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Sample records for chromatin core particle

  1. The structure of the nucleosome core particle of chromatin in chicken erythrocytes visualized by using atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    ZHAOHUI; YIZHANG; 等

    1999-01-01

    The structure of the nuclosome core particle of chromatin in chicken erythrocytes has been examined by using AFM.The 146 bp of DNA wrapped twice around the core histone octamer are clearly visualized.Both the ends of entry/exit of linker DNA are also demonstrated.The dimension of the nucleosome core particles is - 1-4 nm in height and - 13-22 nm in width.In addition,superbeads (width of - 48-57 nm,height of - 2-3 nm )are occasionally revealed,two turns of DNA around the core particles are also detected.

  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. Novel nucleosomal particles containing core histones and linker DNA but no histone H1.

    Science.gov (United States)

    Cole, Hope A; Cui, Feng; Ocampo, Josefina; Burke, Tara L; Nikitina, Tatiana; Nagarajavel, V; Kotomura, Naoe; Zhurkin, Victor B; Clark, David J

    2016-01-29

    Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ∼147 bp of DNA wrapped ∼1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ∼160 bp, and then converts it to a core particle, containing ∼147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these 'proto-chromatosomes' are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1.

  4. Particle-core coupling in 141Nd

    Institute of Scientific and Technical Information of China (English)

    LIU; Minliang(柳敏良); ZHANG; Yuhu(张玉虎); ZHOU; Xiaohong(周小红); GUO; Yingxiang(郭应祥); LIU; Zhong(刘忠); LEI; Xiangguo(雷相国); HE; Jianjun(何建军); ZHENG; Yong(郑勇); LUO; Wanju(罗万居); ZHU; Lihua(竺礼华); WEN; Shuxian(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.

  5. The structure of the core NuRD repression complex provides insights into its interaction with chromatin.

    Science.gov (United States)

    Millard, Christopher J; Varma, Niranjan; Saleh, Almutasem; Morris, Kyle; Watson, Peter J; Bottrill, Andrew R; Fairall, Louise; Smith, Corinne J; Schwabe, John W R

    2016-04-21

    The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle. ...

  7. 4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin – poor tracks

    Directory of Open Access Journals (Sweden)

    Athale Chaitanya

    2004-11-01

    Full Text Available Abstract Background The dynamics of nuclear organization, nuclear bodies and RNPs in particular has been the focus of many studies. To understand their function, knowledge of their spatial nuclear position and temporal translocation is essential. Typically, such studies generate a wealth of data that require novel methods in image analysis and computational tools to quantitatively track particle movement on the background of moving cells and shape changing nuclei. Results We developed a novel 4-D image processing platform (TIKAL for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software. With this new tool, we studied the dynamics of two different types of nuclear particles, namely nuclear bodies made from GFP-NLS-vimentin and microinjected 0.1 μm – wide polystyrene beads, by live cell time-lapse microscopy combined with single particle tracking and mobility analysis. We now provide a tool for the automatic 3-D analysis of particle movement in parallel with the acquisition of chromatin density data. Conclusions Kinetic analysis revealed 4 modes of movement: confined obstructed, normal diffusion and directed motion. Particle tracking on the background of stained chromatin revealed that particle movement is directly related to local reorganization of chromatin. Further a direct comparison of particle movement in the nucleoplasm and the cytoplasm exhibited an entirely different kinetic behaviour of vimentin particles in both compartments. The kinetics of nuclear particles were slightly affected by depletion of ATP and significantly disturbed by disruption of actin and microtubule networks. Moreover, the hydration state of the nucleus had a strong impact on the mobility of nuclear bodies since both normal diffusion and directed motion were entirely abolished when cells were challenged with 0.6 M

  8. 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

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

    Science.gov (United States)

    Rezvanfar, Mohammad Amin; Rezvanfar, Mohammad Ali; Shahverdi, Ahmad Reza; Ahmadi, Abbas; Baeeri, Maryam; Mohammadirad, Azadeh; Abdollahi, Mohammad

    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.

  10. 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.

  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.

  12. Core-shell particles at fluid interfaces

    NARCIS (Netherlands)

    Buchcic, C.

    2016-01-01

    There is a growing interest in the use of particles as stabilizers for foams and emulsions. Applying hard particles for stabilization of fluid interface is referred to as Pickering stabilization. By using hard particles instead of surfactants and polymers, fluid interfaces can be effectively stabili

  13. Magnetic core-shell silica particles

    NARCIS (Netherlands)

    Claesson, E.M.

    2007-01-01

    This thesis deals with magnetic silica core-shell colloids and related functionalized silica structures. Synthesis routes have been developed and optimized. The physical properties of these colloids have been investigated, such as the magnetic dipole moment, dipolar structure formation and rotationa

  14. Development of a particle nanoimprinting technique by core-shell particles.

    Science.gov (United States)

    Watanabe, H; Nishimura, M; Fukui, Y; Fujimoto, K

    2014-02-18

    We developed a particle nanoimprinting technique assisted by the array of core-shell particles. Core-shell particles composed of a solid core of polystyrene and a soft shell were prepared by soap-free emulsion polymerization and subsequently seeded polymerization. By the Langmuir-Blodgett method, particles were arranged into a closely packed 2D array over the water surface and transferred onto a polystyrene (PS) substrate at a regular interval. The PS substrate was heated up above its glass transition temperature (Tg) by either UV irradiation using a high-pressure Hg lamp or heat treatment in a temperature-controlled incubator. It could be observed that a nanopatterned indented surface was formed through the denting of particles into the PS substrate (particle nanoindenting). By the detachment of particles from the substrate by ultrasonication in ethanol, nanoholes were produced over the surface (particle nanoimprinting). The depth and the wall of nanoholes and their interval were tunable by the shell thickness and the 2D packing ratio of core-shell particle monolayers. The contact angle decreased from 70 degrees of the pristine particle monolayer to 13 degrees by the particle nanoindenting, and again increased to 50 degrees by detaching the particles from the substrate to create the nanoholes. The use of nanoholes as zepto-litter volume vessels enabled us to produce and arrange nanocrystals, such as NaCl and CaCO3 (zepto-reactor).

  15. 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....

  16. Hysteresis effects in the cores of particle accelerator magnets

    CERN Document Server

    AUTHOR|(CDS)2086181; Schoerling, Daniel

    A study of the hysteresis effects in the cores of particle accelerator magnets has been performed in the framework of the work presented in this thesis. This study has been focused on normal conducting particle accelerator magnets whose cores are manufactured using ferromagnetic materials. The magnetic circuits have been modelled using the developed models: one model for the magnetic circuit and one for the magnetization of the material in the core. The parameters of the magnetic circuit model have been identified with the help of simulations which rely on the finite element method (Opera 3D), while the parameters of the magnetic hysteresis model have been identified through experimental measurements performed using a method developed in the framework of this work. The modelling results have been validated by means of experimental measurements performed on two magnets: one small size magnet which has been specifically designed and manufactured, and one magnet which is currently used in a particle accelerator ...

  17. PMMA/PMMA core-shell particles with ellipsoidal, fluorescent cores: accessing rotational dynamics.

    Science.gov (United States)

    Klein, Matthias K; Klinkenberg, Nele; Schuetter, Stefan; Saenger, Nicolai; Pfleiderer, Patrick; Zumbusch, Andreas

    2015-03-10

    For several decades, nonaqueous dispersions of PMMA particles have played an important role in colloid research. They have found application as colloidal model systems, which are used to probe glassy dynamics or to explore crystal nucleation. To date, most research has focused on spherical particles, in which only translational motion can be investigated. Recently, however, there has been a surge of interest in analyzing also rotational dynamics. In this contribution, we introduce a new class of core-shell particles, which can be used as rotational probes. The colloids described herein are composed of shape anisotropic, fluorescent cores covered with nonfluorescent PMMA shells. The core-shell particles are built up in four steps. In a first step, we produce fluorescent and photo-cross-linkable PMMA colloids. In the second step, these particles are thermomechanically elongated and fixed in defined ellipsoidal shapes by photo-cross-linking. Subsequently, we cover the cross-linked, fluorescent core with a nonfluorescent PMMA shell. The shape of the resulting core-shell colloids is tunable between the initial anisotropic and perfect spherical shape. For shaping, we apply a simple solvent swelling procedure. As one option, this method yields perfect PMMA spheres with ellipsoidal, fluorescent centers. We also report morphological particle characterization using various fluorescence microscopy techniques. Finally, we demonstrate that the rotational dynamics of individual colloids can be tracked and analyzed.

  18. 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...

  19. Chimeric hepatitis B virus core particles with parts or copies of the hepatitis C virus core protein.

    OpenAIRE

    Yoshikawa, A.; Tanaka, T; Hoshi, Y.; Kato, N; K. Tachibana; Iizuka, H; Machida, A; Okamoto, H; Yamasaki, M.; Miyakawa, Y

    1993-01-01

    Either parts or multiple copies of the core gene of hepatitis C virus (HCV) were fused to the 3' terminus of the hepatitis B virus (HBV) core gene with 34 codons removed. As many as four copies of HCV core protein (720 amino acids) were fused to the carboxy terminus of truncated HBV core protein (149 amino acids) without preventing the assembly of HBV core particles. Chimeric core particles were sandwiched between monoclonal antibody to HBV core and that to HCV core, thereby indicating that a...

  20. The Core Subunit of A Chromatin-Remodeling Complex, ZmCHB101, Plays Essential Roles in Maize Growth and Development.

    Science.gov (United States)

    Yu, Xiaoming; Jiang, Lili; Wu, Rui; Meng, Xinchao; Zhang, Ai; Li, Ning; Xia, Qiong; Qi, Xin; Pang, Jinsong; Xu, Zheng-Yi; Liu, Bao

    2016-12-05

    ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages. Independent ZmCHB101 RNA interference plant lines displayed abaxially curling leaf phenotype due to increase of bulliform cell numbers, and showed impaired development of tassel and cob. RNA-seq-based transcriptome profiling revealed that ZmCHB101 dictated transcriptional reprogramming of a significant set of genes involved in plant development, photosynthesis, metabolic regulation, stress response and gene expressional regulation. Intriguingly, we found that ZmCHB101 was required for maintaining normal nucleosome density and 45 S rDNA compaction. Our findings suggest that the SWI3 protein, ZmCHB101, plays pivotal roles in maize normal growth and development via regulation of chromatin structure.

  1. Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication

    Directory of Open Access Journals (Sweden)

    Belhumeur Pierre

    2008-11-01

    Full Text Available Abstract Background HIV-1 integrase (IN is a key viral enzymatic molecule required for the integration of the viral cDNA into the genome. Additionally, HIV-1 IN has been shown to play important roles in several other steps during the viral life cycle, including reverse transcription, nuclear import and chromatin targeting. Interestingly, previous studies have demonstrated that the expression of HIV-1 IN induces the lethal phenotype in some strains of Saccharomyces cerevisiae. In this study, we performed mutagenic analyses of the C-terminal region of the catalytic core domain of HIV-1 IN in order to delineate the critical amino acid(s and/or motif(s required for the induction of the lethal phenotype in the yeast strain HP16, and to further elucidate the molecular mechanism which causes this phenotype. Results Our study identified three HIV-1 IN mutants, V165A, A179P and KR186,7AA, located in the C-terminal region of the catalytic core domain of IN that do not induce the lethal phenotype in yeast. Chromatin binding assays in yeast and mammalian cells demonstrated that these IN mutants were impaired for the ability to bind chromatin. Additionally, we determined that while these IN mutants failed to interact with LEDGF/p75, they retained the ability to bind Integrase interactor 1. Furthermore, we observed that VSV-G-pseudotyped HIV-1 containing these IN mutants was unable to replicate in the C8166 T cell line and this defect was partially rescued by complementation with the catalytically inactive D64E IN mutant. Conclusion Overall, this study demonstrates that three mutations located in the C-terminal region of the catalytic core domain of HIV-1 IN inhibit the IN-induced lethal phenotype in yeast by inhibiting the binding of IN to the host chromatin. These results demonstrate that the C-terminal region of the catalytic core domain of HIV-1 IN is important for binding to host chromatin and is crucial for both viral replication and the promotion of

  2. 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.

  3. Reprogramming chromatin

    DEFF Research Database (Denmark)

    Ehrensberger, Andreas Hasso; Svejstrup, Jesper Qualmann

    2012-01-01

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

  4. Hollow-Core Photonic Band Gap Fibers for Particle Acceleration

    Energy Technology Data Exchange (ETDEWEB)

    Noble, Robert J.; Spencer, James E.; /SLAC; Kuhlmey, Boris T.; /Sydney U.

    2011-08-19

    Photonic band gap (PBG) dielectric fibers with hollow cores are being studied both theoretically and experimentally for use as laser driven accelerator structures. The hollow core functions as both a longitudinal waveguide for the transverse-magnetic (TM) accelerating fields and a channel for the charged particles. The dielectric surrounding the core is permeated by a periodic array of smaller holes to confine the mode, forming a photonic crystal fiber in which modes exist in frequency pass-bands, separated by band gaps. The hollow core acts as a defect which breaks the crystal symmetry, and so-called defect, or trapped modes having frequencies in the band gap will only propagate near the defect. We describe the design of 2-D hollow-core PBG fibers to support TM defect modes with high longitudinal fields and high characteristic impedance. Using as-built dimensions of industrially-made fibers, we perform a simulation analysis of the first prototype PBG fibers specifically designed to support speed-of-light TM modes.

  5. Core-shell composite particles composed of biodegradable polymer particles and magnetic iron oxide nanoparticles for targeted drug delivery

    Science.gov (United States)

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

    2015-05-01

    Core-shell composite particles with biodegradability and superparamagnetic behavior were prepared using a Pickering emulsion for targeted drug delivery based on magnetic guidance. The composite particles were composed of a core of biodegradable polymer and a shell of assembled magnetic iron oxide nanoparticles. It was found that the dispersibility of the nanoparticles is crucial for controlling the core-shell structure. The addition of a small amount of dispersant into the nanoparticle's suspension could improve the dispersibility and led to the formation of composite particles with a thin magnetic shell covering a polymeric core. The composite particles were also fabricated with a model drug loaded into the core, which was released via hydrolysis of the core under strong alkaline conditions. Because the core can also be biodegraded by lipase, this result suggests that the slow release of the drug from the composite particles should occur inside the body.

  6. Antistatic coating material consisting of poly (butylacrylate-co-styrene) core-nickel shell particle

    Institute of Scientific and Technical Information of China (English)

    Min-Yeong JEONG; Byung-Yoon AHN; Sang-Koul LEE; Won-Ki LEE; Nam-Ju JO

    2009-01-01

    A transparent and antistatic coating material consisting of polymer core-metal shell particle was prepared. As a polymer core, poly(butylacrylate-co-styrene)s ([P(BA-co-sty)s]) with various compositions of butylacrylate and styrene were synthesized by emulsion polymerization. And the effect of comonomer composition on the thermal property of polymer core particle was investigated. By electroless plating method, the nickel particles were formed and deposited on the surface of P(BA-co-Sty) particles to form P(BA-co-Sty) core-nickel shell composite particles. SEM observation confirms that the nickel particles with size of 15 nm are distributed on the surface of the polymer core particles. The surface resistance of P(BA-co-Sty) core-nickel shell composite is 0.8×108Ω/cm2, enough to act as antistatic coating material.

  7. 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.

  8. Morphology and film formation of poly(butyl methacrylate)-polypyrrole core-shell latex particles

    NARCIS (Netherlands)

    Huijs, F; Lang, J

    2000-01-01

    Core-shell latex particles made of a poly(butyl methacrylate) (PBMA) core and a thin polypyrrole (PPy) shell were synthesized by two-stage polymerization. In the first stage, PBMA latex particles were synthesized in a semicontinuous process by free-radical polymerization. PBMA latex particles were l

  9. Chromatin computation.

    Directory of Open Access Journals (Sweden)

    Barbara Bryant

    Full Text Available In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this "chromatin computer" to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal--and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines.

  10. Polystyrene-Core-Silica-Shell Hybrid Particles Containing Gold and Magnetic Nanoparticles.

    Science.gov (United States)

    Tian, Jia; Vana, Philipp

    2016-02-18

    Polystyrene-core-silica-shell hybrid particles were synthesized by combining the self-assembly of nanoparticles and the polymer with a silica coating strategy. The core-shell hybrid particles are composed of gold-nanoparticle-decorated polystyrene (PS-AuNP) colloids as the core and silica particles as the shell. PS-AuNP colloids were generated by the self-assembly of the PS-grafted AuNPs. The silica coating improved the thermal stability and dispersibility of the AuNPs. By removing the "free" PS of the core, hollow particles with a hydrophobic cage having a AuNP corona and an inert silica shell were obtained. Also, Fe3O4 nanoparticles were encapsulated in the core, which resulted in magnetic core-shell hybrid particles by the same strategy. These particles have potential applications in biomolecular separation and high-temperature catalysis and as nanoreactors.

  11. DESIGN AND CONTROL OF SOAP-FREE HYDROPHILIC-HYDROPHOBIC CORE-SHELL LATEX PARTICLES WITH HIGH CARBOXYL CONTENT IN THE CORE OF THE PARTICLES

    Institute of Scientific and Technical Information of China (English)

    Wen-jiao Ji; Yi-ming Jiang; Bo-tian Li; Wei Deng; Cheng-you Kan

    2012-01-01

    Soap-free hydrophilic-hydrophobic core-shell latex particles with high carboxyl content in the core of the particles were synthesized via the seeded emulsion polymerization using methyl methacrylate (MMA),butyl acrylate (BA),methacrylic acid (MAA),styrene (St) and ethylene glycol dimethacrylate (EGDMA) as monomers,and the influences of MMA content used in the core preparation on polymerization,particle size and morphology were investigated by transmission electron microscopy,dynamic light scattering and conductometric titration.The results showed that the seeded emulsion polymerization could be carried out smoothly using "starved monomer feeding process" when MAA content in the core preparation was equal to or less than 24 wt%,and the encapsulating efficiency of the hydrophilic P(MMA-BA-MAA-EGDMA) core with the hydrophobic PSt shell decreased with the increase in MAA content.When an interlayer of P(MMA-MAA-St) with moderate polarity was inserted between the P(MMA-BA-MAA-EGDMA) core and the PSt shell,well designed soap-free hydrophilic-hydrophobic core-shell latex particles with 24 wt% MAA content in the core preparation were obtained.

  12. 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.

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

    Science.gov (United States)

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

    2013-01-01

    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.

  14. Fabrication and characteristics of spindle Fe2O3@Au core/shell particles

    Institute of Scientific and Technical Information of China (English)

    SHEN Hong-xia; YAO Jian-lin; GU Ren-ao

    2009-01-01

    The fabrication and characteristics of spindle Fe2O3@Au core/shell particle were investigated, and the effect of the core/shell nanoparticles as the surface enhanced Raman spectroscopy (SERS)-active substrates was studied. By using the seed-catalyzed reduction technique, anisotropic Fe2O3@Au core/shell particles with spindle morphology were successfully prepared. The Fe2O3 particles with spindle morphology were initially prepared as original cores. The Au nanoparticles of 2 nm were attached onto the Fe2O3 particles through organosilane molecules. Uniform Au shell formed onto Fe2O3 core modified by Au nanoparticles through the in-situ reduction of HAuCl4. The shell thickness was controlled through regulating the concentration of HAuCl4 solution. The results of TEM, XRD and UV-vis characterization show that the core/shell particles with the original shape of the Fe2O3 particles are obtained and these surfaces are covered by Au shell completely. The surface enhanced Raman spectrum of the probe molecules adsorbed on these core/shell substrates is strong and the intensity is enhanced with the increase of the thickness of Au shell or the aspect ratio of particles. The spindle Fe2O3@Au core/shell particles exhibit optimum (SERS) activity.

  15. Trafficking of hepatitis C virus core protein during virus particle assembly.

    Directory of Open Access Journals (Sweden)

    Natalie A Counihan

    2011-10-01

    Full Text Available Hepatitis C virus (HCV core protein is directed to the surface of lipid droplets (LD, a step that is essential for infectious virus production. However, the process by which core is recruited from LD into nascent virus particles is not well understood. To investigate the kinetics of core trafficking, we developed methods to image functional core protein in live, virus-producing cells. During the peak of virus assembly, core formed polarized caps on large, immotile LDs, adjacent to putative sites of assembly. In addition, LD-independent, motile puncta of core were found to traffic along microtubules. Importantly, core was recruited from LDs into these puncta, and interaction between the viral NS2 and NS3-4A proteins was essential for this recruitment process. These data reveal new aspects of core trafficking and identify a novel role for viral nonstructural proteins in virus particle assembly.

  16. Tracing the sources of particles in the East Rongbuk ice core from Mt. Qomolangma

    Institute of Scientific and Technical Information of China (English)

    XU JianZhong; HOU ShuGui; CHEN FuKun; REN JiaWen; QIN DaHe

    2009-01-01

    Sr-Nd-Pb isotopic tracer was applied, for the first time, to identifying the sources of the particles in the East Rongbuk ice core from Mt. Qomalangma (Everest). The results show that the particles in the dirty layers originate mainly from local sources, while the particles in the non-dirty layers are consistent with the features of dust from the arid regions in northwestern India. The HYSPLIT model shows that the air trajectory goes first through northwestern India before reaching the drilling site of ice core when dust storms occur in northwestern India, confirming northwestern India as a possible source of dust in the East Rongbuk ice core.

  17. Core-corona PSt/P(BA-AA) composite particles by two-stage emulsion polymerization

    Science.gov (United States)

    Xie, Delong; Ren, Xiaolin; Zhang, Xinya; Liao, Shijun

    2016-03-01

    Raspberry-shaped composite particles with polystyrene (PSt) as core and poly(n-butyl acrylate-co-acrylic acid) (P(BA-AA)) as corona were synthesized via emulsion polymerization. The random copolymer, P(BA-AA), was pre-prepared and used as a polymeric surfactant, its emulsifying properties adjusted by changing the mass ratio of BA and AA. The morphology of the resulting core-corona composite particles, P(St/P(BA-AA)), could be regulated and controlled by varying the concentrations of P(BA-AA) or the mass ratio of BA:AA in P(BA-AA). The experimental results indicate that 3.0-6.0 wt% of P(BA-AA) is required to obtain stable composite emulsions, and P(BA-AA) with a mass ratio of BA:AA = 1:2 is able to generate distinct core-corona structures. A mechanism of composite particle formation is proposed based on the high affinity between the PSt core and the hydrophobic segments of P(BA-A). The regular morphology of the colloidal film is expected to facilitate potential application of core-corona particles in the field of light scattering. Furthermore, the diversity of core-corona particles can be expanded by replacing P(BA-AA) corona particles with other amphiphilic particles.

  18. 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...

  19. Synthesis of ZnO core spike particles as composite fillers with a high throughput method

    Energy Technology Data Exchange (ETDEWEB)

    Wille, Sebastian; Koschine, Toenjes; Chluba, Christoph; Freitag, Stefan; Mishra, Yogendra Kumar; Adelung, Rainer [Funktionale Nanomaterialien, CAU Kiel (Germany)

    2011-07-01

    ZnO core spike particles are typically micro particles covered with nanoscopic spikes. They show advanced properties compared to conventional fillers like roundish particles and short fibers. An example is a very strong mechanical interlocking behaviors. This property together with its hardness makes this material very interesting for compounds with enhanced mechanical properties. In addition ZnO has very interesting electric and electronic properties, which make the range of possible applications for composites containing ZnO core spike particles very wide. In order to use ZnO core spike particles as filler for bulk materials, considerable amounts are necessary. A problem during the oxidation based synthesis of such particles using Zn-powder as source material is the separation of the single Zn-particles, which is necessary for oxygen supply, for avoiding sinter processes and allowing the nanoscopic spikes to grow. We introduce simple processing routes found as solution for this problem. Large amounts of microscopic Zn-powder can be converted to ZnO core spike particles with a total size from nanometers up to a couple of micrometers. Furthermore by changing the growth parameters it is also possible to modify the particle shape.

  20. Effect of reaction time on formation of silica core/shell particles

    Directory of Open Access Journals (Sweden)

    Milan P. Nikolić

    2015-12-01

    Full Text Available The silica core/shell nanostructures were prepared by a wet-chemical process. Silica core particles were prepared by hydrolysis and condensation of tetraethylorthosilicate. The obtained particles (average size ∼0.4 µm were used as templates for assembling of silica nanoparticles generated from highly basic sodium silicate solution. The silica core particles were functionalized with 3-aminopropyltriethoxysilane (APTES to allow electrostatic assembling of silica nanoparticles on the surface of silica core particles. In order to find the optimal conditions for synthesis of silica core/shell particles with mesoporous shells, the effect of reaction time on formation of silica nanoparticles was investigated. The effect of process parameters on generation and aggregation of silica nanoparticles prepared from highly basic sodium silicate solution was also investigated. It was shown that the size of silica nanoparticles and tendency towards aggregation increase with increasing the reaction time and temperature. These behaviours were reflected on the formation of mesoporous silica shell around silica core particles. Thin and uniform mesoporous silica layers were obtained if reaction times were kept short. When the reaction time was prolonged, the thicker and non-uniform shells were obtained.

  1. Rapid Histone-Catalyzed DNA Lesion Excision and Accompanying Protein Modification in Nucleosomes and Nucleosome Core Particles.

    Science.gov (United States)

    Weng, Liwei; Greenberg, Marc M

    2015-09-01

    C5'-Hydrogen atoms are frequently abstracted during DNA oxidation. The oxidized abasic lesion 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) is an electrophilic product of the C5'-radical. DOB is a potent irreversible inhibitor of DNA polymerase β, and forms interstrand cross-links in free DNA. We examined the reactivity of DOB within nucleosomes and nucleosome core particles (NCPs), the monomeric component of chromatin. Depending upon the position at which DOB is generated within a NCP, it is excised from nucleosomal DNA at a rate 275-1500-fold faster than that in free DNA. The half-life of DOB (7.0-16.8 min) in NCPs is shorter than any other abasic lesion. DOB's lifetime in NCPs is also significantly shorter than the estimated lifetime of an abasic site within a cell, suggesting that the observed chemistry would occur intracellularly. Histones also catalyze DOB excision when the lesion is present in the DNA linker region of a nucleosome. Schiff-base formation between DOB and histone proteins is detected in nucleosomes and NCPs, resulting in pyrrolone formation at the lysine residues. The lysines modified by DOB are often post-translationally modified. Consequently, the histone modifications described herein could affect the regulation of gene expression and may provide a chemical basis for the cytotoxicity of the DNA damaging agents that produce this lesion.

  2. Preparation of hydrogel hollow particles for cell encapsulation by a method of polyester core degradation.

    Science.gov (United States)

    Rabanel, J-M; Hildgen, P

    2004-06-01

    Implantation of encapsulated cells in particles of less than 1 mm (micro-encapsulation) has been proposed as a cell synthesized bio-molecule delivery system. Encapsulation provides immuno-isolation, protecting foreign cells from host immune system while nutrients, oxygen and therapeutic products can diffuse freely across capsule walls. A new method is described for the synthesis of a new family of hollow microparticles for cell encapsulation. Unlike other micro-encapsulation methods, encapsulation in those devices will take place after capsule synthesis, by micro-injection. The microcapsules were prepared by a three-steps original procedure: first, synthesis of a core particle, followed by coating with a layer of epichlorohydrin cross-linked amylo-pectin gel and, finally, selective degradation of the core particle to create the cavity. Initial experiments make use of amylo-pectin cross-linked with trimetaphosphate as core particle material. However, selective degradation was difficult to achieve. In further essays, polyesters were used successfully for the preparation of core particles. Optimizations were carried out and the permeability and morphology of the hollow particles were investigated. The preliminary results show that the new method has the potential to become a standard procedure to obtain hydrogel hollow particles. Moreover, the permeability study seems to be in accordance with specifications for immuno-isolation.

  3. 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.

  4. Drosophila TAP/p32 is a core histone chaperone that cooperates with NAP-1, NLP, and nucleophosmin in sperm chromatin remodeling during fertilization.

    Science.gov (United States)

    Emelyanov, Alexander V; Rabbani, Joshua; Mehta, Monika; Vershilova, Elena; Keogh, Michael C; Fyodorov, Dmitry V

    2014-09-15

    Nuclear DNA in the male gamete of sexually reproducing animals is organized as sperm chromatin compacted primarily by sperm-specific protamines. Fertilization leads to sperm chromatin remodeling, during which protamines are expelled and replaced by histones. Despite our increased understanding of the factors that mediate nucleosome assembly in the nascent male pronucleus, the machinery for protamine removal remains largely unknown. Here we identify four Drosophila protamine chaperones that mediate the dissociation of protamine-DNA complexes: NAP-1, NLP, and nucleophosmin are previously characterized histone chaperones, and TAP/p32 has no known function in chromatin metabolism. We show that TAP/p32 is required for the removal of Drosophila protamine B in vitro, whereas NAP-1, NLP, and Nph share roles in the removal of protamine A. Embryos from P32-null females show defective formation of the male pronucleus in vivo. TAP/p32, similar to NAP-1, NLP, and Nph, facilitates nucleosome assembly in vitro and is therefore a histone chaperone. Furthermore, mutants of P32, Nlp, and Nph exhibit synthetic-lethal genetic interactions. In summary, we identified factors mediating protamine removal from DNA and reconstituted in a defined system the process of sperm chromatin remodeling that exchanges protamines for histones to form the nucleosome-based chromatin characteristic of somatic cells.

  5. Importance of core electrostatic properties on the electrophoresis of a soft particle

    Science.gov (United States)

    De, Simanta; Bhattacharyya, Somnath; Gopmandal, Partha P.

    2016-08-01

    The impact of the volumetric charged density of the dielectric rigid core on the electrophoresis of a soft particle is analyzed numerically. The volume charge density of the inner core of a soft particle can arise for a dendrimer structure or bacteriophage MS2. We consider the electrokinetic model based on the conservation principles, thus no conditions for Debye length or applied electric field is imposed. The fluid flow equations are coupled with the ion transport equations and the equation for the electric field. The occurrence of the induced nonuniform surface charge density on the outer surface of the inner core leads to a situation different from the existing analysis of a soft particle electrophoresis. The impact of this induced surface charge density together with the double-layer polarization and relaxation due to ion convection and electromigration is analyzed. The dielectric permittivity and the charge density of the core have a significant impact on the particle electrophoresis when the Debye length is in the order of the particle size. We find that by varying the ionic concentration of the electrolyte, the particle can exhibit reversal in its electrophoretic velocity. The role of the polymer layer softness parameter is addressed in the present analysis.

  6. 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.

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

    Science.gov (United States)

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

    2009-03-18

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

  8. 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.

  9. Carbonaceous particles in Muztagh Ata ice core, West Kunlun Mountains, China

    Institute of Scientific and Technical Information of China (English)

    LIU XianQin; XU BaiQing; YAO TanDong; WANG NingLian; WU GuangJian

    2008-01-01

    Carbonaceous particles concentrations of OC and EC are determined using a two-step gas chroma-tography system in Muztagh Ata ice core covering the time period of 1955-2000. Over the period rep-resented by the core, OC and EC concentrations appear to have changed significantly, varied in the range of 17.7-216.7 and 6.5-124.6, and averaged 61.8, 32.9 ng·g-1, respectively. The average concen-tration of EC in Muztagh Ata ice core is much lower than that in an Alpine ice core record (100-300 ng·g-1) during the same period, but it is a factor of 14 in Greenland ice core (2.3 ng.g-1), this may induce a strong impact on the snow albedo in the last 46 years in our study area. Observations indicate two periods with obviously high deposition concentrations (1955-1965 and 1974-1989) and two periods with low concentrations (1966-1973 and 1990-1995), as well as a recent increasing trend. By com-paring EC and SO42- concentration variations and deciphering OC/EC ratios recorded in the same ice core, we can judge roughly that the carbonaceous particles deposited in Muztagh Ata ice core were attributed to fossil fuel combustion sources.

  10. Microfluidic conceived pH sensitive core-shell particles for dual drug delivery.

    Science.gov (United States)

    Khan, Ikram Ullah; Stolch, Lukas; Serra, Christophe A; Anton, Nicolas; Akasov, Roman; Vandamme, Thierry F

    2015-01-15

    In current study, we report on the synthesis of core-shell microparticles for dual drug delivery by means of a two co-axial microfluidic device and online UV assisted free radical polymerization. Before developing pH-sensitive particles, ketoprofen loaded poly(methyl acrylate) core-ranitidine HCl loaded poly(acrylamide) shell particles were produced. Influence of inner and outer phases flow rates on particle size, shape, core diameter, shell thickness, and drug release properties was studied. All the particles were monodispersed with coefficient of variation below 5%. Furthermore, their diameter ranged from 100 to 151 μm by increasing continuous (Qc) to middle (Qm) phase flow rate ratio (Qc/Qm). Core diameter varied from 58 to 115 μm by decreasing middle (Qm) to inner (Qi) phase flow rate ratio (Qm/Qi) at constant continuous phase flow rate as confirmed by SEM images. It was observed that an optimum concentration of acrylamide (30 wt%) and an appropriate combination of surfactants were necessary to get core-shell particles otherwise Janus structure was obtained. FTIR confirmed the complete polymerization of core and shell phases. MTT assay showed variation in viability of cells under non-contact and contact conditions with less cytotoxicity for the former. Under non-contact conditions LD50 was 3.1mg/mL. Release studies in USP phosphate buffer solution showed simultaneously release of ketoprofen and ranitidine HCl for non pH-sensitive particles. However, release rates of ranitidine HCl and ketoprofen were higher at low and high pH respectively. To develop pH-sensitive particles for colon targeting, the previous shell phase was admixed with few weight percentage of pH sensitive carboxyethyl acrylate monomer. Core and shell contained the same hydrophobic and hydrophilic model drugs as in previous case. The pH-sensitive shell prevented the release of the two entrapped molecules at low pH while increasing significantly their release rate at higher pH with a maximum

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

    Energy Technology Data Exchange (ETDEWEB)

    V.A. Soukhanovskii; R. Maingi; R. Raman; H.W. Kugel; B.P. LeBlanc; L. Roquemore; C.H. Skinner; NSTX Research Team

    2002-06-12

    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 t {approx} 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. Effects of Heat Treatment on the Magnetic Properties of Polymer-Bound Iron Particle Cores

    Science.gov (United States)

    Namkung, M.; Wincheski, B.; Bryant, R. G.; Buchman, A.

    1998-01-01

    Spherical iron particles of three different size distributions, 6-10 micrometers in diameter, 100 mesh and 30-80 mesh, were mixed with 2.0 wt % of soluble imide and compression molded at 300 C under 131 MPa. Post-fabrication heat treatments were performed at 960 C for 6 h resulting in a significant enhancement of the permeability in low field region for all the specimens except for the one made of 30-80 mesh particles. The rate of core loss of these specimens at a magnetic induction of 5 kG measured up to 1 kHz shows a noticeable. increase after heat treatment which, along with the permeability enhancement, can be explained by the coalescence of particles forming a network of conductivity paths in the specimens. ne scanning electron micrographs taken for the 6-10 micrometer particle specimens show no evidence of heat treatment-induced grain growth. The untreated specimens show a very weak f(sup 2) -dependence of the core loss which clearly indicates a negligible contribution from the eddy current loss. In particular, an almost perfect linearity was found in the frequency dependence of the core loss of the untreated specimen made of 100 mesh iron particles.

  13. Electrorheological Particles Composed of PolyanilineCore and BaTiO3 Layer Shell

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Composite particles consisting of polyaniline(PAn) core and barium titanate (BaTiO3) layer shell were synthesized.The PAn-BaTiO3 composites particles were characterized with TEM and XRD.The dielectric behavior of particles was tested and the electrorheological(ER) behavior of the suspensions of PAn/BaTiO3 particles in chlorinated paraffin oil with a 20vol% was investigated under DC electric field.The results show that the ER effect of composite particle is far stronger than that of pure polyaniline and barium titanate which were synthesized by the same method.pH and thickness of BaTiO3 have an important influence on the ER effects.

  14. 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.

  15. Tuning the Mechanical Properties of Hydrogel Core-Shell Particles by Inwards Interweaving Self-Assembly.

    Science.gov (United States)

    Pan, Houwen Matthew; Seuss, Maximilian; Neubauer, Martin P; Trau, Dieter W; Fery, Andreas

    2016-01-20

    Mechanical properties of hydrogel particles are of importance for their interactions with cells or tissue, apart from their relevance to other applications. While so far the majority of works aiming at tuning particle mechanics relied on chemical cross-linking, we report a novel approach using inwards interweaving self-assembly of poly(allylamine) (PA) and poly(styrenesulfonic acid) (PSSA) on agarose gel beads. Using this technique, shell thicknesses up to tens of micrometers can be achieved from single-polymer incubations and accurately controlled by varying the polymer concentration or incubation period. We quantified the changes in mechanical properties of hydrogel core-shell particles. The effective elastic modulus of core-shell particles was determined from force spectroscopy measurements using the colloidal probe-AFM (CP-AFM) technique. By varying the shell thickness between 10 and 24 μm, the elastic modulus of particles can be tuned in the range of 10-190 kPa and further increased by increasing the layer number. Through fluorescence quantitative measurements, the polymeric shell density was found to increase together with shell thickness and layer number, hence establishing a positive correlation between elastic modulus and shell density of core-shell particles. This is a valuable method for constructing multidensity or single-density shells of tunable thickness and is particularly important in mechanobiology as studies have reported enhanced cellular uptake of particles in the low-kilopascal range (shell particles for the separation of biomolecules or systemic study of stiffness-dependent cellular uptake.

  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. Toll-like receptor 2 senses hepatitis C virus core protein but not infectious viral particles

    Science.gov (United States)

    Hoffmann, Marco; Zeisel, Mirjam B.; Jilg, Nikolaus; Paranhos-Baccalà, Glaucia; Stoll-Keller, Françoise; Wakita, Takaji; Hafkemeyer, Peter; Blum, Hubert E.; Barth, Heidi; Henneke, Philipp; Baumert, Thomas F.

    2009-01-01

    Toll-like receptors (TLRs) are pathogen recognition molecules activating the innate immune system. Cell surface expressed TLRs, such as TLR2 and TLR4 have been shown to play an important role in human host defenses against viruses through sensing of viral structural proteins. In this study, we aimed to elucidate whether TLR2 and TLR4 participate in inducing antiviral immunity against hepatitis C virus by sensing viral structural proteins. We studied TLR2 and TLR4 activation by cell-culture derived infectious virions (HCVcc) and serum-derived virions in comparison to purified recombinant HCV structural proteins and enveloped virus-like particles. Incubation of TLR2 or TLR4 transfected cell lines with recombinant core protein resulted in activation of TLR2-dependent signaling. In contrast, neither infectious virions nor enveloped HCV-like particles triggered TLR2 and TLR4 signaling. These findings suggest that monomeric HCV core protein but not intact infectious particles are sensed by TLR2. Impairment of core-TLR interaction in infectious viral particles may contribute to escape from innate antiviral immune responses. PMID:20375602

  18. Polybutylacrylate/poly(methyl methacrylate) Core-Shell Elastic Particles as Epoxy Resin Toughener:Part Ⅰ Design and Preparation

    Institute of Scientific and Technical Information of China (English)

    Jianli WANG; Myonghoon LEE; Xiaomei YU; Jianbin JI; Kejian YAO

    2004-01-01

    Polybutylacrylate (PBA)/poly(methyl methacrylate) (PM MA) core-shell elastic particles (CSEP), whose rubbery core diameterranged from 0.08 μm to 1.38 μm, were synthesized by using conventional emulsion polymerization, multi-step emulsion polymerization, and soapless polymerization. Allyl methacylate (ALMA) and ethylene glycol dimethacrylate (EGDMA) were selected as crosslinking reagents for core polymerization. Methacrylic acid (MAA) was used as functional co-monomer with methyl methacrylate as shell component. The content of vinyl groups in PBA rubbery core increased with the amount of crosslinking reagents. The core-shell ratio affected great on the morphology of the complex particles. Furthermore, the amounts of carboxyl on the surface of core-shell particles, copolymerized with acrylic acid, were determined by potentiometric titration. Results showed that methylacrylic acid was distributed mostly on the surface of particles.

  19. Partial coherence in the core/halo picture of Bose-Einstein n-particle correlations

    CERN Document Server

    Csörgö, T; Schmidt-Sørensen, J; Ster, A

    1999-01-01

    We study the influence of a possible coherent component in the boson source on the two-, three- and $n$-particle correlation functions in a generalized core/halo type of boson-emitting source. In particular, a simple formula is presented for the strengh of the $n$-particle correlation functions for such systems. Graph rules are obtained to evaluate the correlation functions of arbitrary high order. The importance of experimental determination of the 4-th and 5-th order Bose-Einstein correlation function is emphasized.

  20. Protein encapsulated core-shell structured particles prepared by coaxial electrospraying: investigation on material and processing variables.

    Science.gov (United States)

    Zamani, Maedeh; Prabhakaran, Molamma P; Thian, Eng San; Ramakrishna, Seeram

    2014-10-01

    Biodegradable polymeric particles have been extensively investigated for controlled drug delivery of various therapeutic agents. 'Coaxial' electrospraying was successfully employed in this study, to fabricate core-shell PLGA particles containing bovine serum albumin (BSA) as the model protein, and the results were also compared to particles prepared by 'emulsion' electrospraying. Two different molecular weights of PLGA were employed to encapsulate the protein. Solution properties and processing parameters were found to influence the morphology of the core-shell particles. Depending on the type of solvent used to dissolve the polymer as well as the polymer concentration and molecular weight, the mean diameter of the particles varied between 3.0 to 5.5 μm. Fluorescence microscopic analysis of the electrosprayed particles using FITC-conjugated BSA demonstrated the core-shell structure of the developed particles. The encapsulation efficiency and release behavior of BSA was influenced by shell:core feeding ratio, protein concentration, and the electrospraying method. The encapsulation efficiency of BSA within the core-shell particles of high and low molecular weight PLGA was found 15.7% and 25.1% higher than the emulsion electrosprayed particles, respectively. Moreover, the total amount of BSA released from low molecular weight PLGA particles was significantly higher than high molecular weight PLGA particles within 43 days of release studies, with negligible effect on encapsulation efficiency. The technique of coaxial electrospraying has high potential for encapsulation of susceptible protein-based therapeutic agents such as growth factors for multiple drug delivery applications.

  1. Hierarchically functionalized magnetic core/multishell particles and their postsynthetic conversion to polymer capsules.

    Science.gov (United States)

    Schmitt, Sophia; Silvestre, Martin; Tsotsalas, Manuel; Winkler, Anna-Lena; Shahnas, Artak; Grosjean, Sylvain; Laye, Fabrice; Gliemann, Hartmut; Lahann, Joerg; Bräse, Stefan; Franzreb, Matthias; Wöll, Christof

    2015-01-01

    The controlled synthesis of hierarchically functionalized core/multishell particles is highly desirable for applications in medicine, catalysis, and separation. Here, we describe the synthesis of hierarchically structured metal-organic framework multishells around magnetic core particles (magMOFs) via layer-by-layer (LbL) synthesis. The LbL deposition enables the design of multishell systems, where each MOF shell can be modified to install different functions. Here, we used this approach to create controlled release capsules, in which the inner shell serves as a reservoir and the outer shell serves as a membrane after postsynthetic conversion of the MOF structure to a polymer network. These capsules enable the controlled release of loaded dye molecules, depending on the surrounding media.

  2. 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.

  3. A Reacting-Shrinking Core Model for Pyrolysis and Combustion of a Single Biomass Particle

    Energy Technology Data Exchange (ETDEWEB)

    Gordon, Alfredo L.; Avila, Claudio R.; Garcia, Ximena A. (Dept. of Chemical Engineering, Univ. of Concepcion (Chile)). e-mail: algordon@udec.cl

    2008-10-15

    Consecutive heating and pyrolysis of the solid due to incident heat flow represented by a shrinking reacting core approximation and combustion, described by a shrinking unreacting core description, allow modeling the combustion of a cylindrical biomass particle. A bi-dimensional approach (radial and axial) describes mass and heat balances and first order kinetics characterizes the reaction rates. A finite differences algorithm numerically solved the model. Results showed good agreement with available experimental data. The parameter analysis for the pyrolysis step shows high sensibility to the kinetic constants, the incident heat flow, the initial moisture and particle size. Parameters with a significant effect on combustion are the concentration and effective diffusivity of the oxidizing agent in the atmosphere around the reaction surface

  4. Characterization of monoclonal antibodies to histone 2B. Localization of epitopes and analysis of binding to chromatin.

    Science.gov (United States)

    Whitfield, W G; Fellows, G; Turner, B M

    1986-06-16

    Two mouse monoclonal IgM antibodies have been isolated which bind to histone 2B (H2B), as shown by protein blotting and immunostaining and by solid-phase radioimmunoassay (RIA). One of these (HBC-7) was specific for H2B by both techniques whereas the other (2F8) cross-reacted with histone H1 by RIA. Both antibodies failed to recognize H2B limit peptides from trypsin-digested chromatin and did not bind to Drosophila H2B, which differs extensively from vertebrate H2B only in the N-terminal region. These findings indicate that both antibodies recognize epitopes within the trypsin-sensitive, N-terminal region comprising residues 1-20. Binding of antibody HBC-7 was inhibited by in vitro ADP-ribosylation of H2B at glutamic acid residue 2. This strongly suggests that the epitope recognized by HBC-7 is located at the N-terminus of H2B, probably between residues 1 and 8. We have used solid-phase radioimmunoassay to investigate factors which influence the accessibility of this epitope in chromatin. Removal of H1 ('stripping') from high-molecular-mass chromatin had no effect on HBC-7 binding, nor was any difference observed between binding to stripped chromatin and to 146-base-pair (bp) core particles derived from it by nuclease digestion. These results suggest that accessibility of the N-terminal region of H2B is not influenced by H1 itself or by the size or conformation of linker DNA. In contrast, binding of antibody HBC-7 to 146-bp core particles derived from unstripped chromatin was reduced by up to 70%. Binding was restored by exposure of these core particles to the conditions used for stripping. Analysis of the protein content of core particle preparations from stripped and unstripped chromatin suggests that these findings may be attributable to redistribution of non-histone proteins during nuclease digestion. Pre-treatment of high-molecular-mass chromatin or 146-bp core particles with the intercalating dye ethidium bromide resulted in a severalfold increase in binding

  5. Chromatin is wonderful stuff.

    NARCIS (Netherlands)

    R. van Driel

    2007-01-01

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

  6. 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

    2016-04-21

    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.

  7. 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

  8. 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

  9. 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.

  10. Chromatin Fiber Dynamics under Tension and Torsion

    Directory of Open Access Journals (Sweden)

    Christophe Lavelle

    2010-04-01

    Full Text Available Genetic and epigenetic information in eukaryotic cells is carried on chromosomes, basically consisting of large compact supercoiled chromatin fibers. Micromanipulations have recently led to great advances in the knowledge of the complex mechanisms underlying the regulation of DNA transaction events by nucleosome and chromatin structural changes. Indeed, magnetic and optical tweezers have allowed opportunities to handle single nucleosomal particles or nucleosomal arrays and measure their response to forces and torques, mimicking the molecular constraints imposed in vivo by various molecular motors acting on the DNA. These challenging technical approaches provide us with deeper understanding of the way chromatin dynamically packages our genome and participates in the regulation of cellular metabolism.

  11. Fluorescent core-shell silica nanoparticles: towards "Lab on a Particle" architectures for nanobiotechnology.

    Science.gov (United States)

    Burns, Andrew; Ow, Hooisweng; Wiesner, Ulrich

    2006-11-01

    Novel nanoscale fluorescent materials are integral to the progress of emergent fields such as nanobiotechnology and facilitate new research in a variety of contexts. Sol-gel derived silica is an excellent host material for creating fluorescent nanoparticles by the inclusion of covalently-bound organic dyes. Significant enhancements in the brightness and stability of organic dye emission can be achieved for silica-based core-shell nanoparticle architectures at length scales down to tens of nanometers with narrow size distributions. This tutorial review will highlight these findings and describe the evolution of the fluorescent core-shell silica nanoparticle concept towards integration of multiple functionalities including mesoporosity, metal nanoshells and quantitative chemical sensing. These developments point towards the development of "lab on a particle" architectures with promising prospects for nanobiotechnology, drug development and beyond.

  12. Particle Physics in Ice with IceCube DeepCore

    CERN Document Server

    DeYoung, T

    2011-01-01

    The IceCube Neutrino Observatory is the world's largest high energy neutrino telescope, using the Antarctic ice cap as a Cherenkov detector medium. DeepCore, the low energy extension to IceCube, is an infill array with a fiducial volume of around 30 MTon in the deepest, clearest ice, aiming for an energy threshold as low as 10 GeV and extending IceCube's sensitivity to indirect dark matter searches and atmospheric neutrino oscillation physics. We will discuss the analysis of the first year of DeepCore data, as well as ideas for a further extension of the particle physics program in the ice with a future PINGU detector.

  13. Core-shell hydrogel particles harvest, concentrate and preserve labile low abundance biomarkers.

    Directory of Open Access Journals (Sweden)

    Caterina Longo

    Full Text Available BACKGROUND: The blood proteome is thought to represent a rich source of biomarkers for early stage disease detection. Nevertheless, three major challenges have hindered biomarker discovery: a candidate biomarkers exist at extremely low concentrations in blood; b high abundance resident proteins such as albumin mask the rare biomarkers; c biomarkers are rapidly degraded by endogenous and exogenous proteinases. METHODOLOGY AND PRINCIPAL FINDINGS: Hydrogel nanoparticles created with a N-isopropylacrylamide based core (365 nm-shell (167 nm and functionalized with a charged based bait (acrylic acid were studied as a technology for addressing all these biomarker discovery problems, in one step, in solution. These harvesting core-shell nanoparticles are designed to simultaneously conduct size exclusion and affinity chromatography in solution. Platelet derived growth factor (PDGF, a clinically relevant, highly labile, and very low abundance biomarker, was chosen as a model. PDGF, spiked in human serum, was completely sequestered from its carrier protein albumin, concentrated, and fully preserved, within minutes by the particles. Particle sequestered PDGF was fully protected from exogenously added tryptic degradation. When the nanoparticles were added to a 1 mL dilute solution of PDGF at non detectable levels (less than 20 picograms per mL the concentration of the PDGF released from the polymeric matrix of the particles increased within the detection range of ELISA and mass spectrometry. Beyond PDGF, the sequestration and protection from degradation for a series of additional very low abundance and very labile cytokines were verified. CONCLUSIONS AND SIGNIFICANCE: We envision the application of harvesting core-shell nanoparticles to whole blood for concentration and immediate preservation of low abundance and labile analytes at the time of venipuncture.

  14. A unique missense allele of BAF155, a core BAF chromatin remodeling complex protein, causes neural tube closure defects in mice.

    Science.gov (United States)

    Harmacek, Laura; Watkins-Chow, Dawn E; Chen, Jianfu; Jones, Kenneth L; Pavan, William J; Salbaum, J Michael; Niswander, Lee

    2014-05-01

    Failure of embryonic neural tube closure results in the second most common class of birth defects known as neural tube defects (NTDs). While NTDs are likely the result of complex multigenic dysfunction, it is not known whether polymorphisms in epigenetic regulators may be risk factors for NTDs. Here we characterized Baf155(msp3) , a unique ENU-induced allele in mice. Homozygous Baf155(mps3) embryos exhibit highly penetrant exencephaly, allowing us to investigate the roles of an assembled, but malfunctional BAF chromatin remodeling complex in vivo at the time of neural tube closure. Evidence of defects in proliferation and apoptosis were found within the neural tube. RNA-Seq analysis revealed that surprisingly few genes showed altered expression in Baf155 mutant neural tissue, given the broad epigenetic role of the BAF complex, but included genes involved in neural development and cell survival. Moreover, gene expression changes between individual mutants were variable even though the NTD was consistently observed. This suggests that inconsistent gene regulation contributes to failed neural tube closure. These results shed light on the role of the BAF complex in the process of neural tube closure and highlight the importance of studying missense alleles to understand epigenetic regulation during critical phases of development.

  15. 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......Cl or 0.6M NaCL, and is compact in 0.01 M NaCl solutions if histone H 1 is present. Even high concentrations of urea did not alter the fundamental beaded structure, consisting of 110A beads of 200 base pair content, each joined by thin DNA bridges of 50 base pairs. The physical bead observed by EM...... 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....

  16. Construction of PS/PNIPAM core-shell particles and hollow spheres by using hydrophobic interaction and thermosensitive phase separation

    Institute of Scientific and Technical Information of China (English)

    Dongmei ZHU; Fei WANG; Cuiling GAO; Zheng XU

    2008-01-01

    This paper reports an easy and effective way tofabricate polystyrene/poly (N-isopropylacrylamide) (PS/PNIPAM) core-shell particles and PNIPAM hollow spheres.The main point of the method is to take advantage of the hydrophobic interaction between initiator and PS particles.The hydrophobic azodiisobutyronitriles automat-ically concentrate around the PS particles and initiate poly-merization of N-isopropylacrylamide (NIPAM) and thecrosslinker methylene bisacrylamide (MBA),which dissolve in the aqueous phase,at the surface of the PS nanoparticles.Then,PNIPAM adheres to the PS particles to form a core-shell structure as a result of their hydrophobic interaction.This interaction is due to the unique property of PNIPAM,namely,its ability to transition from hydrophilic to hydro-phobic when the temperature rises to 32℃.Furthermore,the hollow PNIPAM spheres were obtained by etching the PS core with chloroform.

  17. Formation of Core-Shell Particles by Interfacial Radical Polymerization Initiated by a Glucose Oxidase-Mediated Redox System.

    Science.gov (United States)

    Shenoy, Raveesh; Tibbitt, Mark W; Anseth, Kristi S; Bowman, Christopher N

    2013-03-12

    A unique design paradigm to form core-shell particles based on interfacial radical polymerization is described. The interfacial initiation system is comprised of an enzymatic reaction between glucose and glucose oxidase (GOx) to generate hydrogen peroxide, which, in the presence of iron (Fe(2+)), generates hydroxyl radicals that initiate polymerization. Shell formation on prefabricated polymeric cores is achieved by localizing the initiation reaction to the interface of the core and a surrounding aqueous monomer formulation into which it is immersed. The interfacially confined initiation reaction is accomplished by incorporating one or more of the initiating species in the particle core and the remainder of the complementary initiating components in the surrounding media such that interactions and the resulting initiation reaction occur at the interface. This work is focused on engineering the reaction behavior and mass transport processes to promote interfacially confined polymerization, controlling the rate of shell formation, and manipulating the structure of the core-shell particle. Specifically, incorporating GOx in the precursor solution used to fabricate cores ranging from 100 to 200 μm, and the remainder of the complementary initiating components and monomer in the bulk solution prior to interfacial polymerization yielded shells whose average thickness was 20 μm after 4 min of immersion and at a bulk iron concentration of 12.5 mM. When the locations of glucose and GOx are interchanged, the average thickness of the shell was 15 or 100 μm for bulk iron concentrations of 45 and 12.5 mM, respectively. The initial locations of glucose and GOx also determine the degree of interpenetration of the core and the shell. Specifically, for a bulk iron concentration of 45 mM, the thickness of the interpenetrating layer averaged 12 μm when GOx was initially within the core, whereas no interpenetrating layer was observed when glucose was incorporated in the core. The

  18. Meaningful timescales from Monte Carlo simulations of particle systems with hard-core interactions

    Science.gov (United States)

    Costa, Liborio I.

    2016-12-01

    A new Markov Chain Monte Carlo method for simulating the dynamics of particle systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is associated with minima in the energy landscape, in the proposed method, the state of the system is associated with the set of paths traveled by the atoms and the transition probabilities for an atom to be displaced are proportional to the corresponding velocities. In this way, the number of possible state-to-state transitions is reduced to a discrete set, and a direct link between the Monte Carlo time step and true physical time is naturally established. The resulting rejection-free algorithm is validated against event-driven molecular dynamics: the equilibrium and non-equilibrium dynamics of hard disks converge to the exact results with decreasing displacement size.

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

    Science.gov (United States)

    Lopes, Ilídio P; Silk, Joseph

    2002-04-15

    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.

  20. 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.

  1. 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...... intersect. Routes for unicast sessions are agnostic to other sessions and setup beforehand, CORE will then discover and exploit intersecting routes. Our approach allows the inter-session regions to leverage RLNC to compensate for losses or failures in the overhearing or transmitting process. Thus, we...... 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...

  2. Influence of particle size and shell thickness of core-shell packing materials on optimum experimental conditions in preparative chromatography.

    Science.gov (United States)

    Horváth, Krisztián; Felinger, Attila

    2015-08-14

    The applicability of core-shell phases in preparative separations was studied by a modeling approach. The preparative separations were optimized for two compounds having bi-Langmuir isotherms. The differential mass balance equation of chromatography was solved by the Rouchon algorithm. The results show that as the size of the core increases, larger particles can be used in separations, resulting in higher applicable flow rates, shorter cycle times. Due to the decreasing volume of porous layer, the loadability of the column dropped significantly. As a result, the productivity and economy of the separation decreases. It is shown that if it is possible to optimize the size of stationary phase particles for the given separation task, the use of core-shell phases are not beneficial. The use of core-shell phases proved to be advantageous when the goal is to build preparative column for general purposes (e.g. for purification of different products) in small scale separations.

  3. 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...

  4. Magnetically self-assembled SrFe12O19/Fe-Co core/shell particles

    Energy Technology Data Exchange (ETDEWEB)

    Xu, X; Park, J; Hong, YK; Lane, AM

    2015-02-15

    Epitaxial growth to synthesize core/shell-structured materials is limited because large lattice mismatches are common between materials. Magnetically hard/soft, core/shell-structured materials can be potentially used for rare-earth free permanent magnets, but their synthesis presents a challenge. We report a wet chemistry method to synthesize core/shell structured particles consisting of a magnetically hard SrFe12O19 core and a soft Fe-Co shell, with a lattice mismatch of similar to 100%, which cannot be achieved by conventional epitaxial growth or other alternative methods. When decreasing the size of the magnetically soft Fe-Co nanoclusters to below 5 nm, we show that they can be magnetically attracted by the hard SrFe12O19 to form core/shell structured particles. An AC demagnetization experiment demonstrates the formation mechanism of the core/shell particles, and their magnetic hysteresis loop shows potential for use as rare-earth free permanent magnets. Published by Elsevier B.V.

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

    Science.gov (United States)

    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 core-shell-structured composite when the composite particles are prepared by miniemulsion polymerization in which monomers are fed in batch (droplet nucleation). By contrast, hydrophobic butylacrylate promotes the encapsulating efficiency of silica when monomers are fed dropwise (homogeneous nucleation). The morphologies of polyacrylate-nano-SiO2 composites prepared from different feed ratio of methylmethacrylate/butylacrylate (with different hydrophobicity) and by different feed processes are characterized by transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques. The results from SEM and TEM show that the morphologies of the as-prepared polyacrylate/nano-SiO2 composite can be a core-shell structure or a bare acrylic sphere. The stability of resulting emulsions composed of these composite particles is strongly dependent on the surface coverage of silica particles. The emulsion stability is improved by densely silica-packed composite particles.

  6. The influence of some factors on the electrical conductivity and particle size of core/shell polystyrene/polyaniline composites

    Directory of Open Access Journals (Sweden)

    GORDANA D. NESTOROVIC

    2005-11-01

    Full Text Available The electrically conductive, micron-sized, core/shell polystyrene (PS/polyaniline (PANI composite particles were synthesized by chemical oxidative polymerization of aniline in the presence of micron-sized PS particles in 1 M HCl. The conditions of the dispersion polymerization of styrene were optimized. The influence of the initiator type employed for the chemical oxidative polymerization of aniline and the aniline (ANI concentration on the PS/PANI particle size and size distribution and their conductivity was investigated. The obtained results show that the conductivity of the samples increased with increasing ANI concentration. The conductivity of the PS/PANI composite particles obtained with the highest ANI concentration was of the same order of magnitude as that for PANI powder. The particle size did not depend on the concentration of ANI, while the particle size distribution was narrower at higher concentrations of ANI.

  7. Spherical 3D photonic crystal with conducting nanoshell and particle core

    Science.gov (United States)

    Zamudio-Lara, A.; Sánchez-Mondragón, J.; Escobedo-Alatorre, J.; Pérez-Careta, E.; Torres-Cisneros, M.; Tecpoyotl-Torres, Margarita; Vázquez-Buenos Aires, O.

    2009-06-01

    We discuss a structured 3D Dielectric Photonic Crystal with both a metallic core and a metallic shell. We discuss the role of each one, the stack, the core as well as the cavity formed between the core and the shell. The low frequency metallic core features becomes much more significant as it gets smaller and get diluted by the cavity.

  8. 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.

  9. Glass-NiP-CoFeP triplex-shell particles with hollow cores and tunable magnetic properties.

    Science.gov (United States)

    An, Zhenguo; Zhang, Jingjie

    2013-02-01

    Low density (0.55-0.92g/mL, depending on the shell thickness and composition) glass-metal-metal triplex-shell hollow particles (TSHP) were prepared by a three-step route. First, micrometer-sized silicate glass particles with hollow cores, uniform shells, and high sphericity were prepared through spray drying and subsequent melting. NiP shell was uniformly assembled to the previously obtained glass hollow particles by silver seed induced chemical reduction of Ni(2+) by sodium hypophosphite, and glass-NiP double-shell hollow particles (DSHP) with compact and uniform shells were formed. The as-formed NiP particles further acted as the seeds for the directed formation and assembly of the CoFeP shell on the NiP shell to form the final glass-NiP-CoFeP triplex-shell hollow particles (TSHP). The influences of the component of the reaction system on the composition, structure, and magnetic properties of the hollow particles were studied. The multishell hollow particles thus obtained may have some promising applications in the fields of low-density magnetic materials, conduction, microwave absorbers, catalysis, etc. This work provides an additional strategy to fabricate multishell structured hollow particles with tailored shell composition and magnetic properties, which can be extended to the controlled preparation of multishell composite particles with the shells consisting of metal, oxides, or other compounds.

  10. 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...

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

    Science.gov (United States)

    Sun, Li; Zang, Shuying

    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 (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.

  12. Structure of the Particle-Hole Amplitudes in No-core Shell Model Wave Functions

    CERN Document Server

    Hayes, A C

    2009-01-01

    We study the structure of the no-core shell model wave functions for $^6$Li and $^{12}$C by investigating the ground state and first excited state electron scattering charge form factors. In both nuclei, large particle-hole ($ph$) amplitudes in the wave functions appear with the opposite sign to that needed to reproduce the shape of the $(e,e')$ form factors, the charge radii, and the B(E2) values for the lowest two states. The difference in sign appears to arise mainly from the monopole $\\Delta\\hbar\\omega=2$ matrix elements of the kinetic and potential energy (T+V) that transform under the harmonic oscillator SU(3) symmetries as $(\\lambda,\\mu)=(2,0)$. These are difficult to determine self-consistently, but they have a strong effect on the structure of the low-lying states and on the giant monopole and quadrupole resonances. The Lee-Suzuki transformation, used to account for the restricted nature of the space in terms of an effective interaction, introduces large higher-order $\\Delta\\hbar\\omega=n, n>$2, $ph$ ...

  13. Histone variants: key players of chromatin.

    Science.gov (United States)

    Biterge, Burcu; Schneider, Robert

    2014-06-01

    Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.

  14. 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.

  15. A disulfide-bonded dimer of the core protein of hepatitis C virus is important for virus-like particle production.

    Science.gov (United States)

    Kushima, Yukihiro; Wakita, Takaji; Hijikata, Makoto

    2010-09-01

    Hepatitis C virus (HCV) core protein forms the nucleocapsid of the HCV particle. Although many functions of core protein have been reported, how the HCV particle is assembled is not well understood. Here we show that the nucleocapsid-like particle of HCV is composed of a disulfide-bonded core protein complex (dbc-complex). We also found that the disulfide-bonded dimer of the core protein (dbd-core) is formed at the endoplasmic reticulum (ER), where the core protein is initially produced and processed. Mutational analysis revealed that the cysteine residue at amino acid position 128 (Cys128) of the core protein, a highly conserved residue among almost all reported isolates, is responsible for dbd-core formation and virus-like particle production but has no effect on the replication of the HCV RNA genome or the several known functions of the core protein, including RNA binding ability and localization to the lipid droplet. The Cys128 mutant core protein showed a dominant negative effect in terms of HCV-like particle production. These results suggest that this disulfide bond is critical for the HCV virion. We also obtained the results that the dbc-complex in the nucleocapsid-like structure was sensitive to proteinase K but not trypsin digestion, suggesting that the capsid is built up of a tightly packed structure of the core protein, with its amino (N)-terminal arginine-rich region being concealed inside.

  16. 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...

  17. Reprogramming the chromatin landscape

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  18. On the extent of size range and power law scaling for particles of natural carbonate fault cores

    Science.gov (United States)

    Billi, Andrea

    2007-09-01

    To determine the size range and both type and extent of the scaling laws for particles of loose natural carbonate fault rocks, six granular fault cores from Mesozoic carbonate strata of central Italy were sampled. Particle size distributions of twelve samples were determined by combining sieving and sedimentation methods. Results show that, regardless of the fault geometry, kinematics, and tectonic history, the size of fault rock particles respects a power law distribution across approximately four orders of magnitude. The fractal dimension ( D) of the particle size distribution in the analysed samples ranges between ˜2.0 and ˜3.5. A lower bound to the power law trend is evident in all samples except in those with the highest D-values; in these samples, the smallest analysed particles (˜0.0005 mm in diameter) were also included in the power law interval, meaning that the lower size limit of the power law distribution decreases for increasing D-values and that smallest particles start to be comminuted with increasing strain (i.e. increasing fault displacement and D-values). For increasing D-values, also the largest particles tends to decrease in number, but this evidence may be affected by a censoring bias connected with the sample size. Stick-slip behaviour is suggested for the studied faults on the basis of the inferred particle size evolutions. Although further analyses are necessary to make the results of this study more generalizable, the preliminary definition of the scaling rules for fault rock particles may serve as a tool for predicting a large scale of fault rock particles once a limited range is known. In particular, data from this study may result useful as input numbers in numerical models addressing the packing of fault rock particles for frictional and hydraulic purposes.

  19. 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.

  20. Preparation and characterization of inorganic-organic trilayer core-shell polysilsesquioxane/polyacrylate/polydimethylsiloxane hybrid latex particles

    Science.gov (United States)

    Bai, Ruiqin; Qiu, Teng; Han, Feng; He, Lifan; Li, Xiaoyu

    2012-07-01

    The inorganic-organic trilayer core-shell polysilsesquioxane/polyacrylate/polydimethylsiloxane hybrid latex particles have been successfully prepared via seeded emulsion polymerization of acrylate monomers and octamethylcyclotetrasiloxane (D4) gradually, using functional polymethacryloxypropylsilsesquioxane (PSQ) latex particles with reactive methacryloxypropyl groups synthesized by the hydrolysis and polycondensation of (3-methacryloxypropyl)trimethoxysilane in the presence of mixed emulsifiers as seeds. The FTIR spectra show that acrylate monomers and D4 are effectively involved in the emulsion copolymerization and formed the polydimethylsiloxane-containing hybrid latex particles. Transmission electron microscopy (TEM) and dynamic light scattering (DLS) confirm that the resultant hybrid latex particles have evident trilayer core-shell structure and a narrow size distribution. XPS analysis also indicates that polysilsesquioxane/polyacrylate/polydimethylsiloxane hybrid latex particles have been successfully prepared and PDMS is rich in the surface of the hybrid latex film. Additionally, compared with the hybrid latex film without PDMS, the hybrid latex film containing PDMS shows higher hydrophobicity (water contact angle) and lower water absorption.

  1. Preparation and characterization of inorganic-organic trilayer core-shell polysilsesquioxane/polyacrylate/polydimethylsiloxane hybrid latex particles

    Energy Technology Data Exchange (ETDEWEB)

    Bai Ruiqin [College of Materials Science and Engineering, State Key Laboratory of Organic-Inorganic Composite, Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China); Qiu Teng, E-mail: qiuteng@mail.buct.edu.cn [College of Materials Science and Engineering, State Key Laboratory of Organic-Inorganic Composite, Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China); Han Feng; He Lifan [College of Materials Science and Engineering, State Key Laboratory of Organic-Inorganic Composite, Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China); Li Xiaoyu, E-mail: lixy@mail.buct.edu.cn [College of Materials Science and Engineering, State Key Laboratory of Organic-Inorganic Composite, Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029 (China)

    2012-07-15

    The inorganic-organic trilayer core-shell polysilsesquioxane/polyacrylate/polydimethylsiloxane hybrid latex particles have been successfully prepared via seeded emulsion polymerization of acrylate monomers and octamethylcyclotetrasiloxane (D{sub 4}) gradually, using functional polymethacryloxypropylsilsesquioxane (PSQ) latex particles with reactive methacryloxypropyl groups synthesized by the hydrolysis and polycondensation of (3-methacryloxypropyl)trimethoxysilane in the presence of mixed emulsifiers as seeds. The FTIR spectra show that acrylate monomers and D{sub 4} are effectively involved in the emulsion copolymerization and formed the polydimethylsiloxane-containing hybrid latex particles. Transmission electron microscopy (TEM) and dynamic light scattering (DLS) confirm that the resultant hybrid latex particles have evident trilayer core-shell structure and a narrow size distribution. XPS analysis also indicates that polysilsesquioxane/polyacrylate/polydimethylsiloxane hybrid latex particles have been successfully prepared and PDMS is rich in the surface of the hybrid latex film. Additionally, compared with the hybrid latex film without PDMS, the hybrid latex film containing PDMS shows higher hydrophobicity (water contact angle) and lower water absorption.

  2. Generation of nano-sized core-shell particles using a coaxial tri-capillary electrospray-template removal method.

    Science.gov (United States)

    Cao, Lihua; Luo, Jun; Tu, Kehua; Wang, Li-Qun; Jiang, Hongliang

    2014-03-01

    This study proposed a new strategy based on a coaxial tri-capillary electrospray-template removal process for producing nanosized polylactide-b-polyethylene glycol (PLA-PEG) particles with a core-shell structure. Microparticles with core-shell-corona structures were first fabricated by coaxial tri-capillary electrospray, and core-shell nanoparticles less than 200 nm in size were subsequently obtained by removing the PEG template from the core-shell-corona microparticles. The nanoparticle size could be modulated by adjusting the flow rate of corona fluid, and nanoparticles with an average diameter of 106±5 nm were obtained. The nanoparticles displayed excellent dispersion stability in aqueous media and very low cytotoxicity. Paclitaxel was used as a model drug to be incorporated into the core section of the nanoparticles. A drug loading content in the nanoparticles as high as 50.7±1.5 wt% with an encapsulation efficiency of greater than 70% could be achieved by simply increasing the feed rate of the drug solution. Paclitaxel exhibited sustained release from the nanoparticles for more than 40 days. The location of the paclitaxel in the nanoparticles, i.e., in the core or shell layer, did not have a significant effect on its release.

  3. Self-assembled HCV core virus-like particles targeted and inhibited tumor cell migration and invasion

    Science.gov (United States)

    Li, Xiang; Xu, Xuehe; Jin, Aihui; Jia, Qunying; Zhou, Huaibin; Kang, Shuai; Lou, Yongliang; Gao, Jimin; Lu, Jianxin

    2013-09-01

    We used a baculovirus expression system to express fusion proteins of HCV core, RGD (Arg-Gly-Asp) peptide, and IFN-α2a fragments in Sf9 cells. Western blotting and electron microscopy demonstrate that HCV core, peptides RGD, and IFN-α2a fusion proteins assemble into 30 to 40 nm nano-particles (virus-like particles, VLPs). Xenograft assays show that VLPs greatly reduced tumor volume and weight with regard to a nontreated xenograft. Migration and invasion results show that VLPs can inhibit the migration and invasion of the breast cancer cells MDA-MB231. This study will provide theoretical and experimental basis for the establishment of safe and effective tumor-targeted drug delivery systems and clinical application of VLPs carrying cell interacting cargo.

  4. Synthesis of TiO{sub 2} core/RuO{sub 2} shell particles using multistep ultrasonic spray pyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Stopic, Srecko, E-mail: sstopic@ime-aachen.de [IME – Process Metallurgy and Metal Recycling, RWTH Aachen University, Intzestr. 3, D-52056 Aachen (Germany); Friedrich, Bernd [IME – Process Metallurgy and Metal Recycling, RWTH Aachen University, Intzestr. 3, D-52056 Aachen (Germany); Schroeder, Michael [IPC – Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52074 Aachen (Germany); Weirich, Thomas E. [GFE – Central Facility for Electron Microscopy, RWTH Aachen University, Ahornstr. 55, D-52074 Aachen (Germany); AIXTAL – Institute of Crystallography, RWTH Aachen University, Jägerstraße 17–19, D-52066 Aachen (Germany)

    2013-09-01

    Graphical abstract: - Highlights: • TiO{sub 2} core/RuO{sub 2} 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 TiO{sub 2} core–RuO{sub 2} 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 TiO{sub 2} 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.

  5. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    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...

  6. Chromatin dynamics in plants

    NARCIS (Netherlands)

    Fransz, P.F.; Jong, de J.H.

    2002-01-01

    Recent studies in yeast, animals and plants have provided major breakthroughs in unraveling the molecular mechanism of higher-order gene regulation. In conjunction with the DNA code, proteins that are involved in chromatin remodeling, histone modification and epigenetic imprinting form a large netwo

  7. Production of rotavirus core-like particles in Sf9 cells using recombinase-mediated cassette exchange.

    Science.gov (United States)

    Fernandes, Fabiana; Dias, Mafalda M; Vidigal, João; Sousa, Marcos F Q; Patrone, Marco; Teixeira, Ana P; Alves, Paula M

    2014-02-10

    A flexible Sf9 insect cell line was recently developed leveraging the recombinase-mediated cassette exchange (RMCE) technology, which competes with the popular baculovirus expression vector system (BEVS) in terms of speed to produce new proteins. Herein, the ability of this cell platform to produce complex proteins, such as rotavirus core-like particles, was evaluated. A gene construct coding for a VP2-GFP fusion protein was targeted to a pre-characterized high recombination efficiency locus flanked by flipase (Flp) recognition target sites and, after three weeks in selection, an isogenic cell population was obtained. Despite the lower cell specific productivities with respect to those obtained by baculovirus infection, the titers of VP2-GFP reached in shake flask batch cultures were comparable as a result of higher cell densities. To further improve the VP2-GFP levels from stable expression, analysis of exhausted medium was undertaken to design feeding strategies enabling higher cell densities as well as increased culture duration. The implementation of the best strategy allowed reaching 20 million cells per ml in bioreactor cultures; the integrity of the rotavirus core-like particles could be confirmed by electron microscopy. Overall, we show that this Sf9-Flp cell platform represents a valuable alternative to the BEVS for producing complex recombinant proteins, such as rotavirus core-like particles.

  8. Chromatin assembly using Drosophila systems.

    Science.gov (United States)

    Fyodorov, Dmitry V; Levenstein, Mark E

    2002-05-01

    To successfully study chromatin structure and activity in vitro, it is essential to have a chromatin assembly system that will prepare extended nucleosome arrays with highly defined protein content that resemble bulk chromatin isolated from living cell nuclei in terms of periodicity and nucleosome positioning. The Drosophila ATP-dependent chromatin assembly system described in this unit meets these requirements. The end product of the reaction described here has highly periodic extended arrays with physiologic spacing and positioning of the nucleosomes.

  9. 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.

  10. Shape-Controlled Synthesis of Magnetic Iron Oxide@SiO₂-Au@C Particles with Core-Shell Nanostructures.

    Science.gov (United States)

    Li, Mo; Li, Xiangcun; Qi, Xinhong; Luo, Fan; He, Gaohong

    2015-05-12

    The preparation of nonspherical magnetic core-shell nanostructures with uniform sizes still remains a challenge. In this study, magnetic iron oxide@SiO2-Au@C particles with different shapes, such as pseduocube, ellipsoid, and peanut, were synthesized using hematite as templates and precursors of magnetic iron oxide. The as-obtained magnetic particles demonstrated uniform sizes, shapes, and well-designed core-shell nanostructures. Transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDX) analysis showed that the Au nanoparticles (AuNPs) of ∼6 nm were uniformly distributed between the silica and carbon layers. The embedding of the metal nanocrystals into the two different layers prevented the aggregation and reduced the loss of the metal nanocrystals during recycling. Catalytic performance of the peanut-like particles kept almost unchanged without a noticeable decrease in the reduction of 4-nitrophenol (4-NP) in 8 min even after 7 cycles, indicating excellent reusability of the particles. Moreover, the catalyst could be readily recycled magnetically after each reduction by an external magnetic field.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-07-01

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

  12. 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 included...

  13. MICRON CORE-SHELL PARTICLES PREPARED BY GRAFTING POLYMERIZATION OF METHYL METHACRYLATE FROM NARROW DISPERSE SURFACE OF CHLOROMETHYLATED POLYDIVINYLBENZENE VIA ATRP

    Institute of Scientific and Technical Information of China (English)

    Yu-zeng Zhao; Xin-lin Yang; Wen-qiang Huang

    2005-01-01

    Grafting of poly(methyl methacrylate) from narrow disperse polymer particles by surface-initiated atom transfer radical polymerization (ATRP) was investigated. Polydivinylbenzene (PDVB) particles were prepared by dispersion polymerization with poly(N-vinyl pyrrolidone) (PVP) as the stabilizer. Chloromethylated PDVB was used as initiating core sites for subsequent ATRP of methyl methacrylate with CuBr/bpy as catalyst system. It was found that poly(methyl methacrylate) was grafted not only from the particle surfaces but also from within a thin shell layer, leading to particles size increases from 2.38-3.00 μm with a core-shell structure particles. The grafted core-shell particles were characterized with FTIR, SEM, DSC.

  14. Nanoscale indentation of polymer and composite polymer-silica core-shell submicrometer particles by atomic force microscopy.

    Science.gov (United States)

    Armini, Silvia; Vakarelski, Ivan U; Whelan, Caroline M; Maex, Karen; Higashitani, Ko

    2007-02-13

    Atomic force microscopy was employed to probe the mechanical properties of surface-charged polymethylmethacrylate (PMMA)-based terpolymer and composite terpolymer core-silica shell particles in air and water media. The composite particles were achieved with two different approaches: using a silane coupling agent (composite A) or attractive electrostatic interactions (composite B) between the core and the shell. Young's moduli (E) of 4.3+/-0.7, 11.1+/-1.7, and 8.4+/-1.7 GPa were measured in air for the PMMA-based terpolymer, composite A, and composite B, respectively. In water, E decreases to 1.6+/-0.2 GPa for the terpolymer; it shows a slight decrease to 8.0+/-1.2 GPa for composite A, while it decreases to 2.9+/-0.6 GPa for composite B. This trend is explained by considering a 50% swelling of the polymer in water confirmed by dynamic light scattering. Close agreement is found between the absolute values of elastic moduli determined by nanoindentation and known values for the corresponding bulk materials. The thickness of the silica coating affects the mechanical properties of composite A. In the case of composite B, because the silica shell consists of separate particles free to move in the longitudinal direction that do not individually deform when the entire composite deforms, the elastic properties of the composites are determined exclusively by the properties of the polymer core. These results provide a basis for tailoring the mechanical properties of polymer and composite particles in air and in solution, essential in the design of next-generation abrasive schemes for several technological applications.

  15. 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.)

  16. Core-shell diode array for high performance particle detectors and imaging sensors: status of the development

    Science.gov (United States)

    Jia, G.; Hübner, U.; Dellith, J.; Dellith, A.; Stolz, R.; Plentz, J.; Andrä, G.

    2017-02-01

    We propose a novel high performance radiation detector and imaging sensor by a ground-breaking core-shell diode array design. This novel core-shell diode array are expected to have superior performance respect to ultrahigh radiation hardness, high sensitivity, low power consumption, fast signal response and high spatial resolution simultaneously. These properties are highly desired in fundamental research such as high energy physics (HEP) at CERN, astronomy and future x-ray based protein crystallography at x-ray free electron laser (XFEL) etc.. This kind of detectors will provide solutions for these fundamental research fields currently limited by instrumentations. In this work, we report our progress on the development of core-shell diode array for the applications as high performance imaging sensors and particle detectors. We mainly present our results in the preparation of high aspect ratio regular silicon rods by metal assisted wet chemical etching technique. Nearly 200 μm deep and 2 μm width channels with high aspect ratio have been etched into silicon. This result will open many applications not only for the core-shell diode array, but also for a high density integration of 3D microelectronics devices.

  17. 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.

  18. Fused-core particle technology in high-performance liquid chromatography:An overview

    Institute of Scientific and Technical Information of China (English)

    Joseph J. Kirkland; Stephanie A. Schuster; William L. Johnson; Barry E. Boyes

    2013-01-01

    The advent of superficially porous particles (SPPs) for packed HPLC columns has changed the way that many practitioners have approached the problem of developing needed separations. The very high efficiency of such columns, combined with convenient operating conditions, modest back pressures and the ability to use conventional HPLC instruments has resulted in intense basic studies of SPP technology, and widespread applications in many sciences. This report contains an overview of the SPP technology first developed in 2006 by Advanced Materials Technology, Inc., for sub-3-mm particles, then expanded into a family of SPP products with different particle sizes, pore sizes and other physical parameters. This approach was designed so that each particle of the family could be optimized for separating a particular group of compounds, usually based on solute size.

  19. Quantitative cellular uptake of double fluorescent core-shelled model submicronic particles

    Energy Technology Data Exchange (ETDEWEB)

    Leclerc, Lara, E-mail: leclerc@emse.fr [Ecole Nationale Superieure des Mines, CIS-EMSE, LINA (France); Boudard, Delphine [LINA (France); Pourchez, Jeremie; Forest, Valerie [Ecole Nationale Superieure des Mines, CIS-EMSE, LINA (France); Marmuse, Laurence; Louis, Cedric [NANO-H S.A.S (France); Bin, Valerie [LINA (France); Palle, Sabine [Universite Jean Monnet, Centre de Microscopie Confocale Multiphotonique (France); Grosseau, Philippe; Bernache-Assollant, Didier [Ecole Nationale Superieure des Mines, CIS-EMSE, LINA (France); Cottier, Michele [LINA (France)

    2012-11-15

    The relationship between particles' physicochemical parameters, their uptake by cells and their degree of biological toxicity represent a crucial issue, especially for the development of new technologies such as fabrication of micro- and nanoparticles in the promising field of drug delivery systems. This work was aimed at developing a proof-of-concept for a novel model of double fluorescence submicronic particles that could be spotted inside phagolysosomes. Fluorescein isothiocyanate (FITC) particles were synthesized and then conjugated with a fluorescent pHrodo Trade-Mark-Sign probe, red fluorescence of which increases in acidic conditions such as within lysosomes. After validation in acellular conditions by spectral analysis with confocal microscopy and dynamic light scattering, quantification of phagocytosis was conducted on a macrophage cell line in vitro. The biological impact of pHrodo functionalization (cytotoxicity, inflammatory response, and oxidative stress) was also investigated. Results validate the proof-of-concept of double fluorescent particles (FITC + pHrodo), allowing detection of entirely engulfed pHrodo particles (green and red labeling). Moreover incorporation of pHrodo had no major effects on cytotoxicity compared to particles without pHrodo, making them a powerful tool for micro- and nanotechnologies.

  20. Determinants of Sir2-Mediated, Silent Chromatin Cohesion.

    Science.gov (United States)

    Chen, Yu-Fan; Chou, Chia-Ching; Gartenberg, Marc R

    2016-08-01

    Cohesin associates with distinct sites on chromosomes to mediate sister chromatid cohesion. Single cohesin complexes are thought to bind by encircling both sister chromatids in a topological embrace. Transcriptionally repressed chromosomal domains in the yeast Saccharomyces cerevisiae represent specialized sites of cohesion where cohesin binds silent chromatin in a Sir2-dependent fashion. In this study, we investigated the molecular basis for Sir2-mediated cohesion. We identified a cluster of charged surface residues of Sir2, collectively termed the EKDK motif, that are required for cohesin function. In addition, we demonstrated that Esc8, a Sir2-interacting factor, is also required for silent chromatin cohesion. Esc8 was previously shown to associate with Isw1, the enzymatic core of ISW1 chromatin remodelers, to form a variant of the ISW1a chromatin remodeling complex. When ESC8 was deleted or the EKDK motif was mutated, cohesin binding at silenced chromatin domains persisted but cohesion of the domains was abolished. The data are not consistent with cohesin embracing both sister chromatids within silent chromatin domains. Transcriptional silencing remains largely intact in strains lacking ESC8 or bearing EKDK mutations, indicating that silencing and cohesion are separable functions of Sir2 and silent chromatin.

  1. Energy Spectrum of Ground State and Excitation Spectrum of Quasi-particle for Hard-Core Boson in Optical Lattices

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    We investigate the energy spectrum of ground state and quasi-particle excitation spectrum of hard-core bosons, which behave very much like spinless noninteracting fermions, in optical lattices by means of the perturbation expansion and Bogoliubov approach. The results show that the energy spectrum has a single band structure, and the energy is lower near zero momentum; the excitation spectrum gives corresponding energy gap, and the system is in Mott-insulating state at Tonks limit. The analytic result of energy spectrum is in good agreement with that calculated in terms of Green's function at strong correlation limit.

  2. Hollow-core photonic crystal fiber based multifunctional optical system for trapping, position sensing, and detection of fluorescent particles.

    Science.gov (United States)

    Shinoj, V K; Murukeshan, V M

    2012-05-15

    We demonstrate a novel multifunctional optical system that is capable of trapping, imaging, position sensing, and fluorescence detection of micrometer-sized fluorescent test particles using hollow-core photonic crystal fiber (HC-PCF). This multifunctional optical system for trapping, position sensing, and fluorescent detection is designed such that a near-IR laser light is used to create an optical trap across a liquid-filled HC-PCF, and a 473 nm laser is employed as a source for fluorescence excitation. This proposed system and the obtained results are expected to significantly enable an efficient integrated trapping platform employing HC-PCF for diagnostic biomedical applications.

  3. The human chromosome. Electron microscopic observations on chromatin fiber organization.

    Science.gov (United States)

    Abuelo, J G; Moore, D E

    1969-04-01

    Human lymphocytes were grown in short-term tissue culture and were arrested in metaphase with Colcemid. Their chromosomes were prepared by the Langmuir trough-critical point drying technique and were examined under the electron microscope. In addition, some chromosomes were digested with trypsin, Pronase, or DNase. The chromosomes consist entirely of tightly packed, 240 +/- 50-A chromatin fibers. Trypsin and Pronase treatments induce relaxation of fiber packing and reveal certain underlying fiber arrangements. Furthermore, trypsin treatment demonstrates that the chromatin fiber has a 25-50 A trypsin-resistant core surrounded by a trypsin-sensitive sheath. DNase digestion suggests that this core contains DNA.

  4. Structural variation of solid core and thickness of porous shell of 1.7 μm core-shell silica particles on chromatographic performance: narrow bore columns.

    Science.gov (United States)

    Omamogho, Jesse O; Hanrahan, John P; Tobin, Joe; Glennon, Jeremy D

    2011-04-15

    Chromatographic and mass transfer kinetic properties of three narrow bore columns (2.1×50 mm) packed with new core-shell 1.7 μm EIROSHELL™-C(18) (EiS-C(18)) particles have been studied. The particles in each column varied in the solid-core to shell particle size ratio (ρ), of 0.59, 0.71 and 0.82, with a porous silica shell thickness of 350, 250 and 150 nm respectively. Scanning and transmission electron microscopy (SEM and TEM), Coulter counter analysis, gas pycnometry, nitrogen sorption analysis and inverse size exclusion chromatography (ISEC) elucidated the physical properties of these materials. The porosity measurement of the packed HILIC and C(18) modified phases provided the means to estimate the phase ratios of the three different shell columns (EiS-150-C(18), EiS-250-C(18) and EiS-350-C(18)). The dependence of the chromatographic performance to the volume fraction of the porous shell was observed for all three columns. The naphtho[2,3-a]pyrene retention factor of k'∼10 on the three EiS-C(18s) employed to obtain the height equivalents to theoretical plates (HETPs) data were achieved by varying the mobile phase compositions and applying the Wilke and Chang relationship to obtain a parallel reduced linear velocity. The Knox fit model gave the coefficient of the reduce HETPs for the three EiS-C(18s). The reduced plate height minimum h(min)=1.9 was achieved for the EiS-150-C(18) column, and generated an efficiency of over 350,000 N/m and h(min)=2.5 equivalent to an efficiency of 200,000 N/m for the EiS-350-C(18) column. The efficiency loss of the EiS-C18 column emanating from the system extra-column volume was discussed with respect to the porous shell thickness.

  5. Graphene supported Sn-Sb rate at carbon core-shell particles as a superior anode for lithium ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shuangqiang; Chen, Peng; Wang, Yong [Department of Chemical Engineering, School of Environmental and Chemical Engineering, Shanghai University (China); Wu, Minghong; Pan, Dengyu [Institute of Nanochemistry and Nanobiology, Shanghai Univ. (China)

    2010-10-15

    This paper reports the preparation and Li-storage properties of graphene nanosheets(GNS), GNS supported Sn-Sb rate at carbon (50-150 nm) and Sn-Sb nanoparticles (5-10 nm). The best cycling performance and excellent high rate capabilities were observed for GNS-supported Sn-Sb rate at carbon core-shell particles, which exhibited initial capacities of 978, 850 and 668 mAh/g respectively at 0.1C, 2C and 5C (1C = 800 mA/g) with good cyclability. Besides the GNS support, the carbon skin around Sn-Sb particles is believed to be a key factor to improve electrochemical properties of Sn-Sb. (author)

  6. 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

    2016-04-28

    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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Synthesis of Co/MFe(2)O(4) (M = Fe, Mn) Core/Shell Nanocomposite Particles.

    Science.gov (United States)

    Peng, Sheng; Xie, Jin; Sun, Shouheng

    2008-01-01

    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 MFe(2)O(4) (M = Fe, Mn) ferrite shell. Core/shell structured bimagnetic Co/MFe(2)O(4) nanocomposites are prepared with tunable shell thickness (1-5 nm). The Co/MFe(2)O(4) nanocomposites retain the high magnetic moment density from the Co core, while gaining chemical and magnetic stability from the ferrite shell. Comparing to Co NPs, the nanocomposites show much enhanced stability in buffer solution at elevated temperatures, making them promising for biomedical applications.

  12. The optical Tamm states at the interface between a photonic crystal and a nanocomposite containing core-shell particles

    Science.gov (United States)

    Vetrov, S. Ya; Pankin, P. S.; Timofeev, I. V.

    2016-06-01

    We investigate the optical Tamm states (OTSs) localized at the interface between a photonic crystal (PC) and a nanocomposite consisting of spherical nanoparticles with a dielectric core and a metallic shell, which are dispersed in a transparent matrix, and is characterized by the resonance permittivity. Spectra of transmission, reflection, and absorption of normally incident light waves by the investigated structure are calculated. The spectral manifestation of the Tamm states caused by negative values of the real part of the effective permittivity in the visible spectral range is studied. It is demonstrated that, along with the significantly extended band gap of the PC, the transmission spectrum contains an additional stopband caused by nanocomposite absorption near the resonance frequency. It is shown that the OTSs can be implemented in two band gaps of the PCs, each corresponding to a certain plasmon resonance frequency of the nanocomposite. It is established that the characteristics of the Tamm state localized at the edge of the PCs significantly depend on the ratio between the particle core volume and the total particle volume.

  13. Hepatitis B virus DNA-negative dane particles lack core protein but contain a 22-kDa precore protein without C-terminal arginine-rich domain.

    Science.gov (United States)

    Kimura, Tatsuji; Ohno, Nobuhiko; Terada, Nobuo; Rokuhara, Akinori; Matsumoto, Akihiro; Yagi, Shintaro; Tanaka, Eiji; Kiyosawa, Kendo; Ohno, Shinichi; Maki, Noboru

    2005-06-10

    DNA-negative Dane particles have been observed in hepatitis B virus (HBV)-infected sera. The capsids of the empty particles are thought to be composed of core protein but have not been studied in detail. In the present study, the protein composition of the particles was examined using new enzyme immunoassays for the HBV core antigen (HBcAg) and for the HBV precore/core proteins (core-related antigens, HBcrAg). HBcrAg were abundant in fractions slightly less dense than HBcAg and HBV DNA. Three times more Dane-like particles were observed in the HBcrAg-rich fraction than in the HBV DNA-rich fraction by electron microscopy. Western blots and mass spectrometry identified the HBcrAg as a 22-kDa precore protein (p22cr) containing the uncleaved signal peptide and lacking the arginine-rich domain that is involved in binding the RNA pregenome or the DNA genome. In sera from 30 HBV-infected patients, HBcAg represented only a median 10.5% of the precore/core proteins in enveloped particles. These data suggest that most of the Dane particles lack viral DNA and core capsid but contain p22cr. This study provides a model for the formation of the DNA-negative Dane particles. The precore proteins, which lack the arginine-rich nucleotide-binding domain, form viral RNA/DNA-negative capsid-like particles and are enveloped and released as empty particles.

  14. Utterance-final particles in Taiwan Mandarin : contact, context and core functions

    NARCIS (Netherlands)

    Lin, Chin-hui

    2014-01-01

    The use of utterance-final particles (UFPs) is a salient feature of Taiwan Mandarin, a Mandarin variety spoken in Taiwan. Despite their widespread use, Taiwan Mandarin UFPs have not attracted much attention in previous research. One reason for this neglect is that previous studies focus on UFPs that

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

    NARCIS (Netherlands)

    J.G. van Bemmel (Joke)

    2012-01-01

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

  16. Isocratic and gradient impedance plot analysis and comparison of some recently introduced large size core-shell and fully porous particles.

    Science.gov (United States)

    Vanderheyden, Yoachim; Cabooter, Deirdre; Desmet, Gert; Broeckhoven, Ken

    2013-10-18

    The intrinsic kinetic performance of three recently commercialized large size (≥4μm) core-shell particles packed in columns with different lengths has been measured and compared with that of standard fully porous particles of similar and smaller size (5 and 3.5μm, respectively). The kinetic performance is compared in both absolute (plot of t0 versus the plate count N or the peak capacity np for isocratic and gradient elution, respectively) and dimensionless units. The latter is realized by switching to so-called impedance plots, a format which has been previously introduced (as a plot of t0/N(2) or E0 versus Nopt/N) and has in the present study been extended from isocratic to gradient elution (where the impedance plot corresponds to a plot of t0/np(4) versus np,opt(2)/np(2)). Both the isocratic and gradient impedance plot yielded a very similar picture: the clustered impedance plot curves divide into two distinct groups, one for the core-shell particles (lowest values, i.e. best performance) and one for the fully porous particles (highest values), confirming the clear intrinsic kinetic advantage of core-shell particles. If used around their optimal flow rate, the core-shell particles displayed a minimal separation impedance that is about 40% lower than the fully porous particles. Even larger gains in separation speed can be achieved in the C-term regime.

  17. 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 radio-isotopes 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 ...

  18. 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...

  19. 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

  20. Tunable multiple Fano resonances in magnetic single-layered core-shell particles

    CERN Document Server

    Arruda, Tiago Jose; Pinheiro, Felipe Arruda

    2015-01-01

    We investigate multiple Fano, comblike scattering resonances in single-layered, concentric core-shell nanoparticles composed of magnetic materials. Using the Lorenz-Mie theory, we derive, in the long-wavelength limit, an analytical condition for the occurrence of comblike resonances in the single scattering by coated spheres. This condition establishes that comblike scattering response uniquely depends on material parameters and thickness of the shell, provided that it is magnetic and thin compared to the scatterer radius. We also demonstrate that comblike scattering response shows up beyond the long-wavelength limit and it is robust against absorption. Since multiple Fano resonances are shown to depend explicitly on the magnetic permeability of the shell, we argue that both the position and profile of the comblike, morphology-dependent resonances could be externally tuned by exploiting the properties of engineered magnetic materials.

  1. 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

    2014-01-01

    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 ((1)H-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

  2. Nano-magnetic particles used in biomedicine: core and coating materials.

    Science.gov (United States)

    Karimi, Z; Karimi, L; Shokrollahi, H

    2013-07-01

    Magnetic nanoparticles for medical applications have been developed by many researchers. Separation, immunoassay, drug delivery, magnetic resonance imaging and hyperthermia are enhanced by the use of suitable magnetic nanoparticles and coating materials in the form of ferrofluids. Due to their low biocompatibility and low dispersion in water solutions, nanoparticles that are used for biomedical applications require surface treatment. Various kinds of coating materials including organic materials (polymers), inorganic metals (gold, platinum) or metal oxides (aluminum oxide, cobalt oxide) have been attracted during the last few years. Based on the recent advances and the importance of nanomedicine in human life, this paper attempts to give a brief summary on the different ferrite nano-magnetic particles and coatings used in nanomedicine.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kuno, T; Hirao, K [Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, 466-8555 (Japan); Nagata, F; Ohji, T; Kato, K, E-mail: katsuya-kato@aist.go.jp [Advanced Manufacturing Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2266-98, Anagahora, Shimoshidami, Moriyama-ku, Nagoya, 463-8510 (Japan)

    2011-04-15

    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(CH{sub 3}COO){sub 2} and (NH{sub 4}){sub 2}HPO{sub 4}. 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.

  4. [Adsorption of Cu on Core-shell Structured Magnetic Particles: Relationship Between Adsorption Performance and Surface Properties].

    Science.gov (United States)

    Li, Qiu-mei; Chen, Jing; Li, Hai-ning; Zhang, Xiao-lei; Zhang, Gao-sheng

    2015-12-01

    In order to reveal the relationship between the adsorption performance of adsorbents and their compositions, structure, and surface properties, the core-shell structured Fe₃O₄/MnO2 and Fe-Mn/Mn₂2 magnetic particles were systematically characterized using multiple techniques and their Cu adsorption behaviors as well as mechanism were also investigated in details. It was found that both Fe₃O4 and Fe-Mn had spinel structure and no obvious crystalline phase change was observed after coating with MnO₂. The introduction of Mn might improve the affinity between the core and the shell, and therefore enhanced the amount and distribution uniformity of the MnO₂ coated. Consequently, Fe-Mn/MnO₂ exhibited a higher BET specific surface area and a lower isoelectric point. The results of sorption experiments showed that Fe-Mn had a higher maximal Cu adsorption capacity of 33.7 mg · g⁻¹ at pH 5.5, compared with 17.5 mg · g⁻¹ of Fe₃O4. After coating, the maximal adsorption capacity of Fe-Mn/MnO₂ was increased to 58.2 mg · g⁻¹, which was 2.6 times as high as that of Fe₃O₄/MnO₂ and outperformed the majority of magnetic adsorbents reported in literature. In addition, a specific adsorption of Cu occurred at the surface of Fe₃O₄/MnO₂ or Fe-Mn/MnO₂ through the formation of inner-sphere complexes. In conclusion, the adsorption performance of the magnetic particles was positively related to their compositions, structure, and surface properties.

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

    Directory of Open Access Journals (Sweden)

    G. Bocchi

    2016-09-01

    Full Text Available The γ-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 γ-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 μs isomer. Lifetimes analysis, performed by fast-timing techniques with LaBr3(Ce scintillators, revealed 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 in the nature of particle-core excitations with increasing spin.

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

    Science.gov (United States)

    Bocchi, G.; Leoni, S.; Fornal, B.; Colò, G.; Bortignon, P. F.; Bottoni, S.; Bracco, A.; Michelagnoli, C.; Bazzacco, D.; Blanc, A.; de France, G.; Jentschel, M.; Köster, U.; Mutti, P.; Régis, 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-Oryǹczak, N.; Crespi, F. C. L.; Didierjean, F.; Jolie, J.; Korten, W.; Kröll, T.; Lalkovski, S.; Mach, H.; Mărginean, N.; Melon, B.; Mengoni, D.; Million, B.; Nannini, A.; Napoli, D.; Olaizola, B.; Paziy, V.; Podolyák, Zs.; Regan, P. H.; Saed-Samii, N.; Szpak, B.; Vedia, V.

    2016-09-01

    The γ-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 γ-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 μs isomer. Lifetimes analysis, performed by fast-timing techniques with LaBr3(Ce) scintillators, revealed 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 in the nature of particle-core excitations with increasing spin.

  7. Structure of chromatin in spermatozoa.

    Science.gov (United States)

    Björndahl, Lars; Kvist, Ulrik

    2014-01-01

    The specialized structure of the sperm chromatin has a dual function - first to protect the DNA from damage during storage and transport to the oocyte, and then to enable a rapid and complete unpacking of the undamaged paternal genome in the ooplasm. It is evident that zinc has a pivotal role in maintaining the structural stability and in enabling a rapid decondensation at the appropriate time. It is important for the sperm chromatin structure that the spermatozoa are ejaculated together with the zinc-rich prostatic secretion. Early exposure to zinc-binding seminal vesicular fluid can deplete the sperm chromatin of zinc and most likely induce surplus formation of disulfide bridges, likely to cause incomplete and delayed decondensation of the sperm chromatin in the oocyte. A premature decrease in sperm chromatin structure stability is likely to increase the risk for damage to the DNA due to increased access to the genome for DNA damaging compounds. The status of the sperm chromatin structure can vary in vitro depending on the exposure to zinc-depleting conditions when spermatozoa are stored in semen after ejaculation. When sperm DNA damage tests are evaluated and validated, it is therefore essential to also take into account the dynamics of zinc-dependent and zinc-independent sperm chromatin stability.

  8. Synthesis of polystyrene core/SiO2 shell composite particles and fabrication of SiO2 capsules out of them

    Science.gov (United States)

    Terekhin, V.

    2017-01-01

    Systemic studies on the dependence of the morphology of polystyrene core/SiO2 shell composite particles on the conditions of their fabrication have been performed. Spherical polystyrene particles synthesized in the presence of a cationic initiator of polymerization were used as cores. SiO2 shells were formed by modified Stober’s method. Exposure of the synthesized composite particles to high temperatures has been shown to cause destruction of their polystyrene core, thereby allowing the formation of mesoporous SiO2 capsules with a mean pore diameter of ~3 nm and specific surface area of ~270 m2/g. Model experiments on loading the SiO2 capsules with amoxicillin have been carried out. Spectrophotometry in the UV and visible spectral regions has been used to estimate the kinetics of amoxicillin release from the SiO2 capsules.

  9. Polybutylacrylate/poly (methyl methacrylate) Core-Shell Elastic Particles as Epoxy Resin Toughener:Part II Toughness on DGEBA/DDM system

    Institute of Scientific and Technical Information of China (English)

    Jianli WANG; Myonghoon LEE; Kejian YAO; Jianbin JI; Xiaomei YU

    2004-01-01

    Mechanical properties of epoxy resin were investigated by adding core-shell elastic particles (CSEP). The results indicated that optimized core-shell ratio was 60/40 and the loading volume of CSEP was 10 phr (per hundred parts of epoxy resin by weight). The impact strength of modified systems increased apparently with the decrease of core sizes. However, the shearing strength changed gently with the particle sizes. CSEP with lightly crosslinked rubbery core showed more effectiveness on toughness than others. With solution blending, CSEP could be dispersed in epoxy matrix well, and the morphologies of dispersed rubber domains were controlled perfectly by CSEP whose structure was predesigned. A cavitation-shearing band toughness mechanism was observed from the SEM micrographs of fracture surface. It also was found that the deforming temperature (DT) of modified epoxy did not decline apparently.

  10. Application of the isopycnic kinetic plot method for elucidating the potential of sub-2 µm and core-shell particles in SFC.

    Science.gov (United States)

    Delahaye, Sander; Broeckhoven, Ken; Desmet, Gert; Lynen, Frédéric

    2013-11-15

    In this work the isopycnic method to construct kinetic plots for SFC was used to investigate the performance limits of an SFC system when using sub-2 µm fully porous particles and sub-3 µm superficially porous (core-shell) particles. This isopycnic kinetic plot method for SFC was developed and tested earlier for SFC separations on native silica with pure CO2 as mobile phase. In the current work, octadecyl based reversed phase columns were used in combination with a mobile phase that contains 10% methanol as modifier in order to study the applicability of the described methodology to assess the kinetic performance limits of experimental setups in which SFC is used and will, according to all probability, be evolving. SFC and HPLC van Deemter and kinetic plots are constructed for columns packed with fully porous particles with various diameters and for a column packed with core-shell particles. The influence of the experimental kinetic performance limits of the particle diameter and morphology in SFC is shown to be the same as in HPLC. Additionally, kinetic plot predictions were constructed for separations on 1 µm and 0.5 µm particles using the data measured on the 5 µm, 3.5 µm and 1.8 µm fully porous particles. By doing this the potential applicability of 1 µm particles on the contemporary SFC and HPLC systems was demonstrated together with the irrelevance of the use of 0.5 µm particles in SFC.

  11. 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.

  12. 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.

  13. 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...

  14. Glucose sensing through Fano resonances in mesoscale silica core-gold shell particles arrays

    Science.gov (United States)

    Pincella, Francesca; Huang, Zhiwei

    2016-03-01

    We report the development of a versatile, cheap and reusable plasmonic sensor able to detect glucose in the physiological concentration range by means of a simple label-free optical detection scheme. In order to achieve the aforementioned goal we applied a self-assembly deposition technique for the large-scale arraying of mesoscale gold nanoshell particles. Different from metallic nanospheres arrays, the localized surface plasmon resonances of gold nanoshells arrays extend in both the visible and near-infrared range, making them extremely promising for their use in biological media. Furthermore, the optical response of mesoscale gold nanoshells arrays showed another remarkable characteristic, which is the presence of various Fano resonances that have the advantage of enhancing the sensitivity of the plasmonic substrate to the external media thanks to their sharp features and increased spectral contrast. The plasmonic sensor was shown to have an extended working range with a good linear response for large refractive index shifts, where a bulk refractive index sensitivity of 0.93 RIU-1 (RIU, refractive index units) was achieved experimentally. In addition, the plasmonic sensor could detect aqueous glucose solutions in the blood concentration range (0-25 mM), with a sensitivity of 0.24 M-1.

  15. Biomimetic synthesis of raspberry-like hybrid polymer-silica core-shell nanoparticles by templating colloidal particles with hairy polyamine shell.

    Science.gov (United States)

    Pi, Mengwei; Yang, Tingting; Yuan, Jianjun; Fujii, Syuji; Kakigi, Yuichi; Nakamura, Yoshinobu; Cheng, Shiyuan

    2010-07-01

    The nanoparticles composed of polystyrene core and poly[2-(diethylamino)ethyl methacrylate] (PDEA) hairy shell were used as colloidal templates for in situ silica mineralization, allowing the well-controlled synthesis of hybrid silica core-shell nanoparticles with raspberry-like morphology and hollow silica nanoparticles by subsequent calcination. Silica deposition was performed by simply stirring a mixture of the polymeric core-shell particles in isopropanol, tetramethyl orthosilicate (TMOS) and water at 25 degrees C for 2.5h. No experimental evidence was found for nontemplated silica formation, which indicated that silica deposition occurred exclusively in the PDEA shell and formed PDEA-silica hybrid shell. The resulting hybrid silica core-shell particles were characterized by transmission electron microscopy (TEM), thermogravimetry, aqueous electrophoresis, and X-ray photoelectron spectroscopy. TEM studies indicated that the hybrid particles have well-defined core-shell structure with raspberry morphology after silica deposition. We found that the surface nanostructure of hybrid nanoparticles and the composition distribution of PDEA-silica hybrid shell could be well controlled by adjusting the silicification conditions. These new hybrid core-shell nanoparticles and hollow silica nanoparticles would have potential applications for high-performance coatings, encapsulation and delivery of active organic molecules.

  16. 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.

  17. Vernalization-mediated chromatin changes.

    Science.gov (United States)

    Zografos, Brett R; Sung, Sibum

    2012-07-01

    Proper flowering time is vital for reproductive fitness in flowering plants. In Arabidopsis, vernalization is mediated primarily through the repression of a MADS box transcription factor, FLOWERING LOCUS C (FLC). The induction of a plant homeodomain-containing protein, VERNALIZATION INSENSITIVE 3 (VIN3), by vernalizing cold is required for proper repression of FLC. One of a myriad of changes that occurs after VIN3 is induced is the establishment of FLC chromatin at a mitotically repressed state due to the enrichment of repressive histone modifications. VIN3 induction by cold is the earliest known event during the vernalization response and includes changes in histone modifications at its chromatin. Here, the current understanding of the vernalization-mediated chromatin changes in Arabidopsis is discussed, with a focus on the roles of shared chromatin-modifying machineries in regulating VIN3 and FLC gene family expression during the course of vernalization.

  18. Decoding chromatin goes high tech.

    Science.gov (United States)

    Levy, Dan; Gozani, Or

    2010-09-17

    Identifying proteins that recognize histone methylation is critical for understanding chromatin function. Vermeulen et al. (2010) now describe a cutting-edge strategy to identify and characterize several nuclear proteins and complexes that recognize five major histone trimethyl marks.

  19. Computational investigation of longitudinal diffusion, eddy dispersion, and trans-particle mass transfer in bulk, random packings of core-shell particles with varied shell thickness and shell diffusion coefficient.

    Science.gov (United States)

    Daneyko, Anton; Hlushkou, Dzmitry; Baranau, Vasili; Khirevich, Siarhei; Seidel-Morgenstern, Andreas; Tallarek, Ulrich

    2015-08-14

    In recent years, chromatographic columns packed with core-shell particles have been widely used for efficient and fast separations at comparatively low operating pressure. However, the influence of the porous shell properties on the mass transfer kinetics in core-shell packings is still not fully understood. We report on results obtained with a modeling approach to simulate three-dimensional advective-diffusive transport in bulk random packings of monosized core-shell particles, covering a range of reduced mobile phase flow velocities from 0.5 up to 1000. The impact of the effective diffusivity of analyte molecules in the porous shell and the shell thickness on the resulting plate height was investigated. An extension of Giddings' theory of coupled eddy dispersion to account for retention of analyte molecules due to stagnant regions in porous shells with zero mobile phase flow velocity is presented. The plate height equation involving a modified eddy dispersion term excellently describes simulated data obtained for particle-packings with varied shell thickness and shell diffusion coefficient. It is confirmed that the model of trans-particle mass transfer resistance of core-shell particles by Kaczmarski and Guiochon [42] is applicable up to a constant factor. We analyze individual contributions to the plate height from different mass transfer mechanisms in dependence of the shell parameters. The simulations demonstrate that a reduction of plate height in packings of core-shell relative to fully porous particles arises mainly due to reduced trans-particle mass transfer resistance and transchannel eddy dispersion.

  20. 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.

  1. Spreading chromatin into chemical biology.

    Science.gov (United States)

    Allis, C David; Muir, Tom W

    2011-01-24

    Epigenetics, broadly defined as the inheritance of non-Mendelian phenotypic traits, can be more narrowly defined as heritable alterations in states of gene expression ("on" versus "off") that are not linked to changes in DNA sequence. Moreover, these alterations can persist in the absence of the signals that initiate them, thus suggesting some kind of "memory" to epigenetic forms of regulation. How, for example, during early female mammalian development, is one X chromosome selected to be kept in an active state, while the genetically identical sister X chromosome is "marked" to be inactive, even though they reside in the same nucleus, exposed to the same collection of shared trans-factors? Once X inactivation occurs, how are these contrasting chromatin states maintained and inherited faithfully through subsequent cell divisions? Chromatin states, whether active (euchromatic) or silent (heterochromatic) are established, maintained, and propagated with remarkable precision during normal development and differentiation. However, mistakes made in establishing and maintaining these chromatin states, often executed by a variety of chromatin-remodeling activities, can lead to mis-expression or mis-silencing of critical downstream gene targets with far-reaching implications for human biology and disease, notably cancer. Though chromatin biologists have identified many of the "inputs" that are important for controlling chromatin states, the detailed mechanisms by which these processes work remain largely opaque, in part due to the staggering complexity of the chromatin polymer, the physiologically relevant form of our genome. The primary objective of this article is to serve as a "call to arms" for chemists to contribute to the development of the precision tools needed to answer pressing molecular problems in this rapidly moving field.

  2. Chromatin analysis of occluded genes

    Science.gov (United States)

    Lee, Jae Hyun; Gaetz, Jedidiah; Bugarija, Branimir; Fernandes, Croydon J.; Snyder, Gregory E.; Bush, Eliot C.; Lahn, Bruce T.

    2009-01-01

    We recently described two opposing states of transcriptional competency. One is termed ‘competent’ whereby a gene is capable of responding to trans-acting transcription factors of the cell, such that it is active if appropriate transcriptional activators are present, though it can also be silent if activators are absent or repressors are present. The other is termed ‘occluded’ whereby a gene is silenced by cis-acting, chromatin-based mechanisms in a manner that blocks it from responding to trans-acting factors, such that it is silent even when activators are present in the cellular milieu. We proposed that gene occlusion is a mechanism by which differentiated cells stably maintain their phenotypic identities. Here, we describe chromatin analysis of occluded genes. We found that DNA methylation plays a causal role in maintaining occlusion for a subset of occluded genes. We further examined a variety of other chromatin marks typically associated with transcriptional silencing, including histone variants, covalent histone modifications and chromatin-associated proteins. Surprisingly, we found that although many of these marks are robustly linked to silent genes (which include both occluded genes and genes that are competent but silent), none is linked specifically to occluded genes. Although the observation does not rule out a possible causal role of these chromatin marks in occlusion, it does suggest that these marks might be secondary effect rather than primary cause of the silent state in many genes. PMID:19380460

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    J. W. Taylor

    2014-06-01

    Full Text Available 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 nonrefractory material in the particles. Mixing between these two components is often considered using a core/shell coated sphere morphology. The Single Particle Soot Photometer (SP2 is the premier instrument for reporting distributions of both core size and coating thickness. Most studies combine the SP2's incandescence and scattering data to report coating properties, but there is variation in the assumed density and refractive index of the core that are used in these calculations. 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 n = (2.26-1.26i were the most appropriate to use with ambient soot in the Los Angeles area. Using these parameters generated a distribution of shell/core ratio of 1.04 ± 0.21, corresponding to an absolute coating thickness distribution of 1.7 ± 17.5 nm. This demonstrates that using this technique the SP2 can accurately determine the mixing state (externally or internally mixed of ambient soot, but with limited precision. Using other core parameters resulted in an offset in the coating distribution, but similar precision. For comparison, using the core parameters that resulted in the thickest coatings (on the same particles as before generated a distribution of shell/core ratio of 1.40 ± 0.19, corresponding to an absolute coating thickness distribution of 30.3 ± 14.9 nm. Relative changes in coatings associated with secondary aerosol condensation were captured regardless of the assumed core parameters. These results must be taken into account when comparing BC

  5. Chromatin Remodeling and Plant Immunity.

    Science.gov (United States)

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

    2017-01-01

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

  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.

  7. Inhibitory effect of presenilin inhibitor LY411575 on maturation of hepatitis C virus core protein, production of the viral particle and expression of host proteins involved in pathogenicity.

    Science.gov (United States)

    Otoguro, Teruhime; Tanaka, Tomohisa; Kasai, Hirotake; Yamashita, Atsuya; Moriishi, Kohji

    2016-11-01

    Hepatitis C virus (HCV) core protein is responsible for the formation of infectious viral particles and induction of pathogenicity. The C-terminal transmembrane region of the immature core protein is cleaved by signal peptide peptidase (SPP) for maturation of the core protein. SPP belongs to the family of presenilin-like aspartic proteases. Some presenilin inhibitors are expected to suppress HCV infection and production; however, this anti-HCV effect has not been investigated in detail. In this study, presenilin inhibitors were screened to identify anti-HCV compounds. Of the 13 presenilin inhibitors tested, LY411575 was the most potent inhibitor of SPP-dependent cleavage of HCV core protein. Production of intracellular core protein and supernatant infectious viral particles from HCV-infected cells was significantly impaired by LY411575 in a dose-dependent manner (half maximum inhibitory concentration = 0.27 μM, cytotoxic concentration of the extracts to cause death to 50% of viable cells > 10 μM). No effect of LY411575 on intracellular HCV RNA in the subgenomic replicon cells was detected. LY411575 synergistically promoted daclatasvir-dependent inhibition of viral production, but not that of viral replication. Furthermore, LY411575 inhibited HCV-related production of reactive oxygen species and expression of NADPH oxidases and vascular endothelial growth factor. Taken together, our data suggest that LY411575 suppresses HCV propagation through SPP inhibition and impairs host gene expressions related to HCV pathogenicity.

  8. High Photocatalytic Activity of Fe3O4-SiO2-TiO2 Functional Particles with Core-Shell Structure

    Directory of Open Access Journals (Sweden)

    Chenyang Xue

    2013-01-01

    Full Text Available This paper describes a novel method of synthesizing Fe3O4-SiO2-TiO2 functional nanoparticles with the core-shell structure. The Fe3O4 cores which were mainly superparamagnetic were synthesized through a novel carbon reduction method. The Fe3O4 cores were then modified with SiO2 and finally encapsulated with TiO2 by the sol-gel method. The results of characterizations showed that the encapsulated 700 nm Fe3O4-SiO2-TiO2 particles have a relatively uniform size distribution, an anatase TiO2 shell, and suitable magnetic properties for allowing collection in a magnetic field. These magnetic properties, large area, relative high saturation intensity, and low retentive magnetism make the particles have high dispersibility in suspension and yet enable them to be recovered well using magnetic fields. The functionality of these particles was tested by measuring the photocatalytic activity of the decolouring of methyl orange (MO and methylene blue (MB under ultraviolet light and sunlight. The results showed that the introduction of the Fe3O4-SiO2-TiO2 functional nanoparticles significantly increased the decoloration rate so that an MO solution at a concentration of 10 mg/L could be decoloured completely within 180 minutes. The particles were recovered after utilization, washing, and drying and the primary recovery ratio was 87.5%.

  9. Rapid determination of parabens in seafood sauces by high-performance liquid chromatography: A practical comparison of core-shell particles and sub-2 μm fully porous particles.

    Science.gov (United States)

    Ye, Jing; Cao, Xiaoji; Cheng, Zhuo; Qin, Ye; Lu, Yanbin

    2015-12-01

    In this work, the chromatographic performance of superficially porous particles (Halo core-shell C18 column, 50 mm × 2.1 mm, 2.7 μm) was compared with that of sub-2 μm fully porous particles (Acquity BEH C18 , 50 mm × 2.1 mm, 1.7 μm). Four parabens, methylparaben, ethylparaben, propylparaben, and butylparaben, were used as representative compounds for calculating the plate heights in a wide flow rate range and analyzed on the basis of the Van Deemter and Knox equations. Theoretical Poppe plots were constructed for each column to compare their kinetic performance. Both phases gave similar minimum plate heights when using nonreduced coordinates. Meanwhile, the flat C-term of the core-shell column provided the possibilities for applying high flow rates without significant loss in efficiency. The low backpressure of core-shell particles allowed this kind of column, especially compatible with conventional high-performance liquid chromatography systems. Based on these factors, a simple high-performance liquid chromatography method was established and validated for the determination of parabens in various seafood sauces using the Halo core-shell C18 column for separation.

  10. The nuclear matrix and the regulation of chromatin organization and function.

    Science.gov (United States)

    Davie, J R

    1995-01-01

    Nuclear DNA is organized into loop domains, with the base of the loop being bound to the nuclear matrix. Loops with transcriptionally active and/or potentially active genes have a DNase I-sensitive chromatin structure, while repressed chromatin loops have a condensed configuration that is essentially invisible to the transcription machinery. Core histone acetylation and torsional stress appear to be responsible for the generation and/or maintenance of the open potentially active chromatin loops. The transcriptionally active region of the loop makes several dynamic attachments with the nuclear matrix and is associated with core histones that are dynamically acetylated. Histone acetyltransferase and deacetylase, which catalyze this rapid acetylation and deacetylation, are bound to the nuclear matrix. Several transcription factors are components of the nuclear matrix. Histone acetyltransferase, deacetylase, and transcription factors may contribute to the dynamic attachment of the active chromatin domains with the nuclear matrix at sites of ongoing transcription.

  11. 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.

  12. 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....

  13. Biophysical studies of cholesterol effects on chromatin.

    Science.gov (United States)

    Silva, Isabel T G; Fernandes, Vinicius; Souza, Caio; Treptow, Werner; Santos, Guilherme Martins

    2017-03-22

    Changes in chromatin structure regulate gene expression and genome maintenance. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Previous work indicated that cholesterol, a ubiquitous cellular lipid, may bind to chromatin in vivo, suggesting a potential function for lipids in modulating chromatin architecture. However, the molecular mechanisms of cholesterol action on chromatin structure have remained unclear. Here, we explored the biophysical impact of cholesterol on nucleosome and chromatin fibers reconstituted in vitro and characterized in silico the cholesterol binding to nucleosome. Our findings support that cholesterol assists 10nm and 30nm chromatin formation and induces folding of long chromatin fibers as a result of direct interaction of the cholesterol to six nucleosomal binding sites.

  14. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications...

  15. Chromatin structure regulates gene conversion.

    Directory of Open Access Journals (Sweden)

    W Jason Cummings

    2007-10-01

    Full Text Available Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vlambda pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205, expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vlambda donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vlambda array, and altered the outcome of Vlambda diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences.

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

    DEFF Research Database (Denmark)

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

    2000-01-01

    The structure of chromatin regulates the genetic activity of the underlying DNA sequence. We report here that the protein encoded by the proto-oncogene DEK, which is involved in acute myelogenous leukemia, induces alterations of the superhelical density of DNA in chromatin. The change in topology...... protein substantially reduces the replication efficiency of chromatin but not of naked DNA templates.......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...... is observed with chromatin but not with naked DNA and does not involve dissociation of core histones from chromatin. Moreover, these effects require histone H2A/H2B dimers in addition to histone H3/H4. We additionally tested whether the DEK protein affects DNA-utilizing processes and found that the DEK...

  17. The Chd Family of Chromatin Remodelers

    OpenAIRE

    Marfella, Concetta G.A.; Imbalzano, Anthony N.

    2007-01-01

    Chromatin remodeling enzymes contribute to the dynamic changes that occur in chromatin structure during cellular processes such as transcription, recombination, repair, and replication. Members of the chromodomain helicase DNA-binding (Chd) family of enzymes belong to the SNF2 superfamily of ATP-dependent chromatin remodelers. The Chd proteins are distinguished by the presence of two N-terminal chromodomains that function as interaction surfaces for a variety of chromatin components. Genetic,...

  18. A core viral protein binds host nucleosomes to sequester immune danger signals.

    Science.gov (United States)

    Avgousti, Daphne C; Herrmann, Christin; Kulej, Katarzyna; Pancholi, Neha J; Sekulic, Nikolina; Petrescu, Joana; Molden, Rosalynn C; Blumenthal, Daniel; Paris, Andrew J; Reyes, Emigdio D; Ostapchuk, Philomena; Hearing, Patrick; Seeholzer, Steven H; Worthen, G Scott; Black, Ben E; Garcia, Benjamin A; Weitzman, Matthew D

    2016-07-01

    Viral proteins mimic host protein structure and function to redirect cellular processes and subvert innate defenses. Small basic proteins compact and regulate both viral and cellular DNA genomes. Nucleosomes are the repeating units of cellular chromatin and play an important part in innate immune responses. Viral-encoded core basic proteins compact viral genomes, but their impact on host chromatin structure and function remains unexplored. Adenoviruses encode a highly basic protein called protein VII that resembles cellular histones. Although protein VII binds viral DNA and is incorporated with viral genomes into virus particles, it is unknown whether protein VII affects cellular chromatin. Here we show that protein VII alters cellular chromatin, leading us to hypothesize that this has an impact on antiviral responses during adenovirus infection in human cells. We find that protein VII forms complexes with nucleosomes and limits DNA accessibility. We identified post-translational modifications on protein VII that are responsible for chromatin localization. Furthermore, proteomic analysis demonstrated that protein VII is sufficient to alter the protein composition of host chromatin. We found that protein VII is necessary and sufficient for retention in the chromatin of members of the high-mobility-group protein B family (HMGB1, HMGB2 and HMGB3). HMGB1 is actively released in response to inflammatory stimuli and functions as a danger signal to activate immune responses. We showed that protein VII can directly bind HMGB1 in vitro and further demonstrated that protein VII expression in mouse lungs is sufficient to decrease inflammation-induced HMGB1 content and neutrophil recruitment in the bronchoalveolar lavage fluid. Together, our in vitro and in vivo results show that protein VII sequesters HMGB1 and can prevent its release. This study uncovers a viral strategy in which nucleosome binding is exploited to control extracellular immune signaling.

  19. In vitro biocompatibility of magnetic thermo-responsive nanohydrogel particles of poly(N-isopropylacrylamide-co-acrylic acid) with Fe3O4 cores: effect of particle size and chemical composition.

    Science.gov (United States)

    Chou, Feng-Yi; Lai, Jui-Yang; Shih, Chao-Ming; Tsai, Meng-Chao; Lue, Shingjiang Jessie

    2013-04-01

    Biocompatibility is a critical factor in the design and development of candidate materials for biomedical use. This paper reports on the in vitro biocompatibility of magnetic stimuli-sensitive nanohydrogel particles composed of magnetite cores in poly(N-isopropylacrylamide-co-acrylic acid) shells referred to Fe(3)O(4)/P(NIPAAm-co-AAc). The AAc concentration and polymerization time were varied to fabricate magnetic nanoparticles with various AAc levels (1.80-2.37%) and particle sizes (74-213 nm). The P(NIPAAm-co-AAc) shell exhibited thermo-sensitive properties and the Fe(3)O(4) core constituted 2.25-4.10% of the particles by weight. After a 2-day incubation of L929 cells with extract media that had been conditioned with various test samples, the cellular responses were monitored in terms of cell viability and growth. The Live/Dead assays showed that high levels of cellular viability (97.3-98.1%) were observed in all groups, indicating that none of the nanoparticles were cytotoxic. However, the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymetho-xyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assays demonstrated that the activity of mitochondrial dehydrogenase varied significantly in cultures exposed to different magnetic nanohydrogel particles. The murine fibroblasts exposed to the NIP-(AAc5.1-Fe)-2 sample, which contained the highest AAc content and largest particle sizes, were the least metabolically active. In contrast, the activity levels in the cultures treated with the low AAc content and small size particles (NIP-(AAc2.6-Fe)-1) were not significantly different from those in the control group. Our findings suggest that smaller magnetic stimuli-sensitive nanohydrogel particles with a lower AAc content may have little inhibitory impact on cell proliferation. Overall, the in vitro biocompatibilities of the nanoparticles depend on the chemical composition and size of the Fe(3)O(4)/P(NIPAAm-co-AAc) particles.

  20. Investigation of the particle-core structure of odd-mass nuclei in the N sub p N sub n scheme

    Energy Technology Data Exchange (ETDEWEB)

    Bucurescu, D.; Cata, G.; Cutoiu, D.; Dragulescu, E.; Ivascu, M.; Zamfir, N.V. (Institutul Central de Fizica, Bucharest (Romania)); Gizon, A.; Gizon, J. (Grenoble-1 Univ., 38 (France). Inst. des Sciences Nucleaires)

    1989-10-19

    The N{sub p}N{sub n} scheme is applied to data related to collective band structures determined by the unique parity shell model orbitals in odd-A nuclei from the mass regions A{approx equal}80-100 and A{approx equal}130. Simple systematics are obtained which give a synthetic picture of the evolution of the particle-core coupling in these nuclear regions. (orig.).

  1. Impact of chromatin structure on PR signaling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Hager, Gordon L

    2012-01-01

    The progesterone receptor (PR) interacts with chromatin in a highly dynamic manner that requires ongoing chromatin remodeling, interaction with chaparones and activity of the proteasome. Here we discuss dynamic interaction of steroid receptor with chromatin, with special attention not only to PR...

  2. Investigation of a new core-shell particle column for ion-pair reversed-phase liquid chromatography analysis of oligonucleotides.

    Science.gov (United States)

    Biba, Mirlinda; Welch, Christopher J; Foley, Joe P

    2014-08-01

    A new core-shell particle column showed excellent performance and durability for separation of short (∼21-mer) ribonucleic acid (RNA) oligonucleotides by ion-pair reversed-phase liquid chromatography (IP-RPLC). Previously investigated core-shell C18 columns showed excellent peak shapes and separations of closely eluting impurities by IP-RPLC. However, these columns showed only modest long-term stability at the neutral pH and elevated column temperatures of ≥60°C, typically used for IP-RPLC analysis of oligonucleotides. The newly introduced SunShell C18 column provided separations comparable to the previously evaluated core-shell columns, but with significantly improved long-term column stability when operated at neutral pH and elevated column temperature.

  3. Luminescence study on Eu{sup 3+} doped Y{sub 2}O{sub 3} nanoparticles: particle size, concentration and core-shell formation effects

    Energy Technology Data Exchange (ETDEWEB)

    Singh, L Robindro [Department of Physics, Manipur University, Canchipur-795003 (India); Ningthoujam, R S [Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Sudarsan, V [Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Srivastava, Iti [Metallurgical Engineering Department, Institute of Technology, Banaras Hindu University, Varansi (India); Singh, S Dorendrajit [Department of Physics, Manipur University, Canchipur-795003 (India); Dey, G K [Material Science Division, Bhabha Atomic Research Centre, Mumbai-40085 (India); Kulshreshtha, S K [Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2008-02-06

    Nanoparticles of Eu{sup 3+} doped Y{sub 2}O{sub 3} (core) and Eu{sup 3+} doped Y{sub 2}O{sub 3} covered with Y{sub 2}O{sub 3} shell (core-shell) are prepared by urea hydrolysis for 3 h in ethylene glycol medium at a relatively low temperature of 140 deg. C, followed by heating at 500 and 900 deg. C. Particle sizes determined from x-ray diffraction and transmission electron microscopic studies are 11 and 18 nm for 500 and 900 deg. C heated samples respectively. Based on the luminescence studies of 500 and 900 deg. C heated samples, it is confirmed that there is no particle size effect on the peak positions of Eu{sup 3+} emission, and optimum luminescence intensity is observed from the nanoparticles with a Eu{sup 3+} concentration of 4-5 at.%. A luminescence study establishes that the Eu{sup 3+} environment in amorphous Y (OH){sub 3} is different from that in crystalline Y{sub 2}O{sub 3}. For a fixed concentration of Eu{sup 3+} doping, there is a reduction in Eu{sup 3+} emission intensity for core-shell nanoparticles compared to that of core nanoparticles, and this has been attributed to the concentration dilution effect. Energy transfer from the host to Eu{sup 3+} increases with increase of crystallinity.

  4. 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.

  5. Epigenetic regulation and chromatin remodeling in learning and memory

    Science.gov (United States)

    Kim, Somi; Kaang, Bong-Kiun

    2017-01-01

    Understanding the underlying mechanisms of memory formation and maintenance has been a major goal in the field of neuroscience. Memory formation and maintenance are tightly controlled complex processes. Among the various processes occurring at different levels, gene expression regulation is especially crucial for proper memory processing, as some genes need to be activated while some genes must be suppressed. Epigenetic regulation of the genome involves processes such as DNA methylation and histone post-translational modifications. These processes edit genomic properties or the interactions between the genome and histone cores. They then induce structural changes in the chromatin and lead to transcriptional changes of different genes. Recent studies have focused on the concept of chromatin remodeling, which consists of 3D structural changes in chromatin in relation to gene regulation, and is an important process in learning and memory. In this review, we will introduce three major epigenetic processes involved in memory regulation: DNA methylation, histone methylation and histone acetylation. We will also discuss general mechanisms of long-term memory storage and relate the epigenetic control of learning and memory to chromatin remodeling. Finally, we will discuss how epigenetic mechanisms can contribute to the pathologies of neurological disorders and cause memory-related symptoms. PMID:28082740

  6. Analysis of chromatin structure at meiotic DSB sites in yeasts.

    Science.gov (United States)

    Hirota, Kouji; Fukuda, Tomoyuki; Yamada, Takatomi; Ohta, Kunihiro

    2009-01-01

    One of the major features of meiosis is a high frequency of homologous recombination that not only confers genetic diversity to a successive generation but also ensures proper segregation of chromosomes. Meiotic recombination is initiated by DNA double-strand breaks that require many proteins including the catalytic core, Spo11. In this regard, like transcription and repair, etc., recombination is hindered by a compacted chromatin structure because trans-acting factors cannot easily access the DNA. Such inhibitory effects must be alleviated prior to recombination initiation. Indeed, a number of groups showed that chromatin around recombination hotspots is less condensed, by using nucleases as a probe to assess local DNA accessibility. Here we describe a method to analyze chromatin structure of a recombination hotspot in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. This method, combining micrococcal nuclease (MNase) digestion ofchromatin DNA and subsequent Southern blotting, is expected to provide information as to chromatin context around a hotspot. Moreover, by virtue of MNase preferentially targeting linker DNA, positions of several nucleosomes surrounding a hotspot can also be determined. Our protocol is a very powerful way to analyze several-kb regions of interest and can be applied to other purposes.

  7. Nanoscale histone localization in live cells reveals reduced chromatin mobility in response to DNA damage.

    Science.gov (United States)

    Liu, Jing; Vidi, Pierre-Alexandre; Lelièvre, Sophie A; Irudayaraj, Joseph M K

    2015-02-01

    Nuclear functions including gene expression, DNA replication and genome maintenance intimately rely on dynamic changes in chromatin organization. The movements of chromatin fibers might play important roles in the regulation of these fundamental processes, yet the mechanisms controlling chromatin mobility are poorly understood owing to methodological limitations for the assessment of chromatin movements. Here, we present a facile and quantitative technique that relies on photoactivation of GFP-tagged histones and paired-particle tracking to measure chromatin mobility in live cells. We validate the method by comparing live cells to ATP-depleted cells and show that chromatin movements in mammalian cells are predominantly energy dependent. We also find that chromatin diffusion decreases in response to DNA breaks induced by a genotoxic drug or by the ISceI meganuclease. Timecourse analysis after cell exposure to ionizing radiation indicates that the decrease in chromatin mobility is transient and precedes subsequent increased mobility. Future applications of the method in the DNA repair field and beyond are discussed.

  8. 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...

  9. 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.

  10. 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.

  11. Organisation of subunits in chromatin.

    Science.gov (United States)

    Carpenter, B G; Baldwin, J P; Bradbury, E M; Ibel, K

    1976-07-01

    There is considerable current interest in the organisation of nucleosomes in chromatin. A strong X-ray and neutron semi-meridional diffraction peak at approximately 10 nm had previously been attributed to the interparticle specing of a linear array of nucleosomes. This diffraction peak could also result from a close packed helical array of nucleosomes. A direct test of these proposals is whether the 10 nm peak is truly meridional as would be expected for a linear array of nucleosomes or is slightly off the meridian as expected for a helical array. Neutron diffraction studies of H1-depleted chromatin support the latter alternative. The 10 nm peak has maxima which form a cross-pattern with semi-meridional angle of 8 to 9 degrees. This is consistent with a coil of nucleosomes of pitch 10 nm and outer diameter of approximately 30 nm. These dimensions correspond to about six nucleosomes per turn of the coli.

  12. The sustained-release behavior and in vitro and in vivo transfection of pEGFP-loaded core-shell-structured chitosan-based composite particles

    Directory of Open Access Journals (Sweden)

    Wang Y

    2014-10-01

    Full Text Available Yun Wang,1 Fu-xing Lin,2 Yu Zhao,1 Mo-zhen Wang,2 Xue-wu Ge,2 Zheng-xing Gong,1 Dan-dan Bao,1 Yu-fang Gu1 1Department of Plastic Surgery, First Affiliated Hospital of Anhui Medical University, 2CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China Abstract: Novel submicron core-shell-structured chitosan-based composite particles ­encapsulated with enhanced green fluorescent protein plasmids (pEGFP were prepared by complex coacervation method. The core was pEGFP-loaded thiolated N-alkylated chitosan (TACS and the shell was pH- and temperature-responsive hydroxybutyl chitosan (HBC. pEGFP-loaded TACS-HBC composite particles were spherical, and had a mean diameter of approximately 120 nm, as measured by transmission electron microscopy and particle size analyzer. pEGFP showed sustained release in vitro for >15 days. Furthermore, in vitro transfection in human embryonic kidney 293T and human cervix epithelial cells, and in vivo transfection in mice skeletal muscle of loaded pEGFP, were investigated. Results showed that the expression of loaded pEGFP, both in vitro and in vivo, was slow but could be sustained over a long period. pEGFP expression in mice skeletal muscle was sustained for >60 days. This work indicates that these submicron core-shell-structured chitosan-based composite particles could potentially be used as a gene vector for in vivo controlled gene transfection. Keywords: gene therapy, gene transfection, hydroxybutyl chitosan, thiolated N-alkylated chitosan, pEGFP, complex coacervation

  13. 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.

  14. 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

  15. Folic acid-functionalized magnetic ZnFe2O4 hollow microsphere core/mesoporous silica shell composite particles: synthesis and application in drug release.

    Science.gov (United States)

    Yang, Dandan; Wei, Kaiwei; Liu, Qi; Yang, Yong; Guo, Xue; Rong, Hongren; Cheng, Mei-Ling; Wang, Guoxiu

    2013-07-01

    A drug delivery system was designed by deliberately combining the useful functions into one entity, which was composed of magnetic ZnFe2O4 hollow microsphere as the core, and mesoporous silica with folic acid molecules as the outer shell. Amine groups coated magnetic ZnFe2O4 hollow microsphere core/mesoporous silica shell (MZHM-MSS-NH2) composite particles were first synthesized by a one-pot direct co-condensation method. Subsequently a novel kind of folic acid-functionalized magnetic ZnFe2O4 hollow microsphere core/mesoporous silica shell (MZHM-MSS-NHFA) composite particles were synthesized by conjugating folic acid as targeted molecule to MZHM-MSS-NH2. Ibuprofen, a well-known antiphlogistic drug, was used as a model drug to assess the loading and releasing behavior of the composite microspheres. The results show that the MZHM-MSS-NHFA system has the higher capacity of drug storage and good sustained drug-release property.

  16. 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.

  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. Chromatin domains and prediction of MAR sequences.

    Science.gov (United States)

    Boulikas, T

    1995-01-01

    Polynuceosomes are constrained into loops or domains and are insulated from the effects of chromatin structure and torsional strain from flanking domains by the cross-complexation of matrix-attached regions (MARs) and matrix proteins. MARs or SARs have an average size of 500 bp, are spaced about every 30 kb, and are control elements maintaining independent realms of gene activity. A fraction of MARs may cohabit with core origin replication (ORIs) and another fraction might cohabit with transcriptional enhancers. DNA replication, transcription, repair, splicing, and recombination seem to take place on the nuclear matrix. Classical AT-rich MARs have been proposed to anchor the core enhancers and core origins complexed with low abundancy transcription factors to the nuclear matrix via the cooperative binding to MARs of abundant classical matrix proteins (topoisomerase II, histone H1, lamins, SP120, ARBP, SATB1); this creates a unique nuclear microenvironment rich in regulatory proteins able to sustain transcription, replication, repair, and recombination. Theoretical searches and experimental data strongly support a model of activation of MARs and ORIs by transcription factors. A set of 21 characteristics are deduced or proposed for MAR/ORI sequences including their enrichment in inverted repeats, AT tracts, DNA unwinding elements, replication initiator protein sites, homooligonucleotide repeats (i.e., AAA, TTT, CCC), curved DNA, DNase I-hypersensitive sites, nucleosome-free stretches, polypurine stretches, and motifs with a potential for left-handed and triplex structures. We are establishing Banks of ORI and MAR sequences and have undertaken a large project of sequencing a large number of MARs in an effort to determine classes of DNA sequences in these regulatory elements and to understand their role at the origins of replication and transcriptional enhancers.

  19. 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.

  20. Proteomics of a fuzzy organelle: interphase chromatin

    Science.gov (United States)

    Kustatscher, Georg; Hégarat, Nadia; Wills, Karen L H; Furlan, Cristina; Bukowski-Wills, Jimi-Carlo; Hochegger, Helfrid; Rappsilber, Juri

    2014-01-01

    Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology. PMID:24534090

  1. Efficient cell migration requires global chromatin condensation.

    Science.gov (United States)

    Gerlitz, Gabi; Bustin, Michael

    2010-07-01

    Cell migration is a fundamental process that is necessary for the development and survival of multicellular organisms. Here, we show that cell migration is contingent on global condensation of the chromatin fiber. Induction of directed cell migration by the scratch-wound assay leads to decreased DNaseI sensitivity, alterations in the chromatin binding of architectural proteins and elevated levels of H4K20me1, H3K27me3 and methylated DNA. All these global changes are indicative of increased chromatin condensation in response to induction of directed cell migration. Conversely, chromatin decondensation inhibited the rate of cell migration, in a transcription-independent manner. We suggest that global chromatin condensation facilitates nuclear movement and reshaping, which are important for cell migration. Our results support a role for the chromatin fiber that is distinct from its known functions in genetic processes.

  2. Chromatin Modification and Remodeling in Heart Development

    Directory of Open Access Journals (Sweden)

    Paul Delgado-Olguín

    2006-01-01

    Full Text Available In organogenesis, cell types are specified from determined precursors as morphogenetic patterning takes place. These events are largely controlled by tissue-specific transcription factors. These transcription factors must function within the context of chromatin to activate or repress target genes. Recent evidence suggests that chromatin-remodeling and -modifying factors may have tissue-specific function. Here we review the potential roles for chromatin-remodeling and -modifying proteins in the development of the mammalian heart.

  3. Chromatin remodeling in cardiovascular development and physiology

    OpenAIRE

    Han, Pei; Hang, Calvin T.; Yang, Jin; Chang, Ching-Pin

    2011-01-01

    Chromatin regulation provides an important means of controlling cardiac gene expression under different physiological and pathological conditions. Processes that direct the development of normal embryonic hearts and pathology of stressed adult hearts may share general mechanisms that govern cardiac gene expression by chromatin-regulating factors. These common mechanisms may provide a framework for us to investigate the interactions among diverse chromatin remodelers/modifiers and various tran...

  4. Chromatin remodeling and human disease.

    Science.gov (United States)

    Huang, Cheng; Sloan, Emily A; Boerkoel, Cornelius F

    2003-06-01

    In the past few years, there has been a nascent convergence of scientific understanding of inherited human diseases with epigenetics. Identified epigenetic processes involved in human disease include covalent DNA modifications, covalent histone modifications, and histone relocation. Each of these processes influences chromatin structure and thereby regulates gene expression and DNA methylation, replication, recombination, and repair. The importance of these processes for nearly all aspects of normal growth and development is illustrated by the array of multi-system disorders and neoplasias caused by their dysregulation.

  5. Advances in chromatin remodeling and human disease.

    Science.gov (United States)

    Cho, Kyoung Sang; Elizondo, Leah I; Boerkoel, Cornelius F

    2004-06-01

    Epigenetic factors alter phenotype without changing genotype. A primary molecular mechanism underlying epigenetics is the alteration of chromatin structure by covalent DNA modifications, covalent histone modifications, and nucleosome reorganization. Remodeling of chromatin structure regulates DNA methylation, replication, recombination, and repair as well as gene expression. As these functions would predict, dysfunction of the proteins that remodel chromatin causes an array of multi-system disorders and neoplasias. Insights from these diseases suggest that during embryonic and fetal life, environmental distortions of chromatin remodeling encode a 'molecular memory' that predispose the individual to diseases in adulthood.

  6. Probing the nature of particle-core couplings in {sup 49}Ca with {gamma} spectroscopy and heavy-ion transfer reactions

    Energy Technology Data Exchange (ETDEWEB)

    Montanari, D. [Dipartimento di Fisica, University of Milano, Milano (Italy); INFN, Sezione di Milano, Milano (Italy); Leoni, S., E-mail: silvia.leoni@mi.infn.i [Dipartimento di Fisica, University of Milano, Milano (Italy); INFN, Sezione di Milano, Milano (Italy); Mengoni, D. [Dipartimento di Fisica, University of Padova, Padova (Italy); University of the West of Scotland, Paisley (United Kingdom); Benzoni, G.; Blasi, N. [INFN, Sezione di Milano, Milano (Italy); Bocchi, G. [Dipartimento di Fisica, University of Milano, Milano (Italy); Bortignon, P.F.; Bracco, A.; Camera, F.; Colo, G.; Corsi, A.; Crespi, F.C.L. [Dipartimento di Fisica, University of Milano, Milano (Italy); INFN, Sezione di Milano, Milano (Italy); Million, B. [INFN, Sezione di Milano, Milano (Italy); Nicolini, R. [Dipartimento di Fisica, University of Milano, Milano (Italy); INFN, Sezione di Milano, Milano (Italy); Wieland, O. [INFN, Sezione di Milano, Milano (Italy); Valiente-Dobon, J.J.; Corradi, L.; Angelis, G. de; Della Vedova, F.; Fioretto, E. [INFN, Laboratori Nazionali di Legnaro, Padova (Italy)

    2011-03-14

    Neutron rich nuclei around {sup 48}Ca have been measured with the CLARA-PRISMA setup, making use of {sup 48}Ca on {sup 64}Ni binary reactions, at 5.9 MeV/A. Angular distributions of {gamma} rays give evidence, in several transfer channels, for a large spin alignment ({approx}70%) perpendicular to the reaction plane, making it possible to firmly establish spin and parities of the excited states. In the case of {sup 49}Ca, states arising from different types of particle-core couplings are, for the first time, unambiguously identified on basis of angular distribution, polarization and lifetime measurements. Shell model and particle-vibration coupling calculations are used to pin down the nature of the states. Evidence is found for the presence, in the same excitation energy region, of two types of coupled states, i.e. single particle coupled to either {sup 48}Ca or {sup 50}Ca simple configurations, and particle-vibration coupled states based on the 3{sup -} phonon of {sup 48}Ca.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics durin...

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

    NARCIS (Netherlands)

    Driessen, Rosalie Paula Catharina

    2014-01-01

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

  9. Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis-Menten kinetics and assessment of numerical methods.

    Science.gov (United States)

    Pereira, Félix Monteiro; Oliveira, Samuel Conceição

    2016-11-01

    In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.

  10. Fluoride adsorption from aqueous solution by magnetic core-shell Fe3O4@alginate-La particles fabricated via electro-coextrusion

    Science.gov (United States)

    Zhang, Yahui; Lin, Xiaoyan; Zhou, Quisheng; Luo, Xuegang

    2016-12-01

    The magnetic core-shell Fe3O4@Alg-La particles were fabricated successfully by a simple method of electro-coextrusion, and employed as an adsorbent for separation of fluoride from aqueous solution. Main factors affecting the removal of fluoride, including pH, adsorbent dosage, initial concentration, temperature and contact time were investigated. The adsorption isotherm and adsorption kinetics were studied to understand the adsorption process in detail. The experimental data were fitted well by the non-linear Freundlich isotherm and linear pseudo-second-order model, the maximum fluoride adsorption capacity was 45.230 mg/g at pH 4, 298.15 K. Thermodynamic parameters indicated that the fluoride adsorption process was feasible and spontaneous. The presence of other anions like Cl-, SO42-, HCO3- and PO43- had almost no effect on the fluoride adsorption. The adsorbent can be easily separated from the solution by a magnet. The magnetic core-shell Fe3O4@Alg-La particles before and after fluoride adsorption were studied by SEM, FTIR, EDX and XPS, which indicated that the adsorption mechanism may be related to electrostatic attraction and Lewis acid-base interaction.

  11. Pirkle-type chiral stationary phase on core-shell and fully porous particles: Are superficially porous particles always the better choice toward ultrafast high-performance enantioseparations?

    Science.gov (United States)

    Ismail, Omar H; Pasti, Luisa; Ciogli, Alessia; Villani, Claudio; Kocergin, Jelena; Anderson, Scott; Gasparrini, Francesco; Cavazzini, Alberto; Catani, Martina

    2016-09-30

    Pirkle-type Whelk-O1 chiral stationary phase (CSP) was prepared on 2.6μm superficially porous particles (SPPs). The chromatographic behavior of columns packed with this new CSP was compared with that of columns packed respectively with 1.8 and 2.5μm Whelk-O1 fully porous particles (FPPs). In the comparison, both thermodynamic and kinetic aspects were considered. Contrary to initial expectations, chiral columns packed with 2.6μm SPPs were quasi-comparable to those packed with 2.5μm FPPs, apparently due to larger contributions to band broadening from both eddy dispersion and, especially for the second eluted enantiomer, adsorption-desorption kinetics. These findings raise the question if SPPs, in spite of the undeniable advantages of their morphology to speed up mass transfer, are always the best choice for high-efficient ultrafast chiral separations. The last part of the work focuses on the use of short columns (10mm long) and very high flow rates to realize the separation of the enantiomers of trans-stilbene oxide (TSO) in normal phase mode in less than 1s.

  12. Expression-dependent folding of interphase chromatin.

    Directory of Open Access Journals (Sweden)

    Hansjoerg Jerabek

    Full Text Available Multiple studies suggest that chromatin looping might play a crucial role in organizing eukaryotic genomes. To investigate the interplay between the conformation of interphase chromatin and its transcriptional activity, we include information from gene expression profiles into a polymer model for chromatin that incorporates genomic loops. By relating loop formation to transcriptional activity, we are able to generate chromosome conformations whose structural and topological properties are consistent with experimental data. The model particularly allows to reproduce the conformational variations that are known to occur between highly and lowly expressed chromatin regions. As previously observed in experiments, lowly expressed regions of the simulated polymers are much more compact. Due to the changes in loop formation, the distributions of chromatin loops are also expression-dependent and exhibit a steeper decay in highly active regions. As a results of entropic interaction between differently looped parts of the chromosome, we observe topological alterations leading to a preferential positioning of highly transcribed loci closer to the surface of the chromosome territory. Considering the diffusional behavior of the chromatin fibre, the simulations furthermore show that the higher the expression level of specific parts of the chromatin fibre is, the more dynamic they are. The results exhibit that variations of loop formation along the chromatin fibre, and the entropic changes that come along with it, do not only influence the structural parameters on the local scale, but also effect the global chromosome conformation and topology.

  13. Chromatin dynamics resolved with force spectroscopy

    NARCIS (Netherlands)

    Chien, Fan-Tso

    2011-01-01

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

  14. Chromatin Remodelers: From Function to Dysfunction

    Directory of Open Access Journals (Sweden)

    Gernot Längst

    2015-06-01

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

  15. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  16. 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

  17. Chromatin roadblocks to reprogramming 50 years on.

    Science.gov (United States)

    Skene, Peter J; Henikoff, Steven

    2012-10-29

    A half century after John Gurdon demonstrated nuclear reprogramming, for which he was awarded the 2012 Nobel Prize in Physiology or Medicine, his group provides insights into the molecular mechanisms whereby chromatin remodeling is required for nuclear reprogramming. Among the issues addressed in Gurdon's latest work are the chromatin impediments to artificially induced reprogramming, discovered by Shinya Yamanaka, who shared the award with Gurdon.

  18. Identified Particle Spectra for Au+Au Collisions at $\\sqrt{s}$ = 200 GeV from STAR, PHENIX and BRAHMS in Comparison to Core-Corona Model Predictions

    CERN Document Server

    Schreiber, C; Aichelin, J

    2010-01-01

    The core-corona model describes quite successfully the centrality dependence of multiplicity and $$ of identified particles observed in heavy ion reaction at beam energies between $\\sqrt{s}$ = 17 GeV and 200 GeV. Also the centrality dependence of the elliptic flow, $v_2$, for all charged and identified particles could be explained in this model. Here we extend this analysis and study the centrality dependence of single particle spectra of identified particles. We concentrate here on protons, antiprotons, kaons and pions which have all been measured by the PHENIX, STAR and BRAHMS collaborations. We find that an analysis of the spectra in the core-corona model suffers from differences in the data published by the different experimental groups, notably for the pp collisions. For each experience the data agree well with the prediction of the core-corona model but the value of the two necessary parameters depends onthe experiments.

  19. Interactions of transcription factors with chromatin.

    Science.gov (United States)

    van Bakel, Harm

    2011-01-01

    Sequence-specific transcription factors (TFs) play a central role in regulating transcription initiation by directing the recruitment and activity of the general transcription machinery and accessory factors. It is now well established that many of the effects exerted by TFs in eukaryotes are mediated through interactions with a host of coregulators that modify the chromatin state, resulting in a more open (in case of activation) or closed conformation (in case of repression). The relationship between TFs and chromatin is a two-way street, however, as chromatin can in turn influence the recognition and binding of target sequences by TFs. The aim of this chapter is to highlight how this dynamic interplay between TF-directed remodelling of chromatin and chromatin-adjusted targeting of TF binding determines where and how transcription is initiated, and to what degree it is productive.

  20. 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.

  1. Chromatin remodeling in cardiovascular development and physiology.

    Science.gov (United States)

    Han, Pei; Hang, Calvin T; Yang, Jin; Chang, Ching-Pin

    2011-02-04

    Chromatin regulation provides an important means for controlling cardiac gene expression under different physiological and pathological conditions. Processes that direct the development of normal embryonic hearts and pathology of stressed adult hearts may share general mechanisms that govern cardiac gene expression by chromatin-regulating factors. These common mechanisms may provide a framework for us to investigate the interactions among diverse chromatin remodelers/modifiers and various transcription factors in the fine regulation of gene expression, essential for all aspects of cardiovascular biology. Aberrant cardiac gene expression, triggered by a variety of pathological insults, can cause heart diseases in both animals and humans. The severity of cardiomyopathy and heart failure correlates strongly with abnormal cardiac gene expression. Therefore, controlling cardiac gene expression presents a promising approach to the treatment of human cardiomyopathy. This review focuses on the roles of ATP-dependent chromatin-remodeling factors and chromatin-modifying enzymes in the control of gene expression during cardiovascular development and disease.

  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. New insights into protamine-like component organization in Mytilus galloprovincialis' sperm chromatin.

    Science.gov (United States)

    Vassalli, Quirino Attilio; Caccavale, Filomena; Avagnano, Stefano; Murolo, Alessandra; Guerriero, Giulia; Fucci, Laura; Ausió, Juan; Piscopo, Marina

    2015-03-01

    We have analyzed Mytilus galloprovincialis' sperm chromatin, which consists of three protamine-like proteins, PL-II, PL-III, and PL-IV, in addition to a residual amount of the four core histones. We have probed the structure of this sperm chromatin through digestion with micrococcal nuclease (MNase) in combination with salt fractionation. Furthermore, we used the electrophoretic mobility shift assay to define DNA-binding mode of PL-II and PL-III and turbidimetric assays to determine their self-association ability in the presence of sodium phosphate. Although in literature it is reported that M. galloprovincialis' sperm chromatin lacks nucleosomal organization, our results obtained by MNase digestion suggest the existence of a likely unusual organization, in which there would be a more accessible location of PL-II/PL-IV when compared with PL-III and core histones. So, we hypothesize that in M. galloprovincialis' sperm chromatin organization DNA is wrapped around a PL-III protein core and core histones and PL-II and PL-IV are bound to the flanking DNA regions (similarly to somatic histone H1). Furthermore, we propose that PL's K/R ratio affects their DNA-binding mode and self-association ability as reported previously for somatic and sperm H1 histones.

  4. The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex

    NARCIS (Netherlands)

    G.E. Chalkley (Gillian); Y.M. Moshkin (Yuri); K. Langenberg (Karin); K. Bezstarosti (Karel); A. Blastyak (Andras); H. Gyurkovics (Henrik); J.A.A. Demmers (Jeroen); C.P. Verrijzer (Peter)

    2008-01-01

    textabstractSWI/SNF ATP-dependent chromatin remodeling complexes (remodelers) perform critical functions in eukaryotic gene expression control. BAP and PBAP are the fly representatives of the two evolutionarily conserved major subclasses of SWI/SNF remodelers. Both complexes share seven core subunit

  5. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Eun Byul; Lee, Jong-Hyun, E-mail: pljh@snut.ac.kr

    2015-09-15

    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.

  7. Core-coupled states and split proton-neutron quasi-particle multiplets in 122-126Ag

    CERN Document Server

    Lalkovski, S; Jungclaus, A; Gorska, M; Pfutzner, M; Caceres, L; Naqvi, F; Pietri, S; Podolyak, Zs; Simpson, G S; Andgren, K; Bednarczyk, P; Beck, T; Benlliure, J; Benzoni, G; Casarejos, E; Cederwall, B; Crespi, F C L; Cuenca-Garcia, J J; Cullen, I J; Bacelar, A M Denis; Detistov, P; Doornenbal, P; Farrelly, G F; Garnsworthy, A B; Geissel, H; Gelletly, W; Gerl, J; Grebosz, J; Hadinia, B; Hellstrom, M; Hinke, C; Hoischen, R; Ilie, G; Jaworski, G; Jolie, J; Khaplanov, A; Kisyov, S; Kmiecik, M; Kojouharov, I; Kumar, R; Kurz, N; Maj, A; Mandal, S; Modamio, V; Montes, F; Myalski, S; Palacz, M; Prokopowicz, W; Reiter, P; Regan, P H; Rudolph, D; Schaffner, H; Sohler, D; Steer, S J; Tashenov, S; Walker, J; Walker, P M; Weick, H; Werner-Malento, E; Wieland, O; Wollersheim, H J; Zhekova, M

    2012-01-01

    Neutron-rich silver isotopes were populated in the fragmentation of a 136Xe beam and the relativistic fission of 238U. The fragments were mass analyzed with the GSI Fragment separator and subsequently implanted into a passive stopper. Isomeric transitions were detected by 105 HPGe detectors. Eight isomeric states were observed in 122-126Ag nuclei. The level schemes of 122,123,125Ag were revised and extended with isomeric transitions being observed for the first time. The excited states in the odd-mass silver isotopes are interpreted as core-coupled states. The isomeric states in the even-mass silver isotopes are discussed in the framework of the proton-neutron split multiplets. The results of shell-model calculations, performed for the most neutron-rich silver nuclei are compared to the experimental data.

  8. 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.

  9. Embryonic stem cell differentiation: a chromatin perspective.

    Science.gov (United States)

    Rasmussen, Theodore P

    2003-11-13

    Embryonic stem (ES) cells hold immense promise for the treatment of human degenerative disease. Because ES cells are pluripotent, they can be directed to differentiate into a number of alternative cell-types with potential therapeutic value. Such attempts at "rationally-directed ES cell differentiation" constitute attempts to recapitulate aspects of normal development in vitro. All differentiated cells retain identical DNA content, yet gene expression varies widely from cell-type to cell-type. Therefore, a potent epigenetic system has evolved to coordinate and maintain tissue-specific patterns of gene expression. Recent advances show that mechanisms that govern epigenetic regulation of gene expression are rooted in the details of chromatin dynamics. As embryonic cells differentiate, certain genes are activated while others are silenced. These activation and silencing events are exquisitely coordinated with the allocation of cell lineages. Remodeling of the chromatin of developmentally-regulated genes occurs in conjunction with lineage commitment. Oocytes, early embryos, and ES cells contain potent chromatin-remodeling activities, an observation that suggests that chromatin dynamics may be especially important for early lineage decisions. Chromatin dynamics are also involved in the differentiation of adult stem cells, where the assembly of specialized chromatin upon tissue-specific genes has been studied in fine detail. The next few years will likely yield striking advances in the understanding of stem cell differentiation and developmental biology from the perspective of chromatin dynamics.

  10. Embryonic stem cell differentiation: A chromatin perspective

    Directory of Open Access Journals (Sweden)

    Rasmussen Theodore P

    2003-11-01

    Full Text Available Abstract Embryonic stem (ES cells hold immense promise for the treatment of human degenerative disease. Because ES cells are pluripotent, they can be directed to differentiate into a number of alternative cell-types with potential therapeutic value. Such attempts at "rationally-directed ES cell differentiation" constitute attempts to recapitulate aspects of normal development in vitro. All differentiated cells retain identical DNA content, yet gene expression varies widely from cell-type to cell-type. Therefore, a potent epigenetic system has evolved to coordinate and maintain tissue-specific patterns of gene expression. Recent advances show that mechanisms that govern epigenetic regulation of gene expression are rooted in the details of chromatin dynamics. As embryonic cells differentiate, certain genes are activated while others are silenced. These activation and silencing events are exquisitely coordinated with the allocation of cell lineages. Remodeling of the chromatin of developmentally-regulated genes occurs in conjunction with lineage commitment. Oocytes, early embryos, and ES cells contain potent chromatin-remodeling activities, an observation that suggests that chromatin dynamics may be especially important for early lineage decisions. Chromatin dynamics are also involved in the differentiation of adult stem cells, where the assembly of specialized chromatin upon tissue-specific genes has been studied in fine detail. The next few years will likely yield striking advances in the understanding of stem cell differentiation and developmental biology from the perspective of chromatin dynamics.

  11. PARTICLE IMAGE VELOCIMETRY MEASUREMENTS IN A REPRESENTATIVE GAS-COOLED PRISMATIC REACTOR CORE MODEL: FLOW IN THE COOLANT CHANNELS AND INTERSTITIAL BYPASS GAPS

    Energy Technology Data Exchange (ETDEWEB)

    Thomas E. Conder; Richard Skifton; Ralph Budwig

    2012-11-01

    Core bypass flow is one of the key issues with the prismatic Gas Turbine-Modular Helium Reactor, and it refers to the coolant that navigates through the interstitial, non-cooling passages between the graphite fuel blocks instead of traveling through the designated coolant channels. To determine the bypass flow, a double scale representative model was manufactured and installed in the Matched Index-of-Refraction flow facility; after which, stereo Particle Image Velocimetry (PIV) was employed to measure the flow field within. PIV images were analyzed to produce vector maps, and flow rates were calculated by numerically integrating over the velocity field. It was found that the bypass flow varied between 6.9-15.8% for channel Reynolds numbers of 1,746 and 4,618. The results were compared to computational fluid dynamic (CFD) pre-test simulations. When compared to these pretest calculations, the CFD analysis appeared to under predict the flow through the gap.

  12. Fabrication of anode-supported zirconia thin film electrolyte based core-shell particle structure for intermediate temperature solid oxide fuel cells

    Institute of Scientific and Technical Information of China (English)

    Peng Li; John T.S.Irvinen

    2013-01-01

    With a view to produce intermediate temperature SOFCs, yttria and scandia doped zirconia with a core-shell structure was prepared, then an anode supported fuel cell was fabricated by a spray method. The influences of the scandia content in the electrolyte and atmosphere conditions used in the testing experiments on phase composition, microstructure and fuel cell performance were investigated. The electrolyte was composed of cubic and tetragonal phases and SEM pictures revealed very fine grain sizes and a smooth surface of the electrolyte film, though some defects were observed in samples with high Scandia content. Coating scandia on partially stabilized zirconium particles improves both ionic conductivity of the electrolyte and power density of the fuel cell distinctly below 750 1C. Anodes were pre-sintered at 1200 1C before co-sintering with the electrolyte film to ensure that the shrinkage percentage was close to that of the electrolyte during co-sintering, avoiding warping of cell.

  13. Activation of DNA damage response signaling by condensed chromatin.

    Science.gov (United States)

    Burgess, Rebecca C; Burman, Bharat; Kruhlak, Michael J; Misteli, Tom

    2014-12-11

    The DNA damage response (DDR) occurs in the context of chromatin, and architectural features of chromatin have been implicated in DNA damage signaling and repair. Whereas a role of chromatin decondensation in the DDR is well established, we show here that chromatin condensation is integral to DDR signaling. We find that, in response to DNA damage chromatin regions transiently expand before undergoing extensive compaction. Using a protein-chromatin-tethering system to create defined chromatin domains, we show that interference with chromatin condensation results in failure to fully activate DDR. Conversely, forced induction of local chromatin condensation promotes ataxia telangiectasia mutated (ATM)- and ATR-dependent activation of upstream DDR signaling in a break-independent manner. Whereas persistent chromatin compaction enhanced upstream DDR signaling from irradiation-induced breaks, it reduced recovery and survival after damage. Our results demonstrate that chromatin condensation is sufficient for activation of DDR signaling and is an integral part of physiological DDR signaling.

  14. Synthesis of Nanoscale Shell-core Titania Coated Silica Particles in the Presence of Polyether Polyamine and the Phase Transition

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The nanoscale titania coated silica was prepared via a two-step precipitating approach, where the nanoscale silica nuclei were first prepared by passing an aqueous solution of sodium silicate through an ion-exchange resin bed, then coated with the precipitation from hydrolyzed butyl titanate in an ethanol-hexane mixture at a low pH value in the presence of poly(ethylene oxide) polyamine salt(PPA) at a high temperature of 90 ℃. In the second-step precipitating process, the spontaneously precipitated titania shell on the silica nuclei was stabilized in the suspension solution with the help of the adsorption of PPA on the particles. A possible precipitating mechanism was suggested. Furthermore, the amorphous titania shell could undergo crystallization from the amorphous to the anatase structure at a high temperature of 650 ℃, and a further phase transition from the anatase to the rutile structure in the different sintering processes at a rising temperature of 750 ℃.

  15. 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.

  16. Chromatin targeting drugs in cancer and immunity.

    Science.gov (United States)

    Prinjha, Rab; Tarakhovsky, Alexander

    2013-08-15

    Recent advances in the enzymology of transcription and chromatin regulation have led to the discovery of proteins that play a prominent role in cell differentiation and the maintenance of specialized cell functions. Knowledge about post-synthetic DNA and histone modifications as well as information about the rules that guide the formation of multimolecular chromatin-bound complexes have helped to delineate gene-regulating pathways and describe how these pathways are altered in various pathological conditions. The present review focuses on the emerging area of therapeutic interference with chromatin function for the purpose of cancer treatment and immunomodulation.

  17. Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation.

    Science.gov (United States)

    Wakamori, Masatoshi; Fujii, Yoshifumi; Suka, Noriyuki; Shirouzu, Mikako; Sakamoto, Kensaku; Umehara, Takashi; Yokoyama, Shigeyuki

    2015-11-26

    Post-translational modifications (PTMs) of histones, such as lysine acetylation of the N-terminal tails, play crucial roles in controlling gene expression. Due to the difficulty in reconstituting site-specifically acetylated nucleosomes with crystallization quality, structural analyses of histone acetylation are currently performed using synthesized tail peptides. Through engineering of the genetic code, translation termination, and cell-free protein synthesis, we reconstituted human H4-mono- to tetra-acetylated nucleosome core particles (NCPs), and solved the crystal structures of the H4-K5/K8/K12/K16-tetra-acetylated NCP and unmodified NCP at 2.4 Å and 2.2 Å resolutions, respectively. The structure of the H4-tetra-acetylated NCP resembled that of the unmodified NCP, and the DNA wrapped the histone octamer as precisely as in the unmodified NCP. However, the B-factors were significantly increased for the peripheral DNAs near the N-terminal tail of the intra- or inter-nucleosomal H4. In contrast, the B-factors were negligibly affected by the H4 tetra-acetylation in histone core residues, including those composing the acidic patch, and at H4-R23, which interacts with the acidic patch of the neighboring NCP. The present study revealed that the H4 tetra-acetylation impairs NCP self-association by changing the interactions of the H4 tail with DNA, and is the first demonstration of crystallization quality NCPs reconstituted with genuine PTMs.

  18. 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 ...

  19. 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.

  20. Mapping the particle acceleration in the cool core of the galaxy cluster RX J1720.1+2638

    CERN Document Server

    Giacintucci, Simona; Brunetti, Gianfranco; ZuHone, John A; Venturi, Tiziana; Mazzotta, Pasquale; Bourdin, Harve'

    2014-01-01

    We present new deep, high-resolution radio images of the diffuse minihalo in the cool core of the galaxy cluster RX ,J1720.1+2638. The images have been obtained with the Giant Metrewave Radio Telescope at 317, 617 and 1280 MHz and with the Very Large Array at 1.5, 4.9 and 8.4 GHz, with angular resolutions ranging from 1" to 10". This represents the best radio spectral and imaging dataset for any minihalo. Most of the radio flux of the minihalo arises from a bright central component with a maximum radius of ~80 kpc. A fainter tail of emission extends out from the central component to form a spiral-shaped structure with a length of ~230 kpc, seen at frequencies 1.5 GHz and below. We observe steepening of the total radio spectrum of the minihalo at high frequencies. Furthermore, a spectral index image shows that the spectrum of the diffuse emission steepens with the increasing distance along the tail. A striking spatial correlation is observed between the minihalo emission and two cold fronts visible in the Chan...

  1. 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.

  2. Probing the “Dark” Fraction of Core-Shell Quantum Dots by Ensemble and Single Particle pH-Dependent Spectroscopy

    Science.gov (United States)

    Durisic, Nela; Godin, Antoine G.; Walters, Derrel; Grütter, Peter; Wiseman, Paul W.; Heyes, Colin D.

    2011-01-01

    The optical properties of core-shell CdSe-ZnS quantum dots (QDs) are characterized by complex photophysics leading to difficulties in interpreting quantitative measurements based on QD emission. By comparing the pH dependence of fluorescence of single QDs to that of an ensemble, we have been able to propose a molecular scale model of how QD surface chemical and physical processes are affected by protons and oxygen. We show that the connection between the ensemble fluorescence intensity and the single QD fluorescence properties such as dark fraction, blinking, particle brightness and a multi-exponential fluorescence lifetime decay is not trivial. The ensemble fluorescence intensity is more weakly dependent on pH than the single particle fluorescence which, together with fluorescence lifetime analysis, provided evidence that the dark fraction of QDs emits photons with low quantum efficiency and long lifetime. We uncovered two surface-dependent mechanisms that affected the fluorescence emission: an immediate physical effect of charges surrounding the QD and an irreversible chemical effect from reaction of the H+ and O2 with the QD shell surface. These results will have important implications for those using QD-based fluorescence lifetime imaging as well as for proper implementation of these probes for quantitative cellular imaging applications. PMID:22023370

  3. 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.

  4. 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...

  5. Preparation of Micrometer Core-shell Composite Particles via Dispersion Polymerization%分散聚合法制备微米级核壳复合粒子

    Institute of Scientific and Technical Information of China (English)

    张星; 郑玉婴; 陈德贤

    2012-01-01

    在硬脂酸改性纳米CaCO3存在下进行了苯乙烯(St)和丙烯酸正丁酯(nBA)的分散共聚合,制备了平均粒径为1.76 μm、单分散性较好的CaCO3/P(St-co-nBA)核壳复合粒子.包覆层聚合物P(St-co-nBA)与CaCO3粒子之间存在物理吸附和化学键合作用,使其热分解温度比共聚物P(St-co-nBA)高.经热二甲苯抽提后复合物中仍有共聚物存在,这部分共聚物与CaCO3通过化学键牢固的结合.热失重结果表明,CaCO3的稳定包覆率为6.6%.%Narrow dispersed CaCO3/poly ( styrene-co-n-butylacrylate ) ( CaCO3/P ( St-co-nBA ) ) composite particles with average diameter of 1. 76 μm were obtained via a dispersion copolymerization of St and nBA in the presence of stearic acid modified nano-CaCO3 particles. The products were characterized by transmission electron microscopy ( TEM ) , optical microscope ( OM ) , Courier transfer infrared spectroscopy ( FT-IR ) , thermogravimetric analysis ( TGA ) , and X-ray diffraction ( XRD ). The TEM images indicated the composite particles had nano-CaCO3 core and P ( St-co-nBA ) shell structure. The TGA analysis results of composite particles before and after being extracted with dimethylbenzene showed the thermal decomposition temperature of the cladding polymer was higher than that of pure copolymer P( St-co-nBA) , and some copolymer couldn't be extracted. The FT-IR spectra also confirmed the existence of copolymer on the composite particles after extracting. It suggested that the copolymer had chemical bonding with nano-CaCO3. The mass proportion of P( St-co-nBA) which couldn't be extracted with accounted for 6. 6% based on the mass of nano-CaCO3.

  6. Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1.

    Science.gov (United States)

    Nguyen, Vu Q; Ranjan, Anand; Stengel, Florian; Wei, Debbie; Aebersold, Ruedi; Wu, Carl; Leschziner, Andres E

    2013-09-12

    The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.

  7. Interaction of a C-terminal Truncated Hepatitis C Virus Core Protein with Plasmid DNA Vaccine Leads to in vitro Assembly of Heterogeneous Virus-like Particles

    Directory of Open Access Journals (Sweden)

    Nelson Acosta-Rivero

    2005-01-01

    Full Text Available Recently, it has been shown that HCV core proteins (HCcAg with C-terminal deletions assemble in vitro into virus-like particles (VLPs in the presence of structured RNA molecules. Results presented in this work showed that a truncated HCcAg variant covering the first 120 aa (HCcAg.120 with a 32 aa N-terminal fusion peptide (6xHistag-XpressTMepitope interacts with plasmid DNA vaccine. Interestingly, the buoyant density of VLPs containing HCcAg.120 in CsCl gradients changed from 1.15-1,17 g mLˉ1 to 1.30-1.34 g mLˉ1 after addition of plasmid DNA to assembly reactions. In addition, a delay in electrophoretic mobility of HCcAg.120-plasmid samples on agarose gels was observed indicating a direct interaction between VLPs and nucleic acids. Remarkably, addition of either plasmid DNA or tRNA to assembly reactions leaded to heterogeneous and larger VLPs formation than those observed in HCcAg.120 assembly reactions. VLPs containing HCcAg.120 induced a specific IgG antibodies in mice that reacted with hepatocytes from HCV-infected patients. VLPs obtained in this work would be important to elucidate the mechanisms behind the ability of HCcAg to assemble into a nucleocapsid structure. Besides, the capacity of particles containing HCcAg.120 to interact with nucleic acids could be used in the development of DNA vaccines and viral vectors based on these particles.

  8. Chromatin roadblocks to reprogramming 50 years on

    Directory of Open Access Journals (Sweden)

    Skene Peter J

    2012-10-01

    Full Text Available Abstract A half century after John Gurdon demonstrated nuclear reprogramming, for which he was awarded the 2012 Nobel Prize in Physiology or Medicine, his group provides insights into the molecular mechanisms whereby chromatin remodeling is required for nuclear reprogramming. Among the issues addressed in Gurdon's latest work are the chromatin impediments to artificially induced reprogramming, discovered by Shinya Yamanaka, who shared the award with Gurdon. See research article: http://www.epigeneticsandchromatin.com/content/5/1/17

  9. Chromatin Dynamics During DNA Replication and Uncharacterized Replication Factors determined by Nascent Chromatin Capture (NCC) Proteomics

    Science.gov (United States)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; Kustatscher, Georg; Nakamura, Kyosuke; de Lima Alves, Flavia; Menard, Patrice; Mejlvang, Jakob; Rappsilber, Juri; Groth, Anja

    2014-01-01

    SUMMARY To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use Nascent Chromatin Capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity-purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3995 proteins. The replication machinery and 485 chromatin factors like CAF-1, DNMT1, 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, while H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance. PMID:24561620

  10. 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.

  11. Preparation of organic/inorganic hybrid and hollow particles by catalytic deposition of silica onto core/shell heterocoagulates modified with poly[2-(N,N-dimethylamino)ethyl methacrylate].

    Science.gov (United States)

    Taniguchi, Tatsuo; Obi, Shun; Kamata, Yoshitada; Kashiwakura, Takuya; Kasuya, Masakatsu; Ogawa, Tatsuya; Kohri, Michinari; Nakahira, Takayuki

    2012-02-15

    The organic/inorganic hybrid particles PSt/P(St-CPEM)(θ)-g-PDMAEMA/SiO(2) were prepared by catalytic hydrolysis and subsequent polycondensation of tetraethoxysilane in the poly[2-(N,N-dimethylamino)ethyl methacrylate] (PDMAEMA) layers grafted on the PSt/P(St-CPEM)(θ) core/shell heterocoagulates. The micron-sized PSt core and the submicron-sized P(St-CPEM) shell particles bearing ATRP initiating groups were synthesized by dispersion polymerization of styrene (St) and emulsifier-free emulsion polymerization of St with 2-chloropropionyloxyethyl methacrylate (CPEM), respectively. The raspberry-shaped PSt/P(St-CPEM)(θ) heterocoagulates with a controlled surface coverage (θ=0.51, 0.81) were prepared by hydrophobic coagulation between the core and the shell particles in an aqueous NaCl solution near the T(g) of P(St-CPEM). Surface modification of heterocoagulates was carried out by ATRP of DMAEMA from the shell particles adsorbed on the core particles. Silica deposition was performed by simply adding tetraethoxysilane to a water/methanol dispersion of PSt/P(St-CPEM)(θ)-g-PDMAEMA. The SEM and TGA revealed that the resulting PSt/P(St-CPEM)(θ)-g-PDMAEMA/SiO(2) composites maintain a raspberry-like morphology after deposition of silica onto the PDMAEMA layer grafted on heterocoagulates. The micron-sized, raspberry-shaped or the submicron-sized, hole-structured silica hollow particles were obtained selectively by thermal decomposition of the PSt/P(St-CPEM)(θ)-g-PDMAEMA/SiO(2). The oriented particle array was fabricated by dropping anisotropically perforated silica particles onto a glass substrate settled at the bottom of a bottle filled with chloroform.

  12. 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.

  13. Dynamic structures of intact chicken erythrocyte chromatins as studied by 1H-31P cross-polarization NMR.

    Science.gov (United States)

    Akutsu, H; Nishimoto, S; Kyogoku, Y

    1994-08-01

    The dynamic properties of DNA in intact chicken erythrocyte cells, nuclei, nondigested chromatins, digested soluble chromatins, H1, H5-depleted soluble chromatins and nucleosome cores were investigated by means of single-pulse and 1H-31P cross-polarization NMR. The temperature dependence of the phosphorus chemical shift anisotropy was identical for the former three in the presence of 3 mM MgCl2, suggesting that the local higher order structure is identical for these chromatins. The intrinsic phosphorus chemical shift anisotropy of the nucleosome cores was -159 ppm. The chemical shift anisotropy of DNA in the chromatins can be further averaged by the motion of the linker DNA. The spin-lattice relaxation time in the rotating frame of the proton spins (T1p) of the nondigested chromatins was measured at various locking fields. The result was analyzed on the assumption of the isotropic motion to get a rough value of the correlation time of the motion efficient for the relaxation, which was eventually ascribed to the segmental motion of the linker DNA with restricted amplitude. The 30 nm filament structure induced by NaCl was shown to be dynamically different from that induced by MgCl2. Side-by-side compaction of 30-nm filaments was suggested to be induced in the MgCl2 concentration range higher than 0.3 mM. Biological significance of the dynamic structure was discussed in connection with the results obtained.

  14. Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein.

    Science.gov (United States)

    Kurat, Christoph F; Lambert, Jean-Philippe; van Dyk, Dewald; Tsui, Kyle; van Bakel, Harm; Kaluarachchi, Supipi; Friesen, Helena; Kainth, Pinay; Nislow, Corey; Figeys, Daniel; Fillingham, Jeffrey; Andrews, Brenda J

    2011-12-01

    The cell cycle-regulated expression of core histone genes is required for DNA replication and proper cell cycle progression in eukaryotic cells. Although some factors involved in histone gene transcription are known, the molecular mechanisms that ensure proper induction of histone gene expression during S phase remain enigmatic. Here we demonstrate that S-phase transcription of the model histone gene HTA1 in yeast is regulated by a novel attach-release mechanism involving phosphorylation of the conserved chromatin boundary protein Yta7 by both cyclin-dependent kinase 1 (Cdk1) and casein kinase 2 (CK2). Outside S phase, integrity of the AAA-ATPase domain is required for Yta7 boundary function, as defined by correct positioning of the histone chaperone Rtt106 and the chromatin remodeling complex RSC. Conversely, in S phase, Yta7 is hyperphosphorylated, causing its release from HTA1 chromatin and productive transcription. Most importantly, abrogation of Yta7 phosphorylation results in constitutive attachment of Yta7 to HTA1 chromatin, preventing efficient transcription post-recruitment of RNA polymerase II (RNAPII). Our study identified the chromatin boundary protein Yta7 as a key regulator that links S-phase kinases with RNAPII function at cell cycle-regulated histone gene promoters.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    the chromatin-associated scaffold attachment factor SAFB1 as a component of the DNA damage response and show that SAFB1 cooperates with histone acetylation to allow for efficient γH2AX spreading and genotoxic stress signaling. SAFB1 undergoes a highly dynamic exchange at damaged chromatin in a poly...

  16. Magnetic C-C@Fe3O4 double-shelled hollow microspheres via aerosol-based Fe3O4@C-SiO2 core-shell particles.

    Science.gov (United States)

    Zhu, Yangzhi; Li, Xiangcun; He, Gaohong; Qi, Xinhong

    2015-02-18

    Magnetic C-C@Fe3O4 hollow microspheres were prepared by using aerosol-based Fe3O4@C-SiO2 core-shell particles as templates. The magnetic double-shelled microspheres efficiently worked as carriers to load Pt nanoparticles, thus making the catalyst recyclable and reusable.

  17. Chromatin associations in Arabidopsis interphase nuclei

    Directory of Open Access Journals (Sweden)

    Veit eSchubert

    2014-11-01

    Full Text Available The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analysed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fibre movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns.Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its ten centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei.

  18. 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.

  19. Chromatin ring formation at plant centromeres

    Directory of Open Access Journals (Sweden)

    Veit eSchubert

    2016-02-01

    Full Text Available We observed the formation of chromatin ring structures at centromeres of somatic rye and Arabidopsis chromosomes. To test whether this behavior is present also in other plant species and tissues we analyzed Arabidopsis, rye, wheat, Aegilops and barley centromeres during cell divisions and in interphase nuclei by immunostaining and FISH. Furthermore, structured illumination microscopy (super-resolution was applied to investigate the ultrastructure of centromere chromatin beyond the classical refraction limit of light. It became obvious, that a ring formation at centromeres may appear during mitosis, meiosis and in interphase nuclei in all species analyzed. However, varying centromere structures, as ring formations or globular organized chromatin fibers, were identified in different tissues of one and the same species. In addition, we found that a chromatin ring formation may also be caused by subtelomeric repeats in barley. Thus, we conclude that the formation of chromatin rings may appear in different plant species and tissues, but that it is not specific for centromere function. Based on our findings we established a model describing the ultrastructure of plant centromeres and discuss it in comparison to previous models proposed for animals and plants.

  20. Reshaping chromatin after DNA damage: the choreography of histone proteins.

    Science.gov (United States)

    Polo, Sophie E

    2015-02-13

    DNA damage signaling and repair machineries operate in a nuclear environment where DNA is wrapped around histone proteins and packaged into chromatin. Understanding how chromatin structure is restored together with the DNA sequence during DNA damage repair has been a topic of intense research. Indeed, chromatin integrity is central to cell functions and identity. However, chromatin shows remarkable plasticity in response to DNA damage. This review presents our current knowledge of chromatin dynamics in the mammalian cell nucleus in response to DNA double strand breaks and UV lesions. I provide an overview of the key players involved in regulating histone dynamics in damaged chromatin regions, focusing on histone chaperones and their concerted action with histone modifiers, chromatin remodelers and repair factors. I also discuss how these dynamics contribute to reshaping chromatin and, by altering the chromatin landscape, may affect the maintenance of epigenetic information.

  1. Repair of alpha-particle-induced DNA double strand breaks and their localization in chromatin in human lymphocytes%α粒子照射诱发DNA双链断裂修复及其在染色质中的分布

    Institute of Scientific and Technical Information of China (English)

    张亚平; 张旭霞; 王晶; 暴一众; 李佳颖; 殷丽娜; 陈红红

    2014-01-01

    Objective To investigate the characteristics of repair of DNA double strand breaks (DSB) induced by high-LET α-particle irradiation and their relationship with chromatin structure in the G0 lymphocytes of human peripheral blood,in order to provide the experimental basis for the judgement and dose evaluation of internal α-particle radiation.Methods Peripheral whole blood were collected from four healthy adults and lymphocytes were separated.A monocellular layer of human lymphocytes attached in Mylar film were irradiated with 0 and 0.5 Gy of α-particles and the lymphocytes suspensions were irradiated with 0 and 0.5 Gy of γ-rays.The formations of γH2AX foci as a surrogate marker of DSB and Rad51 foci as a marker of homologous recombination (HR) repair and their spatial localization in chromatin structure were measured by immunofluorescence staining technique at 10 min-48 h post-irradiation.Results Linear-γH2AX foci tracks were observe at 10 min-2 h post-irradiation in lymphocytes exposed to α-particle irradiation(t =11.12,14.40,16.56,P < 0.05),and almost completely disppeared at 6 h postirradiation.The frequencies of γH2AX foci peaked at 30 min after α-particle irradiation (t =51.72,P <0.05) and then decreased rapidly during 6 h post-irradiation (t =29.83,P < 0.05).The average number of foci remained only about 16% at 24-48 h post-irradiation.Moreover,27% of γH2AX foci located at DAPI-bright heterochromatin region at 10 min after α-particle radiation,suggesting that the efficacy of DSB repair may be decreased.In contrast,at 10 min-48 h after γ-ray irradiation,no linear γH2AX foci track was observed and the γH2AX foci diffused randomly in nucleus and predominantly located in DAPI-weak euchromatin region.The numbers of formative and residual γH2AX foci after γ-ray irradiation were significantly less than those after α-particle radiation.During 30 min-2 h after α-particle and γ-ray irradiation,the frequencies of Rad51 foci slightly but not

  2. 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 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.

  3. Chromatin Regulators in Pancreas Development and Diabetes.

    Science.gov (United States)

    Campbell, Stephanie A; Hoffman, Brad G

    2016-03-01

    The chromatin landscape of a cell is dynamic and can be altered by chromatin regulators that control nucleosome placement and DNA or histone modifications. Together with transcription factors, these complexes help dictate the transcriptional output of a cell and, thus, balance cell proliferation and differentiation while restricting tissue-specific gene expression. In this review, we describe current research on chromatin regulators and their roles in pancreas development and the maintenance of mature β cell function, which, once elucidated, will help us better understand how β cell differentiation occurs and is maintained. These studies have so far implicated proteins from several complexes that regulate DNA methylation, nucleosome remodeling, and histone acetylation and methylation that could become promising targets for diabetes therapy and stem cell differentiation.

  4. Functions of the Proteasome on Chromatin

    Science.gov (United States)

    McCann, Tyler S.; Tansey, William P.

    2014-01-01

    The proteasome is a large self-compartmentalized protease complex that recognizes, unfolds, and destroys ubiquitylated substrates. Proteasome activities are required for a host of cellular functions, and it has become clear in recent years that one set of critical actions of the proteasome occur on chromatin. In this review, we discuss some of the ways in which proteasomes directly regulate the structure and function of chromatin and chromatin regulatory proteins, and how this influences gene transcription. We discuss lingering controversies in the field, the relative importance of proteolytic versus non-proteolytic proteasome activities in this process, and highlight areas that require further investigation. Our intention is to show that proteasomes are involved in major steps controlling the expression of the genetic information, that proteasomes use both proteolytic mechanisms and ATP-dependent protein remodeling to accomplish this task, and that much is yet to be learned about the full spectrum of ways that proteasomes influence the genome. PMID:25422899

  5. Functions of the Proteasome on Chromatin

    Directory of Open Access Journals (Sweden)

    Tyler S. McCann

    2014-11-01

    Full Text Available The proteasome is a large self-compartmentalized protease complex that recognizes, unfolds, and destroys ubiquitylated substrates. Proteasome activities are required for a host of cellular functions, and it has become clear in recent years that one set of critical actions of the proteasome occur on chromatin. In this review, we discuss some of the ways in which proteasomes directly regulate the structure and function of chromatin and chromatin regulatory proteins, and how this influences gene transcription. We discuss lingering controversies in the field, the relative importance of proteolytic versus non-proteolytic proteasome activities in this process, and highlight areas that require further investigation. Our intention is to show that proteasomes are involved in major steps controlling the expression of the genetic information, that proteasomes use both proteolytic mechanisms and ATP-dependent protein remodeling to accomplish this task, and that much is yet to be learned about the full spectrum of ways that proteasomes influence the genome.

  6. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

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

  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 frequent event in disease, and the first epigenetic-based therapies for cancer treatment have been approved. A generation of new classes of potent and specific inhibitors for several chromatin-associated proteins have shown promise in preclinical trials. Although the biology of epigenetic regulation...

  8. CHD chromatin remodelers and the transcription cycle.

    Science.gov (United States)

    Murawska, Magdalena; Brehm, Alexander

    2011-01-01

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

  9. 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.

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    Saera Hihara

    2012-12-01

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

  12. Chromatin compaction protects genomic DNA from radiation damage.

    Directory of Open Access Journals (Sweden)

    Hideaki Takata

    Full Text Available Genomic DNA is organized three-dimensionally in the nucleus, and is thought to form compact chromatin domains. Although chromatin compaction is known to be essential for mitosis, whether it confers other advantages, particularly in interphase cells, remains unknown. Here, we report that chromatin compaction protects genomic DNA from radiation damage. Using a newly developed solid-phase system, we found that the frequency of double-strand breaks (DSBs in compact chromatin after ionizing irradiation was 5-50-fold lower than in decondensed chromatin. Since radical scavengers inhibited DSB induction in decondensed chromatin, condensed chromatin had a lower level of reactive radical generation after ionizing irradiation. We also found that chromatin compaction protects DNA from attack by chemical agents. Our findings suggest that genomic DNA compaction plays an important role in maintaining genomic integrity.

  13. 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...

  14. 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,

  15. 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

  16. Epigenetic chromatin silencing: bistability and front propagation

    Science.gov (United States)

    Sedighi, Mohammad; Sengupta, Anirvan M.

    2007-12-01

    The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.

  17. Chromatin conformation capture strategies in molecular diagnostics

    NARCIS (Netherlands)

    Vree, P.J.P. de

    2015-01-01

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

  18. The great repression: chromatin and cryptic transcription.

    Science.gov (United States)

    Hennig, Bianca P; Fischer, Tamás

    2013-01-01

    The eukaryotic chromatin structure is essential in correctly defining transcription units. Impairing this structure can activate cryptic promoters, and lead to the accumulation of aberrant RNA transcripts. Here we discuss critical pathways that are responsible for the repression of cryptic transcription and the maintenance of genome integrity.

  19. A study of the interaction between ethidium bromide and rye chromatin: comparison with calf thymus chromatin.

    Science.gov (United States)

    LaRue, H; Pallotta, D

    1976-09-01

    We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change in the binding of ethidium bromide. The subsequent extraction of H2A and H2B produces a 14% increase in the binding, and the removal of H3 and H4, another 54% increase. At this stage, the number of binding sites is still less than that of DNA. This is presumably due to the presence of some tightly bound non-histones. Thus, the arginine-rich histones and the tightly bound non-histones are most responsible for limiting the binding of ethidium bromide to rye chromatin.

  20. Direct chromatin PCR (DC-PCR: hypotonic conditions allow differentiation of chromatin states during thermal cycling.

    Directory of Open Access Journals (Sweden)

    Sergei Vatolin

    Full Text Available Current methods to study chromatin configuration are not well suited for high throughput drug screening since they require large cell numbers and multiple experimental steps that include centrifugation for isolation of nuclei or DNA. Here we show that site specific chromatin analysis can be achieved in one step by simply performing direct chromatin PCR (DC-PCR on cells. The basic underlying observation was that standard hypotonic PCR buffers prevent global cellular chromatin solubilization during thermal cycling while more loosely organized chromatin can be amplified. Despite repeated heating to >90 °C, 41 of 61 tested 5' sequences of silenced genes (CDKN2A, PU.1, IRF4, FOSB, CD34 were not amplifiable while 47 could be amplified from expressing cells. Two gene regions (IRF4, FOSB even required pre-heating of cells in isotonic media to allow this differentiation; otherwise none of 19 assayed sequences yielded PCR products. Cells with baseline expression or epigenetic reactivation gave similar DC-PCR results. Silencing during differentiation of CD34 positive cord blood cells closed respective chromatin while treatment of myeloma cells with an IRF4 transcriptional inhibitor opened a site to DC-PCR that was occupied by RNA polymerase II and NFκB as determined by ChIP. Translation into real-time PCR can not be achieved with commercial real-time PCR buffers which potently open chromatin, but even with simple ethidium bromide addition to standard PCR mastermix we were able to identify hits in small molecules screens that suppressed IRF4 expression or reactivated CDKN2A in myeloma cells using densitometry or visual inspection of PCR plates under UV light. While need in drug development inspired this work, application to genome-wide analysis appears feasible using phi29 for selective amplification of open cellular chromatin followed by library construction from supernatants since such supernatants yielded similar results as gene specific DC-PCR.

  1. Chromatin Dynamics of the mouse β-globin locus

    NARCIS (Netherlands)

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

    2010-01-01

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

  2. The many faces of plant chromatin: Meeting summary of the 4th European workshop on plant chromatin 2015, Uppsala, Sweden.

    Science.gov (United States)

    Mozgová, Iva; Köhler, Claudia; Gaudin, Valérie; Hennig, Lars

    2015-01-01

    In June 2015, the fourth European Workshop on Plant Chromatin took place in Uppsala, Sweden, bringing together 80 researchers studying various aspects of plant chromatin and epigenetics. The intricate relationships between plant chromatin dynamics and gene expression change, chromatin organization within the plant cell nucleus, and the impact of chromatin structure on plant development were discussed. Among the main highlights of the meeting were an ever-growing list of newly identified players in chromatin structure establishment and the development of novel tools and approaches to foster our understanding of chromatin-mediated gene regulation, taking into account the context of the plant cell nucleus and its architecture. In this report, we summarize some of the main advances and prospects of plant chromatin research presented at this meeting.

  3. Chromatin remodelling complex RSC promotes base excision repair in chromatin of Saccharomyces cerevisiae.

    Science.gov (United States)

    Czaja, Wioletta; Mao, Peng; Smerdon, Michael J

    2014-04-01

    The base excision repair (BER) pathway is a conserved DNA repair system required to maintain genomic integrity and prevent mutagenesis in all eukaryotic cells. Nevertheless, how BER operates in vivo (i.e. in the context of chromatin) is poorly understood. We have investigated the role of an essential ATP-dependent chromatin remodelling (ACR) complex RSC (Remodels the Structure of Chromatin) in BER of intact yeast cells. We show that depletion of STH1, the ATPase subunit of RSC, causes enhanced sensitivity to the DNA alkylating agent methyl methanesulfonate (MMS) and results in a substantial inhibition of BER, at the GAL1 locus and in the genome overall. Consistent with this observation, the DNA in chromatin is less accessible to micrococcal nuclease digestion in the absence of RSC. Quantitative PCR results indicate that repair deficiency in STH1 depleted cells is not due to changes in the expression of BER genes. Collectively, our data indicates the RSC complex promotes efficient BER in chromatin. These results provide, for the first time, a link between ATP-dependent chromatin remodelling and BER in living cells.

  4. Luminescence enhancement of Y{sub 2}O{sub 3}:Eu{sup 3+} and Y{sub 2}SiO{sub 5}:Ce{sup 3+},Tb{sup 3+} core particles with SiO{sub 2} shells

    Energy Technology Data Exchange (ETDEWEB)

    Han, J.K. [Material Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093 (United States); Hirata, G.A. [Centro de Nanociencias y Nanotecnolgia, Universidad Nacional Autonoma de Mexico, Ensenada, Baja California, MX CP 22860 (Mexico); Talbot, J.B. [Material Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093 (United States); Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093 (United States); McKittrick, J., E-mail: jmckittrick@ucsd.edu [Material Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093 (United States); Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States)

    2011-03-25

    This paper reports on the luminescence and microstructural features of oxide nano-crystalline (Y{sub 2}O{sub 3}:Eu{sup 3+}) and submicron-sized (Y{sub 2}SiO{sub 5}:Ce{sup 3+},Tb{sup 3+}) phosphor cores, produced by two different synthesis techniques, and subsequently coated by an inert shell of SiO{sub 2} using a sol-gel process. The shells mitigate the detrimental effect of the phosphor particle surfaces on the photoluminescence emission properties, thereby increasing luminous output by 20-90%, depending on the core composition and shell thickness. For Y{sub 2}O{sub 3}:Eu{sup 3+}, uniformly shaped, narrow particle size distribution core/shell particles were successfully fabricated. The photoluminescence emission intensity of core nanoparticles increased with increasing Eu{sup 3+} activator concentration and the luminescence emission intensity of the core/shell particles was 20-50% higher than that of the core particles alone. For Y{sub 2}SiO{sub 5}:Ce{sup 3+},Tb{sup 3+}, the core/shell particles showed enhancement of the luminescence emission intensity of 35-90% that of the core particles, depending on the SiO{sub 2} shell thickness.

  5. SWI/SNF-like chromatin remodeling factor Fun30 supports point centromere function in S. cerevisiae.

    Directory of Open Access Journals (Sweden)

    Mickaël Durand-Dubief

    2012-09-01

    Full Text Available Budding yeast centromeres are sequence-defined point centromeres and are, unlike in many other organisms, not embedded in heterochromatin. Here we show that Fun30, a poorly understood SWI/SNF-like chromatin remodeling factor conserved in humans, promotes point centromere function through the formation of correct chromatin architecture at centromeres. Our determination of the genome-wide binding and nucleosome positioning properties of Fun30 shows that this enzyme is consistently enriched over centromeres and that a majority of CENs show Fun30-dependent changes in flanking nucleosome position and/or CEN core micrococcal nuclease accessibility. Fun30 deletion leads to defects in histone variant Htz1 occupancy genome-wide, including at and around most centromeres. FUN30 genetically interacts with CSE4, coding for the centromere-specific variant of histone H3, and counteracts the detrimental effect of transcription through centromeres on chromosome segregation and suppresses transcriptional noise over centromere CEN3. Previous work has shown a requirement for fission yeast and mammalian homologs of Fun30 in heterochromatin assembly. As centromeres in budding yeast are not embedded in heterochromatin, our findings indicate a direct role of Fun30 in centromere chromatin by promoting correct chromatin architecture.

  6. Granulation of core particles suitable for film coating by agitation fluidized bed III. Effect of scale, agitator rotational speed and blade shape on granule properties and development of a high accuracy scale-up theory.

    Science.gov (United States)

    Hamashita, Tomohiro; Ono, Tetsuo; Ono, Masaki; Tsunenari, Yoshinobu; Aketo, Takao; Watano, Satoru

    2009-04-01

    The preparation of core particles suitable for subsequent film coating was examined using different scales of agitation fluidized beds. Specifically, the effects of agitator rotational speed and agitator blade shape in different scales of granulators on granule properties such as mass median diameter, apparent density, friability and shape factor were studied. As the agitator rotational speed was increased or when the agitator blade height and angle were large, the mass median diameter and friability of the granules decreased, while the apparent density and shape factor increased, in a manner independent of the vessel size because the granules were subjected to greater compression, shearing and rolling effects. The same core particles could not be prepared using granulators with different vessel sizes by simply adopting a conventional scale-up theory(1,2)) based on kinetic energy similarity. Here, a novel scale-up theory that takes into account agitator blade shape factors is proposed.(3)) When the two scale-up theories were compared, our new theory was capable of predicting the granule properties more accurately than the conventional theory. By adopting this novel theory, the same core particles could be prepared under different operating conditions in any scale of granulator.

  7. Statistical mechanics of chromatin: Inferring free energies of nucleosome formation from high-throughput data sets

    Science.gov (United States)

    Morozov, Alexandre

    2009-03-01

    Formation of nucleosome core particles is a first step towards packaging genomic DNA into chromosomes in living cells. Nucleosomes are formed by wrapping 147 base pairs of DNA around a spool of eight histone proteins. It is reasonable to assume that formation of single nucleosomes in vitro is determined by DNA sequence alone: it costs less elastic energy to wrap a flexible DNA polymer around the histone octamer, and more if the polymer is rigid. However, it is unclear to which extent this effect is important in living cells. Cells have evolved chromatin remodeling enzymes that expend ATP to actively reposition nucleosomes. In addition, nucleosome positioning on long DNA sequences is affected by steric exclusion - many nucleosomes have to form simultaneously without overlap. Currently available bioinformatics methods for predicting nucleosome positions are trained on in vivo data sets and are thus unable to distinguish between extrinsic and intrinsic nucleosome positioning signals. In order to see the relative importance of such signals for nucleosome positioning in vivo, we have developed a model based on a large collection of DNA sequences from nucleosomes reconstituted in vitro by salt dialysis. We have used these data to infer the free energy of nucleosome formation at each position along the genome. The method uses an exact result from the statistical mechanics of classical 1D fluids to infer the free energy landscape from nucleosome occupancy. We will discuss the degree to which in vitro nucleosome occupancy profiles are predictive of in vivo nucleosome positions, and will estimate how many nucleosomes are sequence-specific and how many are positioned purely by steric exclusion. Our approach to nucleosome energetics should be applicable across multiple organisms and genomic regions.

  8. Quantification of chromatin condensation level by image processing.

    Science.gov (United States)

    Irianto, Jerome; Lee, David A; Knight, Martin M

    2014-03-01

    The level of chromatin condensation is related to the silencing/activation of chromosomal territories and therefore impacts on gene expression. Chromatin condensation changes during cell cycle, progression and differentiation, and is influenced by various physicochemical and epigenetic factors. This study describes a validated experimental technique to quantify chromatin condensation. A novel image processing procedure is developed using Sobel edge detection to quantify the level of chromatin condensation from nuclei images taken by confocal microscopy. The algorithm was developed in MATLAB and used to quantify different levels of chromatin condensation in chondrocyte nuclei achieved through alteration in osmotic pressure. The resulting chromatin condensation parameter (CCP) is in good agreement with independent multi-observer qualitative visual assessment. This image processing technique thereby provides a validated unbiased parameter for rapid and highly reproducible quantification of the level of chromatin condensation.

  9. Protein-protein Förster resonance energy transfer analysis of nucleosome core particles containing H2A and H2A.Z.

    Science.gov (United States)

    Hoch, Duane A; Stratton, Jessica J; Gloss, Lisa M

    2007-08-24

    A protein-protein Förster resonance energy transfer (FRET) system, employing probes at multiple positions, was designed to specifically monitor the dissociation of the H2A-H2B dimer from the nucleosome core particle (NCP). Tryptophan donors and Cys-AEDANS acceptors were chosen because, compared to previous NCP FRET fluorophores, they: (1) are smaller and less hydrophobic, which should minimize perturbations of histone and NCP structure; and (2) have an R0 of 20 A, which is much less than the dimensions of the NCP (approximately 50 A width and approximately 100 A diameter). Equilibrium protein unfolding titrations indicate that the donor and acceptor moieties have minimal effects on the stability of the H2A-H2B dimer and (H3-H4)2 tetramer. NCPs containing the various FRET pairs were reconstituted with the 601 DNA positioning element. Equilibrium NaCl-induced dissociation of the modified NCPs showed that the 601 sequence stabilized the NCP to dimer dissociation relative to weaker positioning sequences. This finding implies a significant role for the H2A-H2B dimers in determining the DNA sequence dependence of NCP stability. The free energy of dissociation determined from reversible and well-defined sigmoidal transitions revealed two distinct phases reflecting the dissociation of individual H2A-H2B dimers, confirming cooperativity as suggested previously; these data allow quantitative description of the cooperativity. The FRET system was then used to study the effects of the histone variant H2A.Z on NCP stability; previous studies have reported both destabilizing and stabilizing effects. H2A.Z FRET NCP dissociation transitions suggest a slight increase in stability but a significant increase in cooperativity of the dimer dissociations. Thus, the utility of this protein-protein FRET system to monitor the effects of histone variants on NCP dynamics has been demonstrated, and the system appears equally well-suited for dissection of the kinetic processes of dimer

  10. Chromatin structure and DNA damage repair

    Directory of Open Access Journals (Sweden)

    Dinant Christoffel

    2008-11-01

    Full Text Available Abstract The integrity of the genome is continuously challenged by both endogenous and exogenous DNA damaging agents. These damaging agents can induce a wide variety of lesions in the DNA, such as double strand breaks, single strand breaks, oxidative lesions and pyrimidine dimers. The cell has evolved intricate DNA damage response mechanisms to counteract the genotoxic effects of these lesions. The two main features of the DNA damage response mechanisms are cell-cycle checkpoint activation and, at the heart of the response, DNA repair. For both damage signalling and repair, chromatin remodelling is most likely a prerequisite. Here, we discuss current knowledge on chromatin remodelling with respect to the cellular response to DNA damage, with emphasis on the response to lesions resolved by nucleotide excision repair. We will discuss the role of histone modifications as well as their displacement or exchange in nucleotide excision repair and make a comparison with their requirement in transcription and double strand break repair.

  11. Keystone Symposia on Epigenomics and Chromatin Dynamics

    DEFF Research Database (Denmark)

    Ravnskjær, Kim

    2012-01-01

    Keystone Symposia kicked off the start of 2012 with two joint meetings on Epigenomics and Chromatin Dynamics and a star-studded list of speakers. Held in Keystone, CO, January 17-22, and organized by Steven Jacobsen and Steven Henikoff and by Bradley Cairns and Geneviève Almouzni, respectively, t......, there was plenty happening in these sessions that it did not seem to matter that the ski-slope conditions were not ideal....

  12. Toughening Modification of Epoxy Resin with Different Core-Shell Particles%不同结构聚合物核壳粒子对环氧树脂的增韧改性

    Institute of Scientific and Technical Information of China (English)

    汪源; 王源升

    2012-01-01

    The traditional toughening modification of epoxy resin often can't attain ideal effect.After blended with epoxy resin,the core-shell particles can reduce the internal stress and attain significant toughening effect.Meantime,they don't change the thermal deformation temperature.In this paper,lots of core-shell particles were prepared by the soap-free core-shell emulsion polymerization method.The properties of epoxy resin modified by these core-shell particles were analyzed.The mechanical strength and dynamic mechanical analysis were used to analyze the structure of core-shell particles and the toughening mechanism of modified epoxy resin.The results showed that improving the compatibility would make the core part dissipate the energy of external force better.So the impact strength increases further.%传统环氧树脂的增韧改性方法往往达不到理想的效果。核壳粒子与环氧树脂混合,能减小内应力,获得显著的增韧效果,且不改变热变形温度。文中采用微皂核壳乳液的聚合方法合成了不同的核壳粒子,并对这些核壳粒子增韧环氧树脂体系的力学性能进行试验研究、理论分析和数值计算。用力学强度、动态力学分析等表征手段对核壳粒子的结构和改性环氧树脂体系的增韧机理进行了探讨。结果发现,改善核、壳之间或者核壳粒子壳层同环氧树脂之间的相容性和界面粘合力,核层能更好地将能量充分耗散,改性体系的冲击强度得以进一步提高。

  13. A Development of Nucleic Chromatin Measurements as a New Prognostic Marker for Severe Chronic Heart Failure.

    Directory of Open Access Journals (Sweden)

    Machiko Kanzaki

    Full Text Available Accurate prediction of both mortality and morbidity is of significant importance, but it is challenging in patients with severe heart failure. It is especially difficult to detect the optimal time for implanting mechanical circulatory support devices in such patients. We aimed to analyze the morphometric ultrastructure of nuclear chromatin in cardiomyocytes by developing an original clinical histopathological method. Using this method, we developed a biomarker to predict poor outcome in patients with dilated cardiomyopathy (DCM.As a part of their diagnostic evaluation, 171 patients underwent endomyocardial biopsy (EMB. Of these, 63 patients diagnosed with DCM were included in this study. We used electron microscopic imaging of cardiomyocyte nuclei and an automated image analysis software program to assess whether it was possible to detect discontinuity of the nuclear periphery. Twelve months after EMB, all patients with a discontinuous nuclear periphery (Group A, n = 11 died from heart failure or underwent left ventricular assist device (VAD implantation. In contrast, in patients with a continuous nuclear periphery (Group N, n = 52 only 7 patients (13% underwent VAD implantation and there were no deaths (p<0.01. We then evaluated chromatin particle density (Nuc-CS and chromatin thickness in the nuclear periphery (Per-CS in Group N patients; these new parameters were able to identify patients with poor prognosis.We developed novel morphometric methods based on cardiomyocyte nuclear chromatin that may provide pivotal information for early prediction of poor prognosis in patients with DCM.

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

    KAUST Repository

    Jégu, Teddy

    2015-10-12

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

  15. Plant chromatin warms up in Madrid: meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain.

    Science.gov (United States)

    Jarillo, José A; Gaudin, Valérie; Hennig, Lars; Köhler, Claudia; Piñeiro, Manuel

    2014-04-01

    The 3rd European Workshop on Plant Chromatin (EWPC) was held on August 2013 in Madrid, Spain. A number of different topics on plant chromatin were presented during the meeting, including new factors mediating Polycomb Group protein function in plants, chromatin-mediated reprogramming in plant developmental transitions, the role of histone variants, and newly identified chromatin remodeling factors. The function of interactions between chromatin and transcription factors in the modulation of gene expression, the role of chromatin dynamics in the control of nuclear processes and the influence of environmental factors on chromatin organization were also reported. In this report, we highlight some of the new insights emerging in this growing area of research, presented at the 3rd EWPC.

  16. Passive immunity to bovine rotavirus in newborn calves fed colostrum supplements from cows immunized with recombinant SA11 rotavirus core-like particle (CLP) or virus-like particle (VLP) vaccines.

    Science.gov (United States)

    Fernandez, F M; Conner, M E; Hodgins, D C; Parwani, A V; Nielsen, P R; Crawford, S E; Estes, M K; Saif, L J

    1998-03-01

    Heterotypic passive immunity to IND (P/5/G6) bovine rotavirus (BRV) was evaluated. Three groups of calves (n = 5 per group) were fed 1% pooled colostrum supplements (birth to 7 days of age) from BRV seropositive cows vaccinated with recombinant SA11(P/2/G3) rotavirus-like particles (VLPs), recombinant SA11 rotavirus core-like particles (CLPs), or inactivated SA11 rotavirus (SA11). Control calves (n = 5 per group) received either pooled colostrum from unvaccinated (BRV field exposure seropositive) control cows, or no colostrum. IgG1 antibody titers to IND BRV for the pooled colostrum were: 1,048,576 (VLP); 1,048,576 (CLP); 262,144 (SA11); and 16,384 (control colostrum). Elevated titers of BRV neutralizing (VN) antibodies were present in VLP colostrum (98,000), and SA11 colostrum (25,000), but not in CLP colostrum (1400), compared to colostrum from nonvaccinates (2081). Calves were orally inoculated with virulent IND BRV at 2 days of age and challenged at post-inoculation day (PID) 21. Calves were monitored daily for diarrhea and faecal BRV shedding through PID 10 and post-challenge day (PCD) 10. After colostrum feeding, the IgG1 antibody titers were highest in serum and faeces of calves fed VLP and CLP colostrum, but VN and IgA antibodies were highest in calves fed VLP colostrum. After BRV inoculation, calves fed colostrum from vaccinated cows had significantly fewer days of BRV-associated diarrhea and BRV shedding than control calves. All calves fed VLP colostrum were protected from diarrhea after BRV inoculation; two calves shed BRV. In the CLP colostrum group, one calf developed BRV-associated diarrhea and all calves shed virus. In the SA11 colostrum group, three calves developed BRV-associated diarrhea and four calves shed virus. BRV-associated diarrhea and shedding occurred in 9 of 10 control calves. Active IgM antibody responses occurred in faeces and/or serum of most calves after BRV inoculation. However, the highest active antibody responses (IgM and IgG1 in

  17. 改性环氧PBA/PMMA核壳乳胶粒子的制备与应用%Preparation and application of PBA/PMMA core-shell atex particles modified with epoxy resin

    Institute of Scientific and Technical Information of China (English)

    马立群; 李艳东; 王雅珍; 刘洪成; 汪建新

    2012-01-01

    The PBA/P (MMA-ITA-DGEBA) latex particles were prepared by semi-continuous seed emulsion polymerization process. FI-IR was used to characterize latex with core-shell structure. Epoxy resin was toughened by latex particles with an epoxy-based core-shell. Cross section of cured resin was observed by SEM micrograph. A significant effect was significant effect in toughening of modified core-shell latex particles. Compatibility between modified core-shell latex and epoxy resin were improved.%采用半连续种子乳液聚合工艺制备核壳结构的聚丙烯酸丁酯,(聚甲基丙烯酸甲酯-衣康酸-双酚A环氧树脂)(PBA/P(MMA—ITA—DGEBA))乳胶粒子。并通过红外光谱仪(IR)对乳胶粒子进行了表征,证明乳胶粒子具有壮粒子结构。将壳层带有环氧基的核壳乳胶粒子对环氧树脂进行增韧,通过扫描电子显微镜(SEM)对固化物冲击断面进行观测,改性核壳乳胶粒子对环氧树脂起到明显增韧效果,并提升了与环氧树脂的相容性。

  18. Premitotic assembly of human CENPs -T and -W switches centromeric chromatin to a mitotic state.

    Directory of Open Access Journals (Sweden)

    Lisa Prendergast

    2011-06-01

    Full Text Available 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 assembly of a large complex of associated proteins in vertebrates. While CENP-A itself is stably transmitted from one generation to the next, the nature of the template for centromere replication and its relationship to kinetochore function are as yet poorly understood. Here, we investigate the assembly and inheritance of a histone fold complex of the centromere, the CENP-T/W complex, which is integrated with centromeric chromatin in association with canonical histone H3 nucleosomes. We have investigated the cell cycle regulation, timing of assembly, generational persistence, and requirement for function of CENPs -T and -W in the cell cycle in human cells. The CENP-T/W complex assembles through a dynamic exchange mechanism in late S-phase and G2, is required for mitosis in each cell cycle and does not persist across cell generations, properties reciprocal to those measured for CENP-A. We propose that the CENP-A and H3-CENP-T/W nucleosome components of the centromere are specialized for centromeric and kinetochore activities, respectively. Segregation of the assembly mechanisms for the two allows the cell to switch between chromatin configurations that reciprocally support the replication of the centromere and its conversion to a mitotic state on postreplicative chromatin.

  19. 多群粒子输运问题在多核集群系统上的混合并行计算%Hybrid Parallel Computation of Multi-Group Particle transport Equations on Multi-Core Cluster Systems

    Institute of Scientific and Technical Information of China (English)

    迟利华; 刘杰; 龚春叶; 徐涵; 蒋杰; 胡庆丰

    2009-01-01

    The parallel performance of solving the multi-group particle transport equations on the unstructure meshes is analyzed Adapting to the characteristics of multi-core cluster systems, this paper desgins a MPI/OpenMP hybrid parallel code. For the meshes, the space domain decomposition is adopted, and MPI between the computations of multi-core CPU nodes is used. When each MPI process begin to compute the variables of the energy groups, several OpenMP threads will be forked, and the threads start to compute simultaneously in the same mutli-core CPU node. Using the MPI/OpenMP hybrid parallel code, we solve a 2D mutli-group particle transport equation on a cluster with mutli-core CPU nodes, and the results show that the code has good scalability and can be scaled to 1024 CPU cores.%本文分析了非结构网格多群粒子输运Sn方程求解的并行性,拟合多核机群系统的特点,设计了MPI/OpenMP混合程序,针对空间网格点采用区域分解划分,计算结点间基于消息传递MPI编程,每个MPI计算进程在计算过程中碰到关于能群的计算,就生成多个OpenMP线程,计算结点内针对能群进行多线程并行计算.数值测试结果表明,非结构网格上的粒子输运问题的混合并行计算能较好地匹配多核机群系统的硬件结构,具有良好的可扩展性,可以扩展到1 024个CPU核.

  20. Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility

    Science.gov (United States)

    Rueedi, Rico

    2017-01-01

    To better understand genome regulation, it is important to uncover the role of transcription factors in the process of chromatin structure establishment and maintenance. Here we present a data-driven approach to systematically characterise transcription factors that are relevant for this process. Our method uses a linear mixed modelling approach to combine datasets of transcription factor binding motif enrichments in open chromatin and gene expression across the same set of cell lines. Applying this approach to the ENCODE dataset, we confirm already known and imply numerous novel transcription factors that play a role in the establishment or maintenance of open chromatin. In particular, our approach rediscovers many factors that have been annotated as pioneer factors. PMID:28118358

  1. 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.

  2. Spectroscopic study of fast-neutron-irradiated chromatin

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-02-01

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

  3. 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.

  4. 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.

  5. Impact of chromatin structures on DNA processing for genomic analyses.

    Directory of Open Access Journals (Sweden)

    Leonid Teytelman

    Full Text Available Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome.

  6. 填料形状对Fe@Ag核壳复合粒子的电磁特性的影响%INFLUENCE OF THE SHAPE OF SHIELDING FILLERS ON ELECTROMAGNETIC PROPERTIES OF Fe@Ag CORE-SHELL COMPOSITE PARTICLES

    Institute of Scientific and Technical Information of China (English)

    赵素玲; 陈晶; 王一龙

    2012-01-01

    运用液相化学还原Ag技术,制备了球形和片形2种Fe@Ag核壳复合粒子.表征了这2种屏蔽填料的物相、表面形貌和化学组成,研究了其静磁性能,分析了填料的形状对复合材料的复磁导率、电导率和屏蔽效能等电磁特性的影响.结果表明:2种复合粒子均为核壳结构完整的Fe@Ag核壳复合粒子,其Ag壳层均匀且致密;球形和片形Fe @Ag核壳复合粒子均具有良好的软磁性能;与形状各向同性的屏蔽填料相比,以片形Fe@Ag核壳复合粒子为填料的电磁屏蔽复合材料的复磁导率更高,体积电阻率更低,该复合材料在电磁波频率范围为30-1500 MHz内的屏蔽效能(SE)为-51-55 dB,优于以球形Fe@Ag核壳复合粒子为填料的电磁屏蔽复合材料.并且从理论上分析了片形Fe@Ag核壳复合粒子的电磁屏蔽复合材料对电磁波的吸收损耗更强和屏蔽效能更高的物理本质.%Due to the rapid growth of radio frequency radiation sources, electromagnetic shielding composite materials have become a research hotspot in civil control of electromagnetic radiation technology and military equipment shielding technology. The shielding effectiveness (SE) of these electromagnetic shielding composite materials has much to do with the structures, volume resistivity and magnetic properties of the fillers. Spherical and flaky Fe@Ag core-shell composite particles were synthesized by a liquid electroless plating method in this work. The phase, morphology and chemical composition of spherical and flaky particles were characterized. The magnetic property of fillers was analyzed. The effects of the shape of these shielding fillers on complex permeability, conductivity, magnetic properties and shielding effectiveness of their composition material were investigated. The results showed that spherical and flaky carbonyl iron powders/silver core-shell composite particles both had intact core-shell microstructure. Silver coating of these

  7. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling.

    Directory of Open Access Journals (Sweden)

    Mariliis Tark-Dame

    2014-10-01

    Full Text Available Folding of the chromosomal fibre in interphase nuclei is an important element in the regulation of gene expression. For instance, physical contacts between promoters and enhancers are a key element in cell-type-specific transcription. We know remarkably little about the principles that control chromosome folding. Here we explore the view that intrachromosomal interactions, forming a complex pattern of loops, are a key element in chromosome folding. CTCF and cohesin are two abundant looping proteins of interphase chromosomes of higher eukaryotes. To investigate the role of looping in large-scale (supra Mb folding of human chromosomes, we knocked down the gene that codes for CTCF and the one coding for Rad21, an essential subunit of cohesin. We measured the effect on chromosome folding using systematic 3D fluorescent in situ hybridization (FISH. Results show that chromatin becomes more compact after reducing the concentration of these two looping proteins. The molecular basis for this counter-intuitive behaviour is explored by polymer modelling usingy the Dynamic Loop model (Bohn M, Heermann DW (2010 Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 5: e12218.. We show that compaction can be explained by selectively decreasing the number of short-range loops, leaving long-range looping unchanged. In support of this model prediction it has recently been shown by others that CTCF and cohesin indeed are responsible primarily for short-range looping. Our results suggest that the local and the overall changes in of chromosome structure are controlled by a delicate balance between short-range and long-range loops, allowing easy switching between, for instance, open and more compact chromatin states.

  8. 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.

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

    Science.gov (United States)

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

    2016-02-01

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

  10. 功能化PDMS/PMMA核壳乳胶粒子的制备与表征%Preparation and characterization of functional PDMS / PMMA core-shell latex particles

    Institute of Scientific and Technical Information of China (English)

    王权; 刘喜军; 伊海楠

    2012-01-01

    A novel latex particles of polysiloxane/polymethylmethacrylate (PDMS/PMMA) having core-shell structure was successfully synthesized by the pre-emulsion semi-continuous seeded emulsion polymerization. Through the introduction of functional monomer ITA, MAH or GMA to realize the function of core-shell latex particles.Which were characterized by the laser particle size analyzer. Fourier transform infrared spectroscopy (FTIR) and transmission electron microscope (TEM).%采用预乳化-半连续种子乳液聚合工艺合成了聚硅氧烷,聚甲基丙烯酸甲酯(PDMS/PMMA)核壳乳胶粒子,通过引入功能单体ITA、MAH或GMA实现核壳乳胶粒子的功能化。采用激光粒度分析仪、傅立叶变换红外光谱仪(FTIR)和透射电子显微镜(TEM)等手段对核壳乳胶粒子进行了表征。

  11. 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.

  12. NET23/STING promotes chromatin compaction from the nuclear envelope.

    Directory of Open Access Journals (Sweden)

    Poonam Malik

    Full Text Available Changes in the peripheral distribution and amount of condensed chromatin are observed in a number of diseases linked to mutations in the lamin A protein of the nuclear envelope. We postulated that lamin A interactions with nuclear envelope transmembrane proteins (NETs that affect chromatin structure might be altered in these diseases and so screened thirty-one NETs for those that promote chromatin compaction as determined by an increase in the number of chromatin clusters of high pixel intensity. One of these, NET23 (also called STING, MITA, MPYS, ERIS, Tmem173, strongly promoted chromatin compaction. A correlation between chromatin compaction and endogenous levels of NET23/STING was observed for a number of human cell lines, suggesting that NET23/STING may contribute generally to chromatin condensation. NET23/STING has separately been found to be involved in innate immune response signaling. Upon infection cells make a choice to either apoptose or to alter chromatin architecture to support focused expression of interferon genes and other response factors. We postulate that the chromatin compaction induced by NET23/STING may contribute to this choice because the cells expressing NET23/STING eventually apoptose, but the chromatin compaction effect is separate from this as the condensation was still observed when cells were treated with Z-VAD to block apoptosis. NET23/STING-induced compacted chromatin revealed changes in epigenetic marks including changes in histone methylation and acetylation. This indicates a previously uncharacterized nuclear role for NET23/STING potentially in both innate immune signaling and general chromatin architecture.

  13. Assaying chromatin structure and remodeling by restriction enzyme accessibility

    OpenAIRE

    Trotter, Kevin W.; Archer, Trevor K.

    2012-01-01

    The packaging of eukaryotic DNA into nucleosomes, the fundamental unit of chromatin, creates a barrier to nuclear processes, such as transcription, DNA replication, recombination, and repair(1). This obstructive nature of chromatin can be overcome by the enzymatic activity of chromatin remodeling complexes which creates a more favorable environment for the association of essential factors and regulators to sequences within target genes. Here we describe a detailed approach for analyzing chrom...

  14. Chromatin remodeling regulated by steroid and nuclear receptors

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    Coactivators and corepressors regulate transcription by controlling interactions between sequence-specific transcription factors,the basal transcriptional machinery and the chromatin environment,This review consider the access of nuclear and steroid receptors to chromatin,their use of corepressors and coactivators to modify chromatin structure and the implications for transcriptional control.The assembly of specific nucleoprotein architectures and targeted histone modification emerge as central controlling elements for gene expression.

  15. 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 a...

  16. 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...

  17. Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes

    Directory of Open Access Journals (Sweden)

    Hyangyee Oh

    2013-02-01

    Full Text Available The Hippo pathway regulates growth through the transcriptional coactivator Yorkie, but how Yorkie promotes transcription remains poorly understood. We address this by characterizing Yorkie’s association with chromatin and by identifying nuclear partners that effect transcriptional activation. Coimmunoprecipitation and mass spectrometry identify GAGA factor (GAF, the Brahma complex, and the Mediator complex as Yorkie-associated nuclear protein complexes. All three are required for Yorkie’s transcriptional activation of downstream genes, and GAF and the Brahma complex subunit Moira interact directly with Yorkie. Genome-wide chromatin-binding experiments identify thousands of Yorkie sites, most of which are associated with elevated transcription, based on genome-wide analysis of messenger RNA and histone H3K4Me3 modification. Chromatin binding also supports extensive functional overlap between Yorkie and GAF. Our studies suggest a widespread role for Yorkie as a regulator of transcription and identify recruitment of the chromatin-modifying GAF protein and BRM complex as a molecular mechanism for transcriptional activation by Yorkie.

  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.

  19. Interaction of sulfur mustard with rat liver salt fractionated chromatin.

    Science.gov (United States)

    Jafari, Mahvash; Nateghi, M; Rabbani, A

    2010-01-01

    In this study, the interaction of an alkylating agent, sulfur mustard (SM) with rat liver active (S1 and S2) and inactive (P2) chromatin was investigated employing UV/vis spectroscopy and gel electrophoreses. The results show that SM affects the chromatin structure in a dose-dependent manner. The binding of SM to fractions is different. At lower concentrations (<500 microM), SM seems to unfold the structure and at higher concentrations, it induces aggregation and condensation of chromatin possibly via forming cross-links between the chromatin components. The extent of condensation in S2 is higher when compared to the P2 fraction.

  20. Distribution of intercalative dye binding sites in chromatin.

    Science.gov (United States)

    Lurquin, P F; Seligy, V L

    1976-04-01

    Actinomycin D (AMD) and ethidium bromide (EB) were found to bind to chromatin isolated from a variety of gander tissues according to a strong and weak process analogous to that found for deproteinized DNA. Distribution of the dye intercalation sites in chromatin and DNA were evaluated at low r-values (dye bound per nucleotide) by following the appearance of free dye released from chromatin and DNA during thermal denaturation. The AMD dissociation profiles closely resembled the DNA or chromatin-DNA denaturation profiles; whereas the EB derivative dissociation profiles, indicated 3 major transitions for transcriptionally active chromatin with the main component corresponding to the single component which characterizes DNA. The DNA-like component was greatly reduced for mature erythrocyte chromatin but could be generated by removal of histone I and V. Removal of residual non acid-soluble proteins from dehistonized chromatin, urea treatment or dissociation and reconstitution of chromatin favoured conversion to the DNA-like component with loss of the other two. This study indicates that more than one type of binding exists generally in chromatin.

  1. Tandem assays of protein and glucose with functionalized core/shell particles based on magnetic separation and surface-enhanced Raman scattering.

    Science.gov (United States)

    Kong, Xianming; Yu, Qian; Lv, Zhongpeng; Du, Xuezhong

    2013-10-11

    Tandem assays of protein and glucose in combination with mannose-functionalized Fe3 O4 @SiO2 and Ag@SiO2 tag particles have promising potential in effective magnetic separation and highly sensitive and selective SERS assays of biomaterials. It is for the first time that tandem assay of glucose is developed using SERS based on the Con A-sandwiched microstructures between the functionalized magnetic and tag particles.

  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. Sensitivity of Λ single-particle energies to the ΛN spin-orbit coupling and to nuclear core structure in p-shell and sd-shell hypernuclei

    Science.gov (United States)

    Veselý, P.; Hiyama, E.; Hrtánková, J.; Mareš, J.

    2016-10-01

    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 Λ hypernuclei - 13ΛC, 17ΛO, 21ΛNe, 29ΛSi and 41ΛCa. The hypernuclear spectra are compared with the results of a relativistic mean field (RMF) model and available experimental data. The sensitivity of Λ single-particle energies to the nuclear core structure is explored. Special attention is paid to the effect of spin-orbit ΛN interaction on the energy splitting of the Λ 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.

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

    DEFF Research Database (Denmark)

    Comet, Itys; Schuettengruber, Bernd; Sexton, Tom;

    2011-01-01

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

  5. Global chromatin fibre compaction in response to DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, Charlotte [Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Hayward, Richard L. [Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Breakthrough Research Unit, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Gilbert, Nick, E-mail: Nick.Gilbert@ed.ac.uk [Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Breakthrough Research Unit, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom)

    2011-11-04

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

  6. Human sperm chromatin stabilization: a proposed model including zinc bridges.

    Science.gov (United States)

    Björndahl, Lars; Kvist, Ulrik

    2010-01-01

    The primary focus of this review is to challenge the current concepts on sperm chromatin stability. The observations (i) that zinc depletion at ejaculation allows a rapid and total sperm chromatin decondensation without the addition of exogenous disulfide cleaving agents and (ii) that the human sperm chromatin contains one zinc for every protamine for every turn of the DNA helix suggest an alternative model for sperm chromatin structure may be plausible. An alternative model is therefore proposed, that the human spermatozoon could at ejaculation have a rapidly reversible zinc dependent chromatin stability: Zn(2+) stabilizes the structure and prevents the formation of excess disulfide bridges by a single mechanism, the formation of zinc bridges with protamine thiols of cysteine and potentially imidazole groups of histidine. Extraction of zinc enables two biologically totally different outcomes: immediate decondensation if chromatin fibers are concomitantly induced to repel (e.g. by phosphorylation in the ooplasm); otherwise freed thiols become committed into disulfide bridges creating a superstabilized chromatin. Spermatozoa in the zinc rich prostatic fluid (normally the first expelled ejaculate fraction) represent the physiological situation. Extraction of chromatin zinc can be accomplished by the seminal vesicular fluid. Collection of the ejaculate in one single container causes abnormal contact between spermatozoa and seminal vesicular fluid affecting the sperm chromatin stability. There are men in infertile couples with low content of sperm chromatin zinc due to loss of zinc during ejaculation and liquefaction. Tests for sperm DNA integrity may give false negative results due to decreased access for the assay to the DNA in superstabilized chromatin.

  7. The preparation of composite microsphere with hollow core/porous shell structure by self-assembling of latex particles at emulsion droplet interface.

    Science.gov (United States)

    He, Xiao Dong; Ge, Xue Wu; Wang, Mo Zhen; Zhang, Zhi Cheng

    2006-07-15

    A submicrometer-scaled polystyrene/melamine-formaldehyde hollow microsphere composite was prepared by self-assembling of sulfonated polystyrene (SPS) latex particles at the interface of emulsion droplets and then being fixed in place using a hard melamine-formaldehyde (MF) composite layer. For control-released purposes, the influential factors that control the size and uniformity of the packed-droplets and the permeability of the composite shell, including the initial particle location, the hydrophilicity and the size of colloidal templates, the oil phase solvent and reserving time of emulsions after the addition of MF prepolymer, were further studied. Relatively uniform sized particle packed-droplets with an average diameter of 10 microm were obtained. The assembled SPS particles kept ordering and minimal conglutination after the preparation of composite microspheres, which allows of controlling the permeability from the interstices between the particles. Porous-mesh-structured MF composite layer was formed to further control the permeability. The morphology of emulsions and composite microspheres were characterized by optical microscopy, scanning and transmission electron microscopy.

  8. Visualisation of γH2AX foci caused by heavy ion particle traversal; distinction between core track versus non-track damage.

    Directory of Open Access Journals (Sweden)

    Nakako Izumi Nakajima

    Full Text Available Heavy particle irradiation produces complex DNA double strand breaks (DSBs which can arise from primary ionisation events within the particle trajectory. Additionally, secondary electrons, termed delta-electrons, which have a range of distributions can create low linear energy transfer (LET damage within but also distant from the track. DNA damage by delta-electrons distant from the track has not previously been carefully characterised. Using imaging with deconvolution, we show that at 8 hours after exposure to Fe (∼200 keV/µm ions, γH2AX foci forming at DSBs within the particle track are large and encompass multiple smaller and closely localised foci, which we designate as clustered γH2AX foci. These foci are repaired with slow kinetics by DNA non-homologous end-joining (NHEJ in G1 phase with the magnitude of complexity diminishing with time. These clustered foci (containing 10 or more individual foci represent a signature of DSBs caused by high LET heavy particle radiation. We also identified simple γH2AX foci distant from the track, which resemble those arising after X-ray exposure, which we attribute to low LET delta-electron induced DSBs. They are rapidly repaired by NHEJ. Clustered γH2AX foci induced by heavy particle radiation cause prolonged checkpoint arrest compared to simple γH2AX foci following X-irradiation. However, mitotic entry was observed when ∼10 clustered foci remain. Thus, cells can progress into mitosis with multiple clusters of DSBs following the traversal of a heavy particle.

  9. An in vitro assay to study the recruitment and substrate specificity of chromatin modifying enzymes

    Directory of Open Access Journals (Sweden)

    Vermeulen Michiel

    2004-01-01

    Full Text Available Post-translational modifications of core histones play an important role in regulating fundamental biological processes such as DNA repair, transcription and replication. In this paper, we describe a novel assay that allows sequential targeting of distinct histone modifying enzymes to immobilized nucleosomal templates using recombinant chimeric targeting molecules. The assay can be used to study the histone substrate specificity of chromatin modifying enzymes as well as whether and how certain enzymes affect each other's histone modifying activities. As such the assay can help to understand how a certain histone code is established and interpreted.

  10. A Broad Set of Chromatin Factors Influences Splicing

    Science.gov (United States)

    Allemand, Eric; Myers, Michael P.; Garcia-Bernardo, Jose; Harel-Bellan, Annick; Krainer, Adrian R.; Muchardt, Christian

    2016-01-01

    Several studies propose an influence of chromatin on pre-mRNA splicing, but it is still unclear how widespread and how direct this phenomenon is. We find here that when assembled in vivo, the U2 snRNP co-purifies with a subset of chromatin-proteins, including histones and remodeling complexes like SWI/SNF. Yet, an unbiased RNAi screen revealed that the outcome of splicing is influenced by a much larger variety of chromatin factors not all associating with the spliceosome. The availability of this broad range of chromatin factors impacting splicing further unveiled their very context specific effect, resulting in either inclusion or skipping, depending on the exon under scrutiny. Finally, a direct assessment of the impact of chromatin on splicing using an in vitro co-transcriptional splicing assay with pre-mRNAs transcribed from a nucleosomal template, demonstrated that chromatin impacts nascent pre-mRNP in their competence for splicing. Altogether, our data show that numerous chromatin factors associated or not with the spliceosome can affect the outcome of splicing, possibly as a function of the local chromatin environment that by default interferes with the efficiency of splicing. PMID:27662573

  11. 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....

  12. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging.

    Science.gov (United States)

    Tatavosian, Roubina; Zhen, Chao Yu; Duc, Huy Nguyen; Balas, Maggie M; Johnson, Aaron M; Ren, Xiaojun

    2015-11-20

    Epigenetic complexes play an essential role in regulating chromatin structure, but information about their assembly stoichiometry on chromatin within cells is poorly understood. The cellular assembly stoichiometry is critical for appreciating the initiation, propagation, and maintenance of epigenetic inheritance during normal development and in cancer. By combining genetic engineering, chromatin biochemistry, and single-molecule fluorescence imaging, we developed a novel and sensitive approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) to enable investigation of the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was validated by using chromatin complexes with known stoichiometry. The stoichiometry of subunits within a polycomb complex and the assembly stoichiometry of polycomb complexes on chromatin have been extensively studied but reached divergent views. Moreover, the cellular assembly stoichiometry of polycomb complexes on chromatin remains unexplored. Using Sm-ChIPi, we demonstrated that within mouse embryonic stem cells, one polycomb repressive complex (PRC) 1 associates with multiple nucleosomes, whereas two PRC2s can bind to a single nucleosome. Furthermore, we obtained direct physical evidence that the nucleoplasmic PRC1 is monomeric, whereas PRC2 can dimerize in the nucleoplasm. We showed that ES cell differentiation induces selective alteration of the assembly stoichiometry of Cbx2 on chromatin but not other PRC1 components. We additionally showed that the PRC2-mediated trimethylation of H3K27 is not required for the assembly stoichiometry of PRC1 on chromatin. Thus, these findings uncover that PRC1 and PRC2 employ distinct mechanisms to assemble on chromatin, and the novel Sm-ChIPi technique could provide single-molecule insight into other epigenetic complexes.

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

    Science.gov (United States)

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

    2003-10-24

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

  14. 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.

  15. Transcription upregulation via force-induced direct stretching of chromatin

    Science.gov (United States)

    Tajik, Arash; Zhang, Yuejin; Wei, Fuxiang; Sun, Jian; Jia, Qiong; Zhou, Wenwen; Singh, Rishi; Khanna, Nimish; Belmont, Andrew S.; Wang, Ning

    2016-12-01

    Mechanical forces play critical roles in the function of living cells. However, the underlying mechanisms of how forces influence nuclear events remain elusive. Here, we show that chromatin deformation as well as force-induced transcription of a green fluorescent protein (GFP)-tagged bacterial-chromosome dihydrofolate reductase (DHFR) transgene can be visualized in a living cell by using three-dimensional magnetic twisting cytometry to apply local stresses on the cell surface via an Arg-Gly-Asp-coated magnetic bead. Chromatin stretching depended on loading direction. DHFR transcription upregulation was sensitive to load direction and proportional to the magnitude of chromatin stretching. Disrupting filamentous actin or inhibiting actomyosin contraction abrogated or attenuated force-induced DHFR transcription, whereas activating endogenous contraction upregulated force-induced DHFR transcription. Our findings suggest that local stresses applied to integrins propagate from the tensed actin cytoskeleton to the LINC complex and then through lamina-chromatin interactions to directly stretch chromatin and upregulate transcription.

  16. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

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

  17. Control of human adenovirus type 5 gene expression by cellular Daxx/ATRX chromatin-associated complexes.

    Science.gov (United States)

    Schreiner, Sabrina; Bürck, Carolin; Glass, Mandy; Groitl, Peter; Wimmer, Peter; Kinkley, Sarah; Mund, Andreas; Everett, Roger D; Dobner, Thomas

    2013-04-01

    Death domain-associated protein (Daxx) cooperates with X-linked α-thalassaemia retardation syndrome protein (ATRX), a putative member of the sucrose non-fermentable 2 family of ATP-dependent chromatin-remodelling proteins, acting as the core ATPase subunit in this complex, whereas Daxx is the targeting factor, leading to histone deacetylase recruitment, H3.3 deposition and transcriptional repression of cellular promoters. Despite recent findings on the fundamental importance of chromatin modification in host-cell gene regulation, it remains unclear whether adenovirus type 5 (Ad5) transcription is regulated by cellular chromatin remodelling to allow efficient virus gene expression. Here, we focus on the repressive role of the Daxx/ATRX complex during Ad5 replication, which depends on intact protein-protein interaction, as negative regulation could be relieved with a Daxx mutant that is unable to interact with ATRX. To ensure efficient viral replication, Ad5 E1B-55K protein inhibits Daxx and targets ATRX for proteasomal degradation in cooperation with early region 4 open reading frame protein 6 and cellular components of a cullin-dependent E3-ubiquitin ligase. Our studies illustrate the importance and diversity of viral factors antagonizing Daxx/ATRX-mediated repression of viral gene expression and shed new light on the modulation of cellular chromatin remodelling factors by Ad5. We show for the first time that cellular Daxx/ATRX chromatin remodelling complexes play essential roles in Ad gene expression and illustrate the importance of early viral proteins to counteract cellular chromatin remodelling.

  18. Effect of core-shell polymer particles on the coefficient of thermal expansion of epoxy resin%核壳聚合物粒子对环氧树脂热膨胀系数的影响

    Institute of Scientific and Technical Information of China (English)

    赫玉欣; 张丽; 朱伸兵; 姚大虎; 张志强; 张玉清

    2012-01-01

    The epoxy resins were modified by core-shell polymer(CSP) particles.The effect of CSP on the coefficient of thermal expansion(CTE) of modified epoxy resins was investigated by infrared spectroscopy,thermal mechanical analysis and scanning electron microscopy.The results showed that hydrogen bond was formed between C= =O of CSP particle shell and — OH of DGEBA epoxy resin side chain during the curing pocess,thereby strengthening the interface role of core-shell polymer particles and epoxy matrix.The glass transition temperatures of CSP particles modified epoxy resin were decreased and CTE values of modified resin below the Tg range were decreased,then increased compared with that of neat epoxy resins with the increasing of CSP content.The CTE of the resins with 0.5% CSP was decreased by 12.88%.But the CTE values of modified resins were all higher than that of neat epoxy resins above the Tg range.%采用核壳聚合物(Core-Shell Polymer,CSP)粒子改性环氧树脂,通过红外光谱、热力学分析和扫描电镜研究了CSP粒子对环氧树脂基体热膨胀系数(CTE)的影响。结果表明:CSP粒子壳材料分子链中的羰基在环氧树脂固化过程中可与环氧分子侧链上的羟基形成氢键作用,从而加强了核壳聚合物粒子与环氧树脂的界面作用。随着CSP粒子质量分数的增加,改性环氧树脂基体的玻璃化转变温度呈下降趋势;相对于纯环氧树脂,改性环氧树脂在玻璃化转变温度下的CTE呈现先下降后上升的趋势,添加质量分数为0.5%的CSP后,其CTE值降低了12.88%。但在玻璃化转变温度上的热膨胀系数均高于纯环氧树脂。

  19. Effect of DNA groove binder distamycin A upon chromatin structure.

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

    Full Text Available BACKGROUND: Distamycin A is a prototype minor groove binder, which binds to B-form DNA, preferentially at A/T rich sites. Extensive work in the past few decades has characterized the binding at the level of double stranded DNA. However, effect of the same on physiological DNA, i.e. DNA complexed in chromatin, has not been well studied. Here we elucidate from a structural perspective, the interaction of distamycin with soluble chromatin, isolated from Sprague-Dawley rat. METHODOLOGY/PRINCIPAL FINDINGS: Chromatin is a hierarchical assemblage of DNA and protein. Therefore, in order to characterize the interaction of the same with distamycin, we have classified the system into various levels, according to the requirements of the method adopted, and the information to be obtained. Isothermal titration calorimetry has been employed to characterize the binding at the levels of chromatin, chromatosome and chromosomal DNA. Thermodynamic parameters obtained thereof, identify enthalpy as the driving force for the association, with comparable binding affinity and free energy for chromatin and chromosomal DNA. Reaction enthalpies at different temperatures were utilized to evaluate the change in specific heat capacity (ΔCp, which, in turn, indicated a possible binding associated structural change. Ligand induced structural alterations have been monitored by two complementary methods--dynamic light scattering, and transmission electron microscopy. They indicate compaction of chromatin. Using transmission electron microscopy, we have visualized the effect of distamycin upon chromatin architecture at di- and trinucleosome levels. Our results elucidate the simultaneous involvement of linker bending and internucleosomal angle contraction in compaction process induced by distamycin. CONCLUSIONS/SIGNIFICANCE: We summarize here, for the first time, the thermodynamic parameters for the interaction of distamycin with soluble chromatin, and elucidate its effect on

  20. Defining the multivalent functions of CTCF from chromatin state and three-dimensional chromatin interactions.

    Science.gov (United States)

    Lu, Yiming; Shan, Guangyu; Xue, Jiguo; Chen, Changsheng; Zhang, Chenggang

    2016-07-27

    CCCTC-binding factor (CTCF) is a multi-functional protein that is assigned various, even contradictory roles in the genome. High-throughput sequencing-based technologies such as ChIP-seq and Hi-C provided us the opportunity to assess the multivalent functions of CTCF in the human genome. The location of CTCF-binding sites with respect to genomic features provides insights into the possible roles of this protein. Here we present the first genome-wide survey and characterization of three important functions of CTCF: enhancer insulator, chromatin barrier and enhancer linker. We developed a novel computational framework to discover the multivalent functions of CTCF based on chromatin state and three-dimensional chromatin architecture. We applied our method to five human cell lines and identified ∼46 000 non-redundant CTCF sites related to the three functions. Disparate effects of these functions on gene expression were found and distinct genomic features of these CTCF sites were characterized in GM12878 cells. Finally, we investigated the cell-type specificities of CTCF sites related to these functions across five cell types. Our study provides new insights into the multivalent functions of CTCF in the human genome.

  1. 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

  2. The differential mobilization of histones H3.1 and H3.3 by herpes simplex virus 1 relates histone dynamics to the assembly of viral chromatin.

    Science.gov (United States)

    Conn, Kristen L; Hendzel, Michael J; Schang, Luis M

    2013-01-01

    During lytic infections, HSV-1 genomes are assembled into unstable nucleosomes. The histones required for HSV-1 chromatin assembly, however, are in the cellular chromatin. We have shown that linker (H1) and core (H2B and H4) histones are mobilized during HSV-1 infection, and proposed that the mobilized histones are available for assembly into viral chromatin. However, the actual relevance of histone mobilization remained unknown. We now show that canonical H3.1 and variant H3.3 are also mobilized during HSV-1 infection. Mobilization required no HSV-1 protein expression, although immediate early or early proteins enhanced it. We used the previously known differential association of H3.3 and H3.1 with HSV-1 DNA to test the relevance of histone mobilization. H3.3 binds to HSV-1 genomes first, whereas H3.1 only binds after HSV-1 DNA replication initiates. Consistently, H3.3 and H3.1 were differentially mobilized. H3.1 mobilization decreased with HSV-1 DNA replication, whereas H3.3 mobilization was largely unaffected by it. These results support a model in which previously mobilized H3.1 is immobilized by assembly into viral chromatin during HSV-1 DNA replication, whereas H3.3 is mobilized and assembled into HSV-1 chromatin throughout infection. The differential mobilizations of H3.3 and H3.1 are consistent with their differential assembly into viral chromatin. These data therefore relate nuclear histone dynamics to the composition of viral chromatin and provide the first evidence that histone mobilization relates to viral chromatin assembly.

  3. Ice cores

    DEFF Research Database (Denmark)

    Svensson, Anders

    2014-01-01

    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...

  4. 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.

  5. Preparation and characterization of PDMS/PMMA core-shell latex particles having functional group in surface layer%表层功能化PDMS/PMMA核壳乳胶粒子的制备与表征

    Institute of Scientific and Technical Information of China (English)

    张国青; 刘喜军

    2014-01-01

    In this paper, the polydimethyl siloxane/polymethyl methacrylate(PDMS/PMMA)core-shell latex particles (-320 nm)respectively with itaconic acid(ITA),maleic anhydride(MAH)and glycidyl methacrylate(GMA) as functional monomer in surface layer were successfully synthesized employing pre-emulsification semi-continuous process by seeded emulsion polymerization method. Octamethyl cyclotetrasiloxane(D 4 )and Tetravinyl tetramethyl cyelotetrasiloxane as the main monomer were compounded to form PDMS core latex particles with methyl triethoxysilane(MTES)as cross-linking agent. The effects of the reaction time, surfactant and catalyst concentration, and the ratio of D 4 and VD 4 on the polymerization system were studied, and the optimal synthesizing process of PDMS core latex particles was defined.By laser particle size analyzer, Fourier transform infrared spectrometer and transmission electron microscopy analysis showed that the core monomer conversion was nearly 85%and PDMS latex particle size was at about 290 nm when the reaction time was 10 h,surfactant concentration was 5.3%, catalyst concentration was 5.3%,and D4∶VD4=4∶1.%分别以衣康酸(ITA)、马来酸酐(MAH)和甲基丙烯酸缩水甘油酯(GMA)为功能单体,采用预乳化半连续工艺通过种子乳液聚合方法成功合成了表层功能化的聚二甲基硅氧烷/聚甲基丙烯酸甲酯(PDMS/PMMA)核壳乳胶粒子(~320 nm)。PDMS核乳胶粒子以八甲基环四硅氧烷(D 4)和四甲基四乙烯基环四硅氧烷(VD 4)为单体、甲基三乙氧基硅烷(MTES)为交联剂构建而成,实验研究了反应时间、乳化剂和催化剂用量、单体D 4与VD 4比例对聚合体系的影响,并确定了PDMS核乳胶粒子合成最佳工艺。通过激光粒度分析仪、傅里叶变换红外光谱仪、透射电子显微镜等分析表明:当反应时间为10 h、乳化剂用量为核单体总量的5.3%、催化剂用量为核单体总量的5.3%

  6. Fractal Characterization of Chromatin Decompaction in Live Cells.

    Science.gov (United States)

    Yi, Ji; Stypula-Cyrus, Yolanda; Blaha, Catherine S; Roy, Hemant K; Backman, Vadim

    2015-12-01

    Chromatin organization has a fundamental impact on the whole spectrum of genomic functions. Quantitative characterization of the chromatin structure, particularly at submicron length scales where chromatin fractal globules are formed, is critical to understanding this structure-function relationship. Such analysis is currently challenging due to the diffraction-limited resolution of conventional light microscopy. We herein present an optical approach termed inverse spectroscopic optical coherence tomography to characterize the mass density fractality of chromatin, and we apply the technique to observe chromatin decompaction in live cells. The technique makes it possible for the first time, to our knowledge, to sense intracellular morphology with length-scale sensitivity from ∼30 to 450 nm, thus primarily probing the higher-order chromatin structure, without resolving the actual structures. We used chromatin decompaction due to inhibition of histone deacytelases and measured the subsequent changes in the fractal dimension of the intracellular structure. The results were confirmed by transmission electron microscopy and confocal fluorescence microscopy.

  7. 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.

  8. Persistent Chromatin Modifications Induced by High Fat Diet.

    Science.gov (United States)

    Leung, Amy; Trac, Candi; Du, Juan; Natarajan, Rama; Schones, Dustin E

    2016-05-13

    Obesity is a highly heritable complex disease that results from the interaction of multiple genetic and environmental factors. Formerly obese individuals are susceptible to metabolic disorders later in life, even after lifestyle changes are made to mitigate the obese state. This is reminiscent of the metabolic memory phenomenon originally observed for persistent complications in diabetic patients, despite subsequent glycemic control. Epigenetic modifications represent a potential mediator of this observed memory. We previously demonstrated that a high fat diet leads to changes in chromatin accessibility in the mouse liver. The regions of greatest chromatin changes in accessibility are largely strain-dependent, indicating a genetic component in diet-induced chromatin alterations. We have now examined the persistence of diet-induced chromatin accessibility changes upon diet reversal in two strains of mice. We find that a substantial fraction of loci that undergo chromatin accessibility changes with a high fat diet remains in the remodeled state after diet reversal in C57BL/6J mice. In contrast, the vast majority of diet-induced chromatin accessibility changes in A/J mice are transient. Our data also indicate that the persistent chromatin accessibility changes observed in C57BL/6J mice are associated with specific transcription factors and histone post-translational modifications. The persistent loci identified here are likely to be contributing to the overall phenotype and are attractive targets for therapeutic intervention.

  9. 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.

  10. 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.

  11. 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

    2015-02-18

    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 positioning, and

  12. Essential roles of Snf21, a Swi2/Snf2 family chromatin remodeler, in fission yeast mitosis.

    Science.gov (United States)

    Yamada, Kentaro; Hirota, Kouji; Mizuno, Ken-Ichi; Shibata, Takehiko; Ohta, Kunihiro

    2008-10-01

    ATP-dependent chromatin remodelers (ADCRs) convert local chromatin structure into both transcriptional active and repressive state. Recent studies have revealed that ADCRs play diverse regulatory roles in chromosomal events such as DNA repair and recombination. Here we have newly identified a fission yeast gene encoding a Swi2/Snf2 family ADCR. The amino acid sequence of this gene, snf21(+), implies that Snf21 is a fission yeast orthologue of the budding yeast Sth1, the catalytic core of the RSC chromatin remodeling complex. The snf21(+) gene product is a nuclear protein essential to cell viability: the null mutant cells stop growing after several rounds of cell divisions. A temperature sensitive allele of snf21(+), snf21-36 exhibits at non-permissive temperature (34 degrees C) a cell cycle arrest at G2-M phase and defects in chromosome segregation, thereby causing cell elongation, lack of cell growth, and death of some cell population. snf21-36 shows thiabendazole (TBZ) sensitivity even at permissive temperature (25 degrees C). The TBZ sensitivity becomes severer as snf21-36 is combined with the deletion of a centromere-localized Mad2 spindle checkpoint protein. The cell cycle arrest phenotype at 34 degrees C cannot be rescued by the mad2(+) deletion, although it is substantially alleviated at 30 degrees C in mad2Delta. These data suggest that Snf21 plays an essential role in mitosis possibly functioning in centromeric chromatin.

  13. 3D solutions of the Poisson-Vlasov equations for a charged plasma and particle-core model in a line of FODO cells

    Energy Technology Data Exchange (ETDEWEB)

    Turchetti, G.; Rambaldi, S.; Bazzani, A. [Dipartimento di Fisica and INFN, Via Irnerio 46, 40126, Bologna (Italy); Comunian, M.; Pisent, A. [INFN Laboratori Nazionali di Legnaro (Italy)

    2003-09-01

    We consider a charged plasma of positive ions in a periodic focusing channel of quadrupolar magnets in the presence of RF cavities. The ions are bunched into charged triaxial ellipsoids and their description requires the solution of a fully 3D Poisson-Vlasov equation. We also analyze the trajectories of test particles in the exterior of the ion bunches in order to estimate their diffusion rate. This rate is relevant for a high intensity linac (TRASCO project). A numerical PIC scheme to integrate the Poisson-Vlasov equations in a periodic focusing system in 2 and 3 space dimensions is presented. The scheme consists of a single particle symplectic integrator and a Poisson solver based on FFT plus tri-diagonal matrix inversion. In the 2D version arbitrary boundary conditions can be chosen. Since no analytical self-consistent 3D solution is known, we chose an initial Neuffer-KV distribution in phase space, whose electric field is close to the one generated by a uniformly filled ellipsoid. For a matched (periodic) beam the orbits of test particles moving in the field of an ellipsoidal bunch, whose semi-axis satisfy the envelope equations, is similar to the orbits generated by the self-consistent charge distribution obtained from the PIC simulation, even though it relaxes to a Fermi-Dirac-like distribution. After a transient the RMS radii and emittances have small amplitude oscillations. The PIC simulations for a mismatched (quasiperiodic) beam are no longer comparable with the ellipsoidal bunch model even though the qualitative behavior is the same, namely a stronger diffusion due to the increase of resonances. (orig.)

  14. Sperm chromatin structure and male fertility: biological and clinical aspects

    Institute of Scientific and Technical Information of China (English)

    J. Erenpreiss; M. Spano; J. Erenpreisa; M. Bungum; A. Giwercman

    2006-01-01

    Aim: Sperm chromatin/DNA integrity is essential for the accurate transmission of paternal genetic information, and normal sperm chromatin structure is important for sperm fertilizing ability. The routine examination of semen, which includes sperm concentration, motility and morphology, does not identify defects in sperm chromatin structure. The origin of sperm DNA damage and a variety of methods for its assessment are described. Evaluation of sperm DNA damage appears to be a useful tool for assessing male fertility potential both in vivo and in vitro. The possible impact of sperm DNA defects on the offspring is also discussed.

  15. Defective DNA repair and increased chromatin binding of DNA repair factors in Down syndrome fibroblasts.

    Science.gov (United States)

    Necchi, Daniela; Pinto, Antonella; Tillhon, Micol; Dutto, Ilaria; Serafini, Melania Maria; Lanni, Cristina; Govoni, Stefano; Racchi, Marco; Prosperi, Ennio

    2015-10-01

    Down syndrome (DS) is characterized by genetic instability, neurodegeneration, and premature aging. However, the molecular mechanisms leading to this phenotype are not yet well understood. Here, we report that DS fibroblasts from both fetal and adult donors show the presence of oxidative DNA base damage, such as dihydro-8-oxoguanine (8-oxodG), and activation of a DNA damage response (DDR), already during unperturbed growth conditions. DDR with checkpoint activation was indicated by histone H2AX and Chk2 protein phosphorylation, and by increased p53 protein levels. In addition, both fetal and adult DS fibroblasts were more sensitive to oxidative DNA damage induced by potassium bromate, and were defective in the removal of 8-oxodG, as compared with age-matched cells from control healthy donors. The analysis of core proteins participating in base excision repair (BER), such as XRCC1 and DNA polymerase β, showed that higher amounts of these factors were bound to chromatin in DS than in control cells, even in the absence of DNA damage. These findings occurred in concomitance with increased levels of phosphorylated XRCC1 detected in DS cells. These results indicate that DS cells exhibit a BER deficiency, which is associated with prolonged chromatin association of core BER factors.

  16. 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.

  17. 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.

  18. R-loop: an emerging regulator of chromatin dynamics

    Institute of Scientific and Technical Information of China (English)

    Qais Al-Hadid; Yanzhong Yang

    2016-01-01

    The dynamic structure of chromatin,which exists in two conformational states:heterochromatin and euchromatin,alters the accessibility of the DNA to regulatory factors during transcription,replication,recombination,and DNA damage repair.Chemical modifications of histones and DNA,as well as adenosine triphospahate-dependent nucleosome remodeling,have been the major focus of research on chromatin dynamics over the past two decades.However,recent studies using a DNA-RNA hybrid-specific antibody and next-generation seque,ncing approaches have revealed that the formation of R-loops,one of the most common non-canonical DNA structures,is an emerging regulator of chromatin states.This review focuses on recent insights into the interplay between R-loop formation and the epigenetic modifications of chromatin in normal and disease states.

  19. Control of chromatin structure by long noncoding RNA

    Science.gov (United States)

    Böhmdorfer, Gudrun; Wierzbicki, Andrzej T.

    2015-01-01

    Long noncoding RNA (lncRNA) is a pivotal factor regulating various aspects of genome activity. Genome regulation via DNA methylation and posttranslational histone modifications is a well-documented function of lncRNA in plants, fungi, and animals. Here, we summarize evidence showing that lncRNA also controls chromatin structure including nucleosome positioning and chromosome looping. We focus on data from plant experimental systems, discussed in the context of other eukaryotes. We explain the mechanisms of lncRNA-controlled chromatin remodeling and the implications of the functional interplay between noncoding transcription and several different chromatin remodelers. We propose that the unique properties of RNA make it suitable for controlling chromatin modifications and structure. PMID:26410408

  20. 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.

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

    Science.gov (United States)

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

    2012-07-01

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

  2. Chromatin remodeling and cancer, Part I: Covalent histone modifications.

    Science.gov (United States)

    Wang, Gang G; Allis, C David; Chi, Ping

    2007-09-01

    Dynamic chromatin remodeling underlies many, if not all, DNA-templated biological processes, including gene transcription; DNA replication and repair; chromosome condensation; and segregation and apoptosis. Disruption of these processes has been linked to the development and progression of cancer. The mechanisms of dynamic chromatin remodeling include the use of covalent histone modifications, histone variants, ATP-dependent complexes and DNA methylation. Together, these mechanisms impart variation into the chromatin fiber, and this variation gives rise to an 'epigenetic landscape' that extends the biological output of DNA alone. Here, we review recent advances in chromatin remodeling, and pay particular attention to mechanisms that appear to be linked to human cancer. Where possible, we discuss the implications of these advances for disease-management strategies.

  3. 动态优化环境下的群核进化粒子群优化方法%Swarm-Core Evolutionary Particle Swarm Optimization in Dynamic Optimization Environments

    Institute of Scientific and Technical Information of China (English)

    窦全胜; 周春光; 徐中宇; 潘冠宇

    2006-01-01

    粒子群优化方法是由Kennedy和Eberhart于1995年提出的一种基于群体智能(swarm intelligence)的进化计算技术.定义了"群核"(swarm-core)的概念,并在此基础上,提出了基于群核进化的粒子群优化方法(swarm-core evolutionary particle swarm optimization,SCEPSO),在SCEPSO方法中,为增强群体的优化能力,把群体分成了3个子群体,并且每个子群体有各自不同的"分工".同时研究了SCEPSO方法对连续变化的最优点的动态跟踪能力,在3种动态优化模型下进行了实验.实验结果表明,与传统PSO方法相比,SCEPSO方法能够可靠并精确地跟踪连续变化的全局最优解.

  4. Use of a small particle solid-core packing for improved efficiency and rapid measurement of sirolimus and everolimus by LC-MS/MS.

    Science.gov (United States)

    Morgan, Phillip; Nwafor, Magnus; Tredger, Mike

    2016-06-01

    Measurement of whole blood sirolimus and everolimus is required in order to optimize patient treatment following solid organ transplant. Assay by LC-MS/MS is increasingly preferred; however efficient use of the instrument and short turnaround times are crucial. Use of a 1.6 µm solid-core packing HPLC column (Cortecs) gave significant increases in efficiency, sensitivity and throughput compared with an existing method, following simple protein precipitation of small-volume (20 μL) whole blood samples. Sirolimus, everolimus and the stable isotopic internal standard ((13) C2 D4 - everolimus) eluted at around 0.8 min, and total analytical run time was 2.2 min, saving almost 4 min per sample compared with an existing method. Within-assay imprecision (CV) was 3.3-8.5%, and between-assay imprecision was 2.2-10.8%. Retrospective assay of external quality assurance samples and comparison of patient samples assayed in parallel showed only small differences (between +6.8 and -1.9%) in results using the Cortecs column when compared with the existing method. No significant interferences or ion suppression were observed. Copyright © 2015 John Wiley & Sons, Ltd.

  5. Synthesis and drug-loading properties of folic acid-modified superparamagnetic Fe3O4 hollow microsphere core/mesoporous SiO2 shell composite particles

    Science.gov (United States)

    Yang, Yong; Guo, Xue; Wei, Kaiwei; Wang, Lijuan; Yang, Dandan; Lai, Lifang; Cheng, Meiling; Liu, Qi

    2014-01-01

    A drug delivery system, which not only has superparamagnetic property, higher surface area but also has targeting function, has been developed. The core/shell structural magnetic magnetite mesoporous silica microspheres with amine groups (Fe3O4-SiO2-NH2) were first fabricated by a one-pot direct co-condensation method, then folic acid-modified magnetic mesoporous silica composite microspheres (Fe3O4-SiO2-NHFA) were obtained by the bonding of the Fe3O4-SiO2-NH2 with folic acid as targeted molecule. The resultant composite microspheres were characterized by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, scanning electron microscopy, low temperature nitrogen adsorption-desorption, and vibrating sample magnetometer. A well-known inflammational drug ibuprofen was used as a model drug to assess the loading and releasing behavior of the composite microspheres. Fe3O4-SiO2-NHFA system exhibits magnetic properties typical for superparamagnetic material with a higher saturation magnetization value of about 41.2 emu/g and has better capacity of drug storage (32.0 %) and sustained drug-release property. So this system has potential applications in biomedical field.

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

    Science.gov (United States)

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

    2013-01-01

    In order to survive, cells have evolved highly effective repair mechanisms to deal with the potentially lethal DNA damage produced by exposure to endogenous as well as exogenous agents. Ionizing radiation exposure induces highly lethal DNA damage, especially DNA double-strand breaks (DSBs), that is sensed by the cellular machinery and then subsequently repaired by either of two different DSB repair mechanisms: (1) non-homologous end joining, which re-ligates the broken ends of the DNA and (2) homologous recombination, that employs an undamaged identical DNA sequence as a template, to maintain the fidelity of DNA repair. Repair of DSBs must occur within the natural context of the cellular DNA which, along with specific proteins, is organized to form chromatin, the overall structure of which can impede DNA damage site access by repair proteins. The chromatin complex is a dynamic structure and is known to change as required for ongoing cellular processes such as gene transcription or DNA replication. Similarly, during the process of DNA damage sensing and repair, chromatin needs to undergo several changes in order to facilitate accessibility of the repair machinery. Cells utilize several factors to modify the chromatin in order to locally open up the structure to reveal the underlying DNA sequence but post-translational modification of the histone components is one of the primary mechanisms. In this review, we will summarize chromatin modifications by the respective chromatin modifying factors that occur during the DNA damage response. PMID:23346550

  7. Ectopically tethered CP190 induces large-scale chromatin decondensation

    Science.gov (United States)

    Ahanger, Sajad H.; Günther, Katharina; Weth, Oliver; Bartkuhn, Marek; Bhonde, Ramesh R.; Shouche, Yogesh S.; Renkawitz, Rainer

    2014-01-01

    Insulator mediated alteration in higher-order chromatin and/or nucleosome organization is an important aspect of epigenetic gene regulation. Recent studies have suggested a key role for CP190 in such processes. In this study, we analysed the effects of ectopically tethered insulator factors on chromatin structure and found that CP190 induces large-scale decondensation when targeted to a condensed lacO array in mammalian and Drosophila cells. In contrast, dCTCF alone, is unable to cause such a decondensation, however, when CP190 is present, dCTCF recruits it to the lacO array and mediates chromatin unfolding. The CP190 induced opening of chromatin may not be correlated with transcriptional activation, as binding of CP190 does not enhance luciferase activity in reporter assays. We propose that CP190 may mediate histone modification and chromatin remodelling activity to induce an open chromatin state by its direct recruitment or targeting by a DNA binding factor such as dCTCF.

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Elizabeth A Rach

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

  11. Chromatin and Nucleosome Organizations and DNA Replication of Nucleus Reassembled in vitro Using Purified Exogenous DNA and Xenopus Egg Extracts

    Institute of Scientific and Technical Information of China (English)

    张传茂; 张博; 翟中和

    1994-01-01

    It has been demonstrated in the last ten years that the nuclear reassembly may occur in the cell-free systems from frog egg extracts added with exogenous naked DNA. However, there remains an open question : is the cell-free reassembled nucleus structurally similar to the nucleus in the intact cell ? That is, does the cell-free reassembled nucleus contain nucleosomes and chromatin? For this issue, we have designed experiments for identifying the internal structures of the cell-free reassembled nucleus. These experiments show that the nucleus reassembled in vitro also contains chromatin which is composed of typical 10 nm nucleosome fibers of "beads-on-a-string", 30 nm filaments and the next higher-order structures. The digestion experiment with the enzyme micrococcal nuclease has demonstrated that the DNA in the nucleosome of the reconstituted chromatin is about 200 base pairs (bp) in length, of which 165 bp may be in the nucleosome particle, and 35 bp may be in the linker between two particles. Prolongin

  12. The dynamics of individual nucleosomes controls the chromatin condensation pathway: direct AFM visualization of variant chromatin

    CERN Document Server

    Montel, Fabien; Castelnovo, Martin; Bednar, Jan; Dimitrov, Stefan; Angelov, Dimitar; Faivre-Moskalenko, Cendrine

    2009-01-01

    Chromatin organization and dynamics is studied in this work at scales ranging from single nucleosome to nucleosomal array by using a unique combination of biochemical assays, single molecule imaging technique and numerical modeling. We demonstrate that a subtle modification in the nucleosome structure induced by the histone variant H2A.Bbd drastically modifies the higher order organization of the nucleosomal arrays. Importantly, as directly visualized by AFM, conventional H2A nucleosomal arrays exhibit specific local organization, in contrast to H2A.Bbd arrays, which show ?beads on a string? structure. The combination of systematic image analysis and theoretical modeling allows a quantitative description relating the observed gross structural changes of the arrays to their local organization. Our results strongly suggest that higher-order organization of H1-free nucleosomal arrays is mainly determined by the fluctuation properties of individual nucleosomes. Moreover, numerical simulations suggest the existenc...

  13. 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.

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

    Science.gov (United States)

    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, 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

  15. Chromatin dynamics at DNA breaks: what, how and why?

    Directory of Open Access Journals (Sweden)

    Théo Lebeaupin

    2015-09-01

    Full Text Available Chromatin has a complex, dynamic architecture in the interphase nucleus, which regulates the accessibility of the underlying DNA and plays a key regulatory role in all the cellular functions using DNA as a template, such as replication, transcription or DNA damage repair. Here, we review the recent progresses in the understanding of the interplay between chromatin architecture and DNA repair mechanisms. Several reports based on live cell fluorescence imaging show that the activation of the DNA repair machinery is associated with major changes in the compaction state and the mobility of chromatin. We discuss the functional consequences of these changes in yeast and mammals in the light of the different repair pathways utilized by these organisms. In the final section of this review, we show how future developments in high-resolution light microscopy and chromatin modelling by polymer physics should contribute to a better understanding of the relationship between the structural changes in chromatin and the activity of the repair processes.

  16. Chromatin Modifications and the DNA Damage Response to Ionizing Radiation

    Directory of Open Access Journals (Sweden)

    Tej K Pandita

    2013-01-01

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

  17. 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...

  18. Core BPEL

    DEFF Research Database (Denmark)

    Hallwyl, Tim; Højsgaard, Espen

    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......, does not allow omissions, and does not contain ignorable elements. We do so by identifying syntactic sugar, including default values, and ignorable elements in WS-BPEL. The analysis results in a translation from the full language to the core subset. Thus, we reduce the effort needed for working...... formally with WS-BPEL, as one, without loss of generality, need only consider the much simpler Core BPEL. This report may also be viewed as an addendum to the WS-BPEL standard specification, which clarifies the WS-BPEL syntax and presents the essential elements of the language in a more concise way...

  19. RSC Chromatin-Remodeling Complex Is Important for Mitochondrial Function in Saccharomyces cerevisiae.

    Science.gov (United States)

    Imamura, Yuko; Yu, Feifei; Nakamura, Misaki; Chihara, Yuhki; Okane, Kyo; Sato, Masahiro; Kanai, Muneyoshi; Hamada, Ryoko; Ueno, Masaru; Yukawa, Masashi; Tsuchiya, Eiko

    2015-01-01

    RSC (Remodel the Structure of Chromatin) is an ATP-dependent chromatin remodeling complex essential for the growth of Saccharomyces cerevisiae. RSC exists as two distinct isoforms that share core subunits including the ATPase subunit Nps1/Sth1 but contain either Rsc1or Rsc2. Using the synthetic genetic array (SGA) of the non-essential null mutation method, we screened for mutations exhibiting synthetic growth defects in combination with the temperature-sensitive mutant, nps1-105, and found connections between mitochondrial function and RSC. rsc mutants, including rsc1Δ, rsc2Δ, and nps1-13, another temperature-sensitive nps1 mutant, exhibited defective respiratory growth; in addition, rsc2Δ and nps1-13 contained aggregated mitochondria. The rsc2Δ phenotypes were relieved by RSC1 overexpression, indicating that the isoforms play a redundant role in respiratory growth. Genome-wide expression analysis in nps1-13 under respiratory conditions suggested that RSC regulates the transcription of some target genes of the HAP complex, a transcriptional activator of respiratory gene expression. Nps1 physically interacted with Hap4, the transcriptional activator moiety of the HAP complex, and overexpression of HAP4 alleviated respiratory defects in nps1-13, suggesting that RSC plays pivotal roles in mitochondrial gene expression and shares a set of target genes with the HAP complex.

  20. Non-immunospecific association of immunoglobulin G with chromatin during elution from protein A inflates host contamination, aggregate content, and antibody loss.

    Science.gov (United States)

    Gagnon, Pete; Nian, Rui; Yang, Yuansheng; Yang, Qiaohui; Lim, Chiew Ling

    2015-08-21

    Monoclonal IgG at pH 3.5 expressed a tendency to self-associate and associate non-specifically with surfaces, including the surfaces of precipitated chromatin heteroaggregates. The tendency was elevated with protein A-eluted IgG still in elution buffer (100mM acetate, pH 3.5). Association of IgG with chromatin elements under protein A elution conditions amplified host protein contamination of the elution fraction about 15-fold, caused formation of aggregates that persisted after pH neutralization, and imposed an approximate 5% loss on IgG recovery. Neutralization released eluted IgG from its low pH associations with chromatin and caused heteroaggregate remnants to associate into large particles easily removed by microfiltration. Most effective host contaminant clearance was achieved by filtration after neutralization to pH 5.5. All chromatin-mediated liabilities were suspended by extraction of chromatin heteroaggregates in advance of protein A.

  1. Spatial organization of chromatin domains and compartments in single chromosomes.

    Science.gov (United States)

    Wang, Siyuan; Su, Jun-Han; Beliveau, Brian J; Bintu, Bogdan; Moffitt, Jeffrey R; Wu, Chao-ting; Zhuang, Xiaowei

    2016-08-05

    The spatial organization of chromatin critically affects genome function. Recent chromosome-conformation-capture studies have revealed topologically associating domains (TADs) as a conserved feature of chromatin organization, but how TADs are spatially organized in individual chromosomes remains unknown. Here, we developed an imaging method for mapping the spatial positions of numerous genomic regions along individual chromosomes and traced the positions of TADs in human interphase autosomes and X chromosomes. We observed that chromosome folding deviates from the ideal fractal-globule model at large length scales and that TADs are largely organized into two compartments spatially arranged in a polarized manner in individual chromosomes. Active and inactive X chromosomes adopt different folding and compartmentalization configurations. These results suggest that the spatial organization of chromatin domains can change in response to regulation.

  2. Interplay of Dynamic Transcription and Chromatin Remodeling: Lessons from Yeast

    Directory of Open Access Journals (Sweden)

    Eva Klopf

    2011-07-01

    Full Text Available Regulation of transcription involves dynamic rearrangements of chromatin structure. The budding yeast Saccharomyces cerevisiae has a variety of highly conserved factors necessary for these reconstructions. Chromatin remodelers, histone modifiers and histone chaperones directly associate to promoters and open reading frames of exposed genes and facilitate activation and repression of transcription. We compare two distinct patterns of induced transcription: Sustained transcribed genes switch to an activated state where they remain as long as the induction signal is present. In contrast, single pulsed transcribed genes show a quick and strong induction pulse resulting in high transcript levels followed by adaptation and repression to basal levels. We discuss intensively studied promoters and coding regions from both groups for their co-factor requirements during transcription. Interplay between chromatin restructuring factors and dynamic transcription is highly variable and locus dependent.

  3. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis.

    Science.gov (United States)

    Hu, Jialei; Donahue, Greg; Dorsey, Jean; Govin, Jérôme; Yuan, Zuofei; Garcia, Benjamin A; Shah, Parisha P; Berger, Shelley L

    2015-12-01

    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.

  4. 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.

  5. 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.

  6. Human pescadillo induces large-scale chromatin unfolding

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hao; FANG Yan; HUANG Cuifen; YANG Xiao; YE Qinong

    2005-01-01

    The human pescadillo gene encodes a protein with a BRCT domain. Pescadillo plays an important role in DNA synthesis, cell proliferation and transformation. Since BRCT domains have been shown to induce chromatin large-scale unfolding, we tested the role of Pescadillo in regulation of large-scale chromatin unfolding. To this end, we isolated the coding region of Pescadillo from human mammary MCF10A cells. Compared with the reported sequence, the isolated Pescadillo contains in-frame deletion from amino acid 580 to 582. Targeting the Pescadillo to an amplified, lac operator-containing chromosome region in the mammalian genome results in large-scale chromatin decondensation. This unfolding activity maps to the BRCT domain of Pescadillo. These data provide a new clue to understanding the vital role of Pescadillo.

  7. Absence of canonical active chromatin marks in developmentally regulated genes

    Science.gov (United States)

    Ruiz-Romero, Marina; Corominas, Montserrat; Guigó, Roderic

    2015-01-01

    The interplay of active and repressive histone modifications is assumed to play a key role in the regulation of gene expression. In contrast to this generally accepted view, we show that transcription of genes temporally regulated during fly and worm development occurs in the absence of canonically active histone modifications. Conversely, strong chromatin marking is related to transcriptional and post-transcriptional stability, an association that we also observe in mammals. Our results support a model in which chromatin marking is associated to stable production of RNA, while unmarked chromatin would permit rapid gene activation and de-activation during development. In this case, regulation by transcription factors would play a comparatively more important regulatory role. PMID:26280901

  8. TALE proteins bind to both active and inactive chromatin.

    Science.gov (United States)

    Scott, James N F; Kupinski, Adam P; Kirkham, Christopher M; Tuma, Roman; Boyes, Joan

    2014-02-15

    TALE (transcription activator-like effector) proteins can be tailored to bind to any DNA sequence of choice and thus are of immense utility for genome editing and the specific delivery of transcription activators. However, to perform these functions, they need to occupy their sites in chromatin. In the present study, we have systematically assessed TALE binding to chromatin substrates and find that in vitro TALEs bind to their target site on nucleosomes at the more accessible entry/exit sites, but not at the nucleosome dyad. We show further that in vivo TALEs bind to transcriptionally repressed chromatin and that transcription increases binding by only 2-fold. These data therefore imply that TALEs are likely to bind to their target in vivo even at inactive loci.

  9. The telomere binding protein TRF2 induces chromatin compaction.

    Directory of Open Access Journals (Sweden)

    Asmaa M Baker

    Full Text Available Mammalian telomeres are specialized chromatin structures that require the telomere binding protein, TRF2, for maintaining chromosome stability. In addition to its ability to modulate DNA repair activities, TRF2 also has direct effects on DNA structure and topology. Given that mammalian telomeric chromatin includes nucleosomes, we investigated the effect of this protein on chromatin structure. TRF2 bound to reconstituted telomeric nucleosomal fibers through both its basic N-terminus and its C-terminal DNA binding domain. Analytical agarose gel electrophoresis (AAGE studies showed that TRF2 promoted the folding of nucleosomal arrays into more compact structures by neutralizing negative surface charge. A construct containing the N-terminal and TRFH domains together altered the charge and radius of nucleosomal arrays similarly to full-length TRF2 suggesting that TRF2-driven changes in global chromatin structure were largely due to these regions. However, the most compact chromatin structures were induced by the isolated basic N-terminal region, as judged by both AAGE and atomic force microscopy. Although the N-terminal region condensed nucleosomal array fibers, the TRFH domain, known to alter DNA topology, was required for stimulation of a strand invasion-like reaction with nucleosomal arrays. Optimal strand invasion also required the C-terminal DNA binding domain. Furthermore, the reaction was not stimulated on linear histone-free DNA. Our data suggest that nucleosomal chromatin has the ability to facilitate this activity of TRF2 which is thought to be involved in stabilizing looped telomere structures.

  10. Dicer is associated with ribosomal DNA chromatin in mammalian cells.

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    Lasse Sinkkonen

    Full Text Available BACKGROUND: RNA silencing is a common term for pathways utilizing small RNAs as sequence-specific guides to repress gene expression. Components of the RNA silencing machinery are involved in different aspects of chromatin function in numerous organisms. However, association of RNA silencing with chromatin in mammalian cells remains unclear. METHODOLOGY/PRINCIPAL FINDINGS: Immunostaining of mitotic chromosomes with antibodies visualizing either endogenous or ectopically expressed Dicer in mammalian cells revealed association of the protein with ribosomal DNA (rDNA repeats. Chromatin immunoprecipitations and bisulfite sequencing experiments indicated that Dicer is associated with transcribed regions of both active and silenced genes in rDNA arrays of interphase chromosomes. Metabolic labeling of the mouse embryonic stem (ES cells lacking Dicer did not reveal apparent defect in rRNA biogenesis though pre-rRNA synthesis in these cells was decreased, likely as a consequence of their slower growth caused by the loss of miRNAs. We analyzed in detail chromatin structure of rDNA but did not find any epigenetic changes at rDNA loci in Dicer(-/- ES cells. Instead, we found that rDNA methylation is rather low in primary tissues, contrasting with rDNA methylation patterns in transformed cell lines. CONCLUSION/SIGNIFICANCE: We found that Dicer, a key component of RNA silencing pathways, can be detected in association with rDNA chromatin in mammalian cells. The role of this particular localization of Dicer is not readily apparent since the enzyme is associated with rDNA genes regardless of their transcriptional activity. However, localization of Dicer to the transcribed region suggests that transcription may contribute to the Dicer deposition at rDNA chromatin. We hypothesize that Dicer functions in maintaining integrity of rDNA arrays.

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

    Science.gov (United States)

    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 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 across a broad range of

  12. 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

  13. Chromatin structure and evolution in the human genome

    Directory of Open Access Journals (Sweden)

    Dunlop Malcolm G

    2007-05-01

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

  14. SANS spectra of the fractal supernucleosomal chromatin structure models

    Science.gov (United States)

    Ilatovskiy, Andrey V.; Lebedev, Dmitry V.; Filatov, Michael V.; Petukhov, Michael G.; Isaev-Ivanov, Vladimir V.

    2012-03-01

    The eukaryotic genome consists of chromatin—a nucleoprotein complex with hierarchical architecture based on nucleosomes, the organization of higher-order chromatin structures still remains unknown. Available experimental data, including SANS spectra we had obtained for whole nuclei, suggested fractal nature of chromatin. Previously we had built random-walk supernucleosomal models (up to 106 nucleosomes) to interpret our SANS spectra. Here we report a new method to build fractal supernucleosomal structure of a given fractal dimension or two different dimensions. Agreement between calculated and experimental SANS spectra was significantly improved, especially for model with two fractal dimensions—3 and 2.

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

    Science.gov (United States)

    Lieberman, Paul M

    2015-01-01

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

  16. Chromatin modifications, epigenetics, and how protozoan parasites regulate their lives.

    Science.gov (United States)

    Croken, Matthew M; Nardelli, Sheila C; Kim, Kami

    2012-05-01

    Chromatin structure plays a vital role in epigenetic regulation of protozoan parasite gene expression. Epigenetic gene regulation impacts upon parasite virulence, differentiation and cell-cycle control. Recent work in many laboratories has elucidated the functions of proteins that regulate parasite gene expression by chemical modification of constituent nucleosomes. A major focus of investigation has been the characterization of post-translational modifications (PTMs) of histones and the identification of the enzymes responsible. Despite conserved features and specificity common to all eukaryotes, parasite enzymes involved in chromatin modification have unique functions that regulate unique aspects of parasite biology.

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

    Science.gov (United States)

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

    2006-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Bo eDing

    2015-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Andreas H Ehrensberger

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

  20. Instability of trinucleotidic repeats during chromatin remodeling in spermatids.

    Science.gov (United States)

    Simard, Olivier; Grégoire, Marie-Chantal; Arguin, Mélina; Brazeau, Marc-André; Leduc, Frédéric; Marois, Isabelle; Richter, Martin V; Boissonneault, Guylain

    2014-11-01

    Transient DNA breaks and evidence of DNA damage response have recently been reported during the chromatin remodeling process in haploid spermatids, creating a potential window of enhanced genetic instability. We used flow cytometry to achieve separation of differentiating spermatids into four highly purified populations using transgenic mice harboring 160 CAG repeats within exon 1 of the human Huntington disease gene (HTT). Trinucleotic repeat expansion was found to occur immediately following the chromatin remodeling steps, confirming the genetic instability of the process and pointing to the origin of paternal anticipation observed in some trinucleotidic repeats diseases.

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

    DEFF Research Database (Denmark)

    Laugesen, Anne; Helin, Kristian

    2014-01-01

    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......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...... complexes in modulating thresholds for gene activation and their importance for specification and maintenance of cell fate....

  2. The importance of topoisomerases for chromatin regulated genes

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  3. BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization.

    Science.gov (United States)

    Orvis, Tess; Hepperla, Austin; Walter, Vonn; Song, Shujie; Simon, Jeremy; Parker, Joel; Wilkerson, Matthew D; Desai, Nisarg; Major, Michael B; Hayes, D Neil; Davis, Ian J; Weissman, Bernard

    2014-11-15

    SWI/SNF chromatin remodeling complexes regulate critical cellular processes, including cell-cycle control, programmed cell death, differentiation, genomic instability, and DNA repair. Inactivation of this class of chromatin remodeling complex has been associated with a variety of malignancies, including lung, ovarian, renal, liver, and pediatric cancers. In particular, approximately 10% of primary human lung non-small cell lung cancers (NSCLC) display attenuations in the BRG1 ATPase, a core factor in SWI/SNF complexes. To evaluate the role of BRG1 attenuation in NSCLC development, we examined the effect of BRG1 silencing in primary and established human NSCLC cells. BRG1 loss altered cellular morphology and increased tumorigenic potential. Gene expression analyses showed reduced expression of genes known to be associated with progression of human NSCLC. We demonstrated that BRG1 losses in NSCLC cells were associated with variations in chromatin structure, including differences in nucleosome positioning and occupancy surrounding transcriptional start sites of disease-relevant genes. Our results offer direct evidence that BRG1 attenuation contributes to NSCLC aggressiveness by altering nucleosome positioning at a wide range of genes, including key cancer-associated genes.

  4. The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism.

    Science.gov (United States)

    Parnell, Timothy J; Schlichter, Alisha; Wilson, Boris G; Cairns, Bradley R

    2015-01-01

    ISWI family chromatin remodelers typically organize nucleosome arrays, while SWI/SNF family remodelers (RSC) typically disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex or mutations in the 'basic patch' of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism and reveal different mechanisms at two different promoter architectures.

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

    Directory of Open Access Journals (Sweden)

    Nadine Schuler

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

  6. 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.

  7. Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization

    Directory of Open Access Journals (Sweden)

    Peterhansel Christoph

    2007-09-01

    Full Text Available Abstract Background Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. A very useful technique to study these processes is chromatin immunoprecipitation (ChIP. ChIP is widely used for a few model systems, including Arabidopsis, but establishment of the technique for other organisms is still remarkably challenging. Furthermore, quantitative analysis of the precipitated material and normalization of the data is often underestimated, negatively affecting data quality. Results We developed a robust ChIP protocol, using maize (Zea mays as a model system, and present a general strategy to systematically optimize this protocol for any type of tissue. We propose endogenous controls for active and for repressed chromatin, and discuss various other controls that are essential for successful ChIP experiments. We experienced that the use of quantitative PCR (QPCR is crucial for obtaining high quality ChIP data and we explain why. The method of data normalization has a major impact on the quality of ChIP analyses. Therefore, we analyzed different normalization strategies, resulting in a thorough discussion of the advantages and drawbacks of the various approaches. Conclusion Here we provide a robust ChIP protocol and strategy to optimize the protocol for any type of tissue; we argue that quantitative real-time PCR (QPCR is the best method to analyze the precipitates, and present comprehensive insights into data normalization.

  8. Chromatin Structure in Cell Differentiation, Aging and Cancer

    NARCIS (Netherlands)

    S. Kheradmand Kia (Sima)

    2009-01-01

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

  9. 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...

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

    NARCIS (Netherlands)

    Kornet, N.G.

    2008-01-01

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

  11. 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

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

    Directory of Open Access Journals (Sweden)

    Sascha eBeneke

    2012-09-01

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

  13. Is chromatin remodeling required to build sister-chromatid cohesion?

    NARCIS (Netherlands)

    Riedel, Christian G; Gregan, Juraj; Gruber, Stephan; Nasmyth, Kim

    2004-01-01

    Chromosome segregation during mitosis and meiosis depends on the linkage of sister DNA molecules after replication. These links, known as sister-chromatid cohesion, are provided by a multi-subunit complex called cohesin. Recent papers suggest that chromatin-remodeling complexes also have a role in t

  14. Functional Insights into Chromatin Remodelling from Studies on CHARGE Syndrome

    NARCIS (Netherlands)

    Basson, M. Albert; van Ravenswaaij-Arts, Conny

    2015-01-01

    CHARGE syndrome is a rare genetic syndrome characterised by a unique combination of multiple organ anomalies. Dominant loss-of-function mutations in the gene encoding chromodomain helicase DNA binding protein 7 (CHD7), which is an ATP-dependent chromatin remodeller, have been identified as the cause

  15. Trichomonas vaginalis: chromatin and mitotic spindle during mitosis.

    Science.gov (United States)

    Gómez-Conde, E; Mena-López, R; Hernández-Jaúregui, P; González-Camacho, M; Arroyo, R

    2000-11-01

    The mitotic phases and the changes that the chromatin and mitotic microtubules undergo during mitosis in the sexually transmitted parasite Trichomonas vaginalis are described. Parasites arrested in the gap 2 phase of the cell cycle by nutrient starvation were induced to mitosis by addition of fresh whole medium. [(3)H] Thymidine labeling of trichomonad parasites for 24 h showed that parasites have at least four synchronic duplications after mitosis induction. Fixed or live and acridine orange (AO)-stained trichomonads analyzed at different times during mitosis by epifluorescence microscopy showed that mitosis took about 45 min and is divided into five stages: prophase, metaphase, early and late anaphase, early and late telophase, and cytokinesis. The AO-stained nucleus of live trichomonads showed green (DNA) and orange (RNA) fluorescence, and the nucleic acid nature was confirmed by DNase and RNase treatment, respectively. The chromatin appeared partially condensed during interphase. At metaphase, it appeared as six condensed chromosomes, as recently reported, which decondensed at anaphase and migrated to the nuclear poles at telophase. In addition, small bundles of microtubules (as hemispindles) were detected only in metaphase with the polyclonal antibody anti-Entamoeba histolytica alpha-tubulin. This antibody showed that the hemispindle and an atractophore-like structure seem to duplicate and polarize during metaphase. In conclusion, T. vaginalis mitosis involves five mitotic phases in which the chromatin undergoes different degrees of condensation, from chromosomes to decondensed chromatin, and two hemispindles that are observed only in the metaphase stage.

  16. Discovering enhancers by mapping chromatin features in primary tissue.

    Science.gov (United States)

    Bowman, Sarah K

    2015-09-01

    Enhancers work with promoters to refine the timing, location, and level of gene expression. As they perform these functions, active enhancers generate a chromatin environment that is distinct from other areas of the genome. Therefore, profiling enhancer-associated chromatin features can produce genome-wide maps of potential regulatory elements. This review focuses on current technologies used to produce maps of potential tissue-specific enhancers by profiling chromatin from primary tissue. First, cells are separated from whole organisms either by affinity purification, automated cell sorting, or microdissection. Isolating the tissue prior to analysis ensures that the molecular signature of active enhancers will not become lost in an averaged signal from unrelated cell types. After cell isolation, the molecular feature that is profiled will depend on the abundance and quality of the harvested material. The combination of tissue isolation plus genome-wide chromatin profiling has successfully identified enhancers in several pioneering studies. In the future, the regulatory apparatus of healthy and diseased tissues will be explored in this manner, as researchers use the combined techniques to gain insight into how active enhancers may influence disease progression.

  17. The N-terminus of murine leukaemia virus p12 protein is required for mature core stability.

    Directory of Open Access Journals (Sweden)

    Darren J Wight

    2014-10-01

    Full Text Available The murine leukaemia virus (MLV gag gene encodes a small protein called p12 that is essential for the early steps of viral replication. The N- and C-terminal regions of p12 are sequentially acting domains, both required for p12 function. Defects in the C-terminal domain can be overcome by introducing a chromatin binding motif into the protein. However, the function of the N-terminal domain remains unknown. Here, we undertook a detailed analysis of the effects of p12 mutation on incoming viral cores. We found that both reverse transcription complexes and isolated mature cores from N-terminal p12 mutants have altered capsid complexes compared to wild type virions. Electron microscopy revealed that mature N-terminal p12 mutant cores have different morphologies, although immature cores appear normal. Moreover, in immunofluorescent studies, both p12 and capsid proteins were lost rapidly from N-terminal p12 mutant viral cores after entry into target cells. Importantly, we determined that p12 binds directly to the MLV capsid lattice. However, we could not detect binding of an N-terminally altered p12 to capsid. Altogether, our data imply that p12 stabilises the mature MLV core, preventing premature loss of capsid, and that this is mediated by direct binding of p12 to the capsid shell. In this manner, p12 is also retained in the pre-integration complex where it facilitates tethering to mitotic chromosomes. These data also explain our previous observations that modifications to the N-terminus of p12 alter the ability of particles to abrogate restriction by TRIM5alpha and Fv1, factors that recognise viral capsid lattices.

  18. The N-Terminus of Murine Leukaemia Virus p12 Protein Is Required for Mature Core Stability

    Science.gov (United States)

    Wight, Darren J.; Boucherit, Virginie C.; Wanaguru, Madushi; Elis, Efrat; Hirst, Elizabeth M. A.; Li, Wilson; Ehrlich, Marcelo; Bacharach, Eran; Bishop, Kate N.

    2014-01-01

    The murine leukaemia virus (MLV) gag gene encodes a small protein called p12 that is essential for the early steps of viral replication. The N- and C-terminal regions of p12 are sequentially acting domains, both required for p12 function. Defects in the C-terminal domain can be overcome by introducing a chromatin binding motif into the protein. However, the function of the N-terminal domain remains unknown. Here, we undertook a detailed analysis of the effects of p12 mutation on incoming viral cores. We found that both reverse transcription complexes and isolated mature cores from N-terminal p12 mutants have altered capsid complexes compared to wild type virions. Electron microscopy revealed that mature N-terminal p12 mutant cores have different morphologies, although immature cores appear normal. Moreover, in immunofluorescent studies, both p12 and capsid proteins were lost rapidly from N-terminal p12 mutant viral cores after entry into target cells. Importantly, we determined that p12 binds directly to the MLV capsid lattice. However, we could not detect binding of an N-terminally altered p12 to capsid. Altogether, our data imply that p12 stabilises the mature MLV core, preventing premature loss of capsid, and that this is mediated by direct binding of p12 to the capsid shell. In this manner, p12 is also retained in the pre-integration complex where it facilitates tethering to mitotic chromosomes. These data also explain our previous observations that modifications to the N-terminus of p12 alter the ability of particles to abrogate restriction by TRIM5alpha and Fv1, factors that recognise viral capsid lattices. PMID:25356837

  19. Material with core-shell structure

    Science.gov (United States)

    Luhrs, Claudia; Richard, Monique N.; Dehne, Aaron; Phillips, Jonathan; Stamm, Kimber L.; Fanson, Paul T.

    2011-11-15

    Disclosed is a material having a composite particle, the composite particle including an outer shell and a core. The core is made from a lithium alloying material and the outer shell has an inner volume that is greater in size than the core of the lithium alloying material. In some instances, the outer mean diameter of the outer shell is less than 500 nanometers and the core occupies between 5 and 99% of the inner volume. In addition, the outer shell can have an average wall thickness of less than 100 nanometers.

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

    OpenAIRE

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

    2012-01-01

    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 wi...

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

    OpenAIRE

    Nicholas C. Gomez; Austin J. Hepperla; Raluca Dumitru; Jeremy M. Simon; Fang Fang; Ian J. Davis

    2016-01-01

    Chromatin regulation is critical for differentiation and disease. However, features linking the chromatin environment of stem cells with disease remain largely unknown. We explored chromatin accessibility in embryonic and multipotent stem cells and unexpectedly identified widespread chromatin accessibility at repetitive elements. Integrating genomic and biochemical approaches, we demonstrate that these sites of increased accessibility are associated with well-positioned nucleosomes marked by ...

  2. The ING tumor suppressors in cellular senescence and chromatin.

    Science.gov (United States)

    Ludwig, Susann; Klitzsch, Alexandra; Baniahmad, Aria

    2011-07-18

    The Inhibitor of Growth (ING) proteins represent a type II tumor suppressor family comprising five conserved genes, ING1 to ING5. While ING1, ING2 and ING3 proteins are stable components of the mSIN3a-HDAC complexes, the association of ING1, ING4 and ING5 with HAT protein complexes was also reported. Among these the ING1 and ING2 have been analyzed more deeply. Similar to other tumor suppressor factors the ING proteins are also involved in many cellular pathways linked to cancer and cell proliferation such as cell cycle regulation, cellular senescence, DNA repair, apoptosis, inhibition of angiogenesis and modulation of chromatin.A common structural feature of ING factors is the conserved plant homeodomain (PHD), which can bind directly to the histone mark trimethylated lysine of histone H3 (H3K4me3). PHD mutants lose the ability to undergo cellular senescence linking chromatin mark recognition with cellular senescence. ING1 and ING2 are localized in the cell nucleus and associated with chromatin modifying enzymes, linking tumor suppression directly to chromatin regulation. In line with this, the expression of ING1 in tumors is aberrant or identified point mutations are mostly localized in the PHD finger and affect histone binding. Interestingly, ING1 protein levels increase in replicative senescent cells, latter representing an efficient pathway to inhibit cancer proliferation. In association with this, suppression of p33ING1 expression prolongs replicative life span and is also sufficient to bypass oncogene-induced senescence. Recent analyses of ING1- and ING2-deficient mice confirm a tumor suppressive role of ING1 and ING2 and also indicate an essential role of ING2 in meiosis.Here we summarize the activity of ING1 and ING2 as tumor suppressors, chromatin factors and in development.

  3. Modeling Core Collapse Supernovae

    Science.gov (United States)

    Mezzacappa, Anthony

    2017-01-01

    Core collapse supernovae, or the death throes of massive stars, are general relativistic, neutrino-magneto-hydrodynamic events. The core collapse supernova mechanism is still not in hand, though key components have been illuminated, and the potential for multiple mechanisms for different progenitors exists. Core collapse supernovae are the single most important source of elements in the Universe, and serve other critical roles in galactic chemical and thermal evolution, the birth of neutron stars, pulsars, and stellar mass black holes, the production of a subclass of gamma-ray bursts, and as potential cosmic laboratories for fundamental nuclear and particle physics. Given this, the so called ``supernova problem'' is one of the most important unsolved problems in astrophysics. It has been fifty years since the first numerical simulations of core collapse supernovae were performed. Progress in the past decade, and especially within the past five years, has been exponential, yet much work remains. Spherically symmetric simulations over nearly four decades laid the foundation for this progress. Two-dimensional modeling that assumes axial symmetry is maturing. And three-dimensional modeling, while in its infancy, has begun in earnest. I will present some of the recent work from the ``Oak Ridge'' group, and will discuss this work in the context of the broader work by other researchers in the field. I will then point to future requirements and challenges. Connections with other experimental, observational, and theoretical efforts will be discussed, as well.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    of the cell cycle. Sperm nuclei were incubated in Xenopus egg extracts, and chromatin-associated proteins were analyzed by mass spectrometry at different times. Approximately 75% of the proteins varied in abundance on chromatin by more than 15%, suggesting that the chromatin proteome is highly dynamic...

  5. The Emerging Roles of ATP-Dependent Chromatin Remodeling Enzymes in Nucleotide Excision Repair

    Directory of Open Access Journals (Sweden)

    Wioletta Czaja

    2012-09-01

    Full Text Available DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo.

  6. Shape-tunable core-shell microparticles.

    Science.gov (United States)

    Klein, Matthias K; Saenger, Nicolai R; Schuetter, Stefan; Pfleiderer, Patrick; Zumbusch, Andreas

    2014-10-28

    Colloidal polymer particles are an important class of materials finding use in both everyday and basic research applications. Tailoring their composition, shape, and functionality is of key importance. In this article, we describe a new class of shape-tunable core-shell microparticles. They are composed of a cross-linked polystyrene (PS) core and a poly(methyl methacrylate) (PMMA) shell of varying thickness. In the first step, we prepared highly cross-linked PS cores, which are subsequently transferred into a nonpolar dispersant. They serve as the seed dispersion for a nonaqueous dispersion polymerization to generate the PMMA shell. The shape of the particles can subsequently be manipulated. After the shell growth stage, the spherical PS/PMMA core-shell colloids exhibit an uneven and wrinkled surface. An additional tempering procedure allows for smoothing the surface of the core-shell colloids. This results in polymer core-shell particles with a perfectly spherical shape. In addition to this thermal smoothing of the PMMA shell, we generated a selection of shape-anisotropic core-shell particles using a thermomechanical stretching procedure. Because of the unique constitution, we can selectively interrogate molecular vibrations in the PS core or the PMMA shell of the colloids using nonlinear optical microscopy techniques. This is of great interest because no photobleaching occurs, such that the particles can be tracked in real space over long times.

  7. 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 ...

  8. Retroviruses hijack chromatin loops to drive oncogene expression and highlight the chromatin architecture around proto-oncogenic loci.

    Directory of Open Access Journals (Sweden)

    Jillian M Pattison

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

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

    Science.gov (United States)

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

    2015-01-01

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

  10. Chromatin analyses of Zymoseptoria tritici: Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

    Science.gov (United States)

    Soyer, Jessica L; Möller, Mareike; Schotanus, Klaas; Connolly, Lanelle R; Galazka, Jonathan M; Freitag, Michael; Stukenbrock, Eva H

    2015-06-01

    The presence or absence of specific transcription factors, chromatin remodeling machineries, chromatin modification enzymes, post-translational histone modifications and histone variants all play crucial roles in the regulation of pathogenicity genes. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) provides an important tool to study genome-wide protein-DNA interactions to help understand gene regulation in the context of native chromatin. ChIP-seq is a convenient in vivo technique to identify, map and characterize occupancy of specific DNA fragments with proteins against which specific antibodies exist or which can be epitope-tagged in vivo. We optimized existing ChIP protocols for use in the wheat pathogen Zymoseptoria tritici and closely related sister species. Here, we provide a detailed method, underscoring which aspects of the technique are organism-specific. Library preparation for Illumina sequencing is described, as this is currently the most widely used ChIP-seq method. One approach for the analysis and visualization of representative sequence is described; improved tools for these analyses are constantly being developed. Using ChIP-seq with antibodies against H3K4me2, which is considered a mark for euchromatin or H3K9me3 and H3K27me3, which are considered marks for heterochromatin, the overall distribution of euchromatin and heterochromatin in the genome of Z. tritici can be determined. Our ChIP-seq protocol was also successfully applied to Z. tritici strains with high levels of melanization or aberrant colony morphology, and to different species of the genus (Z. ardabiliae and Z. pseudotritici), suggesting that our technique is robust. The methods described here provide a powerful framework to study new aspects of chromatin biology and gene regulation in this prominent wheat pathogen.

  11. Comparative analysis of chromatin binding by Sex Comb on Midleg (SCM) and other polycomb group repressors at a Drosophila Hox gene.

    Science.gov (United States)

    Wang, Liangjun; Jahren, Neal; Miller, Ellen L; Ketel, Carrie S; Mallin, Daniel R; Simon, Jeffrey A

    2010-06-01

    Sex Comb on Midleg (SCM) is a transcriptional repressor in the Polycomb group (PcG), but its molecular role in PcG silencing is not known. Although SCM can interact with Polycomb repressive complex 1 (PRC1) in vitro, biochemical studies have indicated that SCM is not a core constituent of PRC1 or PRC2. Nevertheless, SCM is just as critical for Drosophila Hox gene silencing as canonical subunits of these well-characterized PcG complexes. To address functional relationships between SCM and other PcG components, we have performed chromatin immunoprecipitation studies using cultured Drosophila Schneider line 2 (S2) cells and larval imaginal discs. We find that SCM associates with a Polycomb response element (PRE) upstream of the Ubx gene which also binds PRC1, PRC2, and the DNA-binding PcG protein Pleiohomeotic (PHO). However, SCM is retained at this Ubx PRE despite genetic disruption or knockdown of PHO, PRC1, or PRC2, suggesting that SCM chromatin targeting does not require prior association of these other PcG components. Chromatin immunoprecipitations (IPs) to test the consequences of SCM genetic disruption or knockdown revealed that PHO association is unaffected, but reduced levels of PRE-bound PRC2 and PRC1 were observed. We discuss these results in light of current models for recruitment of PcG complexes to chromatin targets.

  12. Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information.

    Science.gov (United States)

    Corpet, Armelle; Almouzni, Geneviève

    2009-01-01

    Understanding the basic mechanisms underlying chromatin dynamics during DNA replication in eukaryotic cells is of fundamental importance. Beyond DNA compaction, chromatin organization represents a means to regulate genome function. Thus, the inheritance and maintenance of the DNA sequence, along with its organization into chromatin, is central for eukaryotic life. To orchestrate DNA replication in the context of chromatin is a challenge, both in terms of accessibility to the compact structures and maintenance of chromatin organization. To meet the challenge of maintenance, cells have evolved efficient nucleosome dynamics involving assembly pathways and chromatin maturation mechanisms that restore chromatin organization in the wake of DNA replication. In this review, we describe our current knowledge concerning how these pathways operate at the nucleosomal level and highlight the key players, such as histone chaperones, chromatin remodelers or modifiers, involved in the process of chromatin duplication. Major advances have been made recently concerning de novo nucleosome assembly and our understanding of its coordination with recycling of parental histones is progressing. Insights into the transmission of chromatin-based information during replication have important implications in the field of epigenetics to fully comprehend how the epigenetic landscape might, or at times might not, be stably maintained in the face of dramatic changes in chromatin structure.

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

    Directory of Open Access Journals (Sweden)

    Nicholas C. Gomez

    2016-11-01

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

  14. 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.

  15. 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 Ercument; Kou, Yan; Liu, Li; Fromer, Menachem; Walker, Susan; Singh, Tarjinder; Klei, Lambertus; Kosmicki, Jack; Fu, Shih-Chen; Aleksic, Branko; Biscaldi, Monica; Bolton, Patrick F.; Brownfeld, Jessica M.; Cai, Jinlu; Campbell, Nicholas J.; Carracedo, Angel; Chahrour, Maria H.; Chiocchetti, Andreas G.; Coon, Hilary; Crawford, Emily L.; Crooks, Lucy; Curran, Sarah R.; Dawson, Geraldine; Duketis, Eftichia; Fernandez, Bridget A.; Gallagher, Louise; Geller, Evan; Guter, Stephen J.; Hill, R. Sean; Ionita-Laza, Iuliana; Gonzalez, Patricia Jimenez; Kilpinen, Helena; Klauck, Sabine M.; Kolevzon, Alexander; Lee, Irene; Lei, Jing; Lehtimäki, Terho; Lin, Chiao-Feng; Ma'ayan, Avi; Marshall, Christian R.; McInnes, Alison L.; Neale, Benjamin; Owen, Michael J.; Ozaki, Norio; 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; Wang, Li-San; 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, Aarno; Schellenberg, Gerard D.; Sklar, Pamela; State, Matthew W.; Sutcliffe, James S.; Walsh, Christopher A.; Scherer, Stephen W.; Zwick, Michael E.; Barrett, Jeffrey C.; Cutler, David J.; Roeder, Kathryn; Devlin, Bernie; Daly, Mark J.; Buxbaum, Joseph D.

    2014-01-01

    Summary The genetic architecture of autism spectrum disorder involves the interplay of common and rare variation and their impact on hundreds of genes. Using exome sequencing, 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, and 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, transcriptional, and chromatin remodeling pathways. These include voltage-gated ion channels regulating propagation of action potentials, pacemaking, and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodelers, prominently histone post-translational modifications involving lysine methylation/demethylation. PMID:25363760

  16. Cellular Fractionation and Isolation of Chromatin-Associated RNA.

    Science.gov (United States)

    Conrad, Thomas; Ørom, Ulf Andersson

    2017-01-01

    In eukaryotic cells, the synthesis, processing, and functions of RNA molecules are confined to distinct subcellular compartments. Biochemical fractionation of cells prior to RNA isolation thus enables the analysis of distinct steps in the lifetime of individual RNA molecules that would be masked in bulk RNA preparations from whole cells. Here, we describe a simple two-step differential centrifugation protocol for the isolation of cytoplasmic, nucleoplasmic, and chromatin-associated RNA that can be used in downstream applications such as qPCR or deep sequencing. We discuss various aspects of this fractionation protocol, which can be readily applied to many mammalian cell types. For the study of long noncoding RNAs and enhancer RNAs in regulation of transcription especially the preparation of chromatin-associated RNA can contribute significantly to further developments.

  17. Chromatin Assembly in a Yeast Whole-Cell Extract

    Science.gov (United States)

    Schultz, Michael C.; Hockman, Darren J.; Harkness, Troy A. A.; Garinther, Wendy I.; Altheim, Brent A.

    1997-08-01

    A simple in vitro system that supports chromatin assembly was developed for Saccharomyces cerevisiae. The assembly reaction is ATP-dependent, uses soluble histones and assembly factors, and generates physiologically spaced nucleosomes. We analyze the pathway of histone recruitment into nucleosomes, using this system in combination with genetic methods for the manipulation of yeast. This analysis supports the model of sequential recruitment of H3/H4 tetramers and H2A/H2B dimers into nucleosomes. Using a similar approach, we show that DNA ligase I can play an important role in template repair during assembly. These studies demonstrate the utility of this system for the combined biochemical and genetic analysis of chromatin assembly in yeast.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    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......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...... 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...

  19. A quantitative telomeric chromatin isolation protocol identifies different telomeric states

    Science.gov (United States)

    Grolimund, Larissa; Aeby, Eric; Hamelin, Romain; Armand, Florence; Chiappe, Diego; Moniatte, Marc; Lingner, Joachim

    2013-11-01

    Telomere composition changes during tumourigenesis, aging and in telomere syndromes in a poorly defined manner. Here we develop a quantitative telomeric chromatin isolation protocol (QTIP) for human cells, in which chromatin is cross-linked, immunopurified and analysed by mass spectrometry. QTIP involves stable isotope labelling by amino acids in cell culture (SILAC) to compare and identify quantitative differences in telomere protein composition of cells from various states. With QTIP, we specifically enrich telomeric DNA and all shelterin components. We validate the method characterizing changes at dysfunctional telomeres, and identify and validate known, as well as novel telomere-associated polypeptides including all THO subunits, SMCHD1 and LRIF1. We apply QTIP to long and short telomeres and detect increased density of SMCHD1 and LRIF1 and increased association of the shelterins TRF1, TIN2, TPP1 and POT1 with long telomeres. Our results validate QTIP to study telomeric states during normal development and in disease.

  20. ATRX: the case of a peculiar chromatin remodeler.

    Science.gov (United States)

    Ratnakumar, Kajan; Bernstein, Emily

    2013-01-01

    The SWI/SNF-like chromatin remodeler ATRX has recently garnered renewed attention. ATRX mutations were first identified in patients bearing the syndrome after which it is named, alpha thalassemia/mental retardation, X-linked. While ATRX has long been implicated in transcriptional regulation through multiple mechanisms, recent studies have identified a role for ATRX in the regulation of histone variant deposition. In addition, current reports describe ATRX to be mutated at high percentages in multiple tumor types, suggestive of a potential 'driver' role in cancer. Here we discuss the numerous and seemingly diverse roles for ATRX in transcriptional regulation and histone deposition and suggest that ATRX's effects are mediated by its regulation of histones within the chromatin template.

  1. The chromatin remodeller ATRX: a repeat offender in human disease.

    Science.gov (United States)

    Clynes, David; Higgs, Douglas R; Gibbons, Richard J

    2013-09-01

    The regulation of chromatin structure is of paramount importance for a variety of fundamental nuclear processes, including gene expression, DNA repair, replication, and recombination. The ATP-dependent chromatin-remodelling factor ATRX (α thalassaemia/mental retardation X-linked) has emerged as a key player in each of these processes. Exciting recent developments suggest that ATRX plays a variety of key roles at tandem repeat sequences within the genome, including the deposition of a histone variant, prevention of replication fork stalling, and the suppression of a homologous recombination-based pathway of telomere maintenance. Here, we provide a mechanistic overview of the role of ATRX in each of these processes, and propose how they may be connected to give rise to seemingly disparate human diseases.

  2. The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex.

    Science.gov (United States)

    Chalkley, Gillian E; Moshkin, Yuri M; Langenberg, Karin; Bezstarosti, Karel; Blastyak, Andras; Gyurkovics, Henrik; Demmers, Jeroen A A; Verrijzer, C Peter

    2008-05-01

    SWI/SNF ATP-dependent chromatin remodeling complexes (remodelers) perform critical functions in eukaryotic gene expression control. BAP and PBAP are the fly representatives of the two evolutionarily conserved major subclasses of SWI/SNF remodelers. Both complexes share seven core subunits, including the Brahma ATPase, but differ in a few signature subunits; POLYBROMO and BAP170 specify PBAP, whereas OSA defines BAP. Here, we show that the transcriptional coactivator and PHD finger protein SAYP is a novel PBAP subunit. Biochemical analysis established that SAYP is tightly associated with PBAP but absent from BAP. SAYP, POLYBROMO, and BAP170 display an intimately overlapping distribution on larval salivary gland polytene chromosomes. Genome-wide expression analysis revealed that SAYP is critical for PBAP-dependent transcription. SAYP is required for normal development and interacts genetically with core- and PBAP-selective subunits. Genetic analysis suggested that, like BAP, PBAP also counteracts Polycomb silencing. SAYP appears to be a key architectural component required for the integrity and association of the PBAP-specific module. We conclude that SAYP is a signature subunit that plays a major role in the functional specificity of the PBAP holoenzyme.

  3. 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.

  4. 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.

  5. Defining the budding yeast chromatin-associated interactome

    OpenAIRE

    Lambert, Jean-Philippe; Fillingham, Jeffrey; Siahbazi, Mojgan; Greenblatt, Jack; Baetz, Kristin; Figeys, Daniel

    2010-01-01

    The maintenance of cellular fitness requires living organisms to integrate multiple signals into coordinated outputs. Central to this process is the regulation of the expression of the genetic information encoded into DNA. As a result, there are numerous constraints imposed on gene expression. The access to DNA is restricted by the formation of nucleosomes, in which DNA is wrapped around histone octamers to form chromatin wherein the volume of DNA is considerably reduced. As such, nucleosome ...

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

    OpenAIRE

    Ding, Bo; Wang, Guo-Liang

    2015-01-01

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

  7. Chromatin Memory in the Development of Human Cancers

    OpenAIRE

    Yao, Yixin; Des Marais, Thomas L; Costa, Max

    2014-01-01

    Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by car...

  8. ATRX: The case of a peculiar chromatin remodeler

    OpenAIRE

    Ratnakumar, Kajan; Bernstein, Emily

    2013-01-01

    The SWI/SNF-like chromatin remodeler ATRX has recently garnered renewed attention. ATRX mutations were first identified in patients bearing the syndrome after which it is named, alpha thalassemia/mental retardation, X-linked. While ATRX has long been implicated in transcriptional regulation through multiple mechanisms, recent studies have identified a role for ATRX in the regulation of histone variant deposition. In addition, current reports describe ATRX to be mutated at high percentages in ...

  9. Evaluation of DNA fragmentation in llama (Lama glama) sperm using the sperm chromatin dispersion test.

    Science.gov (United States)

    Carretero, M I; Lombardo, D; Arraztoa, C C; Giuliano, S M; Gambarotta, M C; Neild, D M

    2012-03-01

    The integrity of sperm chromatin is now viewed as an important factor in male fertility and in early embryonic development. The objectives of this study were: (1) adapt the simple and inexpensive sperm chromatin dispersion (SCD) test to evaluate DNA fragmentation in llama sperm and establish the halo patterns observed in this species, (2) determine an effective and reliable positive control for this technique and (3) evaluate correlation between the SCD test and the toluidine blue (TB) stain. To adapt the SCD test, three different mercaptoethanol (ME) concentrations were assayed (2.5%, 5% and 10% ME). To determine an effective positive control, three treatments (incubation at 100 °C for 30 min, incubation with 0.3 M NaOH for 30 min at room temperature and exposure to UV light for 2h) were assayed. The concentration selected to use in the SCD test was 5% ME, because it produced the largest halo while still conserving the structure of the core. Four DNA dispersion patterns were clearly observed: (I) nuclei with large DNA dispersion halos; (II) nuclei with medium halos; (III) nuclei with very small halos and (IV) nuclei with no halo. All treatments used as positive controls were effective in producing DNA fragmentation. A high correlation (r=0.84, P=0.03) was observed between spermatozoa without halos and TB positive cells. To conclude, SCD patterns in llama sperm have been established as well as a repeatable positive control for the assay. The SCD test and TB stain are simple and inexpensive techniques that can be used to evaluate DNA damage in llama sperm.

  10. Moving core beam energy absorber and converter

    Science.gov (United States)

    Degtiarenko, Pavel V.

    2012-12-18

    A method and apparatus for the prevention of overheating of laser or particle beam impact zones through the use of a moving-in-the-coolant-flow arrangement for the energy absorbing core of the device. Moving of the core spreads the energy deposition in it in 1, 2, or 3 dimensions, thus increasing the effective cooling area of the device.

  11. Senataxin controls meiotic silencing through ATR activation and chromatin remodeling.

    Science.gov (United States)

    Yeo, Abrey J; Becherel, Olivier J; Luff, John E; Graham, Mark E; Richard, Derek; Lavin, Martin F

    2015-01-01

    Senataxin, defective in ataxia oculomotor apraxia type 2, protects the genome by facilitating the resolution of RNA-DNA hybrids (R-loops) and other aspects of RNA processing. Disruption of this gene in mice causes failure of meiotic recombination and defective meiotic sex chromosome inactivation, leading to male infertility. Here we provide evidence that the disruption of Setx leads to reduced SUMOylation and disruption of protein localization across the XY body during meiosis. We demonstrate that senataxin and other DNA damage repair proteins, including ataxia telangiectasia and Rad3-related protein-interacting partner, are SUMOylated, and a marked downregulation of both ataxia telangiectasia and Rad3-related protein-interacting partner and TopBP1 leading to defective activation and signaling through ataxia telangiectasia and Rad3-related protein occurs in the absence of senataxin. Furthermore, chromodomain helicase DNA-binding protein 4, a component of the nucleosome remodeling and deacetylase chromatin remodeler that interacts with both ataxia telangiectasia and Rad3-related protein and senataxin was not recruited efficiently to the XY body, triggering altered histone acetylation and chromatin conformation in Setx (-/-) pachytene-staged spermatocytes. These results demonstrate that senataxin has a critical role in ataxia telangiectasia and Rad3-related protein- and chromodomain helicase DNA-binding protein 4-mediated transcriptional silencing and chromatin remodeling during meiosis providing greater insight into its critical role in gene regulation to protect against neurodegeneration.

  12. ATM and KAT5 safeguard replicating chromatin against formaldehyde damage.

    Science.gov (United States)

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

    2016-01-08

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

  13. Predicting chromatin architecture from models of polymer physics.

    Science.gov (United States)

    Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario

    2017-01-09

    We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches. To identify the nature of architectural domains and their molecular determinants within a principled approach, we discuss models based on polymer physics. We show that basic concepts of interacting polymer physics explain chromatin spatial organization across chromosomal scales and cell types. The 3D structure of genomic loci can be derived with high accuracy and its molecular determinants identified by crossing information with epigenomic databases. In particular, we illustrate the case of the Sox9 locus, linked to human congenital disorders. The model in-silico predictions on the effects of genomic rearrangements are confirmed by available 5C data. That can help establishing new diagnostic tools for diseases linked to chromatin mis-folding, such as congenital disorders and cancer.

  14. Rsc4 Connects the Chromatin Remodeler RSC to RNA Polymerases‡

    Science.gov (United States)

    Soutourina, Julie; Bordas-Le Floch, Véronique; Gendrel, Gabrielle; Flores, Amando; Ducrot, Cécile; Dumay-Odelot, Hélène; Soularue, Pascal; Navarro, Francisco; Cairns, Bradley R.; Lefebvre, Olivier; Werner, Michel

    2006-01-01

    RSC is an essential, multisubunit chromatin remodeling complex. We show here that the Rsc4 subunit of RSC interacted via its C terminus with Rpb5, a conserved subunit shared by all three nuclear RNA polymerases (Pol). Furthermore, the RSC complex coimmunoprecipitated with all three RNA polymerases. Mutations in the C terminus of Rsc4 conferred a thermosensitive phenotype and the loss of interaction with Rpb5. Certain thermosensitive rpb5 mutations were lethal in combination with an rsc4 mutation, supporting the physiological significance of the interaction. Pol II transcription of ca. 12% of the yeast genome was increased or decreased twofold or more in a rsc4 C-terminal mutant. The transcription of the Pol III-transcribed genes SNR6 and RPR1 was also reduced, in agreement with the observed localization of RSC near many class III genes. Rsc4 C-terminal mutations did not alter the stability or assembly of the RSC complex, suggesting an impact on Rsc4 function. Strikingly, a C-terminal mutation of Rsc4 did not impair RSC recruitment to the RSC-responsive genes DUT1 and SMX3 but rather changed the chromatin accessibility of DNases to their promoter regions, suggesting that the altered transcription of DUT1 and SMX3 was the consequence of altered chromatin remodeling. PMID:16782880

  15. Chromatin immunoprecipitation in microfluidic droplets: towards fast and cheap analyses.

    Science.gov (United States)

    Teste, Bruno; Champ, Jerome; Londono-Vallejo, Arturo; Descroix, Stéphanie; Malaquin, Laurent; Viovy, Jean-Louis; Draskovic, Irena; Mottet, Guillaume

    2017-01-31

    Genetic organization is governed by the interaction of DNA with histone proteins, and differential modifications of these proteins is a fundamental mechanism of gene regulation. Histone modifications are primarily studied through chromatin immunoprecipitation (ChIP) assays, however conventional ChIP procedures are time consuming, laborious and require a large number of cells. Here we report for the first time the development of ChIP in droplets based on a microfluidic platform combining nanoliter droplets, magnetic beads (MB) and magnetic tweezers (MT). The droplet approach enabled compartmentalization and improved mixing, while reducing the consumption of samples and reagents in an integrated workflow. Anti-histone antibodies grafted to MB were used as a solid support to capture and transfer the target chromatin from droplets to droplets in order to perform chromatin immunoprecipitation, washing, elution and purification of DNA. We designed a new ChIP protocol to investigate four different types of modified histones with known roles in gene activation or repression. We evaluated the performances of this new ChIP in droplet assay in comparison with conventional methods. The proposed technology dramatically reduces analytical time from a few days to 7 hours, simplifies the ChIP protocol and decreases the number of cells required by 100 fold while maintaining a high degree of sensitivity and specificity. Therefore this droplet-based ChIP assay represents a new, highly advantageous and convenient approach to epigenetic analyses.

  16. Signaling to the circadian clock: plasticity by chromatin remodeling.

    Science.gov (United States)

    Nakahata, Yasukazu; Grimaldi, Benedetto; Sahar, Saurabh; Hirayama, Jun; Sassone-Corsi, Paolo

    2007-04-01

    Circadian rhythms govern several fundamental physiological functions in almost all organisms, from prokaryotes to humans. The circadian clocks are intrinsic time-tracking systems with which organisms can anticipate environmental changes and adapt to the appropriate time of day. In mammals, circadian rhythms are generated in pacemaker neurons within the suprachiasmatic nuclei (SCN), a small area of the hypothalamus, and are entrained by environmental cues, principally light. Disruption of these rhythms can profoundly influence human health, being linked to depression, insomnia, jet lag, coronary heart disease and a variety of neurodegenerative disorders. It is now well established that circadian clocks operate via transcriptional feedback autoregulatory loops that involve the products of circadian clock genes. Furthermore, peripheral tissues also contain independent clocks, whose oscillatory function is orchestrated by the SCN. The complex program of gene expression that characterizes circadian physiology involves dynamic changes in chromatin transitions. These remodeling events are therefore of great importance to ensure the proper timing and extent of circadian regulation. How signaling influences chromatin remodeling through histone modifications is therefore highly relevant in the context of circadian oscillation. Recent advances in the field have revealed unexpected links between circadian regulators, chromatin remodeling and cellular metabolism.

  17. Balancing chromatin remodeling and histone modifications in transcription.

    Science.gov (United States)

    Petty, Emily; Pillus, Lorraine

    2013-11-01

    Chromatin remodelers use the energy of ATP hydrolysis to reposition or evict nucleosomes or to replace canonical histones with histone variants. By regulating nucleosome dynamics, remodelers gate access to the underlying DNA for replication, repair, and transcription. Nucleosomes are subject to extensive post-translational modifications that can recruit regulatory proteins or alter the local chromatin structure. Just as extensive crosstalk has been observed between different histone post-translational modifications, there is growing evidence for both coordinated and antagonistic functional relations between nucleosome remodeling and modifying machineries. Defining the combined functions of the complexes that alter nucleosome interactions, position, and stability is key to understanding processes that require access to DNA, particularly with growing appreciation of their contributions to human health and disease. Here, we highlight recent advances in the interactions between histone modifications and the imitation-switch (ISWI) and chromodomain helicase DNA-binding protein 1 (CHD1) chromatin remodelers from studies in budding yeast, fission yeast, flies, and mammalian cells, with a focus on yeast.

  18. Histone chaperones link histone nuclear import and chromatin assembly.

    Science.gov (United States)

    Keck, Kristin M; Pemberton, Lucy F

    2013-01-01

    Histone chaperones are proteins that shield histones from nonspecific interactions until they are assembled into chromatin. After their synthesis in the cytoplasm, histones are bound by different histone chaperones, subjected to a series of posttranslational modifications and imported into the nucleus. These evolutionarily conserved modifications, including acetylation and methylation, can occur in the cytoplasm, but their role in regulating import is not well understood. As part of histone import complexes, histone chaperones may serve to protect the histones during transport, or they may be using histones to promote their own nuclear localization. In addition, there is evidence that histone chaperones can play an active role in the import of histones. Histone chaperones have also been shown to regulate the localization of important chromatin modifying enzymes. This review is focused on the role histone chaperones play in the early biogenesis of histones, the distinct cytoplasmic subcomplexes in which histone chaperones have been found in both yeast and mammalian cells and the importins/karyopherins and nuclear localization signals that mediate the nuclear import of histones. We also address the role that histone chaperone localization plays in human disease. This article is part of a Special Issue entitled: Histone chaperones and chromatin assembly.

  19. Repression and activation by multiprotein complexes that alter chromatin structure.

    Science.gov (United States)

    Kingston, R E; Bunker, C A; Imbalzano, A N

    1996-04-15

    Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.

  20. Biphasic Chromatin Structure and FISH Signals Reflect Intranuclear Order

    Directory of Open Access Journals (Sweden)

    Jyoti P. Chaudhuri

    2005-01-01

    Full Text Available Background and Aim: One of the two parental allelic genes may selectively be expressed, regulated by imprinting, X-inactivation or by other less known mechanisms. This study aims to reflect on such genetic mechanisms. Materials and Methods: Slides from short term cultures or direct smears of blood, bone marrow and amniotic fluids were hybridized with FISH probes singly, combined or sequentially. Two to three hundred cells were examined from each preparation. Results and Aignificance: A small number of cells (up to about 5%, more frequent in leukemia cases, showed the twin features: (1 nuclei with biphasic chromatin, one part decondensed and the other condensed; and (2 homologous FISH signals distributed equitably in those two regions. The biphasic chromatin structure with equitable distribution of the homologous FISH signals may correspond to the two sets of chromosomes, supporting observations on ploidywise intranuclear order. The decondensed chromatin may relate to enhanced transcriptions or advanced replications. Conclusions: Transcriptions of only one of the two parental genomes cause allelic exclusion. Genomes may switch with alternating monoallelic expression of biallelic genes as an efficient genetic mechanism. If genomes fail to switch, allelic exclusion may lead to malignancy. Similarly, a genome-wide monoallelic replication may tilt the balance of heterozygosity resulting in aneusomy, initiating early events in malignant transformation and in predicting cancer mortality.

  1. Chromatin structure and ATRX function in mouse oocytes.

    Science.gov (United States)

    De La Fuente, Rabindranath; Baumann, Claudia; Viveiros, Maria M

    2012-01-01

    Differentiation of chromatin structure and function during oogenesis is essential to confer the mammalian oocyte with meiotic and developmental potential. Errors in chromosome segregation during female meiosis and subsequent transmission of an abnormal chromosome complement (aneuploidy) to the early conceptus are one of the leading causes of pregnancy loss in women. The chromatin remodeling protein ATRX (α-thalassemia mental retardation X-linked) has recently emerged as a critical factor involved in heterochromatin formation at mammalian centromeres during meiosis. In mammalian oocytes, ATRX binds to centromeric heterochromatin domains where it is required for accurate chromosome segregation. Loss of ATRX function induces abnormal meiotic chromosome morphology, reduces histone H3 phosphorylation, and promotes a high incidence of aneuploidy associated with severely reduced fertility. The presence of centromeric breaks during the transition to the first mitosis in the early embryo indicates that the role of ATRX in chromosome segregation is mediated through an epigenetic mechanism involving the maintenance of chromatin modifications associated with pericentric heterochromatin (PCH) formation and chromosome condensation. This is consistent with the existence of a potential molecular link between centromeric and PCH in the epigenetic control of centromere function and maintenance of chromosome stability in mammalian oocytes. Dissecting the molecular mechanisms of ATRX function during meiosis will have important clinical implications towards uncovering the epigenetic factors contributing to the onset of aneuploidy in the human oocyte.

  2. 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.

  3. The shades of gray of the chromatin fiber: recent literature provides new insights into the structure of chromatin.

    Science.gov (United States)

    Ausió, Juan

    2015-01-01

    The chromatin fiber consists of a string of nucleosomes connected by linker DNA regions. The hierarchy of folding of this fiber within the cell has long been controversial, and the existence of an originally described 30 nm fiber has been debated and reviewed extensively. This review contextualizes two recent papers on this topic that suggest the 30 nm fiber to be an over-simplification. The idealized model from the first study provides good insight into the constraints and histone participation in the maintenance of the fiber structure. The second paper provides a theoretical description of a more realistic view of the highly heterogeneous and dynamic chromatin organization in the in vivo setting. It is now time to abandon the highly regular "one start" solenoidal 30 nm structure and replace it with a more realistic highly dynamic, polymorphic fiber.

  4. New Evidence for the Theory of Chromosome Organization by Repetitive Elements (CORE).

    Science.gov (United States)

    Tang, Shao-Jun

    2017-02-20

    Repetitive DNA elements were proposed to coordinate chromatin folding and interaction in chromosomes by their intrinsic homology-based clustering ability. A recent analysis of the data sets from chromosome-conformation-capture experiments confirms the spatial clustering of DNA repeats of the same family in the nuclear space, and thus provides strong new support for the CORE theory.

  5. Biological assay of chromatin dispersal simplified for determining absorbed dose of ionizing radiation; Ensayo biologico simplificado de dispersion de cromatina para la determinacion de dosis de radiacion ionizante

    Energy Technology Data Exchange (ETDEWEB)

    Galaz, S.; Perez, G.; Stockert, J. C.; Blazquez-Castro, A.

    2011-07-01

    Currently, the production of nuclear halos chromatin dispersion methods is a good procedure for nuclear analysis by in situ hybridization (Wiegant et al., 1992, Gerdes et al. 1994), to detect apoptosis, DNA fragmentation and cell death rates in cell cultures (Fernandez et al., 2005, Enciso et al. 2006). It is customary to display the nuclear halos by fluorescence microscopy using propidium iodide, ethidium bromide or DAPI (Gerdes et al., 1994, Sestili et al. 2006). Using this technique based on a modified protocol of fast halo assay [FHA],(Sestili et al. 2006), has developed a simplified method to quantify the cytogenetic damage induced by ionizing radiation (dispersion test chromatin in agarose thin smear), which allows visualization of halos after staining for light microscopy or fluorescence and correlating the ratio: total area occuped by the halo nucleus / nucleus (halo-core index [IHN] ) with radiation dose.

  6. The linkage of chromatin remodeling to genome maintenance: contribution from a human disease gene BRIT1/MCPH1

    OpenAIRE

    Peng, Guang; Lin, Shiaw-Yih

    2009-01-01

    Genomic DNA is packed into a highly condensed chromatin structure, which acts as natural barrier preventing accessibility of DNA. In various processes to maintain genomic integrity such as DNA replication, DNA repair, telomere regulation, proteins need to overcome the barrier of condensed chromatin to gain access to DNA. ATP-dependent chromatin remodeling is one of the fundamental mechanisms used by cells to relax chromatin. However, the chromatin remodeling complex does not contain intrinsic...

  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

    2012-10-02

    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.

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

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    replication and chromatin assembly processes in time and space. Dynamic recycling and de novo deposition of histones are fundamental for chromatin restoration. Histone post-translational modifications (PTMs) are thought to have a causal role in establishing distinct chromatin structures. Here we discuss PTMs......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...... present on new and parental histones and how they influence genome stability and restoration of epigenetically defined domains. Newly deposited histones must change their signature in the process of chromatin restoration, this may occur in a step-wise fashion involving replication-coupled processes...

  9. Phosphorylation of the chromatin binding domain of KSHV LANA.

    Directory of Open Access Journals (Sweden)

    Crystal Woodard

    Full Text Available The Kaposi sarcoma associated herpesvirus (KSHV latency associated nuclear antigen (LANA is expressed in all KSHV associated malignancies and is essential for maintenance of KSHV genomes in infected cells. To identify kinases that are potentially capable of modifying LANA, in vitro phosphorylation assays were performed using an Epstein Barr virus plus LANA protein microarray and 268 human kinases purified in active form from yeast. Interestingly, of the Epstein-Barr virus proteins on the array, the EBNA1 protein had the most similar kinase profile to LANA. We focused on nuclear kinases and on the N-terminus of LANA (amino acids 1-329 that contains the LANA chromatin binding domain. Sixty-three nuclear kinases phosphorylated the LANA N-terminus. Twenty-four nuclear kinases phosphorylated a peptide covering the LANA chromatin binding domain (amino acids 3-21. Alanine mutations of serine 10 and threonine 14 abolish or severely diminish chromatin and histone binding by LANA. However, conversion of these residues to the phosphomimetic glutamic acid restored histone binding suggesting that phosphorylation of serine 10 and threonine 14 may modulate LANA function. Serine 10 and threonine 14 were validated as substrates of casein kinase 1, PIM1, GSK-3 and RSK3 kinases. Short-term treatment of transfected cells with inhibitors of these kinases found that only RSK inhibition reduced LANA interaction with endogenous histone H2B. Extended treatment of PEL cell cultures with RSK inhibitor caused a decrease in LANA protein levels associated with p21 induction and a loss of PEL cell viability. The data indicate that RSK phosphorylation affects both LANA accumulation and function.

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

    Directory of Open Access Journals (Sweden)

    Francesca Martinato

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

  11. A unique chromatin signature uncovers early developmental enhancers in humans.

    Science.gov (United States)

    Rada-Iglesias, Alvaro; Bajpai, Ruchi; Swigut, Tomek; Brugmann, Samantha A; Flynn, Ryan A; Wysocka, Joanna

    2011-02-10

    Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.

  12. More on core instabilities of magnetic monopoles

    CERN Document Server

    Striet, J

    2003-01-01

    In this paper we present new results on the core instability of the 't Hooft Polyakov monopoles we reported on before. This instability, where the spherical core decays in a toroidal one, typically occurs in models in which charge conjugation is gauged. In this paper we also discuss a third conceivable configuration denoted as ``split core'', which brings us to some details of the numerical methods we employed. We argue that a core instability of 't Hooft Polyakov type monopoles is quite a generic feature of models with charged Higgs particles.

  13. The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes.

    Science.gov (United States)

    Brown, Emily J; Bachtrog, Doris

    2014-07-01

    The chromatin landscape is key for gene regulation, but little is known about how it differs between sexes or between species. Here, we study the sex-specific chromatin landscape of Drosophila miranda, a species with young sex chromosomes, and compare it with Drosophila melanogaster. We analyze six histone modifications in male and female larvae of D. miranda (H3K4me1, H3K4me3, H3K36me3, H4K16ac, H3K27me3, and H3K9me2), and define seven biologically meaningful chromatin states that show different enrichments for transcribed and silent genes, repetitive elements, housekeeping, and tissue-specific genes. The genome-wide distribution of both active and repressive chromatin states differs between males and females. In males, active chromatin is enriched on the X, relative to females, due to dosage compensation of the hemizygous X. Furthermore, a smaller fraction of the euchromatic portion of the genome is in a repressive chromatin state in males relative to females. However, sex-specific chromatin states appear not to explain sex-biased expression of genes. Overall, conservation of chromatin states between male and female D. miranda is comparable to conservation between D. miranda and D. melanogaster, which diverged >30 MY ago. Active chromatin states are more highly conserved across species, while heterochromatin shows very low levels of conservation. Divergence in chromatin profiles contributes to expression divergence between species, with ∼26% of genes in different chromatin states in the two species showing species-specific or species-biased expression, an enrichment of approximately threefold over null expectation. Our data suggest that heteromorphic sex chromosomes in males (that is, a hypertranscribed X and an inactivated Y) may contribute to global redistribution of active and repressive chromatin marks between chromosomes and sexes.

  14. Assembly of Two Transgenes in an Artificial Chromatin Domain Gives Highly Coordinated Expression in Tobacco

    OpenAIRE

    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 beta-glucuronidase gene and the firefly luciferase gene, driven by different promoters, were placed between copies of the chicken lysozyme A element, a member of the matrix-associated region (MAR) group of chromatin boundary elements, and introduced in tobacco (Nicotiana tab...

  15. Multiple modes of chromatin configuration at natural meiotic recombination hot spots in fission yeast.

    Science.gov (United States)

    Hirota, Kouji; Steiner, Walter W; Shibata, Takehiko; Ohta, Kunihiro

    2007-11-01

    The ade6-M26 meiotic recombination hot spot of fission yeast is defined by a cyclic AMP-responsive element (CRE)-like heptanucleotide sequence, 5'-ATGACGT-3', which acts as a binding site for the Atf1/Pcr1 heterodimeric transcription factor required for hot spot activation. We previously demonstrated that the local chromatin around the M26 sequence motif alters to exhibit higher sensitivity to micrococcal nuclease before the initiation of meiotic recombination. In this study, we have examined whether or not such alterations in chromatin occur at natural meiotic DNA double-strand break (DSB) sites in Schizosaccharomyces pombe. At one of the most prominent DSB sites, mbs1 (meiotic break site 1), the chromatin structure has a constitutively accessible configuration at or near the DSB sites. The establishment of the open chromatin state and DSB formation are independent of the CRE-binding transcription factor, Atf1. Analysis of the chromatin configuration at CRE-dependent DSB sites revealed both differences from and similarities to mbs1. For example, the tdh1+ locus, which harbors a CRE consensus sequence near the DSB site, shows a meiotically induced open chromatin configuration, similar to ade6-M26. In contrast, the cds1+ locus is similar to mbs1 in that it exhibits a constitutive open configuration. Importantly, Atf1 is required for the open chromatin formation in both tdh1+ and cds1+. These results suggest that CRE-dependent meiotic chromatin changes are intrinsic processes related to DSB formation in fission yeast meiosis. In addition, the results suggest that the chromatin configuration in natural meiotic recombination hot spots can be classified into at least three distinct categories: (i) an Atf1-CRE-independent constitutively open chromatin configuration, (ii) an Atf1-CRE-dependent meiotically induced open chromatin configuration, and (iii) an Atf1-CRE-dependent constitutively open chromatin configuration.

  16. Hijacking the chromatin remodeling machinery: impact of SWI/SNF perturbations in cancer

    OpenAIRE

    Weissman, Bernard; Knudsen, Karen E

    2009-01-01

    There is increasing evidence that alterations in chromatin remodeling play a significant role in human disease. The SWI/SNF chromatin remodeling complex family mobilizes nucleosomes and functions as a master regulator of gene expression and chromatin dynamics whose functional specificity is driven by combinatorial assembly of a central ATPase and association with 10-12 unique subunits. While the biochemical consequence of SWI/SNF in model systems has been extensively reviewed, the present art...

  17. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

    OpenAIRE

    Giresi, Paul G.; Lieb, Jason D.

    2009-01-01

    The binding of sequence-specific regulatory factors and the recruitment of chromatin remodeling activities cause nucleosomes to be evicted from chromatin in eukaryotic cells. Traditionally, these active sites have been identified experimentally through their sensitivity to nucleases. Here we describe the details of a simple procedure for the genome-wide isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). We also pro...

  18. Study on Resistance of Human Sperm Chromatin to Heparin Decondensation

    Institute of Scientific and Technical Information of China (English)

    褚劲松; 李建国; 薛同一; 王一飞

    1995-01-01

    Resistance of human sperm chromatin to heparin deeondensatinn was investigated by image analysis. The level of DNA deeondensation was determined by measuring the α, [red fluorescence/(red + green) fluoreseence] of sperm. The optimal experimental conditions were incubating sperms with 1000 IU/ml of heparin at 37℃ for 13 minutes and analysing the sperms with excitation F488, red fluoreseenee F630, green fluoreseence F530. The result showed that 72.93±14.73 percent of 20 fertile human sperms resist heparin deeondensa tion.

  19. Large chromatin domains in pluripotent and differentiated cells

    Institute of Scientific and Technical Information of China (English)

    Shibin Hu; Lu Cheng; Bo Wen

    2012-01-01

    Pluripotent stem cells are able to proliferate unlimitedly and to generate all somatic cell types,thus holding a great promise in medical applications.Epigenetic modifications are believed to play crucial roles in regulating pluripotency and differentiation.Recent genome-wide studies on mammalian systems have revealed several types of large chromatin domains which are associated with higherorder organization of the genome.The elucidation of genomic distribution and dynamics of these domains have shed light on the mechanisms underling pluripotency and lineage commitment.

  20. 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.

  1. Nucleosome conformational flexibility in experiments with single chromatin fibers

    Directory of Open Access Journals (Sweden)

    Sivolob A. V.

    2010-09-01

    Full Text Available 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 a distorted histone octamer. Molecular mechanisms of the nucleosome structural flexibility and its biological relevance are discussed.

  2. Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry.

    Science.gov (United States)

    Dillinger, Stefan; Garea, Ana Villar; Deutzmann, Rainer; Németh, Attila

    2014-01-01

    Chromatin is unevenly distributed within the eukaryote nucleus and it contributes to the formation of morphologically and functionally distinct substructures, called chromatin domains and nuclear bodies. Here we describe an approach to assess specific chromatin features, the histone posttranslational modifications (PTMs), of the largest nuclear sub-compartment, the nucleolus. In this chapter, methods for the isolation of nucleolus-associated chromatin from native or formaldehyde-fixed cells and the effect of experimental procedures on the outcome of mass spectrometry analysis of histone PTMs are compared.

  3. Evolution and genetic architecture of chromatin accessibility and function in yeast.

    Directory of Open Access Journals (Sweden)

    Caitlin F Connelly

    2014-07-01

    Full Text Available Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign.

  4. Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers.

    Science.gov (United States)

    Hayami, Shinya; Kelly, John D; Cho, Hyun-Soo; Yoshimatsu, Masanori; Unoki, Motoko; Tsunoda, Tatsuhiko; Field, Helen I; Neal, David E; Yamaue, Hiroki; Ponder, Bruce A J; Nakamura, Yusuke; Hamamoto, Ryuji

    2011-02-01

    A number of histone demethylases have been identified and biochemically characterized, but the pathological roles of their dysfunction in human disease like cancer have not been well understood. Here, we demonstrate important roles of lysine-specific demethylase 1 (LSD1) in human carcinogenesis. Expression levels of LSD1 are significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (p human embryonic kidney fibroblast cells. Expression profile analysis showed that LSD1 could affect the expression of genes involved in various chromatin-modifying pathways such as chromatin remodeling at centromere, centromeric heterochromatin formation and chromatin assembly, indicating its essential roles in carcinogenesis through chromatin modification.

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

    DEFF Research Database (Denmark)

    Düring, Louis; Thorsen, Michael; Petersen, Darima;

    2012-01-01

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

  6. 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.

  7. 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.

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

    OpenAIRE

    Savic, Velibor

    2013-01-01

    In the last decade, a lot has been done in elucidating the sequence of events that occur at the nascent double strand DNA break. Nevertheless, the overall structure formed by the DNA damage response (DDR) factors around the break site, the repair focus, remains poorly understood. Although most of the data presented so far only address events that occur in chromatin in cis around the break, there are strong indications that in mammalian systems it may also occur in trans, analogous to the rece...

  9. Reactivation of developmentally silenced globin genes by forced chromatin looping.

    Science.gov (United States)

    Deng, Wulan; Rupon, Jeremy W; Krivega, Ivan; Breda, Laura; Motta, Irene; Jahn, Kristen S; Reik, Andreas; Gregory, Philip D; Rivella, Stefano; Dean, Ann; Blobel, Gerd A

    2014-08-14

    Distal enhancers commonly contact target promoters via chromatin looping. In erythroid cells, the locus control region (LCR) contacts β-type globin genes in a developmental stage-specific manner to stimulate transcription. Previously, we induced LCR-promoter looping by tethering the self-association domain (SA) of Ldb1 to the β-globin promoter via artificial zinc fingers. Here, we show that targeting the SA to a developmentally silenced embryonic globin gene in adult murine erythroblasts triggers its transcriptional reactivation. This activity depends on the LCR, consistent with an LCR-promoter looping mechanism. Strikingly, targeting the SA to the fetal γ-globin promoter in primary adult human erythroblasts increases γ-globin promoter-LCR contacts, stimulating transcription to approximately 85% of total β-globin synthesis, with a reciprocal reduction in adult β-globin expression. Our findings demonstrate that forced chromatin looping can override a stringent developmental gene expression program and suggest a novel approach to control the balance of globin gene transcription for therapeutic applications.

  10. 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.

  11. Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and its denucleation

    Directory of Open Access Journals (Sweden)

    He Shuying

    2010-11-01

    Full Text Available Abstract Background Brahma-related gene 1 (Brg1, also known as Smarca4 and Snf2β encodes an adenosine-5'-triphosphate (ATP-dependent catalytical subunit of the (switch/sucrose nonfermentable (SWI/SNF chromatin remodeling complexes. SWI/SNF complexes are recruited to chromatin through multiple mechanisms, including specific DNA-binding factors (for example, heat shock transcription factor 4 (Hsf4 and paired box gene 6 (Pax6, chromatin structural proteins (for example, high-mobility group A1 (HMGA1 and/or acetylated core histones. Previous studies have shown that a single amino acid substitution (K798R in the Brg1 ATPase domain acts via a dominant-negative (dn mechanism. Genetic studies have demonstrated that Brg1 is an essential gene for early (that is, prior implantation mouse embryonic development. Brg1 also controls neural stem cell maintenance, terminal differentiation of multiple cell lineages and organs including the T-cells, glial cells and limbs. Results To examine the roles of Brg1 in mouse lens development, a dnBrg1 transgenic construct was expressed using the lens-specific αA-crystallin promoter in postmitotic lens fiber cells. Morphological studies revealed abnormal lens fiber cell differentiation in transgenic lenses resulting in cataract. Electron microscopic studies showed abnormal lens suture formation and incomplete karyolysis (that is, denucleation of lens fiber cells. To identify genes regulated by Brg1, RNA expression profiling was performed in embryonic day 15.5 (E15.5 wild-type and dnBrg1 transgenic lenses. In addition, comparisons between differentially expressed genes in dnBrg1 transgenic, Pax6 heterozygous and Hsf4 homozygous lenses identified multiple genes coregulated by Brg1, Hsf4 and Pax6. DNase IIβ, a key enzyme required for lens fiber cell denucleation, was found to be downregulated in each of the Pax6, Brg1 and Hsf4 model systems. Lens-specific deletion of Brg1 using conditional gene targeting demonstrated that

  12. Camk2a-Cre-mediated conditional deletion of chromatin remodeler Brg1 causes perinatal hydrocephalus.

    Science.gov (United States)

    Cao, Mou; Wu, Jiang I

    2015-06-15

    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/SmarcA4 or 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 transgene, which mediates Brg1 deletion in a subset of forebrain neurons beginning in the late embryonic stage. Brg1 deletion in these neurons led to severe congenital hydrocephalus with enlargement of the lateral ventricles and attenuation of the cerebral cortex. The Brg1-deficient mice had significantly smaller subcommissural organs and narrower Sylvian aqueducts than mice that express normal levels of Brg1. Effects were non-cell autonomous and may be responsible for the development of the congenital hydrocephalus phenotype. Our study provides evidence indicating that abnormalities in Brg1 function result in defects associated with neurodevelopmental disorders and autism.

  13. Dual-core antiresonant hollow core fibers.

    Science.gov (United States)

    Liu, Xuesong; Fan, Zhongwei; Shi, Zhaohui; Ma, Yunfeng; Yu, Jin; Zhang, Jing

    2016-07-25

    In this work, dual-core antiresonant hollow core fibers (AR-HCFs) are numerically demonstrated, based on our knowledge, for the first time. Two fiber structures are proposed. One is a composite of two single-core nested nodeless AR-HCFs, exhibiting low confinement loss and a circular mode profile in each core. The other has a relatively simple structure, with a whole elliptical outer jacket, presenting a uniform and wide transmission band. The modal couplings of the dual-core AR-HCFs rely on a unique mechanism that transfers power through the air. The core separation and the gap between the two cores influence the modal coupling strength. With proper designs, both of the dual-core fibers can have low phase birefringence and short modal coupling lengths of several centimeters.

  14. 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

  15. Cool Core Clusters from Cosmological Simulations

    CERN Document Server

    Rasia, E; Murante, G; Planelles, S; Beck, A M; Biffi, V; Ragone-Figueroa, C; Granato, G L; Steinborn, L K; Dolag, K

    2015-01-01

    We present results obtained from a set of cosmological hydrodynamic simulations of galaxy clusters, aimed at comparing predictions with observational data on the diversity between cool-core and non-cool-core clusters. Our simulations include the effects of stellar and AGN feedback and are based on an improved version of the Smoothed-Particle-Hydrodynamics code GADGET-3, which ameliorates gas mixing and better captures gas-dynamical instabilities by including a suitable artificial thermal diffusion. In this Letter, we focus our analysis on the entropy profiles, our primary diagnostic to classify the degree of cool-coreness of clusters, and on the iron profiles. In keeping with observations, our simulated clusters display a variety of behaviors in entropy profiles: they range from steadily decreasing profiles at small radii, characteristic of cool-core systems, to nearly flat core isentropic profiles, characteristic of non cool-core systems. Using observational criteria to distinguish between the two classes of...

  16. 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

    2016-08-02

    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.

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

    Directory of Open Access Journals (Sweden)

    Sepideh Babaei

    2015-05-01

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

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

    NARCIS (Netherlands)

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

    2000-01-01

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

  19. 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.

  20. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    Science.gov (United States)

    Lesne, Annick; Bécavin, Christophe; Victor, Jean–Marc

    2012-02-01

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.