee (Belgium)

    2011-08-12

    Highlights: {yields} The SAP-like domain in NuSAP is a functional DNA-binding domain with preference for dsDNA. {yields} This SAP-like domain is essential for chromosome loading during early mitosis. {yields} NuSAP is highly dynamic on mitotic chromatin, as evident from photobleaching experiments. {yields} The SAP-like domain also mediates NuSAP-chromatin interaction in interphase nucleoplasm. -- Abstract: Nucleolar spindle associated protein (NuSAP) is a microtubule-stabilizing protein that localizes to chromosome arms and chromosome-proximal microtubules during mitosis and to the nucleus, with enrichment in the nucleoli, during interphase. The critical function of NuSAP is underscored by the finding that its depletion in HeLa cells results in various mitotic defects. Moreover, NuSAP is found overexpressed in multiple cancers and its expression levels often correlate with the aggressiveness of cancer. Due to its localization on chromosome arms and combination of microtubule-stabilizing and DNA-binding properties, NuSAP takes a special place within the extensive group of spindle assembly factors. In this study, we identify a SAP-like domain that shows DNA binding in vitro with a preference for dsDNA. Deletion of the SAP-like domain abolishes chromosome arm binding of NuSAP during mitosis, but is not sufficient to abrogate its chromosome-proximal localization after anaphase onset. Fluorescence recovery after photobleaching experiments revealed the highly dynamic nature of this NuSAP-chromatin interaction during mitosis. In interphase cells, NuSAP also interacts with chromatin through its SAP-like domain, as evident from its enrichment on dense chromatin regions and intranuclear mobility, measured by fluorescence correlation spectroscopy. The obtained results are in agreement with a model where NuSAP dynamically stabilizes newly formed microtubules on mitotic chromosomes to enhance chromosome positioning without immobilizing these microtubules. Interphase NuSAP-chromatin

  8. SAP-like domain in nucleolar spindle associated protein mediates mitotic chromosome loading as well as interphase chromatin interaction

    International Nuclear Information System (INIS)

    Verbakel, Werner; Carmeliet, Geert; Engelborghs, Yves

    2011-01-01

    Highlights: → The SAP-like domain in NuSAP is a functional DNA-binding domain with preference for dsDNA. → This SAP-like domain is essential for chromosome loading during early mitosis. → NuSAP is highly dynamic on mitotic chromatin, as evident from photobleaching experiments. → The SAP-like domain also mediates NuSAP-chromatin interaction in interphase nucleoplasm. -- Abstract: Nucleolar spindle associated protein (NuSAP) is a microtubule-stabilizing protein that localizes to chromosome arms and chromosome-proximal microtubules during mitosis and to the nucleus, with enrichment in the nucleoli, during interphase. The critical function of NuSAP is underscored by the finding that its depletion in HeLa cells results in various mitotic defects. Moreover, NuSAP is found overexpressed in multiple cancers and its expression levels often correlate with the aggressiveness of cancer. Due to its localization on chromosome arms and combination of microtubule-stabilizing and DNA-binding properties, NuSAP takes a special place within the extensive group of spindle assembly factors. In this study, we identify a SAP-like domain that shows DNA binding in vitro with a preference for dsDNA. Deletion of the SAP-like domain abolishes chromosome arm binding of NuSAP during mitosis, but is not sufficient to abrogate its chromosome-proximal localization after anaphase onset. Fluorescence recovery after photobleaching experiments revealed the highly dynamic nature of this NuSAP-chromatin interaction during mitosis. In interphase cells, NuSAP also interacts with chromatin through its SAP-like domain, as evident from its enrichment on dense chromatin regions and intranuclear mobility, measured by fluorescence correlation spectroscopy. The obtained results are in agreement with a model where NuSAP dynamically stabilizes newly formed microtubules on mitotic chromosomes to enhance chromosome positioning without immobilizing these microtubules. Interphase NuSAP-chromatin interaction

  9. Insulated transcriptional elements enable precise design of genetic circuits.

    Science.gov (United States)

    Zong, Yeqing; Zhang, Haoqian M; Lyu, Cheng; Ji, Xiangyu; Hou, Junran; Guo, Xian; Ouyang, Qi; Lou, Chunbo

    2017-07-03

    Rational engineering of biological systems is often complicated by the complex but unwanted interactions between cellular components at multiple levels. Here we address this issue at the level of prokaryotic transcription by insulating minimal promoters and operators to prevent their interaction and enable the biophysical modeling of synthetic transcription without free parameters. This approach allows genetic circuit design with extraordinary precision and diversity, and consequently simplifies the design-build-test-learn cycle of circuit engineering to a mix-and-match workflow. As a demonstration, combinatorial promoters encoding NOT-gate functions were designed from scratch with mean errors of 96% using our insulated transcription elements. Furthermore, four-node transcriptional networks with incoherent feed-forward loops that execute stripe-forming functions were obtained without any trial-and-error work. This insulation-based engineering strategy improves the resolution of genetic circuit technology and provides a simple approach for designing genetic circuits for systems and synthetic biology.Unwanted interactions between cellular components can complicate rational engineering of biological systems. Here the authors design insulated minimal promoters and operators that enable biophysical modeling of bacterial transcription without free parameters for precise circuit design.

  10. Heat Transfer Modeling for Rigid High-Temperature Fibrous Insulation

    Science.gov (United States)

    Daryabeigi, Kamran; Cunnington, George R.; Knutson, Jeffrey R.

    2012-01-01

    Combined radiation and conduction heat transfer through a high-temperature, high-porosity, rigid multiple-fiber fibrous insulation was modeled using a thermal model previously used to model heat transfer in flexible single-fiber fibrous insulation. The rigid insulation studied was alumina enhanced thermal barrier (AETB) at densities between 130 and 260 kilograms per cubic meter. The model consists of using the diffusion approximation for radiation heat transfer, a semi-empirical solid conduction model, and a standard gas conduction model. The relevant parameters needed for the heat transfer model were estimated from steady-state thermal measurements in nitrogen gas at various temperatures and environmental pressures. The heat transfer modeling methodology was evaluated by comparison with standard thermal conductivity measurements, and steady-state thermal measurements in helium and carbon dioxide gases. The heat transfer model is applicable over the temperature range of 300 to 1360 K, pressure range of 0.133 to 101.3 x 10(exp 3) Pa, and over the insulation density range of 130 to 260 kilograms per cubic meter in various gaseous environments.

  11. Quantum fluctuations in insulating ferroelectrics

    International Nuclear Information System (INIS)

    Riseborough, Peter S.

    2010-01-01

    Graphical abstract: It has been proposed that in a ferroelectric insulator, an applied magnetic field may couple the transverse phonon modes and produce left and right circularly polarized phonon modes which are no longer degenerate. We quantize the theory and examine the effects of quantal fluctuations. In particular, we show that the zero point fluctuations result in a large diamagnetic contribution to the magnetic susceptibility. - Abstract: It has been proposed that in a ferroelectric insulator, an applied magnetic field may couple the transverse phonon modes and produce left and right circularly polarized phonon modes which are no longer degenerate. We quantize the theory and examine the effects of quantal fluctuations. In particular, we show that the zero-point fluctuations result in a large diamagnetic contribution to the magnetic susceptibility.

  12. Multilayer Insulation Ascent Venting Model

    Science.gov (United States)

    Tramel, R. W.; Sutherlin, S. G.; Johnson, W. L.

    2017-01-01

    The thermal and venting transient experienced by tank-applied multilayer insulation (MLI) in the Earth-to-orbit environment is very dynamic and not well characterized. This new predictive code is a first principles-based engineering model which tracks the time history of the mass and temperature (internal energy) of the gas in each MLI layer. A continuum-based model is used for early portions of the trajectory while a kinetic theory-based model is used for the later portions of the trajectory, and the models are blended based on a reference mean free path. This new capability should improve understanding of the Earth-to-orbit transient and enable better insulation system designs for in-space cryogenic propellant systems.

  13. Chiral topological insulator of magnons

    Science.gov (United States)

    Li, Bo; Kovalev, Alexey A.

    2018-05-01

    We propose a magnon realization of 3D topological insulator in the AIII (chiral symmetry) topological class. The topological magnon gap opens due to the presence of Dzyaloshinskii-Moriya interactions. The existence of the topological invariant is established by calculating the bulk winding number of the system. Within our model, the surface magnon Dirac cone is protected by the sublattice chiral symmetry. By analyzing the magnon surface modes, we confirm that the backscattering is prohibited. By weakly breaking the chiral symmetry, we observe the magnon Hall response on the surface due to opening of the gap. Finally, we show that by changing certain parameters, the system can be tuned between the chiral topological insulator, three-dimensional magnon anomalous Hall, and Weyl magnon phases.

  14. Magnetically insulated transmission line oscillator

    Science.gov (United States)

    Bacon, L.D.; Ballard, W.P.; Clark, M.C.; Marder, B.M.

    1987-05-19

    A magnetically insulated transmission line oscillator employs self-generated magnetic fields to generate microwave energy. An anode of the oscillator includes slow-wave structures which are formed of a plurality of thin conductive vanes defining cavities therebetween, and a gap is formed between the anode and a cathode of the oscillator. In response to a pulsed voltage applied to the anode and cathode, self-generated magnetic fields are produced in a cross-field orientation with respect to the orientation of the electric field between the anode and the cathode. The cross-field magnetic fields insulate the flow of electrons in the gap and confine the flow of electrons within the gap. 11 figs.

  15. Insulation assembly for electric machine

    Science.gov (United States)

    Rhoads, Frederick W.; Titmuss, David F.; Parish, Harold; Campbell, John D.

    2013-10-15

    An insulation assembly is provided that includes a generally annularly-shaped main body and at least two spaced-apart fingers extending radially inwards from the main body. The spaced-apart fingers define a gap between the fingers. A slot liner may be inserted within the gap. The main body may include a plurality of circumferentially distributed segments. Each one of the plurality of segments may be operatively connected to another of the plurality of segments to form the continuous main body. The slot liner may be formed as a single extruded piece defining a plurality of cavities. A plurality of conductors (extendable from the stator assembly) may be axially inserted within a respective one of the plurality of cavities. The insulation assembly electrically isolates the conductors in the electric motor from the stator stack and from other conductors.

  16. Secondary electron emission from insulators

    International Nuclear Information System (INIS)

    Kanaya, K.; Ono, S.; Ishigaki, F.

    1978-01-01

    The high yield of secondary electron emission from insulators due to electron bombardment may be the result of an increase of the depth of escape. The free-electron scattering theory is applied to the high energy of primary beams, but cannot be applied to the low energy of secondary escaping beams because of the large energy gap of the insulators. The plasmon loss with the valence electron is considered when the secondary electrons escape. Based on the energy retardation power formula of the penetration and energy loss of an electron probe into solid targets, secondary electron emissions from insulators are calculated from the assumptions that the distribution of the secondary electrons due to both incident and back-scattered electrons within the target is isotropic and that it follows the absorption law of the Lenard type. The universal yield-energy curve of the secondary electron emission, which is deduced as a function of three parameters such as ionisation potential, valence electron and the back-scattered coefficient in addition to the free-electron density effect, is found to be in good agreement with the experimental results. (author)

  17. Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.

    Science.gov (United States)

    Dunaway, Keith W; Islam, M Saharul; Coulson, Rochelle L; Lopez, S Jesse; Vogel Ciernia, Annie; Chu, Roy G; Yasui, Dag H; Pessah, Isaac N; Lott, Paul; Mordaunt, Charles; Meguro-Horike, Makiko; Horike, Shin-Ichi; Korf, Ian; LaSalle, Janine M

    2016-12-13

    Rare variants enriched for functions in chromatin regulation and neuronal synapses have been linked to autism. How chromatin and DNA methylation interact with environmental exposures at synaptic genes in autism etiologies is currently unclear. Using whole-genome bisulfite sequencing in brain tissue and a neuronal cell culture model carrying a 15q11.2-q13.3 maternal duplication, we find that significant global DNA hypomethylation is enriched over autism candidate genes and affects gene expression. The cumulative effect of multiple chromosomal duplications and exposure to the pervasive persistent organic pollutant PCB 95 altered methylation of more than 1,000 genes. Hypomethylated genes were enriched for H2A.Z, increased maternal UBE3A in Dup15q corresponded to reduced levels of RING1B, and bivalently modified H2A.Z was altered by PCB 95 and duplication. These results demonstrate the compounding effects of genetic and environmental insults on the neuronal methylome that converge upon dysregulation of chromatin and synaptic genes. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer

    Directory of Open Access Journals (Sweden)

    Nicholas C. Gomez

    2016-11-01

    Full Text Available Chromatin regulation is critical for differentiation and disease. However, features linking the chromatin environment of stem cells with disease remain largely unknown. We explored chromatin accessibility in embryonic and multipotent stem cells and unexpectedly identified widespread chromatin accessibility at repetitive elements. Integrating genomic and biochemical approaches, we demonstrate that these sites of increased accessibility are associated with well-positioned nucleosomes marked by distinct histone modifications. Differentiation is accompanied by chromatin remodeling at repetitive elements associated with altered expression of genes in relevant developmental pathways. Remarkably, we found that the chromatin environment of Ewing sarcoma, a mesenchymally derived tumor, is shared with primary mesenchymal stem cells (MSCs. Accessibility at repetitive elements in MSCs offers a permissive environment that is exploited by the critical oncogene responsible for this cancer. Our data demonstrate that stem cells harbor a unique chromatin landscape characterized by accessibility at repetitive elements, a feature associated with differentiation and oncogenesis.

  19. Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(DJ Recombination

    Directory of Open Access Journals (Sweden)

    Louise S. Matheson

    2017-11-01

    Full Text Available V(DJ recombination is essential for the generation of diverse antigen receptor (AgR repertoires. In B cells, immunoglobulin kappa (Igκ light chain recombination follows immunoglobulin heavy chain (Igh recombination. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. Integration of VDJ-seq data with genome-wide datasets revealed that two chromatin states at the recombination signal sequence (RSS of VH genes are highly predictive of recombination in mouse pro-B cells. It is unknown whether local chromatin states contribute to Vκ gene choice during Igκ recombination. Here we adapt VDJ-seq to profile the Igκ VκJκ repertoire and present a comprehensive readout in mouse pre-B cells, revealing highly variable Vκ gene usage. Integration with genome-wide datasets for histone modifications, DNase hypersensitivity, transcription factor binding and germline transcription identified PU.1 binding at the RSS, which was unimportant for Igh, as highly predictive of whether a Vκ gene will recombine or not, suggesting that it plays a binary, all-or-nothing role, priming genes for recombination. Thereafter, the frequency with which these genes recombine was shaped both by the presence and level of enrichment of several other chromatin features, including H3K4 methylation and IKAROS binding. Moreover, in contrast to the Igh locus, the chromatin landscape of the promoter, as well as of the RSS, contributes to Vκ gene recombination. Thus, multiple facets of local chromatin features explain much of the variation in Vκ gene usage. Together, these findings reveal shared and divergent roles for epigenetic features and transcription factors in AgR V(DJ recombination and provide avenues for further investigation of chromatin signatures that may underpin V(DJ-mediated chromosomal translocations.

  20. Comparative Investigation of Pollution Accumulation and Natural Cleaning for Different HV Insulators

    Directory of Open Access Journals (Sweden)

    M. Dimitropoulou

    2015-04-01

    Full Text Available High Voltage insulators are scattered throughout any HV network and a single insulator fault may cause an excessive outage. Reliability is a key issue for electric power systems and fault-free performance of insulators greatly reflects on the reliability of the system. Environmental influence is rather important for the optimum selection of outdoor insulators and, therefore, field measurements provide valuable information. Utilities perform such measurements in order to decide upon the location/route of new HV installations (substations, lines etc and also to optimize the selection, maintenance and replacement of already installed insulators. A rather interesting case in Greek territory is the island of Crete, due to the coastal development of the network and the local weather conditions. The Greek utility has employed a variety of remedies to cope with the pollution problem. Following the positive feedback after the installation on certain tower in the past, a large project to replace all ceramic insulators with new polymer ones of hydrophobic surface is now in progress. Polymer coatings have also been extensively applied on substations and also on certain areas/towers of the transmission network in the past. In order to investigate the pollution accumulation and the impact of natural washing on different insulator types, a series of periodical ESDD and NSDD pollution measurements were conducted in HEDNO’s TALOS High Voltage Test Station for a 3-months period. Multiple measurements were performed on each insulator every month in order to collect additional data. Five different insulators were selected based on the types historically used in the Cretan Network. Along with the standard glass disc profile, two strings of glass fog profile (the one coated with RTV and two long-rod composite insulators of different shed profile and material were used. Results are presented and discussed in this paper.

  1. Neutron scatter studies of chromatin structures related to functions

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1992-01-01

    Despite of setbacks in the lack of neutrons for the proposed We have made considerable progress in chromatin reconstitution with the VLR histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized an intrinsically bent DNA region flanking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interatctions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin

  2. Neutron scatter studies of chromatin structures related to functions

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1992-01-01

    We have made considerable progress in chromatin reconstitution with very lysine rich histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized in intrinsically bent DNA region flaking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interactions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear Magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin

  3. Models of chromatin spatial organisation in the cell nucleus

    Science.gov (United States)

    Nicodemi, Mario

    2014-03-01

    In the cell nucleus chromosomes have a complex architecture serving vital functional purposes. Recent experiments have started unveiling the interaction map of DNA sites genome-wide, revealing different levels of organisation at different scales. The principles, though, which orchestrate such a complex 3D structure remain still mysterious. I will overview the scenario emerging from some classical polymer physics models of the general aspect of chromatin spatial organisation. The available experimental data, which can be rationalised in a single framework, support a picture where chromatin is a complex mixture of differently folded regions, self-organised across spatial scales according to basic physical mechanisms. I will also discuss applications to specific DNA loci, e.g. the HoxB locus, where models informed with biological details, and tested against targeted experiments, can help identifying the determinants of folding.

  4. Atomic force microscopy on chromosomes, chromatin and DNA: a review.

    Science.gov (United States)

    Kalle, Wouter; Strappe, Padraig

    2012-12-01

    The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  5. Accumulation of DNA damage-induced chromatin alterations in tissue-specific stem cells: the driving force of aging?

    Directory of Open Access Journals (Sweden)

    Nadine Schuler

    Full Text Available Accumulation of DNA damage leading to stem cell exhaustion has been proposed to be a principal mechanism of aging. Using 53BP1-foci as a marker for DNA double-strand breaks (DSBs, hair follicle stem cells (HFSCs in mouse epidermis were analyzed for age-related DNA damage response (DDR. We observed increasing amounts of 53BP1-foci during the natural aging process independent of telomere shortening and after protracted low-dose radiation, suggesting substantial accumulation of DSBs in HFSCs. Electron microscopy combined with immunogold-labeling showed multiple small 53BP1 clusters diffusely distributed throughout the highly compacted heterochromatin of aged HFSCs, but single large 53BP1 clusters in irradiated HFSCs. These remaining 53BP1 clusters did not colocalize with core components of non-homologous end-joining, but with heterochromatic histone modifications. Based on these results we hypothesize that these lesions were not persistently unrepaired DSBs, but may reflect chromatin rearrangements caused by the repair or misrepair of DSBs. Flow cytometry showed increased activation of repair proteins and damage-induced chromatin modifications, triggering apoptosis and cellular senescence in irradiated, but not in aged HFSCs. These results suggest that accumulation of DNA damage-induced chromatin alterations, whose structural dimensions reflect the complexity of the initial genotoxic insult, may lead to different DDR events, ultimately determining the biological outcome of HFSCs. Collectively, our findings support the hypothesis that aging might be largely the remit of structural changes to chromatin potentially leading to epigenetically induced transcriptional deregulation.

  6. Effects of insulation on potted superconducting coils

    International Nuclear Information System (INIS)

    Zeller, A.F.; DeKamp, J.C.; Magsig, C.T.; Nolen, J.A.; McInturff, A.D.

    1989-01-01

    Test coils using identical wire but with either Formvar or Polyesterimid insulation were fabricated to determine the effects of insulation on training behavior. It was found that the type of insulation did not affect the training behavior. While considerable attention has been paid to epoxy formulations used for superconducting coils, little study has been devoted to the effects of the wire insulation on training behavior. If the insulation does not bind well with the epoxy, the wires will not be held securely in place, and training will be required to make the coil operate at its design limit. In fact, the coil may never reach its design current, showing considerable degredation. Conversely, if the epoxy-insulation reaction is to soften or weaken the insulation, then shorts and/or training may result. The authors have undertaken a study of the effects of the insulation on potted coils wet wound with Stycast 2850 FT epoxy. The wire was insulated with one of two insulting varnishes: Formvar (a polyvinyl formal resin) or Polyesterimid (a phenolic resin). Formvar is the standard insulation in the United States while Polyesterimid the European standard

  7. Histone occurrence in chromatin from Peridinium balticum, a binucleate dinoflagellate.

    Science.gov (United States)

    Rizzo, P J; Cox, E R

    1977-12-23

    Peridinium balticum is one of two dinoflagellates known to have dissimilar nuclei together in the same cell. One nucleus (dinokaryotic) has permanently condensed chromosomes, while the other (eukaryotic) does not have morphologically distinct chromosomes. Acid extracts of chromatin prepared from a mixture of dinokaryotic and eukaryotic nuclei and purified eukaryotic nuclei give four bands that co-migrate with four of the five histones from calf thymus when analyzed in urea-containing polyacrylamide gels.

  8. Light scattering measurements supporting helical structures for chromatin in solution.

    Science.gov (United States)

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

  9. Insulator-insulator and insulator-conductor transitions in the phase diagram of aluminium trichloride

    Directory of Open Access Journals (Sweden)

    Romina Ruberto

    2009-01-01

    Full Text Available We report a classical computer-simulation study of the phase diagram of AlCl3 in the pressure-temperature (p, T plane, showing (i that melting from a layered crystal structure occurs into a molecular liquid at low (p, T and into a dissociated ionic liquid at high (p, T, and (ii that a broad transition from a molecular insulator to an ionic conductor takes place in the liquid state.

  10. Role of Chromatin assembly factor 1 in DNA replication of Plasmodium falciparum.

    Science.gov (United States)

    Gupta, Mohit Kumar; Agarawal, Meetu; Banu, Khadija; Reddy, K Sony; Gaur, Deepak; Dhar, Suman Kumar

    2018-01-01

    Nucleosome assembly in P. falciparum could be the key process in maintaining its genomic integrity as DNA replicates more than once per cell cycle during several stages of its life cycle. Here, we report the functional characterization of P. falciparum chromatin assembly factor 1 (CAF1), which interacts with several proteins namely PfCAF2, Histones, PfHP1 and others. Consistent with the above findings, we demonstrate the presence of PfCAF1 at the telomeric repeat regions, central and subtelomeric var genes of multiple var gene family along with PfHP1. Further, we report the upregulation of PfCAF1 after treatment with genotoxic agents like MMS and HU. Together, these findings establish role of PfCAF1 in heterochromatin maintenance and as histone chaperone in nucleosome assembly and DNA damage repair. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. ATM and KAT5 safeguard replicating chromatin against formaldehyde damage

    Science.gov (United States)

    Ortega-Atienza, Sara; Wong, Victor C.; DeLoughery, Zachary; Luczak, Michal W.; Zhitkovich, Anatoly

    2016-01-01

    Many carcinogens damage both DNA and protein constituents of chromatin, and it is unclear how cells respond to this compound injury. We examined activation of the main DNA damage-responsive kinase ATM and formation of DNA double-strand breaks (DSB) by formaldehyde (FA) that forms histone adducts and replication-blocking DNA-protein crosslinks (DPC). We found that low FA doses caused a strong and rapid activation of ATM signaling in human cells, which was ATR-independent and restricted to S-phase. High FA doses inactivated ATM via its covalent dimerization and formation of larger crosslinks. FA-induced ATM signaling showed higher CHK2 phosphorylation but much lower phospho-KAP1 relative to DSB inducers. Replication blockage by DPC did not produce damaged forks or detectable amounts of DSB during the main wave of ATM activation, which did not require MRE11. Chromatin-monitoring KAT5 (Tip60) acetyltransferase was responsible for acetylation and activation of ATM by FA. KAT5 and ATM were equally important for triggering of intra-S-phase checkpoint and ATM signaling promoted recovery of normal human cells after low-dose FA. Our results revealed a major role of the KAT5-ATM axis in protection of replicating chromatin against damage by the endogenous carcinogen FA. PMID:26420831

  12. [Neutron scatter studies of chromatin structure related to function

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1990-01-01

    This study is concerned with the application of neutron scatter techniques to the different structural states of nucleosomes and chromatin with the long term objective of understanding how the enormous lengths of DNA are folded into chromosomes. Micrococcal nuclease digestion kinetics have defined two subnucleosome particles; the chromatosome with 168 bp DNA, the histone octamer and one H1 and the nucleosome core particle with 146 bp DNA and the histone octamer. As will be discussed, the structure of the 146 bp DNA core particle is known in solution at low resolution from neutron scatter studies and in crystals. Based on this structure, the authors have a working model for the chromatosome and the mode of binding of H1. In order to define the structure of the nucleosome and also the different orders of chromatin structures they need to know the paths of DNA that link nucleosomes and the factors associated with chromosome functions that act on those DNA paths. The major region for this situation is the inherent variabilities in nucleosome DNA sequences, in the histone subtypes and their states of chemical modification and in the precise locations of nucleosomes. Such variabilities obscure the underlying principles that govern the packaging of DNA into the different structural states of nucleosomes and chromatin. The only way to elucidate these principles is to study the structures of nucleosomes and oligonucleosomes that are fully defined. They have largely achieved these objectives

  13. Safe and Effective Gene Therapy for Murine Wiskott-Aldrich Syndrome Using an Insulated Lentiviral Vector

    Directory of Open Access Journals (Sweden)

    Swati Singh

    2017-03-01

    Full Text Available Wiskott-Aldrich syndrome (WAS is a life-threatening immunodeficiency caused by mutations within the WAS gene. Viral gene therapy to restore WAS protein (WASp expression in hematopoietic cells of patients with WAS has the potential to improve outcomes relative to the current standard of care, allogeneic bone marrow transplantation. However, the development of viral vectors that are both safe and effective has been problematic. While use of viral transcriptional promoters may increase the risk of insertional mutagenesis, cellular promoters may not achieve WASp expression levels necessary for optimal therapeutic effect. Here we evaluate a self-inactivating (SIN lentiviral vector combining a chromatin insulator upstream of a viral MND (MPSV LTR, NCR deleted, dl587 PBS promoter driving WASp expression. Used as a gene therapeutic in Was−/− mice, this vector resulted in stable WASp+ cells in all hematopoietic lineages and rescue of T and B cell defects with a low number of viral integrations per cell, without evidence of insertional mutagenesis in serial bone marrow transplants. In a gene transfer experiment in non-human primates, the insulated MND promoter (driving GFP expression demonstrated long-term polyclonal engraftment of GFP+ cells. These observations demonstrate that the insulated MND promoter safely and efficiently reconstitutes clinically effective WASp expression and should be considered for future WAS therapy.

  14. The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication in a chromatin-specific manner

    DEFF Research Database (Denmark)

    Alexiadis, V; Waldmann, T; Andersen, Jens S.

    2000-01-01

    The structure of chromatin regulates the genetic activity of the underlying DNA sequence. We report here that the protein encoded by the proto-oncogene DEK, which is involved in acute myelogenous leukemia, induces alterations of the superhelical density of DNA in chromatin. The change in topology...

  15. Insulation Progress since the Mid-1950s

    Science.gov (United States)

    Timmerhaus, K. D.

    Storage vessel and cryostat design for modern cryogenic systems has become rather routine as the result of the wide use of and application of cryogenic fluids. Such vessels for these fluids range in size from 1 L flasks used in the laboratory for liquid nitrogen to the more than 200,000 m3 double-walled tanks used for temporary storage of liquefied natural gas before being transported overseas to their final destination. These storage vessels for cryogenic fluids range in type from low-performance containers insulated with rigid foam or fibrous insulation to high-performance containers insulated with evacuated multilayer insulations. The overriding factors in the type of container selected normally are of economics and safety. This paper will consider various insulation concepts used in such cryogenic storage systems and will review the progress that has been made over the past 50 years in these insulation systems.

  16. Handleable shapes of thermal insulation material

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, J. T.

    1989-01-17

    Handleable and machineable shapes of thermal insulation material are made by compacting finely divided thermal insulation material into the cells of a reinforcing honeycomb insulation material into the cells of a reinforcing honeycomb structure. The finely divided thermal insulation material may be, for example, silica aerogel, pyrogenic silica, carbon black, silica gel, volatilised silica, calcium silicate, vermiculate or perlite, or finely divided metal oxides such as alumina or titania. The finely divided thermal insulation material may include an infra-red opacifier and/or reinforcing fibres. The reinforcing honeycomb structure may be made from, for example, metals such as aluminium foil, inorganic materials such as ceramics, organic materials such as plastics materials, woven fabrics or paper. A rigidiser may be employed. The shapes of thermal insulation material are substantially rigid and may be machines, for example by mechanical or laser cutting devices, or may be formed, for example by rolling, into curved or other shaped materials. 12 figs.

  17. Hydrogen storage in insulated pressure vessels

    Energy Technology Data Exchange (ETDEWEB)

    Aceves, S.M.; Garcia-Villazana, O. [Lawrence Livermore National Lab., CA (United States)

    1998-08-01

    Insulated pressure vessels are cryogenic-capable pressure vessels that can be fueled with liquid hydrogen (LH{sub 2}) or ambient-temperature compressed hydrogen (CH{sub 2}). Insulated pressure vessels offer the advantages of liquid hydrogen tanks (low weight and volume), with reduced disadvantages (lower energy requirement for hydrogen liquefaction and reduced evaporative losses). This paper shows an evaluation of the applicability of the insulated pressure vessels for light-duty vehicles. The paper shows an evaluation of evaporative losses and insulation requirements and a description of the current analysis and experimental plans for testing insulated pressure vessels. The results show significant advantages to the use of insulated pressure vessels for light-duty vehicles.

  18. ASRM case insulation design and development

    Science.gov (United States)

    Bell, Matthew S.; Tam, William F. S.

    1992-10-01

    This paper describes the achievements made on the Advanced Solid Rocket Motor (ASRM) case insulation design and development program. The ASRM case insulation system described herein protects the metal case and joints from direct radiation and hot gas impingement. Critical failure of solid rocket systems is often traceable to failure of the insulation design. The wide ranging accomplishments included the development of a nonasbestos insulation material for ASRM that replaced the existing Redesigned Solid Rocket Motor (RSRM) asbestos-filled nitrile butadiene rubber (NBR) along with a performance gain of 300 pounds, and improved reliability of all the insulation joint designs, i.e., segmented case joint, case-to-nozzle and case-to-igniter joint. The insulation process development program included the internal stripwinding process. This process advancement allowed Aerojet to match to exceed the capability of other propulsion companies.

  19. Polyester Apparel Cutting Waste as Insulation Material

    OpenAIRE

    Trajković, Dušan; Jordeva, Sonja; Tomovska, Elena; Zafirova, Koleta

    2017-01-01

    Polyester waste is the dominant component of the clothing industry waste stream, yet its recycling in this industry is rarely addressed. This paper proposes using polyester cutting waste as an insulation blanket for roofing and buildings’ internal walls in order to reduce environmental pollution. The designed textile structures used waste cuttings from different polyester fabrics without opening the fabric to fibre. Thermal insulation, acoustic insulation, fire resistance and biodegradation o...

  20. Radiation-resistant plastic insulators

    International Nuclear Information System (INIS)

    Sturm, B.J.; Parkinson, W.W.

    1975-01-01

    A high molecular weight organic composition useful as an electric insulator in radiation fields is provided and comprises normally a solid polymer of an organic compound having a specific resistance greater than 10 19 ohm-cm and containing phenyl groups and 1 to 7.5 weight percent of a high molecular weight organic phosphite. In one embodiment the composition comprises normally solid polystyrene having 7.5 weight percent tris-β-chloroethyl phosphite as an additive; the composition exhibited an increase in the post-irradiation resistivity of over an order of magnitude over the post-irradiation resistivity of pure polystyrene. (Patent Office Record)

  1. Processing of insulators and semiconductors

    Science.gov (United States)

    Quick, Nathaniel R.; Joshi, Pooran C.; Duty, Chad Edward; Jellison, Jr., Gerald Earle; Angelini, Joseph Attilio

    2015-06-16

    A method is disclosed for processing an insulator material or a semiconductor material. The method includes pulsing a plasma lamp onto the material to diffuse a doping substance into the material, to activate the doping substance in the material or to metallize a large area region of the material. The method may further include pulsing a laser onto a selected region of the material to diffuse a doping substance into the material, to activate the doping substance in the material or to metallize a selected region of the material.

  2. Characterization of Microporous Insulation, Microsil

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-06-15

    Microsil microporous insulation has been characterized by Lawrence Livermore National Laboratory for possible use in structural and thermal applications in the DPP-1 design. Qualitative test results have provided mechanical behavioral characteristics for DPP-1 design studies and focused on the material behavioral response to being crushed, cyclically loaded, and subjected to vibration for a confined material with an interference fit or a radial gap. Quantitative test results have provided data to support the DPP-1 FEA model analysis and verification and were used to determine mechanical property values for the material under a compression load. The test results are documented within this report.

  3. Method of manufacturing a thermally insulating body

    Energy Technology Data Exchange (ETDEWEB)

    McWilliams, J.A.; Morgan, D.E.; Jackson, J.D.

    1988-10-11

    A method of manufacturing a microporous thermally insulating body comprises mixing together a finely divided microporous insulating material such as silica aerogel or pyrogenic silica and a solid ammonia-generating compound in particulate form, and compressing the mixture to form a thermally insulating body. The ammonia-generating compound is dispersed evenly throughout the insulating material and may comprise, for example, ammonium carbonate, ammonium acetate or urea. Preferably, the ammonia-generating compound comprises a mixture of about one third by weight of ammonium carbonate and about two thirds by weight of ammonium bicarbonate together with a small proportion of magnesium oxide. Experiments are described which illustrate the manufacturing process. 6 tabs.

  4. Dielectric and Insulating Technology 2004 : Review & Forecast

    Science.gov (United States)

    Okamoto, Tatsuki

    This article reports the state-of-art of DEIS activites. DEIS activiteis are basically based on the activites of 8-10 investigation committees’ under DEIS committee. Recent DEIS activites are categlized into three functions in this article and remarkable activity or trend of each category is mentioned. Those are activities on insulation diagnosis (AI application and asset management), activities on new insulation technology for power tansmission (high Tc super conducting cable insulation and all solid sinulated substation), and activities on new insulating materials (Nanocomposite).

  5. Process insulation. Isolation thermique des equipements

    Energy Technology Data Exchange (ETDEWEB)

    1987-01-01

    A manual is presented to assist managers and operating personnel to recognize industrial energy management opportunities, and provides mathematical equations, general information on proven techniques and technology, and examples. It deals with process insulation, focusing on the insulation of mechanical systems such as piping, process vessels, equipment, and ductwork. The manual describes the effects of insulation materials; commonly encountered types of insulation, coverings and protective finishes as well as common applications; energy management opportunities, divided into housekeeping, low cost, and retrofit; and includes worked examples of each. Includes glossary. 17 figs., 8 tabs.

  6. Low Permeability Polyimide Insulation, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Resodyn Technologies proposes a new technology that enables the application of polyimide based cryogenic insulation with low hydrogen permeability. This effort...

  7. Lateral topological crystalline insulator heterostructure

    Science.gov (United States)

    Sun, Qilong; Dai, Ying; Niu, Chengwang; Ma, Yandong; Wei, Wei; Yu, Lin; Huang, Baibiao

    2017-06-01

    The emergence of lateral heterostructures fabricated by two-dimensional building blocks brings many exciting realms in material science and device physics. Enriching available nanomaterials for creating such heterostructures and enabling the underlying new physics is highly coveted for the integration of next-generation devices. Here, we report a breakthrough in lateral heterostructure based on the monolayer square transition-metal dichalcogenides MX2 (M  =  W, X  =  S/Se) modules. Our results reveal that the MX2 lateral heterostructure (1S-MX2 LHS) can possess excellent thermal and dynamical stability. Remarkably, the highly desired two-dimensional topological crystalline insulator phase is confirmed by the calculated mirror Chern number {{n}\\text{M}}=-1 . A nontrivial band gap of 65 meV is obtained with SOC, indicating the potential for room-temperature observation and applications. The topologically protected edge states emerge at the edges of two different nanoribbons between the bulk band gap, which is consistent with the mirror Chern number. In addition, a strain-induced topological phase transition in 1S-MX2 LHS is also revealed, endowing the potential utilities in electronics and spintronics. Our predictions not only introduce new member and vitality into the studies of lateral heterostructures, but also highlight the promise of lateral heterostructure as appealing topological crystalline insulator platforms with excellent stability for future devices.

  8. Thermal insulation properties of walls

    Directory of Open Access Journals (Sweden)

    Zhukov Aleksey Dmitrievich

    2014-05-01

    Full Text Available Heat-protective qualities of building structures are determined by the qualities of the used materials, adequate design solutions and construction and installation work of high quality. This rule refers both to the structures made of materials similar in their structure and nature and mixed, combined by a construction system. The necessity to ecaluate thermal conductivity is important for a product and for a construction. Methods for evaluating the thermal protection of walls are based on the methods of calculation, on full-scale tests in a laboratory or on objects. At the same time there is a reason to believe that even deep and detailed calculation may cause deviation of the values from real data. Using finite difference method can improve accuracy of the results, but it doesn’t solve all problems. The article discusses new approaches to evaluating thermal insulation properties of walls. The authors propose technique of accurate measurement of thermal insulation properties in single blocks and fragments of walls and structures.

  9. Topological Insulator Nanowires and Nanoribbons

    KAUST Repository

    Kong, Desheng

    2010-01-13

    Recent theoretical calculations and photoemission spectroscopy measurements on the bulk Bi2Se3 material show that it is a three-dimensional topological insulator possessing conductive surface states with nondegenerate spins, attractive for dissipationless electronics and spintronics applications. Nanoscale topological insulator materials have a large surface-to-volume ratio that can manifest the conductive surface states and are promising candidates for devices. Here we report the synthesis and characterization of high quality single crystalline Bi2Se5 nanomaterials with a variety of morphologies. The synthesis of Bi 2Se5 nanowires and nanoribbons employs Au-catalyzed vapor-liquid-solid (VLS) mechanism. Nanowires, which exhibit rough surfaces, are formed by stacking nanoplatelets along the axial direction of the wires. Nanoribbons are grown along [1120] direction with a rectangular cross-section and have diverse morphologies, including quasi-one-dimensional, sheetlike, zigzag and sawtooth shapes. Scanning tunneling microscopy (STM) studies on nanoribbons show atomically smooth surfaces with ∼ 1 nm step edges, indicating single Se-Bi-Se-Bi-Se quintuple layers. STM measurements reveal a honeycomb atomic lattice, suggesting that the STM tip couples not only to the top Se atomic layer, but also to the Bi atomic layer underneath, which opens up the possibility to investigate the contribution of different atomic orbitais to the topological surface states. Transport measurements of a single nanoribbon device (four terminal resistance and Hall resistance) show great promise for nanoribbons as candidates to study topological surface states. © 2010 American Chemical Society.

  10. Aggregation of fragmented chromatin associated with the appearance of products of its nuclease treatment

    International Nuclear Information System (INIS)

    Lobanenkov, V.V.; Mironov, N.M.; Kupriyanova, E.I.; Shapot, V.S.

    1986-01-01

    Isolated cell nuclei were incubated with nucleases, and then the chromatin was extracted with a low-salt buffer. When degradation of the nuclear chromatin DNase I or micrococcal nuclease is intensified, solubilization of the deoxyribonucleoprotein (DNP) in low-salt buffer at first increases, reaching a maximum in the case of hydrolysis of 2-4% of the nuclear DNA, but after intensive treatment with nucleases, it decreases sharply. Soluble fragmented chromatin is aggregated during treatment with DNase I. The addition of exogenous products of nuclease treatment of isolated nuclei to a preparation of gelatinous chromatin induces its aggregation. Pretreatment of nuclear chromatin with RNase prevents the solubilization of DNP by solutions with low ionic strength. Certain experimental data obtained using rigorous nuclease treatment are discussed; for their interpretation it is necessary to consider the effect of aggregation of fragmented chromatin by products of its nuclease degradation

  11. A Poly-ADP-Ribose Trigger Releases the Auto-Inhibition of a Chromatin Remodeling Oncogene

    DEFF Research Database (Denmark)

    Singh, Hari R; Nardozza, Aurelio P; Möller, Ingvar R

    2017-01-01

    DNA damage triggers chromatin remodeling by mechanisms that are poorly understood. The oncogene and chromatin remodeler ALC1/CHD1L massively decompacts chromatin in vivo yet is inactive prior to DNA-damage-mediated PARP1 induction. We show that the interaction of the ALC1 macrodomain......-macrodomain interactions, promotes an ungated conformation, and activates the remodeler's ATPase. ALC1 fragments lacking the regulatory macrodomain relax chromatin in vivo without requiring PARP1 activation. Further, the ATPase restricts the macrodomain's interaction with PARP1 under non-DNA damage conditions. Somatic...... cancer mutants disrupt ALC1's auto-inhibition and activate chromatin remodeling. Our data show that the NAD+-metabolite and nucleic acid PAR triggers ALC1 to drive chromatin relaxation. Modular allostery in this oncogene tightly controls its robust, DNA-damage-dependent activation....

  12. Restoring chromatin after replication: How new and old histone marks come together

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    In dividing cells genome stability and function rely on faithful transmission of both DNA sequence and its organization into chromatin. In the course of DNA replication chromatin undergoes transient genome-wide disruption followed by restoration on new DNA. This involves tight coordination of DNA...... replication and chromatin assembly processes in time and space. Dynamic recycling and de novo deposition of histones are fundamental for chromatin restoration. Histone post-translational modifications (PTMs) are thought to have a causal role in establishing distinct chromatin structures. Here we discuss PTMs...... present on new and parental histones and how they influence genome stability and restoration of epigenetically defined domains. Newly deposited histones must change their signature in the process of chromatin restoration, this may occur in a step-wise fashion involving replication-coupled processes...

  13. Autodigestion of chromatin in some radiosensitive and radioresistant mouse cells. Role of proteolysis and endonucleolysis

    International Nuclear Information System (INIS)

    Suciu, D.; Bojan, O.

    1981-01-01

    Evidence is presented indicating that mouse thymus, spleen, kidney, lung and heart contain a protease activity with relatively high specificity for histones. It is suggested that degradation of chromatin occurring in irradiated lymphoid tissues is produced by the action of alkaline endonuclease in association with this histone protease. The autodigestion of chromatin was assessed by determining the release of soluble chromatin from cells suspended in sucrose media of low ionic strength. It was found that the protease inhibitors, phenylmethylsulphonyl fluoride and especially NaHSO 3 , were also capable of depressing the activity of alkaline endonuclease, the fragmentation of chromatin, and the release of soluble chromatin. The results suggest that the release of histones from irradiated lymphoid tissues cannot be considered as a determinant step in the fragmentation of DNA in chromatin. (author)

  14. Temporal profiling of the chromatin proteome reveals system-wide responses to replication inhibition

    DEFF Research Database (Denmark)

    Khoudoli, Guennadi A; Gillespie, Peter J; Stewart, Graeme

    2008-01-01

    Although the replication, expression, and maintenance of DNA are well-studied processes, the way that they are coordinated is poorly understood. Here, we report an analysis of the changing association of proteins with chromatin (the chromatin proteome) during progression through interphase...... of the cell cycle. Sperm nuclei were incubated in Xenopus egg extracts, and chromatin-associated proteins were analyzed by mass spectrometry at different times. Approximately 75% of the proteins varied in abundance on chromatin by more than 15%, suggesting that the chromatin proteome is highly dynamic....... Proteins were then assigned to one of 12 different clusters on the basis of their pattern of chromatin association. Each cluster contained functional groups of proteins involved in different nuclear processes related to progression through interphase. We also blocked DNA replication by inhibiting either...

  15. DNA repair goes hip-hop: SMARCA and CHD chromatin remodellers join the break dance.

    Science.gov (United States)

    Rother, Magdalena B; van Attikum, Haico

    2017-10-05

    Proper signalling and repair of DNA double-strand breaks (DSB) is critical to prevent genome instability and diseases such as cancer. The packaging of DNA into chromatin, however, has evolved as a mere obstacle to these DSB responses. Posttranslational modifications and ATP-dependent chromatin remodelling help to overcome this barrier by modulating nucleosome structures and allow signalling and repair machineries access to DSBs in chromatin. Here we recap our current knowledge on how ATP-dependent SMARCA- and CHD-type chromatin remodellers alter chromatin structure during the signalling and repair of DSBs and discuss how their dysfunction impacts genome stability and human disease.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'. © 2017 The Authors.

  16. Wongabel Rhabdovirus Accessory Protein U3 Targets the SWI/SNF Chromatin Remodeling Complex

    Science.gov (United States)

    Joubert, D. Albert; Rodriguez-Andres, Julio; Monaghan, Paul; Cummins, Michelle; McKinstry, William J.; Paradkar, Prasad N.; Moseley, Gregory W.

    2014-01-01

    ABSTRACT Wongabel virus (WONV) is an arthropod-borne rhabdovirus that infects birds. It is one of the growing array of rhabdoviruses with complex genomes that encode multiple accessory proteins of unknown function. In addition to the five canonical rhabdovirus structural protein genes (N, P, M, G, and L), the 13.2-kb negative-sense single-stranded RNA (ssRNA) WONV genome contains five uncharacterized accessory genes, one overlapping the N gene (Nx or U4), three located between the P and M genes (U1 to U3), and a fifth one overlapping the G gene (Gx or U5). Here we show that WONV U3 is expressed during infection in insect and mammalian cells and is required for efficient viral replication. A yeast two-hybrid screen against a mosquito cell cDNA library identified that WONV U3 interacts with the 83-amino-acid (aa) C-terminal domain of SNF5, a component of the SWI/SNF chromatin remodeling complex. The interaction was confirmed by affinity chromatography, and nuclear colocalization was established by confocal microscopy. Gene expression studies showed that SNF5 transcripts are upregulated during infection of mosquito cells with WONV, as well as West Nile virus (Flaviviridae) and bovine ephemeral fever virus (Rhabdoviridae), and that SNF5 knockdown results in increased WONV replication. WONV U3 also inhibits SNF5-regulated expression of the cytokine gene CSF1. The data suggest that WONV U3 targets the SWI/SNF complex to block the host response to infection. IMPORTANCE The rhabdoviruses comprise a large family of RNA viruses infecting plants, vertebrates, and invertebrates. In addition to the major structural proteins (N, P, M, G, and L), many rhabdoviruses encode a diverse array of accessory proteins of largely unknown function. Understanding the role of these proteins may reveal much about host-pathogen interactions in infected cells. Here we examine accessory protein U3 of Wongabel virus, an arthropod-borne rhabdovirus that infects birds. We show that U3 enters the

  17. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea

    OpenAIRE

    Guo, Li; Feng, Yingang; Zhang, Zhenfeng; Yao, Hongwei; Luo, Yuanming; Wang, Jinfeng; Huang, Li

    2007-01-01

    Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a high...

  18. Scaffold Attachment Factor B1: A Novel Chromatin Regulator of Prostate Cancer Metabolism

    Science.gov (United States)

    2016-10-01

    AWARD NUMBER: W81XWH-14-1-0152 TITLE: Scaffold Attachment Factor B1: A Novel Chromatin Regulator of Prostate Cancer Metabolism PRINCIPAL...TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-14-1-0152 Scaffold Attachment Factor B1: A Novel Chromatin Regulator of Prostate Cancer Metabolism... chromatin immunoprecipitation-next generation DNA sequencing (ChIP-seq) and integrative network modeling to identify the SAFB1 cistrome and the extent of

  19. Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

    DEFF Research Database (Denmark)

    Rennie, Sarah; Dalby, Maria; van Duin, Lucas

    2018-01-01

    Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it is unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone and how this impacts disease...... proportion of total levels and is highly informative of topological associating domain activities and organisation, revealing boundaries and chromatin compartments. Furthermore, expression data alone accurately predict individual enhancer-promoter interactions, drawing features from expression strength...... between transcription and chromatin architecture....

  20. Osmotic stress alters chromatin condensation and nucleocytoplasmic transport

    Energy Technology Data Exchange (ETDEWEB)

    Finan, John D.; Leddy, Holly A. [Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC (United States); Department of Biomedical Engineering, Duke University, Durham, NC (United States); Guilak, Farshid, E-mail: guilak@duke.edu [Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC (United States); Department of Biomedical Engineering, Duke University, Durham, NC (United States)

    2011-05-06

    Highlights: {yields} The rate of nucleocytoplasmic transport increases under hyper-osmotic stress. {yields} The mechanism is a change in nuclear geometry, not a change in permeability of the nuclear envelope. {yields} Intracytoplasmic but not intranuclear diffusion is sensitive to osmotic stress. {yields} Pores in the chromatin of the nucleus enlarge under hyper-osmotic stress. -- Abstract: Osmotic stress is a potent regulator of biological function in many cell types, but its mechanism of action is only partially understood. In this study, we examined whether changes in extracellular osmolality can alter chromatin condensation and the rate of nucleocytoplasmic transport, as potential mechanisms by which osmotic stress can act. Transport of 10 kDa dextran was measured both within and between the nucleus and the cytoplasm using two different photobleaching methods. A mathematical model was developed to describe fluorescence recovery via nucleocytoplasmic transport. As osmolality increased, the diffusion coefficient of dextran decreased in the cytoplasm, but not the nucleus. Hyper-osmotic stress decreased nuclear size and increased nuclear lacunarity, indicating that while the nucleus was getting smaller, the pores and channels interdigitating the chromatin had expanded. The rate of nucleocytoplasmic transport was increased under hyper-osmotic stress but was insensitive to hypo-osmotic stress, consistent with the nonlinear osmotic properties of the nucleus. The mechanism of this osmotic sensitivity appears to be a change in the size and geometry of the nucleus, resulting in a shorter effective diffusion distance for the nucleus. These results may explain physical mechanisms by which osmotic stress can influence intracellular signaling pathways that rely on nucleocytoplasmic transport.

  1. Chromatin association of UHRF1 during the cell cycle

    KAUST Repository

    Al-Gashgari, Bothayna

    2017-05-01

    Ubiquitin-like with PHD and RING Finger domains 1 (UHRF1) is a nuclear protein that associates with chromatin. Regardless of the various functions of UHRF1 in the cell, one of its more important functions is its role in the maintenance of DNA methylation patterns by the recruitment of DNMT1. Studies on UHRF1 based on this function have revealed the importance of UHRF1 during the cell cycle. Moreover, based on different studies various factors were described to be involved in the regulation of UHRF1 with different functionalities that can control its binding affinity to different targets on chromatin. These factors are regulated differently in a cell cycle specific manner. In light of this, we propose that UHRF1 has different binding behaviors during the cell cycle in regard to its association with chromatin. In this project, we first analyzed the binding behavior of endogenous UHRF1 from different unsynchronized cell systems in pull-down assays with peptides and oligonucleotides. Moreover, to analyze UHRF1 binding behavior during the cell cycle, we used two different approaches. First we sorted Jurkat and HT1080 cells based on their cell cycle stage using FACS analysis. Additionally, we synchronized HeLa cells to different stages of the cell cycle by chemical treatments, and used extracts from cellsorting and cell synchronization experiments for pull-down assays. We observed that UHRF1 in different cell systems has different preferences in regard to its binding to H3 unmodified and H3K9me3. Moreover, we detected that UHRF1, in general, displays different patterns between different stages of cell cycle; however, we cannot draw a final model for UHRF1 binding pattern during cell cycle.

  2. Topological Insulators and Superconductors for Innovative Devices

    Science.gov (United States)

    2015-03-20

    Final 3. DATES COVERED (From - To) 20120321 - 20150320 4. TITLE AND SUBTITLE Topological insulators and superconductors for innovative...locking, which hold promise for various innovative devices. Similarly, topological superconductors are associated with exotic surface states, which...298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 Final Report Title: Topological Insulators and Superconductors for Innovative Devices

  3. Thermal insulation of high temperature reactors

    International Nuclear Information System (INIS)

    Cornille, Y.

    1975-01-01

    Operating conditions of HTR thermal insulation are given and heat insulators currently developed are described (fibers kept in position by metallic structures). For future applications and higher temperatures, research is directed towards solutions using ceramics or associating fibers and ceramics [fr

  4. Quantitative analysis of thermal insulation coatings

    DEFF Research Database (Denmark)

    Kiil, Søren

    2014-01-01

    This work concerns the development of simulation tools for mapping of insulation properties of thermal insulation coatings based on selected functional filler materials. A mathematical model, which includes the underlying physics (i.e. thermal conductivity of a heterogeneous two-component coating...

  5. Study of thermal conductivity of multilayer insulation

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, D; Sundaram, S; Nath, G K; Sethuram, N P; Chandrasekharan, T; Varadarajan, T G [Heavy Water Division, Bhabha Atomic Research Centre, Mumbai (India)

    1994-06-01

    This paper presents experimental determination of the apparent thermal conductivity of multilayer insulation for a cryogenic system. The variation of thermal conductivity with residual gas pressure is studied and the optimum vacuum for good insulating performance is determined. Evaporation loss technique for heat-inleak determination is employed. (author). 3 refs., 3 figs.

  6. Insulation systems for superconducting transmission cables

    DEFF Research Database (Denmark)

    Tønnesen, Ole

    1996-01-01

    the electrical insulation is placed outside both the superconducting tube and the cryostat. The superconducting tube is cooled by liquid nitrogen which is pumped through the hollow part of the tube.2) The cryogenic dielectric design, where the electrical insulation is placed inside the cryostat and thus is kept...

  7. Study of thermal conductivity of multilayer insulation

    International Nuclear Information System (INIS)

    Dutta, D.; Sundaram, S.; Nath, G.K.; Sethuram, N.P.; Chandrasekharan, T.; Varadarajan, T.G.

    1994-01-01

    This paper presents experimental determination of the apparent thermal conductivity of multilayer insulation for a cryogenic system. The variation of thermal conductivity with residual gas pressure is studied and the optimum vacuum for good insulating performance is determined. Evaporation loss technique for heat-inleak determination is employed. (author)

  8. Chromatin structure and epigenetics of tumour cells: A review

    Czech Academy of Sciences Publication Activity Database

    Bártová, Eva; Krejčí, Jana; Hájek, R.; Harničarová, Andrea; Kozubek, Stanislav

    2009-01-01

    Roč. 9, č. 1 (2009), s. 51-61 ISSN 1871-529X R&D Projects: GA AV ČR(CZ) 1QS500040508; GA ČR(CZ) GA204/06/0978 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : tumour cells * chromatin * radiation Subject RIV: BO - Biophysics

  9. Quantitative Immunofluorescence Analysis of Nucleolus-Associated Chromatin.

    Science.gov (United States)

    Dillinger, Stefan; Németh, Attila

    2016-01-01

    The nuclear distribution of eu- and heterochromatin is nonrandom, heterogeneous, and dynamic, which is mirrored by specific spatiotemporal arrangements of histone posttranslational modifications (PTMs). Here we describe a semiautomated method for the analysis of histone PTM localization patterns within the mammalian nucleus using confocal laser scanning microscope images of fixed, immunofluorescence stained cells as data source. The ImageJ-based process includes the segmentation of the nucleus, furthermore measurements of total fluorescence intensities, the heterogeneity of the staining, and the frequency of the brightest pixels in the region of interest (ROI). In the presented image analysis pipeline, the perinucleolar chromatin is selected as primary ROI, and the nuclear periphery as secondary ROI.

  10. Genomic and chromatin signals underlying transcription start-site selection

    DEFF Research Database (Denmark)

    Valen, Eivind; Sandelin, Albin Gustav

    2011-01-01

    A central question in cellular biology is how the cell regulates transcription and discerns when and where to initiate it. Locating transcription start sites (TSSs), the signals that specify them, and ultimately elucidating the mechanisms of regulated initiation has therefore been a recurrent theme....... In recent years substantial progress has been made towards this goal, spurred by the possibility of applying genome-wide, sequencing-based analysis. We now have a large collection of high-resolution datasets identifying locations of TSSs, protein-DNA interactions, and chromatin features over whole genomes...

  11. Aharonov–Bohm interference in topological insulator nanoribbons

    KAUST Repository

    Peng, Hailin; Lai, Keji; Kong, Desheng; Meister, Stefan; Chen, Yulin; Qi, Xiao-Liang; Zhang, Shou-Cheng; Shen, Zhi-Xun; Cui, Yi

    2009-01-01

    Topological insulators represent unusual phases of quantum matter with an insulating bulk gap and gapless edges or surface states. The two-dimensional topological insulator phase was predicted in HgTe quantum wells and confirmed by transport

  12. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription.

    Science.gov (United States)

    Lai, Fan; Orom, Ulf A; Cesaroni, Matteo; Beringer, Malte; Taatjes, Dylan J; Blobel, Gerd A; Shiekhattar, Ramin

    2013-02-28

    Recent advances in genomic research have revealed the existence of a large number of transcripts devoid of protein-coding potential in multiple organisms. Although the functional role for long non-coding RNAs (lncRNAs) has been best defined in epigenetic phenomena such as X-chromosome inactivation and imprinting, different classes of lncRNAs may have varied biological functions. We and others have identified a class of lncRNAs, termed ncRNA-activating (ncRNA-a), that function to activate their neighbouring genes using a cis-mediated mechanism. To define the precise mode by which such enhancer-like RNAs function, we depleted factors with known roles in transcriptional activation and assessed their role in RNA-dependent activation. Here we report that depletion of the components of the co-activator complex, Mediator, specifically and potently diminished the ncRNA-induced activation of transcription in a heterologous reporter assay using human HEK293 cells. In vivo, Mediator is recruited to ncRNA-a target genes and regulates their expression. We show that ncRNA-a interact with Mediator to regulate its chromatin localization and kinase activity towards histone H3 serine 10. The Mediator complex harbouring disease- displays diminished ability to associate with activating ncRNAs. Chromosome conformation capture confirmed the presence of DNA looping between the ncRNA-a loci and its targets. Importantly, depletion of Mediator subunits or ncRNA-a reduced the chromatin looping between the two loci. Our results identify the human Mediator complex as the transducer of activating ncRNAs and highlight the importance of Mediator and activating ncRNA association in human disease.

  13. Nucleolar chromatin organization at different activities of soybean root meristematic cell nucleoli.

    Science.gov (United States)

    Stępiński, Dariusz

    2013-06-01

    Nucleolar chromatin, including nucleolus-associated chromatin as well as active and inactive condensed ribosomal DNA (rDNA) chromatin, derives mostly from secondary constrictions known as nucleolus organizer regions containing rDNA genes on nucleolus-forming chromosomes. This chromatin may occupy different nucleolar positions being in various condensation states which may imply different rDNA transcriptional competence. Sections of nucleoli originating from root meristematic cells of soybean seedlings grown at 25 °C (the control), then subjected to chilling stress (10 °C), and next transferred again to 25 °C (the recovery) were used to measure profile areas occupied by nucleolar condensed chromatin disclosed with sodium hydroxide methylation-acetylation plus uranyl acetate technique. The biggest total area of condensed chromatin was found in the nucleoli of chilled plants, while the smallest was found in those of recovered plants in relation to the amounts of chromatin in the control nucleoli. The condensed nucleolar chromatin, in the form of different-sized and different-shaped clumps, was mainly located in fibrillar centers. One can suppose that changes of condensed rDNA chromatin amounts might be a mechanism controlling the number of transcriptionally active rDNA genes as the nucleoli of plants grown under these experimental conditions show different transcriptional activity and morphology.

  14. MRN1 implicates chromatin remodeling complexes and architectural factors in mRNA maturation

    DEFF Research Database (Denmark)

    Düring, Louis; Thorsen, Michael; Petersen, Darima

    2012-01-01

    A functional relationship between chromatin structure and mRNA processing events has been suggested, however, so far only a few involved factors have been characterized. Here we show that rsc nhp6¿¿ mutants, deficient for the function of the chromatin remodeling factor RSC and the chromatin....... Genetic interactions are observed between 2 µm-MRN1 and the splicing deficient mutants snt309¿, prp3, prp4, and prp22, and additional genetic analyses link MRN1, SNT309, NHP6A/B, SWI/SNF, and RSC supporting the notion of a role of chromatin structure in mRNA processing....

  15. Extracellular Matrix-Induced Chromatin Modifications in Normal and Malignant Human Breast Cells

    National Research Council Canada - National Science Library

    Beyec, Johanne

    2002-01-01

    .... The changes in gene expression that occur during differentiation or tumorigenesis are accompanied by characteristics patterns of chromatin reorganization, modulated, in part, through highly regulated...

  16. Identification of potential nuclear reprogramming and differentiation factors by a novel selection method for cloning chromatin-binding proteins

    International Nuclear Information System (INIS)

    Wang Liu; Zheng Aihua; Yi Ling; Xu Chongren; Ding Mingxiao; Deng Hongkui

    2004-01-01

    Nuclear reprogramming is critical for animal cloning and stem cell creation through nuclear transfer, which requires extensive remodeling of chromosomal architecture involving dramatic changes in chromatin-binding proteins. To understand the mechanism of nuclear reprogramming, it is critical to identify chromatin-binding factors specify the reprogramming process. In this report, we have developed a high-throughput selection method, based on T7 phage display and chromatin immunoprecipitation, to isolate chromatin-binding factors expressed in mouse embryonic stem cells using primary mouse embryonic fibroblast chromatin. Seven chromatin-binding proteins have been isolated by this method. We have also isolated several chromatin-binding proteins involved in hepatocyte differentiation. Our method provides a powerful tool to rapidly and selectively identify chromatin-binding proteins. The method can be used to study epigenetic modification of chromatin during nuclear reprogramming, cell differentiation, and transdifferentiation

  17. Modeling of Dynamic Responses in Building Insulation

    Directory of Open Access Journals (Sweden)

    Anna Antonyová

    2015-10-01

    Full Text Available In this research a measurement systemwas developedfor monitoring humidity and temperature in the cavity between the wall and the insulating material in the building envelope. This new technology does not disturb the insulating material during testing. The measurement system can also be applied to insulation fixed ten or twenty years earlier and sufficiently reveals the quality of the insulation. A mathematical model is proposed to characterize the dynamic responses in the cavity between the wall and the building insulation as influenced by weather conditions.These dynamic responses are manifested as a delay of both humidity and temperature changes in the cavity when compared with the changes in the ambient surrounding of the building. The process is then modeled through numerical methods and statistical analysis of the experimental data obtained using the new system of measurement.

  18. Topological Insulators Dirac Equation in Condensed Matters

    CERN Document Server

    Shen, Shun-Qing

    2012-01-01

    Topological insulators are insulating in the bulk, but process metallic states around its boundary owing to the topological origin of the band structure. The metallic edge or surface states are immune to weak disorder or impurities, and robust against the deformation of the system geometry. This book, Topological insulators, presents a unified description of topological insulators from one to three dimensions based on the modified Dirac equation. A series of solutions of the bound states near the boundary are derived, and the existing conditions of these solutions are described. Topological invariants and their applications to a variety of systems from one-dimensional polyacetalene, to two-dimensional quantum spin Hall effect and p-wave superconductors, and three-dimensional topological insulators and superconductors or superfluids are introduced, helping readers to better understand this fascinating new field. This book is intended for researchers and graduate students working in the field of topological in...

  19. Foam insulated transfer line test report

    International Nuclear Information System (INIS)

    Squier, D.M.

    1994-06-01

    Miles of underground insulated piping will be installed at the Hanford site to transfer liquid waste. Significant cost savings may be realized by using pre-fabricated polyurethane foam insulated piping. Measurements were made on sections of insulated pipe to determine the insulation's resistance to axial expansion of the pipe, the force required to compress the foam in the leg of an expansion loop and the time required for heat up and cool down of a buried piping loop. These measurements demonstrated that the peak axial force increases with the amount of adhesion between the encasement pipe and the insulation. The compressive strength of the foam is too great to accommodate the thermal growth of long straight pipe sections into the expansion loops. Mathematical models of the piping system's thermal behavior can be refined by data from the heated piping loop

  20. Luminescence from metals and insulators

    International Nuclear Information System (INIS)

    Crawford, O.H.

    1985-01-01

    The term luminescence is normally applied to light emission that is not explainable by the mechanisms discussed by the other speakers in this meeting. Specifically, it is not transition radiation, surface plasmon radiation, or bremsstrahlung. One normally thinks of luminescence as arising from one-electron transitions within a medium. This talk consists of an overview of luminescence from condensed matter under irradiation by either energetic particles or photons. The author begins with organic molecules, where luminescence is best understood, and then discusses inorganic insulators and metals. Finally, the dependence of yield upon projectile species and velocity is discussed, and predictions are made concerning the relative effectiveness of electrons, protons, and hydrogen atoms in exciting luminescence

  1. Handbook of Thermal Insulation Applications.

    Science.gov (United States)

    1983-01-01

    Wiuppuoror *tIe beamsWiefag ln~ td ~oair ilmstool beams Plate 18. Metal Building Ceilings - A 18b: Fir* hataird rathge may limit the use of foam Insulation...RFCTANGUI.AR SOL TD A = 2(WxL+LxH+HxW) B V = WxLxH H L TRAPEZOID A 2 (A + B) x H A CONE A -n xRxS+ i xR 2 B V =( /3)x R2 x H TRIANGLE A BxH A- 2 CYLI NDER H 2...FABRICATIIG RECTANGULAR HEATING AND COOLING DUCTWORK. FIBERGLAS DUCT BOARD OWENS-CORNING FIBERGLAS CORP GLASS FIBER RIGID BOARD WITH ALUMINUM 4bD FOIL VAPOR

  2. Electrical resistivity study of insulators

    International Nuclear Information System (INIS)

    Liesegang, J.; Senn, B.C.; Holcombe, S.R.; Pigram, P.J.

    1998-01-01

    Full text: Conventional methods of electrical resistivity measurement of dielectric materials involve the application of electrodes to a sample whereby a potential is applied and a current through the material is measured. Although great care and ingenuity has often been applied to this technique, the recorded values of electrical resistivity (p), especially for insulator materials, show great disparity. In earlier work by the authors, a method for determining surface charge decay [Q(t)], using a coaxial cylindrical capacitor arrangement interfaced to a personal computer, was adapted to allow the relatively straightforward measurement of electrical resistivity in the surface region of charged insulator materials. This method was used to develop an ionic charge transport theory, based on Mott-Gurney diffusion to allow a greater understanding into charge transport behaviour. This theory was extended using numerical analysis to produce a two dimensional (2-D) computational model to allow the direct comparison between experimental and theoretical charge decay data. The work also provided a means for the accurate determination of the diffusion coefficient (D) and the layer of thickness of surface charge (Δz) on the sample. The work outlined here involves an extension of the theoretical approach previously taken, using a computational model based more closely on the 3-D experimental set-up, to reinforce the level of confidence in the results achieved for the simpler 2-D treatment. Initially, a 3-D rectangular box arrangement similar to the experimental set-up was modelled and a theoretical and experimental comparison of voltage decay results made. This model was then transferred into cylindrical coordinates to allow it to be almost identical to the experiment and again a comparison made. In addition, theoretical analysis of the coupled non-linear partial differential equations governing the charge dissipation process has led to a simplification involving directly, the

  3. Thermal Analysis of Low Layer Density Multilayer Insulation Test Results

    Science.gov (United States)

    Johnson, Wesley L.

    2011-01-01

    Investigation of the thermal performance of low layer density multilayer insulations is important for designing long-duration space exploration missions involving the storage of cryogenic propellants. Theoretical calculations show an analytical optimal layer density, as widely reported in the literature. However, the appropriate test data by which to evaluate these calculations have been only recently obtained. As part of a recent research project, NASA procured several multilayer insulation test coupons for calorimeter testing. These coupons were configured to allow for the layer density to be varied from 0.5 to 2.6 layer/mm. The coupon testing was completed using the cylindrical Cryostat-l00 apparatus by the Cryogenics Test Laboratory at Kennedy Space Center. The results show the properties of the insulation as a function of layer density for multiple points. Overlaying these new results with data from the literature reveals a minimum layer density; however, the value is higher than predicted. Additionally, the data show that the transition region between high vacuum and no vacuum is dependent on the spacing of the reflective layers. Historically this spacing has not been taken into account as thermal performance was calculated as a function of pressure and temperature only; however the recent testing shows that the data is dependent on the Knudsen number which takes into account pressure, temperature, and layer spacing. These results aid in the understanding of the performance parameters of MLI and help to complete the body of literature on the topic.

  4. Comparative aspects of basic chromatin proteins in dinoflagellates.

    Science.gov (United States)

    Rizzo, P J

    1981-01-01

    Previous work on histone-like proteins in dinoflagellates is summarized, together with some new data to give an overview of basic proteins in these algae. The first two dinoflagellates studied were both found to contain one major acid-soluble protein that migrated to the same position in acidic-urea gels. When several other genera were studied however, it became apparent that the histone-like proteins from different dinoflagellates were similar but not identical. In view of the great diversity of living dinoflagellates it is speculated that further differences in dinoflagellate basic chromatin proteins will be revealed. Electrophoretic data from the eukaryotic (endosymbiont) nucleus of Peridinium balticum showed the presence of five major components. It is speculated that two of these proteins represent an H1-like doublet and two others correspond to the highly conserved histones H3 and H4. The fifth component is a new histone that may substitute for H2A and H2B in the nucleosome. Because histones and nucleosomes are present in all higher organisms but completely lacking in procaryotes, studies on basic proteins in dinoflagellates will provides insights into the evolution of histones and eucaryotic chromatin organization.

  5. Synaptic, transcriptional and chromatin genes disrupted in autism.

    Science.gov (United States)

    De Rubeis, Silvia; He, Xin; Goldberg, Arthur P; Poultney, Christopher S; Samocha, Kaitlin; Cicek, A Erucment; Kou, Yan; Liu, Li; Fromer, Menachem; Walker, Susan; Singh, Tarinder; Klei, Lambertus; Kosmicki, Jack; Shih-Chen, Fu; Aleksic, Branko; Biscaldi, Monica; Bolton, Patrick F; Brownfeld, Jessica M; Cai, Jinlu; Campbell, Nicholas G; Carracedo, Angel; Chahrour, Maria H; Chiocchetti, Andreas G; Coon, Hilary; Crawford, Emily L; Curran, Sarah R; Dawson, Geraldine; Duketis, Eftichia; Fernandez, Bridget A; Gallagher, Louise; Geller, Evan; Guter, Stephen J; Hill, R Sean; Ionita-Laza, Juliana; Jimenz Gonzalez, Patricia; Kilpinen, Helena; Klauck, Sabine M; Kolevzon, Alexander; Lee, Irene; Lei, Irene; Lei, Jing; Lehtimäki, Terho; Lin, Chiao-Feng; Ma'ayan, Avi; Marshall, Christian R; McInnes, Alison L; Neale, Benjamin; Owen, Michael J; Ozaki, Noriio; Parellada, Mara; Parr, Jeremy R; Purcell, Shaun; Puura, Kaija; Rajagopalan, Deepthi; Rehnström, Karola; Reichenberg, Abraham; Sabo, Aniko; Sachse, Michael; Sanders, Stephan J; Schafer, Chad; Schulte-Rüther, Martin; Skuse, David; Stevens, Christine; Szatmari, Peter; Tammimies, Kristiina; Valladares, Otto; Voran, Annette; Li-San, Wang; Weiss, Lauren A; Willsey, A Jeremy; Yu, Timothy W; Yuen, Ryan K C; Cook, Edwin H; Freitag, Christine M; Gill, Michael; Hultman, Christina M; Lehner, Thomas; Palotie, Aaarno; Schellenberg, Gerard D; Sklar, Pamela; State, Matthew W; Sutcliffe, James S; Walsh, Christiopher A; Scherer, Stephen W; Zwick, Michael E; Barett, Jeffrey C; Cutler, David J; Roeder, Kathryn; Devlin, Bernie; Daly, Mark J; Buxbaum, Joseph D

    2014-11-13

    The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome sequencing, here we show that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR) < 0.05, plus a set of 107 autosomal genes strongly enriched for those likely to affect risk (FDR < 0.30). These 107 genes, which show unusual evolutionary constraint against mutations, incur de novo loss-of-function mutations in over 5% of autistic subjects. Many of the genes implicated encode proteins for synaptic formation, transcriptional regulation and chromatin-remodelling pathways. These include voltage-gated ion channels regulating the propagation of action potentials, pacemaking and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodellers-most prominently those that mediate post-translational lysine methylation/demethylation modifications of histones.

  6. Chromatin Structure and Radiation-Induced Intrachromosome Exchange

    Science.gov (United States)

    Mangala; Zhang, Ye; Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

    2011-01-01

    We have recently investigated the location of breaks involved in intrachromosomal type exchange events, using the multicolor banding in situ hybridization (mBAND) technique for human chromosome 3. In human epithelial cells exposed to both low- and high-LET radiations in vitro, intrachromosome exchanges were found to occur preferentially between a break in the 3p21 and one in the 3q11. Exchanges were also observed between a break in 3p21 and one in 3q26, but few exchanges were observed between breaks in 3q11 and 3q26, even though the two regions were on the same arm of the chromosome. To explore the relationships between intrachromosome exchanges and chromatin structure, we used probes that hybridize the three regions of 3p21, 3q11 and 3q26, and measured the distance between two of the three regions in interphase cells. We further analyzed fragile sites on the chromosome that have been identified in various types of cancers. Our results demonstrated that the distribution of breaks involved in radiation-induced intrachromosome aberrations depends upon both the location of fragile sites and the folding of chromatins

  7. The role of proteins and metal ions in the protection of chromatin DNA at fast neutrons action

    International Nuclear Information System (INIS)

    Radu, L.; Preoteasa, V.; Radulescu, I.; Constantinescu, B.

    1997-01-01

    The role of chromatin proteins and of some ions on the fast neutrons actions on chromatin DNA from rat Walker tumors was analysed. The DNA in chromatin is effectively protected against fast neutrons actions by DNA bound proteins and specially by histones, because of the limited accessibility of the condensed chromatin DNA to hydroxyl radicals and of the scavenging of radicals by the chromatin proteins. The ions utilised protect chromatin DNA against the damage produced ed by fast neutrons, through the induction of structural DNA changes with a less accessibility to OH radicals. (authors)

  8. Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture.

    Science.gov (United States)

    Moriyama, Kenji; Yoshizawa-Sugata, Naoko; Masai, Hisao

    2018-03-09

    Rap1-interacting protein 1 (Rif1) regulates telomere length in budding yeast. We previously reported that, in metazoans and fission yeast, Rif1 also plays pivotal roles in controlling genome-wide DNA replication timing. We proposed that Rif1 may assemble chromatin compartments that contain specific replication-timing domains by promoting chromatin loop formation. Rif1 also is involved in DNA lesion repair, restart after replication fork collapse, anti-apoptosis activities, replicative senescence, and transcriptional regulation. Although multiple physiological functions of Rif1 have been characterized, biochemical and structural information on mammalian Rif1 is limited, mainly because of difficulties in purifying the full-length protein. Here, we expressed and purified the 2418-amino-acid-long, full-length murine Rif1 as well as its partially truncated variants in human 293T cells. Hydrodynamic analyses indicated that Rif1 forms elongated or extended homo-oligomers in solution, consistent with the presence of a HEAT-type helical repeat segment known to adopt an elongated shape. We also observed that the purified murine Rif1 bound G-quadruplex (G4) DNA with high specificity and affinity, as was previously shown for Rif1 from fission yeast. Both the N-terminal (HEAT-repeat) and C-terminal segments were involved in oligomer formation and specifically bound G4 DNA, and the central intrinsically disordered polypeptide segment increased the affinity for G4. Of note, pulldown assays revealed that Rif1 simultaneously binds multiple G4 molecules. Our findings support a model in which Rif1 modulates chromatin loop structures through binding to multiple G4 assemblies and by holding chromatin fibers together. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Labeling and advertising of home insulation

    Energy Technology Data Exchange (ETDEWEB)

    1978-07-01

    This staff report, prepared by the F.T.C.'s Bureau of Consumer Protection for Commission review, includes recommendations as to the final form of a trade regulation rule relating to the labeling and advertising of home insulation. Because of marketing abuses which accompanied the rising demand for home insulation, there has been broad support for a rule requiring information disclosures to help purchasers of home insulation to make an informed decision. The Commission, to provide such rule as quickly as possible, undertook its rulemaking proceeding under its new expedited rulemaking procedure. The rule was proposed on November 18, 1977, and, following a two-month period for written comments, four weeks of hearings were held in Washington, D.C. in February 1978. The record, contributed to by a variety of interests, shows that consumers do not know how to shop for home insulation. The staff-recommended rule, among other things, would require that insulation be tested and R-values (a measure of insulation's ability to retain heat) disclosed on labels and in advertising. To facilitate comparison shopping, the industry would also be required to furnish consumers with fact sheets describing, on a product-to-product basis, factors that can reduce the R-value of insulation.

  10. Slab edge insulating form system and methods

    Science.gov (United States)

    Lee, Brain E [Corral de Tierra, CA; Barsun, Stephan K [Davis, CA; Bourne, Richard C [Davis, CA; Hoeschele, Marc A [Davis, CA; Springer, David A [Winters, CA

    2009-10-06

    A method of forming an insulated concrete foundation is provided comprising constructing a foundation frame, the frame comprising an insulating form having an opening, inserting a pocket former into the opening; placing concrete inside the foundation frame; and removing the pocket former after the placed concrete has set, wherein the concrete forms a pocket in the placed concrete that is accessible through the opening. The method may further comprise sealing the opening by placing a sealing plug or sealing material in the opening. A system for forming an insulated concrete foundation is provided comprising a plurality of interconnected insulating forms, the insulating forms having a rigid outer member protecting and encasing an insulating material, and at least one gripping lip extending outwardly from the outer member to provide a pest barrier. At least one insulating form has an opening into which a removable pocket former is inserted. The system may also provide a tension anchor positioned in the pocket former and a tendon connected to the tension anchor.

  11. Electrical insulator requirements for mirror fusion reactors

    International Nuclear Information System (INIS)

    Condit, R.H.; Van Konynenburg, R.A.

    1977-01-01

    The requirements for mirror fusion electrical insulators are discussed. Insulators will be required at the neutral beam injectors, injector power supplies, direct converters, and superconducting magnets. Insulators placed at the neutral beam injectors will receive the greatest radiation exposure, 10 14 to 10 16 neutrons/m 2 .s and 0.3 to 3 Gy/s (10 5 to 10 6 R/h) of gamma rays, with shielding. Direct converter insulators may receive the highest temperature (up to 1300 0 K), but low voltage holding requirements. Insulators made from organic materials (e.g., plastics) for the magnet coils may be satisfactory. Immediate conductivity increases of all insulators result from gamma irradiation. With an upper limit to gamma flux exposures of 300 Gy/s in a minimally shielded region, the conductivity could reach 10 -6 S/m. Damage from neutron irradiation may not be serious during several years' exposure. Surface changes in ceramics at the neutral beam injector may be serious. The interior of the injector will contain atomic hydrogen, and sputtering may transfer material away from or onto the ceramic insulators. Unknown and potentially damaging interactions between irradiation, electric fields, temperature gradients, cycling of temperature, surface and joint reactions, sputtering, polarization, and electrotransport in the dielectrics are of concern. Materials research to deal with these problems is needed

  12. Excavationless Exterior Foundation Insulation Field Study

    Energy Technology Data Exchange (ETDEWEB)

    Schirber, T.; Mosiman, G.; Ojczyk, C.

    2014-10-01

    Building science research supports installing exterior (soil side) foundation insulation as the optimal method to enhance the hygrothermal performance of new homes. With exterior foundation insulation, water management strategies are maximized while insulating the basement space and ensuring a more even temperature at the foundation wall. However, such an approach can be very costly and disruptive when applied to an existing home, requiring deep excavation around the entire house. The NorthernSTAR Building America Partnership team implemented an innovative, minimally invasive foundation insulation upgrade technique on an existing home. The approach consisted of using hydrovac excavation technology combined with a liquid insulating foam. The team was able to excavate a continuous 4" wide by 4' to 5' deep trench around the entire house, 128 linear feet, except for one small part under the stoop that was obstructed with concrete debris. The combination pressure washer and vacuum extraction technology also enabled the elimination of large trenches and soil stockpiles normally produced by backhoe excavation. The resulting trench was filled with liquid insulating foam, which also served as a water-control layer of the assembly. The insulation was brought above grade using a liquid foam/rigid foam hybrid system and terminated at the top of the rim joist. Cost savings over the traditional excavation process ranged from 23% to 50%. The excavationless process could result in even greater savings since replacement of building structures, exterior features, utility meters, and landscaping would be minimal or non-existent in an excavationless process.

  13. Excavationless Exterior Foundation Insulation Field Study

    Energy Technology Data Exchange (ETDEWEB)

    Schirber, T. [NorthernSTAR, Minneaplolis, MN (United States); Mosiman, G. [NorthernSTAR, Minneaplolis, MN (United States); Ojczyk, C. [NorthernSTAR, Minneaplolis, MN (United States)

    2014-09-01

    Building science research supports installing exterior (soil side) foundation insulation as the optimal method to enhance the hygrothermal performance of new homes. With exterior foundation insulation, water management strategies are maximized while insulating the basement space and ensuring a more even temperature at the foundation wall. However, such an approach can be very costly and disruptive when applied to an existing home, requiring deep excavation around the entire house. The NorthernSTAR Building America Partnership team implemented an innovative, minimally invasive foundation insulation upgrade technique on an existing home. The approach consisted of using hydrovac excavation technology combined with liquid insulating foam. The team was able to excavate a continuous 4 inches wide by 4 feet to 5 feet deep trench around the entire house, 128 linear feet, except for one small part under the stoop that was obstructed with concrete debris. The combination pressure washer and vacuum extraction technology also enabled the elimination of large trenches and soil stockpiles normally produced by backhoe excavation. The resulting trench was filled with liquid insulating foam, which also served as a water-control layer of the assembly. The insulation was brought above grade using a liquid foam/rigid foam hybrid system and terminated at the top of the rim joist. Cost savings over the traditional excavation process ranged from 23% to 50%. The excavationless process could result in even greater savings since replacement of building structures, exterior features, utility meters, and landscaping would be minimal or non-existent in an excavationless process.

  14. Estimation of thermal insulation performance in multi-layer insulator for liquid helium pipe

    International Nuclear Information System (INIS)

    Shibanuma, Kiyoshi; Kuriyama, Masaaki; Shibata, Takemasa

    1991-01-01

    For a multi-layer insulator around the liquid helium pipes for cryopumps of JT-60 NBI, a multi-layer insulator composed of 10 layers, which can be wound around the pipe at the same time and in which the respective layers are in concentric circles by shifting them in arrangement, has been developed and tested. As the result, it was shown that the newly developed multi-layer insulator has better thermal insulation performance than the existing one, i.e. the heat load of the newly developed insulator composed of 10 layers was reduced to 1/3 the heat load of the existing insulator, and the heat leak at the joint of the insulator in longitudinal direction of the pipe was negligible. In order to clarify thermal characteristics of the multi-layer insulator, the heat transfer through the insulator has been analyzed considering the radiation heat transfer by the netting spacer between the reflectors, and the temperature dependence on the emissivities and the heat transmission coefficients of these two components of the insulator. The analytical results were in good agreements with the experimental ones, so that the analytical method was shown to be valid. Concerning the influence of the number of layers and the layer density on the insulation performance of the insulator, analytical results showed that the multi-layer insulator with the number of layer about N = 20 and the layer density below 2.0 layer/mm was the most effective for the liquid helium pipe of a JT-60 cryopump. (author)

  15. Measure Guideline. Hybrid Foundation Insulation Retrofits

    Energy Technology Data Exchange (ETDEWEB)

    Ueno, K. [Building Science Corporation, Somerville, MA (United States); Lstiburek, J. [Building Science Corporation, Somerville, MA (United States)

    2012-05-01

    This measure guideline provides recommendations for designs and variations for retrofit hybrid assemblies in improving interior foundation insulation and water management of basements. Variations include closed cell spray foam (ccSPF) with membrane waterproofing or air gap membrane drainage layers, rigid board foam insulation at flat walls (cast concrete or CMU block), a “partial drainage” detail making use of the bulk water drainage that occurs through the field of a rubble stone wall, and non-drained spray foam assemblies (including slab insulation).

  16. Measure Guideline: Hybrid Foundation Insulation Retrofits

    Energy Technology Data Exchange (ETDEWEB)

    Ueno, K.; Lstiburek, J.

    2012-05-01

    This measure guideline provides recommendations for designs and variations for retrofit hybrid assemblies in improving interior foundation insulation and water management of basements. Variations include closed cell spray foam (ccSPF) with membrane waterproofing or air gap membrane drainage layers, rigid board foam insulation at flat walls (cast concrete or CMU block), a 'partial drainage' detail making use of the bulk water drainage that occurs through the field of a rubble stone wall, and non-drained spray foam assemblies (including slab insulation).

  17. External insulation with cellular plastic materials

    DEFF Research Database (Denmark)

    Sørensen, Lars Schiøtt; Nielsen, Anker

    2014-01-01

    External thermal insulation composite systems (ETICS) can be used as extra insulation of existing buildings. The system can be made of cellular plastic materials or mineral wool. There is a European Technical guideline, ETAG 004, that describe the tests that shall be conducted on such systems....... This paper gives a comparison of systems with mineral wool and cellular plastic, based on experience from practice and literature. It is important to look at the details in the system and at long time stability of the properties such as thermal insulation, moisture and fire. Investigation of fire properties...

  18. Silicon on insulator self-aligned transistors

    Science.gov (United States)

    McCarthy, Anthony M.

    2003-11-18

    A method for fabricating thin-film single-crystal silicon-on-insulator (SOI) self-aligned transistors. Standard processing of silicon substrates is used to fabricate the transistors. Physical spaces, between the source and gate, and the drain and gate, introduced by etching the polysilicon gate material, are used to provide connecting implants (bridges) which allow the transistor to perform normally. After completion of the silicon substrate processing, the silicon wafer is bonded to an insulator (glass) substrate, and the silicon substrate is removed leaving the transistors on the insulator (glass) substrate. Transistors fabricated by this method may be utilized, for example, in flat panel displays, etc.

  19. Gibberellin-induced change in the structure of chromatin in wheat sprouts: decrease in the accessibility of DNA in preparations of soluble chromatin to the action of EcoRII methylase

    International Nuclear Information System (INIS)

    Noskov, V.A.; Kintsurashvili, L.N.; Smirnova, T.A.; Manamsh'yan, T.A.; Kir'yanov, G.I.; Vanyushin, B.F.

    1986-01-01

    A method has been perfected for producing soluble chromatin from whole wheat sprouts at low ionic strength. The chromatin preparations isolated possess a native structure: they have a nucleosome organization. Under identical conditions the soluble wheat chromatin undergoes more profound degradation by DNase I and staphylococcal nuclease than the chromatin from the rat liver. The DNA contained in the isolated chromatin is capable of accepting CHnumber groups from S-[methyl- 3 H]-adenosylmethionine during incubation with DNA methylase EcoRII; not all the CC A/T GG sequences in DNA are methylated in vivo. Chromatin from gibberellin A 3 -treated wheat sprout DNA accepts 40% fewer CH 3 groups than that from the control sprouts, which is probably due to the greater compactness of the chromatin. In the case of longer incubation, the level of methylation of the chromatin falls, which may be associated with the presence of DNA-demethylating activity

  20. Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex

    Science.gov (United States)

    Hulsman, Marc; Lelieveldt, Boudewijn P. F.; de Ridder, Jeroen; Reinders, Marcel

    2015-01-01

    The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains challenging. We address this by characterizing the topology of the cortical chromatin interaction network using scale-aware topological measures. We demonstrate that based on these characterizations it is possible to accurately predict spatial co-expression between genes in the mouse cortex. Consistent with previous findings, we find that the chromatin interaction profile of a gene-pair is a good predictor of their spatial co-expression. However, the accuracy of the prediction can be substantially improved when chromatin interactions are described using scale-aware topological measures of the multi-resolution chromatin interaction network. We conclude that, for co-expression prediction, it is necessary to take into account different levels of chromatin interactions ranging from direct interaction between genes (i.e. small-scale) to chromatin compartment interactions (i.e. large-scale). PMID:25965262

  1. Regular character of chromatin degradation in lymphoid tissues after treatment with biological alkylating agents in vivo

    International Nuclear Information System (INIS)

    Matyasova, J.; Skalka, M.; Cejkova, M.

    1979-01-01

    The chromatin changes are reevaluated occurring in lymphoid tissues of mice treated with alkylating agents of the nitrogen-mustard type in relation to recent evidence on the nucleosomal organization of chromatin and to our new data on the regular character of chromatin degradation in lymphoid tissues of irradiated mice. DNA was isolated from nuclei at various intervals (1 to 18 h) after treatment of mice and subjected to gel electrophoresis in polyacrylamide gels. Thymus chromatin from treated mice has been shown to degrade in a regular fashion and to yield discrete DNA fragments, resembling those that originate in lymphoid tissues of irradiated mice or in thymus nuclei digested with micrococcal nuclease in vitro. With increasing interval after treatment higher amounts of smaller DNA fragments appear. Chromatin in spleen cells responds to treatment in a similar way, whilst no degradation in vivo takes place in liver chromatin. Chromatin of LS/BL lymphosarcoma cells in mice treated with alkylating agents or with irradiation suffers from a similar regular degradation. The results stress the significance of the action of liberated or activated endogenous nuclease(s) in the development of chromatin damage in lymphoid cells after treatment with alkylating agents. (author)

  2. Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes.

    NARCIS (Netherlands)

    Boyer, L.A.; Logie, C.; Bonte, E; Becker, P.B.; Wade, P.A.; Wolff, A.P.; Wu, C.; Imbalzano, A.N.; Peterson, C.L.

    2000-01-01

    ATP-dependent chromatin remodeling enzymes antagonize the inhibitory effects of chromatin. We compare six different remodeling complexes: ySWI/SNF, yRSC, hSWI/SNF, xMi-2, dCHRAC, and dNURF. We find that each complex uses similar amounts of ATP to remodel nucleosomal arrays at nearly identical rates.

  3. Reading the maps: Organization and function of chromatin types in Drosophila

    NARCIS (Netherlands)

    Braunschweig, U.

    2010-01-01

    The work presented in this thesis shows that the Drosophila genome is organized in chromatin domains with many implications for gene regulation, nuclear organization, and evolution. Furthermore it provides examples of how maps of chromatin protein binding, combined with computational approaches, can

  4. Assembly of two transgenes in an artificial chromatin domain gives highly coordinated expression in tobacco

    NARCIS (Netherlands)

    Mlynárová, L.; Loonen, A.; Mietkiewska, E.; Jansen, R.C.; Nao, J.P.

    2002-01-01

    The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli ß-glucuronidase gene and the firefly luciferase gene, driven by different

  5. Assembly of Two Transgenes in an Artificial Chromatin Domain Gives Highly Coordinated Expression in Tobacco

    NARCIS (Netherlands)

    Mlynárová, Ludmila; Loonen, Annelies; Mietkiewska, Elzbieta; Jansen, Ritsert C.; Nap, Jan-Peter

    The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli β-glucuronidase gene and the firefly luciferase gene, driven by different

  6. Friend of Prmt1, a novel chromatin target of protein arginine methyltransferases

    NARCIS (Netherlands)

    T.B. van Dijk (Thamar); N. Gillemans (Nynke); C. Stein (Claudia); P. Fanis (Pavlos); J.A.A. Demmers (Jeroen); M.P.C. van de Corput (Mariëtte); J. Essers (Jeroen); F.G. Grosveld (Frank); U.M. Bauer (Uta-Maria); J.N.J. Philipsen (Sjaak)

    2010-01-01

    textabstractWe describe the isolation and characterization of Friend of Prmt1 (Fop), a novel chromatin target of protein arginine methyltransferases. Human Fop is encoded by C1orf77, a gene of previously unknown function. We show that Fop is tightly associated with chromatin, and that it is modified

  7. Modern human sperm freezing: Effect on DNA, chromatin and acrosome integrity

    Directory of Open Access Journals (Sweden)

    Tahereh Rahiminia

    2017-08-01

    Conclusion: Sperm in Vapour was healthier in terms of DNA, chromatin and acrosome integrity. In contrast of higher motility and normal morphology; DNA, chromatin and acrosome integrity were decreased in Vit. However, these findings were more acceptable in SSV or Vapour.

  8. High-throughput assessment of context-dependent effects of chromatin proteins

    NARCIS (Netherlands)

    Brueckner, L. (Laura); Van Arensbergen, J. (Joris); Akhtar, W. (Waseem); L. Pagie (Ludo); B. van Steensel (Bas)

    2016-01-01

    textabstractBackground: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy

  9. Small chromosomal regions position themselves autonomously according to their chromatin class.

    Science.gov (United States)

    van de Werken, Harmen J G; Haan, Josien C; Feodorova, Yana; Bijos, Dominika; Weuts, An; Theunis, Koen; Holwerda, Sjoerd J B; Meuleman, Wouter; Pagie, Ludo; Thanisch, Katharina; Kumar, Parveen; Leonhardt, Heinrich; Marynen, Peter; van Steensel, Bas; Voet, Thierry; de Laat, Wouter; Solovei, Irina; Joffe, Boris

    2017-06-01

    The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes. © 2017 van de Werken et al.; Published by Cold Spring Harbor Laboratory Press.

  10. Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Persson, Jenna [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); Ekwall, Karl, E-mail: karl.ekwall@ki.se [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); School of Life Sciences, University College Sodertorn, NOVUM, Huddinge (Sweden)

    2010-05-01

    Eukaryotic DNA is packaged around octamers of histone proteins into nucleosomes, the basic unit of chromatin. In addition to enabling meters of DNA to fit within the confines of a nucleus, the structure of chromatin has functional implications for cell identity. Covalent chemical modifications to the DNA and to histones, histone variants, ATP-dependent chromatin remodelers, small noncoding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. The great diversity of epigenomes that can arise from a single genome permits a single, totipotent cell to generate the hundreds of distinct cell types found in humans. Two recent studies in mouse and in fly have highlighted the importance of Chd1 chromatin remodelers for maintaining an open, active chromatin state. Based on evidence from fission yeast as a model system, we speculate that Chd1 remodelers are involved in the disassembly of nucleosomes at promoter regions, thus promoting active transcription and open chromatin. It is likely that these nucleosomes are specifically marked for disassembly by the histone variant H2A.Z.

  11. Induction of stable protein-deoxyribonucleic acid adducts in Chinese hamster cell chromatin by ultraviolet light

    International Nuclear Information System (INIS)

    Strniste, G.F.; Rall, S.C.

    1976-01-01

    Ultraviolet (uv)-light-mediated formation of protein-DNA adducts in Chinese hamster cell chromatin was investigated in an attempt to compare chromatin alterations induced in vitro with those observed in vivo. Three independent methods of analysis indicated stable protein-DNA associations: a membrane filter assay which retained DNA on the filter in the presence of high salt-detergent; a Sepharose 4B column assay in which protein eluted coincident with DNA; and a CsCl density gradient equilibrium assay which showed both protein and DNA banding at densities other than their respective native densities. Treatment of the irradiated chromatin with DNase provided further evidence that protein--DNA and not protein-protein adducts were being observed in the column assay. There is a fluence-dependent response of protein-DNA adduct formation when the chromatin is irradiated at low ionic strength and is linear for protein over the range studied. When the chromatin is exposed to differing conditions of pH, ionic strength, or divalent metal ion concentration, the quantity of adduct formed upon uv irradiation varies. Susceptibility to adduct formation can be partially explained in terms of the condensation state of the chromatin and other factors such as rearrangement, denaturation, and dissociation of the chromatin components. Besides providing information on the biological significance of these types of uv-induced lesions, this technique may be useful as a probe of chromatin structure

  12. Prediction of highly expressed genes in microbes based on chromatin accessibility

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Ussery, David

    2007-01-01

    BACKGROUND: It is well known that gene expression is dependent on chromatin structure in eukaryotes and it is likely that chromatin can play a role in bacterial gene expression as well. Here, we use a nucleosomal position preference measure of anisotropic DNA flexibility to predict highly expressed...

  13. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    International Nuclear Information System (INIS)

    Lesne, Annick; Victor, Jean–Marc; Bécavin, Christophe

    2012-01-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity. (perspective)

  14. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    Science.gov (United States)

    Lesne, Annick; Bécavin, Christophe; Victor, Jean–Marc

    2012-02-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.

  15. Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation

    International Nuclear Information System (INIS)

    Persson, Jenna; Ekwall, Karl

    2010-01-01

    Eukaryotic DNA is packaged around octamers of histone proteins into nucleosomes, the basic unit of chromatin. In addition to enabling meters of DNA to fit within the confines of a nucleus, the structure of chromatin has functional implications for cell identity. Covalent chemical modifications to the DNA and to histones, histone variants, ATP-dependent chromatin remodelers, small noncoding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. The great diversity of epigenomes that can arise from a single genome permits a single, totipotent cell to generate the hundreds of distinct cell types found in humans. Two recent studies in mouse and in fly have highlighted the importance of Chd1 chromatin remodelers for maintaining an open, active chromatin state. Based on evidence from fission yeast as a model system, we speculate that Chd1 remodelers are involved in the disassembly of nucleosomes at promoter regions, thus promoting active transcription and open chromatin. It is likely that these nucleosomes are specifically marked for disassembly by the histone variant H2A.Z.

  16. Targeting of chromatin readers: a novel strategy used by the Shigella flexneri virulence effector OspF to reprogram transcription

    Directory of Open Access Journals (Sweden)

    Habiba Harouz

    2014-12-01

    Full Text Available Shigella flexneri, a gram-negative bacterium responsible of bacillary dysentery, uses multiple strategies to overcome host immune defense. We have decrypted how this bacterium manipulates host-cell chromatin binders to take control of immune gene expression. We found that OspF, an injected virulence factor previously identified as a repressor of immune gene expression, targets the chromatin reader HP1γ. Heterochromatin Protein 1 family members specifically recognize and bind histone H3 methylated at Lys 9. Although initially identified as chromatin-associated transcriptional silencers in heterochromatin, their location in euchromatin indicates an active role in gene expression. Notably, HP1γ phosphorylation at Serine 83 defines a subpopulation exclusively located to euchromatin, targeted to the site of transcriptional elongation. We showed that OspF directly interacts with HP1γ, and causes HP1 dephosphorylation, suggesting a model in which this virulence effector “uses” HP1 proteins as beacons to target and repress immune gene expression (Harouz, et al. EMBO J (2014. OspF alters HP1γ phosphorylation mainly by inactivating the Erk-activated kinase MSK1, spotlighting it as a new HP1 kinase. In vivo, infectious stresses trigger HP1γ phosphorylation in the colon, principally in the lamina propria and the intestinal crypts. Several lines of evidence suggest that HP1 proteins are modified as extensively as histones, and decrypting the impact of these HP1 post-translational modifications on their transcriptional activities in vivo will be the next challenges to be taken up.

  17. Toxic effects of lead and nickel nitrate on rat liver chromatin components.

    Science.gov (United States)

    Rabbani-Chadegani Iii, Azra; Fani, Nesa; Abdossamadi, Sayeh; Shahmir, Nosrat

    2011-01-01

    The biological activity of heavy metals is related to their physicochemical interaction with biological receptors. In the present study, the effect of low concentrations of nickel nitrate and lead nitrate (lead nitrate to chromatin compared to nickel nitrate. Also, the binding affinity of lead nitrate to histone proteins free in solution was higher than nickel. On the basis of the results, it is concluded that lead reacts with chromatin components even at very low concentrations and induce chromatin aggregation through histone-DNA cross-links. Whereas, nickel nitrate is less effective on chromatin at low concentrations, suggesting higher toxicity of lead nitrate on chromatin compared to nickel. Copyright © 2010 Wiley Periodicals, Inc.

  18. High-Frequency Promoter Firing Links THO Complex Function to Heavy Chromatin Formation

    DEFF Research Database (Denmark)

    Mouaikel, John; Causse, Sébastien Z; Rougemaille, Mathieu

    2013-01-01

    The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes...... (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single......-molecule fluorescence insitu hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase...

  19. Time-resolved spectroscopy and fluorescence resonance energy transfer in the study of excimer laser damage of chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [Department of Molecular Genetics and Radiobiology, Babes National Institute, Bucharest (Romania)], E-mail: lilianajradu@yahoo.fr; Mihailescu, I. [Department of Lasers, Laser, Plasma and Radiation Physics Institute, Bucharest (Romania); Radu, S. [Department of Computer Science, Polytechnics University, Bucharest (Romania); Gazdaru, D. [Department of Biophysics, Bucharest University (Romania)

    2007-09-21

    The analysis of chromatin damage produced by a 248 nm excimer laser radiation, for doses of 0.3-3 MJ/m{sup 2} was carried out by time-resolved spectroscopy and fluorescence resonance energy transfer (FRET). The chromatin was extracted from a normal and a tumoral tissue of Wistar rats. The decrease with laser dose of the relative contribution of the excited state lifetimes of ethidium bromide (EtBr) bounded to chromatin constitutes an evidence of the reduction of chromatin deoxyribonucleic acid (DNA) double-strand structure. FRET was performed from dansyl chloride to acridine orange, both coupled to chromatin. The increase of the average distance between these ligands, under the action of laser radiation, reflects a loosening of the chromatin structure. The radiosensitivity of tumor tissue chromatin is higher than that of a normal tissue. The determination of the chromatin structure modification in an excimer laser field can be of interest in laser therapy.

  20. Time-resolved spectroscopy and fluorescence resonance energy transfer in the study of excimer laser damage of chromatin

    International Nuclear Information System (INIS)

    Radu, L.; Mihailescu, I.; Radu, S.; Gazdaru, D.

    2007-01-01

    The analysis of chromatin damage produced by a 248 nm excimer laser radiation, for doses of 0.3-3 MJ/m 2 was carried out by time-resolved spectroscopy and fluorescence resonance energy transfer (FRET). The chromatin was extracted from a normal and a tumoral tissue of Wistar rats. The decrease with laser dose of the relative contribution of the excited state lifetimes of ethidium bromide (EtBr) bounded to chromatin constitutes an evidence of the reduction of chromatin deoxyribonucleic acid (DNA) double-strand structure. FRET was performed from dansyl chloride to acridine orange, both coupled to chromatin. The increase of the average distance between these ligands, under the action of laser radiation, reflects a loosening of the chromatin structure. The radiosensitivity of tumor tissue chromatin is higher than that of a normal tissue. The determination of the chromatin structure modification in an excimer laser field can be of interest in laser therapy

  1. Snake-like chromatin in conjunctival cells of a population aged 30-60 years from Copenhagen City

    DEFF Research Database (Denmark)

    Bjerrum, Kirsten Birgitte

    1998-01-01

    ophthalmology, keratoconjunctivitis sicca, Sjögrens Syndrome, epidemiology, imprint biopsy, snake-like chromatin......ophthalmology, keratoconjunctivitis sicca, Sjögrens Syndrome, epidemiology, imprint biopsy, snake-like chromatin...

  2. Elucidation of Chromatin Remodeling Machinery Involved in Regulation of Estrogen Receptor Alpha Expression in Human Breast Cancer Cells

    National Research Council Canada - National Science Library

    Sharma, Dipali

    2005-01-01

    .... Using chromatin immunoprecipitation (ChIP), we examined the chromatin status and repressor complex associated with silenced ER and changes in the key regulatory factors during reactivation by inhibitors of DNMT...

  3. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-12-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation (MLI) has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five Glenn Research Center (GRC) provided coupons with 25 layers was shown to be +/- 8.4% whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0%. A second group of 10 coupons has been fabricated by Yetispace and tested by Florida State University, the repeatability between coupons has been shown to be +/- 15-25%. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  4. Surface electrical resistivity of insulators

    International Nuclear Information System (INIS)

    Senn, B. C.; Liesegang, J.

    1996-01-01

    A method is presented here for measuring surface charge decay, and theory has been developed so as to produce determinations of resistivity in the surface region of insulator films or wafers. This method incorporates the use of a coaxial cylindrical capacitor arrangement and an electrometer interfaced to a PC. The charge transport theory given here is based on Mott-Gurney diffusion, and allows easy interpretation of the experimental data, especially for the initial phase of surface charge decay. Resistivity measurements are presented for glass, mica, perspex and polyethylene, covering a range of 10 9 to 10 18 Ωm, as an illustration of the useful range of the instrument for static and antistatic materials, particularly in film or sheet form. Values for the surface charge diffusion constants of the materials are also presented. The charge transport theory has also been extended to allow the experimental and computational theoretical comparison of surface charge decay not only over the initial phase of charge decay, but also over longer times. The theoretical predictions show excellent agreement with experiment using the values for the diffusion constants referred to above

  5. Irradiation effects on organic insulators

    International Nuclear Information System (INIS)

    Kasen, M.B.

    1986-01-01

    The overall objective of this work is to contribute to development of organic insulators having the cryogenic neutron irradiation resistance required for MFE systems utilizing superconducting magnet confinement. The system for producing standard 3.2-mm (0.125-in) diameter rod specimens discussed in previous reports has been further refined to permit the fabrication of both fiber-reinforced and heat-resin specimens from hot-melt resin systems. The method has been successfully used to produce very high quality specimens duplicating the G-11CR system and specimens from a variant of that system eliminating a boron-containing additive. We have also produced specimens from an epoxy system suitable for impregnation or potting operations and from a bismaleimide polyimide system. These materials will be used in the first irradiation program in the National Low Temperature Neutron Irradiation Facility (NLTNIF) reactor at Oak Ridge. We have refined the 4-K torsional shear test method for evaluating radiation degradation of the fiber-matrix interface and have developed a method of quantitatively measuring changes in fracture energy as a function of radiation dose. Cooperative work with laboratories in Japan and England in this area is continuing and plans are being formulated for joint production, irradiation, and testing of specimens

  6. Spintronics Based on Topological Insulators

    Science.gov (United States)

    Fan, Yabin; Wang, Kang L.

    2016-10-01

    Spintronics using topological insulators (TIs) as strong spin-orbit coupling (SOC) materials have emerged and shown rapid progress in the past few years. Different from traditional heavy metals, TIs exhibit very strong SOC and nontrivial topological surface states that originate in the bulk band topology order, which can provide very efficient means to manipulate adjacent magnetic materials when passing a charge current through them. In this paper, we review the recent progress in the TI-based magnetic spintronics research field. In particular, we focus on the spin-orbit torque (SOT)-induced magnetization switching in the magnetic TI structures, spin-torque ferromagnetic resonance (ST-FMR) measurements in the TI/ferromagnet structures, spin pumping and spin injection effects in the TI/magnet structures, as well as the electrical detection of the surface spin-polarized current in TIs. Finally, we discuss the challenges and opportunities in the TI-based spintronics field and its potential applications in ultralow power dissipation spintronic memory and logic devices.

  7. Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers.

    Science.gov (United States)

    Deng, Xiang; Zhironkina, Oxana A; Cherepanynets, Varvara D; Strelkova, Olga S; Kireev, Igor I; Belmont, Andrew S

    2016-09-26

    In higher eukaryotic interphase nuclei, the 100- to >1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significant changes in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change in the overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Topological insulators Dirac equation in condensed matter

    CERN Document Server

    Shen, Shun-Qing

    2017-01-01

    This new edition presents a unified description of these insulators from one to three dimensions based on the modified Dirac equation. It derives a series of solutions of the bound states near the boundary, and describes the current status of these solutions. Readers are introduced to topological invariants and their applications to a variety of systems from one-dimensional polyacetylene, to two-dimensional quantum spin Hall effect and p-wave superconductors, three-dimensional topological insulators and superconductors or superfluids, and topological Weyl semimetals, helping them to better understand this fascinating field. To reflect research advances in topological insulators, several parts of the book have been updated for the second edition, including: Spin-Triplet Superconductors, Superconductivity in Doped Topological Insulators, Detection of Majorana Fermions and so on. In particular, the book features a new chapter on Weyl semimetals, a topic that has attracted considerable attention and has already b...

  9. KSI's Cross Insulated Core Transformer Technology

    International Nuclear Information System (INIS)

    Uhmeyer, Uwe

    2009-01-01

    Cross Insulated Core Transformer (CCT) technology improves on Insulated Core Transformer (ICT) implementations. ICT systems are widely used in very high voltage, high power, power supply systems. In an ICT transformer ferrite core sections are insulated from their neighboring ferrite cores. Flux leakage is present at each of these insulated gaps. The flux loss is raised to the power of stages in the ICT design causing output voltage efficiency to taper off with increasing stages. KSI's CCT technology utilizes a patented technique to compensate the flux loss at each stage of an ICT system. Design equations to calculate the flux compensation capacitor value are presented. CCT provides corona free operation of the HV stack. KSI's CCT based High Voltage power supply systems offer high efficiency operation, high frequency switching, low stored energy and smaller size over comparable ICT systems.

  10. Cryogenic Insulation Standard Data and Methodologies

    Data.gov (United States)

    National Aeronautics and Space Administration — Extending some recent developments in the area of technical consensus standards for cryogenic thermal insulation systems, a preliminary Inter-Laboratory Study of...

  11. Electrical breakdown studies with Mycalex insulators

    International Nuclear Information System (INIS)

    Waldron, W.; Greenway, W.; Eylon, S.; Henestroza, E.; Yu, S.

    2003-01-01

    Insulating materials such as alumina and glass-bonded mica (Mycalex) are used in accelerator systems for high voltage feedthroughs, structural supports, and barriers between high voltage insulating oil and the vacuum beam pipe in induction accelerator cells. Electric fields in the triple points should be minimized to prevent voltage breakdown. Mechanical stress can compromise seals and result in oil contamination of the insulator surface. We have tested various insulator cleaning procedures including ultrasonic cleaning with a variety of aqueous-based detergents, and manual scrubbing with various detergents. Water sheeting tests were used to determine the initial results of the cleaning methods. Ultimately, voltage breakdown tests will be used to quantify the benefits of these cleaning procedures

  12. Characterization techniques for ion bombarded insulators

    International Nuclear Information System (INIS)

    Borders, J.A.

    1987-01-01

    The chapter gives a comprehensive review of the experimental methods for the analysis of ion-bombarded insulators including optical and structural methods, resonance, energetic ion methods, and surface techniques. 48 refs.; 34 figs

  13. Corrosion-under-insulation (CUI) guidelines

    CERN Document Server

    Staff, European Federation of Corrosion; Winnik, S

    2014-01-01

    Corrosion under insulation (CUI) refers to the external corrosion of piping and vessels that occurs underneath externally clad/jacketed insulation as a result of the penetration of water. By its very nature CUI tends to remain undetected until the insulation and cladding/jacketing is removed to allow inspection or when leaks occur. CUI is a common problem shared by the refining, petrochemical, power, industrial, onshore and offshore industries. The European Federation of Corrosion (EFC) Working Parties WP13 and WP15 have worked to provide guidelines on managing CUI together with a number of major European refining, petrochemical and offshore companies including BP, Chevron-Texaco, Conoco-Phillips, ENI, Exxon-Mobil, IFP, MOL, Scanraff, Statoil, Shell, Total and Borealis. The guidelines within this document are intended for use on all plants and installations that contain insulated vessels, piping and equipment. The guidelines cover a risk-based inspection methodology for CUI, inspection techniques (including n...

  14. (ajst) effects of ground insulation and greenhouse

    African Journals Online (AJOL)

    NORBERT OPIYO AKECH

    and quality of biogas generation from dairy cattle dung. The effects ... Therefore ground insulation of plastic biogas digester under greenhouse conditions significantly enhances ..... The low values obtained did not suggest failure of the system ...

  15. Improved thermal monitoring of rotating machine insulation

    International Nuclear Information System (INIS)

    Stone, G.C.; Sedding, H.G.; Bernstein, B.S.

    1991-01-01

    Aging of motor and generator insulation is most often induced as a result of operation at high temperatures. In spite of this knowledge, stator and rotor temperatures are only crudely monitored in existing machines. In EPRI project RP2577-1, three new means of detecting machine temperatures were successfully developed. Two of the techniques, the Electronic Rotor Temperature Sensor and the Passive Rotor Temperature Sensor, were specifically developed to give point temperature readings on turbine generator rotor windings. The Insulation Sniffer allows operators to determine when any electrical insulation in a motor is overheating. Another electronic device, called the Thermal Life Indicator, helps operators and maintenance personnel determine how accumulated operation has affected the remaining life of the insulation in rotating machines. These new devices permit nuclear station operators to avoid hazardous operating conditions and will help to determine priorities for maintenance and plant life extension programs

  16. Thermal insulation performance of green roof systems

    Energy Technology Data Exchange (ETDEWEB)

    Celik, Serdar; Morgan, Susan; Retzlaff, William; Once, Orcun [southern Illinois University (United States)], e-mail: scelik@siue.edu, e-mail: smorgan@siue.edu, e-mail: wretzla@siue.edu, e-mail: oonce@siue.edu

    2011-07-01

    With the increasing costs of energy, good building insulation has become increasingly important. Among existing insulation techniques is the green roof system, which consists of covering the roof of a building envelop with plants. The aim of this paper is to assess the impact of vegetation type and growth media on the thermal performance of green roof systems. Twelve different green roof samples were made with 4 different growth media and 3 sedum types. Temperature at the sample base was recorded every 15 minutes for 3 years; the insulation behavior was then analysed. Results showed that the insulation characteristics were achieved with a combination of haydite and sedum sexangulare. This study demonstrated that the choice of growth media and vegetation is important to the green roof system's performance; further research is required to better understand the interactions between growth media and plant roots.

  17. Aluminum nitride insulating films for MOSFET devices

    Science.gov (United States)

    Lewicki, G. W.; Maserjian, J.

    1972-01-01

    Application of aluminum nitrides as electrical insulator for electric capacitors is discussed. Electrical properties of aluminum nitrides are analyzed and specific use with field effect transistors is defined. Operational limits of field effect transistors are developed.

  18. Effect of Sweating on Insulation of Footwear.

    Science.gov (United States)

    Kuklane, Kalev; Holmér, Ingvar

    1998-01-01

    The study aimed to find out the influence of sweating on footwear insulation with a thermal foot model. Simultaneously, the influence of applied weight (35 kg), sock, and steel toe cap were studied. Water to 3 sweat glands was supplied with a pump at the rate of 10 g/hr in total. Four models of boots with steel toe caps were tested. The same models were manufactured also without steel toe. Sweating reduced footwear insulation 19-25% (30-37% in toes). During static conditions, only a minimal amount of sweat evaporated from boots. Weight affected sole insulation: Reduction depended on compressibility of sole material. The influence of steel toe varied with insulation. The method of thermal foot model appears to be a practical tool for footwear evaluation.

  19. Grandstand view of phenolic foam insulation

    Energy Technology Data Exchange (ETDEWEB)

    1987-03-01

    Stadium Insulation Ltd, manufacture pipe sections, tank and vessel insulation products in Lowphen, polyisocyanurate, polyurethane foams and expanded polystyrene, though for certain specialist applications, cork is still employed in small quantities. Currently the emphasis is very much on Lowphen, the company's range of pipe sections based on phenolic foam. The company's manufacturing and marketing effort reflects the increasing market trend towards the use of insulating material capable of withstanding higher temperatures, and phenolic foam neatly satisfies the demand since it is capable of use at temperatures up to 140/sup 0/C. Moreover, phenolic foam has the lowest K value at 0.02W/m/sup 0/C of any of the currently available range of insulating materials, and while the product is slightly more expensive than alternatives such as polyisocyanurate and polyurethane, its high performance offsets that premium.

  20. Transcriptional and chromatin regulation during fasting – The genomic era

    Science.gov (United States)

    Goldstein, Ido; Hager, Gordon L.

    2015-01-01

    An elaborate metabolic response to fasting is orchestrated by the liver and is heavily reliant upon transcriptional regulation. In response to hormones (glucagon, glucocorticoids) many transcription factors (TFs) are activated and regulate various genes involved in metabolic pathways aimed at restoring homeostasis: gluconeogenesis, fatty acid oxidation, ketogenesis and amino acid shuttling. We summarize the recent discoveries regarding fasting-related TFs with an emphasis on genome-wide binding patterns. Collectively, the summarized findings reveal a large degree of co-operation between TFs during fasting which occurs at motif-rich DNA sites bound by a combination of TFs. These new findings implicate transcriptional and chromatin regulation as major determinants of the response to fasting and unravels the complex, multi-TF nature of this response. PMID:26520657

  1. Increased polyamines alter chromatin and stabilize autoantigens in autoimmune diseases

    Directory of Open Access Journals (Sweden)

    Wesley H. Brooks

    2013-04-01

    Full Text Available Polyamines are small cations with unique combinations of charge and length that give them many putative interactions in cells. Polyamines are essential since they are involved in replication, transcription, translation, and stabilization of macro-molecular complexes. However, polyamine synthesis competes with cellular methylation for S-adenosylmethionine, the methyl donor. Also, polyamine degradation can generate reactive molecules like acrolein. Therefore, polyamine levels are tightly controlled. This control may be compromised in autoimmune diseases since elevated polyamine levels are seen in autoimmune diseases. Here a hypothesis is presented explaining how polyamines can stabilize autoantigens. In addition, the hypothesis explains how polyamines can inappropriately activate enzymes involved in NETosis, a process in which chromatin is modified and extruded from cells as extracellular traps that bind pathogens during an immune response. This polyamine-induced enzymatic activity can lead to an increase in NETosis resulting in release of autoantigenic material and tissue damage.

  2. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective

    Directory of Open Access Journals (Sweden)

    Li Shen

    2013-06-01

    Full Text Available A decade-long project, led by several international research groups, called the Encyclopedia of DNA Elements (ENCODE, recently released an unprecedented amount of data. The ambitious project covers transcriptome, cistrome, epigenome, and interactome data from more than 1,600 sets of experiments in human. To make use of this valuable resource, it is important to understand the information it represents and the techniques that were used to generate these data. In this review, we introduce the data that ENCODE generated, summarize the observations from the data analysis, and revisit a computational approach that ENCODE used to predict gene expression, with a focus on the human transcriptome and its association with chromatin modifications.

  3. Causes and consequences of chromatin variation between inbred mice.

    Directory of Open Access Journals (Sweden)

    Mona Hosseini

    2013-06-01

    Full Text Available Variation at regulatory elements, identified through hypersensitivity to digestion by DNase I, is believed to contribute to variation in complex traits, but the extent and consequences of this variation are poorly characterized. Analysis of terminally differentiated erythroblasts in eight inbred strains of mice identified reproducible variation at approximately 6% of DNase I hypersensitive sites (DHS. Only 30% of such variable DHS contain a sequence variant predictive of site variation. Nevertheless, sequence variants within variable DHS are more likely to be associated with complex traits than those in non-variant DHS, and variants associated with complex traits preferentially occur in variable DHS. Changes at a small proportion (less than 10% of variable DHS are associated with changes in nearby transcriptional activity. Our results show that whilst DNA sequence variation is not the major determinant of variation in open chromatin, where such variants exist they are likely to be causal for complex traits.

  4. Chromatin Dynamics in Vivo: A Game of Musical Chairs

    Directory of Open Access Journals (Sweden)

    Daniël P. Melters

    2015-08-01

    Full Text Available Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.

  5. [Effect of irradiation on the degradation of rat thymocyte chromatin].

    Science.gov (United States)

    Tsudzevich, B O; Parkhomets', Iu P; Andriĭchuk, T R; Iurkina, V V

    1998-01-01

    Genome instability of adaptive nature is formed under the experimental influence on a cell. Under critical conditions, strategy of organism is to damage the cells that cannot be restored and controlled by including the program of apoptosis. The ordered internucleosomal DNA degradation is considered to be one of the proof attributes of immunocompetent cell apoptosis. We investigated the effects of various doses of irradiation on the thymocytes chromatine fragmentation in 1,2,3 hours after a single X-ray exposure or after chronic influence in conditions of Chernobyl research base. By the means of electrophoresis in agarose and judging by polydeoxyribonucleotides accumulation we observed the "ladder pattern" of degradation in 3 hr after single 1 Gr irradiation (the smallest dose displaying the effect). We suppose that the influence of both chronic low-intensity irradiation taking place in Chernobyl and single X-ray exposure result in intensifying of DNA fragmentation in the cells of immunocompetent organs.

  6. Chromatin Constrains the Initiation and Elongation of DNA Replication.

    Science.gov (United States)

    Devbhandari, Sujan; Jiang, Jieqing; Kumar, Charanya; Whitehouse, Iestyn; Remus, Dirk

    2017-01-05

    Eukaryotic chromosomal DNA is faithfully replicated in a complex series of cell-cycle-regulated events that are incompletely understood. Here we report the reconstitution of DNA replication free in solution with purified proteins from the budding yeast Saccharomyces cerevisiae. The system recapitulates regulated bidirectional origin activation; synthesis of leading and lagging strands by the three replicative DNA polymerases Pol α, Pol δ, and Pol ε; and canonical maturation of Okazaki fragments into continuous daughter strands. We uncover a dual regulatory role for chromatin during DNA replication: promoting origin dependence and determining Okazaki fragment length by restricting Pol δ progression. This system thus provides a functional platform for the detailed mechanistic analysis of eukaryotic chromosome replication. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Chromatin in fractal globule state: evidence from comet assay

    Directory of Open Access Journals (Sweden)

    Afanasieva K. S.

    2015-04-01

    Full Text Available At higher order levels chromatin is organized into loops that appear as a result of contacts between distant loci. The aim of this work was to investigate the length distribution of the DNA loops in nucleoids obtained after lysis of either whole cells or isolated cell nuclei. Methods. We used single cell gel electrophoresis to analyze the kinetics of the DNA loop migration from the two nucleoid types. Results. The kinetics of the DNA exit was found to have specific features for the two types of nucleoids. At the same time, in both cases, the DNA amount in the electrophoretic track depends linearly on the length of the longest loops in the track. Conclusions. We have concluded that for the loops up to ~ 100 kb the length distribution appears to be consistent with the fractal globule organization.

  8. Pyrimidine dimers in Drosophila chromatin become increasingly accessible after irradiation

    International Nuclear Information System (INIS)

    Harris, P.V.; Boyd, J.B.

    1987-01-01

    A prokaryotic DNA-repair enzyme has been utilized as a probe for changes in the accessibility of pyrimidine dimers in Drosophila chromatin following UV irradiation. The results demonstrate a rapid cellular response to physiologically relevant doses of radiation which results in at least a 40% increase in accessible dimers. This increase occurs in two incision-deficient mutants which indicates that the excision-repair process, at or beyond the incision step, is not required or responsible for the increase. In the absence of excision the increase in accessibility persists for a least 2 days following irradiation. The observed increase in accessibility is inhibited by both novobiocin and coumermycin. These inhibitors do not inhibit the initial rate of incision, but do reduce dimer excision measured over more extended periods. A pre-incision process is proposed which actively exposes DNA lesions to excision repair. A fraction of the genome is postulated to be accessible without the intervention of that process. (Auth.)

  9. Total dose hardening of buried insulator in implanted silicon-on-insulator structures

    International Nuclear Information System (INIS)

    Mao, B.Y.; Chen, C.E.; Pollack, G.; Hughes, H.L.; Davis, G.E.

    1987-01-01

    Total dose characteristics of the buried insulator in implanted silicon-on-insulator (SOI) substrates have been studied using MOS transistors. The threshold voltage shift of the parasitic back channel transistor, which is controlled by charge trapping in the buried insulator, is reduced by lowering the oxygen dose as well as by an additional nitrogen implant, without degrading the front channel transistor characteristics. The improvements in the radiation characteristics of the buried insulator are attributed to the decrease in the buried oxide thickness or to the presence of the interfacial oxynitride layer formed by the oxygen and nitrogen implants

  10. Comparative transmission genetics of introgressed chromatin in Gossypium (cotton) polyploids.

    Science.gov (United States)

    Waghmare, Vijay N; Rong, Junkang; Rogers, Carl J; Bowers, John E; Chee, Peng W; Gannaway, John R; Katageri, Ishwarappa; Paterson, Andrew H

    2016-04-01

    Introgression is widely acknowledged as a potential source of valuable genetic variation, and growing effort is being invested in analysis of interspecific crosses conferring transgressive variation. Experimental backcross populations provide an opportunity to study transmission genetics following interspecific hybridization, identifying opportunities and constraints to introgressive crop improvement. The evolutionary consequences of introgression have been addressed at the theoretical level, however, issues related to levels and patterns of introgression among (plant) species remain inadequately explored, including such factors as polyploidization, subgenome interaction inhabiting a common nucleus, and the genomic distribution and linkage relationships of introgressant alleles. We analyze introgression into the polyploid Gossypium hirsutum (upland cotton) from its sister G. tomentosum and compare the level and pattern with that of G. barbadense representing a different clade tracing to the same polyploidization. Across the genome, recurrent backcrossing to Gossypium hirsutum yielded only one-third of the expected average frequency of the G. tomentosum allele, although one unusual region showed preferential introgression. Although a similar rate of introgression is found in the two subgenomes of polyploid (AtDt) G. hirsutum, a preponderance of multilocus interactions were largely within the Dt subgenome. Skewed G. tomentosum chromatin transmission is polymorphic among two elite G. hirsutum genotypes, which suggests that genetic background may profoundly affect introgression of particular chromosomal regions. Only limited correspondence is found between G. hirsutum chromosomal regions that are intolerant to introgression from the two species, G. barbadense and G. tomentosum, concentrated near possible inversion polymorphisms. Complex transmission of introgressed chromatin highlights the challenges to utilization of exotic germplasm in crop improvement. © 2016

  11. Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2.

    Directory of Open Access Journals (Sweden)

    Nina Winter

    Full Text Available BACKGROUND: HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors. The protein harbours three basically charged DNA binding domains and an acidic protein binding C-terminal domain. DNA binding induces changes of DNA conformation and hence results in global overall change of gene expression patterns. Recently, using a PCR-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment procedure two consensus sequences for HMGA2 binding have been identified. METHODOLOGY/PRINCIPAL FINDINGS: In this investigation chromatin immunoprecipitation (ChIP experiments and bioinformatic methods were used to analyze if these binding sequences can be verified on chromatin of living cells as well. CONCLUSION: After quantification of HMGA2 protein in different cell lines the colon cancer derived cell line HCT116 was chosen for further ChIP experiments because of its 3.4-fold higher HMGA2 protein level. 49 DNA fragments were obtained by ChIP. These fragments containing HMGA2 binding sites have been analyzed for their AT-content, location in the human genome and similarities to sequences generated by a SELEX study. The sequences show a significantly higher AT-content than the average of the human genome. The artificially generated SELEX sequences and short BLAST alignments (11 and 12 bp of the ChIP fragments from living cells show similarities in their organization. The flanking regions are AT-rich, whereas a lower conservation is present in the center of the sequences.

  12. Alternative epigenetic chromatin states of polycomb target genes.

    Directory of Open Access Journals (Sweden)

    Yuri B Schwartz

    2010-01-01

    Full Text Available Polycomb (PcG regulation has been thought to produce stable long-term gene silencing. Genomic analyses in Drosophila and mammals, however, have shown that it targets many genes, which can switch state during development. Genetic evidence indicates that critical for the active state of PcG target genes are the histone methyltransferases Trithorax (TRX and ASH1. Here we analyze the repertoire of alternative states in which PcG target genes are found in different Drosophila cell lines and the role of PcG proteins TRX and ASH1 in controlling these states. Using extensive genome-wide chromatin immunoprecipitation analysis, RNAi knockdowns, and quantitative RT-PCR, we show that, in addition to the known repressed state, PcG targets can reside in a transcriptionally active state characterized by formation of an extended domain enriched in ASH1, the N-terminal, but not C-terminal moiety of TRX and H3K27ac. ASH1/TRX N-ter domains and transcription are not incompatible with repressive marks, sometimes resulting in a "balanced" state modulated by both repressors and activators. Often however, loss of PcG repression results instead in a "void" state, lacking transcription, H3K27ac, or binding of TRX or ASH1. We conclude that PcG repression is dynamic, not static, and that the propensity of a target gene to switch states depends on relative levels of PcG, TRX, and activators. N-ter TRX plays a remarkable role that antagonizes PcG repression and preempts H3K27 methylation by acetylation. This role is distinct from that usually attributed to TRX/MLL proteins at the promoter. These results have important implications for Polycomb gene regulation, the "bivalent" chromatin state of embryonic stem cells, and gene expression in development.

  13. Facility for endurance tests of thermal insulations

    International Nuclear Information System (INIS)

    Mauersberger, R.

    1984-01-01

    In the following report the design and construction of an experimental facility for endurance tests of thermal insulations is presented. It's name in abbreviation is 'ADI' standing for the German words A nlage zum Dauertest von Isolierungen . This test facility was build by HRB in order to investigate the performance of thermal insulation systems of hot gas ducts for the process heat-reactor-project. The tests are intended to simulate the conditions of reactor operation. They include short-time experiments for selection of insulation-concepts and in a second step long-time experiments as performance tests. During these tests are measured the effective heat conductivity the local heat losses the temperature profiles of the insulation, of the fixing elements and along the wall of the duct. The design-data required to perform all these tasks are shown in the first picture: The gas-atmosphere must be Helium in tests like in reactor with regard to the special thermal and hydraulic properties of Helium and to the influence of Helium on mechanic friction and wear. The hot gas temperature in the PNP-reactor will be 950 deg. C and should be equal in the experiments. The temperature on the cold side of the insulation has to be adjustable from 50 deg. C up to 300 deg. C. The Helium pressure in the hot gas ducts of a HTR-plant is about 42 bar. The ADI was laid out for 70 bar to cover the hole range of interest. A Helium mass flow has to stream through the insulated test duct in order to realize equal temperatures on the hot side of the insulation. A flow rate of 4,5 kg/s is sufficient for this requirement. The axial pressure gradient along the insulation must be the same as in the reactor, because this has an essential influence on the heat losses. This pressure gradient is about 40 Pa/m

  14. Status of surface conduction in topological insulators

    International Nuclear Information System (INIS)

    Barua, Sourabh; Rajeev, K. P.

    2014-01-01

    In this report, we scrutinize the thickness dependent resistivity data from the recent literature on electrical transport measurements in topological insulators. A linear increase in resistivity with increase in thickness is expected in the case of these materials since they have an insulating bulk and a conducting surface. However, such a trend is not seen in the resistivity versus thickness data for all the cases examined, except for some samples, where it holds for a range of thickness

  15. Measure Guideline. Internal Insulation of Masonry Walls

    Energy Technology Data Exchange (ETDEWEB)

    Straube, J. F. [Building Science Corporation (BSC), Somerville, MA (United States); Ueno, K. [Building Science Corporation (BSC), Somerville, MA (United States); Schumacher, C. J. [Building Science Corporation (BSC), Somerville, MA (United States)

    2012-07-01

    This measure guideline provides recommendations for interior insulation assemblies that control interstitial condensation and durability risks; recommendations for acceptable thermal performance are also provided. An illustrated guide of high-risk exterior details (which concentrate bulk water), and recommended remediation details is provided. This is followed by a recommended methodology for risk assessment of a masonry interior insulation project: a series of steps are suggested to assess the risks associated with this retrofit, with greater certainty with added steps.

  16. Measure Guideline: Internal Insulation of Masonry Walls

    Energy Technology Data Exchange (ETDEWEB)

    Straube, J. F.; Ueno, K.; Schumacher, C. J.

    2012-07-01

    This measure guideline provides recommendations for interior insulation assemblies that control interstitial condensation and durability risks; recommendations for acceptable thermal performance are also provided. An illustrated guide of high-risk exterior details (which concentrate bulk water), and recommended remediation details is provided. This is followed by a recommended methodology for risk assessment of a masonry interior insulation project: a series of steps are suggested to assess the risks associated with this retrofit, with greater certainty with added steps.

  17. High-voltage polymeric insulated cables

    Energy Technology Data Exchange (ETDEWEB)

    Ross, A

    1987-01-01

    Reviews developments in high-voltage (here defined as 25 kV, 66 kV and 132 kV) polymeric insulated cables in the UK over the period 1979-1986, with particular reference to the experience of the Eastern Electricity Board. Outlines the background to the adoption of XPLE-insulated solid cable, and the design, testing, terminations, jointing and costs of 25 kV, 66 kV and 132 kV cables.

  18. Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans

    Directory of Open Access Journals (Sweden)

    Sha Ky

    2010-08-01

    Full Text Available Abstract Background Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underlying genomic DNA, the epigenome influences the cell's transcriptome and ultimately its function. Existing genomic methods for analyzing cell-type-specific changes in chromatin generally involve two elements: (i a source for purified cells (or nuclei of distinct types, and (ii a specific treatment that partitions or degrades chromatin by activity or structural features. For many cell types of great interest, such assays are limited by our inability to isolate the relevant cell populations in an organism or complex tissue containing an intertwined mixture of other cells. This limitation has confined available knowledge of chromatin dynamics to a narrow range of biological systems (cell types that can be sorted/separated/dissected in large numbers and tissue culture models or to amalgamations of diverse cell types (tissue chunks, whole organisms. Results Transgene-driven expression of DNA/chromatin modifying enzymes provides one opportunity to query chromatin structures in expression-defined cell subsets. In this work we combine in vivo expression of a bacterial DNA adenine methyltransferase (DAM with high throughput sequencing to sample tissue-specific chromatin accessibility on a genome-wide scale. We have applied the method (DALEC: Direct Asymmetric Ligation End Capture towards mapping a cell-type-specific view of genome accessibility as a function of differentiated state. Taking advantage of C. elegans strains expressing the DAM enzyme in diverse tissues (body wall muscle, gut, and hypodermis, our efforts yield a genome-wide dataset measuring chromatin accessibility at each of 538,000 DAM target sites in the C. elegans (diploid genome. Conclusions Validating the DALEC mapping results, we observe a strong association

  19. Snake-like chromatin in conjunctival cells of normal elderly persons and of patients with primary Sjögren's syndrome and other connective tissue diseases

    DEFF Research Database (Denmark)

    Bjerrum, Kirsten Birgitte

    1995-01-01

    Ophthalmology, snake-like chromatin, cytoplasm ratio, keratoconjunctivitis sicca, nucleus, goblet cell......Ophthalmology, snake-like chromatin, cytoplasm ratio, keratoconjunctivitis sicca, nucleus, goblet cell...

  20. Load responsive multilayer insulation performance testing

    International Nuclear Information System (INIS)

    Dye, S.; Kopelove, A.; Mills, G. L.

    2014-01-01

    Cryogenic insulation designed to operate at various pressures from one atmosphere to vacuum, with high thermal performance and light weight, is needed for cryogenically fueled space launch vehicles and aircraft. Multilayer insulation (MLI) performs well in a high vacuum, but the required vacuum shell for use in the atmosphere is heavy. Spray-on foam insulation (SOFI) is often used in these systems because of its light weight, but can have a higher heat flux than desired. We report on the continued development of Load Responsive Multilayer Insulation (LRMLI), an advanced thermal insulation system that uses dynamic beam discrete spacers that provide high thermal performance both in atmosphere and vacuum. LRMLI consists of layers of thermal radiation barriers separated and supported by micromolded polymer spacers. The spacers have low thermal conductance, and self-support a thin, lightweight vacuum shell that provides internal high vacuum in the insulation. The dynamic load responsive spacers compress to support the external load of a vacuum shell in one atmosphere, and decompress under reduced atmospheric pressure for lower heat leak. Structural load testing was performed on the spacers with various configurations. LRMLI was installed on a 400 liter tank and boil off testing with liquid nitrogen performed at various chamber pressures from one atmosphere to high vacuum. Testing was also performed with an MLI blanket on the outside of the LRMLI

  1. Proximity effects in topological insulator heterostructures

    International Nuclear Information System (INIS)

    Li Xiao-Guang; Wu Guang-Fen; Zhang Gu-Feng; Culcer Dimitrie; Zhang Zhen-Yu; Chen Hua

    2013-01-01

    Topological insulators (TIs) are bulk insulators that possess robust helical conducting states along their interfaces with conventional insulators. A tremendous research effort has recently been devoted to Tl-based heterostructures, in which conventional proximity effects give rise to a series of exotic physical phenomena. This paper reviews our recent studies on the potential existence of topological proximity effects at the interface between a topological insulator and a normal insulator or other topologically trivial systems. Using first-principles approaches, we have realized the tunability of the vertical location of the topological helical state via intriguing dual-proximity effects. To further elucidate the control parameters of this effect, we have used the graphene-based heterostructures as prototypical systems to reveal a more complete phase diagram. On the application side of the topological helical states, we have presented a catalysis example, where the topological helical state plays an essential role in facilitating surface reactions by serving as an effective electron bath. These discoveries lay the foundation for accurate manipulation of the real space properties of the topological helical state in TI-based heterostructures and pave the way for realization of the salient functionality of topological insulators in future device applications. (topical review - low-dimensional nanostructures and devices)

  2. Load responsive multilayer insulation performance testing

    Energy Technology Data Exchange (ETDEWEB)

    Dye, S.; Kopelove, A. [Quest Thermal Group, 6452 Fig Street Suite A, Arvada, CO 80004 (United States); Mills, G. L. [Ball Aerospace and Technologies Corp, 1600 Commerce Street, Boulder, CO 80301 (United States)

    2014-01-29

    Cryogenic insulation designed to operate at various pressures from one atmosphere to vacuum, with high thermal performance and light weight, is needed for cryogenically fueled space launch vehicles and aircraft. Multilayer insulation (MLI) performs well in a high vacuum, but the required vacuum shell for use in the atmosphere is heavy. Spray-on foam insulation (SOFI) is often used in these systems because of its light weight, but can have a higher heat flux than desired. We report on the continued development of Load Responsive Multilayer Insulation (LRMLI), an advanced thermal insulation system that uses dynamic beam discrete spacers that provide high thermal performance both in atmosphere and vacuum. LRMLI consists of layers of thermal radiation barriers separated and supported by micromolded polymer spacers. The spacers have low thermal conductance, and self-support a thin, lightweight vacuum shell that provides internal high vacuum in the insulation. The dynamic load responsive spacers compress to support the external load of a vacuum shell in one atmosphere, and decompress under reduced atmospheric pressure for lower heat leak. Structural load testing was performed on the spacers with various configurations. LRMLI was installed on a 400 liter tank and boil off testing with liquid nitrogen performed at various chamber pressures from one atmosphere to high vacuum. Testing was also performed with an MLI blanket on the outside of the LRMLI.

  3. Topological insulators and superconductors from string theory

    International Nuclear Information System (INIS)

    Ryu, Shinsei; Takayanagi, Tadashi

    2010-01-01

    Topological insulators and superconductors in different spatial dimensions and with different discrete symmetries have been fully classified recently, revealing a periodic structure for the pattern of possible types of topological insulators and superconductors, both in terms of spatial dimensions and in terms of symmetry classes. It was proposed that K theory is behind the periodicity. On the other hand, D-branes, a solitonic object in string theory, are also known to be classified by K theory. In this paper, by inspecting low-energy effective field theories realized by two parallel D-branes, we establish a one-to-one correspondence between the K-theory classification of topological insulators/superconductors and D-brane charges. In addition, the string theory realization of topological insulators and superconductors comes naturally with gauge interactions, and the Wess-Zumino term of the D-branes gives rise to a gauge field theory of topological nature, such as ones with the Chern-Simons term or the θ term in various dimensions. This sheds light on topological insulators and superconductors beyond noninteracting systems, and the underlying topological field theory description thereof. In particular, our string theory realization includes the honeycomb lattice Kitaev model in two spatial dimensions, and its higher-dimensional extensions. Increasing the number of D-branes naturally leads to a realization of topological insulators and superconductors in terms of holography (AdS/CFT).

  4. High-Performance Slab-on-Grade Foundation Insulation Retrofits

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Louise F. [NorthernSTAR, St. Paul, MN (United States); Mosiman, Garrett E. [NorthernSTAR, St. Paul, MN (United States)

    2015-09-01

    A more accurate assessment of slab-on-grade foundation insulation energy savings than traditionally possible is now feasible. This has been enabled by advances in whole building energy simulation with 3-dimensional foundation modelling integration at each time step together with an experimental measurement of the site energy savings of SOG foundation insulation. Ten SOG insulation strategies were evaluated on a test building to identify an optimum retrofit insulation strategy in a zone 6 climate (Minneapolis, MN). The optimum insulation strategy in terms of energy savings and cost effectiveness consisted of two components: (a) R-20 XPS insulation above grade, and, (b) R-20 insulation at grade (comprising an outer layer of R-10 insulation and an interior layer of R-12 poured polyurethane insulation) tapering to R-10 XPS insulation at half the below-grade wall height (the lower half of the stem wall was uninsulated).

  5. Magnetic insulation in triplate and coaxial vacuum transmission lines. Report PIFR-1009

    International Nuclear Information System (INIS)

    Di Capua, M.; Pellinen, D.G.

    1980-08-01

    An experimental investigation was made of magnetically insulated transmission lines for use in an electron beam fusion accelerator. The magnetically insulated vacuum transmission lines would transfer the power pulses from many modules to a single diode region or multiple diodes to generate currents on the order of 100 MA. This approach may allow present limits on power flow through dielectric vacuum interfaces to be overcome. We have investigated symmetric parallel plate (triplate) transmission lines with a wave impedance of 24 Ω and a spacing of 1.9 cm, and coaxial transmission lines (coax) with a wave impedance of 42 Ω and a spacing of 2.9 cm

  6. Linear accelerator with x-ray absorbing insulators

    International Nuclear Information System (INIS)

    Rose, P.H.

    1975-01-01

    Annular insulators for supporting successive annular electrodes in a linear accelerator have embedded x-ray absorbing shield structures extending around the accelerating path. The shield members are disposed to intercept x-ray radiation without disrupting the insulative effect of the insulator members. In preferred forms, the structure comprises a plurality of annular members of heavy metal disposed in an x-ray blocking array, spaced from each other by the insulating substance of the insulator member. (auth)

  7. Development of insulating coatings for liquid metal blankets

    International Nuclear Information System (INIS)

    Malang, S.; Borgstedt, H.U.; Farnum, E.H.; Natesan, K.; Vitkovski, I.V.

    1994-07-01

    It is shown that self-cooled liquid metal blankets are feasible only with electrically insulating coatings at the duct walls. The requirements on the insulation properties are estimated by simple analytical models. Candidate insulator materials are selected based on insulating properties and thermodynamic consideration. Different fabrication technologies for insulating coatings are described. The status of the knowledge on the most crucial feasibility issue, the degradation of the resisivity under irradiation, is reviewed

  8. Selection on a Subunit of the NURF Chromatin Remodeler Modifies Life History Traits in a Domesticated Strain of Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Edward E Large

    2016-07-01

    Full Text Available Evolutionary life history theory seeks to explain how reproductive and survival traits are shaped by selection through allocations of an individual's resources to competing life functions. Although life-history traits evolve rapidly, little is known about the genetic and cellular mechanisms that control and couple these tradeoffs. Here, we find that two laboratory-adapted strains of C. elegans descended from a single common ancestor that lived in the 1950s have differences in a number of life-history traits, including reproductive timing, lifespan, dauer formation, growth rate, and offspring number. We identified a quantitative trait locus (QTL of large effect that controls 24%-75% of the total trait variance in reproductive timing at various timepoints. Using CRISPR/Cas9-induced genome editing, we show this QTL is due in part to a 60 bp deletion in the 3' end of the nurf-1 gene, which is orthologous to the human gene encoding the BPTF component of the NURF chromatin remodeling complex. Besides reproduction, nurf-1 also regulates growth rate, lifespan, and dauer formation. The fitness consequences of this deletion are environment specific-it increases fitness in the growth conditions where it was fixed but decreases fitness in alternative laboratory growth conditions. We propose that chromatin remodeling, acting through nurf-1, is a pleiotropic regulator of life history trade-offs underlying the evolution of multiple traits across different species.

  9. An Insulating Glass Knowledge Base

    Energy Technology Data Exchange (ETDEWEB)

    Michael L. Doll; Gerald Hendrickson; Gerard Lagos; Russell Pylkki; Chris Christensen; Charlie Cureija

    2005-08-01

    This report will discuss issues relevant to Insulating Glass (IG) durability performance by presenting the observations and developed conclusions in a logical sequential format. This concluding effort discusses Phase II activities and focuses on beginning to quantifying IG durability issues while continuing the approach presented in the Phase I activities (Appendix 1) which discuss a qualitative assessment of durability issues. Phase II developed a focus around two specific IG design classes previously presented in Phase I of this project. The typical box spacer and thermoplastic spacer design including their Failure Modes and Effect Analysis (FMEA) and Fault Tree diagrams were chosen to address two currently used IG design options with varying components and failure modes. The system failures occur due to failures of components or their interfaces. Efforts to begin quantifying the durability issues focused on the development and delivery of an included computer based IG durability simulation program. The focus/effort to deliver the foundation for a comprehensive IG durability simulation tool is necessary to address advancements needed to meet current and future building envelope energy performance goals. This need is based upon the current lack of IG field failure data and the lengthy field observation time necessary for this data collection. Ultimately, the simulation program is intended to be used by designers throughout the current and future industry supply chain. Its use is intended to advance IG durability as expectations grow around energy conservation and with the growth of embedded technologies as required to meet energy needs. In addition the tool has the immediate benefit of providing insight for research and improvement prioritization. Included in the simulation model presentation are elements and/or methods to address IG materials, design, process, quality, induced stress (environmental and other factors), validation, etc. In addition, acquired data

  10. Biodegradation performance of environmentally-friendly insulating oil

    Science.gov (United States)

    Yang, Jun; He, Yan; Cai, Shengwei; Chen, Cheng; Wen, Gang; Wang, Feipeng; Fan, Fan; Wan, Chunxiang; Wu, Liya; Liu, Ruitong

    2018-02-01

    In this paper, biodegradation performance of rapeseed insulating oil (RDB) and FR3 insulating oil (FR3) was studied by means of ready biodegradation method which was performed with Organization for Economic Co-operation and Development (OECD) 301B. For comparison, the biodegradation behaviour of 25# mineral insulating oil was also characterized with the same method. The testing results shown that the biodegradation degree of rapeseed insulating oil, FR3 insulating oil and 25# mineral insulating oil was 95.8%, 98.9% and 38.4% respectively. Following the “new chemical risk assessment guidelines” (HJ/T 154 - 2004), which illustrates the methods used to identify and assess the process safety hazards inherent. The guidelines can draw that the two vegetable insulating oils, i.e. rapeseed insulating oil and FR3 insulating oil are easily biodegradable. Therefore, the both can be classified as environmentally-friendly insulating oil. As expected, 25# mineral insulating oil is hardly biodegradable. The main reason is that 25# mineral insulating oil consists of isoalkanes, cyclanes and a few arenes, which has few unsaturated bonds. Biodegradation of rapeseed insulating oil and FR3 insulating oil also remain some difference. Biodegradation mechanism of vegetable insulating oil was revealed from the perspective of hydrolysis kinetics.

  11. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration.

    Science.gov (United States)

    Matysiak, Julien; Lesbats, Paul; Mauro, Eric; Lapaillerie, Delphine; Dupuy, Jean-William; Lopez, Angelica P; Benleulmi, Mohamed Salah; Calmels, Christina; Andreola, Marie-Line; Ruff, Marc; Llano, Manuel; Delelis, Olivier; Lavigne, Marc; Parissi, Vincent

    2017-07-28

    Insertion of retroviral genome DNA occurs in the chromatin of the host cell. This step is modulated by chromatin structure as nucleosomes compaction was shown to prevent HIV-1 integration and chromatin remodeling has been reported to affect integration efficiency. LEDGF/p75-mediated targeting of the integration complex toward RNA polymerase II (polII) transcribed regions ensures optimal access to dynamic regions that are suitable for integration. Consequently, we have investigated the involvement of polII-associated factors in the regulation of HIV-1 integration. Using a pull down approach coupled with mass spectrometry, we have selected the FACT (FAcilitates Chromatin Transcription) complex as a new potential cofactor of HIV-1 integration. FACT is a histone chaperone complex associated with the polII transcription machinery and recently shown to bind LEDGF/p75. We report here that a tripartite complex can be formed between HIV-1 integrase, LEDGF/p75 and FACT in vitro and in cells. Biochemical analyzes show that FACT-dependent nucleosome disassembly promotes HIV-1 integration into chromatinized templates, and generates highly favored nucleosomal structures in vitro. This effect was found to be amplified by LEDGF/p75. Promotion of this FACT-mediated chromatin remodeling in cells both increases chromatin accessibility and stimulates HIV-1 infectivity and integration. Altogether, our data indicate that FACT regulates HIV-1 integration by inducing local nucleosomes dissociation that modulates the functional association between the incoming intasome and the targeted nucleosome.

  12. Non coding RNA: sequence-specific guide for chromatin modification and DNA damage signaling

    Directory of Open Access Journals (Sweden)

    Sofia eFrancia

    2015-11-01

    Full Text Available Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports suggest that ncRNAs are involved in DDR signaling and homology-mediated DNA repair. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.

  13. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-05-17

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad hoc parameters. Also, we designed a global and a local alignment algorithms to measure the similarity between the templates and the chromatin struc- tures predicted by different modeling methods. Finally, the results from large-scale comparative tests indicated that our alignment algorithms significantly outperform the algorithms in literature.

  14. The effect of higher order chromatin structure on DNA damage and repair

    International Nuclear Information System (INIS)

    Yasui, L.S.; Warters, R.L.; Higashikubo, R.

    1985-01-01

    Alterations in chromatin structure are thought to play an important role in various radiobiological end points, i.e., DNA damage, DNA damage repair and cell survival. The authors use here the isoleucine deprivation technique to decondense higher order chromatin structure and asses X-ray induced DNA damage, DNA damage repair and cell survival on cells with decondensed chromatin as compared to controls. This chromatin decondensation manifests itself as a 30 fold decrease in nuclear area occupied by heterochromatin, an increased rate of Micrococcal nuclease digestion, 15% increased ethidium bromide intercalation and an altered binding capacity of Hl histone. These chromatin/nuclear changes do not affect X-ray induced DNA damage as measured by the alkaline elution technique or cell survival but slows DNA damage repair by 2 fold. Therefore, even though the chromatin appears more accessible to DNA damage and repair processes, these particular nuclear changes do not affect the DNA damaging effects of X-rays and in addition, repair is not enhanced by the ''relaxed'' state of chromatin. It is proposed that the altered metabolic state of isoleucine deprived cells provides a less efficient system for the repair of X-ray induced DNA damage

  15. [Automated morphometric evaluation of the chromatin structure of liver cell nuclei after vagotomy].

    Science.gov (United States)

    Butusova, N N; Zhukotskiĭ, A V; Sherbo, I V; Gribkov, E N; Dubovaia, T K

    1989-05-01

    The morphometric analysis of the interphase chromatine structure of the hepatic cells nuclei was carried out on the automated TV installation for the quantitative analysis of images "IBAS-2" (by the OPTON firm, the FRG) according to 50 optical and geometric parameters during various periods (1.2 and 4 weeks) after the vagotomy operation. It is determined that upper-molecular organisation of chromatine undergoes the biggest changes one week after operation, and changes of granular component are more informative than changes of the nongranular component (with the difference 15-20%). It was also revealed that chromatine components differ in tinctorial properties, which are evidently dependent on physicochemical characteristics of the chromatine under various functional conditions of the cell. As a result of the correlation analysis the group of morphometric indices of chromatine structure was revealed, which are highly correlated with level of transcription activity of chromatine during various terms after denervation. The correlation quotient of these parameters is 0.85-0.97. The summing up: vagus denervation of the liver causes changes in the morphofunctional organisation of the chromatine.

  16. [Comparative investigation of the non-histone proteins of chromatin from pigeon erythroblasts and erythrocytes].

    Science.gov (United States)

    Fedina, A B; Gazarian, G G

    1976-01-01

    Chromosomal non-histone proteins are obtained from nuclei of two types of pigeon erythroid cells: erythroblasts (cells active in RNA synthesis) and erythrocytes (cells with repressed RNA synthesis). They are well soluble in solutions of low ionic strength. Electrophoretic separation of the obtained non-histone proteins in polyacrylamide gels with urea and SDS shows the presence of qualitative differences in the pattern of non-histone proteins of chromatine from erythroblasts and erythrocytes. By electrophoresis in urea some protein bands of non-histone proteins of chromatine from erythroblasts were found which disappear with the aging of cells. At the same time two protein fractions were observed in chromatine from erythrocytes which were absent in that of erythroblasts. Disappearance of some high molecular weight protein fractions from erythrocyte chromatine as compared to erythroblasts was observed by separation of the non-histone proteins in the presence of SDS. These fractions of the non-histone proteins disappearing during aging of cells are well extractable from erythroblast chromatine by 0.35 M NaCl solution. In the in vitro system with E. coli RNA polymerase addition of non-histone proteins of chromatine from erythroblasts to chromatine from erythrocytes increases RNA synthesis 2--3 times. At the same time addition of non-histone proteins from erythrocytes is either without any influence on this process or somewhat inhibiting.

  17. Real-Time Tracking of Parental Histones Reveals Their Contribution to Chromatin Integrity Following DNA Damage.

    Science.gov (United States)

    Adam, Salomé; Dabin, Juliette; Chevallier, Odile; Leroy, Olivier; Baldeyron, Céline; Corpet, Armelle; Lomonte, Patrick; Renaud, Olivier; Almouzni, Geneviève; Polo, Sophie E

    2016-10-06

    Chromatin integrity is critical for cell function and identity but is challenged by DNA damage. To understand how chromatin architecture and the information that it conveys are preserved or altered following genotoxic stress, we established a system for real-time tracking of parental histones, which characterize the pre-damage chromatin state. Focusing on histone H3 dynamics after local UVC irradiation in human cells, we demonstrate that parental histones rapidly redistribute around damaged regions by a dual mechanism combining chromatin opening and histone mobilization on chromatin. Importantly, parental histones almost entirely recover and mix with new histones in repairing chromatin. Our data further define a close coordination of parental histone dynamics with DNA repair progression through the damage sensor DDB2 (DNA damage-binding protein 2). We speculate that this mechanism may contribute to maintaining a memory of the original chromatin landscape and may help preserve epigenome stability in response to DNA damage. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. High-resolution mapping reveals links of HP1 with active and inactive chromatin components.

    Directory of Open Access Journals (Sweden)

    Elzo de Wit

    2007-03-01

    Full Text Available Heterochromatin protein 1 (HP1 is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. To obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1-binding sites on Chromosomes 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DNA adenine methyltransferase identification (DamID technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5' regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2, which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5' ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

  19. Energy conservation through thermally insulated structures

    International Nuclear Information System (INIS)

    Abu-Dayyeh, Ayoub

    2006-01-01

    The propose of this paper is to explicate its title through investigating the different available thermal insulating materials and the various techniques of application, as practiced in Jordan, in particular, and as practiced in many parts of the world in general, which will satisfy Jordanian standards in terms of heat transmittance and thermal comfort. A brief comparison with international standards will shed some light on the stringent measures enforced in the developed world and on our striving aspirations to keep pace. The paper consists of four main parts, pseudoally divided. The first part will deal with the mechanism of heat loss and heat gain in structures during summer and winter. It will also explain the Time-lag phenomenon which is vital for providing thermal comfort inside the dwellings. The second part will evaluate the damages induced by the temperature gradients on the different elements of the structure, particularly next to exterior opening. The paper will also demonstrate the damages induced by water condensation and fungus growth on the internal surfaces of the structure and within its skeleton. A correlation between condensation and thermal insulation will be established. The third part of the paper will evaluate the different available thermal insulating materials and the application techniques which will satisfy the needs for thermal insulating and thermal comfort at the least cost possible. The criteria of an economical design shall be established. As a conclusion, the paper infers answers to the following different criteria discussed throughout the different parts of the paper. The main theme of questions can be summarized as follows: 1)How energy conservation is possible due to thermal insulation? 2)The feasibility of investing in thermal insulation? 3)Is thermal comfort and a healthy atmosphere possible inside the dwellings during all season! What are the conditions necessary to sustain them? 4)What environmental impacts can exist due to

  20. Insulation systems of the building construtions

    Directory of Open Access Journals (Sweden)

    Rumiantcev Boris

    2016-01-01

    Full Text Available Constructions of the exterior insulation and decoration combines materials of different functionality and constructive solutions allows to these materials to demonstrate their efficiency to the great extent. Fire safety of buildings is mandatory requirement for building systems. Some insulating material may belong to the group of combustible, but their use in structures so as to minimize the risk of fire. On the other hand, there are special designs, in which non-flammable insulation acts as a flame retardant barrier. In the article carried systematization of construction systems used in the flat and pitched roof during the insulation and wall covering and facades. Taking into account the experience of leading firms were considered the application features of using exterior finish systems: construction solutions, requirements for materials and recommendations about the installation these systems.The article deals with the construction ventilated roofing system of two types: flat roof and pitched roof seam. In the first case, the ventilation system is created using milled insulation boards in the second - by a ventilated gap. In both cases the natural convection of air in the air cavities. Ensuring operational stability insulation is laid on the stages of production of heat-insulating materials. It is important: firstly responsible execution of all process operations associated with providing regulatory properties of materials and secondly, the performance of additional operations associated with the produc-tion of materials, working in a specific design. An example of a material whose properties can modify for a particular application, are milled mineral wool (with air channels for systems of ventilated flat roof.