WorldWideScience

Sample records for chromatin core particle

  1. Multiscale modelling of nucleosome core particle aggregation

    Science.gov (United States)

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

    2015-02-01

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

  2. Effective particle magnetic moment of multi-core particles

    Energy Technology Data Exchange (ETDEWEB)

    Ahrentorp, Fredrik; Astalan, Andrea; Blomgren, Jakob; Jonasson, Christian [Acreo Swedish ICT AB, Arvid Hedvalls backe 4, SE-411 33 Göteborg (Sweden); Wetterskog, Erik; Svedlindh, Peter [Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala (Sweden); Lak, Aidin; Ludwig, Frank [Institute of Electrical Measurement and Fundamental Electrical Engineering, TU Braunschweig, D‐38106 Braunschweig Germany (Germany); IJzendoorn, Leo J. van [Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven (Netherlands); Westphal, Fritz; Grüttner, Cordula [Micromod Partikeltechnologie GmbH, D ‐18119 Rostock (Germany); Gehrke, Nicole [nanoPET Pharma GmbH, D ‐10115 Berlin Germany (Germany); Gustafsson, Stefan; Olsson, Eva [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg (Sweden); Johansson, Christer, E-mail: christer.johansson@acreo.se [Acreo Swedish ICT AB, Arvid Hedvalls backe 4, SE-411 33 Göteborg (Sweden)

    2015-04-15

    In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron microscopy (TEM). We also investigate how the effective particle magnetic moment is coupled to the individual moments of the single-domain nanocrystals by using different measurement techniques: DC magnetometry, AC susceptometry, dynamic light scattering and TEM. We have studied two magnetic multi-core particle systems – BNF Starch from Micromod with a median particle diameter of 100 nm and FeraSpin R from nanoPET with a median particle diameter of 70 nm – and one single-core particle system – SHP25 from Ocean NanoTech with a median particle core diameter of 25 nm.

  3. Effective particle magnetic moment of multi-core particles

    Science.gov (United States)

    Ahrentorp, Fredrik; Astalan, Andrea; Blomgren, Jakob; Jonasson, Christian; Wetterskog, Erik; Svedlindh, Peter; Lak, Aidin; Ludwig, Frank; van IJzendoorn, Leo J.; Westphal, Fritz; Grüttner, Cordula; Gehrke, Nicole; Gustafsson, Stefan; Olsson, Eva; Johansson, Christer

    2015-04-01

    In this study we investigate the magnetic behavior of magnetic multi-core particles and the differences in the magnetic properties of multi-core and single-core nanoparticles and correlate the results with the nanostructure of the different particles as determined from transmission electron microscopy (TEM). We also investigate how the effective particle magnetic moment is coupled to the individual moments of the single-domain nanocrystals by using different measurement techniques: DC magnetometry, AC susceptometry, dynamic light scattering and TEM. We have studied two magnetic multi-core particle systems - BNF Starch from Micromod with a median particle diameter of 100 nm and FeraSpin R from nanoPET with a median particle diameter of 70 nm - and one single-core particle system - SHP25 from Ocean NanoTech with a median particle core diameter of 25 nm.

  4. Attenuation of DNA charge transport by compaction into a nucleosome core particle

    OpenAIRE

    Bjorklund, Chad C.; Davis, William B.

    2006-01-01

    The nucleosome core particle (NCP) is the fundamental building block of chromatin which compacts ∼146 bp of DNA around a core histone protein octamer. The effects of NCP packaging on long-range DNA charge transport reactions have not been adequately assessed to date. Here we study DNA hole transport reactions in a 157 bp DNA duplex (AQ-157TG) incorporating multiple repeats of the DNA TG-motif, a strong NCP positioning sequence and a covalently attached Anthraquinone photooxidant. Following a ...

  5. Protection of cisplatin-induced spermatotoxicity, DNA damage and chromatin abnormality by selenium nano-particles

    Energy Technology Data Exchange (ETDEWEB)

    Rezvanfar, Mohammad Amin; Rezvanfar, Mohammad Ali [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of); Shahverdi, Ahmad Reza [Department of Pharmaceutical Biotechnology and Biotechnology Research Centre, Faculty of Pharmacy, TUMS, Tehran (Iran, Islamic Republic of); Ahmadi, Abbas [Department of Histology and Embryology, Faculty of Veterinary Medicine, Urmia University, Urmia (Iran, Islamic Republic of); Baeeri, Maryam; Mohammadirad, Azadeh [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of); Abdollahi, Mohammad, E-mail: mohammad.abdollahi@utoronto.ca [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)

    2013-02-01

    Cisplatin (CIS), an anticancer alkylating agent, induces DNA adducts and effectively cross links the DNA strands and so affects spermatozoa as a male reproductive toxicant. The present study investigated the cellular/biochemical mechanisms underlying possible protective effect of selenium nano-particles (Nano-Se) as an established strong antioxidant with more bioavailability and less toxicity, on reproductive toxicity of CIS by assessment of sperm characteristics, sperm DNA integrity, chromatin quality and spermatogenic disorders. To determine the role of oxidative stress (OS) in the pathogenesis of CIS gonadotoxicity, the level of lipid peroxidation (LPO), antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) and peroxynitrite (ONOO) as a marker of nitrosative stress (NS) and testosterone (T) concentration as a biomarker of testicular function were measured in the blood and testes. Thirty-two male Wistar rats were equally divided into four groups. A single IP dose of CIS (7 mg/kg) and protective dose of Nano-Se (2 mg/kg/day) were administered alone or in combination. The CIS-exposed rats showed a significant increase in testicular and serum LPO and ONOO level, along with a significant decrease in enzymatic antioxidants levels, diminished serum T concentration and abnormal histologic findings with impaired sperm quality associated with increased DNA damage and decreased chromatin quality. Coadministration of Nano-Se significantly improved the serum T, sperm quality, and spermatogenesis and reduced CIS-induced free radical toxic stress and spermatic DNA damage. In conclusion, the current study demonstrated that Nano-Se may be useful to prevent CIS-induced gonadotoxicity through its antioxidant potential. Highlights: ► Cisplatin (CIS) affects spermatozoa as a male reproductive toxicant. ► Effect of Nano-Se on CIS-induced spermatotoxicity was investigated. ► CIS-exposure induces oxidative sperm DNA damage

  6. Core-shell diodes for particle detectors

    Science.gov (United States)

    Jia, Guobin; Plentz, Jonathan; Höger, Ingmar; Dellith, Jan; Dellith, Andrea; Falk, Fritz

    2016-02-01

    High performance particle detectors are needed for fundamental research in high energy physics in the exploration of the Higgs boson, dark matter, anti-matter, gravitational waves and proof of the standard model, which will extend the understanding of our Universe. Future particle detectors should have ultrahigh radiation hardness, low power consumption, high spatial resolution and fast signal response. Unfortunately, some of these properties are counter-influencing for the conventional silicon drift detectors (SDDs), so that they cannot be optimized simultaneously. In this paper, the main issues of conventional SDDs have been analyzed, and a novel core-shell detector design based on micro- and nano-structures etched into Si-wafers is proposed. It is expected to simultaneously reach ultrahigh radiation hardness, low power consumption, fast signal response and high spatial resolution down to the sub-micrometer range, which will probably meet the requirements for the most powerful particle accelerators in the near future. A prototype core-shell detector was fabricated using modern silicon nanotechnology and the functionality was tested using electron-beam-induced current measurements. Such a high performance detector will open many new applications in extreme radiation environments such as high energy physics, astrophysics, high resolution (bio-) imaging and crystallography, which will push these fields beyond their current boundaries.

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

    Directory of Open Access Journals (Sweden)

    Anderly C Chueh

    2009-01-01

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

  8. Particle-core coupling in 141Nd

    Institute of Scientific and Technical Information of China (English)

    柳敏良; 张玉虎; 周小红; 郭应祥; 刘忠; 雷相国; 何建军; 郑勇; 罗万居; 竺礼华; 温书贤

    2003-01-01

    High-spin states in 141Nd have been studied using in-beam γ-ray spectroscopic techniques via the 130Te(16O, 5nγ)141Nd reaction. The level scheme of 141Nd has been extended up to an excitation energy of 7614.5 kev including 12 new γ rays deexciting 15 new levels. According to particle-vibrator coupling and semi-empirical shell model calculations, the level structure of 141Nd can be well interpreted by coupling an h11/2 neutron-hole to the respective excited states in 142Nd core.

  9. Novel nano-composite particles : titania-coated silica cores

    OpenAIRE

    Greenwood, Peter; Gevert, Börje S.; Otterstedt, Jan-Erik; Niklasson, Gunnar; Vargas, William

    2010-01-01

    Purpose - The purpose of this paper is to develop methods to produce white composite pigments consisting of a silica core with a titania shell. Design/methodology/approach - Silica cores were coated with titanium dioxide (TiO2) via forced hydrolysis of a solution prepared from titanium tetrachloride (TiCl4). The morphology, surface charge and particle size of obtained composite particles were studied. Findings - Dispersions of well-dispersed composite particles, having silica cores of uniform...

  10. Salt and divalent cations affect the flexible nature of the natural beaded chromatin structure

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Griffith, J

    1977-01-01

    A natural chromatin containing simian virus 40 (SV40) DNA and histone has been used to examine changes in chromatin structure caused by various physical and chemical treatments. We find that histone H1 depleted chromatin is more compact in solutions of 0.15M NaCl or 2 mM MgCl2 than in 0.01 M Na...... therefore contains more DNA than the 140 base pair "core particle". The natural variation in the bridge length is consistent with the broad bands observed after nuclease digestion of chromatin. Chromatin prepared for EM without fixation containing long 20A to 30A fibers possibly complexed with protein....

  11. Entrapment of carbon dioxide with chitosan-based core-shell particles containing changeable cores.

    Science.gov (United States)

    Dong, Yanrui; Fu, Yinghao; Lin, Xia; Xiao, Congming

    2016-08-01

    Water-soluble chitosan-based core-shell particles that contained changeable cores were successfully applied to anchor carbon dioxide. The entrapment capacity of the particles for carbon dioxide (EC) depended on the cores. It was found that EC of the particles contained aqueous cores was higher than that of the beads with water-soluble chitosan gel cores, which was confirmed with thermogravimetric analysis. In addition, calcium ions and sodium hydroxide were introduced within the particles to examine their effect on the entrapment. EC of the particles was enhanced with sodium hydroxide when the cores were WSC gel. The incorporation of calcium ions was helpful for stabilizing carbon dioxide through the formation of calcium carbonate, which was verified with Fourier transform infrared spectra and scanning electron microscopy/energy-dispersive spectrometry. This phenomenon meant the role of calcium ions for fixating carbon dioxide was significant. PMID:27174910

  12. Prenucleosomes and Active Chromatin

    Science.gov (United States)

    Khuong, Mai T.; Fei, Jia; Ishii, Haruhiko; Kadonaga, James T.

    2016-01-01

    Chromatin consists of nucleosomes as well as nonnucleosomal histone-containing particles. Here we describe the prenucleosome, which is a stable conformational isomer of the nucleosome that associates with ~80 bp DNA. Prenucleosomes are formed rapidly upon the deposition of histones onto DNA and can be converted into canonical nucleosomes by an ATP-driven chromatin assembly factor such as ACF. Different lines of evidence reveal that there are prenucleosome-sized DNA-containing particles with histones in the upstream region of active promoters. Moreover, p300 acetylates histone H3K56 in prenucleosomes but not in nucleosomes, and H3K56 acetylation is found at active promoters and enhancers. These findings therefore suggest that there may be prenucleosomes or prenucleosome-like particles in the upstream region of active promoters. More generally, we postulate that prenucleosomes or prenucleosome-like particles are present at dynamic chromatin, whereas canonical nucleosomes are at static chromatin. PMID:26767995

  13. Core-shell particles as model compound for studying fouling

    DEFF Research Database (Denmark)

    Christensen, Morten Lykkegaard; Nielsen, Troels Bach; Andersen, Morten Boel Overgaard;

    2008-01-01

    Synthetic colloidal particles with hard cores and soft, water-swollen shells were used to study cake formation during ultrafiltration. The total cake resistance was lowest for particles with thick shells, which indicates that interparticular forces between particles (steric hindrance and...... electrostatic repulsion) influenced cake formation. At low pressure the specific cake resistance could be predicted from the Kozeny-Carman equation. At higher pressures, the resistance increased due to cake compression. Both cake formation and compression were reversible. For particles with thick shells the...... permeate flux could be enhanced by lowering the pressure. Hence, the amount of water-swollen material influences both cake thickness and resistance....

  14. Twist Neutrality and the Diameter of the Nucleosome Core Particle

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2012-01-01

    The diameter of the nucleosome core particle is the same for all the eukaryotes. Here we discuss the possibility that this selectiveness is consistent with a propensity for twist neutrality, in particular, for the double helical DNA to stay rotationally neutral when strained. Reorganization of DNA...... cannot be done without some level of temporal tensile stress, and as a consequence chiral molecules, such as helices, will twist under strain. The requirement that the nucleosome, constituting the nucleosome core particle and linker DNA, has a vanishing strain-twist coupling leads to a requirement for...

  15. Blm10 facilitates nuclear import of proteasome core particles

    OpenAIRE

    Weberruss, Marion H; Savulescu, Anca F; Jando, Julia; Bissinger, Thomas; Harel, Amnon; Glickman, Michael H.; Enenkel, Cordula

    2013-01-01

    Short-lived proteins are degraded by proteasome complexes, which contain a proteolytic core particle (CP) but differ in the number of regulatory particles (RPs) and activators. A recently described member of conserved proteasome activators is Blm10. Blm10 contains 32 HEAT-like modules and is structurally related to the nuclear import receptor importin/karyopherin β. In proliferating yeast, RP-CP assemblies are primarily nuclear and promote cell division. During quiescence, RP-CP assemblies di...

  16. Optical properties of core-mantle spheroidal particles

    Science.gov (United States)

    Somsikov, Vadim V.; Farafonov, Victor G.

    1994-12-01

    The new solution of the problem of light scattering by coated spheroids was used to calculate the optical properties of prolate and oblate particles. The solution was obtained by the method of separation of variables for confocal spheroids. We consider the silicate core ice mantle particles and present the extinction cross-sections for prolate and oblate spheroids with the refractive indices mcore equals 1.7 + Oi, 1.7 + 0.1i and mmantle equals 1.3, the aspect ratio (a/b)mantle equals 2 and various volume ratios Vcore/Vtotal. The results are plotted for different size parameters xv equals 2(pi) rv/(lambda) , where rv is the radius of equivolume sphere and (lambda) is the wavelength of incident radiation. The main conclusions are: (a) if Vcore/Vtotal equals 0.5, the optical properties of a core-mantle particle are determined mainly by its core: for prolate non-absorbing spheroids when xv EQ 4.5; for prolate absorbing spheroids when xv EQ 4.5 or xv > 10, for oblate absorbing and non-absorbing spheroids when xv EQ 10. (b) the linear growth of the extinction cross-sections on the volume ratio Vcore/Vtotal is obtained for prolate particles with xv equals 1 and 2. (c) the non-linear increase of cross- sections is obtained for oblate particles with size parameters xv equals 1 - 5. (d) the small imaginary part of the core refractive index m [Im(m) < 0.01] practically does not change the optical properties of an inhomogeneous particle. When the imaginary part reaches 0.1, the noticeable changes of cross-sections may be detected.

  17. Single-epitope recognition imaging of native chromatin

    Directory of Open Access Journals (Sweden)

    Wang Hongda

    2008-12-01

    Full Text Available Abstract Background Direct visualization of chromatin has the potential to provide important insights into epigenetic processes. In particular, atomic force microscopy (AFM can visualize single nucleosomes under physiological ionic conditions. However, AFM has mostly been applied to chromatin that has been reconstituted in vitro, and its potential as a tool for the dissection of native nucleosomes has not been explored. Recently we applied AFM to native Drosophila chromatin containing the centromere-specific histone 3 (CenH3, showing that it is greatly enriched in smaller particles. Taken together with biochemical analyses of CenH3 nucleosomes, we propose that centromeric nucleosomes are hemisomes, with one turn of DNA wrapped around a particle consisting of one molecule each of centromere-specific CenH3, H4, H2A and H2B. Results Here we apply a recognition mode of AFM imaging to directly identify CenH3 within histone core particles released from native centromeric chromatin. More than 90% of these particles were found to be tetrameric in height. The specificity of recognition was confirmed by blocking with a CenH3 peptide, and the strength of the interaction was quantified by force measurements. These results imply that the particles imaged by AFM are indeed mature CenH3-containing hemisomes. Conclusion Efficient and highly specific recognition of CenH3 in histone core particles isolated from native centromeric chromatin demonstrates that tetramers are the predominant form of centromeric nucleosomes in mature tetramers. Our findings provide proof of principle that this approach can yield insights into chromatin biology using direct and rapid detection of native nucleosomes in physiological salt concentrations.

  18. Preparation of porous carbon particle with shell/core structure

    Directory of Open Access Journals (Sweden)

    2007-05-01

    Full Text Available Porous carbon particles with a shell/core structure have been prepared successfully by controlled precipitation of the polymer from droplets of oil-in-water emulsion, followed by curing and carbonization. The droplets of the oil phase are composed of phenolic resin (PFR, a good solvent (ethyl acetate and porogen (Poly(methyl methacrylate, PMMA. The microstructure was characterized in detail by scanning electron microscopy (SEM, transmission electron microscopy (TEM, nitrogen adsorption, and thermo gravimetric analysis (TGA. The obtained carbon particles have a capsular structure with a microporous carbon shell and a mesoporous carbon core. The BET surface area and porous volume are calculated to be 499 m2g-1 and 0.56 cm3g-1, respectively. The effects of the amount of porogen (PMMA, co-solvent (acetone and surfactant on the resultant structure were studied in detail.

  19. Therapeutic activity of modified U1 core spliceosomal particles

    Science.gov (United States)

    Rogalska, Malgorzata Ewa; Tajnik, Mojca; Licastro, Danilo; Bussani, Erica; Camparini, Luca; Mattioli, Chiara; Pagani, Franco

    2016-01-01

    Modified U1 snRNAs bound to intronic sequences downstream of the 5′ splice site correct exon skipping caused by different types of mutations. Here we evaluate the therapeutic activity and structural requirements of these exon-specific U1 snRNA (ExSpeU1) particles. In a severe spinal muscular atrophy, mouse model, ExSpeU1, introduced by germline transgenesis, increases SMN2 exon 7 inclusion, SMN protein production and extends life span. In vitro, RNA mutant analysis and silencing experiments show that while U1A protein is dispensable, the 70K and stem loop IV elements mediate most of the splicing rescue activity through improvement of exon and intron definition. Our findings indicate that precise engineering of the U1 core spliceosomal RNA particle has therapeutic potential in pathologies associated with exon-skipping mutations. PMID:27041075

  20. Spermine-induced aggregation of DNA, nucleosome, and chromatin.

    OpenAIRE

    Raspaud, E.; Chaperon, I; Leforestier, A; Livolant, F

    1999-01-01

    We have analyzed the conditions of aggregation or precipitation of DNA in four different states: double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), mononucleosome core particles (NCP), and H1-depleted chromatin fragments (ChF) in the presence of the multivalent cation spermine (4+). In an intermediate regime of DNA concentration, these conditions are identical for the four states. This result demonstrates that the mechanism involved is general from flexible chains to rigid rods and qua...

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

    Directory of Open Access Journals (Sweden)

    Yanping Fan

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

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

    Science.gov (United States)

    Kwon, So Yeon; Grisan, Valentina; Jang, Boyun; Herbert, John; Badenhorst, Paul

    2016-04-01

    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. PMID:27046080

  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. Characterization of spherical core–shell particles by static light scattering. Estimation of the core- and particle-size distributions

    International Nuclear Information System (INIS)

    A numerical method is proposed for the characterization of core–shell spherical particles from static light scattering (SLS) measurements. The method is able to estimate the core size distribution (CSD) and the particle size distribution (PSD), through the following two-step procedure: (i) the estimation of the bivariate core–particle size distribution (C–PSD), by solving a linear ill-conditioned inverse problem through a generalized Tikhonov regularization strategy, and (ii) the calculation of the CSD and the PSD from the estimated C–PSD. First, the method was evaluated on the basis of several simulated examples, with polystyrene–poly(methyl methacrylate) core–shell particles of different CSDs and PSDs. Then, two samples of hematite–Yttrium basic carbonate core–shell particles were successfully characterized. In all analyzed examples, acceptable estimates of the PSD and the average diameter of the CSD were obtained. Based on the single-scattering Mie theory, the proposed method is an effective tool for characterizing core–shell colloidal particles larger than their Rayleigh limits without requiring any a-priori assumption on the shapes of the size distributions. Under such conditions, the PSDs can always be adequately estimated, while acceptable CSD estimates are obtained when the core/shell particles exhibit either a high optical contrast, or a moderate optical contrast but with a high ‘average core diameter’/‘average particle diameter’ ratio. -- Highlights: ► Particles with core–shell morphology are characterized by static light scattering. ► Core size distribution and particle size distribution are successfully estimated. ► Simulated and experimental examples are used to validate the numerical method. ► The positive effect of a large core/shell optical contrast is investigated. ► No a-priori assumption on the shapes of the size distributions is required.

  5. Conformational changes in the chromatin structure of human peripheral blood mononuclear cells exposed to low dose radiation

    International Nuclear Information System (INIS)

    Ionizing radiations are known to challenge the integrity of the genome by inducing several lesions like double strand breaks, single strand breaks and oxidative base damage in the DNA. Human cells have evolved efficient DNA repair processes in response to DNA damage by which the integrity of genome is maintained. Emerging evidence indicates that various modulations to chromatin structure are centrally important to many aspects of the DNA damage response (DDR). DNA is compacted and packed in the form of chromatin in eukaryotic cells, the basic unit of chromatin is the nucleosome core particle, which consists of ∼ 146 base pairs of DNA wrapped in two left-handed superhelical turns around an octamer of histone proteins. Higher order chromatin packaging acts as a barrier to the detection and repair of DNA damage. Hence, chromatin reorganization is thought to play a crucial role in cellular responses to DNA damage by making damaged sites more accessible to repair as well as transcriptional machinery of the cell. Dynamic light scattering (DLS) is a sensitive and non invasive tool to study the dynamics of biomolecules in solution. Changes in the conformation of chromatin on exposure to gamma radiation were measured in the form of average hydrodynamic diameter of chromatin fragments in irradiated and control cells. In the present study we have used Dynamic Light Scattering (PLS) as a tool to analyze radiation induced conformational changes in the structure of native chromatin in peripheral blood mononuclear cells (PBMCs) at resting stage (G0). Dose response experiments carried out on 10 individuals have shown a significant difference in the average hydrodynamic diameter of chromatin fibers in different dose groups. Our results have also shown significant changes in the chromatin size at low dose groups (25 cGy and 50 cGy) as compared to higher doses. Inter-individual variations in the chromatin dynamics were clearly demonstrated

  6. Preparation of Core-shell Structured Particles and Their Nucleation in Polyester: Ⅰ. Preparation of Monodisperse SiO2/PS Core-shell Composite Particles

    Institute of Scientific and Technical Information of China (English)

    KeYangchuan; WuTianbin; WangYi

    2005-01-01

    To enhance the nucleation and crystallization properties of polyester (e.g., polyethylene terephthalate, PET),core-shell structured particles are used to improve these properties by controlling the inorganic dispersion properties in the polymers. In the paper, monodisperse particles of silica/polystyrene (PS) are prepared with both dispersion and emulsion polymerization techniques. The monodisperse silicon dioxide particles are first prepared with the seed growth method and modified by the coupling agents. Silica is properly modified with KH-570, and its size deviation is 3.0% or so. The modified silica then reacts with the mixture of ethanol, water medium, and monomer of styrene under dispersion polymerization. Results show that the dispersion polymerization technique is more suitable for monodisperse core-shell SiO2/PS particles than that of the emulsion. The morphology and molecular structure of the core-shell particles are investigated with the transmission electron microscope (TEM), and fourier transform infra-red spectroscopy (FTIR). The results show that the modified silica particles are successfully encapsulated with polystyrene. The average number of silica particles encapsulated into each polystyrene sphere decreases when the size of silica particles increases from 50 nm to 600 nm, and will approach one when the silica is greater than 380nm in size. The mass ratio for silica/PS particles in emulsion polymerization is 4.7/1,lower than that of 6.8/1 for dispersion polymerization, which is the first reported optimized data for preparing the similar monodisperse composite particles. Thus, the PS shell in the former is thinner than that in the latter.

  7. Magnetic, Structural, and Particle Size Analysis of Single- and Multi-Core Magnetic Nanoparticles

    DEFF Research Database (Denmark)

    Ludwig, Frank; Kazakova, Olga; Barquin, Luis Fernandez;

    2014-01-01

    We have measured and analyzed three different commercial magnetic nanoparticle systems, both multi-core and single-core in nature, with the particle (core) size ranging from 20 to 100 nm. Complementary analysis methods and same characterization techniques were carried out in different labs and the...... results are compared with each other. The presented results primarily focus on determining the particle size—both the hydrodynamic size and the individual magnetic core size—as well as magnetic and structural properties. The used analysis methods include transmission electron microscopy, static and...... dynamic magnetization measurements, and Mössbauer spectroscopy. We show that particle (hydrodynamic and core) size parameters can be determined from different analysis techniques and the individual analysis results agree reasonably well. However, in order to compare size parameters precisely determined...

  8. Chromatin structure and DNA damage

    International Nuclear Information System (INIS)

    This dissertation examines the structure and structural transitions of chromatin in relation to DNA damage. The ability of intact and histone H1 depleted chromatin fibers to fold into higher ordered structures in vitro was examined following DNA photodamage introduced by two different agents. (1) 254-nm UV radiation and (2) trimethylpsoralen (plus near-UV radiation). Both agents are highly specific for DNA and form adducts predicted to cause different degrees of distortion in the DNA helix. The salt-induced structural transitions of intact and histone H1 depleted chromatin fibers were monitored by both analytical ultracentrifugation and light scattering. Our results show that even in the presence of extremely large, nonphysiological amounts of photodamage by either agent the ability of chromatin to fold into higher ordered structures is not affected. The compact, 30 nm fiber must therefore be able to accommodate a large amount of DNA damage without any measurable changes in the overall size or degree of compaction of this structure. The distribution of pyrimidine dimers was mapped at the single nucleotide level in nucleosome core DNA from UV-irradiated mononucleosomes, chromatin fibers, and human cells in culture using the 3' → 5' exonuclease activity of T4 DNA polymerase

  9. POLYELECTROLYTE CORE/HYDROPHOBIC SHELL POLYMER PARTICLES BY DOUBLE EMULSION TEMPLATING POLYMERISATION FOR ENVIRONMENTAL APPLICATIONS

    OpenAIRE

    Menzel, Cristian

    2015-01-01

    The University of Manchester, Faculty of Engineering and Physical SciencesCristian Adolfo Menzel BuenoA thesis submitted for the degree of Doctor of PhilosophyPolyelectrolyte core/hydrophobic shell polymer particles by double emulsion templating polymerisation for environmental applicationsDate: 25th September 2014Herein two novel synthetic strategies for the synthesis of sub-millimetre sized core–shell particles comprising a polyelectrolyte core and a porous hydrophobic shell are presented.I...

  10. Chimeric hepatitis B virus core particles as probes for studying peptide-integrin interactions.

    OpenAIRE

    Chambers, M A; Dougan, G; Newman, J.; Brown, F.; Crowther, J.; Mould, A P; Humphries, M J; Francis, M. J.; Clarke, B.; Brown, A L; Rowlands, D.

    1996-01-01

    An RGD-containing epitope from the foot-and-mouth disease virus (FMDV) VP1 protein was inserted into the e1 loop of the hepatitis B virus core (HBc) protein. This chimeric protein was expressed at high levels in Escherichia coli and spontaneously assembled into virus-like particles which could be readily purified. These fusion particles elicited high levels of both enzyme-linked immunosorbent assay- and FMDV-neutralizing antibodies in guinea pigs. The chimeric particles bound specifically to ...

  11. Stopping of α particles from the core in corona plasmas

    OpenAIRE

    Mima, Kunioki; Tajima, Toshiki; Alvarez Ruiz, Jesus; Tanaka, K.A.; Perlado Martin, Jose Manuel; Nagatomo, H.; Johzaki, T.; Sunahara, A.

    2012-01-01

    In the laser fusion reactor design, the protection of first wall and the final optics from high energy ions is the key issue. So, it is necessary to predict the precise energy spectra of ions.In the previous reactor designs, the ion energy spectra were provided by the classical ion transport codes. However, this poster shows that the α particle spectrum is significantly modified by the anomalous process in ablated plasmas.

  12. Synthesis and Characterization of Polyvinylpyrrolidone Silica Core-Shell Nanocomposite Particles.

    Science.gov (United States)

    Chen, Lian-Xi; Li, Jie; Li, Xi; Zhang, Zhong-Min; Jiao, Cai-Bin

    2015-03-01

    In this work, a novel and facile strategy for making a new type of polymer/silica nanocomposte particle was proposed. Colloidally stable polyvinypyrrolidone (PVP)/silica core-shell nanocomposite particles have been successfully synthesized using an azo initiator via seed polymerization of N-vinyl-2-pyrrolidone (NVP) and VFSs (VFSs) that were derived from vinyl triethoxysilane (VTES). It was suggested from the FTIR and TGA analysis that the copolymerization reaction of NVP with VFSs has been thoroughly carried out. In addition, SEM images showed that PVP/silica nanocomposite particles have relatively rough surface due to surface polymerization in comparison with VFSs. Furthermore, TEM results proved that the size of VFSs had considerable effects on the appearance of PVP/silica nanocomposite particles. Generally, it presented that several silica nanoparticle cores with an average size of 78 nm mainly pack together within each nanocomposite particle after seed polymerization. Interestingly, the average shell thickness was 59 nm for most PVP/silica nanocomposite particles with cores about 242 nm. However, when the core size was large enough to about 504 nm, a series of PVP/silica nanocomposite particles with a relative thin shell were observed. PMID:26413650

  13. A core-particle model for periodically focused ion beams with intense space-charge

    International Nuclear Information System (INIS)

    A core-particle (CP) model is derived to analyze transverse orbits of test-particles evolving in the presence of a core ion beam that has uniform density within an elliptical cross-section. The model can be applied to both quadrupole and solenoidal focused beams in periodic or aperiodic lattices. Efficient analytical descriptions of electrostatic space-charge fields external to the beam core are derived to simplify model equations. Image-charge effects are analyzed for an elliptical beam centered in a round, conducting pipe to estimate model corrections resulting from image-charge nonlinearities. Transformations are employed in diagnostics to remove coherent flutter motion associated with oscillations of the ion beam core due to rapidly varying, linear applied-focusing forces. Diagnostics for particle trajectories, Poincare phase-space projections, and single-particle emittances based on these transformations better illustrate the effects of nonlinear forces acting on particles evolving outside the core. A numerical code has been written based on this model. Example applications illustrate model characteristics. The CP model described has recently been applied to identify physical processes leading to space-charge transport limits for an rms-envelope matched beam in a periodic quadrupole focusing-channel [S.M. Lund, S.R. Chawla, Nucl. Instr. and Meth. A 561 (2006) 203]. Further characteristics of these processes are presented here

  14. Pre-Stressing Micron-Scale Aluminum Core-Shell Particles to Improve Reactivity

    Science.gov (United States)

    Levitas, Valery I.; McCollum, Jena; Pantoya, Michelle

    2015-01-01

    The main direction in increasing reactivity of aluminum (Al) particles for energetic applications is reduction in their size down to nanoscale. However, Al nanoparticles are 30-50 times more expensive than micron scale particles and possess safety and environmental issues. Here, we improved reactivity of Al micron scale particles by synthesizing pre-stressed core-shell structures. Al particles were annealed and quenched to induce compressive stresses in the alumina passivation shell surrounding Al core. This thermal treatment was designed based on predictions of the melt-dispersion mechanism (MDM); a theory describing Al particle reaction under high heating rate. For all anneal treatment temperatures, experimental flame propagation rates for Al combined with nanoscale copper oxide (CuO) are in quantitative agreement with the theoretical predictions based on the MDM. The best treatment increases flame rate by 36% and achieves 68% of that for the best Al nanoparticles.

  15. Optical detection of antibody using silica-silver core-shell particles

    Science.gov (United States)

    Kalele, S. A.; Ashtaputre, S. S.; Hebalkar, N. Y.; Gosavi, S. W.; Deobagkar, D. N.; Deobagkar, D. D.; Kulkarni, S. K.

    2005-03-01

    Nearly monodispersed spherical particles of silica were synthesized and coated with thin layer of silver nanoparticles. Silver coated silica particles, forming core-shell particles exhibited a strong surface plasmon resonance peak at 453 nm. A very small amount (20 μg) of rabbit immunoglobulin in core-shell particle solution results in to a marked shift in surface plasmon resonance. Addition of 20 μg quantity of goat anti rabbit antibodies results in to a red shift of surface plasmon resonance to 494 nm. This demonstrates that silver coated silica particles are sensitive probes for rapid antibody-anti antibody kind of interaction investigations. Fourier transform infra red spectroscopy and scanning electron microscopy have been used to interpret the optical extinction spectroscopy results.

  16. The Chromatin Fiber: Multiscale Problems and Approaches

    OpenAIRE

    Ozer, Gungor; Luque, Antoni; Schlick, Tamar

    2015-01-01

    The structure of chromatin, affected by many factors from DNA linker lengths to posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined experimental and computational methods have led to new insights into its structural and dynamical features, from interactions due to the flexible core histone tails of the nucleosomes to the physical mechanism driving the formation of chromosomal domains. Here we present a perspective of recent advances in chromatin modelin...

  17. Core Material Preparation of TRISO Coated Particle in HTGR Fuel

    International Nuclear Information System (INIS)

    A VHTR(Very High Temperature Reactor) is being conducted by many countries mainly promoted for electricity production and high temperature process heat. The proposed nuclear fuel for the preliminary reactor concept on these purposes is a TRISO(Tri-Isotropic or multi-layered structure) coated particle prepared by pyro-carbon and silicone coatings on a spherical UO2 kernel surface as a fissile material. Generally, UO2 kernels are prepared by using the modified sol-gel process, wet process, known as the GSP(gel supported precipitation) method. This chemical route was well-known to the potential kernel fabrication process. HTGR nuclear fuel production processes have been classified in five categories of research and development : - Spherical UO2 kernel preparation step - Pyro-carbon(PyC) and silicon carbide(SiC) coatings - Pebble or Prismatic block preparation by using graphite matrix powder - Fuel performance including a fission products release - Advanced and improved fuel development The well-known GSP process is one of the modified processes for an external gelation method developed NUKEM of Germany. As shown in Figure 1, a spherical UO2 kernel particle was prepared by using a modified external gelation process. UO2 kernels are highly dense sintered microsphere of stoichiometric UO2 with a nominal diameter of about 500 μm. The raw material for UO2 kernel preparation is nuclear grade U3O8 powder which will be dissolved with nitric acid to obtain the UN solution. The procedures are formed by mixing the UN solution with organic additives and transferring the aqueous solution to spherical droplets, which are on the surface of liquid droplets slightly hardened by a chemical reaction with ammonia. The necessary viscosity and shape of liquid droplets are achieved by the addition of PVA. THFA solution is added to achieve a controlled shrinkage of the ADU gel particles during gelation, ageing, and washing processes. After ageing in ammonia water and washing with demi

  18. 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

  19. Aligned gold nanorods in silica made by ion irradiation of core-shell colloidal particles

    OpenAIRE

    Roorda, S.; Dillen, T. van; Polman, A.; Graf, C.; Blaaderen, A. van; Kooi, BJ

    2004-01-01

    Colloidal particles with a 14 nm diameter Au core surrounded by a 72 nm thick silica shell have been irradiated with 30 MeV heavy ions. The shell deforms into an oblate ellipsoid, while the core becomes rod-shaped (aspect ratio up to 9) with the major axis along the beam. Optical extinction measurements show evidence for split plasmon bands, characteristic for anisotropic metal nanoparticles.

  20. HCV prototype vaccine based on hepatitis B core virus-like particles

    OpenAIRE

    Marija Mihailova

    2008-01-01

    HCV prototype vaccine based on hepatitis B core virus-like particles Abstract In the current study the C-terminally truncated HBc expression vectors were used for exposure of different hepatitis C virus (HCV) protein (core, E2, and NS3) fragments. All created chimeric constructs directed high level of recombinant protein synthesis in E.coli. However, not all chimeric proteins were able to self-assemble into virus-like particles (VLPs). HBcCterm/HVR1tetramer VLPs turned ou...

  1. How to Determine the Core-Shell Nature in Bimetallic Catalyst Particles?

    Directory of Open Access Journals (Sweden)

    Emma Westsson

    2014-11-01

    Full Text Available Nanometer-sized materials have significantly different chemical and physical properties compared to bulk material. However, these properties do not only depend on the elemental composition but also on the structure, shape, size and arrangement. Hence, it is not only of great importance to develop synthesis routes that enable control over the final structure but also characterization strategies that verify the exact nature of the nanoparticles obtained. Here, we consider the verification of contemporary synthesis strategies for the preparation of bimetallic core-shell particles in particular in relation to potential particle structures, such as partial absence of core, alloying and raspberry-like surface. It is discussed what properties must be investigated in order to fully confirm a covering, pin-hole free shell and which characterization techniques can provide such information. Not uncommonly, characterization strategies of core-shell particles rely heavily on visual imaging like transmission electron microscopy. The strengths and weaknesses of various techniques based on scattering, diffraction, transmission and absorption for investigating core-shell particles are discussed and, in particular, cases where structural ambiguities still remain will be highlighted. Our main conclusion is that for particles with extremely thin or mono-layered shells—i.e., structures outside the limitation of most imaging techniques—other strategies, not involving spectroscopy or imaging, are to be employed. We will provide a specific example of Fe-Pt core-shell particles prepared in bicontinuous microemulsion and point out the difficulties that arise in the characterization process of such particles.

  2. Controlled Release from Core-Shell Nanoporous Silica Particles for Corrosion Inhibition of Aluminum Alloys

    Directory of Open Access Journals (Sweden)

    Xingmao Jiang

    2011-01-01

    Full Text Available Cerium (Ce corrosion inhibitors were encapsulated into hexagonally ordered nanoporous silica particles via single-step aerosol-assisted self-assembly. The core/shell structured particles are effective for corrosion inhibition of aluminum alloy AA2024-T3. Numerical simulation proved that the core-shell nanostructure delays the release process. The effective diffusion coefficient elucidated from release data for monodisperse particles in water was 1.0×10−14 m2s for Ce3+ compared to 2.5×10−13 m2s for NaCl. The pore size, pore surface chemistry, and the inhibitor solubility are crucial factors for the application. Microporous hydrophobic particles encapsulating a less soluble corrosion inhibitor are desirable for long-term corrosion inhibition.

  3. Controlled Release from Core-Shell Nano porous Silica Particles for Corrosion Inhibition of Aluminum Alloys

    International Nuclear Information System (INIS)

    Cerium (Ce) corrosion inhibitors were encapsulated into hexagonally ordered nanoporous silica particles via single-step aerosol-assisted self-assembly. The core/shell structured particles are effective for corrosion inhibition of aluminum alloy AA2024-T3. Numerical simulation proved that the core-shell nanostructure delays the release process. The effective diffusion coefficient elucidated from release data for monodisperse particles in water was 1.0x10-14 m2s for Ce3+ compared to 2.5x10-13 m2s for NaCl. The pore size, pore surface chemistry, and the inhibitor solubility are crucial factors for the application. Microporous hydrophobic particles encapsulating a less soluble corrosion inhibitor are desirable for long-term corrosion inhibition.

  4. Description of the particle core interaction within a projection after variation formalism

    International Nuclear Information System (INIS)

    An interacting system consisting in one particle moving in a spherical oscillator potential and a complex core described by an anharmonic quadrupole Hamiltonian is semiclassically treated. One determined three decoupled modes describing the composite system in the intrinsic frame. On the top of the ground as well as of the one boson states, one builds rotational bands. The projected states may be further used as single particle basis for treating an interacting many body system. (authors)

  5. Spherical core-shell magnetic particles constructed by main-chain palladium N-heterocyclic carbenes

    Science.gov (United States)

    Zhao, Huaixia; Li, Liuyi; Wang, Jinyun; Wang, Ruihu

    2015-02-01

    The encapsulation of the functional species on magnetic core is a facile approach for the synthesis of core-shell magnetic materials, and surface encapsulating matrices play crucial roles in regulating their properties and applications. In this study, two core-shell palladium N-heterocyclic carbene (NHC) particles (Fe3O4@PNP1 and Fe3O4@PNP2) were prepared by a one-pot reaction of semi-rigid tripodal imidazolium salts and palladium acetate in the presence of magnetite nanoparticles. The magnetite nanoparticles are encapsulated inside the main-chain palladium, which act as cores. The conjugated effects of triphenyltriazine and triphenylbenzene in the imidazolium salts have important influence on their physical properties and catalytic performances. Fe3O4@PNP2 shows better recyclability than Fe3O4@PNP1. Unexpectedly, Pd(ii) is well maintained after six consecutive catalytic runs in Fe3O4@PNP2, and Pd(0) and Pd(ii) coexist in Fe3O4@PNP1 under the same conditions; moreover, the morphologies of these spherical core-shell particles show no significant variation after six consecutive catalytic runs.The encapsulation of the functional species on magnetic core is a facile approach for the synthesis of core-shell magnetic materials, and surface encapsulating matrices play crucial roles in regulating their properties and applications. In this study, two core-shell palladium N-heterocyclic carbene (NHC) particles (Fe3O4@PNP1 and Fe3O4@PNP2) were prepared by a one-pot reaction of semi-rigid tripodal imidazolium salts and palladium acetate in the presence of magnetite nanoparticles. The magnetite nanoparticles are encapsulated inside the main-chain palladium, which act as cores. The conjugated effects of triphenyltriazine and triphenylbenzene in the imidazolium salts have important influence on their physical properties and catalytic performances. Fe3O4@PNP2 shows better recyclability than Fe3O4@PNP1. Unexpectedly, Pd(ii) is well maintained after six consecutive catalytic runs in

  6. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles

    Directory of Open Access Journals (Sweden)

    Alexey K. Shaytan

    2016-06-01

    Full Text Available We present here raw trajectories of molecular dynamics simulations for nucleosome with linker DNA strands as well as minimalistic nucleosome core particle model. The simulations were done in explicit solvent using CHARMM36 force field. We used this data in the research article Shaytan et al., 2016 [1]. The trajectory files are supplemented by TCL scripts providing advanced visualization capabilities.

  7. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles

    OpenAIRE

    Shaytan, Alexey K.; Armeev, Grigoriy A.; Goncearenco, Alexander; Zhurkin, Victor B.; Landsman, David; Panchenko, Anna R

    2016-01-01

    We present here raw trajectories of molecular dynamics simulations for nucleosome with linker DNA strands as well as minimalistic nucleosome core particle model. The simulations were done in explicit solvent using CHARMM36 force field. We used this data in the research article Shaytan et al., 2016 [1]. The trajectory files are supplemented by TCL scripts providing advanced visualization capabilities.

  8. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

    Science.gov (United States)

    Shaytan, Alexey K; Armeev, Grigoriy A; Goncearenco, Alexander; Zhurkin, Victor B; Landsman, David; Panchenko, Anna R

    2016-06-01

    We present here raw trajectories of molecular dynamics simulations for nucleosome with linker DNA strands as well as minimalistic nucleosome core particle model. The simulations were done in explicit solvent using CHARMM36 force field. We used this data in the research article Shaytan et al., 2016 [1]. The trajectory files are supplemented by TCL scripts providing advanced visualization capabilities. PMID:27222871

  9. Resonant optical propulsion of a particle inside a hollow-core photonic crystal fiber.

    Science.gov (United States)

    Maslov, A V

    2016-07-01

    Resonant propulsion of small nonresonant particles inside metal waveguides due to the formation of resonant states by the guided modes below their cutoffs has been predicted in the past. Here it is shown that stable resonant propulsion exists in hollow-core photonic crystal fibers, which are all-dielectric structures and are a major platform for various photonic applications. Specific features of the resonant propulsion are discussed together with the fiber design issues. The results may enable power-efficient transport of particles over long distances, particle sorting, and sensitive detection. PMID:27367102

  10. Where splicing joins chromatin

    OpenAIRE

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

    There are numerous data suggesting that two key steps in gene expression—transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and...

  11. Core Fueling and Edge Particle Flux Analysis in Ohmically and Auxiliary Heated NSTX Plasmas

    International Nuclear Information System (INIS)

    The Boundary Physics program of the National Spherical Torus Experiment (NSTX) is focusing on optimization of the edge power and particle flows in b * 25% L- and H-mode plasmas of 0.8 s duration heated by up to 6 MW of high harmonic fast wave and up to 5 MW of neutral beam injection. Particle balance and core fueling efficiencies of low and high field side gas fueling of L-mode homic and NBI heated plasmas have been compared using an analytical zero dimensional particle balance model and measured ion and neutral fluxes. Gas fueling efficiencies are in the range of 0.05-0.20 and do not depend on discharge magnetic configuration, density or poloidal location of the injector. The particle balance modeling indicates that the addition of HFS fueling results in a reversal of the wall loading rate and higher wall inventories. Initial particle source estimates obtained from neutral pressure and spectroscopic measurements indicate that ion flux into the divertor greatly exceeds midplane ion flux from the main plasma, suggesting that the scrape-off cross-field transport plays a minor role in diverted plasmas. Present analysis provides the basis for detailed fluid modeling of core and edge particle flows and particle confinement properties of NSTX plasmas. This research was supported by the U.S. Department of Energy under contracts No. DE-AC02-76CH03073, DE-AC05-00OR22725, and W-7405-ENG-36

  12. Fracture resistance improvement of polypropylene by joint action of core-shell particles and nucleating agent

    International Nuclear Information System (INIS)

    Research highlights: →The core-shell particles, which were prepared from melt blending of POE and nano-CaCO3, and different nucleating agents (α-form NA or β-form NA) were first introduced into PP to prepare the super toughened PP materials. →NAs control the crystalline structures of PP matrix including the spherulites diameter and the crystal form. →NAs and core-shell particles exhibit apparent joint effect in improving the fracture resistance of PP. - Abstract: As a serial work about the fracture resistance improvement of polypropylene (PP), this work reports the joint effect of core-shell particles and nucleating agent (NA) on the microstructure and fracture resistance of PP. Core-shell particles were prepared through melt blending of ethylene-octene copolymer (POE) and calcium carbonate (CaCO3). Different NA, i.e. α-form NA (P-tert-butylbenzoic acid-Al, MD-NA-28) and β-form NA (aryl amides compound, TMB-5) were introduced into PP matrix to control the crystalline structure. The phase morphology of POE and the distribution of CaCO3 were characterized by using scanning electron microscope (SEM), and the crystallization behavior of PP matrix were investigated by using differential scanning calorimetry (DSC), wide angle X-ray diffraction (WAXD) and polarization optical microscope (POM). The mechanical properties were obtained through universal tensile measurement and notched Izod impact measurement. Surprisingly, the results show that through addition of so-called core-shell particles and NA simultaneously, the fracture resistance of PP can be dramatically improved.

  13. Biodegradable and magnetic core-shell composite particle prepared by emulsion solvent diffusion method

    Science.gov (United States)

    Oka, Chiemi; Ushimaru, Kazunori; Horiishi, Nanao; Tsuge, Takeharu; Kitamoto, Yoshitaka

    2016-02-01

    The present paper describes optimization of preparation conditions of a core-shell composite particle, and its heat generation by alternating magnetic fields. The composite particles are prepared with a modified emulsion solvent diffusion method, which is combined with Pickering emulsion stabilized by magnetic nanoparticles. In this method, the magnetic nanoparticles act as an emulsifier, and its amount and size are crucial to morphology of the composite particles. The magnetic nanoparticles of 8-9 nm would be strongly adsorbed at a liquid-liquid interface rather than the larger nanoparticles. At the optimized concentration of the magnetic nanoparticle’s suspension for the preparation, small and uniform composite particles are obtained since the amount of the nanoparticles is enough to prevent coalescence of droplets during the formation of the composites. The heat generation by alternating magnetic fields emerged certainly. This result suggests the composite particles have a property as a heat-generating carrier for hyperthermia treatment.

  14. THE PREPARATION AND CHARACTERIZATION OF SBR/PS CORE-SHELL PARTICLES BY GAMMA IRRADIATION

    Institute of Scientific and Technical Information of China (English)

    Dai-shuang Li; Jing Peng; Xiao-hong Zhang; Jin-liang Qiao; Jiu-qiang Li; Gen-shuan Wei

    2005-01-01

    A kind of core(SBR)-shell(PS) particles was synthesized by using SBR latex and grafting with St under gamma irradiation. The influences of absorbed dose and dose rate on the grafting yield of PS on SBR seed latex have been investigated. Results show there was a transition layer which contained the SBR/PS graft copolymer between the SBR core and PS shell. Dynamic laser scattering (DLS) and differential scanning calorimetry (DSC) results confirm the existence of grafted polystyrene, and transmission electron microscope (TEM) observation verifies the core-shell structure of SBR-g-PS latex. Such SBR/PS core-shell latex could be processed easily to ultrafine rubber powders by using spray drying and expected to be used as an impact modifier for PS.

  15. Highly temperature responsive core-shell magnetic particles: synthesis, characterization and colloidal properties.

    Science.gov (United States)

    Rahman, Md Mahbubor; Chehimi, Mohamed M; Fessi, Hatem; Elaissari, Abdelhamid

    2011-08-15

    Temperature responsive magnetic polymer submicron particles were prepared by two step seed emulsion polymerization process. First, magnetic seed polymer particles were obtained by emulsion polymerization of styrene using potassium persulfate (KPS) as an initiator and divinylbenzne (DVB) as a cross-linker in the presence of oil-in-water magnetic emulsion (organic ferrofluid droplets). Thereafter, DVB cross-linked magnetic polymer particles were used as seed in the precipitation polymerization of N-isopropylacrylamide (NIPAM) to induce thermosensitive PNIPAM shell onto the hydrophobic polymer surface of the cross-linked magnetic polymer particles. To impart cationic functional groups in the thermosensitive PNIPAM backbone, the functional monomer aminoethylmethacrylate hydrochloride (AEMH) was used to polymerize with NIPAM while N,N'-methylenebisacrylamide (MBA) and 2, 2'-azobis (2-methylpropionamidine) dihydrochloride (V-50) were used as a cross-linker and as an initiator respectively. The effect of seed to monomer (w/w) ratio along with seed nature on the final particle morphology was investigated. Dynamic light scattering (DLS) results demonstrated particles swelling at below volume phase transition temperature (VPTT) and deswelling above the VPTT. The perfect core (magnetic) shell (polymer) structure of the particles prepared was confirmed by Transmission Electron Microscopy (TEM). The chemical composition of the particles were determined by thermogravimetric analysis (TGA). The effect of temperature, pH, ionic strength on the colloidal properties such as size and zeta potential of the micron sized thermo-sensitive magnetic particles were also studied. In addition, a short mechanistic discussion on the formation of core-shell morphology of magnetic polymer particles has also been discussed. PMID:21570083

  16. Preparation of sulphonate-containing core/shell latex particles via seeded emulsion copolymerization

    Institute of Scientific and Technical Information of China (English)

    Ji Shuai Wang; Wei Deng; Yun Shen Chen; Cheng You Kan

    2010-01-01

    In this study,P(St-MAA)seed latex particles were first prepared via soap-free emulsion polymerization of styrene(St)and methacrylic acid(MAA),then the seed particles were allowed to swell with St at room temperature,and the P(St-MAA)/P(St-NaSS)core/shell latex particles were then synthesized via seeded emulsion copolymerization of St and sodium styrene sulphonate(NaSS)using AIBN as initiator in the presence of N,N'-methylenebisacrylamide(BAA,water-soluble crosslinker).Results showed that the polymerization could be carried out smoothly when the ratio of BAA to total monomers was less than 3 mol%,the narrow dispersed P(St-MAA)seed particles with the diameter of 150 nm and the P(St-MAA)/P(St-NaSS)core/shell latexes with the particle size of about 200 nm were synthesized.When the 25/75 mole ratio of NaSS/(St+MAA)and 2 mol% of BAA were used in the seeded emulsion polymerization,the resulted P(St-MAA)/P(St-NaSS)latex product showed a low weight loss after water extraction,and the NaSS unit content in the whole particle and in the shell reached 11.7 mol% and 34.6 mol%,respectively.

  17. Design of Gas-phase Synthesis of Core-Shell Particles by Computational Fluid – Aerosol Dynamics

    OpenAIRE

    Buesser, B.; Pratsinis, S.E.

    2011-01-01

    Core-shell particles preserve the bulk properties (e.g. magnetic, optical) of the core while its surface is modified by a shell material. Continuous aerosol coating of core TiO2 nanoparticles with nanothin silicon dioxide shells by jet injection of hexamethyldisiloxane precursor vapor downstream of titania particle formation is elucidated by combining computational fluid and aerosol dynamics. The effect of inlet coating vapor concentration and mixing intensity on product shell thickness distr...

  18. Epoxy-acrylic core-shell particles by seeded emulsion polymerization.

    Science.gov (United States)

    Chen, Liang; Hong, Liang; Lin, Jui-Ching; Meyers, Greg; Harris, Joseph; Radler, Michael

    2016-07-01

    We developed a novel method for synthesizing epoxy-acrylic hybrid latexes. We first prepared an aqueous dispersion of high molecular weight solid epoxy prepolymers using a mechanical dispersion process at elevated temperatures, and we subsequently used the epoxy dispersion as a seed in the emulsion polymerization of acrylic monomers comprising methyl methacrylate (MMA) and methacrylic acid (MAA). Advanced analytical techniques, such as scanning transmission X-ray microscopy (STXM) and peak force tapping atomic force microscopy (PFT-AFM), have elucidated a unique core-shell morphology of the epoxy-acrylic hybrid particles. Moreover, the formation of the core-shell morphology in the seeded emulsion polymerization process is primarily attributed to kinetic trapping of the acrylic phase at the exterior of the epoxy particles. By this new method, we are able to design the epoxy and acrylic polymers in two separate steps, and we can potentially synthesize epoxy-acrylic hybrid latexes with a broad range of compositions. PMID:27078740

  19. Controllable fabrication and characterization of biocompatible core-shell particles and hollow capsules as drug carrier

    Science.gov (United States)

    Hao, Lingyun; Gong, Xinglong; Xuan, Shouhu; Zhang, Hong; Gong, Xiuqing; Jiang, Wanquan; Chen, Zuyao

    2006-10-01

    SiO 2@CdSe core-shell particles were fabricated by controllable deposition CdSe nanoparticles on silica colloidal spheres. Step-wise coating process was tracked by the TEM and XRD measurements. In addition, SiO 2@CdSe/polypyrrole(PPy) multi-composite particles were synthesized based on the as-prepared SiO 2@CdSe particles by cationic polymerization. The direct electrochemistry of myoglobin (Mb) could be performed by immobilizing Mb on the surface of SiO 2@CdSe particles. Immobilized with Mb, SiO 2@CdSe/PPy-Mb also displayed good bioelectrochemical activity. It confirmed the good biocompatible property of the materials with protein. CdSe hollow capsules were further obtained as the removal of the cores of SiO 2@CdSe spheres. Hollow and porous character of CdSe sub-meter size capsules made them becoming hopeful candidates as drug carriers. Doxorubicin, a typical an antineoplastic drug, was introduced into the capsules. A good sustained drug release behavior of the loading capsules was discovered via performing a release test in the PBS buffer (pH 7.4) solution at 310 k. Furthermore, SiO 2@CdSe/PPy could be converted to various smart hollow capsules via selectively removal of their relevant components.

  20. Chromatin deregulation in disease.

    Science.gov (United States)

    Mirabella, Anne C; Foster, Benjamin M; Bartke, Till

    2016-03-01

    The regulation of chromatin by epigenetic mechanisms plays a central role in gene expression and is essential for development and maintenance of cell identity and function. Aberrant chromatin regulation is observed in many diseases where it leads to defects in epigenetic gene regulation resulting in pathological gene expression programmes. These defects are caused by inherited or acquired mutations in genes encoding enzymes that deposit or remove DNA and histone modifications and that shape chromatin architecture. Chromatin deregulation often results in neurodevelopmental disorders and intellectual disabilities, frequently linked to physical and developmental abnormalities, but can also cause neurodegenerative diseases, immunodeficiency, or muscle wasting syndromes. Epigenetic diseases can either be of monogenic origin or manifest themselves as complex multifactorial diseases such as in congenital heart disease, autism spectrum disorders, or cancer in which mutations in chromatin regulators are contributing factors. The environment directly influences the epigenome and can induce changes that cause or predispose to diseases through risk factors such as stress, malnutrition or exposure to harmful chemicals. The plasticity of chromatin regulation makes targeting the enzymatic machinery an attractive strategy for therapeutic intervention and an increasing number of small molecule inhibitors against a variety of epigenetic regulators are in clinical use or under development. In this review, we will give an overview of the molecular lesions that underlie epigenetic diseases, and we will discuss the impact of the environment and prospects for epigenetic therapies. PMID:26188466

  1. 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...

  2. Modification of unsaturated polyester resins using nano-size core-shell particles

    International Nuclear Information System (INIS)

    Unsaturated polyester resinsaresome of the most widely usedplastics for composites as matrices. Their brittle nature,however, makes then susceptible to catastrophic failure. One way of alleviating this property deficiency is to incorporate rubbery particles in the polymer system. Polyester resin blends comprising core-shell particlesof varied particle sizes were prepared and their properties investigated using a variety of techniques. Thermal properties were examined by differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMTA). The morphology of particles and their distribution in the cured resin blends were investigated using transmission electron microscopy (TEM). Tensile tests were carried out to establish the stress-strain behaviour of the resin blends.The results showed that the particles were prepared according to the design in terms of size and morphology. DSC results showed a shift of the peak in the exotherm during programmed heating to higher temperatures but remained unchanged in isothermal measurements. TEM analysis of resin blends showed the particles well distributed in clusters. No deformation mechanisms were discernible in the microgrphs presumably due to relaxation of materialsprior and during analysis.Tensile results showed an increase in ductility and fracture strain while a reduction fracture stress was noted. ( Author)

  3. Nucleosome dynamics during chromatin remodeling in vivo.

    Science.gov (United States)

    Ramachandran, Srinivas; Henikoff, Steven

    2016-01-01

    Precise positioning of nucleosomes around regulatory sites is achieved by the action of chromatin remodelers, which use the energy of ATP to slide, evict or change the composition of nucleosomes. Chromatin remodelers act to bind nucleosomes, disrupt histone-DNA interactions and translocate the DNA around the histone core to reposition nucleosomes. Hence, remodeling is expected to involve nucleosomal intermediates with a structural organization that is distinct from intact nucleosomes. We describe the identification of a partially unwrapped nucleosome structure using methods that map histone-DNA contacts genome-wide. This alternative nucleosome structure is likely formed as an intermediate or by-product during nucleosome remodeling by the RSC complex. Identification of the loss of histone-DNA contacts during chromatin remodeling by RSC in vivo has implications for the regulation of transcriptional initiation. PMID:26933790

  4. Dynamic simulations of colloids by core-modified dissipative particle dynamics.

    Science.gov (United States)

    Whittle, Martin; Travis, Karl P

    2010-03-28

    We develop a core-modified dissipative particle dynamics model of colloidal systems which includes an extra term to counteract depletion forces. Results are presented covering the full range of volume fractions. Radial distribution functions for the suspending fluid are shown to change significantly as the volume fraction of colloid increases. Equilibrium results for the long-time diffusion coefficient behave as expected, but the short-time coefficient is anomalous. The form of the equilibrium stress correlation functions is discussed and the derived Green-Kubo viscosities are compared with expected semiempirical forms. For nonequilibrium shear-field simulations we find that the system temperature is not adequately controlled by the dissipative particle dynamics (DPD) thermostat alone. Results using three alternative auxiliary thermostats are compared; a naive choice leading to a string phase at high shear rate. Using a thermostat based on relative particle velocities, the model reproduced the four classical regions of colloid rheology: a first Newtonian plateau, a shear-thinning region, a second Newtonian plateau, and finally a shear-thickening region at high strain rate. The most unexpected result of this exercise is that the core-modified DPD model without auxiliary thermostat almost exactly follows the same curve despite recording a temperature increase of a factor approximately 2.5 over the range. PMID:20370149

  5. Vaccine delivery system for tuberculosis based on nano-sized hepatitis B virus core protein particles

    Directory of Open Access Journals (Sweden)

    Dhanasooraj D

    2013-02-01

    Full Text Available Dhananjayan Dhanasooraj, R Ajay Kumar, Sathish MundayoorMycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Kerala, IndiaAbstract: Nano-sized hepatitis B virus core virus-like particles (HBc-VLP are suitable for uptake by antigen-presenting cells. Mycobacterium tuberculosis antigen culture filtrate protein 10 (CFP-10 is an important vaccine candidate against tuberculosis. The purified antigen shows low immune response without adjuvant and tends to have low protective efficacy. The present study is based on the assumption that expression of these proteins on HBc nanoparticles would provide higher protection when compared to the native antigen alone. The cfp-10 gene was expressed as a fusion on the major immunodominant region of HBc-VLP, and the immune response in Balb/c mice was studied and compared to pure proteins, a mixture of antigens, and fusion protein-VLP, all without using any adjuvant. The humoral, cytokine, and splenocyte cell proliferation responses suggested that the HBc-VLP bearing CFP-10 generated an antigen-specific immune response in a Th1-dependent manner. By virtue of its self-adjuvant nature and ability to form nano-sized particles, HBc-VLPs are an excellent vaccine delivery system for use with subunit protein antigens identified in the course of recent vaccine research.Keywords: Mycobacterium tuberculosis, VLP, hepatitis B virus core particle, CFP-10, self-adjuvant, vaccine delivery

  6. Mechanical Fracturing of Core-Shell Undercooled Metal Particles for Heat-Free Soldering

    Science.gov (United States)

    Çınar, Simge; Tevis, Ian D.; Chen, Jiahao; Thuo, Martin

    2016-02-01

    Phase-change materials, such as meta-stable undercooled (supercooled) liquids, have been widely recognized as a suitable route for complex fabrication and engineering. Despite comprehensive studies on the undercooling phenomenon, little progress has been made in the use of undercooled metals, primarily due to low yields and poor stability. This paper reports the use of an extension of droplet emulsion technique (SLICE) to produce undercooled core-shell particles of structure; metal/oxide shell-acetate (‘/’ = physisorbed, ‘-’ = chemisorbed), from molten Field’s metal (Bi-In-Sn) and Bi-Sn alloys. These particles exhibit stability against solidification at ambient conditions. Besides synthesis, we report the use of these undercooled metal, liquid core-shell, particles for heat free joining and manufacturing at ambient conditions. Our approach incorporates gentle etching and/or fracturing of outer oxide-acetate layers through mechanical stressing or shearing, thus initiating a cascade entailing fluid flow with concomitant deformation, combination/alloying, shaping, and solidification. This simple and low cost technique for soldering and fabrication enables formation of complex shapes and joining at the meso- and micro-scale at ambient conditions without heat or electricity.

  7. Core/shell silicon/polyaniline particles via in-flight plasma-induced polymerization

    International Nuclear Information System (INIS)

    Although silicon nanoparticles have potential applications in many relevant fields, there is often the need for post-processing steps to tune the property of the nanomaterial and to optimize it for targeted applications. In particular surface modification is generally necessary to both tune dispersibility of the particles in desired solvents to achieve optimal coating conditions, and to interface the particles with other materials to realize functional heterostructures. In this contribution we discuss the realization of core/shell silicon/polymer nanoparticles realized using a plasma-initiated in-flight polymerization process. Silicon particles are produced in a non-thermal plasma reactor using silane as a precursor. After synthesis they are aerodynamically injected into a second plasma reactor into which aniline vapor is introduced. The second plasma initiates the polymerization reactor leading to the formation of a 3–4 nm thick polymer shell surrounding the silicon core. The role of processing conditions on the properties of the polymeric shell is discussed. Preliminary results on the testing of this material as an anode for lithium ion batteries are presented. (paper)

  8. Core/shell silicon/polyaniline particles via in-flight plasma-induced polymerization

    Science.gov (United States)

    Yasar-Inceoglu, Ozgul; Zhong, Lanlan; Mangolini, Lorenzo

    2015-08-01

    Although silicon nanoparticles have potential applications in many relevant fields, there is often the need for post-processing steps to tune the property of the nanomaterial and to optimize it for targeted applications. In particular surface modification is generally necessary to both tune dispersibility of the particles in desired solvents to achieve optimal coating conditions, and to interface the particles with other materials to realize functional heterostructures. In this contribution we discuss the realization of core/shell silicon/polymer nanoparticles realized using a plasma-initiated in-flight polymerization process. Silicon particles are produced in a non-thermal plasma reactor using silane as a precursor. After synthesis they are aerodynamically injected into a second plasma reactor into which aniline vapor is introduced. The second plasma initiates the polymerization reactor leading to the formation of a 3-4 nm thick polymer shell surrounding the silicon core. The role of processing conditions on the properties of the polymeric shell is discussed. Preliminary results on the testing of this material as an anode for lithium ion batteries are presented.

  9. Nanostructured core-shell Ni deposition on SiC particles by alkaline electroless coating

    International Nuclear Information System (INIS)

    In this study, core-shell nanostructured nickel formation on silicon carbide (SiC) ceramic powders was achieved through the electroless deposition method using alkaline solutions. To produce a nano core-shell Ni deposition on the SiC surfaces, process parameters such as pH values, the type of reducer material, deposition temperature, stirring rate and activation procedure among others were determined. Full coverage of core-shell nickel structures on SiC surfaces was achieved with a grain size of between 100 and 300 nm, which was approximately the same deposition thickness on the SiC surfaces. The surface morphology of the coated SiC particles showed a homogenous distribution of nanostructured nickel grains characterized by scanning electron microscopy and X-ray diffraction techniques. The nanostructures of the crystalline Ni coatings were observed to be attractive for achieving both good bonding and dense structure. The thin core shell-structure of Ni on the SiC surfaces was assessed as a beneficial reinforcement for possible metal matrix composite manufacturing.

  10. Nanostructured core-shell Ni deposition on SiC particles by alkaline electroless coating

    Science.gov (United States)

    Uysal, M.; Karslioğlu, R.; Alp, A.; Akbulut, H.

    2011-10-01

    In this study, core-shell nanostructured nickel formation on silicon carbide (SiC) ceramic powders was achieved through the electroless deposition method using alkaline solutions. To produce a nano core-shell Ni deposition on the SiC surfaces, process parameters such as pH values, the type of reducer material, deposition temperature, stirring rate and activation procedure among others were determined. Full coverage of core-shell nickel structures on SiC surfaces was achieved with a grain size of between 100 and 300 nm, which was approximately the same deposition thickness on the SiC surfaces. The surface morphology of the coated SiC particles showed a homogenous distribution of nanostructured nickel grains characterized by scanning electron microscopy and X-ray diffraction techniques. The nanostructures of the crystalline Ni coatings were observed to be attractive for achieving both good bonding and dense structure. The thin core shell-structure of Ni on the SiC surfaces was assessed as a beneficial reinforcement for possible metal matrix composite manufacturing.

  11. A particle-bed gas-cooled fast reactor core design for waste minimization

    International Nuclear Information System (INIS)

    The issue of waste minimization in advanced reactor systems has been investigated using the Particle-Bed Gas-cooled Fast Reactor (PB-GCFR) design being developed and funded under the U.S. Department of Energy Nuclear Energy Research Initiative (USDOE NERI) Programme. Results indicate that for the given core power density and constraint on the maximum TRU enrichment allowable, the lowest amount of radio-toxic transuranics to be processed and hence sent to the repository is obtained for long-life core designs. Calculations were additionally done to investigate long-life core designs using LWR spent fuel TRU and recycle TRU, and different feed, matrix and reflector materials. The recycled TRU and LWR spent TRU fuels give similar core behaviours, because of the fast spectrum environment which does not significantly degrade the TRU composition. Using light elements as reflector material was found to be unattractive because of power peaking problems and large reactivity swings. The application of a lead reflector gave the longest cycle length and lowest TRU processing requirement. Materials compatibility and performance issues require additional investigation. (author)

  12. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

    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 H2O-D2O 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

  13. Solar Neutrinos: Probing the Quasi-Isothermal Solar Core Produced by SUSY Dark Matter Particles

    OpenAIRE

    Lopes, Ilidio; Silk, Joseph

    2001-01-01

    SNO measurements strongly constrain the central temperature of the Sun within a precision of much less than 1%. This result can be used to constrain the parameter space of SUSY dark matter particle candidates. In this first analysis we find a lower limit for the WIMP mass of 60 GeV, well above the WIMP evaporation limit of 10 GeV. Furthermore, in the event that WIMPs create a quasi-isothermal core within the Sun, they will produce a peculiar distribution of the solar neutrino fluxes measured ...

  14. Facile preparation of core@shell and concentration-gradient spinel particles for Li-ion battery cathode materials

    International Nuclear Information System (INIS)

    Core@shell and concentration-gradient particles have attracted much attention as improved cathodes for Li-ion batteries (LIBs). However, most of their preparation routes have employed a precisely-controlled co-precipitation method. Here, we report a facile preparation route of core@shell and concentration-gradient spinel particles by dry powder processing. The core@shell particles composed of the MnO2 core and the Li(Ni,Mn)2O4 spinel shell are prepared by mechanical treatment using an attrition-type mill, whereas the concentration-gradient spinel particles with an average composition of LiNi0.32Mn1.68O4 are produced by calcination of their core@shell particles as a precursor. The concentration-gradient LiNi0.32Mn1.68O4 spinel cathode exhibits the high discharge capacity of 135.3 mA h g−1, the wide-range plateau at a high voltage of 4.7 V and the cyclability with a capacity retention of 99.4% after 20 cycles. Thus, the facile preparation route of the core@shell and concentration-gradient particles may provide a new opportunity for the discovery and investigation of functional materials as well as for the cathode materials for LIBs. (paper)

  15. Purification of infective bluetongue virus particles by immuno-affinity chromatography using anti-core antibody.

    Science.gov (United States)

    Chand, Karam; Biswas, Sanchay K; Mondal, Bimalendu

    2016-03-01

    An immuno-affinity chromatography technique for purification of infective bluetongue virus (BTV) has been descried using anti-core antibodies. BTV anti-core antibodies (prepared in guinea pig) were mixed with cell culture-grown BTV-1 and then the mixture was added to the cyanogens bromide-activated protein-A Sepharose column. Protein A binds to the antibody which in turn binds to the antigen (i.e. BTV). After thorough washing, antigen-antibody and antibody-protein A couplings were dissociated with 4M MgCl2, pH6.5. Antibody molecules were removed by dialysis and virus particles were concentrated by spin column ultrafiltration. Dialyzed and concentrated material was tested positive for BTV antigen by a sandwich ELISA and the infectivity of the chromatography-purified virus was demonstrated in cell culture. This method was applied for selective capture of BTV from a mixture of other viruses. As group-specific antibodies (against BTV core) were used to capture the virus, it is expected that virus of all BTV serotypes could be purified by this method. This method will be helpful for selective capture and enrichment of BTV from concurrently infected blood or tissue samples for efficient isolation in cell culture. Further, this method can be used for small scale purification of BTV avoiding ultracentrifugation. PMID:26925450

  16. TOUGHENING OF POLYCARBONATE WITH PBA-PMMA CORE-SHELL PARTICLES

    Institute of Scientific and Technical Information of China (English)

    Wei-guo Yao; Li-qin Wang; Da-yong He; Shi-chun Jiang; Li-jia An; Hui-xuan Zhang

    2005-01-01

    The miscibility, mechanical properties, morphology and toughening mechanism of PC/PBA-PMMA blends were investigated. The dynamic mechanical results show that PC/PBA-PMMA blend has good miscibility and strong interfacial adhesion. The Izod impact strength of blend PC/PBA-PMMA with 4% (volume fraction) PBA-PMMA core-shell modifier is 16 times higher than that of pure PC. The core-shell volume fraction and thickness of the PMMA shell have effect on the toughness of PC/PBA-PMMA blends. As PMMA volume fraction increases, the toughness of PC/PBA-PMMA blend increases, and reaches a maximum value at 30% volume fraction of PMMA or so. The tensile properties of PC/PBA-PMMA blend with a minimum amount of PBA-PMMA modifier show that brittle-tough transition has no significant variance in comparison with that of pure PC. The scanning electron microscopic (SEM) observation indicates that the toughening mechanism of the blend with the pseudo-ductile matrix modified by small core-shell latex polymer particles is the synergetic effect of cavitation and shear yielding of the matrix.

  17. Chromatin chemistry goes cellular.

    OpenAIRE

    W. Fischle; D. Schwarzer; Mootz, H.

    2015-01-01

    Analysing post-translational modifications of histone proteins as they occur within chromatin is challenging due to their large number and chemical diversity. A major step forward has now been achieved by using split intein chemistry to engineer functionalized histones within cells.

  18. Analysis of Chromatin Organisation

    Science.gov (United States)

    Szeberenyi, Jozsef

    2011-01-01

    Terms to be familiar with before you start to solve the test: chromatin, nucleases, sucrose density gradient centrifugation, melting point, gel electrophoresis, ethidium bromide, autoradiography, Southern blotting, Northern blotting, Sanger sequencing, restriction endonucleases, exonucleases, linker DNA, chloroform extraction, nucleosomes,…

  19. Where splicing joins chromatin

    Czech Academy of Sciences Publication Activity Database

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

    Roč. 2, č. 3 (2011), s. 182-188. ISSN 1949-1034 R&D Projects: GA ČR GAP305/10/0424; GA AV ČR KAN200520801 Institutional research plan: CEZ:AV0Z50520514 Keywords : chromatin * exon * alternative splicing * transcription * snRNP Subject RIV: EB - Genetics ; Molecular Biology

  20. DNA-Protein interactions in nucleosomes and in Chromatin

    International Nuclear Information System (INIS)

    Crosslinking induced by ultraviolet light irradiation at 254 nm has been utilized to investigate the structure of chromatin and isolated nucleosomes. The results presented here imply that the four core histones, as well as histone H1, have reactive groups within a bond length of the DNA bases. In nucleosomes depleted of H1, all of the core histones react similarly with the DNA and form crosslinks. In chromatin, the rate of crosslinking of all histones to DNA is essentially similar. Comparison of mononucleosomes, dinucleosomes and whole chromatin shows that the rate of crosslinking increase significantly with increasing number of connected nucleosomes. These differences in the rate of crosslinking are interpreted in terms of interactions between neighbouring nucleosomes on the chromatin fiber, which are absent in an isolated mononucleosome. (orig.)

  1. 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.

  2. Isostructural solid-solid phase transition in monolayers of soft core-shell particles at fluid interfaces: structure and mechanics.

    Science.gov (United States)

    Rey, Marcel; Fernández-Rodríguez, Miguel Ángel; Steinacher, Mathias; Scheidegger, Laura; Geisel, Karen; Richtering, Walter; Squires, Todd M; Isa, Lucio

    2016-04-13

    We have studied the complete two-dimensional phase diagram of a core-shell microgel-laden fluid interface by synchronizing its compression with the deposition of the interfacial monolayer. Applying a new protocol, different positions on the substrate correspond to different values of the monolayer surface pressure and specific area. Analyzing the microstructure of the deposited monolayers, we discovered an isostructural solid-solid phase transition between two crystalline phases with the same hexagonal symmetry, but with two different lattice constants. The two phases corresponded to shell-shell and core-core inter-particle contacts, respectively; with increasing surface pressure the former mechanically failed enabling the particle cores to come into contact. In the phase-transition region, clusters of particles in core-core contacts nucleate, melting the surrounding shell-shell crystal, until the whole monolayer moves into the second phase. We furthermore measured the interfacial rheology of the monolayers as a function of the surface pressure using an interfacial microdisk rheometer. The interfaces always showed a strong elastic response, with a dip in the shear elastic modulus in correspondence with the melting of the shell-shell phase, followed by a steep increase upon the formation of a percolating network of the core-core contacts. These results demonstrate that the core-shell nature of the particles leads to a rich mechanical and structural behavior that can be externally tuned by compressing the interface, indicating new routes for applications, e.g. in surface patterning or emulsion stabilization. PMID:26948023

  3. Organization of higher-level chromatin structures (chromomere, chromonema and chromatin block) examined using visible light-induced chromatin photo-stabilization.

    Science.gov (United States)

    Sheval, E V; Prusov, A N; Kireev, I I; Fais, D; Polyakov, V Yu

    2002-01-01

    The method of chromatin photo-stabilization by the action of visible light in the presence of ethidium bromide was used for investigation of higher-level chromatin structures in isolated nuclei. As a model we used rat hepatocyte nuclei isolated in buffers which stabilized or destabilized nuclear matrix. Several higher-level chromatin structures were visualized: 100nm globules-chromomeres, chains of chromomeres-chromonemata, aggregates of chromomeres-blocks of condensed chromatin. All these structures were completely destroyed by 2M NaCl extraction independent of the matrix state, and DNA was extruded from the residual nuclei (nuclear matrices) into a halo. These results show that nuclear matrix proteins do not play the main role in the maintenance of higher-level chromatin structures. Preliminary irradiation led to the reduction of the halo width in the dose-dependent manner. In regions of condensed chromatin of irradiated nucleoids there were discrete complexes consisting of DNA fibers radiating from an electron-dense core and resembling the decondensed chromomeres or the rosette-like structures. As shown by the analysis of proteins bound to irradiated nuclei upon high-salt extraction, irradiation presumably stabilized the non-histone proteins. These results suggest that in interphase nuclei loop domains are folded into discrete higher-level chromatin complexes (chromomeres). These complexes are possibly maintained by putative non-histone proteins, which are extracted with high-salt buffers from non-irradiated nuclei. PMID:12127937

  4. Controllable dielectric and electrical performance of polymer composites with novel core/shell-structured conductive particles through biomimetic method

    International Nuclear Information System (INIS)

    Highlights: ► Conductive core/shell-structured particles were synthesized by biomimetic method. ► These particles with silica/poly(dopamine)/silver core and poly(dopamine) shell. ► Dielectric composites were prepared with resulted particles and silicone elastomer. ► The dielectric properties of the composites can be controlled by shell thickness. ► This biomimetic method is simple, nontoxic, efficient and easy to control. - Abstract: Novel silica/poly(dopamine)/silver (from inner to outer) (denoted as SiO2/PDA/Ag) conductive micro-particles were first synthesized by biomimetic poly(dopamine) coating. These micro-particles were then coated with a poly(dopamine) layer to form core/shell-structured particles, with silica/poly(dopamine)/silver core and poly(dopamine) shell (denoted as SiO2/PDA/Ag/PDA). This multilayer core/shell micro-particles were confirmed by scanning electron microscopy, X-ray photoelectron spectroscopy, X-ray diffraction, and transmission electron microscope. Polymer composites were then prepared by mechanical blending of poly(dimethyl siloxane) and the core/shell-structured particles. It was found that the silver layer and the poly(dopamine) shell had good adhesion with substrate and they kept intact even under violent shearing stress during mechanical mixing. The effect of the thickness of outermost poly(dopamine) shell as well as the loading amount of this filler on the dielectric and electrical properties of the composites was further studied. The results showed that the dielectric constant, dielectric loss, and conductivity of the composites decreased with increasing shell thickness (10–53 nm) at the same loading level. And the maximal dielectric constant of composites was achieved in the composites filled with SiO2/PDA/Ag/PDA (with 10–15 nm PDA shell) particles, which was much larger than that of the composite filled with SiO2/PDA/Ag particles without insulative PDA shell. At the same time, the composites can change from

  5. Solar neutrinos: Probing the quasi-isothermal solar core produced by supersymmetric dark matter particles

    International Nuclear Information System (INIS)

    SNO measurements strongly constrain the central temperature of the Sun, to within a precision of much less than 1% . This result can be used to probe the parameter space of supersymmetric dark matter. In this first analysis we find a lower limit for the weakly interacting massive particle (WIMP) mass of 60 GeV. Furthermore, in the event that WIMPs create a quasi-isothermal core, they will produce a peculiar distribution of the solar neutrino fluxes measured on Earth. Typically, a WIMP with a mass of 100 GeV and annihilation cross section of 10-34 cm 3/sec will decrease the neutrino predictions, by up to 4% for the Cl, by 3% for the heavy water, and by 1% for the Ga detectors

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

    Directory of Open Access Journals (Sweden)

    Hua Wong

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

  7. Rayleigh like scattering from silica–titania core-shell particles and their application in protection against harmful ultraviolet rays

    Indian Academy of Sciences (India)

    Sudipta G Dastidar; P Bharath; Arindam Roy

    2011-04-01

    In this article we report experimental and theoretical results of angle-dependent laser light scattering of nano titanium dioxide nucleated on silica particles. It was observed that the experimental scattering profile from nano-titania coated silica (TCS) particle resembles that of a Rayleigh scattering. It can be inferred from the light scattering profile that nucleating fine particles onto a surface of a bigger particle (core), the resulting scattering profile is dominated by the smaller particles. Thin film transmittance measurement of TCS particles also supports this claim. The theoretical scattering predictions do not match with the experimental findings and the reasons for the discrepancies are addressed. This Rayleigh-like scattering property of TCS particles can be used in cosmetic formulations as a replacement for nanoparticles to provide protection from harmful ultraviolet rays. This study helps to provide insights into these systems for their potential usage in cosmetics.

  8. CORE

    DEFF Research Database (Denmark)

    Krigslund, Jeppe; Hansen, Jonas; Hundebøll, Martin;

    2013-01-01

    different flows. Instead of maintaining these approaches separate, we propose a protocol (CORE) that brings together these coding mechanisms. Our protocol uses random linear network coding (RLNC) for intra- session coding but allows nodes in the network to setup inter- session coding regions where flows...... increase the benefits of XORing by exploiting the underlying RLNC structure of individual flows. This goes beyond providing additional reliability to each individual session and beyond exploiting coding opportunistically. Our numerical results show that CORE outperforms both forwarding and COPE......-like schemes in general. More importantly, we show gains of up to 4 fold over COPE-like schemes in terms of transmissions per packet in one of the investigated topologies....

  9. Fast determination of biogenic amines in beverages by a core-shell particle column.

    Science.gov (United States)

    Preti, Raffaella; Antonelli, Marta Letizia; Bernacchia, Roberta; Vinci, Giuliana

    2015-11-15

    A fast and reliable HPLC method for the determination of 11 biogenic amines in beverages has been performed. After pre-column derivatization with dansyl-chloride a Kinetex C18 core-shell particle column (100 mm × 4.6 mm, 2.6 μm particle size) has been employed and the biogenic amines were identified and quantified in a total run time of 13 min with ultraviolet (UV) or fluorescence detection (FLD). Chromatographic conditions such as column temperature (kept at 50 °C), gradient elution and flow rate have been optimized and the method has been tested on red wine and fruit nectar. The proposed method is enhanced in terms of reduced analysis time and eluent consumption with respect of classical HPLC method as to be comparable to UHPLC methods. Green and cost-effective, this method can be used as a quality-control tool for routine quantitative analysis of biogenic amines in beverages for the average laboratory. PMID:25977063

  10. Effect of Ratio of Face to Core Particles on Mechanical and Physical Properties of Particleboard Manufactured from Ethiopian Highland Bamboo

    Institute of Scientific and Technical Information of China (English)

    SEYOUM; Kelemwork; PARIDAH; Md.Tahi; WONG; Ee; Ding; RAHIM; Sudin

    2009-01-01

    The study was conducted to evaluate effect of ratio of face to core particles on mechanical and physical properties of oriented strand board produced from Ethiopian highland bamboo.Three-layered oriented particleboards were manufactured with 4 proportions of face to core particles at 750 kg/m~3 target density.Ten percent urea formaldehyde resin was used as a binder.Strength and dimensional stability performances of all boards were assessed based on ISO standards.The results showed that modulus of rupture...

  11. Magnetic/luminescent core/shell particles synthesized by spray pyrolysis and their application in immunoassays with internal standard

    International Nuclear Information System (INIS)

    Many types of fluorescent nanoparticles have been investigated as alternatives to conventional organic dyes in biochemistry; magnetic beads also have a long history of biological applications. In this work we apply flame spray pyrolysis in order to engineer a novel type of nanoparticle that has both luminescent and magnetic properties. The particles have magnetic cores of iron oxide doped with cobalt and neodymium and luminescent shells of europium-doped gadolinium oxide (Eu:Gd2O3). Measurements by vibrating sample magnetometry showed an overall paramagnetic response of these composite particles. Luminescence spectroscopy showed spectra typical of the Eu ion in a Gd2O3 host-a narrow emission peak centred near 615 nm. Our synthesis method offers a low-cost, high-rate synthesis route that enables a wide range of biological applications of magnetic/luminescent core/shell particles. Using these particles we demonstrate a novel immunoassay format with internal luminescent calibration for more precise measurements

  12. Reaction model for fluorination of uranium dioxide using improved unreacted shrinking core model for expanding spherical particles

    International Nuclear Information System (INIS)

    A gas-solid reaction model is developed to represent the fluorination of uranium dioxide (UO2), which consists of a two-step reaction: the formation of a solid intermediate of uranyl fluoride (UO2F2) on the core of unreacted UO2 and the consumption of UO2F2. The model is an extension of the unreacted shrinking core model with a shrinking spherical particle and takes into account particle expansion resulting from the density difference between UO2 and UO2F2. This model successfully represents the initial expansion of the particle by the formation of the low-density UO2F2 intermediate. The accuracy of this model is higher than that of the original model, which does not allow particle expansion. (author)

  13. Kinetic evaluation of new generation of column packed with 1.3 μm core-shell particles.

    Science.gov (United States)

    Fekete, Szabolcs; Guillarme, Davy

    2013-09-20

    The goal of this study was to critically evaluate a new generation of columns packed with 1.3 μm core-shell particles. The practical possibilities and limitations of this column technology were assessed and performance was compared with other reference columns packed with 1.7, 2.6 and 5 μm core-shell particles. The column efficiency achieved with 1.3 μm core-shell particles was indeed impressive, Hmin value of only 1.95 μm was achieved, this would correspond to an efficiency of more than 500,000 plates/m. The separation impedance of this column was particularly low, Emin=2000, mostly due to a reduced plate height, h of 1.50. Comparing the kinetic performance of 1.3 μm core-shell particles to that of other particle dimensions tested in this study revealed that the 1.3 μm material could provide systematically the shortest analysis time in a range of below 30,000 theoretical plates (Nlimitations of current instrumentation in terms of upper pressure limit and extra-column band broadening: (1) even at 1,200 bar, it was not possible to reach an optimal linear velocity showing minimal plate height value, due to the low permeability of this column (Kv=1.7×10(-11)cm(2)), and (2) for these short narrow bore columns packed with 1.3 μm core shell particles, which is mandatory for performing fast-analysis and preventing the influence of frictional heat on column performance in UHPLC, it was observed that the extra-column band broadening could have a major impact on the apparent kinetic performance. In the present work, significant plate count loss was noticed for retention factors of less than 5, even with the best system on the market (σ(2)ec=2 μL(2)). PMID:23953620

  14. Thermosensitive core-shell particles as model systems for studying the flow behavior of concentrated colloidal dispersions.

    Science.gov (United States)

    Crassous, J J; Siebenbürger, M; Ballauff, M; Drechsler, M; Henrich, O; Fuchs, M

    2006-11-28

    We report on a comprehensive investigation of the flow behavior of colloidal thermosensitive core-shell particles at high densities. The particles consist of a solid core of poly(styrene) onto which a network of cross-linked poly(N-isopropylacrylamide) is affixed. Immersed in water the shell of these particles will swell if the temperature is low. Raising the temperature above 32 degrees C leads to a volume transition within this shell which leads to a marked shrinking of the shell. The particles have well-defined core-shell structure and a narrow size distribution. The remaining electrostatic interactions due to a small number of charges affixed to the core particles can be screened by adding 0.05M KCl to the suspensions. Below the lower critical solution temperature at 32 degrees C the particles are purely repulsive. Above this transition, a thermoreversible coagulation takes place. Lowering the temperature again leads to full dissociation of the aggregates formed by this process. The particles crystallize for effective volume fractions between 0.48 and 0.55. The crystallites can be molten by shear in order to reach a fluid sample again. The reduced shear stress measured in this metastable disordered state was found to be a unique function of the shear rate and the effective volume fraction. These reduced flow curves thus obtained can be described quantitatively by the theory of Fuchs and Cates [Phys. Rev. Lett. 89, 248304 (2002)] which is based on the mode-coupling theory of the glass transition. PMID:17144739

  15. Enrichment of Fetal Nucleated Red Blood Cells by Multi-core Magnetic Composite Particles for Non-invasive Prenatal Diagnosis

    Institute of Scientific and Technical Information of China (English)

    PAN Ying; ZHANG Ai-chen; WANG Qing; HUANG Wen-jun; QIAO Feng-li; LIU Yu-ping; ZHANG Yu-cheng; HAl De-yang; DU Ying-ting; WANG Wen-yue

    2012-01-01

    A novel kind of multi-core magnetic composite particles,the surfaces of which were respectively modified with goat-anti-mouse IgG and antitransferrin receptor(anti-CD71 ),was prepared.The fetal nucleated red blood cells(FNRBCs) in the peripheral blood of a gravida were rapidly and effectively enriched and separated by the modified multi-core magnetic composite particles in an external magnetic field.The obtained FNRBCs were used for the identification of the fetal sex by means of fluorescence in situ hybridization(FISH) technique.The results demonstrate that the multi-core magnetic composite particles meet the requirements for the enrichment and speration of FNRBCs with a low concentration and the accuracy of detetion for the diagnosis of fetal sex reached to 95%.Moreover,the obtained FNRBCs were applied to the non-invasive diagnosis of Down syndrome and chromosome 3p21 was detected.The above facts indicate that the novel multi-core magnetic composite particles-based method is simple,reliable and cost-effective and has opened up vast vistas for the potential application in clinic non-invasive prenatal diagnosis.

  16. 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.

  17. Cas9 Functionally Opens Chromatin

    OpenAIRE

    Barkal, Amira A.; Srinivasan, Sharanya; Hashimoto, Tatsunori; Gifford, David K.; Sherwood, Richard I.

    2016-01-01

    Using a nuclease-dead Cas9 mutant, we show that Cas9 reproducibly induces chromatin accessibility at previously inaccessible genomic loci. Cas9 chromatin opening is sufficient to enable adjacent binding and transcriptional activation by the settler transcription factor retinoic acid receptor at previously unbound motifs. Thus, we demonstrate a new use for Cas9 in increasing surrounding chromatin accessibility to alter local transcription factor binding.

  18. Cas9 Functionally Opens Chromatin

    OpenAIRE

    Barkal, Amira A.; Srinivasan, Sharanya; Gifford, David K.; Sherwood, Richard I.; Hashimoto, Tatsunori Benjamin

    2015-01-01

    Using a nuclease-dead Cas9 mutant, we show that Cas9 reproducibly induces chromatin accessibility at previously inaccessible genomic loci. Cas9 chromatin opening is sufficient to enable adjacent binding and transcriptional activation by the settler transcription factor retinoic acid receptor at previously unbound motifs. Thus, we demonstrate a new use for Cas9 in increasing surrounding chromatin accessibility to alter local transcription factor binding.

  19. Cas9 Functionally Opens Chromatin.

    Directory of Open Access Journals (Sweden)

    Amira A Barkal

    Full Text Available Using a nuclease-dead Cas9 mutant, we show that Cas9 reproducibly induces chromatin accessibility at previously inaccessible genomic loci. Cas9 chromatin opening is sufficient to enable adjacent binding and transcriptional activation by the settler transcription factor retinoic acid receptor at previously unbound motifs. Thus, we demonstrate a new use for Cas9 in increasing surrounding chromatin accessibility to alter local transcription factor binding.

  20. Cas9 Functionally Opens Chromatin

    Science.gov (United States)

    Barkal, Amira A.; Srinivasan, Sharanya; Hashimoto, Tatsunori; Gifford, David K.; Sherwood, Richard I.

    2016-01-01

    Using a nuclease-dead Cas9 mutant, we show that Cas9 reproducibly induces chromatin accessibility at previously inaccessible genomic loci. Cas9 chromatin opening is sufficient to enable adjacent binding and transcriptional activation by the settler transcription factor retinoic acid receptor at previously unbound motifs. Thus, we demonstrate a new use for Cas9 in increasing surrounding chromatin accessibility to alter local transcription factor binding. PMID:27031353

  1. Fabrication and characterization of flaky core-shell particles by magnetron sputtering silver onto diatomite

    Science.gov (United States)

    Wang, Yuanyuan; Zhang, Deyuan; Cai, Jun

    2016-02-01

    Diatomite has delicate porous structures and various shapes, making them ideal templates for microscopic core-shell particles fabrication. In this study, a new process of magnetron sputtering assisted with photoresist positioning was proposed to fabricate lightweight silver coated porous diatomite with superior coating quality and performance. The diatomite has been treated with different sputtering time to investigate the silver film growing process on the surface. The morphologies, constituents, phase structures and surface roughness of the silver coated diatomite were analyzed with SEM, EDS, XRD and AFM respectively. The results showed that the optimized magnetron sputtering time was 8-16 min, under which the diatomite templates were successfully coated with uniform silver film, which exhibits face centered cubic (fcc) structure, and the initial porous structures were kept. Moreover, this silver coating has lower surface roughness (RMS 4.513 ± 0.2 nm) than that obtained by electroless plating (RMS 15.692 ± 0.5 nm). And the infrared emissivity of coatings made with magnetron sputtering and electroless plating silver coated diatomite can reach to the lowest value of 0.528 and 0.716 respectively.

  2. Internal stresses in pre-stressed micron-scale aluminum core-shell particles and their improved reactivity

    Energy Technology Data Exchange (ETDEWEB)

    Levitas, Valery I., E-mail: vlevitas@iastate.edu [Department of Aerospace Engineering, Department of Mechanical Engineering, Department of Material Science and Engineering, Iowa State University, Ames, Iowa 50011 (United States); McCollum, Jena; Pantoya, Michelle L. [Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409 (United States); Tamura, Nobumichi [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2015-09-07

    Dilatation of aluminum (Al) core for micron-scale particles covered by alumina (Al{sub 2}O{sub 3}) shell was measured utilizing x-ray diffraction with synchrotron radiation for untreated particles and particles after annealing at 573 K and fast quenching at 0.46 K/s. Such a treatment led to the increase in flame rate for Al + CuO composite by 32% and is consistent with theoretical predictions based on the melt-dispersion mechanism of reaction for Al particles. Experimental results confirmed theoretical estimates and proved that the improvement of Al reactivity is due to internal stresses. This opens new ways of controlling particle reactivity through creating and monitoring internal stresses.

  3. Internal stresses in pre-stressed micron-scale aluminum core-shell particles and their improved reactivity

    International Nuclear Information System (INIS)

    Dilatation of aluminum (Al) core for micron-scale particles covered by alumina (Al2O3) shell was measured utilizing x-ray diffraction with synchrotron radiation for untreated particles and particles after annealing at 573 K and fast quenching at 0.46 K/s. Such a treatment led to the increase in flame rate for Al + CuO composite by 32% and is consistent with theoretical predictions based on the melt-dispersion mechanism of reaction for Al particles. Experimental results confirmed theoretical estimates and proved that the improvement of Al reactivity is due to internal stresses. This opens new ways of controlling particle reactivity through creating and monitoring internal stresses

  4. Relationship between polycyclic aromatic hydrocarbons (PAHs) and particle size in dated core sediments in Lake Lianhuan, Northeast China

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Li; Zang, Shuying, E-mail: zsy6311@163.com

    2013-09-01

    Atmospheric particle associated with pyrogenic polycyclic aromatic hydrocarbons (PAHs) poses serious threats to human health by inhalation exposure, especially in semiarid areas. Hence, the distributions of PAHs and particle size in two core sediments collected from Lake Lianhuan, Northeast China were studied. The sediments were dated radiometrically, and particle size distribution and PAH concentration were evaluated and potential human health risk was assessed. From 1980 to 2007, the dominant PAHs in the two cores were 2- and 3-ring PAHs, and the concentrations of 3–6 ring PAHs gradually increased from the early 1990s. Diagnostic ratios indicated that pyrogenic PAHs were the main sources of PAHs which changed over time from combustions of wood and coal to liquid fossil fuel sources. Fine particles (< 65 μm) were the predominant particle size (56–97%). Lacustrine source (with the peak towards 200–400 μm) and eolian sources derived from short (2.0–10 and 30–65 μm) and long (0.4–1.0 μm) distance suspension were indentified from frequency distribution pattern of particle size. Significant correlations between 3–6 ring PAHs (especially carcinogenic 5–6 ring PAHs) and 10–35 μm particulate fractions indicated that eolian particles played an important role in adsorbing pyrogenic PAHs. Petroleum source of PAHs was only identified during the 1980s in one core sediments, in which positive correlations between 2-ring PAHs and particulate fractions of > 125 μm were found. Future research should focus on the seven carcinogenic pyrogenic PAHs due to a rapidly increasing trend since 1995 based on the assessment of toxic equivalency factors. - Highlights: • PAHs and particle size in core sediments were used to evaluate the role of eolian particles in delivering pyrogenic PAHs. • Changes of PAH sources closely followed local historical socioeconomic development since 1980s. • Changes of particulate sources from eolian to lacustrine reflected the

  5. Quantum behaved Particle Swarm Optimization with Differential Mutation operator applied to WWER-1000 in-core fuel management optimization

    International Nuclear Information System (INIS)

    Highlights: ► A new method called QPSO-DM is applied to BNPP in-core fuel management optimization. ► It is found that QPSO-DM performs better than PSO and QPSO. ► This method provides a permissible arrangement for optimum loading pattern. - Abstract: This paper presents a new method using Quantum Particle Swarm Optimization with Differential Mutation operator (QPSO-DM) for optimizing WWER-1000 core fuel management. Genetic Algorithm (GA) and Particle Swarm Optimization (PSO) have shown good performance on in-core fuel management optimization (ICFMO). The objective of this paper is to show that QPSO-DM performs very well and is comparable to PSO and Quantum Particle Swarm Optimization (QPSO). Most of the strategies for ICFMO are based on maximizing multiplication factor (keff) to increase cycle length and minimizing power peaking factor (Pq) in order to improve fuel integrity. PSO, QPSO and QPSO-DM have been implemented to fulfill these requirements for the first operating cycle of WWER-1000 Bushehr Nuclear Power Plant (BNPP). The results show that QPSO-DM performs better than the others. A program has been written in MATLAB to map PSO, QPSO and QPSO-DM for loading pattern optimization. WIMS and CITATION have been used to simulate reactor core for neutronic calculations

  6. Fabrication of quantum dot/silica core-shell particles immobilizing Au nanoparticles and their dual imaging functions

    Science.gov (United States)

    Kobayashi, Yoshio; Matsudo, Hiromu; Li, Ting-ting; Shibuya, Kyosuke; Kubota, Yohsuke; Oikawa, Takahiro; Nakagawa, Tomohiko; Gonda, Kohsuke

    2016-03-01

    The present work proposes preparation methods for quantum dot/silica (QD/SiO2) core-shell particles that immobilize Au nanoparticles (QD/SiO2/Au). A colloid solution of QD/SiO2 core-shell particles with an average size of 47.0 ± 6.1 nm was prepared by a sol-gel reaction of tetraethyl orthosilicate in the presence of the QDs with an average size of 10.3 ± 2.1 nm. A colloid solution of Au nanoparticles with an average size of 17.9 ± 1.3 nm was prepared by reducing Au3+ ions with sodium citrate in water at 80 °C. Introduction of amino groups to QD/SiO2 particle surfaces was performed using (3-aminopropyl)-triethoxysilane (QD/SiO2-NH2). The QD/SiO2/Au particles were fabricated by mixing the Au particle colloid solution and the QD/SiO2-NH2 particle colloid solution. Values of radiant efficiency and computed tomography for the QD/SiO2/Au particle colloid solution were 2.23 × 107 (p/s/cm2/sr)/(μW/cm2) at a QD concentration of 8 × 10-7 M and 1180 ± 314 Hounsfield units and an Au concentration of 5.4 × 10-2 M. The QD/SiO2/Au particle colloid solution was injected into a mouse chest wall. Fluorescence emitted from the colloid solution could be detected on the skin covering the chest wall. The colloid solution could also be X-ray-imaged in the chest wall. Consequently, the QD/SiO2/Au particle colloid solution was found to have dual functions, i.e., fluorescence emission and X-ray absorption in vivo, which makes the colloid solution suitable to function as a contrast agent for dual imaging processes.

  7. Self-Assembly of an Alphavirus Core-like Particle Is Distinguished by Strong Intersubunit Association Energy and Structural Defects.

    Science.gov (United States)

    Wang, Joseph Che-Yen; Chen, Chao; Rayaprolu, Vamseedhar; Mukhopadhyay, Suchetana; Zlotnick, Adam

    2015-09-22

    Weak association energy can lead to uniform nanostructures: defects can anneal due to subunit lability. What happens when strong association energy leads to particles where defects are trapped? Alphaviruses are enveloped viruses whose icosahedral nucleocapsid core can assemble independently. We used a simplest case system to study Ross River virus (RRV) core-like particle (CLP) self-assembly using purified capsid protein and a short DNA oligomer. We find that capsid protein binds the oligomer with high affinity to form an assembly competent unit (U). Subsequently, U assembles with concentration dependence into CLPs. We determined that U-U pairwise interactions are very strong (ca. -6 kcal/mol) compared to other virus assembly systems. Assembled RRV CLPs appeared morphologically uniform and cryo-EM image reconstruction with imposed icosahedral symmetry yielded a T = 4 structure. However, 2D class averages of the CLPs show that virtually every class had disordered regions. These results suggested that irregular cores may be present in RRV virions. To test this hypothesis, we determined 2D class averages of RRV virions using authentic virions or only the core from intact virions isolated by computational masking. Virion-based class averages were symmetrical, geometric, and corresponded well to projections of image reconstructions. In core-based class averages, cores and envelope proteins in many classes were disordered. These results suggest that partly disordered components are common even in ostensibly well-ordered viruses, a biological realization of a patchy particle. Biological advantages of partly disordered complexes may arise from their ease of dissociation and asymmetry. PMID:26275088

  8. A description of odd neutron-deficient cadmium isotopes within the rotor-plus-particle model using self-consistent core signle-particle states

    International Nuclear Information System (INIS)

    Single-particle wave functions as obtained from self-consistent calculations for the core are used to calculate within the rotor-plus-quasiparticle model, some spectroscopic properties of odd neutron-deficient cadmium isotopes. From constrained Hartree-Fock calculations including pairing correlations and performed with the SIII Skyrme effective force, the deformation energy curves of 98102106110Cd have been extracted together with the single-particle states corresponding to the equilibrium deformations. The projection of standard unified model wave functions onto eigenfunctions of the core angular momentum has allowed the authors to introduce exactly in the core Hamiltonian the experimental level sequence of the neigbouring even isotopes. Therefore all parameters entering the calculations are either valid for the whole chart of nuclides (effective force parameters) or unambiguously deduced from experimental data (core energies and pairing gaps). In spite of such an absence of free adjustable parameters the recently available experimental data concerning 105107109111Cd isotopes are correctly reproduced both for negative parity (as the expected hsub(11/2) decoupled band) and for positive parity states. In the 105Cd isotope, the authors have interpreted a set of positive parity levels as a gsub(7/2) decoupled band. They have also concluded that a prolate-oblate shape coexistence was probably absent in the low energy spectra of the isotopes considered. (Auth.)

  9. Epigenetics & chromatin: Interactions and processes

    NARCIS (Netherlands)

    S. Henikoff (Steven); F.G. Grosveld (Frank)

    2013-01-01

    textabstractOn 11 to 13 March 2013, BioMed Central will be hosting its inaugural conference, Epigenetics & Chromatin: Interactions and Processes, at Harvard Medical School, Cambridge, MA, USA. Epigenetics & Chromatin has now launched a special article series based on the general themes of the confer

  10. Construction and Immunological Evaluation of Multivalent Hepatitis B Virus (HBV) Core Virus-Like Particles Carrying HBV and HCV Epitopes▿

    OpenAIRE

    Sominskaya, Irina; Skrastina, Dace; Dislers, Andris; Vasiljev, Denis; Mihailova, Marija; Ose, Velta; Dreilina, Dzidra; Pumpens, Paul

    2010-01-01

    A multivalent vaccine candidate against hepatitis B virus (HBV) and hepatitis C virus (HCV) infections was constructed on the basis of HBV core (HBc) virus-like particles (VLPs) as carriers. Chimeric VLPs that carried a virus-neutralizing HBV pre-S1 epitope corresponding to amino acids (aa) 20 to 47 in the major immunodominant region (MIR) and a highly conserved N-terminal HCV core epitope corresponding to aa 1 to 60 at the C terminus of the truncated HBcΔ protein (N-terminal aa 1 to 144 of f...

  11. Rheological properties of magnetorheological suspensions based on core-shell structured polyaniline-coated carbonyl iron particles

    Science.gov (United States)

    Sedlačík, M.; Pavlínek, V.; Sáha, P.; Švrčinová, P.; Filip, P.; Stejskal, J.

    2010-11-01

    The sedimentation caused by the high density of suspended particles used in magnetorheological fluids is a significant obstacle for their wider application. In the present paper, core-shell structured carbonyl iron-polyaniline particles in silicone oil were used as a magnetorheological suspension with enhanced dispersion stability. Bare carbonyl iron particles were suspended in silicone oil to create model magnetorheological suspensions of different loading. For a magnetorheological suspension of polyaniline-coated particles the results show a decrease in the base viscosity. Moreover, the polyaniline coating has a negligible influence on the MR properties under an external magnetic field B. The change in the viscoelastic properties of magnetorheological suspensions in the small-strain oscillatory shear flow as a function of the strain amplitude, the frequency and the magnetic flux density was also investigated.

  12. A particle-core-MD model for intrabeam scattering and halo formation in high current beams in a FODO channel

    CERN Document Server

    Uhlmann, N; Comunian, M; Pisent, A

    2002-01-01

    An essential problem for the successful operation of high current linear ion accelerators is the control of beam losses due to halo particles. As a possible mechanism for the formation of such a halo we concentrate on the interplay between intrabeam scattering (IBS) and the incidence of particles which are driven to high amplitudes by resonances with the nonlinear space charge fields of a mismatched beam. Since a fully microscopic numerical treatment including all the mutual Coulomb interactions between the beam ions requires much too high computational effort, we developed an approximative method. These particle-core-molecular-dynamics (PCMD) simulations suitably join the mean-field description of the time evolution of the beam in framework of the envelope equations and a microscopic calculation of the Coulomb interactions between pseudo-particles with a renormalized charge. With this method we studied matched and mismatched continuous KV-beams in a FODO channel. In first simulation runs we observed a signif...

  13. Synthesis and Characterization of Monodisperse Metallodielectric SiO2@Pt@SiO2 Core-Shell-Shell Particles.

    Science.gov (United States)

    Petrov, Alexey; Lehmann, Hauke; Finsel, Maik; Klinke, Christian; Weller, Horst; Vossmeyer, Tobias

    2016-01-26

    Metallodielectric nanostructured core-shell-shell particles are particularly desirable for enabling novel types of optical components, including narrow-band absorbers, narrow-band photodetectors, and thermal emitters, as well as new types of sensors and catalysts. Here, we present a facile approach for the preparation of submicron SiO2@Pt@SiO2 core-shell-shell particles. As shown by transmission and scanning electron microscopy, the first steps of this approach allow for the deposition of closed and almost perfectly smooth platinum shells onto silica cores via a seeded growth mechanism. By choosing appropriate conditions, the shell thickness could be adjusted precisely, ranging from ∼3 to ∼32 nm. As determined by X-ray diffraction, the crystalline domain sizes of the polycrystalline metal shells were ∼4 nm, regardless of the shell thickness. The platinum content of the particles was determined by atomic absorption spectroscopy and for thin shells consistent with a dense metal layer of the TEM-measured thickness. In addition, we show that the roughness of the platinum shell strongly depends on the storage time of the gold seeds used to initiate reductive platinum deposition. Further, using polyvinylpyrrolidone as adhesion layer, it was possible to coat the metallic shells with very homogeneous and smooth insulating silica shells of well-controlled thicknesses between ∼2 and ∼43 nm. After depositing the particles onto silicon substrates equipped with interdigitated electrode structures, the metallic character of the SiO2@Pt particles and the insulating character of the SiO2 shells of the SiO2@Pt@SiO2 particles were successfully demonstrated by charge transport measurements at variable temperatures. PMID:26731341

  14. An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome

    OpenAIRE

    Förster, Friedrich; Lasker, Keren; Beck, Florian; Nickell, Stephan; Sali, Andrej; Baumeister, Wolfgang

    2009-01-01

    The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) ...

  15. Optimization of fuel core loading pattern design in a VVER nuclear power reactors using Particle Swarm Optimization (PSO)

    International Nuclear Information System (INIS)

    The two main goals in core fuel loading pattern design optimization are maximizing the core effective multiplication factor (Keff) in order to extract the maximum energy, and keeping the local power peaking factor (Pq) lower than a predetermined value to maintain fuel integrity. In this research, a new strategy based on Particle Swarm Optimization (PSO) algorithm has been developed to optimize the fuel core loading pattern in a typical VVER. The PSO algorithm presents a simple social model by inspiration from bird collective behavior in finding food. A modified version of PSO algorithm for discrete variables has been developed and implemented successfully for the multi-objective optimization of fuel loading pattern design with constraints of keeping Pq lower than a predetermined value and maximizing Keff. This strategy has been accomplished using WIMSD and CITATION calculation codes. Simulation results show that this algorithm can help in the acquisition of a new pattern without contravention of the constraints.

  16. The particle-in-cell model for ab initio thermodynamics: implications for the elastic anisotropy of the Earth's inner core

    OpenAIRE

    Gannarelli, C. M. S.; Alfe, D.; Gillan, M. J.

    2003-01-01

    We assess the quantitative accuracy of the particle-in-cell (PIC) approximation used in recent ab initio predictions of the thermodynamic properties of hexagonal-close-packed iron at the conditions of the Earth's inner core. The assessment is made by comparing PIC predictions for a range of thermodynamic properties with the results of more exact calculations that avoid the PIC approximation. It is shown that PIC gives very accurate results for some properties, but that it gives an incorrect t...

  17. Synthesis of TiO2 core/RuO2 shell particles using multistep ultrasonic spray pyrolysis

    International Nuclear Information System (INIS)

    Graphical abstract: - Highlights: • TiO2 core/RuO2 shell submicron-particles were prepared via a sequential spray pyrolysis. • Spherical particles have the mean particle diameters between 200 and 400 nm. • This method is promising for synthesis of core–shell and core–multishell materials. - Abstract: Spherical submicron-particles with TiO2 core–RuO2 shell structure have been synthesized by employing sequential ultrasonic spray pyrolysis. The particles have been investigated by X-ray powder diffraction, scanning electron microscopy and different transmission electron microscopy techniques. The quality of the core–shell structure of the particles has been confirmed by comparison of the experimental data with those generated on the basis of a hard sphere core–shell model. It has been found that the mixing of the Ru-containing aerosol with the TiO2 particle stream has a significant impact on the core–shell formation. The method introduced in this study can probably be applied for preparation of core–shell and core–multishell materials that are difficult to synthesize in a single step spray pyrolysis process

  18. Internal and higher-order structure of chromatin nu bodies

    Energy Technology Data Exchange (ETDEWEB)

    Olins, D E

    1977-01-01

    Based upon current biophysical data (including recent laser-Raman studies) of isolated nu bodies and inner histones, we have proposed that the chromatin subunit consists of a DNA-rich outer domain surrounding a protein core composed of ..cap alpha..-helical-rich histone globular regions, close-packed with dihedral point-group symmetry. Analysis of the effects of urea on isolated nu bodies suggest that these two domains respond differently: the DNA-rich shell exhibits noncooperative destabilization; the protein core undergoes cooperative destabilization. This differential response of the two regions of a nu body to a simple chemical perturbant (i.e., urea) may furnish a model for the conformational differences in nu bodies postulated for active chromatin. Nu bodies are believed to organize into 20-30 nm higher-order fibers in condensed regions of chromatin. However, the integrity of subunits in these thick fibers has recently been seriously challenged. Evidence from our laboratory, presented here, confirms that the 20-30 nm chromatin fibers consists of a close-packing of nu bodies. The chromatin subunits, therefore, retain their integrity within the higher-order fibers.

  19. Chromatin, epigenetics and stem cells.

    Science.gov (United States)

    Roloff, Tim C; Nuber, Ulrike A

    2005-03-01

    Epigenetics is a term that has changed its meaning with the increasing biological knowledge on developmental processes. However, its current application to stem cell biology is often imprecise and is conceptually problematic. This article addresses two different subjects, the definition of epigenetics and chromatin states of stem and differentiated cells. We describe mechanisms that regulate chromatin changes and provide an overview of chromatin states of stem and differentiated cells. Moreover, a modification of the current epigenetics definition is proposed that is not restricted by the heritability of gene expression throughout cell divisions and excludes translational gene expression control. PMID:15819395

  20. Elastic properties of mono- and polydisperse two-dimensional crystals of hard--core repulsive Yukawa particles

    CERN Document Server

    Narojczyk, Jakub W; Wojciechowski, K W; Tretiakov, K V

    2015-01-01

    Monte Carlo simulations of mono-- and polydisperse two--dimensional crystals are reported. The particles in the studied system, interacting through hard--core repulsive Yukawa potential, form a solid phase of hexagonal lattice. The elastic properties of crystalline Yukawa systems are determined in the $NpT$ ensemble with variable shape of the periodic box. Effects of the Debye screening length ($\\kappa^{-1}$), contact value of the potential ($\\epsilon$), and the size polydispersity of particles on elastic properties of the system are studied. The simulations show that the polydispersity of particles strongly influences the elastic properties of the studied system, especially on the shear modulus. It is also found that the elastic moduli increase with density and their growth rate depends on the screening length. Shorter screening length leads to faster increase of elastic moduli with density and decrease of the Poisson's ratio. In contrast to its three-dimensional version, the studied system is non-auxetic, i...

  1. Particle sizes of Pliocene and Pleistocene core sediments from IODP Expedition 323 in the Bering Sea

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data compilation includes the results of grain size analyses of core sediment collected by IODP during Expedition 323 in the Bering Sea. One dataset is...

  2. 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.

  3. Nd-doped calcium molybdate core and particles: synthesis, optical and photoluminescence studies

    Energy Technology Data Exchange (ETDEWEB)

    Ansari, Anees A. [King Saud University, King Abdullah Institute for Nanotechnology, P.O. Box 2455, Riyadh (Saudi Arabia); Alam, Manawwer [King Saud University, Research Center, College of Science, P.O. Box 2455, Riyadh (Saudi Arabia); Parchur, A.K. [Banaras Hindu University, Department of Physics, Varanasi (India)

    2014-09-15

    CaMoO{sub 4}:Nd (core), CaMoO{sub 4}:Nd rate at CaMoO{sub 4} and CaMoO{sub 4}:Nd rate at CaMoO{sub 4} rate at SiO{sub 2} core-shell nanoparticles were synthesized using polyol method under urea hydrolysis. X-ray diffraction and thermogravimetric analysis were employed to examine the structural and thermal properties of the as-prepared core and core-shell nanoparticles. Optical properties of core and core-shell nanoparticles were observed to investigate the influence of surface coating on the spectra of as-prepared nanomaterials in terms of ultraviolet/visible (UV-Vis) absorbance, FTIR, Raman and emission spectra. The optical band gap energy calculated from the UV-Vis absorption spectrum for CaMoO{sub 4}:Nd, CaMoO{sub 4}:Nd rate at CaMoO{sub 4} and CaMoO{sub 4}:Nd rate at CaMoO{sub 4} rate at SiO{sub 2} nanoparticles was 3.09, 2.06 and 1.26 eV, respectively. The photoluminescence spectra of the samples showed broad charge transfer emission band of [MoO{sub 4}]{sup 2-} along with sharp transitions of neodymium ion in the visible and near infrared regions, respectively. (orig.)

  4. Painting a Clearer Picture of Chromatin.

    Science.gov (United States)

    Finn, Elizabeth H; Misteli, Tom; Shachar, Sigal

    2016-02-22

    Elucidating chromatin's 3D shape is critical to understanding its function, but the fine structure of chromatin domains remains poorly resolved. In a recent report in Nature, Boettiger et al. (2016) visualize chromatin in super-resolution, gaining unprecedented insight into chromatin architecture. PMID:26906730

  5. Polystyrene Core-Silica Shell Particles with Defined Nanoarchitectures as a Versatile Platform for Suspension Array Technology.

    Science.gov (United States)

    Sarma, Dominik; Gawlitza, Kornelia; Rurack, Knut

    2016-04-19

    The need for rapid and high-throughput screening in analytical laboratories has led to significant growth in interest in suspension array technologies (SATs), especially with regard to cytometric assays targeting a low to medium number of analytes. Such SAT or bead-based assays rely on spherical objects that constitute the analytical platform. Usually, functionalized polymer or silica (SiO2) microbeads are used which each have distinct advantages and drawbacks. In this paper, we present a straightforward synthetic route to highly monodisperse SiO2-coated polystyrene core-shell (CS) beads for SAT with controllable architectures from smooth to raspberry- and multilayer-like shells by varying the molecular weight of poly(vinylpyrrolidone) (PVP), which was used as the stabilizer of the cores. The combination of both organic polymer core and a structurally controlled inorganic SiO2 shell in one hybrid particle holds great promises for flexible next-generation design of the spherical platform. The particles were characterized by electron microscopy (SEM, T-SEM, and TEM), thermogravimetry, flow cytometry, and nitrogen adsorption/desorption, offering comprehensive information on the composition, size, structure, and surface area. All particles show ideal cytometric detection patterns and facile handling due to the hybrid structure. The beads are endowed with straightforward modification possibilities through the defined SiO2 shells. We successfully implemented the particles in fluorometric SAT model assays, illustrating the benefits of tailored surface area which is readily available for small-molecule anchoring. Very promising assay performance was shown for DNA hybridization assays with quantification limits down to 8 fmol. PMID:27018430

  6. Brain Function and Chromatin Plasticity

    OpenAIRE

    Dulac, Catherine

    2010-01-01

    The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activity and connectivity. Persistent changes in chromatin structure are thought to contribute to mechanisms of epigenetic inheritance. Recent advances in chromatin biology offer new avenues to investig...

  7. Chromatin remodeling, development and disease

    International Nuclear Information System (INIS)

    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

  8. Mobilization and preferential transport of soil particles during infiltration: A core-scale modeling approach

    Science.gov (United States)

    Majdalani, Samer; Michel, Eric; di Pietro, Liliana; Angulo-Jaramillo, Rafael; Rousseau, Marine

    2007-05-01

    Understanding particle movement in soils is a major concern for both geotechnics and soil physics with regard to environmental protection and water resources management. This paper describes a model for mobilization and preferential transport of soil particles through structured soils. The approach combines a kinematic-dispersive wave model for preferential water flow with a convective-dispersive equation subject to a source/sink term for particle transport and mobilization. Particle detachment from macropore walls is considered during both the steady and transient water flow regimes. It is assumed to follow first-order kinetics with a varying detachment efficiency, which depends on the history of the detachment process. Estimates of model parameters are obtained by comparing simulations with experimental particle breakthrough curves obtained during infiltrations through undisturbed soil columns. Both water flux and particle concentrations are satisfactorily simulated by the model. Particle mobilization parameters favoring both attachment and detachment of particles are related to the incoming solution ionic strength by a Fermi-type function.

  9. New Small LWR Core Designs using Particle Burnable Poisons for Low Boron Concentration

    International Nuclear Information System (INIS)

    The soluble boron has two major important roles in commercial PWR operations : 1) the control of the long-term reactivity to maintain criticality under normal operation, and 2) the shutdown of the reactor under accidents. However, the removal of the soluble boron gives several advantages in SMRs (Small Modular Reactor). These advantages resulted from the elimination of soluble boron include the significant simplification of nuclear power plant through the removal of pipes, pumps, and purification systems. Also, the use of soluble boron mitigates corrosion problems on the primary coolant loop. Furthermore, the soluble boron-free operation can remove an inadvertent boron dilution accident (BDA) which can lead to a significant insertion of positive reactivity. From the viewpoint of core physics, the removal of soluble boron or reduction of soluble boron concentration makes the moderator temperature coefficient (MTC) more negative. From the core design studies using new fuel assemblies, it is shown that the cores have very low critical soluble boron concentrations less than 500ppm, low peaking factors within the design targets, strong negative MTCs over cycles, and large enough shutdown margins both at BOC and EOC. However, the present cores have relatively low average discharge burnups of ∼ 30MWD/kg leading to low fuel economy because the cores use lots of non-fuel burnable poison rods to achieve very low critical boron concentrations. So, in the future, we will perform the trade-off study between the fuel discharge burnup and the boron concentrations by changing fuel assembly design and the core loading pattern

  10. An Ensemble Method based on Particle of Swarm for the Reduction of Noise, Outlier and Core Point

    Directory of Open Access Journals (Sweden)

    Satish Dehariya,

    2013-04-01

    Full Text Available The majority voting and accurate prediction ofclassification algorithm in data mining arechallenging task for data classification. For theimprovement of data classification used differentclassifier along with another classifier in a mannerof ensembleprocess. Ensemble process increase theclassification ratio of classification algorithm, nowsuch par diagram of classification algorithm iscalled ensemble classifier. Ensemble learning is atechnique to improve the performance and accuracyof classification and predication of machinelearning algorithm. Many researchers proposed amodel for ensemble classifier for merging adifferent classification algorithm, but theperformance of ensemble algorithm suffered fromproblem of outlier, noise and core pointproblem ofdata from features selection process. In this paperwe combined core, outlier and noise data (COB forfeatures selection process for ensemble model. Theprocess of best feature selection with appropriateclassifier used particle of swarm optimization.

  11. The particle-in-cell model for ab initio thermodynamics: implications for the elastic anisotropy of the Earth's inner core

    CERN Document Server

    Gannarelli, C M S; Gillan, M J

    2003-01-01

    We assess the quantitative accuracy of the particle-in-cell (PIC) approximation used in recent ab initio predictions of the thermodynamic properties of hexagonal-close-packed iron at the conditions of the Earth's inner core. The assessment is made by comparing PIC predictions for a range of thermodynamic properties with the results of more exact calculations that avoid the PIC approximation. It is shown that PIC gives very accurate results for some properties, but that it gives an incorrect treatment of anharmonic lattice vibrations. In addition, our assessment does not support recent PIC-based predictions that the hexagonal c/a ratio increases strongly with increasing temperature, and we point out that this casts doubt on a proposed re-interpretation of the elastic anisotropy of the inner core.

  12. An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.

    Science.gov (United States)

    Förster, Friedrich; Lasker, Keren; Beck, Florian; Nickell, Stephan; Sali, Andrej; Baumeister, Wolfgang

    2009-10-16

    The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) is in excellent agreement with the recently identified base-precursor complexes formed during the assembly of the RP. Furthermore, the atomic CP-AAA-ATPase model suggests that the assembly chaperone Nas6 facilitates CP-RP association by enhancing the shape complementarity between Rpt3 and its binding CP alpha subunits partners. PMID:19653995

  13. High-resolution analytical imaging and electron holography of magnetite particles in amyloid cores of Alzheimer’s disease

    Science.gov (United States)

    Plascencia-Villa, Germán; Ponce, Arturo; Collingwood, Joanna F.; Arellano-Jiménez, M. Josefina; Zhu, Xiongwei; Rogers, Jack T.; Betancourt, Israel; José-Yacamán, Miguel; Perry, George

    2016-04-01

    Abnormal accumulation of brain metals is a key feature of Alzheimer’s disease (AD). Formation of amyloid-β plaque cores (APC) is related to interactions with biometals, especially Fe, Cu and Zn, but their particular structural associations and roles remain unclear. Using an integrative set of advanced transmission electron microscopy (TEM) techniques, including spherical aberration-corrected scanning transmission electron microscopy (Cs-STEM), nano-beam electron diffraction, electron holography and analytical spectroscopy techniques (EDX and EELS), we demonstrate that Fe in APC is present as iron oxide (Fe3O4) magnetite nanoparticles. Here we show that Fe was accumulated primarily as nanostructured particles within APC, whereas Cu and Zn were distributed through the amyloid fibers. Remarkably, these highly organized crystalline magnetite nanostructures directly bound into fibrillar Aβ showed characteristic superparamagnetic responses with saturated magnetization with circular contours, as observed for the first time by off-axis electron holography of nanometer scale particles.

  14. An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome

    International Nuclear Information System (INIS)

    The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) is in excellent agreement with the recently identified base-precursor complexes formed during the assembly of the RP. Furthermore, the atomic CP-AAA-ATPase model suggests that the assembly chaperone Nas6 facilitates CP-RP association by enhancing the shape complementarity between Rpt3 and its binding CP alpha subunits partners.

  15. An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome

    Energy Technology Data Exchange (ETDEWEB)

    Foerster, Friedrich [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany); Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Lasker, Keren [Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv (Israel); Beck, Florian; Nickell, Stephan [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany); Sali, Andrej [Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Baumeister, Wolfgang, E-mail: baumeist@biochem.mpg.de [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany)

    2009-10-16

    The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) is in excellent agreement with the recently identified base-precursor complexes formed during the assembly of the RP. Furthermore, the atomic CP-AAA-ATPase model suggests that the assembly chaperone Nas6 facilitates CP-RP association by enhancing the shape complementarity between Rpt3 and its binding CP alpha subunits partners.

  16. Single Molecule Studies of Chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  17. Chromatin remodelers and their roles in chromatin organization

    OpenAIRE

    Strålfors, Annelie

    2012-01-01

    The DNA in the eukaryotic nucleus is organized into a complex DNA-protein structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around a histone protein octamer. The nucleosomes form a “beads on a string” structure, which can be folded into higherorder structures that allow an extensive degree of DNA compaction. This compaction is so effective that 2 meters of DNA can fit into the human cell nucleus with a ...

  18. Core and grain boundary sensitivity of tungsten-oxide sensor devices by molecular beam assisted particle deposition

    Science.gov (United States)

    Huelser, T. P.; Lorke, A.; Ifeacho, P.; Wiggers, H.; Schulz, C.

    2007-12-01

    In this study, we investigate the synthesis of WO3 and WOx (2.6≥x≤2.8) by adding different concentrations of tungsten hexafluoride (WF6) into a H2/O2/Ar premixed flame within a low-pressure reactor equipped with a particle-mass spectrometer (PMS). The PMS results show that mean particle diameters dp between 5 and 9 nm of the as-synthesized metal-oxides can be obtained by varying the residence time and precursor concentration in the reactor. This result is further validated by N2 adsorption measurements on the particle surface, which yielded a 91 m2/g surface area, corresponding to a spherical particle diameter of 9 nm (Brunauer-Emmett-Teller technique). H2/O2 ratios of 1.6 and 0.63 are selected to influence the stoichiometry of the powders, resulting in blue-colored WOx and white WO3 respectively. X-ray diffraction (XRD) analysis of the as-synthesized materials indicates that the powders are mostly amorphous, and the observed broad reflexes can be attributed to the orthorhombic structure of β-WO3. Thermal annealing at 973 K for 3 h in air resulted in crystalline WO3 comprised of both monoclinic and orthorhombic phases. The transmission electron microscope micrograph analysis shows that the particles exhibit spherical morphology with some degree of agglomeration. Impedance spectroscopy is used for the electrical characterization of tungsten-oxide thin films with a thickness of 50 nm. Furthermore, the temperature-dependent gas-sensing properties of the material deposited on interdigital capacitors are investigated. Sensitivity experiments reveal two contributions to the overall sensitivity, which result from the surface and the core of each particle.

  19. Characterization of polymer-silica nanocomposite particles with core-shell morphologies using Monte Carlo simulations and small angle X-ray scattering.

    Science.gov (United States)

    Balmer, Jennifer A; Mykhaylyk, Oleksandr O; Schmid, Andreas; Armes, Steven P; Fairclough, J Patrick A; Ryan, Anthony J

    2011-07-01

    A two-population model based on standard small-angle X-ray scattering (SAXS) equations is verified for the analysis of core-shell structures comprising spherical colloidal particles with particulate shells. First, Monte Carlo simulations of core-shell structures are performed to demonstrate the applicability of the model. Three possible shell packings are considered: ordered silica shells due to either charge-dependent repulsive or size-dependent Lennard-Jones interactions or randomly arranged silica particles. In most cases, the two-population model produces an excellent fit to calculated SAXS patterns for the simulated core-shell structures, together with a good correlation between the fitting parameters and structural parameters used for the simulation. The limits of application are discussed, and then, this two-population model is applied to the analysis of well-defined core-shell vinyl polymer/silica nanocomposite particles, where the shell comprises a monolayer of spherical silica nanoparticles. Comprehensive SAXS analysis of a series of poly(styrene-co-n-butyl acrylate)/silica colloidal nanocomposite particles (prepared by the in situ emulsion copolymerization of styrene and n-butyl acrylate in the presence of a glycerol-functionalized silica sol) allows the overall core-shell particle diameter, the copolymer latex core diameter and polydispersity, the mean silica shell thickness, the mean silica diameter and polydispersity, the volume fractions of the two components, the silica packing density, and the silica shell structure to be obtained. These experimental SAXS results are consistent with electron microscopy, dynamic light scattering, thermogravimetry, helium pycnometry, and BET surface area studies. The high electron density contrast between the (co)polymer and the silica components, together with the relatively low polydispersity of these core-shell nanocomposite particles, makes SAXS ideally suited for the characterization of this system. Moreover

  20. Hollow and Core-Shell Microgels at Oil-Water Interfaces: Spreading of Soft Particles Reduces the Compressibility of the Monolayer.

    Science.gov (United States)

    Geisel, Karen; Rudov, Andrey A; Potemkin, Igor I; Richtering, Walter

    2015-12-01

    We investigate the influence of a solid core and of the cross-link density on the compression of microgel particles at oil-water interfaces by means of compression isotherms and computer simulations. We investigate particles with different morphology, namely core-shell particles containing a solid silica core surrounded by a cross-linked polymer shell of poly(N-isopropylacrylamide), and the corresponding hollow microgels where the core was dissolved. The polymer shell contains different amounts of cross-linker. The compression isotherms show that the removal of the core leads to an increase of the surface pressure at low compression, and the same effect can be observed when the polymer cross-link density is decreased. Low cross-link density and a missing core thus facilitate spreading of the polymer chains at the interface and, at high compression, hinder the transition to close hexagonal packing. Furthermore, the compression modulus only depends on the cross-link density at low compression, and no difference can be observed between the core-shell particles and the corresponding hollow microgels. It is especially remarkable that a low cross-link density leads to a high compression modulus at low compression, while this behavior is reversed at high compression. Thus, the core does not influence the particle behavior until the polymer shell is highly compressed and the core is directly exposed to the pressure. This is related to an enhanced spreading of polymer chains at the interface and thus high adsorption energy. These conclusions are fully supported by computer simulations which show that the cross-link density of the polymer shell defines the degree of deformation at the interface. Additionally, the core restricts the spreading of polymer chains at the interface. These results illustrate the special behavior of soft microgels at liquid interfaces. PMID:26575794

  1. Determination of antibodies for the core antigen of the hepatitis B virus by means of a direct radioimmunoassay with 32P-marked core particles

    International Nuclear Information System (INIS)

    After characterization of the protein kinase of the hepatitus B virus and the purification of this enzyme, the enzyme was proved to be a component of the core particle with a high affinity for ATP. Based on this a new procedure for the determination of the diagnostically important antibody for HBcAg (anti HBc) is presented, namely the direct radioimmunoassay by means of the marking of HBcAg with 32P. This procedure is much more sensitive than the traditional inhibitory test using an enzyme-marked anti-HBc immunoglobulin as a reagent (EIBA). Using this new RIA anti-HBc was shown to be present in the majority of the EIBA anti-HBc positive serums and also in a large number of EIBA anti-HBc negative serums from a population at high risk for the Hepatitis B virus. The significance of reproducible threshold values was also shown. RIA activity was seldom found in healthy blood donors without HBsAg and anti-HBs. On the other hand blood donors with increased serum transaminase values showed a significantly higher frequency of activity. This weak activity only determinable in dRIA, could be attributed to a very limited heaptitis B viral infection or to a cross-reaction. (TRV)

  2. Smoothed Particle Hydrodynamics simulations of the core-degenerate scenario for Type Ia supernovae

    CERN Document Server

    Aznar-Siguán, G; Lorén-Aguilar, P; Soker, N; Kashi, A

    2015-01-01

    The core-degenerate (CD) scenario for type Ia supernovae (SN Ia) involves the merger of the hot core of an asymptotic giant branch (AGB) star and a white dwarf, and might contribute a non-negligible fraction of all thermonuclear supernovae. Despite its potential interest, very few studies, and based on only crude simplifications, have been devoted to investigate this possible scenario, compared with the large efforts invested to study some other scenarios. Here we perform the first three-dimensional simulations of the merger phase, and find that this process can lead to the formation of a massive white dwarf, as required by this scenario. We consider two situations, according to the mass of the circumbinary disk formed around the system during the final stages of the common envelope phase. If the disk is massive enough, the stars merge on a highly eccentric orbit. Otherwise, the merger occurs after the circumbinary disk has been ejected and gravitational wave radiation has brought the stars close to the Roche...

  3. Effect of Particle-Core-Vibration Coupling Near the Double Closed $^{132}$Sn Nucleus from Precise Magnetic Moment Measurements

    CERN Multimedia

    Postma, H; Heyde, K; Walker, P; Grant, I; Veskovic, M; Stone, N; Stone, J

    2002-01-01

    % IS301 \\\\ \\\\ Low temperature nuclear orientation of isotope-separator implanted short-lived radioisotopes makes possible the measurements of nuclear magnetic dipole moments of oriented ground and excited states with half-lives longer than a few seconds. Coupling schemes characterizing the odd nucleons and ground-state deformations can be extracted from the nuclear moments. \\\\ We thus propose to measure the magnetic dipole moments of $^{127-133}$Sb to high precision using NMR/ON at the NICOLE facility. With (double magic +1) $^{133}$Sb as the reference, the main aim of this experiment is to examine whether the collective component in the 7/2$^+$ Sb ground state magnetic dipole moment varies as expected according to particle-core coupling calculations carried out for the Sb (Z=51) isotopes. Comparison of the 1-proton-particle excitations in Sb to 1-proton-hole states in In nuclei will shed light on differences between particle and hole excitations as understood within the present model. Comparison of r...

  4. 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....

  5. Coming to terms with chromatin structure.

    Science.gov (United States)

    Even-Faitelson, Liron; Hassan-Zadeh, Vahideh; Baghestani, Zahra; Bazett-Jones, David P

    2016-03-01

    Chromatin, once thought to serve only as a means to package DNA, is now recognized as a major regulator of gene activity. As a result of the wide range of methods used to describe the numerous levels of chromatin organization, the terminology that has emerged to describe these organizational states is often imprecise and sometimes misleading. In this review, we discuss our current understanding of chromatin architecture and propose terms to describe the various biochemical and structural states of chromatin. PMID:26223534

  6. Chromatin state dynamics during blood formation

    OpenAIRE

    Lara-Astiaso, David; Weiner, Assaf; Lorenzo-Vivas, Erika; Zaretsky, Irina; Jaitin, Diego Adhemar; David, Eyal; Keren-Shaul, Hadas; Mildner, Alexander; Winter, Deborah; Jung, Steffen; Friedman, Nir; Amit, Ido

    2014-01-01

    Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics, however technical limitations impede profiling of homogeneous differentiation intermediates. We developed a high sensitivity indexing-first chromatin immunoprecipitation approach (iChIP) to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation. We ide...

  7. Predicting chromatin organization using histone marks

    OpenAIRE

    Huang, Jialiang; Marco, Eugenio; Pinello, Luca; Yuan, Guo-Cheng

    2015-01-01

    Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interactions, we have developed a computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries. Our model accurately and robustly predicts these feat...

  8. Self-Propelled Particles with Soft-Core Interactions: Patterns, Stability, and Collapse

    Science.gov (United States)

    D'Orsogna, M. R.; Chuang, Y. L.; Bertozzi, A. L.; Chayes, L. S.

    2006-03-01

    Understanding collective properties of driven particle systems is significant for naturally occurring aggregates and because the knowledge gained can be used as building blocks for the design of artificial ones. We model self-propelling biological or artificial individuals interacting through pairwise attractive and repulsive forces. For the first time, we are able to predict stability and morphology of organization starting from the shape of the two-body interaction. We present a coherent theory, based on fundamental statistical mechanics, for all possible phases of collective motion.

  9. Manipulation of metal-dielectric core-shell particles in optical fields

    Czech Academy of Sciences Publication Activity Database

    Chvátal, Lukáš; Šiler, Martin; Zemánek, Pavel

    Bellingham : SPIE, 2014, 944106:1-6. ISBN 9781628415568. ISSN 0277-786X. [Polish-Slovak-Czech Optical Conference on Wave and Quantum Aspects of Contemporary Optics /19./. Jelenia Góra (PL), 08.09.2014-12.09.2014] R&D Projects: GA TA ČR TE01020233; GA ČR GB14-36681G; GA ČR GPP205/12/P868; GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01 Institutional support: RVO:68081731 Keywords : metals * particles * optical tweezers * apertures * mie scattering * nanoplasmonics * water Subject RIV: BH - Optics, Masers, Lasers

  10. Hybrid space–angle adaptivity for whole-core particle transport calculations

    International Nuclear Information System (INIS)

    Highlights: • A hybrid space–angle refinement for whole-core transport calculations is developed. • Our method is implemented for response matrix and collision probability methods. • The adaptive method leads to substantial reduction of the response matrix dimensions. • A new approach for coupling surface angular flux is introduced. • The results show the ability of the algorithm to obtain a desired accuracy. - Abstract: Adaptive refinement is a powerful method for efficiently solving physical problems. In this paper we present a new coupled space–angle adaptive algorithm for neutron transport calculations. The scheme is specifically employed for the solution of the integral form of transport equation based on the collision probability–response matrix method. The adaptive algorithm is started by first applying angular adaptivity and then projecting the solution to the spatial mesh refinement. A posteriori error estimate is derived by utilizing the flux gradient approach based on the net current leakage of nodes. A new approach is used to apply continuity of flux in the interface between nodes by escalating the order of spherical harmonics expansions of entrance response matrix to the same order of spherical harmonics expansions of outgoing angular flux at the neighboring node. Using an integral transport method within the node and refined space and angle variables, a new method for whole-core transport calculations is introduced. The validity of the developed adaptive strategy is assessed by a series of numerical experiments. Comparisons indicate that the space–angle adaptivity framework is capable of resulting acceptable solution with less number of the degrees of freedom (DOFs)

  11. Impact of Chromatin on HIV Replication

    OpenAIRE

    Agosto, Luis M.; Matthew Gagne; Henderson, Andrew J.

    2015-01-01

    Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.

  12. Silica nanoparticles as the adjuvant for the immunisation of mice using hepatitis B core virus-like particles.

    Science.gov (United States)

    Skrastina, Dace; Petrovskis, Ivars; Lieknina, Ilva; Bogans, Janis; Renhofa, Regina; Ose, Velta; Dishlers, Andris; Dekhtyar, Yuri; Pumpens, Paul

    2014-01-01

    Advances in nanotechnology and nanomaterials have facilitated the development of silicon dioxide, or Silica, particles as a promising immunological adjuvant for the generation of novel prophylactic and therapeutic vaccines. In the present study, we have compared the adjuvanting potential of commercially available Silica nanoparticles (initial particles size of 10-20 nm) with that of aluminium hydroxide, or Alum, as well as that of complete and incomplete Freund's adjuvants for the immunisation of BALB/c mice with virus-like particles (VLPs) formed by recombinant full-length Hepatitis B virus core (HBc) protein. The induction of B-cell and T-cell responses was studied after immunisation. Silica nanoparticles were able to adsorb maximally 40% of the added HBc, whereas the adsorption capacity of Alum exceeded 90% at the same VLPs/adjuvant ratio. Both Silica and Alum formed large complexes with HBc VLPs that sedimented rapidly after formulation, as detected by dynamic light scattering, spectrophotometry, and electron microscopy. Both Silica and Alum augmented the humoral response against HBc VLPs to the high anti-HBc level in the case of intraperitoneal immunisation, whereas in subcutaneous immunisation, the Silica-adjuvanted anti-HBc level even exceeded the level adjuvanted by Alum. The adjuvanting of HBc VLPs by Silica resulted in the same typical IgG2a/IgG1 ratios as in the case of the adjuvanting by Alum. The combination of Silica with monophosphoryl lipid A (MPL) led to the same enhancement of the HBc-specific T-cell induction as in the case of the Alum and MPL combination. These findings demonstrate that Silica is not a weaker putative adjuvant than Alum for induction of B-cell and T-cell responses against recombinant HBc VLPs. This finding may have an essential impact on the development of the set of Silica-adjuvanted vaccines based on a long list of HBc-derived virus-like particles as the biological component. PMID:25436773

  13. Labeling the oily core of nanocapsules and lipid-core nanocapsules with a triglyceride conjugated to a fluorescent dye as a strategy to particle tracking in biological studies

    Science.gov (United States)

    Fiel, Luana Almeida; Contri, Renata Vidor; Bica, Juliane Freitas; Figueiró, Fabrício; Battastini, Ana Maria Oliveira; Guterres, Sílvia Stanisçuaski; Pohlmann, Adriana Raffin

    2014-05-01

    The synthesis of novel fluorescent materials represents a very important step to obtain labeled nanoformulations in order to evaluate their biological behavior. The strategy of conjugating a fluorescent dye with triacylglycerol allows that either particles differing regarding supramolecular structure, i.e., nanoemulsions, nanocapsules, lipid-core nanocapsules, or surface charge, i.e., cationic nanocapsules and anionic nanocapsules, can be tracked using the same labeled material. In this way, a rhodamine B-conjugated triglyceride was obtained to prepare fluorescent polymeric nanocapsules. Different formulations were obtained, nanocapsules (NC) or lipid-core nanocapsules (LNC), using the labeled oil and Eudragit RS100, Eudragit S100, or poly(caprolactone) (PCL), respectively. The rhodamine B was coupled with the ricinolein by activating the carboxylic function using a carbodiimide derivative. Thin layer chromatography, proton nuclear magnetic resonance (1H-NMR), Fourier transform infrared spectroscopy (FTIR), UV-vis, and fluorescence spectroscopy were used to identify the new product. Fluorescent nanocapsule aqueous suspensions were prepared by the solvent displacement method. Their pH values were 4.6 (NC-RS100), 3.5 (NC-S100), and 5.0 (LNC-PCL). The volume-weighted mean diameter ( D 4.3) and polydispersity values were 150 nm and 1.05 (NC-RS100), 350 nm and 2.28 (NC-S100), and 270 nm and 1.67 (LNC-PCL). The mean diameters determined by photon correlation spectroscopy (PCS) ( z-average) were around 200 nm. The zeta potential values were +5.85 mV (NC-RS100), -21.12 mV (NC-S100), and -19.25 mV (LNC-PCL). The wavelengths of maximum fluorescence emission were 567 nm (NC-RS100 and LNC-PCL) and 574 nm (NC-S100). Fluorescence microscopy was used to evaluate the cell uptake (human macrophage cell line) of the fluorescent nanocapsules in order to show the applicability of the approach. When the cells were treated with the fluorescent nanocapsules, red emission was detected

  14. Premitotic Assembly of Human CENPs -T and -W Switches Centromeric Chromatin to a Mitotic State

    OpenAIRE

    Prendergast, Lisa; van Vuuren, Chelly; Kaczmarczyk, Agnieszka; Doering, Volker; Hellwig, Daniela; Quinn, Nadine; Hoischen, Christian; Diekmann, Stephan; Sullivan, Kevin F.

    2011-01-01

    Centromeres are differentiated chromatin domains, present once per chromosome, that direct segregation of the genome in mitosis and meiosis by specifying assembly of the kinetochore. They are distinct genetic loci in that their identity in most organisms is determined not by the DNA sequences they are associated with, but through specific chromatin composition and context. The core nucleosomal protein CENP-A/cenH3 plays a primary role in centromere determination in all species and directs ass...

  15. Density functional formulation of the random-phase approximation for inhomogeneous fluids: Application to the Gaussian core and Coulomb particles

    Science.gov (United States)

    Frydel, Derek; Ma, Manman

    2016-06-01

    Using the adiabatic connection, we formulate the free energy in terms of the correlation function of a fictitious system, hλ(r ,r') , in which interactions λ u (r ,r') are gradually switched on as λ changes from 0 to 1. The function hλ(r ,r') is then obtained from the inhomogeneous Ornstein-Zernike equation and the two equations constitute a general liquid-state framework for treating inhomogeneous fluids. The two equations do not yet constitute a closed set. In the present work we use the closure cλ(r ,r') ≈-λ β u (r ,r') , known as the random-phase approximation (RPA). We demonstrate that the RPA is identical with the variational Gaussian approximation derived within the field-theoretical framework, originally derived and used for charged particles. We apply our generalized RPA approximation to the Gaussian core model and Coulomb charges.

  16. Layer-by-layer assembly of imogolite nanotubes and polyelectrolytes into core-shell particles and their conversion to hierarchically porous spheres

    Directory of Open Access Journals (Sweden)

    Yoshiyuki Kuroda et al

    2008-01-01

    Full Text Available Core-shell particles were prepared by the layer-by-layer (LbL assembly of imogolite (IMO nanotubes and poly(sodium 4-styrenesulfonate (PSS on polystyrene particles (diameter: 800 nm coated preliminarily with poly(diallyldimethylammonium chloride (PDDA. PSS and imogolite were alternately adsorbed on the particles to form core-shell particles with one to three bilayers of PSS/IMO. Macroporous hollow spheres were formed by removing polystyrene cores via heat treatment or extraction when the number of bilayers was 2 or 3. The sample formed by extraction (the number of bilayer was 3 showed only macroporosity and PSS remained in the shell, whereas the heat-treated sample showed hierarchical micro- and macroporosities. When the diameter of polystyrene particles decreased from 800 nm to 300 or 100 nm, hollow spheres were deformed because of the increase in the relative length of imogolite nanotubes against the size of polystyrene particles. Imogolite is a promising building block of hierarchically porous materials with core-shell morphologies using LbL assembly.

  17. Histone H2A (H2A.X and H2A.Z variants in molluscs: molecular characterization and potential implications for chromatin dynamics.

    Directory of Open Access Journals (Sweden)

    Rodrigo González-Romero

    Full Text Available Histone variants are used by the cell to build specialized nucleosomes, replacing canonical histones and generating functionally specialized chromatin domains. Among many other processes, the specialization imparted by histone H2A (H2A.X and H2A.Z variants to the nucleosome core particle constitutes the earliest response to DNA damage in the cell. Consequently, chromatin-based genotoxicity tests have been developed in those cases where enough information pertaining chromatin structure and dynamics is available (i.e., human and mouse. However, detailed chromatin knowledge is almost absent in most organisms, specially protostome animals. Molluscs (which represent sentinel organisms for the study of pollution are not an exception to this lack of knowledge. In the present work we first identified the existence of functionally differentiated histone H2A.X and H2A.Z variants in the mussel Mytilus galloprovincialis (MgH2A.X and MgH2A.Z, a marine organism widely used in biomonitoring programs. Our results support the functional specialization of these variants based on: a their active expression in different tissues, as revealed by the isolation of native MgH2A.X and MgH2A.Z proteins in gonad and hepatopancreas; b the evolutionary conservation of different residues encompassing functional relevance; and c their ability to confer specialization to nucleosomes, as revealed by nucleosome reconstitution experiments using recombinant MgH2A.X and MgH2A.Z histones. Given the seminal role of these variants in maintaining genomic integrity and regulating gene expression, their preliminary characterization opens up new potential applications for the future development of chromatin-based genotoxicity tests in pollution biomonitoring programs.

  18. An Ensemble Method based on Particle of Swarm for the Reduction of Noise, Outlier and Core Point

    Directory of Open Access Journals (Sweden)

    Satish Dehariya

    2013-03-01

    Full Text Available The majority voting and accurate prediction of classification algorithm in data mining are challenging task for data classification. For the improvement of data classification used different classifier along with another classifier in a manner of ensemble process. Ensemble process increase the classification ratio of classification algorithm, now such par diagram of classification algorithm is called ensemble classifier. Ensemble learning is a technique to improve the performance and accuracy of classification and predication of machine learning algorithm. Many researchers proposed a model for ensemble classifier for merging a different classification algorithm, but the performance of ensemble algorithm suffered from problem of outlier, noise and core point problem of data from features selection process. In this paper we combined core, outlier and noise data (COB for features selection process for ensemble model. The process of best feature selection with appropriate classifier used particle of swarm optimization. Empirical results with UCI data set prediction on Ecoil and glass dataset indicate that the proposed COB model optimization algorithm can help to improve accuracy and classification.

  19. Preparation of Surfactant-free Core-Shell Poly(lactic acid) / Calcium Phosphate Hybrid Particles and Their Drug Release Characteristics

    International Nuclear Information System (INIS)

    We propose surfactant-free core-shell poly(lactic acid) (PLA) / calcium phosphate (CaP) hybrid particles as drug delivery carriers. These particles were prepared by biomineralization process using ultrasonic irradiation, and their drug release profiles were investigated. Drug release rate was earlier when particles were prepared by PLA with a low molecular weight, and/or by Ca(CH3COO)2 and (NH4)2HPO4. Also, these were shown good protein adsorption. This work indicates that these particles have sustained-release ability without initial burst and can do targeting capability by biomolecule conjugation.

  20. 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...

  1. Spectroscopic study of laser irradiated chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Radu, Liliana, E-mail: liliana1radu@gmail.com [V. Babes National Institute, Department of Molecular Genetics and Radiobiology (Romania); Mihailescu, I. [National Institute for Lasers, Plasma and Radiation Physics, Department of Lasers (Romania); Gazdaru, Doina [Faculty of Physics, Bucharest University, Department of Biophysics (Romania); Preoteasa, V. [V. Babes National Institute, Department of Molecular Genetics and Radiobiology (Romania)

    2013-04-15

    The effects of three UV excimer laser radiations, with wavelengths of 193, 248 and 282 nm respectively, on the structure of chromatin (the complex of deoxyribonucleic acid with proteins that exists in eukaryotic cells nuclei) were investigated. The chromatin was extracted from livers of Winstar rats. The spectroscopic methods used are: fluorescence (Foerster) resonance energy transfer (FRET), time resolved fluorescence and steady-state fluorescence. A chromatin deoxyribonucleic acid radiolysis, a chromatin proteins damage and a change of the global chromatin structure on lasers action were indicated by this study. It exists some small differences between the actions of these three laser radiations.

  2. Control of the Transition to Flowering by Chromatin Modifications

    Institute of Scientific and Technical Information of China (English)

    Yuehui He

    2009-01-01

    The timing of floral transition is critical to reproductive success in angiosperms and is genetically controlled by a network of flowering genes.In Arabidopsis,expression of certain flowering genes is regulated by various chromatin modifications,among which are two central regulators of flowering,namely FLOWERING LOCUS C(FLC) and FLOWERING LOCUS T(FT).Recent studies have revealed that a number of chromatin-modifying components are involved in activation or repression of FLC expression.Activation of FLC expression is associated with various 'active' chromatin modifications including acetylation of core histone tails,histone H3 lysine-4 (H3K4) methylation,H2B monoubiquitination,H3 lysine-36 (H3K36) di- and tri-methylation and deposition of the histone variant H2A.Z,whereas various 'repressive' histone modifications are associated with FLC repression,including histone deacetylation,H3K4 demethylation,histone H3 lysine-9(H3Kg) and H3 lysine-27 (H3K27) methylation,and histone arginine methylation.In addition,recent studies have revealed that Polycomb group gene-mediated transcriptional-silencing mechanism not only represses FLC expression,but also directly represses FT expression.Regulation of FLC expression provides a paradigm for control of the expression of other developmental genes in plants through chromatin mechanisms.

  3. Antiviral Activity of Gold/Copper Sulfide Core/Shell Nanoparticles against Human Norovirus Virus-Like Particles.

    Directory of Open Access Journals (Sweden)

    Jessica Jenkins Broglie

    Full Text Available Human norovirus is a leading cause of acute gastroenteritis worldwide in a plethora of residential and commercial settings, including restaurants, schools, and hospitals. Methods for easily detecting the virus and for treating and preventing infection are critical to stopping norovirus outbreaks, and inactivation via nanoparticles (NPs is a more universal and attractive alternative to other physical and chemical approaches. Using norovirus GI.1 (Norwalk virus-like particles (VLPs as a model viral system, this study characterized the antiviral activity of Au/CuS core/shell nanoparticles (NPs against GI.1 VLPs for the rapid inactivation of HuNoV. Inactivation of VLPs (GI.1 by Au/CuS NPs evaluated using an absorbance-based ELISA indicated that treatment with 0.083 μM NPs for 10 min inactivated ~50% VLPs in a 0.37 μg/ml VLP solution and 0.83 μM NPs for 10 min completely inactivated the VLPs. Increasing nanoparticle concentration and/or VLP-NP contact time significantly increased the virucidal efficacy of Au/CuS NPs. Changes to the VLP particle morphology, size, and capsid protein were characterized using dynamic light scattering, transmission electron microscopy, and Western blot analysis. The strategy reported here provides the first reported proof-of-concept Au/CuS NPs-based virucide for rapidly inactivating human norovirus.

  4. Preparation by alkaline treatment and detailed characterisation of empty hepatitis B virus core particles for vaccine and gene therapy applications

    Science.gov (United States)

    Strods, Arnis; Ose, Velta; Bogans, Janis; Cielens, Indulis; Kalnins, Gints; Radovica, Ilze; Kazaks, Andris; Pumpens, Paul; Renhofa, Regina

    2015-06-01

    Hepatitis B virus (HBV) core (HBc) virus-like particles (VLPs) are one of the most powerful protein engineering tools utilised to expose immunological epitopes and/or cell-targeting signals and for the packaging of genetic material and immune stimulatory sequences. Although HBc VLPs and their numerous derivatives are produced in highly efficient bacterial and yeast expression systems, the existing purification and packaging protocols are not sufficiently optimised and standardised. Here, a simple alkaline treatment method was employed for the complete removal of internal RNA from bacteria- and yeast-produced HBc VLPs and for the conversion of these VLPs into empty particles, without any damage to the VLP structure. The empty HBc VLPs were able to effectively package the added DNA and RNA sequences. Furthermore, the alkaline hydrolysis technology appeared efficient for the purification and packaging of four different HBc variants carrying lysine residues on the HBc VLP spikes. Utilising the introduced lysine residues and the intrinsic aspartic and glutamic acid residues exposed on the tips of the HBc spikes for chemical coupling of the chosen peptide and/or nucleic acid sequences ensured a standard and easy protocol for the further development of versatile HBc VLP-based vaccine and gene therapy applications.

  5. 3D simulations of young core-collapse supernova remnants undergoing efficient particle acceleration

    CERN Document Server

    Ferrand, Gilles

    2016-01-01

    Within our Galaxy, supernova remnants are believed to be the major sources of cosmic rays up to the "knee". However important questions remain regarding the share of the hadronic and leptonic components, and the fraction of the supernova energy channelled into these components. We address such question by the means of numerical simulations that combine a hydrodynamic treatment of the shock wave with a kinetic treatment of particle acceleration. Performing 3D simulations allows us to produce synthetic projected maps and spectra of the thermal and non-thermal emission, that can be compared with multi-wavelength observations (in radio, X-rays, and gamma-rays). Supernovae come in different types, and although their energy budget is of the same order, their remnants have different properties, and so may contribute in different ways to the pool of Galactic cosmic-rays. Our first simulations were focused on thermonuclear supernovae, like Tycho's SNR, that usually occur in a mostly undisturbed medium. Here we present...

  6. Deoxyribonucleic acid excision repair in chromatin after ultraviolet irradiation of human fibroblasts in culture

    International Nuclear Information System (INIS)

    We have exposed confluent normal human fibroblasts to ultraviolet (UV) fluences of 5, 14, or 40 J/m2 and monitored the specific activity of post-uv repair synthesis in chromatin with [3H]thymidine pulses. We have shown that under conditions where no semiconservative deoxyribonucleic acid (DNA) synthesis is detectable, the specific activity of repair label one-fifth that in bulk DNA at all three uv fluences. On the other hand, the distribution of thymine-containing pyrimidine dimers in bulk and nuclease-resistant regions measured either immediately after irradiation or at later times showed no significant differences; preferential labeling of linker (nuclease-sensitive) DNA during repair synthesis is thus apparently not due to a predominance of uv-induced photoproducts in linker relative to core particle DNA in the nucleosoome. Pulse and pulse-chase experiments at 14 or 40 J/m2 with normal human or repair-deficient xeroderma pigmentosum (XP) cells showed that at most 30% of repair label in all these cells shifts from nuclease-sensitive (linker) DNA to nuclease-resistant (core particle) DNA

  7. Wrinkle-assisted linear assembly of hard-core/soft-shell particles: impact of the soft shell on the local structure.

    Science.gov (United States)

    Müller, Mareen; Karg, Matthias; Fortini, Andrea; Hellweg, Thomas; Fery, Andreas

    2012-04-01

    This article addresses wrinkle assisted assembly of core-shell particles with hard cores and soft poly-(N-isopropylacrylamide) shells. As core materials we chose silica as well as silver nanoparticles. The assembled structures show that the soft shells act as a separator between the inorganic cores. Anisotropic alignment is found on two length scales, macroscopically guided through the wrinkle structure and locally due to deformation of the polymer shell leading to smaller inter-core separations as compared to assembly on flat substrates without confinement. The structures were analysed by means of scanning electron microscopy. Radial distribution functions are shown, clearly highlighting the impact of confinement on nearest neighbour distances and symmetry. The observed ordering is directly compared to Monte-Carlo simulations for hard-core/soft-shell particles, showing that the observed symmetries are a consequence of the soft interaction potential and differ qualitatively from a hard-sphere situation. For the silver-poly-(N-isopropylacrylamide) particles, we show UV-vis absorbance measurements revealing optical anisotropy of the generated structures due to plasmon coupling. Furthermore, the high degree of order of the assembled structures on macroscopic areas is demonstrated by laser diffraction effects. PMID:22395669

  8. Chromatin Dynamics of Circadian Transcription

    OpenAIRE

    Aguilar-Arnal, Lorena; Sassone-Corsi, Paolo

    2015-01-01

    The molecular circadian clock orchestrates the daily cyclical expression of thousands of genes. Disruption of this transcriptional program leads to a variety of pathologies, including insomnia, depression and metabolic disorders. Circadian rhythms in gene expression rely on specific chromatin transitions which are ultimately coordinated by the molecular clock. As a consequence, a highly plastic and dynamic circadian epigenome can be delineated across different tissues and cell types. Intrigui...

  9. An amino-terminal segment of hantavirus nucleocapsid protein presented on hepatitis B virus core particles induces a strong and highly cross-reactive antibody response in mice

    International Nuclear Information System (INIS)

    Previously, we have demonstrated that hepatitis B virus (HBV) core particles tolerate the insertion of the amino-terminal 120 amino acids (aa) of the Puumala hantavirus nucleocapsid (N) protein. Here, we demonstrate that the insertion of 120 amino-terminal aa of N proteins from highly virulent Dobrava and Hantaan hantaviruses allows the formation of chimeric core particles. These particles expose the inserted foreign protein segments, at least in part, on their surface. Analysis by electron cryomicroscopy of chimeric particles harbouring the Puumala virus (PUUV) N segment revealed 90% T = 3 and 10% T = 4 shells. A map computed from T = 3 shells shows additional density splaying out from the tips of the spikes producing the effect of an extra shell of density at an outer radius compared with wild-type shells. The inserted Puumala virus N protein segment is flexibly linked to the core spikes and only partially icosahedrally ordered. Immunisation of mice of two different haplotypes (BALB/c and C57BL/6) with chimeric core particles induces a high-titered and highly cross-reactive N-specific antibody response in both mice strains

  10. Broadband and Low-Loss Plasmonic Light Trapping in Dye-Sensitized Solar Cells Using Micrometer-Scale Rodlike and Spherical Core-Shell Plasmonic Particles.

    Science.gov (United States)

    Malekshahi Byranvand, Mahdi; Nemati Kharat, Ali; Taghavinia, Nima; Dabirian, Ali

    2016-06-29

    Dielectric scattering particles have widely been used as embedded scattering elements in dye-sensitized solar cells (DSCs) to improve the optical absorption of the device. Here we systematically study rodlike and spherical core-shell silica@Ag particles as more effective alternatives to the dielectric scattering particles. The wavelength-scale silica@Ag particles with sufficiently thin Ag shell support hybrid plasmonic-photonic resonance modes that have low parasitic absorption losses and a broadband optical response. Both of these features lead to their successful deployment in light trapping in high-efficiency DSCs. Optimized rodlike silica@Ag@silica particles improve the power conversion efficiency of a DSC from 6.33 to 8.91%. The dimension, surface morphology, and concentration of these particles are optimized to achieve maximal efficiency enhancement. The rodlike silica particles are prepared in a simple one-pot synthesis process and then are coated with Ag in a liquid-phase deposition process by reducing an Ag salt. The aspect ratio of silica rods is tuned by adjusting the temperature and duration of the growth process, whereas the morphology of Ag shell is tailored by controlling the reduction rate of Ag salt, where slower reduction in a polyol process gives a smoother Ag shell. Using optical calculations, the superior performance of the plasmonic core-shell particles is related to the large number of hybrid photonic-plasmonic resonance modes that they support. PMID:27300764

  11. Silica nanoparticles as the adjuvant for the immunisation of mice using hepatitis B core virus-like particles.

    Directory of Open Access Journals (Sweden)

    Dace Skrastina

    Full Text Available Advances in nanotechnology and nanomaterials have facilitated the development of silicon dioxide, or Silica, particles as a promising immunological adjuvant for the generation of novel prophylactic and therapeutic vaccines. In the present study, we have compared the adjuvanting potential of commercially available Silica nanoparticles (initial particles size of 10-20 nm with that of aluminium hydroxide, or Alum, as well as that of complete and incomplete Freund's adjuvants for the immunisation of BALB/c mice with virus-like particles (VLPs formed by recombinant full-length Hepatitis B virus core (HBc protein. The induction of B-cell and T-cell responses was studied after immunisation. Silica nanoparticles were able to adsorb maximally 40% of the added HBc, whereas the adsorption capacity of Alum exceeded 90% at the same VLPs/adjuvant ratio. Both Silica and Alum formed large complexes with HBc VLPs that sedimented rapidly after formulation, as detected by dynamic light scattering, spectrophotometry, and electron microscopy. Both Silica and Alum augmented the humoral response against HBc VLPs to the high anti-HBc level in the case of intraperitoneal immunisation, whereas in subcutaneous immunisation, the Silica-adjuvanted anti-HBc level even exceeded the level adjuvanted by Alum. The adjuvanting of HBc VLPs by Silica resulted in the same typical IgG2a/IgG1 ratios as in the case of the adjuvanting by Alum. The combination of Silica with monophosphoryl lipid A (MPL led to the same enhancement of the HBc-specific T-cell induction as in the case of the Alum and MPL combination. These findings demonstrate that Silica is not a weaker putative adjuvant than Alum for induction of B-cell and T-cell responses against recombinant HBc VLPs. This finding may have an essential impact on the development of the set of Silica-adjuvanted vaccines based on a long list of HBc-derived virus-like particles as the biological component.

  12. Citrullination regulates pluripotency and histone H1 binding to chromatin

    Science.gov (United States)

    Christophorou, Maria A.; Castelo-Branco, Gonçalo; Halley-Stott, Richard P.; Oliveira, Clara Slade; Loos, Remco; Radzisheuskaya, Aliaksandra; Mowen, Kerri A.; Bertone, Paul; Silva, José C. R.; Zernicka-Goetz, Magdalena; Nielsen, Michael L.; Gurdon, John B.; Kouzarides, Tony

    2014-03-01

    Citrullination is the post-translational conversion of an arginine residue within a protein to the non-coded amino acid citrulline. This modification leads to the loss of a positive charge and reduction in hydrogen-bonding ability. It is carried out by a small family of tissue-specific vertebrate enzymes called peptidylarginine deiminases (PADIs) and is associated with the development of diverse pathological states such as autoimmunity, cancer, neurodegenerative disorders, prion diseases and thrombosis. Nevertheless, the physiological functions of citrullination remain ill-defined, although 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 response to infection. Here we show that the expression and enzymatic activity of Padi4 are also induced under conditions of ground-state pluripotency and during reprogramming in mouse. Padi4 is part of the pluripotency transcriptional network, binding to regulatory elements of key stem-cell genes 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 insights into how citrullination regulates chromatin compaction.

  13. Feasibility study of Large-scale helium GFR employing coated particle fuel. Design study of hexagonal matrix-block fuel assembly cores. Annual report of JFY2004

    International Nuclear Information System (INIS)

    Gas-cooled fast reactor has been taken an interest as a future nuclear reactor power source; we JNC have designed large-scale (1124MW electric power), high-temperature (850degC) with high thermodynamic efficiency (around 47%), helium-cooled fast reactors as a part of feasibility study. Hexagonal-block fuel assembly configuration has been considered as a candidate, where a number of coated particles packed in a SiC matrix are cooled indirectly by ascending flow in penetrating tubes. This manuscript describes, as an annual report of JFY2004, technical keys for enhancing core neutronics/thermal-hydraulics performances of the hex-block concepts and the best-to-date core designs. Technical keys for enhancing are from neutronics viewpoints (radial peaking factor, assembly layout and configuration), thermal-hydraulic viewpoints (heat transfer and film temperature rise, thermal conductivity and fuel-matrix temperature rise, core pressure drop, and coolant temperature), and neutronics/and/thermal-hydraulics combinational viewpoints (effective fuel volume fraction, local temperature decrees for increasing Doppler effects). Two issues (reducing contacting heat resistance in a matrix, and lowering core inflow temperature under depressurization transient) are selected from quantitative pre-evaluations; then are applied to select the reference core designs for achieving reduced Pu fissile inventory and improved average discharge burnup. Two reference cores are designed; one is 'breeding' core, which achieves high breeding ratio and high discharge burnup, the other is 'break-even' core, which brings much higher discharge burnup with a breeding ratio of around unity. [Reference core designs (2400MW thermal/1124MW electric outputs)] Core equiv. diameter/Height/Outermost diameter: 5.42m/1.00m/7.49m. Average Discharge Burnup (Seed region average): 121 GWd/t/123 GWd/t. (Entire core average): 69 GWd/t/89 GWd/t. Breeding Ratio: 1.11/1.03. Initial Pu fissile quantity: 7.0 ton/GWe/7.0 ton

  14. Safety and enhanced immunogenicity of a hepatitis B core particle Plasmodium falciparum malaria vaccine formulated in adjuvant Montanide ISA 720 in a phase I trial.

    NARCIS (Netherlands)

    Oliveira, G.A.; Wetzel, K.; Calvo-Calle, J.M.; Nussenzweig, R.; Schmidt, A.; Birkett, A.; Dubovsky, F.; Tierney, E.; Gleiter, C.H.; Boehmer, G.; Luty, A.J.F.; Ramharter, M.; Thornton, G.B.; Kremsner, P.G.; Nardin, E.H.

    2005-01-01

    Highly purified subunit vaccines require potent adjuvants in order to elicit optimal immune responses. In a previous phase I trial, an alum formulation of ICC-1132, a malaria vaccine candidate comprising hepatitis B core (HBc) virus-like particle containing Plasmodium falciparum circumsporozoite (CS

  15. Charged-particle and neutron-capture processes in the high-entropy wind of core-collapse supernovae

    International Nuclear Information System (INIS)

    The astrophysical site of the r-process is still uncertain, and a full exploration of the systematics of this process in terms of its dependence on nuclear properties from stability to the neutron drip-line within realistic stellar environments has still to be undertaken. Sufficiently high neutron-to-seed ratios can only be obtained either in very neutron-rich low-entropy environments or moderately neutron-rich high-entropy environments, related to neutron star mergers (or jets of neutron star matter) and the high-entropy wind of core-collapse supernova explosions. As chemical evolution models seem to disfavor neutron star mergers, we focus here on high-entropy environments characterized by entropy S, electron abundance Ye, and expansion velocity Vexp. We investigate the termination point of charged-particle reactions, and we define a maximum entropy Sfinal for a given Vexp and Ye, beyond which the seed production of heavy elements fails due to the very small matter density. We then investigate whether an r-process subsequent to the charged-particle freeze-out can in principle be understood on the basis of the classical approach, which assumes a chemical equilibrium between neutron captures and photodisintegrations, possibly followed by a β-flow equilibrium. In particular, we illustrate how long such a chemical equilibrium approximation holds, how the freeze-out from such conditions affects the abundance pattern, and which role the late capture of neutrons originating from β-delayed neutron emission can play. Furthermore, we analyze the impact of nuclear properties from different theoretical mass models on the final abundances after these late freeze-out phases and β-decays back to stability. As only a superposition of astrophysical conditions can provide a good fit to the solar r-abundances, the question remains how such superpositions are attained, resulting in the apparently robust r-process pattern observed in low metallicity stars.

  16. Synthesis and characterization of spherical core-shell particles SiO2-AgEu(MoO4)2

    International Nuclear Information System (INIS)

    Submicron spherical SiO2 particles have been coated with AgEu(MoO4)2 phosphor layers by a sol-gel process, followed by surface reaction at high temperature, to get core/shell structured SiO2-AgEu(MoO4)2 particles. X-ray diffraction (XRD), Fourier-transformed infrared spectroscopy (FT-IR), field emission scanning electron microscopy (FE-SEM), and transmission electron microscopy (TEM) were used to characterize the structure and morphology of the resulted core-shell phosphors. The luminescent properties of the core-shell structured phosphors have also been measured at room temperature, and their photoluminescence (PL) spectra are similar to the pure AgEu(MoO4)2 phosphor prepared by the same sol-gel method exhibiting red emission.

  17. Characterization of the RNA content of chromatin

    OpenAIRE

    Mondal, Tanmoy; Rasmussen, Markus; Pandey, Gaurav Kumar; Isaksson, Anders; Kanduri, Chandrasekhar

    2010-01-01

    Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show s...

  18. Induced self-energy on a static scalar charged particle in the spacetime of a global monopole with finite core

    CERN Document Server

    Barbosa, D; de Mello, E R Bezerra

    2010-01-01

    We analyze the induced self-energy and self-force on a scalar point-like charged test particle placed at rest in the spacetime of a global monopole admitting a general spherically symmetric inner structure to it. In order to develop this analysis we calculate the three-dimensional Green function associated with this physical system. We explicitly show that for points outside the monopole's core the scalar self-energy presents two distinct contributions. The first one is induced by the non-trivial topology of the global monopole considered as a point-like defect and the second is a correction induced by the non-vanishing inner structure attributed to it. For points inside the monopole, the self-energy also present a similar structure, where now the first contribution depends on the geometry of the spacetime inside. As illustrations of the general procedure adopted, two specific models, namely flower-pot and the ballpoint-pen, are considered for the region inside. For these two different situations, we were abl...

  19. Induced self-energy on a static scalar charged particle in the spacetime of a global monopole with finite core

    Science.gov (United States)

    Barbosa, D.; de Freitas, U.; Bezerra de Mello, E. R.

    2011-03-01

    We analyze the induced self-energy and self-force on a scalar point-like charged test particle placed at rest in the spacetime of a global monopole admitting a general spherically symmetric inner structure to it. In order to develop this analysis we calculate the three-dimensional Green's function associated with this physical system. We explicitly show that for points outside the monopole's core the scalar self-energy presents two distinct contributions. The first one is induced by the non-trivial topology of the global monopole considered as a point-like defect and the second is a correction induced by the non-vanishing inner structure attributed to it. For points inside the monopole, the self-energy also present a similar structure, where now the first contribution depends on the geometry of the spacetime inside. As illustrations of the general procedure adopted, two specific models, namely flower-pot and the ballpoint-pen, are considered for the region inside. For these two different situations, we were able to obtain exact expressions for the self-energies and self-forces in the regions outside and inside the global monopole.

  20. In vitro assembly into virus-like particles is an intrinsic quality of Pichia pastoris derived HCV core protein

    International Nuclear Information System (INIS)

    Different variants of hepatitis C virus core protein (HCcAg) have proved to self-assemble in vitro into virus-like particles (VLPs). However, difficulties in obtaining purified mature HCcAg have limited these studies. In this study, a high degree of monomeric HCcAg purification was accomplished using chromatographic procedures under denaturing conditions. Size exclusion chromatography and sucrose density gradient centrifugation of renatured HCcAg (in the absence of structured RNA) under reducing conditions suggested that it assembled into empty capsids. The electron microscopy analysis of renatured HCcAg showed the presence of spherical VLPs with irregular shapes and an average diameter of 35 nm. Data indicated that HCcAg monomers assembled in vitro into VLPs in the absence of structured RNA, suggesting that recombinant HCcAg used in this work contains all the information necessary for the assembly process. However, they also suggest that some cellular factors might be required for the proper in vitro assembly of capsids

  1. Controlling Shell Thickness of PS/SiO2 Core-Shell Particles and Their Crystallization into 3-D Ordered Thin Film

    Institute of Scientific and Technical Information of China (English)

    武晓峰; 陈运法; 魏连启; 王奇

    2006-01-01

    PS/SiO2 particles with core-shell structure were synthesized by coating silica on surface of polystyrene (PS)colloidal particles. The reaction parameters, such as initial tetraethyl orthosilicate (TEOS) concentration, water concentration and reaction temperature, have been investigated to control the thickness of silica shells. The shell thickness was prepositional to the square root of the initial concentration of TEOS and first increased with increasing water concentration, reached a maximum at about 2.0 mol/L and then started decreasing beyond that concentration. It was also found that the shell thickness decreased firstly with the reaction temperature added, then tended to a constant. The so-synthesized PS/SiO2 core-shell particles were directly crystallized into 3-D ordered thin film, then sintered at 570 ℃ into the ordered macroporous thin film.Compared with the conditional method, the present approach avoids repeatedly filling the precursor in the templetes and save time more.

  2. Assessment of the sensitivity of core / shell parameters derived using the single-particle soot photometer to density and refractive index

    Science.gov (United States)

    Taylor, J. W.; Allan, J. D.; Liu, D.; Flynn, M.; Weber, R.; Zhang, X.; Lefer, B. L.; Grossberg, N.; Flynn, J.; Coe, H.

    2015-04-01

    Black carbon (BC) is the dominant absorbing aerosol in the atmosphere, and plays an important role in climate and human health. The optical properties and cloud condensation nuclei (CCN) activity of soot depend on the amounts (both relative and absolute) of BC and non-refractory material in the particles. Mixing between these two components is often represented in models by a core / shell coated sphere. The single-particle soot photometer (SP2) is one of, if not the only, instrument capable of reporting distributions of both core size and coating thickness. Most studies combine the SP2's incandescence and 1064 nm scattering data to report coating properties, but to date there is no consistency in the assumed values of density and refractive index of the core that are used in these calculations, which can greatly affect the reported parameters such as coating thickness. Given that such data are providing an important constraint for model comparisons and comparison between large data sets, it is important that this lack of consistency is addressed. In this study we explore the sensitivity of the reported coatings to these parameters. An assessment of the coating properties of freshly emitted, thermodenuded ambient particles demonstrated that a core density of 1.8 g cm-3 and refractive index of (2.26-1.26i) were the most appropriate to use with ambient soot in the Los Angeles area. Using these parameters generated a distribution with median shell / core ratio of 1.02 ± 0.11, corresponding to a median absolute coating thickness of 2 ± 8 nm. The main source of statistical error in the single-particle data was random variation in the incandescence signals. Other than the sensitivity to core refractive index, the incandescence calibration was the main source of uncertainty when optically determining the average coatings. The refractive index of coatings was found to have only a minor influence. This work demonstrates that using this technique the SP2 can accurately

  3. Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.

    Science.gov (United States)

    Luque, Antoni; Ozer, Gungor; Schlick, Tamar

    2016-06-01

    Eukaryotic cells condense their genetic material in the nucleus in the form of chromatin, a macromolecular complex made of DNA and multiple proteins. The structure of chromatin is intimately connected to the regulation of all eukaryotic organisms, from amoebas to humans, but its organization remains largely unknown. The nucleosome repeat length (NRL) and the concentration of linker histones (ρLH) are two structural parameters that vary among cell types and cell cycles; the NRL is the number of DNA basepairs wound around each nucleosome core plus the number of basepairs linking successive nucleosomes. Recent studies have found a linear empirical relationship between the variation of these two properties for different cells, but its underlying mechanism remains elusive. Here we apply our established mesoscale chromatin model to explore the mechanisms responsible for this relationship, by investigating chromatin fibers as a function of NRL and ρLH combinations. We find that a threshold of linker histone concentration triggers the compaction of chromatin into well-formed 30-nm fibers; this critical value increases linearly with NRL, except for long NRLs, where the fibers remain disorganized. Remarkably, the interaction patterns between core histone tails and chromatin elements are highly sensitive to the NRL and ρLH combination, suggesting a molecular mechanism that could have a key role in regulating the structural state of the fibers in the cell. An estimate of the minimized work and volume associated with storage of chromatin fibers in the nucleus further suggests factors that could spontaneously regulate the NRL as a function of linker histone concentration. Both the tail interaction map and DNA packing considerations support the empirical NRL/ρLH relationship and offer a framework to interpret experiments for different chromatin conditions in the cell. PMID:27276249

  4. Particle distributions in approximately 10(14) 10(16) eV air shower cores at sea level

    Science.gov (United States)

    Hodson, A. L.; Ash, A. G.; Bull, R. M.

    1985-01-01

    Experimental evidence is reported for fixed distances (0, 1.0, 2.5 and 4.0 m) from the shower centers and for core flattening. The cores become flatter, on average, as the shower size (primary energy) increases. With improved statistics on 4192 cores, the previous results are exactly confirmed.

  5. Computational strategies to address chromatin structure problems.

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-01-01

    While the genetic information is contained in double helical DNA, gene expression is a complex multilevel process that involves various functional units, from nucleosomes to fully formed chromatin fibers accompanied by a host of various chromatin binding enzymes. The chromatin fiber is a polymer composed of histone protein complexes upon which DNA wraps, like yarn upon many spools. The nature of chromatin structure has been an open question since the beginning of modern molecular biology. Many experiments have shown that the chromatin fiber is a highly dynamic entity with pronounced structural diversity that includes properties of idealized zig-zag and solenoid models, as well as other motifs. This diversity can produce a high packing ratio and thus inhibit access to a majority of the wound DNA. Despite much research, chromatin's dynamic structure has not yet been fully described. Long stretches of chromatin fibers exhibit puzzling dynamic behavior that requires interpretation in the light of gene expression patterns in various tissue and organisms. The properties of chromatin fiber can be investigated with experimental techniques, like in vitro biochemistry, in vivo imagining, and high-throughput chromosome capture technology. Those techniques provide useful insights into the fiber's structure and dynamics, but they are limited in resolution and scope, especially regarding compact fibers and chromosomes in the cellular milieu. Complementary but specialized modeling techniques are needed to handle large floppy polymers such as the chromatin fiber. In this review, we discuss current approaches in the chromatin structure field with an emphasis on modeling, such as molecular dynamics and coarse-grained computational approaches. Combinations of these computational techniques complement experiments and address many relevant biological problems, as we will illustrate with special focus on epigenetic modulation of chromatin structure. PMID:27345617

  6. Core-Shell Soy Protein-Soy Polysaccharide Complex (Nano)particles as Carriers for Improved Stability and Sustained Release of Curcumin.

    Science.gov (United States)

    Chen, Fei-Ping; Ou, Shi-Yi; Tang, Chuan-He

    2016-06-22

    Using soy protein isolate (SPI) and soy-soluble polysaccharides (SSPS) as polymer matrixes, this study reported a novel process to fabricate unique core-shell complex (nano)particles to perform as carriers for curcumin (a typical poorly soluble bioactive). In the process, curcumin-SPI nanocomplexes were first formed at pH 7.0 and then coated by SSPS. At this pH, the core-shell complex was formed in a way the SPI nanoparticles might be incorporated into the interior of SSPS molecules without distinctly affecting the size and morphology of particles. The core-shell structure was distinctly changed by adjusting pH from 7.0 to 4.0. At pH 4.0, SSPS was strongly bound to the surface of highly aggregated SPI nanoparticles, and as a consequence, much larger complexes were formed. The bioaccessibility of curcumin in the SPI-curcumin complexes was unaffected by the SSPS coating. However, the core-shell complex formation greatly improved the thermal stability and controlled release properties of encapsulated curcumin. The improvement was much better at pH 4.0 than that at pH 7.0. All of the freeze-dried core-shell complex preparations exhibited good redispersion behavior. The findings provide a simple approach to fabricate food-grade delivery systems for improved water dispersion, heat stability, and even controlled release of poorly soluble bioactives. PMID:27243766

  7. UV-durable superhydrophobic textiles with UV-shielding properties by coating fibers with ZnO/SiO2 core/shell particles

    International Nuclear Information System (INIS)

    ZnO/SiO2 core/shell particles were fabricated by successive coating of multilayer polyelectrolytes and then a SiO2 shell onto ZnO particles. The as-prepared ZnO/SiO2 core/shell particles were coated on poly(ethylene terephthalate) (PET) textiles, followed by hydrophobization with hexadecyltrimethoxysilane, to fabricate superhydrophobic surfaces with UV-shielding properties. Transmission electron microscopy and ζ potential analysis were employed to evidence the fabrication of ZnO/SiO2 core/shell particles. Scanning electron microscopy and thermal gravimetric analysis were conducted to investigate the surface morphologies of the textile and the coating of the fibers. Ultraviolet-visible spectrophotometry and contact angle measurement indicated that the incorporation of ZnO onto fibers imparted UV-blocking properties to the textile surface, while the coating of SiO2 shell on ZnO prohibited the photocatalytic degradation of hexadecyltrimethoxysilane by ZnO, making the as-treated PET textile surface show stable superhydrophobicity with good UV-shielding properties.

  8. 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 genome

  9. Subunit Protein Vaccine Delivery System for Tuberculosis Based on Hepatitis B Virus Core VLP (HBc-VLP) Particles.

    Science.gov (United States)

    Dhanasooraj, Dhananjayan; Kumar, R Ajay; Mundayoor, Sathish

    2016-01-01

    Despite the development of modern medicine, tuberculosis (TB), caused by the pathogenic bacterium, Mycobacterium tuberculosis (Mtb), remains one of the deadliest diseases. This bacterium can lay dormant in individuals and get activated when immunity goes down and has also shown considerable prowess in mutating into drug resistant forms. The global emergence of such drug resistant Mtb and the lack of efficacy of Bacille Calmette Guérin (BCG), the only vaccine available so far, have resulted in a situation which cries out for a safe and effective tuberculosis vaccine.Number of different strategies has been used for developing new anti-TB vaccines and several protective antigens have been identified so far. One strategy, the use of protein subunits, has the potential to develop into a powerful tuberculosis vaccine, not only because of its efficacy and safety, but also because they are economical. The proper delivery of protein subunit vaccines with adjuvants or novel delivery systems is necessary for inducing protective immune responses. The available adjuvants or delivery systems are inadequate for generating such a response. In the present method, we have constructed a vaccine delivery system for tuberculosis based on Virus-Like Particles (VLPs). Hepatitis B Virus core antigen gene was recombinantly modified using Overlap Extension PCR (OEPCR). The final construct was designed to express HBc-VLP carrying external antigen (fusion VLP). Mycobacterium tuberculosis antigen CFP-10 was used for the construction of fusion VLP. The recombinant gene for the construct was cloned into a pET expression system and transformed into E. coli BL21(DE3) and induced with IPTG to express the protein. The fusion protein was purified using the Histidine tag and allowed to form VLPs. The preformed VLPs were purified by sucrose density gradient centrifugation. The VLPs were characterized using Transmission Electron Microscopy (TEM). PMID:27076312

  10. Chimeric Hepatitis B core antigen virus-like particles displaying the envelope domain III of dengue virus type 2

    Directory of Open Access Journals (Sweden)

    Arora Upasana

    2012-07-01

    Full Text Available Abstract Background Dengue is a global public health problem for which no drug or vaccine is available. Currently, there is increasing interest in developing non-replicating dengue vaccines based on a discrete antigenic domain of the major structural protein of dengue viruses (DENVs, known as envelope domain III (EDIII. The use of bio-nanoparticles consisting of recombinant viral structural polypeptides, better known as virus-like particles (VLPs, has emerged as a potential platform technology for vaccine development. This work explores the feasibility of developing nanoparticles based on E. coli-expressed recombinant Hepatitis B virus core antigen (HBcAg designed to display EDIII moiety of DENV on the surface. Findings We designed a synthetic gene construct encoding HBcAg containing an EDIII insert in its c/e1 loop. The fusion antigen HBcAg-EDIII-2 was expressed in E. coli, purified to near homogeneity using Ni+2 affinity chromatography and demonstrated to assemble into discrete 35–40 nm VLPs by electron microscopy. Competitive ELISA analyses showed that the EDIII-2 moieties of the VLPs are accessible to anti-EDIII-2-specific monoclonal and polyclonal antibodies, suggesting that they are surface-displayed. The VLPs were highly immunogenic eliciting high titer anti-EDIII-2 antibodies that were able to recognize, bind and neutralize infectious DENV based on ELISA, immunofluorescence and virus-neutralization assays. Conclusion This work demonstrates that HBcAg-derived nanoparticles can serve as a useful platform for the display of DENV EDIII. The EDIII-displaying nanoparticles may have potential applications in diagnostics/vaccines for dengue.

  11. Chromatin domain boundaries: insulators and beyond

    Institute of Scientific and Technical Information of China (English)

    Gong Hong WEI; De Pei LIU; Chih Chuan LIANG

    2005-01-01

    The eukaryotic genome is organized into functionally and structurally distinct domains, representing regulatory units for gene expression and chromosome behavior. DNA sequences that mark the border between adjacent domains are the insulators or boundary elements, which are required in maintenance of the function of different domains. Some insulators need others enable to play insulation activity. Chromatin domains are defined by distinct sets of post-translationally modified histones. Recent studies show that these histone modifications are also involved in establishment of sharp chromatin boundaries in order to prevent the spreading of distinct domains. Additionally, in some loci, the high-order chromatin structures for long-range looping interactions also have boundary activities, suggesting a correlation between insulators and chromatin loop domains. In this review, we will discuss recent progress in the field of chromatin domain boundaries.

  12. Computational strategies to address chromatin structure problems

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-06-01

    While the genetic information is contained in double helical DNA, gene expression is a complex multilevel process that involves various functional units, from nucleosomes to fully formed chromatin fibers accompanied by a host of various chromatin binding enzymes. The chromatin fiber is a polymer composed of histone protein complexes upon which DNA wraps, like yarn upon many spools. The nature of chromatin structure has been an open question since the beginning of modern molecular biology. Many experiments have shown that the chromatin fiber is a highly dynamic entity with pronounced structural diversity that includes properties of idealized zig-zag and solenoid models, as well as other motifs. This diversity can produce a high packing ratio and thus inhibit access to a majority of the wound DNA. Despite much research, chromatin’s dynamic structure has not yet been fully described. Long stretches of chromatin fibers exhibit puzzling dynamic behavior that requires interpretation in the light of gene expression patterns in various tissue and organisms. The properties of chromatin fiber can be investigated with experimental techniques, like in vitro biochemistry, in vivo imagining, and high-throughput chromosome capture technology. Those techniques provide useful insights into the fiber’s structure and dynamics, but they are limited in resolution and scope, especially regarding compact fibers and chromosomes in the cellular milieu. Complementary but specialized modeling techniques are needed to handle large floppy polymers such as the chromatin fiber. In this review, we discuss current approaches in the chromatin structure field with an emphasis on modeling, such as molecular dynamics and coarse-grained computational approaches. Combinations of these computational techniques complement experiments and address many relevant biological problems, as we will illustrate with special focus on epigenetic modulation of chromatin structure.

  13. Fabrication and electromagnetic properties of bio-based helical soft-core particles by way of Ni-Fe alloy electroplating

    International Nuclear Information System (INIS)

    Ni-Fe alloy electroplating was used as a bio-limited forming process to fabricate bio-based helical soft-core ferromagnetic particles, and a low frequency vibration device was applied to the cathode to avoid microorganism (Spirulina platens) cells adhesion to the copper net during the course of plating. The morphologies and ingredients of the coated Spirulina cells were characterized using scanning electron microscopy and energy dispersive spectrometer. The complex permittivity and permeability of the samples containing the coated Spirulina cells before and after heat treatment were measured and investigated by a vector network analyzer. The results show that the Spirulina cells after plating keep their initial helical shape, and applying low frequency vibration to the copper net cathode in the plating process can effectively prevent agglomeration and intertwinement of the Spirulina cells. The microwave absorbing and electromagnetic properties of the samples containing the coated Spirulina cells particles with heat treatment are superior to those samples containing the coated Spirulina cells particles without heat treatment. - Highlights: → We used the microorganism cells as forming template to fabricate the bio-based helical soft-core ferromagnetic particles. → Microorganism selected as forming templates was Spirulina platens, which are of natural helical shape and have high aspect ratio. → Coated Spirulina cells were a kind lightweight ferromagnetic particle.

  14. Fabrication and electromagnetic properties of bio-based helical soft-core particles by way of Ni-Fe alloy electroplating

    Energy Technology Data Exchange (ETDEWEB)

    Lan Mingming, E-mail: lan_mingming@163.com [Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, School of Mechanical Engineering and Automation, Beihang University, Beijing 100191 (China); Zhang Deyuan; Cai Jun; Zhang Wenqiang; Yuan Liming [Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, School of Mechanical Engineering and Automation, Beihang University, Beijing 100191 (China)

    2011-12-15

    Ni-Fe alloy electroplating was used as a bio-limited forming process to fabricate bio-based helical soft-core ferromagnetic particles, and a low frequency vibration device was applied to the cathode to avoid microorganism (Spirulina platens) cells adhesion to the copper net during the course of plating. The morphologies and ingredients of the coated Spirulina cells were characterized using scanning electron microscopy and energy dispersive spectrometer. The complex permittivity and permeability of the samples containing the coated Spirulina cells before and after heat treatment were measured and investigated by a vector network analyzer. The results show that the Spirulina cells after plating keep their initial helical shape, and applying low frequency vibration to the copper net cathode in the plating process can effectively prevent agglomeration and intertwinement of the Spirulina cells. The microwave absorbing and electromagnetic properties of the samples containing the coated Spirulina cells particles with heat treatment are superior to those samples containing the coated Spirulina cells particles without heat treatment. - Highlights: > We used the microorganism cells as forming template to fabricate the bio-based helical soft-core ferromagnetic particles. > Microorganism selected as forming templates was Spirulina platens, which are of natural helical shape and have high aspect ratio. > Coated Spirulina cells were a kind lightweight ferromagnetic particle.

  15. The M1 gene is associated with differences in the temperature optimum of the transcriptase activity in reovirus core particles.

    OpenAIRE

    Yin, P.; Cheang, M; Coombs, K M

    1996-01-01

    The reovirus core is a multienzyme complex that contains five different structural proteins and 10 segments of double-stranded RNA. The core is responsible for transcribing mRNA from the enclosed double-stranded RNA. The reovirus transcriptase has an unusual temperature profile, with optimum transcription occurring at approximately 50 degrees C and little activity occurring below 30 or above 60 degrees C. Purified reovirus serotype 1 Lang (T1L) cores transcribed most efficiently at 48 degrees...

  16. Temperature Effects on Retention and Separation of PAHs in Reversed-Phase Liquid Chromatography Using Columns Packed with Fully Porous and Core-Shell Particles

    OpenAIRE

    Christophe Waterlot; Anaïs Goulas

    2016-01-01

    Effects of temperature on the reversed-phase chromatographic behavior of PAHs were investigated on three columns. The first was the recent C18 column (250 mm × 4.6 mm) packed with 5 µm core-shell particles while the others were more conventional C18 columns (250 mm × 4.6 mm) packed with fully porous particles. Among the 16 PAHs studied, special attention has been paid to two pairs of PAHs, fluorene/acenaphthene and chrysene/benzo[a]anthracene, which often present coeluting problems. Due to th...

  17. Synthesis and characterization of Mn-doped Zn2SiO4/SiO2 phosphor particles in core-shell structure

    International Nuclear Information System (INIS)

    Manganese-doped zinc silicate (Zn2SiO4:Mn) is a kind of phosphor material that has a photo-luminescent (PL) and cathode-luminescent (CL) properties with intensive green light emission at 520 nm. The particles consisting of SiO2-Zn2SiO4:Mn (SiO2 core-Zn2SiO4:Mn shell) were synthesized via colloidal process and forced precipitation. After drying, the Zn/Mn precipitates were coated on the surface of SiO2 particles. The Zn/Mn precipitates reacted with SiO2 and transformed to Zn2SiO4:Mn by suitable calcination. The microstructure, crystalline phase, and luminescent characteristics of the products were studied. Besides, a CL device consisting of the core-shell powder was characterized.

  18. Core-shell-structured silica/polyacrylate particles prepared by Pickering emulsion: influence of the nucleation model on particle interfacial organization and emulsion stability

    OpenAIRE

    Ji, Jing; Shu, Shi; Wang, Feng; Li, Zhilin; Liu, Jingjun; Song, Ye; Jia, Yi

    2014-01-01

    This work reports a new evidence of the versatility of silica sol as a stabilizer for Pickering emulsions. The organization of silica particles at the oil-water interface is a function of the nucleation model. The present results show that nucleation model, together with monomer hydrophobicity, can be used as a trigger to modify the packing density of silica particles at the oil-water interface: Less hydrophobic methylmethacrylate, more wettable with silica particles, favors the formation of ...

  19. Detection and Tracking of Dual-Labeled HIV Particles Using Wide-Field Live Cell Imaging to Follow Viral Core Integrity.

    Science.gov (United States)

    Mamede, João I; Hope, Thomas J

    2016-01-01

    Live cell imaging is a valuable technique that allows the characterization of the dynamic processes of the HIV-1 life cycle. Here, we present a method of production and imaging of dual-labeled HIV viral particles that allows the visualization of two events. Varying release of the intravirion fluid phase marker reveals virion fusion and the loss of the integrity of HIV viral cores with the use of live wide-field fluorescent microscopy. PMID:26714704

  20. Phase I Trial of an Alhydrogel Adjuvanted Hepatitis B Core Virus-Like Particle Containing Epitopes of Plasmodium falciparum Circumsporozoite Protein

    OpenAIRE

    Gregson, Aric L.; Giane Oliveira; Caroline Othoro; J. Mauricio Calvo-Calle; Thorton, George B.; Elizabeth Nardin; Robert Edelman

    2008-01-01

    UNLABELLED: The objectives of this non-randomized, non-blinded, dose-escalating Phase I clinical trial were to assess the safety, reactogenicity and immunogenicity of ICC-1132 formulated with Alhydrogel (aluminum hydroxide) in 51 healthy, malaria-naive adults aged 18 to 45 years. ICC-1132 (Malariavax) is a recombinant, virus-like particle malaria vaccine comprised of hepatitis core antigen engineered to express the central repeat regions from Plasmodium falciparum circumsporozoite protein con...

  1. Recognition of chromatin by the plant alkaloid, ellipticine as a dual binder

    International Nuclear Information System (INIS)

    Recognition of core histone components of chromatin along with chromosomal DNA by a class of small molecule modulators is worth examining to evaluate their intracellular mode of action. A plant alkaloid ellipticine (ELP) which is a putative anticancer agent has so far been reported to function via DNA intercalation, association with topoisomerase II and binding to telomere region. However, its effect upon the potential intracellular target, chromatin is hitherto unreported. Here we have characterized the biomolecular recognition between ELP and different hierarchical levels of chromatin. The significant result is that in addition to DNA, it binds to core histone(s) and can be categorized as a ‘dual binder’. As a sequel to binding with histone(s) and core octamer, it alters post-translational histone acetylation marks. We have further demonstrated that it has the potential to modulate gene expression thereby regulating several key biological processes such as nuclear organization, transcription, translation and histone modifications. - Highlights: • Ellipticine acts a dual binder binding to both DNA and core histone(s). • It induces structural perturbations in chromatin, chromatosome and histone octamer. • It alters histones acetylation and affects global gene expression

  2. Recognition of chromatin by the plant alkaloid, ellipticine as a dual binder

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Amrita; Sanyal, Sulagna; Majumder, Parijat [Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal (India); Chakraborty, Payal [Bionivid Technology Pvt Ltd, Kasturi Nagar, Bangalore 560043 (India); Jana, Kuladip [Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal (India); Das, Chandrima, E-mail: chandrima.das@saha.ac.in [Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal (India); Dasgupta, Dipak, E-mail: dipak.dasgupta@saha.ac.in [Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal (India)

    2015-07-10

    Recognition of core histone components of chromatin along with chromosomal DNA by a class of small molecule modulators is worth examining to evaluate their intracellular mode of action. A plant alkaloid ellipticine (ELP) which is a putative anticancer agent has so far been reported to function via DNA intercalation, association with topoisomerase II and binding to telomere region. However, its effect upon the potential intracellular target, chromatin is hitherto unreported. Here we have characterized the biomolecular recognition between ELP and different hierarchical levels of chromatin. The significant result is that in addition to DNA, it binds to core histone(s) and can be categorized as a ‘dual binder’. As a sequel to binding with histone(s) and core octamer, it alters post-translational histone acetylation marks. We have further demonstrated that it has the potential to modulate gene expression thereby regulating several key biological processes such as nuclear organization, transcription, translation and histone modifications. - Highlights: • Ellipticine acts a dual binder binding to both DNA and core histone(s). • It induces structural perturbations in chromatin, chromatosome and histone octamer. • It alters histones acetylation and affects global gene expression.

  3. 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.

  4. Microagglomeration of pulverized pharmaceutical powders using the Wurster process I. Preparation of highly drug-incorporated, subsieve-sized core particles for subsequent microencapsulation by film-coating.

    Science.gov (United States)

    Ichikawa, H; Fukumori, Y

    1999-04-15

    A novel agglomeration process of pulverized pharmaceutical powders into subsieve-sized agglomerates (microagglomeration) was designed for manufacturing highly drug-incorporated core particles for subsequent microencapsulation by film-coating. The microagglomeration of pulverized phenacetin powder, whose mass median diameter was 9 microm, was performed by spraying an aqueous colloidal dispersion of acrylic polymer, Eudragit(R) RS30D, as a binding/coating agent using a spouted bed assisted with a draft tube (the Wurster process), and the effect of process variables was examined. An appropriate spray liquid flow rate made it possible to produce microagglomerates of 20-50 microm with 60% yield. However, 10% of the product still survived as particles smaller than 10 microm even at the elevated liquid flow rate. In contrast, the survived particles smaller than 10 microm tended to be predominantly reduced to 2%, while coarse agglomerates larger than 53 microm were not excessively produced, by additionally setting a fixed bed of glass beads in the spouted bed apparatus. The length of the draft tube influenced compaction of the agglomerates as well as their surface-smoothening. Equipping the fixed bed of the glass beads and the long draft tube in the spouted bed allowed us to prepare microagglomerates of 20-50 microm at yield of 55% applicable as highly drug-incorporated, free-flowing, surface-smoothed, narrowly size-distributed core particles for subsequent microencapsulation by film-coating. PMID:10370190

  5. Low power loss and field-insensitive permeability of Fe-6.5%Si powder cores with manganese oxide-coated particles

    Energy Technology Data Exchange (ETDEWEB)

    Li, Junnan, E-mail: junnanli1991@163.com, E-mail: rzhgong@hust.edu.cn; Wang, Xian; Xu, Xiaojun; Gong, Rongzhou, E-mail: junnanli1991@163.com, E-mail: rzhgong@hust.edu.cn; Feng, Zekun [School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074 (China); Chen, Yajie; Harris, V. G. [Department of Electrical and Computer Engineering, Center for Microwave Magnetic Materials and Integrated Circuits, Northeastern University, Boston, Massachusetts 02115 (United States)

    2015-05-07

    Fe-6.5%Si alloy powders coated with manganese oxides using an innovative in situ process were investigated. The in-situ coating of the insulating oxides was realized with a KMnO{sub 4} solution by a chemical process. The insulating manganese oxides with mixed valance state were verified by X-ray photoelectron spectroscopy analysis. The thickness of the insulating layer on alloy particles was determined to be in a range of 20–210 nm, depending upon the KMnO{sub 4} concentration. The powder core loss and the change in permeability under a DC-bias field were measured at frequencies ranging from 50 to 100 kHz. The experiments indicated that the Fe-6.5%Si powder cores with a 210 nm-thick manganese oxide layer not only showed a low core loss of 459 mW/cm{sup 3} at 100 kHz but also showed a small reduction in permeability (μ(H)/μ(0) = 85% for μ = 42) at a DC-bias field of 80 Oe. This work has defined a novel pathway to realizing low core loss and field-insensitive permeability for Fe-Si powder cores.

  6. Waste Utilization as Fine Coconut Fiber for Core and Wood Waste Bayur to The Face Layer of The Physical and Mechanical Properties of Particle Board Produced

    Directory of Open Access Journals (Sweden)

    Sahadi Didi Ismanto

    2014-01-01

    Full Text Available This study aims to determine the effect of wood particle bayur comparison to the outer layer of coconut husk particle board smooth the physical and mechanical properties of the resulting particle board . The design used was completely randomized design ( CRD with 5 treatments with 3 replications for each treatment used is the use of wood particles bayur as the outer layer of particle board and refined coconut fiber as a core that is 80 % : 20 % , 70 % : 30 % , 60 % : 40 % , 50 % : 50 % , 40 % : 60 % observational data physical and mechanical properties were analyzed using analysis of variance if significantly different then performed with a further test of Duncan's New Multiple Range Test ( DMNRT at the 5% significance level . Observations made on the physical properties of particle board include : water content , water absorption and thickness expansion. The mechanical properties of particle board : strength broken , the pressure parallel and bonding strength. Based on the research that has been carried out showed that the utilization of wood waste bayur as the outer layer of particle board on a percentage varying significantly different effect on strength broken , water content , water absorption , expansion of thick , strength pressure bonding parallel to the internal surface . The results show the percentage of particle board with wood bayur with delicate coconut husk ( 40:60 is the best board with a water content of 6.11% , water absorption 20.56 % 10.93 % thicker expansion, density of 0.84 % , bonding strength of 56.90 kg / cm 2 pressure and parallel fiber determination 146.65 kg /cm 2.

  7. Construction and immunological evaluation of truncated hepatitis B core particles carrying HBsAg amino acids 119-152 in the major immunodominant region (MIR).

    Science.gov (United States)

    Su, Qiudong; Yi, Yao; Guo, Minzhuo; Qiu, Feng; Jia, Zhiyuan; Lu, Xuexin; Meng, Qingling; Bi, Shengli

    2013-09-13

    Hepatitis B capsid protein expressed in Escherichia coli can reassemble into icosahedral particles, which could strongly enhance the immunogenicity of foreign epitopes, especially those inserted into its major immunodominant region. Herein, we inserted the entire 'α' antigenic determinant amino acids (aa) 119-152 of HBsAg into the truncated HBc (aa 1-144), between Asp(78) and Pro(79). Prokaryotic expression showed that the mosaic HBc was mainly in the form of inclusion bodies. After denaturation with urea, it was dialyzed progressively for protein renaturation. We observed that before and after renaturation, mosaic HBc was antigenic as determined by HBsAg ELISA and a lot of viruslike particles were observed after renaturation. Thus, we further purified the mosaic viruslike particles by (NH4)2SO4 precipitation, DEAE chromatography, and Sepharose 4FF chromatography. Negative staining electron microscopy demonstrated the morphology of the viruslike particles. Immunization of Balb/c mice with mosaic particles induced the production of anti-HBs antibody and Th1 cell immune response supported by ELISPOT and CD4/CD8 proportions assay. In conclusion, we constructed mosaic hepatitis core particles displaying the entire 'α' antigenic determinant on the surface and laid a foundation for researching therapeutic hepatits B vaccines. PMID:23969156

  8. 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.

  9. Facile synthesis of QD-anchored composite particles with magnetite cluster cores (nFe3O4@SiO2@QDs)

    International Nuclear Information System (INIS)

    Highlights: ► Triple layered Fe3O4/SiO2/QDs were designed as fluorescent magnetic nanocomposites. ► Magnetite cluster-embedded silica exhibited strong and controllable magnetism. ► Effective conjugation between QDs and magnetic silica occurred at pH3. - Abstract: Magnetism-controlled fluorescent composite particles (nFe3O4@SiO2@QDs) were prepared as QD-anchored silica nanoparticles with magnetite cluster cores. First, citrate-capped magnetites (C-Fe3O4) were prepared by the co-precipitation method and subsequently complexed with 3-aminopropyl-trimethoxysilane (APTMS) at room temperature, consequently leading to the formation of magnetite clusters (A-nFe3O4) with alkoxy terminated interfaces. The sol–gel reaction between A-nFe3O4 and tetraethoxysilane (TEOS) produced the core-shell nFe3O4@SiO2. The resulting core-shell particles exhibited superparamagnetic properties and controllable magnetism simply by adjusting the thickness of nonmagnetic silica layer. After then, amine-terminated nFe3O4@SiO2 (NH2–nFe3O4@SiO2) was conjugated with carboxy quantum dots (QDs) using an EDC coupling agent. The QD conjugation with NH2–nFe3O4@SiO2 of lower pH exhibited the higher photoluminescence (PL) intensity, and the resulting composite particles (nFe3O4@SiO2@QDs) can be a useful biomedical agent. This chemical strategy can be further applied to prepare the core-shell magnetic nanostructure with various oxide layers for specific applications

  10. Pulling chromatin apart: Unstacking or Unwrapping?

    Directory of Open Access Journals (Sweden)

    Victor Jean Marc

    2012-11-01

    Full Text Available Abstract Background Understanding the mechanical properties of chromatin is an essential step towards deciphering the physical rules of gene regulation. In the past ten years, many single molecule experiments have been carried out, and high resolution measurements of the chromatin fiber stiffness are now available. Simulations have been used in order to link those measurements with structural cues, but so far no clear agreement among different groups has been reached. Results We revisit here some of the most precise experimental results obtained with carefully reconstituted fibers. Conclusions We show that the mechanical properties of the chromatin fiber can be quantitatively accounted for by the stiffness of the DNA molecule and the 3D structure of the chromatin fiber.

  11. In vivo binding of retinol to chromatin

    International Nuclear Information System (INIS)

    The authors have previously shown that exposure of responding cells to vitamin A leads to profound modifications of chromatin structure as revealed by an increased susceptibility to DNase I digestion, modified patterns of histone acetylation, and impaired synthesis of a nonhistone chromosomal protein. The present results show that these effects are most probably due to the direct interaction between retinol and chromatin, and analysis of mononucleosomes and higher oligomers obtained from retinol-treated cells shows that retinol is indeed tightly bound to chromatin. Enzymatic digestions of vitamin A containing nucleosomes with proteinase K, phospholipase C, and phospholipase A2 support a model where the final binding of retinol to chromatin is mediated by a lipoprotein: the recognition of the binding sites on DNA being dictated by the proteic component while the hydrophobic retinol is solubilized in the fatty acid moiety

  12. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    OpenAIRE

    Recouvreux, Pierre; Lavelle, Christophe; Barbi, Maria; Conde e Silva, Natalia; Le Cam, Eric; Victor, Jean-Marc; Viovy, Jean-Louis

    2011-01-01

    Genomic DNA in eukaryotic cells is organized in supercoiled chromatin fibers, which undergo dynamic changes during such DNA metabolic processes as transcription or replication. Indeed, DNA-translocating enzymes like polymerases produce physical constraints in vivo. We used single-molecule micromanipulation by magnetic tweezers to study the response of chromatin to mechanical constraints in the same range as those encountered in vivo. We had previously shown that under positive torsional const...

  13. Construction and immunological evaluation of truncated hepatitis B core particles carrying HBsAg amino acids 119–152 in the major immunodominant region (MIR)

    International Nuclear Information System (INIS)

    Highlights: •The conformational HBV neutralization antigen domain was successfully displayed on the surface of truncated HBc particles. •Appropriate dialysis procedures to support the renaturing environment for the protein refolding. •Efficient purification procedures to obtain high purity and icosahedral particles of mosaic HBV antigen. •Strong immune responses not only including neutralization antibody response but also Th1 cell response were induced in mice. -- Abstract: Hepatitis B capsid protein expressed in Escherichia coli can reassemble into icosahedral particles, which could strongly enhance the immunogenicity of foreign epitopes, especially those inserted into its major immunodominant region. Herein, we inserted the entire ‘α’ antigenic determinant amino acids (aa) 119–152 of HBsAg into the truncated HBc (aa 1–144), between Asp78 and Pro79. Prokaryotic expression showed that the mosaic HBc was mainly in the form of inclusion bodies. After denaturation with urea, it was dialyzed progressively for protein renaturation. We observed that before and after renaturation, mosaic HBc was antigenic as determined by HBsAg ELISA and a lot of viruslike particles were observed after renaturation. Thus, we further purified the mosaic viruslike particles by (NH4)2SO4 precipitation, DEAE chromatography, and Sepharose 4FF chromatography. Negative staining electron microscopy demonstrated the morphology of the viruslike particles. Immunization of Balb/c mice with mosaic particles induced the production of anti-HBs antibody and Th1 cell immune response supported by ELISPOT and CD4/CD8 proportions assay. In conclusion, we constructed mosaic hepatitis core particles displaying the entire ‘α’ antigenic determinant on the surface and laid a foundation for researching therapeutic hepatits B vaccines

  14. Construction and immunological evaluation of truncated hepatitis B core particles carrying HBsAg amino acids 119–152 in the major immunodominant region (MIR)

    Energy Technology Data Exchange (ETDEWEB)

    Su, Qiudong; Yi, Yao [National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Changbai Road 155, Changping District, Beijing 102206 (China); Guo, Minzhuo [Beijing Entry-Exit Inspection and Quarantine Beureau, Tianshuiyuan Lane 6, Chaoyang District, Beijing 100026 (China); Qiu, Feng; Jia, Zhiyuan; Lu, Xuexin; Meng, Qingling [National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Changbai Road 155, Changping District, Beijing 102206 (China); Bi, Shengli, E-mail: shengli_bi@163.com [National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Changbai Road 155, Changping District, Beijing 102206 (China)

    2013-09-13

    Highlights: •The conformational HBV neutralization antigen domain was successfully displayed on the surface of truncated HBc particles. •Appropriate dialysis procedures to support the renaturing environment for the protein refolding. •Efficient purification procedures to obtain high purity and icosahedral particles of mosaic HBV antigen. •Strong immune responses not only including neutralization antibody response but also Th1 cell response were induced in mice. -- Abstract: Hepatitis B capsid protein expressed in Escherichia coli can reassemble into icosahedral particles, which could strongly enhance the immunogenicity of foreign epitopes, especially those inserted into its major immunodominant region. Herein, we inserted the entire ‘α’ antigenic determinant amino acids (aa) 119–152 of HBsAg into the truncated HBc (aa 1–144), between Asp{sup 78} and Pro{sup 79}. Prokaryotic expression showed that the mosaic HBc was mainly in the form of inclusion bodies. After denaturation with urea, it was dialyzed progressively for protein renaturation. We observed that before and after renaturation, mosaic HBc was antigenic as determined by HBsAg ELISA and a lot of viruslike particles were observed after renaturation. Thus, we further purified the mosaic viruslike particles by (NH{sub 4}){sub 2}SO{sub 4} precipitation, DEAE chromatography, and Sepharose 4FF chromatography. Negative staining electron microscopy demonstrated the morphology of the viruslike particles. Immunization of Balb/c mice with mosaic particles induced the production of anti-HBs antibody and Th1 cell immune response supported by ELISPOT and CD4/CD8 proportions assay. In conclusion, we constructed mosaic hepatitis core particles displaying the entire ‘α’ antigenic determinant on the surface and laid a foundation for researching therapeutic hepatits B vaccines.

  15. Multi-responsive hybrid particles: thermo-, pH-, photo-, and magneto-responsive magnetic hydrogel cores with gold nanorod optical triggers

    Science.gov (United States)

    Rittikulsittichai, Supparesk; Kolhatkar, Arati G.; Sarangi, Subhasis; Vorontsova, Maria A.; Vekilov, Peter G.; Brazdeikis, Audrius; Randall Lee, T.

    2016-06-01

    The research strategy described in this manuscript harnesses the attractive properties of hydrogels, gold nanorods (Aurods), and magnetic nanoparticles (MNPs) by synthesizing one unique multi-responsive nanostructure. This novel hybrid structure consists of silica-coated magnetic particles encapsulated within a thermo-responsive P(NIPAM-co-AA) hydrogel network on which Aurods are assembled. Furthermore, this research demonstrates that these composite particles respond to several forms of external stimuli (temperature, pH, light, and/or applied magnetic field) owing to their specific architecture. Exposure of the hybrid particles to external stimuli led to a systematic and reversible variation in the hydrodynamic diameter (swelling-deswelling) and thus in the optical properties of the hybrid particles (red-shifting of the plasmon band). Such stimuli-responsive volume changes can be effectively exploited in drug-delivery applications.The research strategy described in this manuscript harnesses the attractive properties of hydrogels, gold nanorods (Aurods), and magnetic nanoparticles (MNPs) by synthesizing one unique multi-responsive nanostructure. This novel hybrid structure consists of silica-coated magnetic particles encapsulated within a thermo-responsive P(NIPAM-co-AA) hydrogel network on which Aurods are assembled. Furthermore, this research demonstrates that these composite particles respond to several forms of external stimuli (temperature, pH, light, and/or applied magnetic field) owing to their specific architecture. Exposure of the hybrid particles to external stimuli led to a systematic and reversible variation in the hydrodynamic diameter (swelling-deswelling) and thus in the optical properties of the hybrid particles (red-shifting of the plasmon band). Such stimuli-responsive volume changes can be effectively exploited in drug-delivery applications. Electronic supplementary information (ESI) available: Contains detailed information about the synthesis of

  16. Etiology and Evaluation of Sperm Chromatin Anomalies

    Directory of Open Access Journals (Sweden)

    Marziyeh Tavalaee

    2008-01-01

    Full Text Available Evidence suggests that human sperm chromatin anomalies adversely affect reproductive outcomesand infertile men possess substantially amount of sperm with chromatin anomalies than fertilemen.Routine semen analysis evaluates parameters such as sperm motility and morphology, but doesnot examine the nuclear DNA integrity of spermatozoa. It has been suggested that altered nuclearchromatin structure or damaged DNA in spermatozoa could modify the special cellular functionsof human spermatozoa, and thereby affect the fertility potential. Intra-cytoplasmic sperm injection(ICSI bypass the barriers to fertilization for such a sperm, then the effect of chromatin anomalies onthe development remains a concern. Therefore, it is essential to develop and use accurate diagnostictests, which may provide better prognostic capabilities than the standard sperm assessments. Thisreview discusses our current understanding of the structure and organization of sperm DNA,the different procedures for assessment of sperm chromatin anomalies including comet assay,Chromomycin A3 (CMA3, sperm chromatin structure assay (SCSA, acridine orange test (AOT,terminal TdT-mediated dUTP-nick-end labelling (TUNEL assay, aniline blue and sperm chromatindispersion (SCD test and the impact of chromatin anomalies on reproductive outcome.

  17. Synthesis of sol–gel silica particles in reverse micelles with mixed-solvent polar cores: tailoring nanoreactor structure and properties

    Energy Technology Data Exchange (ETDEWEB)

    Bürglová, Kristýna; Hlaváč, Jan [Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry (Czech Republic); Bartlett, John R., E-mail: jbartlett@usc.edu.au [University of the Sunshine Coast, Faculty of Science, Health, Education and Engineering (Australia)

    2015-07-15

    In this paper, we describe a new approach for producing metal oxide nano- and microparticles via sol–gel processing in confined media (sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles), in which the chemical and physical properties of the polar aqueous core of the reverse micelles are modulated by the inclusion of a second polar co-solvent. The co-solvents were selected for their capacity to solubilise compounds with low water solubility and included dimethylsulfoxide, dimethylformamide, ethylene glycol, n-propanol, dimethylacetamide and N-methylpyrrolidone. A broad range of processing conditions across the sodium bis(2-ethylhexyl)sulfosuccinate/cyclohexane/water phase diagram were identified that are suitable for preparing particles with dimensions <50 to >500 nm. In contrast, only a relatively narrow range of processing conditions were suitable for preparing such particles in the absence of the co-solvents, highlighting the role of the co-solvent in modulating the properties of the polar core of the reverse micelles. A mechanism is proposed that links the interactions between the various reactive sites on the polar head group of the surfactant and the co-solvent to the nucleation and growth of the particles.

  18. Synthesis of sol–gel silica particles in reverse micelles with mixed-solvent polar cores: tailoring nanoreactor structure and properties

    International Nuclear Information System (INIS)

    In this paper, we describe a new approach for producing metal oxide nano- and microparticles via sol–gel processing in confined media (sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles), in which the chemical and physical properties of the polar aqueous core of the reverse micelles are modulated by the inclusion of a second polar co-solvent. The co-solvents were selected for their capacity to solubilise compounds with low water solubility and included dimethylsulfoxide, dimethylformamide, ethylene glycol, n-propanol, dimethylacetamide and N-methylpyrrolidone. A broad range of processing conditions across the sodium bis(2-ethylhexyl)sulfosuccinate/cyclohexane/water phase diagram were identified that are suitable for preparing particles with dimensions <50 to >500 nm. In contrast, only a relatively narrow range of processing conditions were suitable for preparing such particles in the absence of the co-solvents, highlighting the role of the co-solvent in modulating the properties of the polar core of the reverse micelles. A mechanism is proposed that links the interactions between the various reactive sites on the polar head group of the surfactant and the co-solvent to the nucleation and growth of the particles

  19. Chromatin condensation in terminally differentiating mouse erythroblasts does not involve special architectural proteins but depends on histone deacetylation

    Energy Technology Data Exchange (ETDEWEB)

    Popova, Evgenya Y.; Krauss, Sharon Wald; Short, Sarah A.; Lee, Gloria; Villalobos, Jonathan; Etzell, Joan; Koury, Mark J.; Ney, Paul A.; Chasis, Joel Anne; Grigoryev, Sergei A.

    2008-08-21

    Terminal erythroid differentiation in vertebrates is characterized by progressive heterochromatin formation, chromatin condensation and, in mammals, culminates in nuclear extrusion. To date, although mechanisms regulating avian erythroid chromatin condensation have been identified, little is known regarding this process during mammalian erythropoiesis. To elucidate the molecular basis for mammalian erythroblast chromatin condensation, we used Friend virus-infected murine spleen erythroblasts that undergo terminal differentiation in vitro. Chromatin isolated from early and late stage erythroblasts had similar levels of linker and core histones, only a slight difference in nucleosome repeats, and no significant accumulation of known developmentally-regulated architectural chromatin proteins. However, histone H3(K9) dimethylation markedly increased while histone H4(K12) acetylation dramatically decreased and became segregated from the histone methylation as chromatin condensed. One histone deacetylase, HDAC5, was significantly upregulated during the terminal stages of Friend virus-infected erythroblast differentiation. Treatment with histone deacetylase inhibitor, trichostatin A, blocked both chromatin condensation and nuclear extrusion. Based on our data, we propose a model for a unique mechanism in which extensive histone deacetylation at pericentromeric heterochromatin mediates heterochromatin condensation in vertebrate erythroblasts that would otherwise be mediated by developmentally-regulated architectural proteins in nucleated blood cells.

  20. Study of Molecular Conformation and Activity-Related Properties of Lipase Immobilized onto Core-Shell Structured Polyacrylic Acid-Coated Magnetic Silica Nanocomposite Particles.

    Science.gov (United States)

    Esmaeilnejad-Ahranjani, Parvaneh; Kazemeini, Mohammad; Singh, Gurvinder; Arpanaei, Ayyoob

    2016-04-01

    A facile approach for the preparation of core-shell structured poly(acrylic acid) (PAA)-coated Fe3O4 cluster@SiO2 nanocomposite particles as the support materials for the lipase immobilization is reported. Low- or high-molecular-weight (1800 and 100 000, respectively) PAA molecules were covalently attached onto the surface of amine-functionalized magnetic silica nanoacomposite particles. The successful preparation of particles were verified by scanning transmission electron microscopy (STEM), X-ray diffraction (XRD), vibrating sample magnetometer (VSM), thermogravimetric analysis (TGA), zeta potential measurement, and Fourier-transform infrared (FTIR) techniques. Once lipase is covalently immobilized onto the particles with an average diameter of 210 ± 50 nm, resulting from high binding sites concentrations on the low- and high-molecular-weight PAA-coated particles, high lipase immobilization efficiencies (86.2% and 89.9%, respectively), and loading capacities (786 and 816 mg g(-1), respectively) are obtained. Results from circular dichroism (CD) analysis and catalytic activity tests reveal an increase in the β-sheet content of lipase molecules upon immobilization, along with an enhancement in their activities and stabilities. The lipases immobilized onto the low- and high-molecular-weight PAA-coated particles show maximum activities at 55 and 50 °C, respectively, which are ∼28% and ∼15% higher than that of the free lipase at its own optimum temperature (40 °C), respectively. The immobilized lipases exhibit excellent performance at broader temperature and pH ranges and high thermal and storage stabilities, as well as superior reusability. These prepared magnetic nanocomposite particles can be offered as suitable support materials for efficient immobilization of enzymes and improvement of the immobilized enzymes properties. PMID:26986897

  1. Silica Nanoparticles as the Adjuvant for the Immunisation of Mice Using Hepatitis B Core Virus-Like Particles

    OpenAIRE

    Dace Skrastina; Ivars Petrovskis; Ilva Lieknina; Janis Bogans; Regina Renhofa; Velta Ose; Andris Dishlers; Yuri Dekhtyar; Paul Pumpens

    2014-01-01

    Advances in nanotechnology and nanomaterials have facilitated the development of silicon dioxide, or Silica, particles as a promising immunological adjuvant for the generation of novel prophylactic and therapeutic vaccines. In the present study, we have compared the adjuvanting potential of commercially available Silica nanoparticles (initial particles size of 10-20 nm) with that of aluminium hydroxide, or Alum, as well as that of complete and incomplete Freund's adjuvants for the immunisatio...

  2. Three-dimensional gyrokinetic particle-in-cell simulation of plasmas on a massively parallel computer: Final report on LDRD Core Competency Project, FY 1991--FY 1993

    International Nuclear Information System (INIS)

    One of the programs of the Magnetic fusion Energy (MFE) Theory and computations Program is studying the anomalous transport of thermal energy across the field lines in the core of a tokamak. We use the method of gyrokinetic particle-in-cell simulation in this study. For this LDRD project we employed massively parallel processing, new algorithms, and new algorithms, and new formal techniques to improve this research. Specifically, we sought to take steps toward: researching experimentally-relevant parameters in our simulations, learning parallel computing to have as a resource for our group, and achieving a 100 x speedup over our starting-point Cray2 simulation code's performance

  3. Lateral structuring and stability phenomena induced by block copolymers and core-shell nanogel particles at immiscible polymer/polymer interfaces

    Science.gov (United States)

    Gozen, Arif Omer

    We have investigated the parameters such as copolymer/nanoparticle concentration, architecture and molecular weight combined with film thickness, time and temperature in order to develop a molecular-level insight on how lateral interfacial structuring occurs at immiscible polymer/polymer interfaces. I order to develop a molecular-level understanding of how these 'smart' self-assembling materials and core-shell nanogel particles interact both intra- and inter-molecularly and form ordered structures in bulk, as well as at immiscible interfaces, we first focused on the response of core-shell polymer nanoparticles, designated CSNGs, composed of a cross-linked divinylbenzene core and poly(methyl methacrylate) (PMMA) arms as they segregate from PMMA homopolymer. We have demonstrated that these nanogel particles exhibit autophobic character when dispersed in high molecular weight homopolymer matrices and segregate to the interface with another fluid. We have further explored the migration of these new-generation nanogel particles (CSNG-Rs) segregating from PS homopolymer to PS/PMMA interfaces. Unlike the instability patterns observed with the CSNGs, which exhibit classical nucleation and growth mechanism with circular hole formation, we have observed an intriguing dewetting pattern and CSNG-Rs forming lateral aggregates and tentacle-like structures at the interface. In parallel with our core-shell particle studies, we have also explored the structuring of copolymer molecules that are far from equilibrium in bulk and complex laminate of polymer thin films. Our early triblock copolymer studies have proven that molecular asymmetry has a profound effect on order-disorder transition temperature. We focused primarily on the effect of the copolymer chemical composition (i.e., block sizes) on the dewetting behavior of PS/SM thin films on PMMA. We elucidate the interfacial segregation and concurrent micellization of diblock copolymers in a dynamically evolving environment with

  4. The Role of B-Lactoglobulin in the Development of the Core-and-Lining Structure of Casein Particles in Acid-Heat-Induced Milk Gels

    OpenAIRE

    Harwalkar, V. R.; Kalab, Miloslav

    1988-01-01

    Acid-heat-induced gels were obtained by coagulating casein micelle dispersions at 90 C using glucono-and-lactone. The casein micelles used were isolated from raw skim milk by centrifugation, washed free of whey proteins and soluble salts, and dispersed in water or a milk dialyzate. The pH values of the gels varied from 4.7 to 6.3. A core-and-lining ultrastructure developed in casein particles coagulated at pH 5.2 to 5.5 from casein micelle dispersions in the milk dialyzate provided that B-lac...

  5. Non-classical particle transport with angular-dependent path-length distributions. II: Application to pebble bed reactor cores

    International Nuclear Information System (INIS)

    Highlights: • We construct and analyze random and crystal arrangements of pebble bed cores. • We investigate anisotropic diffusion of neutrons in the interior of the cores. • We generate benchmark numerical results using Monte Carlo. • We obtain model estimates for the anisotropic diffusion coefficients. • We find that the new theory is accurate and able to predict anisotropic diffusion. - Abstract: We describe an analysis of neutron transport in the interior of model pebble bed reactor (PBR) cores, considering both crystal and random pebble arrangements. Monte Carlo codes were developed for (i) generating random realizations of the model PBR core, and (ii) performing neutron transport inside the crystal and random heterogeneous cores; numerical results are presented for two different choices of material parameters. These numerical results are used to investigate the anisotropic behavior of neutrons in each case and to assess the accuracy of estimates for the diffusion coefficients obtained with the diffusion approximations of different models: the atomic mix model, the Behrens correction, the Lieberoth correction, the generalized linear Boltzmann equation (GLBE), and the new GLBE with angular-dependent path-length distributions. This new theory utilizes a non-classical form of the Boltzmann equation in which the locations of the scattering centers in the system are correlated and the distance-to-collision is not exponentially distributed; this leads to an anisotropic diffusion equation. We show that the results predicted using the new GLBE theory are extremely accurate, correctly identifying the anisotropic diffusion in each case and greatly outperforming the other models for the case of random systems

  6. 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.

  7. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    Directory of Open Access Journals (Sweden)

    Arifulin E. A.

    2015-08-01

    Full Text Available Aim. The ultrastructural aspect of replicating chromatin organization is a matter of dispute. Here, we have analyzed the ultrastructural organization of replication foci using prematurely condensed chromosomes (PCC. Methods. To investigate the ultrastructure of replicating chromatin, we have used correlative light and electron microscopy as well as immunogold staining. Results. Replication in PCC occurs in the gaps between condensed chromatin domains. Using correlative light and electron microscopy, we observed that the replication foci contain decondensed chromatin as well as 80 and 130 nm globules, those were also found in condensed non-replicating chromatin domains. Using immunogolding, we demonstrated that DNA replication in S-phase PCC occurs in loose chromatin on the periphery of dense chromatin domains. Conclusion. Replication in PCC occurred in the decondensed chromatin neighboring the condensed chromatin without formation of special structures.

  8. Plasticity of fission yeast CENP-A chromatin driven by relative levels of histone H3 and H4.

    Directory of Open Access Journals (Sweden)

    Araceli G Castillo

    2007-07-01

    Full Text Available The histone H3 variant CENP-A assembles into chromatin exclusively at centromeres. The process of CENP-A chromatin assembly is epigenetically regulated. Fission yeast centromeres are composed of a central kinetochore domain on which CENP-A chromatin is assembled, and this is flanked by heterochromatin. Marker genes are silenced when placed within kinetochore or heterochromatin domains. It is not known if fission yeast CENP-A(Cnp1 chromatin is confined to specific sequences or whether histone H3 is actively excluded. Here, we show that fission yeast CENP-A(Cnp1 can assemble on noncentromeric DNA when it is inserted within the central kinetochore domain, suggesting that in fission yeast CENP-A(Cnp1 chromatin assembly is driven by the context of a sequence rather than the underlying DNA sequence itself. Silencing in the central domain is correlated with the amount of CENP-A(Cnp1 associated with the marker gene and is also affected by the relative level of histone H3. Our analyses indicate that kinetochore integrity is dependent on maintaining the normal ratio of H3 and H4. Excess H3 competes with CENP-A(Cnp1 for assembly into central domain chromatin, resulting in less CENP-A(Cnp1 and other kinetochore proteins at centromeres causing defective kinetochore function, which is manifest as aberrant mitotic chromosome segregation. Alterations in the levels of H3 relative to H4 and CENP-A(Cnp1 influence the extent of DNA at centromeres that is packaged in CENP-A(Cnp1 chromatin and the composition of this chromatin. Thus, CENP-A(Cnp1 chromatin assembly in fission yeast exhibits plasticity with respect to the underlying sequences and is sensitive to the levels of CENP-A(Cnp1 and other core histones.

  9. Plasticity of fission yeast CENP-A chromatin driven by relative levels of histone H3 and H4.

    Science.gov (United States)

    Castillo, Araceli G; Mellone, Barbara G; Partridge, Janet F; Richardson, William; Hamilton, Georgina L; Allshire, Robin C; Pidoux, Alison L

    2007-07-01

    The histone H3 variant CENP-A assembles into chromatin exclusively at centromeres. The process of CENP-A chromatin assembly is epigenetically regulated. Fission yeast centromeres are composed of a central kinetochore domain on which CENP-A chromatin is assembled, and this is flanked by heterochromatin. Marker genes are silenced when placed within kinetochore or heterochromatin domains. It is not known if fission yeast CENP-A(Cnp1) chromatin is confined to specific sequences or whether histone H3 is actively excluded. Here, we show that fission yeast CENP-A(Cnp1) can assemble on noncentromeric DNA when it is inserted within the central kinetochore domain, suggesting that in fission yeast CENP-A(Cnp1) chromatin assembly is driven by the context of a sequence rather than the underlying DNA sequence itself. Silencing in the central domain is correlated with the amount of CENP-A(Cnp1) associated with the marker gene and is also affected by the relative level of histone H3. Our analyses indicate that kinetochore integrity is dependent on maintaining the normal ratio of H3 and H4. Excess H3 competes with CENP-A(Cnp1) for assembly into central domain chromatin, resulting in less CENP-A(Cnp1) and other kinetochore proteins at centromeres causing defective kinetochore function, which is manifest as aberrant mitotic chromosome segregation. Alterations in the levels of H3 relative to H4 and CENP-A(Cnp1) influence the extent of DNA at centromeres that is packaged in CENP-A(Cnp1) chromatin and the composition of this chromatin. Thus, CENP-A(Cnp1) chromatin assembly in fission yeast exhibits plasticity with respect to the underlying sequences and is sensitive to the levels of CENP-A(Cnp1) and other core histones. PMID:17677001

  10. Synthesis of Co/MFe2O4 (M=Fe, Mn) core/shell nanocomposite particles

    International Nuclear Information System (INIS)

    Monodispersed cobalt nanoparticles (NPs) with controllable size (8-14 nm) have been synthesized using thermal decomposition of dicobaltoctacarbonyl in organic solvent. The as-synthesized high magnetic moment (125 emu/g) Co NPs are dispersible in various organic solvents, and can be easily transferred into aqueous phase by surface modification using phospholipids. However, the modified hydrophilic Co NPs are not stable as they are quickly oxidized, agglomerated in buffer. Co NPs are stabilized by coating the MFe2O4 (M=Fe, Mn) ferrite shell. Core/shell structured bimagnetic Co/MFe2O4 nanocomposites are prepared with tunable shell thickness (1-5 nm). The Co/MFe2O4 nanocomposites retain the high magnetic moment density from the Co core, while gaining chemical and magnetic stability from the ferrite shell. Compared to Co NPs, the nanocomposites show much enhanced stability in buffer solution at elevated temperatures, making them promising for biomedical applications. - Graphical abstract: The 10 nm/3 nm Co/MFe2O4 (M=Fe, Mn) bimagnetic core/shell nanocomposites are synthesized from the surface coating of ferrite shell over 10 nm Co nanoparticle seeds. The nanocomposites show much enhanced chemical and magnetic stability in solid state, organic solution and aqueous phase, and are promising for biomedical applications

  11. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    Science.gov (United States)

    Recouvreux, Pierre; Lavelle, Christophe; Barbi, Maria; Conde e Silva, Natalia; Le Cam, Eric; Victor, Jean-Marc; Viovy, Jean-Louis

    2011-01-01

    Genomic DNA in eukaryotic cells is organized in supercoiled chromatin fibers, which undergo dynamic changes during such DNA metabolic processes as transcription or replication. Indeed, DNA-translocating enzymes like polymerases produce physical constraints in vivo. We used single-molecule micromanipulation by magnetic tweezers to study the response of chromatin to mechanical constraints in the same range as those encountered in vivo. We had previously shown that under positive torsional constraints, nucleosomes can undergo a reversible chiral transition toward a state of positive topology. We demonstrate here that chromatin fibers comprising linker histones present a torsional plasticity similar to that of naked nucleosome arrays. Chromatosomes can undergo a reversible chiral transition toward a state of positive torsion (reverse chromatosome) without loss of linker histones. PMID:21641318

  12. Bacterial chromatin: converging views at different scales.

    Science.gov (United States)

    Dame, Remus T; Tark-Dame, Mariliis

    2016-06-01

    Bacterial genomes are functionally organized and compactly folded into a structure referred to as bacterial chromatin or the nucleoid. An important role in genome folding is attributed to Nucleoid-Associated Proteins, also referred to as bacterial chromatin proteins. Although a lot of molecular insight in the mechanisms of operation of these proteins has been generated in the test tube, knowledge on genome organization in the cellular context is still lagging behind severely. Here, we discuss important advances in the understanding of three-dimensional genome organization due to the application of Chromosome Conformation Capture and super-resolution microscopy techniques. We focus on bacterial chromatin proteins whose proposed role in genome organization is supported by these approaches. Moreover, we discuss recent insights into the interrelationship between genome organization and genome activity/stability in bacteria. PMID:26942688

  13. Expression, purification, crystallization and preliminary X-ray crystallographic studies of hepatitis B virus core fusion protein corresponding to octahedral particles

    International Nuclear Information System (INIS)

    Novel hepatitis B virus-like particles of recombinant dimeric core–GFP fusion protein were expressed, purified and crystallized. The crystals diffracted to 2.15 Å resolution and belonged to space group F432, with unit-cell parameters a = b = c = 219.7 Å. Recombinant hepatitis B virus core proteins dimerize to form building blocks that are capable of self-assembly into a capsid. A core capsid protein dimer (CPD) linked to a green fluorescent protein variant, EGFP, at the C-terminus has been designed. The recombinant fusion CPD was expressed in Escherichia coli, assembled into virus-like particles (VLPs), purified and crystallized. The single crystal diffracted to 2.15 Å resolution and belonged to the cubic space group F432, with unit-cell parameters a = b = c = 219.7 Å. The fusion proteins assembled into icosahedral VLPs in aqueous solution, but were rearranged into octahedral symmetry through the crystal-packing process under the crystallization conditions

  14. Alphavirus capsid proteins self-assemble into core-like particles in insect cells: A promising platform for nanoparticle vaccine development.

    Science.gov (United States)

    Hikke, Mia C; Geertsema, Corinne; Wu, Vincen; Metz, Stefan W; van Lent, Jan W; Vlak, Just M; Pijlman, Gorben P

    2016-02-01

    The mosquito-borne chikungunya virus (CHIKV) causes arthritic diseases in humans, whereas the aquatic salmonid alphavirus (SAV) is associated with high mortality in aquaculture of salmon and trout. Using modern biotechnological approaches, promising vaccine candidates based upon highly immunogenic, enveloped virus-like particles (eVLPs) have been developed. However, the eVLP structure (core, lipid membrane, surface glycoproteins) is more complex than that of non-enveloped, protein-only VLPs, which are structurally and morphologically 'simple'. In order to develop an alternative to alphavirus eVLPs, in this paper we engineered recombinant baculovirus vectors to produce high levels of alphavirus core-like particles (CLPs) in insect cells by expression of the CHIKV and SAV capsid proteins. The CLPs localize in dense nuclear bodies within the infected cell nucleus and are purified through a rapid and scalable protocol involving cell lysis, sonication and low-speed centrifugation steps. Furthermore, an immunogenic epitope from the alphavirus E2 glycoprotein can be successfully fused to the N-terminus of the capsid protein without disrupting the CLP self-assembling properties. We propose that immunogenic epitope-tagged alphavirus CLPs produced in insect cells present a simple and perhaps more stable alternative to alphavirus eVLPs. PMID:26287127

  15. On the Origin and Precursor Materials of Glassy Fallback Particles in the Lake Bosumtwi ICDP Cores - Status Report

    Science.gov (United States)

    Luetke, S.; Deutsch, A.; Kreher-Hartmann, B.; Berndt, J.

    2007-03-01

    Major element composition of fallback particles from the Bosumtwi crater matches well with that one of target rocks with intermediate SiO2 content. Variations in CaO and MgO may reflect heterogeneous carbonate distribution in the precursor material.

  16. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    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...... reassembly on nascent DNA strands. The aim of this review is to discuss how histones - new and old - are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms.......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...

  17. Alpha radiation-induced alterations of the proliferation kinetics, chromatin structure and gene expression in mammalian cells

    International Nuclear Information System (INIS)

    Exponentially growing mammalian cells were exposed to 3.4 MeV alpha particles. The chromatin of cells arrested in G2 by alpha irradiation was severely damaged, though all cells were still capable to condensate their chromatin after fusion with mitotic cells. In addition to the common types of aberrations (breaks, gaps, dicentrics and exchanges) cells were found possessing one or more chromosomes with long stretches of undercondensed chromatin. Repair of these lesions was indicated by site specific unscheduled DNA synthesis and by the observation that condensation of these regions improved during G2 arrest. Furthermore, during G2 arrest the synthesis of two cellular proteins was stimulated. This was studied by two-dimensional gel electrophoresis of 35S-methionine labeled cellular proteins. All these findings provided evidence that radiation-induced G2 arrest is caused by chromatin damage, which prevents regular chromosome condensation for mitosis. (orig./MG)

  18. Comparison of fused-core and conventional particle size columns by LC-MS/MS and UV: application to pharmacokinetic study.

    Science.gov (United States)

    Song, Wei; Pabbisetty, Deepthi; Groeber, Elizabeth A; Steenwyk, Rick C; Fast, Douglas M

    2009-10-15

    The chromatographic performance of fused-core (superficially porous) HPLC packing materials was compared with conventional fully porous particle materials for LC-MS/MS analysis of two pharmaceuticals in rat plasma. Two commercially available antidepressants, imipramine and desipramine, were assayed using a conventional analytical C(18) column (5 microm, 2.0 mm x 30 mm) and a fused-core C(18) column (2.7 microm, 2.1 mm x 30 mm). Retention time, column efficiency, pressure drop, resolution, and loading capacity were compared under the same operating conditions. The fused-core column demonstrated reduced assay time by 34% and 2-3-fold increased efficiency (N). Loading capacity up to 25 microl of extract injected on column showed no peak distortion. The registered back-pressure from a flow rate of 1.0 ml/min did not exceed 3400 psi making it compatible with standard HPLC equipment (typically rated to 6000 psi). Two mobile phases were examined, and morpholine as an organic base modifier yielded a 2-5-fold increase in S/N near the limit of detection over triethylamine. The 2.7 microm fused-core column was applied to the analysis of imipramine and desipramine in extracted, protein precipitated rat plasma by LC-MS/MS. The calibration curves were linear in the concentration range of 0.5-1000 ng/ml for both imipramine and desipramine. Intra-run precisions (%CV) and accuracies (%bias) were within +/-7.8% and +/-7.3% at three QC levels and within 14.7% and 14.4% at the LOQ level for both analytes. Following a single method qualification run, the method was applied to the quantitation of pharmacokinetic study samples after oral administration of imipramine to male rats. PMID:19540084

  19. Ethylene glycol-based Ag plating for the wet chemical fabrication of one micrometer Cu/Ag core/shell particles

    International Nuclear Information System (INIS)

    Highlights: • Cu@Ag particles less than one micrometer were fabricated through Ag polyol-plating. • Ag polyol-plating was tried without using additional reagents on Cu core particles. • Continuity, uniformity, and thickness of the Ag shell depended on plating conditions. • The sample showed an excellent oxidation initiation temperature of 280 °C. • Anti-oxidation properties of Cu@Ag powders strongly depend on the Ag shell thickness. - Abstract: With the aim of preparing an inexpensive metal filler that can be added to conductive adhesives used in fine-pitch electronic applications, a polyol solution was used to fabricate Ag-coated Cu (Cu@Ag) particles with a size on the order of one micron without the need for additional reagents. The continuity, uniformity, and thickness of the Ag shell were found to be strongly dependent on the plating conditions, particularly the reaction temperature. The Ag shell prepared at a peak temperature of 180 °C from a precursor with an initial Ag concentration of 15 wt.% was judged to be an optimum one. This same sample also showed an excellent oxidation initiation temperature of approximately 280 °C. It was inferred that the oxidation resistance of the Cu@Ag powder is largely determined by the continuity, uniformity and thickness of the Ag shell

  20. Trends in anomalous small-angle X-ray scattering in grazing incidence for supported nano-alloyed and core-shell metallic nano-particles

    International Nuclear Information System (INIS)

    As atomic structure and morphology of particles are directly correlated to their functional properties, experimental methods probing local and average features of particles at the nano-scale elicit a growing interest. Anomalous small-angle X-ray scattering (ASAXS) is a very attractive technique to investigate the size, shape and spatial distribution of nano-objects embedded in a homogeneous matrix or in porous media. The anomalous variation of the scattering factor close to an absorption edge enables element specific investigations. In the case of supported nano-objects, the use of grazing incidence is necessary to limit the probed depth. The combination of grazing incidence with the anomalous technique provides a powerful new method, anomalous grazing incidence small-angle X-ray scattering (AGISAXS), to disentangle complex chemical patterns in supported multi-component nano-structures. Nevertheless, a proper data analysis requires accurate quantitative measurements associated to an adapted theoretical framework. This paper presents anomalous methods applied to nano-alloys phase separation in the 1-10 nm size range, and focuses on the application of AGISAXS in bimetallic systems: nano-composite films and core-shell supported nano-particles

  1. Painting by Numbers: Increasing the Parts List for Chromatin Domains

    Science.gov (United States)

    Chen, Hsiuyi V.; Rando, Oliver J.

    2014-01-01

    In this issue of Molecular Cell, van Bemmel and colleagues (2013) report the genome-wide mapping of 42 novel chromatin factors, systematically identifying new components of the various chromatin domains present in fly cells. PMID:23438859

  2. 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.

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

    Science.gov (United States)

    Wu, Xiaoyun; Shi, Zhen; Cui, Mingxue; Han, Min; Ruvkun, Gary

    2012-01-01

    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. PMID:22412383

  4. Single Chromatin Fibre Assembly Using Optical Tweezers

    NARCIS (Netherlands)

    Bennink, M.L.; Pope, L.H.; Leuba, S.H.; Grooth, de B.G.; Greve, J.

    2001-01-01

    Here we observe the formation of a single chromatin fibre using optical tweezers. A single -DNA molecule was suspended between two micron-sized beads, one held by a micropipette and the other in an optical trap. The constrained DNA molecule was incubated with Xenopus laevis egg extract in order to r

  5. Chromatin and epigenetics in all their states

    NARCIS (Netherlands)

    Bey, Till; Jamge, Suraj; Klemme, Sonja; Komar, Dorota Natalia; Gall, Le Sabine; Mikulski, Pawel; Schmidt, Martin; Zicola, Johan; Berr, Alexandre

    2016-01-01

    In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meetin

  6. CTCF Binding Polarity Determines Chromatin Looping

    NARCIS (Netherlands)

    de Wit, Elzo; Vos, Erica S M; Holwerda, Sjoerd J B; Valdes-Quezada, Christian; Verstegen, Marjon J A M; Teunissen, Hans; Splinter, Erik; Wijchers, Patrick J; Krijger, Peter H L; de Laat, Wouter

    2015-01-01

    CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that ch

  7. 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 ...

  8. Impact of chromatin structure on PR signaling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Hager, Gordon L

    2012-01-01

    but also to the glucocorticoid receptor (GR), as these receptors share many similarities regarding interaction with, and remodeling of, chromatin. Both receptors can bind nucleosomal DNA and have accordingly been described as pioneering factors. However recent genomic approaches (ChIP-seq and DHS...

  9. Research Discovers Frequent Mutations of Chromatin

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    With the support of National Natural Science Foundation of China, BGI, the largest genomics organization in the world, and Peking University Shenzhen Hospital, published online in Nature Geneticsics that the study on frequent mutations of chromatin remodeling genes in transitional cell carcinoma (TCC) of thebladder on August 8th, 2011. Their study provides a valuable genetic basis for future studies on TCC,

  10. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

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

    2007-01-01

    Chromatin-modifying proteins mold the genome into areas that are accessible for transcriptional activity and areas that are transcriptionally silent. This epigenetic gene regulation allows for different transcriptional programs to be conducted in different cell types at different timepoints-despi...

  11. Factors affecting chromatin stability of bovine spermatozoa.

    Science.gov (United States)

    Khalifa, T A A; Rekkas, C A; Lymberopoulos, A G; Sioga, A; Dimitriadis, I; Papanikolaou, Th

    2008-03-01

    The structural stability of transcriptionally inert paternal chromatin is of vital importance for the fertilization process and early embryonic development. Accordingly, a series of eight experiments were conducted during a 7-month period to investigate: (1) effects of bull breed, individuality, successive ejaculations, semen quality characteristics (SQC), semen dilution rates and hypothermic storage of semen in a Tris-egg yolk extender on incidence of sperm nuclear chromatin instability (NCI), and (2) effects of the interaction between variation of NCI within a frozen ejaculate and variation of oocytes quality due to maturation time and/or season on the efficiency of in vitro embryo production (IVEP). Semen samples were collected once a week from six bulls using an AV and only ejaculates (n=220) of >0.30x10(9) sperm/ml and >or=60% motility were used. NCI was measured by: (1) detection of lysine-rich histones in sperm chromatin using aniline blue staining, (2) sperm susceptibility to acid-induced nuclear DNA denaturation in situ using acridine orange test, and (3) sperm susceptibility to nuclear chromatin decondensation (NCD). Bovine oocytes (n=695) were matured in vitro for 18 or 24 h, fertilized after sperm selection through a swim-up procedure and cultured for 72 h. The results showed that the 2nd ejaculates were superior to the 1st ones with respect to chromatin stability. Dilution of semen to 49.67+/-8.56x10(6) sperm/ml (1:19) decreased resistance of sperm to NCD. Cooling of semen had no significant effect on chromatin stability. Cryopreservation of semen augmented sperm vulnerability to DNA denaturation. Improvement of SQC (semen volume, sperm motility, velocity, viability and morphological normalcy) was generally concomitant with increase of sperm resistance to NCI. While Blonde d'Aquitaine bulls had a resistance to NCD higher than Limousine bulls in fresh semen, the former showed a greater susceptibility to DNA denaturation than the latter in cooled semen

  12. Environmentally friendly electroless plating for Ag/TiO2-coated core-shell magnetic particles using ultrasonic treatment.

    Science.gov (United States)

    Kim, Soo-Dong; Choe, Won-Gyun; Jeong, Jong-Ryul

    2013-11-01

    In this work, high-reflectance brilliant white color magnetic microspheres comprising a Fe/TiO2/Ag core-shell structure with a continuous, uniform compact silver layer were successfully fabricated by TiO2-assisted electroless plating in a simple and eco-friendly method. The coating procedure for TiO2 and Ag involved a sol-gel reaction and electroless plating with ultrasound treatment. The electroless plating step was carried out in an eco-friendly manner in a single process without environmentally toxic additives. The TiO2 layer was used as a modification layer between the Fe microspheres and the silver layer to improve adhesion. A continuous and compact silver layer could be formed with a high degree of morphological control by introducing ultrasonication and adjusting the ammonium hydroxide concentration. PMID:23611665

  13. Camk2a-Cre-Mediated Conditional Deletion of Chromatin Remodeler Brg1 Causes Perinatal Hydrocephalus

    OpenAIRE

    Cao, Mou; Wu, Jiang I.

    2015-01-01

    Mammalian SWI/SNF-like BAF chromatin remodeling complexes are essential for many aspects of neural development. Mutations in the genes encoding the core subunit Brg1/SmarcA4or other complex components cause neurodevelopmental diseases and are associated with autism. Congenital hydrocephalus is a serious brain disorder often experienced by these patients. We report a role of Brg1 in the pathogenesis of hydrocephalus disorder. We discovered an unexpected early activity of mouse Camk2a-Cre trans...

  14. Nanometric core-shell-shell {gamma}-Fe{sub 2}O{sub 3}/SiO{sub 2}/TiO{sub 2} particles

    Energy Technology Data Exchange (ETDEWEB)

    Abramson, Sebastien, E-mail: sebastien.abramson@upmc.fr; Srithammavanh, Liliane; Siaugue, Jean-Michel; Horner, Olivier [Universite Pierre et Marie Curie (UPMC), LI2C-UMR 7612 (UPMC-CNRS-ESPCI) (France); Xu Xiangzhen [Ecole Superieure de Physique et Chimie Industrielle (ESPCI), LPEM-UPR A0005 (France); Cabuil, Valerie [Universite Pierre et Marie Curie (UPMC), LI2C-UMR 7612 (UPMC-CNRS-ESPCI) (France)

    2009-02-15

    The preparation of core-shell-shell {gamma}-Fe{sub 2}O{sub 3}/SiO{sub 2}/TiO{sub 2} nanoparticles of few tens nanometers is performed by successively coating onto magnetic nanoparticles a SiO{sub 2} layer and a TiO{sub 2} layer, using sol-gel methods. The thickness of the two layers and the aggregation state of the particles can be controlled by the experimental conditions used for the two coatings. These composite nanoparticles may find application as magnetic photocatalysts, since they are characterized by their small diameters which allow a good accessibility to the TiO{sub 2} shell.

  15. The mutable nature of particle-core excitations with spin in the one-valence-proton nucleus 133Sb

    CERN Document Server

    Bocchi, G; Fornal, B; Colo', G; Bortignon, P F; Bottoni, S; Bracco, A; Michelagnoli, C; Bazzacco, D; Blanc, A; De France, G; Jentschel, M; Koster, U; Mutti, P; Regis, J -M; Simpson, G; Soldner, T; Ur, C A; Urban, W; Fraile, L M; Lozeva, R; Belvito, B; Benzoni, G; Bruce, A; Carroll, R; Cieplicka-Orynczak, N; Crespi, F C L; Didierjean, F; Jolie, J; Korten, W; Kroll, T; Lalkovski, S; Mach, H; Marginean, N; Melon, B; Mengoni, D; Million, B; Nannini, A; Napoli, D; Olaizola, B; Paziy, V; Podolyakn, Zs; Regann, P H; Saed-Samii, N; Szpak, B; Vedia, V

    2016-01-01

    The gamma-ray decay of excited states of the one-valence-proton nucleus 133Sb has been studied using cold-neutron induced fission of 235U and 241Pu targets, during the EXILL campaign at the ILL reactor in Grenoble. By using a highly efficient HPGe array, coincidences between gamma-rays prompt with the fission event and those delayed up to several tens of microseconds were investigated, allowing to observe, for the first time, high-spin excited states above the 16.6 micros isomer. Lifetimes analysis, performed by fast-timing techniques with LaBr3(Ce) scintillators, reveals a difference of almost two orders of magnitude in B(M1) strength for transitions between positive-parity medium-spin yrast states. The data are interpreted by a newly developed microscopic model which takes into account couplings between core excitations (both collective and non-collective) of the doubly magic nucleus 132Sn and the valence proton, using the Skyrme effective interaction in a consistent way. The results point to a fast change ...

  16. Deletion modification enhances anthrax specific immunity and protective efficacy of a hepatitis B core particle-based anthrax epitope vaccine.

    Science.gov (United States)

    Yin, Ying; Zhang, Sheng; Cai, Chenguang; Zhang, Jun; Dong, Dayong; Guo, Qiang; Fu, Ling; Xu, Junjie; Chen, Wei

    2014-02-01

    Protective antigen (PA) is one of the major virulence factors of anthrax and is also the major constituent of the current anthrax vaccine. Previously, we found that the 2β2-2β3 loop of PA contains a dominant neutralizing epitope, the SFFD. We successfully inserted the 2β2-2β3 loop of PA into the major immunodominant region (MIR) of hepatitis B virus core (HBc) protein. The resulting fusion protein, termed HBc-N144-PA-loop2 (HBcL2), can effectively produce anthrax specific protective antibodies in an animal model. However, the protective immunity caused by HBcL2 could still be improved. In this research, we removed amino acids 79-81 from the HBc MIR of the HBcL2. This region was previously reported to be the major B cell epitope of HBc, and in keeping with this finding, we observed that the short deletion in the MIR not only diminished the intrinsic immunogenicity of HBc but also stimulated a higher titer of anthrax specific immunity. Most importantly, this deletion led to the full protection of the immunized mice against a lethal dose anthrax toxin challenge. We supposed that the conformational changes which occurred after the short deletion and foreign insertion in the MIR of HBc were the most likely reasons for the improvement in the immunogenicity of the HBc-based anthrax epitope vaccine. PMID:24054942

  17. Atmospheric Aerosol Loading and Transport Due to the 1783-84 Laki Eruption in Iceland, Interpreted from Ash Particles and Acidity in the GISP2 Ice Core

    Science.gov (United States)

    Fiacco, R. Joseph; Thordarson, Thorvaldur; Germani, Mark S.; Self, Stephen; Palais, Julie M.; Whitlow, Sallie; Grootes, Peter M.

    1994-11-01

    Glass shards from the A.D. 1783 Laki fissure eruption in Iceland have been identified in the GISP2 ice core from Summit, Greenland, at a level just preceding the major acidity/sulfate peak. Detailed reconstruction of ice stratigraphy, coupled with analyses of solid particles from filtered samples, indicate that a small amount of Laki ash was carried via atmospheric transport to Greenland in the summer of 1783, whereas the main aerosol precipitation occurred in the summer and early fall of 1784. Sulfate concentrations in the ice increase slightly during late summer and fall of 1783 and remain steady throughout the winter due to slow oxidation rates during this season in the Arctic. The sulfate concentration rises dramatically in the spring and summer of 1784, producing a massive sulfate peak, previously believed to have accumulated during the summer of 1783 and commonly used as the marker horizon in Greenland ice core studies. The chronology of ash and acid fallout at the GISP2 site suggests that a significant portion of the Laid eruption plume penetrated the tropopause and that aerosol generated from it remained aloft for at least 1 yr after the eruption. Based on comparisons with other glaciochemical seasonal indicators, abnormally cool conditions prevailed at Summit during the summer of 1784. This further supports the claim that a significant volume of sulfate aerosol remained in the Arctic middle atmosphere well after the eruption had ceased.

  18. Particle distributions in approximately 10(13) - 10(16) eV air shower cores at mountain altitude and comparison with Monte Carlo simulations

    Science.gov (United States)

    Ash, A. G.

    1985-01-01

    Photographs of 521 shower cores in an array of current-limited spark (discharge) chambers at Sacramento Peak (2900m above sea level, 730 g /sq cm.), New Mexico, U.S.A., have been analyzed and the results compared with similar data from Leeds (80m above sea level, 1020 g sq cm.). It was found that the central density differential spectrum is consistent with a power law index of -2 up to approx. 1500/sq m where it steepens, and that shower cores become flatter on average with increasing size. Scaling model predictions for proton primaries with a approx E sup -2.71 energy spectrum account well for the altitude dependence of the data at lower densities. However, deviations at higher densities indicate a change in hadron interaction characteristics between approx few x 10 to the 14th power and 10 to the 15th power eV primary energy causing particles close to the shower axis to be spread further out.

  19. Porous Zr(x)Si(1-x)O₂ shell/void/TiO₂ core particles with enhancing transfer for cleaning water.

    Science.gov (United States)

    Zhang, Yuqing; Zhang, Yunge

    2015-06-15

    In order to immobilize TiO2 and prevent TiO2 nanoparticles from damaging polymeric supporters, the porous Zr(x)Si(1-x)O2 shell/void/TiO2 core particles (Zr-SVTs) were fabricated by the synergistic effect between nonionic surfactant P123 ((EO)20(PO)70(EO)20) and oleic acid (CH3(CH2)7CH=CH(CH2)7COOH) and cohydrolysis between TEOS and ZrOCl2·8H2O. Zr-SVTs were characterized by FT-IR, SEM, TEM, EDX and BET. The results show Zr-SVTs exhibit well-developed spherical shape with channels (approximately 5.5 nm in diameter) in porous Zr(x)Si(1-x)O2 shells. Moreover, the preparation conditions of Zr-SVTs were studied and confirmed, and the photocatalytic activity of Zr-SVTs was studied by photodegrading methyl orange in aqueous solution and oil in sewage containing oil. Alternatively, the photocatalytic activity of Zr-SVTs presents better result compared with SiO2 shell/void/TiO2 core (SVT) without doping Zr into the SiO2 shell, which further demonstrates that the Zr(x)Si(1-x)O2 shell could promote the mass transfer inside channels of Zr-SVTs. It suggests that Zr-SVTs with higher photocatalytic activity are desirable for application in water cleaning. PMID:25780933

  20. Rapid determination of polycyclic aromatic hydrocarbons in rainwater by liquid-liquid microextraction and LC with core-shell particles column and fluorescence detection.

    Science.gov (United States)

    Vinci, Giuliana; Antonelli, Marta L; Preti, Raffaella

    2013-02-01

    Liquid-liquid microextraction coupled to LC with fluorescence detection for the determination of Environmental Protection Agency's 16 priority pollutant polycyclic aromatic hydrocarbons in rainwater has been developed. The optimization of the extraction method has involved several parameters, including the comparison between an ultrasonic bath and a magnetic stirrer as extractant apparatus, the choice of the extractant solvent, and the optimization of the extraction time. Liquid-liquid microextraction gave good results in terms of recoveries (from 73.6 to 102.8% in rainwater) and repeatability, with a very simple procedure and low solvent consumption. The reported chromatographic method uses a Core-Shell technology column, with particle size <3 μm instead of classical 5-μm particles column. The resulting backpressure was below 300 bar, allowing the use of a conventional HPLC system rather than the more expensive ultrahigh performance LC (UHPLC). An average decrease of 59% in run time and 75% in eluent consumption has been obtained, compared to classical HPLC methods, keeping good separation, sensitivity, and repeatability. The proposed conditions were successfully applied to the determinations of polycyclic aromatic hydrocarbons in genuine rainwater samples. PMID:23303536

  1. Interfacial effect on physical properties of composite media: Interfacial volume fraction with non-spherical hard-core-soft-shell-structured particles

    Science.gov (United States)

    Xu, Wenxiang; Duan, Qinglin; Ma, Huaifa; Chen, Wen; Chen, Huisu

    2015-11-01

    Interfaces are known to be crucial in a variety of fields and the interfacial volume fraction dramatically affects physical properties of composite media. However, it is an open problem with great significance how to determine the interfacial property in composite media with inclusions of complex geometry. By the stereological theory and the nearest-surface distribution functions, we first propose a theoretical framework to symmetrically present the interfacial volume fraction. In order to verify the interesting generalization, we simulate three-phase composite media by employing hard-core-soft-shell structures composed of hard mono-/polydisperse non-spherical particles, soft interfaces, and matrix. We numerically derive the interfacial volume fraction by a Monte Carlo integration scheme. With the theoretical and numerical results, we find that the interfacial volume fraction is strongly dependent on the so-called geometric size factor and sphericity characterizing the geometric shape in spite of anisotropic particle types. As a significant interfacial property, the present theoretical contribution can be further drawn into predicting the effective transport properties of composite materials.

  2. Optimized high performance liquid chromatography-ultraviolet detection method using core-shell particles for the therapeutic monitoring of methotrexate$

    Institute of Scientific and Technical Information of China (English)

    Milagros Montemurro; María M. De Zan n; Juan C. Robles

    2016-01-01

    Methotrexate (MTX) is an antineoplastic drug, and due to its high toxicity, the therapeutic drug mon-itoring is strictly conducted in the clinical practice. The chemometric optimization and validation of a high performance liquid chromatography (HPLC) method using core–shell particles is presented for the determination of MTX in plasma during therapeutic monitoring. Experimental design and response surface methodology (RSM) were applied for the optimization of the chromatographic system and the analyte extraction step. A Poroshell 120 EC-C18 (3.0 mm ? 75 mm, 2.7μm) column was used to obtain a fast and efficient separation in a complete run time of 4 min. The optimum conditions for the chroma-tographic system resulted in a mobile phase consisting of acetic acid/sodium acetate buffer solution (85.0 mM, pH¼4.00) and 11.2%of acetonitrile at a flow rate of 0.4 mL/min. Selectivity, linearity, accuracy and precision were demonstrated in a range of 0.10–6.0 mM of MTX. The application of the optimized method required only 150 mL of patient plasma and a low consumption of solvent to provide rapid re-sults.

  3. The landscape of accessible chromatin in mammalian preimplantation embryos.

    Science.gov (United States)

    Wu, Jingyi; Huang, Bo; Chen, He; Yin, Qiangzong; Liu, Yang; Xiang, Yunlong; Zhang, Bingjie; Liu, Bofeng; Wang, Qiujun; Xia, Weikun; Li, Wenzhi; Li, Yuanyuan; Ma, Jing; Peng, Xu; Zheng, Hui; Ming, Jia; Zhang, Wenhao; Zhang, Jing; Tian, Geng; Xu, Feng; Chang, Zai; Na, Jie; Yang, Xuerui; Xie, Wei

    2016-06-30

    In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. PMID:27309802

  4. Diversity in the organization of centromeric chromatin.

    Science.gov (United States)

    Steiner, Florian A; Henikoff, Steven

    2015-04-01

    Centromeric chromatin is distinguished primarily by nucleosomes containing the histone variant cenH3, which organizes the kinetochore that links the chromosome to the spindle apparatus. Whereas budding yeast have simple 'point' centromeres with single cenH3 nucleosomes, and fission yeast have 'regional' centromeres without obvious sequence specificity, the centromeres of most organisms are embedded in highly repetitive 'satellite' DNA. Recent studies have revealed a remarkable diversity in centromere chromatin organization among different lineages, including some that have lost cenH3 altogether. We review recent progress in understanding point, regional and satellite centromeres, as well as less well-studied centromere types, such as holocentromeres. We also discuss the formation of neocentromeres, the role of pericentric heterochromatin, and the structure and composition of the cenH3 nucleosome. PMID:25956076

  5. On the topology of chromatin fibres

    Science.gov (United States)

    Barbi, Maria; Mozziconacci, Julien; Victor, Jean-Marc; Wong, Hua; Lavelle, Christophe

    2012-01-01

    The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method for computing topological properties (twist, writhe and linking number) of the DNA embedded in those fibres. The relevance of the method is reviewed through the analysis of magnetic tweezers single molecule experiments that revealed unexpected properties of the chromatin fibre. Possible biological implications of these results are discussed. PMID:24098838

  6. On the topology of chromatin fibres

    OpenAIRE

    Barbi, Maria; Mozziconacci, Julien; Victor, Jean-Marc; Wong, Hua; Lavelle, Christophe

    2012-01-01

    The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method fo...

  7. Chromatin regulation in drug addiction and depression

    OpenAIRE

    Renthal, William; Nestler, Eric J.

    2009-01-01

    Alterations in gene expression are implicated in the pathogenesis of several neuropsychiatrie disorders, including drug addiction and depression, increasing evidence indicates that changes in gene expression in neurons, in the context of animal models of addiction and depression, are mediated in part by epigenetic mechanisms that alter chromatin structure on specific gene promoters. This review discusses recent findings from behavioral, molecular, and bioinformatic approaches that are being u...

  8. Identification of alternative topological domains in chromatin

    OpenAIRE

    Filippova, Darya; Patro, Rob; Duggal, Geet; Kingsford, Carl

    2014-01-01

    Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various r...

  9. Multiscale Identification of Topological Domains in Chromatin

    OpenAIRE

    Filippova, Darya; Patro, Rob; Duggal, Geet; Kingsford, Carl

    2013-01-01

    Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across va...

  10. Titration and hysteresis in epigenetic chromatin silencing

    International Nuclear Information System (INIS)

    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. 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.

  12. 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.

  13. PTEN Interacts with Histone H1 and Controls Chromatin Condensation

    Directory of Open Access Journals (Sweden)

    Zhu Hong Chen

    2014-09-01

    Full Text Available Chromatin organization and dynamics are integral to global gene transcription. Histone modification influences chromatin status and gene expression. PTEN plays multiple roles in tumor suppression, development, and metabolism. Here, we report on the interplay of PTEN, histone H1, and chromatin. We show that loss of PTEN leads to dissociation of histone H1 from chromatin and decondensation of chromatin. PTEN deletion also results in elevation of histone H4 acetylation at lysine 16, an epigenetic marker for chromatin activation. We found that PTEN and histone H1 physically interact through their C-terminal domains. Disruption of the PTEN C terminus promotes the chromatin association of MOF acetyltransferase and induces H4K16 acetylation. Hyperacetylation of H4K16 impairs the association of PTEN with histone H1, which constitutes regulatory feedback that may reduce chromatin stability. Our results demonstrate that PTEN controls chromatin condensation, thus influencing gene expression. We propose that PTEN regulates global gene transcription profiling through histones and chromatin remodeling.

  14. Inverstigation of chromatin folding patterns by atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    ZHANGYi; OUYANGZhenqian; 等

    1999-01-01

    The chromatin folding patterns in air and liquid were studied by atomic force microscopy(AFM),A gentle water-air interface method was adopted to spread chromatin from interphase nucleus of chicken erythrocyte.The chromatin was absorbed on APS-mica surface and studied with AFM,Beads-on a-string were observed and many higher-order structrues such as superbeads with dimensions 40-60nm in diameter and 4-7nm in height were found to string together to make chromation fibers.When sample spreading and absorbing time were shortened.higher-order chromatin fibers with 60-120nm in width were observed in air as well as under water environment.These chromatin structures may reflect chromatin folding patterns in the living cells.

  15. Prevalence of X-chromatin in Jordanian women

    International Nuclear Information System (INIS)

    This study was conducted to evaluate the distribution of X-chromatin among Jordanian women at different age groups. Results will be compared with other studies for possible racial and environmental effects on X-chromatin distribution. Blood samples were drawn from all women subjected to this study by finger prick and stained with Wright's stain. X-chromatin positive polymorphonuclear cells were counted and corrected for percentage. Samples were taken during the late 2002 and early 2003 from healthy women attending routine checkup in health centers in Northern Jordan. The number of X-chromatin was highest in the 50 and above years age group. The number of X-chromatin was 14-18% in other age groups. These results were in accordance with other studies. It seems that racial and environmental factors are ineffective on distribution of X-chromatin in Jordanian women. These data could be used as as reference for further studies. (author)

  16. Role of histone modifications in defining chromatin structure and function.

    Science.gov (United States)

    Gelato, Kathy A; Fischle, Wolfgang

    2008-04-01

    Chromosomes in eukaryotic cell nuclei are not uniformly organized, but rather contain distinct chromatin elements, with each state having a defined biochemical structure and biological function. These are recognizable by their distinct architectures and molecular components, which can change in response to cellular stimuli or metabolic requirements. Chromatin elements are characterized by the fundamental histone and DNA components, as well as other associated non-histone proteins and factors. Post-translational modifications of histone proteins in particular often correlate with a specific chromatin structure and function. Patterns of histone modifications are implicated as having a role in directing the level of chromatin compaction, as well as playing roles in multiple functional pathways directing the readout of distinct regions of the genome. We review the properties of various chromatin elements and the apparent links of histone modifications with chromatin organization and functional output. PMID:18225984

  17. Long Noncoding RNAs, Chromatin, and Development

    Directory of Open Access Journals (Sweden)

    Daniel P. Caley

    2010-01-01

    Full Text Available The way in which the genome of a multicellular organism can orchestrate the differentiation of trillions of cells and many organs, all from a single fertilized egg, is the subject of intense study. Different cell types can be defined by the networks of genes they express. This differential expression is regulated at the epigenetic level by chromatin modifications, such as DNA and histone methylation, which interact with structural and enzymatic proteins, resulting in the activation or silencing of any given gene. While detailed mechanisms are emerging on the role of different chromatin modifications and how these functions are effected at the molecular level, it is still unclear how their deposition across the epigenomic landscape is regulated in different cells. A raft of recent evidence is accumulating that implicates long noncoding RNAs (lncRNAs in these processes. Most genomes studied to date undergo widespread transcription, the majority of which is not translated into proteins. In this review, we will describe recent work suggesting that lncRNAs are more than transcriptional "noise", but instead play a functional role by acting as tethers and guides to bind proteins responsible for modifying chromatin and mediating their deposition at specific genomic locations. We suggest that lncRNAs are at the heart of developmental regulation, determining the epigenetic status and transcriptional network in any given cell type, and that they provide a means to integrate external differentiation cues with dynamic nuclear responses through the regulation of a metastable epigenome. Better characterization of the lncRNA-protein "interactome" may eventually lead to a new molecular toolkit, allowing researchers and clinicians to modulate the genome at the epigenetic level to treat conditions such as cancer.

  18. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    OpenAIRE

    Arifulin E. A.

    2015-01-01

    Aim. The ultrastructural aspect of replicating chromatin organization is a matter of dispute. Here, we have analyzed the ultrastructural organization of replication foci using prematurely condensed chromosomes (PCC). Methods. To investigate the ultrastructure of replicating chromatin, we have used correlative light and electron microscopy as well as immunogold staining. Results. Replication in PCC occurs in the gaps between condensed chromatin domains. Using correlative light and electron mic...

  19. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

    OpenAIRE

    Cieślik, Marcin; Bekiranov, Stefan

    2014-01-01

    Background Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is the most widely used method for characterizing the epigenetic states of chromatin on a genomic scale. With the recent availability of large genome-wide data sets, often comprising several epigenetic marks, novel approaches are required to explore functionally relevant interactions between histone modifications. Computational discovery of "chromatin states" defined by such combinatorial interactions enabled desc...

  20. Single-epitope recognition imaging of native chromatin

    OpenAIRE

    Wang Hongda; Dalal Yamini; Henikoff Steven; Lindsay Stuart

    2008-01-01

    Abstract Background Direct visualization of chromatin has the potential to provide important insights into epigenetic processes. In particular, atomic force microscopy (AFM) can visualize single nucleosomes under physiological ionic conditions. However, AFM has mostly been applied to chromatin that has been reconstituted in vitro, and its potential as a tool for the dissection of native nucleosomes has not been explored. Recently we applied AFM to native Drosophila chromatin containing the ce...

  1. Hydrogen peroxide mediates higher order chromatin degradation.

    Science.gov (United States)

    Bai, H; Konat, G W

    2003-01-01

    Although a large body of evidence supports a causative link between oxidative stress and neurodegeneration, the mechanisms are still elusive. We have recently demonstrated that hydrogen peroxide (H(2)O(2)), the major mediator of oxidative stress triggers higher order chromatin degradation (HOCD), i.e. excision of chromatin loops at the matrix attachment regions (MARs). The present study was designed to determine the specificity of H(2)O(2) in respect to HOCD induction. Rat glioma C6 cells were exposed to H(2)O(2) and other oxidants, and the fragmentation of genomic DNA was assessed by field inversion gel electrophoresis (FIGE). S1 digestion before FIGE was used to detect single strand fragmentation. The exposure of C6 cells to H(2)O(2) induced a rapid and extensive HOCD. Thus, within 30 min, total chromatin was single strandedly digested into 50 kb fragments. Evident HOCD was elicited by H(2)O(2) at concentrations as low as 5 micro M. HOCD was mostly reversible during 4-8h following the removal of H(2)O(2) from the medium indicating an efficient relegation of the chromatin fragments. No HOCD was induced by H(2)O(2) in isolated nuclei indicating that HOCD-endonuclease is activated indirectly by cytoplasmic signal pathways triggered by H(2)O(2). The exposure of cells to a synthetic peroxide, i.e. tert-butyrylhydroperoxide (tBH) also induced HOCD, but to a lesser extent than H(2)O(2). Contrary to the peroxides, the exposure of cells to equitoxic concentration of hypochlorite and spermine NONOate, a nitric oxide generator, failed to induce rapid HOCD. These results indicate that rapid HOCD is not a result of oxidative stress per se, but is rather triggered by signaling cascades initiated specifically by H(2)O(2). Furthermore, the rapid and extensive HOCD was observed in several rat and human cell lines challenged with H(2)O(2), indicating that the process is not restricted to glial cells, but rather represents a general response of cells to H(2)O(2). PMID:12421592

  2. Evidence for the internucleosomal breakage of chromatin in rat thymocytes irradiated in vitro

    International Nuclear Information System (INIS)

    Low molecular-weight (free) DNA increases in lymphatic cells in association with radiation-induced interphase death. In this report, the size of the free DNA from rat thymocytes irradiated in vitro with 1-kR x rays was analyzed by agarose gel electrophoresis and compared with that of the DNA fragments extracted from micrococcal nuclease-digested thymocyte nuclei and with that of HaeIII-digested phi X-174 RF DNA. Results demonstrated clearly that the free DNA consisted of a series of discretely sized DNA fragments with lengths that were integral multiples of a nucleosomal DNA (180 base pairs), suggesting that internucleosomal chromatin breaks occurred in rat thymocytes after in vitro irradiation. Additional evidence was obtained from an electron microscopic observation on the breakdown of chromatin strands into particle form in the irradiated cells

  3. Polymer-assisted sol–gel process for the preparation of photostimulable core/shell structured SiO2/Zn2SiO4:Mn2+ particles

    International Nuclear Information System (INIS)

    In this study the SiO2/Zn2SiO4:Mn2+ core/shell particles with diameters of about 200 nm were prepared by a modified Pechini sol–gel method. The focus of the study was on the investigation of the shell formation mechanism and on the determination of key synthesis parameters. A precise adjustment of the particle structure is crucial for optical properties. The influence of the organic additives, the pH value of the coating solution and the annealing temperature on the properties of the resulting particles was evaluated. The roles of the influential factors were studied in detail using transmission electron microscopy, X-ray diffraction, Fourier transform infrared and nuclear magnetic resonance spectroscopy. The most homogeneous coating was achieved by employing polyethylene glycol (PEG) at a pH value of 1. The application of citric acid in combination with PEG caused the formation of inhomogeneous shells. The particles showed photoluminescence and photostimulable luminescence of increasing intensities with rising annealing temperatures (1100 °C). These core/shell structured particles have the potential to serve as luminescent labeling agents for biomedical applications. - Highlights: • Core/shell structured SiO2/Zn2SiO4:Mn2+ particles were prepared via a sol–gel process. • Utilizing PEG at pH 1 resulted in the most homogeneous coating. • Interactions involved in the coating process were identified and analyzed. • Particles showed phosphorescence and photostimulated luminescence. • Luminescence intensities were strongly dependent on the annealing temperature

  4. Polymer-assisted sol–gel process for the preparation of photostimulable core/shell structured SiO{sub 2}/Zn{sub 2}SiO{sub 4}:Mn{sup 2+} particles

    Energy Technology Data Exchange (ETDEWEB)

    Milde, Moritz, E-mail: moritz.milde@isc.fraunhofer.de [Fraunhofer Institute for Silicate Research, Neunerplatz 2, 97082 Wuerzburg (Germany); Department of Chemical Technology of Materials Synthesis, University of Wuerzburg, Roentgenring 11, 97070 Wuerzburg (Germany); Dembski, Sofia, E-mail: sofia.dembski@isc.fraunhofer.de [Fraunhofer Institute for Silicate Research, Neunerplatz 2, 97082 Wuerzburg (Germany); Osvet, Andres, E-mail: andres.osvet@ww.uni-erlangen.de [Chair WW6 Materials for Electronics and Energy Technology (i-MEET), University of Erlangen-Nuremberg, Martensstraße 7, 91058 Erlangen (Germany); Batentschuk, Miroslaw, E-mail: mirobat@ww.uni-erlangen.de [Chair WW6 Materials for Electronics and Energy Technology (i-MEET), University of Erlangen-Nuremberg, Martensstraße 7, 91058 Erlangen (Germany); Winnacker, Albrecht, E-mail: albrecht.winnacker@ww.uni-erlangen.de [Chair WW6 Materials for Electronics and Energy Technology (i-MEET), University of Erlangen-Nuremberg, Martensstraße 7, 91058 Erlangen (Germany); Sextl, Gerhard, E-mail: gerhard.sextl@isc.fraunhofer.de [Department of Chemical Technology of Materials Synthesis, University of Wuerzburg, Roentgenring 11, 97070 Wuerzburg (Germany)

    2014-12-15

    In this study the SiO{sub 2}/Zn{sub 2}SiO{sub 4}:Mn{sup 2+} core/shell particles with diameters of about 200 nm were prepared by a modified Pechini sol–gel method. The focus of the study was on the investigation of the shell formation mechanism and on the determination of key synthesis parameters. A precise adjustment of the particle structure is crucial for optical properties. The influence of the organic additives, the pH value of the coating solution and the annealing temperature on the properties of the resulting particles was evaluated. The roles of the influential factors were studied in detail using transmission electron microscopy, X-ray diffraction, Fourier transform infrared and nuclear magnetic resonance spectroscopy. The most homogeneous coating was achieved by employing polyethylene glycol (PEG) at a pH value of 1. The application of citric acid in combination with PEG caused the formation of inhomogeneous shells. The particles showed photoluminescence and photostimulable luminescence of increasing intensities with rising annealing temperatures (1100 °C). These core/shell structured particles have the potential to serve as luminescent labeling agents for biomedical applications. - Highlights: • Core/shell structured SiO{sub 2}/Zn{sub 2}SiO{sub 4}:Mn{sup 2+} particles were prepared via a sol–gel process. • Utilizing PEG at pH 1 resulted in the most homogeneous coating. • Interactions involved in the coating process were identified and analyzed. • Particles showed phosphorescence and photostimulated luminescence. • Luminescence intensities were strongly dependent on the annealing temperature.

  5. Phase I trial of an alhydrogel adjuvanted hepatitis B core virus-like particle containing epitopes of Plasmodium falciparum circumsporozoite protein.

    Directory of Open Access Journals (Sweden)

    Aric L Gregson

    Full Text Available UNLABELLED: The objectives of this non-randomized, non-blinded, dose-escalating Phase I clinical trial were to assess the safety, reactogenicity and immunogenicity of ICC-1132 formulated with Alhydrogel (aluminum hydroxide in 51 healthy, malaria-naive adults aged 18 to 45 years. ICC-1132 (Malariavax is a recombinant, virus-like particle malaria vaccine comprised of hepatitis core antigen engineered to express the central repeat regions from Plasmodium falciparum circumsporozoite protein containing an immunodominant B [(NANP(3] epitope, an HLA-restricted CD4 (NANPNVDPNANP epitope and a universal T cell epitope (T* (amino acids 326-345, NF54 isolate. We assessed an Alhydrogel (aluminum hydroxide-adjuvanted vaccine formulation at three ICC-1132 dose levels, each injected intramuscularly (1.0 mL on study days 0, 56 and 168. A saline vaccine formulation was found to be unstable after prolonged storage and this formulation was subsequently removed from the study. Thirty-two volunteers were followed for one year. Local and systemic adverse clinical events were measured and immune responses to P. falciparum and hepatitis B virus core antigens were determined utilizing the following assays: IgG and IgM ELISA, indirect immunofluorescence against P. falciparum sporozoites, circumsporozoite precipitin (CSP and transgenic sporozoite neutralization assays. Cellular responses were measured by proliferation and IL-2 assays. Local and systemic reactions were similarly mild and well tolerated between dose cohorts. Depending on the ICC-1132 vaccine concentration, 95 to 100% of volunteers developed antibody responses to the ICC-1132 immunogen and HBc after two injections; however, only 29-75% and 29-63% of volunteers, respectively, developed malaria-specific responses measured by the malaria repeat synthetic peptide ELISA and IFA; 2 of 8 volunteers had positive reactions in the CSP assay. Maximal transgenic sporozoite neutralization assay inhibition was 54%. Forty

  6. Application of the Particle Swarm Optimization (PSO) technique to the thermal-hydraulics project of a PWR reactor core in reduced scale

    International Nuclear Information System (INIS)

    The reduced scale models design have been employed by engineers from several different industries fields such as offshore, spatial, oil extraction, nuclear industries and others. Reduced scale models are used in experiments because they are economically attractive than its own prototype (real scale) because in many cases they are cheaper than a real scale one and most of time they are also easier to build providing a way to lead the real scale design allowing indirect investigations and analysis to the real scale system (prototype). A reduced scale model (or experiment) must be able to represent all physical phenomena that occurs and further will do in the real scale one under operational conditions, e.g., in this case the reduced scale model is called similar. There are some different methods to design a reduced scale model and from those two are basic: the empiric method based on the expert's skill to determine which physical measures are relevant to the desired model; and the differential equation method that is based on a mathematical description of the prototype (real scale system) to model. Applying a mathematical technique to the differential equation that describes the prototype then highlighting the relevant physical measures so the reduced scale model design problem may be treated as an optimization problem. Many optimization techniques as Genetic Algorithm (GA), for example, have been developed to solve this class of problems and have also been applied to the reduced scale model design problem as well. In this work, Particle Swarm Optimization (PSO) technique is investigated as an alternative optimization tool for such problem. In this investigation a computational approach, based on particle swarm optimization technique (PSO), is used to perform a reduced scale two loop Pressurized Water Reactor (PWR) core, considering 100% of nominal power operation on a forced flow cooling circulation and non-accidental operating conditions. A performance comparison

  7. The Hepatitis B Virus Core Variants that Expose Foreign C-Terminal Insertions on the Outer Surface of Virus-Like Particles.

    Science.gov (United States)

    Dishlers, Andris; Skrastina, Dace; Renhofa, Regina; Petrovskis, Ivars; Ose, Velta; Lieknina, Ilva; Jansons, Juris; Pumpens, Paul; Sominskaya, Irina

    2015-12-01

    The major immunodominant region (MIR) and N-terminus of the hepatitis B virus (HBV) core (HBc) protein were used to expose foreign insertions on the outer surface of HBc virus-like particles (VLPs). The additions to the HBc positively charged arginine-rich C-terminal (CT) domain are usually not exposed on the VLP surface. Here, we constructed a set of recombinant HBcG vectors in which CT arginine stretches were substituted by glycine residues. In contrast to natural HBc VLPs and recombinant HBc VLP variants carrying native CT domain, the HBcG VLPs demonstrated a lowered capability to pack bacterial RNA during expression in Escherichia coli cells. The C-terminal addition of a model foreign epitope from the HBV preS1 sequence to the HBcG vectors resulted in the exposure of the inserted epitope on the VLP surface, whereas the same preS1 sequences added to the native CT of the natural HBc protein remained buried within the HBc VLPs. Based on the immunisation of mice, the preS1 epitope added to the HBcG vectors as a part of preS1(20-47) and preS1phil sequences demonstrated remarkable immunogenicity. The same epitope added to the original C-terminus of the HBc protein did not induce a notable level of anti-preS1 antibodies. HBcG vectors may contribute to the further development of versatile HBc VLP-based vaccine and gene therapy applications. PMID:26446016

  8. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

    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...

  9. Rapid genome-scale mapping of chromatin accessibility in tissue

    DEFF Research Database (Denmark)

    Grøntved, Lars; Bandle, Russell; John, Sam;

    2012-01-01

    BACKGROUND: The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on la...

  10. 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....

  11. Analysis of chromatin integrity and DNA damage of buffalo spermatozoa.

    Science.gov (United States)

    Mahmoud, K Gh M; El-Sokary, A A E; Abdel-Ghaffar, A E; Abou El-Roos, M E A; Ahmed, Y F

    2015-01-01

    This study was conducted to determine chromatin integrity and DNA damage by DNA electrophoresis and comet assays of buffalo fresh and frozen semen. Semen samples were collected from four buffalo bulls and evaluated after freezing for semen motility, viability, sperm abnormalities, chromatin integrity and DNA damage. A significant variation was found in semen parameters after thawing. Highly significant differences (Partificial insemination. PMID:27175169

  12. Lessons from Anaplasma phagocytophilum: Chromatin Remodeling by Bacterial Effectors

    OpenAIRE

    Rennoll-Bankert, Kristen E.; Dumler, J. Stephen

    2012-01-01

    Bacterial pathogens can alter global host gene expression via histone modifications and chromatin remodeling in order to subvert host responses, including those involved with innate immunity, allowing for bacterial survival. Shigella flexneri, Listeria monocytogenes, Chlamydia trachomatis, and Anaplasma phagocytophilum express effector proteins that modify host histones and chromatin structure. A. phagocytophilum modulates granulocyte respiratory burst in part by dampening transcription of se...

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

    DEFF Research Database (Denmark)

    Hendriks, Ivo A; Treffers, Louise W; Verlaan-de Vries, Matty; Olsen, Jesper V; Vertegaal, Alfred C O

    2015-01-01

    identified 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...

  14. 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.

  15. Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation.

    Directory of Open Access Journals (Sweden)

    Erica Larschan

    Full Text Available Sex chromosome dosage compensation in Drosophila provides a model for understanding how chromatin organization can modulate coordinate gene regulation. Male Drosophila increase the transcript levels of genes on the single male X approximately two-fold to equal the gene expression in females, which have two X-chromosomes. Dosage compensation is mediated by the Male-Specific Lethal (MSL histone acetyltransferase complex. Five core components of the MSL complex were identified by genetic screens for genes that are specifically required for male viability and are dispensable for females. However, because dosage compensation must interface with the general transcriptional machinery, it is likely that identifying additional regulators that are not strictly male-specific will be key to understanding the process at a mechanistic level. Such regulators would not have been recovered from previous male-specific lethal screening strategies. Therefore, we have performed a cell culture-based, genome-wide RNAi screen to search for factors required for MSL targeting or function. Here we focus on the discovery of proteins that function to promote MSL complex recruitment to "chromatin entry sites," which are proposed to be the initial sites of MSL targeting. We find that components of the NSL (Non-specific lethal complex, and a previously unstudied zinc-finger protein, facilitate MSL targeting and display a striking enrichment at MSL entry sites. Identification of these factors provides new insight into how MSL complex establishes the specialized hyperactive chromatin required for dosage compensation in Drosophila.

  16. Phosphorylation of histone variant regions in chromatin: unlocking the linker?

    Science.gov (United States)

    Green, G R

    2001-01-01

    Histone variants illuminate the behavior of chromatin through their unique structures and patterns of postsynthetic modification. This review examines the literature on heteromorphous histone structures in chromatin, structures that are primary targets for histone kinases and phosphatases in vivo. Special attention is paid to certain well-studied experimental systems: mammalian culture cells, chicken erythrocytes, sea urchin sperm, wheat sprouts, Tetrahymena, and budding yeast. A common theme emerges from these studies. Specialized, highly basic structures in histone variants promote chromatin condensation in a variety of developmental situations. Before, and sometimes after condensed chromatin is formed, the chromatin is rendered soluble by phosphorylation of the heteromorphous regions, preventing their interaction with linker DNA. A simple structural model accounting for histone variation and phosphorylation is presented. PMID:11467741

  17. Genome maintenance in the context of 4D chromatin condensation.

    Science.gov (United States)

    Yu, Sonia; Yang, Fan; Shen, Wen H

    2016-08-01

    The eukaryotic genome is packaged in the three-dimensional nuclear space by forming loops, domains, and compartments in a hierarchical manner. However, when duplicated genomes prepare for segregation, mitotic cells eliminate topologically associating domains and abandon the compartmentalized structure. Alongside chromatin architecture reorganization during the transition from interphase to mitosis, cells halt most DNA-templated processes such as transcription and repair. The intrinsically condensed chromatin serves as a sophisticated signaling module subjected to selective relaxation for programmed genomic activities. To understand the elaborate genome-epigenome interplay during cell cycle progression, the steady three-dimensional genome requires a time scale to form a dynamic four-dimensional and a more comprehensive portrait. In this review, we will dissect the functions of critical chromatin architectural components in constructing and maintaining an orderly packaged chromatin environment. We will also highlight the importance of the spatially and temporally conscious orchestration of chromatin remodeling to ensure high-fidelity genetic transmission. PMID:27098512

  18. Data on the kinetics of in vitro assembled chromatin.

    Science.gov (United States)

    Völker-Albert, Moritz Carl; Pusch, Miriam Caroline; Schmidt, Andreas; Imhof, Axel

    2016-09-01

    Here, we use LC-MS/MS and SWATH-MS to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos (DREX). This system allows easy manipulation of distinct aspects of chromatin assembly such as post-translational histone modifications, the levels of histone chaperones and the concentration of distinct DNA binding factors. In total, 480 proteins have been quantified as chromatin enriched factors and their binding kinetics have been monitored in the time course of 15 min, 1 h and 4 h of chromatin assembly. The data accompanying the manuscript on this approach, Völker-Albert et al., 2016 "A quantitative proteomic analysis of in vitro assembled chromatin" [1], has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier submission number PRIDE: PXD002537 and PRIDE: PXD003445. PMID:27331114

  19. On the mechanochemical machinery underlying chromatin remodeling

    Science.gov (United States)

    Yusufaly, Tahir I.

    This dissertation discuss two recent efforts, via a unique combination of structural bioinformatics and density functional theory, to unravel some of the details concerning how molecular machinery within the eukaryotic cell nucleus controls chromatin architecture. The first, a study of the 5-methylation of cytosine in 5'-CG-3' : 5'-CG-3' base-pair steps, reveals that the methyl groups roughen the local elastic energy landscape of the DNA. This enhances the probability of the canonical B-DNA structure transitioning into the undertwisted A-like and overtwisted C-like forms seen in nucleosomes, or looped segments of DNA bound to histones. The second part focuses on the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. The arginine residues are ob- served to apply a tunable mechanical load to the backbone, enabling precision-controlled activation of DNA deformations.

  20. Chromatin structure near transcriptionally active genes

    International Nuclear Information System (INIS)

    Hypersensitive domains are the most prominent features of transcriptionally active chromatin. In the case of the β/sup A/-globin gene, it seems likely that two or more protein factors are capable of binding to the DNA so tightly that the nucleosome is prevented from binding. We have shown that nucleosomes, once bound in the assembly process in vitro, cannot be displaced. The interaction of the 5S gene transcription factor TFIIIA with its target DNA also is blocked by histones, and it has been suggested that the activation of the gene must occur during replication, before histones are reassembled on the DNA. We suppose that a similar mechanism may govern the binding of the hypersensitivity factors. It should be noted that nucleosomes are excluded not only from the sites to which the factors bind, but also from the regions between the two domains and at either side. 12 refs., 6 figs

  1. Histone modifications and lamin A regulate chromatin protein dynamics in early embryonic stem cell differentiation

    OpenAIRE

    Melcer, Shai; Hezroni, Hadas; Rand, Eyal; Nissim-Rafinia, Malka; Skoultchi, Arthur; Stewart, Colin L.; Bustin, Michael; Meshorer, Eran

    2012-01-01

    Embryonic stem cells are characterized by unique epigenetic features including decondensed chromatin and hyperdynamic association of chromatin proteins with chromatin. Here we investigate the potential mechanisms that regulate chromatin plasticity in embryonic stem cells. Using epigenetic drugs and mutant embryonic stem cells lacking various chromatin proteins, we find that histone acetylation, G9a-mediated histone H3 lysine 9 (H3K9) methylation and lamin A expression, all affect chromatin pr...

  2. Development of a candidate influenza vaccine based on virus-like particles displaying influenza M2e peptide into the immunodominant region of hepatitis B core antigen: Broad protective efficacy of particles carrying four copies of M2e.

    Science.gov (United States)

    Tsybalova, Liudmila M; Stepanova, Liudmila A; Kuprianov, Victor V; Blokhina, Elena A; Potapchuk, Marina V; Korotkov, Alexander V; Gorshkov, Andrey N; Kasyanenko, Marina A; Ravin, Nikolai V; Kiselev, Oleg I

    2015-06-26

    A long-term objective when designing influenza vaccines is to create one with broad cross-reactivity that will provide effective control over influenza, no matter which strain has caused the disease. Here we summarize the results from an investigation into the immunogenic and protective capacities inherent in variations of a recombinant protein, HBc/4M2e. This protein contains four copies of the ectodomain from the influenza virus protein M2 (M2e) fused within the immunodominant loop of the hepatitis B virus core antigen (HBc). Variations of this basic design include preparations containing M2e from the consensus human influenza virus; the M2e from the highly pathogenic avian A/H5N1 virus and a combination of two copies from human and two copies from avian influenza viruses. Intramuscular delivery in mice with preparations containing four identical copies of M2e induced high IgG titers in blood sera and bronchoalveolar lavages. It also provoked the formation of memory T-cells and antibodies were retained in the blood sera for a significant period of time post immunization. Furthermore, these preparations prevented the death of 75-100% of animals, which were challenged with lethal doses of virus. This resulted in a 1.2-3.5 log10 decrease in viral replication within the lungs. Moreover, HBc particles carrying only "human" or "avian" M2e displayed cross-reactivity in relation to human (A/H1N1, A/H2N2 and A/H3N2) or A/H5N1 and A(H1N1)pdm09 viruses, respectively; however, with the particles carrying both "human" and "avian" M2e this effect was much weaker, especially in relation to influenza virus A/H5N1. It is apparent from this work that to quickly produce vaccine for a pandemic it would be necessary to have several variations of a recombinant protein, containing four copies of M2e (each one against a group of likely influenza virus strains) with these relevant constructs housed within a comprehensive collection Escherichia coli-producers and maintained ready for use

  3. 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

    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...

  4. The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms

    Directory of Open Access Journals (Sweden)

    Postberg Jan

    2010-08-01

    Full Text Available Abstract Background The phenotype of an organism is an outcome of both its genotype, encoding the primary sequence of proteins, and the developmental orchestration of gene expression. The substrate of gene expression in eukaryotes is the chromatin, whose fundamental units are nucleosomes composed of DNA wrapped around each two of the core histone types H2A, H2B, H3 and H4. Key regulatory steps involved in the determination of chromatin conformations are posttranslational modifications (PTM at histone tails as well as the assembly of histone variants into nucleosomal arrays. Although the mechanistic background is fragmentary understood, it appears that the chromatin signature of metazoan cell types is inheritable over generations. Even less understood is the conservation of epigenetic mechanisms among eukaryotes and their origins. Results In the light of recent progress in understanding the tree of eukaryotic life we discovered the origin of histone H3 by phylogenetic analyses of variants from all supergroups, which allowed the reconstruction of ancestral states. We found that H3 variants evolved frequently but independently within related species of almost all eukaryotic supergroups. Interestingly, we found all core histone types encoded in the genome of a basal dinoflagellate and H3 variants in two other species, although is was reported that dinoflagellate chromatin is not organized into nucleosomes. Most probably one or more animal/nuclearid H3.3-like variants gave rise to H3 variants of all opisthokonts (animals, choanozoa, fungi, nuclearids, Amoebozoa. H3.2 and H3.1 as well as H3.1t are derivatives of H3.3, whereas H3.2 evolved already in early branching animals, such as Trichoplax. H3.1 and H3.1t are probably restricted to mammals. We deduced a model for protoH3 of the last eukaryotic common ancestor (LECA confirming a remarkable degree of sequence conservation in comparison to canonical human H3.1. We found evidence that multiple PTMs are

  5. Three-Dimensional, Live-Cell Imaging of Chromatin Dynamics in Plant Nuclei Using Chromatin Tagging Systems.

    Science.gov (United States)

    Hirakawa, Takeshi; Matsunaga, Sachihiro

    2016-01-01

    In plants, chromatin dynamics spatiotemporally change in response to various environmental stimuli. However, little is known about chromatin dynamics in the nuclei of plants. Here, we introduce a three-dimensional, live-cell imaging method that can monitor chromatin dynamics in nuclei via a chromatin tagging system that can visualize specific genomic loci in living plant cells. The chromatin tagging system is based on a bacterial operator/repressor system in which the repressor is fused to fluorescent proteins. A recent refinement of promoters for the system solved the problem of gene silencing and abnormal pairing frequencies between operators. Using this system, we can detect the spatiotemporal dynamics of two homologous loci as two fluorescent signals within a nucleus and monitor the distance between homologous loci. These live-cell imaging methods will provide new insights into genome organization, development processes, and subnuclear responses to environmental stimuli in plants. PMID:27557696

  6. Minireview: role of kinases and chromatin remodeling in progesterone signaling to chromatin.

    Science.gov (United States)

    Vicent, Guillermo P; Nacht, A Silvina; Zaurín, Roser; Ballaré, Cecilia; Clausell, Jaime; Beato, Miguel

    2010-11-01

    Steroid hormones regulate gene expression by interaction of their receptors with hormone-responsive elements on DNA or with other transcription factors, but they can also activate cytoplasmic signaling cascades. Rapid activation of Erk by progestins via an interaction of the progesterone receptor (PR) with the estrogen receptor is critical for transcriptional activation of the mouse mammary tumor virus (MMTV) promoter and other progesterone target genes. Erk activation leads to the phosphorylation of PR, activation of mitogen- and stress-activated protein kinase 1, and the recruitment of a complex of the three activated proteins and of P300/CBP-associated factor (PCAF) to a single nucleosome, resulting in the phosphoacetylation of histone H3 and the displacement of heterochromatin protein 1γ. Hormone-dependent gene expression requires ATP-dependent chromatin remodeling complexes. Two switch/sucrose nonfermentable-like complexes, Brahma-related gene 1-associated factor (BAF) and polybromo-BAF are present in breast cancer cells, but only BAF is recruited to the MMTV promoter and cooperates with PCAF during activation of hormone-responsive promoters. PCAF acetylates histone H3 at K14, an epigenetic mark recognized by BAF subunits, thus anchoring the complex to chromatin. BAF catalyzes localized displacement of histones H2A and H2B, facilitating access of nuclear factor 1 and additional PR complexes to the hidden hormone-responsive elements on the MMTV promoter. The linker histone H1 is a structural component of chromatin generally regarded as a general repressor of transcription. However, it contributes to a better regulation of the MMTV promoter by favoring a more homogeneous nucleosome positioning, thus reducing basal transcription and actually enhancing hormone induced transcription. During transcriptional activation, H1 is phosphorylated and displaced from the promoter. The kinase cyclin-dependent kinase 2 is activated after progesterone treatment and could

  7. Characteristics of thymine dimer excision from xeroderma pigmentosum chromatin

    International Nuclear Information System (INIS)

    We investigated thymine dimer excision from xeroderma pigmentosum (XP) chromatin in the cell-free reconstruction system. The normal-cell extract performed specific dimer excision from native chromatin and DNA isolated from 100 J/m2-irradiated cells. Such an excision in vitro was rapid and required high concentrations of extract. The extracts of XP group A, C and G cells were unable to excise from their own native-chromatin, but capable of excising from chromatin deprived of loosely bound nonhistone proteins with 0.35 M NaCl, as were from purified DNA. Thus, group A, C and G cells are most likely to be defective in the specific XP factors facilitating the excising activity under multicomponent regulation at the chromatin level. Further, either of group A, C and G extracts successfully complemented the native chromatin of the alternative groups. Uniquely, the XP group D extract excised dimers from native chromatin in the normal fashion under the condition. These results suggest that XP group A, C, D and G cells examined may not be defective in the dimer specific endonuclease and exonuclease per se. 19 references, 3 figures, 2 tables

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Timsy Uppal

    2015-01-01

    Full Text Available 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. Chromatinization of the KSHV Genome During the KSHV Life Cycle

    International Nuclear Information System (INIS)

    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

  12. CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

    Science.gov (United States)

    Handoko, Lusy; Xu, Han; Li, Guoliang; Ngan, Chew Yee; Chew, Elaine; Schnapp, Marie; Lee, Charlie Wah Heng; Ye, Chaopeng; Ping, Joanne Lim Hui; Mulawadi, Fabianus; Wong, Eleanor; Sheng, Jianpeng; Zhang, Yubo; Poh, Thompson; Chan, Chee Seng; Kunarso, Galih; Shahab, Atif; Bourque, Guillaume; Cacheux-Rataboul, Valere; Sung, Wing-Kin; Ruan, Yijun; Wei, Chia-Lin

    2011-01-01

    Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. Yet, little is known about CTCF-associated higher order chromatin structures at a global scale. Here, we applied Chromatin Interaction Analysis by Paired-End-Tag sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, 1,480 cis and 336 trans interacting loci were identified with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive crosstalk between promoters and regulatory elements. This highly complex nuclear organization offers insights towards the unifying principles governing genome plasticity and function. PMID:21685913

  13. 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.

  14. 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.

  15. ATM alters the otherwise robust chromatin mobility at sites of DNA double-strand breaks (DSBs in human cells.

    Directory of Open Access Journals (Sweden)

    Annabelle Becker

    Full Text Available Ionizing radiation induces DNA double strand breaks (DSBs which can lead to the formation of chromosome rearrangements through error prone repair. In mammalian cells the positional stability of chromatin contributes to the maintenance of genome integrity. DSBs exhibit only a small, submicron scale diffusive mobility, but a slight increase in the mobility of chromatin domains by the induction of DSBs might influence repair fidelity and the formation of translocations. The radiation-induced local DNA decondensation in the vicinity of DSBs is one factor potentially enhancing the mobility of DSB-containing chromatin domains. Therefore in this study we focus on the influence of different chromatin modifying proteins, known to be activated by the DNA damage response, on the mobility of DSBs. IRIF (ionizing radiation induced foci in U2OS cells stably expressing 53BP1-GFP were used as a surrogate marker of DSBs. Low angle charged particle irradiation, known to trigger a pronounced DNA decondensation, was used for the defined induction of linear tracks of IRIF. Our results show that movement of IRIF is independent of the investigated chromatin modifying proteins like ACF1 or PARP1 and PARG. Also depletion of proteins that tether DNA strands like MRE11 and cohesin did not alter IRIF dynamics significantly. Inhibition of ATM, a key component of DNA damage response signaling, resulted in a pronounced confinement of DSB mobility, which might be attributed to a diminished radiation induced decondensation. This confinement following ATM inhibition was confirmed using X-rays, proving that this effect is not restricted to densely ionizing radiation. In conclusion, repair sites of DSBs exhibit a limited mobility on a small spatial scale that is mainly unaffected by depletion of single remodeling or DNA tethering proteins. However, it relies on functional ATM kinase which is considered to influence the chromatin structure after irradiation.

  16. Nucleosome positioning and composition modulate in silico chromatin flexibility

    Science.gov (United States)

    Clauvelin, N.; Lo, P.; Kulaeva, O. I.; Nizovtseva, E. V.; Diaz-Montes, J.; Zola, J.; Parashar, M.; Studitsky, V. M.; Olson, W. K.

    2015-02-01

    The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes—the familiar assemblies of ˜150 DNA base pairs and eight histone proteins—found on chromatin fibers. Here we introduce a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs. We explore the effects of nucleosome positioning and the presence or absence of cationic N-terminal histone tails on the ‘local’ inter-nucleosomal interactions and the global deformations of the simulated chains. The correspondence between the predicted and observed effects of nucleosome composition and numbers on the long-range communication between the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We also extract effective nucleosome-nucleosome potentials from the simulations and implement the potentials in a larger-scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable effect of nucleosome spacing on chromatin flexibility, with small changes in DNA linker length significantly altering the interactions of nucleosomes and the dimensions of the fiber as a whole. In addition, we find that these changes in nucleosome positioning influence the statistical properties of long chromatin constructs. That is, simulated chromatin fibers with the same number of nucleosomes exhibit polymeric behaviors ranging from Gaussian to worm-like, depending upon nucleosome spacing. These findings suggest that the physical and mechanical properties of chromatin can span a wide range of behaviors, depending on nucleosome

  17. Interaction and conformational changes of chromatin with divalent ions.

    OpenAIRE

    Borochov, N; Ausio, J; Eisenberg, H

    1984-01-01

    We have investigated the interaction of divalent ions with chromatin towards a closer understanding of the role of metal ions in the cell nucleus. The first row transition metal ion chlorides MnCl2, CoCl2, NiCl2 and CuCl2 lead to precipitation of chicken erythrocyte chromatin at a significantly lower concentration than the alkali earth metal chlorides MgCl2, CaCl2 and BaCl2. A similar distinction can be made for the compaction of chromatin to the "30 nm" solenoid higher order structure which ...

  18. Epigenetic regulation by BAF (mSWI/SNF) chromatin remodeling complexes is indispensable for embryonic development.

    Science.gov (United States)

    Nguyen, Huong; Sokpor, Godwin; Pham, Linh; Rosenbusch, Joachim; Stoykova, Anastassia; Staiger, Jochen F; Tuoc, Tran

    2016-05-18

    The multi-subunit chromatin-remodeling SWI/SNF (known as BAF for Brg/Brm-associated factor) complexes play essential roles in development. Studies have shown that the loss of individual BAF subunits often affects local chromatin structure and specific transcriptional programs. However, we do not fully understand how BAF complexes function in development because no animal mutant had been engineered to lack entire multi-subunit BAF complexes. Importantly, we recently reported that double conditional knock-out (dcKO) of the BAF155 and BAF170 core subunits in mice abolished the presence of the other BAF subunits in the developing cortex. The generated dcKO mutant provides a novel and powerful tool for investigating how entire BAF complexes affect cortical development. Using this model, we found that BAF complexes globally control the key heterochromatin marks, H3K27me2 and -3, by directly modulating the enzymatic activity of the H3K27 demethylases, Utx and Jmjd3. Here, we present further insights into how the scaffolding ability of the BAF155 and BAF170 core subunits maintains the stability of BAF complexes in the forebrain and throughout the embryo during development. Furthermore, we show that the loss of BAF complexes in the above-described model up-regulates H3K27me3 and impairs forebrain development and embryogenesis. These findings improve our understanding of epigenetic mechanisms and their modulation by the chromatin-remodeling SWI/SNF complexes that control embryonic development. PMID:26986003

  19. Lamin C and chromatin organization in Drosophila

    Indian Academy of Sciences (India)

    B. V. Gurudatta; L. S. Shashidhara; Veena K. Parnaik

    2010-04-01

    Drosophila lamin C (LamC) is a developmentally regulated component of the nuclear lamina. The lamC gene is situated in the fifth intron of the essential gene tout velu (ttv). We carried out genetic analysis of lamC during development. Phenotypic analyses of RNAi-mediated downregulation of lamC expression as well as targeted misexpression of lamin C suggest a role for lamC in cell survival. Of particular interest in the context of laminopathies is the caspase-dependent apoptosis induced by the overexpression of lamin C. Interestingly, misexpression of lamin C in the central nervous system, where it is not normally expressed, did not affect organization of the nuclear lamina. lamC mutant alleles suppressed position effect variegation normally displayed at near-centromeric and telomeric regions. Further, both downregulation and misexpression of lamin C affected the distribution of heterochromatin protein 1. Our results suggest that Drosophila lamC has a tissue-specific role during development and is required for chromatin organization.

  20. Centromeric chromatin and its dynamics in plants.

    Science.gov (United States)

    Lermontova, Inna; Sandmann, Michael; Mascher, Martin; Schmit, Anne-Catherine; Chabouté, Marie-Edith

    2015-07-01

    Centromeres are chromatin structures that are required for proper separation of chromosomes during mitosis and meiosis. The centromere is composed of centromeric DNA, often enriched in satellite repeats, and kinetochore complex proteins. To date, over 100 kinetochore components have been identified in various eukaryotes. Kinetochore assembly begins with incorporation of centromeric histone H3 variant CENH3 into centromeric nucleosomes. Protein components of the kinetochore are either present at centromeres throughout the cell cycle or localize to centromeres transiently, prior to attachment of microtubules to each kinetochore in prometaphase of mitotic cells. This is the case for the spindle assembly checkpoint (SAC) proteins in animal cells. The SAC complex ensures equal separation of chromosomes between daughter nuclei by preventing anaphase onset before metaphase is complete, i.e. the sister kinetochores of all chromosomes are attached to spindle fibers from opposite poles. In this review, we focus on the organization of centromeric DNA and the kinetochore assembly in plants. We summarize recent advances regarding loading of CENH3 into the centromere, and the subcellular localization and protein-protein interactions of Arabidopsis thaliana proteins involved in kinetochore assembly and function. We describe the transcriptional activity of corresponding genes based on in silico analysis of their promoters and cell cycle-dependent expression. Additionally, barley homologs of all selected A. thaliana proteins have been identified in silico, and their sequences and domain structures are presented. PMID:25976696

  1. 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.

  2. Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin.

    Science.gov (United States)

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

    2016-02-11

    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, but 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 accumulate DDR signals and become more accessible to telomere-associated proteins. 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

  3. 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.

  4. Does seminal fluid viscosity influence sperm chromatin integrity?

    Science.gov (United States)

    Gopalkrishnan, K; Padwal, V; Balaiah, D

    2000-01-01

    A retrospective study was undertaken to investigate whether viscosity alters sperm chromatin integrity. Semen samples were obtained from 269 men attending the infertility clinic. The viscosity was measured quantitatively by needle and syringe method and the viscosity ratio was calculated against distilled water. The chromatin integrity was evaluated by in vitro decondensation test using 1% SDS and 6 mM EDTA. According to the viscosity ratios the samples were divided into 2 groups: I, normal (ratio 9, n = 30) viscosity. Chromatin integrity was significantly lower in the group with higher viscosity. Significant decrease in sperm count and motility were seen in group II as compared to group I. Thus, hyperviscosity of seminal fluid alters the sperm chromatin integrity. PMID:11028927

  5. Nuclear envelope and chromatin, lock and key of genome integrity.

    Science.gov (United States)

    Gay, Sophie; Foiani, Marco

    2015-01-01

    More than as an inert separation between the inside and outside of the nucleus, the nuclear envelope (NE) constitutes an active toll, which controls the import and export of molecules, and also a hub for a diversity of genomic processes, such as transcription, DNA repair, and chromatin dynamics. Proteins localized at the inner surface of the NE (such as lamins, nuclear pore proteins, lamin-associated proteins) interact with chromatin in a dynamic manner, contributing to the establishment of topological domains. In this review, we address the complex interplay between chromatin and NE. We discuss the divergence of this cross talk during evolution and comment both on the current established models and the most recent findings. In particular, we focus our attention on how the NE cooperates with chromatin in protecting the genome integrity. PMID:26008788

  6. Influence of chromatin condensation on the number of direct DSB damages induced by ions studied using a Monte Carlo code

    International Nuclear Information System (INIS)

    The purpose of this work is to evaluate the influence of the chromatin condensation on the number of direct double-strand break (DSB) damages induced by ions. Two geometries of chromosome territories containing either condensed or de-condensed chromatin were implemented as biological targets in the Geant4 Monte Carlo simulation code and proton and alpha irradiation was simulated using the Geant4-DNA processes. A DBSCAN algorithm was used in order to detect energy deposition clusters that could give rise to single-strand breaks or DSBs on the DNA molecule. The results of this study show an increase in the number and complexity of DNA DSBs in condensed chromatin when compared with de-condensed chromatin. This work aims to evaluate the influence of the chromatin condensation in the number and complexity of direct DSB damages induced by proton and alpha irradiation. With the simulations of this study, the increase in the number and complexity of DSB-like clusters induced by ions in the heterochromatin when compared with euchromatin regions of the cell nucleus has been observed and quantified. These results suggest that condensed chromatin can be the location of more severe radiation-induced lesions, more difficult to repair, than de-condensed chromatin. On the other hand, it was also observed that, whatever the chromatin condensation, more possible damages are found after proton irradiation compared with alpha particles of the same LET. Nevertheless, as already remarked, this study concerns only the direct effect of ionising radiation that can be calculated from the results of the physical stage simulated with Geant4-DNA. To include indirect effects induced by radicals around the DNA molecule, the elements needed for simulating the chemical stage are being developed in the frame of the Geant4-DNA project(15, 16) and they are planned to be included in future work. With a complete calculation (direct + indirect damages) it would then be possible to estimate an energy

  7. Dynamic Hydrogen Production from Methanol/Water Photo-Splitting Using Core@Shell-Structured CuS@TiO2 Catalyst Wrapped by High Concentrated TiO2 Particles

    Directory of Open Access Journals (Sweden)

    Younghwan Im

    2013-01-01

    Full Text Available This study focused on the dynamic hydrogen production ability of a core@shell-structured CuS@TiO2 photocatalyst coated with a high concentration of TiO2 particles. The rectangular-shaped CuS particles, 100 nm in length and 60 nm in width, were surrounded by a high concentration of anatase TiO2 particles (>4~5 mol. The synthesized core@shell-structured CuS@TiO2 particles absorbed a long wavelength (a short band gap above 700 nm compared to that pure TiO2, which at approximately 300 nm, leading to easier electronic transitions, even at low energy. Hydrogen evolution from methanol/water photo-splitting over the core@shell-structured CuS@TiO2 photocatalyst increased approximately 10-fold compared to that over pure CuS. In particular, 1.9 mmol of hydrogen gas was produced after 10 hours when 0.5 g of 1CuS@4TiO2 was used at pH = 7. This level of production was increased to more than 4-fold at higher pH. Cyclic voltammetry and UV-visible absorption spectroscopy confirmed that the CuS in CuS@TiO2 strongly withdraws the excited electrons from the valence band in TiO2 because of the higher reduction potential than TiO2, resulting in a slower recombination rate between the electrons and holes and higher photoactivity.

  8. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in...

  9. The DNA intercalators ethidium bromide and propidium iodide also bind to core histones

    Directory of Open Access Journals (Sweden)

    Amrita Banerjee

    2014-01-01

    Full Text Available Eukaryotic DNA is compacted in the form of chromatin, in a complex with histones and other non-histone proteins. The intimate association of DNA and histones in chromatin raises the possibility that DNA-interactive small molecules may bind to chromatin-associated proteins such as histones. Employing biophysical and biochemical techniques we have characterized the interaction of a classical intercalator, ethidium bromide (EB and its structural analogue propidium iodide (PI with hierarchical genomic components: long chromatin, chromatosome, core octamer and chromosomal DNA. Our studies show that EB and PI affect both chromatin structure and function, inducing chromatin compaction and disruption of the integrity of the chromatosome. Calorimetric studies and fluorescence measurements of the ligands demonstrated and characterized the association of these ligands with core histones and the intact octamer in absence of DNA. The ligands affect acetylation of histone H3 at lysine 9 and acetylation of histone H4 at lysine 5 and lysine 8 ex vivo. PI alters the post-translational modifications to a greater extent than EB. This is the first report showing the dual binding (chromosomal DNA and core histones property of a classical intercalator, EB, and its longer analogue, PI, in the context of chromatin.

  10. Chromatin structure modulates DNA repair by photolyase in vivo.

    OpenAIRE

    Suter, B.; Livingstone-Zatchej, M; Thoma, F

    1997-01-01

    Yeast and many other organisms use nucleotide excision repair (NER) and photolyase in the presence of light (photoreactivation) to repair cyclobutane pyrimidine dimers (CPDs), a major class of DNA lesions generated by UV light. To study the role of photoreactivation at the chromatin level in vivo, we used yeast strains which contained minichromosomes (YRpTRURAP, YRpCS1) with well-characterized chromatin structures. The strains were either proficient (RAD1) or deficient (rad1 delta) in NER. In...

  11. Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

    Science.gov (United States)

    Hoffman, Michael M; Buske, Orion J; Wang, Jie; Weng, Zhiping; Bilmes, Jeff A; Noble, William Stafford

    2012-05-01

    We trained Segway, a dynamic Bayesian network method, simultaneously on chromatin data from multiple experiments, including positions of histone modifications, transcription-factor binding and open chromatin, all derived from a human chronic myeloid leukemia cell line. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, transcriptional regulator CTCF-binding regions and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/proj/segway/. PMID:22426492

  12. Higher order chromatin structure: bridging physics and biology

    OpenAIRE

    Fudenberg, Geoffrey; Mirny, Leonid A.

    2012-01-01

    Recent advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of high-order interph...

  13. How does the chromatin fiber deal with topological constraints?

    OpenAIRE

    Barbi, Maria; Mozziconacci, Julien; Victor, Jean-Marc

    2004-01-01

    In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of the so-called 30 nm chromatin fiber and accordingly imposes strong topological constraints. We present a general method for computing both the twist and the writhe of any winding pattern. An explicit derivation is implemented for the chromatin fiber which ...

  14. 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.

  15. Minor groove binder distamycin remodels chromatin but inhibits transcription.

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

    Full Text Available The condensed structure of chromatin limits access of cellular machinery towards template DNA. This in turn represses essential processes like transcription, replication, repair and recombination. The repression is alleviated by a variety of energy dependent processes, collectively known as "chromatin remodeling". In a eukaryotic cell, a fine balance between condensed and de-condensed states of chromatin helps to maintain an optimum level of gene expression. DNA binding small molecules have the potential to perturb such equilibrium. We present herein the study of an oligopeptide antibiotic distamycin, which binds to the minor groove of B-DNA. Chromatin mobility assays and circular dichroism spectroscopy have been employed to study the effect of distamycin on chromatosomes, isolated from the liver of Sprague-Dawley rats. Our results show that distamycin is capable of remodeling both chromatosomes and reconstituted nucleosomes, and the remodeling takes place in an ATP-independent manner. Binding of distamycin to the linker and nucleosomal DNA culminates in eviction of the linker histone and the formation of a population of off-centered nucleosomes. This hints at a possible corkscrew type motion of the DNA with respect to the histone octamer. Our results indicate that distamycin in spite of remodeling chromatin, inhibits transcription from both DNA and chromatin templates. Therefore, the DNA that is made accessible due to remodeling is either structurally incompetent for transcription, or bound distamycin poses a roadblock for the transcription machinery to advance.

  16. 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.

  17. Surface modification of the core-shell type 198Au SiO2 Nano particles for an organic process media tracing study in refinery/petrochemical industries

    International Nuclear Information System (INIS)

    In this study, the surface of the Au SiO2 nano particle was modified from a hydrophilic type to hydrophobic by introducing 3,5-diphenylisocyanate in order to make use of the particle as a radiotracer in the flow dynamics study for petrochemical process units. The partitioning ratio of the hydrophobic particles between water and toluene was measured and compared as a function of time. It was observed that the partitioning ratio into an organic phase has been dramatically increased after the surface modification reaction. Consequently, the potential of its applicability to petrochemical: process diagnosis was enhanced

  18. Multi-responsive hybrid particles: thermo-, pH-, photo-, and magneto-responsive magnetic hydrogel cores with gold nanorod optical triggers.

    Science.gov (United States)

    Rittikulsittichai, Supparesk; Kolhatkar, Arati G; Sarangi, Subhasis; Vorontsova, Maria A; Vekilov, Peter G; Brazdeikis, Audrius; Randall Lee, T

    2016-06-01

    The research strategy described in this manuscript harnesses the attractive properties of hydrogels, gold nanorods (Aurods), and magnetic nanoparticles (MNPs) by synthesizing one unique multi-responsive nanostructure. This novel hybrid structure consists of silica-coated magnetic particles encapsulated within a thermo-responsive P(NIPAM-co-AA) hydrogel network on which Aurods are assembled. Furthermore, this research demonstrates that these composite particles respond to several forms of external stimuli (temperature, pH, light, and/or applied magnetic field) owing to their specific architecture. Exposure of the hybrid particles to external stimuli led to a systematic and reversible variation in the hydrodynamic diameter (swelling-deswelling) and thus in the optical properties of the hybrid particles (red-shifting of the plasmon band). Such stimuli-responsive volume changes can be effectively exploited in drug-delivery applications. PMID:27227963

  19. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.

    Science.gov (United States)

    Baù, Davide; Sanyal, Amartya; Lajoie, Bryan R; Capriotti, Emidio; Byron, Meg; Lawrence, Jeanne B; Dekker, Job; Marti-Renom, Marc A

    2011-01-01

    We developed a general approach that combines chromosome conformation capture carbon copy (5C) with the Integrated Modeling Platform (IMP) to generate high-resolution three-dimensional models of chromatin at the megabase scale. We applied this approach to the ENm008 domain on human chromosome 16, containing the α-globin locus, which is expressed in K562 cells and silenced in lymphoblastoid cells (GM12878). The models accurately reproduce the known looping interactions between the α-globin genes and their distal regulatory elements. Further, we find using our approach that the domain folds into a single globular conformation in GM12878 cells, whereas two globules are formed in K562 cells. The central cores of these globules are enriched for transcribed genes, whereas nontranscribed chromatin is more peripheral. We propose that globule formation represents a higher-order folding state related to clustering of transcribed genes around shared transcription machineries, as previously observed by microscopy. PMID:21131981

  20. Chromatin perturbations during the DNA damage response in higher eukaryotes.

    Science.gov (United States)

    Bakkenist, Christopher J; Kastan, Michael B

    2015-12-01

    The DNA damage response is a widely used term that encompasses all signaling initiated at DNA lesions and damaged replication forks as it extends to orchestrate DNA repair, cell cycle checkpoints, cell death and senescence. ATM, an apical DNA damage signaling kinase, is virtually instantaneously activated following the introduction of DNA double-strand breaks (DSBs). The MRE11-RAD50-NBS1 (MRN) complex, which has a catalytic role in DNA repair, and the KAT5 (Tip60) acetyltransferase are required for maximal ATM kinase activation in cells exposed to low doses of ionizing radiation. The sensing of DNA lesions occurs within a highly complex and heterogeneous chromatin environment. Chromatin decondensation and histone eviction at DSBs may be permissive for KAT5 binding to H3K9me3 and H3K36me3, ATM kinase acetylation and activation. Furthermore, chromatin perturbation may be a prerequisite for most DNA repair. Nucleosome disassembly during DNA repair was first reported in the 1970s by Smerdon and colleagues when nucleosome rearrangement was noted during the process of nucleotide excision repair of UV-induced DNA damage in human cells. Recently, the multi-functional protein nucleolin was identified as the relevant histone chaperone required for partial nucleosome disruption at DBSs, the recruitment of repair enzymes and for DNA repair. Notably, ATM kinase is activated by chromatin perturbations induced by a variety of treatments that do not directly cause DSBs, including treatment with histone deacetylase inhibitors. Central to the mechanisms that activate ATR, the second apical DNA damage signaling kinase, outside of a stalled and collapsed replication fork in S-phase, is chromatin decondensation and histone eviction associated with DNA end resection at DSBs. Thus, a stress that is common to both ATM and ATR kinase activation is chromatin perturbations, and we argue that chromatin perturbations are both sufficient and required for induction of the DNA damage response

  1. Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains.

    Science.gov (United States)

    Tiana, Guido; Amitai, Assaf; Pollex, Tim; Piolot, Tristan; Holcman, David; Heard, Edith; Giorgetti, Luca

    2016-03-29

    Experiments based on chromosome conformation capture have shown that mammalian genomes are partitioned into topologically associating domains (TADs), within which the chromatin fiber preferentially interacts. TADs may provide three-dimensional scaffolds allowing genes to contact their appropriate distal regulatory DNA sequences (e.g., enhancers) and thus to be properly regulated. Understanding the cell-to-cell and temporal variability of the chromatin fiber within TADs, and what determines them, is thus of great importance to better understand transcriptional regulation. We recently described an equilibrium polymer model that can accurately predict cell-to-cell variation of chromosome conformation within single TADs, from chromosome conformation capture-based data. Here we further analyze the conformational and energetic properties of our model. We show that the chromatin fiber within TADs can easily fluctuate between several conformational states, which are hierarchically organized and are not separated by important free energy barriers, and that this is facilitated by the fact that the chromatin fiber within TADs is close to the onset of the coil-globule transition. We further show that in this dynamic state the properties of the chromatin fiber, and its contact probabilities in particular, are determined in a nontrivial manner not only by site-specific interactions between strongly interacting loci along the fiber, but also by nonlocal correlations between pairs of contacts. Finally, we use live-cell experiments to measure the dynamics of the chromatin fiber in mouse embryonic stem cells, in combination with dynamical simulations, and predict that conformational changes within one TAD are likely to occur on timescales that are much shorter than the duration of one cell cycle. This suggests that genes and their regulatory elements may come together and disassociate several times during a cell cycle. These results have important implications for transcriptional

  2. Sensitivity of {\\Lambda} single-particle energies to the {\\Lambda}N spin-orbit coupling and to nuclear core structure in p-shell and sd-shell hypernuclei

    CERN Document Server

    Veselý, P; Hrtánková, J; Mareš, J

    2016-01-01

    We introduce a mean field model based on realistic 2-body baryon interactions and calculate spectra of a set of p-shell and sd-shell {\\Lambda} hypernuclei - 13{\\Lambda}C, 17{\\Lambda}O, 21{\\Lambda}Ne, 29{\\Lambda}Si and 41{\\Lambda}Ca. The hypernuclear spectra are compared with the results of a relativistic mean field (RMF) model and available experimental data. The sensitivity of {\\Lambda} single-particle energies to the nuclear core structure is explored. Special attention is paid to the effect of spin-orbit {\\Lambda}N interaction on the energy splitting of the {\\Lambda} single particle levels 0p3/2 and 0p1/2. In particular, we analyze the contribution of the symmetric (SLS) and the anti-symmetric (ALS) spin-orbit terms to the energy splitting. We give qualitative predictions for the calculated hypernuclei.

  3. CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor I with chromatin.

    Science.gov (United States)

    Jeffery, Daniel C B; Kakusho, Naoko; You, Zhiying; Gharib, Marlene; Wyse, Brandon; Drury, Erin; Weinreich, Michael; Thibault, Pierre; Verreault, Alain; Masai, Hisao; Yankulov, Krassimir

    2015-01-01

    Chromatin Assembly Factor I (CAF-I) plays a key role in the replication-coupled assembly of nucleosomes. It is expected that its function is linked to the regulation of the cell cycle, but little detail is available. Current models suggest that CAF-I is recruited to replication forks and to chromatin via an interaction between its Cac1p subunit and the replication sliding clamp, PCNA, and that this interaction is stimulated by the kinase CDC7. Here we show that another kinase, CDC28, phosphorylates Cac1p on serines 94 and 515 in early S phase and regulates its association with chromatin, but not its association with PCNA. Mutations in the Cac1p-phosphorylation sites of CDC28 but not of CDC7 substantially reduce the in vivo phosphorylation of Cac1p. However, mutations in the putative CDC7 target sites on Cac1p reduce its stability. The association of CAF-I with chromatin is impaired in a cdc28-1 mutant and to a lesser extent in a cdc7-1 mutant. In addition, mutations in the Cac1p-phosphorylation sites by both CDC28 and CDC7 reduce gene silencing at the telomeres. We propose that this phosphorylation represents a regulatory step in the recruitment of CAF-I to chromatin in early S phase that is distinct from the association of CAF-I with PCNA. Hence, we implicate CDC28 in the regulation of chromatin reassembly during DNA replication. These findings provide novel mechanistic insights on the links between cell-cycle regulation, DNA replication and chromatin reassembly. PMID:25602519

  4. Chromatin: a tunable spring at work inside chromosomes.

    Science.gov (United States)

    Ben-Haïm, E; Lesne, A; Victor, J M

    2001-11-01

    This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give a complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the "extensible wormlike rope," allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations, and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance, in the initiation and regulation of transcription. PMID:11735982

  5. Contribution to the experimental validation of the coupling between a particle accelerator and a subcritical core: Muse-3 and Muse-7 experiments

    International Nuclear Information System (INIS)

    As part of the research on the Hybrid Systems and more specially on the physical phenomena involved in a sub-critical core coupled with an external source, it is necessary to qualify several neutronic parameters. These parameters characterize, on the one hand, the external source supplying the core with neutrons (importance, amplification) and, on the other hand, the sub-critical core (spatial distribution of flux, power emitted from the core, reactivity, influence of a spectrum degraded by the presence of buffers like lead). The MUSE Program consists of parametric studies of configuration with different compositions at different sub-critical levels supplied by different types of external source. The first part of this work concerns the first analyses of the static results obtained during the third phase of this experimental program (MUSE-III experiment) and also the preparation of the fourth phase (MUSE-IV experiment). This study has notably concluded on the superiority of a transition zone in lead compared to a sodium zone in terms of neutronic potential (because of the (n, 2n) reaction) and of the source importance. The second part of this work concerns the interpretation of the dynamic results obtained during the MUSE-III experiment and the realization of calculations on the MUSE-IV configurations. This study has shown the important impact of the hydrogenous materials on the external source for the MUSE-III dynamic results. It has also determined the applicability of the pulsed neutron source reactivity measurement technique and optimized the position of monitors for the future MUSE-IV experiment. (authors)

  6. SplitCore Technology Allows Efficient Production of Virus-Like Particles Presenting a Receptor-Contacting Epitope of Human IgE.

    Science.gov (United States)

    Baltabekova, A Zh; Shagyrova, Zh S; Kamzina, A S; Voykov, M; Zhiyenbay, Ye; Ramanculov, E M; Shustov, A V

    2015-08-01

    Immunoglobulin E (IgE) plays a central role in type I hypersensitivity including allergy and asthma. Novel treatment strategy envisages development of a therapeutic vaccine designed to elicit autologous blocking antibodies against the IgE. We sought to develop an IgE-epitope antigen that induces antibodies against a receptor-contacting epitope on human IgE molecule. We designed the VLP immunogens which utilize hepatitis B virus core protein (HBcAg) as a carrier, and present arrays of the receptor-contacting epitopes of the human IgE on their surfaces. FG loop from the IgE domain Cε3 was engineered into the HBcAg. Two constructs explore a well-established approach of insertion into a main immunodominant region of the HBcAg. Third construct is different in that the carrier is produced in a form of an assembly of two polypeptide chains which upon expression remain associated in a stable VLP-forming subunit (SplitCore technology). No VLPs were isolated from E.coli expressing the IgE-epitope antigens with contiguous sequences. On the contrary, the SplitCore antigen carrying the FG loop efficiently formed the VLPs. Immunization of mice with the VLPs presenting receptor-contacting epitope of the IgE elicited antibodies recognizing the human IgE in ELISA. PMID:25837568

  7. Ice cores

    DEFF Research Database (Denmark)

    Svensson, Anders

    Ice cores from Antarctica, from Greenland, and from a number of smaller glaciers around the world yield a wealth of information on past climates and environments. Ice cores offer unique records on past temperatures, atmospheric composition (including greenhouse gases), volcanism, solar activity......, dustiness, and biomass burning, among others. In Antarctica, ice cores extend back more than 800,000 years before present (Jouzel et al. 2007), whereas. Greenland ice cores cover the last 130,000 years...

  8. CENP-C facilitates the recruitment of M18BP1 to centromeric chromatin.

    Science.gov (United States)

    Dambacher, Silvia; Deng, Wen; Hahn, Matthias; Sadic, Dennis; Fröhlich, Jonathan; Nuber, Alexander; Hoischen, Christian; Diekmann, Stephan; Leonhardt, Heinrich; Schotta, Gunnar

    2012-01-01

    Centromeres are important structural constituents of chromosomes that ensure proper chromosome segregation during mitosis by providing defined sites for kinetochore attachment. In higher eukaryotes, centromeres have no specific DNA sequence and thus, they are rather determined through epigenetic mechanisms. A fundamental process in centromere establishment is the incorporation of the histone variant CENP-A into centromeric chromatin, which provides a binding platform for the other centromeric proteins. The Mis18 complex, and, in particular, its member M18BP1 was shown to be essential for both incorporation and maintenance of CENP-A. Here we show that M18BP1 displays a cell cycle-regulated association with centromeric chromatin in mouse embryonic stem cells. M18BP1 is highly enriched at centromeric regions from late anaphase through to G1 phase. An interaction screen against 16 core centromeric proteins revealed a novel interaction of M18BP1 with CENP-C. We mapped the interaction domain in M18BP1 to a central region containing a conserved SANT domain and in CENP-C to the C-terminus. Knock-down of CENP-C leads to reduced M18BP1 association and lower CENP-A levels at centromeres, suggesting that CENP-C works as an important factor for centromeric M18BP1 recruitment and thus for maintaining centromeric CENP-A. PMID:22540025

  9. 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.

  10. Sliding and peeling of histone during chromatin remodelling

    CERN Document Server

    Garai, Ashok; Chowdhury, Debashish

    2011-01-01

    ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, adenosine triphosphate (ATP). CREs actively participate in many cellular processes that require accessibility of specific stretches of DNA which are packaged as chromatin. The basic unit of chromatin is a nucleosome where 146 bp $\\sim$ 50 nm of a double stranded DNA (dsDNA) is wrapped around a spool formed by histone proteins. We investigate the mechanism of peeling of the histone spool, and its complete detachment, from the dsDNA by a CRE. Our two-state model of a CRE captures effectively two distinct chemical (or conformational) states in the mechano-chemical cycle of each ATP-dependent CRE. We calculate the mean times for histone detachment. Our predictions on the ATP-dependence of the measurable quantities can be tested by carrying out {\\it in-vitro} experiments.

  11. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis

    Directory of Open Access Journals (Sweden)

    Jialei Hu

    2015-12-01

    Full Text Available Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac occurring on the nucleosomal lateral surface. We show that H4K44 is acetylated at pre-meiosis and meiosis and displays genome-wide enrichment at recombination hotspots in meiosis. Acetylation at H4K44 is required for normal meiotic recombination, normal levels of double-strand breaks (DSBs during meiosis, and optimal sporulation. Non-modifiable H4K44R results in increased nucleosomal occupancy around DSB hotspots. Our results indicate that H4K44ac functions to facilitate chromatin accessibility favorable for normal DSB formation and meiotic recombination.

  12. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

    Science.gov (United States)

    Mieczkowski, Jakub; Cook, April; Bowman, Sarah K; Mueller, Britta; Alver, Burak H; Kundu, Sharmistha; Deaton, Aimee M; Urban, Jennifer A; Larschan, Erica; Park, Peter J; Kingston, Robert E; Tolstorukov, Michael Y

    2016-01-01

    Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation. PMID:27151365

  13. Structural plasticity of single chromatin fibers revealed by torsional manipulation

    CERN Document Server

    Bancaud, Aurelien; Barbi, Maria; Wagner, Gaudeline; Allemand, Jean-Francois; Mozziconacci, Julien; Lavelle, Christophe; Croquette, Vincent; Victor, Jean-Marc; Prunell, Ariel; Viovy, Jean-Louis

    2006-01-01

    Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, which are determined by the crossing status of the entry/exit DNAs (positive, null or negative). Torsional strain, in displacing that equilibrium, extensively reorganizes the fiber architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin, and may provide the ground to better understand the dynamic binding of most chromatin-associated proteins.

  14. Rapid genome-scale mapping of chromatin accessibility in tissue

    Directory of Open Access Journals (Sweden)

    Grøntved Lars

    2012-06-01

    Full Text Available Abstract Background The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based procedure to bypass nuclear preparation to interrogate nuclease accessible regions in frozen tissue samples. Results Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh. The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Accessible chromatin identified by TACh overlaps to a large extend with accessible chromatin identified by DNase I using nuclei purified from freshly isolated liver tissue as starting material. The similarities are most pronounced at highly accessible regions, whereas identification of less accessible regions tends to be more divergence between nucleases. Interestingly, we show that some of the differences between DNase I and Benzonase relate to their intrinsic sequence biases and accordingly accessibility of CpG islands is probed more efficiently using TACh. Conclusion The TACh methodology identifies accessible chromatin derived from frozen tissue samples. We propose that this simple, robust approach can be applied

  15. 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

  16. Modulation of chromatin modifying complexes by noncoding RNAs in trans

    OpenAIRE

    Názer, Ezequiel; Lei, Elissa P.

    2014-01-01

    Increasing evidence supports a central role for ncRNA in numerous aspects of chromatin function. For instance, ncRNAs can act as a scaffold for the recruitment of certain chromatin modifying complexes to specific sites within the genome. It is easily imaginable how this can occur in cis, but examples also exist whereby targeting of complexes by ncRNA occurs in trans to the site of transcription. Moreover, association of an ncRNA with a particular locus can trigger localization of the gene to ...

  17. 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 of the...... polycomb repressive complexes, PRC1 and PRC2, and the HDAC1- and HDAC2-containing complexes, NuRD, Sin3, and CoREST, in stem cells, development, and cancer, as well as the ongoing efforts to develop therapies targeting these complexes in human cancer. Furthermore, we discuss the role of repressive...... complexes in modulating thresholds for gene activation and their importance for specification and maintenance of cell fate....

  18. Co@Co3O4 core-shell particle encapsulated N-doped mesoporous carbon cage hybrids as active and durable oxygen-evolving catalysts.

    Science.gov (United States)

    Li, Xinzhe; Fang, Yiyun; Wen, Lixin; Li, Feng; Yin, Guanlin; Chen, Wanmin; An, Xingcai; Jin, Jun; Ma, Jiantai

    2016-04-01

    Cobalt-based nanomaterials are promising candidates as efficient, affordable, and sustainable alternative electrocatalysts for the oxygen evolution reaction (OER). However, the catalytic efficiency of traditional nanomaterials is still far below what is expected, because of their low stability in basic solutions and poor active site exposure yield. Here a unique hybrid nanomaterial comprising Co@Co3O4 core-shell nanoparticle (NP) encapsulated N-doped mesoporous carbon cages on reduced graphene oxide (denoted as Co@Co3O4@NMCC/rGO) is successfully synthesized via a carbonization and subsequent oxidation strategy of a graphene oxide (GO)-based metal-organic framework (MOF). Impressively, the special carbon cage structure is very important for not only leading to a large active surface area, enhanced mass/charge transport capability, and easy release of gas bubbles, but also preventing Co@Co3O4 NPs from aggregation and peeling off during prolonged electrochemical reactions. As a result, in alkaline media, the resulting hybrid materials catalyze the OER with a low onset potential of ∼1.50 V (vs. RHE) and an over-potential of only 340 mV to achieve a stable current density of 10 mA cm(-2) for at least 25 h. In addition, metallic Co cores in Co@Co3O4 provide an alternative way for electron transport and accelerate the OER rate. PMID:26914166

  19. CDC28 phosphorylates Cac1p and regulates the association of chromatin assembly factor i with chromatin

    OpenAIRE

    Jeffery, Daniel CB; Kakusho, Naoko; You, Zhiying; Gharib, Marlene; Wyse, Brandon; Drury, Erin; Weinreich, Michael; Thibault, Pierre; Verreault, Alain; Masai, Hisao; Yankulov, Krassimir

    2015-01-01

    Chromatin Assembly Factor I (CAF-I) plays a key role in the replication-coupled assembly of nucleosomes. It is expected that its function is linked to the regulation of the cell cycle, but little detail is available. Current models suggest that CAF-I is recruited to replication forks and to chromatin via an interaction between its Cac1p subunit and the replication sliding clamp, PCNA, and that this interaction is stimulated by the kinase CDC7. Here we show that another kinase, ...

  20. 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 in the...

  1. Linking Morphogen and Chromatin in the Hair Follicle

    OpenAIRE

    Mesa, Kailin R; Greco, Valentina

    2013-01-01

    In this issue of Developmental Cell, Xiong et al. (2013) identify a critical role for the chromatin remodeler, Brg1, in hair follicle stem cell maintenance and epidermal repair. Brg1 interacts with the Shh9 signaling pathway to create a positive feedback loop that fuels hair follicle growth.

  2. ATP independent and ATP dependent chromatin remodeling in wheat

    International Nuclear Information System (INIS)

    Unraveling the biochemistry of chromatin dynamics during DNA replication, repair, recombination as well as transcription is the current challenge in biology. The nucleosomes containing histone octamer are the crucial elements responsible for winding and unwinding eukaryotic DNA. During DNA centric events, these nucleosomes translocate along the DNA with concomitant covalent modifications of histones. We explored these mechanisms in wheat seedlings after irradiation with survivable dose of 60Co-γ radiations. The histones isolated from irradiated seedlings showed that global acetylation of H3 decreased and H4 increased in dose depend manner till 100 grays. Time course of individual modifications showed that for H3K4 and H3K9 acetylation decreased, whereas H3S10, phosphorylation increased. There were fluctuations in acetylation of H4K5, H4K12 and H4K16, whereas H4K8 showed hyperacetylation. We found ATP-dependent chromatin remodeling activity as trans-transfer of the nucleosomes from wheat native donor chromatin on a labeled nucleosome positioning sequence and cis-transfer of the mononucleosomes in vitro. However, there was no significant change in this activity in extracts obtained from irradiated wheat seedlings. This is the first report on, demonstration of ATP-dependent chromatin remodeling activity and site specific H3 and H4 modifications in response to exposure to ionizing radiation in case of plants. (author)

  3. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

    During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response

  4. Generation of bivalent chromatin domains during cell fate decisions

    Directory of Open Access Journals (Sweden)

    De Gobbi Marco

    2011-06-01

    Full Text Available Abstract Background In self-renewing, pluripotent cells, bivalent chromatin modification is thought to silence (H3K27me3 lineage control genes while 'poising' (H3K4me3 them for subsequent activation during differentiation, implying an important role for epigenetic modification in directing cell fate decisions. However, rather than representing an equivalently balanced epigenetic mark, the patterns and levels of histone modifications at bivalent genes can vary widely and the criteria for identifying this chromatin signature are poorly defined. Results Here, we initially show how chromatin status alters during lineage commitment and differentiation at a single well characterised bivalent locus. In addition we have determined how chromatin modifications at this locus change with gene expression in both ensemble and single cell analyses. We also show, on a global scale, how mRNA expression may be reflected in the ratio of H3K4me3/H3K27me3. Conclusions While truly 'poised' bivalently modified genes may exist, the original hypothesis that all bivalent genes are epigenetically premarked for subsequent expression might be oversimplistic. In fact, from the data presented in the present work, it is equally possible that many genes that appear to be bivalent in pluripotent and multipotent cells may simply be stochastically expressed at low levels in the process of multilineage priming. Although both situations could be considered to be forms of 'poising', the underlying mechanisms and the associated implications are clearly different.

  5. Chromatin-regulating proteins as targets for cancer therapy

    International Nuclear Information System (INIS)

    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)

  6. Chromatin-regulating proteins as targets for cancer therapy.

    Science.gov (United States)

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

    2014-07-01

    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. PMID:24522270

  7. Rearrangement of chromatin domains during development in Xenopus.

    Science.gov (United States)

    Vassetzky, Y; Hair, A; Méchali, M

    2000-06-15

    A dynamic change in the organization of different gene domains transcribed by RNA polymerase I, II, or III occurs during the progression from quiescent [pre-midblastula transition (pre-MBT)] to active (post-MBT) embryos during Xenopus development. In the rDNA, c-myc, and somatic 5S gene domains, a transition from random to specific anchorage to the nuclear matrix occurs when chromatin domains become active. The keratin gene domain was also randomly associated to the nuclear matrix before MBT, whereas a defined attachment site was found in keratinocytes. In agreement with this specification, ligation-mediated (LM)-PCR genomic footprinting carried out on the subpopulation of 5S domains specifically attached to the matrix reveals the hallmarks of determined chromatin after the midblastula transition. In contrast, the same analysis performed on the total 5S gene population does not reveal specific chromatin organization, validating the use of nuclear matrix fractionation to unveil active chromatin domains. These data provide a means for the determination of active chromosomal territories in the embryo and emphasize the role of nuclear architecture in regulated gene expression during development. PMID:10859171

  8. Effect of triiodothyronine on rat liver chromatin protein kinase

    International Nuclear Information System (INIS)

    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 32P when incubated with [γ-32P]ATP than the chromatin proteins from untreated rats. Thyroidectomy reduced the in vitro 32P 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.)

  9. Development and validation of a generic high-performance liquid chromatography for the simultaneous separation and determination of six cough ingredients: Robustness study on core-shell particles.

    Science.gov (United States)

    Yehia, Ali Mohamed; Essam, Hebatallah Mohamed

    2016-09-01

    A generally applicable high-performance liquid chromatographic method for the qualitative and quantitative determination of pharmaceutical preparations containing phenylephrine hydrochloride, paracetamol, ephedrine hydrochloride, guaifenesin, doxylamine succinate, and dextromethorphan hydrobromide is developed. Optimization of chromatographic conditions was performed for the gradient elution using different buffer pH values, flow rates and two C18 stationary phases. The method was developed using a Kinetex® C18 column as a core-shell stationary phase with a gradient profile using buffer pH 5.0 and acetonitrile at 2.0 mL/min flow rate. Detection was carried out at 220 nm and linear calibrations were obtained for all components within the studied ranges. The method was fully validated in agreement with ICH guidelines. The proposed method is specific, accurate and precise (RSD% 10%). Satisfactory results were obtained for commercial combinations analyses. Statistical comparison between the proposed chromatographic and official methods revealed no significant difference. PMID:27404374

  10. Electromagnetic properties of the 2+ state in 134Te: Influence of core excitation on single-particle orbits beyond 132Sn

    Energy Technology Data Exchange (ETDEWEB)

    Stuchbery, Andrew E [ORNL; Allmond, James M [ORNL; Galindo-Uribarri, Alfredo {nmn} [ORNL; Padilla-Rodal, Elizabeth [Universidad Nacional Autonoma de Mexico (UNAM); Radford, David C [ORNL; Stone, N. J. [University of Tennessee, Knoxville (UTK); Batchelder, J. C. [Oak Ridge Associated Universities (ORAU); Beene, James R [ORNL; Benczer-Koller, N. [Rutgers University; Bingham, C. R. [University of Tennessee, Knoxville (UTK); Howard, Meredith E [ORNL; Kumbartzki, G. [Rutgers University; Liang, J Felix [ORNL; Manning, Brett M [ORNL; Stracener, Daniel W [ORNL; Yu, Chang-Hong [ORNL

    2013-01-01

    The g factor and B (E2) of the first excited 2+ state have been measured following Coulomb excitation ofthe neutron-rich semimagic nuclide 134Te (two protons outside 132Sn) produced as a radioactive beam. The precision achieved matches related g-factor measurements on stable beams and distinguishes between alternative models. The B(E2) measurement exposes quadrupole strength in the 2+ state beyond that predicted by current large-basis shell-model calculations. This additional quadrupole strength can be attributed to coupling between the two valence protons and excitations of the 132Sn core. However, the wave functions of the low-excitation positive-parity states in 134Te up to 6+ remain dominated by the (g7/2)2 configuration.

  11. Particle adhesion and removal

    CERN Document Server

    Mittal, K L

    2015-01-01

    The book provides a comprehensive and easily accessible reference source covering all important aspects of particle adhesion and removal.  The core objective is to cover both fundamental and applied aspects of particle adhesion and removal with emphasis on recent developments.  Among the topics to be covered include: 1. Fundamentals of surface forces in particle adhesion and removal.2. Mechanisms of particle adhesion and removal.3. Experimental methods (e.g. AFM, SFA,SFM,IFM, etc.) to understand  particle-particle and particle-substrate interactions.4. Mechanics of adhesion of micro- and  n

  12. The epigenetic regulation of cell cycle and chromatin dynamic by sirtuins

    OpenAIRE

    Martínez Redondo, Paloma

    2014-01-01

    Tesi realitzada a l'Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) The chromatin consists of a hierarchical and dynamical structure that is modulated during the different cell cycle stages in order to maintain genome integrity and preserve the genetic information coded in the DNA. The dynamic structure of the chromatin depends on the coordination of the different chromatin remodeling processes: histone modifications, chromatin remodeling enzymes/complexes, DNA methylation and chr...

  13. Chlamydomonas IFT70/CrDYF-1 is a core component of IFT particle complex B and is required for flagellar assembly.

    Science.gov (United States)

    Fan, Zhen-Chuan; Behal, Robert H; Geimer, Stefan; Wang, Zhaohui; Williamson, Shana M; Zhang, Haili; Cole, Douglas G; Qin, Hongmin

    2010-08-01

    DYF-1 is a highly conserved protein essential for ciliogenesis in several model organisms. In Caenorhabditis elegans, DYF-1 serves as an essential activator for an anterograde motor OSM-3 of intraflagellar transport (IFT), the ciliogenesis-required motility that mediates the transport of flagellar precursors and removal of turnover products. In zebrafish and Tetrahymena DYF-1 influences the cilia tubulin posttranslational modification and may have more ubiquitous function in ciliogenesis than OSM-3. Here we address how DYF-1 biochemically interacts with the IFT machinery by using the model organism Chlamydomonas reinhardtii, in which the anterograde IFT does not depend on OSM-3. Our results show that this protein is a stoichiometric component of the IFT particle complex B and interacts directly with complex B subunit IFT46. In concurrence with the established IFT protein nomenclature, DYF-1 is also named IFT70 after the apparent size of the protein. IFT70/CrDYF-1 is essential for the function of IFT in building the flagellum because the flagella of IFT70/CrDYF-1-depleted cells were greatly shortened. Together, these results demonstrate that IFT70/CrDYF-1 is a canonical subunit of IFT particle complex B and strongly support the hypothesis that the IFT machinery has species- and tissue-specific variations with functional ramifications. PMID:20534810

  14. Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci.

    Science.gov (United States)

    Bonifer, C; Hecht, A; Saueressig, H; Winter, D M; Sippel, A E

    1991-10-01

    It is hypothesized that nuclear DNA is organized in topologically constrained loop domains defining basic units of higher order chromatin structure. Our studies are performed in order to investigate the functional relevance of this structural subdivision of eukaryotic chromatin for the control of gene expression. We used the chicken lysozyme gene locus as a model to examine the relation between chromatin structure and gene function. Several structural features of the lysozyme locus are known: the extension of the region of general DNAasel sensitivity of the active gene, the location of DNA-sequences with high affinity for the nuclear matrix in vitro, and the position of DNAasel hypersensitive chromatin sites (DHSs). The pattern of DHSs changes depending on the transcriptional status of the gene. Functional studies demonstrated that DHSs mark the position of cis-acting regulatory elements. Additionally, we discovered a novel cis-activity of the border regions of the DNAasel sensitive domain (A-elements). By eliminating the position effect on gene expression usually observed when genes are randomly integrated into the genome after transfection, A-elements possibly serve as punctuation marks for a regulatory chromatin domain. Experiments using transgenic mice confirmed that the complete structurally defined lysozyme gene domain behaves as an independent regulatory unit, expressing the gene in a tissue specific and position independent manner. These expression features were lost in transgenic mice carrying a construct, in which the A-elements as well as an upstream enhancer region were deleted, indicating the lack of a locus activation function on this construct. Experiments are designed in order to uncover possible hierarchical relationships between the different cis-acting regulatory elements for stepwise gene activation during cell differentiation. We are aiming at the definition of the basic structural and functional requirements for position independent and high

  15. Intense bundles of particles in cores of nuclear-electromagnetic cascades in the atmosphere with energies around 100 PeV (gamma-families with halo)

    Energy Technology Data Exchange (ETDEWEB)

    Puchkov, V.S.; Borisov, A.S.; Guseva, Z.M.; Denisova, V.G.; Kempa, J.; Kanevskaya, E.A.; Maximenko, V.M.; Mukhamedshin, R.A.; Pyatovsky, S.E.; Slavatinsky, S.A.; Amineva, T.P

    2003-07-01

    An appreciable fraction of gamma-families are accompanied by a halo, a narrow bundle of high-energy particles (energy density > 20 TeV/mm{sup 2}) recorded in X-ray emulsion chambers as a diffuse dark spot in the central region of a gamma-family. Gamma-families in the experiment 'Pamir' are compared with simulations by three different codes of quark-gluon string model (MQ, MCO and QGSJet) based on extrapolating accelerator data up to energy E{sub o} = 3 * 10{sup 18} eV and under various assumptions on mass composition of primary cosmic rays (PCR). The spectrum of halo area, S, is analyzed, especially at S > 100 mm{sup 2}. Simulations by different codes predict that at a PCR energy E{sub o} {approx} 10{sup 18} eV the probability of initiating a halo with S {approx} 1000 mm{sup 2} is 60% for primary protons and 40% for Fe nuclei. The fraction of protons in PCR composition at E{sub 0} = 10{sup 16}/10{sup 17} eV is estimated.

  16. A C-terminal truncated hepatitis C virus core protein variant assembles in vitro into virus-like particles in the absence of structured nucleic acids

    International Nuclear Information System (INIS)

    Little is known about the assembly pathway or structure of the hepatitis C virus (HCV). In this work a truncated HCcAg variant covering the first 120 aa (HCcAg.120) with a 32 aa N-terminal fusion peptide (6x Histag-Xpress epitope) was purified as a monomer under strong denaturing conditions. In addition, minor HCcAg.120 peaks exhibiting little different molecular mass by SDS-PAGE which possibly represents alternative forms harboring the N-termini of HCcAg.120 were detected. Analysis using gel filtration chromatography showed that HCcAg.120 assembled into high molecular weight structures in vitro in the absence of structured nucleic acids. The negative-stain electron microscopy analysis revealed that these structures correspond with spherical VLPs of uniform morphology and size distribution. The diameters of these particles ranged from 20 to 43 nm with an average diameter of approximately 30 nm and were specifically immunolabelled with a mouse monoclonal antibody against the residues 5-35 of HCcAg. Results presented in this work showed that HCcAg.120 assembled in vitro into VLPs in the absence of structured nucleic acids with similar morphology and size distribution to those found in sera and hepatocytes from HCV-infected patients. Therefore, these VLPs would be important to elucidate the mechanisms behind the ability of HCcAg to assemble into a nucleocapsid structure

  17. Chromatin structure analysis based on a hierarchic texture model.

    Science.gov (United States)

    Wolf, G; Beil, M; Guski, H

    1995-02-01

    The quantification of chromatin structures is an important part of nuclear grading of malignant and premalignant lesions. In order to achieve high accuracy, computerized image analysis systems have been applied in this process. Chromatin texture analysis of cell nuclei requires a suitable texture model. A hierarchic model seemed to be most compatible for this purpose. It assumes that texture consists of homogeneous regions (textons). Based on this model, two approaches to texture segmentation and feature extraction were investigated using sections of cervical tissue. We examined the reproducibility of the measurement under changing optical conditions. The coefficients of variations of the texture features ranged from 2.1% to 16.9%. The features were tested for their discriminating capability in a pilot study including 30 cases of cervical dysplasia and carcinoma. The overall classification accuracy reached 65%. This study presents an automated technique for texture analysis that is similar to human perception. PMID:7766266

  18. Proteomics and the genetics of sperm chromatin condensation

    Institute of Scientific and Technical Information of China (English)

    Rafael Oliva; Judit Castillo

    2011-01-01

    Spermatogenesis involves extremely marked cellular, genetic and chromatin changes resulting in the generation of the highly specialized sperm cell. Proteomics allows the identification of the proteins that compose the spermatogenic cells and the study of their function. The recent developments in mass spectrometry (MS) have markedly increased the throughput to identify and to study the sperm proteins. Catalogs of thousands of testis and spermatozoan proteins in human and different model species are becoming available, setting up the basis for subsequent research, diagnostic applications and possibly the future development of specific treatments. The present review intends to summarize the key genetic and chromatin changes at the different stages of spermatogenesis and in the mature sperm cell and to comment on the presently available proteomic studies.

  19. Integrative annotation of chromatin elements from ENCODE data

    OpenAIRE

    Hoffman, Michael M.; Ernst, Jason; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Kellis, Manolis; Noble, William Stafford

    2012-01-01

    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learnin...

  20. Unsupervised pattern discovery in human chromatin structure through genomic segmentation

    OpenAIRE

    Hoffman, Michael M.; Buske, Orion J; Wang, Jie; Weng, Zhiping; Bilmes, Jeff A.; Noble, William Stafford

    2012-01-01

    We applied a dynamic Bayesian network method that identifies joint patterns from multiple functional genomics experiments to ChIP-seq histone modification and transcription factor data, and DNaseI-seq and FAIRE-seq open chromatin readouts from the human cell line K562. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, CTCF elements, and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/...

  1. Effect of saffron on rat sperm chromatin integrity

    OpenAIRE

    Mohammad Mardani; Ahmad Vaez; Shahnaz Razavi

    2014-01-01

    Background: Currently, relation between reactive oxygen species (ROS) ROS concentration and semen quality was indicated. Saffron has traditionally been not only considered as a food additive but also as a medicinal herb, which has a good antioxidant properties. Objective: The aim of this study was to evaluate the protection potency of saffron and vitamin E on sperm chromatin integrity. Materials and Methods: Thirty adult male Wistar rats divided equally into saffron (100 mg/kg), vitamin E (10...

  2. Chromatin condensation of Xist genomic loci during oogenesis in mice.

    Science.gov (United States)

    Fukuda, Atsushi; Mitani, Atsushi; Miyashita, Toshiyuki; Umezawa, Akihiro; Akutsu, Hidenori

    2015-12-01

    Repression of maternal Xist (Xm-Xist) during preimplantation in mouse embryos is essential for establishing imprinted X chromosome inactivation. Nuclear transplantation (NT) studies using nuclei derived from non-growing (ng) and full-grown (fg) oocytes have indicated that maternal-specific repressive modifications are imposed on Xm-Xist during oogenesis, as well as on autosomal imprinted genes. Recent studies have revealed that histone H3 lysine 9 trimethylation (H3K9me3) enrichments on Xm-Xist promoter regions are involved in silencing at the preimplantation stages. However, whether H3K9me3 is imposed on Xm-Xist during oogenesis is not known. Here, we dissected the chromatin states in ng and fg oocytes and early preimplantation stage embryos. Chromatin immunoprecipitation experiments against H3K9me3 revealed that there was no significant enrichment within the Xm-Xist region during oogenesis. However, NT embryos with ng nuclei (ngNT) showed extensive Xm-Xist derepression and H3K9me3 hypomethylation of the promoter region at the 4-cell stage, which corresponds to the onset of paternal Xist expression. We also found that the chromatin state at the Xist genomic locus became markedly condensed as oocyte growth proceeded. Although the condensed Xm-Xist genomic locus relaxed during early preimplantation phases, the extent of the relaxation across Xm-Xist loci derived from normally developed oocytes was significantly smaller than those of paternal-Xist and ngNT-Xist genomic loci. Furthermore, Xm-Xist from 2-cell metaphase nuclei became derepressed following NT. We propose that chromatin condensation is associated with imprinted Xist repression and that skipping of the condensation step by NT leads to Xist activation during the early preimplantation phase. PMID:26459223

  3. Nucleosome conformational flexibility in experiments with single chromatin fibers

    OpenAIRE

    Sivolob A. V.

    2010-01-01

    Studies on the chromatin nucleosome organization play an ever increasing role in our comprehension of mechanisms of the gene activity regulation. This minireview describes the results on the nucleosome conformational flexibility, which were obtained using magnetic tweezers to apply torsion to oligonucleosome fibers reconstituted on single DNA molecules. Such an approach revealed a new structural form of the nucleosome, the reversome, in which DNA is wrapped in a right-handed superhelix around...

  4. Chromatin-regulating proteins as targets for cancer therapy

    OpenAIRE

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

  5. Chaperone-mediated assembly of centromeric chromatin in vitro

    OpenAIRE

    Furuyama, Takehito; Dalal, Yamini; Henikoff, Steven

    2006-01-01

    Every eukaryotic chromosome requires a centromere for attachment to spindle microtubules for chromosome segregation. Although centromeric DNA sequences vary greatly among species, centromeres are universally marked by the presence of a centromeric histone variant, centromeric histone 3 (CenH3), which replaces canonical histone H3 in centromeric nucleosomes. Conventional chromatin is maintained in part by histone chaperone complexes, which deposit the S phase-limited (H3) and constitutive (H3....

  6. 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 ostatní: GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : tumour cells * chromatin * radiation Subject RIV: BO - Biophysics

  7. Chromatin structure in relation to telomere length maintenance in plants

    Czech Academy of Sciences Publication Activity Database

    Fajkus, Jiří; Mozgová, I.; Procházková Schrumpfová, P.; Majerová, E.; Fojtová, M.

    Zürich, 2009. s. 1. [European Workshop on Plant Chromatin. 03.09.2009-04.09.2009, Zürich] R&D Projects: GA ČR(CZ) GD204/08/H054; GA ČR(CZ) GA204/08/1530; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : telomere * HMGB1 protein * DNA methylation Subject RIV: BO - Biophysics

  8. Transcription within Condensed Chromatin: Steric Hindrance Facilitates Elongation

    OpenAIRE

    Bécavin, Christophe; Barbi, Maria; Victor, Jean-Marc; Lesne, Annick

    2010-01-01

    During eukaryotic transcription, RNA-polymerase activity generates torsional stress in DNA, having a negative impact on the elongation process. Using our previous studies of chromatin fiber structure and conformational transitions, we suggest that this torsional stress can be alleviated, thanks to a tradeoff between the fiber twist and nucleosome conformational transitions into an activated state named “reversome”. Our model enlightens the origin of polymerase pauses, and leads to the counter...

  9. Structural plasticity of single chromatin fibers revealed by torsional manipulation

    OpenAIRE

    Bancaud, Aurelien; Silva, Natalia Conde e; Barbi, Maria; Wagner, Gaudeline; Allemand, Jean-Francois; Mozziconacci, Julien; Lavelle, Christophe; Croquette, Vincent; Victor, Jean-Marc; Prunell, Ariel; Viovy, Jean-Louis

    2007-01-01

    Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucle...

  10. Quality of histone modification antibodies undermines chromatin biology research

    OpenAIRE

    Goran Kungulovski; Albert Jeltsch

    2015-01-01

    Histone post-translational modification (PTM) antibodies are essential research reagents in chromatin biology. However, they suffer from variable properties and insufficient documentation of quality. Antibody manufacturers and vendors should provide detailed lot-specific documentation of quality, rendering further quality checks by end-customers unnecessary. A shift from polyclonal antibodies towards sustainable reagents like monoclonal or recombinant antibodies or histone binding domains wou...

  11. Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

    OpenAIRE

    Fudenberg, Geoffrey; Mirny, Leonid A.; Doyle, Boryana G.; Imakaev, Maksim Viktorovich

    2014-01-01

    The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equi...

  12. Changes in chromatin state in donors subjected to physical stress

    OpenAIRE

    Shckorbatov, Yuriy; Samokhvalov, Valeriy; Bevziuk, Dariya; Kovaliov, Maxim

    2009-01-01

    The purpose of the present study is to evaluate changes in chromatin of human buccal epithelium under the influence of stressing factor - dosed physical activity. Investigations were performed in a group of students (13 men) of age 19-23. Cells were stained on a slide by a 2% orcein solution in 45% acetic acid during 1 h. The following physiological indexes were determined: arterial blood pressure, pulse frequency, and frequency of breathing. The physical stress produced by the dosed physical...

  13. 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. PMID:662693

  14. Ice Cores

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Records of past temperature, precipitation, atmospheric trace gases, and other aspects of climate and environment derived from ice cores drilled on glaciers and ice...

  15. Radiosensitivity: a role of ATM in chromatin modification

    International Nuclear Information System (INIS)

    Chromatin architecture plays an important role in DNA-template based processes, including transcription, DNA damage repair, replication, and apoptosis. Post-translational modification of histones and non-histone proteins through actions of histone acetyltransferase (HAT) and histone deacetylase (HDAC) regulates chromatin conformation, resulting in the control of accessibility of proteins to target sites. Some of these proteins are involved in cell cycle regulation and DNA damage repair process (ie. Rb, E2F1, p21, p53 and BRCA 1 and 2). However, the mechanism underlying the role of chromatin modification on cellular intrinsic radiation sensitivity is poorly understood. Ataxia-telangiectasia mutated (ATM), the product of the gene mutated in cells from patients with the radiation sensitivity syndrome of ataxia-telangiectasia, has been shown to be involved in multiple DNA damage-induced signal transduction pathways. Previously, we have observed that ATM interacts with histone deacetylase HDAC1 both in vivo and in vitro and its complex exhibits deacetylase activity in response to ionizing radiation. Further studies have suggested that ATM is involved in the regulation of p53 via post-translational modification. Using isogenic AT cell lines, which show radiation sensitivity differences (Do 0.7 and 1.4 Gy), we performed microarray analyses of gene expression at various intervals following irradiation. These data provide evidence for distinctive ATM-dependent or -independent radiation-mediated gene regulation patterns

  16. Novel chromatin texture features for the classification of pap smears

    Science.gov (United States)

    Bejnordi, Babak E.; Moshavegh, Ramin; Sujathan, K.; Malm, Patrik; Bengtsson, Ewert; Mehnert, Andrew

    2013-03-01

    This paper presents a set of novel structural texture features for quantifying nuclear chromatin patterns in cells on a conventional Pap smear. The features are derived from an initial segmentation of the chromatin into bloblike texture primitives. The results of a comprehensive feature selection experiment, including the set of proposed structural texture features and a range of different cytology features drawn from the literature, show that two of the four top ranking features are structural texture features. They also show that a combination of structural and conventional features yields a classification performance of 0.954±0.019 (AUC±SE) for the discrimination of normal (NILM) and abnormal (LSIL and HSIL) slides. The results of a second classification experiment, using only normal-appearing cells from both normal and abnormal slides, demonstrates that a single structural texture feature measuring chromatin margination yields a classification performance of 0.815±0.019. Overall the results demonstrate the efficacy of the proposed structural approach and that it is possible to detect malignancy associated changes (MACs) in Papanicoloau stain.

  17. High sperm chromatin stability in semen with high viscosity.

    Science.gov (United States)

    Gonzales, G F; Sánchez, A

    1994-01-01

    This study was designed to determine the effects of high semen viscosity on sperm chromatin stability. Semen samples obtained from men with normal and high viscosity were studied. Sperm chromatin stability was tested by exposure to sodium dodecyl sulfate (SDS) only and SDS together with a zinc-chelating agent, disodium ethylene diamine tetraacetate (SDS+EDTA). After SDS incubation, stable sperm was 61.36 +/- 3.0 and 54.71 +/- 3.42% for normal and high semen viscosity, respectively (P:NS), and after SDS+EDTA, it was further reduced to 12.48 +/- 0.99% in semen samples with normal consistency and in a less magnitude in semen samples with high viscosity (25.6 +/- 5.2). Comparing values obtained in SDS+EDTA, a high sperm stability was observed in samples with hyperviscosity (p hyperviscosity is associated with a high sperm chromatin stability in situations when a zinc-chelating agent is present. PMID:8122934

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

    Directory of Open Access Journals (Sweden)

    Ivo A. Hendriks

    2015-03-01

    Full Text Available Small ubiquitin-like modifiers play critical roles in the DNA damage response (DDR. To increase our understanding of SUMOylation in the mammalian DDR, we employed a quantitative proteomics approach in order to identify dynamically regulated SUMO-2 conjugates and modification sites upon treatment with the DNA damaging agent methyl methanesulfonate (MMS. We have uncovered a dynamic set of 20 upregulated and 33 downregulated SUMO-2 conjugates, and 755 SUMO-2 sites, of which 362 were dynamic in response to MMS. In contrast to yeast, where a response is centered on homologous recombination, we identified 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. Plasmodium falciparum Histone Acetyltransferase, a Yeast GCN5 Homologue Involved in Chromatin Remodeling

    Institute of Scientific and Technical Information of China (English)

    QiFan; LijiaAn; LiwangCui

    2005-01-01

    The yeast transcriptional coactivator GCN5 (yGCN5), a histone acetyltransferase (HAT), is part of large multimeric complexes that are required for chromatin remodeling and transcriptional activation. Like other eukaryotes, the malaria parasite DNA is organized into nucleosomes and the genome encodes components of chromatin-remodeling complexes. Here we show that GCN5 is conserved in Plasmodium species and that the most homologous regions are within the HAT domain and the bromodomain. The Plasmodiumfalclparum GCN5 homologue (PfGCN5) is spliced with three introns, encoding a protein of 1,464 residues. Mapping of the ends of the PfGCN5 transcript suggests that the mRNA is 5.2 to 5.4 kb, consistent with the result from Northern analysis. Using free core histones, we determined that recombinant PfGCN5 proteins have conserved HAT activity with a substrate preference for histone H3. Using substrate-specific antibodies, we determined that both Lys-8 and -14 of H3 were acetylated by the recombinant PfGCN5. In eukaryotes, GCN5 homologues interact with yeast ADA2 homologues and form large multiprotein HAT complexes. We have identified an ADA2 homologue in P. falciparum, PfADA2. Yeast two-hybrid and in vitro binding assays verified the interactions between PfGCN5 and PfADA2, suggesting that they may be associated with each other in vivo. The conserved function of the HAT domain in PfGCN5 was further illustrated with yeast complementation experiments, which showed that the PfGCN5 region corresponding to the full-length yGCN5 could partially complement the yGCN5 deletion mutation. Furthermore, a chimera comprising the PfGCN5 HAT domain fused to the remainder of yeast GCN5 (yGCN5) fully rescued the yGCN5 deletion mutant. These data demonstrate that PfGCN5 is an authentic GCN5 family member and may exist in chromatin-remodeling complexes to regulate gene expression in P. falciparum.

  20. 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.; Mann, M; Knippers, R; Gruss, C

    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...

  1. FANCD2-Controlled Chromatin Access of the Fanconi-Associated Nuclease FAN1 Is Crucial for the Recovery of Stalled Replication Forks

    Science.gov (United States)

    Chaudhury, Indrajit; Stroik, Daniel R.

    2014-01-01

    Fanconi anemia (FA) is a cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand cross-links (ICLs). Within the FA pathway, an upstream core complex monoubiquitinates and recruits the FANCD2 protein to ICLs on chromatin. Ensuing DNA repair involves the Fanconi-associated nuclease 1 (FAN1), which interacts selectively with monoubiquitinated FANCD2 (FANCD2Ub) at ICLs. Importantly, FANCD2 has additional independent functions: it binds chromatin and coordinates the restart of aphidicolin (APH)-stalled replication forks in concert with the BLM helicase, while protecting forks from nucleolytic degradation by MRE11. We identified FAN1 as a new crucial replication fork recovery factor. FAN1 joins the BLM-FANCD2 complex following APH-mediated fork stalling in a manner dependent on MRE11 and FANCD2, followed by FAN1 nuclease-mediated fork restart. Surprisingly, APH-induced activation and chromatin recruitment of FAN1 occur independently of the FA core complex or the FAN1 UBZ domain, indicating that the FANCD2Ub isoform is dispensable for functional FANCD2-FAN1 cross talk during stalled fork recovery. In the absence of FANCD2, MRE11 exonuclease-promoted access of FAN1 to stalled forks results in severe FAN1-mediated nucleolytic degradation of nascent DNA strands. Thus, FAN1 nuclease activity at stalled replication forks requires tight regulation: too little inhibits fork restart, whereas too much causes fork degradation. PMID:25135477

  2. Particle flow code simulation of hydraulic fracturing in high core wall rockfill dams%高心墙堆石坝心墙水力劈裂的颗粒流模拟

    Institute of Scientific and Technical Information of China (English)

    杨艳; 周伟; 常晓林; 花俊杰

    2012-01-01

    目前针对堆石或土石坝的心墙水力劈裂问题虽然已取得了不少成果,但现有的成果大多从宏观的角度进行研究,对心墙水力劈裂发生机制的认识尚未达成一致的观点.采用颗粒流方法从细观角度对心墙水力劈裂问题进行初步研究,模拟了心墙水力劈裂发生和发展的过程.计算结果表明,劈裂水压力Pf随着竖向应力的增大而增大,且两者基本呈线性关系,与室内成果的规律基本一致;心墙在高水力梯度作用下,形成的水楔效应降低了裂缝尖端区附近的最大主应力,当该值小于或接近心墙上游的外水压力时则会导致水力劈裂的发生.此外,计算结果还证明了心墙发生水力劈裂的主要力学原因是由于心墙中的张拉应力超过了土体的抗拉强度.%Recently, increasing attention has been given to hydraulic fracturing phenomena in core wall of rockfill or soil dams. However, most of the studies are carried out from the macro prospective, and the fracturing mechanism is still disputable. In this paper, the hydraulic fracturing problem is analyzed using the particle flow code (PFC) from the micro prospective. The occurrence and development of hydraulic fracturing is simulated. Results show that the fracturing pressure P/ increases with the increasing of the vertical stress in an approximately linear way, which agrees well with experimental results. Under the high hydraulic gradient condition, the maximum principal stress near crack tip is decreased because of the wedge effect of water. Hydraulic fracturing will probably occur when the maximum principal stress is less than or close to the water pressure of upstream of core wall. In addition, it is also illustrated that the main reason of hydraulic fracturing in core wall is that the tension stress exceeds the tensile strength of the soil.

  3. Core transfer

    Science.gov (United States)

    Good news for all petroleum geoscientists, mining and environmental scientists, university researchers, and the like: Shell Oil Company has deeded its Midland core and sample repository to the Bureau of Economic Geology (BEG) at the University of Texas at Austin. The Midland repository includes more than 1 million linear meters of slab, whole core, and prepared cuttings. Data comprising one of the largest U.S. core collections—the geologic samples from wells drilled in Texas and 39 other states—are now public data and will be incorporated into the existing BEG database. Both Shell and the University of Texas at Austin are affiliated with the American Geological Institute, which assisted in arranging the transfer as part of its goal to establish a National Geoscience Data Repository System at regional centers across the United States.

  4. Core strengthening.

    Science.gov (United States)

    Arendt, Elizabeth A

    2007-01-01

    Several recent studies have evaluated interventional techniques designed to reduce the risk of serious knee injuries, particularly noncontact anterior cruciate ligament injuries in female athletes. Maintenance of rotational control of the limb underneath the pelvis, especially in response to cutting and jumping activities, is a common goal in many training programs. Rotational control of the limb underneath the pelvis is mediated by a complex set of factors including the strength of the trunk muscles and the relationship between the core muscles. It is important to examine the interrelationship between lower extremity function and core stability. PMID:17472321

  5. Core BPEL

    DEFF Research Database (Denmark)

    Hallwyl, Tim; Højsgaard, Espen

    The Web Services Business Process Execution Language (WS-BPEL) is a language for expressing business process behaviour based on web services. The language is intentionally not minimal but provides a rich set of constructs, allows omission of constructs by relying on defaults, and supports language...... extensions. Combined with the fact that the language definition does not provide a formal semantics, it is an arduous task to work formally with the language (e.g. to give an implementation). In this paper we identify a core subset of the language, called Core BPEL, which has fewer and simpler constructs...

  6. Preliminary study of sperm chromatin characteristics of the brachyuran crab Maja brachydactyla. Histones and nucleosome-like structures in decapod crustacean sperm nuclei previously described without SNBPs.

    Science.gov (United States)

    Kurtz, K; Ausió, J; Chiva, M

    2009-10-01

    An interesting characteristic of decapod crustacean sperm nuclei is that they do not contain highly packaged chromatin. In the present study we re-examine the presence of DNA-interacting proteins in sperm nuclei of the brachyuran Maja brachydactyla. Although previous reports have indicated that, unlike the majority of sperm cells, DNA of decapod sperm is not organized by basic proteins, in this work we show that: (1) histones are present in sperm of M. brachydactyla; (2) histones are associated with sperm DNA; (3) histone H3 appears in lower proportions than the other core histones, while histone H2B appears in higher proportions; and (4) histone H3 in sperm nuclei is acetylated. This work complements a previous study of sperm histones of Cancer pagurus and supports the suggestion that decapod crustacean sperm chromatin deserves further attention. PMID:19324386

  7. Complexity of chromatin folding is captured by the strings and binders switch model.

    Science.gov (United States)

    Barbieri, Mariano; Chotalia, Mita; Fraser, James; Lavitas, Liron-Mark; Dostie, Josée; Pombo, Ana; Nicodemi, Mario

    2012-10-01

    Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the "strings and binders switch" model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed "fractal-globule" model, but only as one of many possible transient conformations. PMID:22988072

  8. 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.

  9. Effective medium theory expressions for the effective diffusion in chromatographic beds filled with porous, non-porous and porous-shell particles and cylinders. Part II: Numerical verification and quantitative effect of solid core on expected B-term band broadening.

    Science.gov (United States)

    Deridder, Sander; Desmet, Gert

    2011-01-01

    The results of a numerical simulation study of the diffusion and retention in fully porous spheres and cylinders are compared with some of the high order accuracy analytical solutions for the effective diffusion coefficient that have been derived from the effective medium theory (EMT) theory in part I of the present study. A variety of different ordered (spheres and cylinders) and disordered (cylinders) packings arrangements has been considered. The agreement between simulations and theory was always excellent, lying within the (very tight) accuracy limits of the simulations over the full range of retention factor and diffusion constant values that is practically relevant for most LC applications. Subsequently filling up the spheres and cylinders with a central solid core, while keeping the same packing geometry and the same mobile phase (same thermodynamic retention equilibrium), it was found that the core induces an additional obstruction which reduces the effective intra-particle diffusion coefficient exactly with a factor γ(part)=2/(2+ρ³) for spherical particles and γ(part)=1/(1+ρ²) for cylinders (ρ is the ratio of the core to the particle diameter, ρ=d(core)/d(part)). These expressions hold independently of the packing geometry, the value of the diffusion coefficients and the equilibrium constant or the size of the core. The expressions also imply that, if considering equal mobile phase conditions, the presence of the solid core will never reduce the particle contribution to the B-term band broadening with more than 33% (50% in case of cylindrical pillars). PMID:21122871

  10. Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61 or McaS) and its interaction with RNA polymerase core may link transcription to mRNA fate.

    Science.gov (United States)

    van Nues, Rob W; Castro-Roa, Daniel; Yuzenkova, Yulia; Zenkin, Nikolay

    2016-04-01

    Coupled transcription and translation in bacteria are tightly regulated. Some small RNAs (sRNAs) control aspects of this coupling by modifying ribosome access or inducing degradation of the message. Here, we show that sRNA IsrA (IS61 or McaS) specifically associates with core enzyme of RNAPin vivoandin vitro, independently of σ factor and away from the main nucleic-acids-binding channel of RNAP. We also show that, in the cells, IsrA exists as ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase. Our findings suggest that IsrA might be directly involved in transcription or can participate in regulation of gene expression by delivering proteins associated with it to target mRNAs through its interactions with transcribing RNAP and through regions of sequence-complementarity with the target. In this eukaryotic-like model only in the context of a complex with its target, IsrA and its associated proteins become active. In this manner, in the form of sRNPs, bacterial sRNAs could regulate a number of targets with various outcomes, depending on the set of associated proteins. PMID:26609136

  11. Direct Measurement of Local Chromatin Fluidity Using Optical Trap Modulation Force Spectroscopy

    OpenAIRE

    Roopa, T.; Shivashankar, G. V.

    2006-01-01

    Chromatin assembly is condensed by histone tail-tail interactions and other nuclear proteins into a highly compact structure. Using an optical trap modulation force spectroscopy, we probe the effect of tail interactions on local chromatin fluidity. Chromatin fibers, purified from mammalian cells, are tethered between a microscope coverslip and a glass micropipette. Mechanical unzipping of tail interactions, using the micropipette, lead to the enhancement of local fluidity. This is measured us...

  12. Chromatin preparation and ChIP from Drosophila brain and discs tissues

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Constance Richter, Katarzyna Oktaba, Juerg Mueller & Juergen A. Knoblich ### Abstract Chromatin preparation and chromatin immunoprecipitation (ChIP) protocol as described in Oktaba et al., 2008, Dev Cell, 15, 877-89. The protocol includes description of chromatin preparation from larval tissues, ChIP and quantitative analysis of ChIP material. ### Procedure **1. First “fast” dissection**: Dissect for 20 minutes third instar larvae in ice-cold PBS and remove gu...

  13. The Proteomic Investigation of Chromatin Functional Domains Reveals Novel Synergisms among Distinct Heterochromatin Components*

    OpenAIRE

    Soldi, Monica; Bonaldi, Tiziana

    2013-01-01

    Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent ...

  14. A chromatin activity based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing

    OpenAIRE

    Liu, Cui; Yu, Yanbao; Liu, Feng; Wei, Xin; Wrobel, John A; Gunawardena, Harsha P.; Zhou, Li; Jin, Jian; Chen, Xian

    2014-01-01

    Immune cells develop endotoxin tolerance (ET) after prolonged stimulation. ET increases the level of a repression mark H3K9me2 in the transcriptional-silent chromatin specifically associated with pro-inflammatory genes. However, it is not clear what proteins are functionally involved in this process. Here we show that a novel chromatin activity based chemoproteomic (ChaC) approach can dissect the functional chromatin protein complexes that regulate ET-associated inflammation. Using UNC0638 th...

  15. A critical role for chromatin in mounting a synergistic transcriptional response to GAL4-VP16.

    OpenAIRE

    Chang, C; Gralla, J D

    1994-01-01

    The role of chromatin in mounting a synergistic transcriptional response to GAL4-VP16 was investigated. Strong synergy was observed when chromatin templates were used in vitro. The synergy was severely reduced when naked DNA templates were transcribed. In vivo synergy was strong when nonreplicating templates were used. However, the use of replicating templates, which involved transient disruptions of chromatin, led to strong reductions in synergy. In both of these low-synergy responses, trans...

  16. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species

    OpenAIRE

    Lee, Hye-Ran; Zhang, Wenli; Langdon, Tim; Jin, Weiwei; Yan, Huihuang; Cheng, Zhukuan; Jiang, Jiming

    2005-01-01

    The functional centromeres of rice (Oryza sativa, AA genome) chromosomes contain two key DNA components: the CRR centromeric retrotransposons and a 155-bp satellite repeat, CentO. However, several wild Oryza species lack the CentO repeat. We developed a chromatin immunoprecipitation-based technique to clone DNA fragments derived from chromatin containing the centromeric histone H3 variant CenH3. Chromatin immunoprecipitation cloning was carried out in the CentO-less species Oryza rhizomatis (...

  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. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

    OpenAIRE

    Monica Soldi; Alessandro Cuomo; Michael Bremang; Tiziana Bonaldi

    2013-01-01

    Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, re...

  19. Evolution of histone 2A for chromatin compaction in eukaryotes

    OpenAIRE

    Macadangdang, Benjamin R; Oberai, Amit; Spektor, Tanya; Campos, Oscar A; Sheng, Fang; Carey, Michael F.; Vogelauer, Maria; Kurdistani, Siavash K

    2014-01-01

    eLife digest There are up to three meters of DNA in a human cell. To fit this length into the cell's nucleus in an organized manner, DNA is wrapped around proteins called histones and then tightly packaged to form a structure called chromatin. The interaction between the histones and the DNA is helped by certain amino acids on the surface of the histones fitting snugly into the DNA molecule. Plants and animals have genomes that are significantly larger than those of single-celled organisms. H...

  20. Effects of nuclear isolation on psoralen affinity for chromatin

    International Nuclear Information System (INIS)

    We have tested the effects of nuclear isolation on intercalation of TMP (a psoralen) at specific sequences and in total DNA of cultured human cells. DNA in nuclei photobound about 20% more TMP than in cells and about 10% as much as purified DNA. In contrast, a transcribed ras gene and a randomly selected polymorphic sequence each bound about 20% more TMP than total DNA in cells. However, in nuclei, as in purified DNA, both sequences were just as sensitive as total DNA. Apparently, chromatin in cells exists within diverse TMP-binding environments and some of this diversity was lost upon nuclear isolation

  1. Chromatin immunoselection defines a TAL-1 target gene.

    OpenAIRE

    Cohen-Kaminsky, S; Maouche-Chrétien, L; Vitelli, L; Vinit, M A; Blanchard, I; M. Yamamoto; Peschle, C; Roméo, P H

    1998-01-01

    Despite the major functions of the basic helix-loop-helix transcription factor TAL-1 in hematopoiesis and T-cell leukemogenesis, no TAL-1 target gene has been identified. Using immunoprecipitation of genomic fragments bound to TAL-1 in the chromatin of murine erythro-leukemia (MEL) cells, we found that 10% of the immunoselected fragments contained a CAGATG or a CAGGTG E-box, followed by a GATA site. We studied one of these fragments containing two E-boxes, CAGATG and CAGGTC, followed by a GAT...

  2. Evaluation of sperm chromatin structure in boar semen

    Directory of Open Access Journals (Sweden)

    Banaszewska Dorota

    2015-06-01

    Full Text Available This study was an attempt to evaluate sperm chromatin structure in the semen of insemination boars. Preparations of semen were stained with acridine orange, aniline blue, and chromomycin A3. Abnormal protamination occurred more frequently in young individuals whose sexual development was not yet complete, but may also be an individual trait. This possibility is important to factor into the decision regarding further exploitation of insemination boars. Thus a precise assessment of abnormalities in the protamination process would seem to be expedient as a tool supplementing morphological and molecular evaluation of semen. Disruptions in nucleoprotein structure can be treated as indicators of the biological value of sperm cells.

  3. Condensation of interphase chromatin in nuclei of synchronized chinese hamster ovary (CHO-K1) cells.

    Science.gov (United States)

    Gacsi, Mariann; Nagy, Gabor; Pinter, Gabor; Basnakian, Alexei G; Banfalvi, Gaspar

    2005-01-01

    Reversibly permeabilized cells have been used to visualize interphase chromatin structures in the presence and absence of biotinylated nucleotides. By reversing permeabilization, it was possible to confirm the existence of a flexible chromatin folding pattern through a series of transient geometric forms such as supercoiled, circular forms, chromatin bodies, thin and thick fibers, and elongated chromosomes. Our results show that the incorporation of biotin-11-dUTP interferes with chromatin condensation, leading to the accumulation of decondensed chromatin structures. Chromatin condensation without nucleotide incorporation was also studied in cell populations synchronized by centrifugal elutriation. After reversal of permeabilization, nuclei were isolated and chromatin structures were visualized after DAPI staining by fluorescent microscopy. Decondensed veil-like structures were observed in the early S phase (at an average C-value of 2.21), supercoiled chromatin later in the early S (2, 55 C), fibrous structures in the early mid S phase (2, 76 C), ribboned structures in the mid-S phase (2, 98 C), continuous chromatin strings later in the mid-S phase (3,28), elongated prechromosomes in the late S-phase (3, 72 C), precondensed chromosomes at the end and after the S phase (3, 99 C). Fluorescent microscopy revealed that neither interphase nor metaphase chromosomes are separate entities but form a linear array arranged in a semicircle. Linear arrangement was confirmed by computer image analysis. PMID:15684719

  4. Erythroid-specific gene chromatin has an altered association with linker histones.

    OpenAIRE

    Ridsdale, J A; Rattner, J.B.; Davie, J R

    1988-01-01

    The chromatin of several genes was assayed for sensitivity to DNAase I and for solubility as polynucleosomes in 0.15 M NaCl. The degree of solubility of chromatin fragments as polynucleosomes in 0.15 M NaCl correlates well with the sensitivity to DNAase I for several genes. Chromatin of repressed, housekeeping and erythroid-specific genes can be distinguished as distinct groups by the degree to which they display these properties. NaCl precipitation of chromatin fragments stripped and then re...

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

    Institute of Scientific and Technical Information of China (English)

    LiuWang; AihuaZheng; LingYi; ChongrenXu; MingxiaoDing; HongkuiDeng

    2005-01-01

    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.

  6. Chromatin Assembly at Kinetochores Is Uncoupled from DNA Replication

    Science.gov (United States)

    Shelby, Richard D.; Monier, Karine; Sullivan, Kevin F.

    2000-01-01

    The specification of metazoan centromeres does not depend strictly on centromeric DNA sequences, but also requires epigenetic factors. The mechanistic basis for establishing a centromeric “state” on the DNA remains unclear. In this work, we have directly examined replication timing of the prekinetochore domain of human chromosomes. Kinetochores were labeled by expression of epitope-tagged CENP-A, which stably marks prekinetochore domains in human cells. By immunoprecipitating CENP-A mononucleosomes from synchronized cells pulsed with [3H]thymidine we demonstrate that CENP-A–associated DNA is replicated in mid-to-late S phase. Cytological analysis of DNA replication further demonstrated that centromeres replicate asynchronously in parallel with numerous other genomic regions. In contrast, quantitative Western blot analysis demonstrates that CENP-A protein synthesis occurs later, in G2. Quantitative fluorescence microscopy and transient transfection in the presence of aphidicolin, an inhibitor of DNA replication, show that CENP-A can assemble into centromeres in the absence of DNA replication. Thus, unlike most genomic chromatin, histone synthesis and assembly are uncoupled from DNA replication at the kinetochore. Uncoupling DNA replication from CENP-A synthesis suggests that regulated chromatin assembly or remodeling could play a role in epigenetic centromere propagation. PMID:11086012

  7. 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. PMID:25363760

  8. Chromatin factors affecting DNA repair in mammalian cell nuclei

    International Nuclear Information System (INIS)

    We are investigating chromatin factors that participate in the incision step of DNA repair in eukaryotic cells. Localization of repair activity within nuclei, the stability and extractability of activity, the specificity for recognizing damage in chromatin or purified DNA as substrates are of interest in this investigation of human cells, CHO cells, and their radiation sensitive mutants. We have developed procedures that provide nuclei in which their DNA behaves as a collection of circular molecules. The integrity of the DNA in human nuclei can be maintained during incubation in appropriate buffers for as long as 60 minutes. When cells or nuclei are exposed to uv light prior to incubation, incisions presumably associated with DNA repair can be demonstrated. Incision activity is stable to prior extraction of nuclei with 0.6 M NaCl, which removes many nonhistone proteins. Our studies are consistent with an hypothesis that factors responsible for initiating DNA repair are localized in the nuclear matrix. 18 references, 3 figures

  9. SF3B1 Association with Chromatin Determines Splicing Outcomes

    Directory of Open Access Journals (Sweden)

    Nir Kfir

    2015-04-01

    Full Text Available Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. One probable explanation lies in differences in chromatin organization between exons and introns. Proteomic, co-immunoprecipitation, and sedimentation analyses described here indicate that SF3B1, an essential splicing component of the U2 snRNP complex, is strongly associated with nucleosomes. ChIP-seq and RNA-seq analyses reveal that SF3B1 specifically binds nucleosomes located at exonic positions. SF3B1 binding is enriched at nucleosomes positioned over short exons flanked by long introns that are also characterized by differential GC content between exons and introns. Disruption of SF3B1 binding to such nucleosomes affects splicing of these exons similarly to SF3B1 knockdown. Our findings suggest that the association of SF3B1 with nucleosomes is functionally important for splice-site recognition and that SF3B1 conveys splicing-relevant information embedded in chromatin structure.

  10. Dynamic Recruitment of Functionally Distinct Swi/Snf Chromatin Remodeling Complexes Modulates Pdx1 Activity in Islet β Cells

    Directory of Open Access Journals (Sweden)

    Brian McKenna

    2015-03-01

    Full Text Available Pdx1 is a transcription factor of fundamental importance to pancreas formation and adult islet β cell function. However, little is known about the positive- and negative-acting coregulators recruited to mediate transcriptional control. Here, we isolated numerous Pdx1-interacting factors possessing a wide range of cellular functions linked with this protein, including, but not limited to, coregulators associated with transcriptional activation and repression, DNA damage response, and DNA replication. Because chromatin remodeling activities are essential to developmental lineage decisions and adult cell function, our analysis focused on investigating the influence of the Swi/Snf chromatin remodeler on Pdx1 action. The two mutually exclusive and indispensable Swi/Snf core ATPase subunits, Brg1 and Brm, distinctly affected target gene expression in β cells. Furthermore, physiological and pathophysiological conditions dynamically regulated Pdx1 binding to these Swi/Snf complexes in vivo. We discuss how context-dependent recruitment of coregulatory complexes by Pdx1 could impact pancreas cell development and adult islet β cell activity.

  11. Tissue Microarray-Based Evaluation of Chromatin Assembly Factor-1 (CAF-1/p60 as Tumour Prognostic Marker

    Directory of Open Access Journals (Sweden)

    Stefania Staibano

    2012-09-01

    Full Text Available In this study we aimed to confirm the emerging role of Chromatin Assembly Factor 1 (CAF-1 p60 as a new proliferation and prognostic marker for cancer and to test the usefulness of the tissue microarray technique (TMA for CAF-1 p60 rapid screening in several human malignancies. CAF-1 is a histone chaperone, regulating chromatin dynamics during DNA replication and repair in eukaryotics. TMA is a powerful high-throughput methodology in the study of cancer, allowing simultaneous assessment of different biomarkers within large numbers of tissue specimens. We generated TMA taking 3 mm diameter-core biopsies from oral squamous cell carcinoma, prostate cancer, salivary gland tumours and skin melanoma specimens, which had been previously tested for CAF-1 p60 on routine tissue sections. We also analysed, for the first time, 30 larynx and 30 skin squamous cell carcinomas. CAF-1 p60 resulted over-expressed in both the tissue sections and the TMA specimens, with the highest levels of expression in tumours which were more aggressive and metastasizing. Notably, a high degree of agreement was found between the CAF-1 p60 assessment on TMAs and on routine tissue sections. Our findings confirm the prognostic role of CAF-1 p60 and indicate TMA as a really advantageous method for CAF-1 p60 immunohistochemical screening, allowing savings on both tissue quantity and operator-time.

  12. 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

  13. Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 - 15, 2016 - Strasbourg, France.

    Science.gov (United States)

    Bey, Till; Jamge, Suraj; Klemme, Sonja; Komar, Dorota Natalia; Le Gall, Sabine; Mikulski, Pawel; Schmidt, Martin; Zicola, Johan; Berr, Alexandre

    2016-08-01

    In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meeting to remember. In this article we summarize some of the new insights into chromatin, epigenetics, and epigenomics research and highlight nascent ideas and emerging concepts in this exciting area of research. PMID:27184433

  14. Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications

    Directory of Open Access Journals (Sweden)

    Wang Jiang

    2009-07-01

    Full Text Available Abstract Background ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated. Results In this paper, we have developed a computational method to generate the first genome-wide landscape of interactions between ATP-dependent chromatin remodeling and the covalent modification of histones in Saccharomyces cerevisiae. Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. Our results also demonstrate that most chromatin remodeling-modification interactions act via interactions of remodelers with both histone-modifying enzymes and histone residues. We also found that the co-occurrence of both modification and remodeling has significantly different influences on multiple gene features (e.g. nucleosome occupancy compared with the presence of either one. Conclusion We gave the first genome-wide picture of ATP-dependent chromatin remodeling-histone modification interactions. We also revealed how these two activities work together to regulate chromatin structure and function. Our results suggest that distinct strategies for regulating chromatin activity are selectively employed by genes with different properties.

  15. Radiolysis of chromatin extracted from cultured mammalian cells: formation of DNA-protein cross links

    International Nuclear Information System (INIS)

    Chromatin extracted from Chinese hamster lung fibroblasts has been examined for the formation of radiation-induced DNA-protein cross links, using a membrane filter assay. The relative efficiencies of the aqueous radical intermediates, 0H., esub(aq)- and 02-, were investigated. Cross links were found in gamma-irradiated isolated chromatin and in chromatin irradiated in the cell before isolation. When isolated chromatin was irradiated under conditions in which the chromosomal proteins were dissociated from the DNA, no cross links were detectable. The most efficient radical for the production of cross links in irradiated, isolated chromatin was found to be the hydroxyl radical, whereas, the superoxide radical was essentially ineffective. For chromatin irradiated in the cell before isolation, the greatest effect was seen for cells irradiated in an atmosphere of nitrous oxide, suggesting the hydroxyl radical may be involved in the formation of cross links in intact cells also. The formation of cross links in chromatin irradiated in cells before isolation was considerably less efficient than in irradiated, isolated chromatin. (author)

  16. Induction of stable protein-deoxyribonucleic acid adducts in Chinese hamster cell chromatin by ultraviolet light

    International Nuclear Information System (INIS)

    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

  17. Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Waterfall, Joshua J; Kim, Dong Wook;

    2015-01-01

    facilitates recruitment of co-activators to activate transcription. Here we show that in addition to hormone-independent TR occupancy, ChIP-seq against endogenous TR in mouse liver tissue demonstrates considerable hormone-induced TR recruitment to chromatin associated with chromatin remodelling and activated...

  18. 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.

  19. A Testis-Specific Chaperone and the Chromatin Remodeler ISWI Mediate Repackaging of the Paternal Genome

    Directory of Open Access Journals (Sweden)

    Cécile M. Doyen

    2015-11-01

    Full Text Available During spermatogenesis, the paternal genome is repackaged into a non-nucleosomal, highly compacted chromatin structure. Bioinformatic analysis revealed that Drosophila sperm chromatin proteins are characterized by a motif related to the high-mobility group (HMG box, which we termed male-specific transcript (MST-HMG box. MST77F is a MST-HMG-box protein that forms an essential component of sperm chromatin. The deposition of MST77F onto the paternal genome requires the chaperone function of tNAP, a testis-specific NAP protein. MST77F, in turn, enables the stable incorporation of MST35Ba and MST35Bb into sperm chromatin. Following MST-HMG-box protein deposition, the ATP-dependent chromatin remodeler ISWI mediates the appropriate organization of sperm chromatin. Conversely, at fertilization, maternal ISWI targets the paternal genome and drives its repackaging into de-condensed nucleosomal chromatin. Failure of this transition in ISWI mutant embryos is followed by mitotic defects, aneuploidy, and haploid embryonic divisions. Thus, ISWI enables bi-directional transitions between two fundamentally different forms of chromatin.

  20. A Model of Repetitive-DNA-Organized Chromatin Network of Interphase Chromosomes

    Directory of Open Access Journals (Sweden)

    Shao-Jun Tang

    2012-03-01

    Full Text Available During interphase, chromosomes are relatively de-condensed in the nuclear space. Interphase chromosomes are known to occupy nuclear space in a non-random manner (chromosome territory; however, their internal structures are poorly defined. In particular, little is understood about the molecular mechanisms that govern the internal organization of interphase chromosomes. The author recently proposed that pairing (or interaction of repetitive DNA-containing chromatin regions is a critical driving force that specifies the higher-order organization of eukaryotic chromosomes. Guided by this theoretical framework and published experimental data on the structure of interphase chromosomes and the spatial distribution of repetitive DNA in interphase nuclei, I postulate here a molecular structure of chromatin organization in interphase chromosomes. According to this model, an interphase chromosome is a chromatin mesh (or lattice that is formed by repeat pairing (RP. The mesh consists of two types of structural components: chromosome nodes and loose chromatin fibers. Chromosome nodes are DNA repeat assemblies (RAs that are formed via RP, while loose fibers include chromatin loops that radiate from the nodes. Different loops crosslink by RPs and form a large integrated chromatin network. I suggest that the organization of the chromatin network of a given interphase chromosome is intrinsically specified by the distribution of repetitive DNA elements on the linear chromatin. The stability of the organization is governed by the collection of RA-formed nodes, and the dynamics of the organization is driven by the assembling and disassembling of the nodes.

  1. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    International Nuclear Information System (INIS)

    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)

  2. 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...

  3. 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

    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 β-glucuronidase gene and the firefly luciferase gene, driven by different prom

  4. The enzymes LSD1 and Set1A cooperate with the viral protein HBx to establish an active hepatitis B viral chromatin state

    Science.gov (United States)

    Alarcon, Valentina; Hernández, Sergio; Rubio, Lorena; Alvarez, Francisca; Flores, Yvo; Varas-Godoy, Manuel; De Ferrari, Giancarlo V.; Kann, Michael; Villanueva, Rodrigo A.; Loyola, Alejandra

    2016-01-01

    With about 350 million people chronically infected around the world hepatitis B is a major health problem. Template for progeny HBV synthesis is the viral genome, organized as a minichromosome (cccDNA) inside the hepatocyte nucleus. How viral cccDNA gene expression is regulated by its chromatin structure; more importantly, how the modulation of this structure impacts on viral gene expression remains elusive. Here, we found that the enzyme SetDB1 contributes to setting up a repressed cccDNA chromatin state. This repressive state is activated by the histone lysine demethylase-1 (LSD1). Consistently, inhibiting or reducing LSD1 levels led to repression of viral gene expression. This correlates with the transcriptionally repressive mark H3K9 methylation and reduction on the activating marks H3 acetylation and H3K4 methylation on viral promoters. Investigating the importance of viral proteins we found that LSD1 recruitment to viral promoters was dependent on the viral transactivator protein HBx. Moreover, the histone methyltransferase Set1A and HBx are simultaneously bound to the core promoter, and Set1A expression correlates with cccDNA H3K4 methylation. Our results shed light on the mechanisms of HBV regulation mediated by the cccDNA chromatin structure, offering new therapeutic targets to develop drugs for the treatment of chronically infected HBV patients. PMID:27174370

  5. The enzymes LSD1 and Set1A cooperate with the viral protein HBx to establish an active hepatitis B viral chromatin state.

    Science.gov (United States)

    Alarcon, Valentina; Hernández, Sergio; Rubio, Lorena; Alvarez, Francisca; Flores, Yvo; Varas-Godoy, Manuel; De Ferrari, Giancarlo V; Kann, Michael; Villanueva, Rodrigo A; Loyola, Alejandra

    2016-01-01

    With about 350 million people chronically infected around the world hepatitis B is a major health problem. Template for progeny HBV synthesis is the viral genome, organized as a minichromosome (cccDNA) inside the hepatocyte nucleus. How viral cccDNA gene expression is regulated by its chromatin structure; more importantly, how the modulation of this structure impacts on viral gene expression remains elusive. Here, we found that the enzyme SetDB1 contributes to setting up a repressed cccDNA chromatin state. This repressive state is activated by the histone lysine demethylase-1 (LSD1). Consistently, inhibiting or reducing LSD1 levels led to repression of viral gene expression. This correlates with the transcriptionally repressive mark H3K9 methylation and reduction on the activating marks H3 acetylation and H3K4 methylation on viral promoters. Investigating the importance of viral proteins we found that LSD1 recruitment to viral promoters was dependent on the viral transactivator protein HBx. Moreover, the histone methyltransferase Set1A and HBx are simultaneously bound to the core promoter, and Set1A expression correlates with cccDNA H3K4 methylation. Our results shed light on the mechanisms of HBV regulation mediated by the cccDNA chromatin structure, offering new therapeutic targets to develop drugs for the treatment of chronically infected HBV patients. PMID:27174370

  6. Herpes simplex virus 1 induces egress channels through marginalized host chromatin.

    Science.gov (United States)

    Myllys, Markko; Ruokolainen, Visa; Aho, Vesa; Smith, Elizabeth A; Hakanen, Satu; Peri, Piritta; Salvetti, Anna; Timonen, Jussi; Hukkanen, Veijo; Larabell, Carolyn A; Vihinen-Ranta, Maija

    2016-01-01

    Lytic infection with herpes simplex virus type 1 (HSV-1) induces profound modification of the cell nucleus including formation of a viral replication compartment and chromatin marginalization into the nuclear periphery. We used three-dimensional soft X-ray tomography, combined with cryogenic fluorescence, confocal and electron microscopy, to analyse the transformation of peripheral chromatin during HSV-1 infection. Our data showed an increased presence of low-density gaps in the marginalized chromatin at late infection. Advanced data analysis indicated the formation of virus-nucleocapsid-sized (or wider) channels extending through the compacted chromatin of the host. Importantly, confocal and electron microscopy analysis showed that these gaps frequently contained viral nucleocapsids. These results demonstrated that HSV-1 infection induces the formation of channels penetrating the compacted layer of cellular chromatin and allowing for the passage of progeny viruses to the nuclear envelope, their site of nuclear egress. PMID:27349677

  7. Early aberrations in chromatin dynamics in embryos produced under In vitro conditions

    DEFF Research Database (Denmark)

    Deshmukh, Rahul Shahaji; Østrup, Olga; Strejcek, Frantisek;

    2012-01-01

    standard to that of embryos produced by IVF, parthenogenetic activation (PA), or SCNT. In contrast to IV embryos, chromatin spatial and temporal dynamics in PA, IVF, and SCNT embryos were altered; starting with aberrant chromatin-nuclear envelope interactions at the two-cell stage, delayed chromatin...... decondensation and nucleolar development at the four-cell stage, and ultimately culminating in failure of proper first lineage segregation at the blastocyst stage, demonstrated by poorly defined inner cell mass. Interestingly, in vitro produced (IVP) embryos also lacked a heterochromatin halo around nucleolar...... precursors, indicating imperfections in global chromatin remodeling after fertilization/activation. Porcine IV-produced zygotes and embryos display a well-synchronized pattern of chromatin dynamics compatible with genome activation and regular nucleolar formation at the four-cell stage. Production of porcine...

  8. Time-resolved spectroscopy and fluorescence resonance energy transfer in the study of excimer laser damage of chromatin

    Science.gov (United States)

    Radu, L.; Mihailescu, I.; Radu, S.; Gazdaru, D.

    2007-09-01

    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.

  9. Assembly of telomeric chromatin to create ALTernative endings.

    Science.gov (United States)

    O'Sullivan, Roderick J; Almouzni, Genevieve

    2014-11-01

    Circumvention of the telomere length-dependent mechanisms that control the upper boundaries of cellular proliferation is necessary for the unlimited growth of cancer. Most cancer cells achieve cellular immortality by up-regulating the expression of telomerase to extend and maintain their telomere length. However, a small but significant number of cancers do so via the exchange of telomeric DNA between chromosomes in a pathway termed alternative lengthening of telomeres, or ALT. Although it remains to be clarified why a cell chooses the ALT pathway and how ALT is initiated, recently identified mutations in factors that shape the chromatin and epigenetic landscape of ALT telomeres are shedding light on these mechanisms. In this review, we examine these recent findings and integrate them into the current models of the ALT mechanism. PMID:25172551

  10. 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.

  11. 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

    protein- protein interaction network. We determined the Haspin consensus motif and the co-crystal structure of the kinase with the histone H3 tail. The structure revealed a unique bent substrate binding mode positioning the histone H3 residues Arg2 and Lys4 adjacent to the Haspin phosphorylated threonine......Recent discoveries have highlighted the importance of Haspin kinase activity for the correct positioning of the kinase Aurora B at the centromere. Haspin phosphorylates Thr3 of the histone H3 (H3), which provides a signal for Aurora B to localize to the centromere of mitotic chromosomes. To date......, 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...

  12. Live visualization of chromatin dynamics with fluorescent TALEs.

    Science.gov (United States)

    Miyanari, Yusuke; Ziegler-Birling, Céline; Torres-Padilla, Maria-Elena

    2013-11-01

    The spatiotemporal organization of genomes in the nucleus is an emerging key player to regulate genome function. Live imaging of nuclear organization dynamics would be a breakthrough toward uncovering the functional relevance and mechanisms regulating genome architecture. Here, we used transcription activator-like effector (TALE) technology to visualize endogenous repetitive genomic sequences. We established TALE-mediated genome visualization (TGV) to label genomic sequences and follow nuclear positioning and chromatin dynamics in cultured mouse cells and in the living organism. TGV is highly specific, thus allowing differential labeling of parental chromosomes by distinguishing between single-nucleotide polymorphisms (SNPs). Our findings provide a framework to address the function of genome architecture through visualization of nuclear dynamics in vivo. PMID:24096363

  13. Impact of sperm DNA chromatin in the clinic.

    Science.gov (United States)

    Ioannou, Dimitrios; Miller, David; Griffin, Darren K; Tempest, Helen G

    2016-02-01

    The paternal contribution to fertilization and embryogenesis is frequently overlooked as the spermatozoon is often considered to be a silent vessel whose only function is to safely deliver the paternal genome to the maternal oocyte. In this article, we hope to demonstrate that this perception is far from the truth. Typically, infertile men have been unable to conceive naturally (or through regular IVF), and therefore, a perturbation of the genetic integrity of sperm heads in infertile males has been under-considered. The advent of intracytoplasmic sperm injection (ICSI) however has led to very successful treatment of male factor infertility and subsequent widespread use in IVF clinics worldwide. Until recently, little concern has been raised about the genetic quality of sperm in ICSI patients or the impact genetic aberrations could have on fertility and embryogenesis. This review highlights the importance of chromatin packaging in the sperm nucleus as essential for the establishment and maintenance of a viable pregnancy. PMID:26678492

  14. H3K9 acetylation and radial chromatin positioning

    Czech Academy of Sciences Publication Activity Database

    Strašák, Luděk; Bártová, Eva; Harničarová, Andrea; Galiová-Šustáčková, Gabriela; Krejčí, Jana; Kozubek, Stanislav

    2009-01-01

    Roč. 220, č. 1 (2009), s. 91-101. ISSN 0021-9541 R&D Projects: GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535; GA AV ČR(CZ) 1QS500040508; GA AV ČR(CZ) IAA5004306; GA ČR(CZ) GA204/06/0978 Grant ostatní: GA ČR(CZ) GP310/07/P480 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : chromatin structure * RIDGE and anti-RIDGE regions * H3K9 acetylation Subject RIV: BO - Biophysics Impact factor: 4.586, year: 2009

  15. Mutations in chromatin machinery and pediatric high-grade glioma.

    Science.gov (United States)

    Lulla, Rishi R; Saratsis, Amanda Muhs; Hashizume, Rintaro

    2016-03-01

    Pediatric central nervous system tumors are the most common solid tumor of childhood. Of these, approximately one-third are gliomas that exhibit diverse biological behaviors in the unique context of the developing nervous system. Although low-grade gliomas predominate and have favorable outcomes, up to 20% of pediatric gliomas are high-grade. These tumors are a major contributor to cancer-related morbidity and mortality in infants, children, and adolescents, with long-term survival rates of only 10 to 15%. The recent discovery of somatic oncogenic mutations affecting chromatin regulation in pediatric high-grade glioma has markedly improved our understanding of disease pathogenesis, and these findings have stimulated the development of novel therapeutic approaches targeting epigenetic regulators for disease treatment. We review the current perspective on pediatric high-grade glioma genetics and epigenetics, and discuss the emerging and experimental therapeutics targeting the unique molecular abnormalities present in these deadly childhood brain tumors. PMID:27034984

  16. 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. PMID:27576710

  17. Chromatin remodeling by curcumin alters endogenous aryl hydrocarbon receptor signaling.

    Science.gov (United States)

    Mohammadi-Bardbori, Afshin; Akbarizadeh, Amin Reza; Delju, Fatemeh; Rannug, Agneta

    2016-05-25

    The aim of this study was to gain more information about the mechanisms that regulate expression of the aryl hydrocarbon receptor (AHR) target gene CYP1A1. Human hepatoma cells (HepG2 and Huh7) and human immortalized keratinocytes (HaCaT) were treated with different concentrations of the dietary polyphenolic compound curcumin (CUR) alone or in combination with the natural AHR agonist 6-formylindolo[3,2-b]carbazole (FICZ). In an earlier study, we described that CUR can activate the AHR indirectly by inhibiting metabolic clearance of FICZ. Here, we measured cell viability, activation of AHR signaling, oxidative stress and histone modifying activities in response to CUR at concentrations ranging from 0.1 to 50 μM. We observed apparent non-linear responses on cell viability and activation of AHR signaling. The CYP1A1 expression and the CYP1A1 enzyme activity in the presence of CUR reflected the histone acetylation efficiency observed in nuclear extracts. At the lowest concentration, CUR significantly decreased histone deacetylase activity and increased the FICZ-induced CYP1A1 activity. In contrast, at the highest concentration, CUR increased the formation of reactive oxygen species, significantly inhibited histone acetylation, and temporally decreased FICZ-induced CYP1A1 activity. The results suggest that CUR can both increase and decrease the accessibility of DNA and thereby influence transcriptional responses to the ligand-activated AHR. This suggestion was supported by the fact that chromatin remodeling treatments with trichostatin A, p300, or 5-aza-dC increased CYP1A1 transcription. We conclude that the AHR-dependent transcriptional efficiency is modified by factors that influence the cellular redox status and the chromatin structure. PMID:27041069

  18. Genomic aberrations frequently alter chromatin regulatory genes in chordoma.

    Science.gov (United States)

    Wang, Lu; Zehir, Ahmet; Nafa, Khedoudja; Zhou, Nengyi; Berger, Michael F; Casanova, Jacklyn; Sadowska, Justyna; Lu, Chao; Allis, C David; Gounder, Mrinal; Chandhanayingyong, Chandhanarat; Ladanyi, Marc; Boland, Patrick J; Hameed, Meera

    2016-07-01

    Chordoma is a rare primary bone neoplasm that is resistant to standard chemotherapies. Despite aggressive surgical management, local recurrence and metastasis is not uncommon. To identify the specific genetic aberrations that play key roles in chordoma pathogenesis, we utilized a genome-wide high-resolution SNP-array and next generation sequencing (NGS)-based molecular profiling platform to study 24 patient samples with typical histopathologic features of chordoma. Matching normal tissues were available for 16 samples. SNP-array analysis revealed nonrandom copy number losses across the genome, frequently involving 3, 9p, 1p, 14, 10, and 13. In contrast, copy number gain is uncommon in chordomas. Two minimum deleted regions were observed on 3p within a ∼8 Mb segment at 3p21.1-p21.31, which overlaps SETD2, BAP1 and PBRM1. The minimum deleted region on 9p was mapped to CDKN2A locus at 9p21.3, and homozygous deletion of CDKN2A was detected in 5/22 chordomas (∼23%). NGS-based molecular profiling demonstrated an extremely low level of mutation rate in chordomas, with an average of 0.5 mutations per sample for the 16 cases with matched normal. When the mutated genes were grouped based on molecular functions, many of the mutation events (∼40%) were found in chromatin regulatory genes. The combined copy number and mutation profiling revealed that SETD2 is the single gene affected most frequently in chordomas, either by deletion or by mutations. Our study demonstrated that chordoma belongs to the C-class (copy number changes) tumors whose oncogenic signature is non-random multiple copy number losses across the genome and genomic aberrations frequently alter chromatin regulatory genes. © 2016 Wiley Periodicals, Inc. PMID:27072194

  19. Plasticity of Fission Yeast CENP-A Chromatin Driven by Relative Levels of Histone H3 and H4

    OpenAIRE

    Castillo, Araceli G.; Mellone, Barbara G; Partridge, Janet F; William Richardson; Hamilton, Georgina L.; Allshire, Robin C.; Pidoux, Alison L.

    2007-01-01

    The histone H3 variant CENP-A assembles into chromatin exclusively at centromeres. The process of CENP-A chromatin assembly is epigenetically regulated. Fission yeast centromeres are composed of a central kinetochore domain on which CENP-A chromatin is assembled, and this is flanked by heterochromatin. Marker genes are silenced when placed within kinetochore or heterochromatin domains. It is not known if fission yeast CENP-A(Cnp1) chromatin is confined to specific sequences or whether histone...

  20. Particle Pollution

    Science.gov (United States)

    ... Your Health Particle Pollution Public Health Issues Particle Pollution Recommend on Facebook Tweet Share Compartir Particle pollution ... see them in the air. Where does particle pollution come from? Particle pollution can come from two ...

  1. Nuclear stiffening and chromatin softening with progerin expression leads to an attenuated nuclear response to force.

    Science.gov (United States)

    Booth, Elizabeth A; Spagnol, Stephen T; Alcoser, Turi A; Dahl, Kris Noel

    2015-08-28

    Progerin is a mutant form of the nucleoskeletal protein lamin A, and its expression results in the rare premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). Patients with HGPS demonstrate several characteristic signs of aging including cardiovascular and skeletal dysfunction. Cells from HGPS patients show several nuclear abnormalities including aberrant morphology, nuclear stiffening and loss of epigenetic modifications including heterochromatin territories. However, it is unclear why these changes disproportionately impact mechanically-responsive tissues. Using micropipette aspiration, we show that nuclei in progerin-expressing cells are stiffer than control cells. Conversely, our particle tracking reveals the nuclear interior becomes more compliant in cells from HGPS patients or with progerin expression, as consistent with decreased chromatin condensation as shown previously. Additionally, we find the nuclear interior is less responsive to external mechanical force from shear or compression likely resulting from damped force propagation due to nucleoskeletal stiffening. Collectively our findings suggest that force is similarly transduced into the nuclear interior in normal cells. In HGPS cells a combination of a stiffened nucleoskeleton and softened nuclear interior leads to mechanical irregularities and dysfunction of mechanoresponsive tissues in HGPS patients. PMID:26171741

  2. Chromatin Targeting of de Novo DNA Methyltransferases by the PWWP Domain

    Institute of Scientific and Technical Information of China (English)

    Ying-ZiGe; Min-TiePu; HumairaGowher; Hai-PingWu; Jian-PingDing; AlbertJeltsch; Guo-LiangXu

    2005-01-01

    DNA methylation patterns of mammalian genomes are generated in gametogenesis and early embryonic development. Two de novo DNA methyltransferases, Dnmt3a and Dnmt3b, are responsible for the process. Both en-zymes contain a long N-terminal regulatory region linked to a conserved C-terminal domain responsible forthe catalytic activity. Although a PWWP domain in the N-terminal region has been shown to bind DNA in vitro, it is unclear how the DNA methyltransferases access their substrate in chromatin in vivo. We show here that the two proteins are associated with chromatin including mitotic chromosomes in mammalian cells, and the PWWP domain is essential for the chromatin targeting of the enzymes. The functional significance of PWWPmediated chromatin targeting is suggested by the fact that a missense mutation in this domain of human DNMT3B causes immunodeficiency, centromeric heterochromatin instability, facial anomalies (ICF) syndrome, which is characterized by loss of methylation insatellite DNA, pericentromeric instability, and immunodeficiency. We demonstrate that the mutant protein completely loses its chromatin targeting capacity. Our data establish the PWWP domain as a novel chromatin/chromosome-targeting module and suggest that the PWWP-mediated chromatin association is essential for the function of the de novo methyltransferases during development.

  3. Organophosphorous pesticide exposure alters sperm chromatin structure in Mexican agricultural workers

    International Nuclear Information System (INIS)

    Our objective was to evaluate alterations in sperm chromatin structure in men occupationally exposed to a mixture of organophosphorus pesticides (OP) because these alterations have been proposed to compromise male fertility and offspring development. Chromatin susceptibility to in situ acid-induced denaturation structure was assessed by the sperm chromatin structure assay (SCSA). Urinary levels of alkylphosphates (DAP) were used to assess exposure. Diethylthiophosphate (DETP) was the most frequent OP metabolite found in urine samples indicating that compounds derived from thiophosphoric acid were mainly used. Chromatin structure was altered in most samples. About 75% of semen samples were classified as having poor fertility potential (>30% of Percentage of DNA Fragmentation Index [DFI%]), whereas individuals without OP occupational exposure showed average DFI% values of 9.9%. Most parameters of conventional semen analysis were within normality except for the presence of immature cells (IGC) in which 82% of the samples were above reference values. There were significant direct associations between urinary DETP concentrations and mean DFI and SD-DFI but marginally (P = 0.079) with DFI%, after adjustment for potential confounders, including IGC. This suggests that OP exposure alters sperm chromatin condensation, which could be reflected in an increased number of cells with greater susceptibility to DNA denaturation. This study showed that human sperm chromatin is a sensitive target to OP exposure and may contribute to adverse reproductive outcomes. Further studies on the relevance of protein phosphorylation as a possible mechanism by which OP alter sperm chromatin are required

  4. 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.

  5. 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.

  6. Structural hierarchy of chromatin in chicken erythrocyte nuclei based on small-angle neutron scattering: Fractal nature of the large-scale chromatin organization

    International Nuclear Information System (INIS)

    The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 x 10-1 to 10-4 A-1 with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 μm and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm

  7. Nucleosomal organization of chromatin in sperm nuclei of the bivalve mollusc Aulacomya ater.

    Science.gov (United States)

    Olivares, C; Ruiz, S

    1991-03-13

    The sperm nuclei of Aulacomya ater, family Mitylidae, contain three proteins (X, Aa5 and Aa6) which are specific to this cell type coexisting with a set of five somatic-type histones. Information about the chromatin structure resulting from this kind of association is scarce. Therefore, we have probed the structure of this sperm chromatin through digestion with micrococcal nuclease in combination with salt fractionation. The data obtained have allowed us to propose a nucleosomal arrangement for this chromatin. However, two types of nucleosomes would be present in agreement with their protein components. PMID:1861676

  8. Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape.

    Science.gov (United States)

    Winter, Deborah R; Jung, Steffen; Amit, Ido

    2015-09-15

    Recent technological advances have enabled researchers to accurately and efficiently assay the chromatin dynamics of scarce cell populations. In this Opinion article, we advocate the application of these technologies to central questions in immunology. Unlike changes to other molecular structures in the cell, chromatin features can reveal the past (developmental history), present (current activity) and future (potential response to challenges) of a given immune cell type; chromatin profiling is therefore an important new tool for studying the immune-regulatory networks of health and disease. PMID:26272294

  9. Data on force-dependent structural changes of chromatin fibers measured with magnetic tweezers

    Directory of Open Access Journals (Sweden)

    Fan-Tso Chien

    2014-12-01

    Full Text Available The compaction of chromatin fibers regulates the accessibility of embedded DNA, highly associated with transcriptional activities [1]. Single molecule force spectroscopy has revealed the great details of the structural changes of chromatin fibers in the presence of external exerted force [2–7]. However, most of the studies focus on a specific force regime [2,3,8,9]. The data here show force-extension (FE traces of chromatin fibers as measured with magnetic tweezers, covering the force regime from 0 pN to 27 pN. Those traces provide information for further studies at varied force regimes.

  10. Genome-wide profiling of salt fractions maps physical properties of chromatin

    OpenAIRE

    Henikoff, Steven; Henikoff, Jorja G.; Sakai, Akiko; Loeb, Gabriel B.; Ahmad, Kami

    2009-01-01

    We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical “active” chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA ...

  11. Hybrid particles and associated methods

    Science.gov (United States)

    Fox, Robert V; Rodriguez, Rene; Pak, Joshua J; Sun, Chivin

    2015-02-10

    Hybrid particles that comprise a coating surrounding a chalcopyrite material, the coating comprising a metal, a semiconductive material, or a polymer; a core comprising a chalcopyrite material and a shell comprising a functionalized chalcopyrite material, the shell enveloping the core; or a reaction product of a chalcopyrite material and at least one of a reagent, heat, and radiation. Methods of forming the hybrid particles are also disclosed.

  12. Tagging of MADS domain proteins for chromatin immunoprecipitation

    Directory of Open Access Journals (Sweden)

    van Zuijlen Lisette GC

    2007-09-01

    Full Text Available Abstract Background Most transcription factors fulfill their role in complexes and regulate their target genes upon binding to DNA motifs located in upstream regions or introns. To date, knowledge about transcription factor target genes and their corresponding transcription factor binding sites are still very limited. Two related methods that allow in vivo identification of transcription factor binding sites are chromatin immunoprecipitation (ChIP and chromatin affinity purification (ChAP. For ChAP, the protein of interest is tagged with a peptide or protein, which can be used for affinity purification of the protein-DNA complex and hence, the identification of the target gene. Results Here, we present the results of experiments aiming at the development of a generic tagging approach for the Arabidopsis MADS domain proteins AGAMOUS, SEPALLATA3, and FRUITFULL. For this, Arabidopsis wild type plants were transformed with constructs containing a MADS-box gene fused to either a double Strep-tag® II-FLAG-tag, a triple HA-tag, or an eGFP-tag, all under the control of the constitutive double 35S Cauliflower Mosaic Virus (CaMV promoter. Strikingly, in all cases, the number of transformants with loss-of-function phenotypes was much larger than those with an overexpression phenotype. Using endogenous promoters in stead of the 35S CaMV resulted in a dramatic reduction in the frequency of loss-of-function phenotypes. Furthermore, pleiotropic defects occasionally caused by an overexpression strategy can be overcome by using the native promoter of the gene. Finally, a ChAP result is presented using GFP antibody on plants carrying a genomic fragment of a MADS-box gene fused to GFP. Conclusion This study revealed that MADS-box proteins are very sensitive to fusions with small peptide tags and GFP tags. Furthermore, for the expression of chimeric versions of MADS-box genes it is favorable to use the entire genomic region in frame to the tag of choice

  13. Circulating chromatin-anti-chromatin antibody complexes bind with high affinity to dermo-epidermal structures in murine and human lupus nephritis

    DEFF Research Database (Denmark)

    Fismen, S; Hedberg, A; Fenton, K A;

    2009-01-01

    Murine and human lupus nephritis are characterized by glomerular deposits of electron-dense structures (EDS). Dominant components of EDS are chromatin fragments and IgG antibodies. Whether glomerular EDS predispose for similar deposits in skin is unknown. We analysed (i) whether dermo...... (NZBxNZW)F1 and MRL-lpr/lpr mice and from five patients with lupus nephritis were analysed by immunofluorescence, immune electron microscopy (IEM) and co-localization TUNEL IEM. Affinity of chromatin fragments for membrane structures was determined by surface plasmon resonance. Results demonstrated (i...... were present in capillary lumina in glomeruli and skin of all nephritic individuals. Thus, chromatin-IgG complexes accounting for lupus nephritis seem to reach skin through circulation, but other undetermined factors are required for these complexes to deposit within skin membranes....

  14. Chromatin and Cell Wall Staining of Schizosaccharomyces pombe.

    Science.gov (United States)

    Hagan, Iain M

    2016-01-01

    Fission yeasts grow by tip extension, maintaining a constant width until they reach a critical size threshold and divide. Division by medial fission-which gives these yeast their name-generates a new end that arises from the site of cytokinesis. The old end, which was produced during the previous cell cycle, initiates progression of the new cell cycle, and in G2, the new end is activated in a process termed new-end takeoff (NETO). In this protocol, the fluorescent stains calcofluor and 4',6-diamidino-2-phenylindole (DAPI) are used to give a rapid and informative assessment of morphogenesis and cell-cycle progression in the fission yeast Schizosaccharomyces pombe Calcofluor reveals the timing of NETO because it stains the birth scars that are generated at new ends by cytokinesis less efficiently than the rest of the cell wall. Intense calcofluor staining of the septum and measurement of cell length are also widely used to identify dividing cells and to gauge the timing of mitotic commitment. Staining nuclei with DAPI identifies mono- and binucleated cells and complements the calcofluor staining procedure to evaluate the stages of the cell cycle and identify mitotic errors. Equally simple DAPI staining procedures reveal chromatin structure in higher resolution, facilitating more accurate staging of mitotic progression and characterization of mitotic errors. PMID:27250942

  15. First Exon Length Controls Active Chromatin Signatures and Transcription

    Directory of Open Access Journals (Sweden)

    Nicole I. Bieberstein

    2012-07-01

    Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

  16. The paternal hidden agenda: Epigenetic inheritance through sperm chromatin.

    Science.gov (United States)

    Puri, Deepika; Dhawan, Jyotsna; Mishra, Rakesh K

    2010-07-01

    Epigenetic modifications play a crucial role in developmental gene regulation. These modifications, being reversible, provide a layer of information over and above the DNA sequence, that has plasticity and leads to the generation of cell type-specific epigenomes during cellular differentiation. In almost all higher eukaryotes, the oocyte provides not only its cytoplasm, mitochondria, maternally deposited RNA and proteins but also an epigenetic component in the form of DNA and histone-modifications. During spermeiogenesis however, most of the histones are replaced by protamines, leading to a loss of the epigenetic component. The sperm is, therefore, viewed as a passive carrier of the paternal genome with a disproportionate, lower epigenetic contribution except for DNA methylation, to the next generation. A recent study overturns this view by demonstrating a locus-specific retention of histones, with specific modifications in the sperm chromatin at the promoters of developmentally important genes. This programmed retention of epigenetic marks with a role in embryonic development is suggested to offset, in some measure, the dominant maternal effect. This new finding helps in addressing the question of epigenetic transmission of environmental and 'lifestyle' experiences across generations and raises the question of 'parental conflict' at the loci that may be differentially marked. PMID:20448473

  17. Gene Expression and Chromatin Modifications Associated with Maize Centromeres

    Directory of Open Access Journals (Sweden)

    Hainan Zhao

    2016-01-01

    Full Text Available Centromeres are defined by the presence of CENH3, a variant of histone H3. Centromeres in most plant species contain exclusively highly repetitive DNA sequences, which has hindered research on structure and function of centromeric chromatin. Several maize centromeres have been nearly completely sequenced, providing a sequence-based platform for genomic and epigenomic research of plant centromeres. Here we report a high resolution map of CENH3 nucleosomes in the maize genome. Although CENH3 nucleosomes are spaced ∼190 bp on average, CENH3 nucleosomes that occupied CentC, a 156-bp centromeric satellite repeat, showed clear positioning aligning with CentC monomers. Maize centromeres contain alternating CENH3-enriched and CENH3-depleted subdomains, which account for 87% and 13% of the centromeres, respectively. A number of annotated genes were identified in the centromeres, including 11 active genes that were located exclusively in CENH3-depleted subdomains. The euchromatic histone modification marks, including H3K4me3, H3K36me3 and H3K9ac, detected in maize centromeres were associated mainly with the active genes. Interestingly, maize centromeres also have lower levels of the heterochromatin histone modification mark H3K27me2 relative to pericentromeric regions. We conclude that neither H3K27me2 nor the three euchromatic histone modifications are likely to serve as functionally important epigenetic marks of centromere identity in maize.

  18. Gene Expression and Chromatin Modifications Associated with Maize Centromeres.

    Science.gov (United States)

    Zhao, Hainan; Zhu, Xiaobiao; Wang, Kai; Gent, Jonathan I; Zhang, Wenli; Dawe, R Kelly; Jiang, Jiming

    2016-01-01

    Centromeres are defined by the presence of CENH3, a variant of histone H3. Centromeres in most plant species contain exclusively highly repetitive DNA sequences, which has hindered research on structure and function of centromeric chromatin. Several maize centromeres have been nearly completely sequenced, providing a sequence-based platform for genomic and epigenomic research of plant centromeres. Here we report a high resolution map of CENH3 nucleosomes in the maize genome. Although CENH3 nucleosomes are spaced ∼190 bp on average, CENH3 nucleosomes that occupied CentC, a 156-bp centromeric satellite repeat, showed clear positioning aligning with CentC monomers. Maize centromeres contain alternating CENH3-enriched and CENH3-depleted subdomains, which account for 87% and 13% of the centromeres, respectively. A number of annotated genes were identified in the centromeres, including 11 active genes that were located exclusively in CENH3-depleted subdomains. The euchromatic histone modification marks, including H3K4me3, H3K36me3 and H3K9ac, detected in maize centromeres were associated mainly with the active genes. Interestingly, maize centromeres also have lower levels of the heterochromatin histone modification mark H3K27me2 relative to pericentromeric regions. We conclude that neither H3K27me2 nor the three euchromatic histone modifications are likely to serve as functionally important epigenetic marks of centromere identity in maize. PMID:26564952

  19. Relocalization of human chromatin remodeling cofactor TIP48 in mitosis

    International Nuclear Information System (INIS)

    TIP48 is a highly conserved eukaryotic AAA+ protein which is an essential cofactor for several complexes involved in chromatin acetylation and remodeling, transcriptional and developmental regulation and nucleolar organization and trafficking. We show that TIP48 abundance in HeLa cells did not change during the cell cycle, nor did its distribution in various biochemical fractions. However, we observed distinct changes in the subcellular localization of TIP48 during M phase using immunofluorescence microscopy. Our studies demonstrate that in interphase cells TIP48 was found mainly in the nucleus and exhibited a distinct localization in the nuclear periphery. As the cells entered mitosis, TIP48 was excluded from the condensing chromosomes but showed association with the mitotic apparatus. During anaphase, some TIP48 was detected in the centrosome colocalizing with tubulin but the strongest staining appeared in the mitotic equator associated with the midzone central spindle. Accumulation of TIP48 in the midzone and the midbody was observed in late telophase and cytokinesis. This redeployment of TIP48 during anaphase and cytokinesis was independent of microtubule assembly. The relocation of endogenous TIP48 to the midzone/midbody under physiological conditions suggests a novel and distinct function for TIP48 in mitosis and possible involvement in the exit of mitosis

  20. Dual Chromatin and Cytoskeletal Remodeling by SETD2.

    Science.gov (United States)

    Park, In Young; Powell, Reid T; Tripathi, Durga Nand; Dere, Ruhee; Ho, Thai H; Blasius, T Lynne; Chiang, Yun-Chen; Davis, Ian J; Fahey, Catherine C; Hacker, Kathryn E; Verhey, Kristen J; Bedford, Mark T; Jonasch, Eric; Rathmell, W Kimryn; Walker, Cheryl Lyn

    2016-08-11

    Posttranslational modifications (PTMs) of tubulin specify microtubules for specialized cellular functions and comprise what is termed a "tubulin code." PTMs of histones comprise an analogous "histone code," although the "readers, writers, and erasers" of the cytoskeleton and epigenome have heretofore been distinct. We show that methylation is a PTM of dynamic microtubules and that the histone methyltransferase SET-domain-containing 2 (SETD2), which is responsible for H3 lysine 36 trimethylation (H3K36me3) of histones, also methylates α-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy. These data now identify SETD2 as a dual-function methyltransferase for both chromatin and the cytoskeleton and show a requirement for methylation in maintenance of genomic stability and the integrity of both the tubulin and histone codes. PMID:27518565

  1. HJURP is involved in the expansion of centromeric chromatin.

    Science.gov (United States)

    Perpelescu, Marinela; Hori, Tetsuya; Toyoda, Atsushi; Misu, Sadahiko; Monma, Norikazu; Ikeo, Kazuho; Obuse, Chikashi; Fujiyama, Asao; Fukagawa, Tatsuo

    2015-08-01

    The CENP-A-specific chaperone HJURP mediates CENP-A deposition at centromeres. The N-terminal region of HJURP is responsible for binding to soluble CENP-A. However, it is unclear whether other regions of HJURP have additional functions for centromere formation and maintenance. In this study, we generated chicken DT40 knockout cell lines and gene replacement constructs for HJURP to assess the additional functions of HJURP in vivo. Our analysis revealed that the middle region of HJURP associates with the Mis18 complex protein M18BP1/KNL2 and that the HJURP-M18BP1 association is required for HJURP function. In addition, on the basis of the analysis of artificial centromeres induced by ectopic HJURP localization, we demonstrate that HJURP exhibits a centromere expansion activity that is separable from its CENP-A-binding activity. We also observed centromere expansion surrounding natural centromeres after HJURP overexpression. We propose that this centromere expansion activity reflects the functional properties of HJURP, which uses this activity to contribute to the plastic establishment of a centromeric chromatin structure. PMID:26063729

  2. On simultaneous s-cores/t-cores

    OpenAIRE

    Aukerman, D; Kane, B.; Sze, L

    2009-01-01

    In this paper, the authors investigate the question of when a partition of n∈N is an s-core and also a t-core when s and t are not relatively prime. A characterization of all such s/t-cores is given, as well as a generating function dependent upon the polynomial generating functions for s/t-cores when s and t are relatively prime. Furthermore, characterizations and generating functions are given for s/t-cores which are self-conjugate and also for (e,r)/(e′,r)-cores.

  3. Hollow carbon nanospheres prepared by carbonizing polymethylmethacrylate/polyacrylonitrile core/shell polymer particles%炭化聚甲基丙烯酸甲酯/聚丙烯腈核壳聚合物制备炭纳米空心球

    Institute of Scientific and Technical Information of China (English)

    杨光智; 徐日升; 陈敏; 王霞; 凌立成; 张睿; 杨俊和

    2008-01-01

    Hollow carbon nanospheres (HCNs) were synthesized by carbonizing fine core/shell particles of polymeth-ylmethacrylate (PMMA)/polyacrylonitrile (PAN). The PMMA/PAN core/shell particles were prepared using two-stage soapless emulsion polymerization. PMMA spheres with a diameter of approximately 200 nm were first synthesised by batch mode polymerization and then a PAN shell with a thickness of approximately 30nm was polymerized on the sur-face of PMMA spheres by drop-wise addition of acrylonitrile monomer. After freeze drying, PMMA/PAN composite particles were stabilized in air at 250℃ and then carbonized in nitrogen at 1000℃. Transmission electron microscopy of the final sample showed that all PMMA cores turned into pores and all PAN shells developed into carbon shells. The PMMA/PAN composite particles were converted to HCNs with some adhering with each other and some breaking of the carbon shells.%采用炭化聚甲基丙烯酸甲酯(PMMA)/聚丙烯腈(PAN)核壳聚合物的方法制备了炭纳米空心球.以两步无皂乳液聚合法制备了PMMA/PAN核壳粒子:首先以间歇无皂乳聚合法制备出直径约200 nm的PMMA粒子乳液,再以其作为种子乳液,以饥饿滴定法在PMMA外表而聚合一层厚度约30 nm的PAN外壳.将制备的PMMA/PAN乳液冷冻干燥后,分别经过250℃预氧化及1000℃炭化工艺,制备了炭纳米空心球.透射电镜结果显示所有核壳粒子均炭化成空心球并呈现交联状态.

  4. A phylogenetic study of SPBP and RAI1: evolutionary conservation of chromatin binding modules.

    Directory of Open Access Journals (Sweden)

    Sagar Darvekar

    Full Text Available Our genome is assembled into and array of highly dynamic nucleosome structures allowing spatial and temporal access to DNA. The nucleosomes are subject to a wide array of post-translational modifications, altering the DNA-histone interaction and serving as docking sites for proteins exhibiting effector or "reader" modules. The nuclear proteins SPBP and RAI1 are composed of several putative "reader" modules which may have ability to recognise a set of histone modification marks. Here we have performed a phylogenetic study of their putative reader modules, the C-terminal ePHD/ADD like domain, a novel nucleosome binding region and an AT-hook motif. Interactions studies in vitro and in yeast cells suggested that despite the extraordinary long loop region in their ePHD/ADD-like chromatin binding domains, the C-terminal region of both proteins seem to adopt a cross-braced topology of zinc finger interactions similar to other structurally determined ePHD/ADD structures. Both their ePHD/ADD-like domain and their novel nucleosome binding domain are highly conserved in vertebrate evolution, and construction of a phylogenetic tree displayed two well supported clusters representing SPBP and RAI1, respectively. Their genome and domain organisation suggest that SPBP and RAI1 have occurred from a gene duplication event. The phylogenetic tree suggests that this duplication has happened early in vertebrate evolution, since only one gene was identified in insects and lancelet. Finally, experimental data confirm that the conserved novel nucleosome binding region of RAI1 has the ability to bind the nucleosome core and histones. However, an adjacent conserved AT-hook motif as identified in SPBP is not present in RAI1, and deletion of the novel nucleosome binding region of RAI1 did not significantly affect its nuclear localisation.

  5. Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics

    Science.gov (United States)

    Aguilar, Carlos A.; Craighead, Harold G.

    2013-10-01

    Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin -- a dynamic complex of nucleic acids and proteins -- is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.

  6. Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres.

    Science.gov (United States)

    Choi, Eun Shik; Strålfors, Annelie; Castillo, Araceli G; Durand-Dubief, Mickaël; Ekwall, Karl; Allshire, Robin C

    2011-07-01

    The histone H3 variant CENP-A is the most favored candidate for an epigenetic mark that specifies the centromere. In fission yeast, adjacent heterochromatin can direct CENP-A(Cnp1) chromatin establishment, but the underlying features governing where CENP-A(Cnp1) chromatin assembles are unknown. We show that, in addition to centromeric regions, a low level of CENP-A(Cnp1) associates with gene promoters where histone H3 is depleted by the activity of the Hrp1(Chd1) chromatin-remodeling factor. Moreover, we demonstrate that noncoding RNAs are transcribed by RNA polymerase II (RNAPII) from CENP-A(Cnp1) chromatin at centromeres. These analyses reveal a similarity between centromeres and a subset of RNAPII genes and suggest a role for remodeling at RNAPII promoters within centromeres that influences the replacement of histone H3 with CENP-A(Cnp1). PMID:21531710

  7. Physiological and Pathological Aging Affects Chromatin Dynamics, Structure and Function at the Nuclear Edge.

    Science.gov (United States)

    Robin, Jérôme D; Magdinier, Frédérique

    2016-01-01

    Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains. We will discuss here the impact of A-type Lamins loss on alterations of chromatin organization and formation of chromatin domains and how disorganization of the lamina contributes to the patho-physiology of premature aging syndromes. PMID:27602048

  8. Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Valeria Visone

    2014-09-01

    Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  9. Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome

    Science.gov (United States)

    Ernst, Jason; Kellis, Manolis

    A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, their combinatorial patterns are still unresolved and their potential for systematic de novo genome annotation remains untapped. Here, we use a multivariate Hidden Markov Model to reveal chromatin states in human T cells, based on recurrent and spatially coherent combinations of chromatin marks.We define 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, largescale repressed and repeat-associated states. Each chromatin state shows specific enrichments in functional annotations, sequence motifs and specific experimentally observed characteristics, suggesting distinct biological roles. This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function.

  10. Active remodeling of chromatin and implications for in-vivo folding

    CERN Document Server

    Ramakrishnan, N; Kuttippurathu, Lakshmi; Kumar, P B Sunil; Rao, Madan

    2015-01-01

    Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to such specific statistical conformations. Here, we show that an active chromatin model of in-vivo folding, based on the interplay between polymer elasticity, confinement, topological constraints and active stresses arising from the (un)binding of ATP-dependent chromatin-remodeling proteins gives rise to steady state conformations consistent with these experiments. Our results lead us to conjecture that the chromatin conformation resulting from this active folding optimizes information storage by co-locating gene loci which share transcription resources.

  11. Changes in chromatin-associated proteins of virus-infected tobacco leaves

    OpenAIRE

    Telgen, van, H.J.

    1985-01-01

    Symptoms of viral infections in plants often resemble disturbances in growth and development. Therefore, symptoms appear to result from an interference of the virus with the regulation of growth and development of the host plant. Particularly the non-histone chromatin- associated proteins are considered to be the regulators of specific gene expression. The aim of the present study was to elucidate whether upon infection of a plant with a virus, alterations occur in the non-histone chromatin-a...

  12. Protocol: methodology for chromatin immunoprecipitation (ChIP) in Chlamydomonas reinhardtii

    OpenAIRE

    Strenkert Daniela; Schmollinger Stefan; Schroda Michael

    2011-01-01

    Abstract We report on a detailed chromatin immunoprecipitation (ChIP) protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example f...

  13. An in vitro reconstitution system for the assessment of chromatin protein fluidity during Xenopus development

    International Nuclear Information System (INIS)

    Research highlights: → An in vitro reconstitution system was established with isolated nuclei and cytoplasm. → Chromatin fluidities were measured in the system using FRAP. → Chromatin fluidities were higher in the cytoplasm of earlier-stage embryos. → Chromatin fluidities were higher in the earlier-stage nuclei with egg-extract. → Chromatin fluidity may decrease during embryonic development. -- Abstract: Chromatin fluidity, which is one of the indicators of higher-order structures in chromatin, is associated with cell differentiation. However, little is known about the relationships between chromatin fluidity and cell differentiation status in embryonic development. We established an in vitro reconstitution system that uses isolated nuclei and cytoplasmic extracts of Xenopus embryos and a fluorescence recovery after photobleaching assay to measure the fluidities of heterochromatin protein 1 (HP1) and histone H1 during development. The HP1 and H1 fluidities of nuclei isolated from the tailbuds of early tadpole stage (stage 32) embryos in the cytoplasmic extracts of eggs and of late blastula stage (stage 9) embryos were higher than those in the cytoplasmic extracts of mid-neurula stage (stage 15) embryos. The HP1 fluidities of nuclei isolated from animal cap cells of early gastrula stage (stage 10) embryos and from the neural plates of neural stage (stage 20) embryos were higher than those isolated from the tailbuds of stage 32 embryos in egg extracts, whereas the HP1 fluidities of these nuclei were the same in the cytoplasmic extracts of stage 15 embryos. These results suggest that chromatin fluidity is dependent upon both cytoplasmic and nuclear factors and decreases during development.

  14. Alternative Lengthening of Telomeres is characterized by reduced compaction of telomeric chromatin.

    OpenAIRE

    Episkopou, Charikleia; Draskovic, Irena; Van Beneden, Amandine; Tilman, Gaëlle; Mattiussi, Marina; Gobin, Matthieu; Arnoult, Nausica; Londoño-Vallejo, Arturo; Decottignies, Anabelle

    2014-01-01

    International audience Proper telomeric chromatin configuration is thought to be essential for telomere homeostasis and stability. Previous studies in mouse suggested that loss of heterochromatin marks at telomeres might favor onset of Alternative Lengthening of Telomeres (ALT) pathway, by promoting homologous recombination. However, analysis of chromatin status at human ALT telomeres has never been reported. Here, using isogenic human cell lines and cellular hybrids, which rely either on ...

  15. Sequential chromatin immunoprecipitation protocol for global analysis through massive parallel sequencing (reChIP-seq)

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Marco Antonio Mendoza-Parra, Shankaranarayanan Pattabhiraman & Hinrich Gronemeyer ### Abstract Chromatin immunoprecipitation combined with massive parallel sequencing (ChIP-seq) is increasingly used to study protein-chromatin interactions or local epigenetic modifications at genome-wide scale. ChIP-seq can be performed directly with several ng of immunoprecipitated DNA, which is generally obtained from a several million cells, depending on the quality of the antibody. ChI...

  16. Genome Wide Analysis of Chromatin Regulation by Cocaine Reveals a Novel Role for Sirtuins

    OpenAIRE

    Renthal, William; Kumar, Arvind; Xiao, Guanghua; Wilkinson, Matthew; Covington, Herbert E.; Maze, Ian; Sikder, Devanjan; Robison, Alfred J.; LaPlant, Quincey; Dietz, David M.; Russo, Scott J.; Vialou, Vincent; Chakravarty, Sumana; Kodadek, Thomas J.; Stack, Ashley

    2009-01-01

    Changes in gene expression contribute to the long-lasting regulation of the brain’s reward circuitry seen in drug addiction, however, the specific genes regulated and the transcriptional mechanisms underlying such regulation remain poorly understood. Here, we used chromatin immunoprecipitation coupled with promoter microarray analysis to characterize genome-wide chromatin changes in the mouse nucleus accumbens, a crucial brain reward region, after repeated cocaine administration. Our findings...

  17. Complete in vitro DNA replication of SV40 chromatin in digitonin-treated permeable cells.

    OpenAIRE

    Oda,Takuzo; Watanabe,Sekiko; Hanakawa,Shiro; Nakamura, Takashi

    1980-01-01

    A permeable cell system has been developed by treatment with digitonin for studying in vitro DNA replication of chromatin. DNA replication of simian virus 40 nucleoprotein complexes (SV40 chromatin) in digitonin-treated permeable cells was analyzed by electrophoresis in agarose-gel. Autoradiography of the agarose-gel revealed that [32P]dCTP was incorporated in SV40 DNA I, II and replicating intermediates. The time course of the incorporation indicated the complete replication of SV40 DNA and ...

  18. An in vitro reconstitution system for the assessment of chromatin protein fluidity during Xenopus development

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, Ryuta; Inui, Masafumi; Hayashi, Yohei; Sedohara, Ayako [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Okabayashi, Koji [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); ICORP Organ Regeneration Project, Japan Science and Technology Agency (JST), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Ohnuma, Kiyoshi, E-mail: kohnuma@vos.nagaokaut.ac.jp [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Murata, Masayuki [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Asashima, Makoto, E-mail: asashi@bio.c.u-tokyo.ac.jp [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); ICORP Organ Regeneration Project, Japan Science and Technology Agency (JST), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Organ Development Research Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562 (Japan)

    2010-09-17

    Research highlights: {yields} An in vitro reconstitution system was established with isolated nuclei and cytoplasm. {yields} Chromatin fluidities were measured in the system using FRAP. {yields} Chromatin fluidities were higher in the cytoplasm of earlier-stage embryos. {yields} Chromatin fluidities were higher in the earlier-stage nuclei with egg-extract. {yields} Chromatin fluidity may decrease during embryonic development. -- Abstract: Chromatin fluidity, which is one of the indicators of higher-order structures in chromatin, is associated with cell differentiation. However, little is known about the relationships between chromatin fluidity and cell differentiation status in embryonic development. We established an in vitro reconstitution system that uses isolated nuclei and cytoplasmic extracts of Xenopus embryos and a fluorescence recovery after photobleaching assay to measure the fluidities of heterochromatin protein 1 (HP1) and histone H1 during development. The HP1 and H1 fluidities of nuclei isolated from the tailbuds of early tadpole stage (stage 32) embryos in the cytoplasmic extracts of eggs and of late blastula stage (stage 9) embryos were higher than those in the cytoplasmic extracts of mid-neurula stage (stage 15) embryos. The HP1 fluidities of nuclei isolated from animal cap cells of early gastrula stage (stage 10) embryos and from the neural plates of neural stage (stage 20) embryos were higher than those isolated from the tailbuds of stage 32 embryos in egg extracts, whereas the HP1 fluidities of these nuclei were the same in the cytoplasmic extracts of stage 15 embryos. These results suggest that chromatin fluidity is dependent upon both cytoplasmic and nuclear factors and decreases during development.

  19. Chromatin Adaptor Brd4 Modulates E2 Transcription Activity and Protein Stability*

    OpenAIRE

    Lee, A-Young; Chiang, Cheng-Ming

    2009-01-01

    Brd4 is a chromatin adaptor containing tandem bromodomains binding to acetylated histone H3 and H4. Although Brd4 has been implicated in the transcriptional control of papillomavirus-encoded E2 protein, it is unclear how Brd4 regulates E2 function and whether the involvement of Brd4 in transactivation and transrepression is common to different types of E2 proteins. Using DNase I footprinting performed with in vitro reconstituted human papillomavirus (HPV) chromatin and...

  20. SWI/SNF-like chromatin remodeling factor Fun30 supports point centromere function in S. cerevisiae

    OpenAIRE

    Durand-Dubief, Mickaël; Will, William Ryan; Petrini, Edoardo; Theodorou, Delphine; Harris, Rachael R.; Crawford, Margaret R.; Paszkiewicz, Konrad; Krueger, Felix; Correra, Rosa Maria; Vetter, Anna T.; Miller, J. Ross; Kent, Nicholas A.; Varga-Weisz, Patrick

    2012-01-01

    Author Summary Centromeres are essential to chromatin structures, providing a binding platform for the mitotic spindle. Defects in centromere structure or function can lead to chromosome missegregation or chromosome breakage. This, in turn, can cause cancer in metazoans. Centromeres are defined by specialized chromatin that contains the histone H3 variant CENP-A (also called CenH3, or Cse4 in budding yeast), and transcription over centromeres is tightly controlled. Budding yeast centromeres a...