WorldWideScience

Sample records for characterizing nucleosome dynamics

  1. Nucleosome dynamics: Sequence matters.

    Science.gov (United States)

    Eslami-Mossallam, Behrouz; Schiessel, Helmut; van Noort, John

    2016-06-01

    About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly conserved in evolution, nucleosomes can be very different from each other due to posttranslational modifications of the histones. Another crucial factor in making nucleosomes unique has so far been underappreciated: the sequence of their DNA. This review provides an overview of the experimental and theoretical progress that increasingly points to the importance of the nucleosomal base pair sequence. Specifically, we discuss the role of the underlying base pair sequence in nucleosome positioning, sliding, breathing, force-induced unwrapping, dissociation and partial assembly and also how the sequence can influence higher-order structures. A new view emerges: the physical properties of nucleosomes, especially their dynamical properties, are determined to a large extent by the mechanical properties of their DNA, which in turn depends on DNA sequence. PMID:26896338

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

    Directory of Open Access Journals (Sweden)

    Anna Schrader

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

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

    Directory of Open Access Journals (Sweden)

    Alexey K. Shaytan

    2016-06-01

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

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

    OpenAIRE

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

  6. 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

  7. Structure, dynamics, and evolution of centromeric nucleosomes

    OpenAIRE

    Dalal, Yamini; Furuyama, Takehito; Vermaak, Danielle; Henikoff, Steven

    2007-01-01

    Centromeres are defining features of eukaryotic chromosomes, providing sites of attachment for segregation during mitosis and meiosis. The fundamental unit of centromere structure is the centromeric nucleosome, which differs from the conventional nucleosome by the presence of a centromere-specific histone variant (CenH3) in place of canonical H3. We have shown that the CenH3 nucleosome core found in interphase Drosophila cells is a heterotypic tetramer, a “hemisome” consisting of one molecule...

  8. Rigid-body molecular dynamics of DNA inside a nucleosome.

    Science.gov (United States)

    Fathizadeh, Arman; Berdy Besya, Azim; Reza Ejtehadi, Mohammad; Schiessel, Helmut

    2013-03-01

    The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use Kramers theory to calculate nucleosome sliding caused by such defects. It is shown that the twist defect scenario together with the sequence-dependent elasticity of DNA can explain the slow time scales observed for nucleosome mobility along DNA. With this method we also show how the twist defect mechanism leads to a higher mobility of DNA in the presence of sin mutations near the dyad axis. Finally, by performing simulations on 5s rDNA, 601, and telomeric base pair sequences, it is demonstrated that the current model is a powerful tool to predict nucleosome positioning. PMID:23475204

  9. Biophysical Characterization of the Centromere-specific Nucleosome from Budding Yeast*

    OpenAIRE

    Kingston, Isabel J.; Yung, Jasmine S. Y.; Singleton, Martin R

    2010-01-01

    The centromeric DNA of all eukaryotes is assembled upon a specialized nucleosome containing a histone H3 variant known as CenH3. Despite the importance and conserved nature of this protein, the characteristics of the centromeric nucleosome are still poorly understood. In particular, the stoichiometry and DNA-binding properties of the CenH3 nucleosome have been the subject of some debate. We have characterized the budding yeast centromeric nucleosome by biochemical and biophysical methods and ...

  10. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

    Science.gov (United States)

    Pasi, Marco; Lavery, Richard

    2016-01-01

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

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

    Directory of Open Access Journals (Sweden)

    Steven E Weicksel

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

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

    OpenAIRE

    Fransz, P.; Jong, de, M.C.M.

    2011-01-01

    Gene activity is controlled at different levels of chromatin organization, which involve genomic sequences, nucleosome structure, chromatin folding and chromosome arrangement. These levels are interconnected and influence each other. At the basic level nucleosomes generally occlude the DNA sequence from interacting with DNA-binding proteins. Evidently, nucleosome positioning is a major factor in gene control and chromatin organization. Understanding the biological rules that govern the deposi...

  13. 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

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

    Directory of Open Access Journals (Sweden)

    Rifka Vlijm

    2015-01-01

    Full Text Available DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length of single DNA molecules, we monitor the real-time loading of tetramers or complete histone octamers onto DNA by Nucleosome Assembly Protein-1 (NAP1. Remarkably, we find that tetrasomes exhibit spontaneous flipping between a preferentially occupied left-handed state (ΔLk = −0.73 and a right-handed state (ΔLk = +1.0, separated by a free energy difference of 2.3 kBT (1.5 kcal/mol. This flipping occurs without concomitant changes in DNA end-to-end length. The application of weak positive torque converts left-handed tetrasomes into right-handed tetrasomes, whereas nucleosomes display more gradual conformational changes. Our findings reveal unexpected dynamical rearrangements of the nucleosomal structure, suggesting that chromatin can serve as a “twist reservoir,” offering a mechanistic explanation for the regulation of DNA supercoiling in chromatin.

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

    OpenAIRE

    Yingxue Ren; Vera, Daniel L.; Kimberly A. Hughes; Dennis, Jonathan H.

    2015-01-01

    In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, nucleosome dynamics during a genome response have not been well characterized [1,2]. We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the imm...

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

    Science.gov (United States)

    Howell, Steven C.

    Chromatin conformation and dynamics remains unsolved despite the critical role of the chromatin in fundamental genetic functions such as transcription, replication, and repair. At the molecular level, chromatin can be viewed as a linear array of nucleosomes, each consisting of 147 base pairs (bp) of double-stranded DNA (dsDNA) wrapped around a protein core and connected by 10 to 90 bp of linker dsDNA. Using small-angle X-ray scattering (SAXS), we investigated how the conformations of model nucleosome arrays in solution are modulated by ionic condition as well as the effect of linker histone proteins. To facilitate ensemble modeling of these SAXS measurements, we developed a simulation method that treats coarse-grained DNA as a Markov chain, then explores possible DNA conformations using Metropolis Monte Carlo (MC) sampling. This algorithm extends the functionality of SASSIE, a program used to model intrinsically disordered biological molecules, adding to the previous methods for simulating protein, carbohydrates, and single-stranded DNA. Our SAXS measurements of various nucleosome arrays together with the MC generated models provide valuable solution structure information identifying specific differences from the structure of crystallized arrays.

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

    Science.gov (United States)

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

    2014-08-01

    In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. We show that the regulatory properties of the two promoter types are remarkably similar, suggesting that they are determined to a large extent by Rap1 and the Fhl1/Ifh1 pair. Rapid depletion experiments allowed us to define a hierarchy of TF binding in which Rap1 acts as a pioneer factor required for binding of all other TFs. We also uncovered unexpected features underlying recruitment of Fhl1, whose forkhead DNA-binding domain is not required for binding at most promoters, and Hmo1, whose binding is supported by repeated motifs. Finally, we describe unusually micrococcal nuclease (MNase)-sensitive nucleosomes at all RPG promoters, located between the canonical +1 and -1 nucleosomes, which coincide with sites of Fhl1/Ifh1 and Hmo1 binding. We speculate that these "fragile" nucleosomes play an important role in regulating RPG transcriptional output. PMID:25085421

  18. Nucleosome Organization in Human Embryonic Stem Cells.

    Directory of Open Access Journals (Sweden)

    Puya G Yazdi

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

  19. Effects of macroH2A and H2A.Z on nucleosome structure and dynamics as elucidated by molecular dynamics simulations

    CERN Document Server

    Bowerman, Samuel

    2015-01-01

    Eukaryotes tune the transcriptional activity of their genome by altering the nucleosome core particle through multiple chemical processes. In particular, replacement of the canonical H2A histone with the variants macroH2A and H2A.Z has been shown to affect DNA accessibility and nucleosome stability; however, the processes by which this occurs remain poorly understood. Here, we elucidate the molecular mechanisms of these variants with an extensive molecular dynamics study of the canonical nucleosome along with three variant-containing structures: H2A.Z, macroH2A, and an H2A mutant with macroH2A-like L1 loops. Simulation results show that variant L1 loops play a pivotal role in stabilizing DNA binding to the octamer through direct interactions, core structural rearrangements, and altered allosteric networks in the nucleosome. All variants influence dynamics; however, macroH2A-like systems have the largest effect on energetics. In addition, we provide a comprehensive analysis of allosteric networks in the nucleo...

  20. UV Damage in DNA Promotes Nucleosome Unwrapping*

    OpenAIRE

    Duan, Ming-Rui; Smerdon, Michael J.

    2010-01-01

    The association of DNA with histones in chromatin impedes DNA repair enzymes from accessing DNA lesions. Nucleosomes exist in a dynamic equilibrium in which portions of the DNA molecule spontaneously unwrap, transiently exposing buried DNA sites. Thus, nucleosome dynamics in certain regions of chromatin may provide the exposure time and space needed for efficient repair of buried DNA lesions. We have used FRET and restriction enzyme accessibility to study nucleosome dynamics following DNA dam...

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

    Directory of Open Access Journals (Sweden)

    Yingxue Ren

    2015-03-01

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

  2. Two distinct modes of nucleosome modulation associated with different degrees of dependence of nucleosome positioning on the underlying DNA sequence

    Directory of Open Access Journals (Sweden)

    Wang Jiang

    2009-01-01

    Full Text Available Abstract Background The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning plays a central role in diverse cellular processes that rely on access to genomic DNA. Experimental evidence suggests that the genomic DNA sequence is one important determinant of nucleosome positioning. Yet it is less clear whether the role of the underlying DNA sequence in nucleosome positioning varies across different promoters. Whether different determinants of nucleosome positioning have characteristic influences on nucleosome modulation also remains to be elucidated. Results We identified two typical promoter classes in yeast associated with high or low dependence of nucleosome positioning on the underlying DNA sequence, respectively. Importantly, the two classes have low or high intrinsic sequence preferences for nucleosomes, respectively. The two classes are further distinguished by multiple promoter features, including nucleosome occupancy, nucleosome fuzziness, H2A.Z occupancy, changes in nucleosome positions before and after transcriptional perturbation, and gene activity. Both classes have significantly high turnover rates of histone H3, but employ distinct modes of nucleosome modulation: The first class is characterized by hyperacetylation, whereas the second class is highly regulated by ATP-dependent chromatin remodelling. Conclusion Our results, coupled with the known features of nucleosome modulation, suggest that the two distinct modes of nucleosome modulation selectively employed by different genes are linked with the intrinsic sequence preferences for nucleosomes. The difference in modes of nucleosome modulation can account for the difference in the contribution of DNA sequence to nucleosome positioning between both promoter classes.

  3. Methylation of Lysine 9 in Histone H3 Directs Alternative Modes of Highly Dynamic Interaction of Heterochromatin Protein hHP1β with the Nucleosome*

    Science.gov (United States)

    Munari, Francesca; Soeroes, Szabolcs; Zenn, Hans Michael; Schomburg, Adrian; Kost, Nils; Schröder, Sabrina; Klingberg, Rebecca; Rezaei-Ghaleh, Nasrollah; Stützer, Alexandra; Gelato, Kathy Ann; Walla, Peter Jomo; Becker, Stefan; Schwarzer, Dirk; Zimmermann, Bastian; Fischle, Wolfgang; Zweckstetter, Markus

    2012-01-01

    Binding of heterochromatin protein 1 (HP1) to the histone H3 lysine 9 trimethylation (H3K9me3) mark is a hallmark of establishment and maintenance of heterochromatin. Although genetic and cell biological aspects have been elucidated, the molecular details of HP1 binding to H3K9me3 nucleosomes are unknown. Using a combination of NMR spectroscopy and biophysical measurements on fully defined recombinant experimental systems, we demonstrate that H3K9me3 works as an on/off switch regulating distinct binding modes of hHP1β to the nucleosome. The methyl-mark determines a highly flexible and very dynamic interaction of the chromodomain of hHP1β with the H3-tail. There are no other constraints of interaction or additional multimerization interfaces. In contrast, in the absence of methylation, the hinge region and the N-terminal tail form weak nucleosome contacts mainly with DNA. In agreement with the high flexibility within the hHP1β-H3K9me3 nucleosome complex, the chromoshadow domain does not provide a direct binding interface. Our results report the first detailed structural analysis of a dynamic protein-nucleosome complex directed by a histone modification and provide a conceptual framework for understanding similar interactions in the context of chromatin. PMID:22815475

  4. Methylation of lysine 9 in histone H3 directs alternative modes of highly dynamic interaction of heterochromatin protein hHP1β with the nucleosome.

    Science.gov (United States)

    Munari, Francesca; Soeroes, Szabolcs; Zenn, Hans Michael; Schomburg, Adrian; Kost, Nils; Schröder, Sabrina; Klingberg, Rebecca; Rezaei-Ghaleh, Nasrollah; Stützer, Alexandra; Gelato, Kathy Ann; Walla, Peter Jomo; Becker, Stefan; Schwarzer, Dirk; Zimmermann, Bastian; Fischle, Wolfgang; Zweckstetter, Markus

    2012-09-28

    Binding of heterochromatin protein 1 (HP1) to the histone H3 lysine 9 trimethylation (H3K9me3) mark is a hallmark of establishment and maintenance of heterochromatin. Although genetic and cell biological aspects have been elucidated, the molecular details of HP1 binding to H3K9me3 nucleosomes are unknown. Using a combination of NMR spectroscopy and biophysical measurements on fully defined recombinant experimental systems, we demonstrate that H3K9me3 works as an on/off switch regulating distinct binding modes of hHP1β to the nucleosome. The methyl-mark determines a highly flexible and very dynamic interaction of the chromodomain of hHP1β with the H3-tail. There are no other constraints of interaction or additional multimerization interfaces. In contrast, in the absence of methylation, the hinge region and the N-terminal tail form weak nucleosome contacts mainly with DNA. In agreement with the high flexibility within the hHP1β-H3K9me3 nucleosome complex, the chromoshadow domain does not provide a direct binding interface. Our results report the first detailed structural analysis of a dynamic protein-nucleosome complex directed by a histone modification and provide a conceptual framework for understanding similar interactions in the context of chromatin. PMID:22815475

  5. Why Do Nucleosomes Unwrap Asymmetrically?

    Science.gov (United States)

    de Bruin, Lennart; Tompitak, Marco; Eslami-Mossallam, Behrouz; Schiessel, Helmut

    2016-07-01

    Nucleosomes, DNA spools with a protein core, engage about three-quarters of eukaryotic DNA and play a critical role in chromosomal processes, ranging from gene regulation, recombination, and replication to chromosome condensation. For more than a decade, micromanipulation experiments where nucleosomes are put under tension, as well as the theoretical interpretations of these experiments, have deepened our understanding of the stability and dynamics of nucleosomes. Here we give a theoretical explanation for a surprising new experimental finding: nucleosomes wrapped onto the 601 positioning sequence (the sequence used in most laboratories) respond highly asymmetrically to external forces by always unwrapping from the same end. Using a computational nucleosome model, we show that this asymmetry can be explained by differences in the DNA mechanics of two very short stretches on the wrapped DNA portion. Our finding suggests that the physical properties of nucleosomes, here the response to forces, can be tuned locally by the choice of the underlying base-pair sequence. This leads to a new view of nucleosomes: a physically highly varied set of DNA-protein complexes whose properties can be tuned on evolutionary time scales to their specific function in the genomic context. PMID:26991771

  6. Monitoring Conformational Dynamics with Single-Molecule Fluorescence Energy Transfer: Applications in Nucleosome Remodeling

    Science.gov (United States)

    Deindl, Sebastian; Zhuang, Xiaowei

    2016-01-01

    Due to its ability to track distance changes within individual molecules or molecular complexes on the nanometer scale and in real time, single-molecule fluorescence resonance energy transfer (single-molecule FRET) is a powerful tool to tackle a wide range of important biological questions. Using our recently developed single-molecule FRET assay to monitor nucleosome translocation as an illustrative example, we describe here in detail how to set up, carry out, and analyze single-molecule FRET experiments that provide time-dependent information on biomolecular processes. PMID:22929765

  7. Sequence-dependent nucleosome structural and dynamic polymorphism. Potential involvement of histone H2B N-terminal tail proximal domain.

    Science.gov (United States)

    Sivolob, Andrei; Lavelle, Christophe; Prunell, Ariel

    2003-02-01

    Relaxation of nucleosomes on an homologous series (pBR) of ca 350-370 bp DNA minicircles originating from plasmid pBR322 was recently used as a tool to study their structure and dynamics. These nucleosomes thermally fluctuated between three distinct DNA conformations within a histone N-terminal tail-modulated equilibrium: one conformation was canonical, with 1.75 turn wrapping and negatively crossed entering and exiting DNAs; another was also "closed", but with these DNAs positively crossed; and the third was "open", with a lower than 1.5 turn wrapping and uncrossed DNAs. In this work, a new minicircle series (5S) of similar size was used, which contained the 5S nucleosome positioning sequence. Results showed that DNA in pBR nucleosomes was untwisted by approximately 0.2 turn relative to 5S nucleosomes, which DNase I footprinting confirmed in revealing a approximately 1 bp untwisting at each of the two dyad-distal sites where H2B N-terminal tails pass between the two gyres. In contrast, both nucleosomes showed untwistings at the dyad-proximal sites, i.e. on the other gyre, which were also observed in the high-resolution crystal structure. 5S nucleosomes also differ with respect to their dynamics: they hardly accessed the positively crossed conformation, but had an easier access to the negatively crossed conformation. Simulation showed that such reverse effects on the conformational free energies could be simply achieved by slightly altering the trajectories of entering and exiting DNAs. We propose that this is accomplished by H2B tail untwisting at the distal sites through action at a distance ( approximately 20 bp) on H3-tail interactions with the small groove at the nucleosome entry-exit. These results may help to gain a first glimpse into the two perhaps most intriguing features of the high-resolution structure: the alignment of the grooves on the two gyres and the passage of H2B and H3 N-terminal tails between them. PMID:12547190

  8. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.

    Science.gov (United States)

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

    2016-01-16

    An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies. PMID:26699921

  9. AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and sliding

    CERN Document Server

    Montel, Fabien; Saint-Jean, Philippe; Castelnovo, Martin; Moskalenko-Faivre, Cendrine

    2007-01-01

    We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA complexed length distribution and nucleosome position in various contexts. First, we show that differences in the nucleo-proteic structure observed between conventional H2A and H2A.Bbd variant nucleosomes induce quantitative changes in the in the length distribution of DNA complexed with histones. Then, the sliding action of remodeling complex SWI/SNF is characterized through the evolution of the nucleosome position and wrapped DNA length mapping. Using a linear energetic model for the distribution of DNA complexed length, we extract the net wrapping energy of DNA onto the histone octamer, and compare it to previous studies.

  10. Theoretical analysis of epigenetic cell memory by nucleosome modification.

    Science.gov (United States)

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

    2007-05-18

    Chromosomal regions can adopt stable and heritable alternative states resulting in bistable gene expression without changes to the DNA sequence. Such epigenetic control is often associated with alternative covalent modifications of histones. The stability and heritability of the states are thought to involve positive feedback where modified nucleosomes recruit enzymes that similarly modify nearby nucleosomes. We developed a simplified stochastic model for dynamic nucleosome modification based on the silent mating-type region of the yeast Schizosaccharomyces pombe. We show that the mechanism can give strong bistability that is resistant both to high noise due to random gain or loss of nucleosome modifications and to random partitioning upon DNA replication. However, robust bistability required: (1) cooperativity, the activity of more than one modified nucleosome, in the modification reactions and (2) that nucleosomes occasionally stimulate modification beyond their neighbor nucleosomes, arguing against a simple continuous spreading of nucleosome modification. PMID:17512413

  11. Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae

    OpenAIRE

    Hongde Liu; Pingyan Wang; Lingjie Liu; Zhu Min; Kun Luo; Yakun Wan

    2015-01-01

    Nucleosome organization exhibits dynamic properties depending on the cell state and environment. Histone proteins, fundamental components of nucleosomes, are subject to chemical modifications on particular residues. We examined the effect of substituting modifiable residues of four core histones with the non-modifiable residue alanine on nucleosome dynamics. We mapped the genome-wide nucleosomes in 22 histone mutants of Saccharomyces cerevisiae and compared the nucleosome alterations relative...

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

    Directory of Open Access Journals (Sweden)

    Amber N Brown

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

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

    Science.gov (United States)

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

    2015-01-01

    Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug naïve positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse. PMID:26414157

  14. Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae

    Science.gov (United States)

    Liu, Hongde; Wang, Pingyan; Liu, Lingjie; Min, Zhu; Luo, Kun; Wan, Yakun

    2015-01-01

    Nucleosome organization exhibits dynamic properties depending on the cell state and environment. Histone proteins, fundamental components of nucleosomes, are subject to chemical modifications on particular residues. We examined the effect of substituting modifiable residues of four core histones with the non-modifiable residue alanine on nucleosome dynamics. We mapped the genome-wide nucleosomes in 22 histone mutants of Saccharomyces cerevisiae and compared the nucleosome alterations relative to the wild-type strain. Our results indicated that different types of histone mutation resulted in different phenotypes and a distinct reorganization of nucleosomes. Nucleosome occupancy was altered at telomeres, but not at centromeres. The first nucleosomes upstream (−1) and downstream (+1) of the transcription start site (TSS) were more dynamic than other nucleosomes. Mutations in histones affected the nucleosome array downstream of the TSS. Highly expressed genes, such as ribosome genes and genes involved in glycolysis, showed increased nucleosome occupancy in many types of histone mutant. In particular, the H3K56A mutant exhibited a high percentage of dynamic genomic regions, decreased nucleosome occupancy at telomeres, increased occupancy at the +1 and −1 nucleosomes, and a slow growth phenotype under stress conditions. Our findings provide insight into the influence of histone mutations on nucleosome dynamics. PMID:26498326

  15. Dynamic Histone Acetylation of H3K4me3 Nucleosome Regulates MCL1 Pre-mRNA Splicing.

    Science.gov (United States)

    Khan, Dilshad H; Gonzalez, Carolina; Tailor, Nikesh; Hamedani, Mohammad K; Leygue, Etienne; Davie, James R

    2016-10-01

    Pre-mRNA splicing is a cotranscriptional process affected by the chromatin architecture along the body of coding genes. Recruited to the pre-mRNA by splicing factors, histone deacetylases (HDACs) and K-acetyltransferases (KATs) catalyze dynamic histone acetylation along the gene. In colon carcinoma HCT 116 cells, HDAC inhibition specifically increased KAT2B occupancy as well as H3 and H4 acetylation of the H3K4 trimethylated (H3K4me3) nucleosome positioned over alternative exon 2 of the MCL1 gene, an event paralleled with the exclusion of exon 2. These results were reproduced in MDA-MB-231, but not in MCF7 breast adenocarcinoma cells. These later cells have much higher levels of demethylase KDM5B than either HCT 116 or MDA-MB-231 cells. We show that H3K4me3 steady-state levels and H3K4me3 occupancy at the end of exon 1 and over exon 2 of the MCL1 gene were lower in MCF7 than in MDA-MB-231 cells. Furthermore, in MCF7 cells, there was minimal effect of HDAC inhibition on H3/H4 acetylation and H3K4me3 levels along the MCL1 gene and no change in pre-mRNA splicing choice. These results show that, upon HDAC inhibition, the H3K4me3 mark plays a critical role in the exclusion of exon 2 from the MCL1 pre-mRNA. J. Cell. Physiol. 231: 2196-2204, 2016. © 2016 Wiley Periodicals, Inc. PMID:26864447

  16. Tetrameric Structure of Centromeric Nucleosomes in Interphase Drosophila Cells

    OpenAIRE

    Dalal, Yamini; Wang, Hongda; Lindsay, Stuart; Henikoff, Steven

    2007-01-01

    Author Summary The octameric structure of eukaryotic nucleosomes is universally accepted as the basic unit of chromatin. This is certainly the case for the vast bulk of nucleosomes; however, there have been no reports of the in vivo structure of nucleosomes associated with centromeres. Though centromeres make up only a minute fraction of the genomic landscape, their role in segregating chromosomes during mitosis is essential for maintaining genomic integrity. We report the characterization of...

  17. 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

  18. Nucleosome Positioning and Epigenetics

    Science.gov (United States)

    Schwab, David; Bruinsma, Robijn

    2008-03-01

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

  19. Baculoviruses and nucleosome management

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-15

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

  20. The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

    International Nuclear Information System (INIS)

    Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure. In this paper, we use normal mode analysis to detect significant structural deformations of nucleosomal DNA and investigate the relationship between periodic dinucleotides and DNA motions. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing that they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently

  1. Nucleosomes undergo slow spontaneous gaping

    OpenAIRE

    Ngo, Thuy T.M.; Ha, Taekjip

    2015-01-01

    In eukaryotes, DNA is packaged into a basic unit, the nucleosome which consists of 147 bp of DNA wrapped around a histone octamer composed of two copies each of the histones H2A, H2B, H3 and H4. Nucleosome structures are diverse not only by histone variants, histone modifications, histone composition but also through accommodating different conformational states such as DNA breathing and dimer splitting. Variation in nucleosome structures allows it to perform a variety of cellular functions. ...

  2. Centromeric nucleosomes induce positive supercoils

    OpenAIRE

    Furuyama, Takehito; Henikoff, Steven

    2009-01-01

    Centromeres of higher eukaryotes are epigenetically maintained, however, the mechanism that underlies centromere inheritance is unknown. Centromere identity and inheritance require the assembly of nucleosomes containing the CenH3 histone variant in place of canonical H3. Whereas H3 nucleosomes wrap DNA in a left-handed manner and induce negative supercoils, we show here that CenH3 nucleosomes that are reconstituted from Drosophila histones induce positive supercoils. Furthermore, we show that...

  3. DiNuP: a systematic approach to identify regions of differential nucleosome positioning

    OpenAIRE

    Fu, Kai; Tang, Qianzi; Feng, Jianxing; Liu, Xiaole Shirley; Zhang, Yong

    2012-01-01

    Motivation: With the rapid development of high-throughput sequencing technologies, the genome-wide profiling of nucleosome positioning has become increasingly affordable. Many future studies will investigate the dynamic behaviour of nucleosome positioning in cells that have different states or that are exposed to different conditions. However, a robust method to effectively identify the regions of differential nucleosome positioning (RDNPs) has not been previously available. Results: We descr...

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

    Science.gov (United States)

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

    2016-05-01

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

  6. New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome

    Directory of Open Access Journals (Sweden)

    Deng Yangyang

    2010-01-01

    discrepancy and consistency, reflects the mechanisms of nucleosome packaging in vivo more faithfully than individual studies. Furthermore, nucleosomes can be divided into two classes according to their stable and dynamic characteristics. We found that two different nucleosome-positioning characteristics may significantly impact transcription programs. Besides, some positioned-nucleosomes are involved in the transition from stable state to dynamic state in response to abrupt environmental changes.

  7. Divalent Metal- and High Mobility Group N Protein-Dependent Nucleosome Stability and Conformation

    Directory of Open Access Journals (Sweden)

    Michelle S. Ong

    2010-01-01

    Full Text Available High mobility group N proteins (HMGNs bind specifically to the nucleosome core and act as chromatin unfolding and activating factors. Using an all-Xenopus system, we found that HMGN1 and HMGN2 binding to nucleosomes results in distinct ion-dependent conformation and stability. HMGN2 association with nucleosome core particle or nucleosomal array in the presence of divalent metal triggers a reversible transition to a species with much reduced electrophoretic mobility, consistent with a less compact state of the nucleosome. Residues outside of the nucleosome binding domain are required for the activity, which is also displayed by an HMGN1 truncation product lacking part of the regulatory domain. In addition, thermal denaturation assays show that the presence of 1 mM Mg2+> or Ca2+ gives a reduction in nucleosome core terminus stability, which is further substantially diminished by the binding of HMGN2 or truncated HMGN1. Our findings emphasize the importance of divalent metals in nucleosome dynamics and suggest that the differential biological activities of HMGNs in chromatin activation may involve different conformational alterations and modulation of nucleosome core stability.

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

    Directory of Open Access Journals (Sweden)

    Gracey Lia E

    2010-07-01

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

  9. Methylation of K9 in histone H3 directs alternative modes of highly dynamic interaction of heterochromatin protein hHP1β with the nucleosome.

    OpenAIRE

    Munari, F; Soeroes, S.; Zenn, H.; Schomburg, A.; Kost, N.; Schröder, S.; Klingberg, R.; Rezaei-Ghaleh, N.; Stützer, A.; Gelato, K.; Walla, P; Becker, S.; Schwarzer, D; Zimmermann, B.; Fischle, W

    2012-01-01

    Binding of heterochromatin protein 1 (HP1) to the histone H3 lysine 9 trimethylation (H3K9me3) mark is a hallmark of establishment and maintenance of heterochromatin. Although genetic and cell biological aspects have been elucidated, the molecular details of HP1 binding to H3K9me3 nucleosomes are unknown. Using a combination of NMR spectroscopy and biophysical measurements on fully defined recombinant experimental systems, we demonstrate that H3K9me3 works as an on/off switch regulating disti...

  10. The size of the nucleosome

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2011-01-01

    dictated by the fulfillment of two criteria: One is optimizing the volume fraction of the DNA double helix; this requirement for close-packing has its root in optimizing atomic and molecular interactions. The other criterion being that of having a zero strain-twist coupling; being a zero-twist structure is......-pairs of the linker-DNA is included the estimate of the size of an ideal nucleosome is in close agreement with the experimental numbers. Interestingly, the size of the nucleosome is shown to be a consequence of intrinsic properties of the DNA double helix....

  11. Conditions for positioning of nucleosomes on DNA

    CERN Document Server

    Sheinman, Michael

    2015-01-01

    Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single nucleosome to different locations along the DNA and some as interactions between neighboring nucleosomes. In this study we analyzed how well nucleosomes are positioned along the DNA as a function of strength of the preferential binding, correlation length of the binding energy landscape, interactions between neighboring nucleosomes and others relevant system properties. We analyze different scenarios: designed energy landscapes and generically disordered ones and derive conditions for good positioning. Using analytic and numerical approaches we find that, even if the binding preferences are very weak, synergistic interplay between the interactions and the binding preferences is essential for a good positioning of nucleosomes, especially on correlated energy landscapes. Ana...

  12. Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome

    Science.gov (United States)

    Winogradoff, David; Zhao, Haiqing; Dalal, Yamini; Papoian, Garegin A.

    2015-11-01

    The centromeric nucleosome is a key epigenetic determinant of centromere identity and function. Consequently, deciphering how CENP-A containing nucleosomes contribute structurally to centromere function is a fundamental question in chromosome biology. Here, we performed microsecond timescale all-atom molecular dynamics (MD) simulations of CENP-A and H3 nucleosomes, and report that the octameric CENP-A core particles and nucleosomes display different dynamics from their canonical H3-containing counterparts. The most significant motion observed is within key interactions at the heart of the CENP-A octameric core, wherein shearing of contacts within the CENP-A:CENP-A’ dimerization interface results in a weaker four helix bundle, and an extrusion of 10-30 bp of DNA near the pseudo-dyad. Coupled to other local and global fluctuations, the CENP-A nucleosome occupies a more rugged free energy landscape than the canonical H3 nucleosome. Taken together, our data suggest that CENP-A encodes enhanced distortability to the octameric nucleosome, which may allow for enhanced flexing of the histone core in vivo.

  13. Insights into DNA signals for nucleosome positioning

    Institute of Scientific and Technical Information of China (English)

    Zhiming DAI; Xianhua DAI; Jihua FENG; Qian XIANG; Yangyang DENG; Jiang WANG

    2008-01-01

    The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning in the promoter region plays a central role in regulating gene transcription. Experimental evidence suggests that the genomic DNA sequence is one important determinant of nucleosome positioning. Several approaches have been developed to predict nucleosome positions based on DNA sequence features, but the results indicate that there is room for improvement. This paper presents a new computational approach to predict genome-wide nucleosome locations in promoter regions. Importantly, the proposed approach outperforms existing approaches in yeast. Further anal-ysis demonstrates that DNA signals for nucleosome posi-tioning vary with species and composition of histones. Analysis of individual genes reveals that the role of the underlying DNA sequence in nucleosome positioning var-ies with genes.

  14. Characterisation of CenH3 nucleosomes

    OpenAIRE

    Miell, Matthew Daniel David

    2013-01-01

    As a centromere-specific protein complex in direct contact with the DNA, CenH3-containing nucleosomes are generally thought to act as the distinguishing epigenetic mark of active centromere location. Confusingly, seemingly disparate models have been proposed for the structure of CenH3 nucleosomes. The most widely supported model is an octameric structure that, like histone H3 nucleosomes, contains two subunits of each histone. Another more contentious, yet persistent model i...

  15. Nucleosomes shape DNA polymorphism and divergence.

    Directory of Open Access Journals (Sweden)

    Sasha A Langley

    2014-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Soler-López Montserrat

    2011-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Guillem Portella

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

  18. Relating periodicity of nucleosome organization and gene regulation

    OpenAIRE

    Wan, Jun; Lin, Jimmy; Zack, Donald J.; Qian, Jiang

    2009-01-01

    Motivation: The relationship between nucleosome positioning and gene regulation is fundamental yet complex. Previous studies on genomic nucleosome positions have revealed a correlation between nucleosome occupancy on promoters and gene expression levels. Many of these studies focused on individual nucleosomes, especially those proximal to transcription start sites. To study the collective effect of multiple nucleosomes on the gene expression, we developed a mathematical approach based on auto...

  19. The unconventional structure of centromeric nucleosomes

    OpenAIRE

    Henikoff, Steven; Furuyama, Takehito

    2012-01-01

    The centromere is a defining feature of the eukaryotic chromosome, required for attachment to spindle microtubules and segregation to the poles at both mitosis and meiosis. The fundamental unit of centromere identity is the centromere-specific nucleosome, in which the centromeric histone 3 (cenH3) variant takes the place of H3. The structure of the cenH3 nucleosome has been the subject of controversy, as mutually exclusive models have been proposed, including conventional and unconventional l...

  20. Characterizing and modeling citation dynamics

    CERN Document Server

    Eom, Young-Ho; 10.1371/journal.pone.0024926

    2011-01-01

    Citation distributions are crucial for the analysis and modeling of the activity of scientists. We investigated bibliometric data of papers published in journals of the American Physical Society, searching for the type of function which best describes the observed citation distributions. We used the goodness of fit with Kolmogorov-Smirnov statistics for three classes of functions: log-normal, simple power law and shifted power law. The shifted power law turns out to be the most reliable hypothesis for all citation networks we derived, which correspond to different time spans. We find that citation dynamics is characterized by bursts, usually occurring within a few years since publication of a paper, and the burst size spans several orders of magnitude. We also investigated the microscopic mechanisms for the evolution of citation networks, by proposing a linear preferential attachment with time dependent initial attractiveness. The model successfully reproduces the empirical citation distributions and accounts...

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    Yanping Fan

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

  3. Insights into distinct regulatory modes of nucleosome positioning

    Directory of Open Access Journals (Sweden)

    Feng Jihua

    2009-12-01

    Full Text Available Abstract Background The nucleosome is the fundamental unit of eukaryotic genomes. Experimental evidence suggests that the genomic DNA sequence and a variety of protein factors contribute to nucleosome positioning in vivo. However, how nucleosome positioning is determined locally is still largely unknown. Results We found that transcription factor binding sites (TFBSs with particular nucleosomal contexts show a preference to reside on specific chromosomes. We identified four typical gene classes associated with distinct regulatory modes of nucleosome positioning, and further showed that they are distinguished by transcriptional regulation patterns. The first mode involves the cooperativity between chromatin remodeling and stable transcription factor (TF-DNA binding that is linked to high intrinsic DNA binding affinities, evicting nucleosomes from favorable DNA sequences. The second is the DNA-encoded low nucleosome occupancy that is associated with high gene activity. The third is through chromatin remodeling and histone acetylation, sliding nucleosomes along DNA. This mode is linked to more cryptic sites for TF binding. The last consists of the nucleosome-enriched organization driven by other factors that overrides nucleosome sequence preferences. In addition, we showed that high polymerase II (Pol II occupancy is associated with high nucleosome occupancy around the transcription start site (TSS. Conclusions We identified four different regulatory modes of nucleosome positioning and gave insights into mechanisms that specify promoter nucleosome location. We suggest two distinct modes of recruitment of Pol II, which are selectively employed by different genes.

  4. Characterizing and modeling citation dynamics.

    Directory of Open Access Journals (Sweden)

    Young-Ho Eom

    Full Text Available Citation distributions are crucial for the analysis and modeling of the activity of scientists. We investigated bibliometric data of papers published in journals of the American Physical Society, searching for the type of function which best describes the observed citation distributions. We used the goodness of fit with Kolmogorov-Smirnov statistics for three classes of functions: log-normal, simple power law and shifted power law. The shifted power law turns out to be the most reliable hypothesis for all citation networks we derived, which correspond to different time spans. We find that citation dynamics is characterized by bursts, usually occurring within a few years since publication of a paper, and the burst size spans several orders of magnitude. We also investigated the microscopic mechanisms for the evolution of citation networks, by proposing a linear preferential attachment with time dependent initial attractiveness. The model successfully reproduces the empirical citation distributions and accounts for the presence of citation bursts as well.

  5. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

    OpenAIRE

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-01-01

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agre...

  6. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers.

    Science.gov (United States)

    Shaytan, Alexey K; Landsman, David; Panchenko, Anna R

    2015-06-01

    Nucleosome variability is essential for their functions in compacting the chromatin structure and regulation of transcription, replication and cell reprogramming. The DNA molecule in nucleosomes is wrapped around an octamer composed of four types of core histones (H3, H4, H2A, H2B). Nucleosomes represent dynamic entities and may change their conformation, stability and binding properties by employing different sets of histone variants or by becoming post-translationally modified. There are many variants of histones H2A and H2B. Specific H2A and H2B variants may preferentially associate with each other resulting in different combinations of variants and leading to the increased combinatorial complexity of nucleosomes. In addition, the H2A-H2B dimer can be recognized and substituted by chaperones/remodelers as a distinct unit, can assemble independently and is stable during nucleosome unwinding. In this review we discuss how sequence and structural variations in H2A-H2B dimers may provide necessary complexity and confer the nucleosome functional variability. PMID:25731851

  7. Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes

    Directory of Open Access Journals (Sweden)

    Trifonov Edward N

    2011-05-01

    Full Text Available Abstract Background The periodical occurrence of dinucleotides with a period of 10.4 bases now is undeniably a hallmark of nucleosome positioning. Whereas many eukaryotic genomes contain visible and even strong signals for periodic distribution of dinucleotides, the human genome is rather featureless in this respect. The exact sequence features in the human genome that govern the nucleosome positioning remain largely unknown. Results When analyzing the human genome sequence with the positional autocorrelation method, we found that only the dinucleotide CG shows the 10.4 base periodicity, which is indicative of the presence of nucleosomes. There is a high occurrence of CG dinucleotides that are either 31 (10.4 × 3 or 62 (10.4 × 6 base pairs apart from one another - a sequence bias known to be characteristic of Alu-sequences. In a similar analysis with repetitive sequences removed, peaks of repeating CG motifs can be seen at positions 10, 21 and 31, the nearest integers of multiples of 10.4. Conclusions Although the CG dinucleotides are dominant, other elements of the standard nucleosome positioning pattern are present in the human genome as well. The positional autocorrelation analysis of the human genome demonstrates that the CG dinucleotide is, indeed, one visible element of the human nucleosome positioning pattern, which appears both in Alu sequences and in sequences without repeats. The dominant role that CG dinucleotides play in organizing human chromatin is to indicate the involvement of human nucleosomes in tuning the regulation of gene expression and chromatin structure, which is very likely due to cytosine-methylation/-demethylation in CG dinucleotides contained in the human nucleosomes. This is further confirmed by the positions of CG-periodical nucleosomes on Alu sequences. Alu repeats appear as monomers, dimers and trimers, harboring two to six nucleosomes in a run. Considering the exceptional role CG dinucleotides play in the

  8. Tension-dependent Free Energies of Nucleosome Unwrapping

    CERN Document Server

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

    2016-01-01

    Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome, and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails are crucial f...

  9. Characterizing popularity dynamics of online videos

    Science.gov (United States)

    Ren, Zhuo-Ming; Shi, Yu-Qiang; Liao, Hao

    2016-07-01

    Online popularity has a major impact on videos, music, news and other contexts in online systems. Characterizing online popularity dynamics is nature to explain the observed properties in terms of the already acquired popularity of each individual. In this paper, we provide a quantitative, large scale, temporal analysis of the popularity dynamics in two online video-provided websites, namely MovieLens and Netflix. The two collected data sets contain over 100 million records and even span a decade. We characterize that the popularity dynamics of online videos evolve over time, and find that the dynamics of the online video popularity can be characterized by the burst behaviors, typically occurring in the early life span of a video, and later restricting to the classic preferential popularity increase mechanism.

  10. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output.

    Directory of Open Access Journals (Sweden)

    Barbara Celona

    2011-06-01

    Full Text Available The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1 contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation.

  11. 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

  12. [The effect of DNA supercoiling DNA on nucleosome structure].

    Science.gov (United States)

    Sivolob, A V; Khrapunov, S N

    1991-01-01

    The circular DNA which contains nucleosomes and additional supercoils has been considered theoretically. The different possible effect of increased negative supercoiling on the nucleosome structure have been studied. According to the model proposed all supercoils in the nucleosome-containing circular DNA are realized as torsional deformations of the double helix. The free energy of both supercoiling (torsional deformations) and nucleosome stabilization have been taken into consideration to obtain the equation for free energy of nucleosome-containing circular DNA. The analysis of this equation and the experimental data by Garner et al. (II Psoc. Natl. Acad. Sci. USA. 1987. P. 2620-2623) about the maximum amount of supercoiling obtained by DNA-topoisomerase II treatment of nucleosome-containing pBR322 plasmid has been performed. It has been shown that two possibilities are consistent with both the equation and experimental data. These are: (1) the increased supercoiling induces the torsional strains not only in linker regions but also in nucleosome DNA and thus supercoiling causes an instability on nucleosome structure; (2) increased supercoiling induces a structural change of nucleosome which is accompanied by nucleosome DNA unwinding and its transition into form with approximately 11 base pairs per turn of double helix. It has been evaluated that in the first case the average torsional rigidity of nucleosome DNA should be approximately 2.5 times as much and in the second case--much more than the rigidity of naked DNA. Both types of nucleosome structural changes may cause its transition to a potentially active state for transcription. It is suggested that increased supercoiling can be a switch mechanism of chromatin activation. PMID:1654518

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

    OpenAIRE

    Isaac, RS; Jiang, F; Doudna, JA; Lim, WA; Narlikar, GJ; De Almeida, R

    2016-01-01

    The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to ...

  14. 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...

  15. Automatic characterization of dynamics in Absence Epilepsy

    DEFF Research Database (Denmark)

    Petersen, Katrine N. H.; Nielsen, Trine N.; Kjær, Troels W.;

    2013-01-01

    Dynamics of the spike-wave paroxysms in Childhood Absence Epilepsy (CAE) are automatically characterized using novel approaches. Features are extracted from scalograms formed by Continuous Wavelet Transform (CWT). Detection algorithms are designed to identify an estimate of the temporal development...

  16. 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.

  17. A deformation energy-based model for predicting nucleosome dyads and occupancy

    Science.gov (United States)

    Liu, Guoqing; Xing, Yongqiang; Zhao, Hongyu; Wang, Jianying; Shang, Yu; Cai, Lu

    2016-01-01

    Nucleosome plays an essential role in various cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to decode the mechanism of nucleosome positioning and identify nucleosome positions in the genome. In this paper, we present a model for predicting nucleosome positioning based on DNA deformation, in which both bending and shearing of the nucleosomal DNA are considered. The model successfully predicted the dyad positions of nucleosomes assembled in vitro and the in vitro map of nucleosomes in Saccharomyces cerevisiae. Applying the model to Caenorhabditis elegans and Drosophila melanogaster, we achieved satisfactory results. Our data also show that shearing energy of nucleosomal DNA outperforms bending energy in nucleosome occupancy prediction and the ability to predict nucleosome dyad positions is attributed to bending energy that is associated with rotational positioning of nucleosomes. PMID:27053067

  18. Vocal Dynamic Visual Pattern for voice characterization

    International Nuclear Information System (INIS)

    Voice assessment requires simple and painless exams. Modern technologies provide the necessary resources for voice signal processing. Techniques based on nonlinear dynamics seem to asses the complexity of voice more accurately than other methods. Vocal dynamic visual pattern (VDVP) is based on nonlinear methods and provides qualitative and quantitative information. Here we characterize healthy and Reinke's edema voices by means of perturbation measures and VDVP analysis. VDPD and jitter show different results for both groups, while amplitude perturbation has no difference. We suggest that VDPD analysis improve and complement the evaluation methods available for clinicians.

  19. Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

    Science.gov (United States)

    Meyer, Sam; Everaers, Ralf

    2015-02-01

    The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

  20. Sequence structure of Lowary/Widom clones forming strong nucleosomes.

    Science.gov (United States)

    Trifonov, Edward N

    2016-04-01

    Lowary and Widom selected from random sequences those which form exceptionally stable nucleosomes, including clone 601, the current champion of strong nucleosome (SN) sequences. This unique sequence database (LW sequences) carries sequence elements which confer stability on the nucleosomes formed on the sequences, and, thus, may serve as source of information on the structure of "ideal" or close to ideal nucleosome DNA sequence. An important clue is also provided by crystallographic study of Vasudevan and coauthors on clone 601 nucleosomes. It demonstrated that YR·YR dinucleotide stacks (primarily TA·TA) follow one another at distances 10 or 11 bases or multiples thereof, such that they all are located on the interface between DNA and histone octamer. Combining this important information with alignment of the YR-containing 10-mers and 11-mers from LW sequences, the bendability matrices of the stable nucleosome DNA are derived. The matrices suggest that the periodically repeated TA (YR), RR, and YY dinucleotides are the main sequence features of the SNs. This consensus coincides with the one for recently discovered SNs with visibly periodic DNA sequences. Thus, the experimentally observed stable LW nucleosomes and SNs derived computationally appear to represent the same entity - exceptionally stable SNs. PMID:26208855

  1. Roles of histones and nucleosomes in gene transcription

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This article reviews the latest research developments in the field of eukaryotic gene regulation by the structural alterations of chromatin and nucleosomes. The following issues are briefly addressed: (ⅰ) nucleosome and histone modifications by both the ATP-dependent remodel- ing com-plexes and the histone acetyltransferases and their roles in gene activation; (ⅱ) competitive binding of histones and transcription factors on gene promoters, and transcription repression by nucleosomes; and (ⅲ) influences of linker histone H1 on gene regulation. Meanwhile, the significance and impact of these new research progresses, as well as issues worthwhile for further study are commented.

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

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2012-01-01

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

  3. Triple helix DNA alters nucleosomal histone-DNA interactions and acts as a nucleosome barrier.

    OpenAIRE

    Westin, L; Blomquist, P.; Milligan, J F; Wrange, O

    1995-01-01

    Oligonucleotides which form triple helical complexes on double-stranded DNA have been previously reported to selectively inhibit transcription both in vitro and in vivo by physically blocking RNA polymerase or transcription factor access to the DNA template. Here we show that a 16mer oligonucleotide, which forms triple helix DNA by binding to a 16 bp homopurine segment, alters the formation of histone-DNA contacts during in vitro nucleosome reconstitution. This effect was DNA sequence-specifi...

  4. DPNuc: Identifying Nucleosome Positions Based on the Dirichlet Process Mixture Model.

    Science.gov (United States)

    Chen, Huidong; Guan, Jihong; Zhou, Shuigeng

    2015-01-01

    Nucleosomes and the free linker DNA between them assemble the chromatin. Nucleosome positioning plays an important role in gene transcription regulation, DNA replication and repair, alternative splicing, and so on. With the rapid development of ChIP-seq, it is possible to computationally detect the positions of nucleosomes on chromosomes. However, existing methods cannot provide accurate and detailed information about the detected nucleosomes, especially for the nucleosomes with complex configurations where overlaps and noise exist. Meanwhile, they usually require some prior knowledge of nucleosomes as input, such as the size or the number of the unknown nucleosomes, which may significantly influence the detection results. In this paper, we propose a novel approach DPNuc for identifying nucleosome positions based on the Dirichlet process mixture model. In our method, Markov chain Monte Carlo (MCMC) simulations are employed to determine the mixture model with no need of prior knowledge about nucleosomes. Compared with three existing methods, our approach can provide more detailed information of the detected nucleosomes and can more reasonably reveal the real configurations of the chromosomes; especially, our approach performs better in the complex overlapping situations. By mapping the detected nucleosomes to a synthetic benchmark nucleosome map and two existing benchmark nucleosome maps, it is shown that our approach achieves a better performance in identifying nucleosome positions and gets a higher F-score. Finally, we show that our approach can more reliably detect the size distribution of nucleosomes. PMID:26671796

  5. Multiscale modelling of nucleosome core particle aggregation

    Science.gov (United States)

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

    2015-02-01

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

  6. 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.)

  7. Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach.

    Science.gov (United States)

    Eslami-Mossallam, Behrouz; Schram, Raoul D; Tompitak, Marco; van Noort, John; Schiessel, Helmut

    2016-01-01

    Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function. PMID:27272176

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

    Directory of Open Access Journals (Sweden)

    Alberto J Lopez

    2015-04-01

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

  9. Nucleosomes determine their own patch size in base excision repair.

    Science.gov (United States)

    Meas, Rithy; Smerdon, Michael J

    2016-01-01

    Base excision repair (BER) processes non-helix distorting lesions (e.g., uracils and gaps) and is composed of two subpathways that differ in the number of nucleotides (nts) incorporated during the DNA synthesis step: short patch (SP) repair incorporates 1 nt and long patch (LP) repair incorporates 2-12 nts. This choice for either LP or SP repair has not been analyzed in the context of nucleosomes. Initial studies with uracil located in nucleosome core DNA showed a distinct DNA polymerase extension profile in cell-free extracts that specifically limits extension to 1 nt, suggesting a preference for SP BER. Therefore, we developed an assay to differentiate long and short repair patches in 'designed' nucleosomes containing a single-nucleotide gap at specific locations relative to the dyad center. Using cell-free extracts or purified enzymes, we found that DNA lesions in the nucleosome core are preferentially repaired by DNA polymerase β and there is a significant reduction in BER polymerase extension beyond 1 nt, creating a striking bias for incorporation of short patches into nucleosomal DNA. These results show that nucleosomes control the patch size used by BER. PMID:27265863

  10. The universality of nucleosome organization: from yeast to human

    Science.gov (United States)

    Chereji, Razvan

    The basic units of DNA packaging are called nucleosomes. Their locations on the chromosomes play an essential role in gene regulation. We study nucleosome positioning in yeast, fly, mouse, and human, and build biophysical models in order to explain the genome-wide nucleosome organization. We show that DNA sequence alone is not able to generate the phased arrays of nucleosomes observed in vivo near the transcription start sites. We discuss simple models which can account for the formation of nucleosome depleted regions and nucleosome phasing at the gene promoters. We show that the same principles apply to different organisms. References: [1] RV Chereji, D Tolkunov, G Locke, AV Morozov - Phys. Rev. E 83, 050903 (2011) [2] RV Chereji, AV Morozov - J. Stat. Phys. 144, 379 (2011) [3] RV Chereji, AV Morozov - Proc. Natl. Acad. Sci. U.S.A. 111, 5236 (2014) [4] RV Chereji, T-W Kan, et al. - Nucleic Acids Res. (2015) doi: 10.1093/nar/gkv978 [5] RV Chereji, AV Morozov - Brief. Funct. Genomics 14, 50 (2015) [6] HA Cole, J Ocampo, JR Iben, RV Chereji, DJ Clark - Nucleic Acids Res. 42, 12512 (2014) [7] D Ganguli, RV Chereji, J Iben, HA Cole, DJ Clark - Genome Res. 24, 1637 (2014)

  11. Characterization of majorization monotone quantum dynamics

    OpenAIRE

    Yuan, Haidong

    2015-01-01

    In this article I study the dynamics of open quantum system in Markovian environment. I give necessary and sufficient conditions for such dynamics to be majorization monotone, which are those dynamics always mixing the states.

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

    Directory of Open Access Journals (Sweden)

    Chuong D Pham

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

  13. Integrated molecular mechanism directing nucleosome reorganization by human FACT.

    Science.gov (United States)

    Tsunaka, Yasuo; Fujiwara, Yoshie; Oyama, Takuji; Hirose, Susumu; Morikawa, Kosuke

    2016-03-15

    Facilitates chromatin transcription (FACT) plays essential roles in chromatin remodeling during DNA transcription, replication, and repair. Our structural and biochemical studies of human FACT-histone interactions present precise views of nucleosome reorganization, conducted by the FACT-SPT16 (suppressor of Ty 16) Mid domain and its adjacent acidic AID segment. AID accesses the H2B N-terminal basic region exposed by partial unwrapping of the nucleosomal DNA, thereby triggering the invasion of FACT into the nucleosome. The crystal structure of the Mid domain complexed with an H3-H4 tetramer exhibits two separate contact sites; the Mid domain forms a novel intermolecular β structure with H4. At the other site, the Mid-H2A steric collision on the H2A-docking surface of the H3-H4 tetramer within the nucleosome induces H2A-H2B displacement. This integrated mechanism results in disrupting the H3 αN helix, which is essential for retaining the nucleosomal DNA ends, and hence facilitates DNA stripping from histone. PMID:26966247

  14. nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning

    OpenAIRE

    Alharbi, Bader A.; Alshammari, Thamir H.; Felton, Nathan L.; Zhurkin, Victor B.; Cui, Feng

    2014-01-01

    Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic...

  15. Cse4 is Part of an Octameric Nucleosome in Budding Yeast

    OpenAIRE

    Camahort, Raymond; Shivaraju, Manjunatha; Mattingly, Mark; Li, Bing; Nakanishi, Shima; Zhu, Dongxiao; Shilatifard, Ali; Workman, Jerry L.; Gerton, Jennifer L.

    2009-01-01

    The budding yeast CenH3 histone variant Cse4 localizes to centromeric nucleosomes and is required for kinetochore assembly and chromosome segregation. The exact composition of centromeric Cse4–containing nucleosomes is a subject of debate. ChIP-chip experiments and high resolution quantitative PCR confirm that there is a single Cse4 nucleosome at each centromere, and additional regions of the genome contain Cse4 nucleosomes at low levels. Using unbiased biochemical, cell biological, and genet...

  16. Dynamic characterization of the CAREM fuel element prototype

    International Nuclear Information System (INIS)

    As a previous step to make a complete test plan to evaluate the hydrodynamic behavior of the present configuration of the CAREM type fuel element, a dynamic characterization analysis is required, without the dynamic response induced by the flowing fluid. This paper presents the tests made, the methods and instrumentation used, and the results obtained in order to obtain a complete dynamic characterization of the CAREM type fuel element. (author)

  17. Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

    Directory of Open Access Journals (Sweden)

    Nikolaou Christoforos

    2010-11-01

    Full Text Available Abstract Background Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process of nucleosome positioning, for which several models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. In this paper, we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences. Results We compared the complete sets of nucleosome positions for the budding yeast (Saccharomyces cerevisiae as defined in the output of two independent experiments with the use of two different experimental techniques. We found that Conclusion Our findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints that further shape the structure of the underlying DNA. We were able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore, we found that both consistently positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency towards conservation of this structural feature.

  18. Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response

    Science.gov (United States)

    Sexton, Brittany S.; Druliner, Brooke R.; Vera, Daniel L.; Avey, Denis; Zhu, Fanxiu; Dennis, Jonathan H.

    2016-01-01

    Nucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of all human genes. Nucleosomes underwent widespread changes in organization 24 hours after KSHV reactivation and returned to their basal nucleosomal architecture 48 hours after KSHV reactivation. The widespread changes consisted of an indiscriminate remodeling event resulting in the loss of nucleosome rotational phasing signals. Additionally, one in six TSSs in the human genome possessed nucleosomes that are translationally remodeled. 72% of the loci with translationally remodeled nucleosomes have nucleosomes that moved to positions encoded by the underlying DNA sequence. Finally we demonstrated that these widespread alterations in nucleosomal architecture potentiated regulatory factor binding. These descriptions of nucleosomal architecture changes provide a new framework for understanding the role of chromatin in the genomic response, and have allowed us to propose a hierarchical model for chromatin-based regulation of genome response. PMID:26771136

  19. Reactivity in ELISA with DNA-loaded nucleosomes in patients with proliferative lupus nephritis

    NARCIS (Netherlands)

    Dieker, J.W.; Schlumberger, W.; McHugh, N.; Hamann, P.; Vlag, J. van der; Berden, J.H.M.

    2015-01-01

    Autoantibodies against nucleosomes are considered a hallmark of systemic lupus erythematosus (SLE). We compared in patients with proliferative lupus nephritis the diagnostic usefulness of a dsDNA-loaded nucleosome ELISA (anti-dsDNA-NcX) with ELISAs in which dsDNA or nucleosomes alone were coated. Fi

  20. Characterization of quantum dynamics using quantum error correction

    OpenAIRE

    Omkar, S.; Srikanth, R.; Banerjee, S.

    2014-01-01

    Characterizing noisy quantum processes is important to quantum computation and communication (QCC), since quantum systems are generally open. To date, all methods of characterization of quantum dynamics (CQD), typically implemented by quantum process tomography, are \\textit{off-line}, i.e., QCC and CQD are not concurrent, as they require distinct state preparations. Here we introduce a method, "quantum error correction based characterization of dynamics", in which the initial state is any ele...

  1. DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo.

    Science.gov (United States)

    Gangadharan, Sunil; Mularoni, Loris; Fain-Thornton, Jennifer; Wheelan, Sarah J; Craig, Nancy L

    2010-12-21

    Transposons are mobile genetic elements that are an important source of genetic variation and are useful tools for genome engineering, mutagenesis screens, and vectors for transgenesis including gene therapy. We have used second-generation sequencing to analyze ≈2 × 10(5) unique de novo transposon insertion sites of the transposon Hermes in the Saccharomyces cerevisiae genome from both in vitro transposition reactions by using purified yeast genomic DNA, to better characterize intrinsic sequence specificity, and sites recovered from in vivo transposition events, to characterize the effect of intracellular factors such as chromatin on target site selection. We find that Hermes transposon targeting in vivo is profoundly affected by chromatin structure: The subset of genome-wide target sites used in vivo is strongly associated (P < 2e-16 by Fisher's exact test) with nucleosome-free chromatin. Our characterization of the insertion site preferences of Hermes not only assists in the future use of this transposon as a molecular biology tool but also establishes methods to more fully determine targeting mechanisms of other transposons. We have also discovered a long-range sequence motif that defines S. cerevisiae nucleosome-free regions. PMID:21131571

  2. Effect of the Spiroiminodihydantoin Lesion on Nucleosome Stability and Positioning.

    Science.gov (United States)

    Norabuena, Erika M; Barnes Williams, Sara; Klureza, Margaret A; Goehring, Liana J; Gruessner, Brian; Radhakrishnan, Mala L; Jamieson, Elizabeth R; Núñez, Megan E

    2016-04-26

    DNA is constantly under attack by oxidants, generating a variety of potentially mutagenic covalently modified species, including oxidized guanine base products. One such product is spiroiminodihydantoin (Sp), a chiral, propeller-shaped lesion that strongly destabilizes the DNA helix in its vicinity. Despite its unusual shape and thermodynamic effect on double-stranded DNA structure, DNA duplexes containing the Sp lesion form stable nucleosomes upon being incubated with histone octamers. Indeed, among six different combinations of lesion location and stereochemistry, only two duplexes display a diminished ability to form nucleosomes, and these only by ∼25%; the other four are statistically indistinguishable from the control. Nonetheless, kinetic factors also play a role: when the histone proteins have less time during assembly of the core particle to sample both lesion-containing and normal DNA strands, they are more likely to bind the Sp lesion DNA than during slower assembly processes that better approximate thermodynamic equilibrium. Using DNase I footprinting and molecular modeling, we discovered that the Sp lesion causes only a small perturbation (±1-2 bp) on the translational position of the DNA within the nucleosome. Each diastereomeric pair of lesions has the same effect on nucleosome positioning, but lesions placed at different locations behave differently, illustrating that the location of the lesion and not its shape serves as the primary determinant of the most stable DNA orientation. PMID:27074396

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

    OpenAIRE

    Lopez, Alberto J.; Wood, Marcelo A.

    2015-01-01

    It is becoming increasingly important to understand how epigenetic mechanisms control gene expression during neurodevelopment. Two epigenetic mechanisms that have received considerable attention are DNA methylation and histone acetylation. Human exome sequencing and genome-wide association studies have linked several neurobiological disorders to genes whose products actively regulate DNA methylation and histone acetylation. More recently, a third major epigenetic mechanism, nucleosome remodel...

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

    Science.gov (United States)

    Quintales, Luis; Vázquez, Enrique; Antequera, Francisco

    2015-07-01

    Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use. PMID:25296770

  5. Using DNA mechanics to predict intrinsic and extrinsic nucleosome positioning signals

    Science.gov (United States)

    Morozov, Alexandre

    2008-03-01

    In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are determined by sequence alone, in vivo competition with other DNA-binding factors and action of chromatin remodeling enzymes play a role that needs to be quantified. We developed a biophysical, DNA mechanics-based model for the sequence dependence of DNA bending energies, and validated it against a collection of in vitro free energies of nucleosome formation and a nucleosome crystal structure; we also successfully designed both strong and poor histone binding sequences ab initio. For in vivo data from S.cerevisiae, the strongest positioning signal came from the competition with other factors rather than intrinsic nucleosome sequence preferences. Based on sequence alone, our model predicts that functional transcription factor binding sites tend to be covered by nucleosomes, yet are uncovered in vivo because functional sites cluster within a single nucleosome footprint and thus make transcription factors bind cooperatively. Similarly a weak enhancement of nucleosome binding in the TATA region becomes a strong depletion when the TATA-binding protein is included, in quantitative agreement with experiment. Our model distinguishes multiple ways in which genomic sequence influences nucleosome positions, and thus provides alternative explanations for several genome-wide experimental findings. In the future our approach will be used to rationally alter gene expression levels in model systems through redesign of nucleosome occupancy profiles.

  6. Discovery, Characterization, and Dynamics of Transiting Exoplanets

    DEFF Research Database (Denmark)

    Van Eylen, Vincent

    2015-01-01

    present the first results of this study, constraining the masses and bulk compositions of three planets. The second part of this thesis focuses on dynamics of exoplanets. All the solar system planets orbit in nearly the same plane, and that plane is also aligned with the equatorial plane of the Sun. That....... The measurement joins a handful of obliquity measurements, so far suggesting multi-planet systems are mostly aligned. This favors theories suggesting that hot Jupiter migration is responsible for creating misaligned planets. Moreover, unlike the planets in the solar system, which have nearly circular...... are similar to the solar system, but differ from the highly eccentric orbits seen for some massive planets....

  7. 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.

  8. Differential dynamic microscopy to characterize Brownian motion and bacteria motility

    Science.gov (United States)

    Germain, David; Leocmach, Mathieu; Gibaud, Thomas

    2016-03-01

    We have developed a lab module for undergraduate students, which involves the process of quantifying the dynamics of a suspension of microscopic particles using Differential Dynamic Microscopy (DDM). DDM is a relatively new technique that constitutes an alternative method to more classical techniques such as dynamic light scattering (DLS) or video particle tracking (VPT). The technique consists of imaging a particle dispersion with a standard light microscope and a camera and analyzing the images using a digital Fourier transform to obtain the intermediate scattering function, an autocorrelation function that characterizes the dynamics of the dispersion. We first illustrate DDM in the textbook case of colloids under Brownian motion, where we measure the diffusion coefficient. Then we show that DDM is a pertinent tool to characterize biological systems such as motile bacteria.

  9. High Dynamic Range Characterization of the Trauma Patient Plasma Proteome

    OpenAIRE

    Liu, Tao; Qian, Wei-Jun; Gritsenko, Marina A.; Xiao, Wenzhong; Moldawer, Lyle L; Kaushal, Amit; Monroe, Matthew E.; Susan M Varnum; Moore, Ronald J.; Purvine, Samuel O; Ronald V Maier; Davis, Ronald W; Tompkins, Ronald G.; Camp II, David G.; Smith, Richard D.

    2006-01-01

    While human plasma represents an attractive sample for disease biomarker discovery, the extreme complexity and large dynamic range in protein concentrations present significant challenges for characterization, candidate biomarker discovery, and validation. Herein, we describe a strategy that combines immunoaffinity subtraction and subsequent chemical fractionation based on cysteinyl peptide and N-glycopeptide captures with 2D-LC-MS/MS to increase the dynamic range of analysis for plasma. Appl...

  10. Preferential Nucleosome Assembly at DNA Triplet Repeats from the Myotonic Dystrophy Gene

    Science.gov (United States)

    Wang, Yuh-Hwa; Amirhaeri, Sorour; Kang, Seongman; Wells, Robert D.; Griffith, Jack D.

    1994-07-01

    The expansion of CTG repeats in DNA occurs in or near genes involved in several human diseases, including myotonic dystrophy and Huntington's disease. Nucleosomes, the basic structural element of chromosomes, consist of 146 base pairs of DNA coiled about an octamer of histone proteins and mediate general transcriptional repression. Electron microscopy was used to examine in vitro the nucleosome assembly of DNA containing repeating CTG triplets. The efficiency of nucleosome formation increased with expanded triplet blocks, suggesting that such blocks may repress transcription through the creation of stable nucleosomes.

  11. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

    Science.gov (United States)

    Kelly, Theresa K.; Liu, Yaping; Lay, Fides D.; Liang, Gangning; Berman, Benjamin P.; Jones, Peter A.

    2012-01-01

    DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome-depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule, and thus, single cell level, that can be used to monitor disease progression and response to therapy. PMID:22960375

  12. Activator control of nucleosome occupancy in activation and repression of transcription.

    Directory of Open Access Journals (Sweden)

    Gene O Bryant

    2008-12-01

    Full Text Available The relationship between chromatin structure and gene expression is a subject of intense study. The universal transcriptional activator Gal4 removes promoter nucleosomes as it triggers transcription, but how it does so has remained obscure. The reverse process, repression of transcription, has often been correlated with the presence of nucleosomes. But it is not known whether nucleosomes are required for that effect. A new quantitative assay describes, for any given location, the fraction of DNA molecules in the population that bears a nucleosome at any given instant. This allows us to follow the time courses of nucleosome removal and reformation, in wild-type and mutant cells, upon activation (by galactose and repression (by glucose of the GAL genes of yeast. We show that upon being freed of its inhibitor Gal80 by the action of galactose, Gal4 quickly recruits SWI/SNF to the genes, and that nucleosome "remodeler" rapidly removes promoter nucleosomes. In the absence of SWI/SNF, Gal4's action also results in nucleosome removal and the activation of transcription, but both processes are significantly delayed. Addition of glucose to cells growing in galactose represses transcription. But if galactose remains present, Gal4 continues to work, recruiting SWI/SNF and maintaining the promoter nucleosome-free despite it being repressed. This requirement for galactose is obviated in a mutant in which Gal4 works constitutively. These results show how an activator's recruiting function can control chromatin structure both during gene activation and repression. Thus, both under activating and repressing conditions, the activator can recruit an enzymatic machine that removes promoter nucleosomes. Our results show that whereas promoter nucleosome removal invariably accompanies activation, reformation of nucleosomes is not required for repression. The finding that there are two routes to nucleosome removal and activation of transcription-one that requires the

  13. Characterizing detonator output using dynamic witness plates

    International Nuclear Information System (INIS)

    A sub-microsecond, time-resolved micro-particle-image velocimetry (PIV) system is developed to investigate the output of explosive detonators. Detonator output is directed into a transparent solid that serves as a dynamic witness plate and instantaneous shock and material velocities are measured in a two-dimensional plane cutting through the shock wave as it propagates through the solid. For the case of unloaded initiators (e.g. exploding bridge wires, exploding foil initiators, etc.) the witness plate serves as a surrogate for the explosive material that would normally be detonated. The velocity-field measurements quantify the velocity of the shocked material and visualize the geometry of the shocked region. Furthermore, the time-evolution of the velocity-field can be measured at intervals as small as 10 ns using the PIV system. Current experimental results of unloaded exploding bridge wire output in polydimethylsiloxane (PDMS) witness plates demonstrate 20 MHz velocity-field sampling just 300 ns after initiation of the wire.

  14. Modal analysis application for dynamic characterization of simple structures

    International Nuclear Information System (INIS)

    The knowledge of the dynamic characteristics of a structure helps to foresee the vibrating behaviour under operating conditions. The modal analysis techniques offer a method to perform the dynamic characterization of a studied structure from the vibration modes of such structure. A hammer provided with a loaded cell to excite a wide frequency band and accelerometer and, on the basis of a measurement of the transfer function at different points, various simple structures were given with a dynamic structures analysis (of the type of Fourier's rapidly transformation) and the results were compared with those obtained by other methods. Different fields where these techniques are applied, are also enumerated. (Author)

  15. 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

  16. 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.

  17. Reactivity in ELISA with DNA-loaded nucleosomes in patients with proliferative lupus nephritis.

    Science.gov (United States)

    Dieker, Jürgen; Schlumberger, Wolfgang; McHugh, Neil; Hamann, Philip; van der Vlag, Johan; Berden, Jo H

    2015-11-01

    Autoantibodies against nucleosomes are considered a hallmark of systemic lupus erythematosus (SLE). We compared in patients with proliferative lupus nephritis the diagnostic usefulness of a dsDNA-loaded nucleosome ELISA (anti-dsDNA-NcX) with ELISAs in which dsDNA or nucleosomes alone were coated. First, we analysed whether DNA loading on nucleosomes led to masking of epitopes by using defined monoclonal anti-DNA, anti-histone and nucleosome-specific autoantibodies to evaluate the accessibility of nucleosomal epitopes in the anti-dsDNA-NcX ELISA. Second, autoantibody levels were measured in these 3 ELISAs in 100 patients with proliferative lupus nephritis (LN) before immunosuppressive treatment and in 128 non-SLE disease controls. In patients with LN inter-assay comparisons and associations with clinical and serological parameters were analysed. The panel of monoclonal antibodies revealed that all epitopes were equally accessible in the anti-dsDNA-NcX ELISA as in the two other ELISAs. Patients with proliferative lupus nephritis were positive with dsDNA-loaded nucleosomes in 86%, with DNA in 66% and with nucleosomes in 85%. In the non-lupus disease control group these frequencies were 1.6% (2 out of 128) for both the anti-dsDNA-NcX and the anti-dsDNA ELISA and 0% in the anti-nucleosome ELISA. The levels in the anti-dsDNA-NcX ELISA were high in a group of patients with LN that showed absent reactivity in the anti-DNA or low levels in the anti-nucleosome ELISA. Anti-dsDNA-NcX positivity was associated with higher SLEDAI scores within this group. Within nucleosome-based ELISAs, we propose the anti-dsDNA-NcX ELISA as the preferred test system. PMID:26597199

  18. “Point” Centromeres of Saccharomyces Harbor Single Centromere-Specific Nucleosomes

    OpenAIRE

    Henikoff, Steven; Henikoff, Jorja G.

    2012-01-01

    The “point” centromere of budding yeast is genetically defined by an ∼125-bp sequence. Recent fluorescence measurements of kinetochore clusters have suggested that this sequence specifies multiple centromere histone 3 (CenH3) nucleosomes. However, high-resolution mapping demonstrates that there is only one CenH3 nucleosome per centromere, providing biochemical confirmation of the point centromere model.

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

    NARCIS (Netherlands)

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

    2003-01-01

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

  20. RSC remodeling of oligo-nucleosomes: an atomic force microscopy study

    CERN Document Server

    Montel, Fabien; Menoni, Hervé; Angelov, Dimitar; Dimitrov, Stéfan; Faivre-Moskalenko, Cendrine

    2010-01-01

    RSC is an essential chromatin remodeling factor that is required for the control of several processes including transcription, repair and replication. The ability of RSC to relocate centrally positioned mononucleosomes at the end of nucleosomal DNA is firmly established, but the data on RSC action on oligo-nucleosomal templates remains still scarce. By using Atomic Force Microscopy (AFM) imaging, we have quantitatively studied the RSC- induced mobilization of positioned di- and trinucleosomes as well as the directionality of mobilization on mononucleosomal template labeled at one end with streptavidin. AFM imaging showed only a limited set of distinct configurational states for the remodeling products. No stepwise or preferred directionality of the nucleosome motion was observed. Analysis of the corresponding reaction pathways allows deciphering the mechanistic features of RSC-induced nucleosome relocation. The final outcome of RSC remodeling of oligosome templates is the packing of the nucleosomes at the edg...

  1. Dynamic characterization of the cutting conditions in dry turning

    International Nuclear Information System (INIS)

    Machining instability in the form of violent vibrations or chatter is a physical process characterized by extreme cutting force at the cutting point. The process has very negative impact on machine integrity, tool life, surface quality and dimensional accuracy. Thus it could significantly compromise productivity and manufacturing quality. In the present paper, the importance of characterization and identification of dynamic instability in dry turning operation are shown. The stability behaviour of machine vibration or chatter has been examined and the various relevant parameters are studied and discuted. For chatter detection and identification of the transition between stable and unstable states, different methods are used. Results obtained proof the accuracy of these methods.

  2. Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning

    Directory of Open Access Journals (Sweden)

    Gent Jonathan I

    2011-02-01

    Full Text Available Abstract Background Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. The histone H3 variant CENH3 (centromeric histone H3 is viewed as the key element of centromere chromatin and its interaction with centromere DNA is epigenetic in that its localization to centromeres is not sequence-dependent. Results In order to investigate what influence the DNA sequence exerts on CENH3 chromatin structure, we examined CENH3 nucleosome footprints on maize centromere DNA. We found a predominant average nucleosome spacing pattern of roughly 190-bp intervals, which was also the dominant arrangement for nucleosomes genome-wide. For CENH3-containing nucleosomes, distinct modes of nucleosome positioning were evident within that general spacing constraint. Over arrays of the major ~156-bp centromeric satellite sequence (tandem repeat CentC, nucleosomes were not positioned in register with CentC monomers but in conformity with a striking ~10-bp periodicity of AA/TT dimers within the sequence. In contrast, nucleosomes on a class of centromeric retrotransposon (CRM2 lacked a detectable AA/TT periodicity but exhibited tightly phased positioning. Conclusions These data support a model in which general chromatin factors independent of both DNA sequence and CENH3 enforce roughly uniform centromeric nucleosome spacing while allowing flexibility in the mode in which nucleosomes are positioned. In the case of tandem repeat DNA, the natural bending effects related to AA/TT periodicity produce an energetically-favourable arrangement consistent with conformationally rigid nucleosomes and stable chromatin at centromeres.

  3. Escherichia coli activity characterization using a laser dynamic speckle technique

    CERN Document Server

    Ramírez-Miquet, Evelio E; Contreras-Alarcón, Orestes R

    2012-01-01

    The results of applying a laser dynamic speckle technique to characterize bacterial activity are presented. The speckle activity was detected in two-compartment Petri dishes. One compartment was inoculated and the other one was left as a control blank. The speckled images were processed by the recently reported temporal difference method. Three inoculums of 0.3, 0.5, and 0.7 McFarland units of cell concentration were tested; each inoculum was tested twice for a total of six experiments. The dependences on time of the mean activity, the standard deviation of activity and other descriptors of the speckle pattern evolution were calculated for both the inoculated compartment and the blank. In conclusion the proposed dynamic speckle technique allows characterizing the activity of Escherichia coli bacteria in solid medium.

  4. Dynamic Propagation Channel Characterization and Modeling for Human Body Communication

    OpenAIRE

    Lei Wang; Jingjing Ma; Zhicheng Li; Hong Chen; Zedong Nie

    2012-01-01

    This paper presents the first characterization and modeling of dynamic propagation channels for human body communication (HBC). In-situ experiments were performed using customized transceivers in an anechoic chamber. Three HBC propagation channels, i.e., from right leg to left leg, from right hand to left hand and from right hand to left leg, were investigated under thirty-three motion scenarios. Snapshots of data (2,800,000) were acquired from five volunteers. Various path gains caused by di...

  5. Some Characterization Results on Dynamic Cumulative Residual Tsallis Entropy

    Directory of Open Access Journals (Sweden)

    Madan Mohan Sati

    2015-01-01

    Full Text Available We propose a generalized cumulative residual information measure based on Tsallis entropy and its dynamic version. We study the characterizations of the proposed information measure and define new classes of life distributions based on this measure. Some applications are provided in relation to weighted and equilibrium probability models. Finally the empirical cumulative Tsallis entropy is proposed to estimate the new information measure.

  6. Thermal characterization of green roofs through dynamic simulation

    OpenAIRE

    Gorrino, Alice; Corrado, Vincenzo; Capozzoli, Alfonso

    2013-01-01

    The aim of this study is to evaluate a simplified parameter to characterize green roofs summer dynamic thermal performance through a mathematical approach. The inside face surface conduction in a green roof component is calculated through the Fast all-season soil strength (FASST) model. A parametric analysis is carried out to evaluate which roof design options have the greatest effect on the green roof Thermal behavior during the summer period. The results show the relevance of the leaf area ...

  7. Characterizing and modeling the dynamics of online popularity

    CERN Document Server

    Ratkiewicz, Jacob; Fortunato, Santo; Flammini, Alessandro; Vespignani, Alessandro

    2010-01-01

    Online popularity has enormous impact on opinions, culture, policy, and profits. We provide a quantitative, large scale, longitudinal analysis of the dynamics of online content popularity in two massive model systems, the Wikipedia and an entire country's Web space. We find that the dynamics of popularity are characterized by bursts, displaying characteristic features of critical systems such as fat-tailed distributions of magnitude and inter-event time. We propose a minimal model combining the classic preferential popularity increase mechanism with the occurrence of random popularity shift due to exogenous factors. The model recovers the critical features observed in the empirical analysis of the systems analyzed here, highlighting the key factors needed in the description of popularity dynamics.

  8. Universality in survivor distributions: Characterizing the winners of competitive dynamics

    Science.gov (United States)

    Luck, J. M.; Mehta, A.

    2015-11-01

    We investigate the survivor distributions of a spatially extended model of competitive dynamics in different geometries. The model consists of a deterministic dynamical system of individual agents at specified nodes, which might or might not survive the predatory dynamics: all stochasticity is brought in by the initial state. Every such initial state leads to a unique and extended pattern of survivors and nonsurvivors, which is known as an attractor of the dynamics. We show that the number of such attractors grows exponentially with system size, so that their exact characterization is limited to only very small systems. Given this, we construct an analytical approach based on inhomogeneous mean-field theory to calculate survival probabilities for arbitrary networks. This powerful (albeit approximate) approach shows how universality arises in survivor distributions via a key concept—the dynamical fugacity. Remarkably, in the large-mass limit, the survivor probability of a node becomes independent of network geometry and assumes a simple form which depends only on its mass and degree.

  9. A high-resolution map of nucleosome positioning on a fission yeast centromere.

    Science.gov (United States)

    Song, Jun S; Liu, Xingkun; Liu, X Shirley; He, Xiangwei

    2008-07-01

    A key element for defining the centromere identity is the incorporation of a specific histone H3, CENPA, known as Cnp1p in Schizosaccharomyces pombe. Previous studies have suggested that functional S. pombe centromeres lack regularly positioned nucleosomes and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are, in fact, positioned in regular intervals in the core of centromere 2, providing the first high-resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore protein genes cnp1, mis18, mis12, nuf2, mal2; overexpression of cnp1; or the deletion of ams2, which encodes a GATA-like factor participating in CENPA incorporation. Bioinformatics analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence bias in nucleosome positioning. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites of Ams2p. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence. PMID:18411404

  10. Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.

    Directory of Open Access Journals (Sweden)

    Karin Schwarzbauer

    Full Text Available To gain deeper insights into principles of cell biology, it is essential to understand how cells reorganize their genomes by chromatin remodeling. We analyzed chromatin remodeling on next generation sequencing data from resting and activated T cells to determine a whole-genome chromatin remodeling landscape. We consider chromatin remodeling in terms of nucleosome repositioning which can be observed most robustly in long nucleosome-free regions (LNFRs that are occupied by nucleosomes in another cell state. We found that LNFR sequences are either AT-rich or GC-rich, where nucleosome repositioning was observed much more prominently in GC-rich LNFRs - a considerable proportion of them outside promoter regions. Using support vector machines with string kernels, we identified a GC-rich DNA sequence pattern indicating loci of nucleosome repositioning in resting T cells. This pattern appears to be also typical for CpG islands. We found out that nucleosome repositioning in GC-rich LNFRs is indeed associated with CpG islands and with binding sites of the CpG-island-binding ZF-CXXC proteins KDM2A and CFP1. That this association occurs prominently inside and also prominently outside of promoter regions hints at a mechanism governing nucleosome repositioning that acts on a whole-genome scale.

  11. Dynamic characterization of oil fields, complex stratigraphically using genetic algorithms

    International Nuclear Information System (INIS)

    A novel methodology is presented in this paper for the characterization of highly heterogeneous oil fields by integration of the oil fields dynamic information to the static updated model. The objective of the oil field's characterization process is to build an oil field model, as realistic as possible, through the incorporation of all the available information. The classical approach consists in producing a model based in the oil field's static information, having as the process final stage the validation model with the dynamic information available. It is important to clarify that the term validation implies a punctual process by nature, generally intended to secure the required coherence between productive zones and petrophysical properties. The objective of the proposed methodology is to enhance the prediction capacity of the oil field's model by previously integrating, parameters inherent to the oil field's fluid dynamics by a process of dynamic data inversion through an optimization procedure based on evolutionary computation. The proposed methodology relies on the construction of the oil field's high-resolution static model, escalated by means of hybrid techniques while aiming to preserve the oil field's heterogeneity. Afterwards, using an analytic simulator as reference, the scaled model is methodically modified by means of an optimization process that uses genetic algorithms and production data as conditional information. The process's final product is a model that observes the static and dynamic conditions of the oil field with the capacity to minimize the economic impact that generates production historical adjustments to the simulation tasks. This final model features some petrophysical properties (porosity, permeability and water saturation), as modified to achieve a better adjustment of the simulated production's history versus the real one history matching. Additionally, the process involves a slight modification of relative permeability, which has

  12. Association of a centromere specific nucleosome with the yeast plasmid partitioning locus: Implications beyond plasmid partitioning

    OpenAIRE

    Jayaram, Makkuni

    2011-01-01

    The genetically defined point centromeres of budding yeasts and the epigenetically specified regional centromeres of all other eukaryotes harbor a common epigenetic mark in the form of a non-standard nucleosome. Although, the composition of the protein core of the centromere specific nucleosome and the nature of the DNA wrap around it are at present controversial, there is no doubt that this specialized nucleosome harbors a variant of the standard histone H3 (cenH3). The association of cenH3,...

  13. The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere

    OpenAIRE

    Cole, Hope A.; Howard, Bruce H.; David J Clark

    2011-01-01

    The centromeres of budding yeast are ∼120 bp in size and contain three functional elements: an AT-rich region flanked by binding sites for Cbf1 and CBF3. A specialized nucleosome containing the H3 variant Cse4 (CenH3) is formed at the centromere. Our genome-wide paired-end sequencing of nucleosomal DNA reveals that the centromeric nucleosome contains a micrococcal nuclease-resistant kernel of 123–135 bp, depending on the centromere, and is therefore significantly shorter than the canonical nu...

  14. Dynamic response modelling and characterization of a vertical electrothermal actuator

    International Nuclear Information System (INIS)

    Mathematical modelling and characterization of the dynamic response of a microelectromechanical system (MEMS) electrothermal actuator are presented in this paper. The mathematical model is based on a second-order partial differential equation (one-dimensional heat transfer) and a second-order ordinary differential equation (mechanical dynamic equation). The simulations are implemented using the piecewise finite difference method and the Runge–Kutta algorithm. The electrothermal modelling includes thermal conduction, convective thermal loss and radiation effects. The temperature dependence of resistivity and thermal conductivity of single crystal silicon have also been taken into consideration in the electrothermal modelling. It is calculated from the simulation results that the 'cold' beam of the electrothermal actuator is not only a mechanical constraint but also a thermal response compensation structure. The 0–90% electrothermal rise times for the individual 'hot' and 'cold' beams are calculated to be 32.9 ms and 42.8 ms, respectively, while the 0–90% electrothermal rise time for the whole actuator is calculated to be 17.3 ms. Nonlinear cubic stiffness has been considered in the thermal-mechanical modelling. Dynamic performances of the device have been characterized using a laser vibrometer, and the 0–90% thermal response time of the whole structure has been measured to be 16.8 ms, which matches well with the modelling results. The displacements of the device under different driving conditions and at resonant frequency have been modelled and measured, and the results from both modelling and experiment agree reasonably well. This work provides a comprehensive understanding of the dynamic behaviour of the electrothermal actuation mechanism. The model will be useful for designing control systems for microelectrothermal actuated devices

  15. Characterization of a periodically driven chaotic dynamical system

    CERN Document Server

    Crisanti, A; Lacorata, G; Purini, R; Crisanti, A

    1996-01-01

    We discuss how to characterize the behavior of a chaotic dynamical system depending on a parameter that varies periodically in time. In particular, we study the predictability time, the correlations and the mean responses, by defining a local--in--time version of these quantities. In systems where the time scale related to the time periodic variation of the parameter is much larger than the ``internal'' time scale, one has that the local quantities strongly depend on the phase of the cycle. In this case, the standard global quantities can give misleading information.

  16. Nucleosome structure of the yeast CHA1 promoter

    DEFF Research Database (Denmark)

    Moreira, José Manuel Alfonso; Holmberg, S

    1998-01-01

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

  17. Analytical model for nanoscale viscoelastic properties characterization using dynamic nanoindentation

    Science.gov (United States)

    Yuya, Philip A.; Patel, Nimitt G.

    2014-08-01

    In the last few decades, nanoindentation has gained widespread acceptance as a technique for materials properties characterization at micron and submicron length scales. Accurate and precise characterization of material properties with a nanoindenter is critically dependent on the ability to correctly model the response of the test equipment in contact with the material. In dynamic nanoindention analysis, a simple Kelvin-Voigt model is commonly used to capture the viscoelastic response. However, this model oversimplifies the response of real viscoelastic materials such as polymers. A model is developed that captures the dynamic nanoindentation response of a viscoelastic material. Indenter tip-sample contact forces are modelled using a generalized Maxwell model. The results on a silicon elastomer were analysed using conventional two element Kelvin-Voigt model and contrasted to analysis done using the Maxwell model. The results show that conventional Kelvin-Voigt model overestimates the storage modulus of the silicone elastomer by ~30%. Maxwell model represents a significant improvement in capturing the viscoelastic material behaviour over the Voigt model.

  18. nuMap: a web platform for accurate prediction of nucleosome positioning.

    Science.gov (United States)

    Alharbi, Bader A; Alshammari, Thamir H; Felton, Nathan L; Zhurkin, Victor B; Cui, Feng

    2014-10-01

    Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site. PMID:25220945

  19. nuMap:A Web Platform for Accurate Prediction of Nucleosome Positioning

    Institute of Scientific and Technical Information of China (English)

    Bader A Alharbi; Thamir H Alshammari; Nathan L Felton; Victor B Zhurkin; Feng Cui

    2014-01-01

    Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and param-eters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.

  20. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

    Science.gov (United States)

    Hu, Gangqing; Schones, Dustin E.; Cui, Kairong; Ybarra, River; Northrup, Daniel; Tang, Qingsong; Gattinoni, Luca; Restifo, Nicholas P.; Huang, Suming; Zhao, Keji

    2011-01-01

    Enhancers of transcription activate transcription via binding of sequence-specific transcription factors to their target sites in chromatin. In this report, we identify GATA1-bound distal sites genome-wide and find a global reorganization of the nucleosomes at these potential enhancers during differentiation of hematopoietic stem cells (HSCs) to erythrocytes. We show that the catalytic subunit BRG1 of BAF complexes localizes to these distal sites during differentiation and generates a longer nucleosome linker region surrounding the GATA1 sites by shifting the flanking nucleosomes away. Intriguingly, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1 and is linked to subsequent transcriptional regulation of target genes. PMID:21795385

  1. Statistical characterization of spatiotemporal sediment dynamics in the Venice lagoon

    Science.gov (United States)

    Carniello, Luca; D'Alpaos, Andrea; Botter, Gianluca; Rinaldo, Andrea

    2016-05-01

    Characterizing the dynamics of suspended sediment is crucial when investigating the long-term evolution of tidal landscapes. Here we apply a widely tested mathematical model which describes the dynamics of cohesive and noncohesive sediments, driven by the combined effect of tidal currents and wind waves, using 1 year long time series of observed water levels and wind data from the Venice lagoon. The spatiotemporal evolution of the computed suspended sediment concentration (SSC) is analyzed on the basis of the "peak over threshold" theory. Our analysis suggests that events characterized by high SSC can be modeled as a marked Poisson process over most of the lagoon. The interarrival time between two consecutive over threshold events, the intensity of peak excesses, and the duration are found to be exponentially distributed random variables over most of tidal flats. Our study suggests that intensity and duration of over threshold events are temporally correlated, while almost no correlation exists between interarrival times and both durations and intensities. The benthic vegetation colonizing the central southern part of the Venice lagoon is found to exert a crucial role on sediment dynamics: vegetation locally decreases the frequency of significant resuspension events by affecting spatiotemporal patterns of SSCs also in adjacent areas. Spatial patterns of the mean interarrival of over threshold SSC events are found to be less heterogeneous than the corresponding patterns of mean interarrivals of over threshold bottom shear stress events because of the role of advection/dispersion processes in mixing suspended sediments within the lagoon. Implications for long-term morphodynamic modeling of tidal environments are discussed.

  2. Pixel Analysis and Plasma Dynamics Characterized by Photospheric Spectral Data

    Science.gov (United States)

    Rasca, Anthony P.; Chen, James; Pevtsov, Alexei A.

    2016-05-01

    Recent observations of the photosphere using high spatial and temporal resolutions show small dynamic features at the resolving limit during emerging flux events. However, line-of-sight (LOS) magnetogram pixels only contain the net uncanceled magnetic flux, which is expected to increase for fixed regions as resolution limits improve. A new pixel dynamics method uses spectrographic images to characterize photospheric absorption line profiles by variations in line displacement, width, asymmetry, and peakedness and is applied to quiet-sun regions, active regions with no eruption, and an active region with an ongoing eruption. Using Stokes I images from SOLIS/VSM on 2012 March 13, variations in line width and peakedness of Fe I 6301.5 Å are shown to have a strong spatial and temporal relationship with an M7.9 X-ray flare originating from NOAA 11429. This relationship is observed as a flattening in the line profile as the X-ray flare approaches peak intensity and was not present in area scans of a non-eruptive active region on 2011 April 14. These results are used to estimate dynamic plasma properties on sub-pixel scales and provide both spatial and temporal information of sub-pixel activity at the photosphere. The analysis can be extended to include the full Stokes parameters and study signatures of magnetic fields and coupled plasma properties.

  3. High Dynamic Range Characterization of the Trauma Patient Plasma Proteome

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Tao; Qian, Weijun; Gritsenko, Marina A.; Xiao, Wenzhong; Moldawer, Lyle L.; Kaushal, Amit; Monroe, Matthew E.; Varnum, Susan M.; Moore, Ronald J.; Purvine, Samuel O.; Maier, Ronald V.; Davis, Ronald W.; Tompkins, Ronald G.; Camp, David G.; Smith, Richard D.

    2006-06-08

    While human plasma represents an attractive sample for disease biomarker discovery, the extreme complexity and large dynamic range in protein concentrations present significant challenges for characterization, candidate biomarker discovery, and validation. Herein, we describe a strategy that combines immunoaffinity subtraction and chemical fractionation based on cysteinyl peptide and N-glycopeptide captures with 2D-LC-MS/MS to increase the dynamic range of analysis for plasma. Application of this ''divide-and-conquer'' strategy to trauma patient plasma significantly improved the overall dynamic range of detection and resulted in confident identification of 22,267 unique peptides from four different peptide populations (cysteinyl peptides, non-cysteinyl peptides, N-glycopeptides, and non-glycopeptides) that covered 3654 nonredundant proteins. Numerous low-abundance proteins were identified, exemplified by 78 ''classic'' cytokines and cytokine receptors and by 136 human cell differentiation molecules. Additionally, a total of 2910 different N-glycopeptides that correspond to 662 N-glycoproteins and 1553 N-glycosylation sites were identified. A panel of the proteins identified in this study is known to be involved in inflammation and immune responses. This study established an extensive reference protein database for trauma patients, which provides a foundation for future high-throughput quantitative plasma proteomic studies designed to elucidate the mechanisms that underlie systemic inflammatory responses.

  4. Serum nucleosomes during neoadjuvant chemotherapy in patients with cervical cancer. Predictive and prognostic significance

    Directory of Open Access Journals (Sweden)

    Cetina Lucely

    2005-06-01

    Full Text Available Abstract Background It has been shown that free DNA circulates in serum plasma of patients with cancer and that at least part is present in the form of oligo- and monucleosomes, a marker of cell death. Preliminary data has shown a good correlation between decrease of nucleosomes with response and prognosis. Here, we performed pre- and post-chemotherapy determinations of serum nucleosomes with an enzyme-linked immunosorbent assay (ELISA method in a group of patients with cervical cancer receiving neoadjuvant chemotherapy. Methods From December 2000 to June 2001, 41 patients with cervical cancer staged as FIGO stages IB2-IIIB received three 21-day courses of carboplatin and paclitaxel, both administered at day 1; then, patients underwent radical hysterectomy. Nucleosomes were measured the day before (baseline, at day seven of the first course and day seven of the third course of chemotherapy. Values of nucleosomes were analyzed with regard to pathologic response and to time to progression-free and overall survival. Results All patients completed chemotherapy, were evaluable for pathologic response, and had nucleosome levels determined. At a mean follow-up of 23 months (range, 7–26 months, projected progression time and overall survival were 80.3 and 80.4%, respectively. Mean differential values of nucleosomes were lower in the third course as compared with the first course (p >0.001. The decrease in the third course correlated with pathologic response (p = 0.041. Survival analysis showed a statistically significant, better progression-free and survival time in patients who showed lower levels at the third course (p = 0.0243 and p = 0.0260, respectively. Cox regression analysis demonstrated that nucleosome increase in the third course increased risk of death to 6.86 (95% confidence interval [CI 95%], 0.84–56.0. Conclusion Serum nucleosomes may have a predictive role for response and prognostic significance in patients with cervical cancer

  5. A high-resolution map of nucleosome positioning on a fission yeast centromere

    OpenAIRE

    Song, Jun S.; Liu, Xingkun; Liu, X. Shirley; He, Xiangwei

    2008-01-01

    A key element for defining the centromere identity is the incorporation of a specific histone H3, CENPA, known as Cnp1p in Schizosaccharomyces pombe. Previous studies have suggested that functional S. pombe centromeres lack regularly positioned nucleosomes and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are, in fact, positioned in regular intervals in the core of centromere 2, providing the first high-resolution m...

  6. Contribution of dynamic focusing to ultrasonic defect characterization

    International Nuclear Information System (INIS)

    Non destructive testing of vessels of pressurized water reactors uses ultrasonic focused transducers, with spherically shaped emitting surface or requiring an acoustic lens. But a mechanically focused transducer has to be used for a given inspection zone and for a fixed control configuration. The aim of this thesis is to improve ultrasonic defect characterization using adaptive dynamic focusing. Such a technique makes use of a ultrasonic defect characterization using adaptive dynamic focusing. Such a technique makes use of an ultrasonic transducer split into an array of individually controlled elements, allowing to apply delay and amplitude laws, calculated from modeling or experimentally deduced. Acoustical characteristics of the ultrasonic beam in the inspected specimen this can be electronically controlled; refraction angle, depth focusing, beam width. We briefly describe in the first chapter a theoretical modeling of the ultrasonic field radiated through a fluid/solid interface, extended to phase array transducers. This model is based on the integral formulation of Rayleigh, modified to take into account transmission through a fluid/solid (homogeneous and isotropic), of planar or cylindrical shape. In the second chapter an experimental study of this technique, with delay and amplitude laws given from the model, is presented, showing the efficiency of this method to adjust the acoustic performances. In he third chapter, experimental delay laws, extracted from the time distribution of signals received by the array (issued from a preliminary detected reflector), are used to provide an optimal imaging of the defect. This self-focusing procedure shows to adapt to a defect without using theoretical delays. The last chapter is dedicated to different applications devoted to improved defect characterization. The first application uses amplitude distribution received by the array, pointing out geometric characteristics of the reflector, while the second application

  7. Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic states.

    Science.gov (United States)

    Dodd, Ian B; Sneppen, Kim

    2011-12-01

    Positive feedback in nucleosome modification has been proposed to allow large chromatin regions to exist stably and heritably in distinct expression states. However, modeling has shown that such epigenetic bistability requires that modifying enzymes recruited by nucleosomes are active on distant nucleosomes, potentially allowing uncontrollable spreading of modification. By modeling the silencing of mating-type loci in Saccharomyces cerevisiae, we show that a modification reaction that combines a long-range component and a locally acting component can provide bistability and can be blocked by simple barriers that interrupt the nucleosome chain. We find that robust containment of the silenced region could be achieved by the presence of a number of weak simple barriers in the surrounding chromatin and a limited capacity of the positive feedback reaction. In addition, we show that the state of the silenced region can be regulated by silencer elements acting only on neighboring nucleosomes. Thus, a relatively simple set of nucleosome-modifying enzymes and recognition domains is all that is needed to make chromatin-based epigenetics useful and safe. PMID:22037584

  8. A 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNA

    CERN Document Server

    Tesoro, S; Morozov, A N; Sulaiman, N; Marenduzzo, D

    2015-01-01

    The first level of folding of DNA in eukaryotes is provided by the so called '10nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging 'bead on a string' structure. In this work we present a one dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We consider both the case of homogeneous DNA, where the problem can be mapped to a Tonks gas, and that of genomic sheep DNA, where our modelling is informed by high-resolution nucleosome positioning data. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally, we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on ...

  9. Organisation of nucleosomal arrays reconstituted with repetitive African green monkey α-satellite DNA as analysed by atomic force microscopy

    OpenAIRE

    Bussiek, Malte; Müller, Gabriele; Waldeck, Waldemar; Diekmann, Stephan; Langowski, Jörg

    2007-01-01

    Alpha-satellite DNA (AS) is part of centromeric DNA and could be relevant for centromeric chromatin structure: its repetitive character may generate a specifically ordered nucleosomal arrangement and thereby facilitate kinetochore protein binding and chromatin condensation. Although nucleosomal positioning on some satellite sequences had been shown, including AS from African green monkey (AGM), the sequence-dependent nucleosomal organisation of repetitive AS of this species has so far not bee...

  10. Nucleosome transactions on the Hypocrea jecorina (Trichoderma reesei) cellulase promoter cbh2 associated with cellulase induction.

    Science.gov (United States)

    Zeilinger, S; Schmoll, M; Pail, M; Mach, R L; Kubicek, C P

    2003-10-01

    The 5' regulatory region of the cbh2 gene of Hypocrea jecorina contains the cbh2 activating element (CAE) which is essential for induction of cbh2 gene expression by sophorose and cellulose. The CAE consists of two motifs, a CCAAT box on the template strand and a GTAATA box on the coding strand, which cooperate during induction. Northern analyses of cbh2 gene expression has revealed an absolute dependence on induction, but no direct effect of Cre1-mediated carbon catabolite repression. Investigation of the chromatin structure in the wild-type strain showed that, under repressing conditions, there is a nucleosome free region (nfr) around the CAE, which is flanked by strictly positioned nucleosomes. Induction results in a loss of positioning of nucleosomes -1 and -2 downstream of the CAE, thus making the TATA box accessible. Simultaneous mutation of both motifs of the CAE, or of the CCAAT-box alone, also leads to shifting of nucleosome -1, which normally covers the TATA-box under repressing conditions, whereas mutation of the GTAATA element results in a narrowing of the nfr, indicating that the proteins that bind to both motifs in the CAE interact with chromatin, although in different ways. A cellulase-negative mutant strain, which has previously been shown to be altered in protein binding to the CAE, still displayed the induction-specific changes in nucleosome structure, indicating that none of the proteins that directly interact with CAE are affected, and that nucleosome rearrangement and induction of cbh2 expression are uncoupled. Interestingly, the carbon catabolite repressor Cre1 is essential for strict nucleosome positioning in the 5' regulatory sequences of cbh2 under all of the conditions tested, and induction can occur in a promoter that lacks positioned nucleosomes. These data suggest that Cre1, the Hap2/3/5 complex and the GTAATA-binding protein are all involved in nucleosome assembly on the cbh2 promoter, and that the latter two respond to inducing

  11. Characterization and Modeling of Segmental Dynamics in Silicone Based Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, R S; Baumann, T; Gee, R; Maiti, A; Patel, M; Lewicki, J

    2009-03-27

    The addition of nano-particles with novel chemical, optical, or barrier properties further opens the door to the development of so-called multifunctional materials (1). Key to developing robust, tailored composites is a detailed understanding of the structural contributions to the engineering properties of the composite and how they may change with time in harsh service conditions. The segmental dynamics and local order underlie much of the fundamental physics that influence the performance of elastomers and can serve as important diagnostics for reinforcement and other fundamental properties (e.g., network topology, cross-link density, the number and distance between chemical and physical (entanglements) cross-links, the type and volume fraction of filler) and thus provide a route to this fundamental understanding. {sup 1}H MQ-NMR spectroscopy has shown the ability to provide more reliable and quantitative information regarding the elastomer network structure and heterogeneities (2). {sup 1}H MQ-NMR methods allow for the measurement of absolute residual dipolar couplings (<{Omega}{sub d}>) and thus the segmental/cooperative dynamics Thus, the MQ-NMR method allows for the direct measure of network topology and in many cases, filler-particle interactions. The ability of MD methods to uncover structural motifs and dynamics at the atomistic scale is well known. In polymer systems, however, the relationship to bulk material properties can be somewhat tenuous due to often limited number of atoms and short time durations that can be studied. Extending these MD simulations to large assemblies of atoms and extending them to longer times using state of the art computational resources has allowed us to probe some useful relationships. MD provides static and dynamic properties for a collection of particles that allow atomic scale insights that are difficult to gain otherwise. We have been exploiting these methods to characterize the effects of network structure and filler

  12. Dynamic Characterization of Cercal Mechanosensory Hairs of Crickets

    Directory of Open Access Journals (Sweden)

    Joel M. Book

    2012-10-01

    Full Text Available Previous dynamic characterizations of the cercal mechanosensory hairs of crickets have generally been limited to the first resonant frequency and associated deflection shape. A more complete description of the mechanical dynamics of these structures could be obtained by an experimental modal analysis. This paper describes a method by which a full experimental modal analysis, giving natural frequency, mode shape, and modal damping ratio, of these sense organs can be performed. Results of this analysis, employing an unmeasured moving-air excitation and non-contact vibration measurement with an output-only identification method are presented. Two distinct types of behaviour were observed, one of which was a good match for the behaviour expected based on the literature, and one of which was quite different. These two behaviours had distinct patterns of modal parameters. The method described in this paper has been shown to be able to estimate the modal parameters, including natural frequency, modal damping ratio, and normalized mode shape, for the first mode of cercal mechanosensory hairs of crickets. The method could practically be extended to higher modes and a wide variety of other sound and vibration sense organs with the selection of appropriate excitation and specimen supports.

  13. A spatiotemporal characterization method for the dynamic cytoskeleton.

    Science.gov (United States)

    Alhussein, Ghada; Shanti, Aya; Farhat, Ilyas A H; Timraz, Sara B H; Alwahab, Noaf S A; Pearson, Yanthe E; Martin, Matthew N; Christoforou, Nicolas; Teo, Jeremy C M

    2016-05-01

    The significant gap between quantitative and qualitative understanding of cytoskeletal function is a pressing problem; microscopy and labeling techniques have improved qualitative investigations of localized cytoskeleton behavior, whereas quantitative analyses of whole cell cytoskeleton networks remain challenging. Here we present a method that accurately quantifies cytoskeleton dynamics. Our approach digitally subdivides cytoskeleton images using interrogation windows, within which box-counting is used to infer a fractal dimension (Df ) to characterize spatial arrangement, and gray value intensity (GVI) to determine actin density. A partitioning algorithm further obtains cytoskeleton characteristics from the perinuclear, cytosolic, and periphery cellular regions. We validated our measurement approach on Cytochalasin-treated cells using transgenically modified dermal fibroblast cells expressing fluorescent actin cytoskeletons. This method differentiates between normal and chemically disrupted actin networks, and quantifies rates of cytoskeletal degradation. Furthermore, GVI distributions were found to be inversely proportional to Df , having several biophysical implications for cytoskeleton formation/degradation. We additionally demonstrated detection sensitivity of differences in Df and GVI for cells seeded on substrates with varying degrees of stiffness, and coated with different attachment proteins. This general approach can be further implemented to gain insights on dynamic growth, disruption, and structure of the cytoskeleton (and other complex biological morphology) due to biological, chemical, or physical stimuli. © 2016 Wiley Periodicals, Inc. PMID:27015595

  14. iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.

    Directory of Open Access Journals (Sweden)

    Wei Chen

    Full Text Available Nucleosome positioning has important roles in key cellular processes. Although intensive efforts have been made in this area, the rules defining nucleosome positioning is still elusive and debated. In this study, we carried out a systematic comparison among the profiles of twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome. We found that nucleosomal sequences have some position-specific physicochemical features, which can be used for in-depth studying nucleosomes. Meanwhile, a new predictor, called iNuc-PhysChem, was developed for identification of nucleosomal sequences by incorporating these physicochemical properties into a 1788-D (dimensional feature vector, which was further reduced to a 884-D vector via the IFS (incremental feature selection procedure to optimize the feature set. It was observed by a cross-validation test on a benchmark dataset that the overall success rate achieved by iNuc-PhysChem was over 96% in identifying nucleosomal or linker sequences. As a web-server, iNuc-PhysChem is freely accessible to the public at http://lin.uestc.edu.cn/server/iNuc-PhysChem. For the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented just for the integrity in developing the predictor. Meanwhile, for those who prefer to run predictions in their own computers, the predictor's code can be easily downloaded from the web-server. It is anticipated that iNuc-PhysChem may become a useful high throughput tool for both basic research and drug design.

  15. Characterization of dynamic loads on the LMFBR rotating shield

    International Nuclear Information System (INIS)

    The rotating shields structure is a potential weak point of some current designs of primary containment against postulated whole core explosions. The calculation of the effect of transient loads on this structure, resulting from such an explosion, is therefore important in developing a safety case. The transient loads are usually calculated by computer codes such as ASTARTE, SEURBNUK, REXCO or ICECO and the effect of these loads on the structure by a suitable finite element code. Such procedure can be lengthly and costly. The present paper proposed a procedure which allows the consequences of changes in the transient loads, resulting from design changes for example, to be quickly and simply gauged. The load-impulse method of characterizing dynamic response of a structural system is well established. Provided loads with a similar temporal variation are compared, it can be shown that the dynamic response depends on only two features of the load, an average load and a time intregrated load or impulse. The scope of this approach has been extended by Youngdahl who has shown, for structures which deform in a rigid-plastic manner, that complex laoding histories can be equated to a rectangular form of loading, in a precise manner for simple structures and in an approximate manner for more complicated structures. This paper proposes that the failure characteristics of the rotating shields for which extensive plastic deformation is involved, be calculated for rectangular type loadings. The complex transient loadings calculated for various explosions and various changes in the primary vessel design can then be reduced to an equivalent rectangular form and the consequencial response of the shields structure deduced. (orig.)

  16. A one-dimensional statistical mechanics model for nucleosome positioning on genomic DNA

    Science.gov (United States)

    Tesoro, S.; Ali, I.; Morozov, A. N.; Sulaiman, N.; Marenduzzo, D.

    2016-02-01

    The first level of folding of DNA in eukaryotes is provided by the so-called ‘10 nm chromatin fibre’, where DNA wraps around histone proteins (∼10 nm in size) to form nucleosomes, which go on to create a zig-zagging bead-on-a-string structure. In this work we present a one-dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We focus on the case of genomic sheep DNA, and we start from effective potentials valid at infinite dilution and determined from high-resolution in vitro salt dialysis experiments. We study positioning within a polynucleosome chain, and compare the results for genomic DNA to that obtained in the simplest case of homogeneous DNA, where the problem can be mapped to a Tonks gas [1]. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point-like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on experimentally observable quantities in experiments on polynucleosome chromatin fibres reconstituted in vitro.

  17. Characterization of Affective States by Pupillary Dynamics and Autonomic Correlates

    Directory of Open Access Journals (Sweden)

    Francesco eOnorati

    2013-11-01

    Full Text Available With the recent advent of new recording devices and an easier access to signal processing tools, researchers are increasingly exploring and studying the Pupil Dilation (PD signal. Recently, numerous studies pointed out the relations between PD dynamics and psychophysiological states. Although it is well known that PD is controlled by the Autonomic Nervous System (ANS, and ANS responses are related to emotional events/stimuli, the relationship between emotional states and PD is still an open issue. The aim of this study is to define the statistical properties of the PD signal, to understand its relation with ANS correlates such as Heart Rate Variability (HRV and respiration, and to explore if PD could provide information for the evaluation of the psychophysiological response of ANS to affective triggering events. ECG, respiration (RESP and Pupil Dilation (PD data from 13 normal subjects were recorded during a memory recall paradigm, and processed with spectral and cross-spectral analysis. Our results demonstrate that variability indices extracted from fast PD oscillations, not observable through standard cardiorespiratory identification in the frequency domain, would be able to discern psychophysiological responses elicited by basic emotional stimuli. A strong linear coupling was found between the variables, due to the influence of RESP on both PD and HRV within the High Frequency (HF band, from 0.15 and 0.45 Hz. Most importantly, our results point at PD features as possible candidates for characterizing basic emotional stimuli.

  18. Characterizing the nonlinear and dynamical properties of thermionic conversion

    Energy Technology Data Exchange (ETDEWEB)

    Irvin, A.D.; Tanner, P.; Fraser, D.; Dewson, T.

    1998-07-01

    The conversion process of thermal power to electrical power is represented as a mixed linear-nonlinear convolution form of the Onsager equations. A moment hierarchy method is presented that transforms the Volterra functional expansion into a linear algebraic form, which is trivial to invert. The method is nonparametric and can be used to estimate both the form and amplitude of the ascending order multivariate nonlinear response functions that characterize the conversion and transport processes from the discrete vector time data. A multi-channel input-output representation for causal thermal and electrical processes is discussed with reference to the physical significance of the estimated response function. This representation is then used to develop a multi-convolution percolation theory for coupled thermal electric processes in ceramic materials. In addition to the Volterra approach a numerical calculation procedure is being developed that can model the transport properties in both the electrodes and the inter-electrode plasma. The starting point for this is the plasma physics particle in a cell model KARAT. This simulation model is presently being validated against available empirical data and some provisional results are presented here. In order to design and understand the properties of ceramically coated electrodes that have thermodynamic forces acting to modify the generation and overall transport properties of the diode KARAT is being extended to include the nonlinear dynamic effects of combined temperature and species gradients in the electrode surface layers.

  19. Characterizing the Human Cone Photoreceptor Mosaic via Dynamic Photopigment Densitometry

    Science.gov (United States)

    Sabesan, Ramkumar; Hofer, Heidi; Roorda, Austin

    2015-01-01

    Densitometry is a powerful tool for the biophysical assessment of the retina. Until recently, this was restricted to bulk spatial scales in living humans. The application of adaptive optics (AO) to the conventional fundus camera and scanning laser ophthalmoscope (SLO) has begun to translate these studies to cellular scales. Here, we employ an AOSLO to perform dynamic photopigment densitometry in order to characterize the optical properties and spectral types of the human cone photoreceptor mosaic. Cone-resolved estimates of optical density and photosensitivity agree well with bulk estimates, although show smaller variability than previously reported. Photopigment kinetics of individual cones derived from their selective bleaching allowed efficient mapping of cone sub-types in human retina. Estimated uncertainty in identifying a cone as long vs middle wavelength was less than 5%, and the total time taken per subject ranged from 3–9 hours. Short wavelength cones were delineated in every subject with high fidelity. The lack of a third cone-type was confirmed in a protanopic subject. In one color normal subject, cone assignments showed 91% correspondence against a previously reported cone-typing method from more than a decade ago. Combined with cone-targeted stimulation, this brings us closer in studying the visual percept arising from a specific cone type and its implication for color vision circuitry. PMID:26660894

  20. Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.

    Science.gov (United States)

    Ichikawa, Yuichi; Morohashi, Nobuyuki; Tomita, Nobuyuki; Mitchell, Aaron P; Kurumizaka, Hitoshi; Shimizu, Mitsuhiro

    2016-07-22

    Nucleosome-depleted regions (NDRs) (also called nucleosome-free regions or NFRs) are often found in the promoter regions of many yeast genes, and are formed by multiple mechanisms, including the binding of activators and enhancers, the actions of chromatin remodeling complexes, and the specific DNA sequences themselves. However, it remains unclear whether NDR formation per se is essential for transcriptional activation. Here, we examined the relationship between nucleosome organization and gene expression using a defined yeast reporter system, consisting of the CYC1 minimal core promoter and the lacZ gene. We introduced simple repeated sequences that should be either incorporated in nucleosomes or excluded from nucleosomes in the site upstream of the TATA boxes. The (CTG)12, (GAA)12 and (TGTAGG)6 inserts were incorporated into a positioned nucleosome in the core promoter region, and did not affect the reporter gene expression. In contrast, the insertion of (CGG)12, (TTAGGG)6, (A)34 or (CG)8 induced lacZ expression by 10-20 fold. Nucleosome mapping analyses revealed that the inserts that induced the reporter gene expression prevented nucleosome formation, and created an NDR upstream of the TATA boxes. Thus, our results demonstrated that NDR formation dictated by DNA sequences is sufficient for transcriptional activation from the core promoter in vivo. PMID:27208777

  1. RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response.

    Science.gov (United States)

    Groocock, Lynda M; Nie, Minghua; Prudden, John; Moiani, Davide; Wang, Tao; Cheltsov, Anton; Rambo, Robert P; Arvai, Andrew S; Hitomi, Chiharu; Tainer, John A; Luger, Karolin; Perry, J Jefferson P; Lazzerini-Denchi, Eros; Boddy, Michael N

    2014-05-01

    The post-translational modification of DNA repair and checkpoint proteins by ubiquitin and small ubiquitin-like modifier (SUMO) critically orchestrates the DNA damage response (DDR). The ubiquitin ligase RNF4 integrates signaling by SUMO and ubiquitin, through its selective recognition and ubiquitination of SUMO-modified proteins. Here, we define a key new determinant for target discrimination by RNF4, in addition to interaction with SUMO. We identify a nucleosome-targeting motif within the RNF4 RING domain that can bind DNA and thereby enables RNF4 to selectively ubiquitinate nucleosomal histones. Furthermore, RNF4 nucleosome-targeting is crucially required for the repair of TRF2-depleted dysfunctional telomeres by 53BP1-mediated non-homologous end joining. PMID:24714598

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

    Science.gov (United States)

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

    2016-06-01

    Nuclear receptor-binding SET domain protein 2 (NSD2) is a histone H3 lysine 36 (H3K36)-specific methyltransferase enzyme that is overexpressed in a number of cancers, including multiple myeloma. NSD2 binds to S-adenosyl-l-methionine (SAM) and nucleosome substrates to catalyze the transfer of a methyl group from SAM to the ε-amino group of histone H3K36. Equilibrium binding isotope effects and density functional theory calculations indicate that the SAM methyl group is sterically constrained in complex with NSD2, and that this steric constraint is released upon nucleosome binding. Together, these results show that nucleosome binding to NSD2 induces a significant change in the chemical environment of enzyme-bound SAM. PMID:27183271

  3. 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.

  4. Nucleosomal organization of chromatin in sperm nuclei of the bivalve mollusc Aulacomya ater.

    Science.gov (United States)

    Olivares, C; Ruiz, S

    1991-03-13

    The sperm nuclei of Aulacomya ater, family Mitylidae, contain three proteins (X, Aa5 and Aa6) which are specific to this cell type coexisting with a set of five somatic-type histones. Information about the chromatin structure resulting from this kind of association is scarce. Therefore, we have probed the structure of this sperm chromatin through digestion with micrococcal nuclease in combination with salt fractionation. The data obtained have allowed us to propose a nucleosomal arrangement for this chromatin. However, two types of nucleosomes would be present in agreement with their protein components. PMID:1861676

  5. Differential Dynamic Microscopy to characterize Brownian motion and bacteria motility

    OpenAIRE

    Germain, David; Leocmach, Mathieu; Gibaud, Thomas

    2015-01-01

    We have developed a lab work module where we teach undergraduate students how to quantify the dynamics of a suspension of microscopic particles, measuring and analyzing the motion of those particles at the individual level or as a group. Differential Dynamic Microscopy (DDM) is a relatively recent technique that precisely does that and constitutes an alternative method to more classical techniques such as dynamics light scattering (DLS) or video particle tracking (VPT). DDM consists in imagin...

  6. Industry review: Locomotive dynamic characterization test-analysis

    Science.gov (United States)

    1981-01-01

    Data are given relative to tests performed on locomotive components. Dynamic characteristics related to safety are described. Suspension systems, shock absorbers, data processing, bearings, and damping are discussed.

  7. Comparative studies of genome-wide maps of nucleosomes between deletion mutants of elp3 and hos2 genes of Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Takashi Matsumoto

    Full Text Available In order to elucidate the influence of histone acetylation upon nucleosomal DNA length and nucleosome position, we compared nucleosome maps of the following three yeast strains; strain BY4741 (control, the elp3 (one of histone acetyltransferase genes deletion mutant, and the hos2 (one of histone deactylase genes deletion mutant of Saccharomyces cerevisiae. We sequenced mononucleosomal DNA fragments after treatment with micrococcal nuclease. After mapping the DNA fragments to the genome, we identified the nucleosome positions. We showed that the distributions of the nucleosomal DNA lengths of the control and the hos2 disruptant were similar. On the other hand, the distribution of the nucleosomal DNA lengths of the elp3 disruptant shifted toward shorter than that of the control. It strongly suggests that inhibition of Elp3-induced histone acetylation causes the nucleosomal DNA length reduction. Next, we compared the profiles of nucleosome mapping numbers in gene promoter regions between the control and the disruptant. We detected 24 genes with low conservation level of nucleosome positions in promoters between the control and the elp3 disruptant as well as between the control and the hos2 disruptant. It indicates that both Elp3-induced acetylation and Hos2-induced deacetylation influence the nucleosome positions in the promoters of those 24 genes. Interestingly, in 19 of the 24 genes, the profiles of nucleosome mapping numbers were similar between the two disruptants.

  8. Organisation of nucleosomal arrays reconstituted with repetitive African green monkey α-satellite DNA as analysed by atomic force microscopy

    Science.gov (United States)

    Bussiek, Malte; Müller, Gabriele; Waldeck, Waldemar; Diekmann, Stephan

    2007-01-01

    Alpha-satellite DNA (AS) is part of centromeric DNA and could be relevant for centromeric chromatin structure: its repetitive character may generate a specifically ordered nucleosomal arrangement and thereby facilitate kinetochore protein binding and chromatin condensation. Although nucleosomal positioning on some satellite sequences had been shown, including AS from African green monkey (AGM), the sequence-dependent nucleosomal organisation of repetitive AS of this species has so far not been analysed. We therefore studied the positioning of reconstituted nucleosomes on AGM AS tandemly repeated DNA. Enzymatic analysis of nucleosome arrays formed on an AS heptamer as well as the localisation of mononucleosomes on an AS dimer by atomic force microscopy (AFM) showed one major positioning frame, in agreement with earlier results. The occupancy of this site was in the range of 45–50%, in quite good agreement with published in vivo observations. AFM measurements of internucleosomal distances formed on the heptamer indicated that the nucleosomal arrangement is governed by sequence-specific DNA-histone interactions yielding defined internucleosomal distances, which, nevertheless, are not compatible with a uniform phasing of the nucleosomes with the AGM AS repeats. PMID:17503032

  9. Global analysis of core histones reveals nucleosomal surfaces required for chromosome bi-orientation

    OpenAIRE

    Kawashima, Satoshi; Nakabayashi, Yu; Matsubara, Kazuko; Sano, Norihiko; Enomoto, Takemi; Tanaka, Kozo; Seki, Masayuki; Horikoshi, Masami

    2011-01-01

    Kinetochore assembly requires centromere-specific nucleosomes that contain the histone H3 variant CenH3, but less is known about the role of canonical histones in this process. This study reports on the function of histones H2A, H2B, H3, and H4 in chromosome segregation.

  10. Small-Activating RNA Can Change Nucleosome Positioning in Human Fibroblasts.

    Science.gov (United States)

    Wang, Bin; Sun, Jing; Shi, Jiandong; Guo, Qing; Tong, Xiangrong; Zhang, Jin; Hu, Ningzhu; Hu, YunZhang

    2016-07-01

    RNA activation (RNAa) is a mechanism of positive gene expression regulation mediated by small-activating RNAs (saRNAs), which target gene promoters and have been used as tools to manipulate gene expression. Studies have shown that RNAa is associated with epigenetic modifications at promoter regions; however, it is unclear whether these modifications are the cause or a consequence of RNAa. In this study, we examined changes in nucleosome repositioning and the involvement of RNA polymerase II (RNAPII) in this process. We screened saRNAs for OCT4 (POU5F1), SOX2, and NANOG, and identified several novel saRNAs. We found that nucleosome positioning was altered after saRNA treatment and that the formation of nucleosome-depleted regions (NDRs) contributed to RNAa at sites of RNAPII binding, such as the TATA box, CpG islands (CGIs), proximal enhancers, and proximal promoters. Moreover, RNAPII appeared to be bound specifically to NDRs. These results suggested that changes in nucleosome positions resulted from RNAa. We thus propose a hypothesis that targeting promoter regions using exogenous saRNAs can induce the formation of NDRs, exposing regulatory binding sites to recruit RNAPII, a key component of preinitiation complex, and leading to increased initiation of transcription. PMID:26993320

  11. Dynamic Simulation of VEGA SRM Bench Firing By Using Propellant Complex Characterization

    Science.gov (United States)

    Di Trapani, C. D.; Mastrella, E.; Bartoccini, D.; Squeo, E. A.; Mastroddi, F.; Coppotelli, G.; Linari, M.

    2012-07-01

    During the VEGA launcher development, from the 2004 up to now, 8 firing tests have been performed at Salto di Quirra (Sardinia, Italy) and Kourou (Guyana, Fr) with the objective to characterize and qualify of the Zefiros and P80 Solid Rocket Motors (SRM). In fact the VEGA launcher configuration foreseen 3 solid stages based on P80, Z23 and Z9 Solid Rocket Motors respectively. One of the primary objectives of the firing test is to correctly characterize the dynamic response of the SRM in order to apply such a characterization to the predictions and simulations of the VEGA launch dynamic environment. Considering that the solid propellant is around 90% of the SRM mass, it is very important to dynamically characterize it, and to increase the confidence in the simulation of the dynamic levels transmitted to the LV upper part from the SRMs. The activity is articulated in three parts: • consolidation of an experimental method for the dynamic characterization of the complex dynamic elasticity modulus of elasticity of visco-elastic materials applicable to the SRM propellant operative conditions • introduction of the complex dynamic elasticity modulus in a numerical FEM benchmark based on MSC NASTRAN solver • analysis of the effect of the introduction of the complex dynamic elasticity modulus in the Zefiros FEM focusing on experimental firing test data reproduction with numerical approach.

  12. Autoantibodies to histone, DNA and nucleosome antigens in canine systemic lupus erythematosus.

    Science.gov (United States)

    Monestier, M; Novick, K E; Karam, E T; Chabanne, L; Monier, J C; Rigal, D

    1995-01-01

    Dogs can develop systemic lupus erythematosus syndromes that are clinically similar to those seen in humans. In contrast, previous observations suggest differences in their autoantibody reactivity patterns against histones and DNA which are components of the nucleosome in chromatin. The objective of this study was to assess comprehensively the levels of autoantibodies against histone, DNA and nucleosome antigens in a population of lupus dogs. The specificities of antibodies in lupus and control dog sera were determined using IgM- and IgG-specific reagents in an ELISA against a variety of chromatin antigens. When compared with control sera, IgG antibodies to individual histones H1, H2A, H3 and H4 were significantly higher in the lupus group. In contrast, we did not detect IgG antibodies specific for H2B, H2A-H2B, DNA, H2A-H2B-DNA or nucleosome in lupus dogs. There was no significant increase in any of the IgM specificities tested. Therefore, the reactivity pattern to nucleosome antigens in canine lupus is restricted to IgG antibodies against individual histones H1, H2A, H3 and H4. This stands in contrast with human and murine lupus, where autoantibodies are directed against a wide variety of nucleosomal determinants, suggesting that unique mechanisms lead to the expansion of anti-histone antibody clones in canine lupus. The high incidence of glomerulonephritis in dog lupus suggests that anti-DNA antibodies are not required for the development of this complication, whereas IgG anti-histone antibodies may be relevant to its pathogenesis. PMID:7529150

  13. Dynamic Characterization of Materials from a Refrigerator Compartment

    OpenAIRE

    Ilka, Bringhenti; Martinez, Jesus Alberto Ortiz; Lenzi, Arcanjo; Pellegrini, Claudio

    2012-01-01

    The dynamic properties of materials are important parameters for numerical vibro-acoustics analysis of a household refrigerator. The compartment of a household refrigerator is typically composed by three types of materials: hot rolled steel, polyurethane rigid foam (PUR) and high impact polystyrene (HIPS). In this work, the mechanical properties (dynamical Young‟s modulus and loss factor) of these materials were determinate in order to comprehend its frequency-dependent behavior to use them p...

  14. Effective Transmission Coverage Area-Based Link Dynamics Characterization of VANET in Highway Scenario

    OpenAIRE

    Chunfeng Liu; Oliver; Yang; Gen Li; Yantai Shu

    2015-01-01

    This paper uses the concept of effective transmission coverage area as a model for the derivation of analytic expressions in order to characterize the dynamic statistics of link lifetime, new link arrival rate, new link interarrival time, link breakage interarrival time, and so forth. Extensive simulations have been undertaken to verify the derived analytical expressions via generated mobility traces. Results demonstrate that the proposed analytical model can characterize the dynamic statisti...

  15. Cost effective ER data acquisition using a dynamic characterization strategy

    International Nuclear Information System (INIS)

    The important first step in remediating contaminated sites is completing characterization. The process for characterization of natural environmental media (i.e., soil, sediment, surface water, groundwater) involves three basic steps: (1) develop a plan, (2) implement the plan by collecting information necessary to define the nature and extent of contaminants in the natural media, and (3) integrate, interpret and report the results. Because of budgetary constraints, these three steps are typically applied linearly with the expectation that by the end of one application of the process the site will be characterized with sufficient resolution to make decisions about remedial actions. Our experience over the past 13 years at a complex site in Tennessee has shown that this linear approach to characterization does not produce the desired resolution. Because characterization is typically a process of defining unknowns the inflexible nature of the linear approach makes it impractical to react as the conceptual understanding of site contaminants changes in response to the acquisition of new data. An alternative, flexible approach to characterization has been developed based on lessons learned. Over the past 3 years the flexible approach has cost-effectively produced the information needed for decision making. (authors)

  16. Label-free characterization of biomembranes: from structure to dynamics

    NARCIS (Netherlands)

    Mashaghi, A.; Mashaghi, S.; Reviakine, I.; Heeren, R.M.A.; Sandoghdarf, V.; Bonn, M.

    2013-01-01

    We review recent progress in the study of the structure and dynamics of phospholipid membranes and associated proteins, using novel label-free analytical tools. We describe these techniques and illustrate them with examples highlighting current capabilities and limitations. Recent advances in applyi

  17. Label-free characterization of biomembranes: from structure to dynamics

    OpenAIRE

    Mashaghi, A.; Mashaghi, S.; Reviakine, I.; Heeren, R.M.A.; Sandoghdarf, V.; Bonn, M. (Marie-Luise)

    2013-01-01

    We review recent progress in the study of the structure and dynamics of phospholipid membranes and associated proteins, using novel label-free analytical tools. We describe these techniques and illustrate them with examples highlighting current capabilities and limitations. Recent advances in applying such techniques to biological and model membranes for biophysical studies and biosensing applications are presented, and future prospects are discussed.

  18. A Chemical Biology Approach to Reveal Sirt6-targeted Histone H3 Sites in Nucleosomes.

    Science.gov (United States)

    Wang, Wesley Wei; Zeng, Yu; Wu, Bo; Deiters, Alexander; Liu, Wenshe R

    2016-07-15

    As a member of a highly conserved family of NAD(+)-dependent histone deacetylases, Sirt6 is a key regulator of mammalian genome stability, metabolism, and life span. Previous studies indicated that Sirt6 is hardwired to remove histone acetylation at H3K9 and H3K56. However, how Sirt6 recognizes its nucleosome substrates has been elusive due to the difficulty of accessing homogeneous acetyl-nucleosomes and the low activity of Sirt6 toward peptide substrates. Based on the fact that Sirt6 has an enhanced activity to remove long chain fatty acylation from lysine, we developed an approach to recombinantly synthesize histone H3 with a fatty acylated lysine, N(ε)-(7-octenoyl)-lysine (OcK), installed at a number of lysine sites and used these acyl-H3 proteins to assemble acyl-nucleosomes as active Sirt6 substrates. A chemical biology approach that visualizes OcK in nucleosomes and therefore allows direct sensitization of Sirt6 activities on its acyl-nucleosome substrates was also formulated. By combining these two approaches, we showed that Sirt6 actively removes acylation from H3K9, H3K18, and H3K27; has relatively low activities toward H3K4 and K3K23; but sluggishly removes acylation at H3K14, H3K36, H3K56, and H3K79. Overexpressing Sirt6 in 293T cells led to downregulated acetylation at H3K18 and K3K27, confirming these two novel Sirt6-targeted nucleosome lysine sites in cells. Given that downregulation of H3K18 acetylation is correlated with a poor prognosis of several cancer types and H3K27 acetylation antagonizes repressive gene regulation by di- and trimethylation at H3K27, our current study implies that Sirt6 may serve as a target for cancer intervention and regulatory pathway investigation in cells. PMID:27152839

  19. Effect of glycerol on the separation of nucleosomes and bent DNA in low ionic strength polyacrylamide gel electrophoresis.

    OpenAIRE

    Pennings, S; Meersseman, G; Bradbury, E M

    1992-01-01

    We report that glycerol changes the separation characteristics of polyacrylamide nucleoprotein gels in which it is included as a stabilizing agent. Polyacrylamide gel electrophoresis fractionates DNA and nucleosomes according to net negative charge, mass and conformation. With glycerol included, fractionation seems to be largely based on particle mass and charge. The conformation factor in separation is progressively lost with increasing glycerol concentrations. Nucleosome positions on the sa...

  20. Fresh-frozen plasma resuscitation after traumatic brain injury and shock attenuates extracellular nucleosome levels and deoxyribonuclease 1 depletion

    DEFF Research Database (Denmark)

    Sillesen, Martin; Jin, Guang; Oklu, Rahmi; Albadawi, Hassan; Imam, Ayesha M; Jepsen, Cecilie H; Hwabejire, John O; Ostrowski, Sisse R; Johansson, Pär I; Rasmussen, Lars S; Alam, Hasan B

    2013-01-01

    Traumatic brain injury and shock are among the leading causes of trauma-related mortality. We have previously shown that fresh-frozen plasma (FFP) resuscitation reduces the size of brain lesion and associated swelling compared with crystalloids. We hypothesized that this effect would be associate...... with an attenuation of circulating nucleosome levels, a biomarker of injury with cytotoxic potential, through reconstitution of circulating deoxyribonuclease-1 (DNAse1), an enzyme identified as critical in nucleosome clearance from the circulation....

  1. Microstructural characterization of nickel subjected to dynamic plastic deformation

    DEFF Research Database (Denmark)

    Luo, Z.P.; Mishin, Oleg; Zhang, Yubin; Zhang, H.W.; Lu, K.

    2012-01-01

    Average microstructural parameters and the extent of microstructural heterogeneity in nickel deformed at a high strain rate have been characterized quantitatively and compared to those after compression at a quasi-static strain rate. The microstructure in the high strain rate sample was found to ...

  2. Dynamic mechanical characterization of CNT-PP nanocomposites.

    Science.gov (United States)

    Mandal, A; Singh, S P; Prasad, R

    2016-03-01

    In this study, molecular dynamic simulations were used to carry out a dynamic mechanical analysis of polymer nanocomposites (PNC) containing polypropylene (PP) and various volume fractions of single walled carbon nanotubes (SWCNTs). After assembling the composite unit cell, relaxation studies were performed by loading the specimen to a predetermined strain under quasistatic loading and then sustaining the strain while allowing the material to relax. Nano level readjustments of the polymer chains took place during this process, reducing the overall stress levels in the specimen. Free volumes and small voids permitted chain mobility around the carbon nanotubes. By fitting a standard relaxation curve, the nano relaxation parameters of the PNCs were deduced. Relaxation studies were also conducted at different equilibrium temperatures. Using the time temperature transformation relation, a master curve was generated for the nanocomposite with 1.0% SWCNTs in order to obtain results over an extended period of time. PMID:26920022

  3. In vitro molecular magnetic resonance imaging detection and measurement of apoptosis using superparamagnetic iron oxide + antibody as ligands for nucleosomes

    International Nuclear Information System (INIS)

    Recent research in cell biology as well as oncology research has focused on apoptosis or programmed cell death as a means of quantifying the induced effects of treatment. A hallmark of late-stage apoptosis is nuclear fragmentation in which DNA is degraded to release nucleosomes with their associated histones. In this work, a method was developed for detecting and measuring nucleosome concentration in vitro with magnetic resonance imaging (MRI). The indirect procedure used a commercially available secondary antibody-superparamagnetic iron oxide (SPIO) particle complex as a contrast agent that bound to primary antibodies against nucleosomal histones H4, H2A and H2B. Using a multiple-echo spin-echo sequence on a 1.5 T clinical MRI scanner, significant T2 relaxation enhancement as a function of in vitro nucleosomal concentration was measured. In addition, clustering or aggregation of the contrast agent was demonstrated with its associated enhancement in T2 effects. The T2 clustering enhancement showed a complex dependence on relative concentrations of nucleosomes, primary antibody and secondary antibody + SPIO. The technique supports the feasibility of using MRI measurements of nucleosome concentration in blood as a diagnostic, prognostic and predictive tool in the management of cancer. (paper)

  4. Characterizing Protein Structure, Dynamics and Conformation in Lyophilized Solids

    OpenAIRE

    Moorthy, Balakrishnan S.; Iyer, Lavanya K.; Topp, Elizabeth M.

    2015-01-01

    The long-term stability of protein therapeutics in the solid-state depends on the preservation of native structure during lyophilization and in the lyophilized powder. Proteins can reversibly or irreversibly unfold upon lyophilization, acquiring conformations susceptible to degradation during storage. Therefore, characterizing proteins in the dried state is crucial for the design of safe and efficacious formulations. This review summarizes the basic principles and applications of the analytic...

  5. Thermal characterization of nanoscale phononic crystals using supercell lattice dynamics

    Directory of Open Access Journals (Sweden)

    Bruce L. Davis

    2011-12-01

    Full Text Available The concept of a phononic crystal can in principle be realized at the nanoscale whenever the conditions for coherent phonon transport exist. Under such conditions, the dispersion characteristics of both the constitutive material lattice (defined by a primitive cell and the phononic crystal lattice (defined by a supercell contribute to the value of the thermal conductivity. It is therefore necessary in this emerging class of phononic materials to treat the lattice dynamics at both periodicity levels. Here we demonstrate the utility of using supercell lattice dynamics to investigate the thermal transport behavior of three-dimensional nanoscale phononic crystals formed from silicon and cubic voids of vacuum. The periodicity of the voids follows a simple cubic arrangement with a lattice constant that is around an order of magnitude larger than that of the bulk crystalline silicon primitive cell. We consider an atomic-scale supercell which incorporates all the details of the silicon atomic locations and the void geometry. For this supercell, we compute the phonon band structure and subsequently predict the thermal conductivity following the Callaway-Holland model. Our findings dictate that for an analysis based on supercell lattice dynamics to be representative of the properties of the underlying lattice model, a minimum supercell size is needed along with a minimum wave vector sampling resolution. Below these minimum values, a thermal conductivity prediction of a bulk material based on a supercell will not adequately recover the value obtained based on a primitive cell. Furthermore, our results show that for the relatively small voids and void spacings we consider (where boundary scattering is dominant, dispersion at the phononic crystal unit cell level plays a noticeable role in determining the thermal conductivity.

  6. Dynamic FDG PET in characterizing and staging lung cancer

    International Nuclear Information System (INIS)

    CT has proven inadequate for staging lung cancer. This study evaluates F-18 deoxyglucose (FDG) positron emission tomography (PET) in assessing mediastinal metastases of lung tumors, differentiating benign from malignant parenchymal masses, and complementing radiographic and laboratory findings in lymphoma. The authors of this paper examined 13 patients with pulmonary masses as determined by chest radiographs and CT scans. PET scans were obtained with 255.3-592 MBq FDG scanned in dynamic mode at 5 minutes per frame for 45 minutes and one 15 minutes per frame. Image analysis included visual inspection, time activity curves (TAC), and calculation of differential uptake ratio (DUR) in regions of interest versus normal tissue

  7. Dynamical characterization of the last prolonged solar minima

    OpenAIRE

    Cionco, Rodolfo Gustavo; Compagnucci, Rosa Hilda

    2012-01-01

    The planetary hypothesis of the solar cycle is an old idea in which the gravitational influence of the planets has a non-negligible effect on the causes of the solar magnetic cycle. In this work we looked for a possible causal link in relation with solar barycentric dynamics and prolonged minima events. We searched for particular changes in the Sun's acceleration and concentrated on long-term variations of the solar cycle. We show how the orbital angular momentum of the Sun evolves and how th...

  8. Materials Characterization at High Speed by Dynamic Tensile Tests

    OpenAIRE

    Changgang, Geng; Xiangping, Li; Xin, Lu

    2006-01-01

    In this paper, the dynamic deformation behaviors of 2 aluminum alloys (AA6016, AA5182) and 2 steels (v 1158, FeP04) are investigated. Firstly, the test method, an improved Hopkinson pressure bar test, is introduced. Then, the test results are presented and analyzed. The strain rate range used in this study is between 290 s^(-1) and 1750 s^(-1).The test results show that the yield stresses of all four tested materials increase along with the increase of strain rate, but the ductility does not....

  9. Rapid accessibility of nucleosomal DNA in yeast on a second time scale

    OpenAIRE

    Bucceri, Andrea; Kapitza, Kristin; Thoma, Fritz

    2006-01-01

    Packaging DNA in nucleosomes and higher-order chromatin structures restricts its accessibility and constitutes a barrier for all DNA transactions including gene regulation and DNA repair. How and how fast proteins find access to DNA buried in chromatin of living cells is poorly understood. To address this question in a real time in vivo approach, we investigated DNA repair by photolyase in yeast. We show that overexpressed photolyase, a light-dependent DNA-repair enzyme, recognizes and repair...

  10. Theory of Nucleosome Corkscrew Sliding in the Presence of Synthetic DNA Ligands

    OpenAIRE

    Mohammad-Rafiee, Farshid; Kulic, Igor M.; Schiessel, H.

    2004-01-01

    Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong through one-basepair twist defects and through ten-basepair bulge defects. A recent experiment demonstrated that the repositioning is strongly suppressed in the presence of minor-groove binding DNA ligands. In the present study we give a quantitative theory f...

  11. Charge State of the Globular Histone Core Controls Stability of the Nucleosome

    OpenAIRE

    Fenley, Andrew T.; Adams, David A.; Onufriev, Alexey V.

    2010-01-01

    Presented here is a quantitative model of the wrapping and unwrapping of the DNA around the histone core of the nucleosome that suggests a mechanism by which this transition can be controlled: alteration of the charge state of the globular histone core. The mechanism is relevant to several classes of posttranslational modifications such as histone acetylation and phosphorylation; several specific scenarios consistent with recent in vivo experiments are considered. The model integrates a descr...

  12. Charge State of the Globular Histone Core Controls Stability of the Nucleosome

    OpenAIRE

    Fenley, Andrew T.; Adams, D. A.; Onufriev, Alexey V.

    2010-01-01

    Presented here is a quantitative model of the wrapping and unwrapping of the DNA around the histone core of the nucleosome that suggests a mechanism by which this transition can be controlled: alteration of the charge state of the globular histone core. The mechanism is relevant to several classes of posttranslational modifications such as histone acetylation and phosphorylation; several specific scenarios consistent with recent in vivo experiments are considered. The model integrates a descr...

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

    OpenAIRE

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

    2015-01-01

    Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or coca...

  14. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples

    OpenAIRE

    Chun-nan Dong; Ya-dong Yang; Shu-jin Li; Ya-ran Yang; Xiao-jing Zhang; Xiang-dong Fang; Jiang-wei Yan; Bin Cong

    2016-01-01

    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and ident...

  15. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition

    OpenAIRE

    Visnapuu, Mari-Liis; Greene, Eric C.

    2009-01-01

    Here we use single-molecule imaging to determine coarse-grained intrinsic energy landscapes for nucleosome deposition on model DNA substrates. Our results reveal distributions that are correlated with recent in silico predictions, reinforcing the hypothesis that DNA contains some intrinsic positioning information. We also show that cis-regulatory sequences in human DNA coincide with peaks in the intrinsic landscape, whereas valleys correspond to non-regulatory regions, and we present evidence...

  16. Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription ▿

    OpenAIRE

    Yadon, Adam N.; Mark, Daniel; Basom, Ryan; Delrow, Jeffrey; Whitehouse, Iestyn; Tsukiyama, Toshio

    2010-01-01

    Nucleosome-free regions (NFRs) at the 5′ and 3′ ends of genes are general sites of transcription initiation for mRNA and noncoding RNA (ncRNA). The presence of NFRs within transcriptional regulatory regions and the conserved location of transcription start sites at NFRs strongly suggest that the regulation of NFRs profoundly affects transcription initiation. To date, multiple factors are known to facilitate transcription initiation by positively regulating the formation and/or size of NFRs in...

  17. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

    OpenAIRE

    Hu, Gangqing; Dustin E Schones; Cui, Kairong; Ybarra, River; Northrup, Daniel; Tang, Qingsong; Gattinoni, Luca; Restifo, Nicholas P; Huang, Suming; Zhao, Keji

    2011-01-01

    Enhancers of transcription activate transcription via binding of sequence-specific transcription factors to their target sites in chromatin. In this report, we identify GATA1-bound distal sites genome-wide and find a global reorganization of the nucleosomes at these potential enhancers during differentiation of hematopoietic stem cells (HSCs) to erythrocytes. We show that the catalytic subunit BRG1 of BAF complexes localizes to these distal sites during differentiation and generates a longer ...

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

    OpenAIRE

    Bjorklund, Chad C.; Davis, William B.

    2006-01-01

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

  19. Characterization of groundwater dynamics in landslides in varved clays

    Directory of Open Access Journals (Sweden)

    J. E. van der Spek

    2013-01-01

    Full Text Available Groundwater dynamics may play a significant role in landslides. A detailed model is developed of the groundwater dynamics in landslides in varved clays in the Trièves area in the French Alps. The varved clays consist of a sequence of alternating silt and clay layers, covered by a colluvium layer and cut through by fissures. The hydraulic conductivity of the clay layers is negligible compared to the silt layers. It is conceptualized that fissures form a hydraulic connection between the colluvium and the varved clays. Groundwater recharge flows through the colluvium into the fissures where water is exchanged horizontally between the fissure and the silt layers of the varved clays. Groundwater flow in the colluvium is simulated with the Boussinesq equation while flow in the silt layers of the varved clays is simulated with the Richards' equation. Longitudinal outflow from the fissure is simulated with a linear-reservoir model. Scattered data of relatively short monitoring periods is available for several landslides in the region. A good similarity between observed and simulated heads is obtained, especially when considering the lack of important physical parameters such as the fissure width and the distance between the monitoring point and the fissure. A simulation for the period 1959–2004 showed some correlation between peaks in the simulated heads and the recorded occurrence of landslides while the bottom of the varved clays remained saturated during the entire simulation period.

  20. Dynamic characterization of a laminated composite magnetorheological fluid sandwich plate

    International Nuclear Information System (INIS)

    This study investigates the dynamic properties of a laminated composite magnetorheological (MR) fluid sandwich plate. The governing differential equations of motion of a sandwich plate embedding a MR fluid layer as the core layer and laminated composite plates as the face layers are presented in a finite element formulation. The validity of the developed finite element formulation is demonstrated by comparing the results in terms of the natural frequencies derived from the present finite element formulation with those in the available literature. Various parametric studies are also performed to investigate the effect of a magnetic field on the variation of the natural frequencies and loss factors of the MR fluid composite sandwich plate under various boundary conditions. Furthermore, the effect of the thickness of the MR fluid layer and the ply orientation of the composite face layers on the variation of the natural frequencies and loss factors are studied. The free vibration mode shapes under various boundary conditions of a MR fluid laminated composite sandwich plate are also presented. The forced vibration response of a MR fluid composite plate is investigated to study the dynamic response of the sandwich plate under harmonic force excitations in various magnetic fields. The study suggests that the natural frequency increases with increasing magnetic field, irrespective of the boundary conditions. The reduction in peak deflection at each mode under a harmonic excitation force with variation of the applied magnetic field shows the effectiveness of the MR fluid layer in reducing the vibration amplitude of the composite sandwich plate. (paper)

  1. Characterization of axisymmetric disruption dynamics toward VDE avoidance in tokamaks

    International Nuclear Information System (INIS)

    Experiments and axisymmetric MHD simulations on tokamak disruptions have explicated the underlying mechanisms of Vertical Displacement Events (VDEs) and a diversity of disruption dynamics. First, the neutral point, which is known as an advantageous vertical plasma position to avoiding VDEs during the plasma current quench, is shown to be fairly insensitive to plasma shape and current profile parameters. Secondly, a rapid flattening of the plasma current profile frequently seen at thermal quench is newly clarified to play a substantial role in dragging a single null-diverted plasma vertically towards the divertor. As a consequence, the occurrence of downward-going VDEs predominates over the upward-going ones in bottom-diverted discharges. This dragging effect is absent in up-down symmetric limiter discharges. These simulation results are consistent with experiments. Together with the attractive force that arises from passive shell currents and essentially vanishes at the neutral point, the dragging effect explains many details of the VDE dynamics over the whole period of the disruptive termination. (author)

  2. Characterizing and modeling the dynamics of activity and popularity.

    Directory of Open Access Journals (Sweden)

    Peng Zhang

    Full Text Available Social media, regarded as two-layer networks consisting of users and items, turn out to be the most important channels for access to massive information in the era of Web 2.0. The dynamics of human activity and item popularity is a crucial issue in social media networks. In this paper, by analyzing the growth of user activity and item popularity in four empirical social media networks, i.e., Amazon, Flickr, Delicious and Wikipedia, it is found that cross links between users and items are more likely to be created by active users and to be acquired by popular items, where user activity and item popularity are measured by the number of cross links associated with users and items. This indicates that users generally trace popular items, overall. However, it is found that the inactive users more severely trace popular items than the active users. Inspired by empirical analysis, we propose an evolving model for such networks, in which the evolution is driven only by two-step random walk. Numerical experiments verified that the model can qualitatively reproduce the distributions of user activity and item popularity observed in empirical networks. These results might shed light on the understandings of micro dynamics of activity and popularity in social media networks.

  3. Kinematic measurements for the characterization of the dynamics of hopping

    International Nuclear Information System (INIS)

    The study of human movement requires the accurate measurement of the forces and of the kinematic quantities involved. Here we consider hopping, that deserves great attention in the literature, since it combines the activation of a complex sensorimotor control with the relative simplicity of the gesture. The movement of the center of mass and the contact conditions are of special interest. Thus a measuring system that combines digital image acquisition, force measurement based on a force plate and extensive use of inertial sensors, for linear and rotational motion, has been developed and characterized. The results concerning the accurate measurement of contact conditions are specially outlined

  4. Dynamic Characterization of an Inflatable Concentrator for Solar Thermal Propulsion

    Science.gov (United States)

    Leigh, Larry M.; Tinker, Michael L.; McConnaughey, Paul (Technical Monitor)

    2002-01-01

    Solar-thermal propulsion is a concept for producing thrust sufficient for orbital transfers and requires innovative, lightweight structures. This note presents a description of an inflatable concentrator that consists of a torus, lens simulator, and three tapered struts. Modal testing was discussed for characterization and verification of the solar concentrator assembly. Finite element shell models of the concentrator were developed using a two-step nonlinear approach, and results were compared to test data. Reasonable model-to-test agreement was achieved for the torus, and results for the concentrator assembly were comparable to the test for several modes.

  5. Wafer-scale characterization of carrier dynamics in graphene

    DEFF Research Database (Denmark)

    Buron, Jonas Christian Due; Petersen, Dirch Hjorth; Bøggild, Peter;

    2015-01-01

    The electronic properties of single-layer graphene, such as surface conductance, carrier concentration, scattering time and mobility, can be characterized in a noncontact manner by THz time-domain spectroscopy. Standard spectroscopic imaging reveals the AC conductance over large areas with a few...... hundred μm resolution, and spectroscopic imaging on back-gated graphene allows for extraction of both the carrier concentration and the mobility. We find that spatial variations of the conductance of single-layer CVD-grown graphene are predominantly due to variations in mobility rather than in carrier...

  6. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples.

    Science.gov (United States)

    Dong, Chun-Nan; Yang, Ya-Dong; Li, Shu-Jin; Yang, Ya-Ran; Zhang, Xiao-Jing; Fang, Xiang-Dong; Yan, Jiang-Wei; Cong, Bin

    2016-01-01

    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these "nucleosome protected STRs" (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types. PMID:27189082

  7. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples

    Science.gov (United States)

    Dong, Chun-nan; Yang, Ya-dong; Li, Shu-jin; Yang, Ya-ran; Zhang, Xiao-jing; Fang, Xiang-dong; Yan, Jiang-wei; Cong, Bin

    2016-01-01

    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these “nucleosome protected STRs” (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types. PMID:27189082

  8. Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

    CERN Document Server

    Meyer, Sam

    2014-01-01

    The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unkown despite a growing structural knowledge of the complex. Here, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We apply the procedure on a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at the sites of histone-DNA contact, the DNA base-pairs are locally shifted outwards, consistent with locally repulsive forces exerted by the histones. In a second step, we show that the various force profiles of the analyzed structures derive locally from a unique, sequence-independent, quadratic repulsive force field, while the sequence preferences are entirely due to the internal DNA mechanics. We thus obtain the first knowledge-derived nanosca...

  9. Molecular dynamics characterization of as-implanted damage in silicon

    International Nuclear Information System (INIS)

    We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions

  10. Molecular dynamics characterization of as-implanted damage in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Ivan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)]. E-mail: ivasan@ele.uva.es; Marques, Luis A. [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Pelaz, Lourdes [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Lopez, Pedro [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Aboy, Maria [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Barbolla, Juan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)

    2005-12-05

    We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions.

  11. Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription

    Science.gov (United States)

    García, Patricia; Paulo, Esther; Gao, Jun; Wahls, Wayne P.; Ayté, José; Lowy, Ernesto; Hidalgo, Elena

    2014-01-01

    Schizosaccharomyces pombe displays a large transcriptional response common to several stress conditions, regulated primarily by the transcription factor Atf1. Atf1-dependent promoters contain especially broad nucleosome depleted regions (NDRs) prior to stress imposition. We show here that basal binding of Atf1 to these promoters competes with histones to create wider NDRs at stress genes. Moreover, deletion of atf1 results in nucleosome disorganization specifically at stress coding regions and derepresses antisense transcription. Our data indicate that the transcription factor binding to promoters acts as an effective barrier to fix the +1 nucleosome and phase downstream nucleosome arrays to prevent cryptic transcription. PMID:25122751

  12. Characterizing Self-Heating Dynamics Using Cyclostationary Measurements

    CERN Document Server

    Shin, SangHoon; Alam, Muhammad Ashraful

    2016-01-01

    Self-heating in surrounding gate transistors can degrade its on-current performance and reduce lifetime. If a transistor heats/cools with time-constants less than the inverse of the operating frequency, a predictable, frequency-independent performance is expected; if not, the signal pattern must be optimized for highest performance. Typically, time-constants are measured by expensive, ultra-fast instruments with high temporal resolution. Instead, here we demonstrate an alternate, inexpensive, cyclostationary measurement technique to characterize self-heating (and cooling) with sub-microsecond resolution. The results are independently confirmed by direct imaging of the transient heating/cooling of the channel temperature by the thermoreflectance (TR) method. A routine use of the proposed technique will help improve the surrounding gate transistor design and shorten the design cycle.

  13. Characterization of sediment dynamics in an estuary environment using acoustic techniques

    OpenAIRE

    Hermand, J.-P.; L. Perichon; Verbanck, M.

    2006-01-01

    In recent years, acoustic-based methods have been developed to characterize the dynamical behavior of loose sediments and bed deposits in very shallow water environments. In this paper, we present preliminary results on the estimation of the dynamic changes in an estuarine environment using data from dual-frequency echosounding at high resolution and contemporaneous hydrological measurements including suspended matter concentration, density subbottom profiling, and data assimilation based on ...

  14. Characterization of Various Plant-Produced Asphalt Concrete Mixtures Using Dynamic Modulus Test

    OpenAIRE

    Muhammad Irfan; Asad S. Waraich; Sarfraz Ahmed; Yasir Ali

    2016-01-01

    This research characterizes the performance of various plant-produced asphalt concrete mixtures by dynamic modulus |E∗| test using asphalt mixture performance tester (AMPT). Marshall designed specimens of seven different mixtures were prepared using the Superpave gyratory compactor and subjected to sinusoidal compressive loading at various temperatures (4.4 to 54.4°C) and loading frequencies (0.1 to 25 Hz). A catalog of default dynamic modulus values for typical asphalt concrete mixtures of P...

  15. Acoustic characterization of slow compaction dynamics in noncohesive disordered granular media

    OpenAIRE

    Legland, Jean-Baptiste; Tournat, Vincent; Gusev, Vitaly

    2012-01-01

    Noncohesive disordered granular media are well known to exhibit very complex behaviour when being excited by mechanical solicitations. This work presents our studies of the slow dynamics in granular media undergoing a compaction process. The characterization of slow dynamics is performed by an acoustic probing of the packing after mechanical solicitation. With this aim we have built a special setup to increase the density of the granular medium and to probe its elastic properties by the acous...

  16. Characterizing and Modeling the Dynamics of Activity and Popularity

    CERN Document Server

    Zhang, Peng; Gao, Liang; Fan, Ying; Di, Zengru

    2013-01-01

    Social media, regarded as two-layer networks consisting of users and items, turn out to be the most important channels for access to massive information in the era of Web 2.0. The dynamics of human activity and item popularity is a crucial issue in social media networks. In this paper, by analyzing the growth of user activity and item popularity in four empirical social media networks, i.e., Amazon, Flickr, Delicious and Wikipedia, it is found that cross links between users and items are more likely to be created by active users and to be acquired by popular items, where user activity and item popularity are measured by the number of cross links associated with users and items. This indicates that users generally trace popular items, overall. However, it is found that the inactive users much more severely trace popular items than the active users. Inspired by empirical analysis, we propose an evolving model for such networks, in which the evolution is driven only by two-step random walk. Numerical experiments...

  17. Dynamic Characterization of Crystalline Supramolecular Rotors Assembled through Halogen Bonding.

    Science.gov (United States)

    Catalano, Luca; Pérez-Estrada, Salvador; Terraneo, Giancarlo; Pilati, Tullio; Resnati, Giuseppe; Metrangolo, Pierangelo; Garcia-Garibay, Miguel A

    2015-12-16

    A modular molecular kit for the preparation of crystalline molecular rotors was devised from a set of stators and rotators to gain simple access to a large number of structures with different dynamic performance and physical properties. In this work, we have accomplished this with crystalline molecular rotors self-assembled by halogen bonding of diazabicyclo[2.2.2]octane, acting as a rotator, and a set of five fluorine-substituted iodobenzenes that take the role of the stator. Using variable-temperature (1)H T1 spin-lattice relaxation measurements, we have shown that all structures display ultrafast Brownian rotation with activation energies of 2.4-4.9 kcal/mol and pre-exponential factors of the order of (1-9) × 10(12) s(-1). Line shape analysis of quadrupolar echo (2)H NMR measurements in selected examples indicated rotational trajectories consistent with the 3-fold or 6-fold symmetric potential of the rotator. PMID:26583701

  18. Dynamic characterization of satellite components through non-invasive methods

    Energy Technology Data Exchange (ETDEWEB)

    Mullins, Joshua G [Los Alamos National Laboratory; Wiest, Heather K [Los Alamos National Laboratory; Mascarenas, David D. L. [Los Alamos National Laboratory; Macknelly, David [INST-OFF/AWE; Park, Gyuhae [Los Alamos National Laboratory

    2010-10-21

    The rapid deployment of satellites is hindered by the need to flight-qualify their components and the resulting mechanical assembly. Conventional methods for qualification testing of satellite components are costly and time consuming. Furthermore, full-scale vehicles must be subjected to launch loads during testing. This harsh testing environment increases the risk of component damage during qualification. The focus of this research effort was to assess the performance of Structural Health Monitoring (SHM) techniques as a replacement for traditional vibration testing. SHM techniques were applied on a small-scale structure representative of a responsive satellite. The test structure consisted of an extruded aluminum space-frame covered with aluminum shear plates, which was assembled using bolted joints. Multiple piezoelectric patches were bonded to the test structure and acted as combined actuators and sensors. Various methods of SHM were explored including impedance-based health monitoring, wave propagation, and conventional frequency response functions. Using these methods in conjunction with finite element modelling, the dynamic properties of the test structure were established and areas of potential damage were identified and localized. The adequacy of the results from each SHM method was validated by comparison to results from conventional vibration testing.

  19. Dynamic characterization of satellite components through non-invasive methods

    Energy Technology Data Exchange (ETDEWEB)

    Mullens, Joshua G [Los Alamos National Laboratory; Wiest, Heather K [Los Alamos National Laboratory; Mascarenas, David D [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory

    2011-01-24

    The rapid deployment of satellites is hindered by the need to flight-qualify their components and the resulting mechanical assembly. Conventional methods for qualification testing of satellite components are costly and time consuming. Furthermore, full-scale vehicles must be subjected to launch loads during testing. The harsh testing environment increases the risk of component damage during qualification. The focus of this research effort was to assess the performance of Structural Health Monitoring (SHM) techniques as replacement for traditional vibration testing. SHM techniques were applied on a small-scale structure representative of a responsive satellite. The test structure consisted of an extruded aluminum space-frame covered with aluminum shear plates, which was assembled using bolted joints. Multiple piezoelectric patches were bonded to the test structure and acted as combined actuators and sensors. Various methods of SHM were explored including impedance-based health monitoring, wave propagation, and conventional frequency response functions. Using these methods in conjunction with finite element modeling, the dynamic properties of the test structure were established and areas of potential damage were identified and localized. The adequacy of the results from each SHM method was validated by comparison to results from conventional vibration testing.

  20. Characterizing the transmission dynamics and control of ebola virus disease.

    Directory of Open Access Journals (Sweden)

    Gerardo Chowell

    2015-01-01

    Full Text Available Carefully calibrated transmission models have the potential to guide public health officials on the nature and scale of the interventions required to control epidemics. In the context of the ongoing Ebola virus disease (EVD epidemic in Liberia, Drake and colleagues, in this issue of PLOS Biology, employed an elegant modeling approach to capture the distributions of the number of secondary cases that arise in the community and health care settings in the context of changing population behaviors and increasing hospital capacity. Their findings underscore the role of increasing the rate of safe burials and the fractions of infectious individuals who seek hospitalization together with hospital capacity to achieve epidemic control. However, further modeling efforts of EVD transmission and control in West Africa should utilize the spatial-temporal patterns of spread in the region by incorporating spatial heterogeneity in the transmission process. Detailed datasets are urgently needed to characterize temporal changes in population behaviors, contact networks at different spatial scales, population mobility patterns, adherence to infection control measures in hospital settings, and hospitalization and reporting rates.

  1. Design and characterization of a dynamic multileaf collimator

    International Nuclear Information System (INIS)

    The characteristics of a prototype computer-assisted dynamic multileaf collimator (DMLC), specifically designed for small-field conformal radiotherapy, were evaluated at the Istituto Nazionale Tumori of Milan. The collimating device consists of two opposing banks of 16 pairs of 8 cm thick, 3.6 mm wide tungsten leaves and allows shaping of a radiation field up to a size of 10x10cm2 at the isocentre. The screening thickness of each leaf is 6.25 mm at the accelerator gantry isocentre. The leaves have a trapezoidal cross section and move along an arched path, thus providing a 'double focused' collimation system. The DMLC was installed on the head of a Varian Clinac 2100C linear accelerator. Mechanical and dosimetric evaluations were performed to test the stability of the mechanical isocentre and to determine leaf leakage, penumbra width, accuracy of leaf positions and uniformity of leaf speed. Displacement of the mechanical isocentre was less than 1 mm at all gantry angles. Standard radiographic films exposed to 6 MV x-ray radiation were used for dosimetric evaluations. Leakage between leaves was less than 2.5%, and leakage through abutted leaves was less than 5.5%. The penumbra width between 20% and 80% isodose at different positions of leaf banks was 2.7 mm in the direction of the leaf motion and 3.1 mm along the side of the leaf with a standard deviation of 0.2 mm in both directions. Accuracy in the positioning of the leaf was 0.3 mm, whereas the maximum repositioning error was less than 0.2 mm. Finally, during movement of the leaves at the maximum speed of 0.5 mm s-1, the standard deviation of the leaf positioning error was 0.2 mm, proving an accurate uniformity of leaf speed. (author)

  2. Characterization of degeneration process in combustion instability based on dynamical systems theory.

    Science.gov (United States)

    Gotoda, Hiroshi; Okuno, Yuta; Hayashi, Kenta; Tachibana, Shigeru

    2015-11-01

    We present a detailed study on the characterization of the degeneration process in combustion instability based on dynamical systems theory. We deal with combustion instability in a lean premixed-type gas-turbine model combustor, one of the fundamentally and practically important combustion systems. The dynamic behavior of combustion instability in close proximity to lean blowout is dominated by a stochastic process and transits to periodic oscillations created by thermoacoustic combustion oscillations via chaos with increasing equivalence ratio [Chaos 21, 013124 (2011); Chaos 22, 043128 (2012)]. Thermoacoustic combustion oscillations degenerate with a further increase in the equivalence ratio, and the dynamic behavior leads to chaotic fluctuations via quasiperiodic oscillations. The concept of dynamical systems theory presented here allows us to clarify the nonlinear characteristics hidden in complex combustion dynamics. PMID:26651761

  3. Experimental characterization of energetic material dynamics for multiphase blast simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Beresh, Steven Jay; Wagner, Justin L.; Kearney, Sean Patrick; Wright, Elton K.; Baer, Melvin R.; Pruett, Brian Owen Matthew

    2011-09-01

    experiments. The development of the Multiphase Shock Tube and associated diagnostic capabilities offers experimental capability to a previously inaccessible regime, which can provide unprecedented data concerning particle dynamics of dense gas-solid flows.

  4. 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...

  5. Characterizing system dynamics with a weighted and directed network constructed from time series data

    International Nuclear Information System (INIS)

    In this work, we propose a novel method to transform a time series into a weighted and directed network. For a given time series, we first generate a set of segments via a sliding window, and then use a doubly symbolic scheme to characterize every windowed segment by combining absolute amplitude information with an ordinal pattern characterization. Based on this construction, a network can be directly constructed from the given time series: segments corresponding to different symbol-pairs are mapped to network nodes and the temporal succession between nodes is represented by directed links. With this conversion, dynamics underlying the time series has been encoded into the network structure. We illustrate the potential of our networks with a well-studied dynamical model as a benchmark example. Results show that network measures for characterizing global properties can detect the dynamical transitions in the underlying system. Moreover, we employ a random walk algorithm to sample loops in our networks, and find that time series with different dynamics exhibits distinct cycle structure. That is, the relative prevalence of loops with different lengths can be used to identify the underlying dynamics

  6. Relevance of circulating nucleosomes and oncological biomarkers for predicting response to transarterial chemoembolization therapy in liver cancer patients

    Directory of Open Access Journals (Sweden)

    Durner Jürgen

    2011-05-01

    Full Text Available Abstract Background Transarterial chemoembolization (TACE therapy is an effective locoregional treatment in hepatocellular cancer (HCC patients. For early modification of therapy, markers predicting therapy response are urgently required. Methods Here, sera of 50 prospectively and consecutively included HCC patients undergoing 71 TACE therapies were taken before and 3 h, 6 h and 24 h after TACE application to analyze concentrations of circulating nucleosomes, cytokeratin-19 fragments (CYFRA 21-1, alpha fetoprotein (AFP, C-reactive protein (CRP and several liver biomarkers, and to compare these with radiological response to therapy. Results While nucleosomes, CYFRA 21-1, CRP and some liver biomarkers increased already 24 h after TACE, percental changes of nucleosome concentrations before and 24 h after TACE and pre- and posttherapeutic values of AFP, gamma-glutamyl-transferase (GGT and alkaline phosphatase (AP significantly indicated the later therapy response (39 progression versus 32 no progression. In multivariate analysis, nucleosomes (24 h, AP (24 h and TACE number were independent predictive markers. The risk score of this combination model achieved an AUC of 81.8% in receiver operating characteristic (ROC curves and a sensitivity for prediction of non-response to therapy of 41% at 97% specificity, and of 72% at 78% specificity. Conclusion Circulating nucleosomes and liver markers are valuable tools for early estimation of the efficacy of TACE therapy in HCC patients.

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

    Science.gov (United States)

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

    2016-01-14

    Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA (cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo nucleosome occupancy and found that short cfDNA fragments harbor footprints of transcription factors. The cfDNA nucleosome occupancies correlate well with the nuclear architecture, gene structure, and expression observed in cells, suggesting that they could inform the cell type of origin. Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how nucleosome footprints can be used to infer cell types contributing to cfDNA in pathological states such as cancer. Since this strategy does not rely on genetic differences to distinguish between contributing tissues, it may enable the noninvasive monitoring of a much broader set of clinical conditions than currently possible. PMID:26771485

  8. Relevance of circulating nucleosomes and oncological biomarkers for predicting response to transarterial chemoembolization therapy in liver cancer patients

    International Nuclear Information System (INIS)

    Transarterial chemoembolization (TACE) therapy is an effective locoregional treatment in hepatocellular cancer (HCC) patients. For early modification of therapy, markers predicting therapy response are urgently required. Here, sera of 50 prospectively and consecutively included HCC patients undergoing 71 TACE therapies were taken before and 3 h, 6 h and 24 h after TACE application to analyze concentrations of circulating nucleosomes, cytokeratin-19 fragments (CYFRA 21-1), alpha fetoprotein (AFP), C-reactive protein (CRP) and several liver biomarkers, and to compare these with radiological response to therapy. While nucleosomes, CYFRA 21-1, CRP and some liver biomarkers increased already 24 h after TACE, percental changes of nucleosome concentrations before and 24 h after TACE and pre- and posttherapeutic values of AFP, gamma-glutamyl-transferase (GGT) and alkaline phosphatase (AP) significantly indicated the later therapy response (39 progression versus 32 no progression). In multivariate analysis, nucleosomes (24 h), AP (24 h) and TACE number were independent predictive markers. The risk score of this combination model achieved an AUC of 81.8% in receiver operating characteristic (ROC) curves and a sensitivity for prediction of non-response to therapy of 41% at 97% specificity, and of 72% at 78% specificity. Circulating nucleosomes and liver markers are valuable tools for early estimation of the efficacy of TACE therapy in HCC patients

  9. Characterization and diagnostics of combustion thermoacoustic instabilities using nonlinear dynamics and topological methods

    CERN Document Server

    Gianni, G; Paganini, E; Sello, S

    2003-01-01

    The onset of thermoacoustic instabilities in lean-premixed gas-turbine combustors is a crucial problem leading to degradation in engine and emissions performance and shortened component life. The main aim of this study is to propose a methodology based both on concepts of nonlinear dynamics and on geometric-topological invariants, for the characterization of attractors related to measurements based on the flame spontaneous light emission, like OH* radical, in order to classify different phases of the combustion process and to better recognize the transition mechanisms leading to the thermoacoustic instabilities. Preliminary results, clearly show the powerfulness of the approach to show the dynamical evolution of the flame and to evidence the onset of the thermoacoustic instabilities: in particular the topological invariant index (genus and related quantities) appear s as the best candidate for an early indicator of the dynamical transition, characterized by the onset of a more persistent, low entropy torus (q...

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

    KAUST Repository

    Cui, Peng

    2011-08-19

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues...

  12. Numerical characterization of nonlinear dynamical systems using parallel computing: The role of GPUS approach

    Science.gov (United States)

    Fazanaro, Filipe I.; Soriano, Diogo C.; Suyama, Ricardo; Madrid, Marconi K.; Oliveira, José Raimundo de; Muñoz, Ignacio Bravo; Attux, Romis

    2016-08-01

    The characterization of nonlinear dynamical systems and their attractors in terms of invariant measures, basins of attractions and the structure of their vector fields usually outlines a task strongly related to the underlying computational cost. In this work, the practical aspects related to the use of parallel computing - specially the use of Graphics Processing Units (GPUS) and of the Compute Unified Device Architecture (CUDA) - are reviewed and discussed in the context of nonlinear dynamical systems characterization. In this work such characterization is performed by obtaining both local and global Lyapunov exponents for the classical forced Duffing oscillator. The local divergence measure was employed by the computation of the Lagrangian Coherent Structures (LCSS), revealing the general organization of the flow according to the obtained separatrices, while the global Lyapunov exponents were used to characterize the attractors obtained under one or more bifurcation parameters. These simulation sets also illustrate the required computation time and speedup gains provided by different parallel computing strategies, justifying the employment and the relevance of GPUS and CUDA in such extensive numerical approach. Finally, more than simply providing an overview supported by a representative set of simulations, this work also aims to be a unified introduction to the use of the mentioned parallel computing tools in the context of nonlinear dynamical systems, providing codes and examples to be executed in MATLAB and using the CUDA environment, something that is usually fragmented in different scientific communities and restricted to specialists on parallel computing strategies.

  13. Crystalline and liquid Si3 N4 characterization by first-principles molecular dynamics simulations

    Science.gov (United States)

    Mauri, Aurelio; Celino, Massimo; Castellani, Niccoló; Erbetta, Davide

    2011-05-01

    Silicon nitride (Si3 N4) has a wide range of engineering applications where its mechanical and electronic properties can be effectively exploited. In particular, in the microelectronics field, the amorphous silicon nitride films are widely used as charge storage layer in metal-alumina-nitrideoxide nonvolatile memory devices. Atomic structure of amorphous silicon nitride is characterized by an high concentration of traps that control the electric behavior of the final device by the trappingde-trapping mechanism of the electrical charge occurring in its traps. In order to have a deep understanding of the material properties and, in particular, the nature of the electrical active traps a detailed numerical characterization of the crystalline and liquid phases is mandatory. For these reasons first-principles molecular dynamics simulations are extensively employed to simulate the crystalline Si3 N4 in its crystalline and liquid phases. Good agreement with experimental results is obtained in terms of density and formation entalpy. Detailed characterization of c-Si3 N4 electronic properties is performed in terms of band structure and band gap. Then constant temperature and constant volume first-principles molecular dynamics is used to disorder a stoichiometric sample of Si3 N4 . Extensive molecular dynamics simulations are performed to obtain a reliable liquid sample whose atomic structure does not depend on the starting atomic configuration. Detailed characterization of the atomic structure is achieved in terms of radial distribution functions and total structure factor.

  14. High-Bandwidth Dynamic Full-Field Profilometry for Nano-Scale Characterization of MEMS

    International Nuclear Information System (INIS)

    The article describes an innovative optical interferometric methodology to delivery dynamic surface profilometry with a measurement bandwidth up to 10MHz or higher and a vertical resolution up to 1 nm. Previous work using stroboscopic microscopic interferometry for dynamic characterization of micro (opto)electromechanical systems (M(O)EMS) has been limited in measurement bandwidth mainly within a couple of MHz. For high resonant mode analysis, the stroboscopic light pulse is insufficiently short to capture the moving fringes from dynamic motion of the detected structure. In view of this need, a microscopic prototype based on white-light stroboscopic interferometry with an innovative light superposition strategy was developed to achieve dynamic full-field profilometry with a high measurement bandwidth up to 10MHz or higher. The system primarily consists of an optical microscope, on which a Mirau interferometric objective embedded with a piezoelectric vertical translator, a high-power LED light module with dual operation modes and light synchronizing electronics unit are integrated. A micro cantilever beam used in AFM was measured to verify the system capability in accurate characterisation of dynamic behaviours of the device. The full-field seventh-mode vibration at a vibratory frequency of 3.7MHz can be fully characterized and nano-scale vertical measurement resolution as well as tens micrometers of vertical measurement range can be performed

  15. Characterization of Various Plant-Produced Asphalt Concrete Mixtures Using Dynamic Modulus Test

    Directory of Open Access Journals (Sweden)

    Muhammad Irfan

    2016-01-01

    Full Text Available This research characterizes the performance of various plant-produced asphalt concrete mixtures by dynamic modulus |E∗| test using asphalt mixture performance tester (AMPT. Marshall designed specimens of seven different mixtures were prepared using the Superpave gyratory compactor and subjected to sinusoidal compressive loading at various temperatures (4.4 to 54.4°C and loading frequencies (0.1 to 25 Hz. A catalog of default dynamic modulus values for typical asphalt concrete mixtures of Pakistan was established by developing stress-dependent master curves separately, for wearing and base course mixtures. The sensitivity of temperature and loading frequency on determination of dynamic modulus value was observed by typical isothermal and isochronal curves, respectively. Also, the effects of various variables on dynamic modulus were investigated using statistical technique of two-level factorial design of experiment. Furthermore, two dynamic modulus prediction models, namely, Witczak and Hirsch, were evaluated for their regional applicability. Results indicated that both the Witczak and Hirsch models mostly underpredict the value of dynamic modulus for the selected conditions/mixtures. The findings of this study are envisaged to facilitate the implementation of relatively new performance based mechanistic-empirical structural design and analysis approach.

  16. Dynamic adsorption properties of xenon on activated carbons and their structure characterization

    International Nuclear Information System (INIS)

    Background: In recent years, adsorption of radioactive xenon by activated carbon has been increasingly applied to the treatment of off-gas in nuclear power project. Though pore structure of activated carbon has a great impact on its dynamic adsorption coefficients for xenon, the concerned research is rare. Purpose: It is very necessary to figure out the relationship between the pore structure and the dynamic adsorption coefficients for the purpose of the selection and development of activated carbon. Methods: In this study, the dynamic adsorption coefficients of xenon on four kinds of activated carbons were measured on a dynamic adsorption platform under the condition of 25℃, OMPa (gauge pressure). And these four kinds of activated carbons were characterized by nitrogen adsorption and SEM. Results: The results show that the activated carbon of JH12-16 with the specific surface area of 991.9 m2·g-1 has the largest xenon dynamic adsorption coefficient among these activated carbons. Conclusions: The dynamic adsorption coefficient of xenon on activated carbon doesn't increase with the specific surface area or the pore volume. The mesopore and macropore only play the role of passageway for xenon adsorption. The most suitable pore for xenon adsorption is the pore with the pore size ranged from 0.55 to 0.6 nm. (authors)

  17. Spatially Distributed Characterization of Soil Dynamics Using Travel-Time Distributions

    OpenAIRE

    Heße, Falk; Zink, Matthias; Kumar, Rohini; Samaniego, Luis; Attinger, Sabine

    2016-01-01

    Travel-time distributions are a comprehensive tool for the characterization of hydrological system dynamics. Unlike streamflow hydrographs, they describe the movement and storage of water inside and through the hydrological system. Until recently, studies using such travel-time distributions have generally either been applied to simple (artificial toy) models or to real-world catchments using available time series, e.g. stable isotopes. Whereas the former are limited in their realism, the lat...

  18. Observation and characterization of chimera states in coupled dynamical systems with nonlocal coupling

    OpenAIRE

    Gopal, R; Chandrasekar, V. K.; Venkatesan, A.; Lakshmanan, M.

    2014-01-01

    By developing the concepts of strength of incoherence and discontinuity measure, we show that a distinct quantitative characterization of chimera and multichimera states which occur in networks of coupled nonlinear dynamical systems admitting nonlocal interactions of finite radius can be made. These measures also clearly distinguish between chimera or multichimera states (both stable and breathing types) and coherent and incoherent as well as cluster states....

  19. Dynamic Light Scattering for the Characterization of Polydisperse Fractal Systems by the Example of Pyrogenic Silica

    OpenAIRE

    Kätzel, Uwe

    2007-01-01

    Dynamic light scattering (DLS) is a method to size submicron particles by measuring their thermal motion (diffusion) in suspensions and emulsions. However, the validity of the Stokes-Einstein equation that relates the diffusion coefficient and the particle size is limited to spherical particles and very low concentrations. Within this thesis, DLS is used for the characterization of suspensions of pyrogenic silica which consists of fractal-like aggregates composed of sintered spherical primary...

  20. A self-test and dynamics characterization circuit for MEMS electrostatic actuators

    OpenAIRE

    Fernández Martínez, Daniel; Madrenas Boadas, Jordi; Cosp Vilella, Jordi

    2011-01-01

    This paper presents a high-bandwidth capacitance estimation and driving circuit especially tailored for its use with MEMS electrostatic actuators. The circuit can be integrated as a part of a system comprising an electrostatic actuator to provide self-testing and failure prediction capabilities and also as a simple and low-cost actuator dynamics characterization system capable of measuring both periodic and nonperiodic movements. Peer Reviewed

  1. Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

    CERN Document Server

    Singh, Raghvendra Pratap; Cleri, Fabrizio

    2013-01-01

    We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to...

  2. Dynamic high-temperature characterization of an iridium alloy in tension

    Energy Technology Data Exchange (ETDEWEB)

    Song, Bo [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Nelson, Kevin [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Jin, Helena [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Lipinski, Ronald J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bignell, John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ulrich, G. B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); George, E. P. [Ruhr Univ., Bochum (Germany)

    2015-09-01

    Iridium alloys have been utilized as structural materials for certain high-temperature applications, due to their superior strength and ductility at elevated temperatures. The mechanical properties, including failure response at high strain rates and elevated temperatures of the iridium alloys need to be characterized to better understand high-speed impacts at elevated temperatures. A DOP-26 iridium alloy has been dynamically characterized in compression at elevated temperatures with high-temperature Kolsky compression bar techniques. However, the dynamic high-temperature compression tests were not able to provide sufficient dynamic high-temperature failure information of the iridium alloy. In this study, we modified current room-temperature Kolsky tension bar techniques for obtaining dynamic tensile stress-strain curves of the DOP-26 iridium alloy at two different strain rates (~1000 and ~3000 s-1) and temperatures (~750°C and ~1030°C). The effects of strain rate and temperature on the tensile stress-strain response of the iridium alloy were determined. The DOP-26 iridium alloy exhibited high ductility in stress-strain response that strongly depended on both strain rate and temperature.

  3. Multiple aspects of atp-dependent nucleosome translocation by rsc and mi-2 are directed by the underlying DNA sequence

    NARCIS (Netherlands)

    Vugt, J. van; Jager, M. de; Murawska, M.; Brehm, A.; Noort, J. van; Logie, C.

    2009-01-01

    Background Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the

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

    Directory of Open Access Journals (Sweden)

    Marcia W Carneiro

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

  5. The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling.

    NARCIS (Netherlands)

    Sengupta, S.M.; Kanegan, M. van; Persinger, J.; Logie, C.; Cairns, B.R.; Peterson, C.L.; Bartholomew, B.

    2001-01-01

    Interactions of the yeast chromatin-remodeling complexes SWI/SNF and RSC with nucleosomes were probed using site-specific DNA photoaffinity labeling. 5 S rDNA was engineered with photoreactive nucleotides incorporated at different sites in DNA to scan for the subunits of SWI/SNF in close proximity t

  6. Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

    Energy Technology Data Exchange (ETDEWEB)

    Lee, A L [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the {delta}-Al-{var_epsilon} activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a {beta}{alpha}{beta}-{beta}{alpha}{beta} pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel {beta}-sheet. In addition {sup 15}N T{sub 1}, T{sub 2}, and {sup 15}N/{sup 1}H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone {sup 1}H, {sup 13}C, and {sup 15}N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and {sup 15}N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

  7. Crystalline and liquid Si3 N4 characterization by first-principles molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Castellani Niccoló

    2011-05-01

    Full Text Available Silicon nitride (Si3 N4 has a wide range of engineering applications where its mechanical and electronic properties can be effectively exploited. In particular, in the microelectronics field, the amorphous silicon nitride films are widely used as charge storage layer in metal-alumina-nitrideoxide nonvolatile memory devices. Atomic structure of amorphous silicon nitride is characterized by an high concentration of traps that control the electric behavior of the final device by the trappingde-trapping mechanism of the electrical charge occurring in its traps. In order to have a deep understanding of the material properties and, in particular, the nature of the electrical active traps a detailed numerical characterization of the crystalline and liquid phases is mandatory. For these reasons first-principles molecular dynamics simulations are extensively employed to simulate the crystalline Si3 N4 in its crystalline and liquid phases. Good agreement with experimental results is obtained in terms of density and formation entalpy. Detailed characterization of c-Si3 N4 electronic properties is performed in terms of band structure and band gap. Then constant temperature and constant volume first-principles molecular dynamics is used to disorder a stoichiometric sample of Si3 N4 . Extensive molecular dynamics simulations are performed to obtain a reliable liquid sample whose atomic structure does not depend on the starting atomic configuration. Detailed characterization of the atomic structure is achieved in terms of radial distribution functions and total structure factor.

  8. 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.

  9. Magnetic tweezers based force spectroscopy studies of the structure and dynamics of nucleosomes and chromatin

    NARCIS (Netherlands)

    Kruithof, Maarten Christiaan

    2009-01-01

    Animals and plants are build from a large number of cells. These cells continuously respond to signals from outside and inside the cell by producing various kinds of proteins. The blueprints of these proteins are stored in genes. The genes, in cells with a nucleus, are carried in chromosomes: thread

  10. Magnetic tweezers based force spectroscopy studies of the structure and dynamics of nucleosomes and chromatin

    OpenAIRE

    Kruithof, Maarten Christiaan

    2009-01-01

    Animals and plants are build from a large number of cells. These cells continuously respond to signals from outside and inside the cell by producing various kinds of proteins. The blueprints of these proteins are stored in genes. The genes, in cells with a nucleus, are carried in chromosomes: threadlike structures in the nucleus of a cell that become visible when the cell, upon dividing, condenses these structures. Chromosomes consist of roughly two parts: proteins, that take care of the cond...

  11. Dynamic characterization of silicon nanowires using a terahertz optical asymmetric demultiplexer-based pump-probe scheme

    DEFF Research Database (Denmark)

    Ji, Hua; Cleary, C. S.; Dailey, J. M.;

    2012-01-01

    Dynamic phase and amplitude all-optical responses of silicon nanowires are characterized using a terahertz optical asymmetric demultiplexer (TOAD) based pump-probe scheme. Ultra-fast recovery is observed for moderate pump powers.......Dynamic phase and amplitude all-optical responses of silicon nanowires are characterized using a terahertz optical asymmetric demultiplexer (TOAD) based pump-probe scheme. Ultra-fast recovery is observed for moderate pump powers....

  12. Final rubbery state characterization using a hollow cylinder dynamic shear sample on DMA7

    Directory of Open Access Journals (Sweden)

    Vilaiporn Luksameevanish

    2004-09-01

    Full Text Available Dynamic properties of raw natural rubber were examined using a hollow cylinder shaped samplesubjected to shear deformation on a laboratory Dynamic Mechanical Analyser. According to Cox-Merz’s study, dynamic complex viscosity obtained by this method showed a good agreement with shear flow viscosity measured by capillary rheometer. A master curve derived from the dynamic properties were then characterized. A crossing point of storage modulus (G’ and loss modulus (G’’ curves in the master curves was used to identify the final rubbery state, which indicated the transition of rubbery state and molten state. The position of this point depends on quantities and types of reinforcing or non-reinforcing fillers. The final rubbery state was shifted to higher frequency or lower temperature. It was found that the final rubbery state of CaCO3-filled rubber compounds was shifted to higher frequency or lower temperature by approximately 4 decades, while the translation of carbon black-filled rubber compounds was lower than unfilled rubber by about 1 decade. This phenomenon can be used to explain rubber elasticity, i.e. a decreasing of die swell of CaCO3 filled compounds at any high processing temperature. On the other hand, high magnitude of die swell for carbon black filled compound was still obtained.

  13. Characterizing the dynamics of a flexible rod wrapped by transverse repeated ribs subjected to axial flow

    Energy Technology Data Exchange (ETDEWEB)

    Perets, Y., E-mail: yaronprts@gmail.com [Department of Mechanical Engineering, Ben-Gurion University of the Negev, Beer-Sheva (Israel); Sher, E. [Faculty of Aerospace Engineering, Technion – Israel Institute of Technology, Haifa (Israel); Harari, R. [Nuclear Research Center – Negev (NRCN), Beer-Sheva (Israel)

    2014-04-01

    Highlights: • The dynamic instability of a repeated ribs cylindrical rod in annular axial flow geometry was studied. • The results indicate a strong dependency between rod instability and rib roughness. • The rod dynamics become stabilized when the pitch-to-height ratio of the ribs increases. • Increase of the rib width-to-height ratio destabilizes the rod. • The nonlinear model confirms the existence of post critical instability and the reliability of the linear results. - Abstract: This study focuses on the dynamics of a flexible cylindrical structure wrapped by repeated transverse rectangular ribs, in an annular flow geometry, under two boundary conditions: simply supported ends and clamped ends. The dynamics is predicted by linear and nonlinear theories. Based on the linear equation a straightforward nonlinear equation can be derived. A parametric investigation of the effect of the ribs’ dimensionless geometry characterized by the pitch-to-height and width-to-height ratios, on the fluid-elastic instability characteristics is considered. The results of the present study indicate a strong dependency between rod instability and rib roughness. The nonlinear model confirms the existence of post critical instability and the reliability of the linear results.

  14. Divergence-based characterization of fundamental limitations of adaptive dynamical systems

    CERN Document Server

    Raginsky, Maxim

    2010-01-01

    Adaptive dynamical systems arise in a multitude of contexts, e.g., optimization, control, communications, signal processing, and machine learning. A precise characterization of their fundamental limitations is therefore of paramount importance. In this paper, we consider the general problem of adaptively controlling and/or identifying a stochastic dynamical system, where our {\\em a priori} knowledge allows us to place the system in a subset of a metric space (the uncertainty set). We present an information-theoretic meta-theorem that captures the trade-off between the metric complexity (or richness) of the uncertainty set, the amount of information acquired online in the process of controlling and observing the system, and the residual uncertainty remaining after the observations have been collected. Following the approach of Zames, we quantify {\\em a priori} information by the Kolmogorov (metric) entropy of the uncertainty set, while the information acquired online is expressed as a sum of information diverg...

  15. Dynamic tunneling force microscopy for characterizing electronic trap states in non-conductive surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Wang, R.; Williams, C. C., E-mail: clayton@physics.utah.edu [Department of Physics and Astronomy, University of Utah, Salt Lake City, Utah 84112 (United States)

    2015-09-15

    Dynamic tunneling force microscopy (DTFM) is a scanning probe technique for real space mapping and characterization of individual electronic trap states in non-conductive films with atomic scale spatial resolution. The method is based upon the quantum mechanical tunneling of a single electron back and forth between a metallic atomic force microscopy tip and individual trap states in completely non-conducting surface. This single electron shuttling is measured by detecting the electrostatic force induced on the probe tip at the shuttling frequency. In this paper, the physical basis for the DTFM method is unfolded through a physical model and a derivation of the dynamic tunneling signal as a function of several experimental parameters is shown. Experimental data are compared with the theoretical simulations, showing quantitative consistency and verifying the physical model used. The experimental system is described and representative imaging results are shown.

  16. Dynamic tunneling force microscopy for characterizing electronic trap states in non-conductive surfaces

    International Nuclear Information System (INIS)

    Dynamic tunneling force microscopy (DTFM) is a scanning probe technique for real space mapping and characterization of individual electronic trap states in non-conductive films with atomic scale spatial resolution. The method is based upon the quantum mechanical tunneling of a single electron back and forth between a metallic atomic force microscopy tip and individual trap states in completely non-conducting surface. This single electron shuttling is measured by detecting the electrostatic force induced on the probe tip at the shuttling frequency. In this paper, the physical basis for the DTFM method is unfolded through a physical model and a derivation of the dynamic tunneling signal as a function of several experimental parameters is shown. Experimental data are compared with the theoretical simulations, showing quantitative consistency and verifying the physical model used. The experimental system is described and representative imaging results are shown

  17. Rearrangement of nucleosome structure during excision repair in xeroderma pigmentosum (group A) human fibroblasts

    International Nuclear Information System (INIS)

    Rearrangements of chromatic structure during excision repair were examined in xeroderma pigmentosum (XP; complementation group A) human fibroblasts treated with the small-molecule alkylating agent methyl methanesulfonate (MMS). We observed normal levels of repair synthesis in these cells during the first 12 h after exposure to MMS, in contrast to the near zero incorporation of repair patches following exposure to u.v. light. Our results indicate that the relative nuclease sensitivity of newly repaired regions in MMS-treated XP (group A) cells is quantitatively similar to that of newly repaired regions in MMS-treated normal human fibroblasts. This enhanced sensitivity is accompanied by a marked under-representation of repair-incorporated nucleotides in isolated nucleosome core DNA. Pulse-chase experiments demonstrated that these regions rapidly undergo rearrangements in chromatin structure, and both the rate and extent of these rearrangements are similar to those observed in normal cells. (author)

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

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed M Vargas; Parker, Brian J; Rasmussen, Morten; Lindgreen, Stinus; Lilje, Berit; Tobin, Desmond J; Kelly, Theresa K; Vang, Søren; Andersson, Robin; Jones, Peter A; Hoover, Cindi A; Tikhonov, Alexei; Prokhortchouk, Egor; Rubin, Edward M; Sandelin, Albin; Gilbert, M Thomas P; Krogh, Anders; Willerslev, Eske; Orlando, Ludovic

    2014-01-01

    expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues......Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into...

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

    International Nuclear Information System (INIS)

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

  20. Possible role of Cl ions in DNA-protein interactions in the nucleosomes

    Science.gov (United States)

    Bende, Attila; Bogár, Ferenc; Ladik, János

    2012-02-01

    The interactions of the PO4- groups of DNA and the positive parts of lysine/arginine were calculated in the nucleosomes using the ONIOM method. For the model system (3HO,K ion, PO4- group, positive side chains of lysine, arginine, resp., Cl) a triple-ζ basis set with polarization functions was applied both at the HF and MP2 levels. For the real system two dezoxyriboses and two guanines were added, the calculations were performed with a double-ζ basis set at the HF level. The direct PO4-⋯Lys/Arg bonds are ˜5 eV strong. These decrease by ˜4 eV due to the Cl ions. The water-mediated PO4-⋯HO⋯Lys/Arg bonds are ˜1 eV strong and the Cl-s hardly change their strength.

  1. PARP3 is a sensor of nicked nucleosomes and monoribosylates histone H2BGlu2

    Science.gov (United States)

    Grundy, Gabrielle J.; Polo, Luis M.; Zeng, Zhihong; Rulten, Stuart L.; Hoch, Nicolas C.; Paomephan, Pathompong; Xu, Yingqi; Sweet, Steve M.; Thorne, Alan W.; Oliver, Antony W.; Matthews, Steve J.; Pearl, Laurence H.; Caldecott, Keith W.

    2016-01-01

    PARP3 is a member of the ADP-ribosyl transferase superfamily that we show accelerates the repair of chromosomal DNA single-strand breaks in avian DT40 cells. Two-dimensional nuclear magnetic resonance experiments reveal that PARP3 employs a conserved DNA-binding interface to detect and stably bind DNA breaks and to accumulate at sites of chromosome damage. PARP3 preferentially binds to and is activated by mononucleosomes containing nicked DNA and which target PARP3 trans-ribosylation activity to a single-histone substrate. Although nicks in naked DNA stimulate PARP3 autoribosylation, nicks in mononucleosomes promote the trans-ribosylation of histone H2B specifically at Glu2. These data identify PARP3 as a molecular sensor of nicked nucleosomes and demonstrate, for the first time, the ribosylation of chromatin at a site-specific DNA single-strand break. PMID:27530147

  2. Characterization and application of microearthquake clusters to problems of scaling, fault zone dynamics, and seismic monitoring at Parkfield, California

    Energy Technology Data Exchange (ETDEWEB)

    Nadeau, R.M.

    1995-10-01

    This document contains information about the characterization and application of microearthquake clusters and fault zone dynamics. Topics discussed include: Seismological studies; fault-zone dynamics; periodic recurrence; scaling of microearthquakes to large earthquakes; implications of fault mechanics and seismic hazards; and wave propagation and temporal changes.

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

    Science.gov (United States)

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

    2016-03-15

    The Chromatin Accessibility Complex (CHRAC) consists of the ATPase ISWI, the large ACF1 subunit and a pair of small histone-like proteins, CHRAC-14/16. CHRAC is a prototypical nucleosome sliding factor that mobilizes nucleosomes to improve the regularity and integrity of the chromatin fiber. This may facilitate the formation of repressive chromatin. Expression of the signature subunit ACF1 is restricted during embryonic development, but remains high in primordial germ cells. Therefore, we explored roles for ACF1 during Drosophila oogenesis. ACF1 is expressed in somatic and germline cells, with notable enrichment in germline stem cells and oocytes. The asymmetrical localization of ACF1 to these cells depends on the transport of the Acf1 mRNA by the Bicaudal-D/Egalitarian complex. Loss of ACF1 function in the novel Acf1(7) allele leads to defective egg chambers and their elimination through apoptosis. In addition, we find a variety of unusual 16-cell cyst packaging phenotypes in the previously known Acf1(1) allele, with a striking prevalence of egg chambers with two functional oocytes at opposite poles. Surprisingly, we found that the Acf1(1) deletion - despite disruption of the Acf1 reading frame - expresses low levels of a PHD-bromodomain module from the C-terminus of ACF1 that becomes enriched in oocytes. Expression of this module from the Acf1 genomic locus leads to packaging defects in the absence of functional ACF1, suggesting competitive interactions with unknown target molecules. Remarkably, a two-fold overexpression of CHRAC (ACF1 and CHRAC-16) leads to increased apoptosis and packaging defects. Evidently, finely tuned CHRAC levels are required for proper oogenesis. PMID:26851213

  4. Experimental dynamical characterization of five autonomous chaotic oscillators with tunable series resistance

    Energy Technology Data Exchange (ETDEWEB)

    Minati, Ludovico, E-mail: lminati@ieee.org, E-mail: ludovico.minati@unitn.it [MR-Lab, Center for Mind/Brain Science, University of Trento, Trento, Italy and Scientific Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan (Italy)

    2014-09-01

    In this paper, an experimental characterization of the dynamical properties of five autonomous chaotic oscillators, based on bipolar-junction transistors and obtained de-novo through a genetic algorithm in a previous study, is presented. In these circuits, a variable resistor connected in series to the DC voltage source acts as control parameter, for a range of which the largest Lyapunov exponent, correlation dimension, approximate entropy, and amplitude variance asymmetry are calculated, alongside bifurcation diagrams and spectrograms. Numerical simulations are compared to experimental measurements. The oscillators can generate a considerable variety of regular and chaotic sine-like and spike-like signals.

  5. Experimental characterization and damage model of the human skin response to dynamic loadings

    OpenAIRE

    JACQUEMOUD,C; Coret, M; BRUYERE-GARNIER,K; Brunet, M.

    2007-01-01

    The objective of this work is to characterize and to model the damage of planar and fibrous soft tissues at high strain rate. As first step, we choose to study the human skin. A dynamic tensile test up to failure is performed on 10x30mm human skin samples. The test is based on the drop test principle and allows loading of samples at a strain rate close to 40 s-1. Classical measurement techniques give global strains whereas a full local strain field is measured on the sample surface by an Imag...

  6. Synthesis, characterization and dynamic NMR studies of a novel chalcone based N-substituted morpholine derivative

    Science.gov (United States)

    Baskar, R.; Baby, C.; Moni, M. S.; Subramanian, K.

    2013-05-01

    The synthesis of a novel chalcone based N-substituted morpholine derivative namely, (E)-1-(biphenyl-4-yl)-3-(4-(5-morpholinopentyloxy) phenyl) prop-2-en-1-one (BMPP), using a two step protocol is reported. The compound is characterized by FTIR, GC-MS and FTNMR spectroscopy techniques. Advanced 2D NMR techniques such as gradient enhanced COSY, HSQC, HMBC and NOESY were employed to establish through-bond and through-space correlations. Dynamic NMR measurements were carried out to obtain the energy barrier to ring inversion of the morpholine moiety.

  7. Characterization of a dynamic multi-leaf collimator for stereotactic radiotherapy applications.

    Science.gov (United States)

    Godwin, G A; Simpson, J B; Mugabe, K V

    2012-07-21

    The Apex® dynamic mini-multileaf collimator has recently been released by Elekta and attaches directly to the linear accelerator head. This paper details the work and results obtained in characterizing this mini-MLC for stereotactic usage within our department. A range of mechanical and dosimetric characteristics were investigated which included inter and intra leaf leakage, light/radiation field congruence, leaf position reproducibility, radiation penumbra, total scatter factors and mechanical rotational stability with the additional mini-MLC weight. PMID:22750675

  8. Characterization of a dynamic multi-leaf collimator for stereotactic radiotherapy applications

    International Nuclear Information System (INIS)

    The Apex® dynamic mini-multileaf collimator has recently been released by Elekta and attaches directly to the linear accelerator head. This paper details the work and results obtained in characterizing this mini-MLC for stereotactic usage within our department. A range of mechanical and dosimetric characteristics were investigated which included inter and intra leaf leakage, light/radiation field congruence, leaf position reproducibility, radiation penumbra, total scatter factors and mechanical rotational stability with the additional mini-MLC weight. (paper)

  9. 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.

  10. Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

    Science.gov (United States)

    Samb, Rawane; Khadraoui, Khader; Belleau, Pascal; Deschênes, Astrid; Lakhal-Chaieb, Lajmi; Droit, Arnaud

    2015-12-01

    Genome-wide mapping of nucleosomes has revealed a great deal about the relationships between chromatin structure and control of gene expression. Recent next generation CHIP-chip and CHIP-Seq technologies have accelerated our understanding of basic principles of chromatin organization. These technologies have taught us that nucleosomes play a crucial role in gene regulation by allowing physical access to transcription factors. Recent methods and experimental advancements allow the determination of nucleosome positions for a given genome area. However, most of these methods estimate the number of nucleosomes either by an EM algorithm using a BIC criterion or an effective heuristic strategy. Here, we introduce a Bayesian method for identifying nucleosome positions. The proposed model is based on a Multinomial-Dirichlet classification and a hierarchical mixture distributions. The number and the positions of nucleosomes are estimated using a reversible jump Markov chain Monte Carlo simulation technique. We compare the performance of our method on simulated data and MNase-Seq data from Saccharomyces cerevisiae against PING and NOrMAL methods. PMID:26656614

  11. Developments in ambient noise analysis for the characterization of dynamic response of slopes to seismic shaking

    Science.gov (United States)

    Del Gaudio, Vincenzo; Wasowski, Janusz

    2016-04-01

    In the last few decades, we have witnessed a growing awareness of the role of site dynamic response to seismic shaking in slope failures during earthquakes. Considering the time and costs involved in acquiring accelerometer data on landslide prone slopes, the analysis of ambient noise offers a profitable investigative alternative. Standard procedures of ambient noise analysis, according to the technique known as HVNR or Nakamura's method, were originally devised to interpret data under simple site conditions similar to 1D layering (flat horizontal layering infinitely extended). In such cases, conditions of site amplification, characterized by a strong impedance contrast between a soft surface layer and a stiff bedrock, result in a single pronounced isotropic maximum of spectral ratios between horizontal and vertical component of ambient noise. However, previous studies have shown that the dynamic response of slopes affected by landslides is rather complex, being characterized by multiple resonance peaks with directional variability, thus, the use of standard techniques can encounter difficulties in providing reliable information. A new approach of data analysis has recently been proposed to exploit the potential of information content of Rayleigh waves present in ambient noise, with regard to the identification of frequency and orientation of directional resonance. By exploiting ground motion ellipticity this approach can also provide information on vertical distribution of S-wave velocity, which controls site amplification factors. The method, based on the identification of Rayleigh wave packets from instantaneous polarization properties of ambient noise, was first tested using synthetic signals in order to optimize the data processing system. Then the improved processing scheme is adopted to re-process and re-interpret the ambient noise data acquired on landslide prone slopes around Caramanico Terme (central Italy), at sites monitored also with accelerometer

  12. Applying non-linear dynamics to atrial appendage flow data to understand and characterize atrial arrhythmia

    International Nuclear Information System (INIS)

    The aim of this study was to better understand and characterize left atrial appendage flow in atrial fibrillation. Atrial fibrillation and flutter are the most common cardiac arrhythmias affecting 15% of the older population. The pulsed Doppler velocity profile data was recorded from the left atrial appendage of patients using transesophageal echocardiography. The data was analyzed using Fourier analysis and nonlinear dynamical tools. Fourier analysis showed that appendage mechanical frequency (ff) for patients in sinus rhythm was always lower (around1 Hz) than that in atrial fibrillation (5-8 Hz). Among patients with atrial fibrillation spectral power below ff was significantly different suggesting variability within this group of patients. Results that suggested the presence of nonlinear dynamics were: a) the existence of two arbitrary peak frequencies f1, f2, and other peak frequencies as linear combinations thereof (mf1±nf2), and b) the similarity between the spectrum of patient data and that obtained using the Lorenz equation. Nonlinear analysis tools, including Phase plots and differential radial plots, were also generated from the velocity data using a delay of 10. In the phase plots, some patients displayed a torus-like structure, while others had a more random-like pattern. In the differential radial plots, the first set of patients (with torus-like phase plots) showed fewer values crossing an arbitrary threshold of 10 than did the second set (8 vs. 27 in one typical example). The outcome of cardioversion was different for these two set of patients. Fourier analysis helped to: differentiate between sinus rhythm and atrial fibrillation, understand the characteristics of the wide range of atrial fibrillation patients, and provide hints that atrial fibrillation could be a nonlinear process. Nonlinear dynamical tools helped to further characterize and sub-classify atrial fibrillation

  13. Experimental Characterization of the Anatomical Structures of the Lumbar Spine Under Dynamic Sagittal Bending.

    Science.gov (United States)

    Bradfield, C A; Demetropoulos, C K; Luongo, M E; Pyles, C O; Armiger, R S; Merkle, A C

    2015-01-01

    Underbody blast (UBB) events transmit high-rate vertical loads through the seated occupant’s lumbar spine and have a high probability of inducing severe injury. While previous studies have characterized the lumbar spine under quasi-static loading, additional work should focus on the complex kinetic and kinematic response under high loading rates. To discern the biomechanical influence of the lumbar spine’s anatomical structures during dynamic loading, the axial force, flexion-extension moments and range of motion for lumbar motion segments (n=18) were measured during different states of progressive dissection. Pre-compression was applied using a static mass while dynamic bending was applied using an offset drop mass. Dynamic loading resulted in peak axial loads of 4,224±133 N, while maximum peak extension and flexion moments were 19.6±12.5 and -44.8±8.6 Nm in the pre-dissected state, respectively. Upon dissection, transection of the interspinous ligament, ligamentum flavum and facet capsules resulted in significantly larger flexion angles, while the removal of the posterior elements increased the total peak angular displacement in extension from 3.3±1.5 to 5.0±1.7 degrees (p=0.002). This study provides insight on the contribution of individual anatomical components on overall lumbar response under high-rate loading, as well as validation data for numerical models. PMID:25996712

  14. Dynamic Characterization of Galfenol (Fe81.6Ga18.4)

    Science.gov (United States)

    Scheidler, Justin J.; Asnani, Vivake M.; Dapino, Marcelo J.

    2016-01-01

    Galfenol has the potential to transform the smart materials industry by allowing for the development of multifunctional, load-bearing devices. One of the primary technical challenges faced by this development is the very limited experimental data on Galfenol's frequency-dependent response to dynamic stress, which is critically important for the design of such devices. This report details a novel and precise characterization of the constitutive behavior of polycrystalline Galfenol (Fe81.6Ga18.4) under quasi-static (1 Hz) and dynamic (4 to 1000 Hz) stress loadings. Mechanical loads are applied using a high-frequency load frame. Quasi-static minor and major hysteresis loop measurements of magnetic flux density and strain are presented for constant electromagnet currents (0 to 1.1 A) and constant magnetic fields 0 to 14 kA/m (0 to 180 Oe). The dynamic stress amplitude for minor and major loops is 2.88 and 31.4 MPa (418 and 4550 psi), respectively. Quasi-static material properties closely match published values for similar Galfenol materials. Quasi-static actuation responses are also measured and compared to quasi-static sensing responses; the high degree of reversibility seen in the comparison is consistent with published measurements and modeling results. Dynamic major and minor loops are measured for dynamic stresses up to 31 MPa (4496 psi) and 1 kHz, and the bias condition resulting in maximum, quasi-static sensitivity. Eddy current effects are quantified by considering solid and laminated Galfenol rods. Three key sources of error in the dynamic measurements are accounted for: (1) electromagnetic noise in strain signals due to Galfenol's magnetic response, (2) error in load signals due to the inertial force of fixturing, and (3) phase misalignment between signals due to conditioning electronics. For dynamic characterization, strain error is kept below 1.2 percent of full scale by wiring two collocated gauges in series (noise cancellation) and through leadwire

  15. Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1.

    OpenAIRE

    Eisfeld, K; Candau, R; Truss, M; Beato, M

    1997-01-01

    To analyse the role of rotational orientation and translational positioning of nucleosomal DNA on transcription factor binding we have generated a series of mutant MMTV promoters containing insertions of various lengths between the hormone-responsive region and the binding site for NF1. These various MMTV promoter fragments were assembled in mononucleosomes and used for structural studies and binding experiments. We show that the insertions change the rotational phase and translational positi...

  16. Rapid deamination of cyclobutane pyrimidine dimer photoproducts at TCG sites in a translationally and rotationally positioned nucleosome in vivo.

    Science.gov (United States)

    Cannistraro, Vincent J; Pondugula, Santhi; Song, Qian; Taylor, John-Stephen

    2015-10-30

    Sunlight-induced C to T mutation hot spots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. The C and 5-methyl-C in CPDs are not stable and deaminate to U and T, respectively, which leads to the insertion of A by the DNA damage bypass polymerase η, thereby defining a probable mechanism for the origin of UV-induced C to T mutations. Deamination rates for T(m)CG CPDs have been found to vary 12-fold with rotational position in a nucleosome in vitro. To determine the influence of nucleosome structure on deamination rates in vivo, we determined the deamination rates of CPDs at TCG sites in a stably positioned nucleosome within the FOS promoter in HeLa cells. A procedure for in vivo hydroxyl radical footprinting with Fe-EDTA was developed, and, together with results from a cytosine methylation protection assay, we determined the translational and rotational positions of the TCG sites. Consistent with the in vitro observations, deamination was slower for one CPD located at an intermediate rotational position compared with two other sites located at outside positions, and all were much faster than for CPDs at non-TCG sites. Photoproduct formation was also highly suppressed at one site, possibly due to its interaction with a histone tail. Thus, it was shown that CPDs of TCG sites deaminate the fastest in vivo and that nucleosomes can modulate both their formation and deamination, which could contribute to the UV mutation hot spots and cold spots. PMID:26354431

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

    OpenAIRE

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

    2014-01-01

    The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is n...

  18. Decoherence of many-spin systems in NMR: From molecular characterization to an environmentally induced quantum dynamical phase transition

    CERN Document Server

    Alvarez, Gonzalo A

    2007-01-01

    The control of open quantum systems has a fundamental relevance for fields ranging from quantum information processing to nanotechnology. Typically, the system whose coherent dynamics one wants to manipulate, interacts with an environment that smoothly degrades its quantum dynamics. Thus, a precise understanding of the inner mechanisms of this process, called "decoherence", is critical to develop strategies to control the quantum dynamics. In this thesis we solved the generalized Liouville-von Neumann quantum master equation to obtain the dynamics of many-spin systems interacting with a spin bath. We also solve the spin dynamics within the Keldysh formalism. Both methods lead to identical solutions and together gave us the possibility to obtain numerous physical predictions that contrast well with Nuclear Magnetic Resonance experiments. We applied these tools for molecular characterizations, development of new numerical methodologies and the control of quantum dynamics in experimental implementations. But, mo...

  19. New Dilated LMI Characterization for the Multiobjective Full-Order Dynamic Output Feedback Synthesis Problem

    Directory of Open Access Journals (Sweden)

    Zrida Jalel

    2010-01-01

    Full Text Available This paper introduces new dilated LMI conditions for continuous-time linear systems which not only characterize stability and performance specifications, but also, performance specifications. These new conditions offer, in addition to new analysis tools, synthesis procedures that have the advantages of keeping the controller parameters independent of the Lyapunov matrix and offering supplementary degrees of freedom. The impact of such advantages is great on the multiobjective full-order dynamic output feedback control problem as the obtained dilated LMI conditions always encompass the standard ones. It follows that much less conservatism is possible in comparison to the currently used standard LMI based synthesis procedures. A numerical simulation, based on an empirically abridged search procedure, is presented and shows the advantage of the proposed synthesis methods.

  20. Characterization of drying paint coatings by dynamic speckle and holographic interferometry measurements.

    Science.gov (United States)

    Budini, N; Mulone, C; Balducci, N; Vincitorio, F M; López, A J; Ramil, A

    2016-06-10

    In this work we implemented dynamic speckle and holographic interferometry techniques to characterize the drying process of solvent-based paint coatings. We propose a simple way to estimate drying time by measuring speckle activity and incrementally fitting experimental data through standard regression algorithms. This allowed us to predict drying time after about 20-30 min of paint application, which is fast compared to usual times required to reach the so-called tack-free state (≈2  h). In turn, we used holographic interferometry to map small thickness variations in the coating surface during drying. We also demonstrate that results obtained from both techniques correlate with each other, which allows us to improve the accuracy of the drying time estimation. PMID:27409029

  1. Differential Dynamic Microscopy: a High-Throughput Method for Characterizing the Motility of Microorganism

    CERN Document Server

    Martinez, Vincent A; Croze, Ottavio A; Tailleur, Julien; Reufer, Mathias; Schwarz-Linek, Jana; Wilson, Laurence G; Bees, Martin A; Poon, Wilson C K

    2012-01-01

    We present a fast, high-throughput method for characterizing the motility of microorganisms in 3D based on standard imaging microscopy. Instead of tracking individual cells, we analyse the spatio-temporal fluctuations of the intensity in the sample from time-lapse images and obtain the intermediate scattering function (ISF) of the system. We demonstrate our method on two different types of microorganisms: bacteria, both smooth swimming (run only) and wild type (run and tumble) Escherichia coli, and the bi-flagellate alga Chlamydomonas reinhardtii. We validate the methodology using computer simulations and particle tracking. From the ISF, we are able to extract (i) for E. coli: the swimming speed distribution, the fraction of motile cells and the diffusivity, and (ii) for C. reinhardtii: the swimming speed distribution, the amplitude and frequency of the oscillatory dynamics. In both cases, the motility parameters are averaged over \\approx 10^4 cells and obtained in a few minutes.

  2. Dynamic characterization of crystalline and glass phases of deuterated 1,1,2,2 tetrachloroethane

    Energy Technology Data Exchange (ETDEWEB)

    Pérez, Silvina C., E-mail: clyde@famaf.unc.edu.ar; Zuriaga, Mariano, E-mail: zuriaga@famaf.unc.edu.ar; Serra, Pablo, E-mail: serra@famaf.unc.edu.ar; Wolfenson, Alberto, E-mail: wolf@famaf.unc.edu.ar [Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba and IFEG-CONICET, Ciudad Universitaria, X5016LAE Córdoba (Argentina); Negrier, Philippe, E-mail: philippe.negrier@u-bordeaux.fr [Université Bordeaux, LOMA, UMR 5798, F-33400 Talence, France and LOMA, UMR 5798, F-33400 Talence (France); Tamarit, Josep Lluis, E-mail: josep.lluis.tamarit@upc.edu [Grup de Caracterització de Materials, Departament de Física i Enginyeria Nuclear, ETSEIB, Diagonal 647, Universitat Politècnica de Catalunya, 08028 Barcelona, Catalonia (Spain)

    2015-10-07

    A thorough characterization of the γ, β, and glass phases of deuterated 1,1,2,2 tetrachloroethane (C{sub 2}D{sub 2}Cl{sub 4}) via nuclear quadrupole resonance and Molecular Dynamic Simulations (MDSs) is reported. The presence of molecular reorientations was experimentally observed in the glass phase and in the β phase. In the β phase, and from MDS, these reorientations are attributed to two possible movements, i.e., a 180°  reorientation around the C{sub 2} molecular symmetry axis and a reorientation of the molecule between two non-equivalent positions. In the glass phase, the spin-lattice relaxation time T{sub 1} is of the order of 16 times lower than in the crystalline phase and varies as T{sup −1} below 100 K in good agreement with the strong quadrupolar relaxation observed in amorphous materials and in the glassy state of molecular organic systems. The activation energy of molecular reorientations in the glass phase (19 kJ/mol) is comparable to that observed in the glassy crystal of a “molecular cousin” compound, Freon 112 (C{sub 2}F{sub 2}Cl{sub 4}), for the secondary β-relaxation. Moreover, the on-site orientational motion of tetrachloroethane molecules offers a new indirect evidence of the prominent role of such orientational disorder in glassy dynamics.

  3. Characterizing regulated reservoirs dynamics in regional to global scale hydrologic models

    Science.gov (United States)

    Beighley, E.; Yoon, Y.; Lee, H.; Pavelsky, T.; Allen, G. H.

    2015-12-01

    Lakes and reservoirs are widely used for water supply and flood control resulting in regulated release of outflows that are nonconcurrent with inflows. In hydrologic modeling applications, accounting for the regulated behavior of reservoirs distributed throughout a river system poses a significant challenge because detailed reservoir operation rules or strategies can be difficult or not possible to obtain. Building on this problem, this study addresses the science questions: Can we model reservoir water storage changes and outlet discharges based on satellite measurements of river water surface elevation and inundated area, and How does repeat cycle, mission duration and measurement uncertainty impact our ability to characterize reservoir behavior? A modeling framework suitable for regional to global applications and based on the forthcoming Surface Water and Ocean Topography (SWOT) satellite mission is presented. Although our framework can be combined with data assimilation techniques for real-time flood forecasting, our goal is to represent reservoir storage patterns in large-scale hydrologic models for simulating: (i) impacts of future climate and/or land cover conditions on water resources, and (ii) synthetic storm events (e.g., 100-yr flood) or event catalogs for flood hazard and risk assessments. In-situ and remotely sensed reservoir dynamics are presented for select locations in the Mississippi River Basin and used in the Hillslope River Routing (HRR) hydrologic model to simulate downstream flow dynamics.

  4. TRAJELIX: a computational tool for the geometric characterization of protein helices during molecular dynamics simulations.

    Science.gov (United States)

    Mezei, Mihaly; Filizola, Marta

    2006-02-01

    We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework (http://inka.mssm.edu/~mezei/simulaid/) that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs. PMID:16783601

  5. Size graded sediment dynamics: from the processes characterization to the transport modelling in the English Channel

    International Nuclear Information System (INIS)

    The purpose of this work is the implementation of a sediment transport model in the English Channel. The design of such a model requires the identification of the physical processes, their modelling and their in-situ validation. Because of the sedimentary particularities of the study area, modelling of the mechanical behaviour of a non uniform mixture of sediments and particularly of the fine grains within a coarse matrix is required. This study focused on the characterization of the relevant processes by acquisition of experimental and in-situ data. Data acquired in hydro-sedimentary conditions comparable to those found in the English Channel are scarce. A new instrument and image processing technique were specifically conceived and implemented in-situ to observe and measure, with a high temporal resolution, the dynamics of a strongly heterogeneous mixture of particles in a grain-size scale. The data collected compared well with several existing formulations. One of these formulations was chosen to be adapted. The transfer dynamics of fine grains in coarse sediments and their depth of penetration were acquired from stratigraphic samples. The sediment transport model deals with multi-size grains and multi sedimentary layers, it is forced by swell and currents, and accounts for bead load and suspended load transports. It was applied to realistic scenarios for the English Channel. (author)

  6. Dynamic characterization of crystalline and glass phases of deuterated 1,1,2,2 tetrachloroethane

    International Nuclear Information System (INIS)

    A thorough characterization of the γ, β, and glass phases of deuterated 1,1,2,2 tetrachloroethane (C2D2Cl4) via nuclear quadrupole resonance and Molecular Dynamic Simulations (MDSs) is reported. The presence of molecular reorientations was experimentally observed in the glass phase and in the β phase. In the β phase, and from MDS, these reorientations are attributed to two possible movements, i.e., a 180°  reorientation around the C2 molecular symmetry axis and a reorientation of the molecule between two non-equivalent positions. In the glass phase, the spin-lattice relaxation time T1 is of the order of 16 times lower than in the crystalline phase and varies as T−1 below 100 K in good agreement with the strong quadrupolar relaxation observed in amorphous materials and in the glassy state of molecular organic systems. The activation energy of molecular reorientations in the glass phase (19 kJ/mol) is comparable to that observed in the glassy crystal of a “molecular cousin” compound, Freon 112 (C2F2Cl4), for the secondary β-relaxation. Moreover, the on-site orientational motion of tetrachloroethane molecules offers a new indirect evidence of the prominent role of such orientational disorder in glassy dynamics

  7. The role of anti-nucleosome antibodies in systemic lupus erythematosus. Results of a study of patients with systemic lupus erythematosus and other connective tissue diseases

    Directory of Open Access Journals (Sweden)

    V. Tigano

    2011-09-01

    Full Text Available Objective: The aim of our study was to investigate the prevalence and the disease specificity of anti-nucleosome antibodies in systemic lupus erythematosus and their association with disease activity and renal involvement. Methods: Anti-nucleosome antibodies were measured by ELISA in the sera of patients with systemic lupus erythematosus (SLE (47, rheumatoid arthritis (RA (22, mixed connective tissue disease (MCTD (19, systemic sclerosis (SSc (11 and Siögren’s syndrome (SS (10. Anti-dsDNA antibodies were measured by IIF on Chritidia luciliae. In the patients with SLE serum levels of C3 and C4 complement components were also measured. Sera of 22 healthy individuals were assayed as controls. SLE activity was evaluated by the ECLAM score. Results: Anti-nucleosome antibodies were found in 40 patients with SLE (85.1%, in 10 with RA (45.4%, in 8 with MCTD (42.1%, in 4 with SSc (36.3%, in 1 with SS (10% and in none of the healthy controls. Anti-dsDNA antibodies were found in 23 patients with SLE and were absent in the patients with other CTD and in controls. All the patients with SLE and renal involvement were positive both for anti-dsDNA antibodies and anti-nucleosome antibodies. No significant correlation was observed between anti-nucleosome antibodies and disease activity and renal involvement. Conclusion: Anti-nucleosome antibodies are present in a high percentage of the patients with SLE but they don’t seem to be specific markers of the desease. Our data don’t support a clear correlation between anti-nucleosome antibodies and disease activity and renal involvement.

  8. Apoptosis-related deregulation of proteolytic activities and high serum levels of circulating nucleosomes and DNA in blood correlate with breast cancer progression

    International Nuclear Information System (INIS)

    As cell-free circulating DNA exists predominantly as mono- and oligonucleosomes, the focus of the current study was to examine the interplay of circulating nucleosomes, DNA, proteases and caspases in blood of patients with benign and malignant breast diseases. The concentrations of cell-free DNA and nucleosomes as well as the protease and caspase activities were measured in serum of patients with benign breast disease (n = 20), primary breast cancer (M0, n = 31), metastatic breast cancer (M1, n = 32), and healthy individuals (n = 28) by PicoGreen, Cell Death Detection ELISA, Protease Fluorescent Detection Kit and Caspase-Glo®3/7 Assay, respectively. Patients with benign and malignant tumors had significantly higher levels of circulating nucleic acids in their blood than healthy individuals (p = 0.001, p = 0.0001), whereas these levels could not discriminate between benign and malignant lesions. Our analyses of all serum samples revealed significant correlations of circulating nucleosome with DNA concentrations (p = 0.001), nucleosome concentrations with caspase activities (p = 0.008), and caspase with protease activities (p = 0.0001). High serum levels of protease and caspase activities associated with advanced tumor stages (p = 0.009). Patients with lymph node-positive breast cancer had significantly higher nucleosome levels in their blood than node-negative patients (p = 0.004). The presence of distant metastases associated with a significant increase in serum nucleosome (p = 0.01) and DNA levels (p = 0.04), and protease activities (p = 0.008). Our findings demonstrate that high circulating nucleic acid concentrations in blood are no indicators of a malignant breast tumor. However, the observed changes in apoptosis-related deregulation of proteolytic activities along with the elevated serum levels of nucleosomes and DNA in blood are linked to breast cancer progression

  9. Evaluation and characterization of bacterial metabolic dynamics with a novel profiling technique, real-time metabolotyping.

    Directory of Open Access Journals (Sweden)

    Shinji Fukuda

    Full Text Available BACKGROUND: Environmental processes in ecosystems are dynamically altered by several metabolic responses in microorganisms, including intracellular sensing and pumping, battle for survival, and supply of or competition for nutrients. Notably, intestinal bacteria maintain homeostatic balance in mammals via multiple dynamic biochemical reactions to produce several metabolites from undigested food, and those metabolites exert various effects on mammalian cells in a time-dependent manner. We have established a method for the analysis of bacterial metabolic dynamics in real time and used it in combination with statistical NMR procedures. METHODOLOGY/PRINCIPAL FINDINGS: We developed a novel method called real-time metabolotyping (RT-MT, which performs sequential (1H-NMR profiling and two-dimensional (2D (1H, (13C-HSQC (heteronuclear single quantum coherence profiling during bacterial growth in an NMR tube. The profiles were evaluated with such statistical methods as Z-score analysis, principal components analysis, and time series of statistical TOtal Correlation SpectroScopY (TOCSY. In addition, using 2D (1H, (13C-HSQC with the stable isotope labeling technique, we observed the metabolic kinetics of specific biochemical reactions based on time-dependent 2D kinetic profiles. Using these methods, we clarified the pathway for linolenic acid hydrogenation by a gastrointestinal bacterium, Butyrivibrio fibrisolvens. We identified trans11, cis13 conjugated linoleic acid as the intermediate of linolenic acid hydrogenation by B. fibrisolvens, based on the results of (13C-labeling RT-MT experiments. In addition, we showed that the biohydrogenation of polyunsaturated fatty acids serves as a defense mechanism against their toxic effects. CONCLUSIONS: RT-MT is useful for the characterization of beneficial bacterium that shows potential for use as probiotic by producing bioactive compounds.

  10. Fluid dynamics characterization of riser in a FCC cold flow model using gas radiotracer

    International Nuclear Information System (INIS)

    Was carried out the characterization of a diameter small riser of a cold flow model of a circulating fluidized bed (CFB), with aid of a radioactive tracer. Compressed air and catalytic cracking of petroleum flow through solids pneumatic transport regime, made of transparent material (glass, acrylic, PVC, polycarbonate) for study of problems in Fluid Catalytic Cracking (FCC) unit and development of methods of measurement of fluid dynamic parameters. The CFB model consisted of a mixer component solid-gas (compressed air at 25 deg C and 200 kN/m2; cracking catalyst with an average diameter of 72μm and specific mass of 1,500 kg/m3), comprising a riser pipe glass 0.02m internal diameter and 1.8m height, a gas solid separation vessel by flash effect, with the filter in the gas outlet, and a return column (a glass tube with an internal diameter of 0.0254m) to redirect the catalyst for the riser base. Recorded data allowed studies on residence time distribution of the gaseous phase in the riser, with the identification and characterization of the flow of gas-solid components in the CFB riser of small diameter. A plug flow type with deviations due to back mixing of catalyst close to the walls, associated with the density difference between this component was observed. (author)

  11. Radiation damage characterization in non-stoichiometric uranium dioxide by molecular dynamics simulations

    International Nuclear Information System (INIS)

    In this work, we perform a characterization of the radiation damage induced in non-stoichiometric UO2±x by means of molecular dynamics (MD) simulations using the CP2K program package. The radiation damage characterization we are studying corresponds to the distribution of point defects and their corresponding clusters after a displacement cascade initiated by a uranium primary knock-on atom (PKA) energy of 10 keV. The study is carried out at 1000 K which represents an average temperature of the fuel under operating conditions. All simulations are performed in a cubic simulation box with an edge length of about 23 nm. The non-stoichiometric structures are constructed based on the stoichiometric UO2.00 structure either by randomly adding interstitial oxygen atoms in octahedral lattice sites (hyper-stoichiometric) or by randomly creating oxygen vacancies (hypo-stoichiometric). The fission products in the fuel matrix are not considered. We compare the results for stoichiometric UO2.00 with two hypo-stoichiometric (UO1.95 and UO1.99) and two hyper-stoichiometric (UO2.01 and UO2.05) structures. For each stoichiometry several simulations are run to estimate the statistical error

  12. Combined Dynamic Light Scattering and Raman Spectroscopy Approach for Characterizing the Aggregation of Therapeutic Proteins

    Directory of Open Access Journals (Sweden)

    E. Neil Lewis

    2014-12-01

    Full Text Available Determination of the physicochemical properties of protein therapeutics and their aggregates is critical for developing formulations that enhance product efficacy, stability, safety and manufacturability. Analytical challenges are compounded for materials: (1 that are formulated at high concentration, (2 that are formulated with a variety of excipients, and (3 that are available only in small volumes. In this article, a new instrument is described that measures protein secondary and tertiary structure, as well as molecular size, over a range of concentrations and formulation conditions of low volume samples. Specifically, characterization of colloidal and conformational stability is obtained through a combination of two well-established analytical techniques: dynamic light scattering (DLS and Raman spectroscopy, respectively. As the data for these two analytical modalities are collected on the same sample at the same time, the technique enables direct correlation between them, in addition to the more straightforward benefit of minimizing sample usage by providing multiple analytical measurements on the same aliquot non-destructively. The ability to differentiate between unfolding and aggregation that the combination of these techniques provides enables insights into underlying protein aggregation mechanisms. The article will report on mechanistic insights for aggregation that have been obtained from the application of this technique to the characterization of lysozyme, which was evaluated as a function of concentration and pH.

  13. Optimized Temporal Window for Detection and Characterization of Renal Cell Carcinomas with Dynamic CT Scanning

    Institute of Scientific and Technical Information of China (English)

    Jinhong Wang; Peijun Wang; Xiaohu Zhao; Xinqin Mao; Xiaolong Gao; Jun Liu

    2005-01-01

    OBJECTIVE To investigate the optimized time period for detection and characterization of renal cell carcinomas (RCC) when the specific CT features appear during spiral dynamic CT scanning, and to optimize an effective scanning protocol of spiral CT for evaluating RCC.METHODS Twenty-four patients with RCC verified by pathology had undergone a dynamic CT (D-CT) scan. A plain scan was employed to select the target slice. Single-level dynamic scanning started at 14-17 s after the intravenous contrast media had been administered, with a scan interval of 4.9 s acquiring a total number of 17~24 frames. A regular CT scan of the whole kidney followed by a delayed single slice acquisition through the target slice in the excretory phase was performed. Images were assessed in two ways: (1) A group of experienced radiologists reviewed the CT images to find when the specific signs appeared and when the CT features of RCC were optimally displayed; (2) Data measurement of the time-density curves (T-DC) of RCC. The exact time was obtained when the densities of the tumor, renal parenchyma, medulla and aorta reached their peak enhancement, thus also the time when the density difference between tumor and parenchyma was at maximum (Max T-M). Based on the slope of the contrast media uptake curve, T-DC types were ranked from the smallest to the biggest of slope as type A, B and C.RESULTS 1. The review of the CT images by the radiologists showed that the CT features of RCC were optimally demonstrated at 70.2 s. The earliest time at which RCC CT features were examined was at 23.9 s. 2. Image data analysis: the time that the density (or CT value) of the tumor mass reached peak enhancement was at 54 s and peak value was at 80.4 Hu for RCC. The time of the maximal difference of densities between tumor and renal parenchyma was at 102 s.CONCLUSION The following proposal is the scanning protocol for detecting RCC recommended by our research: After a plain scan to determine the target level, a

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

    Directory of Open Access Journals (Sweden)

    Justin W Leung

    2014-03-01

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

  15. Dynamic Mechanical Behavior Characterization of Epoxy-Cast Al + Fe2O3 Thermite Mixture Composites

    Science.gov (United States)

    Ferranti, Louis; Thadhani, Naresh N.

    2007-11-01

    The dynamic mechanical behavior characterization of epoxy-cast stoichiometric mixtures of nano- or micron-scale aluminum and hematite (Fe2O3) powders is investigated in this work. Experiments conducted on rod-shaped samples, using instrumented reverse Taylor impact tests employing high-speed imaging and velocity interferometry, show that these composites exhibit viscoelastic deformation and brittle fracture behaviors. Upon impact, the samples display significant elastic and plastic deformation during both the loading and unloading stages, as determined from quantitative high-speed camera measurements of the transient deformation states. Approximately 50 pct elastic recovery of total axial strain was observed to occur rapidly (within tens of microseconds) after impact. A one-dimensional elastic-plastic wave propagation analysis was used for estimating the composite’s dynamic average yield stress and total plastic strain. The results reveal that the nano-Al + Fe2O3-containing epoxy composite is most resilient, has the highest strength, and is more capable of absorbing impact energy. The analysis additionally provides detailed information about elastic and plastic wave interactions for discrete times, up to the final state of the material. Calculations and observations through the coupling of high-speed camera images and velocity interferometry (VISAR) measurements show that the elastic recovery coincides with peak axial strain and the interaction of elastic and plastic waves propagating within the rod-shaped specimen. Hence, such an instrumented Taylor test provides a detailed view of the general wave structure within the material upon impact and, at the same time, enables a complete description of the stress-strain response.

  16. Dynamics and polyphasic characterization of odor-producing cyanobacterium Tychonema bourrellyi from Lake Erhai, China.

    Science.gov (United States)

    Zhang, Hang; Song, Gaofei; Shao, Jihai; Xiang, Xianfen; Li, Qi; Chen, Youxin; Yang, Ping; Yu, Gongliang

    2016-03-01

    The previous studies indicated that Tychonema-like strains from Lake Erhai could release geosmin so that the species was listed as the potential harmful cyanobacteria influencing the drinking water safety around Lake Erhai. But, the dynamics and biological information of this species were too limited. In this study, the polyphasic approach was used to reveal its biological characterization and the dynamics in Lake Erhai. The characters of trichomes, including filaments with solitary or bundle state, reddish-brown or blue-green color, planktonic habitat, and presence of keritomized content, were examined by the microscopic method. The 16S rDNA sequences of these strains were used for phylogenetic analysis and molecular identification. The strains were morphologically classified as Tychonema bourrellyi, and geosmin and β-ionone were identified as the major volatile substances using gas chromatography-mass spectrometry (GC-MS) analysis. No strains of T. bourrellyi were found to produce microcystin by the HPLC and mcy gene approaches. Cell numbers at 12 sampling sites in Lake Erhai were shown as an average of 3 × 10(4) cells L(-1) in 2009 and 2010. The obvious peaks occurred in July and August each year. This was the first report on occurrence of T. bourrellyi from outside of Europe, and T. bourrellyi was also a newly recorded species in China. Such a result demonstrated that T. bourrellyi could distribute extending from cold waters in North Europe to the warm waters in subtropical regions. It was interesting to observe the coincidence of the occurrence of T. bourrellyi with slightly eutrophicated waters since Lake Erhai had been regarded as an early phase of eutrophicated lake. PMID:26564199

  17. Fluid-dynamic characterization of real-scale raceway reactors for microalgae production

    International Nuclear Information System (INIS)

    The fluid dynamic characterization of a 100 m length × 1 m wide channel raceway photobioreactor was carried out. The effects of water depth, liquid velocity and the presence, or absence, of sump baffles to improve the CO2 supply transfer were considered in relation to on the power consumption, residence time and mixing in the reactor was studied. When operated at a depth of 20 cm, the power consumption was between 1.5 and 8.4 W m−3 depending on the forward velocity, with higher values occurring when the baffle was in place. Residence times and the degree of mixing at each section of the raceway (paddlewheel, bends, channels and sump) were measured experimentally. Mixing occurred mainly in the sump, paddlewheel and bends, with a maximum dispersion coefficient of 0.07 m2 s−1. These sections, however, only contributed a small fraction to the total volume of the raceway. Bodenstein numbers from 200 to 540 for the channel sections indicated plug-flow characteristics. Mixing times ranged from 1.4 to 6 h, with the presence of the baffle greatly increasing these times despite higher specific power consumption. A total of 15–20 circuits of the raceway were needed to achieve complete mixing without the baffle, compared to 30–40 cycles with the baffle. Vertical mixing was very poor whereas axial mixing was similar to that achieved in closed photobioreactors. The methodologies applied were shown to be useful in determining the fluid dynamics of a raceway photobioreactor. Equations useful in simulating the power consumption as a function of the design and operation parameters have been validated. -- Highlights: •Power consumption due to accessories can limit the use of raceway reactors for energy purposes. •Use of baffle to enhance mass transfer dramatically increases the power consumption in this type of photobioreactors. •High mixing time, in the order of hours, in raceway reactors limits the operation mode of these systems

  18. Mechanical Characterization of Immature Porcine Brainstem in Tension at Dynamic Strain Rates

    Science.gov (United States)

    Zhao, Hui; Yin, Zhiyong; Li, Kui; Liao, Zhikang; Xiang, Hongyi; Zhu, Feng

    2016-01-01

    Background Many brain injury cases involve pediatric road traffic accidents, and among these, brainstem injury causes disastrous outcomes. A thorough understanding of the tensile characterization of immature brainstem tissue is crucial in modeling traumatic brain injury sustained by children, but limited experimental data in tension is available for the immature brain tissue at dynamic strain rates. Material/Methods We harvested brainstem tissue from immature pigs (about 4 weeks old, and at a developmental stage similar to that of human toddlers) as a byproduct from a local slaughter house and very carefully prepared the samples. Tensile tests were performed on specimens at dynamic strain rates of 2/s, 20/s, and 100/s using a biological material instrument. The constitutive models, Fung, Ogden, Gent, and exponential function, for immature brainstem tissue material property were developed for the recorded experimental data using OriginPro® 8.0 software. The t test was performed for infinitesimal shear modules. Results The curves of stress-versus-stretch ratio were convex in shape, and inflection points were found in all the test groups at the strain of about 2.5%. The average Lagrange stress of the immature brainstem specimen at the 30% strain at the strain rates of 2, 20, and 100/s was 273±114, 515±107, and 1121±197 Pa, respectively. The adjusted R-Square (R2) of Fung, Ogden, Gent, and exponential model was 0.820≤R2≤0.933, 0.774≤R2≤0.940, 0.650≤R2≤0.922, and 0.852≤R2≤0.981, respectively. The infinitesimal shear modulus of the strain energy functions showed a significant association with the strain rate (p<0.01). Conclusions The immature brainstem is a rate-dependent material in dynamic tensile tests, and the tissue becomes stiffer with increased strain rate. The reported results may be useful in the study of brain injuries in children who sustain injuries in road traffic accidents. Further research in more detail should be performed in the

  19. A simulation analysis to characterize the dynamics of vaccinating behaviour on contact networks

    Directory of Open Access Journals (Sweden)

    Bauch Chris T

    2009-05-01

    Full Text Available Abstract Background Human behavior influences infectious disease transmission, and numerous "prevalence-behavior" models have analyzed this interplay. These previous analyses assumed homogeneously mixing populations without spatial or social structure. However, spatial and social heterogeneity are known to significantly impact transmission dynamics and are particularly relevant for certain diseases. Previous work has demonstrated that social contact structure can change the individual incentive to vaccinate, thus enabling eradication of a disease under a voluntary vaccination policy when the corresponding homogeneous mixing model predicts that eradication is impossible due to free rider effects. Here, we extend this work and characterize the range of possible behavior-prevalence dynamics on a network. Methods We simulate transmission of a vaccine-prevetable infection through a random, static contact network. Individuals choose whether or not to vaccinate on any given day according to perceived risks of vaccination and infection. Results We find three possible outcomes for behavior-prevalence dynamics on this type of network: small final number vaccinated and final epidemic size (due to rapid control through voluntary ring vaccination; large final number vaccinated and significant final epidemic size (due to imperfect voluntary ring vaccination, and little or no vaccination and large final epidemic size (corresponding to little or no voluntary ring vaccination. We also show that the social contact structure enables eradication under a broad range of assumptions, except when vaccine risk is sufficiently high, the disease risk is sufficiently low, or individuals vaccinate too late for the vaccine to be effective. Conclusion For populations where infection can spread only through social contact network, relatively small differences in parameter values relating to perceived risk or vaccination behavior at the individual level can translate into large

  20. Decoherence of many-spin systems in NMR: From molecular characterization to an environmentally induced quantum dynamical phase transition

    Science.gov (United States)

    Alvarez, Gonzalo A.

    2007-05-01

    The control of open quantum systems has a fundamental relevance for fields ranging from quantum information processing to nanotechnology. Typically, the system whose coherent dynamics one wants to manipulate, interacts with an environment that smoothly degrades its quantum dynamics. Thus, a precise understanding of the inner mechanisms of this process, called "decoherence", is critical to develop strategies to control the quantum dynamics. In this thesis we solved the generalized Liouville-von Neumann quantum master equation to obtain the dynamics of many-spin systems interacting with a spin bath. We also solve the spin dynamics within the Keldysh formalism. Both methods lead to identical solutions and together gave us the possibility to obtain numerous physical predictions that contrast well with Nuclear Magnetic Resonance experiments. We applied these tools for molecular characterizations, development of new numerical methodologies and the control of quantum dynamics in experimental implementations. But, more important, these results contributed to fundamental physical interpretations of how quantum dynamics behaves in open systems. In particular, we found a manifestation of an environmentally induced quantum dynamical phase transition.

  1. Structure/property (constitutive and dynamic strength/damage) characterization of additively manufactured 316L SS

    Science.gov (United States)

    Gray, G. T., III; Livescu, V.; Rigg, P. A.; Trujillo, C. P.; Cady, C. M.; Chen, S. R.; Carpenter, J. S.; Lienert, T. J.; Fensin, S.

    2015-09-01

    For additive manufacturing (AM), the certification and qualification paradigm needs to evolve as there exists no "ASTM-type" additive manufacturing certified process or AM-material produced specifications. Accordingly, utilization of AM materials to meet engineering applications requires quantification of the constitutive properties of these evolving materials in comparison to conventionally-manufactured metals and alloys. Cylinders of 316L SS were produced using a LENS MR-7 laser additive manufacturing system from Optomec (Albuquerque, NM) equipped with a 1kW Yb-fiber laser. The microstructure of the AM-316L SS is detailed in both the as-built condition and following heat-treatments designed to obtain full recrystallization. The constitutive behavior as a function of strain rate and temperature is presented and compared to that of nominal annealed wrought 316L SS plate. The dynamic damage evolution and failure response of all three materials was probed using flyer-plate impact driven spallation experiments at a peak stress of 4.5 GPa to examine incipient spallation response. The spall strength of AM-produced 316L SS was found to be very similar for the peak shock stress studied to that of annealed wrought or AM-316L SS following recrystallization. The damage evolution as a function of microstructure was characterized using optical metallography.

  2. Methods for dynamic characterization of the major muscles activating the lower limb joints in cycling motion

    Directory of Open Access Journals (Sweden)

    Navit Roth

    2014-04-01

    Full Text Available The functional activation, through electrical stimulation, of the lower limb consisting of several deficient muscles requires well-patterned and coordinated activation of these muscles. This study presents a method for characterizing the parameters of the major muscle groups controlling the ankle and knee joints in cycling motion, the latter having particular significance in the rehabilitation of locomotion. To lower mechanical indeterminacy in the joints the system is reduced by grouping the muscles acting in synergism. The joint torques were calculated by inverse dynamics methods from cycling motion data, including kinematics and foot/pedal reaction loads (forces, moments. The mechanical indeterminacy was resolved by applying optimization criteria and the individual muscle torques were parceled-out from the joint torques. System identification of the individual muscles, part of which being bi-articular, in this non-isometric condition was performed from the relationship between the evaluated force and the measured EMG of each the muscles, using both first and second order linear transfer functions. Feasibility of the presented method was demonstrated through the computation of the coefficients of the muscles involved and validating the results on the experimental data obtained from one subject.

  3. Methods for dynamic characterization of the major muscles activating the lower limb joints in cycling motion

    Directory of Open Access Journals (Sweden)

    Navit Roth

    2014-09-01

    Full Text Available The functional activation, through electrical stimulation, of the lower limb consisting of several deficient muscles requires well-patterned and coordinated activation of these muscles. This study presents a method for characterizing the parameters of the major muscle groups controlling the ankle and knee joints in cycling motion, the latter having particular significance in the rehabilitation of locomotion. To lower mechanical indeterminacy in the joints the system is reduced by grouping the muscles acting in synergism. The joint torques were calculated by inverse dynamics methods from cycling motion data, including kinematics and foot/pedal reaction loads (forces, moments. The mechanical indeterminacy was resolved by applying optimization criteria and the individual muscle torques were parceled-out from the joint torques. System identification of the individual muscles, part of which being bi-articular, in this non-isometric condition was performed from the relationship between the evaluated force and the measured EMG of each the muscles, using both first and second order linear transfer functions. Feasibility of the presented method was demonstrated through the computation of the coefficients of the muscles involved and validating the results on the experimental data obtained from one subject.

  4. Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors.

    Science.gov (United States)

    Kougias, Panagiotis G; Treu, Laura; Campanaro, Stefano; Zhu, Xinyu; Angelidaki, Irini

    2016-01-01

    The process stability of biogas plants is often deteriorated by the accumulation of Long Chain Fatty Acids (LCFA). The microbial community shifts due to LCFA disturbances have been poorly understood as the molecular techniques used were not able to identify the genome characteristics of uncultured microorganisms, and additionally, the presence of limited number of reference genomes in public databases prevented the comprehension of specific functional roles characterizing these microorganisms. The present study is the first research which deciphers by means of high throughput shotgun sequencing the dynamics of the microbial community during an inhibitory shock load induced by single pulses of unsaturated LCFA at two different concentrations (i.e. 2 g/L-reactor and 3 g/L-reactor). The metagenomic analysis showed that only the microbes associated with LCFA degradation could encode proteins related to "chemotaxis" and "flagellar assembly", which promoted the ability to move towards the LCFA sources so as to degrade them. Moreover, the syntrophic interactions found between Syntrophomonas sp. together with Methanosarcina sp. were possibly assigned to the menaquinone-electron transfer. Finally, it was proven that a previously exposed to LCFA inoculum is more efficient in the degradation process of LCFA due to the specialization of the microbial consortium. PMID:27353502

  5. Structure/property (constitutive and dynamic strength/damage characterization of additively manufactured 316L SS

    Directory of Open Access Journals (Sweden)

    Gray III G.T.

    2015-01-01

    Full Text Available For additive manufacturing (AM, the certification and qualification paradigm needs to evolve as there exists no “ASTM-type” additive manufacturing certified process or AM-material produced specifications. Accordingly, utilization of AM materials to meet engineering applications requires quantification of the constitutive properties of these evolving materials in comparison to conventionally-manufactured metals and alloys. Cylinders of 316L SS were produced using a LENS MR-7 laser additive manufacturing system from Optomec (Albuquerque, NM equipped with a 1kW Yb-fiber laser. The microstructure of the AM-316L SS is detailed in both the as-built condition and following heat-treatments designed to obtain full recrystallization. The constitutive behavior as a function of strain rate and temperature is presented and compared to that of nominal annealed wrought 316L SS plate. The dynamic damage evolution and failure response of all three materials was probed using flyer-plate impact driven spallation experiments at a peak stress of 4.5 GPa to examine incipient spallation response. The spall strength of AM-produced 316L SS was found to be very similar for the peak shock stress studied to that of annealed wrought or AM-316L SS following recrystallization. The damage evolution as a function of microstructure was characterized using optical metallography.

  6. Characterizing the dynamic behavior of nano-TiO2 agglomerates in suspensions by photocorrelation spectroscopy

    International Nuclear Information System (INIS)

    Metal oxide nanoparticles are small but easily form agglomerates in suspension, depending on the strength of particle–particle and particle–media interactions. To understand the agglomeration behavior of nanoparticles in media and relate to it to product performance testing, measurement methods are desired to characterize highly scattering metal oxide nanoparticle suspensions without dilution. In this article, we describe the advantages of using photocorrelation spectroscopy (PCS) in a backscattering detection configuration to carry out a realistic agglomerate size measurement in multiple scattering media found in most metal oxide nanoparticle suspensions. The dynamic behavior of nano-titanium dioxide (TiO2) particles in buffer solutions of different chemical composition and pH values was investigated as a sample system using PCS. The resulting autocorrelation functions (AFs) at different time intervals, particle concentrations, and pH values were measured at several detection angles. The AF exhibits a multi-mode relaxation time feature and the calculated hydrodynamic diameters strongly depended on media composition and detection angle. This result indicates that the size and dispersion of nano-TiO2 agglomerates are significantly affected by solution media. A measurement protocol for determining size and dispersion of metal oxide particles in media is proposed and related to a performance test found in industry.

  7. Dynamic characterization of crystalline and glass phases of deuterated 1,1,2,2 Tetrachloroethane

    CERN Document Server

    Perez, Silvina; Serra, Pablo; Wolfenson, Alberto; Negrier, Philippe; Tamarit, Josep

    2015-01-01

    A thorough characterization of the {\\gamma}, {\\beta} and glass phases of deuterated 1,1,2,2 Tetrachloroethane (C2D2Cl4) via Nuclear Quadrupole Resonance and Molecular Dynamic Simulations (MDS) is reported. The presence of molecular reorientations was experimentally observed in the glass phase and in the {\\beta} phase. In the {\\beta} phase, and from MDS, these reorientations are attributed to two possible movements, i.e. a $180^o$ reorientation around the C2 molecular symmetry axis and a reorientation of the molecule between non-equivalent positions. In the glass phase, the spin-lattice relaxation time T1 is of the order of 16 times lower that T1 in the crystalline phase and varies as $T^{-1}$ below 100 K in good agreement with the strong quadrupolar relaxation observed in amorphous materials and in the glassy state of molecular organic systems. The activation energy of molecular reorientations in the glass phase (19 kJ/mol) is comparable to that observed in the glassy crystal of a "molecular cousin" compound,...

  8. The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres

    OpenAIRE

    Tao ZHANG; Talbert, Paul B; Zhang, Wenli; Wu, Yufeng; Yang, Zujun; Henikoff, Jorja G.; Henikoff, Steven; Jiang, Jiming

    2013-01-01

    Centromeres are sites on chromosomes that mediate attachment to microtubules for chromosome segregation and often comprise tandemly repeated “satellite” sequences. The function of these repeats is unclear because centromeres can be formed on single-copy DNA by the presence of nucleosomes containing a centromere-specific variant of histone H3 (cenH3). Rice has centromeres composed of both the 155-bp CentO satellite repeat and single-copy non-CentO sequences. This study shows that rice cenH3 nu...

  9. Ubiquitous human ‘master’ origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers

    Science.gov (United States)

    Drillon, Guénola; Audit, Benjamin; Argoul, Françoise; Arneodo, Alain

    2015-02-01

    As the elementary building block of eukaryotic chromatin, the nucleosome is at the heart of the compromise between the necessity of compacting DNA in the cell nucleus and the required accessibility to regulatory proteins. The recent availability of genome-wide experimental maps of nucleosome positions for many different organisms and cell types has provided an unprecedented opportunity to elucidate to what extent the DNA sequence conditions the primary structure of chromatin and in turn participates in the chromatin-mediated regulation of nuclear functions, such as gene expression and DNA replication. In this study, we use in vivo and in vitro genome-wide nucleosome occupancy data together with the set of nucleosome-free regions (NFRs) predicted by a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix, to investigate the role of intrinsic nucleosome occupancy in the regulation of the replication spatio-temporal programme in human. We focus our analysis on the so-called replication U/N-domains that were shown to cover about half of the human genome in the germline (skew-N domains) as well as in embryonic stem cells, somatic and HeLa cells (mean replication timing U-domains). The ‘master’ origins of replication (MaOris) that border these megabase-sized U/N-domains were found to be specified by a few hundred kb wide regions that are hyper-sensitive to DNase I cleavage, hypomethylated, and enriched in epigenetic marks involved in transcription regulation, the hallmarks of localized open chromatin structures. Here we show that replication U/N-domain borders that are conserved in all considered cell lines have an environment highly enriched in nucleosome-excluding-energy barriers, suggesting that these ubiquitous MaOris have been selected during evolution. In contrast, MaOris that are cell-type-specific are mainly regulated epigenetically and are no longer favoured by a local abundance of intrinsic NFRs

  10. Flow Characterization and Dynamic Analysis of a Radial Compressor with Passive Method of Surge Control

    Science.gov (United States)

    Guillou, Erwann

    Due to recent emission regulations, the use of turbochargers for force induction of internal combustion engines has increased. Actually, the trend in diesel engines is to downsize the engine by use of turbochargers that operate at higher pressure ratio. Unfortunately, increasing the rotational speed tends to reduce the turbocharger radial compressor range of operation which is limited at low mass flow rate by the occurrence of surge. In order to extent the operability of turbochargers, compressor housings can be equipped with a passive surge control device also known as ported shroud. This specific casing treatment has been demonstrated to enhance surge margin with minor negative impact on the compressor efficiency. However, the actual working mechanisms of the bypass system remain not well understood. In order to optimize the design of the ported shroud, it is then crucial to identify the dynamic flow changes induced by the implementation of the device to control instabilities. Experimental methods were used to assess the development of instabilities from stable, stall and eventually surge regimes of a ported shroud centrifugal compressor. Systematic comparison was conducted with the same compressor design without ported shroud. Hence, the full pressure dynamic survey of both compressors' performance characteristics converged toward two different and probably interrelated driving mechanisms to the development and/or propagation of unsteadiness within each compressor. One related the pressure disturbances at the compressor inlet, and notably the more apparent development of perturbations in the non-ported compressor impeller, whereas the other was attributed to the pressure distortions induced by the presence of the tongue in the asymmetric design of the compressor volute. Specific points of operation were selected to carry out planar flow measurements. At normal working, both standard and stereoscopic particle imaging velocimetry (PIV) measurements were performed

  11. Dynamic characterization of hydrophobic and hydrophilic solutes in oleic-acid enhanced transdermal delivery using two-photon fluorescence microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, Te-Yu; Yang, Chiu-Sheng; Chen, Yang-Fang [Department of Physics, National Taiwan University, Taipei, Taiwan (China); Tsai, Tsung-Hua [Department of Dermatology, Far Eastern Memorial Hospital, New Taipei City, Taiwan (China); Dong, Chen-Yuan, E-mail: cydong@phys.ntu.edu.tw [Department of Physics, National Taiwan University, Taipei, Taiwan (China); Center for Quantum Science and Engineering, National Taiwan University, Taipei, Taiwan (China); Center for Optoelectronic Biomedicine, National Taiwan University, Taipei, Taiwan (China)

    2014-10-20

    In this letter, we propose an efficient methodology of investigating dynamic properties of sulforhodamine B and rhodamine B hexyl ester molecules transporting across ex-vivo human stratum corneum with and without oleic acid enhancement. Three-dimensional, time-lapse fluorescence images of the stratum corneum can be obtained using two-photon fluorescence microscopy. Furthermore, temporal quantifications of transport enhancements in diffusion parameters can be achieved with the use of Fick's second law. Dynamic characterization of solutes transporting across the stratum corneum is an effective method for understanding transient phenomena in transdermal delivery of probe molecules, leading to improved delivery strategies of molecular species for therapeutic purposes.

  12. Dynamic characterization of hydrophobic and hydrophilic solutes in oleic-acid enhanced transdermal delivery using two-photon fluorescence microscopy

    Science.gov (United States)

    Tseng, Te-Yu; Yang, Chiu-Sheng; Tsai, Tsung-Hua; Chen, Yang-Fang; Dong, Chen-Yuan

    2014-10-01

    In this letter, we propose an efficient methodology of investigating dynamic properties of sulforhodamine B and rhodamine B hexyl ester molecules transporting across ex-vivo human stratum corneum with and without oleic acid enhancement. Three-dimensional, time-lapse fluorescence images of the stratum corneum can be obtained using two-photon fluorescence microscopy. Furthermore, temporal quantifications of transport enhancements in diffusion parameters can be achieved with the use of Fick's second law. Dynamic characterization of solutes transporting across the stratum corneum is an effective method for understanding transient phenomena in transdermal delivery of probe molecules, leading to improved delivery strategies of molecular species for therapeutic purposes.

  13. Rheological and dynamical characterization of blood analogue flows in a slit

    International Nuclear Information System (INIS)

    Highlights: • We study blood analogue potential of H2O/glycerine/xanthan mixtures through viscosity. • Water/glycerine (35% w/w)/xanthan (0.02% w/w) solution mimics well blood viscosity. • We characterize dynamics of blood analogue flows in open slits with μPIV and CFD. • Results refer to flow rates 4.3 ⩽ Q ⩽ 25.3 L/h. • Wall shear stresses are bellow haemolysis threshold but may trigger thrombus formation. - Abstract: Thrombus formation and haemolysis are blood destructive phenomena depending on the flow hydrodynamics, particularly the shear stresses. This work addresses this issue by characterizing experimentally (using the micro-PIV technique) and numerically (using CFD) steady-state Newtonian (water and water/glycerine solutions) fluid flows and non-Newtonian (water/glycerine/xanthan) blood analogue flows, in a slit with a height of 1.3 mm and a width of 30 mm. The results obtained may provide useful information in the design of extracorporeal devices manipulating blood for diagnosis and therapeutics. Results from CFD showed that the Herschel–Bulkley viscosity model yields velocity predictions in excellent agreement with the experimental data obtained with the micro-PIV. Viscosity measurements evidenced that the water/glycerine (35% w/w)/xanthan (0.02% w/w) solution mimics well the blood global viscosity, exhibiting velocity profile shapes in fully developed flows flattened at the centre, typical of shear-thinning fluids. The maximum shear stresses obtained experimentally (1.39–3.11 Pa) for the blood analogue flows at the studied rates (6.7–25.3 L/h) evidence that haemolysis is unlikely to occur since lysis threshold values are 150 Pa for erythrocytes, 10 Pa for leucocytes and 7.5 Pa for platelets. However, the smallest flow rate cases may be of concern in blood circulation by yielding clot formation near the walls since the shear stresses there are bellow the thrombus/coagulation threshold (1.0–1.8 Pa)

  14. Real-time measurements to characterize dynamics of emulsion interface during simulated intestinal digestion.

    Science.gov (United States)

    Pan, Yuanjie; Nitin, N

    2016-05-01

    Efficient delivery of bioactives remains a critical challenge due to their limited bioavailability and solubility. While many encapsulation systems are designed to modulate the digestion and release of bioactives within the human gastrointestinal tract, there is limited understanding of how engineered structures influence the delivery of bioactives. The objective of this study was to develop a real-time quantitative method to measure structural changes in emulsion interface during simulated intestinal digestion and to correlate these changes with the release of free fatty acids (FFAs). Fluorescence resonant energy transfer (FRET) was used for rapid in-situ measurement of the structural changes in emulsion interface during simulated intestinal digestion. By using FRET, changes in the intermolecular spacing between the two different fluorescent probes labeled emulsifier were characterized. Changes in FRET measurements were compared with the release of FFAs. The results showed that bile salts and pancreatic lipase interacted immediately with the emulsion droplets and disrupted the emulsion interface as evidenced by reduction in FRET efficacy compared to the control. Similarly, a significant amount of FFAs was released during digestion. Moreover, addition of a second layer of polymers at emulsion interface decreased the extent of interface disruption by bile salts and pancreatic lipase and impacted the amount or rate of FFA release during digestion. These results were consistent with the lower donor/acceptor ratio of the labeled probes from the FRET result. Overall, this study provides a novel approach to analyze the dynamics of emulsion interface during digestion and their relationship with the release of FFAs. PMID:26854582

  15. Characterization of flow conditions in 2 L and 20 L wave bioreactors using computational fluid dynamics.

    Science.gov (United States)

    Oncül, Alper A; Kalmbach, Andreas; Genzel, Yvonne; Reichl, Udo; Thévenin, Dominique

    2010-01-01

    Characterization of flow conditions is of great importance to control cell growth and cell damage in animal cell culture because cell viability is influenced by the flow properties in bioreactors. Alternative reactor types like Wave Bioreactors have been proposed in recent years, leading to markedly different results in cell growth and product formation. An advantage of Wave Bioreactors is the disposability of the Polyethylenterephthalet-bags after one single use (fast setup of new production facilities). Another expected advantage is a lower shear stress compared to classical stirred-tank reactors, due to the gentle liquid motion in the rocking cellbag. This property would considerably reduce possible cell damage. The purpose of the present study is to investigate in a quantitative manner the key flow properties in Wave Bioreactors, both numerically and experimentally. To describe accurately flow conditions and shear stress in Wave Bioreactors using numerical simulations, it is necessary to compute the unsteady flow applying Computational Fluid Dynamics (CFD). Corresponding computations for two reactor scales (2 L and 20 L cellbags) are presented using the CFD code ANSYS-FLUENT. To describe correctly the free liquid surface, the present simulations employ the Volume of Fluid (VOF) method. Additionally, experimental measurements have been carried out to determine liquid level, flow velocity and liquid shear stress, which are used as a validation of the present CFD simulations. It is shown that the obtained flows stay in the laminar regime. Furthermore, the obtained shear stress levels are well below known threshold values leading to damage of animal cells. PMID:19918766

  16. Detection and Characterization of Package Defects and Integrity Failure using Dynamic Scanning Infrared Thermography (DSIRT).

    Science.gov (United States)

    Morris, Scott A

    2016-02-01

    A dynamic scanning infrared thermography (DSIRT) system developed at the Univ. of Illinois Urbana-Champaign (UIUC) Packaging Lab relies on variation in transient thermal artifacts to indicate defects, and offers the possibility of characterization of many types of materials and structures. These include newer polymer and laminate-based structures for shelf-stable foods that lack a reliable, nondestructive method for inspection, which is a continuing safety issue. Preliminary trials were conducted on a polyester/aluminum foil/polypropylene retort pouch laminate containing artificially-induced failed seal and insulating inclusion defects ranging from 1 to 10 mm wide in the plane of the seal. The samples were placed in relative motion to a laterally positioned infrared laser, inducing heating through the plane of the seal. The emergent thermal artifact on the obverse side was sensed using either a bolometer camera or a thermopile sensor, with thermal anomalies indicating potential defects and the results of each sensors were compared. The bolometer camera detected defects to the limit of its measured optical resolution-approximately 1 mm at 20 cm-although the lower-resolution thermopile sensors were only capable of detecting 5 mm defects even at closer distances of approximately 5 mm. In addition, a supplementary magnification system was fitted to the bolometer camera which increased resolution but reduced field of view and would require a much higher frame rate to be useful. Automatic processing of the image data rapidly detected the model defects and can lead to development of an automated inspection system.  Much higher material throughput speeds are feasible using faster instruments, and the system is scalable. PMID:26720916

  17. Closed-loop digital control of nuclear reactors characterized by spatial dynamics

    International Nuclear Information System (INIS)

    This report describes the theoretical development and the evaluation via both simulation and, to a lesser degree, experiment of a digital method for the closed-loop control of power and temperature in reactors characterized by spatial dynamics. The major conclusions of the research are that (1) the sophistication of advanced reactor physics and thermal-hydraulic nodal methods is now such that accurate, real-time models of spatially-dependent, heterogeneous reactor cores can be run on present-generation minicomputers; (2) operation of both present-day commercial reactors as well as the multi-modular reactors now being considered for construction in the United States could be significantly improved by incorporating model-generated information on in-core conditions in a digital controller; and (3) digital controllers for spatially-dependent reactors should have a hierarchical or multi-tiered structure consisting of supervisory algorithms that preclude challenges to the safety system, global control laws designed to provide an optimal response to temperature and power perturbations, and local control laws that maintain parameters such as the margin to departure from nucleate boiling within specification. The technology described is appropriate to present-day pressurized water reactors and to the proposed multi-modular designs. The end-product of this research was a (near) real-time analytic plant-estimation code that was given the acronym POPSICLE for POwer Plant SImulator and ControlLEr. POPSICLE's core neutronics model is based on a quasi-static transient solution of the analytic nodal diffusion equations. 126 refs., 159 figs., 17 tabs

  18. Characterization of a linear device developed for research on advanced plasma imaging and dynamics

    International Nuclear Information System (INIS)

    Within the scope of long term research on imaging diagnostics for steady-state plasmas and understanding of edge plasma physics through diagnostics with conventional spectroscopic methods, we have constructed a linear electron cyclotron resonance (ECR) plasma device named Research on Advanced Plasma Imaging and Dynamics (RAPID). It has a variety of axial magnetic field profiles provided by eight water-cooled magnetic coils and two dc power supplies. The positions of the magnetic coils are freely adjustable along the axial direction and the power supplies can be operated with many combinations of electrical wiring to the coils. Here, a 6 kW 2.45 GHz magnetron is used to produce steady-state hydrogen, helium, and argon plasmas with central magnetic fields of 875 and/or 437.5 G (second harmonic). In order to achieve the highest possible plasma performance within the limited input parameters, wall conditioning experiments were carried out. Chamber bake-out was achieved with heating coils that were wound covering the vessel, and long-pulse electron cyclotron heating discharge cleaning was also followed after 4 days of bake-out. A uniform bake-out temperature (150 deg. C) was achieved by wrapping the vessel in high temperature thermal insulation textile and by controlling the heating coil current using a digital control system. The partial pressure changes were observed using a residual gas analyzer, and a total system pressure of 5x10-8 Torr was finally reached. Diagnostic systems including a millimeter-wave interferometer, a high resolution survey spectrometer, a Langmuir probe, and an ultrasoft x-ray detector were used to provide the evidence that the plasma performance was improved as we desired. In this work, we present characterization of the RAPID device for various system conditions and configurations.

  19. Characterization and Dynamics of Aggresome Formation by a Cytosolic Gfp-Chimera✪

    Science.gov (United States)

    García-Mata, Rafael; Bebök, Zsuzsa; Sorscher, Eric J.; Sztul, Elizabeth S.

    1999-01-01

    Formation of a novel structure, the aggresome, has been proposed to represent a general cellular response to the presence of misfolded proteins (Johnston, J.A., C.L. Ward, and R.R. Kopito. 1998. J. Cell Biol. 143:1883–1898; Wigley, W.C., R.P. Fabunmi, M.G. Lee, C.R. Marino, S. Muallem, G.N. DeMartino, and P.J. Thomas. 1999. J. Cell Biol. 145:481–490). To test the generality of this finding and characterize aspects of aggresome composition and its formation, we investigated the effects of overexpressing a cytosolic protein chimera (GFP-250) in cells. Overexpression of GFP-250 caused formation of aggresomes and was paralleled by the redistribution of the intermediate filament protein vimentin as well as by the recruitment of the proteasome, and the Hsp70 and the chaperonin systems of chaperones. Interestingly, GFP-250 within the aggresome appeared not to be ubiquitinated. In vivo time-lapse analysis of aggresome dynamics showed that small aggregates form within the periphery of the cell and travel on microtubules to the MTOC region where they remain as distinct but closely apposed particulate structures. Overexpression of p50/dynamitin, which causes the dissociation of the dynactin complex, significantly inhibited the formation of aggresomes, suggesting that the minus-end–directed motor activities of cytoplasmic dynein are required for aggresome formation. Perinuclear aggresomes interfered with correct Golgi localization and disrupted the normal astral distribution of microtubules. However, ER-to-Golgi protein transport occurred normally in aggresome containing cells. Our results suggest that aggresomes can be formed by soluble, nonubiquitinated proteins as well as by integral transmembrane ubiquitinated ones, supporting the hypothesis that aggresome formation might be a general cellular response to the presence of misfolded proteins. PMID:10491388

  20. Characterization and dynamics of aggresome formation by a cytosolic GFP-chimera.

    Science.gov (United States)

    García-Mata, R; Bebök, Z; Sorscher, E J; Sztul, E S

    1999-09-20

    Formation of a novel structure, the aggresome, has been proposed to represent a general cellular response to the presence of misfolded proteins (Johnston, J.A., C.L. Ward, and R.R. Kopito. 1998. J. Cell Biol. 143:1883-1898; Wigley, W.C., R.P. Fabunmi, M.G. Lee, C.R. Marino, S. Muallem, G.N. DeMartino, and P.J. Thomas. 1999. J. Cell Biol. 145:481-490). To test the generality of this finding and characterize aspects of aggresome composition and its formation, we investigated the effects of overexpressing a cytosolic protein chimera (GFP-250) in cells. Overexpression of GFP-250 caused formation of aggresomes and was paralleled by the redistribution of the intermediate filament protein vimentin as well as by the recruitment of the proteasome, and the Hsp70 and the chaperonin systems of chaperones. Interestingly, GFP-250 within the aggresome appeared not to be ubiquitinated. In vivo time-lapse analysis of aggresome dynamics showed that small aggregates form within the periphery of the cell and travel on microtubules to the MTOC region where they remain as distinct but closely apposed particulate structures. Overexpression of p50/dynamitin, which causes the dissociation of the dynactin complex, significantly inhibited the formation of aggresomes, suggesting that the minus-end-directed motor activities of cytoplasmic dynein are required for aggresome formation. Perinuclear aggresomes interfered with correct Golgi localization and disrupted the normal astral distribution of microtubules. However, ER-to-Golgi protein transport occurred normally in aggresome containing cells. Our results suggest that aggresomes can be formed by soluble, nonubiquitinated proteins as well as by integral transmembrane ubiquitinated ones, supporting the hypothesis that aggresome formation might be a general cellular response to the presence of misfolded proteins. PMID:10491388

  1. Coastal and mesoscale dynamics characterization combining glider and altimetry: case study over the Western Mediterranean Sea

    Science.gov (United States)

    Jerome, Bouffard; Pascual, Ananda; Ruiz, Simon; Isabelle Pujol, Marie; Faugere, Yannice; Larnicol, Gilles; Tintore, Joaquin

    the oceanic circulation characteristics at the regional scales. In summary, these studies highlight the relevance of multi-sensor approaches and the need of oceanic topography measurements at several spatial/temporal sampling requirements in view of the coastal and mesoscale dynamics characterizations.

  2. A dynamical systems approach to characterizing the contribution of neurogenesis to neural coding

    Directory of Open Access Journals (Sweden)

    Merav Stern

    2014-03-01

    that agreed with experimental measurements (Cameron and McKay, 2001; Deng et al., 2010; Tashiro et al., 2007, with no adjustable parameters. It is also important to note that the optimal regime for encoding input signals is often poised near an instability associated with chaotic dynamics (Aljadeff et al., 2013; Sompolinsky et al., 1988. This observation could explain the frequent occurrence of seizures at the early stages of Alzheimer’s disease (Palop and Mucke, 2010a; Palop and Mucke, 2010b. To that extent, we analytically derive conditions for observing chaotic dynamics in networks with of an arbitrary number of neuron types. The analytical results accurately mirrored simulation in predicting the composition of the network (fraction of young neurons and the difference in their excitability and number of synapses when the networks undergoes transformation from stable to chaotic dynamics (Figure 2. Overall, these results demonstrate how a small fraction of neurons can increase the representational capacity of the neural circuit as a whole in a distributed way and provide a quantitative framework for characterizing more heterogeneous networks composed of multiple types of neurons. Figure 1. The representational capacity of a heterogeneous network. Results are shown as a function of the fraction of young neurons (y-axis and the ratio of their hyper-excitability relatively to mature neurons (x-axis. The synaptic weights between neurons are initially set to random values drawn from a Gaussian distribution. In the case of young neurons we used a distribution with larger variance compared to the value used for mature neurons. The networks were tasked with encoding a desired input pattern; the connection weights were adjusted using the algorithm from (Sussillo and Abbott, 2009. The average representation error divided by the average activity of the network is the “learning capacity index” (color. Black lines are contour plots of equal magnitude. The learning capacity

  3. Nucleosome disassembly during human non-homologous end joining followed by concerted HIRA- and CAF-1-dependent reassembly

    Science.gov (United States)

    Li, Xuan; Tyler, Jessica K

    2016-01-01

    The cell achieves DNA double-strand break (DSB) repair in the context of chromatin structure. However, the mechanisms used to expose DSBs to the repair machinery and to restore the chromatin organization after repair remain elusive. Here we show that induction of a DSB in human cells causes local nucleosome disassembly, apparently independently from DNA end resection. This efficient removal of histone H3 from the genome during non-homologous end joining was promoted by both ATM and the ATP-dependent nucleosome remodeler INO80. Chromatin reassembly during DSB repair was dependent on the HIRA histone chaperone that is specific to the replication-independent histone variant H3.3 and on CAF-1 that is specific to the replication-dependent canonical histones H3.1/H3.2. Our data suggest that the epigenetic information is re-established after DSB repair by the concerted and interdependent action of replication-independent and replication-dependent chromatin assembly pathways. DOI: http://dx.doi.org/10.7554/eLife.15129.001 PMID:27269284

  4. lncRNA-Induced Nucleosome Repositioning Reinforces Transcriptional Repression of rRNA Genes upon Hypotonic Stress

    Directory of Open Access Journals (Sweden)

    Zhongliang Zhao

    2016-03-01

    Full Text Available The activity of rRNA genes (rDNA is regulated by pathways that target the transcription machinery or alter the epigenetic state of rDNA. Previous work has established that downregulation of rRNA synthesis in quiescent cells is accompanied by upregulation of PAPAS, a long noncoding RNA (lncRNA that recruits the histone methyltransferase Suv4-20h2 to rDNA, thus triggering trimethylation of H4K20 (H4K20me3 and chromatin compaction. Here, we show that upregulation of PAPAS in response to hypoosmotic stress does not increase H4K20me3 because of Nedd4-dependent ubiquitinylation and proteasomal degradation of Suv4-20h2. Loss of Suv4-20h2 enables PAPAS to interact with CHD4, a subunit of the chromatin remodeling complex NuRD, which shifts the promoter-bound nucleosome into the transcriptional “off” position. Thus, PAPAS exerts a “stress-tailored” dual function in rDNA silencing, facilitating either Suv4-20h2-dependent chromatin compaction or NuRD-dependent changes in nucleosome positioning.

  5. Characterization of the JWST Pathfinder Mirror Dynamics Using the Center of Curvature Optical Assembly (CoCOA)

    Science.gov (United States)

    Wells, Conrad; Hadaway, James B.; Olczak, Gene; Cosentino, Joseph; Johnston, John D.; Whitman, Tony; Connolly, Mark; Chaney, David; Knight, J. Scott; Telfer, Randal

    2016-01-01

    The JWST (James Webb Space Telescope) Optical Telescope Element (OTE) consists of a 6.6 meter clear aperture, 18-segment primary mirror, all-reflective, three-mirror anastigmat operating at cryogenic temperatures. To verify performance of the primary mirror, a full aperture center of curvature optical null test is performed under cryogenic conditions in Chamber A at NASA Johnson Space Center using an instantaneous phase measuring interferometer. After phasing the mirrors during the JWST Pathfinder testing, the interferometer is utilized to characterize the mirror relative piston and tilt dynamics under different facility configurations. The correlation between the motions seen on detectors at the focal plane and the interferometer validates the use of the interferometer for dynamic investigations. The success of planned test hardware improvements will be characterized by the multi-wavelength interferometer (MWIF) at the Center of Curvature Optical Assembly (CoCOA).

  6. Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements

    International Nuclear Information System (INIS)

    The dynamics of three synthetic oligonucleotides d(CG)4, d(CG)6, and d(CGCGTTGTTCGCG) of different length and shape were studied in solution by depolarized dynamic light scattering (DDLS) and time-resolved nuclear Overhauser effect cross-relaxation measurements. For cylindrically symmetric molecules the DDLS spectrum is dominated by the rotation of the main symmetry axis of the cylinder. The experimental correlation times describe the rotation of the oligonucleotides under hydrodynamic stick boundary conditions. It is shown that the hydrodynamic theory of Tirado and Garcia de la Torre gives good predictions of the rotational diffusion coefficients of cylindrically symmetric molecules of the small axial ratios studied here. These relations are used to calculate the solution dimensions of the DNA fragments from measured correlation times. The DDLS relaxations measurements provide a power method for distinguishing between different conformations of the oligonucleotides. Furthermore, the rotational correlation times are a very sensitive probe of the length of different fragments. The NMR results reflect the anisotropic motion of the molecules as well as the amount of local internal motion present. The experimental correlation time from NMR is determined by the rotation of both the short and long axes of the oligonucleotide. The authors results are compared with those from NMR relaxation measurements on other short oligonucleotides with lengths of up to 20 base pairs. Various dynamic models for the reorientation of the internuclear vector are applied to their interpretation

  7. Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries

    OpenAIRE

    Lauren A Rogers; Daniel E Schindler; Lisi, Peter J.; Gordon W Holtgrieve; Leavitt, Peter R.; Bunting, Lynda; Finney, Bruce P.; Selbie, Daniel T.; Chen, Guangjie; Gregory-Eaves, Irene; Lisac, Mark J.; Walsh, Patrick B.

    2013-01-01

    Observational data from the past century have highlighted the importance of interdecadal modes of variability in fish population dynamics, but how these patterns of variation fit into a broader temporal and spatial context remains largely unknown. We analyzed time series of stable nitrogen isotopes from the sediments of 20 sockeye salmon nursery lakes across western Alaska to characterize temporal and spatial patterns in salmon abundance over the past ∼500 y. Although some stocks varied on in...

  8. Thermo-fluid dynamic characterization and technical optimization of structured open-cell metal foams by means of numerical simulation

    OpenAIRE

    Horneber, Tobias

    2015-01-01

    The present contribution provides a fluid dynamic and thermal characterization of structured representatives of open-cell foams. Geometric and analytic methods as well as numeric simulations serve as tools for technical optimization. Three different types of structures are analyzed: a simple cubic structure, a Kelvin cell structure, and a diamond structure. These structures are used as carrier structures in catalysis and make up the inner part of a reactor which is built in its entirety u...

  9. PlanetPack: a radial-velocity time-series analysis tool facilitating exoplanets detection, characterization, and dynamical simulations

    OpenAIRE

    Baluev, Roman V.

    2013-01-01

    We present PlanetPack, a new software tool that we developed to facilitate and standardize the advanced analysis of radial velocity (RV) data for the goal of exoplanets detection, characterization, and basic dynamical $N$-body simulations. PlanetPack is a command-line interpreter, that can run either in an interactive mode or in a batch mode of automatic script interpretation. Its major abilities include: (i) Advanced RV curve fitting with the proper maximum-likelihood treatment of unknown RV...

  10. Dynamics and Characterization of Soil Organic Matter on Mine Soils 16 Years after Amendment with Topsoil, Sawdust, and Sewage Sludge.

    OpenAIRE

    Bendfeldt, Eric S.

    1999-01-01

    DYNAMICS AND CHARACTERIZATION OF SOIL ORGANIC MATTER IN MINE SOILS 16 YEARS AFTER AMENDMENT WITH TOPSOIL, SAWDUST, AND SEWAGE SLUDGE. by Eric S. Bendfeldt Committee Chairman: Dr. James A. Burger Department of Forestry (ABSTRACT) The present state and future prospect of the world's soil resources has prompted scientists and researchers to address the issue of soil quality and sustainable land management. Soil quality research has focused on intensively-managed agricultural a...

  11. Multidimensional characterization of stochastic dynamical systems based on multiple perturbations and measurements

    Energy Technology Data Exchange (ETDEWEB)

    Kryvohuz, Maksym, E-mail: mkryvohu@uci.edu; Mukamel, Shaul [Chemistry Department, University of California, Irvine, California 92697-2025 (United States)

    2015-06-07

    Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequency domains. Closed expressions for GRFs in stochastic dynamical systems are derived and compared with numerical non-equilibrium simulations. Several types of perturbations are considered: impulsive and periodic perturbations of temperature and impulsive perturbations of coordinates. The present approach can be used to study various types of stochastic processes ranging from single-molecule conformational dynamics to chemical kinetics of finite-size reactors such as biocells.

  12. Multidimensional characterization of stochastic dynamical systems based on multiple perturbations and measurements.

    Science.gov (United States)

    Kryvohuz, Maksym; Mukamel, Shaul

    2015-06-01

    Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequency domains. Closed expressions for GRFs in stochastic dynamical systems are derived and compared with numerical non-equilibrium simulations. Several types of perturbations are considered: impulsive and periodic perturbations of temperature and impulsive perturbations of coordinates. The present approach can be used to study various types of stochastic processes ranging from single-molecule conformational dynamics to chemical kinetics of finite-size reactors such as biocells. PMID:26049450

  13. Multidimensional characterization of stochastic dynamical systems based on multiple perturbations and measurements

    International Nuclear Information System (INIS)

    Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequency domains. Closed expressions for GRFs in stochastic dynamical systems are derived and compared with numerical non-equilibrium simulations. Several types of perturbations are considered: impulsive and periodic perturbations of temperature and impulsive perturbations of coordinates. The present approach can be used to study various types of stochastic processes ranging from single-molecule conformational dynamics to chemical kinetics of finite-size reactors such as biocells

  14. Analytic Characterization of the Dynamic Regimes of Quantum-Dot Lasers

    Directory of Open Access Journals (Sweden)

    Benjamin Lingnau

    2015-04-01

    Full Text Available We present analytic treatment of the three different dynamic regimes found in quantum-dot laser turn-on and modulation dynamics. A dynamic coupling, and thus density-dependent scattering lifetimes between dots and reservoir, are identified to be crucial for a realistic modeling. We derive a minimal model for the quantum-dot laser dynamics that can be seeded with experimentally accessible parameters, and give explicit analytic equations that are able to predict relaxation-oscillation frequency and damping rate.

  15. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available H2A.Z is an evolutionary conserved histone variant involved in transcriptional regulation, antisilencing, silencing, and genome stability. The mechanism(s by which H2A.Z regulates these various biological functions remains poorly defined, in part due to the lack of knowledge regarding its physical location along chromosomes and the bearing it has in regulating chromatin structure. Here we mapped H2A.Z across the yeast genome at an approximately 300-bp resolution, using chromatin immunoprecipitation combined with tiling microarrays. We have identified 4,862 small regions--typically one or two nucleosomes wide--decorated with H2A.Z. Those "Z loci" are predominantly found within specific nucleosomes in the promoter of inactive genes all across the genome. Furthermore, we have shown that H2A.Z can regulate nucleosome positioning at the GAL1 promoter. Within HZAD domains, the regions where H2A.Z shows an antisilencing function, H2A.Z is localized in a wider pattern, suggesting that the variant histone regulates a silencing and transcriptional activation via different mechanisms. Our data suggest that the incorporation of H2A.Z into specific promoter-bound nucleosomes configures chromatin structure to poise genes for transcriptional activation. The relevance of these findings to higher eukaryotes is discussed.

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

    Science.gov (United States)

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

    2013-06-28

    Nucleosomes containing the specific histone H3 variant CENP-A mark the centromere locus on each chromatin and initiate kinetochore assembly. For the common type of regional centromeres, little is known in molecular detail of centromeric chromatin organization, its propagation through cell division, and how distinct organization patterns may facilitate kinetochore assembly. Here, we show that in the fission yeast S. pombe, a relatively small number of CENP-A/Cnp1 nucleosomes are found within the centromeric core and that their positioning relative to underlying DNA varies among genetically homogenous cells. Consistent with the flexible positioning of Cnp1 nucleosomes, a large portion of the endogenous centromere is dispensable for its essential activity in mediating chromosome segregation. We present biochemical evidence that Cnp1 occupancy directly correlates with silencing of the underlying reporter genes. Furthermore, using a newly developed pedigree analysis assay, we demonstrated the epigenetic inheritance of Cnp1 positioning and quantified the rate of occasional repositioning of Cnp1 nucleosomes throughout cell generations. Together, our results reveal the plasticity and the epigenetically inheritable nature of centromeric chromatin organization. PMID:23661703

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

    DEFF Research Database (Denmark)

    Rasmussen, Louise; Herzog, Marielle; Aastrup rømer, Eva Christine;

    2016-01-01

    AIM: To evaluate pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA (5mC) or histone modification H3K9Me3 (H3K9Me3). MATERIALS AND METHODS: Six studies were designed to assess the possible influence of pre-analytical variables. Study 1: influence of stasis...

  18. Dynamic quantification of canopy structure to characterize early plant vigour in wheat genotypes.

    Science.gov (United States)

    Duan, T; Chapman, S C; Holland, E; Rebetzke, G J; Guo, Y; Zheng, B

    2016-08-01

    Early vigour is an important physiological trait to improve establishment, water-use efficiency, and grain yield for wheat. Phenotyping large numbers of lines is challenging due to the fast growth and development of wheat seedlings. Here we developed a new photo-based workflow to monitor dynamically the growth and development of the wheat canopy of two wheat lines with a contrasting early vigour trait. Multiview images were taken using a 'vegetation stress' camera at 2 d intervals from emergence to the sixth leaf stage. Point clouds were extracted using the Multi-View Stereo and Structure From Motion (MVS-SFM) algorithm, and segmented into individual organs using the Octree method, with leaf midribs fitted using local polynomial function. Finally, phenotypic parameters were calculated from the reconstructed point cloud including: tiller and leaf number, plant height, Haun index, phyllochron, leaf length, angle, and leaf elongation rate. There was good agreement between the observed and estimated leaf length (RMSE=8.6mm, R (2)=0.98, n=322) across both lines. Significant contrasts of phenotyping parameters were observed between the two lines and were consistent with manual observations. The early vigour line had fewer tillers (2.4±0.6) and larger leaves (308.0±38.4mm and 17.1±2.7mm for leaf length and width, respectively). While the phyllochron of both lines was quite similar, the non-vigorous line had a greater Haun index (more leaves on the main stem) on any date, as the vigorous line had slower development of its first two leaves. The workflow presented in this study provides an efficient method to phenotype individual plants using a low-cost camera (an RGB camera is also suitable) and could be applied in phenotyping for applications in both simulation modelling and breeding. The rapidity and accuracy of this novel method can characterize the results of specific selection criteria (e.g. width of leaf three, number of tillers, rate of leaf appearance) that have

  19. Dynamic quantification of canopy structure to characterize early plant vigour in wheat genotypes

    Science.gov (United States)

    Duan, T.; Chapman, S.C.; Holland, E.; Rebetzke, G.J.; Guo, Y.; Zheng, B.

    2016-01-01

    Early vigour is an important physiological trait to improve establishment, water-use efficiency, and grain yield for wheat. Phenotyping large numbers of lines is challenging due to the fast growth and development of wheat seedlings. Here we developed a new photo-based workflow to monitor dynamically the growth and development of the wheat canopy of two wheat lines with a contrasting early vigour trait. Multiview images were taken using a ‘vegetation stress’ camera at 2 d intervals from emergence to the sixth leaf stage. Point clouds were extracted using the Multi-View Stereo and Structure From Motion (MVS-SFM) algorithm, and segmented into individual organs using the Octree method, with leaf midribs fitted using local polynomial function. Finally, phenotypic parameters were calculated from the reconstructed point cloud including: tiller and leaf number, plant height, Haun index, phyllochron, leaf length, angle, and leaf elongation rate. There was good agreement between the observed and estimated leaf length (RMSE=8.6mm, R 2=0.98, n=322) across both lines. Significant contrasts of phenotyping parameters were observed between the two lines and were consistent with manual observations. The early vigour line had fewer tillers (2.4±0.6) and larger leaves (308.0±38.4mm and 17.1±2.7mm for leaf length and width, respectively). While the phyllochron of both lines was quite similar, the non-vigorous line had a greater Haun index (more leaves on the main stem) on any date, as the vigorous line had slower development of its first two leaves. The workflow presented in this study provides an efficient method to phenotype individual plants using a low-cost camera (an RGB camera is also suitable) and could be applied in phenotyping for applications in both simulation modelling and breeding. The rapidity and accuracy of this novel method can characterize the results of specific selection criteria (e.g. width of leaf three, number of tillers, rate of leaf appearance) that

  20. Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations

    CERN Document Server

    Manetti, C; Giuliani, A; Webber, C L; Zbilut, J P; Manetti, Cesare; Ceruso, Marc-Antoine; Giuliani, Alessandro; Webber, Charles L.; Zbilut, Joseph P.

    1998-01-01

    A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG) simulated in water are analyzed by recurrence quantification. The results demonstrate the sensitivity of the technique for the discrimination of phase sensitive dynamics. Physical interpretation of the recurrence parameters is also discussed.

  1. Characterization of Austenite Dynamic Recrystallization under Different Z Parameters in a Microalloyed Steel

    Institute of Scientific and Technical Information of China (English)

    M. Shaban; B. Eghbali

    2011-01-01

    A low carbon Nb-Ti microalloyed steel was subjected to hot torsion testing over the temperature range 850-1100℃ and strain rates 0.01-1 s-1 to study the influence of deformation conditions on the dynamic recrystallization characteristics of austenite. The results show that dynamic recrystallization occurs more easily with the decrease of strain rate and the increase of deformation temperature. The complete dynamically recrystallized grain size as a function of Zener-Hollomon parameter was established. It was found that dynamically recrystallized grain sizes decrease with increasing strain rate and decreasing deformation temperature. The effect of microalloying elements on peak strain was investigated and the solute drag corrected peak strain was determined. Also, the dynamic recrystallization map of austenite was obtained by using recrystallization critical parameters.

  2. Characterizing dynamic hysteresis and fractal statistics of chaotic two-phase flow and application to fuel cells

    Science.gov (United States)

    Burkholder, Michael B.; Litster, Shawn

    2016-05-01

    In this study, we analyze the stability of two-phase flow regimes and their transitions using chaotic and fractal statistics, and we report new measurements of dynamic two-phase pressure drop hysteresis that is related to flow regime stability and channel water content. Two-phase flow dynamics are relevant to a variety of real-world systems, and quantifying transient two-phase flow phenomena is important for efficient design. We recorded two-phase (air and water) pressure drops and flow images in a microchannel under both steady and transient conditions. Using Lyapunov exponents and Hurst exponents to characterize the steady-state pressure fluctuations, we develop a new, measurable regime identification criteria based on the dynamic stability of the two-phase pressure signal. We also applied a new experimental technique by continuously cycling the air flow rate to study dynamic hysteresis in two-phase pressure drops, which is separate from steady-state hysteresis and can be used to understand two-phase flow development time scales. Using recorded images of the two-phase flow, we show that the capacitive dynamic hysteresis is related to channel water content and flow regime stability. The mixed-wettability microchannel and in-channel water introduction used in this study simulate a polymer electrolyte fuel cell cathode air flow channel.

  3. Predictive and prognostic value of circulating nucleosomes and serum biomarkers in patients with metastasized colorectal cancer undergoing Selective Internal Radiation Therapy

    International Nuclear Information System (INIS)

    Selective Internal Radiation Therapy (SIRT) is a new and effective locoregional anticancer therapy for colorectal cancer patients with liver metastases. Markers for prediction of therapy response and prognosis are needed for the individual management of those patients undergoing SIRT. Blood samples were prospectively and consecutively taken from 49 colorectal cancer patients with extensive hepatic metastases before, three, six, 24 and 48 h after SIRT to analyze the concentrations of nucleosomes and further laboratory parameters, and to compare them with the response to therapy regularly determined 3 months after therapy and with overall survival. Circulating nucleosomes, cytokeratin-19 fragments (CYFRA 21-1), carcinoembryonic antigen (CEA), C-reactive protein (CRP) and various liver markers increased already 24 h after SIRT. Pretherapeutical levels of CYFRA 21-1, CEA, cancer antigen 19-9 (CA 19-9), asparate-aminotransferase (AST) and lactate dehydrogenase (LDH) as well as 24 h values of nucleosomes were significantly higher in patients suffering from disease progression (N = 35) than in non-progressive patients (N = 14). Concerning overall survival, CEA, CA 19-9, CYFRA 21-1, CRP, LDH, AST, choline esterase (CHE), gamma-glutamyl-transferase, alkaline phosphatase, and amylase (all 0 h, 24 h) and nucleosomes (24 h) were found to be prognostic relevant markers in univariate analyses. In multivariate Cox-Regression analysis, the best prognostic model was obtained for the combination of CRP and AST. When 24 h values were additionally included, nucleosomes (24 h) further improved the existing model. Panels of biochemical markers are helpful to stratify pretherapeutically colorectal cancer patients for SIR-therapy and to early estimate the response to SIR-therapy

  4. Characterization of viscoelastic materials by quasi-static and dynamic indentation

    International Nuclear Information System (INIS)

    This paper describes the experimental measurements of the elastic modulus and hardness of viscoelastic materials under quasi-static and dynamic depth-sensing indentation using a homemade tribology probe microscope (TPM). The indentation measurements were performed using a sapphire sphere tip under various conditions. Materials such as polytetrafluoroethylene, styrene rubber and nitrile rubber were tested in both quasi-static and dynamic experiments. In quasi-static mode, the loading and unloading force curves were obtained from these specimens, and the results show a significant load effect on the measured hardness and elastic modulus. The dynamic indentation tests were conducted under a range of loading forces with various frequencies. The values of storage modulus, loss modulus and damping factor were determined by dynamic indentation. To get an accurate measurement, the stiffness and damping of the instrument were rigorously analyzed. Using dynamic indentation, it was confirmed that the variation in the frequency of the oscillation force has a significant effect on the measured results of the materials. Comparing the results obtained from the quasi-static and dynamic indentations, for the viscoelastic properties, dynamic indentation offers an advantage over the quasi-static method. Collectively, these results clearly demonstrate the capability of our homemade TPM facility to determine the constitutive behavior of viscoelastic solids in the frequency domain. (paper)

  5. Cognitive Network Modeling as a Basis for Characterizing Human Communication Dynamics and Belief Contagion in Technology Adoption

    Science.gov (United States)

    Hutto, Clayton; Briscoe, Erica; Trewhitt, Ethan

    2012-01-01

    Societal level macro models of social behavior do not sufficiently capture nuances needed to adequately represent the dynamics of person-to-person interactions. Likewise, individual agent level micro models have limited scalability - even minute parameter changes can drastically affect a model's response characteristics. This work presents an approach that uses agent-based modeling to represent detailed intra- and inter-personal interactions, as well as a system dynamics model to integrate societal-level influences via reciprocating functions. A Cognitive Network Model (CNM) is proposed as a method of quantitatively characterizing cognitive mechanisms at the intra-individual level. To capture the rich dynamics of interpersonal communication for the propagation of beliefs and attitudes, a Socio-Cognitive Network Model (SCNM) is presented. The SCNM uses socio-cognitive tie strength to regulate how agents influence--and are influenced by--one another's beliefs during social interactions. We then present experimental results which support the use of this network analytical approach, and we discuss its applicability towards characterizing and understanding human information processing.

  6. Nonlinear digital signal processing in mental health: characterization of major depression using instantaneous entropy measures of heartbeat dynamics

    Science.gov (United States)

    Valenza, Gaetano; Garcia, Ronald G.; Citi, Luca; Scilingo, Enzo P.; Tomaz, Carlos A; Barbieri, Riccardo

    2015-01-01

    Nonlinear digital signal processing methods that address system complexity have provided useful computational tools for helping in the diagnosis and treatment of a wide range of pathologies. More specifically, nonlinear measures have been successful in characterizing patients with mental disorders such as Major Depression (MD). In this study, we propose the use of instantaneous measures of entropy, namely the inhomogeneous point-process approximate entropy (ipApEn) and the inhomogeneous point-process sample entropy (ipSampEn), to describe a novel characterization of MD patients undergoing affective elicitation. Because these measures are built within a nonlinear point-process model, they allow for the assessment of complexity in cardiovascular dynamics at each moment in time. Heartbeat dynamics were characterized from 48 healthy controls and 48 patients with MD while emotionally elicited through either neutral or arousing audiovisual stimuli. Experimental results coming from the arousing tasks show that ipApEn measures are able to instantaneously track heartbeat complexity as well as discern between healthy subjects and MD patients. Conversely, standard heart rate variability (HRV) analysis performed in both time and frequency domains did not show any statistical significance. We conclude that measures of entropy based on nonlinear point-process models might contribute to devising useful computational tools for care in mental health. PMID:25821435

  7. Characterization of Adenomatous Polyposis Coli Protein Dynamics and Localization at the Centrosome

    OpenAIRE

    Christina Lui; Myth T. S. Mok; Henderson, Beric R.

    2016-01-01

    The adenomatous polyposis coli (APC) tumor suppressor is a multifunctional regulator of Wnt signaling and acts as a mobile scaffold at different cellular sites. APC was recently found to stimulate microtubule (MT) growth at the interphase centrosome; however, little is known about its dynamics and localization at this site. To address this, we analysed APC dynamics in fixed and live cells by fluorescence microscopy. In detergent-extracted cells, we discovered that APC was only weakly retained...

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

    Directory of Open Access Journals (Sweden)

    Nagaraj M Gowda

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

  9. Processing of styrene butadiene rubber-carbon black nanocomposites with gradation of crosslink density: Static and dynamic mechanical characterization

    International Nuclear Information System (INIS)

    The concentrations of sulfur and accelerator were varied in the nanocomposites of carbon black (CB)-filled styrene-butadiene rubber (SBR) matrix to introduce the gradation of the crosslink density. These curatives were varied from 1 to 11 phr (per hundred rubber) along the span of 3-mm thick sheet using the construction-based layering method. The static and dynamic mechanical characterizations of these functionally graded polymeric nanocomposites (FGPNCs) were carried out. With increasing crosslink density along thickness, hardness and modulus increase while the ultimate properties like tensile strength and elongation at break droop down. The dynamic mechanical analysis of FGPNCs exhibits the increment in the storage modulus than the uniformly dispersed polymeric nanocomposites (UDPNCs) employing the same average amount of curatives. The peak position of tan δmax remains at the same temperature while the value mitigates in FGPNCs. In FGPNCs, tan δ peak intimates the broadness in the transition region

  10. Soil organic matter dynamics as characterized with 1H and 13C solid-state NMR techniques

    Science.gov (United States)

    Jäger, Alex; Schwarz, Jette; Bertmer, Marko; Schaumann, Gabriele E.

    2010-05-01

    Soil organic matter (SOM) is a complex and heterogeneous matter. Characterization by solid-state NMR methods on 1H and 13C nuclei is therefore demanding. Our goal is to obtain information on the dynamic behaviour of soil samples and to study the influence of external parameters on both structure and dynamics. We regard water molecules to be the pivotal agent of soil dynamics by generating a network between organic matter via intermolecular hydrogen bonding, which leads to cross linking of organic matter and increases its rigidity. Although 1H solid-state NMR on non-rotating samples are not so commonly used for soil characterization, they enable the differentiation of proton mobilities via their linewidths which are resulting from differences in the dipole-dipole coupling strengths. Therefore, even weak molecular interactions such as hydrogen bonding can be differentiated and changes due to heat treatments and the short and long term behaviour followed. Though in principle a simple technique, static 1H measurements are complicated by several means, one of them is the high abundance in almost all matter including probe head material that has to be excluded for analysis. Finally, we selected 1H DEPTH [1] and Hahn-echo sequences to distinguish different mobilities in soil, mainly free moving water and water fixed in the soil matrix. After decomposition using Gaussian and Lorentzian lineshapes, the relative amounts of mobile and rigid water molecules can be obtained. By heating the samples above 100°C in sealed glass tubes, the proposed water network is destroyed and able to rebuild after cooling. This long term behaviour is studied on the course of months. Furthermore, the instant changes before and after heating are shown for a series of soil samples to characterize soils based on this water network model. To combine the information obtained on the 1H mobility with focus on water dynamics, 13C 2D WISE (wideline separation) measurements were done. This method yields 1

  11. Characterizing and correcting for the effect of sensor noise in the dynamic mode decomposition

    CERN Document Server

    Dawson, Scott T M; Williams, Matthew O; Rowley, Clarence W

    2015-01-01

    Dynamic mode decomposition (DMD) provides a practical means of extracting insightful dynamical information from fluids datasets. Like any data processing technique, DMD's usefulness is limited by its ability to extract real and accurate dynamical features from noise-corrupted data. Here we show analytically that DMD is biased to sensor noise, and quantify how this bias depends on the size and noise level of the data. We present three modifications to DMD that can be used to remove this bias: (i) a direct correction of the identified bias using known noise properties, (ii) combining the results of performing DMD forwards and backwards in time, and (iii) a total least-squares-inspired algorithm. We discuss the relative merits of each algorithm, and demonstrate the performance of these modifications on a range of synthetic, numerical, and experimental datasets. We further compare our modified DMD algorithms with other variants proposed in recent literature.

  12. Characterizing and correcting for the effect of sensor noise in the dynamic mode decomposition

    Science.gov (United States)

    Dawson, Scott T. M.; Hemati, Maziar S.; Williams, Matthew O.; Rowley, Clarence W.

    2016-03-01

    Dynamic mode decomposition (DMD) provides a practical means of extracting insightful dynamical information from fluids datasets. Like any data processing technique, DMD's usefulness is limited by its ability to extract real and accurate dynamical features from noise-corrupted data. Here, we show analytically that DMD is biased to sensor noise, and quantify how this bias depends on the size and noise level of the data. We present three modifications to DMD that can be used to remove this bias: (1) a direct correction of the identified bias using known noise properties, (2) combining the results of performing DMD forwards and backwards in time, and (3) a total least-squares-inspired algorithm. We discuss the relative merits of each algorithm and demonstrate the performance of these modifications on a range of synthetic, numerical, and experimental datasets. We further compare our modified DMD algorithms with other variants proposed in the recent literature.

  13. Characterization of degeneration process in thermo-acoustic combustion instability using dynamical systems theory

    Science.gov (United States)

    Hayashi, Kenta; Gotoda, Hiroshi; Okuno, Yuta; Tachibana, Shigeru; Tokyo University of Science Collaboration; Japan Aerospace Exploration Agency Collaboration

    2015-11-01

    We have experimentally investigated the degeneration process of combustion instability in a lean premixed gas-turbine model combustor on the basis of dynamical systems theory. Our previous study reported that with increasing the equivalence ratio, the dynamical behavior of combustion state close to lean blowout transits from stochastic fluctuations to periodic thermoacoustic combustion oscillations via low-dimensional chaotic oscillations. The further increase in the equivalence ratio gives rise to the quasi-periodic oscillations and the subsequent chaotic oscillations with small amplitudes. The route to chaotic oscillations is quantitatively shown by the use of nonlinear time series analysis involving the color recurrence plots, permutation entropy and local predictor.

  14. Characterization of Adenomatous Polyposis Coli Protein Dynamics and Localization at the Centrosome.

    Science.gov (United States)

    Lui, Christina; Mok, Myth T S; Henderson, Beric R

    2016-01-01

    The adenomatous polyposis coli (APC) tumor suppressor is a multifunctional regulator of Wnt signaling and acts as a mobile scaffold at different cellular sites. APC was recently found to stimulate microtubule (MT) growth at the interphase centrosome; however, little is known about its dynamics and localization at this site. To address this, we analysed APC dynamics in fixed and live cells by fluorescence microscopy. In detergent-extracted cells, we discovered that APC was only weakly retained at the centrosome during interphase suggesting a rapid rate of exchange. This was confirmed in living cells by fluorescence recovery after photobleaching (FRAP), which identified two pools of green fluorescent protein (GFP)-APC: a major rapidly exchanging pool (~86%) and minor retained pool (~14%). The dynamic exchange rate of APC was unaffected by C-terminal truncations implicating a targeting role for the N-terminus. Indeed, we mapped centrosome localization to N-terminal armadillo repeat (ARM) domain amino acids 334-625. Interestingly, the rate of APC movement to the centrosome was stimulated by intact MTs, and APC dynamics slowed when MTs were disrupted by nocodazole treatment or knockdown of γ-tubulin. Thus, the rate of APC recycling at the centrosome is enhanced by MT growth, suggesting a positive feedback to stimulate its role in MT growth. PMID:27144584

  15. Characterization of Adenomatous Polyposis Coli Protein Dynamics and Localization at the Centrosome

    Directory of Open Access Journals (Sweden)

    Christina Lui

    2016-04-01

    Full Text Available The adenomatous polyposis coli (APC tumor suppressor is a multifunctional regulator of Wnt signaling and acts as a mobile scaffold at different cellular sites. APC was recently found to stimulate microtubule (MT growth at the interphase centrosome; however, little is known about its dynamics and localization at this site. To address this, we analysed APC dynamics in fixed and live cells by fluorescence microscopy. In detergent-extracted cells, we discovered that APC was only weakly retained at the centrosome during interphase suggesting a rapid rate of exchange. This was confirmed in living cells by fluorescence recovery after photobleaching (FRAP, which identified two pools of green fluorescent protein (GFP-APC: a major rapidly exchanging pool (~86% and minor retained pool (~14%. The dynamic exchange rate of APC was unaffected by C-terminal truncations implicating a targeting role for the N-terminus. Indeed, we mapped centrosome localization to N-terminal armadillo repeat (ARM domain amino acids 334–625. Interestingly, the rate of APC movement to the centrosome was stimulated by intact MTs, and APC dynamics slowed when MTs were disrupted by nocodazole treatment or knockdown of γ-tubulin. Thus, the rate of APC recycling at the centrosome is enhanced by MT growth, suggesting a positive feedback to stimulate its role in MT growth.

  16. Complete characterization of the stability of cluster synchronization in complex dynamical networks.

    Science.gov (United States)

    Sorrentino, Francesco; Pecora, Louis M; Hagerstrom, Aaron M; Murphy, Thomas E; Roy, Rajarshi

    2016-04-01

    Synchronization is an important and prevalent phenomenon in natural and engineered systems. In many dynamical networks, the coupling is balanced or adjusted to admit global synchronization, a condition called Laplacian coupling. Many networks exhibit incomplete synchronization, where two or more clusters of synchronization persist, and computational group theory has recently proved to be valuable in discovering these cluster states based on the topology of the network. In the important case of Laplacian coupling, additional synchronization patterns can exist that would not be predicted from the group theory analysis alone. Understanding how and when clusters form, merge, and persist is essential for understanding collective dynamics, synchronization, and failure mechanisms of complex networks such as electric power grids, distributed control networks, and autonomous swarming vehicles. We describe a method to find and analyze all of the possible cluster synchronization patterns in a Laplacian-coupled network, by applying methods of computational group theory to dynamically equivalent networks. We present a general technique to evaluate the stability of each of the dynamically valid cluster synchronization patterns. Our results are validated in an optoelectronic experiment on a five-node network that confirms the synchronization patterns predicted by the theory. PMID:27152349

  17. Characterization of volatiles from cultured dairy spreads during storage by dynamic headspace GC/MS

    DEFF Research Database (Denmark)

    Lund, Pia; Hølmer, Gunhild Kofoed

    2001-01-01

    The effect of storage time and storage temperature on the formation of volatile compounds in dairy spreads was investigated. Dairy spreads were stored for 10 weeks at -18, 5 and 20 degreesC, respectively, and analyzed after 0, 38, 54 and 67 days of storage. By means of a dynamic headspace GC/MS...

  18. Dynamic Characterization and Impulse Response Modeling of Amplitude and Phase Response of Silicon Nanowires

    DEFF Research Database (Denmark)

    Cleary, Ciaran S.; Ji, Hua; Dailey, James M.;

    2013-01-01

    Amplitude and phase dynamics of silicon nanowires were measured using time-resolved spectroscopy. Time shifts of the maximum phase change and minimum amplitude as a function of pump power due to saturation of the free-carrier density were observed. A phenomenological impulse response model used to......, for silicon nanowires with lengths varying from 3.6 to 14.9 mm....

  19. A Nonlinear Dynamic Characterization of The Universal Scrape-off Layer Plasma Fluctuations

    CERN Document Server

    Mekkaoui, A

    2012-01-01

    A stochastic differential equation of plasma density dynamic is derived, consistent with the experimentally measured pdf and the theoretical quadratic nonlinearity. The plasma density evolves on the turbulence correlation time scale and is driven by a stochastic white noise proportional to the turbulence fluctuations amplitude, while the linear growth is quadratically damped by the fluctuation level $n_e(t)/\\bar{n}_e$.

  20. Crossfit analysis: a novel method to characterize the dynamics of induced plant responses

    Directory of Open Access Journals (Sweden)

    Smilde Age K

    2009-12-01

    Full Text Available Abstract Background Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model. Results This study therefore aims to describe the dynamics of the glucosinolate response, measured at three time points after induction in a feral Brassica, by a three-faceted approach, based on Principal Component Analysis. First the large-scale aspects of the response are described in a 'global model' and then each time-point in the experiment is individually described in 'local models' that focus on phenomena that occur at specific moments in time. Although each local model describes the variation among the plants at one time-point as well as possible, the response dynamics are lost. Therefore a novel method called the 'Crossfit' is described that links the local models of different time-points to each other. Conclusions Each element of the described analysis approach reveals different aspects of the response. The crossfit shows that smaller dynamic changes may occur in the response that are overlooked by global models, as illustrated by the analysis of a metabolic profiling dataset of the same samples.

  1. Characterization of dynamic change of Fan-delta reservoir properties in water-drive development

    Energy Technology Data Exchange (ETDEWEB)

    Wu Shenghe; Xiong Qihua; Liu Yuhong [Univ. of Petroleum Changping, Beijing (China)

    1997-08-01

    Fan-delta reservoir in Huzhuangji oil field of east China, is a typical highly heterogeneous reservoir. The oil field has been developed by water-drive for 10 years, but the oil recovery is less than 12%, and water cut is over 90%, resulting from high heterogeneity and serious dynamic change of reservoir properties. This paper aims at the study of dynamic change of reservoir properties in water-drive development. Through quantitative imaging analysis and mercury injection analysis of cores from inspection wells, the dynamic change of reservoir pore structure in water-drive development was studied. The results show that the {open_quotes}large pore channels{close_quotes} develop in distributary channel sandstone and become larger in water-drive development, resulting in more serious pore heterogeneity. Through reservoir sensitivity experiments, the rock-fluid reaction in water-drive development is studied. The results show the permeability of some distal bar sandstone and deserted channel sandstone becomes lower due to swelling of I/S clay minerals in pore throats. OD the other hand, the permeability of distributary channel and mouth bar sandstone become larger because the authigenic Koalinites in pore throats are flushed away with the increase of flow rate of injection water. Well-logging analysis of flooded reservoirs are used to study the dynamic change of reservoir properties in various flow units. The distribution of remaining oil is closely related to the types and distribution of flow units.

  2. Electron diffraction tomography and dynamical refinement for crystal-structure characterization of nanocrystalline materials

    Czech Academy of Sciences Publication Activity Database

    Correa, Cinthia Antunes; Klementová, Mariana; Palatinus, Lukáš

    Warsaw : Polish Academy of Sciences, 2015, s. 651-653. ISSN 0587-4246. [International Symposium on Physics of Materials /13./. Praha (CZ), 31.08.2014-04.09.2014] R&D Projects: GA ČR GA13-25747S Institutional support: RVO:68378271 Keywords : dynamical diffraction * nanocrystal * structure analysis Subject RIV: BM - Solid Matter Physics ; Magnetism

  3. The Magnetic Nanoparticle Movement in Magnetic Fluid Characterized by the Laser Dynamic Speckle Interferometry

    Directory of Open Access Journals (Sweden)

    Xijun Wang

    2014-01-01

    Full Text Available A dual scanning laser speckle interferometry experiment was designed to observe the dynamic behavior of the magnetic fluid actuated by a magnetic field. In order to improve the spatial resolution of the dynamic speckle measurement, the phase delay scanning was used to compensate the additional phase variation which was caused by the transverse scanning. The correlation coefficients corresponding to the temporal dynamic speckle patterns within the same time interval scattering from the nanoparticles were calculated in the experiment on nanoscale magnetic clusters. In the experiment, the speckle of the magnetic nanoparticle fluid movement has been recorded by the lens unmounted CCD within the interferometry strips, although the speckle led to the distinguished annihilation of the light coherence. The results have showed that the nanoparticle fluid dynamic properties appeared synergistically in the fringe speckles. The analyses of the nanoparticle's relative speed and the speckle pattern moving amount in the fringes have proved the nanoparticle’s movement in a laminar flow in the experiment.

  4. Characterization of time-enhancement curves of benign and malignant prostate tissue at dynamic MR imaging

    International Nuclear Information System (INIS)

    Our objectives were to determine time-enhancement curves of prostate cancer, peripheral zone, and adenoma at gadolinium-enhanced MR imaging, and to determine if a high-spatial/low-temporal dynamic imaging could be accurate in depicting prostate cancer, or if a higher temporal resolution (and a lower spatial resolution) should be favored. Thirty-nine patients with prostate cancer underwent MR imaging before radical prostatectomy by using T1- and T2-weighted axial images and a single-slice dynamic gadolinium-enhanced sequence (40 images; one image per 6 s; injection of 20 ml at 2 ml/s). After analysis of the pathologic specimens, four region-of-interest (ROI) cursors (cancer, peripheral zone, adenoma, and muscle) were retrospectively placed on dynamic images. Time-enhancement curves of the ROIs were obtained. The theoretical accuracy of a 30-s dynamic multislice MR sequence in depicting cancer within peripheral zone and adenoma (ROC curves) was calculated from these curves. On average, prostate cancer enhanced more and earlier than peripheral zone and adenoma, but there were great interindividual variations. For start delays ranging from 12 to 84 s, the areas under the ROC curves ranged from 0.602 to 0.698 for the depiction of cancer within adenoma and from 0.614 to 0.827 for the depiction of cancer within peripheral zone. The best results were obtained with a 36-s start delay. In conclusion, we found a 30-s scanning window which seems to allow a good depiction of cancer within peripheral zone. Because of largely overlapping enhancement patterns, cancer will probably not be depicted within adenoma by dynamic imaging, at least by using low temporal resolution. (orig.)

  5. Applications of hydrogen deuterium exchange (HDX for the characterization of conformational dynamics in light-activated photoreceptors

    Directory of Open Access Journals (Sweden)

    Robert eLindner

    2015-06-01

    Full Text Available Rational design of optogenetic tools is inherently linked to the understanding of photoreceptor function. Structural analysis of elements involved in signal integration in individual sensor domains provides an initial idea of their mode of operation, but understanding how local structural rearrangements eventually affect signal transmission to output domains requires inclusion of the effector regions in the characterization. However, the dynamic nature of these assemblies renders their structural analysis challenging and therefore a combination of high- and low-resolution techniques is required to appreciate functional aspects of photoreceptors.This review focuses on the potential of Hydrogen-Deuterium exchange coupled to mass spectrometry (HDX-MS for complementing the structural characterization of photoreceptors. In this respect, the ability of HDX-MS to provide information on the conformational dynamics and the possibility to address multiple functionally relevant states in solution render this methodology ideally suitable. We highlight recent examples demonstrating the potential of HDX-MS and discuss how these results can help to improve existing optogenetic systems or guide the design of novel optogenetic tools.

  6. Distinguishing linear, nonlinear, transient and persistent vegetation dynamics to characterize empirical signatures of ecological resilience

    Science.gov (United States)

    Background/Question/Methods To characterize and interpret ecological resilience and state change is a fundamental question in ecology. In the same ecosystem, across different communities, one can encounter relative stability, abrupt directional shifts, transient reversible change, as well as nondire...

  7. Characterizing a Dynamic Land Cover Change Frontier Using MODIS Phenology Metrics: Cropland Expansion in Mato Grosso, Brazil

    Science.gov (United States)

    Morton, D. C.; Defries, R. S.; Shimabukuro, Y. E.; Morisette, J.

    2005-12-01

    The state of Mato Grosso, Brazil experienced the most rapid agricultural expansion of any region in the Amazon Basin during the existing MODIS data record. Rapid conversion of Amazon forest, transitional tropical forest, and cerrado woodland-savanna for cattle ranching and grain production continues to fragment large tracts of these biomes. Tropical forest loss is estimated annually, yet the fate of cleared lands and losses of transitional forest or cerrado have not been well characterized in this region. Using phenological information from time series of MODIS 16-day composite data, it is possible to capture the temporal dynamism of land cover change and accurately separate primary and secondary land use transitions. We use time series of cloud-cleaned MODIS NDVI and EVI at 250 m resolution to characterize land cover based on metrics of wet-season, dry-season, and annual phenology from 2000-2004. Distinct phenological signatures for forest, pasture and natural grasslands, cerrado, and cropland enable accurate classification of land cover types when compared to field validation data (overall accuracy = 85%). We estimate that more than 1.6 million hectares were converted to cropland between 2000 and 2004. The majority of new cropland resulted from the direct conversion of cerrado (35%) or forest (29%); conversion of natural grassland areas or planted pasture accounted for 36% of new cropland areas. While secondary transitions from existing cattle pasture to cropland are an important source of new agricultural production, our findings contradict recent statements that cropland agriculture is not directly associated with new deforestation activities. Separation of more seasonal cerrado vegetation from transitional tropical forest based on vegetation phenology highlights land cover dynamics in regions with no previous deforestation monitoring. Phenological information from MODIS is extremely important to monitor land cover dynamics, separate forest types, and estimate

  8. Characterization of the High-Speed-Stage Bearing Skidding of Wind Turbine Gearboxes Induced by Dynamic Electricity Grid Events: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Helsen, Jan; Guillaume, Patrick; Guo, Yi; Keller, Jonathan

    2016-05-18

    Bearing behavior is an important factor for wind turbine drivetrain reliability. Extreme loads and dynamic excitations pose challenges to the bearing design and therefore its performance. Excessive skidding of the bearing rollers should be avoided because it can cause scuffing failures. Excitations coming from wind and the electricity grid can subject the drivetrain to fluctuating torque and nontorque loads. Wind-induced excitations have been investigated predominantly in literature. However, modern wind turbines are subjected more and more to grid-induced loads because of stricter electricity grid regulations. For example, during fault-ride-through events, turbines are required to stay connected for a longer period of time during the grid failure. This work investigates the influence of electrically induced excitations on the skidding behaviour of the tapered roller bearings on the high-speed stage of a wind turbine gearbox. This skidding behaviour during dynamic events is described as a potential bearing failure initiator by many researchers; however, only limited full-scale dynamic testing is documented. Therefore, a dedicated gridloss-type event is defined in the paper and conducted in a dynamometer test on a full-scale wind turbine nacelle. During the event, a complete electricity grid failure is simulated while the turbine is at rated speed and predefined torque levels. Particular focus is on the characterization of the high-speed shaft tapered roller bearing slip behavior. Strain-gauge bridges in grooves along the circumference of the outer ring are used to characterize the bearing load zone in detail. It is shown that during the torque reversals of the transient event, roller slip can be induced. This indicates the potential of the applied load case to go beyond the preload of the tapered roller bearing. Furthermore, the relation between the applied torque and skidding level is studied.

  9. Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries.

    Science.gov (United States)

    Rogers, Lauren A; Schindler, Daniel E; Lisi, Peter J; Holtgrieve, Gordon W; Leavitt, Peter R; Bunting, Lynda; Finney, Bruce P; Selbie, Daniel T; Chen, Guangjie; Gregory-Eaves, Irene; Lisac, Mark J; Walsh, Patrick B

    2013-01-29

    Observational data from the past century have highlighted the importance of interdecadal modes of variability in fish population dynamics, but how these patterns of variation fit into a broader temporal and spatial context remains largely unknown. We analyzed time series of stable nitrogen isotopes from the sediments of 20 sockeye salmon nursery lakes across western Alaska to characterize temporal and spatial patterns in salmon abundance over the past ∼500 y. Although some stocks varied on interdecadal time scales (30- to 80-y cycles), centennial-scale variation, undetectable in modern-day catch records and survey data, has dominated salmon population dynamics over the past 500 y. Before 1900, variation in abundance was clearly not synchronous among stocks, and the only temporal signal common to lake sediment records from this region was the onset of commercial fishing in the late 1800s. Thus, historical changes in climate did not synchronize stock dynamics over centennial time scales, emphasizing that ecosystem complexity can produce a diversity of ecological responses to regional climate forcing. Our results show that marine fish populations may alternate between naturally driven periods of high and low abundance over time scales of decades to centuries and suggest that management models that assume time-invariant productivity or carrying capacity parameters may be poor representations of the biological reality in these systems. PMID:23322737

  10. Electron beam crosslinked gels-Preparation, characterization and their effect on the mechanical, dynamic mechanical and rheological properties of rubbers

    Energy Technology Data Exchange (ETDEWEB)

    Mitra, Suman; Chattopadhyay, Santanu [Rubber Technology Centre, Indian Institute of Technology, Kharagpur 721302 (India); Sabharwal, Sunil [Radiation Technology Development Section, Bhabha Atomic Research Center, Trombay, Mumbai 400085 (India); Bhowmick, Anil K., E-mail: anilkb@rtc.iitkgp.ernet.i [Rubber Technology Centre, Indian Institute of Technology, Kharagpur 721302 (India)

    2010-03-15

    Electron beam (EB) crosslinked natural rubber (NR) gels were prepared by curing NR latex with EB irradiation over a range of doses from 2.5 to 20 kGy using butyl acrylate as sensitizer. The NR gels were systematically characterized by solvent swelling, dynamic light scattering, mechanical and dynamic mechanical properties. These gels were introduced in virgin NR and styrene butadiene rubber (SBR) matrices at 2, 4, 8 and 16 phr concentration. Addition of the gels improved the mechanical and dynamic mechanical properties of NR and SBR considerably. For example, 16 phr of 20 kGy EB-irradiated gel-filled NR showed a tensile strength of 3.53 MPa compared to 1.85 MPa of virgin NR. Introduction of gels in NR shifted the glass transition temperature to a higher temperature. A similar effect was observed in the case of NR gel-filled SBR systems. Morphology of the gel-filled systems was studied with atomic force microscopy. The NR gels also improved the processability of the virgin rubbers greatly. Both the shear viscosity and the die swell values of EB-irradiated gel-filled NR and SBR were lower than their virgin counterparts as investigated by capillary rheometer.

  11. On the testing, characterization, and evaluation of PV inverters and dynamic MPPT performance under real varying operating conditions

    Energy Technology Data Exchange (ETDEWEB)

    Sanchis, P.; Lopez, J.; Ursua, A.; Gubia, E.; Marroyo, L. [Public University of Navarra, Pamplona (Spain). Department of Electrical and Electronic Engineering

    2006-07-01

    The increasing number of photovoltaic inverters that are coming on the PV market stresses the need to carry out a dynamic characterization of these elements and their maximum power point tracking (MPPT) algorithms under real operating conditions. In order to make these conditions repeatable at the laboratory, PV array simulators are used. However, actual simulators, including the commercial simulators, recreate only a single or small set of PV array characteristic curves in which quite commonly theoretical calculations are included in order to simulate irradiance and temperature artificial variations. This is far from being a recreation of the real and long dynamic behavior of a PV array or generator. The testing and evaluation of the performance of PV inverters and MPPT algorithms has to be carried out when the PV system moves dynamically according to real operating conditions, including processes such as rapidly changing atmospheric conditions, partial shadows, dawn, and nightfall. This paper tries to contribute to the analysis of this problem by means of an electronic system that both measures the real evolution of the characteristic curves of PV arrays at outdoor operation and then recreates them at the laboratory to test PV inverters. This way the equipment can highlight the different performances of PV inverters and MPPT techniques when they operate under real operating conditions. As an example, two commercial inverters are tested and analyzed under the recreated behavior of a PV generator during 2 singular days that include processes of partial shading and fast irradiance variations. (author)

  12. Far-field characterization of the thermal dynamics in lasing microspheres

    CERN Document Server

    Ramirez, J M; Capuj, N E; Berencen, Y; Pitanti, A; Garrido, B; Tredicucci, A

    2015-01-01

    This work reports the dynamical thermal behavior of lasing microspheres placed on a dielectric substrate while they are homogeneously heated-up by the top-pump laser used to excite the active medium. The lasing modes are collected in the far-field and their temporal spectral traces show characteristic lifetimes of about 2 ms. The latter values scale with the microsphere radius and are independent of the pump power in the studied range. Finite-Element Method simulations reproduce the experimental results, revealing that the thermal dynamics is dominated by the heat dissipated towards the substrate through the medium surrounding the contact point. The characteristic system scale regarding thermal transport is of few hundreds of nanometers, thus enabling an effective toy model for investigating heat conduction in non-continuum gaseous media and near-field radiative energy transfer.

  13. Characterization of Thin Film Polymers Through Dynamic Mechanical Analysis and Permeation

    Science.gov (United States)

    Herring, Helen

    2003-01-01

    Thin polymer films are being considered, as candidate materials to augment the permeation resistance of cryogenic hydrogen fuel tanks such as would be required for future reusable launch vehicles. To evaluate performance of candidate films after environmental exposure, an experimental study was performed to measure the thermal/mechanical and permeation performance of six, commercial-grade materials. Dynamic storage modulus, as measured by Dynamic Mechanical Analysis, was found over a range of temperatures. Permeability, as measured by helium gas diffusion, was found at room temperature. Test data was correlated with respect to film type and pre-test exposure to moisture, elevated temperature, and cryogenic temperature. Results indicated that the six films were comparable in performance and their resistance to environmental degradation.

  14. Laser-Induced Fluorescence Photogrammetry for Dynamic Characterization of Transparent and Aluminized Membrane Structures

    Science.gov (United States)

    Dorrington, Adrian A.; Jones, Thomas W.; Danehy, Paul M.; Pappa, Richard S.

    2003-01-01

    Photogrammetry has proven to be a valuable tool for static and dynamic profiling of membrane based inflatable and ultra-lightweight space structures. However, the traditional photogrammetric targeting techniques used for solid structures, such as attached retro-reflective targets and white-light dot projection, have some disadvantages and are not ideally suited for measuring highly transparent or reflective membrane structures. In this paper, we describe a new laser-induced fluorescence based target generation technique that is more suitable for these types of structures. We also present several examples of non-contact non-invasive photogrammetric measurements of laser-dye doped polymers, including the dynamic measurement and modal analysis of a 1m-by-1m aluminized solar sail style membrane.

  15. Characterization of biogenic gas dynamics in low-latitude peat soils using hydrogeophysical methods

    Science.gov (United States)

    Comas, X.; Wright, W. J.

    2011-12-01

    Peatlands are well recognized carbon reservoirs that account for about 33% of the global soil carbon pool and about 5 to 10% of methane (CH4) flux to the atmosphere while acting as a net sink for atmospheric carbon dioxide (CO2). Although wetland distribution is roughly bimodal with approximately 50% located in boreal and arctic regions and about 35% located in tropical/subtropical regions, most studies investigating biogenic gas dynamics (i.e. accumulation and/or releases) from peat soils are based on boreal peatlands while low-latitude systems have traditionally been less studied. The work presented here focuses on the use of hydrogeophysical methods (mostly ground penetrating radar, GPR) to investigate biogenic gas build up and release from low-latitude peat soils in the Everglades at both the laboratory and field-scale. GPR is a geophysical method based on measuring the travel times of high-frequency electromagnetic (EM) waves primarily controlled by changes in water content and thus gas content. This method has been effectively applied as a non-invasive technique for investigating biogenic gas dynamics in peat soils over a wide range of spatial and temporal scales. Several applications of GPR at both the laboratory and field scale are presented here in order to investigate the temporal dynamics of biogenic gases in peat soils from several locations in the Everglades. Geophysical measurements are constrained temporally by measuring flux using gas chambers fitted with time-lapse cameras, and gas composition is determined using gas analyzers. Further recommendations for future applications of hydrogeophysical methods for investigating gas distribution and dynamics in peat soils in low-latitude systems are also proposed.

  16. Characterization and modeling of intermittent locomotor dynamics in clock gene-deficient mice.

    Directory of Open Access Journals (Sweden)

    Toru Nakamura

    Full Text Available The scale-invariant and intermittent dynamics of animal behavior are attracting scientific interest. Recent findings concerning the statistical laws of behavioral organization shared between healthy humans and wild-type mice (WT and their alterations in human depression patients and circadian clock gene (Period 2; Per2 mutant mice indicate that clock genes play functional roles in intermittent, ultradian locomotor dynamics. They also claim the clinical and biological importance of the laws as objective biobehavioral measures or endophenotypes for psychiatric disorders. In this study, to elucidate the roles of breakdown of the broader circadian regulatory circuit in intermittent behavioral dynamics, we studied the statistical properties and rhythmicity of locomotor activity in Per2 mutants and mice deficient in other clock genes (Bmal1, Clock. We performed wavelet analysis to examine circadian and ultradian rhythms and estimated the cumulative distributions of resting period durations during which locomotor activity levels are continuously lower than a predefined threshold value. The wavelet analysis revealed significant amplification of ultradian rhythms in the BMAL1-deficient mice, and instability in the Per2 mutants. The resting period distributions followed a power-law form in all mice. While the distributions for the BMAL1-deficient and Clock mutant mice were almost identical to those for the WT mice, with no significant differences in their parameter (power-law scaling exponent, only the Per2 mutant mice showed consistently and significantly lower values of the scaling exponent, indicating the increased intermittency in ultradian locomotor dynamics. Furthermore, based on a stochastic priority queuing model, we explained the power-law nature of resting period distributions, as well as its alterations shared with human depressive patients and Per2 mutant mice. Our findings lead to the development of a novel mathematical model for abnormal

  17. Temporal Dynamics of the Default Mode Network Characterize Meditation-Induced Alterations in Consciousness

    Science.gov (United States)

    Panda, Rajanikant; Bharath, Rose D.; Upadhyay, Neeraj; Mangalore, Sandhya; Chennu, Srivas; Rao, Shobini L.

    2016-01-01

    Current research suggests that human consciousness is associated with complex, synchronous interactions between multiple cortical networks. In particular, the default mode network (DMN) of the resting brain is thought to be altered by changes in consciousness, including the meditative state. However, it remains unclear how meditation alters the fast and ever-changing dynamics of brain activity within this network. Here we addressed this question using simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) to compare the spatial extents and temporal dynamics of the DMN during rest and meditation. Using fMRI, we identified key reductions in the posterior cingulate hub of the DMN, along with increases in right frontal and left temporal areas, in experienced meditators during rest and during meditation, in comparison to healthy controls (HCs). We employed the simultaneously recorded EEG data to identify the topographical microstate corresponding to activation of the DMN. Analysis of the temporal dynamics of this microstate revealed that the average duration and frequency of occurrence of DMN microstate was higher in meditators compared to HCs. Both these temporal parameters increased during meditation, reflecting the state effect of meditation. In particular, we found that the alteration in the duration of the DMN microstate when meditators entered the meditative state correlated negatively with their years of meditation experience. This reflected a trait effect of meditation, highlighting its role in producing durable changes in temporal dynamics of the DMN. Taken together, these findings shed new light on short and long-term consequences of meditation practice on this key brain network. PMID:27499738

  18. Crossfit analysis: a novel method to characterize the dynamics of induced plant responses

    OpenAIRE

    Smilde Age K; Hoefsloot Huub CJ; van Dam Nicole M; Jansen Jeroen J

    2009-01-01

    Abstract Background Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced r...

  19. Characterization of heat dynamics of an arctic low-energy house with floor heating

    DEFF Research Database (Denmark)

    Andersen, Philip Hvidthøft Delff; Jiménez, María José; Madsen, Henrik;

    2014-01-01

    the fast responses to mechanical ventilation and solar radiation through a large window facade, and the slow responses to floor heating and outdoor temperature. To successfully describe the dynamics of the system, solar radiation is given special attention in modeling of both the physical system...... and the observational noise. The estimated physical parameters which include UA-value, total heat capacity, and time constants for the apartment are discussed. Simulations are performed to illustrate step and impulse responses of inputs....

  20. MISTY ECHO Tunnel Dynamics Experiment--Data report: Volume 1; Yucca Mountain Site Characterization Project

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, J.S.; Luke, B.A.; Long, J.W.; Lee, J.G.

    1992-04-01

    Tunnel damage resulting from seismic loading is an important issue for the Yucca Mountain nuclear waste repository. The tunnel dynamics experiment was designed to obtain and document ground motions, permanent displacements, observable changes in fracture patterns, and visible damage at ground motion levels of interest to the Yucca Mountain Project. Even though the maximum free-field loading on this tunnel was 28 g, the damage observed was minor. Fielding details, data obtained, and supporting documentation are reported.

  1. Contribution of dynamic focusing to ultrasonic defect characterization; Contribution de la focalisation dynamique a la caracterisation ultrasonore des defauts

    Energy Technology Data Exchange (ETDEWEB)

    Mahaut, S. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. des Procedes et Systemes Avances]|[Paris-7 Univ., 75 (France)

    1997-12-31

    Non destructive testing of vessels of pressurized water reactors uses ultrasonic focused transducers, with spherically shaped emitting surface or requiring an acoustic lens. But a mechanically focused transducer has to be used for a given inspection zone and for a fixed control configuration. The aim of this thesis is to improve ultrasonic defect characterization using adaptive dynamic focusing. Such a technique makes use of a ultrasonic defect characterization using adaptive dynamic focusing. Such a technique makes use of an ultrasonic transducer split into an array of individually controlled elements, allowing to apply delay and amplitude laws, calculated from modeling or experimentally deduced. Acoustical characteristics of the ultrasonic beam in the inspected specimen this can be electronically controlled; refraction angle, depth focusing, beam width. We briefly describe in the first chapter a theoretical modeling of the ultrasonic field radiated through a fluid/solid interface, extended to phase array transducers. This model is based on the integral formulation of Rayleigh, modified to take into account transmission through a fluid/solid (homogeneous and isotropic), of planar or cylindrical shape. In the second chapter an experimental study of this technique, with delay and amplitude laws given from the model, is presented, showing the efficiency of this method to adjust the acoustic performances. In he third chapter, experimental delay laws, extracted from the time distribution of signals received by the array (issued from a preliminary detected reflector), are used to provide an optimal imaging of the defect. This self-focusing procedure shows to adapt to a defect without using theoretical delays. The last chapter is dedicated to different applications devoted to improved defect characterization. The first application uses amplitude distribution received by the array, pointing out geometric characteristics of the reflector, while the second application

  2. Linear response range characterization and in vivo application of laser speckle imaging of blood flow dynamics

    Science.gov (United States)

    Choi, Bernard; Ramírez-San-Juan, Julio C.; Lotfi, Justin; Nelson, J. S.

    2006-07-01

    Noninvasive blood flow imaging can provide critical information on the state of biological tissue and the efficacy of approaches to treat disease. With laser speckle imaging (LSI), relative changes in blood flow are typically reported, with the assumption that the measured values are on a linear scale. A linear relationship between the measured and actual flow rate values has been suggested. The actual flow rate range, over which this linear relationship is valid, is unknown. Herein we report the linear response range and velocity dynamic range (VDR) of our LSI instrument at two relevant camera integration times. For integration times of 1 and 10 ms, the best case VDR was 80 and 60 dB, respectively, and the worst case VDR was 20 and 50 dB. The best case VDR values were similar to those reported in the literature for optical Doppler tomography. We also demonstrate the potential of LSI for monitoring blood flow dynamics in the rodent dorsal skinfold chamber model. These findings imply that LSI can provide accurate wide-field maps of microvascular blood flow rate dynamics and highlight heterogeneities in flow response to the application of exogenous agents.

  3. Dynamics

    CERN Document Server

    Goodman, Lawrence E

    2001-01-01

    Beginning text presents complete theoretical treatment of mechanical model systems and deals with technological applications. Topics include introduction to calculus of vectors, particle motion, dynamics of particle systems and plane rigid bodies, technical applications in plane motions, theory of mechanical vibrations, and more. Exercises and answers appear in each chapter.

  4. Immunogenic DNA-related factors. Nucleosomes spontaneously released from normal murine lymphoid cells stimulate proliferation and immunoglobulin synthesis of normal mouse lymphocytes.

    OpenAIRE

    Bell, D. A.; Morrison, B; VandenBygaart, P

    1990-01-01

    The cell-free supernatants of normal spleen and thymus lymphocytes in short-term culture release low molecular weight (LMW) DNA protein molecules that have an immunoproliferative effect (polyclonal B cell activation) in vitro. We have determined that the protein-LMW DNA complexes responsible for these effects are nucleosomal constituents of chromatin, since the mitogenically active fractions of these cell-free supernatants contain the constituents of core histones (H3, H2A, H2B, H4) together ...

  5. Broadband electrical impedance spectroscopy for dynamic electrical bio-impedance characterization

    OpenAIRE

    Sánchez Terrones, Benjamín

    2012-01-01

    The electrical impedance of biological samples is known in the literature as Electrical Bioimpedance (EBI). The Electrical Bioimpedance enables to characterize physiological conditions and events that are interesting for physiological research and medical diagnosis. Although the Electrical Bioimpedance weakness is that it depends on many physiological parameters, on the other hand, it is suitable for many medical applications where minimally invasive and real-time measurements with simple and...

  6. Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region.

    Science.gov (United States)

    Kasahara, Koji; Ohyama, Yoshifumi; Kokubo, Tetsuro

    2011-05-01

    Saccharomyces cerevisiae Hmo1 binds to the promoters of ∼ 70% of ribosomal protein genes (RPGs) at high occupancy, but is observed at lower occupancy on the remaining RPG promoters. In Δhmo1 cells, the transcription start site (TSS) of the Hmo1-enriched RPS5 promoter shifted upstream, while the TSS of the Hmo1-limited RPL10 promoter did not shift. Analyses of chimeric RPS5/RPL10 promoters revealed a region between the RPS5 upstream activating sequence (UAS) and core promoter, termed the intervening region (IVR), responsible for strong Hmo1 binding and an upstream TSS shift in Δhmo1 cells. Chromatin immunoprecipitation analyses showed that the RPS5-IVR resides within a nucleosome-free region and that pre-initiation complex (PIC) assembly occurs at a site between the IVR and a nucleosome overlapping the TSS (+1 nucleosome). The PIC assembly site was shifted upstream in Δhmo1 cells on this promoter, indicating that Hmo1 normally masks the RPS5-IVR to prevent PIC assembly at inappropriate site(s). This novel mechanism ensures accurate transcriptional initiation by delineating the 5'- and 3'-boundaries of the PIC assembly zone. PMID:21288884

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

    Directory of Open Access Journals (Sweden)

    Sharma Shikhar

    2012-01-01

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

  8. Microwave dynamic large signal waveform characterization of advanced InGaP HBT for power amplifiers

    Energy Technology Data Exchange (ETDEWEB)

    Zhao Lixin; Jin Zhi; Liu Xinyu, E-mail: zhaolixin@ime.ac.c [Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029 (China)

    2009-12-15

    In wireless mobile communications and wireless local area networks (WLAN), advanced InGaP HBT with power amplifiers are key components. In this paper, the microwave large signal dynamic waveform characteristics of an advanced InGaP HBT are investigated experimentally for 5.8 GHz power amplifier applications. The microwave large signal waveform distortions at various input power levels, especially at large signal level, are investigated and the reasons are analyzed. The output power saturation is also explained. These analyses will be useful for power amplifier designs. (semiconductor devices)

  9. Characterization of the time dynamics of monthly satellite snow cover data on Mountain Chains in Lebanon

    OpenAIRE

    Telesca, L.; Shaban, A.; Gascoin, S.; Darwich, T.; Drapeau, Laurent; El Hage, M.; Faour, G.

    2014-01-01

    In this study, the time dynamics of the monthly means of the snow cover have been on Lebanese Mountain Chains from 2000 to 2012, derived from the MODIS Aqua/Terra satellite snow products was analyzed. This represents the longest satellite-based snow cover time series produced for Lebanon so far. Field survey was also carried out over the last three years in order to measure the in-situ snow/water equivalent and depth in different localities. Analyzing the regime of the snow cover in Mount-Leb...

  10. Microwave dynamic large signal waveform characterization of advanced InGaP HBT for power amplifiers

    International Nuclear Information System (INIS)

    In wireless mobile communications and wireless local area networks (WLAN), advanced InGaP HBT with power amplifiers are key components. In this paper, the microwave large signal dynamic waveform characteristics of an advanced InGaP HBT are investigated experimentally for 5.8 GHz power amplifier applications. The microwave large signal waveform distortions at various input power levels, especially at large signal level, are investigated and the reasons are analyzed. The output power saturation is also explained. These analyses will be useful for power amplifier designs. (semiconductor devices)

  11. Characterizing the dynamics of soil organic carbon in grasslands on the Qinghai-Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    ZHANG YongQiang; TANG YanHong; JIANG Jie; YANG YongHui

    2007-01-01

    Carbon dynamics of grasslands on the Qinghai-Tibetan Plateau may play an important role in regional and global carbon cycles. The CENTURY model (Version 4.5) is used to examine temporal and spatial variations of soil organic carbon (SOC) in grasslands on the Plateau for the period from 1960 to 2002. The model successfully simulates the dynamics of aboveground carbon and soil surface SOC at the soil depth of 0-20 cm and the simulated results agree well to the measurements. Examination of SOC for eight typical grasslands shows different patterns of temporal variation in different ecosystems in 1960-2002. The extent of temporal variation increases with the increase of SOC of ecosystem. SOC increases first and decreases quickly then during the period from 1990 to 2000. Spatially, SOC density obtained for the equilibrium condition declines gradually from the southeast to the northwest on the plateau and showed a high heterogeneity in the eastern plateau. The results suggest that (i) SOC density in the alpine grasslands shows remarkable response to climate change during the 42 years, and (ii) the net carbon exchange rate between the alpine grassland ecosystems and the atmosphere increases from 1990 to 2000 as compared with that before 1990.

  12. Characterizing the dynamics of soil organic carbon in grasslands on the Qinghai-Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Carbon dynamics of grasslands on the Qinghai-Tibetan Plateau may play an important role in regional and global carbon cycles. The CENTURY model (Version 4.5) is used to examine temporal and spatial variations of soil organic carbon (SOC) in grasslands on the Plateau for the period from 1960 to 2002. The model successfully simulates the dynamics of aboveground carbon and soil surface SOC at the soil depth of 0-20 cm and the simulated results agree well to the measurements. Examination of SOC for eight typical grasslands shows different patterns of temporal variation in different ecosystems in 1960-2002. The extent of temporal variation increases with the increase of SOC of ecosystem. SOC increases first and decreases quickly then during the period from 1990 to 2000. Spatially, SOC density obtained for the equilibrium condition declines gradually from the southeast to the northwest on the plateau and showed a high heterogeneity in the eastern plateau. The results suggest that (i) SOC den-sity in the alpine grasslands shows remarkable response to climate change during the 42 years, and (ii) the net carbon exchange rate between the alpine grassland ecosystems and the atmosphere increases from 1990 to 2000 as compared with that before 1990.

  13. The role of shallow traps in dynamic characterization of organic semiconductor devices

    Science.gov (United States)

    Knapp, Evelyne; Ruhstaller, Beat

    2012-07-01

    We present an analysis of charge mobility determination methods for the steady as well as the transient state and investigate shallow charge traps with respect to their dynamic behavior. We distinguish between fast and slow trap states in our numerical model corresponding to two characteristic regimes. The two regimes manifest themselves in both impedance spectroscopy and dark injection transient currents (DITC). Further we investigate the charge mobility obtained from dynamic simulations and relate it to the extracted charge mobility from steady-state current-voltage curves. To demonstrate the practical impact of these regimes, we apply our numerical model to the DITC that have commonly been used to determine the charge mobility in organic semiconductor devices. The obtained results from DITC studies strongly depend on the measurement conditions. Therefore we analyze the measurements of reference [Esward et al., J. Appl. Phys. 109, 093707 (2011)] and reproduce the effects of varying pulse off-times on the transient current qualitatively. Thus, our simulations are able to explain the experimental observations with the help of relaxation effects due to shallow traps.

  14. Real-Time Intensity Domain Characterization of Fibre Lasers Using Spatio-Temporal Dynamics

    Directory of Open Access Journals (Sweden)

    Srikanth Sugavanam

    2016-02-01

    Full Text Available Fibre lasers are light sources that are synonymous with stability. They can give rise to highly coherent continuous-wave radiation, or a stable train of mode locked pulses with well-defined characteristics. However, they can also exhibit an exceedingly diverse range of nonlinear operational regimes spanning a multi-dimensional parameter space. The complex nature of the dynamics poses significant challenges in the theoretical and experimental studies of such systems. Here, we demonstrate how the real-time experimental methodology of spatio-temporal dynamics can be used to unambiguously identify and discern between such highly complex lasing regimes. This two-dimensional representation of laser intensity allows the identification and tracking of individual features embedded in the radiation as they make round-trip circulations inside the cavity. The salient features of this methodology are highlighted by its application to the case of Raman fibre lasers and a partially mode locked ring fibre laser operating in the normal dispersion regime.

  15. Evaluation of sliding window correlation performance for characterizing dynamic functional connectivity and brain states.

    Science.gov (United States)

    Shakil, Sadia; Lee, Chin-Hui; Keilholz, Shella Dawn

    2016-06-01

    A promising recent development in the study of brain function is the dynamic analysis of resting-state functional MRI scans, which can enhance understanding of normal cognition and alterations that result from brain disorders. One widely used method of capturing the dynamics of functional connectivity is sliding window correlation (SWC). However, in the absence of a "gold standard" for comparison, evaluating the performance of the SWC in typical resting-state data is challenging. This study uses simulated networks (SNs) with known transitions to examine the effects of parameters such as window length, window offset, window type, noise, filtering, and sampling rate on the SWC performance. The SWC time course was calculated for all node pairs of each SN and then clustered using the k-means algorithm to determine how resulting brain states match known configurations and transitions in the SNs. The outcomes show that the detection of state transitions and durations in the SWC is most strongly influenced by the window length and offset, followed by noise and filtering parameters. The effect of the image sampling rate was relatively insignificant. Tapered windows provide less sensitivity to state transitions than rectangular windows, which could be the result of the sharp transitions in the SNs. Overall, the SWC gave poor estimates of correlation for each brain state. Clustering based on the SWC time course did not reliably reflect the underlying state transitions unless the window length was comparable to the state duration, highlighting the need for new adaptive window analysis techniques. PMID:26952197

  16. Inward open characterization of EmrD transporter with molecular dynamics simulation.

    Science.gov (United States)

    Tan, Xianwei; Wang, Boxiong

    2016-06-10

    EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. PMID:27055595

  17. Thermal and dynamic mechanical characterization of thermoplastic polyurethane/organoclay nanocomposites prepared by melt compounding

    International Nuclear Information System (INIS)

    Thermoplastic polyurethane (TPU) nanocomposites based on organically modified layered silicate (OMLS) were prepared by melt intercalation process followed by compression molding. Different percentage of organoclays was incorporated into the TPU matrix in order to examine the influence of the nanoscaled fillers on nanostructure morphology and material properties. The microscopic morphology of the nanocomposites was evaluated by wide angle X-ray diffraction (WAXD), transmission electron microscopy (TEM), and atomic force microscopy (AFM). The observation revealed that both nanoclay-polymer interactions and shear stress developed during melt mixing are responsible for the effectively organoclay dispersion in TPU matrix resulting intercalated/exfoliated morphology. Thermal stability of the nanocomposites measured by thermogravimetric analysis (TGA) was improved significantly with the addition of nanoclay. The differential scanning calorimetry (DSC) analysis reveals that melting point of the nanocomposites increased with incorporation of nanoclay. The dynamic mechanical properties of the TPU nanocomposites were analyzed using a dynamic mechanical thermal analyzer (DMTA), which indicates that the storage modulus (E'), loss modulus (E''), and glass transition temperature (Tg) are significantly increased with increasing nanoclay content.

  18. Dynamic Mechanical Characterizations and Road Performances of Flame Retardant Asphalt Mortars and Concretes

    Institute of Scientific and Technical Information of China (English)

    QIN Xiantao; ZHU Siyue; LI Zuzhong; CHEN Shuanfa

    2015-01-01

    To research the dynamic mechanical properties and road performances of flame retardant asphalt mortars and mixtures, four different asphalt mortars/mixtures were prepared: a reference group and three asphalt mortars/mixtures containing composite lfame retardant materials (M-FRs) of different proportions. Temperature sweep, frequency sweep, repeated creep test, force ductility test and bending beam rheological test were carried out to research the dynamic mechanical properties of asphalt mortars containing M-FRs; wheel-tracking test, low-temperature bending test and freeze-thaw split test were used to study the road performances of asphalt mixtures containing M-FRs. The results show that high-temperature performances of the three lfame retardant asphalt mortars improve greatly, while low-temperature cracking resistances decline. Both high-temperature performances and water stabilities of asphalt mixtures containing M-FRs are quite good and exceed the speciifcation requirements. However, their low-temperature performances decline in different degrees. In summary, besides their good lfame retardancy, the lfame retardant asphalt mortars and mixtures also exhibit acceptable road performance.

  19. Spectroscopic detection, characterization and dynamics of free radicals relevant to combustion processes

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Terry [The Ohio State Univ., Columbus, OH (United States)

    2015-06-04

    Combustion chemistry is enormously complex. The chemical mechanisms involve a multitude of elementary reaction steps and a comparable number of reactive intermediates, many of which are free radicals. Computer simulations based upon these mechanisms are limited by the validity of the mechanisms and the parameters characterizing the properties of the intermediates and their reactivity. Spectroscopy can provide data for sensitive and selective diagnostics to follow their reactions. Spectroscopic analysis also provides detailed parameters characterizing the properties of these intermediates. These parameters serve as experimental gold standards to benchmark predictions of these properties from large-scale, electronic structure calculations. This work has demonstrated the unique capabilities of near-infrared cavity ringdown spectroscopy (NIR CRDS) to identify, characterize and monitor intermediates of key importance in complex chemical reactions. Our studies have focussed on the large family of organic peroxy radicals which are arguably themost important intermediates in combustion chemistry and many other reactions involving the oxidation of organic compounds. Our spectroscopic studies have shown that the NIR Ã - ˜X electronic spectra of the peroxy radicals allows one to differentiate among chemical species in the organic peroxy family and also determine their isomeric and conformic structure in many cases. We have clearly demonstrated this capability on saturated and unsaturated peroxy radicals and β-hydroxy peroxy radicals. In addition we have developed a unique dual wavelength CRDS apparatus specifically for the purpose of measuring absolute absorption cross section and following the reaction of chemical intermediates. The utility of the apparatus has been demonstrated by measuring the cross-section and self-reaction rate constant for ethyl peroxy.

  20. Integrating structural and functional connectivity to characterize sediment dynamics in a small Alpine catchment

    Science.gov (United States)

    Cavalli, Marco; Crema, Stefano; Blok, Michiel; Lucía, Ana; Comiti, Francesco; Marchi, Lorenzo; Keesstra, Saskia

    2016-04-01

    Sediment connectivity can be regarded as a descriptor of the internal linkages between different landscape components within a catchment. The recent focus of the scientific community on connectivity related topics, both concerning hydrological and sediment connectivity, stresses the importance of understanding the main active pathways for a better estimation of energy and matter transfer at catchment scale. This task can be addressed using topography-based indices that analyse the linkages between landscape units. This approach to characterize connectivity is known as structural connectivity. The main limitation of structural connectivity is that it does not account for the processes driving sediment and energy fluxes (i.e., functional connectivity). In this work the integration between structural and functional approaches is proposed for characterizing sediment connectivity in mountain catchments. The structural approach, based on a topography-based sediment connectivity index, was used for assessing hillslope-to-channel connectivity. Since field data on processes driving sediment transport along the channel network are available, a functional approach has been devised to estimate within-channel connectivity. An index of unit stream power computed from the hydraulic properties of the channel (i.e., discharge, slope and channel width) has been compared with the critical unit stream power computed from incipient motion thresholds derived from field data to identify the cells of the Digital Terrain Model (DTM) in which sediment can be mobilized under near-bankfull conditions. The index expressing the within-channel connectivity is given by the length of the reaches consisting of contiguous cells that exceed the critical unit stream power. During high-magnitude floods, when unit stream power values exceed the threshold for incipient motion, channels experience an increase in both hydrological and sediment connectivity. The proposed index characterizes those sections

  1. Characterizing the emissivity of materials under dynamic compression (final report for LDRD project 79877)

    International Nuclear Information System (INIS)

    Temperature measurements are crucial to equation of state development, but difficult to perform reliably. In the case of infrared pyrometry, a large uncertainty comes from the fact that sample emissivity (the deviation from a blackbody) is unknown. In this project, a method for characterizing the emissivity of shocked materials was developed. By coupling infrared radiation from the National Synchrotron Light Source to a gas gun system, broad spectrum emissivity changes were studied to a peak stress of 8 GPa. Emissivity measurements were performed on standard metals (Al, Cr, Cu, and Pt) as well as a high emissivity coating developed at Sandia

  2. Crystalline and liquid Si3 N4 characterization by first-principles molecular dynamics simulations

    OpenAIRE

    Castellani Niccoló; Celino Massimo; Mauri Aurelio; Erbetta Davide

    2011-01-01

    Silicon nitride (Si3 N4) has a wide range of engineering applications where its mechanical and electronic properties can be effectively exploited. In particular, in the microelectronics field, the amorphous silicon nitride films are widely used as charge storage layer in metal-alumina-nitrideoxide nonvolatile memory devices. Atomic structure of amorphous silicon nitride is characterized by an high concentration of traps that control the electric behavior of the final device by the trappingde-trap...

  3. Characterizing the emissivity of materials under dynamic compression (final report for LDRD project 79877).

    Energy Technology Data Exchange (ETDEWEB)

    Dolan, Daniel H.

    2007-10-01

    Temperature measurements are crucial to equation of state development, but difficult to perform reliably. In the case of infrared pyrometry, a large uncertainty comes from the fact that sample emissivity (the deviation from a blackbody) is unknown. In this project, a method for characterizing the emissivity of shocked materials was developed. By coupling infrared radiation from the National Synchrotron Light Source to a gas gun system, broad spectrum emissivity changes were studied to a peak stress of 8 GPa. Emissivity measurements were performed on standard metals (Al, Cr, Cu, and Pt) as well as a high emissivity coating developed at Sandia.

  4. Characterization and Dynamics of Aggresome Formation by a Cytosolic Gfp-Chimera✪

    OpenAIRE

    García-Mata, Rafael; Bebök, Zsuzsa; Sorscher, Eric J.; Sztul, Elizabeth S

    1999-01-01

    Formation of a novel structure, the aggresome, has been proposed to represent a general cellular response to the presence of misfolded proteins (Johnston, J.A., C.L. Ward, and R.R. Kopito. 1998. J. Cell Biol. 143:1883–1898; Wigley, W.C., R.P. Fabunmi, M.G. Lee, C.R. Marino, S. Muallem, G.N. DeMartino, and P.J. Thomas. 1999. J. Cell Biol. 145:481–490). To test the generality of this finding and characterize aspects of aggresome composition and its formation, we investigated the effects of over...

  5. Complete structural characterization of metallacyclic complexes in solution-phase using simultaneously X-ray diffraction and molecular dynamics simulation.

    Science.gov (United States)

    Megyes, Tünde; Bálint, Szabolcs; Bakó, Imre; Grósz, Tamás; Pálinkás, Gábor

    2008-07-23

    Wide-angle X-ray diffraction and molecular dynamics simulation has been used to perform complete structural characterization of nitromethane solution of a 16-membered gold(I) ring. The joint application of these two methods was an adequate tool to describe not only the structure of the complex but also the solvation properties of the complex in nitromethane and the effect of the solvation on the bulk structure. It has been found that a relatively diffuse slightly distorted solvation shell is formed around the complex, following the shape of the molecule. Nitromethane molecules in the solvation sphere are distributed randomly; no special orientation can be detected. The interaction energy of the complex with nitromethane molecules is attractive. In bulk, besides the antiparallel orientation of the nitromethane molecules, T-shape orientation and long-range order in antidipole orientation can also be detected. PMID:18576617

  6. Characterization of a Measurement System for Dynamic Effects in Large-Aperture SC Quadrupole Magnets

    CERN Document Server

    Buzio, M; Deferne, G; Dunkel, O; Fiscarelli, L; Russenschuck, S; Giloteaux, D; Walckiers, L

    2012-01-01

    A new measurement system, based on a large-diameter search-coil rotating in the superfluid helium, a fast digital integrator, a motor drive unit with slip rings, and a flexible software environment was developed at CERN for the measurement of dynamic effects in superconducting magnets. This system has made it possible the measure, with a resolution of up to 1 Hz, the multipole field errors due to superconductor magnetization and interstrand coupling currents. In this paper we present the development and calibration of the measurement system, its installation in the vertical cryostat of CERN’s recently refurbished test station, and its application to the US-LARP built, 120-mm aperture Nb3Sn quadrupole magnet (HQ01e) for the upgrade of the LHC insertion regions.

  7. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

    DEFF Research Database (Denmark)

    Nagarajan, Harish; Embree, Mallory; Rotaru, Amelia-Elena;

    2013-01-01

    complex nutritional and energetic dependencies and their functioning. Here we apply a multi-omic modelling workflow that combines genomic, transcriptomic and physiological data with genome-scale models to investigate dynamics and electron flow mechanisms in the syntrophic association of Geobacter......Syntrophic associations are central to microbial communities and thus have a fundamental role in the global carbon cycle. Despite biochemical approaches describing the physiological activity of these communities, there has been a lack of a mechanistic understanding of the relationship between...... metallireducens and Geobacter sulfurreducens. Genome-scale modelling of direct interspecies electron transfer reveals insights into the energetics of electron transfer mechanisms. While G. sulfurreducens adapts to rapid syntrophic growth by changes at the genomic and transcriptomic level, G. metallireducens...

  8. Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2

    Energy Technology Data Exchange (ETDEWEB)

    Gattin, Zrinka; Schneider, Robert; Laukat, Yvonne; Giller, Karin [Max Planck Institute for Biophysical Chemistry (Germany); Maier, Elke [Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Lehrstuhl für Biotechnologie (Germany); Zweckstetter, Markus; Griesinger, Christian [Max Planck Institute for Biophysical Chemistry (Germany); Benz, Roland [Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Lehrstuhl für Biotechnologie (Germany); Becker, Stefan; Lange, Adam, E-mail: alange@fmp-berlin.de [Max Planck Institute for Biophysical Chemistry (Germany)

    2015-04-15

    The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to study the structure of the human VDAC isoform 2 in a lipid bilayer environment. We find that the structure of hVDAC2 is similar to the structure of hVDAC1, in line with recent investigations on zfVDAC2. However, hVDAC2 appears to exhibit an increased conformational heterogeneity compared to hVDAC1 which is reflected in broader solid-state NMR spectra and less defined electrophysiological profiles.

  9. Characterizing and correcting for the dynamic response of a bag-in-box system.

    Science.gov (United States)

    Bates, J H; Prisk, G K; Tanner, T E; McKinnon, A E

    1984-01-01

    A bag-in-box system (BBS) whose volume is monitored by a mechanical spirometer tends to have a slow response if the volume of the box is large, and this may significantly affect its measurement of gas flow. We describe a device for creating reproducible gas flows with which the impulse response of a BBS may be conveniently determined. Two computational techniques for correcting a BBS flow measurement for the effects of the impulse response were investigated: 1) an exponential model method that assumes a second-order model of the BBS dynamics and 2) a Fourier transform-based method of deconvolution known as Wiener filtering. Both correction methods produced a significant increase in the accuracy of BBS flow estimations, with the Wiener filter giving superior results. PMID:6693330

  10. Characterization of volatiles from cultured dairy spreads during storage by dynamic headspace GC/MS

    DEFF Research Database (Denmark)

    Lund, Pia; Hølmer, Gunhild Kofoed

    2001-01-01

    The effect of storage time and storage temperature on the formation of volatile compounds in dairy spreads was investigated. Dairy spreads were stored for 10 weeks at -18, 5 and 20 degreesC, respectively, and analyzed after 0, 38, 54 and 67 days of storage. By means of a dynamic headspace GC....../MS method using Tenax traps the dairy spreads were analyzed for volatile aromatic compounds. 61 components were identified and their relative content was followed during the storage period. Among these were four alcohols, 17 aldehydes, four esters, ten alkanes, 11 ketones and six lactones. A general...... increase in the concentration of most of the volatile compounds during storage was found. The content of volatile compounds in dairy spreads stored at -18 OC was nearly constant or showed a rather low increase in the content during the storage period. Storage at higher temperatures (5 and 20 degrees...

  11. Dynamical and stabilometric measures are complementary for the characterization of postural fluctuations in older women.

    Science.gov (United States)

    Tallon, Guillaume; Blain, Hubert; Seigle, Benoît; Bernard, Pierre Louis; Ramdani, Sofiane

    2013-05-01

    We investigate the complementarities of several measures extracted from center of pressure (COP) recordings during quiet standing, in older women. The selected variables include classical stabilometric measures (SMs) and several dynamical measures (DMs). The computed DMs quantify various features of the temporal structure of COP signals, including predictability, regularity and smoothness of the trajectories. The postural fluctuations of a group of 101 healthy older women were recorded by means of a force platform. After estimating the SMs and DMs from the COP data, we used principal components analysis (PCA) to quantify the contribution of each measure. The results suggest that SMs and DMs are complementary. In addition, the different DMs are globally not redundant. This finding is a reinforcement argument in favor of the use of DMs as postural signatures. PMID:23206901

  12. Characterizing and modeling dynamic processes in the cochlea using otoacoustic emissions

    DEFF Research Database (Denmark)

    Verhulst, Sarah

    2010-01-01

    An important characteristic of human hearing is that it amplifies weak sounds while attenuating louder ones. This gain transformation takes place in the inner ear (i.e., cochlea), and is responsible for a compressive relation between the level of the presented and perceived sound. The cochlear gain...... mechanism is essential for our hearing and degrades when hearing impairment develops. A comprehensive understanding of the gain involved in the intact human cochlea is crucial, as hearing instruments try to compensate for the loss in cochlear gain caused by hearing damage. This thesis investigates dynamic...... such a time constant in cochlear compression may be of interest for the future development of signal processing in hearing instruments....

  13. Scaling law characterizing the dynamics of the transition of HIV-1 to error catastrophe

    Science.gov (United States)

    Gupta, Vipul; Dixit, Narendra M.

    2015-10-01

    Increasing the mutation rate, μ , of viruses above a threshold, {μ }c, has been predicted to trigger a catastrophic loss of viral genetic information and is being explored as a novel intervention strategy. Here, we examine the dynamics of this transition using stochastic simulations mimicking within-host HIV-1 evolution. We find a scaling law governing the characteristic time of the transition: τ ≈ 0.6/≤ft(μ -{μ }c\\right). The law is robust to variations in underlying evolutionary forces and presents guidelines for treatment of HIV-1 infection with mutagens. We estimate that many years of treatment would be required before HIV-1 can suffer an error catastrophe.

  14. CHARACTERIZING THE BROWN DWARF FORMATION CHANNELS FROM THE INITIAL MASS FUNCTION AND BINARY-STAR DYNAMICS

    International Nuclear Information System (INIS)

    The stellar initial mass function (IMF) is a key property of stellar populations. There is growing evidence that the classical star-formation mechanism by the direct cloud fragmentation process has difficulties reproducing the observed abundance and binary properties of brown dwarfs and very-low-mass stars. In particular, recent analytical derivations of the stellar IMF exhibit a deficit of brown dwarfs compared to observational data. Here we derive the residual mass function of brown dwarfs as an empirical measure of the brown dwarf deficiency in recent star-formation models with respect to observations and show that it is compatible with the substellar part of the Thies-Kroupa IMF and the mass function obtained by numerical simulations. We conclude that the existing models may be further improved by including a substellar correction term that accounts for additional formation channels like disk or filament fragmentation. The term ''peripheral fragmentation'' is introduced here for such additional formation channels. In addition, we present an updated analytical model of stellar and substellar binarity. The resulting binary fraction and the dynamically evolved companion mass-ratio distribution are in good agreement with observational data on stellar and very-low-mass binaries in the Galactic field, in clusters, and in dynamically unprocessed groups of stars if all stars form as binaries with stellar companions. Cautionary notes are given on the proper analysis of mass functions and the companion mass-ratio distribution and the interpretation of the results. The existence of accretion disks around young brown dwarfs does not imply that these form just like stars in direct fragmentation

  15. Discovery and dynamical characterization of the Amor-class asteroid 2012 XH16

    Science.gov (United States)

    Wlodarczyk, I.; Cernis, K.; Boyle, R. P.; Laugalys, V.

    2014-03-01

    The near-Earth asteroid belt is continuously replenished with material originally moving in Amor-class orbits. Here, the orbit of the dynamically interesting Amor-class asteroid 2012 XH16 is analysed. This asteroid was discovered with the Vatican Advanced Technology Telescope (VATT) at the Mt Graham International Observatory as part of an ongoing asteroid survey focused on astrometry and photometry. The orbit of the asteroid was computed using 66 observations (57 obtained with VATT and 9 from the Lunar and Planetary Laboratory-Spacewatch II project) to give a = 1.63 au, e = 0.36, i = 3.76°. The absolute magnitude of the asteroid is 22.3 which translates into a diameter in the range 104-231 m, assuming the average albedos of S-type and C-type asteroids, respectively. We have used the current orbit to study the future dynamical evolution of the asteroid under the perturbations of the planets and the Moon, relativistic effects, and the Yarkovsky force. Asteroid 2012 XH16 is locked close to the strong 1:2 mean motion resonance with the Earth. The object shows stable evolution and could survive in near-resonance for a relatively long period of time despite experiencing frequent close encounters with Mars. Moreover, results of our computations show that the asteroid 2012 XH16 can survive in the Amor region at most for about 200-400 Myr. The evolution is highly chaotic with a characteristic Lyapunov time of 245 yr. Jupiter is the main perturber but the effects of Saturn, Mars and the Earth-Moon system are also important. In particular, secular resonances with Saturn are significant.

  16. CHARACTERIZING THE BROWN DWARF FORMATION CHANNELS FROM THE INITIAL MASS FUNCTION AND BINARY-STAR DYNAMICS

    Energy Technology Data Exchange (ETDEWEB)

    Thies, Ingo; Pflamm-Altenburg, Jan; Kroupa, Pavel; Marks, Michael [Helmholtz-Institut für Strahlen- und Kernphysik (HISKP), Universität Bonn, Nussallee 14-16, D-53115 Bonn (Germany)

    2015-02-10

    The stellar initial mass function (IMF) is a key property of stellar populations. There is growing evidence that the classical star-formation mechanism by the direct cloud fragmentation process has difficulties reproducing the observed abundance and binary properties of brown dwarfs and very-low-mass stars. In particular, recent analytical derivations of the stellar IMF exhibit a deficit of brown dwarfs compared to observational data. Here we derive the residual mass function of brown dwarfs as an empirical measure of the brown dwarf deficiency in recent star-formation models with respect to observations and show that it is compatible with the substellar part of the Thies-Kroupa IMF and the mass function obtained by numerical simulations. We conclude that the existing models may be further improved by including a substellar correction term that accounts for additional formation channels like disk or filament fragmentation. The term ''peripheral fragmentation'' is introduced here for such additional formation channels. In addition, we present an updated analytical model of stellar and substellar binarity. The resulting binary fraction and the dynamically evolved companion mass-ratio distribution are in good agreement with observational data on stellar and very-low-mass binaries in the Galactic field, in clusters, and in dynamically unprocessed groups of stars if all stars form as binaries with stellar companions. Cautionary notes are given on the proper analysis of mass functions and the companion mass-ratio distribution and the interpretation of the results. The existence of accretion disks around young brown dwarfs does not imply that these form just like stars in direct fragmentation.

  17. Characterizing mercury concentrations and fluxes in a Coastal Plain watershed: Insights from dynamic modeling and data

    Science.gov (United States)

    Golden, H.E.; Knightes, C.D.; Conrads, P.A.; Davis, G.M.; Feaster, T.D.; Journey, C.A.; Benedict, S.T.; Brigham, M.E.; Bradley, P.M.

    2012-01-01

    Mercury (Hg) is one of the leading water quality concerns in surface waters of the United States. Although watershed-scale Hg cycling research has increased in the past two decades, advances in modeling watershed Hg processes in diverse physiographic regions, spatial scales, and land cover types are needed. The goal of this study was to assess Hg cycling in a Coastal Plain system using concentrations and fluxes estimated by multiple watershed-scale models with distinct mathematical frameworks reflecting different system dynamics. We simulated total mercury (Hg T, the sum of filtered and particulate forms) concentrations and fluxes from a Coastal Plain watershed (McTier Creek) using three watershed Hg models and an empirical load model. Model output was compared with observed in-stream Hg T. We found that shallow subsurface flow is a potentially important transport mechanism of particulate Hg T during periods when connectivity between the uplands and surface waters is maximized. Other processes (e.g., stream bank erosion, sediment re-suspension) may increase particulate Hg T in the water column. Simulations and data suggest that variable source area (VSA) flow and lack of rainfall interactions with surface soil horizons result in increased dissolved Hg T concentrations unrelated to DOC mobilization following precipitation events. Although flushing of DOC-Hg T complexes from surface soils can also occur during this period, DOC-complexed Hg T becomes more important during base flow conditions. TOPLOAD simulations highlight saturated subsurface flow as a primary driver of daily Hg T loadings, but shallow subsurface flow is important for Hg T loads during high-flow events. Results suggest limited seasonal trends in Hg T dynamics. Copyright 2012 by the American Geophysical Union.

  18. Characterizing Hot-Spot Dynamics of Direct-Drive Cryogenic Implosions on OMEGA

    Science.gov (United States)

    Anderson, K. S.; McKenty, P. W.; Shvydky, A.; Knauer, J. P.; Collins, T. J. B.; Delettrez, J. A.; Keller, D.; Marinak, M. M.

    2015-11-01

    In direct-drive inertial confinement fusion, nonuniformities in laser drive, capsule manufacture, and target positioning lead to non-radial hydrodynamic flow in the hot spot at stagnation. Characterizing such flow in the hot spot requires simulating the entire capsule in three dimensions to remove symmetry boundary conditions, which artificially constrain hot-spot flow. This paper will present results from 3-D simulations of cryogenic implosions on OMEGA using HYDRA. Low-mode asymmetries and their contributions to residual hot-spot kinetic energy will be discussed. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944 and performed under the auspices of LLNL under Contract No. DE-AC52-07NA27344.

  19. Dynamics and morphometric characterization of hippocampus neurons using digital holographic microscopy

    Science.gov (United States)

    Elkatlawy, Saeid; Gomariz, María.; Soto-Sánchez, Cristina; Martínez Navarrete, Gema; Fernández, Eduardo; Fimia, Antonio

    2014-05-01

    In this paper we report on the use of digital holographic microscopy for 3D real time imaging of cultured neurons and neural networks, in vitro. Digital holographic microscopy is employed as an assessment tool to study the biophysical origin of neurodegenerative diseases. Our study consists in the morphological characterization of the axon, dendrites and cell bodies. The average size and thickness of the soma were 21 and 13 μm, respectively. Furthermore, the average size and diameter of some randomly selected neurites were 4.8 and 0.89 μm, respectively. In addition, the spatiotemporal growth process of cellular bodies and extensions was fitted to by a non-linear behavior of the nerve system. Remarkably, this non-linear process represents the relationship between the growth process of cellular body with respect to the axon and dendrites of the neurons.

  20. Static and dynamic characterization of robust superhydrophobic surfaces built from nano-flowers on silicon micro-post arrays

    KAUST Repository

    Chen, Longquan

    2010-09-01

    Superhydrophobic nano-flower surfaces were fabricated using MEMS technology and microwave plasma-enhanced chemical vapor deposition (MPCVD) of carbon nanotubes on silicon micro-post array surfaces. The nano-flower structures can be readily formed within 1-2 min on the micro-post arrays with the spacing ranging from 25 to 30 μm. The petals of the nano-flowers consisted of clusters of multi-wall carbon nanotubes. Patterned nano-flower structures were characterized using various microscopy techniques. After MPCVD, the apparent contact angle (160 ± 0.2°), abbreviated as ACA (defined as the measured angle between the apparent solid surface and the tangent to the liquid-fluid interface), of the nano-flower surfaces increased by 139% compared with that of the silicon micro-post arrays. The measured ACA of the nano-flower surface is consistent with the predicted ACA from a modified Cassie-Baxter equation. A high-speed CCD camera was used to study droplet impact dynamics on various micro/nanostructured surfaces. Both static testing (ACA and sliding angle) and droplet impact dynamics demonstrated that, among seven different micro/nanostructured surfaces, the nano-flower surfaces are the most robust superhydrophobic surfaces. © 2010 IOP Publishing Ltd.

  1. Usability of ECT for quantitative and qualitative characterization of trickle-bed flow dynamics experiencing filtration conditions

    Energy Technology Data Exchange (ETDEWEB)

    Tibirna, C.; Fortin, A. [Laval Univ., Quebec City, PQ (Canada). GIREF; Edouard, D.; Larachi, F. [Laval Univ., Quebec City, PQ (Canada). Dept. of Chemical Engineering

    2006-07-01

    The feasibility of using electrical capacitance tomography (ECT) as an imaging method for trickle-bed reaction processes was examined in this study. In particular, the advantages and disadvantages of using ECT to characterize the flow dynamics in a four-phase trickle bed reactor were investigated. This work was part of a larger study to extend the service life of catalyst beds used during the hydrotreatment of some oil fractions, such as Athabasca bitumen. A better understanding of the flow dynamics and clogging physics in trickle-bed reactors is needed in order to prevent clogging in the catalyst bed. This study focused on several aspects of the ECT as a non-intrusive imaging method for such processes. This paper described the experimental setup in detail. The ECT equipment allowed for up to 100 tomograms per second to be recorded. The clogging experiments lasted about 30 hours from a completely clean catalyst bed to a stable, non-filtering clogging state. A series of algorithms for ECT image reconstruction were presented. Truncated and filtered single value decomposition (SVD) and Landweber methods were found to be the most appropriate. ECT was shown to be faster and less expensive than nuclear ionizing, non-ionizing and other tomography methods. However, the main advantage of ECT was its non-intrusive attributes. It was also suggested that the complex technologies involved in ECT still require further refinement and better calibration methods. 9 refs., 5 figs.

  2. PlanetPack: a radial-velocity time-series analysis tool facilitating exoplanets detection, characterization, and dynamical simulations

    CERN Document Server

    Baluev, Roman V

    2013-01-01

    We present PlanetPack, a new software tool that we developed to facilitate and standardize the advanced analysis of radial velocity (RV) data for the goal of exoplanets detection, characterization, and basic dynamical $N$-body simulations. PlanetPack is a command-line interpreter, that can run either in an interactive mode or in a batch mode of automatic script interpretation. Its major abilities include: (i) Advanced RV curve fitting with the proper maximum-likelihood treatment of unknown RV jitter; (ii) User-friendly multi-Keplerian as well as Newtonian $N$-body RV fits; (iii) Use of more efficient maximum-likelihood periodograms that involve the full multi-planet fitting (sometimes called as ``residual'' or ``recursive'' periodograms); (iv) Easily calculatable parametric 2D likelihood function level contours, reflecting the asymptotic confidence regions; (v) Fitting under some useful functional constraints is user-friendly; (vi) Basic tasks of short- and long-term planetary dynamical simulation using a fas...

  3. Static and dynamic characterization of robust superhydrophobic surfaces built from nano-flowers on silicon micro-post arrays

    International Nuclear Information System (INIS)

    Superhydrophobic nano-flower surfaces were fabricated using MEMS technology and microwave plasma-enhanced chemical vapor deposition (MPCVD) of carbon nanotubes on silicon micro-post array surfaces. The nano-flower structures can be readily formed within 1–2 min on the micro-post arrays with the spacing ranging from 25 to 30 µm. The petals of the nano-flowers consisted of clusters of multi-wall carbon nanotubes. Patterned nano-flower structures were characterized using various microscopy techniques. After MPCVD, the apparent contact angle (160 ± 0.2°), abbreviated as ACA (defined as the measured angle between the apparent solid surface and the tangent to the liquid–fluid interface), of the nano-flower surfaces increased by 139% compared with that of the silicon micro-post arrays. The measured ACA of the nano-flower surface is consistent with the predicted ACA from a modified Cassie–Baxter equation. A high-speed CCD camera was used to study droplet impact dynamics on various micro/nanostructured surfaces. Both static testing (ACA and sliding angle) and droplet impact dynamics demonstrated that, among seven different micro/nanostructured surfaces, the nano-flower surfaces are the most robust superhydrophobic surfaces

  4. Elastic line deformed on a surface by an external field: Intrinsic formulation and preliminary application to nucleosome energetics

    International Nuclear Information System (INIS)

    If an elastically resilient thin rod (elastic line) is subjected to a static force field, it adopts a trajectory that minimizes the sum of its elastic energy and its energy of interaction with the field. Using ''intrinsic'' methods of differential geometry and variational calculus, we formulate and solve this problem for an elastic line confined to a general surface. The biological structure known as the nucleosome core particle provides motivation to apply the solution to an elastic line (DNA) subject to a centrosymmetric force emanating from a circle. In this case the surface is a plane (although the surface will be curved in a more accurate model). In preliminary numerical work we are able to represent the angular deviation of the elastic line to fifth order in powers of arc length. The result of greatest interest may be that the equilibrium trajectory appears not to approach the circle progressively with increasing strength of the attraction between line and circle. Instead, the line approaches a ''barrier'' trajectory and, as it does, becomes unstable relative to the circular arc

  5. The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules.

    Science.gov (United States)

    Zhang, W; Aubert, A; Gomez de Segura, J M; Karuppasamy, M; Basu, S; Murthy, A S; Diamante, A; Drury, T A; Balmer, J; Cramard, J; Watson, A A; Lando, D; Lee, S F; Palayret, M; Kloet, S L; Smits, A H; Deery, M J; Vermeulen, M; Hendrich, B; Klenerman, D; Schaffitzel, C; Berger, I; Laue, E D

    2016-07-17

    The nucleosome remodeling deacetylase (NuRD) complex is a highly conserved regulator of chromatin structure and transcription. Structural studies have shed light on this and other chromatin modifying machines, but much less is known about how they assemble and whether stable and functional sub-modules exist that retain enzymatic activity. Purification of the endogenous Drosophila NuRD complex shows that it consists of a stable core of subunits, while others, in particular the chromatin remodeler CHD4, associate transiently. To dissect the assembly and activity of NuRD, we systematically produced all possible combinations of different components using the MultiBac system, and determined their activity and biophysical properties. We carried out single-molecule imaging of CHD4 in live mouse embryonic stem cells, in the presence and absence of one of core components (MBD3), to show how the core deacetylase and chromatin-remodeling sub-modules associate in vivo. Our experiments suggest a pathway for the assembly of NuRD via preformed and active sub-modules. These retain enzymatic activity and are present in both the nucleus and the cytosol, an outcome with important implications for understanding NuRD function. PMID:27117189

  6. Silver Nanoscale Hexagonal Column Chips for Detecting Cell-free DNA and Circulating Nucleosomes in Cancer Patients

    Science.gov (United States)

    Ito, Hiroaki; Hasegawa, Katsuyuki; Hasegawa, Yuuki; Nishimaki, Tadashi; Hosomichi, Kazuyoshi; Kimura, Satoshi; Ohba, Motoi; Yao, Hiroshi; Onimaru, Manabu; Inoue, Ituro; Inoue, Haruhiro

    2015-01-01

    Blood tests, which are commonly used for cancer screening, generally have low sensitivity. Here, we developed a novel rapid and simple method to generate silver nanoscale hexagonal columns (NHCs) for use in surface-enhanced Raman scattering (SERS). We reported that the intensity of SERS spectra of clinical serum samples obtained from gastrointestinal cancer patients is was significantly higher than that of SERS spectra of clinical serum samples obtained from non-cancer patients. We estimated the combined constituents on silver NHCs by using a field emission-type scanning electron microscope, Raman microscopes, and a 3D laser scanning confocal microscope. We obtained the Raman scattering spectra of samples of physically fractured cells and clinical serum. No spectra were obtained for chemically lysed cultured cells and DNA, RNA, and protein extracted from cultured cells. We believe that our method, which uses SERS with silver NHCs to detect circulating nucleosomes bound by methylated cell-free DNA, may be successfully implemented in blood tests for cancer screening. PMID:25994878

  7. PGC1α -1 Nucleosome Position and Splice Variant Expression and Cardiovascular Disease Risk in Overweight and Obese Individuals.

    Science.gov (United States)

    Henagan, Tara M; Stewart, Laura K; Forney, Laura A; Sparks, Lauren M; Johannsen, Neil; Church, Timothy S

    2014-01-01

    PGC1α, a transcriptional coactivator, interacts with PPARs and others to regulate skeletal muscle metabolism. PGC1α undergoes splicing to produce several mRNA variants, with the NTPGC1α variant having a similar biological function to the full length PGC1α (FLPGC1α). CVD is associated with obesity and T2D and a lower percentage of type 1 oxidative fibers and impaired mitochondrial function in skeletal muscle, characteristics determined by PGC1α expression. PGC1α expression is epigenetically regulated in skeletal muscle to determine mitochondrial adaptations, and epigenetic modifications may regulate mRNA splicing. We report in this paper that skeletal muscle PGC1α  -1 nucleosome (-1N) position is associated with splice variant NTPGC1α but not FLPGC1α expression. Division of participants based on the -1N position revealed that those individuals with a -1N phased further upstream from the transcriptional start site (UP) expressed lower levels of NTPGC1α than those with the -1N more proximal to TSS (DN). UP showed an increase in body fat percentage and serum total and LDL cholesterol. These findings suggest that the -1N may be a potential epigenetic regulator of NTPGC1α splice variant expression, and -1N position and NTPGC1α variant expression in skeletal muscle are linked to CVD risk. This trial is registered with clinicaltrials.gov, identifier NCT00458133. PMID:25614734

  8. PGC1α −1 Nucleosome Position and Splice Variant Expression and Cardiovascular Disease Risk in Overweight and Obese Individuals

    Directory of Open Access Journals (Sweden)

    Tara M. Henagan

    2014-01-01

    Full Text Available PGC1α, a transcriptional coactivator, interacts with PPARs and others to regulate skeletal muscle metabolism. PGC1α undergoes splicing to produce several mRNA variants, with the NTPGC1α variant having a similar biological function to the full length PGC1α (FLPGC1α. CVD is associated with obesity and T2D and a lower percentage of type 1 oxidative fibers and impaired mitochondrial function in skeletal muscle, characteristics determined by PGC1α expression. PGC1α expression is epigenetically regulated in skeletal muscle to determine mitochondrial adaptations, and epigenetic modifications may regulate mRNA splicing. We report in this paper that skeletal muscle PGC1α  −1 nucleosome (−1N position is associated with splice variant NTPGC1α but not FLPGC1α expression. Division of participants based on the −1N position revealed that those individuals with a −1N phased further upstream from the transcriptional start site (UP expressed lower levels of NTPGC1α than those with the −1N more proximal to TSS (DN. UP showed an increase in body fat percentage and serum total and LDL cholesterol. These findings suggest that the −1N may be a potential epigenetic regulator of NTPGC1α splice variant expression, and −1N position and NTPGC1α variant expression in skeletal muscle are linked to CVD risk. This trial is registered with clinicaltrials.gov, identifier NCT00458133.

  9. On the characterization of inhomogeneity of the density distribution in supercritical fluids via molecular dynamics simulation and data mining analysis.

    Science.gov (United States)

    Idrissi, Abdenacer; Vyalov, Ivan; Georgi, Nikolaj; Kiselev, Michael

    2013-10-10

    We combined molecular dynamics simulation and DBSCAN algorithm (Density Based Spatial Clustering of Application with Noise) in order to characterize the local density inhomogeneity distribution in supercritical fluids. The DBSCAN is an algorithm that is capable of finding arbitrarily shaped density domains, where domains are defined as dense regions separated by low-density regions. The inhomogeneity of density domain distributions of Ar system in sub- and supercritical conditions along the 50 bar isobar is associated with the occurrence of a maximum in the fluctuation of number of particles of the density domains. This maximum coincides with the temperature, Tα, at which the thermal expansion occurs. Furthermore, using Voronoi polyhedral analysis, we characterized the structure of the density domains. The results show that with increasing temperature below Tα, the increase of the inhomogeneity is mainly associated with the density fluctuation of the border particles of the density domains, while with increasing temperature above Tα, the decrease of the inhomogeneity is associated with the core particles. PMID:24015951

  10. Characterization of energy use in 300 mm DRAM (Dynamic Random Access Memory) wafer fabrication plants (fabs) in Taiwan

    International Nuclear Information System (INIS)

    Driven by technology advances and demand for enhanced productivity, migration of wafer fabrication for DRAM (Dynamic Random Access Memory) toward increased wafer size has become the fast-growing trend in semiconductor industry. Taiwan accounts for about 18% of the total DRAM wafer production in the world. The energy use required for operating wafer fabrication plants (fabs) is intensive and has become one of the major concerns to production power reliability in the island. This paper characterizes the energy use in four 300 mm DRAM wafer fabs in Taiwan through performing surveys and on-site measurements. Specifically, the objectives of this study are to characterize the electric energy consumption and production of 300 mm DRAM fabs by using various performance metrics, including PEI ((production efficiency index), annual electric power consumption normalized by annual produced wafer area) and EUI ((electrical utilization index), annual electric power consumption normalized by UOP (units of production), which is defined as the product of annual produced wafer area and the average number of mask layers of a wafer). The results show that the PEI and EUI values are 0.743 kWh/cm2 and 0.0272 kWh/UOP, respectively. Using EUI in assessing energy efficiency of the fab production provides more consistent comparisons than using PEI alone.

  11. Hemodynamic and metabolic characterization of orthotopic rat prostate carcinomas using dynamic MRI and proton magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    The aim of this study was the noninvasive characterization of prostate carcinoma orthotopically implanted in rats using Gd-DTPA-assisted dynamic MRI (dMRI) and proton magnetic resonance spectroscopy (1H-MRS). After surgical exposure of the prostate, Dunning R3327 orthotopic prostate carcinoma was induced by injecting cells of the MAT-LyLu subline. Six rats were examined 5 and 14 days after tumor induction with dMRI and 1H-MRS at 1.5 T. Six tumor-free rats served as controls. Using an open two-compartment model, the parameters A (amplitude) and kep (exchange rate constants) were calculated from the signal time curves of the dMRI. The relative signal intensities (Cho/Cr) of the resonances of choline (Cho) and the creatine-phosphocreatine complex (Cr) were computed from the MR spectra. Already after 5 days, the tumors in the prostate could be clearly identified based on the decrease in signal intensity to T2w and increase of A and kep. High Cho/Cr levels and resonances of two lipid fractions (Lip1 at 0.8-1.5 ppm and Lip2 at 2.0-2.2 ppm) were observed by MRS in the highly necrotic tumors. The orthotopic rat prostate carcinoma model resembles human prostate carcinoma in regard to MR morphology, dMRI, and 1H-MRS. The noninvasive characterization of perfusion and metabolism makes a comparative examination of different treatment modalities possible. (orig.)

  12. Indium–tin nanoscaled oxides synthesized under hydrothermal supercritical and postannealing pathway: Phase dynamics and characterization

    International Nuclear Information System (INIS)

    With the aim of synthesizing the mixed nanoparticle system xIn2O3–(1−x)SnO2 over all molar concentration range 0 ≤ x ≤ 1, Δx = 0.1, we performed hydrothermal supercritical experiments on indium–tin hydrogel resulted from InCl3–SnCl4 water solution. Nanophases isostructural with InOOH and SnO2 were obtained by hydrothermal reaction at 400 °C, in the molar concentration range of 0.1 ≤ x ≤ 0.7; at x = 0.8 and x = 0.9 only one phase, isostructural with InOOH, was observed. Samples calcined at 500 °C with x in the range of 0.2 ≤ x ≤ 0.7 contain a nanoscaled phase isostructural with rhombohedral In2O3 and a second one isostructural with tetrahedral SnO2. At x = 0.8 and x = 0.9 only one phase isostructural with rhombohedral In2O3 appears: rhombohedral ITO phase. The determined band gap energies could recommend the rhombohedral ITO structure for visible light photocatalytic applications. The phase dynamics together with the concentration range for existence of the solid solutions in the InOOH–SnO2 and In2O3–SnO2 composite semiconducting nanoparticle systems have been evidenced and discussed. - Highlights: • Phase dynamics study on SnCl4–InCl3 water solution under hydrothermal conditions. • InOOH–SnO2, In2O3–SnO2 nanopowders obtained by hydrothermal and postannealing route. • In the presence of Sn4+ ions, InOOH phase goes into rhombohedral In2O3 at 500 °C. • ITO like phases based on rhombohedral In2O3 have been obtained. • Solubility limits in the InOOH–SnO2 and In2O3–SnO2 nanoparticles systems evidenced

  13. Indium–tin nanoscaled oxides synthesized under hydrothermal supercritical and postannealing pathway: Phase dynamics and characterization

    Energy Technology Data Exchange (ETDEWEB)

    Diamandescu, L., E-mail: diamand@infim.ro [National Institute of Materials Physics, Atomistilor 105 Bis, P.O. Box MG-7, Bucharest-Magurele 77125 (Romania); Tarabasanu-Mihaila, D.; Feder, M.; Enculescu, M.; Teodorescu, V.S.; Constantinescu, S.; Popescu, T.; Bartha, C. [National Institute of Materials Physics, Atomistilor 105 Bis, P.O. Box MG-7, Bucharest-Magurele 77125 (Romania); Pap, Zs. [Institute of Material Science and Engineering, University of Szeged, Szeged H-6701, P.O. Box 440 (Hungary)

    2014-02-14

    With the aim of synthesizing the mixed nanoparticle system xIn{sub 2}O{sub 3}–(1−x)SnO{sub 2} over all molar concentration range 0 ≤ x ≤ 1, Δx = 0.1, we performed hydrothermal supercritical experiments on indium–tin hydrogel resulted from InCl{sub 3}–SnCl{sub 4} water solution. Nanophases isostructural with InOOH and SnO{sub 2} were obtained by hydrothermal reaction at 400 °C, in the molar concentration range of 0.1 ≤ x ≤ 0.7; at x = 0.8 and x = 0.9 only one phase, isostructural with InOOH, was observed. Samples calcined at 500 °C with x in the range of 0.2 ≤ x ≤ 0.7 contain a nanoscaled phase isostructural with rhombohedral In{sub 2}O{sub 3} and a second one isostructural with tetrahedral SnO{sub 2}. At x = 0.8 and x = 0.9 only one phase isostructural with rhombohedral In{sub 2}O{sub 3} appears: rhombohedral ITO phase. The determined band gap energies could recommend the rhombohedral ITO structure for visible light photocatalytic applications. The phase dynamics together with the concentration range for existence of the solid solutions in the InOOH–SnO{sub 2} and In{sub 2}O{sub 3}–SnO{sub 2} composite semiconducting nanoparticle systems have been evidenced and discussed. - Highlights: • Phase dynamics study on SnCl{sub 4}–InCl{sub 3} water solution under hydrothermal conditions. • InOOH–SnO{sub 2}, In{sub 2}O{sub 3}–SnO{sub 2} nanopowders obtained by hydrothermal and postannealing route. • In the presence of Sn{sup 4+} ions, InOOH phase goes into rhombohedral In{sub 2}O{sub 3} at 500 °C. • ITO like phases based on rhombohedral In{sub 2}O{sub 3} have been obtained. • Solubility limits in the InOOH–SnO{sub 2} and In{sub 2}O{sub 3}–SnO{sub 2} nanoparticles systems evidenced.

  14. High-Data-Rate Quadrax Cable Microwave Characterization at the NASA Glenn Structural Dynamics Laboratory

    Science.gov (United States)

    Theofylaktos, Onoufrios; Warner, Joseph D.; Sheehe, Charles J.

    2012-01-01

    An experiment was performed to determine the degradation in the bit-error-rate (BER) in the high-data-rate cables chosen for the Orion Service Module due to extreme launch conditions of vibrations with a magnitude of 60g. The cable type chosen for the Orion Service Module was no. 8 quadrax cable. The increase in electrical noise induced on these no. 8 quadrax cables was measured at the NASA Glenn vibration facility in the Structural Dynamics Laboratory. The intensity of the vibrations was set at 32g, which was the maximum available level at the facility. The cable lengths used during measurements were 1, 4, and 8 m. The noise measurements were done in an analog fashion using a performance network analyzer (PNA) by recording the standard deviation of the transmission scattering parameter S(sub 21) over the frequency range of 100 to 900 MHz. The standard deviation of S(sub 210 was measured before, during, and after the vibration of the cables at the vibration facility. We observed an increase in noise by a factor of 2 to 6. From these measurements we estimated the increase expected in the BER for a cable length of 25 m and concluded that these findings are large enough that the noise increase due to vibration must be taken in to account for the design of the communication system for a BER of 10(exp -8).

  15. System dynamics model for hospital waste characterization and generation in developing countries.

    Science.gov (United States)

    Eleyan, Derar; Al-Khatib, Issam A; Garfield, Joy

    2013-10-01

    Waste management policy makers always face the problem of how to predict the future amount and composition of medical solid waste, which, in turn, helps to determine the most appropriate treatment, recycling and disposal strategy. An accurate prediction can assist in both the planning and design of medical solid waste management systems. Insufficient budget and unavailable management capacity are the main reasons for the scarcity of medical solid waste quantities and components historical records, which are so important in long-term system planning and short-term expansion programs. This article presents a new technique, using System Dynamics modeling, to predict generated medical solid waste in a developing urban area, based on a set of limited samples from Jenin District hospitals, Palestine. The findings of the model present the trend of medical solid waste generation together with its different components and indicate that a new forecasting approach may cover a variety of possible causative models and track inevitable uncertainties when traditional statistical least-squared regression methods are unable to handle such issues. PMID:23743573

  16. Characterization and Dynamics of Agrarian Structures in Bouna, Northeast of Côte d'Ivoire

    Directory of Open Access Journals (Sweden)

    Yao-Kouame Albert

    2013-06-01

    Full Text Available In order to better reproduction of the information that is as close as possible to reality, we have established a procedure for analyzing images based on visual interpretation and digital processing. In digital processing, supervised classification by maximum likelihood, based on a fieldwork allowed to discriminate elements of land. Recovery of geometric shapes by scanning fallow and bare soil from panchromatic Spot image yielded the map of agrarian structures. Different queries and statistical operations performed were used to assess the areas of agrarian structures. The analysis of the dynamics of agrarian structures showed that the period 1986 - 2000 was marked by environmental degradation, while the period 2000 - 2004 has seen a regeneration of the natural environment. Treatments applied to images and ensuing results indicate the feasibility of monitoring by remote sensing of agricultural structures in northeastern area of Côte d'Ivoire. This research shows that the Geographic Information System is an effective tool for the evaluation of agrarian structures. However, manual scanning of elements in the environment requires careful attention to avoid skewing the results.

  17. Characterization of expression dynamics of WOX homeodomain transcription factors during somatic embryogenesis in Vitis vinifera.

    Science.gov (United States)

    Gambino, Giorgio; Minuto, Martina; Boccacci, Paolo; Perrone, Irene; Vallania, Rosalina; Gribaudo, Ivana

    2011-01-01

    Different cultivars of Vitis vinifera vary in their potential to form embryogenic tissues. The WUSCHEL (WUS)-related homeobox (WOX) genes have been shown to play an important role in coordinating the gene transcription involved in the early phases of embryogenesis. The expression dynamics of 12 VvWOX genes present in the V. vinifera genome in embryogenic and other tissues of 'Chardonnay' were analysed. In order to understand the influence of WOX genes on the somatic embryogenic process, their expression profiles were compared in two cultivars of V. vinifera ('Chardonnay' and 'Cabernet Sauvignon') that show different aptitudes for embryogenesis. The expression of all VvWOX genes was influenced by culture conditions. VvWOX2 and VvWOX9 were the principal WOX genes expressed during the somatic embryogenesis process, and the low aptitude for embryogenesis of 'Cabernet Sauvignon' was generally correlated with the low expression levels of these VvWOX genes. VvWOX3 and VvWOX11 were strongly activated in correspondence to torpedo and cotyledonary stages of somatic embryos, with low expression in the earlier developmental stages (pre-embryogenic masses and globular embryos) and during embryo germination. VvWOX genes appeared to be key regulators of somatic embryogenesis in grapevine, and the regulation of these genes during early phases of somatic embryogenesis differed between the two cultivars of the same species. PMID:21127025

  18. Characterization of moisture-protective polymer coatings using differential scanning calorimetry and dynamic vapor sorption.

    Science.gov (United States)

    Bley, O; Siepmann, J; Bodmeier, R

    2009-02-01

    The aim of this study was to evaluate the moisture-protective ability of different polymeric coatings. Free films and film-coated tablets (with cores containing freeze-dried garlic powder) were prepared using aqueous solutions/dispersions of hydroxypropyl methylcellulose (HPMC), Opadry AMB [a poly(vinylalcohol)-based formulation] and Eudragit E PO [a poly(methacrylate-methylmethacrylate)]. The water content of the systems upon open storage at 75% relative humidity (RH) and 22 degrees C (room temperature) was followed gravimetrically. Furthermore, polymer powders, free films and coated tablets were analyzed by differential scanning calorimetry (DSC) and dynamic vapor sorption (DVS). The type of polymer strongly affected the resulting water uptake kinetics of the free films and coated tablets. DSC analysis revealed whether or not significant physical changes occurred in the coatings during storage, and whether the water vapor permeability was water concentration dependent. Using DVS analysis the critical glass transition RH of Opadry AMB powder and Opadry AMB-coated tablets at 25 degrees C could be determined: 44.0% and 72.9% RH. Storage below these threshold values significantly reduces water penetration. Thus, DVS and DSC measurements can provide valuable information on the nature of polymers used for moisture protection. PMID:18481311

  19. Characterizing magnetopause shadowing effects on the radiation belt's dynamic: modelling and comparison to observations.

    Science.gov (United States)

    Maget, Vincent; Bourdarie, Sebastien; Boscher, Daniel

    2014-05-01

    The dynamic of the Earth's electron radiation belts are mainly governed by internal processes enhanced during period of electromagnetic disturbances. In the framework of the EU-FP7 SPACECAST project, the modelling of many of them has been improved and implemented into the ONERA Salammbô code (radial diffusion, wave-particle interactions, and boundary conditions). Furthermore, the modelling of drop-outs has also been investigated. Such a global magnetospheric process can drastically modify the shape of the outer radiation belts during magnetic storms. In the present talk, we aim at showing how magnetopause shadowing primarily contributes to drop-outs of > 300 keV electrons in the outer radiation belt. In particular, the impact of the combination of all the improvements conducted during the SPACECAST project are highlighted and compared to recent data. SPACECAST has received fundings from the European Community's Seventh Framework Programme (FP7-SPACE-.2010-1, SP1 Cooperation, Collaborative project) under grant agreement n262468. This paper reflects only the authors' views and the European Union is not liable for any use that may be made of the information contained therein.

  20. Characterization of Terrestrial Water Dynamics in the Congo Basin Using GRACE and Satellite Radar Altimetry

    Science.gov (United States)

    Lee, Hyongki; Beighley, R. Edward; Alsdorf, Douglas; Jung, Hahn Chul; Shum, C. K.; Duan, Jianbin; Guo, Junyi; Yamazaki, Dai; Andreadis, Konstantinos

    2011-01-01

    The Congo Basin is the world's third largest in size (approx.3.7 million sq km), and second only to the Amazon River in discharge (approx.40,200 cu m/s annual average). However, the hydrological dynamics of seasonally flooded wetlands and floodplains remains poorly quantified. Here, we separate the Congo wetland into four 3deg 3deg regions, and use remote sensing measurements (i.e., GRACE, satellite radar altimeter, GPCP, JERS-1, SRTM, and MODIS) to estimate the amounts of water filling and draining from the Congo wetland, and to determine the source of the water. We find that the amount of water annually filling and draining the Congo wetlands is 111 cu km, which is about one-third the size of the water volumes found on the mainstem Amazon floodplain. Based on amplitude comparisons among the water volume changes and timing comparisons among their fluxes, we conclude that the local upland runoff is the main source of the Congo wetland water, not the fluvial process of river-floodplain water exchange as in the Amazon. Our hydraulic analysis using altimeter measurements also supports our conclusion by demonstrating that water surface elevations in the wetlands are consistently higher than the adjacent river water levels. Our research highlights differences in the hydrology and hydrodynamics between the Congo wetland and the mainstem Amazon floodplain.

  1. Molecular dynamics characterization of five pathogenic factor X mutants associated with decreased catalytic activity

    KAUST Repository

    Abdel-Azeim, Safwat

    2014-11-11

    Factor X (FX) is one of the major players in the blood coagulation cascade. Upon activation to FXa, it converts prothrombin to thrombin, which in turn converts fibrinogen into fibrin (blood clots). FXa deficiency causes hemostasis defects, such as intracranial bleeding, hemathrosis, and gastrointestinal blood loss. Herein, we have analyzed a pool of pathogenic mutations, located in the FXa catalytic domain and directly associated with defects in enzyme catalytic activity. Using chymotrypsinogen numbering, they correspond to D102N, T135M, V160A, G184S, and G197D. Molecular dynamics simulations were performed for 1.68 μs on the wild-type and mutated forms of FXa. Overall, our analysis shows that four of the five mutants considered, D102N, T135M, V160A, and G184S, have rigidities higher than those of the wild type, in terms of both overall protein motion and, specifically, subpocket S4 flexibility, while S1 is rather insensitive to the mutation. This acquired rigidity can clearly impact the substrate recognition of the mutants.

  2. Characterizing soil water dynamics on steep hillslopes from long-term lysimeter data

    Science.gov (United States)

    Augenstein, Michael; Goeppert, Nadine; Goldscheider, Nico

    2015-10-01

    Understanding soil water dynamics on hillslopes is of crucial importance to the prediction of floods and other hydrological events in mountainous catchments, to the identification of natural vegetation patterns, and to the optimization of agricultural land use. In principle, such information can be obtained from lysimeters, but most experimental lysimeter facilities have been installed on flat terrain. This study presents a long-term and high-resolution investigation of soil moisture, surface and subsurface flow using three large-scale lysimeters on a slope with 23.5° inclination on a landfill site in Karlsruhe, Germany. Data from a 10-year observation period were evaluated for this study, including weekly soil moisture data obtained by neutron probes, continuous discharge data from the land surface and several layers within the soil zone, and hydrometeorological data from a climate station. The results reveal (i) clear temporal and spatial patterns of soil moisture variations down to a depth of 250 cm, (ii) substantially higher discharge and faster percolation rates in the lower part of the lysimeter field, indicating significant downhill flow at various depths within the soil profile, (iii) characteristic threshold values for flow processes in the soil, associated with a hysteresis effect between soil moisture and flow processes. These results can be used as a basis of improved numerical models for the simulation of floods, soil moisture distributions, and vegetation patterns.

  3. Characterization of Terrestrial Water Dynamics in the Congo Basin Using GRACE and Satellite Radar Altimetry

    Science.gov (United States)

    Lee, Lyongki; Beighley, R. Edward; Alsdorf, Douglas; Jung, Hahn Chul; Shum, C. K.; Duan, Jianbin; Guo, Junyi; Yamazaki, Dai; Andreadis, Konstantinos

    2011-01-01

    The Congo Basin is the world's third largest in size (approximately 3.7 million km^2), and second only to the Amazon River in discharge (approximately 40,200 cms annual average). However, the hydrological dynamics of seasonally flooded wetlands and floodplains remains poorly quantified. Here, we separate the Congo wetland into four 3 degree x 3 degree regions, and use remote sensing measurements (i.e., GRACE, satellite radar altimeter, GPCP, JERS-1, SRTM, and MODIS) to estimate the amounts of water filling and draining from the Congo wetland, and to determine the source of the water. We find that the amount of water annually filling and draining the Congo wetlands is 111 km^3, which is about one-third the size of the water volumes found on the mainstem Amazon floodplain. Based on amplitude comparisons among the water volume changes and timing comparisons among their fluxes, we conclude that the local upland runoff is the main source of the Congo wetland water, not the fluvial process of river-floodplain water exchange as in the Amazon. Our hydraulic analysis using altimeter measurements also supports our conclusion by demonstrating that water surface elevations in the wetlands are consistently higher than the adjacent river water levels. Our research also highlights differences in the hydrology and hydrodynamics between the Congo wetland and the mainstem Amazon floodplain.

  4. Characterization of immobilized enzymes in polyurethane foams in a dynamic bed reactor.

    Science.gov (United States)

    Hu, Z C; Korus, R A; Stormo, K E

    1993-06-01

    beta-D-Galactosidase (E 3.2.1.23) from Aspergillus oryzae was immobilized with polyurethane foam (PUF). Among several immobilization methods attempted in this work, the immobilized enzyme preparation by in-situ co-polymerization between enzyme and prepolymer HYPOL 3000 showed the highest activity. The intrinsic kinetics of PUF-immobilized enzyme was determined in a dynamic bed reactor, used to increase transport rates. The immobilization mechanism in PUF was studied by measurements of immobilized enzyme kinetics and by using scanning electron microscopy combined with immuno-gold labeling techniques. The results showed that immobilization was predominantly by covalent bonding between primary amino groups of beta-D-galactosidase and isocyanate groups of the prepolymers. Entrapment in the PUF micropores assisted the immobilization of enzymes, and adsorption on the surface of macropores was not important for immobilization. The bicinchoninic acid method was applied for the determination of PUF loading capacity and specific enzyme activity and used to determine enzyme deactivation during immobilization. PMID:7763711

  5. Characterization of Cetyltrimethylammonium Bromide/Hexanol Reverse Micelles by Experimentally Benchmarked Molecular Dynamics Simulations.

    Science.gov (United States)

    Fuglestad, Brian; Gupta, Kushol; Wand, A Joshua; Sharp, Kim A

    2016-02-23

    Encapsulation of small molecules, proteins, and other macromolecules within the protective water core of reverse micelles is emerging as a powerful strategy for a variety of applications. The cationic surfactant cetyltrimethylammonium bromide (CTAB) in combination with hexanol as a cosurfactant is particularly useful in the context of solution NMR spectroscopy of encapsulated proteins. Small-angle X-ray and neutron scattering is employed to investigate the internal structure of the CTAB/hexanol reverse micelle particle under conditions appropriate for high-resolution NMR spectroscopy. The scattering profiles are used to benchmark extensive molecular dynamics simulations of this reverse micelle system and indicate that the parameters used in these simulations recapitulate experimental results. Scattering profiles and simulations indicate formation of homogeneous solutions of small approximately spherical reverse micelle particles at a water loading of 20 composed of ∼150 CTAB and 240 hexanol molecules. The 3000 waters comprising the reverse micelle core show a gradient of translational diffusion that reaches that of bulk water at the center. Rotational diffusion is slowed relative to bulk throughout the water core, with the greatest slowing near the CTAB headgroups. The 5 Å thick interfacial region of the micelle consists of overlapping layers of Br(-) enriched water, CTAB headgroups, and hexanol hydroxyl groups, containing about one-third of the total water. This study employs well-parametrized MD simulations, X-ray and neutron scattering, and electrostatic theory to illuminate fundamental properties of CTAB/hexanol reverse micelle size, shape, partitioning, and water behavior. PMID:26840651

  6. The dynamics of ant mosaics in tropical rainforests characterized using the Self-Organizing Map algorithm.

    Science.gov (United States)

    Dejean, Alain; Azémar, Frédéric; Céréghino, Régis; Leponce, Maurice; Corbara, Bruno; Orivel, Jérôme; Compin, Arthur

    2016-08-01

    Ants, the most abundant taxa among canopy-dwelling animals in tropical rainforests, are mostly represented by territorially dominant arboreal ants (TDAs) whose territories are distributed in a mosaic pattern (arboreal ant mosaics). Large TDA colonies regulate insect herbivores, with implications for forestry and agronomy. What generates these mosaics in vegetal formations, which are dynamic, still needs to be better understood. So, from empirical research based on 3 Cameroonian tree species (Lophira alata, Ochnaceae; Anthocleista vogelii, Gentianaceae; and Barteria fistulosa, Passifloraceae), we used the Self-Organizing Map (SOM, neural network) to illustrate the succession of TDAs as their host trees grow and age. The SOM separated the trees by species and by size for L. alata, which can reach 60 m in height and live several centuries. An ontogenic succession of TDAs from sapling to mature trees is shown, and some ecological traits are highlighted for certain TDAs. Also, because the SOM permits the analysis of data with many zeroes with no effect of outliers on the overall scatterplot distributions, we obtained ecological information on rare species. Finally, the SOM permitted us to show that functional groups cannot be selected at the genus level as congeneric species can have very different ecological niches, something particularly true for Crematogaster spp., which include a species specifically associated with B. fistulosa, nondominant species and TDAs. Therefore, the SOM permitted the complex relationships between TDAs and their growing host trees to be analyzed, while also providing new information on the ecological traits of the ant species involved. PMID:25684460

  7. Mechanical Characterization of Brain Tissue in Compression at Dynamic Strain Rates

    CERN Document Server

    Rashid, Badar; Gilchrist, Michael; 10.1016/j.jmbbm.2012.01.022

    2013-01-01

    Traumatic brain injury (TBI) occurs when local mechanical load exceeds certain tolerance levels for brain tissue. Extensive research has been done previously for brain matter experiencing compression at quasistatic loading; however, limited data is available to model TBI under dynamic impact conditions. In this research, an experimental setup was developed to perform unconfined compression tests and stress relaxation tests at strain rates < 90/s. The brain tissue showed a stiffer response with increasing strain rates, showing that hyperelastic models are not adequate. Specifically, the compressive nominal stress at 30% strain was 8.83 +/- 1.94, 12.8 +/- 3.10 and 16.0 +/- 1.41 kPa (mean +/- SD) at strain rates of 30, 60 and 90/s, respectively. Relaxation tests were also conducted at 10%-50% strain with the average rise time of 10 ms, which can be used to derive time dependent parameters. Numerical simulations were performed using one-term Ogden model with initial shear modulus mu_0 = 6.06 +/- 1.44, 9.44 +/-...

  8. On the Characterization of Revisitation Patterns in Complex Human Dynamics - A Data Science Approach

    Science.gov (United States)

    Barbosa Filho, Hugo Serrano

    When it comes to visitation patterns, humans beings are extremely regular and predictable, with recurrent activities responsible for most of our movements. In recent years, we have seen scientists attempt to model and explain human dynamics and in particular human movement. Akin to other human behaviors, traveling patterns evolve from the convolution between internal and external factors. A better understanding on the mechanisms responsible for transforming and incorporating individual events into regular patterns is of fundamental importance. Many aspects of our complex lives are affected by human movements such as disease spread and epidemics modeling, city planning, wireless network development, and disaster relief, to name a few. Given the myriad of applications, it is clear that a complete understanding of how people move in space can lead to considerable benefits to our society. In most of the recent works, scientists have focused on the idea that people movements are biased towards frequently-visited locations. According to them, human movement is based on a exploration/exploitation dichotomy in which individuals choose new locations (exploration) or return to frequently-visited locations (exploitation). In this dissertation we present some of our contributions to the field, such as the presence of a recency effect in human mobility and Web browsing behaviors as well as the Returner vs. Explorers dichotomy in Web browsing trajectories.

  9. A Highly Miniaturized, Wireless Inertial Measurement Unit for Characterizing the Dynamics of Pitched Baseballs and Softballs

    Directory of Open Access Journals (Sweden)

    Noel C. Perkins

    2012-08-01

    Full Text Available Baseball and softball pitch types are distinguished by the path and speed of the ball which, in turn, are determined by the angular velocity of the ball and the velocity of the ball center at the instant of release from the pitcher’s hand. While radar guns and video-based motion capture (mocap resolve ball speed, they provide little information about how the angular velocity of the ball and the velocity of the ball center develop and change during the throwing motion. Moreover, mocap requires measurements in a controlled lab environment and by a skilled technician. This study addresses these shortcomings by introducing a highly miniaturized, wireless inertial measurement unit (IMU that is embedded in both baseballs and softballs. The resulting “ball-embedded” sensor resolves ball dynamics right on the field of play. Experimental results from ten pitches, five thrown by one softball pitcher and five by one baseball pitcher, demonstrate that this sensor technology can deduce the magnitude and direction of the ball’s velocity at release to within 4.6% of measurements made using standard mocap. Moreover, the IMU directly measures the angular velocity of the ball, which further enables the analysis of different pitch types.

  10. Characterizing Psychological Dimensions in Non-Pathological Subjects through Autonomic Nervous System Dynamics

    Directory of Open Access Journals (Sweden)

    Mimma eNardelli

    2015-03-01

    Full Text Available The objective assessment of psychological traits of healthy subjects and psychiatric patients has been growing interest in clinical and bioengineering research fields during the last decade. Several experimental evidences strongly suggest that a link between Autonomic Nervous System (ANS dynamics and specific dimensions such as anxiety, social phobia, stress and emotional regulation might exist. Nevertheless, an extensive investigation on a wide range of psycho-cognitive scales and ANS non-invasive markers gathered from standard and nonlinear analysis still needs to be addressed. In this study, we analyzed the discerning and correlation capabilities of a comprehensive set of ANS features and psycho-cognitive scales in 29 non-pathological subjects monitored during resting conditions. In particular, the state of the art of standard and nonlinear analysis was performed on Heart Rate Variability, InterBreath Interval series, and Inter-Beat Respiration series, which were considered as monovariate and multivariate measurements. Experimental results show that each ANS feature is linked to specific psychological traits. Moreover, nonlinear analysis outperforms the psychological assessment with respect to standard analysis. Considering that the current clinical practice relies only on subjective scores from interviews and questionnaires, this study provides objective tools for the assessment of psychological dimensions.

  11. Fluid-dynamic characterization of a radio-frequency induction thermal plasma system for nanoparticle synthesis

    International Nuclear Information System (INIS)

    The fluid flow in a radio-frequency induction thermal plasma (RF-ITP) system for the synthesis of nanoparticles has been characterized using three- and two-dimensional modelling supported by enthalpy probe and calorimetric measurements in order to provide insights for the improvement of the process. The RF-ITP system is composed of a commercial inductively coupled plasma torch mounted on a reaction chamber that is equipped with viewports for diagnostics. The three-dimensional model predicted an almost axisymmetric temperature field in the reaction chamber in agreement with enthalpy probe measurements performed along two perpendicular scan axes, whereas recirculating flow patterns resulted in being strongly non-axisymmetric. Temperature profiles at two distances (60 mm and 100 mm) from the torch outlet have been calculated using two-dimensional modelling and compared with enthalpy probe measurements for different operating conditions with the aim of validating the predictive ability of the modelling tool. Calorimetric measurements have been performed in order to estimate the power coupled to the torch, which is usually an arbitrary input parameter for the models. Poor agreement was obtained between energy balances from modelling and from calorimetric measurements and, starting from this, a discussion on the uncertainties in the calculation of the radiative losses has been proposed. Finally, new insights for the improvement of the process of nanoparticle synthesis in the RF-ITP system are suggested. (paper)

  12. Multifrequency simultaneous bioimpedance measurements using multitone burst signals for dynamic tissue characterization

    Science.gov (United States)

    Sanchez, B.; Bragos, R.

    2010-04-01

    In this paper we present the keypoints to perform multifrequency simultaneous bioimpedance measurements using multitone signals. Concerning the frequency distribution, tones are spread over 1kHz to 1MHz range using a custom frequency distribution which we called Bilateral Quasi Logarithmic (BQL). BQL concentrates a higher number of tones around the impedance relaxation and contains a frequency plan algorithm. It minimizes the intermodulation effects due to non-linearities behaviours of the DUT and electrodes by slightly shifting the original tones in order to guarantee a guard bandwith. Regarding the multitone phase distribution, a Genetic Algorithm (GA) has been developed to minimize multitone Crest Factor (CF). This allow us to maximize the resultant Signal to Noise Ratio (SNR) of the acquisition system. This paper also presents the relation between parameters such as sampling frequency and ADC bits with the SNR and the effect in the overall amplitude and phase error when using multitone signals as excitation waveforms. Finally, we present characterization results from a measurement system based on a modular PXI architecture.

  13. Characterizing Spatial Dynamics of Bifurcation to Alternans in Isolated Whole Rabbit Hearts Based on Alternate Pacing

    Directory of Open Access Journals (Sweden)

    Kanchan Kulkarni

    2015-01-01

    Full Text Available Sudden cardiac death instigated by ventricular fibrillation (VF is the largest cause of natural death in the USA. Alternans, a beat-to-beat alternation in the action potential duration, has been implicated as being proarrhythmic. The onset of alternans is mediated via a bifurcation, which may occur through either a smooth or a border-collision mechanism. The objective of this study was to characterize the mechanism of bifurcation to alternans based on experiments in isolated whole rabbit hearts. High resolution optical mapping was performed and the electrical activity was recorded from the left ventricle (LV epicardial surface of the heart. Each heart was paced using an “alternate pacing protocol,” where the basic cycle length (BCL was alternatively perturbed by ±δ. Local onset of alternans in the heart, BCLstart, was measured in the absence of perturbations (δ=0 and was defined as the BCL at which 10% of LV exhibited alternans. The influences of perturbation size were investigated at two BCLs: one prior to BCLstart (BCLprior=BCLstart+20 ms and one preceding BCLprior (BCLfar=BCLstart+40 ms. Our results demonstrate significant spatial correlation of the region exhibiting alternans with smooth bifurcation characteristics, indicating that transition to alternans in isolated rabbit hearts occurs predominantly through smooth bifurcation.

  14. Static and dynamic electronic characterization of organic monolayers grafted on a silicon surface.

    Science.gov (United States)

    Pluchery, O; Zhang, Y; Benbalagh, R; Caillard, L; Gallet, J J; Bournel, F; Lamic-Humblot, A-F; Salmeron, M; Chabal, Y J; Rochet, F

    2016-02-01

    Organic layers chemically grafted on silicon offer excellent interfaces that may open up the way for new organic-inorganic hybrid nanoelectronic devices. However, technological achievements rely on the precise electronic characterization of such organic layers. We have prepared ordered grafted organic monolayers (GOMs) on Si(111), sometimes termed self-assembled monolayers (SAMs), by a hydrosilylation reaction with either a 7-carbon or an 11-carbon alkyl chain, with further modification to obtain amine-terminated surfaces. X-ray photoelectron spectroscopy (XPS) is used to determine the band bending (∼ 0.3 eV), and ultraviolet photoelectron spectroscopy (UPS) to measure the work function (∼ 3.4 eV) and the HOMO edge. Scanning tunneling microscopy (STM) confirms that the GOM surface is clean and smooth. Finally, conductive AFM is used to measure electron transport through the monolayer and to identify transition between the tunneling and the field emission regimes. These organic monolayers offer a promising alternative to silicon dioxide thin films for fabricating metal-insulator-semiconductor (MIS) junctions. We show that gold nanoparticles can be covalently attached to mimic metallic nano-electrodes and that the electrical quality of the GOMs is completely preserved in the process. PMID:26757829

  15. Value of dynamic contrast-enhanced MRI for tissue characterization of ovarian teratomas: Correlation with histopathology

    International Nuclear Information System (INIS)

    Aim: To analyse the value of double contrast-enhanced (DCE) magnetic resonance imaging (MRI) in addition to conventional MRI to characterize ovarian teratomas subtypes with histological correlation. Materials and methods: From January 2005 to December 2008, 38 women undergoing MRI and subsequent resection of ovarian teratomas were identified [40 mature cystic teratomas (MCT), two struma ovarii, three immature teratomas]. MRI images were analysed blindly by two radiologists according to morphological and vascular abnormalities. An experienced histopathologist reviewed all slides to determine the presence and histological composition of Rokitansky protuberances. Results: Thirty-one MCT (77%) had at least one small, regular Rokitansky protuberance presenting at an acute angle with the cyst wall. Ten out of 31 MCT did not display any enhancement on contrast-enhanced MRI related to sebaceous glands, adipose lobules, keratin, and pilosebaceous adnexa at histology. Three different time–intensity curve (TIC), types 1, 2, and 3, were related to presence of smooth muscular cells and fibrous, neuroglial, or thyroid tissue, respectively, found at histology of MCT. Type 3 TIC was also present in one struma ovarii and two immature teratomas. Conclusion: TIC types are related to the specific content of the solid tissue of ovarian teratomas but cannot be used to differentiate benign and malignant ovarian teratomas

  16. Interconverting conformations of variants of the human amyloidogenic protein beta2-microglobulin quantitatively characterized by dynamic capillary electrophoresis and computer simulation

    DEFF Research Database (Denmark)

    Heegaard, Niels H H; Jørgensen, Thomas J D; Cheng, Lei; Schou, Christian; Nissen, Mogens H; Trapp, Oliver

    2006-01-01

    unified theory for dynamic chromatography and dynamic electrophoresis. The results are correlated with the outcome of independent experiments based on mass spectrometric measurement of H/D exchange. This study illustrates that dynamic capillary electrophoresis is suitable for the investigation of the......Capillary electrophoretic separation profiles of cleaved variants of beta2-microglobulin (beta2m) reflect the conformational equilibria existing in solutions of these proteins. The characterization of these equilibria is of interest since beta2m is responsible for amyloid formation in dialysis...

  17. Characterization of BRCA1 Protein Targeting, Dynamics, and Function at the Centrosome

    Science.gov (United States)

    Brodie, Kirsty M.; Henderson, Beric R.

    2012-01-01

    BRCA1 is a DNA damage response protein and functions in the nucleus to stimulate DNA repair and at the centrosome to inhibit centrosome overduplication in response to DNA damage. The loss or mutation of BRCA1 causes centrosome amplification and abnormal mitotic spindle assembly in breast cancer cells. The BRCA1-BARD1 heterodimer binds and ubiquitinates γ-tubulin to inhibit centrosome amplification and promote microtubule nucleation; however regulation of BRCA1 targeting and function at the centrosome is poorly understood. Here we show that both N and C termini of BRCA1 are required for its centrosomal localization and that BRCA1 moves to the centrosome independently of BARD1 and γ-tubulin. Mutations in the C-terminal phosphoprotein-binding BRCT domain of BRCA1 prevented localization to centrosomes. Photobleaching experiments identified dynamic (60%) and immobilized (40%) pools of ectopic BRCA1 at the centrosome, and these are regulated by the nuclear export receptor CRM1 (chromosome region maintenance 1) and BARD1. CRM1 mediates nuclear export of BRCA1, and mutation of the export sequence blocked BRCA1 regulation of centrosome amplification in irradiated cells. CRM1 binds to undimerized BRCA1 and is displaced by BARD1. Photobleaching assays implicate CRM1 in driving undimerized BRCA1 to the centrosome and revealed that when BRCA1 subsequently binds to BARD1, it is less well retained at centrosomes, suggesting a mechanism to accelerate BRCA1 release after formation of the active heterodimer. Moreover, Aurora A binding and phosphorylation of BRCA1 enhanced its centrosomal retention and regulation of centrosome amplification. Thus, CRM1, BARD1 and Aurora A promote the targeting and function of BRCA1 at centrosomes. PMID:22262852

  18. Characterization of the time dynamics of monthly satellite snow cover data on Mountain Chains in Lebanon

    Science.gov (United States)

    Telesca, Luciano; Shaban, Amin; Gascoin, Simon; Darwich, Talal; Drapeau, Laurent; Hage, Mhamad El; Faour, Ghaleb

    2014-11-01

    In this study, the time dynamics of the monthly means of the snow cover have been on Lebanese Mountain Chains from 2000 to 2012, derived from the MODIS Aqua/Terra satellite snow products was analyzed. This represents the longest satellite-based snow cover time series produced for Lebanon so far. Field survey was also carried out over the last three years in order to measure the in-situ snow/water equivalent and depth in different localities. Analyzing the regime of the snow cover in Mount-Lebanon (Western Mountain Chains) region, it was found that: (i) snowmelt accounts for about 31% of the rivers and springs discharge in Lebanon; (ii) consecutive peaks in the snow cover time series, representing the change-point between accumulation phase and ablation phase are present in three different patterns (edged, non-edged and double peaked); (iii) the areal snow coverage has big diversity between different years; (iv) the annual periodicity represents the most statistically significant and predominant frequency of the series contributing for about the 40% of the total variance of the snow cover series; (v) the long-term trend, totally hidden by the more powerful yearly component and detected by using the singular spectrum analysis (SSA), accounts for about the 33% of the total variance of the series; (vi) the long-term trend shows an apparent cyclic behavior with an estimated period (interval between the two minima) of about nine years; (vii) the comparison of the long-term trend with the North Atlantic Oscillation (NAO) monthly index reveals that the minima in 2009-2010 of the SSA long-term component coincides with a persistent negative phase in the NAO Index.

  19. Structural and dynamic properties of linker histone H1 binding to DNA

    OpenAIRE

    Dootz, Rolf; Toma, Adriana C.; Pfohl, Thomas

    2010-01-01

    Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists from a chromatin organization deciphering point of view, and for physicists from the study of polyelectrolyte interactions point of view. Hence, H1/DNA binding processes, structural and dynamical information about these self-assemblies is of broad importance. ...

  20. Characterizing Spatiotemporal Dynamics of Methane Emissions from Rice Paddies in Northeast China from 1990 to 2010

    Science.gov (United States)

    Zhang, Yuan; Su, Shiliang; Zhang, Feng; Shi, Runhe; Gao, Wei

    2012-01-01

    Background Rice paddies have been identified as major methane (CH4) source induced by human activities. As a major rice production region in Northern China, the rice paddies in the Three-Rivers Plain (TRP) have experienced large changes in spatial distribution over the recent 20 years (from 1990 to 2010). Consequently, accurate estimation and characterization of spatiotemporal patterns of CH4 emissions from rice paddies has become an pressing issue for assessing the environmental impacts of agroecosystems, and further making GHG mitigation strategies at regional or global levels. Methodology/Principal Findings Integrating remote sensing mapping with a process-based biogeochemistry model, Denitrification and Decomposition (DNDC), was utilized to quantify the regional CH4 emissions from the entire rice paddies in study region. Based on site validation and sensitivity tests, geographic information system (GIS) databases with the spatially differentiated input information were constructed to drive DNDC upscaling for its regional simulations. Results showed that (1) The large change in total methane emission that occurred in 2000 and 2010 compared to 1990 is distributed to the explosive growth in amounts of rice planted; (2) the spatial variations in CH4 fluxes in this study are mainly attributed to the most sensitive factor soil properties, i.e., soil clay fraction and soil organic carbon (SOC) content, and (3) the warming climate could enhance CH4 emission in the cool paddies. Conclusions/Significance The study concluded that the introduction of remote sensing analysis into the DNDC upscaling has a great capability in timely quantifying the methane emissions from cool paddies with fast land use and cover changes. And also, it confirmed that the northern wetland agroecosystems made great contributions to global greenhouse gas inventory. PMID:22235268

  1. Molecular characterization, distribution, and dynamics of hepatitis C virus genotypes in blood donors in Colombia.

    Science.gov (United States)

    Mora, Mónica Viviana Alvarado; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutiérrez, Maria Fernanda; Carrilho, Flair José; Pinho, João Renato Rebello

    2010-11-01

    Hepatitis C virus (HCV) is a frequent cause of acute and chronic hepatitis and a leading cause for cirrhosis of the liver and hepatocellular carcinoma. HCV is classified in six major genotypes and more than 70 subtypes. In Colombian blood banks, serum samples were tested for anti-HCV antibodies using a third-generation ELISA. The aim of this study was to characterize the viral sequences in plasma of 184 volunteer blood donors who attended the "Banco Nacional de Sangre de la Cruz Roja Colombiana," Bogotá, Colombia. Three different HCV genomic regions were amplified by nested PCR. The first of these was a segment of 180 bp of the 5'UTR region to confirm the previous diagnosis by ELISA. From those that were positive to the 5'UTR region, two further segments were amplified for genotyping and subtyping by phylogenetic analysis: a segment of 380 bp from the NS5B region; and a segment of 391 bp from the E1 region. The distribution of HCV subtypes was: 1b (82.8%), 1a (5.7%), 2a (5.7%), 2b (2.8%), and 3a (2.8%). By applying Bayesian Markov chain Monte Carlo simulation, it was estimated that HCV-1b was introduced into Bogotá around 1950. Also, this subtype spread at an exponential rate between about 1970 to about 1990, after which transmission of HCV was reduced by anti-HCV testing of this population. Among Colombian blood donors, HCV genotype 1b is the most frequent genotype, especially in large urban conglomerates such as Bogotá, as is the case in other South American countries. PMID:20872715

  2. Crystallographic, Microstructural, and Mechanical Characterization of Dynamically Processed EP741NP Superalloy

    Science.gov (United States)

    Sharma, A. D.; Sharma, A. K.; Thakur, N.

    2016-08-01

    Considerable progress has been made for the solidification of metal powders with improved properties by using varieties of metallurgical methods. However, solidification of superalloy powders offers many difficulties under traditional processes. This article outlines an extensive program being undertaken to produce monoliths of superalloys with enhanced microstructural and mechanical properties. EP741NP superalloy has been subjected to explosive shock wave loading to obtain uniform and crack-free monoliths. An axisymmetric cylindrical configuration with a plastic explosive of high-detonation velocity has been used to consolidate the superalloy powder nearer to its theoretical density (~98 pct). By careful design of experiments, detonation velocity has been measured vis-à-vis compaction of metal powders in a single-shot experiment by employing instrumented detonics. The shock-processed specimens characterized for phase, lattice parameter, and structural variation by X-ray diffraction technique show intact crystalline structure. Results obtained from Williamson-Hall method indicate small micro-strain (2.8 × 10-3) and decreased crystallite size. Energy-dispersive spectroscopy suggests no segregation within the specimens. Scanning electron microscopy shows fracture-less and micro-cracks/void-free compacts of superalloy indicating satisfactory sub-structural strength. Indentation experiments with variable loads (1.96 N and 2.94 N) performed on the shock-processed specimen cut along transverse section show high order of Vicker's micro-hardness value up to 486 H v. The tensile and compressive strengths of the superalloy monoliths cut along the consolidation axes have been found to be 824 and 834 MPa, respectively.

  3. Characterizing spatiotemporal dynamics of methane emissions from rice paddies in Northeast China from 1990 to 2010.

    Directory of Open Access Journals (Sweden)

    Yuan Zhang

    Full Text Available BACKGROUND: Rice paddies have been identified as major methane (CH(4 source induced by human activities. As a major rice production region in Northern China, the rice paddies in the Three-Rivers Plain (TRP have experienced large changes in spatial distribution over the recent 20 years (from 1990 to 2010. Consequently, accurate estimation and characterization of spatiotemporal patterns of CH₄ emissions from rice paddies has become an pressing issue for assessing the environmental impacts of agroecosystems, and further making GHG mitigation strategies at regional or global levels. METHODOLOGY/PRINCIPAL FINDINGS: Integrating remote sensing mapping with a process-based biogeochemistry model, Denitrification and Decomposition (DNDC, was utilized to quantify the regional CH(4 emissions from the entire rice paddies in study region. Based on site validation and sensitivity tests, geographic information system (GIS databases with the spatially differentiated input information were constructed to drive DNDC upscaling for its regional simulations. Results showed that (1 The large change in total methane emission that occurred in 2000 and 2010 compared to 1990 is distributed to the explosive growth in amounts of rice planted; (2 the spatial variations in CH₄ fluxes in this study are mainly attributed to the most sensitive factor soil properties, i.e., soil clay fraction and soil organic carbon (SOC content, and (3 the warming climate could enhance CH₄ emission in the cool paddies. CONCLUSIONS/SIGNIFICANCE: The study concluded that the introduction of remote sensing analysis into the DNDC upscaling has a great capability in timely quantifying the methane emissions from cool paddies with fast land use and cover changes. And also, it confirmed that the northern wetland agroecosystems made great contributions to global greenhouse gas inventory.

  4. Dynamic characterization of external and internal mass transport in heterotrophic biofilms from microsensors measurements.

    Science.gov (United States)

    Guimerà, Xavier; Dorado, Antonio David; Bonsfills, Anna; Gabriel, Gemma; Gabriel, David; Gamisans, Xavier

    2016-10-01

    Knowledge of mass transport mechanisms in biofilm-based technologies such as biofilters is essential to improve bioreactors performance by preventing mass transport limitation. External and internal mass transport in biofilms was characterized in heterotrophic biofilms grown on a flat plate bioreactor. Mass transport resistance through the liquid-biofilm interphase and diffusion within biofilms were quantified by in situ measurements using microsensors with a high spatial resolution (based on the Fisher Information Matrix to increase the reliability of experimental data and minimize confidence intervals of estimated mass transport coefficients. The sensitivity of external and internal mass transport resistances to flow conditions within the range of typical fluid velocities over biofilms (Reynolds numbers between 0.5 and 7) was assessed. Estimated external mass transfer coefficients at different liquid phase flow velocities showed discrepancies with studies considering laminar conditions in the diffusive boundary layer near the liquid-biofilm interphase. The correlation of effective diffusivity with flow velocities showed that the heterogeneous structure of biofilms defines the transport mechanisms inside biofilms. Internal mass transport was driven by diffusion through cell clusters and aggregates at Re below 2.8. Conversely, mass transport was driven by advection within pores, voids and water channels at Re above 5.6. Between both flow velocities, mass transport occurred by a combination of advection and diffusion. Effective diffusivities estimated at different biofilm densities showed a linear increase of mass transport resistance due to a porosity decrease up to biofilm densities of 50 g VSS·L(-1). Mass transport was strongly limited at higher biofilm densities. Internal mass transport results were used to propose an empirical correlation to assess the effective diffusivity within biofilms considering the influence of hydrodynamics and biofilm density. PMID

  5. Crystallographic, Microstructural, and Mechanical Characterization of Dynamically Processed EP741NP Superalloy

    Science.gov (United States)

    Sharma, A. D.; Sharma, A. K.; Thakur, N.

    2016-05-01

    Considerable progress has been made for the solidification of metal powders with improved properties by using varieties of metallurgical methods. However, solidification of superalloy powders offers many difficulties under traditional processes. This article outlines an extensive program being undertaken to produce monoliths of superalloys with enhanced microstructural and mechanical properties. EP741NP superalloy has been subjected to explosive shock wave loading to obtain uniform and crack-free monoliths. An axisymmetric cylindrical configuration with a plastic explosive of high-detonation velocity has been used to consolidate the superalloy powder nearer to its theoretical density (~98 pct). By careful design of experiments, detonation velocity has been measured vis-à-vis compaction of metal powders in a single-shot experiment by employing instrumented detonics. The shock-processed specimens characterized for phase, lattice parameter, and structural variation by X-ray diffraction technique show intact crystalline structure. Results obtained from Williamson-Hall method indicate small micro-strain (2.8 × 10-3) and decreased crystallite size. Energy-dispersive spectroscopy suggests no segregation within the specimens. Scanning electron microscopy shows fracture-less and micro-cracks/void-free compacts of superalloy indicating satisfactory sub-structural strength. Indentation experiments with variable loads (1.96 N and 2.94 N) performed on the shock-processed specimen cut along transverse section show high order of Vicker's micro-hardness value up to 486 H v. The tensile and compressive strengths of the superalloy monoliths cut along the consolidation axes have been found to be 824 and 834 MPa, respectively.

  6. Characterization of 4-HNE modified L-FABP reveals alterations in structural and functional dynamics.

    Directory of Open Access Journals (Sweden)

    Rebecca L Smathers

    Full Text Available 4-Hydroxynonenal (4-HNE is a reactive α,β-unsaturated aldehyde produced during oxidative stress and subsequent lipid peroxidation of polyunsaturated fatty acids. The reactivity of 4-HNE towards DNA and nucleophilic amino acids has been well established. In this report, using proteomic approaches, liver fatty acid-binding protein (L-FABP is identified as a target for modification by 4-HNE. This lipid binding protein mediates the uptake and trafficking of hydrophobic ligands throughout cellular compartments. Ethanol caused a significant decrease in L-FABP protein (P<0.001 and mRNA (P<0.05, as well as increased poly-ubiquitinated L-FABP (P<0.001. Sites of 4-HNE adduction on mouse recombinant L-FABP were mapped using MALDI-TOF/TOF mass spectrometry on apo (Lys57 and Cys69 and holo (Lys6, Lys31, His43, Lys46, Lys57 and Cys69 L-FABP. The impact of 4-HNE adduction was found to occur in a concentration-dependent manner; affinity for the fluorescent ligand, anilinonaphthalene-8-sulfonic acid, was reduced from 0.347 µM to Kd(1 = 0.395 µM and Kd(2 = 34.20 µM. Saturation analyses revealed that capacity for ligand is reduced by approximately 50% when adducted by 4-HNE. Thermal stability curves of apo L-FABP was also found to be significantly affected by 4-HNE adduction (ΔTm = 5.44°C, P<0.01. Computational-based molecular modeling simulations of adducted protein revealed minor conformational changes in global protein structure of apo and holo L-FABP while more apparent differences were observed within the internal binding pocket, revealing reduced area and structural integrity. New solvent accessible portals on the periphery of the protein were observed following 4-HNE modification in both the apo and holo state, suggesting an adaptive response to carbonylation. The results from this study detail the dynamic process associated with L-FABP modification by 4-HNE and provide insight as to how alterations in structural integrity and ligand

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  8. PlanetPack: A radial-velocity time-series analysis tool facilitating exoplanets detection, characterization, and dynamical simulations

    Science.gov (United States)

    Baluev, Roman V.

    2013-08-01

    We present PlanetPack, a new software tool that we developed to facilitate and standardize the advanced analysis of radial velocity (RV) data for the goal of exoplanets detection, characterization, and basic dynamical N-body simulations. PlanetPack is a command-line interpreter, that can run either in an interactive mode or in a batch mode of automatic script interpretation. Its major abilities include: (i) advanced RV curve fitting with the proper maximum-likelihood treatment of unknown RV jitter; (ii) user-friendly multi-Keplerian as well as Newtonian N-body RV fits; (iii) use of more efficient maximum-likelihood periodograms that involve the full multi-planet fitting (sometimes called as “residual” or “recursive” periodograms); (iv) easily calculatable parametric 2D likelihood function level contours, reflecting the asymptotic confidence regions; (v) fitting under some useful functional constraints is user-friendly; (vi) basic tasks of short- and long-term planetary dynamical simulation using a fast Everhart-type integrator based on Gauss-Legendre spacings; (vii) fitting the data with red noise (auto-correlated errors); (viii) various analytical and numerical methods for the tasks of determining the statistical significance. It is planned that further functionality may be added to PlanetPack in the future. During the development of this software, a lot of effort was made to improve the calculational speed, especially for CPU-demanding tasks. PlanetPack was written in pure C++ (standard of 1998/2003), and is expected to be compilable and useable on a wide range of platforms.

  9. Toll-Like Receptor (TLR) and Nucleosome-binding Oligomerization Domain (NOD) gene polymorphisms and endometrial cancer risk

    International Nuclear Information System (INIS)

    Endometrial cancer is the most common gynaecological malignancy in women of developed countries. Many risk factors implicated in endometrial cancer trigger inflammatory events; therefore, alterations in immune response may predispose an individual to disease. Toll-like receptors (TLRs) and nucleosome-binding oligomerization domain (NOD) genes are integral to the recognition of pathogens and are highly polymorphic. For these reasons, the aim of the study was to assess the frequency of polymorphic variants in TLR and NOD genes in an Australian endometrial cancer population. Ten polymorphisms were genotyped in 191 endometrial cancer cases and 291 controls using real-time PCR: NOD1 (rs2075822, rs2907749, rs2907748), NOD2 (rs5743260, rs2066844, rs2066845), TLR2 (rs5743708), TLR4 (rs4986790) and TLR9 (rs5743836, rs187084). Haplotype analysis revealed that the combination of the variant alleles of the two TLR9 polymorphisms, rs5743836 and rs187084, were protective for endometrial cancer risk: OR 0.11, 95% CI (0.03-0.44), p = 0.002. This result remained highly significant after adjustment for endometrial cancer risk factors and Bonferroni correction for multiple testing. There were no other associations observed for the other polymorphisms in TLR2, TLR4, NOD1 and NOD2. The variant 'C' allele of rs5743836 causes greater TLR9 transcriptional activity compared to the 'T' allele, therefore, higher TLR9 activity may be related to efficient removal of microbial pathogens within the endometrium. Clearly, the association of these TLR9 polymorphisms and endometrial cancer risk must be further examined in an independent population. The results point towards the importance of examining immune response in endometrial tumourigenesis to understand new pathways that may be implicated in disease

  10. Molecular dynamics characterization of void defects in crystalline (1,3,5-trinitro-1,3,5-triazacyclohexane).

    Science.gov (United States)

    Boyd, Sylke; Murray, Jane S; Politzer, Peter

    2009-11-28

    In the context of a continuing investigation of factors that affect the sensitivities of energetic materials to detonation initiation, we have carried out a molecular dynamics characterization of void defects in crystalline (1,3,5-trinitro-1,3,5-triazacyclo-hexane). An empirical force field that is capable of handling flexible molecules in a pliable crystal was used. Voids ranging in size from 2 to 30 adjacent vacated sites were created in model lattices of 216 or 512 molecules. Energetic and geometric ground state properties were determined. The void formation energy per molecule removed was found to decrease from 50 kcal/mol for a single vacancy to about 23+/-2 kcal/mol for voids larger than one unit cell (8 molecules). Analysis of the local binding energies in the vicinity of a void reveals not only the expected decrease for molecules directly on the void surface but also a wide spread of values in the first 5-10 A away from the surface; this includes some molecules with local binding energies significantly higher than in the defect-free lattice. Molecular conformational changes and reorientations begin to be found in the vicinities of voids larger than one unit cell. Thermal behavior investigated includes void and molecular diffusion coefficients and fluctuations in void size. PMID:19947705

  11. Mechanical and microstructural characterization of Al7075/SiC nanocompo-sites fabricated by dynamic compaction

    Institute of Scientific and Technical Information of China (English)

    A. Atrian; G.H. Majzoobi; M.H. Enayati; H. Bakhtiari

    2014-01-01

    This paper describes the synthesis of Al7075 metal matrix composites reinforced with SiC, and the characterization of their microstructure and mechanical behavior. The mechanically milled Al7075 micron-sized powder and SiC nanoparticles are dynamically com-pacted using a drop hammer device. This compaction is performed at different temperatures and for various volume fractions of SiC nanoparticles. The relative density is directly related to the compaction temperature rise and indirectly related to the content of SiC nanopar-ticle reinforcement, respectively. Furthermore, increasing the amount of SiC nanoparticles improves the strength, stiffness, and hardness of the compacted specimens. The increase in hardness and strength may be attributed to the inherent hardness of the nanoparticles, and other phenomena such as thermal mismatch and crack shielding. Nevertheless, clustering of the nanoparticles at aluminum particle boundaries make these regions become a source of concentrated stress, which reduces the load carrying capacity of the compacted nanocomposite.

  12. Design and characterization of the ePix10k: a high dynamic range integrating pixel ASIC for LCLS detectors

    Science.gov (United States)

    Caragiulo, P.; Dragone, A.; Markovic, B.; Herbst, R.; Nishimura, K.; Reese, B.; Herrmann, S.; Hart, P.; Blaj, G.; Segal, J.; Tomada, A.; Hasi, J.; Carini, G.; Kenney, C.; Haller, G.

    2015-05-01

    ePix10k is a variant of a novel class of integrating pixel ASICs architectures optimized for the processing of signals in second generation LINAC Coherent Light Source (LCLS) X-Ray cameras. The ASIC is optimized for high dynamic range application requiring high spatial resolution and fast frame rates. ePix ASICs are based on a common platform composed of a random access analog matrix of pixel with global shutter, fast parallel column readout, and dedicated sigma-delta analog to digital converters per column. The ePix10k variant has 100um×100um pixels arranged in a 176×192 matrix, a resolution of 140e- r.m.s. and a signal range of 3.5pC (10k photons at 8keV). In its final version it will be able to sustain a frame rate of 2kHz. A first prototype has been fabricated and characterized. Performance in terms of noise, linearity, uniformity, cross-talk, together with preliminary measurements with bump bonded sensors are reported here.

  13. Test Area for Remedial Actions (TARA) site characterization and dynamic compaction of low-level radioactive waste trenches

    Energy Technology Data Exchange (ETDEWEB)

    Davis, E.C.; Spalding, B.P.; Lee, S.Y.; Hyder, L.K.

    1989-01-01

    As part of a low-level radioactive waste burial ground stabilization and closure technology demonstration project, a group of five burial trenches in Oak Ridge National Laboratory (ORNL) Solid Waste Storage Area (SWSA) 6 was selected as a demonstration site for testing trench compaction, trench grouting, and trench cap installation and performance. This report focuses on site characterization, trench compaction, and grout-trench leachate compatibility. Trench grouting and cap design and construction will be the subject of future reports. The five trenches, known as the Test Area for Remedial Actions (TARA) site, are contained within a hydrologically isolated area of SWSA 6; for that reason, any effects of stabilization activities on site performance and groundwater quality will be separable from the influence of other waste disposal units in SWSA 6. To obviate the chronic problem of burial trench subsidence and to provide support for an infiltration barrier cap, these five trenches were dynamically compacted by repeated dropping of a 4-ton weight onto each trench from heights of approximately 7 m.

  14. Characterization of nanoparticles of lidocaine in w/o microemulsions using small-angle neutron scattering and dynamic light scattering

    Indian Academy of Sciences (India)

    A Shukla; M A Kiselev; A Hoell; R H H Neubert

    2004-08-01

    Microemulsions (MEs) are of special interest because a variety of reactants can be introduced into the nanometer-sized aqueous domains, leading to materials with controlled size and shape [1,2]. In the past few years, significant research has been conducted in the reverse ME-mediated synthesis of organic nanoparticles [3,4]. In this study, a w/o ME medium was employed for the synthesis of lidocaine by direct precipitation in w/o microemulsion systems: water/isopropylpalmitat/Tween80/Span80. The particle size as well as the location of nanoparticles in the ME droplet were characterized by means of dynamic light scattering (DLS) and small angle neutron scattering (SANS). It is observed that lidocaine precipitated in the aqueous cores because of its insolubility in water. Hydrodynamic radius and gyration radius of microemulsion droplets were estimated as ∼ 15 nm and ∼ 4.50 nm from DLS and SANS respectively. Furthermore, different size parameters obtained by DLS and SANS experiments were compared

  15. Bolus arrival time and its effect on tissue characterization with dynamic contrast-enhanced magnetic resonance imaging.

    Science.gov (United States)

    Mehrtash, Alireza; Gupta, Sandeep N; Shanbhag, Dattesh; Miller, James V; Kapur, Tina; Fennessy, Fiona M; Kikinis, Ron; Fedorov, Andriy

    2016-01-01

    Matching the bolus arrival time (BAT) of the arterial input function (AIF) and tissue residue function (TRF) is necessary for accurate pharmacokinetic (PK) modeling of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). We investigated the sensitivity of volume transfer constant ([Formula: see text]) and extravascular extracellular volume fraction ([Formula: see text]) to BAT and compared the results of four automatic BAT measurement methods in characterization of prostate and breast cancers. Variation in delay between AIF and TRF resulted in a monotonous change trend of [Formula: see text] and [Formula: see text] values. The results of automatic BAT estimators for clinical data were all comparable except for one BAT estimation method. Our results indicate that inaccuracies in BAT measurement can lead to variability among DCE-MRI PK model parameters, diminish the quality of model fit, and produce fewer valid voxels in a region of interest. Although the selection of the BAT method did not affect the direction of change in the treatment assessment cohort, we suggest that BAT measurement methods must be used consistently in the course of longitudinal studies to control measurement variability. PMID:26989759

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

    OpenAIRE

    Sharma Shikhar; Gerke Daniel S; Han Han F; Jeong Shinwu; Stallcup Michael R; Jones Peter A; Liang Gangning

    2012-01-01

    Abstract Background DNA methylation, histone modifications and nucleosome occupancy act in concert for regulation of gene expression patterns in mammalian cells. Recently, G9a, a H3K9 methyltransferase, has been shown to play a role in establishment of DNA methylation at embryonic gene targets in ES cells through recruitment of de novo DNMT3A/3B enzymes. However, whether G9a plays a similar role in maintenance of DNA methylation in somatic cells is still unclear. Results Here we show that G9a...

  17. Dynamic response characterization of complex systems through operational identification and dynamic substructuring- An application to gear noise propagation in the automotive industry

    NARCIS (Netherlands)

    De Klerk, D.

    2009-01-01

    This thesis deals with new methods, which can determine the dynamic response of a complex system identified in operation, based on the knowledge of its subsystem dynamics and excitation. In the first part of this thesis, the identification of component excitation and its transmission into the total

  18. Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program

    OpenAIRE

    Cornelia Amariei; Rainer Machné; Viktor Stolc; Tomoyoshi Soga; Masaru Tomita; Murray, Douglas B.

    2014-01-01

    The structural dynamics of chromatin have been implicated in the regulation of fundamental eukaryotic processes, such as DNA transcription, replication and repair. Although previous studies have revealed that the chromatin landscape, nucleosome remodeling and histone modification events are intimately tied into cellular energetics and redox state, few studies undertake defined time-resolved measurements of these state variables. Here, we use metabolically synchronous, continuously-grown yeast...

  19. Nuclear magnetic resonance characterization of the stationary dynamics of partially saturated media during steady-state infiltration flow

    Science.gov (United States)

    Rassi, Erik M.; Codd, Sarah L.; Seymour, Joseph D.

    2011-01-01

    Flow in porous media and the resultant hydrodynamics are important in fields including but not limited to the hydrology, chemical, medical and petroleum industries. The observation and understanding of the hydrodynamics in porous media are critical to the design and optimal utilization of porous media, such as those seen in trickle-bed reactors, medical filters, subsurface flows and carbon sequestration. Magnetic resonance (MR) provides for a non-invasive technique that can probe the hydrodynamics on pore and bulk scale lengths; many previous works have characterized fully saturated porous media, while rapid MR imaging (MRI) methods in particular have previously been applied to partially saturated flows. We present time- and ensemble-averaged MR measurements to observe the effects on a bead pack partially saturated with air under flowing water conditions. The 10 mm internal diameter bead pack was filled with 100 μm borosilicate glass beads. Air was injected into the bead pack as water flowed simultaneously through the sample at 25 ml h-1. The initial partially saturated state was characterized with MRI density maps, free induction decay (FID) experiments, propagators and velocity maps before the water flow rate was increased incrementally from 25 to 500 ml h-1. After the maximum flow rate of 500 ml h-1, the MRI density maps, FID experiments, propagators and velocity maps were repeated and compared to the data taken before the maximum flow rate. This work shows that a partially saturated single-phase flow has global flow dynamics that return to characteristic flow statistics once a steady-state high flow rate has been reached. This high flow rate pushed out a significant amount of the air in the bead pack and caused the return of a preferential flow pattern. Velocity maps indicated that local flow statistics were not the same for the before and after blow out conditions. It has been suggested and shown previously that a flow pattern can return to

  20. Nuclear magnetic resonance characterization of the stationary dynamics of partially saturated media during steady-state infiltration flow

    International Nuclear Information System (INIS)

    Flow in porous media and the resultant hydrodynamics are important in fields including but not limited to the hydrology, chemical, medical and petroleum industries. The observation and understanding of the hydrodynamics in porous media are critical to the design and optimal utilization of porous media, such as those seen in trickle-bed reactors, medical filters, subsurface flows and carbon sequestration. Magnetic resonance (MR) provides for a non-invasive technique that can probe the hydrodynamics on pore and bulk scale lengths; many previous works have characterized fully saturated porous media, while rapid MR imaging (MRI) methods in particular have previously been applied to partially saturated flows. We present time- and ensemble-averaged MR measurements to observe the effects on a bead pack partially saturated with air under flowing water conditions. The 10 mm internal diameter bead pack was filled with 100 μm borosilicate glass beads. Air was injected into the bead pack as water flowed simultaneously through the sample at 25 ml h-1. The initial partially saturated state was characterized with MRI density maps, free induction decay (FID) experiments, propagators and velocity maps before the water flow rate was increased incrementally from 25 to 500 ml h-1. After the maximum flow rate of 500 ml h-1, the MRI density maps, FID experiments, propagators and velocity maps were repeated and compared to the data taken before the maximum flow rate. This work shows that a partially saturated single-phase flow has global flow dynamics that return to characteristic flow statistics once a steady-state high flow rate has been reached. This high flow rate pushed out a significant amount of the air in the bead pack and caused the return of a preferential flow pattern. Velocity maps indicated that local flow statistics were not the same for the before and after blow out conditions. It has been suggested and shown previously that a flow pattern can return to similar statistics

  1. iNuc-STNC: a sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept of SAAC and Chou's PseAAC.

    Science.gov (United States)

    Tahir, Muhammad; Hayat, Maqsood

    2016-07-19

    The nucleosome is the fundamental unit of eukaryotic chromatin, which participates in regulating different cellular processes. Owing to the huge exploration of new DNA primary sequences, it is indispensable to develop an automated model. However, identification of novel protein sequences using conventional methods is difficult or sometimes impossible because of vague motifs and the intricate structure of DNA. In this regard, an effective and high throughput automated model "iNuc-STNC" has been proposed in order to identify accurately and reliably nucleosome positioning in genomes. In this proposed model, DNA sequences are expressed into three distinct feature extraction strategies containing dinucleotide composition, trinucleotide composition and split trinucleotide composition (STNC). Various statistical models were utilized as learner hypotheses. Jackknife test was employed to evaluate the success rates of the proposed model. The experiential results expressed that SVM, in combination with STNC, has obtained an outstanding performance on all benchmark datasets. The predicted outcomes of the proposed model "iNuc-STNC" is higher than current state of the art methods in the literature so far. It is ascertained that the "iNuc-STNC" model will provide a rudimentary framework for the pharmaceutical industry in the development of drug design. PMID:27271822

  2. Structural and dynamical characterization of the Miz-1 zinc fingers 5-8 by solution-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, David; Bedard, Mikaeel; Bilodeau, Josee; Lavigne, Pierre, E-mail: pierre.lavigne@usherbrooke.ca [Universite de Sherbrooke, Departement de Biochimie, Faculte de Medecine et des Sciences de la Sante, Institut de Pharmacologie de Sherbrooke (Canada)

    2013-10-15

    Myc-interacting zinc finger protein-1 (Miz-1) is a BTB/POZ transcription factor that activates the transcription of cytostatic genes, such as p15{sup INK4B} or p21{sup CIP1}. The C-terminus of Miz-1 contains 13 consensus C{sub 2}H{sub 2} zinc finger domains (ZF). ZFs 1-4 have been shown to interact with SMAD3/4, while the remaining ZFs are expected to bind the promoters of target genes. We have noted unusual features in ZF 5 and the linker between ZFs 5 and 6. Indeed, a glutamate is found instead of the conserved basic residue two positions before the second zinc-coordinating histidine on the ZF 5 helix, and the linker sequence is DTDKE in place of the classical TGEKP sequence. In a canonical {beta}{beta}{alpha} fold, such unusual primary structure elements should cause severe electrostatic repulsions. In this context, we have characterized the structure and the dynamics of a Miz-1 construct comprising ZFs 5-8 (Miz 5-8) by solution-state NMR. Whilst ZFs 5, 7 and 8 were shown to adopt the classical {beta}{beta}{alpha} fold for C{sub 2}H{sub 2} ZFs, the number of long-range NOEs was insufficient to define a classical fold for ZF 6. We show by using {sup 15}N-relaxation dispersion experiments that this lack of NOEs is due to the presence of extensive motions on the {mu}s-ms timescale. Since this negatively charged region would have to be located near the phosphodiester backbone in a DNA complex, we propose that in addition to promoting conformational searches, it could serve as a hinge region to keep ZFs 1-4 away from DNA.

  3. Characterization of the Free State Ensemble of the CoRNR Box Motif by Molecular Dynamics Simulations.

    Science.gov (United States)

    Cino, Elio A; Choy, Wing-Yiu; Karttunen, Mikko

    2016-02-18

    Intrinsically disordered proteins (IDPs) and regions are highly prevalent in eukaryotic proteomes, and like folded proteins, they perform essential biological functions. Interaction sites in folded proteins are generally formed by tertiary structures, whereas IDPs use short segments called linear motifs (LMs). Despite their short length and lack of stable structure, LMs may have considerable structural propensities, which often resemble bound-state conformations with targets. Structural data is crucial for understanding the molecular basis of protein interactions and development of targeted pharmaceuticals, but IDPs present considerable challenges to experimental techniques. As a result, IDPs are largely underrepresented in the Protein Data Bank. In the face of experimental challenges, molecular dynamics (MD) simulations have proven to be a useful tool for structural characterization of IDPs. Here, the free state ensemble of the nuclear receptor corepressor 1 (NCOR1) CoRNR box 3 motif, which is important for binding to nuclear receptors to control gene expression, is studied using MD simulations of a total of 8 μs. Transitions between disordered and α-helical conformations resembling a bound-state structure were observed throughout the trajectory, indicating that the motif may have a natural conformational bias toward bound-state structures. The data shows that the disordered and folded populations are separated by a low energy (4-6 kJ/mol) barrier, and the presence of off-pathway intermediates, leading to a C-terminally folded species that cannot efficiently transition into a completely folded conformation. Structural transitions and folding pathways within the free state ensemble were well-described by principal component analysis (PCA) of the peptide backbone dihedral angles, with the analysis providing insight for increasing structural homogeneity of the ensemble. PMID:26794929

  4. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

    Directory of Open Access Journals (Sweden)

    Sansavini Silviero

    2010-10-01

    Full Text Available Abstract Background Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-Methylcyclopropene. Results To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies, we utilized both homologous and heterologous (tomato microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. Conclusion Our combined strategy based on microarray hybridization enabled transcriptome characterization

  5. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased Molecular Dynamics simulations and spectral algorithms

    OpenAIRE

    Sgourakis, Nikolaos G.; Merced-Serrano, Myrna; Boutsidis, Christos; Drineas, Petros; Du, Zheming; Wang, Chunyu; Garcia, Angel E.

    2010-01-01

    Aβ(1-42) is the highly pathologic isoform of amyloid-β, the peptide constituent of fibrils and neurotoxic oligomers involved in Alzheimer’s disease. Recent studies on the structural features of Aβ in water have suggested that the system can be described as an ensemble of distinct conformational species in fast exchange. Here, we use replica exchange molecular dynamics simulations (REMD) to characterize the conformations accessible to Aβ42 in explicit water solvent, under the ff99SB forcefield...

  6. Space Shuttle Main Engine Low Pressure Oxidizer Turbo-Pump Inducer Dynamic Environment Characterization through Water Model and Hot-Fire Testing

    Science.gov (United States)

    Arellano, Patrick; Patton, Marc; Schwartz, Alan; Stanton, David

    2006-01-01

    The Low Pressure Oxidizer Turbopump (LPOTP) inducer on the Block II configuration Space Shuttle Main Engine (SSME) experienced blade leading edge ripples during hot firing. This undesirable condition led to a minor redesign of the inducer blades. This resulted in the need to evaluate the performance and the dynamic environment of the redesign, relative to the current configuration, as part of the design acceptance process. Sub-scale water model tests of the two inducer configurations were performed, with emphasis on the dynamic environment due to cavitation induced vibrations. Water model tests were performed over a wide range of inlet flow coefficient and pressure conditions, representative of the scaled operating envelope of the Block II SSME, both in flight and in ground hot-fire tests, including all power levels. The water test hardware, facility set-up, type and placement of instrumentation, the scope of the test program, specific test objectives, data evaluation process and water test results that characterize and compare the two SSME LPOTP inducers are discussed. In addition, dynamic characteristics of the two water models were compared to hot fire data from specially instrumented ground tests. In general, good agreement between the water model and hot fire data was found, which confirms the value of water model testing for dynamic characterization of rocket engine turbomachinery.

  7. Continuous wave W- and D-Band EPR spectroscopy offer “sweet-spots” for characterizing conformational changes and dynamics in intrinsically disordered proteins

    International Nuclear Information System (INIS)

    Highlights: • W- and D-Band line shapes are sensitive to motions in the 0.1–2 ns time regime. • These frequencies effectively report on conformational dynamics of IDPs. • W-band spectra reflecting helical formation in IA3 is experimentally demonstrated. - Abstract: Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for characterizing conformational sampling and dynamics in biological macromolecules. Here we demonstrate that nitroxide spectra collected at frequencies higher than X-band (∼9.5 GHz) have sensitivity to the timescale of motion sampled by highly dynamic intrinsically disordered proteins (IDPs). The 68 amino acid protein IA3, was spin-labeled at two distinct sites and a comparison of X-band, Q-band (35 GHz) and W-band (95 GHz) spectra are shown for this protein as it undergoes the helical transition chemically induced by tri-fluoroethanol. Experimental spectra at W-band showed pronounced line shape dispersion corresponding to a change in correlation time from ∼0.3 ns (unstructured) to ∼0.6 ns (α-helical) as indicated by comparison with simulations. Experimental and simulated spectra at X- and Q-bands showed minimal dispersion over this range, illustrating the utility of SDSL EPR at higher frequencies for characterizing structural transitions and dynamics in IDPs

  8. Decoherence of many-spin systems in NMR: From molecular characterization to an environmentally induced quantum dynamical phase transition

    OpenAIRE

    Alvarez, Gonzalo A.

    2007-01-01

    The control of open quantum systems has a fundamental relevance for fields ranging from quantum information processing to nanotechnology. Typically, the system whose coherent dynamics one wants to manipulate, interacts with an environment that smoothly degrades its quantum dynamics. Thus, a precise understanding of the inner mechanisms of this process, called "decoherence", is critical to develop strategies to control the quantum dynamics. In this thesis we solved the generalized Liouville-vo...

  9. Characterization of age-related modifications of upper limb motor control strategies in a new dynamic environment

    Directory of Open Access Journals (Sweden)

    Dario Paolo

    2008-11-01

    Full Text Available Abstract Background In the past, several research groups have shown that when a velocity dependent force field is applied during upper limb movements subjects are able to deal with this external perturbation after some training. This adaptation is achieved by creating a new internal model which is included in the normal unperturbed motor commands to achieve good performance. The efficiency of this motor control mechanism can be compromised by pathological disorders or by muscular-skeletal modifications such as the ones due to the natural aging process. In this respect, the present study aimed at identifying the age-related modifications of upper limb motor control strategies during adaptation and de-adaptation processes in velocity dependent force fields. Methods Eight young and eight elderly healthy subjects were included in the experiment. Subjects were instructed to perform pointing movements in the horizontal plane both in a null field and in a velocity dependent force field. The evolution of smoothness and hand path were used to characterize the performance of the subjects. Furthermore, the ability of modulating the interactive torque has been used as a paradigm to explain the observed discoordinated patterns during the adaptation process. Results The evolution of the kinematics during the experiments highlights important behavioural differences between the two groups during the adaptation and de-adaptation processes. In young subjects the improvement of movement smoothness was in accordance with the expected learning trend related to the consolidation of the internal model. On the contrary, elders did not show a coherent learning process. The kinetic analysis pointed out the presence of different strategies for the compensation of the external perturbation: older people required an increased involvement of the shoulder with a different modulation of joint torque components during the evolution of the experiments. Conclusion The results

  10. Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Amaro, Rommie E [ORNL; Cheng, Xiaolin [ORNL; Ivanov, Ivaylo N [ORNL; Xu, Dong [ORNL; McCammon, Jonathan [ORNL

    2009-01-01

    The comparative dynamics and inhibitor binding free energies of group-1 and group-2 pathogenic influenza A subtype neuraminidase (NA) enzymes are of fundamental biological interest and relevant to structure-based drug design studies for antiviral compounds. In this work, we present seven generalized Born molecular dynamics simulations of avian (N1)- and human (N9)-type NAs in order to probe the comparative flexibility of the two subtypes, both with and without the inhibitor oseltamivir bound. The enhanced sampling obtained through the implicit solvent treatment suggests several provocative insights into the dynamics of the two subtypes, including that the group-2 enzymes may exhibit similar motion in the 430-binding site regions but different 150-loop motion. End-point free energy calculations elucidate the contributions to inhibitor binding free energies and suggest that entropic considerations cannot be neglected when comparing across the subtypes. We anticipate the findings presented here will have broad implications for the development of novel antiviral compounds against both seasonal and pandemic influenza strains.

  11. Evaluation of the role of dynamic 64-MDCT in the characterization and work up of breast cancer

    OpenAIRE

    Moustafa A. Kader A. Wahab; Hoda Abdel Kareem

    2015-01-01

    Background: Imaging of the breast is a vital component not only for breast cancer screening, but also for diagnosis and treatment. Dynamic MDCT has a very promising role as diagnostic tool in breast cancer patients. Objective: This study aimed to emphasize the role of 64 MDCT in the work up of breast cancer. Patients and methods: Between October 2012 to April 2014, 100 consecutive patients with suspicious breast lesions underwent bilateral mammography, breast ultrasound and dynamic MDCT...

  12. Characterizing real-time forest disturbance in a dynamic land surface model with implications for operational streamflow forecasting using WRF-Hydro

    Science.gov (United States)

    Dugger, A. L.; Gochis, D. J.; McCreight, J. L.; Yu, W.

    2014-12-01

    Forest cover changes have potential to induce large shifts in water fluxes, including short-term responses like changing downstream flood risk and longer-term feedbacks between land surface water and the atmosphere that can influence local and regional weather patterns. Two main challenges in capturing vegetation changes within hydrological forecasting systems, however, are finding real-time data streams to characterize these changes and the ability to accurately translate readily observable qualities such as "greenness" to modelled biophysical and biochemical properties. Here we investigate the feasibility of using near real-time remote sensing products paired with a continuous-running atmosphere - land surface - hydrology model to characterize vegetation disturbance and regrowth dynamics, with the ultimate goal of improving short-range (hourly to daily) and mid-range (weekly to monthly) operational streamflow forecasts. We use WRF-Hydro, a framework for coupling components of land surface models, hydrologic models, and the Weather Research and Forecasting (WRF) atmospheric model. We take advantage of newly implemented data assimilation techniques in WRF-Hydro to assimilate MODIS near real-time observations into the NoahMP dynamic vegetation model to simulate disturbance and regrowth following (1) wildfire in the Southwest U.S. and (2) plantation forestry management in the Southeast U.S. Ranges of modeled vegetation structural (leaf and stem area, height, canopy organization) and biochemical (chlorophyll content) characteristics consistent with MODIS observations are used to estimate uncertainty ranges in downstream flow predictions. The WRF-Hydro framework allows us to characterize changes in streamflow behavior expected after these modeled forest disturbances, evaluate when and where assimilation of vegetation characteristics from remote sensing is most important to streamflow prediction, and quantify the role of recovering vegetation biophysical

  13. Hovering and forward flight of the hawkmoth Manduca sexta: trim search and 6-DOF dynamic stability characterization.

    Science.gov (United States)

    Kim, Joong-Kwan; Han, Jong-Seob; Lee, Jun-Seong; Han, Jae-Hung

    2015-10-01

    We show that the forward flight speed affects the stability characteristics of the longitudinal and lateral dynamics of a flying hawkmoth; dynamic modal structures of both the planes of motion are altered due to variations in the stability derivatives. The forward flight speed u e is changed from 0.00 to 1.00 m s(-1) with an increment of 0.25 m s(-1). (The equivalent advance ratio is 0.00 to 0.38; the advance ratio is the ratio of the forward flight speed to the average wing tip speed.) As the flight speed increases, for the longitudinal dynamics, an unstable oscillatory mode becomes more unstable. Also, we show that the up/down (w(b)) dynamics become more significant at a faster flight speed due to the prominent increase in the stability derivative Z(u) (up/down force due to the forward/backward velocity). For the lateral dynamics, the decrease in the stability derivative L(v) (roll moment due to side slip velocity) at a faster flight speed affects a slightly damped stable oscillatory mode, causing it to become more stable; however, the t(half) (the time taken to reach half the amplitude) of this slightly damped stable oscillatory mode remains relatively long (∼12T at u(e) = 1 m s(-1); T is wingbeat period) compared to the other modes of motion, meaning that this mode represents the most vulnerable dynamics among the lateral dynamics at all flight speeds. To obtain the stability derivatives, trim conditions for linearization are numerically searched to find the exact trim trajectory and wing kinematics using an algorithm that uses the gradient information of a control effectiveness matrix and fully coupled six-degrees of freedom nonlinear multibody equations of motion. With this algorithm, trim conditions that consider the coupling between the dynamics and aerodynamics can be obtained. The body and wing morphology, and the wing kinematics used in this study are based on actual measurement data from the relevant literature. The aerodynamic model of the flapping

  14. Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations

    NARCIS (Netherlands)

    Soto, P; Colombo, G

    2004-01-01

    Molecular dynamics (MD) simulations have been performed on a series of mutants of the 20 amino acid peptide Betanova in order to critically assess the ability of MD simulations to reproduce the folding and stability of small beta-sheet-forming peptides on currently accessible timescales. Simulations

  15. The linear and non-linear characterization of dust ion acoustic mode in complex plasma in presence of dynamical charging of dust

    International Nuclear Information System (INIS)

    A systematic theoretical investigation has been carried out on the role of dust charging dynamics on the nature and stability of DIA (Dust Ion Acoustic) mode in complex plasma. The study has been made for both linear and non-linear scale regime of DIA mode. The observed results have been characterized in terms of background plasma responses towards dust surface responsible for dust charge fluctuation, invoking important dusty plasma parameters, especially the ion flow speed and dust size. The linear analyses confirm the nature of instability in DIA mode in presence of dust charge fluctuation. The instability shows a damping of DIA mode in subsonic flow regime followed by a gradual growth in instability in supersonic limit of ion flow. The strength of non-linearity and their existence domain is found to be driven by different dusty plasma parameters. As dust is ubiquitous in interstellar medium with plasma background, the study also addresses the possible effect of dust charging dynamics in gravito-electrostatic characterization and the stability of dust molecular clouds especially in proto-planetary disc. The observations are influential and interesting towards the understanding of dust settling mechanism and formation of dust environments in different regions in space

  16. Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program

    Directory of Open Access Journals (Sweden)

    Cornelia Amariei

    2014-09-01

    Full Text Available The structural dynamics of chromatin have been implicated in the regulation of fundamental eukaryotic processes, such as DNA transcription, replication and repair. Although previous studies have revealed that the chromatin landscape, nucleosome remodeling and histone modification events are intimately tied into cellular energetics and redox state, few studies undertake defined time-resolved measurements of these state variables. Here, we use metabolically synchronous, continuously-grown yeast cultures to measure DNA occupancy and track global patterns with respect to the metabolic state of the culture. Combined with transcriptome analyses and ChIP-qPCR experiments, these paint an intriguing picture where genome-wide nucleosome focusing occurs during the recovery of energy charge, followed by clearance of the promoter regions and global transcriptional slow-down, thus indicating a nucleosome-mediated “reset point” for the cycle. The reset begins at the end of the catabolic and stress-response transcriptional programs and ends prior to the start of the anabolic and cell-growth transcriptional program, and the histones on genes from both the catabolic and anabolic superclusters are deacetylated.

  17. Characterization of adenomas and metastases in the adrenals: comparison between spin-echo sequences and Gd-DTPA enhanced dynamic studies

    International Nuclear Information System (INIS)

    Nineteen patients with adrenal masses (9 metastases and 10 adenomas) were studied with magnetic resonance spin-echo sequences and with dynamic perfusion with gradient-echo (GE) sequences after gadolinium diethylenetriamine-pentaacetic acid injection. In studies following Gd-DTPA injection, sequential imaging during suspended respiration was obtained. Signal intensities of adrenal masses and retroperitonel fat were measured in the region of interest. The relative signal intensities of lesion and fat were determined and compared in dynamic contrast-enhanced studies. Results were tabulated and plotted in diagrams as a function of time. Sixteen lesions out of 19 were correctly classified by means of SE sequences, with an 84% diagnostic accuracy, whereas 18 out of 19 lesions were characterized by means of GE sequences, with a 95% accuracy. In the dynamic study, adenomas showed mild enhancement and quicker washout than metastases which, in turn, showed a strong enhancement and a much slower washout. The most significant values were obtained in scans taken after 10 min, where adenomas showed signal to lesion/signal to fat values lower than 1.1, whereas metastases showed much higher values in all cases. (orig.)

  18. Fluid Dynamic Characterization of a Polymeric Heart Valve Prototype (Poli-Valve) tested under Continuous and Pulsatile Flow Conditions

    OpenAIRE

    Gaetano, Francesco De; Serrani, Marta; Bagnoli, Paola; Brubert, Jacob; Stasiak, Joanna; Moggridge, Geoff D.; Costantino, Maria Laura

    2015-01-01

    Purpose Only mechanical and biological heart valve prostheses are currently commercially available. The former show longer durability but require anticoagulant therapy; the latter display better fluid dynamic behavior but do not have adequate durability. New Polymeric Heart Valves (PHVs) could potentially combine the hemodynamic properties of biological valves with the durability of mechanical valves. This work presents a hydrodynamic evaluation of 2 groups of newly developed supra-annula...

  19. A critical role for heat shock transcription factor in establishing a nucleosome-free region over the TATA-initiation site of the yeast HSP82 heat shock gene.

    OpenAIRE

    Gross, D S; Adams, C C; Lee, S; Stentz, B

    1993-01-01

    Heat shock genes are poised for rapid transcriptional activation in response to environmental stress. A universal structural characteristic of such genes is the presence of a nucleosome-free, DNase I hypersensitive promoter region. Here we investigate the structural and functional effects of mutating HSE1, the preferred heat shock factor (HSF) binding site upstream of the yeast HSP82 gene. In situ deletion or substitution of this sequence reduces both basal and induced transcription by at lea...

  20. Advanced solid-state NMR techniques for characterization of membrane protein structure and dynamics: Application to Anabaena Sensory Rhodopsin

    Science.gov (United States)

    Ward, Meaghan E.; Brown, Leonid S.; Ladizhansky, Vladimir

    2015-04-01

    Studies of the structure, dynamics, and function of membrane proteins (MPs) have long been considered one of the main applications of solid-state NMR (SSNMR). Advances in instrumentation, and the plethora of new SSNMR methodologies developed over the past decade have resulted in a number of high-resolution structures and structural models of both bitopic and polytopic α-helical MPs. The necessity to retain lipids in the sample, the high proportion of one type of secondary structure, differential dynamics, and the possibility of local disorder in the loop regions all create challenges for structure determination. In this Perspective article we describe our recent efforts directed at determining the structure and functional dynamics of Anabaena Sensory Rhodopsin, a heptahelical transmembrane (7TM) protein. We review some of the established and emerging methods which can be utilized for SSNMR-based structure determination, with a particular focus on those used for ASR, a bacterial protein which shares its 7TM architecture with G-protein coupled receptors.