WorldWideScience

Sample records for chromatin fiber dynamics

  1. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    OpenAIRE

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

    2011-01-01

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

  2. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    Science.gov (United States)

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

    2011-01-01

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

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

    OpenAIRE

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

    2004-01-01

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

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

    Science.gov (United States)

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

    2016-03-29

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

  5. The Chromatin Fiber: Multiscale Problems and Approaches

    OpenAIRE

    Ozer, Gungor; Luque, Antoni; Schlick, Tamar

    2015-01-01

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

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

    CERN Document Server

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

    2006-01-01

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

  7. Chromatin state dynamics during blood formation

    OpenAIRE

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

    2014-01-01

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

  8. Chromatin Dynamics of Circadian Transcription

    OpenAIRE

    Aguilar-Arnal, Lorena; Sassone-Corsi, Paolo

    2015-01-01

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

  9. Nucleosome conformational flexibility in experiments with single chromatin fibers

    OpenAIRE

    Sivolob A. V.

    2010-01-01

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

  10. 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.

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

    OpenAIRE

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

    2007-01-01

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

  12. Centromeric chromatin and its dynamics in plants.

    Science.gov (United States)

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

    2015-07-01

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

  13. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

    International Nuclear Information System (INIS)

    Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity. (perspective)

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

    OpenAIRE

    Meshorer, Eran; Herrmann, Harald; Raška, Ivan

    2011-01-01

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

  15. Data on force-dependent structural changes of chromatin fibers measured with magnetic tweezers

    Directory of Open Access Journals (Sweden)

    Fan-Tso Chien

    2014-12-01

    Full Text Available The compaction of chromatin fibers regulates the accessibility of embedded DNA, highly associated with transcriptional activities [1]. Single molecule force spectroscopy has revealed the great details of the structural changes of chromatin fibers in the presence of external exerted force [2–7]. However, most of the studies focus on a specific force regime [2,3,8,9]. The data here show force-extension (FE traces of chromatin fibers as measured with magnetic tweezers, covering the force regime from 0 pN to 27 pN. Those traces provide information for further studies at varied force regimes.

  16. Nucleosome dynamics during chromatin remodeling in vivo.

    Science.gov (United States)

    Ramachandran, Srinivas; Henikoff, Steven

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Hinde Elizabeth

    2012-12-01

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

  18. New insights into chromatin folding and dynamics from multi-scale modeling

    Science.gov (United States)

    Olson, Wilma

    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 roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed 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 with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.

  19. Insights into Chromatin Structure and Dynamics in Plants

    Directory of Open Access Journals (Sweden)

    Stefanie Rosa

    2013-11-01

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

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

    Science.gov (United States)

    Hirakawa, Takeshi; Matsunaga, Sachihiro

    2016-01-01

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

  1. Visualization and Characterization of High-Order Chromatin Fibers under Light Microscope during Interphase and Mitotic Stages in Plants

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Using genomic in situ hybridization with genomic DNA.high-order chromatin fibers were successfully exhibited under a light microscope through the cell cycle in barley,rice,maize and field bean.From the interphase to prophase and metaphase of mitosis,the fibers were basically similar.Each was estimated to be around 200 nm in diameter,but the strength of signals was not the same along the fiber length.Through the cell cycle a series of dynamic distribution changes occurred in the fibers.In the interphase,they were unraveled.At the early prophase they were arranged with parallel and mirror symmetry.During late-prophase and metaphase,the fibers were bundled and became different visible chromosomes.The parallel coiling and mirror symmetry structures were visible clearly until the metaphase.In anaphase they disappeared.During telophase,in peripheral regions of congregated chromosome group,borderlines of the chromosomes disappeared and the fibers were unraveled.This demonstrated that mitotic chromosomes are assembled and organized by parallel and adjacent coiling of the fibers and the fibers should be the highest order structure for DNA coiling.

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

    OpenAIRE

    Martínez Redondo, Paloma

    2014-01-01

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

  3. Live visualization of chromatin dynamics with fluorescent TALEs.

    Science.gov (United States)

    Miyanari, Yusuke; Ziegler-Birling, Céline; Torres-Padilla, Maria-Elena

    2013-11-01

    The spatiotemporal organization of genomes in the nucleus is an emerging key player to regulate genome function. Live imaging of nuclear organization dynamics would be a breakthrough toward uncovering the functional relevance and mechanisms regulating genome architecture. Here, we used transcription activator-like effector (TALE) technology to visualize endogenous repetitive genomic sequences. We established TALE-mediated genome visualization (TGV) to label genomic sequences and follow nuclear positioning and chromatin dynamics in cultured mouse cells and in the living organism. TGV is highly specific, thus allowing differential labeling of parental chromosomes by distinguishing between single-nucleotide polymorphisms (SNPs). Our findings provide a framework to address the function of genome architecture through visualization of nuclear dynamics in vivo. PMID:24096363

  4. Computational strategies to address chromatin structure problems.

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-01-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC...

  7. Early aberrations in chromatin dynamics in embryos produced under In vitro conditions

    DEFF Research Database (Denmark)

    Deshmukh, Rahul Shahaji; Østrup, Olga; Strejcek, Frantisek;

    2012-01-01

    standard to that of embryos produced by IVF, parthenogenetic activation (PA), or SCNT. In contrast to IV embryos, chromatin spatial and temporal dynamics in PA, IVF, and SCNT embryos were altered; starting with aberrant chromatin-nuclear envelope interactions at the two-cell stage, delayed chromatin...... decondensation and nucleolar development at the four-cell stage, and ultimately culminating in failure of proper first lineage segregation at the blastocyst stage, demonstrated by poorly defined inner cell mass. Interestingly, in vitro produced (IVP) embryos also lacked a heterochromatin halo around nucleolar...... precursors, indicating imperfections in global chromatin remodeling after fertilization/activation. Porcine IV-produced zygotes and embryos display a well-synchronized pattern of chromatin dynamics compatible with genome activation and regular nucleolar formation at the four-cell stage. Production of porcine...

  8. Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription

    Directory of Open Access Journals (Sweden)

    Davood Norouzi

    2015-11-01

    Full Text Available The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10-70 bp (nucleosome repeat length NRL = 157-217 bp. In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers—one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers—that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: the fibers with linkers L = 10n and 10n + 5 bp have DNA linking numbers per nucleosome DLk >>-1.5 and -1.0, respectively. In other words, the level of DNA supercoiling is directly related to the length of the inter-nucleosome linker in the chromatin fiber (and therefore, to NRL. We hypothesize that this topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. A genome-wide analysis of the NRL distribution in active and silent yeast genes yielded results consistent with this assumption.

  9. 30 nm染色质的体外组装和电镜分析%In vitro Assembly and Electron Microscopic Analysis of 30 nm Chromatin Fibers

    Institute of Scientific and Technical Information of China (English)

    孙大鹏; 宋峰; 黄丽; 张阔; 季刚; 陈萍; 朱平

    2013-01-01

    Abstract Genomic DNA in the eukaryotic nucleus is hierarchically packaged by histones into chromatin.The plasticity and dynamics of higher-order chromatin fiber have been widely thought as the key regulators of transcription and other biological processes inherent to DNA.Elucidating how nucleosomal arrays can be folded into higher-order chromatin fibers is essential to understand the dynamics of chromatin structure.Although the structure of nucleosomes,the fundamental repeating unit of chromatin,which comprises 147 base pairs of DNA wrapped in 1.7 superhelical turns around an octamer ofhistones,has been solved at the atomic resolution,there is still much controversy over the chromatin structure at the higher-order level.Here,we built an in vitro chromatin reconstitution system which adopts histone octamers and arrays of 177 bp and 200 bp repeat of the Widom 601 DNA sequence.Taking advantage of this system,we have obtained highly regular spaced and soluble nucleosome arrays,and folded the arrays into 30 nm chromatin fibers with the existence of linker histone H1 or MgCh respectively.Several electron microscopic techniques,including metal shadowing,negative staining and Cryo-EM,have been used to investigate the morphology of the reconstituted 30 nm chromatin fibers.Our results suggest that both histone H1 and divalent Mg2+ can help the formation of 30 nm chromatin fibers,but the resulted chromatin fibers display different topologically architectures.To investigate how the length of linker histone may affect the architecture of chromatin,we measured the diameters of the reconstituted 30 nm chromatin fibers with different nucleosome repeat lengths (NRLs) of 177 and 200 bp and found that these two classes of chromatin fibers present different diameters (P < 0.05).%真核生物的基因组以染色质的形式存在,染色质在真核生物的基因表达调控及胚胎发育过程中起重要作用,为表观遗传提供一个重要的信息整合平台.染

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

    Science.gov (United States)

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

    1991-10-01

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

  11. Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics

    Science.gov (United States)

    Aguilar, Carlos A.; Craighead, Harold G.

    2013-10-01

    Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin -- a dynamic complex of nucleic acids and proteins -- is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.

  12. Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Valeria Visone

    2014-09-01

    Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  13. Macronuclear chromatin structure dynamics in Colpoda inflata (Protista, Ciliophora) resting encystment.

    Science.gov (United States)

    Tiano, L; Chessa, M G; Carrara, S; Tagliafierro, G; Delmonte Corrado, M U

    1999-01-01

    The chromatin structure dynamics of the Colpoda inflata macronucleus have been investigated in relation to its functional condition, concerning chromatin body extrusion regulating activity. Samples of 2- and 25-day-old resting cysts derived from a standard culture, and of 1-year-old resting cysts derived from a senescent culture, were examined by means of histogram analysis performed on acquired optical microscopy images. Three groups of histograms were detected in each sample. Histogram classification, clustering and matching were assessed in order to obtain the mean histogram of each group. Comparative analysis of the mean histogram showed a similarity in the grey level range of 25-day- and 1-year-old cysts, unlike the wider grey level range found in 2-day-old cysts. Moreover, the respective mean histograms of the three cyst samples appeared rather similar in shape. All this implies that macronuclear chromatin structural features of 1-year-old cysts are common to both cyst standard cultures. The evaluation of the acquired images and their respective histograms evidenced a dynamic state of the macronuclear chromatin, appearing differently condensed in relation to the chromatin body extrusion regulating activity of the macronucleus. The coexistence of a chromatin-decondensed macronucleus with a pycnotic extrusion body suggests that chromatin unable to decondense, thus inactive, is extruded. This finding, along with the presence of chromatin structural features common to standard and senescent cyst populations, supports the occurrence of 'rejuvenated' cell lines from 1-year-old encysted senescent cells, a phenomenon which could be a result of accomplished macronuclear renewal. PMID:10439214

  14. A high throughput Chromatin ImmunoPrecipitation approach reveals principles of dynamic gene regulation in mammals

    OpenAIRE

    Garber, Manuel; Yosef, Nir; Goren, Alon; Raychowdhury, Raktima; Thielke, Anne; Guttman, Mitchell; Robinson, James; Minie, Brian; Chevrier, Nicolas; Itzhaki, Zohar; Blecher-Gonen, Ronnie; Bornstein, Chamutal; Amann-Zalcenstein, Daniela; Weiner, Assaf; Friedrich, Dennis

    2012-01-01

    Understanding the principles governing mammalian gene regulation has been hampered by the difficulty in measuring in-vivo binding dynamics of large numbers of transcription factors (TF) to DNA. Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA interactions. HT-ChIP was applied to define the dynamics of DNA binding by 25 TFs and 4 chromatin marks at 4 time-points following pathogen stimulus of dendritic cells. Analyzing over 180...

  15. Chromatin Dynamics in Vivo: A Game of Musical Chairs

    Directory of Open Access Journals (Sweden)

    Daniël P. Melters

    2015-08-01

    Full Text Available Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.

  16. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.

    2014-08-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  17. Modal dynamics in multimode fibers

    CERN Document Server

    Fridman, Moti; Nixon, Micha; Friesem, Asher A; Davidson, Nir

    2010-01-01

    The dynamics of modes and their states of polarizations in multimode fibers as a function of time, space, and wavelength are experimentally and theoretically investigated. The results reveal that the states of polarizations are displaced in Poincare sphere representation when varying the angular orientations of the polarization at the incident light. Such displacements, which complicates the interpretation of the results, are overcome by resorting to modified Poincare spheres representation. With such modification it should be possible to predict the output modes and their state of polarization when the input mode and state of polarization are known.

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

    Directory of Open Access Journals (Sweden)

    Hua Wong

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

  19. Time-Lapse Dynamics of the Mouse Oocyte Chromatin Organisation during Meiotic Resumption

    Directory of Open Access Journals (Sweden)

    Martina Belli

    2014-01-01

    Full Text Available In the mammalian oocyte, distinct patterns of centromeres and pericentromeric heterochromatin localisation correlate with the gamete’s developmental competence. Mouse antral oocytes display two main types of chromatin organisation: SN oocytes, with a ring of Hoechst-positive chromatin surrounding the nucleolus, and NSN oocytes lacking this ring. When matured to MII and fertilised, only SN oocytes develop beyond the 2-cell, and reach full term. To give detailed information on the dynamics of the SN or NSN chromatin during meiosis resumption, we performed a 9 hr time-lapse observation. The main significant differences recorded are: (1 reduction of the nuclear area only in SN oocytes; (2 ~17 min delay of GVBD in NSN oocytes; (3 chromatin condensation, after GVBD, in SN oocytes; (4 formation of 4-5 CHCs in SN oocytes; (5 increase of the perivitelline space, ~57 min later in NSN oocytes; (6 formation of a rosette-like disposition of CHCs, ~84 min later in SN oocytes; (7 appearance of the MI plate ~40 min later in NSN oocytes. Overall, we described a pathway of transition from the GV to the MII stage that is punctuated of discrete recordable events showing their specificity and occurring with different time kinetics in the two types of oocytes.

  20. Time-Lapse Dynamics of the Mouse Oocyte Chromatin Organisation during Meiotic Resumption

    Science.gov (United States)

    Redi, Carlo Alberto; Zuccotti, Maurizio

    2014-01-01

    In the mammalian oocyte, distinct patterns of centromeres and pericentromeric heterochromatin localisation correlate with the gamete's developmental competence. Mouse antral oocytes display two main types of chromatin organisation: SN oocytes, with a ring of Hoechst-positive chromatin surrounding the nucleolus, and NSN oocytes lacking this ring. When matured to MII and fertilised, only SN oocytes develop beyond the 2-cell, and reach full term. To give detailed information on the dynamics of the SN or NSN chromatin during meiosis resumption, we performed a 9 hr time-lapse observation. The main significant differences recorded are: (1) reduction of the nuclear area only in SN oocytes; (2) ~17 min delay of GVBD in NSN oocytes; (3) chromatin condensation, after GVBD, in SN oocytes; (4) formation of 4-5 CHCs in SN oocytes; (5) increase of the perivitelline space, ~57 min later in NSN oocytes; (6) formation of a rosette-like disposition of CHCs, ~84 min later in SN oocytes; (7) appearance of the MI plate ~40 min later in NSN oocytes. Overall, we described a pathway of transition from the GV to the MII stage that is punctuated of discrete recordable events showing their specificity and occurring with different time kinetics in the two types of oocytes. PMID:24864231

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

    OpenAIRE

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

    2012-01-01

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

  2. Dynamics of flexible fibers in shear flow

    International Nuclear Information System (INIS)

    Dynamics of flexible non-Brownian fibers in shear flow at low-Reynolds-number are analyzed numerically for a wide range of the ratios A of the fiber bending force to the viscous drag force. Initially, the fibers are aligned with the flow, and later they move in the plane perpendicular to the flow vorticity. A surprisingly rich spectrum of different modes is observed when the value of A is systematically changed, with sharp transitions between coiled and straightening out modes, period-doubling bifurcations from periodic to migrating solutions, irregular dynamics, and chaos

  3. Dynamics of flexible fibers in shear flow

    Energy Technology Data Exchange (ETDEWEB)

    Słowicka, Agnieszka M.; Wajnryb, Eligiusz; Ekiel-Jeżewska, Maria L., E-mail: mekiel@ippt.pan.pl [Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5b, 02-106 Warsaw (Poland)

    2015-09-28

    Dynamics of flexible non-Brownian fibers in shear flow at low-Reynolds-number are analyzed numerically for a wide range of the ratios A of the fiber bending force to the viscous drag force. Initially, the fibers are aligned with the flow, and later they move in the plane perpendicular to the flow vorticity. A surprisingly rich spectrum of different modes is observed when the value of A is systematically changed, with sharp transitions between coiled and straightening out modes, period-doubling bifurcations from periodic to migrating solutions, irregular dynamics, and chaos.

  4. Chromatin Dynamics and the Development of the TCRα and TCRδ Repertoires.

    Science.gov (United States)

    Carico, Zachary; Krangel, Michael S

    2015-01-01

    The adaptive immune system allows vertebrates to orchestrate highly specific responses to a virtually unlimited milieu of antigens. Effective adaptive immune responses depend on the capacity of T and B lymphocytes to generate diverse repertoires of antigen receptors through the recombination of variable (V), diversity (D), and joining (J) gene segments at antigen receptor loci. V(D)J recombination must be carefully regulated during the early stages of T and B lymphocyte development to ensure the proper development of lymphocyte subsets and to maximize antigen receptor combinatorial diversity. Among all T cell receptor (TCR) and immunoglobulin loci, the TCRα/δ (Tcra/Tcrd) locus is unique in its complexity since it undergoes recombination at two distinct stages of T cell development to create distinct TCR proteins that are used by different lineages of T cells. Here, we review the mechanisms that regulate V(D)J recombination at the Tcra/Tcrd locus, with a focus on the dynamic chromatin environment and how it instructs the assembly of the Tcra and Tcrd repertoires. We discuss the dynamics of Tcra and Tcrd repertoire formation in the context of T cell development, and we consider how the recombination program is directed by localized changes in chromatin structure that regulate the accessibility of Tcra and Tcrd gene segments to the V(D)J recombinase. We then move beyond local to address spatial relationships in the nucleus, emphasizing the three-dimensional organization of the Tcra/Tcrd locus as a critical player in understanding long-distance interactions between chromatin regulatory elements as well as long-distance interactions between recombination substrates. PMID:26477370

  5. ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas.

    Science.gov (United States)

    Yang, Hanseul; Schramek, Daniel; Adam, Rene C; Keyes, Brice E; Wang, Ping; Zheng, Deyou; Fuchs, Elaine

    2015-01-01

    Tumor-initiating stem cells (SCs) exhibit distinct patterns of transcription factors and gene expression compared to healthy counterparts. Here, we show that dramatic shifts in large open-chromatin domain (super-enhancer) landscapes underlie these differences and reflect tumor microenvironment. By in vivo super-enhancer and transcriptional profiling, we uncover a dynamic cancer-specific epigenetic network selectively enriched for binding motifs of a transcription factor cohort expressed in squamous cell carcinoma SCs (SCC-SCs). Many of their genes, including Ets2 and Elk3, are themselves regulated by SCC-SC super-enhancers suggesting a cooperative feed-forward loop. Malignant progression requires these genes, whose knockdown severely impairs tumor growth and prohibits progression from benign papillomas to SCCs. ETS2-deficiency disrupts the SCC-SC super-enhancer landscape and downstream cancer genes while ETS2-overactivation in epidermal-SCs induces hyperproliferation and SCC super-enhancer-associated genes Fos, Junb and Klf5. Together, our findings unearth an essential regulatory network required for the SCC-SC chromatin landscape and unveil its importance in malignant progression. PMID:26590320

  6. Nucleosome positioning and composition modulate in silico chromatin flexibility

    Science.gov (United States)

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

    2015-02-01

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

  7. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

    OpenAIRE

    Monica Soldi; Alessandro Cuomo; Michael Bremang; Tiziana Bonaldi

    2013-01-01

    Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, re...

  8. Fiber optics opens window on stream dynamics

    OpenAIRE

    J. Selker; N. C. van de Giesen; M. Westhoff; Luxemburg, W.; Parlange, M.B.

    2006-01-01

    A new approach to monitoring surface waters using distributed fiber optic temperature sensing is presented, allowing resolutions of temperature of 0.01°C every meter along a fiber optic cable of up to 10,000 m in length. We illustrate the potential of this approach by quantifying both stream temperature dynamics and groundwater inflows to the Maisbich, a first-order stream in Luxembourg (49°47'N, 6°02'E). The technique provides a very rich dataset, which may be of interest to many types of en...

  9. Dynamic Strength of Fiber Glass Shells

    OpenAIRE

    Syrunin, M.; Fedorenko, A.; Ivanov, A

    1997-01-01

    This paper presents generalization of results, obtained by experimental investigations of dynamic response, strength, and load-bearing ability of cylindrical and spherical shells, manufactured from composite materials on the basis of fiber glass, under loading them by explosion of compact high-explosive charges on the inside. The paper describes mechanisms and criteria of destruction of such shells, methods to improve their specific load-bearing ability. Results of experiments concerning inve...

  10. Physiological and Pathological Aging Affects Chromatin Dynamics, Structure and Function at the Nuclear Edge.

    Science.gov (United States)

    Robin, Jérôme D; Magdinier, Frédérique

    2016-01-01

    Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains. We will discuss here the impact of A-type Lamins loss on alterations of chromatin organization and formation of chromatin domains and how disorganization of the lamina contributes to the patho-physiology of premature aging syndromes. PMID:27602048

  11. Dynamic pulsing of a MOPA fiber laser

    Science.gov (United States)

    Romero, Rosa; Guerreiro, Paulo T.; Hendow, Sami T.; Salcedo, José R.

    2011-05-01

    Dynamic Pulsing is demonstrated using a pulsed MOPA fiber laser at 1064nm. The output of the MOPA laser is a pulsed profile consisting of a burst of closely spaced pulses. Tests were performed under several materials with pulse bursts ranging from 10ns to 1μs and operating from 500kHz down to single shot. In particular, percussion drilling in stainless steel is demonstrated showing improvements in quality and speed of the process. These profiles allow high flexibility and optimization of the process addressing the specificity of the end application. Dynamic Pulsing allows the same MOPA fiber laser to be used in diverse materials as well as different processes such us marking, drilling, scribing and engraving. The pulsed fiber laser used in this study is a MOPA-DY by Multiwave Photonics. It is based on a modulated seed laser followed by a series of fiber amplifiers and ending with an optically isolated collimator. This pulsed laser model has an output in such a way that each trigger produces a fast burst of pulses, with a repetition frequency within the burst of the order of tens of MHz. Within the burst it is possible to change the number of pulses, the individual pulse profile, burst pulse period and even to generate non-periodic burst pulse separations. The laser allows full freedom for all these combinations. The study here reported compares the impact of pulse peak power, number of pulses within a burst and the pulse burst period, on process quality (heat affected zone, debris, hole uniformity) and drilling yield.

  12. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

    Directory of Open Access Journals (Sweden)

    Monica Soldi

    2013-03-01

    Full Text Available Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

  13. Prenucleosomes and Active Chromatin

    Science.gov (United States)

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

    2016-01-01

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

  14. A Model of Repetitive-DNA-Organized Chromatin Network of Interphase Chromosomes

    Directory of Open Access Journals (Sweden)

    Shao-Jun Tang

    2012-03-01

    Full Text Available During interphase, chromosomes are relatively de-condensed in the nuclear space. Interphase chromosomes are known to occupy nuclear space in a non-random manner (chromosome territory; however, their internal structures are poorly defined. In particular, little is understood about the molecular mechanisms that govern the internal organization of interphase chromosomes. The author recently proposed that pairing (or interaction of repetitive DNA-containing chromatin regions is a critical driving force that specifies the higher-order organization of eukaryotic chromosomes. Guided by this theoretical framework and published experimental data on the structure of interphase chromosomes and the spatial distribution of repetitive DNA in interphase nuclei, I postulate here a molecular structure of chromatin organization in interphase chromosomes. According to this model, an interphase chromosome is a chromatin mesh (or lattice that is formed by repeat pairing (RP. The mesh consists of two types of structural components: chromosome nodes and loose chromatin fibers. Chromosome nodes are DNA repeat assemblies (RAs that are formed via RP, while loose fibers include chromatin loops that radiate from the nodes. Different loops crosslink by RPs and form a large integrated chromatin network. I suggest that the organization of the chromatin network of a given interphase chromosome is intrinsically specified by the distribution of repetitive DNA elements on the linear chromatin. The stability of the organization is governed by the collection of RA-formed nodes, and the dynamics of the organization is driven by the assembling and disassembling of the nodes.

  15. Effects of interfacial debonding and fiber breakage on static and dynamic buckling of fibers in matrices.

    OpenAIRE

    Serttunc, Metin

    1992-01-01

    Approved for public release; distribution is unlimited Analyses were performed for static and dynamic buckling of a continuous fiber embedded in a matrix and fiber breakage in order to determine the effects of interfacial debonding on the critical buckling load and the domain of instability. A beam on elastic foundation model was used for this study. The study showed that a local interfacial debonding between a fiber and a surrounding matrix resulted in an increase of the waveleng...

  16. Dynamic Recruitment of Functionally Distinct Swi/Snf Chromatin Remodeling Complexes Modulates Pdx1 Activity in Islet β Cells

    Directory of Open Access Journals (Sweden)

    Brian McKenna

    2015-03-01

    Full Text Available Pdx1 is a transcription factor of fundamental importance to pancreas formation and adult islet β cell function. However, little is known about the positive- and negative-acting coregulators recruited to mediate transcriptional control. Here, we isolated numerous Pdx1-interacting factors possessing a wide range of cellular functions linked with this protein, including, but not limited to, coregulators associated with transcriptional activation and repression, DNA damage response, and DNA replication. Because chromatin remodeling activities are essential to developmental lineage decisions and adult cell function, our analysis focused on investigating the influence of the Swi/Snf chromatin remodeler on Pdx1 action. The two mutually exclusive and indispensable Swi/Snf core ATPase subunits, Brg1 and Brm, distinctly affected target gene expression in β cells. Furthermore, physiological and pathophysiological conditions dynamically regulated Pdx1 binding to these Swi/Snf complexes in vivo. We discuss how context-dependent recruitment of coregulatory complexes by Pdx1 could impact pancreas cell development and adult islet β cell activity.

  17. Dynamic Characterization of Polymer Optical Fibers

    DEFF Research Database (Denmark)

    Stefani, Alessio; Andresen, Søren; Yuan, Wu;

    2012-01-01

    With the increasing interest in fiber sensors based on polymer optical fibers, it becomes fundamental to determine the real applicability and reliability of this type of sensor. The viscoelastic nature of polymers gives rise to questions about the mechanical behavior of the fibers. In particular,......-relaxation experiment for larger deformations (2.8%) is also reported and a relaxation time around 5 s is measured, defining a viscosity of 20 GPa·s....

  18. Effects of Fibers on the Dynamic Properties of Asphalt Mixtures

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The dynamic characteristics of fiber-modified asphalt mixture were investigated. Cellulose fiber, polyester fiber and mineral fiber were used as additives for asphalt mixture, and the dosage was 0.3%, 0.3%,0.4%, respectively. Dynamic modulus test using SuperPave simple performance tester (SPT) was conducted to study the dynamic modulus (E*) and phase angle (δ) for the control asphalt mixture and fiber-modified ones at various temperatures and frequencies. Experimental results show that all fiber-modified asphalt mixtures have higher dynamic modulus compared with control mixture. The dynamic modulus master curves of each type of asphalt mixtures are determined based on nonlinear least square regression in accordance with the timetemperature superposition theory at a control temperature (21.1 ℃). The fatigue parameter E*×sinδ and rutting parameter E*/sinδ of asphalt mixture are adopted to study the fatigue and rutting-resistance properties, and experimental results indicate that such properties can be improved by fiber additives.

  19. The dynamic response of carbon fiber-filled polymer composites

    OpenAIRE

    Patterson B.; Orler E.B.; Furmanski J.; Rigg P.A.; Scharff R.J.; Stahl D.B.; Sheffield S.A.; Gustavsen R.L.; Dattelbaum D.M.; Coe J.D.

    2012-01-01

    The dynamic (shock) responses of two carbon fiber-filled polymer composites have been quantified using gas gun-driven plate impact experimentation. The first composite is a filament-wound, highly unidirectional carbon fiber-filled epoxy with a high degree of porosity. The second composite is a chopped carbon fiber- and graphite-filled phenolic resin with little-to-no porosity. Hugoniot data are presented for the carbon fiber-epoxy (CE) composite to 18.6 GPa in the through-thickness direction,...

  20. Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development.

    Science.gov (United States)

    Zylicz, Jan J; Dietmann, Sabine; Günesdogan, Ufuk; Hackett, Jamie A; Cougot, Delphine; Lee, Caroline; Surani, M Azim

    2015-01-01

    Early mouse development is accompanied by dynamic changes in chromatin modifications, including G9a-mediated histone H3 lysine 9 dimethylation (H3K9me2), which is essential for embryonic development. Here we show that genome-wide accumulation of H3K9me2 is crucial for postimplantation development, and coincides with redistribution of enhancer of zeste homolog 2 (EZH2)-dependent histone H3 lysine 27 trimethylation (H3K27me3). Loss of G9a or EZH2 results in upregulation of distinct gene sets involved in cell cycle regulation, germline development and embryogenesis. Notably, the H3K9me2 modification extends to active enhancer elements where it promotes developmentally-linked gene silencing and directly marks promoters and gene bodies. This epigenetic mechanism is important for priming gene regulatory networks for critical cell fate decisions in rapidly proliferating postimplantation epiblast cells. PMID:26551560

  1. Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus

    DEFF Research Database (Denmark)

    Launholt, Dorte; Merkle, Thomas; Houben, Andreas;

    2006-01-01

    acidic C-terminal domain interferes with nucleolar targeting of HMGB1. Fluorescence recovery after photobleaching experiments revealed that HMGA and HMGB proteins are extremely dynamic in the nucleus, indicating that they bind chromatin only transiently before moving on to the next site, thereby...

  2. Chromatin structure and DNA damage

    International Nuclear Information System (INIS)

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

  3. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis

    Directory of Open Access Journals (Sweden)

    Mayuri Rege

    2015-11-01

    Full Text Available The histone variant H2A.Z is a hallmark of nucleosomes flanking promoters of protein-coding genes and is often found in nucleosomes that carry lysine 56-acetylated histone H3 (H3-K56Ac, a mark that promotes replication-independent nucleosome turnover. Here, we find that H3-K56Ac promotes RNA polymerase II occupancy at many protein-coding and noncoding loci, yet neither H3-K56Ac nor H2A.Z has a significant impact on steady-state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on RNA levels are revealed only in the absence of the nuclear RNA exosome. H2A.Z is also necessary for the expression of divergent, promoter-proximal noncoding RNAs (ncRNAs in mouse embryonic stem cells. Finally, we show that H2A.Z functions with H3-K56Ac to facilitate formation of chromosome interaction domains (CIDs. Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher-order chromatin structures.

  4. Chromatin dynamics during cell cycle mediate conversion of DNA damage into chromatid breaks and affect formation of chromosomal aberrations: Biological and clinical significance

    Energy Technology Data Exchange (ETDEWEB)

    Terzoudi, Georgia I.; Hatzi, Vasiliki I. [Institute of Radioisotopes and Radiodiagnostic Products, National Centre for Scientific Research ' Demokritos' , 15310 Ag. Paraskevi Attikis, Athens (Greece); Donta-Bakoyianni, Catherine [Oral Diagnosis and Radiology, University of Athens Dental School, Athens (Greece); Pantelias, Gabriel E., E-mail: gabriel@ipta.demokritos.gr [Institute of Radioisotopes and Radiodiagnostic Products, National Centre for Scientific Research ' Demokritos' , 15310 Ag. Paraskevi Attikis, Athens (Greece)

    2011-06-03

    The formation of diverse chromosomal aberrations following irradiation and the variability in radiosensitivity at different cell-cycle stages remain a long standing controversy, probably because most of the studies have focused on elucidating the enzymatic mechanisms involved using simple DNA substrates. Yet, recognition, processing and repair of DNA damage occur within the nucleoprotein complex of chromatin which is dynamic in nature, capable of rapid unfolding, disassembling, assembling and refolding. The present work reviews experimental work designed to investigate the impact of chromatin dynamics and chromosome conformation changes during cell-cycle in the formation of chromosomal aberrations. Using conventional cytogenetics and premature chromosome condensation to visualize interphase chromatin, the data presented support the hypothesis that chromatin dynamic changes during cell-cycle are important determinants in the conversion of sub-microscopic DNA lesions into chromatid breaks. Consequently, the type and yield of radiation-induced chromosomal aberrations at a given cell-cycle-stage depends on the combined effect of DNA repair processes and chromatin dynamics, which is cell-cycle-regulated and subject to up- or down-regulation following radiation exposure or genetic alterations. This new hypothesis is used to explain the variability in radiosensitivity observed at various cell-cycle-stages, among mutant cells and cells of different origin, or among different individuals, and to revisit unresolved issues and unanswered questions. In addition, it is used to better understand hypersensitivity of AT cells and to provide an improved predictive G2-assay for evaluating radiosensitivity at individual level. Finally, experimental data at single cell level obtained using hybrid cells suggest that the proposed hypothesis applies only to the irradiated component of the hybrid.

  5. Molecular dynamics in electrospun amorphous plasticized polylactide fibers

    OpenAIRE

    MONNIER, X; DELPOUVE, N; BASSON, N; GUINAULT, A; DOMENEK, S; Saiter, A; MALLON, P.E; Dargent, E

    2015-01-01

    The molecular dynamics in the amorphous phase of electrospun fibers of polylactide (PLA) has been investigated using the cooperative rearranging region concept. An unusual and significant increase of the cooperativity length at the glass transition induced by the electrospinning has been observed. This behavior is attributed to the singularity of the amorphous phase organization. Electrospun PLA fibers rearrange in a pre-ordered metastable state which is characterized by highly oriented but n...

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

    International Nuclear Information System (INIS)

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

  7. Dynamically tunable optical bottles from an optical fiber

    DEFF Research Database (Denmark)

    Chen, Yuhao; Yan, Lu; Rishøj, Lars Søgaard;

    2012-01-01

    Optical fibers have long been used to impose spatial coherence to shape free-space optical beams. Recent work has shown that one can use higher order fiber modes to create more exotic beam profiles. We experimentally generate optical bottles from Talbot imaging in the coherent superposition of two...... fiber modes excited with long period gratings, and obtain a 28 μm × 6 μm bottle with controlled contrast up to 10.13 dB. Our geometry allows for phase tuning of one mode with respect to the other, which enables us to dynamically move the bottle in free space....

  8. Mitigation of mode instabilities by dynamic excitation of fiber modes

    Science.gov (United States)

    Otto, Hans-Jürgen; Jauregui, Cesar; Stutzki, Fabian; Jansen, Florian; Limpert, Jens; Tünnermann, Andreas

    2013-03-01

    By dynamically varying the power content of the excited fiber modes of the main amplifier of a fiber-based MOPA system at high average output power levels, it was possible to mitigate mode instabilities to a large extent. In order to achieve the excitation variation, we used an acousto-optic deflector in front of the Yb-doped rod-type fiber. Therewith, it was possible to significantly increase both the average and the instantaneous minimum power content of the fundamental mode. This, consequently, led to a substantial improvement of the beam quality and pointing stability at power levels well beyond the threshold of mode instabilities.

  9. Pulling chromatin apart: Unstacking or Unwrapping?

    Directory of Open Access Journals (Sweden)

    Victor Jean Marc

    2012-11-01

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

  10. Chromatin compensation and dynamic aperture of the Sibir'-2 electron storage ring (numerical simulation)

    International Nuclear Information System (INIS)

    Effect of regular qudratic nonlinear fields (sextupole lenses) intended for compensation of linear chromatism nonlinear errors of magnet fields and quadrupole lenses with an account of particle nonequilibrium pulse on the particle dynamics in the Sibir' storage ring was stided by numerical simulation method. 16 refs

  11. The dynamic response of carbon fiber-filled polymer composites

    Directory of Open Access Journals (Sweden)

    Patterson B.

    2012-08-01

    Full Text Available The dynamic (shock responses of two carbon fiber-filled polymer composites have been quantified using gas gun-driven plate impact experimentation. The first composite is a filament-wound, highly unidirectional carbon fiber-filled epoxy with a high degree of porosity. The second composite is a chopped carbon fiber- and graphite-filled phenolic resin with little-to-no porosity. Hugoniot data are presented for the carbon fiber-epoxy (CE composite to 18.6 GPa in the through-thickness direction, in which the shock propagates normal to the fibers. The data are best represented by a linear Rankine-Hugoniot fit: Us = 2.87 + 1.17 ×up(ρ0 = 1.536g/cm3. The shock wave structures were found to be highly heterogeneous, both due to the anisotropic nature of the fiber-epoxy microstructure, and the high degree of void volume. Plate impact experiments were also performed on a carbon fiber-filled phenolic (CP composite to much higher shock input pressures, exceeding the reactants-to-products transition common to polymers. The CP was found to be stiffer than the filament-wound CE in the unreacted Hugoniot regime, and transformed to products near the shock-driven reaction threshold on the principal Hugoniot previously shown for the phenolic binder itself. [19] On-going research is focused on interrogating the direction-dependent dyanamic response and dynamic failure strength (spall for the CE composite in the TT and 0∘ (fiber directions.

  12. Function of chromatin structure and dynamics in DNA damage, repair and misrepair: γ-rays and protons in action

    International Nuclear Information System (INIS)

    According to their physical characteristics, protons and ion beams promise a revolution in cancer radiotherapy. Curing protocols however reflect rather the empirical knowledge than experimental data on DNA repair. This especially holds for the spatio-temporal organization of repair processes in the context of higher-order chromatin structure—the problematics addressed in this work. The consequences for the mechanism of chromosomal translocations are compared for gamma rays and proton beams. - Highlights: ► The majority of DSBs are repaired individually close to the sites of their origin. ► Decondensation of damaged chromatin domains can potentiate clustering of lesions. ► DSB clustering might increase the risk of chromatin translocation. ► Distances of lesions and higher-order chromatin structure influence DSB clustering. ► The conclusions seem to hold both for DSB damage caused by γ-radiation and protons

  13. Dynamics of Soliton Cascades in Fiber Amplifiers

    CERN Document Server

    Arteaga-Sierra, F R; Agrawal, Govind P

    2016-01-01

    We study numerically the formation of cascading solitons when femtosecond optical pulses are launched into a fiber amplifier with less energy than required to form a soliton of equal duration. As the pulse is amplified, cascaded fundamental solitons are created at different distances, without soliton fission, as each fundamental soliton moves outside the gain bandwidth through the Raman-induced spectral shifts. As a result, each input pulse creates multiple, temporally separated, ultrashort pulses of different wavelengths at the amplifier output. The number of pulses depends not only on the total gain of the amplifier but also on the width of input pulses.

  14. Dynamic fiber Bragg grating sensing method

    Science.gov (United States)

    Ho, Siu Chun Michael; Ren, Liang; Li, Hongnan; Song, Gangbing

    2016-02-01

    The measurement of high frequency vibrations is important in many scientific and engineering problems. This paper presents a novel, cost effective method using fiber optic fiber Bragg gratings (FBGs) for the measurement of high frequency vibrations. The method uses wavelength matched FBG sensors, with the first sensor acting as a transmission filter and the second sensor acting as the sensing portion. Energy fluctuations in the reflection spectrum of the second FBG due to wavelength mismatch between the sensors are captured by a photodiode. An in-depth analysis of the optical circuit is provided to predict the behavior of the method as well as identify ways to optimize the method. Simple demonstrations of the method were performed with the FBG sensing system installed on a piezoelectric transducer and on a wind turbine blade. Vibrations were measured with sampling frequencies up to 1 MHz for demonstrative purposes. The sensing method can be multiplexed for use with multiple sensors, and with care, can be retrofitted to work with FBG sensors already installed on a structure.

  15. Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations

    Science.gov (United States)

    Goldar, A.; Arneodo, A.; Audit, B.; Argoul, F.; Rappailles, A.; Guilbaud, G.; Petryk, N.; Kahli, M.; Hyrien, O.

    2016-03-01

    We propose a non-local model of DNA replication that takes into account the observed uncertainty on the position and time of replication initiation in eukaryote cell populations. By picturing replication initiation as a two-state system and considering all possible transition configurations, and by taking into account the chromatin’s fractal dimension, we derive an analytical expression for the rate of replication initiation. This model predicts with no free parameter the temporal profiles of initiation rate, replication fork density and fraction of replicated DNA, in quantitative agreement with corresponding experimental data from both S. cerevisiae and human cells and provides a quantitative estimate of initiation site redundancy. This study shows that, to a large extent, the program that regulates the dynamics of eukaryotic DNA replication is a collective phenomenon that emerges from the stochastic nature of replication origins initiation.

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

    Directory of Open Access Journals (Sweden)

    Rodrigo González-Romero

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

  17. Interplay of ribosomal DNA loci in nucleolar dominance: dominant NORs are up-regulated by chromatin dynamics in the wheat-rye system.

    Directory of Open Access Journals (Sweden)

    Manuela Silva

    Full Text Available BACKGROUND: Chromatin organizational and topological plasticity, and its functions in gene expression regulation, have been strongly revealed by the analysis of nucleolar dominance in hybrids and polyploids where one parental set of ribosomal RNA (rDNA genes that are clustered in nucleolar organizing regions (NORs, is rendered silent by epigenetic pathways and heterochromatization. However, information on the behaviour of dominant NORs is very sparse and needed for an integrative knowledge of differential gene transcription levels and chromatin specific domain interactions. METHODOLOGY/PRINCIPAL FINDINGS: Using molecular and cytological approaches in a wheat-rye addition line (wheat genome plus the rye nucleolar chromosome pair 1R, we investigated transcriptional activity and chromatin topology of the wheat dominant NORs in a nucleolar dominance situation. Herein we report dominant NORs up-regulation in the addition line through quantitative real-time PCR and silver-staining technique. Accompanying this modification in wheat rDNA trascription level, we also disclose that perinucleolar knobs of ribosomal chromatin are almost transcriptionally silent due to the residual detection of BrUTP incorporation in these domains, contrary to the marked labelling of intranucleolar condensed rDNA. Further, by comparative confocal analysis of nuclei probed to wheat and rye NORs, we found that in the wheat-rye addition line there is a significant decrease in the number of wheat-origin perinucleolar rDNA knobs, corresponding to a diminution of the rDNA heterochromatic fraction of the dominant (wheat NORs. CONCLUSIONS/SIGNIFICANCE: We demonstrate that inter-specific interactions leading to wheat-origin NOR dominance results not only on the silencing of rye origin NOR loci, but dominant NORs are also modified in their transcriptional activity and interphase organization. The results show a cross-talk between wheat and rye NORs, mediated by ribosomal chromatin

  18. Dynamics of non-Brownian fiber suspensions under periodic shear.

    Science.gov (United States)

    Franceschini, Alexandre; Filippidi, Emmanouela; Guazzelli, Elisabeth; Pine, David J

    2014-09-21

    We report experiments studying the dynamics of dense non-Brownian fiber suspensions subjected to periodic oscillatory shear. We find that periodic shear initially causes fibers to collide and to undergo irreversible diffusion. As time progresses, the fibers tend to orient in the vorticity direction while the number of collisions decreases. Ultimately, the system goes to one of two steady states: an absorbing steady state, where collisions cease and the fibers undergo reversible trajectories; an active state, where fibers continue to collide causing them to diffuse and undergo irreversible trajectories. Collisions between fibers can be characterized by an effective volume fraction Φ with a critical volume fraction Φc that separates absorbing from active (diffusing) steady states. The effective volume fraction Φ depends on the mean fiber orientation and thus decreases in time as fibers progressively orient under periodic shear. In the limit that the temporal evolution of Φ is slow compared to the activity relaxation time τ, all the data for all strain amplitudes and all concentrations can be scaled onto a single master curve with a functional dependence well-described by t(-β/ν)R(e(-t)R), where tR is the rescaled time. As Φ → Φc, τ diverges. Therefore, for experiments in which Φ(t) starts above Φc but goes to a steady state below Φc, departures from scaling are observed for Φ very near Φc. The critical exponents are measured to be β = 0.84 ± 0.04 and ν = 1.1 ± 0.1, which is consistent with the Manna universality class for directed percolation. PMID:25068577

  19. ELASTIC WAVE SCATTERING AND DYNAMIC STRESS IN COMPOSITE WITH FIBER

    Institute of Scientific and Technical Information of China (English)

    胡超; 李凤明; 黄文虎

    2003-01-01

    Based on the theory of elastic dynamics, multiple scattering of elastic waves and dynamic stress concentrations in fiber-reinforced composite were studied. The analyticalexpressions of elastic waves in different region were presented and an analytic method tosolve this problem was established. The mode coefficients of elastic waves were determinedin accordance with the continuous conditiors of displacement and stress on the boundary ofthe multi-interfaces. By making use of the addition theorem of Hankel functions, theformulations of scattered wave fields in different local coordinates were transformed intothose in one local coordinate to determine the unknown coefficients and dynamic stressconcentration factors. The influence of distance between two inclusions, material propertiesand structural size on the dynamic stress concentration factors near the interfaces wasanalyzed. It indicates in the analysis that distance between two inclusions, materialproperties and structural size has great influence on the dynamic properties of fiber-reinforced composite near the interfaces. As examples, the numerical results of dynamicstress concentration factors near the interfaces in a fiber- reinforced composite are presentedand discussed.

  20. Study on the Dynamic Performance of Polypropylene Fiber Reinforced Concrete

    OpenAIRE

    Zhang Ying; Zheng Chunhang; Wu Rujun; Chen Xi; Guoping Jiang

    2013-01-01

    The dynamic performance of polypropylene fiber reinforced concrete is studied with the SHPB experiment. The relationship of the strain-stress curves are all obtained in the experiment. The crack characteristics of polypropylene reinforced concrete and plain concrete are also investigated. Analyzed the relation between the character on the crack surface of concrete and material properties and the impact pressure. Also the multi-fractal characteristics are given on the crack surface of concrete...

  1. Regular modes in a mixed-dynamics-based optical fiber.

    Science.gov (United States)

    Michel, C; Allgaier, M; Doya, V

    2016-02-01

    A multimode optical fiber with a truncated transverse cross section acts as a powerful versatile support to investigate the wave features of complex ray dynamics. In this paper, we concentrate on the case of a geometry inducing mixed dynamics. We highlight that regular modes associated with stable periodic orbits present an enhanced spatial intensity localization. We report the statistics of the inverse participation ratio whose features are analogous to those of Anderson localized modes. Our study is supported by both numerical and experimental results on the spatial localization and spectral regularity of the regular modes. PMID:26986325

  2. Nuclear organization and dynamics of the DSB-repair. Direct visualization of double strand breaks in functionally different chromatin domains

    Czech Academy of Sciences Publication Activity Database

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

    La Jolla, 2007. s. 46-46. [Symposium on Biological Complexity: Diseases of Transcription. 11.01.2007-14.01.2007, La Jolla] R&D Projects: GA ČR(CZ) GP204/06/P349; GA MŠk(CZ) 1P05OC084 Institutional research plan: CEZ:AV0Z50040507 Keywords : double-strand breaks (DSB) * DSB-repair * higher-order chromatin structure Subject RIV: BO - Biophysics

  3. Dynamic and static strain gauge using superimposed fiber Bragg gratings

    International Nuclear Information System (INIS)

    This paper demonstrates a simple and fast interrogation method for the dynamic and/or static strain gauge using a reflection spectrum from two superimposed fiber Bragg gratings (FBGs). The superimposed FBGs are designed to decrease nonequidistant space of generated a sensing pulse train in a time domain during dynamic strain gauge. By combining centroid finding with smooth filtering methods, both the interrogation speed and accuracy are improved. A four times increase in the interrogation speed of dynamic strain, by generating a 2 kHz optical sensing pulse train from a 500 Hz scanning frequency, is demonstrated experimentally. The interrogation uncertainty and total harmonic distortion characterization of superimposed FBGs are tested and less than 4 pm standard deviation is obtained. (paper)

  4. Temporal nonlinear beam dynamics in infiltrated photonic crystal fibers

    DEFF Research Database (Denmark)

    Bennet, Francis; Rosberg, Christian Romer; Neshev, Dragomir N.;

    -sensing as well as active devices for all-optical switching at low (mW) laser powers. Commercially available PCFs infiltrated with liquids also provide a versatile and compact tool for exploration of the fundamentals of nonlinear beam propagation in periodic photonic structures. To explore the full...... scientific and technological potential of liquid-infiltrated PCFs it is important to understand the temporal dynamics of nonlinear beam propagation in such structures. In this work we consider thermally induced spatial nonlinear effects in infiltrated photonic crystal fibers. We experimentally study the...... temporal dynamics of nonlinear beam reshaping occurring on a short time scale before the establishment of a steady state regime. In experiment, a 532nm laser beam can be injected into a single hole of an infiltrated PCF cladding structure, and the temporal dynamics of the nonlinear response is measured by...

  5. Dynamic modulus and damping of boron, silicon carbide, and alumina fibers

    Science.gov (United States)

    Dicarlo, J. A.; Williams, W.

    1980-01-01

    The dynamic modulus and damping capacity for boron, silicon carbide, and silicon carbide-coated boron fibers were measured from -190 to 800 C. The single fiber vibration test also allowed measurement of transverse thermal conductivity for the silicon carbide fibers. Temperature-dependent damping capacity data for alumina fibers were calculated from axial damping results for alumina-aluminum composites. The dynamic fiber data indicate essentially elastic behavior for both the silicon carbide and alumina fibers. In contrast, the boron-based fibers are strongly anelastic, displaying frequency-dependent moduli and very high microstructural damping. The single fiber damping results were compared with composite damping data in order to investigate the practical and basic effects of employing the four fiber types as reinforcement for aluminum and titanium matrices.

  6. Dynamic crack growth in a fiber-reinforced composite plate

    Institute of Scientific and Technical Information of China (English)

    LIU Kaixin; LIU Weifu; Zhang Jinxiang; LI Rong; ZHANG Guohua; FU Bin

    2005-01-01

    This paper reports an experiment on the failure of a precracked plate made of unidirectional glass-epoxy fiber-reinforced composites subjected to three-point bending impact load. In the experiment, the whole process of crack growth was recorded by using high-speed photographic technique, in which a transmitted light path was adopted. Moreover, a new phenomenon of dynamic fracture has been observed. Based on the results, some preliminary studies have been carried out on the rate and path of the crack growth, as well as the failure mode.

  7. Dynamic gate algorithm for multimode fiber Bragg grating sensor systems.

    Science.gov (United States)

    Ganziy, D; Jespersen, O; Woyessa, G; Rose, B; Bang, O

    2015-06-20

    We propose a novel dynamic gate algorithm (DGA) for precise and accurate peak detection. The algorithm uses a threshold-determined detection window and center of gravity algorithm with bias compensation. We analyze the wavelength fit resolution of the DGA for different values of the signal-to-noise ratio and different peak shapes. Our simulations and experiments demonstrate that the DGA method is fast and robust with better stability and accuracy than conventional algorithms. This makes it very attractive for future implementation in sensing systems, especially based on multimode fiber Bragg gratings. PMID:26193010

  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. Viscoelastic limit of polymer optical fibers: characterization of the dynamic response

    DEFF Research Database (Denmark)

    Stefani, Alessio; Yuan, Scott Wu; Andresen, S.;

    2011-01-01

    Characterization of polymer optical fibers (POFs) in terms of dynamic behavior is important for many sensors applications for which this type of fibers offers big advantages. We report measurements of the Young’s modulus on microstructured and step index polymer optical fibers and their comparison...

  10. Dynamic Landslide Deformation Monitoring with Fiber Bragg Grating Sensors

    Science.gov (United States)

    Moore, J. R.; Gischig, V.; Button, E.; Loew, S.

    2009-12-01

    Fiber optic (FO) strain sensors are a promising new technology for in-situ landslide monitoring. General performance advantages include high resolution, fast sampling rate, and insensitivity to electrical disturbances. Here we describe a new FO monitoring system based on long-gage fiber Bragg grating sensors installed at the Randa Rockslide Laboratory in southern Switzerland. We highlight the advantages and disadvantages of the system, describe relevant first results, and compare FO data to that from traditional instruments already installed on site. The Randa rock slope has been the subject of intensive research since its failure in 1991. Around 5 million cubic meters of rock remains unstable today, moving at rates up to 20 mm / year. Traditional in-situ monitoring techniques have been employed to understand the mechanics and driving forces of the currently unstable rock mass, however these investigations are limited by the resolution and low sampling rate of the sensors. The new FO monitoring system has micro-strain resolution and offers the capability to detect sub-micrometer scale deformations in both triggered-dynamic and continuous measurements. Two types of sensors have been installed: fully-embedded borehole sensors encased in grout at depths of 38, 40, and 68 m, and surface extensometers spanning active tension cracks. Dynamic measurements are triggered by sensor deformation and recorded at 100 Hz, while continuous measurements are logged every 5 minutes. Since installation in August 2008, the FO monitoring system has been operational 90% of the time. Time series deformation data show movement rates consistent with previous borehole extensometer surveys. Accelerated displacements following installation are likely related to long-term curing and dewatering of the grout. A number of interesting transients have been recorded, which in some cases were large enough to trigger rapid sampling. The combination of short- and long-term observation offers new

  11. 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.

  12. Identification of Novel Proteins Co-Purifying with Cockayne Syndrome Group B (CSB Reveals Potential Roles for CSB in RNA Metabolism and Chromatin Dynamics.

    Directory of Open Access Journals (Sweden)

    Serena Nicolai

    Full Text Available The CSB protein, a member of the SWI/SNF ATP dependent chromatin remodeling family of proteins, plays a role in a sub-pathway of nucleotide excision repair (NER known as transcription coupled repair (TCR. CSB is frequently mutated in Cockayne syndrome group B, a segmental progeroid human autosomal recessive disease characterized by growth failure and degeneration of multiple organs. Though initially classified as a DNA repair protein, recent studies have demonstrated that the loss of CSB results in pleiotropic effects. Identification of novel proteins belonging to the CSB interactome may be useful not only for predicting the molecular basis for diverse pathological symptoms of CS-B patients but also for unraveling the functions of CSB in addition to its authentic role in DNA repair. In this study, we performed tandem affinity purification (TAP technology coupled with mass spectrometry and co-immunoprecipitation studies to identify and characterize the proteins that potentially interact with CSB-TAP. Our approach revealed 33 proteins that were not previously known to interact with CSB. These newly identified proteins indicate potential roles for CSB in RNA metabolism involving repression and activation of transcription process and in the maintenance of chromatin dynamics and integrity.

  13. Function of chromatin structure and dynamics in DNA damage, repair and misrepair: gamma-rays and protons in action

    Czech Academy of Sciences Publication Activity Database

    Ježková, L.; Falk, Martin; Falková, Iva; Davídková, Marie; Bačíková, Alena; Štefančíková, Lenka; Vachelová, Jana; Michaelidesová, Anna; Lukášová, Emilie; Boreyko, A.; Krasavin, E.; Kozubek, Stanislav

    2014-01-01

    Roč. 83, SI (2014), s. 128-136. ISSN 0969-8043 R&D Projects: GA MŠk(CZ) EE2.3.30.0030; GA ČR(CZ) GBP302/12/G157; GA ČR(CZ) GAP302/10/1022; GA ČR(CZ) GBP108/12/G108; GA MŠk(CZ) LD12039; GA MŠk(CZ) LD12008 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : DNA double-strand breaks * Higher-order chromatin structure and DSB repair * Formation of chromosomal translocations Subject RIV: BO - Biophysics; BO - Biophysics (UJF-V) Impact factor: 1.231, year: 2014

  14. 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

  15. A FRACTURE STUDY IN GLASS FIBER COMPOSITES IN DYNAMIC TENSION BY MECHANICAL LUMINESCENCE METHOD

    OpenAIRE

    Tamuzh, V.; Krauja, U.; Kalninsh, P.

    1985-01-01

    Some dependencies of the fracture development in glass fiber composites under dynamic tension have been established. A stageful character of the fracture of an angle-ply glass fiber composite has been shown. The onset of the very initial fracture events within the range of the linear material behavior has been detected. The fracture development in glass fiber composites under dynamic tension depends both on the reinforcement layup and strain rate of specimens.

  16. STUDY OF CYANOETHYLATED ALFA FIBER REINFORCED COMPOSITES BY DYNAMIC MECHANICAL ANALYSIS

    OpenAIRE

    Moufida, Ben; Ridha, Ben

    2008-01-01

    Cyanoethylation of long alfa fibers was studied, and these chemically modified fibers were used to manufacture alfa-polyester composites. The dynamic mechanical thermal properties of an unsaturated polyester resin (cured) and of composites of unmodified and chemically modified alfa-polyester were studied using a dynamic mechanical analyzer over a wide temperature range. The data suggest that in spite of the fragility of the cyanoethylated alfa fibers compared to the unmodified ones, both unmo...

  17. Fiber

    Science.gov (United States)

    Diet - fiber; Roughage; Bulk ... Dietary fiber adds bulk to your diet. Because it makes you feel full faster, it can help with ... Elsevier Saunders; 2016:chap 213. National Research Council. ... Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids ( ...

  18. Fiber

    Science.gov (United States)

    Diet - fiber; Roughage; Bulk ... Dietary fiber adds bulk to your diet. Because it makes you feel full faster, it can help with weight control. Fiber aids digestion and helps prevent constipation . It is ...

  19. Experiment investigation for dynamic behavior of hybrid fiber effects on reactive powder concrete

    Science.gov (United States)

    Wang, Liwen; Pang, Baojun; Yang, Zhenqi; Chi, Runqiang

    2010-03-01

    The influences of different hybrid fibers (steel fibers add polyvinyl-alcohol fibers) mixture rates for reactive power concrete's (RPC) dynamic mechanical behavior after high temperature burnt was investigated by the Split Hopkinson pressure bar (SHPB) device. A plumbic pulse shaper technique was applied in the experiment, PVDF stress gauge was used to monitor the stress uniformity state within the specimen. The strain rate was between 75~85s-1, base on the stressstrain curves and dynamic modes of concrete specimen, the hybrid fiber effect on the dynamic properties was determined. The results show, dynamic compression strength of specimens which mixed with steel fibers (1.0%,1.5%,2.0% vol. rate) and 0.1% PVA fibers is higher than normal reactive powder concrete (NRPC), but the toughness improves unconspicuous; while strength of the one which has both steel fiber (1.0%,1.5%,2.0% vol. rate) and 0.2%PVA fiber declines than NRPC but the toughness improves and the plastic behaviors strengthened, stress-strain curve has evident rising and plate portions. It can be deduced that the concrete with mixed two kinds of fibers has improved dynamic mechanical properties after high temperature burnt. By compounding previous literature results, the mechanism of the experimental results can be explained.

  20. Where splicing joins chromatin

    OpenAIRE

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

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

  1. Unsteady Dynamics of free falling of multi flexible fibers in moderate Reynolds number flows

    Science.gov (United States)

    Qi, Dewei

    2007-11-01

    The direct simulations of sedimentation of single and multi flexible fibers are conducted in moderate Reynolds number flows by using a newly developed method. In the method, for fluid domain, the lattice Boltzmann equations are used to solve the Navier Stokes equations. For solid domain, a fiber is discretized as a chain of rigid segments. The segments are connected through ball and socket joints and can be bent and twisted. Constraint forces are introduced at each joint. Translation and rotation matrix of fiber are linearized with respect to the constraint forces up to a second order of time step. Thus, motion of the fiber under the constraint and hydrodynamic forces could be solved by using a modified leap-frog algorithm. Effects of many body interaction on fiber fluttering are studied. It is found that in the same conditions initial fluttering may be damped by fluid viscosity for a single flexible fiber while irregular and persistent fluttering, rocking and oscillation may occur for a multi- fiber system. It is evident that clusters, such as doublets and triplets, are spontaneously formed and have a profound impact on unsteady dynamics of fibers. Two mechanisms contribute to an increase in unsteadiness. First the clusters have larger local settling velocity than a single fiber. Second, closely packed fibers become more ``fat'' or ``thick'' body and have a lower effective aspect ratio. The flows behind the 'fat' clusters tend to be more unsteady and induce vortex shedding that causes fibers persistently fluttering, rocking or oscillating. It is found that a fiber chain with a long vertical dimension is not stable. They will break down and become more flat structure. This property is directly related to that the fiber is preferentially oriented in horizontal direction due to inertia. In addition, the effects of flexibility on unsteady dynamics of sedimentation of flexible fiber are studied in a given range of Re. We find that when stiffness is very large, the

  2. Simulating Fiber Ordering and Aggregation In Shear Flow Using Dissipative Particle Dynamics

    Science.gov (United States)

    Stimatze, Justin T.

    We have developed a mesoscale simulation of fiber aggregation in shear flow using LAMMPS and its implementation of dissipative particle dynamics. Understanding fiber aggregation in shear flow and flow-induced microstructural fiber networks is critical to our interest in high-performance composite materials. Dissipative particle dynamics enables the consideration of hydrodynamic interactions between fibers through the coarse-grained simulation of the matrix fluid. Correctly simulating hydrodynamic interactions and accounting for fluid forces on the microstructure is required to correctly model the shear-induced aggregation process. We are able to determine stresses, viscosity, and fiber forces while simulating the evolution of a model fiber system undergoing shear flow. Fiber-fiber contact interactions are approximated by combinations of common pairwise forces, allowing the exploration of interaction-influenced fiber behaviors such as aggregation and bundling. We are then able to quantify aggregate structure and effective volume fraction for a range of relevant system and fiber-fiber interaction parameters. Our simulations have demonstrated several aggregate types dependent on system parameters such as shear rate, short-range attractive forces, and a resistance to relative rotation while in contact. A resistance to relative rotation at fiber-fiber contact points has been found to strongly contribute to an increased angle between neighboring aggregated fibers and therefore an increase in average aggregate volume fraction. This increase in aggregate volume fraction is strongly correlated with a significant enhancement of system viscosity, leading us to hypothesize that controlling the resistance to relative rotation during manufacturing processes is important when optimizing for desired composite material characteristics.

  3. All-optical calculus based on dynamic Brillouin grating reflectors in optical fibers

    OpenAIRE

    Primerov, Nikolay; Chin, Sang Hoon; Thévenaz, Luc; Ursini, Leonora; Santagiustina, Marco

    2011-01-01

    We experimentally demonstrate that all-optical signal calculus can be realized based on dynamic Brillouin gratings in optical fibers. Temporal integration and first-order differentiation were performed for optical pulse with various waveforms.

  4. Effects of Non-fiber Carbohydrate to Neutral Detergent Fiber Ratios on Ruminal pH Dynamics in Dairy Goats

    Institute of Scientific and Technical Information of China (English)

    HU Hong-lian; LU De-xun; LIU Da-cheng

    2011-01-01

    IntroductionSubacute ruminal acidosis (SARA)has become common and important economic and health issues for high-yielding dairy cows.Rumen pH takes a central position in the pathogenesis of SARA.So monitoring of rumen pH is play important role in recognizing,quantifying and subsequently controlling this disorder.The objective of the present study was to determine effects of different non-fiber carbohydrate to neutral detergent fiber ratios on ruminal pH dynamics.

  5. Tunable and reconfigurable multi-tap microwave photonic filter based on dynamic Brillouin gratings in fibers

    OpenAIRE

    Sancho Durá, Juan; Sales Maicas, Salvador; Primerov, N.; Chin, S; Antman, Y.; Zadok, A; Thevenaz, L.

    2012-01-01

    We propose and experimentally demonstrate new architectures to realize multi-tap microwave photonic filters, based on the generation of a single or multiple dynamic Brillouin gratings in polarization maintaining fibers. The spectral range and selectivity of the proposed periodic filters is extensively tunable, simply by reconfiguring the positions and the number of dynamic gratings along the fiber respectively. In this paper, we present a complete analysis of three different configurations co...

  6. Anomalous thermal dynamics of Bragg gratings inscribed in germanosilicate optical fiber

    OpenAIRE

    Rahman, A.; Madhav, Venu K; B. Srinivasan; S. Asokan

    2009-01-01

    An interesting, periodic appearance of a new peak has been observed in the reflected spectrum of a Fiber Bragg Grating (FBG) inscribed in a germanosilicate fiber during thermal treatment. The new peak occurs on the longer wavelength side of the spectrum during heating and on the shorter wavelength side during cooling, following an identical reverse dynamics. Comparison with a commercial grating with 99.9% reflectivity shows a similar decay dynamics. It is proposed that the distortion due to s...

  7. Dynamic Strain Measured by Mach-Zehnder Interferometric Optical Fiber Sensors

    OpenAIRE

    Shiuh-Chuan Her; Chih-Min Yang

    2012-01-01

    Optical fibers possess many advantages such as small size, light weight and immunity to electro-magnetic interference that meet the sensing requirements to a large extent. In this investigation, a Mach-Zehnder interferometric optical fiber sensor is used to measure the dynamic strain of a vibrating cantilever beam. A 3 × 3 coupler is employed to demodulate the phase shift of the Mach-Zehnder interferometer. The dynamic strain of a cantilever beam subjected to base excitation is determined by ...

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

    Science.gov (United States)

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

    2016-06-30

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

  9. Molecular dynamics simulation of {beta}-sheet formation in self-assembled peptide amphiphile fibers

    Energy Technology Data Exchange (ETDEWEB)

    Lee, One-Sun; Liu Yamei; Schatz, George C., E-mail: schatz@chem.northwestern.edu [Northwestern University, Department of Chemistry (United States)

    2012-08-15

    The influence of amino acid sequence on the secondary structure of peptide amphiphile (PAs) cylindrical micelles and fibers that are self-assembled in solution is studied using molecular dynamics simulations. Simulations for two choices of PAs were performed, starting with structures that have the correct overall shape, but which restructure considerably during the simulation, with one fiber being composed of valine rich PAs and the other of alanine rich PAs. Self-assembly is similar in both simulations, with stable fibers (diameter is 7.7-8 nm) obtained after 40 ns. We find that the valine rich PA fiber has a higher {beta}-sheet population than the alanine rich fiber, and that the number of hydrogen bonds is higher. This behavior of the valine rich fiber is consistent with experimental measurements of higher stiffness, and it shows that stiffness can be varied while still maintaining self-assembly.

  10. A novel Toxoplasma gondii nuclear factor TgNF3 is a dynamic chromatin-associated component, modulator of nucleolar architecture and parasite virulence.

    Directory of Open Access Journals (Sweden)

    Alejandro Olguin-Lamas

    2011-03-01

    Full Text Available In Toxoplasma gondii, cis-acting elements present in promoter sequences of genes that are stage-specifically regulated have been described. However, the nuclear factors that bind to these cis-acting elements and regulate promoter activities have not been identified. In the present study, we performed affinity purification, followed by proteomic analysis, to identify nuclear factors that bind to a stage-specific promoter in T. gondii. This led to the identification of several nuclear factors in T. gondii including a novel factor, designated herein as TgNF3. The N-terminal domain of TgNF3 shares similarities with the N-terminus of yeast nuclear FK506-binding protein (FKBP, known as a histone chaperone regulating gene silencing. Using anti-TgNF3 antibodies, HA-FLAG and YFP-tagged TgNF3, we show that TgNF3 is predominantly a parasite nucleolar, chromatin-associated protein that binds specifically to T. gondii gene promoters in vivo. Genome-wide analysis using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq identified promoter occupancies by TgNF3. In addition, TgNF3 has a direct role in transcriptional control of genes involved in parasite metabolism, transcription and translation. The ectopic expression of TgNF3 in the tachyzoites revealed dynamic changes in the size of the nucleolus, leading to a severe attenuation of virulence in vivo. We demonstrate that TgNF3 physically interacts with H3, H4 and H2A/H2B assembled into bona fide core and nucleosome-associated histones. Furthermore, TgNF3 interacts specifically to histones in the context of stage-specific gene silencing of a promoter that lacks active epigenetic acetylated histone marks. In contrast to virulent tachyzoites, which express the majority of TgNF3 in the nucleolus, the protein is exclusively located in the cytoplasm of the avirulent bradyzoites. We propose a model where TgNF3 acts essentially to coordinate nucleolus and nuclear functions by modulating

  11. Air-clad fibers: pump absorption assisted by chaotic wave dynamics?

    OpenAIRE

    Mortensen, Niels Asger

    2007-01-01

    Wave chaos is a concept which has already proved its practical usefulness in design of double-clad fibers for cladding-pumped fiber lasers and fiber amplifiers. In general, classically chaotic geometries will favor strong pump absorption and we address the extent of chaotic wave dynamics in typical air-clad geometries. While air-clad structures supporting sup-wavelength convex air-glass interfaces (viewed from the high-index side) will promote chaotic dynamics we find guidance of regular whis...

  12. Dynamic Strain Measured by Mach-Zehnder Interferometric Optical Fiber Sensors

    Directory of Open Access Journals (Sweden)

    Shiuh-Chuan Her

    2012-03-01

    Full Text Available Optical fibers possess many advantages such as small size, light weight and immunity to electro-magnetic interference that meet the sensing requirements to a large extent. In this investigation, a Mach-Zehnder interferometric optical fiber sensor is used to measure the dynamic strain of a vibrating cantilever beam. A 3 × 3 coupler is employed to demodulate the phase shift of the Mach-Zehnder interferometer. The dynamic strain of a cantilever beam subjected to base excitation is determined by the optical fiber sensor. The experimental results are validated with the strain gauge.

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

    Science.gov (United States)

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

    2001-11-01

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

  14. Chromatin deregulation in disease.

    Science.gov (United States)

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

    2016-03-01

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

  15. Dynamic characterization of small fibers based on the flexural vibrations of a piezoelectric cantilever probe

    Science.gov (United States)

    Zhang, Xiaofei; Ye, Xuan; Li, Xide

    2016-08-01

    In this paper, we present a cantilever-probe system excited by a piezoelectric actuator, and use it to measure the dynamic mechanical properties of a micro- and nanoscale fiber. Coupling the fiber to the free end of the cantilever probe, we found the dynamic stiffness and damping coefficient of the fiber from the resonance frequency and the quality factor of the fiber-cantilever-probe system. The properties of Bacillus subtilis fibers measured using our proposed system agreed with tensile measurements, validating our method. Our measurements show that the piezoelectric actuator coupled to cantilever probe can be made equivalent to a clamped cantilever with an effective length, and calculated results show that the errors of measured natural frequency of the system can be ignored if the coupled fiber has an inclination angle of alignment of less than 10°. A sensitivity analysis indicates that the first or second resonant mode is the sensitive mode to test the sample’s dynamic stiffness, while the damping property has different sensitivities for the first four modes. Our theoretical analysis demonstrates that the double-cantilever probe is also an effective sensitive structure that can be used to perform dynamic loading and characterize dynamic response. Our method has the advantage of using amplitude-frequency curves to obtain the dynamic mechanical properties without directly measuring displacements and forces as in tensile tests, and it also avoids the effects of the complex surface structure and deformation presenting in contact resonance method. Our method is effective for measuring the dynamic mechanical properties of fiber-like one-dimensional (1D) materials.

  16. Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons.

    Science.gov (United States)

    Jonkers, Iris; Kwak, Hojoong; Lis, John T

    2014-01-01

    Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ∼3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.DOI: http://dx.doi.org/10.7554/eLife.02407.001. PMID:24843027

  17. 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...

  18. 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.

  19. 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.

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

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Griffith, J

    1977-01-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    identified dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors, and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1, and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the...

  2. FEM Analysis of Dynamic Response of Buried Fiber Reinforced Plastic Matrix Pipe under Seismic Load

    OpenAIRE

    Xu Lei; Ye Zhicai; Ren Qingwen; Zhang Lei

    2013-01-01

    Fiber reinforced plastic matrix pipes have been widely used in the field of civil engineering and hydraulic engineering. In general, the existing FEM models used in the seismic analysis of buried pipes do not fully consider the dynamic interaction between pipe and surrounding soil, and most of the models are proposed for homogeneous pipe. Therefore, the existing models cannot be directly applied to the seismic analysis of fiber reinforced plastic matrix pipes with laminated structure. Based o...

  3. Computational Model of Cellular Metabolic Dynamics in Skeletal Muscle Fibers during Moderate Intensity Exercise

    OpenAIRE

    Li, Yanjun; Lai, Nicola; Kirwan, John P; Saidel, Gerald M.

    2012-01-01

    Human skeletal muscles have different fiber types with distinct metabolic functions and physiological properties. The quantitative metabolic responses of muscle fibers to exercise provide essential information for understanding and modifying the regulatory mechanisms of skeletal muscle. Since in vivo data from skeletal muscle during exercise is limited, a computational, physiologically based model has been developed to quantify the dynamic metabolic responses of many key chemical species. Thi...

  4. A computational study of stress fiber-focal adhesion dynamics governing cell contractility

    OpenAIRE

    Maraldi, Mirko; Valero, Clara; Garikipati, Krishna

    2014-01-01

    We apply a recently developed model of cytoskeletal force generation to study a cell intrinsic contractility, as well as its response to external loading. The model is based on a non-equilibrium thermodynamic treatment of the mechano-chemistry governing force in the stress fiber-focal adhesion system. Our computational study suggests that the mechanical coupling between the stress fibers and focal adhesions leads to a complex, dynamic, mechano-chemical response. We collect the results in resp...

  5. Soliton dynamics in gas-filled hollow-core photonic crystal fibers

    CERN Document Server

    Saleh, Mohammed F

    2015-01-01

    Gas-filled hollow-core photonic crystal fibers offer unprecedented opportunities to observe novel nonlinear phenomena. The various properties of gases that can be used to fill these fibers give additional degrees of freedom for investigating nonlinear pulse propagation in a wide range of different media. In this review, we will consider some of the the new nonlinear interactions that have been discovered in recent years, in particular those which are based on soliton dynamics.

  6. Soliton dynamics in gas-filled hollow-core photonic crystal fibers

    International Nuclear Information System (INIS)

    Gas-filled hollow-core photonic crystal fibers offer unprecedented opportunities to observe novel nonlinear phenomena. The various properties of gases that can be used to fill these fibers give additional degrees of freedom for investigating nonlinear pulse propagation in a wide range of different media. In this review, we will consider some of the the new nonlinear interactions that have been discovered in recent years, in particular those which are based on soliton dynamics. (topical review)

  7. Air-clad fibers: pump absorption assisted by chaotic wave dynamics?

    DEFF Research Database (Denmark)

    Mortensen, Niels Asger

    2007-01-01

    Wave chaos is a concept which has already proved its practical usefulness in design of double-clad fibers for cladding-pumped fiber lasers and fiber amplifiers. In general, classically chaotic geometries will favor strong pump absorption and we address the extent of chaotic wave dynamics in typical...... air-clad structures may thus suppress the pump-absorption efficiency η below the ergodic scaling law η∞ Ac/Acl, where Ac and Acl are the areas of the rare-earth doped core and the cladding, respectively....

  8. Static and dynamic mechanical properties of alkali treated unidirectional continuous Palmyra Palm Leaf Stalk Fiber/jute fiber reinforced hybrid polyester composites

    International Nuclear Information System (INIS)

    Highlights: • New type of hybrid composite with Palmyra Palm Leaf Stalk Fibers (PPLSF) and jute. • Composites fabricated with continuous, unidirectional fibers. • Alkali treatment and hybridizing jute imparted good static and dynamic properties. • Properties are comparable with well know natural/glass fiber composites. • New hybrid composite can be an alternative in place of synthetic fiber composites. - Abstract: Alkali treated continuous Palmyra Palm Leaf Stalk Fiber (PPLSF) and jute fibers were used as reinforcement in unsaturated polyester matrix and their static and dynamic mechanical properties were evaluated. Continuous PPLSF and jute fibers were aligned unidirectionally in bi-layer arrangement and the hybrid composites were fabricated by compression molding process. Positive hybrid effect was observed for the composites due to hybridization. Increasing jute fiber loading showed a considerable increase in tensile and flexural properties of the hybrid composites as compared to treated PPLSF composites. Scanning Electron microscopy (SEM) of the fractured surfaces showed the nature of fiber/matrix interface. The impact strength of the hybrid composites were observed to be less compared to pure PPLSF composites. Addition of jute fibers to PPLSF and alkali treatment of the fibers has enhanced the storage and loss modulus of the hybrid composites. A positive shift of Tan δ peaks to higher temperature and reduction in the peak height of the composites was also observed. The composites with higher jute loading showed maximum damping behavior. Overall the hybridization was found to be efficient showing increased static and dynamic mechanical properties. A comparative study of properties of this hybrid composite with other hybrids made out of using natural/glass fibers is elaborated. Hybridization of alkali treated jute and PPLSF has resulted in enhanced properties which are comparable with other natural/glass fiber composites thus increasing the scope of

  9. Dynamics of Cancer Cell near Collagen Fiber Chain

    Science.gov (United States)

    Kim, Jihan; Sun, Bo

    Cell migration is an integrated process that is important in life. Migration is essential for embryonic development as well as homeostatic processes such as wound healing and immune responses. When cell migrates through connective extracellular matrix (ECM), it applies cellular traction force to ECM and senses the rigidity of their local environment. We used human breast cancer cell (MDA-MB-231) which is highly invasive and applies strong traction force to ECM. As cancer cell applies traction force to type I collage-based ECM, it deforms collagen fibers near the surface. Patterns of deforming collagen fibers are significantly different with pairs of cancer cells compared to a single cancer cell. While a pair of cancer cells within 60 um creates aligned collagen fiber chains between them permanently, a single cancer cell does not form any fiber chains. In this experiment we measured a cellular response and an interaction between a pair of cells through the chain. Finally, we analyzed correlation of directions between cancer cell migration and the collagen chain alignment.

  10. Dynamic gate algorithm for multimode fiber Bragg grating sensor systems

    DEFF Research Database (Denmark)

    Ganziy, Denis; Jespersen, O.; Woyessa, Getinet;

    2015-01-01

    -to-noise ratio and different peak shapes. Our simulations and experiments demonstrate that the DGA method is fast and robust with better stability and accuracy than conventional algorithms. This makes it very attractive for future implementation in sensing systems, especially based on multimode fiber Bragg...

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

    Energy Technology Data Exchange (ETDEWEB)

    Olins, D E

    1977-01-01

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

  12. Experimental Study on Common and Steel Fiber Reinforced Concrete Under Dynamic Tensile Stress

    Institute of Scientific and Technical Information of China (English)

    董新龙; 陈江瑛; 高培正; 祁振林; 王永忠; 王永刚; 王礼立

    2004-01-01

    Split Hopkinson technique has been developed to test the strength of common concrete and steel fiber reinforced concrete under dynamic tensile stress. Two types of test methods are considered, the splitting tensile test and a modified spalling test in which a specimen is loaded under uniaxial stress. The result shows that the dynamic strength enhancement of concrete is remarkable by using the reinforcing fiber. But for the common concrete, the base of compressive strength seems to show little effect on the tensile strength under dynamic loading. The experimental results also show that the resistance to tensile fracture of the steel fiber reinforced concrete for C100-mix is higher than those of C40-mix.

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

    Science.gov (United States)

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

    2002-01-01

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

  14. Chromatin chemistry goes cellular.

    OpenAIRE

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

    2015-01-01

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

  15. Analysis of Chromatin Organisation

    Science.gov (United States)

    Szeberenyi, Jozsef

    2011-01-01

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

  16. Where splicing joins chromatin

    Czech Academy of Sciences Publication Activity Database

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

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

  17. Determination of Water Diffusion Coefficients and Dynamics in Adhesive/ Carbon Fiber Reinforced Epoxy Resin Composite Joints

    Institute of Scientific and Technical Information of China (English)

    WANG Chao; WANG Zhi; WANG Jing; SU Tao

    2007-01-01

    To determinate the water diffusion coefficients and dynamics in adhesive/carbon fiber reinforced epoxy resin composite joints, energy dispersive X-ray spectroscopy analysis(EDX) is used to establish the content change of oxygen in the adhesive in adhesive/carbon fiber reinforced epoxy resin composite joints. As water is made up of oxygen and hydrogen, the water diffusion coefficients and dynamics in adhesive/carbon fiber reinforced epoxy resin composite joints can be obtained from the change in the content of oxygen in the adhesive during humidity aging, via EDX analysis. The authors have calculated the water diffusion coefficients and dynamics in the adhesive/carbon fiber reinforced epoxy resin composite joints with the aid of both energy dispersive X-ray spectroscopy and elemental analysis. The determined results with EDX analysis are almost the same as those determined with elemental analysis and the results also show that the durability of the adhesive/carbon fiber reinforced epoxy resin composite joints subjected to silane coupling agent treatment is better than those subjected to sand paper burnishing treatment and chemical oxidation treatment.

  18. Direct Measurement of Local Chromatin Fluidity Using Optical Trap Modulation Force Spectroscopy

    OpenAIRE

    Roopa, T.; Shivashankar, G. V.

    2006-01-01

    Chromatin assembly is condensed by histone tail-tail interactions and other nuclear proteins into a highly compact structure. Using an optical trap modulation force spectroscopy, we probe the effect of tail interactions on local chromatin fluidity. Chromatin fibers, purified from mammalian cells, are tethered between a microscope coverslip and a glass micropipette. Mechanical unzipping of tail interactions, using the micropipette, lead to the enhancement of local fluidity. This is measured us...

  19. 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.

  20. Air-clad fibers: pump absorption assisted by chaotic wave dynamics?

    CERN Document Server

    Mortensen, Niels Asger

    2007-01-01

    Wave chaos is a concept which has already proved its practical usefulness in design of double-clad fibers for cladding-pumped fiber lasers and fiber amplifiers. In general, classically chaotic geometries will favor strong pump absorption and we address the extent of chaotic wave dynamics in typical air-clad geometries. While air-clad structures supporting sup-wavelength convex air-glass interfaces (viewed from the high-index side) will promote chaotic dynamics we find guidance of regular whispering-gallery modes in air-clad structures resembling an overall cylindrical symmetry. Highly symmetric air-clad structures may thus suppress the pump-absorption efficiency eta below the ergodic scaling law eta proportional to Ac/Acl, where Ac and Acl are the areas of the rare-earth doped core and the cladding, respectively.

  1. Variable optical attenuator and dynamic mode group equalizer for few mode fibers.

    Science.gov (United States)

    Blau, Miri; Weiss, Israel; Gerufi, Jonathan; Sinefeld, David; Bin-Nun, Moran; Lingle, Robert; Grüner-Nielsen, Lars; Marom, Dan M

    2014-12-15

    Variable optical attenuation (VOA) for three-mode fiber is experimentally presented, utilizing an amplitude spatial light modulator (SLM), achieving up to -28dB uniform attenuation for all modes. Using the ability to spatially vary the attenuation distribution with the SLM, we also achieve up to 10dB differential attenuation between the fiber's two supported mode group (LP₀₁ and LP₁₁). The spatially selective attenuation serves as the basis of a dynamic mode-group equalizer (DME), potentially gain-balancing mode dependent optical amplification. We extend the experimental three mode DME functionality with a performance analysis of a fiber supporting 6 spatial modes in four mode groups. The spatial modes' distribution and overlap limit the available dynamic range and performance of the DME in the higher mode count case. PMID:25606998

  2. Tunable and reconfigurable multi-tap microwave photonic filter based on dynamic Brillouin gratings in fibers.

    Science.gov (United States)

    Sancho, J; Primerov, N; Chin, S; Antman, Y; Zadok, A; Sales, S; Thévenaz, L

    2012-03-12

    We propose and experimentally demonstrate new architectures to realize multi-tap microwave photonic filters, based on the generation of a single or multiple dynamic Brillouin gratings in polarization maintaining fibers. The spectral range and selectivity of the proposed periodic filters is extensively tunable, simply by reconfiguring the positions and the number of dynamic gratings along the fiber respectively. In this paper, we present a complete analysis of three different configurations comprising a microwave photonic filter implementation: a simple notch-type Mach-Zehnder approach with a single movable dynamic grating, a multi-tap performance based on multiple dynamic gratings and finally a stationary grating configuration based on the phase modulation of two counter-propagating optical waves by a common pseudo-random bit sequence (PRBS). PMID:22418495

  3. Reflective SOA fiber cavity adaptive laser source for measuring dynamic strains

    Science.gov (United States)

    Wei, Heming; Tao, Chuanyi; Krishnaswamy, Sridhar

    2016-04-01

    Smart sensors based on Optical fiber Bragg gratings (FBGs) are suitable for structural health monitoring of dynamic strains in civil, aerospace, and mechanical structures. In these structures, dynamic strains with high frequencies reveal acoustic emissions cracking or impact loading. It is necessary to find a practical tool for monitoring such structural damages. In this work, we explore an intelligent system based on a reflective semiconductor optical amplifier (RSOA)- FBG composed as a fiber cavity for measuring dynamic strain in intelligent structures. The ASE light emitted from a RSOA laser and reflected by a FBG is amplified in the fiber cavity and coupled out by a 90:10 coupler, which is demodulated by a low frequency compensated Michelson interferometer using a proportional-integral-derivative (PID) controller and is monitored via a photodetector. As the wavelength of the FBG shifts due to dynamic strain, the wavelength of the optical output from the laser cavity shifts accordingly, which is demodulated by the Michelson Interferometer. Because the RSOA has a quick transition time, the RSOA- FBG fiber cavity shows an ability of high frequency response to the FBG reflective spectrum shift, with frequency response extending to megahertz.

  4. DNA-Protein interactions in nucleosomes and in Chromatin

    International Nuclear Information System (INIS)

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

  5. Fiber

    Science.gov (United States)

    ... a fiber-rich sandwich with whole-grain bread, peanut butter, and bananas. Use whole-grain spaghetti and other ... cookies and muffins. Top whole-wheat crackers with peanut butter or low-fat cheese. Go easy on the ...

  6. Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2002-01-01

    textabstractTo approach by virtual microscopy the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was fold

  7. Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2003-01-01

    textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the M

  8. Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2002-01-01

    textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the Mu

  9. Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2002-01-01

    textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the M

  10. Chromatin dynamics in pollen mother cells underpin a common scenario at the somatic-to-reproductive fate transition of both the male and female lineages in Arabidopsis

    OpenAIRE

    She, Wenjing; Baroux, Célia

    2015-01-01

    Unlike animals, where the germline is established early during embryogenesis, plants set aside their reproductive lineage late in development in dedicated floral organs. The specification of pollen mother cells (PMC) committed to meiosis takes place in the sporogenous tissue in anther locules and marks the somatic-to-reproductive cell fate transition toward the male reproductive lineage. Here we show that Arabidopsis PMC differentiation is accompanied by large-scale changes in chromatin organ...

  11. Chromatin dynamics in Pollen Mother Cells underpin a common scenario at the somatic-to-reproductive fate transition of both the male and female lineages in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Wenjing eShe

    2015-04-01

    Full Text Available Unlike animals, where the germline is established early during embryogenesis, plants set aside their reproductive lineage late in development in dedicated floral organs. The specification of pollen mother cells (PMCs committed to meiosis takes place in the sporogenous tissue in anther locules and marks the somatic-to-reproductive cell fate transition towards the male reproductive lineage. Here we show that Arabidopsis PMCs differentiation is accompanied by large-scale changes in chromatin organization. This is characterized by significant increase in nuclear volume, chromatin decondensation, reduction in heterochromatin, eviction of linker histones and the H2AZ histone variant. These structural alterations are accompanied by dramatic, quantitative changes in histone modifications levels compared to that of surrounding somatic cells that do not share a sporogenic fate. All these changes are highly reminiscent of those we have formerly described in female megaspore mother cells (MMCs. This indicates that chromatin reprogramming is a common underlying scenario in the somatic-to-reproductive cell fate transition in both male and female lineages.

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

    Science.gov (United States)

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

    2016-08-01

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

  13. Transcription within Condensed Chromatin: Steric Hindrance Facilitates Elongation

    OpenAIRE

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

    2010-01-01

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

  14. Wide and Fast Wavelength-Swept Fiber Laser Based on Dispersion Tuning for Dynamic Sensing

    OpenAIRE

    Osamu Kusakari; Ryosei Konishi; Yuichi Nakazaki; Shinji Yamashita

    2009-01-01

    We have developed a unique wide and fast wavelength-swept fiber laser for dynamic and accurate fiber sensing. The wavelength tuning is based on the dispersion tuning technique, which simply modulates the loss/gain in the dispersive laser cavity. By using wideband semiconductor optical amplifiers (SOAs), the sweep range could be as wide as ∼180 nm. Since the cavity contains no mechanical components, such as tunable filters, we could achieve very high sweep rate, as high as ∼200 kHz. We have re...

  15. Carbon Fiber Strand Tensile Failure Dynamic Event Characterization

    Science.gov (United States)

    Johnson, Kenneth L.; Reeder, James

    2016-01-01

    There are few if any clear, visual, and detailed images of carbon fiber strand failures under tension useful for determining mechanisms, sequences of events, different types of failure modes, etc. available to researchers. This makes discussion of physics of failure difficult. It was also desired to find out whether the test article-to-test rig interface (grip) played a part in some failures. These failures have nothing to do with stress rupture failure, thus representing a source of waste for the larger 13-00912 investigation into that specific failure type. Being able to identify or mitigate any competing failure modes would improve the value of the 13-00912 test data. The beginnings of the solution to these problems lay in obtaining images of strand failures useful for understanding physics of failure and the events leading up to failure. Necessary steps include identifying imaging techniques that result in useful data, using those techniques to home in on where in a strand and when in the sequence of events one should obtain imaging data.

  16. Hierarchy, dimension, attractor and self-organization -- dynamics of mode-locked fiber lasers

    CERN Document Server

    Wei, Huai; Shi, Wei; Zhu, Xiushan; Norwood, Robert A; Peyghambarian, Nasser; Jian, Shuisheng

    2016-01-01

    Mode-locked fiber lasers are one of the most important sources of ultra-short pulses. However, A unified description for the rich variety of states and the driving forces behind the complex and diverse nonlinear behavior of mode-locked fiber lasers have yet to be developed. Here we present a comprehensive theoretical framework based upon complexity science, thereby offering a fundamentally new way of thinking about the behavior of mode-locked fiber lasers. This hierarchically structured frame work provide a model with and changeable variable dimensionality resulting in a simple and elegant view, with which numerous complex states can be described systematically. The existence of a set of new mode-locked fiber laser states is proposed for the first time. Moreover, research into the attractors' basins reveals the origin of stochasticity, hysteresis and multistability in these systems. These findings pave the way for dynamics analysis and new system designs of mode-locked fiber lasers. The paradigm will have a w...

  17. Cas9 Functionally Opens Chromatin

    OpenAIRE

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

    2016-01-01

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

  18. Cas9 Functionally Opens Chromatin

    OpenAIRE

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

    2015-01-01

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

  19. Cas9 Functionally Opens Chromatin.

    Directory of Open Access Journals (Sweden)

    Amira A Barkal

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

  20. Cas9 Functionally Opens Chromatin

    Science.gov (United States)

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

    2016-01-01

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

  1. On the topology of chromatin fibres

    OpenAIRE

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

    2012-01-01

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

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

    Science.gov (United States)

    Gay, Sophie; Foiani, Marco

    2015-01-01

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

  3. Dynamics analysis of microsphere in a dual-beam fiber-optic trap with transverse offset.

    Science.gov (United States)

    Chen, Xinlin; Xiao, Guangzong; Luo, Hui; Xiong, Wei; Yang, Kaiyong

    2016-04-01

    A comprehensive dynamics analysis of microsphere has been presented in a dual-beam fiber-optic trap with transverse offset. As the offset distance between two counterpropagating beams increases, the motion type of the microsphere starts with capture, then spiral motion, then orbital rotation, and ends with escape. We analyze the transformation process and mechanism of the four motion types based on ray optics approximation. Dynamic simulations show that the existence of critical offset distances at which different motion types transform. The result is an important step toward explaining physical phenomena in a dual-beam fiber-optic trap with transverse offset, and is generally applicable to achieving controllable motions of microspheres in integrated systems, such as microfluidic systems and lab-on-a-chip systems. PMID:27137046

  4. Dynamic tensile response of a carbon-fiber-reinforced LCP composite and its temperature sensitivity

    Science.gov (United States)

    Shim, Victor P. W.; Yuan, J.; Lim, C. T.

    2001-06-01

    The tensile mechanical behavior of a short carbon fiber filled liquid crystalline polymer (LCP) composite, Vectra A230, was examined under static extension and dynamic loading at three temperatures. Dynamic tension was applied using a pendulum-type tensile spilt Hopkinson bar device. Specimens fabricated according to both the mould flow and transverse directions were tested. The stress-strain curves at various strain rates and temperatures were determined and found to be sensitive to strain rate as well as temperature for both types of specimens. With reference to the properties of pure LCP, mechanical anisotropy and fiber reinforcement effects were characterized and are discussed. Failed specimens were observed suing an optical microscope. Deformation and failure mechanisms in the microstructure of the LCP composite were studied to understand the effects of strain rate and temperature on material strength and failure strain.

  5. The Proteomic Investigation of Chromatin Functional Domains Reveals Novel Synergisms among Distinct Heterochromatin Components*

    OpenAIRE

    Soldi, Monica; Bonaldi, Tiziana

    2013-01-01

    Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent ...

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

    Science.gov (United States)

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

    2012-05-01

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

  7. Complex dynamics of a fiber laser in non-stationary pulsed operation.

    Science.gov (United States)

    Garcia-Sanchez, E; Pottiez, O; Bracamontes-Rodriguez, Y; Lauterio-Cruz, J P; Ibarra-Villalon, H E; Hernandez-Garcia, J C; Bello-Jimenez, M; Kuzin, E A

    2016-08-22

    Conventional mode locking is characterized by the generation of a stable train of optical pulses. Even in the noise-like pulsing regime of fiber lasers, sometimes described as partial mode locking, a periodic train of waveforms is still generated. In this work we study the dynamics of a figure-eight fiber laser away from the stable noise-like pulsing regime. By analyzing sequences of time-domain measurements performed with ns resolution, we reveal a wide range of puzzling dynamics, in which sub-structures emerge and drift away from the main bunch, decay or grow in a step-like manner, before vanishing abruptly. In some cases, sub-packets also concentrate in the central part of the period, forming one or multiple wide clouds that merge or split over time scales of seconds or minutes. Spontaneous transitions between these multiple states occur in a non-periodic manner, so that no quasi-stationary behavior is found over long time scales. These results provide a dramatic illustration of the extremely rich dynamics taking place in fiber lasers at the frontier of mode locking. PMID:27557173

  8. Discrete meso-element simulation of the failure behavior of short-fiber composites under dynamic loading

    Science.gov (United States)

    Liu, Wenyan; Tang, Z. P.; Liu, Yunxin

    2000-04-01

    In recent years, more attention has been paid to a better understanding of the failure behavior and mechanism of heterogeneous materials at the meso-scale level. In this paper, the crack initiation and development in epoxy composites reinforced with short steel fibers under dynamic loading were simulated and analyzed with the 2D Discrete Meso-Element Dynamic Method. Results show that the damage process depends greatly on the binding property between matrix and fibers.

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

    Directory of Open Access Journals (Sweden)

    Vuthy Ea

    2015-07-01

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

  10. 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.

  11. Saving entangled photons from sudden death is a single-mode fiber --- Interplay of Decoherence and dynamical decoupling

    Science.gov (United States)

    Gupta, Manish Kumar; You, Chenglong; Dowling, Jonathan P.; Lee, Hwang

    2016-05-01

    We study the dynamics of decoherence in an optical fiber for the case of entangled photons. Such a study will allow us to increase the physical length of fiber for transmission of entangled photon from the sources such as SPDC. We analytically derive the model for Decoherence of entangled state photons in a single-mode fiber. We also show that entanglement lifetime can be increased for Bell state and Werner state with open loop control technique called Dynamical decoupling. The authors would like to acknowledge support from the Air Force Office of Scientific Research, the Army Research Office, the National Science Foundation and the Northrop Grumman Corporation.

  12. 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

  13. 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.

  14. Molecular Dynamics Modeling of PPTA Crystals in Aramid Fibers

    Energy Technology Data Exchange (ETDEWEB)

    Mercer, Brian Scott [Univ. of California, Berkeley, CA (United States)

    2016-05-19

    In this work, molecular dynamics modeling is used to study the mechanical properties of PPTA crystallites, which are the fundamental microstructural building blocks of polymer aramid bers such as Kevlar. Particular focus is given to constant strain rate axial loading simulations of PPTA crystallites, which is motivated by the rate-dependent mechanical properties observed in some experiments with aramid bers. In order to accommodate the covalent bond rupture that occurs in loading a crystallite to failure, the reactive bond order force eld ReaxFF is employed to conduct the simulations. Two major topics are addressed: The rst is the general behavior of PPTA crystallites under strain rate loading. Constant strain rate loading simulations of crystalline PPTA reveal that the crystal failure strain increases with increasing strain rate, while the modulus is not a ected by the strain rate. Increasing temperature lowers both the modulus and the failure strain. The simulations also identify the C N bond connecting the aromatic rings as weakest primary bond along the backbone of the PPTA chain. The e ect of chain-end defects on PPTA micromechanics is explored, and it is found that the presence of a chain-end defect transfers load to the adjacent chains in the hydrogen-bonded sheet in which the defect resides, but does not in uence the behavior of any other chains in the crystal. Chain-end defects are found to lower the strength of the crystal when clustered together, inducing bond failure via stress concentrations arising from the load transfer to bonds in adjacent chains near the defect site. The second topic addressed is the nature of primary and secondary bond failure in crystalline PPTA. Failure of both types of bonds is found to be stochastic in nature and driven by thermal uctuations of the bonds within the crystal. A model is proposed which uses reliability theory to model bonds under constant strain rate loading as components with time-dependent failure rate

  15. Time Prediction of Dynamic Behavior of Glass Fiber Reinforced Polyester Composites Subjected to Fluctuating Varied Temperatures

    Directory of Open Access Journals (Sweden)

    Louay S. Yousuf

    2009-01-01

    Full Text Available The reduction of vibration properties for composite material (woven roving E-glass fiber plies in thermosetting polyester matrix is investigated at the prediction time under varied combined temperatures (60 to -15 using three types of boundary conditions like (CFCF, CCCF, and CFCC. The vibration properties are the amplitude, natural frequency, dynamic elastic moduli (young modulus in x, y directions and shear modulus in 1, 2 plane and damping factor. The natural frequency of a system is a function of its elastic properties, dimensions, and mass. The woven roving glass fiber has been especially engineered for polymer reinforcement; but the unsaturated thermosetting polyester is widely used, offering a good balance of vibration properties at moderate or ambient temperatures, and also at relatively low cost. The mismatch between matrix and fiber yarns gives a predominant role for the fiber's mechanics where the matrix is the area where most damage mechanisms develop. The free vibration test was carried out for (5, 10, 15, 20, 25, 30 minutes. The composite plate was exposed to (75 of thermal gradient for ten times in various times at different stages. The results were classified into experimental and finite element using software ANSYS Ver. 9.

  16. Dynamic Mechanical Behaviour of Ultra-high Performance Fiber Reinforced Concretes

    Institute of Scientific and Technical Information of China (English)

    LAI Jianzhong; SUN Wei

    2008-01-01

    Ultra-high performance fiber reinforced concretes (UHPFRC) were prepared by replacing 60% of cement with ultra-fine industrial waste powder.The dynamic mechanical behaviour of UHPFRC with different fiber volume fraction was researched on repeated compressive impact in four kinds of impact modes through split Hopkinson pressure bar (SHPB).The experimental results show that the peak stress and elastic modulus decrease and the strain rate and peak strain increase gradually with the increasing of impact times.The initial material damage increases and the peak stress of the specimen decreases from the second impact with the increasing of the initial incident wave.Standard strength on repeated impact is defined to compare the ability of resistance against repeated impact among different materials.The rate of reduction of standard strength is decreased by fiber reinforcement under repeated impact.The material damage is reduced and the ability of repeated impact resistance of UHPFRC is improved with the increasing of fiber volume fraction.

  17. On the topology of chromatin fibres

    Science.gov (United States)

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

    2012-01-01

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

  18. Radio-over-fiber DSB-to-SSB conversion using semiconductor lasers at stable locking dynamics.

    Science.gov (United States)

    Hsieh, Kun-Lin; Hung, Yu-Han; Hwang, Sheng-Kwang; Lin, Chien-Chung

    2016-05-01

    In radio-over-fiber systems, optical single-sideband (SSB) modulation signals are preferred to optical double-sideband (DSB) modulation signals for fiber distribution in order to mitigate the microwave power fading effect. However, typically adopted modulation schemes generate DSB signals, making DSB-to-SSB conversion necessary before or after fiber distribution. This study investigates a semiconductor laser at stable locking dynamics for such conversion. The conversion relies solely on the nonlinear dynamical interaction between an input DSB signal and the laser. Only a typical semiconductor laser is therefore required as the key conversion unit, and no pump or probe signal is necessary. The conversion can be achieved for a broad tunable range of microwave frequency up to at least 60 GHz. In addition, the conversion can be carried out even when the microwave frequency, the power of the input DSB signal, or the frequency of the input DSB signal fluctuates over a wide range, leading to high adaptability and stability of the conversion system. After conversion, while the microwave phase quality, such as linewidth and phase noise, is mainly preserved, a bit-error ratio down to 10-9 is achieved for a data rate up to at least 8 Gb/s with a detection sensitivity improvement of more than 1.5 dB. PMID:27137598

  19. Multimodality Neurological Data Visualization With Multi-VOI-Based DTI Fiber Dynamic Integration.

    Science.gov (United States)

    Zhang, Qi; Alexander, Murray; Ryner, Lawrence

    2016-01-01

    Brain lesions are usually located adjacent to critical spinal structures, so it is a challenging task for neurosurgeons to precisely plan a surgical procedure without damaging healthy tissues and nerves. The advancement of medical imaging technologies produces a large amount of neurological data, which are capable of showing a wide variety of brain properties. Advanced algorithms of medical data computing and visualization are critically helpful in efficiently utilizing the acquired data for disease diagnosis and brain function and structure exploration, which is helpful for treatment planning. In this paper, we describe new algorithms and a software framework for multiple volume of interest specified diffusion tensor imaging (DTI) fiber dynamic visualization. The displayed results have been integrated with a volume rendering pipeline for multimodality neurological data exploration. A depth texture indexing algorithm is used to detect DTI fiber tracts in graphics process units (GPUs), which makes fibers to be displayed and interactively manipulated with brain data acquired from functional magnetic resonance imaging, T1- and T2-weighted anatomic imaging, and angiographic imaging. The developed software platform is built on an object-oriented structure, which is transparent and extensible. It provides a comprehensive human-computer interface for data exploration and information extraction. The GPU-accelerated high-performance computing kernels have been implemented to enable our software to dynamically visualize neurological data. The developed techniques will be useful in computer-aided neurological disease diagnosis, brain structure exploration, and general cognitive neuroscience. PMID:25376048

  20. Insight into fiber Bragg sensor response at 100-MHz interrogation rates under various dynamic loading conditions

    Science.gov (United States)

    Rodriguez, George; Jaime, Marcelo; Mielke, Chuck H.; Balakirev, Fedor F.; Azad, Abul; Sandberg, Richard L.; Marshall, Bruce; La Lone, Brandon M.; Henson, Bryan F.; Smilowitz, Laura; Marr-Lyon, Mark; Sandoval, Tom

    2015-05-01

    A 100 MHz fiber Bragg grating (FBG) interrogation system is described and applied to strain, pressure, and shock position sensing. The approach relies on coherent pulse illumination of the FBG sensor with a broadband short pulse from a femtosecond modelocked erbium fiber laser. After interrogation of the FBG sensor, a long multi-kilometer run of single mode fiber was used for chromatic dispersion to temporally stretch the spectral components of the reflected pulse from the FBG sensor. Dynamic strain or pressure induced spectral shifts in the FBG sensor were detected as a pulsed time domain waveform shift after encoding by the chromatic dispersive line. Signals were recorded using a single 35 GHz photodetector and a 25 GHz bandwidth digitizing oscilloscope. Application of this approach to high-speed strain sensing of magnetic materials in pulsed magnetic fields to ~150 T is demonstrated. The FBG wavelength shifts were used to study magnetic field driven magnetostriction effects in LaCoO3. A sub-microsecond temporal shift in the FBG sensor wavelength attached to the sample under first order phase change appears as a fractional length change (strain: ΔL/L<10-4) in the material. A second application to FBG sensing of pressure dynamics to nearly 2 GPa in the thermal ignition of the high explosive PBX-9501 is also demonstrated. Then, as final demonstration, we use a chirped FBG (CFBG) to resolve shock propagation dynamics in 1-D from an explosive detonation that produces fragmentation in an inert confinement vessel. These applications demonstrate the use of this FBG interrogation system in dynamical extreme conditions that would otherwise not be possible using traditional FBG interrogation approaches that are deemed too slow to resolve such events.

  1. Optical Switching for Dynamic Distribution of Wireless-Over-Fiber Signals in Active Optical Networks

    DEFF Research Database (Denmark)

    Vegas Olmos, Juan José; Rodes, Guillermo; Tafur Monroy, Idelfonso

    2012-01-01

    In this paper, we report on an experimental validation of dynamic distribution of wireless-over-fiber by employing optical switching using semiconductor optical amplifiers; we also provide a channel distribution scheme and a generic topology for such an optical switch. The experiment consists of a...... results show a negligible power penalty on each channel for both the best and the worst case in terms of inter-channel crosstalk. The presented system is highly scalable both in terms of port count and throughput, a desirable feature in highly branched access networks, and is modulation- and frequency...... four wavelength-division-multiplexed channel system operating on a WiMax frequency band and employing an orthogonal-frequency-division-multiplexing modulation at 625 Mbits/s per channel, transmission of the data over 20 km of optical fiber, and active switching in a 1 × 16 active optical switch. The...

  2. Optical Switching for Dynamic Distribution of Wireless-over-Fiber Signals

    DEFF Research Database (Denmark)

    Rodes Lopez, Guillermo Arturo; Vegas Olmos, Juan José; Karinou, Fotini;

    2012-01-01

    In this paper, we report on an experimental validation of dynamic distribution of wireless-over-fiber by employing optical switching using semiconductor optical amplifiers; the rest of the network was designed according to the channel distribution over the optical spectra required by the optical...... switch. An experimental validation was also conducted. The experiment consists of a four wavelength division multiplexed (WDM) channel system operating on a WiMax frequency band, and employing an orthogonal frequency-division multiplexing (OFDM) modulation at 625 Mbit/s per channel, transmission of the...... data over 20 km of optical fiber, and active switching in a one-by-sixteen active optical switch. The results show a negligible power penalty on each channel, for both the best and the worst case in terms of inter-channel crosstalk....

  3. Dynamics of soliton explosions in passively mode-locked fiber lasers

    CERN Document Server

    Runge, Antoine F J; Erkintalo, Miro

    2015-01-01

    A soliton explosion is an instability whereby a dissipative soliton undergoes a sudden structural collapse, but remarkably returns back to its original shape after a short transient. We recently reported the first experimental observation of this effect in a fiber laser (A. F. J. Runge et al., Optica 2, 36 (2015)). Here, we expand on our initial work, presenting a more detailed experimental and numerical study of the characteristics and dynamics of soliton explosions in passively mode-locked fiber lasers. Specifically, we explore different cavity configurations and gain levels, observing and characterizing explosion events using spectral and temporal real-time single-shot techniques. Our results highlight that the explosion characteristics observed in experiments depend critically on the position in the cavity where the output coupler is located. Furthermore, we find that the frequency at which explosions occur can be controlled by adjusting the pump power. We also identify a new kind of ``partial'' explosion...

  4. Efficiency of fiber reinforced concrete application in structures subjected to dynamic effects

    Directory of Open Access Journals (Sweden)

    Morozov Valeriy Ivanovich

    2014-03-01

    Full Text Available Fiber reinforced concretes possess high strength under dynamic loadings, which include impact loads, thanks to their high structural viscosity. This is the reason for using them in difficult operating conditions, where increasing the performance characteristics and the structure durability is of prime importance, and the issues of the cost become less significant. Applying methods of disperse reinforcement is most challenging in case of subtle high-porous materials on mineral binders, for example foamed concrete. At the same time, the experiments conducted in Russia and abroad show, that also in other cases the concrete strength resistance several times increases as a result of disperse reinforcement. This doesn't depend on average density of the concrete and type of fiber used. In the article the fibre reinforced concrete impact resistance is analysed. Recommendations are given in regard to fibre concrete application in manufacture of monolithic floor units for industrial buildings and precast piles.

  5. Plasma dynamics studies on the Los Alamos Solid Fiber Z-Pinch

    International Nuclear Information System (INIS)

    The Los Alamos High Density Z Pinch-II (HDZP-II) experiments is being used to study the dynamics of z-pinch plasmas generated from thin solid fibers of deuterated polyethylene (CD2). A model has been developed which incorporates anomalous heating due to instability-generated turbulence. HDZP-II uses a pulsed-power generator that delivers a current of up to 1 MA with a 100 ns rise-time through an inductive load. The surface of the solid fiber, with a 5-cm length and 3-50μm radius, immediately ionizes and rapidly expands in radius. As the plasma is heated, more and more of the fiber is ablated until the entire fiber is ionized. The fully ionized fiber continues to expand radially. Diagnostics include a multi-frame shadowgraph, a three channel X-ray crystal reflection monochromometer, a single frame point-diffraction interferometer, neutron detectors, and generator monitors. The shadowgraph provides the plasma shape in seven frames taken at 10-ns intervals. This has shown very strong m=0 instability at the onset of current, even for small pre-pulse currents. The interferometer provides the plasma line density and, assuming cylindrical symmetry, the electron density. This is used to open-quotes calibrateclose quotes how much of the plasma is contained in the shape given by the shadowgraphs. The author have chosen a small enough aperture to have most of the plasma in the shadowgraph. The X-ray monochromometer provides the electron temperature as a function of time. The temperature generally rises to 90 eV at 40 ns into the current and remains very flat until near the end of the current ramp. The results from these diagnostics and their bearing on anomalous turbulent heating will be presented

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

    Science.gov (United States)

    Luque, Antoni; Ozer, Gungor; Schlick, Tamar

    2016-06-01

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

  7. Chromatin, epigenetics and stem cells.

    Science.gov (United States)

    Roloff, Tim C; Nuber, Ulrike A

    2005-03-01

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

  8. Condensation of interphase chromatin in nuclei of synchronized chinese hamster ovary (CHO-K1) cells.

    Science.gov (United States)

    Gacsi, Mariann; Nagy, Gabor; Pinter, Gabor; Basnakian, Alexei G; Banfalvi, Gaspar

    2005-01-01

    Reversibly permeabilized cells have been used to visualize interphase chromatin structures in the presence and absence of biotinylated nucleotides. By reversing permeabilization, it was possible to confirm the existence of a flexible chromatin folding pattern through a series of transient geometric forms such as supercoiled, circular forms, chromatin bodies, thin and thick fibers, and elongated chromosomes. Our results show that the incorporation of biotin-11-dUTP interferes with chromatin condensation, leading to the accumulation of decondensed chromatin structures. Chromatin condensation without nucleotide incorporation was also studied in cell populations synchronized by centrifugal elutriation. After reversal of permeabilization, nuclei were isolated and chromatin structures were visualized after DAPI staining by fluorescent microscopy. Decondensed veil-like structures were observed in the early S phase (at an average C-value of 2.21), supercoiled chromatin later in the early S (2, 55 C), fibrous structures in the early mid S phase (2, 76 C), ribboned structures in the mid-S phase (2, 98 C), continuous chromatin strings later in the mid-S phase (3,28), elongated prechromosomes in the late S-phase (3, 72 C), precondensed chromosomes at the end and after the S phase (3, 99 C). Fluorescent microscopy revealed that neither interphase nor metaphase chromosomes are separate entities but form a linear array arranged in a semicircle. Linear arrangement was confirmed by computer image analysis. PMID:15684719

  9. Parametric Study on Dynamic Response of Fiber Reinforced Polymer Composite Bridges

    Directory of Open Access Journals (Sweden)

    Woraphot Prachasaree

    2015-01-01

    Full Text Available Because of high strength and stiffness to low self-weight ratio and ease of field installation, fiber reinforced polymer (FRP composite materials are gaining popularity as the materials of choice to replace deteriorated concrete bridge decks. FRP bridge deck systems with lower damping compared to conventional bridge decks can lead to higher amplitudes of vibration causing dynamically active bridge deck leading serviceability problems. The FRP bridge models with different bridge configurations and loading patterns were simulated using finite element method. The dynamic response results under varying FRP deck system parameters were discussed and compared with standard specifications of bridge deck designs under dynamic loads. In addition, the dynamic load allowance equation as a function of natural frequency, span length, and vehicle speed was proposed in this study. The proposed dynamic load allowance related to the first flexural frequency was presented herein. The upper and lower bounds’ limits were established to provide design guidance in selecting suitable dynamic load allowance for FRP bridge systems.

  10. Angiogenin enhances cell migration by regulating stress fiber assembly and focal adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Saisai Wei

    Full Text Available Angiogenin (ANG acts on both vascular endothelial cells and cancer cells, but the underlying mechanism remains elusive. In this study, we carried out a co-immunoprecipitation assay in HeLa cells and identified 14 potential ANG-interacting proteins. Among these proteins, β-actin, α-actinin 4, and non-muscle myosin heavy chain 9 are stress fiber components and involved in cytoskeleton organization and movement, which prompted us to investigate the mechanism of action of ANG in cell migration. Upon confirmation of the interactions between ANG and the three proteins, further studies revealed that ANG co-localized with β-actin and α-actinin 4 at the leading edge of migrating cells. Down-regulation of ANG resulted in fewer but thicker stress fibers with less dynamics, which was associated with the enlargements of focal adhesions. The focal adhesion kinase activity and cell migration capacity were significantly decreased in ANG-deficient cells. Taken together, our data demonstrated that the existence of ANG in the cytoplasm optimizes stress fiber assembly and focal adhesion formation to accommodate cell migration. The finding that ANG promoted cancer cell migration might provide new clues for tumor metastasis research.

  11. Painting a Clearer Picture of Chromatin.

    Science.gov (United States)

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

    2016-02-22

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

  12. Brain Function and Chromatin Plasticity

    OpenAIRE

    Dulac, Catherine

    2010-01-01

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

  13. Chromatin remodeling, development and disease

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

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

    2014-01-01

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

  15. Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains

    CERN Document Server

    Brackley, C A; Michieletto, D; Mouvet, F; Cook, P R; Marenduzzo, D

    2016-01-01

    Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins; these proteins switch between two states -- active (binding) and inactive (non-binding). This system provides a model for any DNA-binding protein that can be modified post-translationally to change its affinity for DNA (e.g., like the phosphorylation of a transcription factor). Due to this out-of-equilibrium process, proteins spontaneously assemble into clusters of self-limiting size, as individual proteins in a cluster exchange with the soluble pool with kinetics like those seen in photo-bleaching experiments. This behavior contrasts sharply with that exhibited by "equilibrium", or non-switching, proteins that exis...

  16. Application of nonlinear compensation to limit input dynamic range in analog optical fiber links

    Directory of Open Access Journals (Sweden)

    R. Garduno

    2010-08-01

    Full Text Available The dynamic range of a signal at the input of a measurement system during a short circuit test is increased severaltimes by the nominal input voltage. Saturation of the measurement system may occur in a device under failure test.This paper introduces the application of a nonlinear compensation to limit the voltage range at the input of a voltagecontrolled oscillator which is used to produce the pulsed frequency modulation needed to transmit the analog signalsover the optical fiber links. The proposed dynamic range compensation system is based on non-linear circuits toaccommodate the input range of the voltage controlled oscillator. This approach increases the transient signalhandling capabilities of the measuring system. This work demonstrates that the nonlinear compensated optical fiberapproach yields a unique, electrically isolated, lightning-proof analog data transmission system for remote measuringsystems in the highly aggressive EMI environment of high-power test laboratories.

  17. Dynamic stress analysis of smooth and notched fiber composite flexural specimens

    Science.gov (United States)

    Murthy, P. L. N.; Chamis, C. C.

    1986-01-01

    A detailed analysis of the dynamic stress field in smooth and notched fiber composite (Charpy-type) specimens is reported in this paper. The analysis is performed with the aid of the direct transient response analysis solution sequence of MSC/NASTRAN. Three unidirectional composites were chosen for the study. They are S-Glass/Epoxy, Kevlar/Epoxy and T-300/Epoxy composite systems. The specimens are subjected to an impact load which is modeled as a triangular impulse with a maximum of 2000 lb and a duration of 1 ms. The results are compared with those of static analysis of the specimens subjected to a peak load of 2000 lb. For the geometry and type of materials studied, the static analysis results gave close conservative estimates for the dynamic stresses. Another interesting inference from the study is that the impact induced effects are felt by S-Glass/Epoxy specimens sooner than Kevlar/Epoxy or T-300/Epoxy specimens.

  18. Effect of temperature on the dynamic characteristics of the glass-carbon fiber hybrid composites

    Science.gov (United States)

    Hidayat, Yon Afif; Susilo, Didik Djoko; Raharjo, Wijang W.

    2016-03-01

    This study aimed to investigate the effect of temperature on the dynamic characteristics of hybrid composites. Hybrid composites consisting of unsaturated polyester resin and glass fiber reinforced with carbon fiber. The volume fraction used in this study was 0.4. The hybrid composite was made using hand lay-up technique. The dynamic characteristics were obtained through vibration testing. The testing was conducted according to ASTM E756. The variables studied were composite without heating, heating at 100 °C, 200 °C and 280 °C. The experiments were done in three mounting configurations, i.e. upright, downward and horizontal configurations. The natural frequency and damping ratio was determined using half-power bandwidth method. The results showed that heating of composite structure affects the natural frequency and damping ratio of the hybrid composite. Heating until 100 °C will increase the natural frequency of the hybrid composite and decrease the damping ratio, but heating at the temperature above 100 °C will decrease the natural frequency and will damage the hybrid composite structure. The composite mounting configurations do not give significant effect to natural frequency and damping ratio of the hybrid composites.

  19. Dynamics of tropomyosin in muscle fibers as monitored by saturation transfer EPR of bi-functional probe.

    Directory of Open Access Journals (Sweden)

    Roni F Rayes

    Full Text Available The dynamics of four regions of tropomyosin was assessed using saturation transfer electron paramagnetic resonance in the muscle fiber. In order to fully immobilize the spin probe on the surface of tropomyosin, a bi-functional spin label was attached to i,i+4 positions via cysteine mutagenesis. The dynamics of bi-functionally labeled tropomyosin mutants decreased by three orders of magnitude when reconstituted into "ghost muscle fibers". The rates of motion varied along the length of tropomyosin with the C-terminus position 268/272 being one order of magnitude slower then N-terminal domain or the center of the molecule. Introduction of troponin decreases the dynamics of all four sites in the muscle fiber, but there was no significant effect upon addition of calcium or myosin subfragment-1.

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

    Science.gov (United States)

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

    2012-10-01

    Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the "strings and binders switch" model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed "fractal-globule" model, but only as one of many possible transient conformations. PMID:22988072

  1. Visualization of chromatin folding patterns in chicken erythrocytes by atomic force microscopy (AFM)

    Institute of Scientific and Technical Information of China (English)

    QIANRUOLAN; ZHENGXIALIU; 等

    1997-01-01

    The organization of the higher order structure of chromatin in chicken erythrocytes has been examined with tapping-mode scanning force microscopy under conditions close to their native envirinment.Reproducible highresolution AFM images of chromatin compaction at several levels can be demonstrated.An extended beads-on-astring (width of - 15-20nm,height of - 2-3nm for each individual nucleosome) can be consistently observed.Furthermore,superbeade (width of - 40nm,height of - 7nm) are demonstrated.Visualization of the solenoid conformation at the level of 30nm chromatin fiber is attained either by using AFM or by using electron microscopy.In addition,tightly coiled chromatin fibers (- 50-60nm and - 90-110nm) can be revealed.Our data suggest that the chromatin in the interphase nucleus of chicken erythrocyte represents a high-order conformation and AFM provides useful high-resolution structural information concerning the folding pattern of interphase chromatin fibers.

  2. Dynamic tensile behavior of two-dimensional carbon fiber reinforced silicon carbide matrix composites

    International Nuclear Information System (INIS)

    Graphical abstract: The dynamic tensile behavior of 2D C/SiC composites was experimentally investigated by means of SHTB. Both the fracture surface and bundle fracture surfaces of composites were observed. The strain rate sensitivity of in-bundle interface was concluded as the dominant contributor to the strain rate sensitivity of the tensile strength. Highlights: → The tensile strength increases with strain rate. → The tensile failure strain remains independent of strain rate. → Macro-structural morphology reveals rough fracture surface under dynamic loading. → SEM morphology reveals integrated bundle pull-out under dynamic loading. → Strain rate sensitivity of in-bundle interface leads to that of the tensile strength. - Abstract: An investigation has been undertaken to determine the dynamic and quasi-static tensile behavior of two-dimensional carbon fiber reinforced silicon carbide matrix (2D-C/SiC) composites by means of the split Hopkinson tension bar and an electronic universal test machine respectively. The results indicate that the tensile strength of 2D C/SiC composites is increased at high strain rate. Furthermore, coated specimens show not only a 15% improvement in tensile strength but heightened strain rate sensitivity compared with uncoated ones. It is also shown that the tensile failure strain is strain rate insensitive and remains around 0.4%. Optical macrograph of failed specimens under dynamic loading revealed jagged fracture surfaces characterized by delamination and crack deviation, together with obvious fiber pull-out/splitting, in contrast with the smooth fracture surfaces under quasi-static loading. Scanning electron microscopy micrograph of fracture surface under dynamic loading clearly displayed integrated bundle pull-out which implies suppressed in-bundle debonding and enhanced in-bundle interfacial strengthening, in contrast with extensive in-bundle debonding under quasi-static loading. Thus we conclude that, with 2D C

  3. Chromatin remodelers and their roles in chromatin organization

    OpenAIRE

    Strålfors, Annelie

    2012-01-01

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

  4. High Pressure Sensing and Dynamics Using High Speed Fiber Bragg Grating Interrogation Systems

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, G. [LANL; Sandberg, R. L. [LANL; Lalone, B. M. [NSTec; Marshall, B. R. [NSTec; Grover, M. [NSTec; Stevens, G. D. [NSTec; Udd, E. [Columbia Gorge Research

    2014-06-01

    Fiber Bragg gratings (FBGs) are developing into useful sensing tools for measuring high pressure dynamics in extreme environments under shock loading conditions. Approaches using traditional diode array coupled FBG interrogation systems are often limited to readout speeds in the sub-MHz range. For shock wave physics, required detection speeds approaching 100 MHz are desired. We explore the use of two types of FBG sensing systems that are aimed at applying this technology as embedded high pressure probes for transient shock events. Both approaches measure time resolved spectral shifts in the return light from short (few mm long) uniform FBGs at 1550 nm. In the first approach, we use a fiber coupled spectrometer to demultiplex spectral channels into an array (up to 12) of single element InGaAs photoreceivers. By monitoring the detectors during a shock impact event with high speed recording, we are able to track the pressure induced spectral shifting in FBG down to a time resolution of 20 ns. In the second approach, developed at the Special Technologies Lab, a coherent mode-locked fiber laser is used to illuminate the FBG sensor. After the sensor, wavelength-to-time mapping is accomplished with a chromatic dispersive element, and entire spectra are sampled using a single detector at the modelocked laser repetition rate of 50 MHz. By sampling with a 12 GHz InGaAs detector, direct wavelength mapping in time is recorded, and the pressure induced FBG spectral shift is sampled at 50 MHz. Here, the sensing systems are used to monitor the spectral shifts of FBGs that are immersed into liquid water and shock compressed using explosives. In this configuration, the gratings survive to pressures approaching 50 kbar. We describe both approaches and present the measured spectral shifts from the shock experiments.

  5. Dynamics of myosin II organization into contractile networks and fibers at the medial cell cortex

    Science.gov (United States)

    Nie, Wei

    The cellular morphology of adhered cells depends crucially on the formation of a contractile meshwork of parallel and cross-linked stress fibers along the contacting surface. The motor activity and mini-filament assembly of non-muscle myosin II is an important component of cell-level cytoskeletal remodeling during mechanosensing. To monitor the dynamics of non-muscle myosin II, we used confocal microscopy to image cultured HeLa cells that stably express myosin regulatory light chain tagged with GFP (MRLC-GFP). MRLC-GFP was monitored in time-lapse movies at steady state and during the response of cells to varying concentrations of blebbistatin (which disrupts actomyosin stress fibers). Using image correlation spectroscopy analysis, we quantified the kinetics of disassembly and reassembly of actomyosin networks and compared to studies by other groups. This analysis suggested the following processes: myosin minifilament assembly and disassembly; aligning and contraction; myosin filament stabilization upon increasing contractile tension. Numerical simulations that include those processes capture some of the main features observed in the experiments. This study provides a framework to help interpret how different cortical myosin remodeling kinetics may contribute to different cell shape and rigidity depending on substrate stiffness. We discuss methods to monitor myosin reorganization using non-linear imaging methods.

  6. Structural Role of RKS Motifs in Chromatin Interactions: A Molecular Dynamics Study of HP1 Bound to a Variably Modified Histone Tail

    OpenAIRE

    Papamokos, George V.; Tziatzos, George; Papageorgiou, Dimitrios G.; Georgatos, Spyros D.; Politou, Anastasia S.; Kaxiras, Efthimios

    2012-01-01

    The current understanding of epigenetic signaling assigns a central role to post-translational modifications that occur in the histone tails. In this context, it has been proposed that methylation of K9 and phosphorylation of S10 in the tail of histone H3 represent a binary switch that controls its reversible association to heterochromatin protein 1 (HP1). To test this hypothesis, we performed a comprehensive molecular dynamics study in which we analyzed a crystallographically defined complex...

  7. A procedure to estimate the dynamic damped behavior of fiber reinforced composite beams submitted to flexural vibrations

    Directory of Open Access Journals (Sweden)

    Volnei Tita

    2001-10-01

    Full Text Available This work proposes a procedure to estimate the dynamic damped behavior of fiber reinforced composite beams in flexural vibrations. A set of experimental dynamic tests were carried out in order to investigate the natural frequencies and modal shapes. These results are used to evaluate the damping factors by the program FREQ. These damping factors are then used as input to a damped dynamic analysis by the Finite Element Method, using Rayleigh Model. A good agreement between theoretical and experimental results was obtained. Thus, it became possible to validate the proposed procedure to evaluate dynamic damped behavior of composite beams.

  8. Dynamic mechanical properties of 3D fiber-deposited PEOT/PBT scaffolds: An experimental and numerical analysis

    NARCIS (Netherlands)

    Moroni, L.; Poort, G.; Keulen, van F.; Wijn, de J.R.; Blitterswijk, van C.A.

    2006-01-01

    Mechanical properties of three-dimensional (3D) scaffolds can be appropriately modulated through novel fabrication techniques like 3D fiber deposition (3DF), by varying scaffold's pore size and shape. Dynamic stiffness, in particular, can be considered as an important property to optimize the scaffo

  9. Changes in human muscle oxygen saturation and mean fiber conduction velocity during intense dynamic exercise - effect of muscular training status

    DEFF Research Database (Denmark)

    Kilen, Anders; Gizzi, Leonardo; Jensen, Bente Rona;

    2012-01-01

    Introduction: In this study we investigated whether an association exists between muscle fiber conduction velocity (MFCV) and local muscle oxygen saturation (StO(2) ) in the superficial part of the latissimus dorsi muscle of runners and swimmers during exhaustive dynamic exercise. Methods: Partic...

  10. 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.

  11. 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....

  12. Compact fiber Bragg grating dynamic strain sensor cum broadband thermometer for thermally unstable ambience

    International Nuclear Information System (INIS)

    An instrument for simultaneous measurement of dynamic strain and temperature in a thermally unstable ambience has been proposed, based on fiber Bragg grating technology. The instrument can function as a compact and stand-alone broadband thermometer and a dynamic strain gauge. It employs a source wavelength tracking procedure for linear dependence of the output on the measurand, offering high dynamic range. Two schemes have been demonstrated with their relative merits. As a thermometer, the present instrumental configuration can offer a linear response in excess of 500 °C that can be easily extended by adding a suitable grating and source without any alteration in the procedure. Temperature sensitivity is about 0.06 °C for a bandwidth of 1 Hz. For the current grating, the upper limit of strain measurement is about 150 µε with a sensitivity of about 80 nε Hz−1/2. The major source of uncertainty associated with dynamic strain measurement is the laser source intensity noise, which is of broad spectral band. A low noise source device or the use of optical power regulators can offer improved performance. The total harmonic distortion is less than 0.5% up to about 50 µε,1.2% at 100 µε and about 2.3% at 150 µε. Calibrated results of temperature and strain measurement with the instrument have been presented. Traces of ultrasound signals recorded by the system at 200 kHz, in an ambience of 100–200 °C temperature fluctuation, have been included. Also, the vibration spectrum and engine temperature of a running internal combustion engine has been recorded as a realistic application of the system

  13. Coming to terms with chromatin structure.

    Science.gov (United States)

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

    2016-03-01

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

  14. Predicting chromatin organization using histone marks

    OpenAIRE

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

    2015-01-01

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

  15. Impact of Chromatin on HIV Replication

    OpenAIRE

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

    2015-01-01

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

  16. Dynamic Response of Tapered Optical Multimode Fiber Coated with Carbon Nanotubes for Ethanol Sensing Application

    OpenAIRE

    Arafat Shabaneh; Saad Girei; Punitha Arasu; Mohd Mahdi; Suraya Rashid; Suriati Paiman; Mohd Yaacob

    2015-01-01

    Ethanol is a highly combustible chemical universally designed for biomedical applications. In this paper, optical sensing performance of tapered multimode fiber tip coated with carbon nanotube (CNT) thin film towards aqueous ethanol with different concentrations is investigated. The tapered optical multimode fiber tip is coated with CNT using drop-casting technique and is annealed at 70 °C to enhance the binding of the nanomaterial to the silica fiber tip. The optical fiber tip and the CNT se...

  17. Wide-Range Tunable Dynamic Property of Carbon Nanotube-Based Fibers

    OpenAIRE

    Zhao, Jingna; ZHANG, XIAOHUA; Pan, Zhijuan; Li, Qingwen

    2015-01-01

    Carbon nanotube (CNT) fiber is formed by assembling millions of individual tubes. The assembly feature provides the fiber with rich interface structures and thus various ways of energy dissipation, as reflected by the non-zero loss tangent (>0.028--0.045) at low vibration frequencies. A fiber containing entangled CNTs possesses higher loss tangents than a fiber spun from aligned CNTs. Liquid densification and polymer infiltration, the two common ways to increase the interfacial friction and t...

  18. Dynamic vortex interactions with flexible fibers and edges for prediction of owl noise suppression

    Science.gov (United States)

    Korykora, Sarah; Jaworski, Justin

    2015-11-01

    The compliant trailing-edge fringe of owls and the soft downy material on their upper wing surfaces are thought to enable their silent flight by weakening the interaction of boundary layer turbulence with these flexible structures. Previous analysis of turbulence noise generation by wave-bearing elastic edges have shown that the far-field acoustic power scaling can be weakened by up to the square of the Mach number relative to a rigid edge. However, it is unclear whether or not the wave-bearing feature or simply the flexible nature of the edge scatterer produces this noise suppression. To assess this distinction, a dynamic vortex interaction model is developed whereby the motion of a line vortex round a rigid but elastically-restrained wall-mounted fiber or trailing edge is determined numerically. Special attention is paid to the dynamic interaction between the flexible structure and vortex, which is accomplished via a conformal mapping relationship determined in closed form. Results from this analysis seek to develop a vortex sound model to discern the effect of flexible versus wave-bearing scatterers on turbulence noise suppression and help explain the mechanisms of silent owl flight.

  19. MULTIPLE SCATTERING AND DYNAMIC STRESS ANALYSIS OF ELASTIC WAVES IN A FIBER-REINFORCED COMPOSITE WITH INTERFACES

    Institute of Scientific and Technical Information of China (English)

    李凤明; 胡超; 徐敏强; 黄文虎

    2003-01-01

    Based on the theory of elastic dynamics,multiple scattering of elastic waves and dynamic stress concentrations in fiber-reinforced composite are studied.The analytical expressions of elastic waves in different regions are presented.The mode coefficients of elastic waves are determined in accordance with the continuous conditions of displacement and stress on the boundary of the multiinterfaces.By using the addition theorem of Hankel functions,the formula of scattered wave fields in different local coordinates are transformed into those in one local coordinate to determine the unknown coefficients and dynamic stress concentration factors (DSCFs).The influences of the distance between two inclusions,material properties and structural size on the DSCFs near the interfaces are analyzed.As examples,the numerical results of DSCFs near the interfaces for two kinds of fiber-reinforced composites are presented and discussed.

  20. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain;

    2007-01-01

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

  1. Spectroscopic study of laser irradiated chromatin

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-04-15

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

  2. Nonlinear compensation to enhance the input dynamic range in analog optical fiber links for the high current short circuit test

    Science.gov (United States)

    Rodriguez, Joaquin; Garduno, Raul; Velazquez, Jose; Montero, Julio

    2010-06-01

    Due to their galvanic insulation and EMI immunity properties, optical fiber links have been used in the transmitter-receiver system of an analog voltage measuring system at a high-power mid-voltage testing laboratory with a highly aggressive EMI environment. This paper introduces the application of a nonlinear compensation to limit the voltage range at the input of a voltage-controlled oscillator, which is used to produce the pulsed frequency modulation needed to transmit the analog signals over the optical fiber links. The proposed dynamic range compensation system is based on nonlinear circuits to accommodate the input range of the voltage-controlled oscillator. This approach increases the transient signal handling capabilities of the measuring system. This work demonstrates that the nonlinear compensated optical fiber approach yields a unique, electrically isolated, lightning-proof analog data transmission system, for remote measuring systems in the highly aggressive EMI environment of high-power test laboratories.

  3. Dynamics of dissipative solitons in a high repetition rate normal-dispersion erbium-doped fiber laser

    CERN Document Server

    Luo, Yiyang; Zhao, Luming; Sun, Qizhen; Wu, Zhichao; Xu, Zhilin; Fu, Songnian; Liu, Deming

    2016-01-01

    The dynamics of dissipative solitons (DSs) are explored in a high repetition rate normal-dispersion erbium-doped fiber laser for the first time. Despite of the high fundamental repetition rate of 129 MHz and thus the low pulse energy, a DS train with a dechirped pulse width of 418 fs, period-doubling of single and dual DSs, as well as 258 MHz 2nd-order harmonic mode-locking of DSs can be observed in the fiber laser with increasing pump power and appropriate settings. A transmitted semiconductor saturable absorber and a wavelength division multiplexer/isolator/tap hybrid module are employed to simplify the laser configuration, thus not only increasing the repetition rate, but also enhancing the stability and robustness of the fiber laser due to the commercial availability of all the components.

  4. Nonlinear compensation to enhance the input dynamic range in analog optical fiber links for the high current short circuit test

    International Nuclear Information System (INIS)

    Due to their galvanic insulation and EMI immunity properties, optical fiber links have been used in the transmitter–receiver system of an analog voltage measuring system at a high-power mid-voltage testing laboratory with a highly aggressive EMI environment. This paper introduces the application of a nonlinear compensation to limit the voltage range at the input of a voltage-controlled oscillator, which is used to produce the pulsed frequency modulation needed to transmit the analog signals over the optical fiber links. The proposed dynamic range compensation system is based on nonlinear circuits to accommodate the input range of the voltage-controlled oscillator. This approach increases the transient signal handling capabilities of the measuring system. This work demonstrates that the nonlinear compensated optical fiber approach yields a unique, electrically isolated, lightning-proof analog data transmission system, for remote measuring systems in the highly aggressive EMI environment of high-power test laboratories

  5. ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes

    OpenAIRE

    Ura, Kiyoe; Araki, Marito; Saeki, Hideaki; Masutani, Chikahide; Ito, Takashi; Iwai, Shigenori; Mizukoshi, Toshimi; Kaneda, Yasufumi; Hanaoka, Fumio

    2001-01-01

    To investigate the relationship between chromatin dynamics and nucleotide excision repair (NER), we have examined the effect of chromatin structure on the formation of two major classes of UV-induced DNA lesions in reconstituted dinucleosomes. Furthermore, we have developed a model chromatin-NER system consisting of purified human NER factors and dinucleosome substrates that contain pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) either at the center of the nucleosome or in the linker DNA....

  6. Fast negative feedback enables mammalian auditory nerve fibers to encode a wide dynamic range of sound intensities.

    Directory of Open Access Journals (Sweden)

    Mark Ospeck

    Full Text Available Mammalian auditory nerve fibers (ANF are remarkable for being able to encode a 40 dB, or hundred fold, range of sound pressure levels into their firing rate. Most of the fibers are very sensitive and raise their quiescent spike rate by a small amount for a faint sound at auditory threshold. Then as the sound intensity is increased, they slowly increase their spike rate, with some fibers going up as high as ∼300 Hz. In this way mammals are able to combine sensitivity and wide dynamic range. They are also able to discern sounds embedded within background noise. ANF receive efferent feedback, which suggests that the fibers are readjusted according to the background noise in order to maximize the information content of their auditory spike trains. Inner hair cells activate currents in the unmyelinated distal dendrites of ANF where sound intensity is rate-coded into action potentials. We model this spike generator compartment as an attenuator that employs fast negative feedback. Input current induces rapid and proportional leak currents. This way ANF are able to have a linear frequency to input current (f-I curve that has a wide dynamic range. The ANF spike generator remains very sensitive to threshold currents, but efferent feedback is able to lower its gain in response to noise.

  7. Measurement of dynamic viscoelasticity of confined lubricant by using oscillating optical fiber probe

    International Nuclear Information System (INIS)

    When a liquid is confined in molecularly narrow gaps, it shows characteristic viscoelasticity such as enhanced viscosity or prolonged relaxation time. In order to investigate the dynamic viscoelasticity of the confined liquid, we developed a new shear force measuring method that uses a ball-ended optical fiber as a shearing probe. Our method can measure the shear force of 0.1 nN order with the oscillation frequency of up to 10 kHz. In addition, the gap that confines the liquid can be set at any constant value ranging from 10 μm to 0.1 nm. In this study, we measured the gap dependence of viscoelasticity of confined liquid lubricants. The gap ranged from 200 nm to a few nm. The tested lubricant was Fomblin Z03 and Zdo14000. A magnetic disk was used as the solid substrate. Oscillation frequency was set at 800 Hz. The experiment showed the viscosity of both Z03 and Zdo14000 gradually increased as the confining gap decreased. The gap width where the viscosity increase started was wider than 100 nm, which is dozens of times larger than the gyration diameter of lubricant molecules. Although Z03 and Zdo14000 have negligibly small elasticity in a bulk state, elasticity suddenly appeared at gaps less than about 8 nm with Zdo14000, and at gaps less than about 4 nm with Z03. Stronger affinity of Zdo14000 molecules to the solid substrate could cause the wider gap width of elasticity appearance

  8. Dynamic range of analog fiber optic links used in microcellular mobile radio applications

    OpenAIRE

    Kelkar, Anish S

    1994-01-01

    The use of analog fiber optic links for microcellular mobile radio comminications has been the focus of considerable research recently. These systems have the advantages relative to coaxial cable of low noise and enormous bandwidth. Analog subcarrier multiplexing techniques are used for transmitting the mobile signals over the fiber. Use of this technology however presents some unique problems due to the nonlinearities of the fiber optics system and the noise introduced by it. ...

  9. Propagation dynamics of femtosecond laser pulses in a hollow fiber filled with argon: constant gas pressure versus differential gas pressure

    Science.gov (United States)

    Nurhuda, Muhammad; Suda, Akira; Midorikawa, Katsumi; Hatayama, Masatoshi; Nagasaka, Keigo

    2003-09-01

    We investigate the dynamics of femtosecond laser pulses propagating in a hollow fiber filled with argon, through a full numerical solution of the nonlinear Schrödinger equation. The simulation results show that, if the intensity is low and no ionization takes place, the spatial profile of the beam does not change very much so that its propagation model may be simplified to a one-dimensional model. If the intensity is high and ionization takes place, the spatial dynamics as well as temporal dynamics become very complicated because of self-focusing and defocusing. It is found that, for the same value of the B integral, self-focusing inside a hollow fiber can be substantially suspended by a differential gas pressure technique, where the gas pressure is set to be a minimum at the entrance and then increased with the propagation distance. Numerical simulations show that using such a technique, the energy transmitted during propagation inside hollow fiber is significantly enhanced, and the spatial phase is also improved.

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

    Directory of Open Access Journals (Sweden)

    Ivo A. Hendriks

    2015-03-01

    Full Text Available Small ubiquitin-like modifiers play critical roles in the DNA damage response (DDR. To increase our understanding of SUMOylation in the mammalian DDR, we employed a quantitative proteomics approach in order to identify dynamically regulated SUMO-2 conjugates and modification sites upon treatment with the DNA damaging agent methyl methanesulfonate (MMS. We have uncovered a dynamic set of 20 upregulated and 33 downregulated SUMO-2 conjugates, and 755 SUMO-2 sites, of which 362 were dynamic in response to MMS. In contrast to yeast, where a response is centered on homologous recombination, we identified dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors, and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1, and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the SUMO-targeted ubiquitin ligase RNF4 and degraded by the proteasome in response to DNA damage, JARID1C was SUMOylated and recruited to the chromatin to demethylate histone H3K4.

  11. Chromatin dynamics during plant sexual reproduction

    OpenAIRE

    She, Wenjing; Baroux, Célia

    2014-01-01

    Plants have the remarkable ability to establish new cell fates throughout their life cycle, in contrast to most animals that define all cell lineages during embryogenesis. This ability is exemplified during sexual reproduction in flowering plants where novel cell types are generated in floral tissues of the adult plant during sporogenesis, gametogenesis, and embryogenesis. While the molecular and genetic basis of cell specification during sexual reproduction is being studied for a long time, ...

  12. Scroll-wave dynamics in human cardiac tissue: lessons from a mathematical model with inhomogeneities and fiber architecture.

    Directory of Open Access Journals (Sweden)

    Rupamanjari Majumder

    Full Text Available Cardiac arrhythmias, such as ventricular tachycardia (VT and ventricular fibrillation (VF, are among the leading causes of death in the industrialized world. These are associated with the formation of spiral and scroll waves of electrical activation in cardiac tissue; single spiral and scroll waves are believed to be associated with VT whereas their turbulent analogs are associated with VF. Thus, the study of these waves is an important biophysical problem. We present a systematic study of the combined effects of muscle-fiber rotation and inhomogeneities on scroll-wave dynamics in the TNNP (ten Tusscher Noble Noble Panfilov model for human cardiac tissue. In particular, we use the three-dimensional TNNP model with fiber rotation and consider both conduction and ionic inhomogeneities. We find that, in addition to displaying a sensitive dependence on the positions, sizes, and types of inhomogeneities, scroll-wave dynamics also depends delicately upon the degree of fiber rotation. We find that the tendency of scroll waves to anchor to cylindrical conduction inhomogeneities increases with the radius of the inhomogeneity. Furthermore, the filament of the scroll wave can exhibit drift or meandering, transmural bending, twisting, and break-up. If the scroll-wave filament exhibits weak meandering, then there is a fine balance between the anchoring of this wave at the inhomogeneity and a disruption of wave-pinning by fiber rotation. If this filament displays strong meandering, then again the anchoring is suppressed by fiber rotation; also, the scroll wave can be eliminated from most of the layers only to be regenerated by a seed wave. Ionic inhomogeneities can also lead to an anchoring of the scroll wave; scroll waves can now enter the region inside an ionic inhomogeneity and can display a coexistence of spatiotemporal chaos and quasi-periodic behavior in different parts of the simulation domain. We discuss the experimental implications of our study.

  13. ATP independent and ATP dependent chromatin remodeling in wheat

    International Nuclear Information System (INIS)

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

  14. Rearrangement of chromatin domains during development in Xenopus.

    Science.gov (United States)

    Vassetzky, Y; Hair, A; Méchali, M

    2000-06-15

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

  15. Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape.

    Science.gov (United States)

    Winter, Deborah R; Jung, Steffen; Amit, Ido

    2015-09-15

    Recent technological advances have enabled researchers to accurately and efficiently assay the chromatin dynamics of scarce cell populations. In this Opinion article, we advocate the application of these technologies to central questions in immunology. Unlike changes to other molecular structures in the cell, chromatin features can reveal the past (developmental history), present (current activity) and future (potential response to challenges) of a given immune cell type; chromatin profiling is therefore an important new tool for studying the immune-regulatory networks of health and disease. PMID:26272294

  16. Characterization of the RNA content of chromatin

    OpenAIRE

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

    2010-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

  18. High-pass filtering and dynamic gain regulation enhance vertical bursts transmission along the mossy fiber pathway of cerebellum

    Directory of Open Access Journals (Sweden)

    Jonathan Mapelli

    2010-05-01

    Full Text Available Signal elaboration in the cerebellum mossy fiber input pathway presents controversial aspects, especially concerning gain regulation and the spot-like (rather than beam-like appearance of granular-to-molecular layer transmission. By using voltage-sensitive dye (VSD imaging in rat cerebellar slices (Mapelli et al., 2010, we found that mossy fiber bursts optimally excited the granular layer above ~50 Hz and the overlaying molecular layer above ~100 Hz, thus generating a cascade of high-pass filters. NMDA receptors enhanced transmission in the granular, while GABA-A receptors depressed transmission in both the granular and molecular layer. Burst transmission gain was controlled through a dynamic frequency-dependent involvement of these receptors. Moreover, while high-frequency transmission was enhanced along vertical lines connecting the granular to molecular layer, no high-frequency enhancement was observed along the parallel fiber axis in the molecular layer. This was probably due to the stronger effect of Purkinje cell GABA-A receptor-mediated inhibition occurring along the parallel fibers than along the granule cell axon ascending branch. The consequent amplification of burst responses along vertical transmission lines could explain the spot-like activation of Purkinje cells observed following punctuate stimulation in vivo .

  19. Studies on mechanical, thermal and dynamic mechanical properties of untreated (raw) and treated coconut sheath fiber reinforced epoxy composites

    International Nuclear Information System (INIS)

    Highlights: • UTCSE and TCSE composites have been fabricated by compression molding technique. • The prepared specimens were characterized by FTIR, DMA, TGA and SEM techniques. • TCSE composite showed higher mechanical properties compared to UTCSE composite. • DMA showed that TCSE composite exhibited higher storage modulus than UTCSE composite. • TCSE composite showed higher thermal stability than UTCSE composite. - Abstract: The untreated (raw) coconut sheath fiber reinforced epoxy (UTCSE) composite and treated coconut sheath fiber reinforced epoxy (TCSE) composite have been fabricated using hand layup followed by compression molding technique. The prepared specimens were characterized by Fourier transform infrared spectroscopy (FTIR), dynamic mechanical analysis (DMA), thermo gravimetric analysis (TGA) and scanning electron microscopy (SEM) techniques. The prepared specimens are cut as per ASTM Standards to measure tensile, flexural and impact strengths by using universal testing machine and izod impact tester respectively. The treated coconut sheath fiber reinforced epoxy composite (TCSE) posses higher mechanical strength and thermal stability compared to untreated (raw) coconut sheath fiber reinforced epoxy composite (UTCSE). In the SEM fracture analysis, TCSE composite showed better fiber–matrix bonding and absence of voids compared to UTCSE composite

  20. Dynamic behaviors of various volume rate steel-fiber reinforced reactive powder concrete after high temperature burnt

    Science.gov (United States)

    Pang, Baojun; Wang, Liwen; Yang, Zhenqi; Chi, Runqiang

    2009-06-01

    Dynamic strain-stress curves of reactive powder concrete under high strain rate (10/s-100/s) were determined by improved split Hopkinson pressure bar (SHPB) system. A plumbum pulse shaper was used to ensure the symmetrical stress in the specimens before fracture and avoid the fluctuation of test data due to input shaky stress pulse. A time modified method was induced for data processing in order to get accurate SHPB results. The results of experiment showed after high temperature burnt, different volume rate (0.0%, 0.5%, 1.0%, 1.5%) steel-fiber reinforced reactive power concrete had the same changing tendency of residual mechanics behaviors, e.g. after 400 centigrade burnt, the residual compression strength was about 70% of material strength without burnt under 100/s. After 800 centigrade burnt, the compression strength is about 30% under 100/s while the deformation ability increased. At meanwhile, steel fiber had improved the mechanism of reinforcing effect and toughening effect of concrete material after burnt. With increasing of steel fiber volume rate, dynamic residual behavior of samples was improved. Microcosmic characteristics and energy absorption were induced for explaining the experiment results.

  1. Generation and Purification of Human INO80 Chromatin Remodeling Complexes and Subcomplexes

    OpenAIRE

    Chen, Lu; Ooi, Soon-Keat; Conaway, Ronald C.; Conaway, Joan W

    2014-01-01

    INO80 chromatin remodeling complexes regulate nucleosome dynamics and DNA accessibility by catalyzing ATP-dependent nucleosome remodeling. Human INO80 complexes consist of 14 protein subunits including Ino80, a SNF2-like ATPase, which serves both as the catalytic subunit and the scaffold for assembly of the complexes. Functions of the other subunits and the mechanisms by which they contribute to the INO80 complex's chromatin remodeling activity remain poorly understood, in part due to the cha...

  2. Multi-pulses dynamic patterns in a topological insulator mode-locked ytterbium-doped fiber laser

    Science.gov (United States)

    Peiguang, Yan; Rongyong, Lin; Han, Zhang; Zhiteng, Wang; Han, Chen; Shuangchen, Ruan

    2015-01-01

    Multi-pulse dynamic patterns have been experimentally observed in an Ytterbium-doped fiber laser passively mode locked by a topological insulator (TI) Bi2Te3 saturable absorber (SA). The fundamental mode-locking operation with a repetition rate of ~1.10 MHz was achieved under a pump power of ~160 mW with an appropriate setting of the polarization controller (PC). It was found that through either changing the pump power or rotating the orientation of intra-cavity PC, several characteristic modes have been experimentally observed, including disordered multi-pulses, bunch of pulses, and soliton rains. Simultaneously, quasi-square pulses have also been observed in the laser cavity. Our systematic study clearly demonstrated that TI could be developed as an effective SA for the generation of different pulse operation states in a passively mode-locked all-normal-dispersion Ytterbium-doped fiber laser.

  3. Dynamic Response of Tapered Optical Multimode Fiber Coated with Carbon Nanotubes for Ethanol Sensing Application

    Directory of Open Access Journals (Sweden)

    Arafat Shabaneh

    2015-05-01

    Full Text Available Ethanol is a highly combustible chemical universally designed for biomedical applications. In this paper, optical sensing performance of tapered multimode fiber tip coated with carbon nanotube (CNT thin film towards aqueous ethanol with different concentrations is investigated. The tapered optical multimode fiber tip is coated with CNT using drop-casting technique and is annealed at 70 °C to enhance the binding of the nanomaterial to the silica fiber tip. The optical fiber tip and the CNT sensing layer are micro-characterized using FESEM and Raman spectroscopy techniques. When the developed sensor was exposed to different concentrations of ethanol (5% to 80%, the sensor reflectance reduced proportionally. The developed sensors showed high sensitivity, repeatability and fast responses (<55 s towards ethanol.

  4. Dynamic Characterization of Fiber Optical Chirped Pulse Amplification for Sub-ps Pulses

    DEFF Research Database (Denmark)

    Cristofori, Valentina; Lali-Dastjerdi, Zohreh; Rishøj, Lars Søgaard;

    2013-01-01

    We investigate experimentally the propagation of sub-picosecond pulses in fiber optical parametric chirped pulse amplifiers, showing a significant broadening of the pulses from 450 fs up to 720 fs due to dispersion and self-phase modulation.......We investigate experimentally the propagation of sub-picosecond pulses in fiber optical parametric chirped pulse amplifiers, showing a significant broadening of the pulses from 450 fs up to 720 fs due to dispersion and self-phase modulation....

  5. Micro-Structured Sapphire Fiber Sensors for Simultaneous Measurements of High-T and Dynamic Gas Pressure in Harsh Environments

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Hai; Tsai, Hai-Lung; Dong, Junhang

    2014-09-30

    This is the final report for the program “Micro-Structured Sapphire Fiber Sensors for Simultaneous Measurements of High Temperature and Dynamic Gas Pressure in Harsh Environments”, funded by NETL, and performed by Missouri University of Science and Technology, Clemson University and University of Cincinnati from October 1, 2009 to September 30, 2014. Securing a sustainable energy economy by developing affordable and clean energy from coal and other fossil fuels is a central element to the mission of The U.S. Department of Energy’s (DOE) National Energy Technology Laboratory (NETL). To further this mission, NETL funds research and development of novel sensor technologies that can function under the extreme operating conditions often found in advanced power systems. The main objective of this research program is to conduct fundamental and applied research that will lead to successful development and demonstration of robust, multiplexed, microstructured silica and single-crystal sapphire fiber sensors to be deployed into the hot zones of advanced power and fuel systems for simultaneous measurements of high temperature and gas pressure. The specific objectives of this research program include: 1) Design, fabrication and demonstration of multiplexed, robust silica and sapphire fiber temperature and dynamic gas pressure sensors that can survive and maintain fully operational in high-temperature harsh environments. 2) Development and demonstration of a novel method to demodulate the multiplexed interferograms for simultaneous measurements of temperature and gas pressure in harsh environments. 3) Development and demonstration of novel sapphire fiber cladding and low numerical aperture (NA) excitation techniques to assure high signal integrity and sensor robustness.

  6. Dynamic angular velocity modeling and error compensation of one-fiber fiber optic gyroscope (OFFOG) in the whole temperature range

    International Nuclear Information System (INIS)

    Dynamic angular velocity modeling and error compensation of VG095M in the whole temperature range, based on a radial basis function (RBF) neural network, is presented in this paper. With gyro output voltage and environmental temperature as the input and angular velocity as the output, an RBF neural network model is established. The model is trained and validated by the experiment data. The fitting error of the model is 4.3818 × 10−6 deg s−1, which shows that the model has high precision. The experiment data except the data used for modeling were processed with this model. The results show that the maximum, minimum and mean square error of the angular velocity were reduced to 4.6%, 4.3% and 4.7% respectively after compensation

  7. 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

  8. 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.

  9. Nuclear deformability and telomere dynamics are regulated by cell geometric constraints.

    Science.gov (United States)

    Makhija, Ekta; Jokhun, D S; Shivashankar, G V

    2016-01-01

    Forces generated by the cytoskeleton can be transmitted to the nucleus and chromatin via physical links on the nuclear envelope and the lamin meshwork. Although the role of these active forces in modulating prestressed nuclear morphology has been well studied, the effect on nuclear and chromatin dynamics remains to be explored. To understand the regulation of nuclear deformability by these active forces, we created different cytoskeletal states in mouse fibroblasts using micropatterned substrates. We observed that constrained and isotropic cells, which lack long actin stress fibers, have more deformable nuclei than elongated and polarized cells. This nuclear deformability altered in response to actin, myosin, formin perturbations, or a transcriptional down-regulation of lamin A/C levels in the constrained and isotropic geometry. Furthermore, to probe the effect of active cytoskeletal forces on chromatin dynamics, we tracked the spatiotemporal dynamics of heterochromatin foci and telomeres. We observed increased dynamics and decreased correlation of the heterochromatin foci and telomere trajectories in constrained and isotropic cell geometry. The observed enhanced dynamics upon treatment with actin depolymerizing reagents in elongated and polarized geometry were regained once the reagent was washed off, suggesting an inherent structural memory in chromatin organization. We conclude that active forces from the cytoskeleton and rigidity from lamin A/C nucleoskeleton can together regulate nuclear and chromatin dynamics. Because chromatin remodeling is a necessary step in transcription control and its memory, genome integrity, and cellular deformability during migration, our results highlight the importance of cell geometric constraints as critical regulators in cell behavior. PMID:26699462

  10. EFFECT OF LAYERING PATTERN ON THE DYNAMIC MECHANICAL PROPERTIES AND THERMAL DEGRADATION OF OIL PALM-JUTE FIBERS REINFORCED EPOXY HYBRID COMPOSITE

    Directory of Open Access Journals (Sweden)

    M. Jawaid

    2011-04-01

    Full Text Available Dynamic mechanical and thermal analysis of oil palm empty fruit bunches (EFB/jute fiber reinforced epoxy hybrid composites were carried out. The effect of layering pattern on dynamic mechanical properties (storage modulus (E’, loss modulus (E”, and tan δ was investigated as a function of temperature. The storage modulus (E’ was found to be decreased with temperature in all cases, and hybrid composites had almost the same values of E’ at glass transition temperature (Tg. The tan δ peak height was minimum for jute composites and maximum for epoxy matrix. Layering pattern affected the dynamic mechanical properties of hybrid composites. Cole-Cole analysis was carried out to understand the phase behaviour of the composite samples. Thermogravimetric analysis (TGA results indicated an increase in thermal stability of pure EFB composite with the incorporation of jute fibers. The overall results showed that hybridization with jute fibers enhanced the dynamic mechanical and thermal properties.

  11. A High Sensitivity and Wide Dynamic Range Fiber-Optic Sensor for Low-Concentration VOC Gas Detection

    Directory of Open Access Journals (Sweden)

    Md. Rajibur Rahaman Khan

    2014-12-01

    Full Text Available In this paper, we propose a volatile organic compound (VOC gas sensing system with high sensitivity and a wide dynamic range that is based on the principle of the heterodyne frequency modulation method. According to this method, the time period of the sensing signal shift when Nile Red containing a VOC-sensitive membrane of a fiber-optic sensing element comes into contact with a VOC. This sensing membrane produces strong, fast and reversible signals when exposed to VOC gases. The response and recovery times of the proposed sensing system were less than 35 s, and good reproducibility and accuracy were obtained.

  12. Dephasing of Single-Photon Orbital Angular Momentum Qudit States in Fiber: Limits to Correction via Dynamical Decoupling

    Science.gov (United States)

    Gupta, Manish K.; Dowling, Jonathan P.

    2016-06-01

    We analytically derive a decoherence model for orbital angular momentum states of a photon in a multimode optical fiber and show that the rate of decoherence scales approximately exponentially with l2, where l is the azimuthal mode order. We also show numerically that for large values of l the orbital angular momentum photon state completely dephases. However, for lower values of l the decoherence can be minimized by using dynamical decoupling to allow for qudit high-bandwidth quantum communication and similar applications.

  13. [Research on the reflection spectrum of linear chirped fiber bragg grating under the impact of dynamic stress].

    Science.gov (United States)

    Wang, Jing; Jiang, Shan-chao; Shi, Bin; Sui, Qing-mei; Wang, Zheng-fang; Li, Xiao-fei; Wang, Ning; Yang, Shuai

    2014-08-01

    Dynastic stress field detection based on the linear chirped fiber Bragg grating (LCFBG) was proposed. Firstly, the reflectance spectra strain sensing model of LCFBG adopting the transfer matrix method was constructed, and attenuation sine function was used to simulate the dynamic stress field along LCFBG. In the simulation experiment, the responding character of LCFBG reflection spectrum to different amplitude, different attenuation coefficient and different propagation speed of dynamic stress was studied in detail. The simulation results show that the reflectivity, wavelength and spectral shape of LCFBG reflection spec- trum are related to the dynamic stress. However, the LCFBG reflection spectrum has different response to different parameters of dynamic stress. In a range, maximum reflectivity of LCFBG reflectance spectra increases when the amplitude and propagation speed of dynastic stress field becomes larger, but it decreases when the attenuation coefficient increases. Eventually, vibration sensor using LCFBG as the sensing element was designed, and then LCFBG dynamic stress fluctuations experiment platform was build. The data obtained from experiment agrees with the simulation results. Therefore, a novel detection method of dynamic stress field through real-time acquisition of LCFBG full spectral information is proposed in this article. PMID:25508706

  14. Synaptic dynamics on different time scales in a parallel fiber feedback pathway of the weakly electric fish.

    Science.gov (United States)

    Lewis, John E; Maler, Leonard

    2004-02-01

    Synaptic dynamics comprise a variety of interacting processes acting on a wide range of time scales. This enables a synapse to perform a large array of computations, from temporal and spatial filtering to associative learning. In this study, we describe how changing synaptic gain via long-term plasticity can act to shape the temporal filtering of a synapse through modulation of short-term plasticity. In the weakly electric fish, parallel fibers from cerebellar granule cells provide massive feedback inputs to the pyramidal neurons of the electrosensory lateral line lobe. We demonstrate a long-term synaptic enhancement (LTE) of these synapses that is biochemically similar to the presynaptic long-term potentiation expressed by parallel fibers in the mammalian cerebellum. Using a novel stimulation protocol and a simple modeling paradigm, we then quantify the changes in short-term plasticity during the induction of LTE and show that these changes can be explained by gradual changes in only one model parameter, that which is associated with the baseline probability of transmitter release. These changes lead to a shift in the spike frequency preference of the synapse, suggesting that long-term plasticity is not only involved in controlling the gain of the parallel fiber synapse, but also provides a means of controlling synaptic filtering over multiple time scales. PMID:14602840

  15. A projection operator approach for computing the dynamics of AS2S3 chalcogenide birefringent photonic crystal fiber coupler

    Science.gov (United States)

    Uthayakumar, T.; Vasantha Jayakantha Raja, R.; Porsezian, K.

    2015-02-01

    A variety of AS2S3 chalcogenide photonic crystal fiber coupler of special properties are proposed to study the role of birefringence in all optical coupling characteristics based on the projection operator method (POM). The equations of motion describing the dynamics of the individual pulse parameters through x- and y-polarized modes are arrived at by employing POM from the coupled nonlinear Schrödinger equations. From the pulse parameter dynamics, it is observed that the amplitudes of the polarization components are significantly influenced by the pulse being introduced with different polarizing angle even at low input power level. Such a selective polarizing angles of the input pulse will provide efficient control over the desired splitting ratio as well as the ability to decide the desired polarization component.

  16. Dynamics of noise-like pulsing at sub-ns scale in a passively mode-locked fiber laser.

    Science.gov (United States)

    Santiago-Hernandez, H; Pottiez, O; Duran-Sanchez, M; Alvarez-Tamayo, R I; Lauterio-Cruz, J P; Hernandez-Garcia, J C; Ibarra-Escamilla, B; Kuzin, E A

    2015-07-27

    We report an original noise-like pulse dynamics observed in a figure-eight fiber laser, in which fragments are continually released from a main waveform that circulates in the cavity. Particularly, we report two representative cases of the dynamics: in the first case the released fragments drift away from the main bunch and decay over a fraction of the round-trip time, and then vanish suddenly; in the second case, the sub-packets drift without decaying over the complete cavity round-trip time, until they eventually merge again with the main waveform. The most intriguing result is that these fragments, as well as the main waveform, are formed of units with sub-ns duration and roughly the same energy. PMID:26367548

  17. A Numerical Development in the Dynamical Equations of Solitons in Optical Fibers

    Directory of Open Access Journals (Sweden)

    Érica Regina Takano Natti

    2006-02-01

    Full Text Available It was evaluated the numerical resolution of a nonlinear differential equations system that describes the solitons propagation in dielectric optical fibers, through the method of finite elements, which is implemented based on Streamline Upwind Petrov-Galerkin (SUPG and Consistent Approximate Upwind (CAU formulations.

  18. Dynamic characterization and amplification of sub-picosecond pulses in fiber optical parametric chirped pulse amplifiers

    DEFF Research Database (Denmark)

    Cristofori, Valentina; Lali-Dastjerdi, Zohreh; Rishøj, Lars Søgaard;

    2013-01-01

    We show a first-time demonstration of amplification of 400 fs pulses in a fiber optical parametric amplifier. The 400 fs signal is stretched in time, amplified by 26 dB and compressed back to 500 fs. A significant broadening of the pulses is experimentally shown due to dispersion and limited gain...

  19. Transient Dynamics of Fluoride-Based High Concentration Erbium/Cerium Co-Doped Fiber Amplifier

    Institute of Scientific and Technical Information of China (English)

    S. S-H. Yam; Y. Akasaka; Y. Kubota; R. Huang; D. L. Harris; J. Pan

    2003-01-01

    We designed and evaluated a fluoride-based high concentration erbium/ cerium co-doped fiber amplifier. It is suitable for Metropolitan Area Networks due to faster transient, flatter (unfiltered) gain, smaller footprint and gain excursion than its silica-based counterpart.

  20. 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.

  1. Dynamics and mechanisms of asbestos-fiber aggregate growth in water

    Science.gov (United States)

    Wu, L.; Ortiz, C. P.; Jerolmack, D. J.

    2015-12-01

    Most colloidal particles including asbestos fibers form aggregates in water, when solution chemistry provides favorable conditions. To date, the growth of colloidal aggregates has been observed in many model systems under optical and scanning electron microscopy; however, all of these studies have used near-spherical particles. The highly elongated nature of asbestos fibers may cause anomalous aggregate growth and morphology, but this has never been examined. Although the exposure pathway of concern for asbestos is through the air, asbestos particles typically reside in soil that is at least partially saturated, and aggregates formed in the aqueous phase may influence the mobility of particles in the environment. Here we study solution-phase aggregation kinetics of asbestos fibers using a liquid-cell by in situ microscopy, over micron to centimeter length scales and from a tenth of a second to hours. We employ an elliptical particle tracking technique to determine particle trajectories and to quantify diffusivity. Experiments reveal that diffusing fibers join by cross linking, but that such linking is sometimes reversible. The resulting aggregates are very sparse and non-compact, with a fractal dimension that is lower than any previously reported value. Their morphology, growth rate and particle size distribution exhibit non-classical behavior that deviates significantly from observations of aggregates composed of near-spherical particles. We also perform experiments using synthetic colloidal particles, and compare these to asbestos in order to separate the controls of particle shape vs. material properties. This direct method for quantitatively observing aggregate growth is a first step toward predicting asbestos fiber aggregate size distributions in the environment. Moreover, many emerging environmental contaminants - such as carbon nanotubes - are elongated colloids, and our work suggests that theories for aggregate growth may need to be modified in order to

  2. 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.

  3. In vivo binding of retinol to chromatin

    International Nuclear Information System (INIS)

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

  4. Mimicking the nonlinear dynamics of optical fibers with waveguide arrays: towards a spatiotemporal supercontinuum generation

    CERN Document Server

    Tran, Truong X

    2013-01-01

    We numerically demonstrate the formation of the spatiotemporal version of the so-called diffractive resonant radiation generated in waveguide arrays with Kerr nonlinearity when a long pulse is launched into the system. The phase matching condition for the diffractive resonant radiation that we have found earlier for CW beams also works well in the spatiotemporal case. By introducing a linear potential, one can introduce a continuous shift of the central wavenumber of a linear pulse, whereas in the nonlinear case one can demonstrate that the soliton self-wavenumber shift can be compensated by the emission of diffractive resonant radiation, in a very similar fashion as it is done in optical fibers. This work paves the way for designing unique optical devices that generate spectrally broad supercontinua with a controllable directionality by taking advantage of the combined physics of optical fibers and waveguide arrays.

  5. Changes in large-scale chromatin structure and function during oogenesis: a journey in company with follicular cells.

    Science.gov (United States)

    Luciano, Alberto M; Franciosi, Federica; Dieci, Cecilia; Lodde, Valentina

    2014-09-01

    The mammalian oocyte nucleus or germinal vesicle (GV) exhibits characteristic chromatin configurations, which are subject to dynamic modifications through oogenesis. Aim of this review is to highlight how changes in chromatin configurations are related to both functional and structural modifications occurring in the oocyte nuclear and cytoplasmic compartments. During the long phase of meiotic arrest at the diplotene stage, the chromatin enclosed within the GV is subjected to several levels of regulation. Morphologically, the chromosomes lose their individuality and form a loose chromatin mass. The decondensed configuration of chromatin then undergoes profound rearrangements during the final stages of oocyte growth that are tightly associated with the acquisition of meiotic and developmental competence. Functionally, the discrete stages of chromatin condensation are characterized by different level of transcriptional activity, DNA methylation and covalent histone modifications. Interestingly, the program of chromatin rearrangement is not completely intrinsic to the oocyte, but follicular cells exert their regulatory actions through gap junction mediated communications and intracellular messenger dependent mechanism(s). With this in mind and since oocyte growth mostly relies on the bidirectional interaction with the follicular cells, a connection between cumulus cells gene expression profile and oocyte developmental competence, according to chromatin configuration is proposed. This analysis can help in identifying candidate genes involved in the process of oocyte developmental competence acquisition and in providing non-invasive biomarkers of oocyte health status that can have important implications in treating human infertility as well as managing breeding schemes in domestic mammals. PMID:25028181

  6. Efficient multiple time scale method for modeling compressible vapor plume dynamics inside transient keyhole during fiber laser welding

    Science.gov (United States)

    Pang, Shengyong; Chen, Xin; Li, Wen; Shao, Xinyu; Gong, Shuili

    2016-03-01

    Efficient coupling modeling of multiple time scale interactions between keyhole, weld pool and compressible vapor plume during laser welding has long been limited. To address this problem, we present a highly efficient multiple time scale method combining a novel dual-time stepping and Ghost Fluid interpolation strategy with incompressible and compressible fluid solvers, which allows us predicting the compressible plume dynamics inside transient keyhole in fiber laser welding for the first time. In our method, the compressible dynamic vapor inside the transient keyhole is solved with a Roe scheme based algorithm and the incompressible molten liquid of weld pool is calculated by a Projection method. A novel temperature dependent boundary condition of vapor plume is also proposed for the consideration of the dynamic evaporation phenomena on the transient keyhole wall. It is found that the time dependent distributions of vapor plume characteristics, including temperature, pressure, velocity, density and Mach number distributions inside the transient keyhole induced by laser welding can be reasonably predicted by comparing to experimental and literature data. It is also shown that the proposed multiple time scale method is around 60 times faster than the vapor plume modeling method using a single nanosecond scale time step. For the vapor plume in a typical fiber laser welding process, the results indicate that the peak pressure can be greater than 2.0 atmospheric pressures; the average density is around 0.15-0.3 kg/m3 which is much smaller than the air density; and the local Mach number can be greater than 0.8 or even 1.0 Mach which demonstrates the necessity to treat the vapor plume as a compressible fluid.

  7. 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.

  8. Nonlinear polarization dynamics in a weakly birefringent all-normal dispersion photonic crystal fiber : toward a practical coherent fiber supercontinuum laser

    DEFF Research Database (Denmark)

    Tu, Haohua; Liu, Yuan; Liu, Xiaomin;

    2012-01-01

    be qualitatively or semi-quantitatively understood by the coupled GNLSE that takes into account the form-birefringence. The nonlinear polarization effects induced by the birefringence significantly distort the otherwise simple spectrotemporal field of the SC pulses. We therefore propose the...... fabrication of polarization-maintaining DFDD-ANDi fibers to avoid these adverse effects in pursuing a practical coherent fiber SC laser....

  9. Experimental and Numerical Evaluation of the Mechanical Behavior of Strongly Anisotropic Light-Weight Metallic Fiber Structures under Static and Dynamic Compressive Loading

    Directory of Open Access Journals (Sweden)

    Olaf Andersen

    2016-05-01

    Full Text Available Rigid metallic fiber structures made from a variety of different metals and alloys have been investigated mainly with regard to their functional properties such as heat transfer, pressure drop, or filtration characteristics. With the recent advent of aluminum and magnesium-based fiber structures, the application of such structures in light-weight crash absorbers has become conceivable. The present paper therefore elucidates the mechanical behavior of rigid sintered fiber structures under quasi-static and dynamic loading. Special attention is paid to the strongly anisotropic properties observed for different directions of loading in relation to the main fiber orientation. Basically, the structures show an orthotropic behavior; however, a finite thickness of the fiber slabs results in moderate deviations from a purely orthotropic behavior. The morphology of the tested specimens is examined by computed tomography, and experimental results for different directions of loading as well as different relative densities are presented. Numerical calculations were carried out using real structural data derived from the computed tomography data. Depending on the direction of loading, the fiber structures show a distinctively different deformation behavior both experimentally and numerically. Based on these results, the prevalent modes of deformation are discussed and a first comparison with an established polymer foam and an assessment of the applicability of aluminum fiber structures in crash protection devices is attempted.

  10. Multiple fiber Bragg grating sensor network with a rapid response and wide spectral dynamic range using code division multiple access

    Science.gov (United States)

    Kim, Youngbok; Jeon, Sie-Wook; Park, Chang-Soo

    2011-05-01

    Fiber Bragg grating (FBG) sensor networks have been intensively researched in optical sensor area and it developed in wavelength division multiplexing (WDM) and time division multiplexing (TDM) technologies which was adopted for its interrogating many optical sensors. In particular, WDM technology can be easily employed to interrogate FBG sensor however, the number of FBG sensors is limited. On the other hand, the TDM technique can extremely expand the number of sensor because the FBG sensors have same center wavelength. However, it suffers from a reduced sensor output power due to low reflectivity of FBG sensor. In this paper, we proposed and demonstrated the FBG sensor network based on code division multiple access (CDMA) with a rapid response and wide spectral dynamic range. The reflected semiconductor optical amplifier (RSOA) as a light source was directly modulated by the generated pseudorandom binary sequence (PRBS) code and the modulated signal is amplified and goes through FBG sensors via circulator. When the modulated optical signal experienced FBG sensor array, the optical signal which was consistent with center wavelength of FBGs is reflected and added from each sensors. The added signal goes into dispersion compensating fiber (DCF) as a dispersion medium. After through the DCF, the optical signal is converted into electrical signal by using photodetector (PD). For separate individual reflected sensor signal, the sliding correlation method was used. The proposed method improves the code interference and it also has advantages such as a large number of sensors, continuously measuring individual sensors, and decreasing the complexity of the sensor network.

  11. The adsorption of lead(II) ions by dynamic high pressure micro-fluidization treated insoluble soybean dietary fiber.

    Science.gov (United States)

    Wang, Hui; Huang, Tao; Tu, Zong-Cai; Ruan, Chuan-Ying; Lin, Derong

    2016-06-01

    Insoluble dietary fiber from soybean residue (SIDF) was treated with dynamic high-pressure microfluidization (DHPM) and used as adsorbent for Pb(II) ion. The effects of pressure on the Pb(II) adsorption capacity, primary cilia structure and surface topography of SIDF were determined using a gastrointestinal simulated model in vitro. SIDF (at pH 7.0) showed maximum binding capacity (261.42 ± 2.77 μmol/g), which was about 1.13 times higher than that of untreated sample (233.47 ± 1.84 μmol/g), when pressure reached 80 MPa. However, the net adsorption value of SIDF in a simulated small intestine (~ 9 μmol/g) was significantly lower than that in the stomach (~ 48 μmol/g), because of the competitive adsorption of Pb(2+) by pancreatin, cholate and several enzymes in the small intestine. In addition, the adsorption capacity of SIDF exhibited good linear relationship with the physicochemical properties of total negative charges, and the adsorption behavior presumably occurred on the surface area of granules fiber. PMID:27478208

  12. Chromatin remodeling enzyme Snf2h regulates embryonic lens differentiation and denucleation.

    Science.gov (United States)

    He, Shuying; Limi, Saima; McGreal, Rebecca S; Xie, Qing; Brennan, Lisa A; Kantorow, Wanda Lee; Kokavec, Juraj; Majumdar, Romit; Hou, Harry; Edelmann, Winfried; Liu, Wei; Ashery-Padan, Ruth; Zavadil, Jiri; Kantorow, Marc; Skoultchi, Arthur I; Stopka, Tomas; Cvekl, Ales

    2016-06-01

    Ocular lens morphogenesis is a model for investigating mechanisms of cellular differentiation, spatial and temporal gene expression control, and chromatin regulation. Brg1 (Smarca4) and Snf2h (Smarca5) are catalytic subunits of distinct ATP-dependent chromatin remodeling complexes implicated in transcriptional regulation. Previous studies have shown that Brg1 regulates both lens fiber cell differentiation and organized degradation of their nuclei (denucleation). Here, we employed a conditional Snf2h(flox) mouse model to probe the cellular and molecular mechanisms of lens formation. Depletion of Snf2h induces premature and expanded differentiation of lens precursor cells forming the lens vesicle, implicating Snf2h as a key regulator of lens vesicle polarity through spatial control of Prox1, Jag1, p27(Kip1) (Cdkn1b) and p57(Kip2) (Cdkn1c) gene expression. The abnormal Snf2h(-/-) fiber cells also retain their nuclei. RNA profiling of Snf2h(-/) (-) and Brg1(-/-) eyes revealed differences in multiple transcripts, including prominent downregulation of those encoding Hsf4 and DNase IIβ, which are implicated in the denucleation process. In summary, our data suggest that Snf2h is essential for the establishment of lens vesicle polarity, partitioning of prospective lens epithelial and fiber cell compartments, lens fiber cell differentiation, and lens fiber cell nuclear degradation. PMID:27246713

  13. Dynamic strain detection using a fiber Bragg grating sensor array for geotechnical applications

    Science.gov (United States)

    Schmidt-Hattenberger, Cornelia; Naumann, M.; Borm, Gunter

    2003-03-01

    In recent years fiber Bragg gratings have been successfully introduced as sensors for strain, temperature and pressure variations. Their performance and reliability has been proven in many practical applications including strain monitoring in civil engineering and tunneling, downhole monitoring in oil reservoirs and flow assurance monitoring in pipelines. The gratings have great potential to at as true structurally integrated sensor elements. They can be embedded in typical structural or reinforcing elements of civil and geotechnical buildings. Several methods of interrogation schemes are established depending on the desired accuracy and resolution of the measurement. The most important methods are the linear discriminator, the tunable Fbry-Perot filter technique, and several interferometer setups.

  14. Dynamic pulsing of a MOPA fiber laser for enhanced material processing

    Science.gov (United States)

    Hendow, Sami T.; Salcedo, José R.; Romero, Rosa; Guerreiro, Paulo T.

    2011-02-01

    Pulse bursting is demonstrated using a pulsed MOPA fiber laser at 1064 nm for percussion drilling of stainless steel. Bursts are configured as fast pulse sequences at tens of MHz, with a temporal envelope in the range from 10 to 420 ns. Their use rapidly enhances the efficiency of material removal by enhancing pulse energy deposition, and quality improvement. Results are shown for various pulse conditions by changing number of pulses, spacing and peak powers. Each pulse burst is collectively triggered and amplified as a single pulse group, at repetition frequencies from singleshot to hundreds of kHz.

  15. Pump-induced carrier envelope offset frequency dynamics and stabilization of an Yb-doped fiber frequency comb

    International Nuclear Information System (INIS)

    In this paper, we demonstrate a carrier envelope phase-stabilized Yb-doped fiber frequency comb seeding by a nonlinear-polarization-evolution (NPE) mode-locked laser at a repetition rate of 60 MHz with a pulse duration of 191 fs. The pump-induced carrier envelope offset frequency (f0) nonlinear tuning is discussed and further explained by the spectrum shift of the laser pulse. Through the environmental noise suppression, the drift of the free-running f0 is reduced down to less than 3 MHz within an hour. By feedback control on the pump power with a self-made phase-lock loop (PLL) electronics the carrier envelope offset frequency is well phase-locked with a frequency jitter of 85 mHz within an hour. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  16. EFFECT OF LAYERING PATTERN ON THE DYNAMIC MECHANICAL PROPERTIES AND THERMAL DEGRADATION OF OIL PALM-JUTE FIBERS REINFORCED EPOXY HYBRID COMPOSITE

    OpenAIRE

    Jawaid, M.; H. P. S. Abdul Khalil

    2011-01-01

    Dynamic mechanical and thermal analysis of oil palm empty fruit bunches (EFB)/jute fiber reinforced epoxy hybrid composites were carried out. The effect of layering pattern on dynamic mechanical properties (storage modulus (E’), loss modulus (E”), and tan δ) was investigated as a function of temperature. The storage modulus (E’) was found to be decreased with temperature in all cases, and hybrid composites had almost the same values of E’ at glass transition temperature (Tg). The tan δ peak h...

  17. Annihilation dynamics of topological monopoles on a fiber in nematic liquid crystals

    Science.gov (United States)

    Nikkhou, M.; Škarabot, M.; Muševič, I.

    2016-06-01

    We use the laser tweezers to create isolated pairs of topological point defects in a form of radial and hyperbolic hedgehogs, located close and attracted to a thin fiber with perpendicular surface orientation of nematic liquid crystal molecules in a thin planar nematic cell. We study the time evolution of the interaction between the two monopoles by monitoring their movement and reconstructing their trajectories and velocities. We find that there is a crossover in the pair interaction force between the radial and hyperbolic hedgehog. At small separation d , the elastic force between the opposite monopoles results in an increase of the attractive force with respect to the far field, and their relative velocity v scales as a v (d ) ∝d-2 ±0.2 power law. At large separations, the two oppositely charged monopoles can either attract or repel with constant interaction force. We explain this strange far-field behavior by the experimental inaccuracy in setting the fiber exactly perpendicular to the cell director.

  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. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

    It is clear that a knowledge of the basic molecular structure of chromatin is a prerequisite for any progress toward an understanding of chromosome organization. With a two-component system, protein and nucleic acid, neutrons have a particularly powerful application to studies of the spatial arrangements of these components because of the ability, by contrast matching with H2O-D2O mixtures, to obtain neutron-scattering data on the individual components. With this approach it has been shown that the neutron diffraction of chromatin is consistent with a ''beads on a string'' model in which the bead consists of a protein core with DNA coiled on the outside. However, because chromatin is a gel and gives limited structural data, confirmation of such a model requires extension of the neutron studies by deuteration of specific chromatin components and the isolation of chromatin subunits. Although these studies are not complete, the neutron results so far obtained support the subunit model described above

  20. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    Directory of Open Access Journals (Sweden)

    Arifulin E. A.

    2015-08-01

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

  1. UV-induced pyrimidine dimers and trimethylpsoralen cross-links do not alter chromatin folding in vitro

    International Nuclear Information System (INIS)

    We have examined the ability of intact and histone H1 depleted chromatin fibers to fold into higher ordered structures in vitro following DNA damage by two different agents: UV irradiation at 254 nm and trimethylpsoralen plus near-UV light. Both agents damage DNA specifically, yet cause different degrees of unwinding (and possibly bending) of the DNA helix. In addition, trimethylpsoralen forms interstrand DNA cross-links. The structural transitions of intact and histone H1 depleted chromatin fibers, induced by NaCl, were monitored by analytical ultracentrifugation, light scattering, and circular dichroism. Our results indicate that when chromatin fibers contain even large, nonphysiological amounts of DNA photodamage by either agent, the salt-induced folding of these fibers into higher ordered structures is unaffected. The compact 30-nm fiber must therefore be able to accommodate a large amount of DNA photodamage (greater than one UV-induced photoproduct or trimethylpsoralen interstrand cross-link per nucleosome) with little or no change in the overall size or compaction of this structure

  2. Activation of tachykinin Neurokinin 3 receptors affects chromatin structure and gene expression by means of histone acetylation

    OpenAIRE

    Thakar, Amit; Sylar, Elise; Flynn, Francis W.

    2012-01-01

    The tachykinin, neurokinin 3 receptor (NK3R) is a g-protein coupled receptor that is broadly distributed in the nervous system and exerts its diverse physiological actions through multiple signaling pathways. Despite the role of the receptor system in a range of biological functions, the effects of NK3R activation on chromatin dynamics and gene expression have received limited attention. The present work determined the effects of senktide, a selective NK3R agonist, on chromatin organization, ...

  3. The Chromatin-Modifying Enzyme Ezh2 Is Critical for the Maintenance of Regulatory T Cell Identity after Activation

    OpenAIRE

    DuPage, Michel; Chopra, Gaurav; Quiros, Jason; Rosenthal, Wendy L.; Morar, Malika M.; Holohan, Dan; Zhang, Ruan; Turka, Laurence; Marson, Alexander; Bluestone, Jeffrey A.

    2015-01-01

    Regulatory T cells (Treg cells) are required for immune homeostasis. Chromatin remodeling is essential for establishing diverse cellular identities, but how the epigenetic program in Treg cells is maintained throughout the dynamic activation process remains unclear. Here we have shown that CD28 co-stimulation, an extracellular cue intrinsically required for Treg cell maintenance, induced the chromatin-modifying enzyme, Ezh2. Treg-specific ablation of Ezh2 resulted in spontaneous autoimmunity ...

  4. Bacterial chromatin: converging views at different scales.

    Science.gov (United States)

    Dame, Remus T; Tark-Dame, Mariliis

    2016-06-01

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

  5. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...... reassembly on nascent DNA strands. The aim of this review is to discuss how histones - new and old - are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms.......Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...

  6. Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters.

    Science.gov (United States)

    Ma, Zhibo; Li, Mo; Roy, Sharmila; Liu, Kevin J; Romine, Matthew L; Lane, Derrick C; Patel, Sapna K; Cai, Haini N

    2016-08-26

    The three-dimensional (3D) organization of the eukaryotic genome is critical for its proper function. Evidence suggests that extensive chromatin loops form the building blocks of the genomic architecture, separating genes and gene clusters into distinct functional domains. These loops are anchored in part by a special type of DNA elements called chromatin boundary elements (CBEs). CBEs were originally found to insulate neighboring genes by blocking influences of transcriptional enhancers or the spread of silent chromatin. However, recent results show that chromatin loops can also play a positive role in gene regulation by looping out intervening DNA and "delivering" remote enhancers to gene promoters. In addition, studies from human and model organisms indicate that the configuration of chromatin loops, many of which are tethered by CBEs, is dynamically regulated during cell differentiation. In particular, a recent work by Li et al has shown that the SF1 boundary, located in the Drosophila Hox cluster, regulates local genes by tethering different subsets of chromatin loops: One subset enclose a neighboring gene ftz, limiting its access by the surrounding Scr enhancers and restrict the spread of repressive histones during early embryogenesis; and the other loops subdivide the Scr regulatory region into independent domains of enhancer accessibility. The enhancer-blocking activity of these CBE elements varies greatly in strength and tissue distribution. Further, tandem pairing of SF1 and SF2 facilitate the bypass of distal enhancers in transgenic flies, providing a mechanism for endogenous enhancers to circumvent genomic interruptions resulting from chromosomal rearrangement. This study demonstrates how a network of chromatin boundaries, centrally organized by SF1, can remodel the 3D genome to facilitate gene regulation during development. PMID:27621770

  7. Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters

    Science.gov (United States)

    Ma, Zhibo; Li, Mo; Roy, Sharmila; Liu, Kevin J; Romine, Matthew L; Lane, Derrick C; Patel, Sapna K; Cai, Haini N

    2016-01-01

    The three-dimensional (3D) organization of the eukaryotic genome is critical for its proper function. Evidence suggests that extensive chromatin loops form the building blocks of the genomic architecture, separating genes and gene clusters into distinct functional domains. These loops are anchored in part by a special type of DNA elements called chromatin boundary elements (CBEs). CBEs were originally found to insulate neighboring genes by blocking influences of transcriptional enhancers or the spread of silent chromatin. However, recent results show that chromatin loops can also play a positive role in gene regulation by looping out intervening DNA and “delivering” remote enhancers to gene promoters. In addition, studies from human and model organisms indicate that the configuration of chromatin loops, many of which are tethered by CBEs, is dynamically regulated during cell differentiation. In particular, a recent work by Li et al has shown that the SF1 boundary, located in the Drosophila Hox cluster, regulates local genes by tethering different subsets of chromatin loops: One subset enclose a neighboring gene ftz, limiting its access by the surrounding Scr enhancers and restrict the spread of repressive histones during early embryogenesis; and the other loops subdivide the Scr regulatory region into independent domains of enhancer accessibility. The enhancer-blocking activity of these CBE elements varies greatly in strength and tissue distribution. Further, tandem pairing of SF1 and SF2 facilitate the bypass of distal enhancers in transgenic flies, providing a mechanism for endogenous enhancers to circumvent genomic interruptions resulting from chromosomal rearrangement. This study demonstrates how a network of chromatin boundaries, centrally organized by SF1, can remodel the 3D genome to facilitate gene regulation during development.

  8. Dynamic Fracture of Nanocomposites and Response of Fiber Composite Panels to Shock Loading

    Science.gov (United States)

    Shukla, Arun

    2009-06-01

    This lecture will present studies on the response of novel engineering materials to extreme dynamic loadings. In particular, the talk will focus on the behavior of sandwich composite materials to shock loading and dynamic fracture of nano-composite materials. Results from an experimental study on the response of sandwich materials to controlled blast loading will be presented. In this study, a shock tube facility was utilized to apply blast loading to simply supported plates of E-glass vinyl ester/PVC foam sandwich composite materials. Pressure sensors were mounted at the end of the muzzle section of the shock tube to measure the incident pressure and the reflected pressure profiles during the experiment. A high speed digital camera was utilized to capture the real time side deformation of the materials, as well as the development and progression of damage. Macroscopic and microscopic examination was then implemented to study the post-mortem damage. Conclusions on the relative performance of sandwich composites under blast loadings will also be discussed. Results from an experimental investigation conducted to evaluate the mechanical properties of novel materials fabricated using nano sized particles in polymer matrix will also be presented. Unsaturated polyester resin specimens embedded with small loadings of nano sized particles of TiO2 and Al2O3 were fabricated using a direct ultrasonification method to study the effects of nanosized particles on nanocomposite fracture properties. The ultrasonification method employed produced nanocomposites with excellent particle dispersion as verified by TEM. Experiments were conducted to investigate the dynamic crack initiation and rapid crack propagation in theses particle reinforced materials. High-speed digital imaging was employed along with dynamic photoelasticity to obtain real time, full-field quantification of the stress field associated with the dynamic fracture process. Birefringent coatings were used to conduct

  9. The influence of annealing on dynamical mechanical properties of polyamide 6 / fiber glass composites

    Directory of Open Access Journals (Sweden)

    J. Koszkul

    2006-10-01

    Full Text Available Purpose: of this paper is analysis the the influence of annealing on dynamical mechanical properties ofcomposites PA6 with fiberglass.Design/methodology/approach: Polamide 6 thermoplastic polymer of trade name Tarnamid T-27 produced byZakłady Azotowe S.A. in Tarnów (Poland was used for examinations. E glass fibre, made of non-alkaline boron– aluminium – silicon glass of alkaline oxides content less than 1%, was used for polyamide 6 reinforcement.Polyamide and its composites filled with 10, 30 and 50% of glass fibre were tested. Dynamical mechanicalproperties of composite matrix were testes for comparative reasons. In order to examine the influence of annealingon mechanical dynamical properties a part of samples were annealed in the air at temperature 170°C. In the testthe annealing rate was 0.015°C/s, time 900s per 1mm thickness and the cooling rate 0.01°C/s. Before examinationstest specimens were conditioned at 23±20C temperature and 50±5% relative humidity, during 16 h. Test specimenswere bent at the frequency 1 Hz and 10 Hz, in the range of temperature from – 100°C to 200°C, at a heating rate5 deg/min. Deformation amplitude was 16μm. Dynamical properties of polyamide and glass fibre filled compositeswere examined by the DMTA general – purpose apertures for dynamical tests (Polymer Laboratories.Findings: DMTA method was used to determine the influence of a fiberglass content on dynamical propertiesof polyamide composites. The effect of annealing on the plastic properties was also described.Research limitations/implications: DMTA method was used to determine the influence of a talc content ondynamical properties of polyamide 6 composites in the future.Practical implications: The results of experiments will allow to determine the recommendations referring to theoptimization of processing conditions, and as a result of this polymer will have high mechanical propertiesOriginality/value: Measurements of dynamical properties are a

  10. Matrix Dominated Failure of Fiber-Reinforced Composite Laminates Under Static and Dynamic Loading

    Science.gov (United States)

    Schaefer, Joseph Daniel

    Hierarchical material systems provide the unique opportunity to connect material knowledge to solving specific design challenges. Representing the quickest growing class of hierarchical materials in use, fiber-reinforced polymer composites (FRPCs) offer superior strength and stiffness-to-weight ratios, damage tolerance, and decreasing production costs compared to metals and alloys. However, the implementation of FRPCs has historically been fraught with inadequate knowledge of the material failure behavior due to incomplete verification of recent computational constitutive models and improper (or non-existent) experimental validation, which has severely slowed creation and development. Noted by the recent Materials Genome Initiative and the Worldwide Failure Exercise, current state of the art qualification programs endure a 20 year gap between material conceptualization and implementation due to the lack of effective partnership between computational coding (simulation) and experimental characterization. Qualification processes are primarily experiment driven; the anisotropic nature of composites predisposes matrix-dominant properties to be sensitive to strain rate, which necessitates extensive testing. To decrease the qualification time, a framework that practically combines theoretical prediction of material failure with limited experimental validation is required. In this work, the Northwestern Failure Theory (NU Theory) for composite lamina is presented as the theoretical basis from which the failure of unidirectional and multidirectional composite laminates is investigated. From an initial experimental characterization of basic lamina properties, the NU Theory is employed to predict the matrix-dependent failure of composites under any state of biaxial stress from quasi-static to 1000 s-1 strain rates. It was found that the number of experiments required to characterize the strain-rate-dependent failure of a new composite material was reduced by an order of

  11. Dynamic Microwave Photonic Filter Using Separate Carrier Tuning Based on Stimulated Brillouin Scattering in Fibers

    OpenAIRE

    Sancho J.; Chin S.; Sagues M.; Loayssa A.; Lloret J.; Gasulla I.; Sales S.; Thevenaz L.; Capmany J.

    2010-01-01

    Dynamic reconfiguration of a microwave photonic filter by tuning its basic delay based on stimulated Brillouin scattering-induced slow light and optical phase shift of the optical carrier is experimentally implemented. The measurements confirm that the free spectral range of the filter changes when a Brillouin pump is applied. These results demonstrate the potential of the separate carrier technique in microwave photonics applications.

  12. Dynamic fiber Bragg gratings based health monitoring system of composite aerospace structures

    Science.gov (United States)

    Panopoulou, A.; Loutas, T.; Roulias, D.; Fransen, S.; Kostopoulos, V.

    2011-09-01

    The main purpose of the current work is to develop a new system for structural health monitoring of composite aerospace structures based on real-time dynamic measurements, in order to identify the structural state condition. Long-gauge Fibre Bragg Grating (FBG) optical sensors were used for monitoring the dynamic response of the composite structure. The algorithm that was developed for structural damage detection utilizes the collected dynamic response data, analyzes them in various ways and through an artificial neural network identifies the damage state and its location. Damage was simulated by slightly varying locally the mass of the structure (by adding a known mass) at different zones of the structure. Lumped masses in different locations upon the structure alter the eigen-frequencies in a way similar to actual damage. The structural dynamic behaviour has been numerically simulated and experimentally verified by means of modal testing on two different composite aerospace structures. Advanced digital signal processing techniques, e.g. the wavelet transform (WT), were used for the analysis of the dynamic response for feature extraction. WT's capability of separating the different frequency components in the time domain without loosing frequency information makes it a versatile tool for demanding signal processing applications. The use of WT is also suggested by the no-stationary nature of dynamic response signals and the opportunity of evaluating the temporal evolution of their frequency contents. Feature extraction is the first step of the procedure. The extracted features are effective indices of damage size and location. The classification step comprises of a feed-forward back propagation network, whose output determines the simulated damage location. Finally, dedicated training and validation activities were carried out by means of numerical simulations and experimental procedures. Experimental validation was performed initially on a flat stiffened panel

  13. Dynamic characteristics and mechanisms of compressible metallic vapor plume behaviors in transient keyhole during deep penetration fiber laser welding

    Science.gov (United States)

    Pang, Shengyong; Shao, Xinyu; Li, Wen; Chen, Xin; Gong, Shuili

    2016-07-01

    The compressible metallic vapor plume or plasma plume behaviors in the keyhole during deep penetration laser welding have significant effects on the joint quality. However, these behaviors and their responses to process parameter variations have not been well understood. In this paper, we first systematically study the dynamic characteristics and mechanisms of compressible metallic vapor plume behaviors in transient keyhole during fiber laser welding of 304 stainless steels based on a multiple timescale multiphase model. The time-dependent temperature, pressure, velocity and Mach number distributions of vapor plume under different process parameters are theoretically predicted. It is found that the distributions of the main physical characteristics of vapor plume such as pressure, velocity as well as Mach number in keyhole are usually highly uneven and highly time dependent. The peak difference of the velocity, pressure, temperature and Mach number of the vapor plume in a keyhole could be greater than 200 m/s, 20 kPa, 1000 K and 0.6 Mach, respectively. The vapor plume characteristics in a transient keyhole can experience significant changes within several hundreds of nanoseconds. The formation mechanisms of these dynamic characteristics are mainly due to the mesoscale keyhole hump (sized in several tens of microns) dynamics. It is also demonstrated that it is possible to suppress the oscillations of compressible vapor plume in the keyhole by improving the keyhole stability through decreasing the heat input. However, stabilizing the keyhole could only weaken, but not eliminate, the observed highly uneven and transient characteristics. This finding may pose new challenges for accurate experimental measurements of vapor plume induced by laser welding.

  14. RNF20-SNF2H Pathway of Chromatin Relaxation in DNA Double-Strand Break Repair

    Directory of Open Access Journals (Sweden)

    Akihiro Kato

    2015-07-01

    Full Text Available Rapid progress in the study on the association of histone modifications with chromatin remodeling factors has broadened our understanding of chromatin dynamics in DNA transactions. In DNA double-strand break (DSB repair, the well-known mark of histones is the phosphorylation of the H2A variant, H2AX, which has been used as a surrogate marker of DSBs. The ubiquitylation of histone H2B by RNF20 E3 ligase was recently found to be a DNA damage-induced histone modification. This modification is required for DSB repair and regulated by a distinctive pathway from that of histone H2AX phosphorylation. Moreover, the connection between H2B ubiquitylation and the chromatin remodeling activity of SNF2H has been elucidated. In this review, we summarize the current knowledge of RNF20-mediated processes and the molecular link to H2AX-mediated processes during DSB repair.

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

    Science.gov (United States)

    Chen, Hsiuyi V.; Rando, Oliver J.

    2014-01-01

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

  16. Single Chromatin Fibre Assembly Using Optical Tweezers

    NARCIS (Netherlands)

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

    2001-01-01

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

  17. 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

  18. CTCF Binding Polarity Determines Chromatin Looping

    NARCIS (Netherlands)

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

    2015-01-01

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

  19. 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 ...

  20. Impact of chromatin structure on PR signaling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Hager, Gordon L

    2012-01-01

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

  1. 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,

  2. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  3. Factors affecting chromatin stability of bovine spermatozoa.

    Science.gov (United States)

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

    2008-03-01

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

  4. The Effects of Five-Order Nonlinear on the Dynamics of Dark Solitons in Optical Fiber

    Directory of Open Access Journals (Sweden)

    Feng-Tao He

    2013-01-01

    Full Text Available We study the influence of five-order nonlinear on the dynamic of dark soliton. Starting from the cubic-quintic nonlinear Schrodinger equation with the quadratic phase chirp term, by using a similarity transformation technique, we give the exact solution of dark soliton and calculate the precise expressions of dark soliton's width, amplitude, wave central position, and wave velocity which can describe the dynamic behavior of soliton's evolution. From two different kinds of quadratic phase chirps, we mainly analyze the effect on dark soliton’s dynamics which different fiver-order nonlinear term generates. The results show the following two points with quintic nonlinearities coefficient increasing: (1 if the coefficients of the quadratic phase chirp term relate to the propagation distance, the solitary wave displays a periodic change and the soliton’s width increases, while its amplitude and wave velocity reduce. (2 If the coefficients of the quadratic phase chirp term do not depend on propagation distance, the wave function only emerges in a fixed area. The soliton’s width increases, while its amplitude and the wave velocity reduce.

  5. Monitoring borehole flow dynamics using heated fiber optic DTS in a fractured rock aquifer

    Science.gov (United States)

    Coleman, Thomas; Chalari, Athena; Parker, Beth; Munn, Jonathan; Mondanos, Michael

    2014-05-01

    Temperature profiles in fractured rock have long been used to identify and characterize flow in the rock formation or in the borehole. Fiber optic distributed temperature sensing (DTS) is a tool that allows for continuous borehole temperature profiling in space and time. Recent technology advancements in the spatial, temperature, and temporal resolutions of DTS systems now allow temperature profiling methods to offer improved insight into fractured rock hydrogeologic processes. An innovation in shallow borehole temperature logging utilizes high resolution DTS temperature profiling in sealed and heated boreholes to identify fractures with natural gradient groundwater flow by creating a thermal disequilibrium and monitoring the temperature response. This technique can also be applied to open well conditions to monitor borehole flow distributions caused by hydraulic perturbations such as pumping or injection. A field trial was conducted in Guelph, Ontario, Canada to determine the capabilities of heated DTS for flow monitoring in both open and sealed wells. Intelligent distributed acoustic sensing (iDAS) measurements for vertical seismic profiling were carried out simultaneously with the DTS measurements to assist with characterization of the fractured aquifer system. DTS heat pulse tests were conducted in a single well under sealed conditions for natural gradient flow measurements and open conditions to monitor flow distributions during injection and pumping. The results of these tests indicate that borehole flow distributions can be monitored using DTS and that active heating allows for further information about the hydrogeologic system to be determined than from the passive measurements alone. Depth-continuous transmissivity data from the borehole correlate well with the DTS testing results. DTS based flow monitoring systems may be useful for monitoring transient production and injection processes for a variety of applications including groundwater remediation

  6. Progressive Chromatin Condensation and H3K9 Methylation Regulate the Differentiation of Embryonic and Hematopoietic Stem Cells.

    Science.gov (United States)

    Ugarte, Fernando; Sousae, Rebekah; Cinquin, Bertrand; Martin, Eric W; Krietsch, Jana; Sanchez, Gabriela; Inman, Margaux; Tsang, Herman; Warr, Matthew; Passegué, Emmanuelle; Larabell, Carolyn A; Forsberg, E Camilla

    2015-11-10

    Epigenetic regulation serves as the basis for stem cell differentiation into distinct cell types, but it is unclear how global epigenetic changes are regulated during this process. Here, we tested the hypothesis that global chromatin organization affects the lineage potential of stem cells and that manipulation of chromatin dynamics influences stem cell function. Using nuclease sensitivity assays, we found a progressive decrease in chromatin digestion among pluripotent embryonic stem cells (ESCs), multipotent hematopoietic stem cells (HSCs), and mature hematopoietic cells. Quantitative high-resolution microscopy revealed that ESCs contain significantly more euchromatin than HSCs, with a further reduction in mature cells. Increased cellular maturation also led to heterochromatin localization to the nuclear periphery. Functionally, prevention of heterochromatin formation by inhibition of the histone methyltransferase G9A resulted in delayed HSC differentiation. Our results demonstrate global chromatin rearrangements during stem cell differentiation and that heterochromatin formation by H3K9 methylation regulates HSC differentiation. PMID:26489895

  7. Progressive Chromatin Condensation and H3K9 Methylation Regulate the Differentiation of Embryonic and Hematopoietic Stem Cells

    Directory of Open Access Journals (Sweden)

    Fernando Ugarte

    2015-11-01

    Full Text Available Epigenetic regulation serves as the basis for stem cell differentiation into distinct cell types, but it is unclear how global epigenetic changes are regulated during this process. Here, we tested the hypothesis that global chromatin organization affects the lineage potential of stem cells and that manipulation of chromatin dynamics influences stem cell function. Using nuclease sensitivity assays, we found a progressive decrease in chromatin digestion among pluripotent embryonic stem cells (ESCs, multipotent hematopoietic stem cells (HSCs, and mature hematopoietic cells. Quantitative high-resolution microscopy revealed that ESCs contain significantly more euchromatin than HSCs, with a further reduction in mature cells. Increased cellular maturation also led to heterochromatin localization to the nuclear periphery. Functionally, prevention of heterochromatin formation by inhibition of the histone methyltransferase G9A resulted in delayed HSC differentiation. Our results demonstrate global chromatin rearrangements during stem cell differentiation and that heterochromatin formation by H3K9 methylation regulates HSC differentiation.

  8. DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure

    International Nuclear Information System (INIS)

    Interstitial Telomeric Sequences (ITS) are over-involved in spontaneous and radiationinduced chromosome aberrations in chinese hamster cells. We have performed a study to investigate the origin of their instability, spontaneously or after low doses irradiation. Our results demonstrate that ITS have a particular chromatin structure: short nucleotide repeat length, less compaction of the 30 nm chromatin fiber, presence of G-quadruplex structures. These features would modulate breaks production and would favour the recruitment of alternative DNA repair mechanisms, which are prone to produce chromosome aberrations. These pathways could be at the origin of chromosome aberrations in ITS whereas NHEJ and HR Double Strand Break repair pathways are rather required for a correct repair in these regions. (author)

  9. The influence of annealing on dynamical mechanical properties of polyamide 6 / fiber glass composites

    OpenAIRE

    J. Koszkul; Kwiatkowski, D.

    2006-01-01

    Purpose: of this paper is analysis the the influence of annealing on dynamical mechanical properties ofcomposites PA6 with fiberglass.Design/methodology/approach: Polamide 6 thermoplastic polymer of trade name Tarnamid T-27 produced byZakłady Azotowe S.A. in Tarnów (Poland) was used for examinations. E glass fibre, made of non-alkaline boron– aluminium – silicon glass of alkaline oxides content less than 1%, was used for polyamide 6 reinforcement.Polyamide and its composites filled with 10, 3...

  10. Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

    OpenAIRE

    Knoch, Tobias

    2002-01-01

    textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the Multi-Loop-Subcompartment (MLS) model, in which ~100 kbp loops form rosettes, connected by a linker, and the Random-Walk/Giant-Loop (RW/GL) topology, in which 1-5 Mbp loops are attached to a flexible bac...

  11. Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

    OpenAIRE

    Knoch, Tobias

    2003-01-01

    textabstractTo approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the Multi-Loop-Subcompartment (MLS) model, in which ~100 kbp loops form rosettes, connected by a linker, and the Random-Walk/Giant-Loop (RW/GL) topology, in which 1-5 Mbp loops are attached to a flexible bac...

  12. Approaching the Three-Dimensional Organization and Dynamics of the Human Genome

    OpenAIRE

    Knoch, Tobias

    2002-01-01

    textabstractTo approach by virtual microscopy the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics methods. The 30 nm chromatin fiber was folded according to the Multi-Loop- Subcompartment (MLS) model, in which ~100 kbp loops form rosettes, connected by a linker, and the Random- Walk/Giant-Loop (RW/GL) topology, in which 1-5 Mbp loops are at...

  13. Assessment of dynamic modulus of high density polypropylene waste fiber reinforcement in asphalt concrete

    Directory of Open Access Journals (Sweden)

    Hassan S. OTUOZE

    2015-12-01

    Full Text Available Traditional asphalt tests like Hveem and Marshall tests are at best mere characterization than effective test of pavement field performance because of complex viscoelastic behavior of asphalt. Mechanical properties otherwise called simple performance tests (SPT are performance criteria of asphalt. Dynamic modulus among other SPT’s like permanent deformation, fatigue cracking, thermal cracking, moisture susceptibility, shear and friction properties; determines stress-strain to time-temperature relationships that imparts on strength, service life and durability. The test followed the recommendations of NCHRP 1-37a (2004 and mixes were prepared using 0, 0.5, 1.0 and 1.5% HDPP contents. The parameters tested for dynamic modulus, /E*/, are stiffness, recoverable strain (ε, and phase angle (ξ. Time – temperature superposition (TTS called master curve was fitted using sigmoidal curve to interpolate the parameters beyond measured data set so as to observe the viscoelastic behavior outside the physical properties. The performance of 0.5% HDPP asphalt is better enhanced than the conventional asphalt to improve upon strength, service and durability.

  14. Role of stationary invariant manifolds in the spatiotemporal dynamics of a nonlinear-wave system of finite extension: Application to polarization attraction in optical fibers

    Science.gov (United States)

    Hamraoui, K.; Guasoni, M.; Picozzi, A.; Assémat, E.; Jauslin, H. R.; Sugny, D.

    2016-05-01

    The study of the spatiotemporal dynamics of two counterpropagating beams in optical fibers has recently been the subject of a growing renewed interest. This system has been shown to exhibit a phenomenon of polarization attraction which can be used to achieve a complete polarization of an initially unpolarized beam, almost without any loss of energy. In previous works, a theoretical description of this phenomenon has been developed in the particular case where the underlying stationary system exhibits the important property of integrability. Our aim here is to provide a generalization of the theoretical description to nonintegrable stationary systems. The analysis reveals that the spatiotemporal dynamics of the system relaxes towards a stationary trajectory whose geometric structure is revealed by the stable and unstable manifolds of some singular fixed points of the stationary system. We illustrate the theory by considering the representative and concrete example of a weakly birefringent optical fiber system.

  15. Photonic microwave amplification for radio-over-fiber links using period-one nonlinear dynamics of semiconductor lasers.

    Science.gov (United States)

    Hung, Yu-Han; Hwang, Sheng-Kwang

    2013-09-01

    For radio-over-fiber links, microwave-modulated optical carriers with high optical modulation depth are preferred because high optical modulation depth allows generation of high microwave power after photodetection, leading to high detection sensitivity, long transmission distance, and large link gain. This study investigates the period-one nonlinear dynamics of semiconductor lasers for optical modulation depth improvement to achieve photonic microwave amplification through modulation sideband enhancement. In our scheme, only typical semiconductor lasers are required as the amplification unit. The amplification is achieved for a broad microwave range, from less than 25 GHz to more than 60 GHz, and for a wide gain range, from less than 10 dB to more than 30 dB. The microwave phase quality is mainly preserved while the microwave power is largely amplified, improving the signal-to-noise ratio up to at least 25 dB. The bit-error ratio at 1.25 Gbits/s is better than 10(-9), and a sensitivity improvement of up to at least 15 dB is feasible. PMID:23988956

  16. Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy.

    Science.gov (United States)

    Suzuki, Yuki; Higuchi, Yuji; Hizume, Kohji; Yokokawa, Masatoshi; Yoshimura, Shige H; Yoshikawa, Kenichi; Takeyasu, Kunio

    2010-05-01

    Nucleosome is a fundamental structural unit of chromatin, and the exposure from or occlusion into chromatin of genomic DNA is closely related to the regulation of gene expression. In this study, we analyzed the molecular dynamics of poly-nucleosomal arrays in solution by fast-scanning atomic force microscopy (AFM) to obtain a visual glimpse of nucleosome dynamics on chromatin fiber at single molecule level. The influence of the high-speed scanning probe on nucleosome dynamics can be neglected since bending elastic energy of DNA molecule showed similar probability distributions at different scan rates. In the sequential images of poly-nucleosomal arrays, the sliding of the nucleosome core particle and the dissociation of histone particle were visualized. The sliding showed limited fluctuation within approximately 50nm along the DNA strand. The histone dissociation occurs by at least two distinct ways: a dissociation of histone octamer or sequential dissociations of tetramers. These observations help us to develop the molecular mechanisms of nucleosome dynamics and also demonstrate the ability of fast-scanning AFM for the analysis of dynamic protein-DNA interaction in sub-seconds time scale. PMID:20236766

  17. Enhancement of Mechanical and Dynamic Mechanical Properties of Hydrophilic Nanoclay Reinforced Polylactic Acid/Polycaprolactone/Oil Palm Mesocarp Fiber Hybrid Composites

    OpenAIRE

    Chern Chiet Eng; Nor Azowa Ibrahim; Norhazlin Zainuddin; Hidayah Ariffin; Wan Md Zin Wan Yunus; Yoon Yee Then

    2014-01-01

    In previous studies, the effect of the addition of 1 wt% hydrophilic nanoclay on polylactic acid (PLA)/polycaprolactone (PCL)/oil palm mesocarp fiber (OPMF) biocomposites was investigated by tensile properties, thermogravimetric analysis (TGA), and scanning electron microscopy (SEM). The current studies focus on the effect of addition of 1 wt% hydrophilic nanoclay on mechanical (flexural and impact properties) and dynamic mechanical properties of composites. The composites were characterized ...

  18. Elastic Properties of UHMWPE-SWCNT Nanocomposites' Fiber: An Experimental, Theoretic, and Molecular Dynamics Evaluation

    Science.gov (United States)

    Khan, Mujibur R.; Mahfuz, Hassan; Adnan, Ashfaq; Shabib, Ishraq; Leventouri, Theodora

    2013-06-01

    Ultrahigh molecular weight polyethylene (PE) filaments were reinforced with 2 wt.% of single-walled carbon nanotubes (SWCNTs). The solution spinning method was used to produce both neat and reinforced PE filaments. Tensile tests and strain hardening through repeated loading-unloading cycles of the filaments revealed a spectacular contribution of the SWCNTs in enhancing the elastic properties, e.g., strength and modulus. The theoretic strength and modulus of the reinforced PE were predicted using the shear lag model and micromechanics-based model, respectively, and verifying with experimental results. It was observed that the predicted strength and modulus were comparable only with those obtained after strain hardening. In the next step, a molecular dynamic simulation was conducted by simulating a unit cell containing a SWCNT surrounded by PE matrix subjected to uniaxial tensile strain. The strength and modulus of the simulated structure showed an agreement, to certain extent, with experimental observations of strain-hardened nanocomposites.

  19. Diversity in the organization of centromeric chromatin.

    Science.gov (United States)

    Steiner, Florian A; Henikoff, Steven

    2015-04-01

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

  20. Dynamic Sensing Performance of a Point-Wise Fiber Bragg Grating Displacement Measurement System Integrated in an Active Structural Control System

    Directory of Open Access Journals (Sweden)

    Chien-Ching Ma

    2011-12-01

    Full Text Available In this work, a fiber Bragg grating (FBG sensing system which can measure the transient response of out-of-plane point-wise displacement responses is set up on a smart cantilever beam and the feasibility of its use as a feedback sensor in an active structural control system is studied experimentally. An FBG filter is employed in the proposed fiber sensing system to dynamically demodulate the responses obtained by the FBG displacement sensor with high sensitivity. For comparison, a laser Doppler vibrometer (LDV is utilized simultaneously to verify displacement detection ability of the FBG sensing system. An optical full-field measurement technique called amplitude-fluctuation electronic speckle pattern interferometry (AF-ESPI is used to provide full-field vibration mode shapes and resonant frequencies. To verify the dynamic demodulation performance of the FBG filter, a traditional FBG strain sensor calibrated with a strain gauge is first employed to measure the dynamic strain of impact-induced vibrations. Then, system identification of the smart cantilever beam is performed by FBG strain and displacement sensors. Finally, by employing a velocity feedback control algorithm, the feasibility of integrating the proposed FBG displacement sensing system in a collocated feedback system is investigated and excellent dynamic feedback performance is demonstrated. In conclusion, our experiments show that the FBG sensor is capable of performing dynamic displacement feedback and/or strain measurements with high sensitivity and resolution.

  1. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  2. Chromatin regulation in drug addiction and depression

    OpenAIRE

    Renthal, William; Nestler, Eric J.

    2009-01-01

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

  3. Identification of alternative topological domains in chromatin

    OpenAIRE

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

    2014-01-01

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

  4. Multiscale Identification of Topological Domains in Chromatin

    OpenAIRE

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

    2013-01-01

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

  5. Carbon-Coated-Nylon-Fiber-Reinforced Cement Composites as an Intrinsically Smart Concrete for Damage Assessment during Dynamic Loading

    Institute of Scientific and Technical Information of China (English)

    Zhenjun ZHOU; Zhiguo XIAO; Wei PAN; Zhipeng XIE; Xixian LUO; Lei JIN

    2003-01-01

    Concrete containing short carbon-coated-nylon fibers (0.4~2.0 vol. pct) exhibited quasi-ductile response by developing a large damage zone prior to fracture localization. In the damage zone, the material was microcracked but continued to local strain-harden. The carbon-coated-nylon-fiber-reinforced concrete composites (NFRC) were found to be an intrinsically smart concrete that could sense elastic and inelastic deformation, as well as fracture. The fibers served to bridge the cracks and the carbon coating gave the conduction path. The signal provided came from the change in electrical resistance, which was reversible for elastic deformation and irreversible for inelastic deformation and fracture. The resistance decrease was due to the reduction of surface touch resistance between fiber and matrix and the crack closure. The resistance irreversible increase resulted from the crack opening and breakage of the carbon coating on nylon fiber.

  6. Titration and hysteresis in epigenetic chromatin silencing

    International Nuclear Information System (INIS)

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

  7. Quantitative Immunofluorescence Analysis of Nucleolus-Associated Chromatin.

    Science.gov (United States)

    Dillinger, Stefan; Németh, Attila

    2016-01-01

    The nuclear distribution of eu- and heterochromatin is nonrandom, heterogeneous, and dynamic, which is mirrored by specific spatiotemporal arrangements of histone posttranslational modifications (PTMs). Here we describe a semiautomated method for the analysis of histone PTM localization patterns within the mammalian nucleus using confocal laser scanning microscope images of fixed, immunofluorescence stained cells as data source. The ImageJ-based process includes the segmentation of the nucleus, furthermore measurements of total fluorescence intensities, the heterogeneity of the staining, and the frequency of the brightest pixels in the region of interest (ROI). In the presented image analysis pipeline, the perinucleolar chromatin is selected as primary ROI, and the nuclear periphery as secondary ROI. PMID:27576710

  8. 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.

  9. Assessment of a fiber-optic distributed-temperature-sensing system to monitor the thermal dynamics of vegetated roof

    Science.gov (United States)

    Cousiño, J. A.; Hausner, M. B.; Victorero, F.; Bonilla, C.; Gironas, J. A.; Vera, S.; Bustamante, W.; Rojas, V.; Pasten, P.; Suarez, F. I.

    2014-12-01

    Vegetated (green) roofs include a growing media and vegetation layer, and offer a range of benefits such as the reduction of: the heat island effect, rooftop runoff peak flows, roof surface temperatures, energy used for cooling or heating buildings, and noise levels inside infrastructures. Vegetated roofs also offer aesthetic benefits and increase the biodiversity of the urban environment, and are increasingly used in sustainable urban development. Understanding the thermal dynamics of vegetated roofs will make it possible to improve their design and to better assess their impacts on energy efficiency. Here, we evaluate the first vertical high-resolution distributed-temperature-sensing (DTS) system installed in a vegetated roof. This system allows a continuous measurement of the thermal profile within a vegetated roof - going from the interior, upward through the drainage layers and soil substrate of the vegetated roof and ending in the air above the vegetation. Temperatures can be observed as frequently as every 30 s at a spatial resolution on the order of centimeters. This DTS system was installed in the "Laboratory of Vegetal Infrastructure of Buildings" (LIVE - its acronym in Spanish), located in the San Joaquín Campus of the Pontifical Catholic University, Santiago, Chile. The laboratory features 18 experimental modules to investigate different configurations of the vegetated roof layers. The LIVE was designed with the installation of the optical fibers in mind, and the DTS system allows simultaneous monitoring of three or four modules of the LIVE. In this work, we describe the design of this DTS deployment, the calibration metrics obtained using the software provided by the manufacturers, and other calibration algorithms previously developed. We compare the results obtained using single- and double-ended measurements, highlighting strengths and weaknesses of DTS methods. Finally, we present the observations obtained from this biophysical environment

  10. Chromatin-based epigenetics of adult subventricular zone neural stem cells

    Directory of Open Access Journals (Sweden)

    Gabriel eGonzales-Roybal

    2013-10-01

    Full Text Available In specific regions of the adult mammalian brain, neural stem cells (NSCs generate new neurons throughout life. Emerging evidence indicate that chromatin-based transcriptional regulation is a key epigenetic mechanism for the life-long function of adult NSCs. In the adult mouse brain, NSCs in the subventricular zone (SVZ retain the ability to produce both neurons and glia for the life of the animal. In this review, we discuss the origin and function of SVZ NSCs as they relate to key epigenetic concepts of development and potential underlying mechanism of chromatin-based transcriptional regulation. A central point of discussion is how SVZ NSCs – which possess many characteristics of mature, non-neurogenic astrocytes – maintain a youthful ability to produce both neuronal and glial lineages. In addition to reviewing data regarding the function of chromatin-modifying factors in SVZ neurogenesis, we incorporate our growing understanding that long noncoding RNAs (lncRNAs serve as an important element to chromatin-based transcriptional regulation, including that of SVZ NSCs. Discoveries regarding the epigenetic mechanisms of adult SVZ NSCs may provide key insights into fundamental principles of adult stem cell biology as well as the more complex and dynamic developmental environment of the embryonic brain.

  11. Dynamic Strain Measurements on Automotive and Aeronautic Composite Components by Means of Embedded Fiber Bragg Grating Sensors

    OpenAIRE

    Alfredo Lamberti; Gabriele Chiesura; Geert Luyckx; Joris Degrieck; Markus Kaufmann; Steve Vanlanduit

    2015-01-01

    The measurement of the internal deformations occurring in real-life composite components is a very challenging task, especially for those components that are rather difficult to access. Optical fiber sensors can overcome such a problem, since they can be embedded in the composite materials and serve as in situ sensors. In this article, embedded optical fiber Bragg grating (FBG) sensors are used to analyze the vibration characteristics of two real-life composite components. The first component...

  12. Prevalence of X-chromatin in Jordanian women

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Gelato, Kathy A; Fischle, Wolfgang

    2008-04-01

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

  14. Epigenetic dynamics across the cell cycle

    DEFF Research Database (Denmark)

    Kheir, Tony Bou; Lund, Anders H.

    2010-01-01

    Progression of the mammalian cell cycle depends on correct timing and co-ordination of a series of events, which are managed by the cellular transcriptional machinery and epigenetic mechanisms governing genome accessibility. Epigenetic chromatin modifications are dynamic across the cell cycle...... a correct inheritance of epigenetic chromatin modifications to daughter cells. In this chapter, we summarize the current knowledge on the dynamics of epigenetic chromatin modifications during progression of the cell cycle....

  15. Distributed fiber Brillouin strain sensing by correlation-based continuous-wave technique: cm-order spatial resolution and dynamic strain measurement

    Science.gov (United States)

    Hotate, Kazuo; Ong, Sean S.

    2002-09-01

    This paper describes a novel correlation-based technique for fiber optic distributed strain sensors using Brillouin scattering. Conventional Brillouin-based sensors utilize a pulsed-pump similar to that of OTDR and are capable of distributed strain sensing over large distances, but suffer an inherent spatial resolution limit of around 1m. In addition, unlike FBG-based strain sensors which are competent of measuring dynamic strain, the pulse-based Brillouin sensors have large measurement times of several minutes, making them inadequate for dynamic strain measurements. On the other hand, using the correlation-based continuous-wave technique, we have achieved static distributed strain measurements of up to 1cm spatial resolution, and dynamic strain measurements of up to 8.8Hz from a 5cm strained section.

  16. Principal modes in fiber amplifiers

    CERN Document Server

    Fridman, Moti; Dubinskii, Mark; Friesem, Asher A; Davidson, Nir

    2010-01-01

    The dynamics of the state of polarization in single mode and multimode fiber amplifiers are presented. The experimental results reveal that although the state of polarizations at the output can vary over a large range when changing the temperatures of the fiber amplifiers, the variations are significantly reduced when resorting to the principal states of polarization in single mode fiber amplifiers and principal modes in multimode fiber amplifiers.

  17. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

    DEFF Research Database (Denmark)

    Räschle, Markus; Smeenk, Godelieve; Hansen, Rebecca K;

    2015-01-01

    technique called chromatin mass spectrometry (CHROMASS) to study protein recruitment dynamics during perturbed DNA replication in Xenopus egg extracts. Using CHROMASS, we systematically monitored protein assembly and disassembly on ICL-containing chromatin. Among numerous prospective DNA repair factors, we...

  18. A Method to Study the Epigenetic Chromatin States of Rare Hematopoietic Stem and Progenitor Cells; MiniChIP–Chip

    Directory of Open Access Journals (Sweden)

    Weishaupt Holger

    2010-01-01

    Full Text Available Abstract Dynamic chromatin structure is a fundamental property of gene transcriptional regulation, and has emerged as a critical modulator of physiological processes during cellular differentiation and development. Analysis of chromatin structure using molecular biology and biochemical assays in rare somatic stem and progenitor cells is key for understanding these processes but poses a great challenge because of their reliance on millions of cells. Through the development of a miniaturized genome-scale chromatin immunoprecipitation method (miniChIP–chip, we have documented the genome-wide chromatin states of low abundant populations that comprise hematopoietic stem cells and immediate progeny residing in murine bone marrow. In this report, we describe the miniChIP methodology that can be used for increasing an understanding of the epigenetic mechanisms underlying hematopoietic stem and progenitor cell function. Application of this method will reveal the contribution of dynamic chromatin structure in regulating the function of other somatic stem cell populations, and how this process becomes perturbed in pathological conditions. Additional file 1 Click here for file

  19. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    OpenAIRE

    Arifulin E. A.

    2015-01-01

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

  20. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

    OpenAIRE

    Cieślik, Marcin; Bekiranov, Stefan

    2014-01-01

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

  1. Single-epitope recognition imaging of native chromatin

    OpenAIRE

    Wang Hongda; Dalal Yamini; Henikoff Steven; Lindsay Stuart

    2008-01-01

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

  2. The role of chromatin insulators in nuclear architecture and genome function

    OpenAIRE

    Van Bortle, Kevin; Corces, Victor G.

    2013-01-01

    Eukaryotic genomes are intricately arranged into highly organized yet dynamic structures that underlie patterns of gene expression and cellular identity. The recent adaptation of novel genomic strategies for assaying nuclear architecture has significantly extended and accelerated our ability to query the nature of genome organization and the players involved. In particular, recent explorations of physical arrangements and chromatin landscapes in higher eukaryotes have demonstrated that chroma...

  3. High-Frequency Promoter Firing Links THO Complex Function to Heavy Chromatin Formation

    DEFF Research Database (Denmark)

    Mouaikel, John; Causse, Sébastien Z; Rougemaille, Mathieu; Daubenton-Carafa, Yves; Blugeon, Corinne; Lemoine, Sophie; Devaux, Frédéric; Darzacq, Xavier; Libri, Domenico

    2013-01-01

    The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes...... occupancy genome wide. We propose that the THO complex is required for tuning the dynamic of gene-nuclear pore association and mRNP release to the same high pace of transcription initiation...

  4. Aberrant Neural Stem Cell Proliferation and Increased Adult Neurogenesis in Mice Lacking Chromatin Protein HMGB2

    OpenAIRE

    Abraham, Ariel B; Robert Bronstein; Avanish S Reddy; Mirjana Maletic-Savatic; Adan Aguirre; Tsirka, Stella E.

    2013-01-01

    Neural stem and progenitor cells (NSCs/NPCs) are distinct groups of cells found in the mammalian central nervous system (CNS). Previously we determined that members of the High Mobility Group (HMG) B family of chromatin structural proteins modulate NSC proliferation and self-renewal. Among them HMGB2 was found to be dynamically expressed in proliferating and differentiating NSCs, suggesting that it may regulate NSC maintenance. We report now that Hmgb2(-/-) mice exhibit SVZ hyperproliferation...

  5. The evolution of chromatin folding in mammals: a role for CTCF

    OpenAIRE

    Vietri Rudan, M.

    2015-01-01

    The organisation of the DNA inside eukaryotic cell nuclei is not random. Rather than being intermingled with one another, chromosomes are compacted in a hierarchical manner which is conserved throughout eukaryote evolution. Topological domains have recently emerged as key architectural building blocks of chromosomes in complex genomes. This thesis aimed to explore the evolutionary dynamics of chromatin architecture in order to shed light on its functional relevance and on how architectural pr...

  6. Hydrogen peroxide mediates higher order chromatin degradation.

    Science.gov (United States)

    Bai, H; Konat, G W

    2003-01-01

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

  7. A Polymer Model with Epigenetic Recolouring Reveals a Pathway for the de novo Establishment and 3D Organisation of Chromatin Domains

    CERN Document Server

    Michieletto, Davide; Marenduzzo, Davide

    2016-01-01

    One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a "recolouring" process modelling the writing of epigenetic marks. Because many intra-chromatin interactions are mediated by bridging proteins, we consider a "two-state" model with self-attractive interactions between two epigenetic marks which are alike (either active or inactive). This model displays a first-order-like transition between a swollen, epigenetically disordered, phase, and a compact, epigenetically coherent, chromatin globule. If the self-attraction strength exceeds a threshold, the chromatin dynamics becomes glassy, and the corresponding interaction network freezes. By modifying the epigenetic read-write process according to more biologically-inspired assumptions, our polymer model with recolouring recapitulates the ultrasensitive response of epigenetic switches t...

  8. Dietary Fiber

    Science.gov (United States)

    Fiber is a substance in plants. Dietary fiber is the kind you eat. It's a type of carbohydrate. You may also see it listed on a food label as soluble fiber or insoluble fiber. Both types have important health benefits. Good sources of dietary fiber include Whole grains Nuts ...

  9. Phosphorylation-Dependent Targeting of Tetrahymena HP1 to Condensed Chromatin.

    Science.gov (United States)

    Yale, Katerina; Tackett, Alan J; Neuman, Monica; Bulley, Emily; Chait, Brian T; Wiley, Emily

    2016-01-01

    The evolutionarily conserved proteins related to heterochromatin protein 1 (HP1), originally described in Drosophila, are well known for their roles in heterochromatin assembly and gene silencing. Targeting of HP1 proteins to specific chromatin locales is mediated, at least in part, by the HP1 chromodomain, which binds to histone H3 methylated at lysine 9 that marks condensed regions of the genome. Mechanisms that regulate HP1 targeting are emerging from studies with yeast and metazoans and point to roles for posttranslational modifications. Here, we report that modifications of an HP1 homolog (Hhp1) in the ciliate model Tetrahymena thermophila correlated with the physiological state and with nuclear differentiation events involving the restructuring of chromatin. Results support the model in which Hhp1 chromodomain binds lysine 27-methylated histone H3, and we show that colocalization with this histone mark depends on phosphorylation at a single Cdc2/Cdk1 kinase site in the "hinge region" adjacent to the chromodomain. These findings help elucidate important functional roles of reversible posttranslational modifications of proteins in the HP1 family, in this case, regulating the targeting of a ciliate HP1 to chromatin regions marked with methylated H3 lysine 27. IMPORTANCE Compacting the genome to various degrees influences processes that use DNA as a template, such as gene transcription and replication. This project was aimed at learning more about the cellular mechanisms that control genome compaction. Posttranslational modifications of proteins involved in genome condensation are emerging as potentially important points of regulation. To help elucidate protein modifications and how they affect the function of condensation proteins, we investigated the phosphorylation of the chromatin protein called Hhp1 in the ciliated protozoan Tetrahymena thermophila. This is one of the first functional investigations of these modifications of a nonhistone chromatin

  10. SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair

    DEFF Research Database (Denmark)

    McCord, Ronald A; Michishita, Eriko; Hong, Tao;

    2009-01-01

    -dependent protein kinase) and promotes DNA DSB repair. In response to DSBs, SIRT6 associates dynamically with chromatin and is necessary for an acute decrease in global cellular acetylation levels on histone H3 Lysine 9. Moreover, SIRT6 is required for mobilization of the DNA-PK catalytic subunit (DNA-PKcs) to...

  11. In Search of Multi-Peaked Reflective Spectrum with Optic Fiber Bragg Grating Sensor for Dynamic Strain Measurement

    Science.gov (United States)

    Tai, Hsiang

    2006-01-01

    In a typical optic fiber Bragg grating (FBG) strain measurement, unless in an ideal static laboratory environment, the presence of vibration or often disturbance always exists, which often creates spurious multiple peaks in the reflected spectrum, resulting in a non-unique determination of strain value. In this report we attempt to investigate the origin of this phenomenon by physical arguments and simple numerical simulation. We postulate that the fiber gratings execute small amplitude transverse vibrations changing the optical path in which the reflected light traverses slightly and non-uniformly. Ultimately, this causes the multi-peak reflected spectrum.

  12. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

    formation of oncogenic chromosomal translocations. In this review, we focus the discussion on how chromatin-modifying activities and -binding proteins contribute to the native chromatin environment in which AID-induced DNA damage is targeted and repaired. Outstanding questions remain regarding the direct...

  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 on la...

  14. 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....

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

    Science.gov (United States)

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

    2015-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

  17. Characterization of fatigue damage in adhesively bonded lap joints through dynamic, full-spectral interrogation of fiber Bragg grating sensors: 1. Experiments

    International Nuclear Information System (INIS)

    In this study we measure the in situ response of a fiber Bragg grating (FBG) sensor embedded in the adhesive layer of a single composite lap joint, subjected to harmonic excitation after fatigue loading. After a fully reversed cyclic fatigue loading is applied to the composite lap joint, the full-spectral response of the sensor is interrogated at 100 kHz during two loading conditions: with and without an added harmonic excitation. The full-spectral information avoided dynamic measurement errors often experienced using conventional peak wavelength and edge filtering techniques. The short-time Fourier transform (STFT) is computed for the extracted peak wavelength information to reveal time-dependent frequencies and amplitudes of the dynamic FBG sensor response. The dynamic response of the FBG sensor indicated a transition to strong nonlinear dynamic behavior as fatigue-induced damage progressed. The ability to measure the dynamic response of the lap joint through sensors embedded in the adhesive layer can provide in situ monitoring of the lap joint condition. (paper)

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

    Science.gov (United States)

    Green, G R

    2001-01-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

  20. Enhancement of Mechanical and Dynamic Mechanical Properties of Hydrophilic Nanoclay Reinforced Polylactic Acid/Polycaprolactone/Oil Palm Mesocarp Fiber Hybrid Composites

    Directory of Open Access Journals (Sweden)

    Chern Chiet Eng

    2014-01-01

    Full Text Available In previous studies, the effect of the addition of 1 wt% hydrophilic nanoclay on polylactic acid (PLA/polycaprolactone (PCL/oil palm mesocarp fiber (OPMF biocomposites was investigated by tensile properties, thermogravimetric analysis (TGA, and scanning electron microscopy (SEM. The current studies focus on the effect of addition of 1 wt% hydrophilic nanoclay on mechanical (flexural and impact properties and dynamic mechanical properties of composites. The composites were characterized by the Fourier transform infrared spectroscopy (FTIR and dynamic mechanical analysis (DMA. FTIR spectra show that peak shifting occurs when 1 wt% hydrophilic nanoclay was added to composites. The addition of 1 wt% hydrophilic nanoclay successfully improves the flexural properties and impact resistance of the biocomposites. The storage modulus of biocomposites was decreased when nanoclay was added which indicates that the stiffness of biocomposites was reduced. The loss modulus curve shows that the addition of nanoclay shift two tg in composites become closer to each other which indicates that the incorporation of nanoclay slightly compatibilizes the biocomposites. Tan δ indicated that hybrid composites dissipate less energy compared to biocomposites indicate that addition of clay to biocomposites improves fiber/matrix adhesion. Water sorption test shows that the addition of nanoclay enhances water resistance of composites.

  1. On the mechanochemical machinery underlying chromatin remodeling

    Science.gov (United States)

    Yusufaly, Tahir I.

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

  2. Chromatin structure near transcriptionally active genes

    International Nuclear Information System (INIS)

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

  3. 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

    Regulation of gene expression involves long-distance communication between regulatory elements and target promoters, but how this is achieved remains unknown. Insulator elements have been proposed to modulate the communication between regulatory elements and promoters due to their ability to insu...

  4. Fiber dielectrophoresis

    International Nuclear Information System (INIS)

    Dielectrophoresis is the motion of uncharged particles in nonuniform electric fields. We find that the theoretical dielectrophoretic velocity of a conducting fiber in an insulating medium is proportional to the square of the fiber length, and is virtually independent of fiber diameter. This prediction has been verified experimentally. The results point to the development of a fiber length classifier based on dielectrophoresis. (author)

  5. Failure properties of fiber bundle models

    OpenAIRE

    Pradhan, Srutarshi; Chakrabarti, Bikas K.

    2003-01-01

    We study the failure properties of fiber bundles when continuous rupture goes on due to the application of external load on the bundles. We take the two extreme models: equal load sharing model (democratic fiber bundles) and local load sharing model. The strength of the fibers are assumed to be distributed randomly within a finite interval. The democratic fiber bundles show a solvable phase transition at a critical stress (load per fiber). The dynamic critical behavior is obtained analyticall...

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

    Science.gov (United States)

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

    2010-11-01

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

  7. X-ray fiber diffraction analysis shows dynamic changes in axial tubulin repeats in native microtubules depending on paclitaxel content, temperature and GTP-hydrolysis.

    Science.gov (United States)

    Kamimura, Shinji; Fujita, Yosuke; Wada, Yuuko; Yagi, Toshiki; Iwamoto, Hiroyuki

    2016-03-01

    Microtubules are key components of the cytoskeleton in eukaryotic cells. The dynamics between assembled microtubules and free tubulin dimers in the cytoplasm is closely related to the active shape changes of microtubule networks. One of the most fundamental questions is the association of microtubule dynamics with the molecular conformation of tubulin within microtubules. To address this issue, we applied a new technique for the rapid shear-flow alignment of biological filaments, enabling us to acquire the structural periodicity data of microtubules by X-ray fiber diffraction under various physiological conditions. We classified microtubules into three main groups on the basis of distinct axial tubulin periodicities and mean microtubule diameters that varied depending on GTP hydrolysis and the content of paclitaxel, a microtubule stabilizer. Paclitaxel induced rapid changes in tubulin axial repeats in a cooperative manner. This is the first demonstration of dynamic changes of axial tubulin repeats within native microtubules without fixation. We also found extraordinary features of negative thermal expansion of axial tubulin repeats in both paclitaxel-stabilized and GMPCPP-containing microtubules. Our results suggest that even in assembled microtubules, both GTP- and GDP-tubulin dimers can undergo dynamic conversion between at least two different states: short and long configurations. © 2016 Wiley Periodicals, Inc. PMID:26873786

  8. Dynamic Strain Measurements on Automotive and Aeronautic Composite Components by Means of Embedded Fiber Bragg Grating Sensors

    Directory of Open Access Journals (Sweden)

    Alfredo Lamberti

    2015-10-01

    Full Text Available The measurement of the internal deformations occurring in real-life composite components is a very challenging task, especially for those components that are rather difficult to access. Optical fiber sensors can overcome such a problem, since they can be embedded in the composite materials and serve as in situ sensors. In this article, embedded optical fiber Bragg grating (FBG sensors are used to analyze the vibration characteristics of two real-life composite components. The first component is a carbon fiber-reinforced polymer automotive control arm; the second is a glass fiber-reinforced polymer aeronautic hinge arm. The modal parameters of both components were estimated by processing the FBG signals with two interrogation techniques: the maximum detection and fast phase correlation algorithms were employed for the demodulation of the FBG signals; the Peak-Picking and PolyMax techniques were instead used for the parameter estimation. To validate the FBG outcomes, reference measurements were performed by means of a laser Doppler vibrometer. Sensors 2015, 15 27175 The analysis of the results showed that the FBG sensing capabilities were enhanced when the recently-introduced fast phase correlation algorithm was combined with the state-of-the-art PolyMax estimator curve fitting method. In this case, the FBGs provided the most accurate results, i.e. it was possible to fully characterize the vibration behavior of both composite components. When using more traditional interrogation algorithms (maximum detection and modal parameter estimation techniques (Peak-Picking, some of the modes were not successfully identified.

  9. Dynamic Strain Measurements on Automotive and Aeronautic Composite Components by Means of Embedded Fiber Bragg Grating Sensors.

    Science.gov (United States)

    Lamberti, Alfredo; Chiesura, Gabriele; Luyckx, Geert; Degrieck, Joris; Kaufmann, Markus; Vanlanduit, Steve

    2015-01-01

    The measurement of the internal deformations occurring in real-life composite components is a very challenging task, especially for those components that are rather difficult to access. Optical fiber sensors can overcome such a problem, since they can be embedded in the composite materials and serve as in situ sensors. In this article, embedded optical fiber Bragg grating (FBG) sensors are used to analyze the vibration characteristics of two real-life composite components. The first component is a carbon fiber-reinforced polymer automotive control arm; the second is a glass fiber-reinforced polymer aeronautic hinge arm. The modal parameters of both components were estimated by processing the FBG signals with two interrogation techniques: the maximum detection and fast phase correlation algorithms were employed for the demodulation of the FBG signals; the Peak-Picking and PolyMax techniques were instead used for the parameter estimation. To validate the FBG outcomes, reference measurements were performed by means of a laser Doppler vibrometer. Sensors 2015, 15 27175 The analysis of the results showed that the FBG sensing capabilities were enhanced when the recently-introduced fast phase correlation algorithm was combined with the state-of-the-art PolyMax estimator curve fitting method. In this case, the FBGs provided the most accurate results, i.e. it was possible to fully characterize the vibration behavior of both composite components. When using more traditional interrogation algorithms (maximum detection) and modal parameter estimation techniques (Peak-Picking), some of the modes were not successfully identified. PMID:26516854

  10. Characteristics of thymine dimer excision from xeroderma pigmentosum chromatin

    International Nuclear Information System (INIS)

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

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Timsy Uppal

    2015-01-01

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

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

    International Nuclear Information System (INIS)

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

  14. CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

    Science.gov (United States)

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

    2011-01-01

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

  15. 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.

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

    OpenAIRE

    Borochov, N; Ausio, J; Eisenberg, H

    1984-01-01

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

  17. Dual Chromatin and Cytoskeletal Remodeling by SETD2.

    Science.gov (United States)

    Park, In Young; Powell, Reid T; Tripathi, Durga Nand; Dere, Ruhee; Ho, Thai H; Blasius, T Lynne; Chiang, Yun-Chen; Davis, Ian J; Fahey, Catherine C; Hacker, Kathryn E; Verhey, Kristen J; Bedford, Mark T; Jonasch, Eric; Rathmell, W Kimryn; Walker, Cheryl Lyn

    2016-08-11

    Posttranslational modifications (PTMs) of tubulin specify microtubules for specialized cellular functions and comprise what is termed a "tubulin code." PTMs of histones comprise an analogous "histone code," although the "readers, writers, and erasers" of the cytoskeleton and epigenome have heretofore been distinct. We show that methylation is a PTM of dynamic microtubules and that the histone methyltransferase SET-domain-containing 2 (SETD2), which is responsible for H3 lysine 36 trimethylation (H3K36me3) of histones, also methylates α-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy. These data now identify SETD2 as a dual-function methyltransferase for both chromatin and the cytoskeleton and show a requirement for methylation in maintenance of genomic stability and the integrity of both the tubulin and histone codes. PMID:27518565

  18. Chromatin dynamics of plant telomeres and ribosomal genes

    Czech Academy of Sciences Publication Activity Database

    Dvořáčková, Martina; Fojtová, Miloslava; Fajkus, Jiří

    2015-01-01

    Roč. 83, č. 1 (2015), s. 18-37. ISSN 0960-7412 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GA13-06943S; GA ČR(CZ) GP13-11563P Grant ostatní: GA ČR(CZ) GAP501/11/0289 Institutional support: RVO:68081707 Keywords : HISTONE VARIANT H3.3 * ASSEMBLY FACTOR-I * REPLICATION FORK PROGRESSION Subject RIV: BO - Biophysics Impact factor: 5.972, year: 2014

  19. A Computational Fluid Dynamics Modeling and Experimental Study of the Mixing Process for the Dispersion of the Synthetic Fibers in Wet-Lay Forming

    Directory of Open Access Journals (Sweden)

    Melur K. Ramasubramanian, Ph.D.

    2008-03-01

    Full Text Available In this paper, we present results from a computational fluid dynamics (CFD model for the mixing process used to disperse synthetic fibers in wet-lay process. We used CFD software, FLUENT, together with the MIXSIM user interface to accurately model the impeller geometry. A multiple reference frame (MRF model and standard k-e turbulence model were used to model the problem. After obtaining a converged solution for the mixing tank with water, a discrete phase model was constructed by injecting spherical particles into the flow. A mixing tank with baffles and a centrally located impeller was used in experiments. PET fibers (1.5 denier, 6.35, 12.7, and 38.7 mm at a concentration of 0.01% were mixed in water for the study. In regions behind the baffles, where the model predicted higher concentration of particles, experimental results showed a 34% higher concentration relative to the region in the high turbulence zone near the center. Instantaneous sheets were formed by rapidly dipping and removing a flat wire mesh strainer into the tank at two different locations to assess the state of dispersion in the tank. The sheets were transferred onto a blotting paper and examined under a microscope to count defects. Results show that the number of rope defects was 43% higher in sheets drawn from the region behind the baffles than in the sheets drawn from regions near the center of the tank. Changing baffles from a rectangular to a triangular cross section decreased the number of rope defects, but increased the number of log defects in the sample sheets at the same location. The CFD model can be used to optimize mixing tank design for wet lay fiber dispersion. The model provides further insight into the mixing process by predicting the effect of changes in design parameters on dispersion quality.

  20. The methylated N-terminal tail of RCC1 is required for stabilisation of its interaction with chromatin by Ran in live cells

    Directory of Open Access Journals (Sweden)

    Sanderson Helen S

    2010-06-01

    Full Text Available Abstract Background Regulator of chromosome condensation 1 (RCC1 is the guanine nucleotide exchange factor for Ran GTPase. Localised generation of Ran-GTP by RCC1 on chromatin is critical for nucleocytoplasmic transport, mitotic spindle assembly and nuclear envelope formation. Both the N-terminal tail of RCC1 and its association with Ran are important for its interaction with chromatin in cells. In vitro, the association of Ran with RCC1 induces a conformational change in the N-terminal tail that promotes its interaction with DNA. Results We have investigated the mechanism of the dynamic interaction of the α isoform of human RCC1 (RCC1α with chromatin in live cells using fluorescence recovery after photobleaching (FRAP of green fluorescent protein (GFP fusions. We show that the N-terminal tail stabilises the interaction of RCC1α with chromatin and this function can be partially replaced by another lysine-rich nuclear localisation signal. Removal of the tail prevents the interaction of RCC1α with chromatin from being stabilised by RanT24N, a mutant that binds stably to RCC1α. The interaction of RCC1α with chromatin is destabilised by mutation of lysine 4 (K4Q, which abolishes α-N-terminal methylation, and this interaction is no longer stabilised by RanT24N. However, α-N-terminal methylation of RCC1α is not regulated by the binding of RanT24N. Conversely, the association of Ran with precipitated RCC1α does not require the N-terminal tail of RCC1α or its methylation. The mobility of RCC1α on chromatin is increased by mutation of aspartate 182 (D182A, which inhibits guanine-nucleotide exchange activity, but RCC1αD182A can still bind nucleotide-free Ran and its interaction with chromatin is stabilised by RanT24N. Conclusions These results show that the stabilisation of the dynamic interaction of RCC1α with chromatin by Ran in live cells requires the N-terminal tail of RCC1α. α-N-methylation is not regulated by formation of the binary

  1. Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression.

    Science.gov (United States)

    Franz, André; Pirson, Paul A; Pilger, Domenic; Halder, Swagata; Achuthankutty, Divya; Kashkar, Hamid; Ramadan, Kristijan; Hoppe, Thorsten

    2016-01-01

    The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin-associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging. PMID:26842564

  2. An Allosteric Interaction Links USP7 to Deubiquitination and Chromatin Targeting of UHRF1

    Directory of Open Access Journals (Sweden)

    Zhi-Min Zhang

    2015-09-01

    Full Text Available The protein stability and chromatin functions of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1 are regulated in a cell-cycle-dependent manner. We report a structural characterization of the complex between UHRF1 and the deubiquitinase USP7. The first two UBL domains of USP7 bind to the polybasic region (PBR of UHRF1, and this interaction is required for the USP7-mediated deubiquitination of UHRF1. Importantly, we find that the USP7-binding site of the UHRF1 PBR overlaps with the region engaging in an intramolecular interaction with the N-terminal tandem Tudor domain (TTD. We show that the USP7-UHRF1 interaction perturbs the TTD-PBR interaction of UHRF1, thereby shifting the conformation of UHRF1 from a TTD-“occluded” state to a state open for multivalent histone binding. Consistently, introduction of a USP7-interaction-defective mutation to UHRF1 significantly reduces its chromatin association. Together, these results link USP7 interaction to the dynamic deubiquitination and chromatin association of UHRF1.

  3. The ING1b tumor suppressor facilitates nucleotide excision repair by promoting chromatin accessibility to XPA

    International Nuclear Information System (INIS)

    ING1b is the most studied ING family protein and perhaps the most ubiquitously and abundantly expressed. This protein is involved in the regulation of various biological functions ranging from senescence, cell cycle arrest, apoptosis, to DNA repair. ING1b is upregulated by UV irradiation and enhances the removal of bulky nucleic acid photoproducts. In this study, we provide evidence that ING1b mediates nucleotide excision repair by facilitating the access to damaged nucleosomal DNA. We demonstrate that ING1b is not recruited to UV-induced DNA lesions but enhances nucleotide excision repair only in XPC-proficient cells, implying an essential role in early steps of the 'access, repair, restore' model. We also find that ING1b alters histone acetylation dynamics upon exposure to UV radiation and induces chromatin relaxation in microccocal nuclease digestion assay, revealing that ING1b may allow better access to nucleotide excision repair machinery. More importantly, ING1b associates with chromatin in a UV-inducible manner and facilitates DNA access to nucleotide excision repair factor XPA. Furthermore, depletion of the endogenous ING1b results to the sensitization of cells at S-phase to UV irradiation. Taken together, these observations establish a role of ING1b acting as a chromatin accessibility factor for DNA damage recognition proteins upon genotoxic injury

  4. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

    Science.gov (United States)

    Schep, Alicia N; Buenrostro, Jason D; Denny, Sarah K; Schwartz, Katja; Sherlock, Gavin; Greenleaf, William J

    2015-11-01

    Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and use this distinctive two-dimensional nucleosomal "fingerprint" as the basis for a new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in S. cerevisiae, Schizosaccharomyces pombe, and human cells. We demonstrate the application of NucleoATAC to a number of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis of nucleosome occupancy and transcription factor binding. PMID:26314830

  5. 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.

  6. 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.

  7. A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules

    OpenAIRE

    Shah, Akshay; Oldenburg, Anja; Collas, Philippe

    2014-01-01

    Background Chromatin remodeling is crucial for proper programing of developmental gene expression. Recent work provides a dynamic view of post-translational histone modifications during differentiation; however there is little insight on the evolution of combinatorial genome-wide patterns of chromatin marks, excluding an essential aspect of developmental gene regulation. Results We report here a 15-chromatin state Hidden Markov Model which describes changes in chromatin signatures in relation...

  8. Fiber optic LDF to monitor vascular dynamics of urticarial dermographism in pressure-tested patients before and after treatment with antihistamines

    Science.gov (United States)

    Eikje, Natalja Skrebova; Arase, Seiji

    2008-02-01

    The local microcirculatory dynamics underlying phenomenon of urticarial dermographism (UD) are not yet sufficiently elucidated in dermatological patients. A fiber optic laser Doppler flowmeter (LDF) was used to monitor skin blood flow (SBF) changes on the back of the patients with UD before and after application of the series of pressure stimuli (9.8×10 4, 14.7×10 4, 19.6×10 4 and 24.5×10 4 Pa). All patients acted as self-controls to assess their disease activity by means of SBF values based on response to pressure stimuli before and after treatment with antihistamines, when compared to baseline SBF. Throughout 30 minutes evaluation inter-subject SBF values at pressure-tested sites were noticeably distinguished as high, moderate and low. By LDF we could differentiate the highest development of vascular dynamics after 5 minutes, coming back to normal within about 30 minutes in one group of patients, and the vascular dynamics reaching its maximum in 15 minutes, but with no fade after 30 minutes, in another group of patients. All treatment regimens in both groups of patients by LDF produced a measurable reduction already during 1-2 days of therapy, accompanied by a reduction in SBF baseline values in patients with severe and moderate symptoms of UD.

  9. A wide dynamics and fast scan interrogating method for a fiber Bragg grating sensor network implemented using code division multiple access.

    Science.gov (United States)

    Kim, Youngbok; Jeon, Sie-Wook; Kwon, Won-Bae; Park, Chang-Soo

    2012-01-01

    We propose and demonstrate a fiber Bragg grating (FBG) sensor network employing the code division multiple access (CDMA) technique to identify information from individual sensors. To detect information without considering time delays between sensors, a sliding correlation method is applied, in which two different signals with the same pseudo-random binary sequence (PRBS) pattern, but slightly different frequencies, are applied to the source and detector sides. Moreover, for time domain detection, a wavelength-to-time conversion technique using a wavelength dispersive medium is introduced. The experimental results show that the proposed sensor network has a wide strain dynamic range of 2,400 με and a low crosstalk of 950:1. PMID:22778619

  10. A Wide Dynamics and Fast Scan Interrogating Method for a Fiber Bragg Grating Sensor Network Implemented Using Code Division Multiple Access

    Directory of Open Access Journals (Sweden)

    Chang-Soo Park

    2012-05-01

    Full Text Available We propose and demonstrate a fiber Bragg grating (FBG sensor network employing the code division multiple access (CDMA technique to identify information from individual sensors. To detect information without considering time delays between sensors, a sliding correlation method is applied, in which two different signals with the same pseudo-random binary sequence (PRBS pattern, but slightly different frequencies, are applied to the source and detector sides. Moreover, for time domain detection, a wavelength-to-time conversion technique using a wavelength dispersive medium is introduced. The experimental results show that the proposed sensor network has a wide strain dynamic range of 2,400 μe and a low crosstalk of 950:1.

  11. 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.

  12. Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin.

    Science.gov (United States)

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

    2016-02-11

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

  13. 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.

  14. Does seminal fluid viscosity influence sperm chromatin integrity?

    Science.gov (United States)

    Gopalkrishnan, K; Padwal, V; Balaiah, D

    2000-01-01

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

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

    OpenAIRE

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

    1997-01-01

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

  16. Higher order chromatin structure: bridging physics and biology

    OpenAIRE

    Fudenberg, Geoffrey; Mirny, Leonid A.

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

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

  18. Fiber optics standard dictionary

    CERN Document Server

    Weik, Martin H

    1997-01-01

    Fiber Optics Vocabulary Development In 1979, the National Communications System published Technical InfonnationBulle­ tin TB 79-1, Vocabulary for Fiber Optics and Lightwave Communications, written by this author. Based on a draft prepared by this author, the National Communications System published Federal Standard FED-STD-1037, Glossary of Telecommunications Terms, in 1980 with no fiber optics tenns. In 1981, the first edition of this dictionary was published under the title Fiber Optics and Lightwave Communications Standard Dictionary. In 1982, the then National Bureau of Standards, now the National Institute of Standards and Technology, published NBS Handbook 140, Optical Waveguide Communications Glossary, which was also published by the General Services Admin­ istration as PB82-166257 under the same title. Also in 1982, Dynamic Systems, Inc. , Fiberoptic Sensor Technology Handbook, co-authored and edited by published the this author, with an extensive Fiberoptic Sensors Glossary. In 1989, the handbook w...

  19. Optical Fiber Embedded in Epoxy Glass Unidirectional Fiber Composite System

    OpenAIRE

    Irina Severin; Rochdi El Abdi; Guillaume Corvec; Mihai Caramihai

    2013-01-01

    We aimed to embed silica optical fibers in composites (epoxy vinyl ester matrix reinforced with E-glass unidirectional fibers in mass fraction of 60%) in order to further monitor the robustness of civil engineering structures (such as bridges). A simple system was implemented using two different silica optical fibers (F1—double coating of 172 µm diameter and F2—single coating of 101.8 µm diameter respectively). The optical fibers were dynamically tensile tested and Weibull plots were traced. ...

  20. Modeling and prototyping of a fiber Bragg grating-based dynamic micro-coordinate measuring machine probe

    Science.gov (United States)

    Liu, Fangfang; Chen, Lijuan; Wang, Jingfan; Xia, Haojie; Li, Ruijun; Yu, Liandong; Fei, Yetai

    2016-02-01

    Higher-accuracy measurements of the 3D metrology of nano- and micro-structures are increasingly demanded. This paper details the prototyping of a novel 3D micro-scale coordinate measuring machine probe based on fiber Bragg grating sensors for true 3D measurements at micro- and nanometer scales. A new manufacturing technique for the high-precision cantilever used in the probe is also reported. Simulations are performed during the design and testing to help to test important aspects of the probe and to gain understanding about the influence of the probe geometrical parameters on the sensor sensitivity. The initial performance of the probe has been tested in both the vertical and horizontal directions, and the characterization results are promising. Further experimental results demonstrate that the probe is not affected by surface interaction forces.

  1. Water Fibers

    CERN Document Server

    Douvidzon, Mark L; Martin, Leopoldo L; Carmon, Tal

    2016-01-01

    Fibers constitute the backbone of modern communication and are used in laser surgeries; fibers also genarate coherent X-ray, guided-sound and supercontinuum. In contrast, fibers for capillary oscillations, which are unique to liquids, were rarely considered in optofluidics. Here we fabricate fibers by water bridging an optical tapered-coupler to a microlensed coupler. Our water fibers are held in air and their length can be longer than a millimeter. These hybrid fibers co-confine two important oscillations in nature: capillary- and electromagnetic-. We optically record vibrations in the water fiber, including an audio-rate fundamental and its 3 overtones in a harmonic series, that one can hear in soundtracks attached. Transforming Micro-Electro-Mechanical-Systems [MEMS] to Micro-Electro-Capillary-Systems [MECS], boosts the device softness by a million to accordingly improve its response to minute forces. Furthermore, MECS are compatible with water, which is a most important liquid in our world.

  2. Characterization of fatigue damage in adhesively bonded lap joints through dynamic, full-spectral interrogation of fiber Bragg grating sensors: 2. Simulations

    International Nuclear Information System (INIS)

    In this paper, we simulate the response of fiber Bragg grating (FBG) sensors embedded in the adhesive layer of a composite lap that is subjected to harmonic excitation. To simulate accumulated fatigue damage at the adhesive layer, two forms of numerical nonlinearities are introduced into the model: (1) progressive plastic deformation of the adhesive and (2) changing the boundary of an interfacial defect at the adhesive layer across the overlap shear area. The simulation results are compared with previous measurements of the dynamic, full-spectral response of such FBG sensors for condition monitoring of the lap joint. Short-time Fourier transforms (STFT) of the locally extracted axial strain time histories reveal a transition to nonlinear behavior of the composite lap joint by means of intermittent frequencies that were observed in the experimental measurements and are not associated with the external excitation. The simulation results verify that the nonlinear changes in measured dynamic FBG responses are due to the progression of damage in the lap joint. (paper)

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

    Science.gov (United States)

    Bakkenist, Christopher J; Kastan, Michael B

    2015-12-01

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

  4. Impact resistance of fiber composites

    Science.gov (United States)

    Chamis, C. C.; Sinclair, J. H.

    1982-01-01

    Stress-strain curves are obtained for a variety of glass fiber and carbon fiber reinforced plastics in dynamic tension, over the stress-strain range of 0.00087-2070/sec. The test method is of the one-bar block-to-bar type, using a rotating disk or a pendulum as the loading apparatus and yielding accurate stress-strain curves up to the breaking strain. In the case of glass fiber reinforced plastic, the tensile strength, strain to peak impact stress, total strain and total absorbed energy all increase significantly as the strain rate increases. By contrast, carbon fiber reinforced plastics show lower rates of increase with strain rate. It is recommended that hybrid composites incorporating the high strength and rigidity of carbon fiber reinforced plastic with the high impact absorption of glass fiber reinforced plastics be developed for use in structures subjected to impact loading.

  5. Drop impact on a fiber

    Science.gov (United States)

    Kim, Sung-Gil; Kim, Wonjung

    2016-04-01

    We present the results of a combined experimental and theoretical investigation of drop impact on a thin fiber. Using high-speed videography, we analyze the dynamics of droplet collision with a fiber. Based on the systematic experiments, we identify three outcomes of collision: capturing, single drop falling, and splitting. The outcomes are presented in a regime map, where the regime boundaries are explained through a scale analysis of forces. We also measure the liquid retention on the fiber after the droplet impact. By considering a liquid film on the fiber, we develop a mechanical model that predicts the residual water mass. Our model reveals that the residual mass depends critically on the fiber thickness and less on the impact speed. Our study can be extended to predicting the remaining droplet, critical problems in air filtration, water collection, and fiber coating.

  6. Chromatin plasticity as a differentiation index during muscle differentiation of C2C12 myoblasts

    International Nuclear Information System (INIS)

    Highlights: ► Change in the epigenetic landscape during myogenesis was optically investigated. ► Mobility of nuclear proteins was used to state the epigenetic status of the cell. ► Mobility of nuclear proteins decreased as myogenesis progressed in C2C12. ► Differentiation state diagram was developed using parameters obtained. -- Abstract: Skeletal muscle undergoes complicated differentiation steps that include cell-cycle arrest, cell fusion, and maturation, which are controlled through sequential expression of transcription factors. During muscle differentiation, remodeling of the epigenetic landscape is also known to take place on a large scale, determining cell fate. In an attempt to determine the extent of epigenetic remodeling during muscle differentiation, we characterized the plasticity of the chromatin structure using C2C12 myoblasts. Differentiation of C2C12 cells was induced by lowering the serum concentration after they had reached full confluence, resulting in the formation of multi-nucleated myotubes. Upon induction of differentiation, the nucleus size decreased whereas the aspect ratio increased, indicating the presence of force on the nucleus during differentiation. Movement of the nucleus was also suppressed when differentiation was induced, indicating that the plasticity of chromatin changed upon differentiation. To evaluate the histone dynamics during differentiation, FRAP experiment was performed, which showed an increase in the immobile fraction of histone proteins when differentiation was induced. To further evaluate the change in the histone dynamics during differentiation, FCS was performed, which showed a decrease in histone mobility on differentiation. We here show that the plasticity of chromatin decreases upon differentiation, which takes place in a stepwise manner, and that it can be used as an index for the differentiation stage during myogenesis using the state diagram developed with the parameters obtained in this study.

  7. Chromatin plasticity as a differentiation index during muscle differentiation of C2C12 myoblasts

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Tomonobu M. [Laboratory for Comprehensive Bioimaging, Riken Qbic, Osaka 565-0874 (Japan); World Premier Initiative, iFREC, Osaka University, Osaka 565-0871 (Japan); Higuchi, Sayaka [Laboratory for Comprehensive Bioimaging, Riken Qbic, Osaka 565-0874 (Japan); Kawauchi, Keiko [Mechanobiology Institute, National University of Singapore, Singapore 117411 (Singapore); Tsukasaki, Yoshikazu; Ichimura, Taro [Laboratory for Comprehensive Bioimaging, Riken Qbic, Osaka 565-0874 (Japan); Fujita, Hideaki, E-mail: hideaki.fujita@riken.jp [Laboratory for Comprehensive Bioimaging, Riken Qbic, Osaka 565-0874 (Japan)

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer Change in the epigenetic landscape during myogenesis was optically investigated. Black-Right-Pointing-Pointer Mobility of nuclear proteins was used to state the epigenetic status of the cell. Black-Right-Pointing-Pointer Mobility of nuclear proteins decreased as myogenesis progressed in C2C12. Black-Right-Pointing-Pointer Differentiation state diagram was developed using parameters obtained. -- Abstract: Skeletal muscle undergoes complicated differentiation steps that include cell-cycle arrest, cell fusion, and maturation, which are controlled through sequential expression of transcription factors. During muscle differentiation, remodeling of the epigenetic landscape is also known to take place on a large scale, determining cell fate. In an attempt to determine the extent of epigenetic remodeling during muscle differentiation, we characterized the plasticity of the chromatin structure using C2C12 myoblasts. Differentiation of C2C12 cells was induced by lowering the serum concentration after they had reached full confluence, resulting in the formation of multi-nucleated myotubes. Upon induction of differentiation, the nucleus size decreased whereas the aspect ratio increased, indicating the presence of force on the nucleus during differentiation. Movement of the nucleus was also suppressed when differentiation was induced, indicating that the plasticity of chromatin changed upon differentiation. To evaluate the histone dynamics during differentiation, FRAP experiment was performed, which showed an increase in the immobile fraction of histone proteins when differentiation was induced. To further evaluate the change in the histone dynamics during differentiation, FCS was performed, which showed a decrease in histone mobility on differentiation. We here show that the plasticity of chromatin decreases upon differentiation, which takes place in a stepwise manner, and that it can be used as an index for the differentiation stage

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

    Science.gov (United States)

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

    2015-01-01

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

  9. Numerical Simulation of Dynamic Response of Fiber Reinforced Ceramic Matrix Composite Beam with Matrix Cracks Using Multiscale Modeling

    Institute of Scientific and Technical Information of China (English)

    Gao Xiguang; Song Yingdong; Sun Zhigang; Hu Xuteng

    2010-01-01

    A multiscale method for simulating the dynamic response of ceramic matrix composite (CMC) with matrix cracks is developed.At the global level,the finite element method is employed to simulate the dynamic response ofa CMC beam.While at the local level,the multiscale mechanical method is used to estimate the stress/strain response of the material.A distributed computing system is developed to speed up the simulation.The simulation of dynamic response of a Nicalon/CAS-Ⅱ beam being subjected to harmonic loading is performed as a numerical example.The results show that both the stress/strain responses under tension and compressive loading are nonlinear.These conditions result in a different response compared with that of elastic beam,such as:1) the displacement response is not symmetric about the axis of time;2) in the condition of small external load,the response at first order natural frequency is limited within a finite range;3) decreasing the matrix crack space will increase the displacement response of the beam.

  10. Novel insights into the dynamics of cold-air drainage and pooling on a gentle slope from fiber-optic distributed temperature sensing

    Science.gov (United States)

    Pfister, Lena; Sigmund, Armin; Olesch, Johannes; Thomas, Christoph

    2016-04-01

    Urban climate can benefit from cold-air drainage as it may help alleviate the urban heat island. In contrast, stable cold-air pools can damage plants especially in rural areas. In this study, we examined the dynamics of cold-air drainage and pooling in a peri-urban setting over a period of 47 days along a 170 m long slope with an inclination of 1.3° located in the Ecological Botany Gardens of the University of Bayreuth. Air and soil temperatures were measured using distributed temperature sensing of an 2-dimensional fiber-optic array at six heights (-2 cm to 100 cm) along the slope sampling every 1 min and every 1 m. Ancillary measurements of winds, turbulence intensity and momentum exchange were collected using two ultrasonic anemometers installed at 0.1 m and 17 m height at the center of the transect. We hypothesized that cold-air drainage, here defined as a gravity-driven density flow near the bottom originating from local radiative cooling of the surface, is decoupled from non-local flows and can thus be predicted from the local topography. The nocturnal data were stratified by classes of longwave radiation balance, wind speed, and wind direction at 0.1 m agl. The four most abundant classes were tested further for decoupling of wind velocities and directions between 17 and 0.1 m. We further computed the vertical and horizontal temperature perturbations of the fiber-optic array as evaluated for these cases, as well as subject the temperature data to a multiresolution decomposition to investigate the spatial two-point correlation coefficient along the transect. Finally, the cold pool intensity was calculated. The results revealed none of the four most abundant classes followed classical textbook knowledge of locally produced cold-air drainage. Instead, we found that the near-surface flow was strongly forced by two possibly competing non-local flow modes. The first mode caused weak (depression the Botanical Gardens are located in. Here, the deeper cold

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-08-12

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

  13. 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.

  14. 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.

  15. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis

    Directory of Open Access Journals (Sweden)

    Jialei Hu

    2015-12-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  17. Activation of tachykinin, neurokinin 3 receptors affects chromatin structure and gene expression by means of histone acetylation.

    Science.gov (United States)

    Thakar, Amit; Sylar, Elise; Flynn, Francis W

    2012-12-01

    The tachykinin, neurokinin 3 receptor (NK3R) is a g-protein coupled receptor that is broadly distributed in the nervous system and exerts its diverse physiological actions through multiple signaling pathways. Despite the role of the receptor system in a range of biological functions, the effects of NK3R activation on chromatin dynamics and gene expression have received limited attention. The present work determined the effects of senktide, a selective NK3R agonist, on chromatin organization, acetylation, and gene expression, using qRT-PCR, in a hypothalamic cell line (CLU 209) that expresses the NK3R. Senktide (1 nM, 10nM) caused a relaxation of chromatin, an increase in global acetylation of histone H3 and H4, and an increase in the expression of a common set of genes involved in cell signaling, cell growth, and synaptic plasticity. Pretreatment with histone acetyltransferase (HAT) inhibitor (garcinol and 2-methylene y-butylactone), that inhibits p300, p300/CREB binding protein (CBP) associated factor (PCAF), and GCN 5, prevented the senktide-induced increase in expression of most, but not all, of the genes upregulated in response to 1 nM and 10nM senktide. Treatment with 100 nM had the opposite effect: a reduction in chromatin relaxation and decreased acetylation. The expression of four genes was significantly decreased and the HAT inhibitor had a limited effect in blocking the upregulation of genes in response to 100 nM senktide. Activation of the NK3R appears to recruit multiple pathways, including acetylation, and possibly histone deactylases, histone methylases, or DNA methylases to affect chromatin structure and gene expression. PMID:22985858

  18. Shear induced fiber orientation, fiber breakage and matrix molecular orientation in long glass fiber reinforced polypropylene composites

    International Nuclear Information System (INIS)

    Research highlights: → Shear affects the tensile strength negatively despite the better orientation. → Fiber length overweighs orientation in determining the tensile strength. → Fibers with higher lengths would suffer more severe breakage. → Matrix molecular orientation degree decreases with fiber content. - Abstract: Long fiber reinforcement is well known to offer thermoplastic materials with high performances. But little work has been done to systematically investigate the effect of shear on the structures and properties of long glass fiber reinforced thermoplastics. The purpose of this work is to investigate the effect of shear on fiber orientation, fiber breakage and matrix molecular orientation in long glass fiber reinforced polypropylene composites, and to construct the structure-property relations. A so-called dynamic packing injection molding (DPIM) technique, which imposed oscillatory shear (10 s-1) on the gradually cooled melt during the packing solidification stage, was used to prepare the dynamic samples, and optical microscope (OM), scanning electron microscope (SEM), micro-Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) were used to characterize the samples. The results show that despite the well-published enhanced fiber and matrix orientation, shear will cause a remarkable fiber breakage. Combined effect of fiber breakage and orientation on the mechanical properties of the composites was qualitatively investigated and tensile properties of the dynamic samples, the conventional injection molded samples and the short glass fiber reinforced samples were compared. It is demonstrated that shear will induce more severe fiber breakage in long glass fiber reinforced polypropylene than in short glass fiber reinforced polypropylene, and that compromising the decreased strength caused by the severe fiber breakage is very difficult.

  19. Breaking an Epigenetic Chromatin Switch: Curious Features of Hysteresis in Saccharomyces cerevisiae Telomeric Silencing

    Science.gov (United States)

    Nagaraj, Vijayalakshmi H.; Mukhopadhyay, Swagatam; Dayarian, Adel; Sengupta, Anirvan M.

    2014-01-01

    In addition to gene network switches, local epigenetic modifications to DNA and histones play an important role in all-or-none cellular decision-making. Here, we study the dynamical design of a well-characterized epigenetic chromatin switch: the yeast SIR system, in order to understand the origin of the stability of epigenetic states. We study hysteresis in this system by perturbing it with a histone deacetylase inhibitor. We find that SIR silencing has many characteristics of a non-linear bistable system, as observed in conventional genetic switches, which are based on activities of a few promoters affecting each other through the abundance of their gene products. Quite remarkably, our experiments in yeast telomeric silencing show a very distinctive pattern when it comes to the transition from bistability to monostability. In particular, the loss of the stable silenced state, upon increasing the inhibitor concentration, does not seem to show the expected saddle node behavior, instead looking like a supercritical pitchfork bifurcation. In other words, the ‘off’ state merges with the ‘on’ state at a threshold concentration leading to a single state, as opposed to the two states remaining distinct up to the threshold and exhibiting a discontinuous jump from the ‘off’ to the ‘on’ state. We argue that this is an inevitable consequence of silenced and active regions coexisting with dynamic domain boundaries. The experimental observations in our study therefore have broad implications for the understanding of chromatin silencing in yeast and beyond. PMID:25536038

  20. Breaking an epigenetic chromatin switch: curious features of hysteresis in Saccharomyces cerevisiae telomeric silencing.

    Directory of Open Access Journals (Sweden)

    Vijayalakshmi H Nagaraj

    Full Text Available In addition to gene network switches, local epigenetic modifications to DNA and histones play an important role in all-or-none cellular decision-making. Here, we study the dynamical design of a well-characterized epigenetic chromatin switch: the yeast SIR system, in order to understand the origin of the stability of epigenetic states. We study hysteresis in this system by perturbing it with a histone deacetylase inhibitor. We find that SIR silencing has many characteristics of a non-linear bistable system, as observed in conventional genetic switches, which are based on activities of a few promoters affecting each other through the abundance of their gene products. Quite remarkably, our experiments in yeast telomeric silencing show a very distinctive pattern when it comes to the transition from bistability to monostability. In particular, the loss of the stable silenced state, upon increasing the inhibitor concentration, does not seem to show the expected saddle node behavior, instead looking like a supercritical pitchfork bifurcation. In other words, the 'off' state merges with the 'on' state at a threshold concentration leading to a single state, as opposed to the two states remaining distinct up to the threshold and exhibiting a discontinuous jump from the 'off' to the 'on' state. We argue that this is an inevitable consequence of silenced and active regions coexisting with dynamic domain boundaries. The experimental observations in our study therefore have broad implications for the understanding of chromatin silencing in yeast and beyond.

  1. 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

  2. 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.

  3. 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

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

    OpenAIRE

    Názer, Ezequiel; Lei, Elissa P.

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Laugesen, Anne; Helin, Kristian

    2014-01-01

    The chromatin environment is essential for the correct specification and preservation of cell identity through modulation and maintenance of transcription patterns. Many chromatin regulators are required for development, stem cell maintenance, and differentiation. Here, we review the roles of the...... polycomb repressive complexes, PRC1 and PRC2, and the HDAC1- and HDAC2-containing complexes, NuRD, Sin3, and CoREST, in stem cells, development, and cancer, as well as the ongoing efforts to develop therapies targeting these complexes in human cancer. Furthermore, we discuss the role of repressive...... complexes in modulating thresholds for gene activation and their importance for specification and maintenance of cell fate....

  6. Self-pulsation in Raman fiber amplifiers

    DEFF Research Database (Denmark)

    Pedersen, Martin Erland Vestergaard; Ott, Johan Raunkjær; Rottwitt, Karsten

    2009-01-01

    Dynamic behavior caused by Brillouin scattering in Raman fiber amplifiers is studied. Modes of self-pulsation steady state oscillations are found. Their dependence on amplification scheme is demonstrated.......Dynamic behavior caused by Brillouin scattering in Raman fiber amplifiers is studied. Modes of self-pulsation steady state oscillations are found. Their dependence on amplification scheme is demonstrated....

  7. Involvement of Plasmodium falciparum protein kinase CK2 in the chromatin assembly pathway

    Directory of Open Access Journals (Sweden)

    Dastidar Eeshita G

    2012-01-01

    Full Text Available Abstract Background Protein kinase CK2 is a pleiotropic serine/threonine protein kinase with hundreds of reported substrates, and plays an important role in a number of cellular processes. The cellular functions of Plasmodium falciparum CK2 (PfCK2 are unknown. The parasite's genome encodes one catalytic subunit, PfCK2α, which we have previously shown to be essential for completion of the asexual erythrocytic cycle, and two putative regulatory subunits, PfCK2β1 and PfCK2β2. Results We now show that the genes encoding both regulatory PfCK2 subunits (PfCK2β1 and PfCK2β2 cannot be disrupted. Using immunofluorescence and electron microscopy, we examined the intra-erythrocytic stages of transgenic parasite lines expressing hemagglutinin (HA-tagged catalytic and regulatory subunits (HA-CK2α, HA-PfCK2β1 or HA-PfCK2β2, and localized all three subunits to both cytoplasmic and nuclear compartments of the parasite. The same transgenic parasite lines were used to purify PfCK2β1- and PfCK2β2-containing complexes, which were analyzed by mass spectrometry. The recovered proteins were unevenly distributed between various pathways, with a large proportion of components of the chromatin assembly pathway being present in both PfCK2β1 and PfCK2β2 precipitates, implicating PfCK2 in chromatin dynamics. We also found that chromatin-related substrates such as nucleosome assembly proteins (Naps, histones, and two members of the Alba family are phosphorylated by PfCK2α in vitro. Conclusions Our reverse-genetics data show that each of the two regulatory PfCK2 subunits is required for completion of the asexual erythrocytic cycle. Our interactome study points to an implication of PfCK2 in many cellular pathways, with chromatin dynamics being identified as a major process regulated by PfCK2. This study paves the way for a kinome-wide interactomics-based approach to elucidate protein kinase function in malaria parasites.

  8. STUDIES ON THE DYNAMIC COMPETITIVE ADSORPTION OF ORGANIC VAPORS ON THE ACTIVATED CARBON FIBERS ACTIVATED WITH PHOSPHORIC ACID

    Institute of Scientific and Technical Information of China (English)

    FURuowen; LIULing; 等

    2000-01-01

    The dynamic competititve adsorption behaviors of different binary organic vapor mixtures on ACF-Ps under different operation conditons were investigated by gas chromatography in this paper,The studied mixtrues included benzene/toluene,toluene/xylene,benzene/isopropylbenzene ethly acetate/toluene and benzene/ethyl acetate.Experimental results show that various ACF-Ps,as with ACF-W,can remove both vapors in binary vapor mixtures with over 99% of removal efficiency before the breakthrough point of the more weakly adsorbed vapor,In dynamic competitive adsorption,the more weakly weakle adsorbed vapor noe only penetrates early,but also will be displaced and desorbed consequently by stronger adsorbate and therefore produces a rolling up in the breakthrough curve,The ACF-Ps prepared at different temperatuers have somewhat different adsorption selectivity,The feed concentration ratio of vapros,the length/diameter ratio and the thick of bed have effect on competitive adsorption.The competitive adsorption ability of a vapor is mainly related to its boiling point.Usually,the higher the boiling point ,the stronger the vapor adsorbed on ACF-P.

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

    OpenAIRE

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

    2015-01-01

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

  10. Optical Fiber Embedded in Epoxy Glass Unidirectional Fiber Composite System

    Directory of Open Access Journals (Sweden)

    Irina Severin

    2013-12-01

    Full Text Available We aimed to embed silica optical fibers in composites (epoxy vinyl ester matrix reinforced with E-glass unidirectional fibers in mass fraction of 60% in order to further monitor the robustness of civil engineering structures (such as bridges. A simple system was implemented using two different silica optical fibers (F1—double coating of 172 µm diameter and F2—single coating of 101.8 µm diameter respectively. The optical fibers were dynamically tensile tested and Weibull plots were traced. Interfacial adhesion stress was determined using pull-out test and stress values were correlated to fracture mechanisms based on SEM observations. In the case of the optical fiber (OF (F1/resin system and OF (F1/composite system, poor adhesion was reported that may be correlated to interface fracture at silica core level. Relevant applicable results were determined for OF (F2/composite system.

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

    DEFF Research Database (Denmark)

    Lichota, J.; Grasser, Klaus D.

    2003-01-01

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

  12. Linking Morphogen and Chromatin in the Hair Follicle

    OpenAIRE

    Mesa, Kailin R; Greco, Valentina

    2013-01-01

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

  13. 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

  14. 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.

  15. Chromatin-regulating proteins as targets for cancer therapy

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2014-07-01

    Chromatin-regulating proteins represent a large class of novel targets for cancer therapy. In the context of radiotherapy, acetylation and deacetylation of histones by histone acetyltransferases (HATs) and histone deacetylases (HDACs) play important roles in the repair of DNA double-strand breaks generated by ionizing irradiation, and are therefore attractive targets for radiosensitization. Small-molecule inhibitors of HATs (garcinol, anacardic acid and curcumin) and HDACs (vorinostat, sodium butyrate and valproic acid) have been shown to sensitize cancer cells to ionizing irradiation in preclinical models, and some of these molecules are being tested in clinical trials, either alone or in combination with radiotherapy. Meanwhile, recent large-scale genome analyses have identified frequent mutations in genes encoding chromatin-regulating proteins, especially in those encoding subunits of the SWI/SNF chromatin-remodeling complex, in various human cancers. These observations have driven researchers toward development of targeted therapies against cancers carrying these mutations. DOT1L inhibition in MLL-rearranged leukemia, EZH2 inhibition in EZH2-mutant or MLL-rearranged hematologic malignancies and SNF5-deficient tumors, BRD4 inhibition in various hematologic malignancies, and BRM inhibition in BRG1-deficient tumors have demonstrated promising anti-tumor effects in preclinical models, and these strategies are currently awaiting clinical application. Overall, the data collected so far suggest that targeting chromatin-regulating proteins is a promising strategy for tomorrow's cancer therapy, including radiotherapy and molecularly targeted chemotherapy. PMID:24522270

  17. Effect of triiodothyronine on rat liver chromatin protein kinase

    International Nuclear Information System (INIS)

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

  18. 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.

  19. Two Fiber Optical Fiber Thermometry

    Science.gov (United States)

    Jones, Mathew R.; Farmer, Jeffery T.; Breeding, Shawn P.

    2000-01-01

    An optical fiber thermometer consists of an optical fiber whose sensing tip is given a metallic coating. The sensing tip of the fiber is essentially an isothermal cavity, so the emission from this cavity will be approximately equal to the emission from a blackbody. Temperature readings are obtained by measuring the spectral radiative heat flux at the end of the fiber at two wavelengths. The ratio of these measurements and Planck's Law are used to infer the temperature at the sensing tip. Optical fiber thermometers have high accuracy, excellent long-term stability and are immune to electromagnetic interference. In addition, they can be operated for extended periods without requiring re-calibration. For these reasons. it is desirable to use optical fiber thermometers in environments such as the International Space Station. However, it has recently been shown that temperature readings are corrupted by emission from the fiber when extended portions of the probe are exposed to elevated temperatures. This paper will describe several ways in which the reading from a second fiber can be used to correct the corrupted temperature measurements. The accuracy and sensitivity to measurement uncertainty will be presented for each method.

  20. Mechanical Behavior of Polyester and Fiber Glass as a Composite Material used in a Vehicle under Dynamic Loading

    Directory of Open Access Journals (Sweden)

    Ahmed Naif Al-Khazraji* Ali Yasser Hassa * Emad Abdul Hussein Abdul Sahib

    2014-04-01

    Full Text Available The automobile industry has shown increased interest in the replacement of steel spring with fiberglass composite leaf spring due to high strength compared to weight. The aim of this paper is to study two kinds of fiberglass, regular direction (0-90 and random direction immersed in polyester resin. They were tested under static load, as tensile test for their mechanical properties, and under dynamic load in fully reversible bending tests as fatigue test, to estimate S-N curves, and impact test for their mechanical properties. Results from the tensile tests showed that the tensile strength of the regular type is greater than random type. The fatigue test results showed that the number of cycles to failure in regular type of composite material is greater than that of the random type and the endurance limit is also greater than in random, the increase percentage in endurance limit is 7.5%. Results due to impact test showed that there were on increasing in fracture energy for the random type the increase ratio is 13.9%. The Important characteristics of composites that make them excellent for leaf spring instead of steel are higher strength-to-weight ratio, superior fatigue strength. Application of composite structures reduces the weight of leaf spring without any reduction on the load carrying capacity and stiffness in automobile suspension system.

  1. 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.

  2. Neuronal accumulation of unrepaired DNA in a novel specific chromatin domain: structural, molecular and transcriptional characterization.

    Science.gov (United States)

    Mata-Garrido, Jorge; Casafont, Iñigo; Tapia, Olga; Berciano, Maria T; Lafarga, Miguel

    2016-01-01

    There is growing evidence that defective DNA repair in neurons with accumulation of DNA lesions and loss of genome integrity underlies aging and many neurodegenerative disorders. An important challenge is to understand how neurons can tolerate the accumulation of persistent DNA lesions without triggering the apoptotic pathway. Here we study the impact of the accumulation of unrepaired DNA on the chromatin architecture, kinetics of the DNA damage response and transcriptional activity in rat sensory ganglion neurons exposed to 1-to-3 doses of ionizing radiation (IR). In particular, we have characterized the structural, molecular and transcriptional compartmentalization of unrepaired DNA in persistent DNA damaged foci (PDDF). IR induced the formation of numerous transient foci, which repaired DNA within the 24 h post-IR, and a 1-to-3 PDDF. The latter concentrate DNA damage signaling and repair factors, including γH2AX, pATM, WRAP53 and 53BP1. The number and size of PDDF was dependent on the doses of IR administered. The proportion of neurons carrying PDDF decreased over time of post-IR, indicating that a slow DNA repair occurs in some foci. The fine structure of PDDF consisted of a loose network of unfolded 30 nm chromatin fiber intermediates, which may provide a structural scaffold accessible for DNA repair factors. Furthermore, the transcription assay demonstrated that PDDF are transcriptionally silent, although transcription occurred in flanking euchromatin. Therefore, the expression of γH2AX can be used as a reliable marker of gene silencing in DNA damaged neurons. Moreover, PDDF were located in repressive nuclear environments, preferentially in the perinucleolar domain where they were frequently associated with Cajal bodies or heterochromatin clumps forming a structural triad. We propose that the sequestration of unrepaired DNA in discrete PDDF and the transcriptional silencing can be essential to preserve genome stability and prevent the synthesis of

  3. All-optical storage and processing in optical fibers

    OpenAIRE

    Thévenaz, Luc; Primerov, Nikolay; Chin, Sanghoon; Antman, Yair; Denisov, Andrey; Zadok, Avi; Santagiustina, Marco

    2012-01-01

    The recent possibility to generate and read dynamic Bragg gratings in optical fibers by the interaction of multiple optical waves through stimulated Brillouin scattering has opened a new field to realize all-optical fiber-based functions.

  4. Fission yeast Scm3 mediates stable assembly of Cnp1/CENP-A into centromeric chromatin.

    Science.gov (United States)

    Williams, Jessica S; Hayashi, Takeshi; Yanagida, Mitsuhiro; Russell, Paul

    2009-02-13

    Mis16 and Mis18 are subunits of a protein complex required for incorporation of the histone H3 variant CenH3 (Cnp1/CENP-A) into centromeric chromatin in Schizosaccharomyces pombe and mammals. How the Mis16-Mis18 complex performs this function is unknown. Here, we report that the Mis16-Mis18 complex is required for centromere localization of Scm3(Sp), a Cnp1-binding protein related to Saccharomyces cerevisiae Scm3. Scm3(Sp) is required for centromeric localization of Cnp1, while Scm3(Sp) localizes at centromeres independently of Cnp1. Like the Mis16-Mis18 complex but unlike Cnp1, Scm3(Sp) dissociates from centromeres during mitosis. Inactivation of Scm3(Sp) or Mis18 increases centromere localization of histones H3 and H2A/H2B, which are largely absent from centromeres in wild-type cells. Whereas S. cerevisiae Scm3 is proposed to replace histone H2A/H2B in centromeric nucleosomes, the dynamic behavior of S. pombe Scm3 suggests that it acts as a Cnp1 assembly/maintenance factor that directly mediates the stable deposition of Cnp1 into centromeric chromatin. PMID:19217403

  5. Fission Yeast Scm3 Mediates Stable Assembly of Cnp1 (CENP-A) into Centromeric Chromatin

    Science.gov (United States)

    Williams, Jessica S.; Hayashi, Takeshi; Yanagida, Mitsuhiro; Russell, Paul

    2009-01-01

    Summary Mis16 and Mis18 are subunits of a protein complex required for incorporation of the histone H3 variant CenH3 (Cnp1/CENP-A) into centromeric chromatin in Schizosaccharomyces pombe and mammals. How the Mis16-Mis18 complex performs this function is unknown. Here we report that the Mis16-Mis18 complex is required for centromere localization of Scm3Sp, a Cnp1-binding protein related to Saccharomyces cerevisiae Scm3. Scm3Sp is required for centromeric localization of Cnp1, whilst Scm3Sp localizes at centromeres independently of Cnp1. Like the Mis16-Mis18 complex but unlike Cnp1, Scm3Sp dissociates from centromeres during mitosis. Inactivation of Scm3Sp or Mis18 increases centromere localization of histones H3 and H2A/H2B, which are largely absent from centromeres in wild type cells. Whereas S. cerevisiae Scm3 is proposed to replace histone H2A/H2B in centromeric nucleosomes, the dynamic behavior of S. pombe Scm3 suggests that it acts as a Cnp1 assembly/maintenance factor that directly mediates the stable deposition of Cnp1 into centromeric chromatin. PMID:19217403

  6. Optical Fiber Strain Sensor Application in Safety Inspection Under Dynamic Loading%光纤应变传感器在振动检测和安全评估中的应用

    Institute of Scientific and Technical Information of China (English)

    孙雨; 吴江; 李旭强

    2012-01-01

    介绍了一种利用光纤应变传感器进行动载作用下构件安全性检测的方法,以国内某过山车基础支撑为例,介绍了光纤应变传感器的安装和使用方法,并通过对传感器采集到的应变数据进行分析,结合其他现场检测数据,对受测构件安全性给出了评价.%The method of using fiber optic strain sensors for safety inspection of structural elements under dynamic loading is introduced. In the study with fiber optic strain sensor in an in-situ test of the structural supporting system of a roller coaster, the method of installation and operation of fiber optic strain sensors is elaborated. In the comparison of the data collected from the fiber optic strain sensors and other test method, analysis is carried out to estimate the safety of the structural system.

  7. Novel insights into the dynamics of cold-air drainage and pooling on a gentle slope from fiber-optic distributed temperature sensing

    Science.gov (United States)

    Pfister, Lena; Sigmund, Armin; Olesch, Johannes; Thomas, Christoph

    2016-04-01

    Urban climate can benefit from cold-air drainage as it may help alleviate the urban heat island. In contrast, stable cold-air pools can damage plants especially in rural areas. In this study, we examined the dynamics of cold-air drainage and pooling in a peri-urban setting over a period of 47 days along a 170 m long slope with an inclination of 1.3° located in the Ecological Botany Gardens of the University of Bayreuth. Air and soil temperatures were measured using distributed temperature sensing of an 2-dimensional fiber-optic array at six heights (-2 cm to 100 cm) along the slope sampling every 1 min and every 1 m. Ancillary measurements of winds, turbulence intensity and momentum exchange were collected using two ultrasonic anemometers installed at 0.1 m and 17 m height at the center of the transect. We hypothesized that cold-air drainage, here defined as a gravity-driven density flow near the bottom originating from local radiative cooling of the surface, is decoupled from non-local flows and can thus be predicted from the local topography. The nocturnal data were stratified by classes of longwave radiation balance, wind speed, and wind direction at 0.1 m agl. The four most abundant classes were tested further for decoupling of wind velocities and directions between 17 and 0.1 m. We further computed the vertical and horizontal temperature perturbations of the fiber-optic array as evaluated for these cases, as well as subject the temperature data to a multiresolution decomposition to investigate the spatial two-point correlation coefficient along the transect. Finally, the cold pool intensity was calculated. The results revealed none of the four most abundant classes followed classical textbook knowledge of locally produced cold-air drainage. Instead, we found that the near-surface flow was strongly forced by two possibly competing non-local flow modes. The first mode caused weak (< 0.4 ms‑1) near-surface winds directed perpendicular to the local slope and

  8. Bound soliton fiber laser

    OpenAIRE

    Tang, D. Y.; B. Zhao; Shen, D. Y.; Lu, C.

    2009-01-01

    Experimental study on the soliton dynamics of a passively mode locked fiber ring laser firstly revealed a state of bound soliton operation in the laser, where two solitons bind together tightly with fixed pulse separation. We further report on the properties of the bound-soliton emission of the laser. In particular, we demonstrate both experimentally and numerically that, like the single pulse soliton operation of the laser, the bound soliton emission is another intrinsic feature of the laser.

  9. Numerical approach of the injection molding process of fiber-reinforced composite with considering fiber orientation

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen Thi, T. B., E-mail: thanhbinh.skku@gmail.com, E-mail: yokoyama@kit.ac.jp; Yokoyama, A., E-mail: thanhbinh.skku@gmail.com, E-mail: yokoyama@kit.ac.jp [Department of Advanced Fibro-Science, Kyoto Institute of Technology (Japan); Ota, K., E-mail: kei-ota@toyobo.jp, E-mail: katsuhiro-kodama@toyobo.jp, E-mail: katsuhisa-yamashita@toyobo.jp, E-mail: yumiko-isogai@toyobo.jp, E-mail: kenji-furuichi@toyobo.jp, E-mail: chisato-nonomura@toyobo.jp; Kodama, K., E-mail: kei-ota@toyobo.jp, E-mail: katsuhiro-kodama@toyobo.jp, E-mail: katsuhisa-yamashita@toyobo.jp, E-mail: yumiko-isogai@toyobo.jp, E-mail: kenji-furuichi@toyobo.jp, E-mail: chisato-nonomura@toyobo.jp; Yamashita, K., E-mail: kei-ota@toyobo.jp, E-mail: katsuhiro-kodama@toyobo.jp, E-mail: katsuhisa-yamashita@toyobo.jp, E-mail: yumiko-isogai@toyobo.jp, E-mail: kenji-furuichi@toyobo.jp, E-mail: chisato-nonomura@toyobo.jp; Isogai, Y., E-mail: kei-ota@toyobo.jp, E-mail: katsuhiro-kodama@toyobo.jp, E-mail: katsuhisa-yamashita@toyobo.jp, E-mail: yumiko-isogai@toyobo.jp, E-mail: kenji-furuichi@toyobo.jp, E-mail: chisato-nonomura@toyobo.jp; Furuichi, K., E-mail: kei-ota@toyobo.jp, E-mail: katsuhiro-kodama@toyobo.jp, E-mail: katsuhisa-yamashita@toyobo.jp, E-mail: yumiko-isogai@toyobo.jp, E-mail: kenji-furuichi@toyobo.jp, E-mail: chisato-nonomura@toyobo.jp; Nonomura, C., E-mail: kei-ota@toyobo.jp, E-mail: katsuhiro-kodama@toyobo.jp, E-mail: katsuhisa-yamashita@toyobo.jp, E-mail: yumiko-isogai@toyobo.jp, E-mail: kenji-furuichi@toyobo.jp, E-mail: chisato-nonomura@toyobo.jp [Toyobo Co., LTD. Research Center (Japan)

    2014-05-15

    One of the most important challenges in the injection molding process of the short-glass fiber/thermoplastic composite parts is being able to predict the fiber orientation, since it controls the mechanical and the physical properties of the final parts. Folgar and Tucker included into the Jeffery equation a diffusive type of term, which introduces a phenomenological coefficient for modeling the randomizing effect of the mechanical interactions between the fibers, to predict the fiber orientation in concentrated suspensions. Their experiments indicated that this coefficient depends on the fiber volume fraction and aspect ratio. However, a definition of the fiber interaction coefficient, which is very necessary in the fiber orientation simulations, hasn't still been proven yet. Consequently, this study proposed a developed fiber interaction model that has been introduced a fiber dynamics simulation in order to obtain a global fiber interaction coefficient. This supposed that the coefficient is a sum function of the fiber concentration, aspect ratio, and angular velocity. The proposed model was incorporated into a computer aided engineering simulation package C-Mold. Short-glass fiber/polyamide-6 composites were produced in the injection molding with the fiber weight concentration of 30 wt.%, 50 wt.%, and 70 wt.%. The physical properties of these composites were examined, and their fiber orientation distributions were measured by micro-computed-tomography equipment μ-CT. The simulation results showed a good agreement with experiment results.

  10. Numerical approach of the injection molding process of fiber-reinforced composite with considering fiber orientation

    International Nuclear Information System (INIS)

    One of the most important challenges in the injection molding process of the short-glass fiber/thermoplastic composite parts is being able to predict the fiber orientation, since it controls the mechanical and the physical properties of the final parts. Folgar and Tucker included into the Jeffery equation a diffusive type of term, which introduces a phenomenological coefficient for modeling the randomizing effect of the mechanical interactions between the fibers, to predict the fiber orientation in concentrated suspensions. Their experiments indicated that this coefficient depends on the fiber volume fraction and aspect ratio. However, a definition of the fiber interaction coefficient, which is very necessary in the fiber orientation simulations, hasn't still been proven yet. Consequently, this study proposed a developed fiber interaction model that has been introduced a fiber dynamics simulation in order to obtain a global fiber interaction coefficient. This supposed that the coefficient is a sum function of the fiber concentration, aspect ratio, and angular velocity. The proposed model was incorporated into a computer aided engineering simulation package C-Mold. Short-glass fiber/polyamide-6 composites were produced in the injection molding with the fiber weight concentration of 30 wt.%, 50 wt.%, and 70 wt.%. The physical properties of these composites were examined, and their fiber orientation distributions were measured by micro-computed-tomography equipment μ-CT. The simulation results showed a good agreement with experiment results

  11. Numerical approach of the injection molding process of fiber-reinforced composite with considering fiber orientation

    Science.gov (United States)

    Nguyen Thi, T. B.; Yokoyama, A.; Ota, K.; Kodama, K.; Yamashita, K.; Isogai, Y.; Furuichi, K.; Nonomura, C.

    2014-05-01

    One of the most important challenges in the injection molding process of the short-glass fiber/thermoplastic composite parts is being able to predict the fiber orientation, since it controls the mechanical and the physical properties of the final parts. Folgar and Tucker included into the Jeffery equation a diffusive type of term, which introduces a phenomenological coefficient for modeling the randomizing effect of the mechanical interactions between the fibers, to predict the fiber orientation in concentrated suspensions. Their experiments indicated that this coefficient depends on the fiber volume fraction and aspect ratio. However, a definition of the fiber interaction coefficient, which is very necessary in the fiber orientation simulations, hasn't still been proven yet. Consequently, this study proposed a developed fiber interaction model that has been introduced a fiber dynamics simulation in order to obtain a global fiber interaction coefficient. This supposed that the coefficient is a sum function of the fiber concentration, aspect ratio, and angular velocity. The proposed model was incorporated into a computer aided engineering simulation package C-Mold. Short-glass fiber/polyamide-6 composites were produced in the injection molding with the fiber weight concentration of 30 wt.%, 50 wt.%, and 70 wt.%. The physical properties of these composites were examined, and their fiber orientation distributions were measured by micro-computed-tomography equipment μ-CT. The simulation results showed a good agreement with experiment results.

  12. The microtubule aster formation and its role in nuclear envelope assembly around the sperm chromatin in Xenopus egg extracts

    Institute of Scientific and Technical Information of China (English)

    YANG Ning; CHEN Zhongcai; LU Ping; ZHANG Chuanmao; ZHAI Zhonghe; TANG Xiaowei

    2003-01-01

    Nuclear envelope is a dynamic structure in the cell cycle. At the beginning of mitosis, nuclear envelope breaks down and its components disperse into the cytoplasm. At the end of mitosis, nuclear envelope reassembles using the dispersed components. Searching for the mechanisms of the nuclear disassembly and reassembly has for a long time been one of the key projects for cell biologists. In this report we show that microtubules take a role in the nuclear envelope assembly around the sperm chromatin in Xenopus egg extracts. Microtubule cytoskeleton has been demonstrated to take roles in the transport of intracellular membranes such as Golgi and ER vesicles. We found that the nuclear envelope assembly needs functional microtubules. At the beginning of the nuclear assembly, microtubules nucleated to form a microtubule aster around the centrosome at the base of the sperm head. Using the microtubule drug colchicine to disrupt the microtubule nucleation, nuclear envelope reassembly was seriously inhibited. If the microtubules were stabilized by taxol, another microtubule drug, the nuclear envelope reassembly was also interfered, although a significantly large aster formed around the chromatin. Based on these observations, we propose that microtubules play an important role in the nuclear envelope reassembly maybe by transporting the nuclear envelope precursors to the chromatin surfaces.

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

    Science.gov (United States)

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

    2016-04-01

    NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx)) has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions. PMID:27046080

  14. 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.

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

    Science.gov (United States)

    Wolf, G; Beil, M; Guski, H

    1995-02-01

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

  16. 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.

  17. Integrative annotation of chromatin elements from ENCODE data

    OpenAIRE

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

    2012-01-01

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

  18. Effect of saffron on rat sperm chromatin integrity

    OpenAIRE

    Mohammad Mardani; Ahmad Vaez; Shahnaz Razavi

    2014-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  20. Chromatin-regulating proteins as targets for cancer therapy

    OpenAIRE

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

    2014-01-01

    Chromatin-regulating proteins represent a large class of novel targets for cancer therapy. In the context of radiotherapy, acetylation and deacetylation of histones by histone acetyltransferases (HATs) and histone deacetylases (HDACs) play important roles in the repair of DNA double-strand breaks generated by ionizing irradiation, and are therefore attractive targets for radiosensitization. Small-molecule inhibitors of HATs (garcinol, anacardic acid and curcumin) and HDACs (vorinostat, sodium...

  1. Chaperone-mediated assembly of centromeric chromatin in vitro

    OpenAIRE

    Furuyama, Takehito; Dalal, Yamini; Henikoff, Steven

    2006-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2009-01-01

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

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

    OpenAIRE

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

    1999-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

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

  5. Quality of histone modification antibodies undermines chromatin biology research

    OpenAIRE

    Goran Kungulovski; Albert Jeltsch

    2015-01-01

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

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

    OpenAIRE

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

    2009-01-01

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

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

    Science.gov (United States)

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

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model. PMID:662693

  8. Molecular alignment relaxation in polymer optical fibers for sensing applications

    Science.gov (United States)

    Stajanca, Pavol; Cetinkaya, Onur; Schukar, Marcus; Mergo, Pawel; Webb, David J.; Krebber, Katerina

    2016-03-01

    A systematic study of annealing behavior of drawn PMMA fibers was performed. Annealing dynamics were investigated under different environmental conditions by fiber longitudinal shrinkage monitoring. The shrinkage process was found to follow a stretched exponential decay function revealing the heterogeneous nature of the underlying molecular dynamics. The complex dependence of the fiber shrinkage on initial degree of molecular alignment in the fiber, annealing time and temperature was investigated and interpreted. Moreover, humidity was shown to have a profound effect on the annealing process, which was not recognized previously. Annealing was also shown to have considerable effect on the fiber mechanical properties associated with the relaxation of molecular alignment in the fiber. The consequences of fiber annealing for the climatic stability of certain polymer optical fiber-based sensors are discussed, emphasizing the importance of fiber controlled pre-annealing with respect to the foreseeable operating conditions.

  9. Radiosensitivity: a role of ATM in chromatin modification

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2013-03-01

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

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

    Science.gov (United States)

    Gonzales, G F; Sánchez, A

    1994-01-01

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

  12. Purification of nanoparticles by hollow fiber diafiltration

    International Nuclear Information System (INIS)

    Hollow Fiber Diafiltration (Hollow Fiber Tangential Flow Filtration) is an efficient and rapid alternative to traditional methods of nanoparticle purification such as ultracentrifugation, stirred cell filtration, dialysis or chromatography. Hollow Fiber Diafiltration can be used to purify a wide range of nanoparticles including liposomes, colloids, magnetic particles and nanotubes. Hollow Fiber Diafiltration is a membrane based method where pore size determines the retention or transmission of solution components. It is a flow process where the sample is gently circulated through a tubular membrane. With controlled replacement of the permeate or (dialysate), pure nanoparticles can be attained. Hollow Fiber Diafiltration can be directly scaled up from R and D volumes to production. By adding more membrane fibers and maintaining the operating parameters, large volumes can be processed in the same time with the same pressure, and flow dynamics as bench-scale volumes. Keywords: hollow fiber, Diafiltration, filtration, purification, tangential flow filtration.

  13. Purification of nanoparticles by hollow fiber diafiltration

    Science.gov (United States)

    Veeken, J.

    2012-09-01

    Hollow Fiber Diafiltration (Hollow Fiber Tangential Flow Filtration) is an efficient and rapid alternative to traditional methods of nanoparticle purification such as ultracentrifugation, stirred cell filtration, dialysis or chromatography. Hollow Fiber Diafiltration can be used to purify a wide range of nanoparticles including liposomes, colloids, magnetic particles and nanotubes. Hollow Fiber Diafiltration is a membrane based method where pore size determines the retention or transmission of solution components. It is a flow process where the sample is gently circulated through a tubular membrane. With controlled replacement of the permeate or (dialysate), pure nanoparticles can be attained. Hollow Fiber Diafiltration can be directly scaled up from R&D volumes to production. By adding more membrane fibers and maintaining the operating parameters, large volumes can be processed in the same time with the same pressure, and flow dynamics as bench-scale volumes. Keywords: hollow fiber, Diafiltration, filtration, purification, tangential flow filtration.

  14. High Temperature Endurable Fiber Optic Accelerometer

    OpenAIRE

    Yeon-Gwan Lee; Jin-Hyuk Kim; Chun-Gon Kim

    2014-01-01

    This paper presents a low frequency fiber optic accelerometer for application in high temperature environments of civil engineering structures. The reflection-based extrinsic fiber optic accelerometer developed in this study consists of a transmissive grating panel, reflective mirror, and two optical fiber collimators as the transceiver whose function can be maintained up to 130°C. The dynamic characteristics of the sensor probe were investigated and the correlation between the natural freque...

  15. [RNA responsible for conferring a DNase I sensitive structure on albumin gene in assembled chromatin].

    Science.gov (United States)

    Lv, Zhan-Jun; Wang, Xiu-Fang; Zhai, Yu; Song, Shu-Xia

    2003-01-01

    Although the set of genes is virtually the same in all tissues,differential gene expression is appeared in cells of different kinds. Differentiation and ageing are associated with regulation of gene expression that is a fundamental mechanism in eukaryotic development and survival. The sensitivity to DNase I of actively transcribed genes seems to be a general phenomenon. The purpose of the study is to test whether RNAs obtained from different organs or cells can enhance susceptibility of albumin gene to DNase I digestion in BALB/c mouse brain chromatin assembled.RNAs extracted from rat liver, lung, kidney, brain, tRNA from yeast and synthesized RNAs (23 nt completed with mouse alb gene) were added to a system of chromatin reconstitution that was achieved by dialysis from high ionic strength solution. Assembled chromatin was digested with DNase I (12.5 microg/mL) at 20 degrees for 1 min, then PCR assay was used to detect the level of albumin gene digested. PCR products (1200 bp) were run on a 6% polyacylamide gel and analyzed by silver stain assay. RNAs from different organs and synthesized RNAs all increased the sensitivity of albumin gene to DNase I attack in mouse assembled chromatin. The effect was more obvious in liver and lung RNAs than in kidney and brain ones. tRNA from yeast did not enhance the sensitivity of albumin gene to DNase I digestion. RNA increased albumin gene sensitivity to DNase I in a dose-dependent manner. We report here for the first time that RNAs can enhance susceptibility of albumin gene to DNase I digestion. The effect is associated with RNA sources or sequences. It is generally agreed that the formation of gene sensitivity to DNase I, by unfolding of a tightly packed chromatin fiber, is the first step in gene activation, then RNAs that recognize complementary DNA sequences may be the specific factors that affect DNA supercoiling and determine the sensitivity of gene to DNase I digestion. Here we describes "RNA Population Gene Activating

  16. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

    Science.gov (United States)

    Sanborn, Adrian; Rao, Suhas; Huang, Su-Chen; Durand, Neva; Huntley, Miriam; Jewett, Andrew; Bochkov, Ivan; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher; McKenna, Doug; Stamenova, Elena; Gnirke, Andreas; Melnikov, Alexandre; Lander, Eric; Aiden, Erez

    Our recent kilobase-resolution genome-wide maps of DNA self-contacts demonstrated that mammalian genomes are organized into domains and loops demarcated by the DNA-binding protein CTCF. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that domains are inconsistent with equilibrium and fractal models. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during condensation leads to formation of an anisotropic ``tension globule.'' In the other, CTCF and cohesin act together to extrude unknotted loops. Both models are consistent with the observed domains and loops. However, the extrusion model explains a far wider array of observations, such as why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The extrusion model predicts in silico the experimental maps using only CTCF-binding sites. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

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

    DEFF Research Database (Denmark)

    Alexiadis, V; Waldmann, T; Andersen, Jens S.; Mann, M; Knippers, R; Gruss, C

    2000-01-01

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

  18. Soluble vs. insoluble fiber

    Science.gov (United States)

    Insoluble vs. soluble fiber; Fiber - soluble vs. insoluble ... There are two different types of fiber -- soluble and insoluble. Both are important for health, digestion, and preventing diseases. Soluble fiber attracts water and turns to gel during digestion. ...

  19. Spatiotemporal dynamics of re-innervation and hyperinnervation patterns by uninjured CGRP fibers in the rat foot sole epidermis after nerve injury

    Directory of Open Access Journals (Sweden)

    Duraku Liron S

    2012-08-01

    Full Text Available Abstract The epidermis is innervated by fine nerve endings that are important in mediating nociceptive stimuli. However, their precise role in neuropathic pain is still controversial. Here, we have studied the role of epidermal peptidergic nociceptive fibers that are located adjacent to injured fibers in a rat model of neuropathic pain. Using the Spared Nerve Injury (SNI model, which involves complete transections of the tibial and common peroneal nerve while sparing the sural and saphenous branches, mechanical hypersensitivity was induced of the uninjured lateral (sural and medial (saphenous area of the foot sole. At different time points, a complete foot sole biopsy was taken from the injured paw and processed for Calcitonin Gene-Related Peptide (CGRP immunohistochemistry. Subsequently, a novel 2D-reconstruction model depicting the density of CGRP fibers was made to evaluate the course of denervation and re-innervation by uninjured CGRP fibers. The results show an increased density of uninjured CGRP-IR epidermal fibers on the lateral and medial side after a SNI procedure at 5 and 10 weeks. Furthermore, although in control animals the density of epidermal CGRP-IR fibers in the footpads was lower compared to the surrounding skin of the foot, 10 weeks after the SNI procedure, the initially denervated footpads displayed a hyper-innervation. These data support the idea that uninjured fibers may play a considerable role in development and maintenance of neuropathic pain and that it is important to take larger biopsies to test the relationship between innervation of injured and uninjured nerve areas.

  20. Reorganization of Damaged Chromatin by the Exchange of Histone Variant H2A.Z-2

    Energy Technology Data Exchange (ETDEWEB)

    Nishibuchi, Ikuno [Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima (Japan); Department of Radiation Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima (Japan); Department of Radiation Oncology, Hiroshima Prefectural Hospital, Hiroshima (Japan); Suzuki, Hidekazu; Kinomura, Aiko; Sun, Jiying; Liu, Ning-Ang [Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima (Japan); Horikoshi, Yasunori [Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima (Japan); Research Center for Mathematics of Chromatin Live Dynamics, Hiroshima University, Hiroshima (Japan); Shima, Hiroki [Department of Biochemistry, Graduate School of Medical Sciences, Tohoku University, Sendai (Japan); Kusakabe, Masayuki; Harata, Masahiko [Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai (Japan); Fukagawa, Tatsuo [Department of Molecular Genetics, National Institute of Genetics and The Graduate University for Advanced Studies, Mishima (Japan); Ikura, Tsuyoshi [Laboratory of Chromatin Regulatory Network, Department of Mutagenesis, Radiation Biology Center, Kyoto University, Kyoto (Japan); Ishida, Takafumi [Department of Cardiovascular Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima (Japan); Nagata, Yasushi [Department of Radiation Oncology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima (Japan); Tashiro, Satoshi, E-mail: ktashiro@hiroshima-u.ac.jp [Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima (Japan); Research Center for Mathematics of Chromatin Live Dynamics, Hiroshima University, Hiroshima (Japan)

    2014-07-15

    Purpose: The reorganization of damaged chromatin plays an important role in the regulation of the DNA damage response. A recent study revealed the presence of 2 vertebrate H2A.Z isoforms, H2A.Z-1 and H2A.Z-2. However, the roles of the vertebrate H2A.Z isoforms are still unclear. Thus, in this study we examined the roles of the vertebrate H2A.Z isoforms in chromatin reorganization after the induction of DNA double-strand breaks (DSBs). Methods and Materials: To examine the dynamics of H2A.Z isoforms at damaged sites, we constructed GM0637 cells stably expressing each of the green fluorescent protein (GFP)-labeled H2A.Z isoforms, and performed fluorescence recovery after photobleaching (FRAP) analysis and inverted FRAP analysis in combination with microirradiation. Immunofluorescence staining using an anti-RAD51 antibody was performed to study the kinetics of RAD51 foci formation after 2-Gy irradiation of wild-type (WT), H2A.Z-1- and H2A.Z-2-deficient DT40 cells. Colony-forming assays were also performed to compare the survival rates of WT, H2A.Z-1-, and H2A.Z-2-deficient DT40 cells with control, and H2A.Z-1- and H2A.Z-2-depleted U2OS cells after irradiation. Results: FRAP analysis revealed that H2A.Z-2 was incorporated into damaged chromatin just after the induction of DSBs, whereas H2A.Z-1 remained essentially unchanged. Inverted FRAP analysis showed that H2A.Z-2 was released from damaged chromatin. These findings indicated that H2A.Z-2 was exchanged at DSB sites immediately after the induction of DSBs. RAD51 focus formation after ionizing irradiation was disturbed in H2A.Z-2-deficient DT40 cells but not in H2A.Z-1-deficient cells. The survival rate of H2A.Z-2-deficient cells after irradiation was lower than those of WT and H2A.Z-1- DT40 cells. Similar to DT40 cells, H2A.Z-2-depleted U2OS cells were also radiation-sensitive compared to control and H2A.Z-1-depleted cells. Conclusions: We found that vertebrate H2A.Z-2 is involved in the regulation of the DNA

  1. Reorganization of Damaged Chromatin by the Exchange of Histone Variant H2A.Z-2

    International Nuclear Information System (INIS)

    Purpose: The reorganization of damaged chromatin plays an important role in the regulation of the DNA damage response. A recent study revealed the presence of 2 vertebrate H2A.Z isoforms, H2A.Z-1 and H2A.Z-2. However, the roles of the vertebrate H2A.Z isoforms are still unclear. Thus, in this study we examined the roles of the vertebrate H2A.Z isoforms in chromatin reorganization after the induction of DNA double-strand breaks (DSBs). Methods and Materials: To examine the dynamics of H2A.Z isoforms at damaged sites, we constructed GM0637 cells stably expressing each of the green fluorescent protein (GFP)-labeled H2A.Z isoforms, and performed fluorescence recovery after photobleaching (FRAP) analysis and inverted FRAP analysis in combination with microirradiation. Immunofluorescence staining using an anti-RAD51 antibody was performed to study the kinetics of RAD51 foci formation after 2-Gy irradiation of wild-type (WT), H2A.Z-1- and H2A.Z-2-deficient DT40 cells. Colony-forming assays were also performed to compare the survival rates of WT, H2A.Z-1-, and H2A.Z-2-deficient DT40 cells with control, and H2A.Z-1- and H2A.Z-2-depleted U2OS cells after irradiation. Results: FRAP analysis revealed that H2A.Z-2 was incorporated into damaged chromatin just after the induction of DSBs, whereas H2A.Z-1 remained essentially unchanged. Inverted FRAP analysis showed that H2A.Z-2 was released from damaged chromatin. These findings indicated that H2A.Z-2 was exchanged at DSB sites immediately after the induction of DSBs. RAD51 focus formation after ionizing irradiation was disturbed in H2A.Z-2-deficient DT40 cells but not in H2A.Z-1-deficient cells. The survival rate of H2A.Z-2-deficient cells after irradiation was lower than those of WT and H2A.Z-1- DT40 cells. Similar to DT40 cells, H2A.Z-2-depleted U2OS cells were also radiation-sensitive compared to control and H2A.Z-1-depleted cells. Conclusions: We found that vertebrate H2A.Z-2 is involved in the regulation of the DNA

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

    Directory of Open Access Journals (Sweden)

    Antonio Rodríguez-Campos

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

  3. Reliability of hard plastic clad silica fibers

    Science.gov (United States)

    Skutnik, Bolesh J.; Spaniol, Stefan

    2006-04-01

    New formulations of cladding materials have become available in recent times for Hard Plastic Clad Silica (HPCS) fibers, Initial data showed gains in some properties, particularly dynamic strength, especially for high numerical aperture (NA) fibers. A systematic study has been undertaken to determine the full strength and fatigue behavior of these HPCS fibers and to make comparisons to earlier HPCS fibers. Preliminary results, now confirmed, has shown improved median dynamic strength and higher Weibull slope. Full results are presented below including fatigue behavior and optical properties. These fibers have many applications and benefits in the high power delivery and medical laser uses as highlighted below. High power diode laser systems with their laser diode bars and arrays not only require special fibers to couple directly to the diode emitters, but also require special fibers to couple from the laser to application sites. These latter power delivery fibers are much larger than the internal fibers but still must be flexible, and have not only good strength but also good fatigue behavior. This particularly important industrial systems using robotic arms to apply the high power laser energy at a treatment site. The optical properties of HPCS fibers are well suited for the needs of the delivery of high power from diode laser bars and arrays to an application site. Benefits of strong median dynamic strengths and tighter flaw distributions in such cases will be discussed. Many medical applications, especially endoscopic ones, can benefit from the use of highly flexible, high NA, cost effective, HPCS optical fibers. Benefits of high strength and good fatigue behavior for such fibers in endoscopic procedures, including laser surgery, are discussed briefly including implications for mechanical reliability in medical and industrial settings.

  4. Carcinogen-inflicted DNA damage causes a dramatic increase in the degradation of chromatin-bound poly(ADP-ribose) in mammalian cells

    International Nuclear Information System (INIS)

    A characteristic response of eukaryotic cells to treatment with carcinogens is de novo poly(ADP-ribosylation) of chromatin proteins, a reaction which acts to modulate subsequent DNA excision repair by a hitherto unidentified molecular mechanism. DNA strand breaks represent the molecular signal which activates the chromatin enzyme poly(ADP-ribose) polymerase and thus stimulates poly(ADP-ribose) biosynthesis. They have now observed that carcinogen-inflicted DNA damage may also cause a more than 600-fold stimulation of the degradation of protein-bound poly(ADP-ribose) in chromatin of rat hepatocytes in primary culture. As a consequence, the metabolic half-life of the polymer decreases from 7.7 h in undamaged control cells to 5.5 min and 2.5 min following damage of cells with 45 and 150 J/m2 of UV light of 254 nm, respectively. Similarly, damage of hepatocellular DNA inflicted with either 20, 50 or 200 μM N-methyl-N'-nitro-N-nitrosoguanidine, a monofunctional alkylating agent, caused a dramatic decrease in the polymer half-life to 5.1 min, 2.3 min, and 41 sec, respectively. Therefore, their results suggest that the dynamic removal of polymeric ADP-ribose residues from their chromatin acceptors represents an obligatory postincisional event in DNA excision repair of mammalian cells

  5. Chromatin preparation and ChIP from Drosophila brain and discs tissues

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Constance Richter, Katarzyna Oktaba, Juerg Mueller & Juergen A. Knoblich ### Abstract Chromatin preparation and chromatin immunoprecipitation (ChIP) protocol as described in Oktaba et al., 2008, Dev Cell, 15, 877-89. The protocol includes description of chromatin preparation from larval tissues, ChIP and quantitative analysis of ChIP material. ### Procedure **1. First “fast” dissection**: Dissect for 20 minutes third instar larvae in ice-cold PBS and remove gu...

  6. A chromatin activity based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing

    OpenAIRE

    Liu, Cui; Yu, Yanbao; Liu, Feng; Wei, Xin; Wrobel, John A; Gunawardena, Harsha P.; Zhou, Li; Jin, Jian; Chen, Xian

    2014-01-01

    Immune cells develop endotoxin tolerance (ET) after prolonged stimulation. ET increases the level of a repression mark H3K9me2 in the transcriptional-silent chromatin specifically associated with pro-inflammatory genes. However, it is not clear what proteins are functionally involved in this process. Here we show that a novel chromatin activity based chemoproteomic (ChaC) approach can dissect the functional chromatin protein complexes that regulate ET-associated inflammation. Using UNC0638 th...

  7. A critical role for chromatin in mounting a synergistic transcriptional response to GAL4-VP16.

    OpenAIRE

    Chang, C; Gralla, J D

    1994-01-01

    The role of chromatin in mounting a synergistic transcriptional response to GAL4-VP16 was investigated. Strong synergy was observed when chromatin templates were used in vitro. The synergy was severely reduced when naked DNA templates were transcribed. In vivo synergy was strong when nonreplicating templates were used. However, the use of replicating templates, which involved transient disruptions of chromatin, led to strong reductions in synergy. In both of these low-synergy responses, trans...

  8. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species

    OpenAIRE

    Lee, Hye-Ran; Zhang, Wenli; Langdon, Tim; Jin, Weiwei; Yan, Huihuang; Cheng, Zhukuan; Jiang, Jiming

    2005-01-01

    The functional centromeres of rice (Oryza sativa, AA genome) chromosomes contain two key DNA components: the CRR centromeric retrotransposons and a 155-bp satellite repeat, CentO. However, several wild Oryza species lack the CentO repeat. We developed a chromatin immunoprecipitation-based technique to clone DNA fragments derived from chromatin containing the centromeric histone H3 variant CenH3. Chromatin immunoprecipitation cloning was carried out in the CentO-less species Oryza rhizomatis (...

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

    OpenAIRE

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

    2007-01-01

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

  10. Tunable Beam Diffraction in Infiltrated Microstructured Fibers

    DEFF Research Database (Denmark)

    Rosberg, Christian Romer; Bennet, Francis H.; Neshev, Dragomir N.;

    We experimentally study beam propagation in two dimensional photonic lattices in microstructured optical fibers infiltrated with high index liquids. We demonstrate strongly tunable beam diffraction by dynamically varying the coupling between individual lattice sites.......We experimentally study beam propagation in two dimensional photonic lattices in microstructured optical fibers infiltrated with high index liquids. We demonstrate strongly tunable beam diffraction by dynamically varying the coupling between individual lattice sites....

  11. Evolution of histone 2A for chromatin compaction in eukaryotes

    OpenAIRE

    Macadangdang, Benjamin R; Oberai, Amit; Spektor, Tanya; Campos, Oscar A; Sheng, Fang; Carey, Michael F.; Vogelauer, Maria; Kurdistani, Siavash K

    2014-01-01

    eLife digest There are up to three meters of DNA in a human cell. To fit this length into the cell's nucleus in an organized manner, DNA is wrapped around proteins called histones and then tightly packaged to form a structure called chromatin. The interaction between the histones and the DNA is helped by certain amino acids on the surface of the histones fitting snugly into the DNA molecule. Plants and animals have genomes that are significantly larger than those of single-celled organisms. H...

  12. Effects of nuclear isolation on psoralen affinity for chromatin

    International Nuclear Information System (INIS)

    We have tested the effects of nuclear isolation on intercalation of TMP (a psoralen) at specific sequences and in total DNA of cultured human cells. DNA in nuclei photobound about 20% more TMP than in cells and about 10% as much as purified DNA. In contrast, a transcribed ras gene and a randomly selected polymorphic sequence each bound about 20% more TMP than total DNA in cells. However, in nuclei, as in purified DNA, both sequences were just as sensitive as total DNA. Apparently, chromatin in cells exists within diverse TMP-binding environments and some of this diversity was lost upon nuclear isolation

  13. Chromatin immunoselection defines a TAL-1 target gene.

    OpenAIRE

    Cohen-Kaminsky, S; Maouche-Chrétien, L; Vitelli, L; Vinit, M A; Blanchard, I; M. Yamamoto; Peschle, C; Roméo, P H

    1998-01-01

    Despite the major functions of the basic helix-loop-helix transcription factor TAL-1 in hematopoiesis and T-cell leukemogenesis, no TAL-1 target gene has been identified. Using immunoprecipitation of genomic fragments bound to TAL-1 in the chromatin of murine erythro-leukemia (MEL) cells, we found that 10% of the immunoselected fragments contained a CAGATG or a CAGGTG E-box, followed by a GATA site. We studied one of these fragments containing two E-boxes, CAGATG and CAGGTC, followed by a GAT...

  14. 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.

  15. Specialty fibers for high power fiber lasers

    OpenAIRE

    Jayanta K. Sahu; Jain, Deepak; Jung, Yongmin

    2015-01-01

    This paper reviews our recent work on novel large-mode area fibers for high power lasers and amplifiers. An ultra-low-NA fiber and single-trench fiber have been proposed for mode area scaling of the fundamental mode. In case of single trench fiber design, resonant coupling of the higher order modes has been exploited to achieve effective single mode operation in fiber with large effective mode area. Our proposed fiber designs are easy to fabricate using conventional low-loss fiber fabrication...

  16. Erythroid-specific gene chromatin has an altered association with linker histones.

    OpenAIRE

    Ridsdale, J A; Rattner, J.B.; Davie, J R

    1988-01-01

    The chromatin of several genes was assayed for sensitivity to DNAase I and for solubility as polynucleosomes in 0.15 M NaCl. The degree of solubility of chromatin fragments as polynucleosomes in 0.15 M NaCl correlates well with the sensitivity to DNAase I for several genes. Chromatin of repressed, housekeeping and erythroid-specific genes can be distinguished as distinct groups by the degree to which they display these properties. NaCl precipitation of chromatin fragments stripped and then re...

  17. Protein phosphatases and chromatin modifying complexes in the inflammatory cascade in acute pancreatitis

    Directory of Open Access Journals (Sweden)

    Javier Escobar

    2010-06-01

    Full Text Available Acute pancreatitis is an inflammation of the pancreas that may lead to systemic inflammatory response syndrome and death due to multiple organ failure. Acinar cells, together with leukocytes, trigger the inflammatory cascade in response to local damage of the pancreas. Amplification of the inflammatory cascade requires up-regulation of pro-inflammatory cytokines and this process is mediated not only by nuclear factor κB but also by chromatin modifying complexes and chromatin remodeling. Among the different families of histone acetyltransferases, the p300/CBP family seems to be particularly associated with the inflammatory process. cAMP activates gene expression via the cAMP-responsive element (CRE and the transcription factor CRE-binding protein (CREB. CREB can be phosphorylated and activated by different kinases, such as protein kinase A and MAPK, and then it recruits the histone acetyltransferase co-activator CREB-binding protein (CBP and its homologue p300. The recruitment of CBP/p300 and changes in the level of histone acetylation are required for transcription activation. Transcriptional repression is also a dynamic and essential mechanism of down-regulation of genes for resolution of inflammation, which seems to be mediated mainly by protein phosphatases (PP1, PP2A and MKP1 and histone deacetylases (HDACs. Class II HDACs are key transcriptional regulators whose activities are controlled via phosphorylation-dependent nucleo/cytoplasmic shuttling. PP2A is responsible for dephosphorylation of class II HDACs, triggering nuclear localization and repression of target genes, whereas phosphorylation triggers cytoplasmic localization leading to activation of target genes. The potential benefit from treatment with phosphodiesterase inhibitors and histone deacetylase inhibitors is discussed.

  18. Overexpression of Chromatin Assembly Factor-1/p60 helps to predict the prognosis of melanoma patients

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    Nugnes Loredana

    2010-02-01

    Full Text Available Abstract Background Cutaneous melanoma (CM is the most lethal form of skin malignancy, which registers a constant increase in incidence worldwide. The identification of molecular alteration(s involved in its biological aggressiveness represents a major challenge for researchers, considering that existing therapies are ineffective to treat metastasizing cases. The epigenetic control of chromatin dynamics during DNA synthesis, replication, and repair is fundamental for the orderly progression of cell proliferation. The Chromatin Assembly Factor 1 (CAF-1 complex acts as a major regulator of this process; its intermediate (p60 subunit has been recently proposed as a novel proliferation and prognostic marker for several tumors. We aimed to establish if the evaluation of the expression of CAF-1/p60 in primary CM may help define the prevision of outcome of patients. Methods Immunohistochemistry with anti-CAF-1/p60 was performed on paraffin-embedded tissue sections of 130 cases of primary CM retrieved from the archive files of the Department of Biomorphological and Functional Sciences, Section of Pathology, University "Federico II" of Naples, Italy. Results were compared with histopathological and follow-up data of patients. Results CAF-1/p60 was expressed in all CM. A significant statistical association between the overexpression of the protein and the occurrence of skin, node and/or distant metastases (P Conclusions CAF-1/p60 looks promising as a new prognostic marker for CM and sheds new light on the molecular events associated with photocancerogenesis and melanoma biology. The screening for CAF-1/p60 might contribute to the molecular sub-classification of CM, with improved translational outcomes.

  19. Virion protein 16 induces demethylation of DNA integrated within chromatin in a novel mammalian cell model

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    Lu Yang; Huijun Wang; Xin Luo; Pengliang Mao; Weidong Tian; Yujiang Shi; Guoying Huang; Jin Zhang; Duan Ma

    2012-01-01

    DNA methylation and demethylation play important roles in mediating epigenetic regulation.So far,the mechanism of DNA demethylation remains elusive and controversial.Here,we constructed a plasmid,named with pCBS-luc,that contained an artificial CpG island,eight Gal4 DNA-binding domain binding site,an SV40 promoter,and a firefly luciferase reporter gene.The linearized pCBS-luc plasmid was methylated in vitro by DNA methyltransferase, and transfected into the HEK293 cells.The stable HEK293 transfectants with methylated pCBS-luc (me-pCBS-luc) were selected and obtained.The methylation status of the selected stable cell lines were confirmed by bisulfite sequencing polymerase chain reaction amplification.The methylation status could be maintained even after 15 passages.The virion protein 16 (VP16) was reported to enhance DNA demethylation around its binding sites of the promoter region in Xenopus fertilized eggs.Using our me-pCBS-luc model,we found that VP16 also had the ability to activate the expression of methylated luciferase reporter gene and induce DNA demethylation in chromatin DNA in mammalian cells.Altogether,we constructed a cell model stably integrated with the me-pCBS-luc reporter plasmid,and in this model we found that VP16 could lead to DNA demethylation.We believe that this cell model will have many potential applications in the future research on DNA demethylation and dynamic process of chromatin modification.

  20. Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger

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    Wang, Gang G.; Song, Jikui; Wang, Zhanxin; Dormann, Holger L.; Casadio, Fabio; Li, Haitao; Luo, Jun-Li; Patel, Dinshaw J.; Allis, C. David; (MSKCC); (Scripps); (Rockefeller)

    2009-07-21

    Histone H3 lysine4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98-PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development.