WorldWideScience

Sample records for chromatin architecture reflects

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

    KAUST Repository

    Jégu, Teddy

    2015-10-12

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

  2. Chromatin architecture and gene expression in Escherichia coli

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Ussery, David

    2004-01-01

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

  3. A Declarative Approach to Architectural Reflection

    DEFF Research Database (Denmark)

    Ingstrup, Mads; Hansen, Klaus Marius

    2005-01-01

    Recent research shows runtime architectural reflection is instrumental in, for instance, building adaptive and flexible systems or checking correspondence between design and implementation. Moreover, experience with computational reflection in various branches of computer science shows that the...... interface through which the meta-information of the running system is accessed, and possibly modified, lies at the heart of designing reflective systems. This paper proposes that such an interface should be like a database: accessed through queries expressed using the concepts with which architecture is...... described. Specifically, our contributions are: (1) a presentation of the general idea of a query-based approach to architectural reflection, (2) a definition of an Architectural Query Language (AQL) in which perspectives on an architectural model can be expressed as queries, (3) a prototype of a system...

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

    Directory of Open Access Journals (Sweden)

    Valeria Visone

    2014-09-01

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

  5. Runtime software architecture based on reflective middleware

    Institute of Scientific and Technical Information of China (English)

    HUANG Gang; MEI Hong; YANG Fuqing

    2004-01-01

    There exists a consensus that software architecture (SA) plays a central role in software development and also plays an important role in the lifecycle phases after software delivery. Particularly, SA can be used to reduce the great difficulty and cost of software maintenance and evolution. In this paper, runtime software architecture (RSA) based on reflective middleware is proposed to support architecture-based software maintenance and evolution. In this approach, the actual states and behaviors of the runtime system can be observed and manipulated in a consistent and understandable way through its architectural view. Being an accurate, up-to-date, semantic and operable view of SA, RSA looks components and connectors as "white-box" entities to accurately and thoroughly describe the runtime system, extends traditional architecture description languages to formally describe itself and naturally inherit plentiful semantics in traditional views of SA, and utilizes reflective middleware to observe and manipulate the runtime system. In order to demonstrate the feasibility of this approach, a reflective J2EE application server, called PKUAS, is implemented to observe and manipulate the components, connectors and constraints in the runtime system. Finally, the performance evaluation proves that making RSA explicit and operable at runtime has little effect on the runtime system.

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

    Science.gov (United States)

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

    2016-08-26

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    OpenAIRE

    Van Bortle, Kevin; Corces, Victor G.

    2013-01-01

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

  9. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-08-21

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

  11. Reflective Subjects in Kant and Architectural Design Education

    Science.gov (United States)

    Rawes, Peg

    2007-01-01

    In architectural design education, students develop drawing, conceptual, and critical skills which are informed by their ability to reflect upon the production of ideas in design processes and in the urban, environmental, social, historical, and cultural context that define architecture and the built environment. Reflective actions and thinking…

  12. The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues.

    Science.gov (United States)

    Cuadrado, Ana; Remeseiro, Silvia; Graña, Osvaldo; Pisano, David G; Losada, Ana

    2015-03-31

    Cohesin, which in somatic vertebrate cells consists of SMC1, SMC3, RAD21 and either SA1 or SA2, mediates higher-order chromatin organization. To determine how cohesin contributes to the establishment of tissue-specific transcriptional programs, we compared genome-wide cohesin distribution, gene expression and chromatin architecture in cerebral cortex and pancreas from adult mice. More than one third of cohesin binding sites differ between the two tissues and these show reduced overlap with CCCTC-binding factor (CTCF) and are enriched at the regulatory regions of tissue-specific genes. Cohesin/CTCF sites at active enhancers and promoters contain, at least, cohesin-SA1. Analyses of chromatin contacts at the Protocadherin (Pcdh) and Regenerating islet-derived (Reg) gene clusters, mostly expressed in brain and pancreas, respectively, revealed remarkable differences that correlate with the presence of cohesin. We could not detect significant changes in the chromatin contacts at the Pcdh locus when comparing brains from wild-type and SA1 null embryos. In contrast, reduced dosage of SA1 altered the architecture of the Reg locus and decreased the expression of Reg genes in the pancreas of SA1 heterozygous mice. Given the role of Reg proteins in inflammation, such reduction may contribute to the increased incidence of pancreatic cancer observed in these animals. PMID:25735743

  13. Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality

    Directory of Open Access Journals (Sweden)

    Ian C. Welsh

    2015-10-01

    Full Text Available Expression of Pitx2 on the left side of the embryo patterns left-right (LR organs including the dorsal mesentery (DM, whose asymmetric cell behavior directs gut looping. Despite the importance of organ laterality, chromatin-level regulation of Pitx2 remains undefined. Here, we show that genes immediately neighboring Pitx2 in chicken and mouse, including a long noncoding RNA (Pitx2 locus-asymmetric regulated RNA or Playrr, are expressed on the right side and repressed by Pitx2. CRISPR/Cas9 genome editing of Playrr, 3D fluorescent in situ hybridization (FISH, and variations of chromatin conformation capture (3C demonstrate that mutual antagonism between Pitx2 and Playrr is coordinated by asymmetric chromatin interactions dependent on Pitx2 and CTCF. We demonstrate that transcriptional and morphological asymmetries driving gut looping are mirrored by chromatin architectural asymmetries at the Pitx2 locus. We propose a model whereby Pitx2 auto-regulation directs chromatin topology to coordinate LR transcription of this locus essential for LR organogenesis.

  14. Chromatin architecture, CTCF and V(D)J recombination: managing long-distance relationships at antigen receptor loci1

    OpenAIRE

    Shih, Han-Yu; Krangel, Michael S.

    2013-01-01

    The rearrangement of T and B lymphocyte antigen receptor loci occurs within a highly complex chromosomal environment and is orchestrated through complex mechanisms. Over the past decade, a large body of literature has highlighted the significance of chromatin architecture at antigen receptor loci in supporting the genomic assembly process: in preparation for recombination, these loci tend to contract and form multiple loops that shorten the distances between gene segments and facilitate recom...

  15. Echo thresholds for reflections from acoustically diffusive architectural surfaces.

    Science.gov (United States)

    Robinson, Philip W; Walther, Andreas; Faller, Christof; Braasch, Jonas

    2013-10-01

    When sound reflects from an irregular architectural surface, it spreads spatially and temporally. Extensive research has been devoted to prediction and measurement of diffusion, but less has focused on its perceptual effects. This paper examines the effect of temporal diffusion on echo threshold. There are several notable differences between the waveform of a reflection identical to the direct sound and one from an architectural surface. The onset and offset are damped and the energy is spread in time; hence, the reflection response has a lower peak amplitude, and is decorrelated from the direct sound. The perceptual consequences of these differences are previously undocumented. Echo threshold tests are conducted with speech and music signals, using direct sound and a simulated reflection that is either identical to the direct sound or has various degrees of diffusion. Results indicate that for a speech signal, diffuse reflections are less easily detectable as a separate auditory event than specular reflections of the same total energy. For a music signal, no differences are observed between the echo thresholds for reflections with and without temporal diffusion. Additionally, echo thresholds are found to be shorter for speech than for music, and shorter for spatialized than for diotic presentation of signals. PMID:24116414

  16. High-order chromatin architecture shapes the landscape of chromosomal alterations in cancer

    Science.gov (United States)

    Fudenberg, Geoffrey; Getz, Gad; Meyerson, Matthew; Mirny, Leonid

    2012-02-01

    The rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the evidence for two major forces, spatial chromosome structure and purifying (or negative) selection, that shape the landscape of somatic copy-number alterations (SCNAs) in cancer (Beroukhim et al, 2010). Using a maximum likelihood framework we compare SCNA maps and three-dimensional genome architecture as determined by genome-wide chromosome conformation capture (HiC) and described by the proposed fractal-globule (FG) model (Lieberman-Aiden and Van Berkum et al, 2009). This analysis provides evidence that the distribution of chromosomal alterations in cancer is spatially related to three-dimensional genomic architecture and additionally suggests that purifying selection as well as positive selection shapes the landscape of SCNAs during somatic evolution of cancer cells.

  17. Personality is reflected in the brain's intrinsic functional architecture.

    Directory of Open Access Journals (Sweden)

    Jonathan S Adelstein

    Full Text Available Personality describes persistent human behavioral responses to broad classes of environmental stimuli. Investigating how personality traits are reflected in the brain's functional architecture is challenging, in part due to the difficulty of designing appropriate task probes. Resting-state functional connectivity (RSFC can detect intrinsic activation patterns without relying on any specific task. Here we use RSFC to investigate the neural correlates of the five-factor personality domains. Based on seed regions placed within two cognitive and affective 'hubs' in the brain--the anterior cingulate and precuneus--each domain of personality predicted RSFC with a unique pattern of brain regions. These patterns corresponded with functional subdivisions responsible for cognitive and affective processing such as motivation, empathy and future-oriented thinking. Neuroticism and Extraversion, the two most widely studied of the five constructs, predicted connectivity between seed regions and the dorsomedial prefrontal cortex and lateral paralimbic regions, respectively. These areas are associated with emotional regulation, self-evaluation and reward, consistent with the trait qualities. Personality traits were mostly associated with functional connections that were inconsistently present across participants. This suggests that although a fundamental, core functional architecture is preserved across individuals, variable connections outside of that core encompass the inter-individual differences in personality that motivate diverse responses.

  18. Nuclear organization and 3D chromatin architecture in cognition and neuropsychiatric disorders.

    Science.gov (United States)

    Medrano-Fernández, Alejandro; Barco, Angel

    2016-01-01

    The current view of neuroplasticity depicts the changes in the strength and number of synaptic connections as the main physical substrate for behavioral adaptation to new experiences in a changing environment. Although transcriptional regulation is known to play a role in these synaptic changes, the specific contribution of activity-induced changes to both the structure of the nucleus and the organization of the genome remains insufficiently characterized. Increasing evidence indicates that plasticity-related genes may work in coordination and share architectural and transcriptional machinery within discrete genomic foci. Here we review the molecular and cellular mechanisms through which neuronal nuclei structurally adapt to stimuli and discuss how the perturbation of these mechanisms can trigger behavioral malfunction. PMID:27595843

  19. Painting a Clearer Picture of Chromatin.

    Science.gov (United States)

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

    2016-02-22

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

  20. Gray level co-occurrence matrix algorithm as pattern recognition biosensor for oxidopamine-induced changes in lymphocyte chromatin architecture.

    Science.gov (United States)

    Pantic, Igor; Dimitrijevic, Draga; Nesic, Dejan; Petrovic, Danica

    2016-10-01

    We demonstrate that a proapoptotic chemical agent, oxidopamine, induces dose dependent changes in chromatin textural patterns which can be quantified using the Gray level co-occurrence matrix (GLCM) method. Peripheral blood (heparin-pretreated) samples were treated with oxidopamine (6-OHDA, 6-hydroxydopamine) to achieve effective concentrations of 100, 200 and 300µM. The samples were smeared on microscope slides and fixated in methanol. The smears were stained using a modification of Feulgen method for DNA visualization. For each stained smear, a sample of 30 lymphocyte chromatin structures were visualized and analyzed. This way, textural parameters for a total of 120 nuclei micrographs were calculated. For each chromatin structure, five different GLCM features were calculated: angular second moment, GLCM entropy, inverse difference moment, GLCM correlation, and GLCM variance. Oxidopamine induced the rise of the values of GLCM entropy and variance, and the reduction of angular second moment, correlation, and inverse difference moment. The trends for GLCM parameter changes were found to be highly significant (palgorithm might be successfully used in detection and evaluation of discrete early apoptotic structural changes in Feulgen-stained chromatin of peripheral blood lymphocytes that are not detectable using conventional microscopy/cell biology techniques. PMID:27424557

  1. The influence of acoustic reflections from diffusive architectural surfaces on spatial auditory perception

    Science.gov (United States)

    Robinson, Philip W.

    This thesis addresses the effect of reflections from diffusive architectural surfaces on the perception of echoes and on auditory spatial resolution. Diffusive architectural surfaces play an important role in performance venue design for architectural expression and proper sound distribution. Extensive research has been devoted to the prediction and measurement of the spatial dispersion. However, previous psychoacoustic research on perception of reflections and the precedence effect has focused on specular reflections. This study compares the echo threshold of specular reflections, against those for reflections from realistic architectural surfaces, and against synthesized reflections that isolate individual qualities of reflections from diffusive surfaces, namely temporal dispersion and spectral coloration. In particular, the activation of the precedence effect, as indicated by the echo threshold is measured. Perceptual tests are conducted with direct sound, and simulated or measured reflections with varying temporal dispersion. The threshold for reflections from diffusive architectural surfaces is found to be comparable to that of a specular re ection of similar energy rather than similar amplitude. This is surprising because the amplitude of the dispersed re ection is highly attenuated, and onset cues are reduced. This effect indicates that the auditory system is integrating re ection response energy dispersed over many milliseconds into a single stream. Studies on the effect of a single diffuse reflection are then extended to a full architectural enclosure with various surface properties. This research utilizes auralizations from measured and simulated performance venues to investigate spatial discrimination of multiple acoustic sources in rooms. It is found that discriminating the lateral arrangement of two sources is possible at narrower separation angles when reflections come from at rather than diffusive surfaces. Additionally, subjective impressions are

  2. H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

    LENUS (Irish Health Repository)

    Shieh, Grace S.

    2011-12-22

    Abstract Background The packaging of DNA into chromatin regulates transcription from initiation through 3\\' end processing. One aspect of transcription in which chromatin plays a poorly understood role is the co-transcriptional splicing of pre-mRNA. Results Here we provide evidence that H2B monoubiquitylation (H2BK123ub1) marks introns in Saccharomyces cerevisiae. A genome-wide map of H2BK123ub1 in this organism reveals that this modification is enriched in coding regions and that its levels peak at the transcribed regions of two characteristic subgroups of genes. First, long genes are more likely to have higher levels of H2BK123ub1, correlating with the postulated role of this modification in preventing cryptic transcription initiation in ORFs. Second, genes that are highly transcribed also have high levels of H2BK123ub1, including the ribosomal protein genes, which comprise the majority of intron-containing genes in yeast. H2BK123ub1 is also a feature of introns in the yeast genome, and the disruption of this modification alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3), which functionally correlates with alternative RNA splicing in humans. In addition, the deletion of genes encoding the U2 snRNP subunits, Lea1 or Msl1, in combination with an htb-K123R mutation, leads to synthetic lethality. Conclusion These data suggest that H2BK123ub1 facilitates cross talk between chromatin and pre-mRNA splicing by modulating the distribution of intronic and exonic histone modifications.

  3. From Molecular Gastronomy to Molecular Architecture: Reflections towards a new architectural praxis

    OpenAIRE

    Rocha, Joao

    2011-01-01

    The relationship between architecture and research has been barely discussed and by making use of critical reading this paper proposes to investigate how other disciplines started to use Research and Development (R&D) as part of their creative processes. In particular it explores how gastronomy has unfolded new R&D paths through the revolutionary work of three leading chefs: Ferrian Adria, Rene Redzepi and Grant Achatz, illustrating the deep impact that the use of R&D had in this field and ho...

  4. Morphological changes of nuclear and chromatin architecture after microwave electromagnetic field exposure in 3T3 fibroblast cell cultures

    International Nuclear Information System (INIS)

    It is already demonstrated in the literature that electromagnetic fields, particularly the microwave irradiation could be a powerful weapon against human tumors , but also against human body itself, depending on the wave parameters and irradiation time. The effects of microwave electromagnetic fields on living systems were studied in detail all over the world and, furthermore, the potential of intracellular damages by cytoskeleton, nuclear, chromatin and DNA alterations were carefully evaluated. In this study, the authors emphasize the morphological changes of nucleus and chromatin in fibroblast cell line 3T3 after microwave exposure with progressive increasing powers and times of irradiation. It was used a pulsed wave with 915 MHz frequency, with forward power ranging between 3 - 10 W, emitted by a helical microwave antenna placed into the cell culture medium, close to the cell monolayer. The authors tried to define certain severity stages of nuclear material alterations following different wave intensities and to compare these effects with other cytoplasmic organelle alterations. It was found that the nuclear material is the most sensitive intracellular structure in microwave electromagnetic field exposure. Also the authors tried to establish a well-defined protocol of irradiation with microwave electromagnetic fields in order to destroy the microtubule system of cytoskeleton in different types of cellular lines, in vitro. The cytoskeleton structure was evaluated by immunofluorescence methods. In non-muscle cells the cytoskeleton stability is achieved by interaction between microtubule system and actin filaments. Microtubule depolymerization by microwave exposure produces a secondary instability of cytoskeleton, the actin filaments coupling and cell contractility. The increasing of fibroblast contractility allows a more efficient treatment of the wounds with low spontaneous healing. Electromagnetic therapy could be an alternative therapy in plastic surgery

  5. Chromatin deregulation in disease.

    Science.gov (United States)

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

    2016-03-01

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

  6. Coming to terms with chromatin structure.

    Science.gov (United States)

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

    2016-03-01

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

  7. What Went Wrong? Reflections on the Condition of Architecture and Urbanism in Lebanon

    Directory of Open Access Journals (Sweden)

    Elie Haddad

    2012-11-01

    Full Text Available In a short article presented at a conference in New York City two years ago, Joan Ockman lucidly diagnosed the contemporary dilemma faced by architecture, i.e. how to insert itself between a pessimistic discourse that warns of the end of time, and an uncritical surrender to globalization. This dilemma is now universal(i. It applies to New York City, where in the same context Kenneth Frampton commented on the dystopia of an “oddly paranoid, rather ruthless, instrumental and resentful landscape”(ii, as well as to other cities around the world, especially in the Third World, where more difficult conditions permeate architectural practice, resulting in even more devastated landscapes. This article will discuss issues that relate to architectural practice and pedagogy, drawing on specific examples in the context of Beirut, Lebanon, and reflecting on the impact of‘architectural education’ and the transformations within the architectural profession in this context. One can no longer deny the negative impact of economics on a profession that has been, for the most part, idealistic in its approach to the built environment, but the responsibility of architects and architectural education, can no longer beminimized in assessing the problems that cities like Beirut face today. i The conference was organized at Columbia University, andpublished as The State of Architecture at the Beginning of the21st Century, New York: Monacelli Press, 2003. See JoanOckman’s “Criticism in the Age of Globalization” [78-9]ii “Brief Reflections on the Predicament of Urbanism” , ibidem[13

  8. Estimation of vegetation LAI from hyperspectral reflectance data: Effects of soil type and plant architecture

    Science.gov (United States)

    Darvishzadeh, Roshanak; Skidmore, Andrew; Atzberger, Clement; van Wieren, Sip

    2008-09-01

    The retrieval of canopy biophysical variables is known to be affected by confounding factors such as plant type and background reflectance. The effects of soil type and plant architecture on the retrieval of vegetation leaf area index (LAI) from hyperspectral data were assessed in this study. In situ measurements of LAI were related to reflectances in the red and near-infrared and also to five widely used spectral vegetation indices (VIs). The study confirmed that the spectral contrast between leaves and soil background determines the strength of the LAI-reflectance relationship. It was shown that within a given vegetation species, the optimum spectral regions for LAI estimation were similar across the investigated VIs, indicating that the various VIs are basically summarizing the same spectral information for a given vegetation species. Cross-validated results revealed that, narrow-band PVI was less influenced by soil background effects (0.15 ≤ RMSE cv ≤ 0.56). The results suggest that, when using remote sensing VIs for LAI estimation, not only is the choice of VI of importance but also prior knowledge of plant architecture and soil background. Hence, some kind of landscape stratification is required before using hyperspectral imagery for large-scale mapping of vegetation biophysical variables.

  9. Remotely amplified combined ring-tree dense access network architecture using reflective RSOA-based ONU

    Science.gov (United States)

    Lazaro, Jose A.; Bock, Carlos; Polo, Victor; Martinez, Reynaldo I.; Prat, Josep

    2007-06-01

    A highly scalable access architecture achieving high density and featuring resiliency, centralized light-generation control, remote amplification, and colorless optical network unit with reflective semiconductor optical amplifier (RSOA) for upstream modulation is presented and experimentally demonstrated. It is based on a user-single-fiber completely passive outside plant and provides broadband connections to >1000 users distributed along large distances. It is believed to represent an intermediate step toward metro-access convergence and offers flexible configurations covering high- and low-density population areas.

  10. Reflections on architectural design education: The return of rationalism in the studio

    Directory of Open Access Journals (Sweden)

    Fathi Bashier

    2014-12-01

    The Department of Architecture and Urban Planning at the Ethiopian Institute of Technology EiT of Mekelle University (MU is currently developing a research program in which the development of and reflection on design methods is a key research area. Within this framework, the present study is intends to be an introductory effort to guide future empirical research. The present study aims to describe the design process of architects, and introduces theoretical and technical frameworks. The integrated design paradigm as a system of inquiry within the spatial relationship strategy is framed.

  11. Reflections on architectural design education: The return of rationalism in the studio

    OpenAIRE

    Fathi Bashier

    2014-01-01

    The design studio environment has remained the same throughout the past century. As the Studio Culture Task Force of the American Institute of Architecture Students (AIAS) (Koch et al., 2006) noted, the ongoing changes in architecture education are not aligned with today׳s fast-changing world, especially in the context of architectural practice. The AIAS analyzed the design studio problem and expressed doubts on the effectiveness of current studio practices in providing adequate design-thinki...

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

    Directory of Open Access Journals (Sweden)

    Alejandro Olguin-Lamas

    2011-03-01

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

  13. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

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

  14. Morphology of muscle attachment sites in the modern human hand does not reflect muscle architecture.

    Science.gov (United States)

    Williams-Hatala, E M; Hatala, K G; Hiles, S; Rabey, K N

    2016-01-01

    Muscle attachment sites (entheses) on dry bones are regularly used by paleontologists to infer soft tissue anatomy and to reconstruct behaviors of extinct organisms. This method is commonly applied to fossil hominin hand bones to assess their abilities to participate in Paleolithic stone tool behaviors. Little is known, however, about how or even whether muscle anatomy and activity regimes influence the morphologies of their entheses, especially in the hand. Using the opponens muscles from a sample of modern humans, we tested the hypothesis that aspects of hand muscle architecture that are known to be influenced by behavior correlate with the size and shape of their associated entheses. Results show no consistent relationships between these behaviorally-influenced aspects of muscle architecture and entheseal morphology. Consequently, it is likely premature to infer patterns of behavior, such as stone tool making in fossil hominins, from these same entheses. PMID:27334440

  15. Evidence-based design: theoretical and practical reflections of an emerging approach in office architecture

    OpenAIRE

    Sailer, K.; Budgen, A.; Lonsdale, N; Turner, A.; A Penn

    2008-01-01

    Evidence-based design is a practice that has emerged only relatively recently, inspired by a growing popularity of evidence-based approaches in other professions such as medicine. It has received greatest attention in design for the health sector, but has received less in office architecture, although this would seem not only to be beneficial for clients, but increasingly important in a changing business environment. This paper outlines the history and origins of evidence-based practice, its ...

  16. CTCF Binding Polarity Determines Chromatin Looping

    NARCIS (Netherlands)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

  18. Where splicing joins chromatin

    OpenAIRE

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

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

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

    Science.gov (United States)

    Gelato, Kathy A; Fischle, Wolfgang

    2008-04-01

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

  20. Vital architecture, slow momentum policy

    DEFF Research Database (Denmark)

    Braae, Ellen Marie

    2010-01-01

    A reflection on the relation between Danish landscape architecture policy and the statements made through current landscape architectural project.......A reflection on the relation between Danish landscape architecture policy and the statements made through current landscape architectural project....

  1. Electroactive semi-interpenetrating polymer networks architecture with tunable IR reflectivity

    Science.gov (United States)

    Chevrot, C.; Teyssié, D.; Verge, P.; Goujon, L.; Tran-Van, F.; Vidal, F.; Aubert, P. H.; Peralta, S.; Sauques, L.

    2011-04-01

    A promising alternative of multi-layered devices showing electrochromic properties results from the design of a self-supported semi-interpenetrating polymer network (semi-IPN) including an electronic conductive polymer (ECP) formed within. The formation of the ECP in the network has already been described by oxidative polymerization using iron trichloride as an oxidant and leading to conducting semi-IPN with mixed electronic and ionic conductivities as well as convenient mechanical properties. This presentation relates to the elaboration of such semi-IPN using polyethyleneoxide (PEO) network or a PEO/NBR (Nitrile Butadiene Rubber) IPN in which a linear poly (3,4-ethylenedioxythiophene) (PEDOT) is formed symmetrically and selectively as very thin layers very next to the two main faces of the film matrix. PEO/PEDOT semi-IPNs lead to interesting optical reflective properties in the IR between 0.8 and 25 μm. Reflectance contrasts up to 35 % is observed when, after swelling in an ionic liquid, a low voltage is applied between the two main faces of the film. However the low flexibility and brittleness of the film and a slow degradation in air at temperature up from 60°C prompted to replace the PEO matrix by a flexible PEO/NBR IPN one. Indeed, the combination of NBR and PEO in an IPN leads to materials possessing flexible properties, good ionic conductivity at 25°C as well as a better resistance to thermal ageing. Finally, NBR/PEO/PEDOT semi-IPNs allow observing comparable reflectance contrast in the IR range than those shown by PEO/PEDOT semi-IPNs.

  2. Seismic architecture of the Chalk Group from onshore reflection data in eastern Denmark

    DEFF Research Database (Denmark)

    Moreau, Julien; Anderskouv, Kresten; Boldreel, Lars Ole;

    The Upper Cretaceous-Danian chalk is well exposed in the 14 km long coastal cliff of Stevns Klint (eastern Denmark). The cliff is a world renowned for its spectacular exposure of the Cretaceous-Palaeogene boundary. Based on regional geological knowledge of the field and cores, the characteristics...... completed with the acquisition of an extensive set of subsurface data. The data include high resolution 2D multichannel seismics onshore and offshore, a seismic refraction profile, two entirely cored boreholes including wireline logs, GPR cross-hole tomography, thermographic analysis, etc. We intend...... to compile and merge the geological and geophysical datasets to investigate the variation of the Chalk Group properties and their signature in the subsurface. In this communication, the seismic reflection data are being analysed. Very high resolution litho-, bio- and cyclostratigraphy can be correlated...

  3. Inverstigation of chromatin folding patterns by atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    ZHANGYi; OUYANGZhenqian; 等

    1999-01-01

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

  4. 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.

  5. Prenucleosomes and Active Chromatin

    Science.gov (United States)

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

    2016-01-01

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

  6. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    LiuWang; AihuaZheng; LingYi; ChongrenXu; MingxiaoDing; HongkuiDeng

    2005-01-01

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

  8. Chromatin chemistry goes cellular.

    OpenAIRE

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

    2015-01-01

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

  9. Analysis of Chromatin Organisation

    Science.gov (United States)

    Szeberenyi, Jozsef

    2011-01-01

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

  10. Where splicing joins chromatin

    Czech Academy of Sciences Publication Activity Database

    Hnilicová, Jarmila; Staněk, David

    2011-01-01

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

  11. Proteomic interrogation of human chromatin.

    Directory of Open Access Journals (Sweden)

    Mariana P Torrente

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

  12. The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

    OpenAIRE

    Chan, Clara S.; McAllister, Sean M.; Leavitt, Anna H.; Brian T. Glazer; Krepski, Sean T.; Emerson, David

    2016-01-01

    Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respecti...

  13. Reflection on Full Life Cycle Green Architectural Design of Passive Priority---Taking the Award Design of China Merchants Property 2013 Green Architectural Design Competition as an Example

    Institute of Scientific and Technical Information of China (English)

    ZhenHe Fan; Yan Qiao

    2014-01-01

    In the China merchants property 2013 green architectural design competition, feature of this award-winning program is the design method based on the principles of passive priority and comprehensive utilization of full life cycle. The passive priority can be achieved by building form derived from the simulation and analysis of wind environment, improvement of the building envelope insulation and the dehumidification of fresh air, the use of solar energy. The full life cycle utilization can be accomplished by the combination of exhibition and residents’ leisure activities, and the integration with local cultural tradition, thereby improving energy efficiency and the utilization of the building.

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

    CERN Document Server

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

    2006-01-01

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

  15. Looking back on 10 years of the ATLAS Metadata Interface. Reflections on architecture, code design and development methods

    International Nuclear Information System (INIS)

    The 'ATLAS Metadata Interface' framework (AMI) has been developed in the context of ATLAS, one of the largest scientific collaborations. AMI can be considered to be a mature application, since its basic architecture has been maintained for over 10 years. In this paper we describe briefly the architecture and the main uses of the framework within the experiment (TagCollector for release management and Dataset Discovery). These two applications, which share almost 2000 registered users, are superficially quite different, however much of the code is shared and they have been developed and maintained over a decade almost completely by the same team of 3 people. We discuss how the architectural principles established at the beginning of the project have allowed us to continue both to integrate the new technologies and to respond to the new metadata use cases which inevitably appear over such a time period.

  16. Expression of acyl-CoA synthetase 5 reflects the state of villus architecture in human small intestine

    DEFF Research Database (Denmark)

    Gassler, Nikolaus; Kopitz, Jürgen; Tehrani, Arman;

    2004-01-01

    -CoA synthetase 5 pattern correlate with conversion of intestinal epithelial cells to a gastric phenotype. These results suggest that deranged acyl-CoA synthetase 5 expression, synthesis, and activity are closely related to the state of villus architecture and epithelial homeostasis in human small intestine.......Several disorders of the small intestine are associated with disturbances in villus architecture. Thus, an understanding of the molecular mechanisms associated with the differentiation of villi represents an important step in the improvement of the understanding of small intestinal pathology...

  17. Cas9 Functionally Opens Chromatin

    OpenAIRE

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

    2016-01-01

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

  18. Cas9 Functionally Opens Chromatin

    OpenAIRE

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

    2015-01-01

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

  19. Cas9 Functionally Opens Chromatin.

    Directory of Open Access Journals (Sweden)

    Amira A Barkal

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

  20. Cas9 Functionally Opens Chromatin

    Science.gov (United States)

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

    2016-01-01

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

  1. Chromosome Architecture and Genome Organization

    Science.gov (United States)

    Bernardi, Giorgio

    2015-01-01

    How the same DNA sequences can function in the three-dimensional architecture of interphase nucleus, fold in the very compact structure of metaphase chromosomes and go precisely back to the original interphase architecture in the following cell cycle remains an unresolved question to this day. The strategy used to address this issue was to analyze the correlations between chromosome architecture and the compositional patterns of DNA sequences spanning a size range from a few hundreds to a few thousands Kilobases. This is a critical range that encompasses isochores, interphase chromatin domains and boundaries, and chromosomal bands. The solution rests on the following key points: 1) the transition from the looped domains and sub-domains of interphase chromatin to the 30-nm fiber loops of early prophase chromosomes goes through the unfolding into an extended chromatin structure (probably a 10-nm “beads-on-a-string” structure); 2) the architectural proteins of interphase chromatin, such as CTCF and cohesin sub-units, are retained in mitosis and are part of the discontinuous protein scaffold of mitotic chromosomes; 3) the conservation of the link between architectural proteins and their binding sites on DNA through the cell cycle explains the “mitotic memory” of interphase architecture and the reversibility of the interphase to mitosis process. The results presented here also lead to a general conclusion which concerns the existence of correlations between the isochore organization of the genome and the architecture of chromosomes from interphase to metaphase. PMID:26619076

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

    Directory of Open Access Journals (Sweden)

    Vuthy Ea

    2015-07-01

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

  3. Humanizing Architecture

    DEFF Research Database (Denmark)

    Toft, Tanya Søndergaard

    2015-01-01

    The article proposes the urban digital gallery as an opportunity to explore the relationship between ‘human’ and ‘technology,’ through the programming of media architecture. It takes a curatorial perspective when proposing an ontological shift from considering media facades as visual spectacles to...... agency and a sense of being by way of dematerializing architecture. This is achieved by way of programming the symbolic to provide new emotional realizations and situations of enlightenment in the public audience. This reflects a greater potential to humanize the digital in media architecture....

  4. Architectural technology

    DEFF Research Database (Denmark)

    2005-01-01

    The booklet offers an overall introduction to the Institute of Architectural Technology and its projects and activities, and an invitation to the reader to contact the institute or the individual researcher for further information. The research, which takes place at the Institute of Architectural...... Technology at the Roayl Danish Academy of Fine Arts, School of Architecture, reflects a spread between strategic, goal-oriented pilot projects, commissioned by a ministry, a fund or a private company, and on the other hand projects which originate from strong personal interests and enthusiasm of individual...

  5. Statistics of genome architecture

    International Nuclear Information System (INIS)

    The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well fitted by the different statistical approximations, the interpretation of observed regularities may strongly depend on the chosen scheme. We discuss the possible evolution scenarios and describe the main characteristics obtained with different distributions. The expression for the assessment of levels in hierarchical chromatin folding is derived and the quantitative measure of genome architecture inhomogeneity is suggested. This theory provides the ground for the regular statistical study of genome architecture and genome tracks.

  6. The architecture of iron microbial mats reflects the adaptation of chemolithotrophic iron oxidation in freshwater and marine environments

    Directory of Open Access Journals (Sweden)

    Clara S Chan

    2016-06-01

    Full Text Available Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to

  7. The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

    Science.gov (United States)

    Chan, Clara S.; McAllister, Sean M.; Leavitt, Anna H.; Glazer, Brian T.; Krepski, Sean T.; Emerson, David

    2016-01-01

    Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe

  8. Epigenetics & chromatin: Interactions and processes

    NARCIS (Netherlands)

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

  10. Time-resolved spectroscopy and fluorescence resonance energy transfer in the study of excimer laser damage of chromatin

    Science.gov (United States)

    Radu, L.; Mihailescu, I.; Radu, S.; Gazdaru, D.

    2007-09-01

    The analysis of chromatin damage produced by a 248 nm excimer laser radiation, for doses of 0.3-3 MJ/m 2 was carried out by time-resolved spectroscopy and fluorescence resonance energy transfer (FRET). The chromatin was extracted from a normal and a tumoral tissue of Wistar rats. The decrease with laser dose of the relative contribution of the excited state lifetimes of ethidium bromide (EtBr) bounded to chromatin constitutes an evidence of the reduction of chromatin deoxyribonucleic acid (DNA) double-strand structure. FRET was performed from dansyl chloride to acridine orange, both coupled to chromatin. The increase of the average distance between these ligands, under the action of laser radiation, reflects a loosening of the chromatin structure. The radiosensitivity of tumor tissue chromatin is higher than that of a normal tissue. The determination of the chromatin structure modification in an excimer laser field can be of interest in laser therapy.

  11. Chromatin, epigenetics and stem cells.

    Science.gov (United States)

    Roloff, Tim C; Nuber, Ulrike A

    2005-03-01

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

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

    OpenAIRE

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

    2007-01-01

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

  13. Brain Function and Chromatin Plasticity

    OpenAIRE

    Dulac, Catherine

    2010-01-01

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

  14. Chromatin remodeling, development and disease

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    Vietri Rudan, M.

    2015-01-01

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

  16. On the mechanochemical machinery underlying chromatin remodeling

    Science.gov (United States)

    Yusufaly, Tahir I.

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

  17. Architectural Engineers

    DEFF Research Database (Denmark)

    Petersen, Rikke Premer

    engineering is addresses from two perspectives – as an educational response and an occupational constellation. Architecture and engineering are two of the traditional design professions and they frequently meet in the occupational setting, but at educational institutions they remain largely estranged. The...... paper builds on a multi-sited study of an architectural engineering program at the Technical University of Denmark and an architectural engineering team within an international engineering consultancy based on Denmark. They are both responding to new tendencies within the building industry where the...... role of engineers and architects increasingly overlap during the design process, but their approaches reflect different perceptions of the consequences. The paper discusses some of the challenges that design education, not only within engineering, is facing today: young designers must be equipped with...

  18. Chromatin structure and DNA damage

    International Nuclear Information System (INIS)

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

  19. Single Molecule Studies of Chromatin

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-02-06

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

  20. Chromatin remodelers and their roles in chromatin organization

    OpenAIRE

    Strålfors, Annelie

    2012-01-01

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

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

    Science.gov (United States)

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

    2001-11-01

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

  2. Rearrangement of chromatin domains during development in Xenopus.

    Science.gov (United States)

    Vassetzky, Y; Hair, A; Méchali, M

    2000-06-15

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

  3. Software Architecture: Architecture Constraints

    OpenAIRE

    Tibermacine, Chouki

    2014-01-01

    International audience In this chapter, we introduce an additional, yet essential, concept in describing software architectures : architecture constraints. We explain the precise role of these entities and their importance in object-oriented, component-based or service-oriented software engi-neering. We then describe the way in which they are specified and interpreted. An architect can define architecture constraints and then associate them to architectural descriptions to limit their stru...

  4. Architecture on Architecture

    DEFF Research Database (Denmark)

    Olesen, Karen

    2016-01-01

    how recognising the autonomy of architecture, not as an esoteric concept but as a valid source of information in a pragmatic design practice, may help us overcome the often-proclaimed dichotomy between formal autonomy and a societally committed architecture. It follows that in architectural education...

  5. Guarding against Collateral Damage during Chromatin Transactions

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Lukas, Jiri

    2013-01-01

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

  6. Chromatin state dynamics during blood formation

    OpenAIRE

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

    2014-01-01

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

  7. Predicting chromatin organization using histone marks

    OpenAIRE

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

    2015-01-01

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

  8. Impact of Chromatin on HIV Replication

    OpenAIRE

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

    2015-01-01

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

  9. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  10. Spectroscopic study of laser irradiated chromatin

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-04-15

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

  11. Chromatin structure and evolution in the human genome

    Directory of Open Access Journals (Sweden)

    Dunlop Malcolm G

    2007-05-01

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

  12. Quantifying Reflection

    DEFF Research Database (Denmark)

    Alcock, Gordon Lindsay

    2013-01-01

    This paper documents 1st semester student reflections on “learning to learn” in a team-based PBL environment with quantitative and qualitative student reflective feedback on the learning gains of 60 Architectural Technology and Construction Management students at VIA University College, Denmark. It...... contrasts the students’ self-assessment in a range of ‘product’ skills such as Revit, Structural Design, Mathematics of construction, Technical Installations; as well as ‘process’ competencies such as ‘Working in a team’, Sharing knowledge, Maintaining a portfolio and Reflecting ON learning and FOR learning...

  13. Chromatin Dynamics of Circadian Transcription

    OpenAIRE

    Aguilar-Arnal, Lorena; Sassone-Corsi, Paolo

    2015-01-01

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

  14. Generation of bivalent chromatin domains during cell fate decisions

    Directory of Open Access Journals (Sweden)

    De Gobbi Marco

    2011-06-01

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

  15. Architecture on Architecture

    DEFF Research Database (Denmark)

    Olesen, Karen

    2016-01-01

    This paper will discuss the challenges faced by architectural education today. It takes as its starting point the double commitment of any school of architecture: on the one hand the task of preserving the particular knowledge that belongs to the discipline of architecture, and on the other hand...... the obligation to prepare students to perform in a profession that is largely defined by forces outside that discipline. It will be proposed that the autonomy of architecture can be understood as a unique kind of information: as architecture’s self-reliance or knowledge-about itself. A knowledge that...... is not scientific or academic but is more like a latent body of data that we find embedded in existing works of architecture. This information, it is argued, is not limited by the historical context of the work. It can be thought of as a virtual capacity – a reservoir of spatial configurations that...

  16. Radiosensitivity: a role of ATM in chromatin modification

    International Nuclear Information System (INIS)

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

  17. Characterization of the RNA content of chromatin

    OpenAIRE

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

    2010-01-01

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

  18. Live visualization of chromatin dynamics with fluorescent TALEs.

    Science.gov (United States)

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

    2013-11-01

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

  19. Organophosphorous pesticide exposure alters sperm chromatin structure in Mexican agricultural workers

    International Nuclear Information System (INIS)

    Our objective was to evaluate alterations in sperm chromatin structure in men occupationally exposed to a mixture of organophosphorus pesticides (OP) because these alterations have been proposed to compromise male fertility and offspring development. Chromatin susceptibility to in situ acid-induced denaturation structure was assessed by the sperm chromatin structure assay (SCSA). Urinary levels of alkylphosphates (DAP) were used to assess exposure. Diethylthiophosphate (DETP) was the most frequent OP metabolite found in urine samples indicating that compounds derived from thiophosphoric acid were mainly used. Chromatin structure was altered in most samples. About 75% of semen samples were classified as having poor fertility potential (>30% of Percentage of DNA Fragmentation Index [DFI%]), whereas individuals without OP occupational exposure showed average DFI% values of 9.9%. Most parameters of conventional semen analysis were within normality except for the presence of immature cells (IGC) in which 82% of the samples were above reference values. There were significant direct associations between urinary DETP concentrations and mean DFI and SD-DFI but marginally (P = 0.079) with DFI%, after adjustment for potential confounders, including IGC. This suggests that OP exposure alters sperm chromatin condensation, which could be reflected in an increased number of cells with greater susceptibility to DNA denaturation. This study showed that human sperm chromatin is a sensitive target to OP exposure and may contribute to adverse reproductive outcomes. Further studies on the relevance of protein phosphorylation as a possible mechanism by which OP alter sperm chromatin are required

  20. The Matrix Regained: Reflections on the Use of the Grid in the Architectural Theories of Nicolaus Goldmann and Jean-Nicolas-Louis Durand

    Directory of Open Access Journals (Sweden)

    Jeroen Goudeau

    2015-05-01

    Full Text Available In addition to the superficial visual similarities between the architectural theories of the Silesian-born, seventeenth-century Dutch mathematician Nicolaus Goldmann and the early nineteenth-century French architect Jean-Nicolas-Louis Durand, there is a more profound interconnection: their use of the grid. This article evaluates the relation between the two theories and argues how Durand could have been influenced by Goldmann’s writings. It turns out to be more than likely that the two were linked by Durand´s German pupils who brought the tradition of German eighteenth-century architectural theory with them. This corpus was nourished by Leonhard Christoph Sturm´s ‘Goldmannic’ architecture.

  1. MeCP2 Rett mutations affect large scale chromatin organization

    DEFF Research Database (Denmark)

    Gupta, Noopur Agarwal; Becker, Annette; Jost, K Laurence;

    2011-01-01

    Rett syndrome is a neurological, X chromosomal-linked disorder associated with mutations in the MECP2 gene. MeCP2 protein has been proposed to play a role in transcriptional regulation as well as in chromatin architecture. Since MeCP2 mutant cells exhibit surprisingly mild changes in gene...... expression, we have now explored the possibility that Rett mutations may affect the ability of MeCP2 to bind and organize chromatin. We found that all but one of the 21 missense MeCP2 mutants analyzed accumulated at heterochromatin and about half of them were significantly affected. Furthermore, two...

  2. Computational strategies to address chromatin structure problems.

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-01-01

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

  3. A Long-Distance Chromatin Affair

    NARCIS (Netherlands)

    Denker, Annette; de Laat, Wouter

    2015-01-01

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

  4. Chromatin domain boundaries: insulators and beyond

    Institute of Scientific and Technical Information of China (English)

    Gong Hong WEI; De Pei LIU; Chih Chuan LIANG

    2005-01-01

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

  5. Computational strategies to address chromatin structure problems

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-06-01

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

  6. Architectural Slicing

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak; Hansen, Klaus Marius

    2013-01-01

    Architectural prototyping is a widely used practice, con- cerned with taking architectural decisions through experiments with light- weight implementations. However, many architectural decisions are only taken when systems are already (partially) implemented. This is prob- lematic in the context of...... architectural prototyping since experiments with full systems are complex and expensive and thus architectural learn- ing is hindered. In this paper, we propose a novel technique for harvest- ing architectural prototypes from existing systems, \\architectural slic- ing", based on dynamic program slicing. Given a...... system and a slicing criterion, architectural slicing produces an architectural prototype that contain the elements in the architecture that are dependent on the ele- ments in the slicing criterion. Furthermore, we present an initial design and implementation of an architectural slicer for Java....

  7. Architecture as Ars Combinatoria

    Directory of Open Access Journals (Sweden)

    Francesco Cacciatore

    2015-11-01

    Full Text Available Architecture today, no longer reflects the limits of experimentation and innovation. An extremely low-tech art whose field of possibilities consists of choosing and using that which has already been done in the past. It is because of this that the key skill a designer should have is the ability to recognize the complexity in forms around them: cities have the widest programming opportunities for architecture, in the two-way relationship that is established from the city that takes form in architecture and an architecture that finds its place in the contemporary city. Thus, architecture has its foundation in hospitality, an element that differentiates it significantly from the design.

  8. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.

    2013-10-17

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

  9. Architectural Prototyping

    DEFF Research Database (Denmark)

    Bardram, Jakob; Christensen, Henrik Bærbak; Hansen, Klaus Marius

    2004-01-01

    A major part of software architecture design is learning how specific architectural designs balance the concerns of stakeholders. We explore the notion of "architectural prototypes", correspondingly architectural prototyping, as a means of using executable prototypes to investigate stakeholders......' concerns with respect to a system under development. An architectural prototype is primarily a learning and communication vehicle used to explore and experiment with alternative architectural styles, features, and patterns in order to balance different architectural qualities. The use of architectural...... prototypes in the development process is discussed, and we argue that such prototypes can play a role throughout the entire process. The use of architectural prototypes is illustrated by three distinct cases of creating software systems. We argue that architectural prototyping can provide key insights that...

  10. Architectural prototyping

    DEFF Research Database (Denmark)

    Bardram, Jakob Eyvind; Christensen, Henrik Bærbak; Hansen, Klaus Marius

    2004-01-01

    A major part of software architecture design is learning how specific architectural designs balance the concerns of stakeholders. We explore the notion of "architectural prototypes", correspondingly architectural prototyping, as a means of using executable prototypes to investigate stakeholders......' concerns with respect to a system under development. An architectural prototype is primarily a learning and communication vehicle used to explore and experiment with alternative architectural styles, features, and patterns in order to balance different architectural qualities. The use of architectural...... prototypes in the development process is discussed, and we argue that such prototypes can play a role throughout the entire process. The use of architectural prototypes is illustrated by three distinct cases of creating software systems. We argue that architectural prototyping can provide key insights that...

  11. 关于中国石化品牌架构的思考%Reflections on SINOPEC’s BrandArchitecture

    Institute of Scientific and Technical Information of China (English)

    刘晓宇; 童宁

    2014-01-01

    Brand architecture is a structure of brands that specifies the roles of different brands of a company and the logical relationships between the brands, and is designed to take advantage of the collective force of different brands and maximize the brand equity of the company. To improve SINOPEC’s brand architecture in future requires a systematic thinking from four aspects: the driving roles of brand elements, the collective force of brands, brand extension capabilities and integration of acquired businesses.%品牌架构用来描述企业中不同品牌的角色以及品牌之间的逻辑关系,目的是发挥不同品牌的协同效应,最大限度地壮大企业的品牌资产。未来中国石化品牌架构的完善,需要从品牌元素的驱动作用、品牌之间的协同作用、品牌的延伸能力、收购业务的整合四个方面进行系统思考。

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

    KAUST Repository

    Bigeard, Jean

    2014-07-10

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

  13. Pulling chromatin apart: Unstacking or Unwrapping?

    Directory of Open Access Journals (Sweden)

    Victor Jean Marc

    2012-11-01

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

  14. In vivo binding of retinol to chromatin

    International Nuclear Information System (INIS)

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

  15. Undifferentiated embryonic cell transcription factor 1 regulates ESC chromatin organization and gene expression

    DEFF Research Database (Denmark)

    Kooistra, Susanne M; van den Boom, Vincent; Thummer, Rajkumar P;

    2010-01-01

    to dimethyl sulfoxide (DMSO) or after LIF withdrawal and display increased colony formation. UTF1 KD ES cells display extensive chromatin decondensation, reflected by a dramatic increase in nucleosome release on micrococcal nuclease (MNase) treatment and enhanced MNase sensitivity of UTF1 target...

  16. The Chromatin Fiber: Multiscale Problems and Approaches

    OpenAIRE

    Ozer, Gungor; Luque, Antoni; Schlick, Tamar

    2015-01-01

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

  17. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    OpenAIRE

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2014-11-13

    The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome sequencing, here we show that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR) < 0.05, plus a set of 107 autosomal genes strongly enriched for those likely to affect risk (FDR < 0.30). These 107 genes, which show unusual evolutionary constraint against mutations, incur de novo loss-of-function mutations in over 5% of autistic subjects. Many of the genes implicated encode proteins for synaptic formation, transcriptional regulation and chromatin-remodelling pathways. These include voltage-gated ion channels regulating the propagation of action potentials, pacemaking and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodellers-most prominently those that mediate post-translational lysine methylation/demethylation modifications of histones. PMID:25363760

  19. Etiology and Evaluation of Sperm Chromatin Anomalies

    Directory of Open Access Journals (Sweden)

    Marziyeh Tavalaee

    2008-01-01

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

  20. Architectural Contestation

    OpenAIRE

    Merle, J.

    2012-01-01

    This dissertation addresses the reductive reading of Georges Bataille's work done within the field of architectural criticism and theory which tends to set aside the fundamental ‘broken’ totality of Bataille's oeuvre and also to narrowly interpret it as a mere critique of architectural form, consequently presenting it either as the negation of all form of architecture or as the critique of 'classical' architectural forms. Against this ‘appropriation’, i.e. this reductive reading and the subse...

  1. Architectural Theatricality

    DEFF Research Database (Denmark)

    Tvedebrink, Tenna Doktor Olsen; Fisker, Anna Marie; Kirkegaard, Poul Henning

    2013-01-01

    and recovery through the architecture framing eating experiences, this article examines, from a theoretical perspective, two less debated concepts relating to hospitality called food design and architectural theatricality. In architectural theory the nineteenth century German architect Gottfried...... Semper is known for his writings on theatricality, understood as a holistic design approach emphasizing the contextual, cultural, ritual and social meanings rooted in architecture. Relative hereto, the International Food Design Society recently argued, in a similar holistic manner, that the methodology...

  2. VLSI architecture

    Energy Technology Data Exchange (ETDEWEB)

    Randell, B.; Treleaven, P.C.

    1983-01-01

    This book is a collection of course papers which discusses the latest (1982) milestone of electronic building blocks and its effect on computer architecture. Contributions range from selecting a VLSI process technology to Japan's Fifth Generation Computer Architecture. Contents, abridged: VLSI and machine architecture. Graphic design aids: HED and FATFREDDY. On the LUCIFER system. Clocking of VLSI circuits. Decentralised computer architectures for VLSI. Index.

  3. My Reflective Practice as Research.

    Science.gov (United States)

    Pereira, Marcia A.

    1999-01-01

    Using Schon's concepts and definition of reflective practice, this article elaborates a model used to analyze the author's own processes of "reflection-in-action" and "reflection-on-action" in teaching first-year architectural students. Emphasizes the importance of the concept of "role-frame" in informing the whole reflective process. (EV)

  4. Architecture in the network society

    DEFF Research Database (Denmark)

    2004-01-01

    Under the theme Architecture in the Network Society, participants were invited to focus on the dialog and sharing of knowledge between architects and other disciplines and to reflect on, and propose, new methods in the design process, to enhance and improve the impact of information technology...... on architecture. This conference and the past history of eCAADe is an example on establishing a social network for the sharing of knowledge regarding the use of computers in architectural education and research....

  5. Architecture & Environment

    Science.gov (United States)

    Erickson, Mary; Delahunt, Michael

    2010-01-01

    Most art teachers would agree that architecture is an important form of visual art, but they do not always include it in their curriculums. In this article, the authors share core ideas from "Architecture and Environment," a teaching resource that they developed out of a long-term interest in teaching architecture and their fascination with the…

  6. Remodeling of nuclear architecture by the thiodioxoxpiperazine metabolite chaetocin

    International Nuclear Information System (INIS)

    Extensive changes of higher order chromatin arrangements can be observed during prometaphase, terminal cell differentiation and cellular senescence. Experimental systems where major reorganization of nuclear architecture can be induced under defined conditions, may help to better understand the functional implications of such changes. Here, we report on profound chromatin reorganization in fibroblast nuclei by chaetocin, a thiodioxopiperazine metabolite. Chaetocin induces strong condensation of chromosome territories separated by a wide interchromatin space largely void of DNA. Cell viability is maintained irrespective of this peculiar chromatin phenotype. Cell cycle markers, histone signatures, and tests for cellular senescence and for oxidative stress indicate that chaetocin induced chromatin condensation/clustering (CICC) represents a distinct entity among nuclear phenotypes associated with condensed chromatin. The territorial organization of entire chromosomes is maintained in CICC nuclei; however, the conventional nuclear architecture harboring gene-dense chromatin in the nuclear interior and gene-poor chromatin at the nuclear periphery is lost. Instead gene-dense and transcriptionally active chromatin is shifted to the periphery of individual condensed chromosome territories where nascent RNA becomes highly enriched around their outer surface. This chromatin reorganization makes CICC nuclei an attractive model system to study this border zone as a distinct compartment for transcription. Induction of CICC is fully inhibited by thiol-dependent antioxidants, but is not related to the production of reactive oxygen species. Our results suggest that chaetocin functionally impairs the thioredoxin (Trx) system, which is essential for deoxynucleotide synthesis, but in addition involved in a wide range of cellular functions. The mechanisms involved in CICC formation remain to be fully explored.

  7. DNA topology confers sequence specificity to nonspecific architectural proteins.

    Science.gov (United States)

    Wei, Juan; Czapla, Luke; Grosner, Michael A; Swigon, David; Olson, Wilma K

    2014-11-25

    Topological constraints placed on short fragments of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural proteins into tightly organized 3D structures. The bacterial heat-unstable (HU) protein builds up, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles and loops. Moreover, the placement of HU along loops with the "wild-type" spacing found in the Escherichia coli lactose (lac) and galactose (gal) operons precludes access to key recognition elements on DNA. The HU protein introduces a unique spatial pathway in the DNA upon closure. The many ways in which the protein induces nearly the same closed circular configuration point to the statistical advantage of its nonspecificity. The rotational settings imposed on DNA by the repressor proteins, by contrast, introduce sequential specificity in HU placement, with the nonspecific protein accumulating at particular loci on the constrained duplex. Thus, an architectural protein with no discernible DNA sequence-recognizing features becomes site-specific and potentially assumes a functional role upon loop formation. The locations of HU on the closed DNA reflect long-range mechanical correlations. The protein responds to DNA shape and deformability—the stiff, naturally straight double-helical structure—rather than to the unique features of the constituent base pairs. The structures of the simulated loops suggest that HU architecture, like nucleosomal architecture, which modulates the ability of regulatory proteins to recognize their binding sites in the context of chromatin, may influence repressor-operator interactions in the context of the bacterial nucleoid. PMID:25385626

  8. Assessment of chromatin status (SCSA) in epididymal and ejaculated sperm in Iberian red deer, ram and domestic dog.

    Science.gov (United States)

    Garcia-Macias, Vanesa; Martinez-Pastor, Felipe; Alvarez, Mercedes; Garde, Jose Julian; Anel, Enrique; Anel, Luis; de Paz, Paulino

    2006-11-01

    Abnormal chromatin condensation is not detected using classical techniques for sperm analysis. SCSA has demonstrated its usefulness in sperm chromatin analysis in several species (human, bull, stallion and boar). In this work, we studied sperm samples from red deer, ram and dog to analyze the differentiation of chromatin structure applying SCSA in epididymal and ejaculated spermatozoa. Epididymal samples were obtained from the caput, corpus and cauda by means of cuts, and ejaculated ones were obtained by electroejaculation (deer), artificial vagina (ram) and digital manipulation (dog). SCSA results suggested different critical points in sperm maturation (spermatozoa with loose chromatin to more condensed chromatin) among species: from corpus to cauda in ram and from caput to corpus in deer and dog. Moreover, we also detected differences in ruminants and dog, reflected in the appearance of SCSA plots. Indeed, ram and deer samples rendered two peaks within the sperm main population (sperm with condensed chromatin), whereas only one was detected in dog. Although some differences were observed between cauda and ejaculated samples, SCSA parameters indicated good chromatin condensation, making these samples suitable for germplasm banking. Some species-dependent modifications in the analysis of the results may be necessary to take full advantage of its analytical power. PMID:16790270

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

    Directory of Open Access Journals (Sweden)

    Xiaoyun Wu

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

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

    Science.gov (United States)

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

    2012-01-01

    The retinoblastoma (Rb) tumor suppressor acts with a number of chromatin cofactors in a wide range of species to suppress cell proliferation. The Caenorhabditis elegans retinoblastoma gene and many of these cofactors, called synMuv B genes, were identified in genetic screens for cell lineage defects caused by growth factor misexpression. Mutations in many synMuv B genes, including lin-35/Rb, also cause somatic misexpression of the germline RNA processing P granules and enhanced RNAi. We show here that multiple small RNA components, including a set of germline-specific Argonaute genes, are misexpressed in the soma of many synMuv B mutant animals, revealing one node for enhanced RNAi. Distinct classes of synMuv B mutants differ in the subcellular architecture of their misexpressed P granules, their profile of misexpressed small RNA and P granule genes, as well as their enhancement of RNAi and the related silencing of transgenes. These differences define three classes of synMuv B genes, representing three chromatin complexes: a LIN-35/Rb-containing DRM core complex, a SUMO-recruited Mec complex, and a synMuv B heterochromatin complex, suggesting that intersecting chromatin pathways regulate the repression of small RNA and P granule genes in the soma and the potency of RNAi. Consistent with this, the DRM complex and the synMuv B heterochromatin complex were genetically additive and displayed distinct antagonistic interactions with the MES-4 histone methyltransferase and the MRG-1 chromodomain protein, two germline chromatin regulators required for the synMuv phenotype and the somatic misexpression of P granule components. Thus intersecting synMuv B chromatin pathways conspire with synMuv B suppressor chromatin factors to regulate the expression of small RNA pathway genes, which enables heightened RNAi response. Regulation of small RNA pathway genes by human retinoblastoma may also underlie its role as a tumor suppressor gene. PMID:22412383

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

    International Nuclear Information System (INIS)

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

  12. New mitotic regulators released from chromatin

    Directory of Open Access Journals (Sweden)

    Hideki eYokoyama

    2013-12-01

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

  13. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

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

  14. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    Directory of Open Access Journals (Sweden)

    Arifulin E. A.

    2015-08-01

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

  15. Architectural Theatricality

    DEFF Research Database (Denmark)

    Tvedebrink, Tenna Doktor Olsen

    This PhD thesis is motived by a personal interest in the theoretical, practical and creative qualities of architecture. But also a wonder and curiosity about the cultural and social relations architecture represents through its occupation with both the sciences and the arts. Inspired by present...... initiatives in Aalborg Hospital to overcome patient undernutrition by refurbishing eating environments, this thesis engages in an investigation of the interior architectural qualities of patient eating environments. The relevance for this holistic perspective, synthesizing health, food and architecture, is...... the current building of a series of Danish ‘super hospitals’ and an increased focus among architectural practices on research-based knowledge produced with the architectural sub-disciplines Healing Architecture and Evidence-Based Design. The problem is that this research does not focus on patient...

  16. Nucleosome dynamics during chromatin remodeling in vivo.

    Science.gov (United States)

    Ramachandran, Srinivas; Henikoff, Steven

    2016-01-01

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

  17. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    Science.gov (United States)

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

    2011-01-01

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

  18. Bacterial chromatin: converging views at different scales.

    Science.gov (United States)

    Dame, Remus T; Tark-Dame, Mariliis

    2016-06-01

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

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

    International Nuclear Information System (INIS)

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

  20. Architectural freedom and industrialised architecture

    DEFF Research Database (Denmark)

    Vestergaard, Inge

    2012-01-01

    Architectural freedom and industrialized architecture. Inge Vestergaard, Associate Professor, Cand. Arch. Aarhus School of Architecture, Denmark Noerreport 20, 8000 Aarhus C Telephone +45 89 36 0000 E-mai l inge.vestergaard@aarch.dk Based on the repetitive architecture from the "building boom" 1960...... to 1973 it is discussed how architects can handle these Danish element and montage buildings through the transformation to upgraded aesthetical, functional and energy efficient architecture. The method used is analysis of cases, parallels to literature studies and producer interviews. This analysis...... compares "best practice" in Denmark and "best practice" in Austria. The modern architects accepted the fact that industrialized architecture told the storey of repetition and monotonous as basic condition. This article aims to explain that architecture can be thought as a complex and diverse design through...

  1. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

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

  2. Influence of oncogenic transcription factors on chromatin conformation and implications in prostate cancer

    Directory of Open Access Journals (Sweden)

    Yang YA

    2014-05-01

    Full Text Available Yeqing Angela Yang,1 Jung Kim,1 Jindan Yu1,21Division of Hematology/Oncology, Department of Medicine, 2Robert H Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL, USAAbstract: In recent years, facilitated by rapid technological advances, we are becoming more adept at probing the molecular processes, which take place in the nucleus, that are crucial for the hierarchical regulation and organization of chromatin architecture. With an unprecedented level of resolution, a detailed atlas of chromosomal structures (histone displacement, variants, modifications, chromosome territories, and DNA looping and mechanisms underlying their establishment, provides invaluable insight into physiological as well as pathological phenomena. In this review, we will focus on prostate cancer, a prevalent malignancy in men worldwide, and for which a curative treatment strategy is yet to be attained. We aim to catalog the most frequently observed oncogenic alterations associated with chromatin conformation, while emphasizing the TMPRSS2-ERG fusion, which is found in more than one-half of prostate cancer patients and its functions in compromising the chromatin landscape in prostate cancer.Keywords: chromatin conformation, ERG, prostate cancer

  3. John Hejduk's Pursuit of an Architectural Ethos

    DEFF Research Database (Denmark)

    Søberg, Martin

    2012-01-01

    Reflected, artistic practices and design-based research are drastically expanding fields within architectural academia. However, the interest in uniting theory and practice is not entirely new. Just a few decades ago, before a ‘death of theory’ was proclaimed, questions of architectural epistemol...... – an embracing pursuit of an architectural ethos....

  4. Architecture Sustainability

    OpenAIRE

    Avgeriou, Paris; Stal, Michael; Hilliard, Rich

    2013-01-01

    Software architecture is the foundation of software system development, encompassing a system's architects' and stakeholders' strategic decisions. A special issue of IEEE Software is intended to raise awareness of architecture sustainability issues and increase interest and work in the area. The first Web extra at http://youtu.be/wUGHvocfix0 is an audio interview in which Davide Falessi speaks with guest editors Paris Avgeriou and Rich Hilliard about the importance of architecture sustainabil...

  5. Software architecture

    CERN Document Server

    Vogel, Oliver; Chughtai, Arif

    2011-01-01

    As a software architect you work in a wide-ranging and dynamic environment. You have to understand the needs of your customer, design architectures that satisfy both functional and non-functional requirements, and lead development teams in implementing the architecture. And it is an environment that is constantly changing: trends such as cloud computing, service orientation, and model-driven procedures open up new architectural possibilities. This book will help you to develop a holistic architectural awareness and knowledge base that extends beyond concrete methods, techniques, and technologi

  6. Catalyst Architecture

    DEFF Research Database (Denmark)

    Kiib, Hans; Marling, Gitte; Hansen, Peter Mandal

    2014-01-01

    How can architecture promote the enriching experiences of the tolerant, the democratic, and the learning city - a city worth living in, worth supporting and worth investing in? Catalyst Architecture comprises architectural projects, which, by virtue of their location, context and their combination...... of programs, have a role in mediating positive social and/or cultural development. In this sense, we talk about architecture as a catalyst for: sustainable adaptation of the city’s infrastructure appropriate renovation of dilapidated urban districts strengthening of social cohesiveness in the city...

  7. Reflecting Reflective Practice

    Science.gov (United States)

    Galea, Simone

    2012-01-01

    This paper demystifies reflective practice on teaching by focusing on the idea of reflection itself and how it has been conceived by two philosophers, Plato and Irigaray. It argues that reflective practice has become a standardized method of defining the teacher in teacher education and teacher accreditation systems. It explores how practices of…

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

    Science.gov (United States)

    Chen, Hsiuyi V.; Rando, Oliver J.

    2014-01-01

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

  9. Single Chromatin Fibre Assembly Using Optical Tweezers

    NARCIS (Netherlands)

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

    2001-01-01

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

  10. Chromatin and epigenetics in all their states

    NARCIS (Netherlands)

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

    2016-01-01

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

  11. Chromatin proteins and modifications as drug targets

    DEFF Research Database (Denmark)

    Helin, Kristian; Dhanak, Dashyant

    2013-01-01

    A plethora of groundbreaking studies have demonstrated the importance of chromatin-associated proteins and post-translational modifications of histones, proteins and DNA (so-called epigenetic modifications) for transcriptional control and normal development. Disruption of epigenetic control is a ...

  12. Impact of chromatin structure on PR signaling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Hager, Gordon L

    2012-01-01

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

  13. Research Discovers Frequent Mutations of Chromatin

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

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

  14. Chromatin-modifying proteins in cancer

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  15. Factors affecting chromatin stability of bovine spermatozoa.

    Science.gov (United States)

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

    2008-03-01

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

  16. Reflecting reflection in supervision

    DEFF Research Database (Denmark)

    Lystbæk, Christian Tang

    Reflection has moved from the margins to the mainstream in supervision. Notions of reflection have become well established since the late 1980s. These notions have provided useful framing devices to help conceptualize some important processes in guidance and counseling. However, some applications...... previously associated with reflection and an exploration of alternative conceptions that view reflection within the context of settings which have a more group- and team-based orientation. Drawing on an action research project on health care supervision, the paper questions whether we should reject earlier...... views of reflection, rehabilitate them in order to capture broader connotations or move to new ways of regarding reflection that are more in keeping with not only reflective but also emotive, normative and formative views on supervision. The paper presents a critical perspective on supervision that...

  17. Systemic Architecture

    DEFF Research Database (Denmark)

    Poletto, Marco; Pasquero, Claudia

    2012-01-01

    This is a manual investigating the subject of urban ecology and systemic development from the perspective of architectural design. It sets out to explore two main goals: to discuss the contemporary relevance of a systemic practice to architectural design, and to share a toolbox of informational...... design protocols developed to describe the city as a territory of self-organization. Collecting together nearly a decade of design experiments by the authors and their practice, ecoLogicStudio, the book discusses key disciplinary definitions such as ecologic urbanism, algorithmic architecture, bottom......-up or tactical design, behavioural space and the boundary of the natural and the artificial realms within the city and architecture. A new kind of "real-time world-city" is illustrated in the form of an operational design manual for the assemblage of proto-architectures, the incubation of proto...

  18. Reflecting on Cherenkov reflections

    OpenAIRE

    Fargion, D.; Gaug, M.; Oliva, P.

    2007-01-01

    Magic Telescope may observe and reveal at horizons lights from air-shower Cherenkov reflections. The ground, the sea, the cloudy sky (below the mountain) may reflect PeVs-EeV UHECR Cherenkov lights observable by MAGIC telescopes. Even rarest UHE neutrino skimming the atmosphere or skimming the Earth may induce upward-horizontal airshowers: a new Neutrino Astronomy. These fluorescence signals or the Cherenkov reflections in upper cloudy sky may flash in correlated BL-Lac or GRB shining at oppo...

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

    Science.gov (United States)

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

    2016-06-30

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

  20. GRC3_ALIVE ARCHITECTURE

    OpenAIRE

    Pferdmenges, Petra

    2011-01-01

    The search for the clean and the perfect in our cities is reflected in the spatial exclusion of certain people, especially those on the margin of society. New immigrants, prostitutes and voyageurs are part of those communities often placed in invaluable districts. The concept of the city with a rich diversity of cultures and social backgrounds becomes increasingly a fairy tale, far from reality.As curator of the 4th International Architecture Biennale in Rotterdam (2010) Kees Christiaanse rev...

  1. Diversity in the organization of centromeric chromatin.

    Science.gov (United States)

    Steiner, Florian A; Henikoff, Steven

    2015-04-01

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

  2. On the topology of chromatin fibres

    Science.gov (United States)

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

    2012-01-01

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

  3. Architectural Mealscapes

    DEFF Research Database (Denmark)

    Tvedebrink, Tenna Doktor Olsen; Fisker, Anna Marie; Kirkegaard, Poul Henning

    2012-01-01

    German architect Gottfried Semper developed a theory on the “four elements of Architecture” tracing the origin of architecture back to the rise of the early human settlement and the creation of fire. With the notion ‘hearth’ as the first motive in architecture and the definition of three enclosing...... motives; mounding, enclosure and roof, Semper linked the cultural and social values of the primordial fireplace with the order and shape of architecture. He claimed that any building ever made was nothing but a variation of the first primitive shelters erected around the fireplace, and that the three...... enclosing motives existed only as defenders of the “sacred flame”. In that way Semper developed the idea that any architectural scenery can be described, analyzed and explained by understanding the contextual, symbolic and social values of how the four basic motives of hearth, mounding, enclosure, and roof...

  4. On the topology of chromatin fibres

    OpenAIRE

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

    2012-01-01

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

  5. Chromatin regulation in drug addiction and depression

    OpenAIRE

    Renthal, William; Nestler, Eric J.

    2009-01-01

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

  6. Identification of alternative topological domains in chromatin

    OpenAIRE

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

    2014-01-01

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

  7. Multiscale Identification of Topological Domains in Chromatin

    OpenAIRE

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

    2013-01-01

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

  8. Framing Architecture

    OpenAIRE

    Shirey, David E.

    2002-01-01

    The following thesis is comprised of a pair of projects focused on the making of architecture through the concept of framing. The work was conducted at the Academia dà ­Architettura in Mendrisio, Switzerland, under the direction of Peter Zumthor, Miguel Kreisler and Myriam Sterling, emphasizing the relationship between ordered structures and contextual propriety. The making of architecture is inherently most pure when approached as the subtraction of unnecessary elements and a distillation ...

  9. Textile Architecture

    OpenAIRE

    Maurin, Bernard; Motro, René

    2013-01-01

    The basic idea for a textile architecture project originates during early meetings between the architect and the engineer. The morphologic richness of such projects is provided by the varying curvatures of shapes, in contradiction with a classical straight line and orthogonal architecture. However the rules of construction are quite different in terms of realisation and of mechanical behaviour: textile membranes are subjected to a pre-stress conferring them their rigidity, and a major objecti...

  10. Fractal Architecture

    OpenAIRE

    Rumież, Agnieszka

    2013-01-01

    Research focuses on the recognition of the disposition of natural environment, which serves as an inspiration for cultural creation as it has always been in the history of architecture. Modern mathematical model of fractal geometry has been used to understand patterns occurring in the surrounding. The comparative analysis has been conducted between the abstract mathematical model and architectural composition in the view of contemporary cognitive paradigms. In conclusion, a hypothesis of a ne...

  11. IAIMS Architecture

    OpenAIRE

    Hripcsak, George

    1997-01-01

    An information system architecture defines the components of a system and the interfaces among the components. A good architecture is essential for creating an Integrated Advanced Information Management System (IAIMS) that works as an integrated whole yet is flexible enough to accommodate many users and roles, multiple applications, changing vendors, evolving user needs, and advancing technology. Modularity and layering promote flexibility by reducing the complexity of...

  12. How architecture students gain and apply knowledge of sustainable architecture

    DEFF Research Database (Denmark)

    Donovan, Elizabeth; Holder, Anna

    2016-01-01

    This paper will reflect on understandings of architectural pedagogy and the integration of sustainability into architectural design education. This is framed within an understanding of the construction industry’s role in the production of waste. Despite the complexity of global environmental crises......, architectural educators have the opportunity to do more to address this. We begin with a discussion of contemporary literature and policy concerning education for sustainability in architecture, articulating the particular approaches in development within higher education. This is then compared with critical...... understandings of how architects synthesise different types of knowledge while designing, raising questions about the ‘match’ between educational experiences and subsequent behaviours in practice. Taking an example from Denmark, we outline the approach of Aarhus School of Architecture, where sustainability...

  13. Titration and hysteresis in epigenetic chromatin silencing

    International Nuclear Information System (INIS)

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

  14. Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events.

    Science.gov (United States)

    Johnson, Graham D; Jodar, Meritxell; Pique-Regi, Roger; Krawetz, Stephen A

    2016-01-01

    Nuclear remodeling to a condensed state is a hallmark of spermatogenesis. This is achieved by replacement of histones with protamines. Regions retaining nucleosomes may be of functional significance. To determine their potential roles, sperm from wild type and transgenic mice harboring a single copy insert of the human protamine cluster were subjected to Micrococcal Nuclease-seq. CENTIPEDE, a hierarchical Bayesian model, was used to identify multiple spatial patterns, "footprints", of MNase-seq reads along the sperm genome. Regions predicted by CENTIPEDE analysis to be bound by a regulatory factor in sperm were correlated with genomic landmarks and higher order chromatin structure datasets to identify potential roles for these factors in regulating either prior or post spermatogenic, i.e., early embryonic events. This approach linked robust endogenous protamine transcription and transgene suppression to its chromatin environment within topologically associated domains. Of the candidate enhancer-bound regulatory proteins, Ctcf, was associated with chromatin domain boundaries in testes and embryonic stem cells. The continuity of Ctcf binding through the murine germline may permit rapid reconstitution of chromatin organization following fertilization. This likely reflects its preparation for early zygotic genome activation and comparatively accelerated preimplantation embryonic development program observed in mouse as compared to human and bull. PMID:27184706

  15. Transverse pumped laser amplifier architecture

    Science.gov (United States)

    Bayramian, Andrew James; Manes, Kenneth; Deri, Robert; Erlandson, Al; Caird, John; Spaeth, Mary

    2013-07-09

    An optical gain architecture includes a pump source and a pump aperture. The architecture also includes a gain region including a gain element operable to amplify light at a laser wavelength. The gain region is characterized by a first side intersecting an optical path, a second side opposing the first side, a third side adjacent the first and second sides, and a fourth side opposing the third side. The architecture further includes a dichroic section disposed between the pump aperture and the first side of the gain region. The dichroic section is characterized by low reflectance at a pump wavelength and high reflectance at the laser wavelength. The architecture additionally includes a first cladding section proximate to the third side of the gain region and a second cladding section proximate to the fourth side of the gain region.

  16. Architectural Theory: A Construction Site

    Directory of Open Access Journals (Sweden)

    Ákos Moravánszky

    2014-07-01

    Full Text Available Around 1968 we saw the birth of a new architectural theory as the conjunction of architectural history and politically engaged architectural criticism. Not the aesthetics of architecture, but architecture itself in its structural relations with social life became the focus of attention. As a result of this development, it is no longer possible to study architectural history without a critical reflection on the method of the study itself and without a grade of interdisciplinarity. Traditional methods of historiography and iconography have been replaced by new approaches configured by psychoanalysis, deconstruction, cultural studies etc. Appropriation has become the proof of criticality both in architectural theory and in design; however, the understanding of the concepts and methods of other disciplines is basically metaphorical. The problem for a school of architecture lies not in the ‘criticality’ of the kind of architectural theory we described as emerging from the spirit of 1968, but in its discursive nature. The disciplinary specificity of architecture resists a discursive approach, and architectural students frequently question the usefulness of theory which undermines the notion of the ‘project’, without articulating a constructive proposal. Projectivity does not seem to provide an answer; its claim of performativity lacks the program to regain its organising power over contributions from other specialised disciplines and practices. Theory should focus on the terms of our discipline, which are so close to our ‘core beliefs’ regarding architecture that we usually take their meaning for granted. It would be wrong to see this focus of theory as a withdrawal into the realm of language. Indeed, after a period of theory alienating architects and the general public, it could now create a rhetoric to influence our understanding of our environment, which is itself organised on the level of language. The requirement that theory should

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

    Directory of Open Access Journals (Sweden)

    Justin W Walley

    2008-12-01

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

  18. PTEN Interacts with Histone H1 and Controls Chromatin Condensation

    Directory of Open Access Journals (Sweden)

    Zhu Hong Chen

    2014-09-01

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

  19. First Exon Length Controls Active Chromatin Signatures and Transcription

    Directory of Open Access Journals (Sweden)

    Nicole I. Bieberstein

    2012-07-01

    Full Text Available Here, we explore the role of splicing in transcription, employing both genome-wide analysis of human ChIP-seq data and experimental manipulation of exon-intron organization in transgenic cell lines. We show that the activating histone modifications H3K4me3 and H3K9ac map specifically to first exon-intron boundaries. This is surprising, because these marks help recruit general transcription factors (GTFs to promoters. In genes with long first exons, promoter-proximal levels of H3K4me3 and H3K9ac are greatly reduced; consequently, GTFs and RNA polymerase II are low at transcription start sites (TSSs and exhibit a second, promoter-distal peak from which transcription also initiates. In contrast, short first exons lead to increased H3K4me3 and H3K9ac at promoters, higher expression levels, accuracy in TSS usage, and a lower frequency of antisense transcription. Therefore, first exon length is predictive for gene activity. Finally, splicing inhibition and intron deletion reduce H3K4me3 levels and transcriptional output. Thus, gene architecture and splicing determines transcription quantity and quality as well as chromatin signatures.

  20. Chromatin remodeling by curcumin alters endogenous aryl hydrocarbon receptor signaling.

    Science.gov (United States)

    Mohammadi-Bardbori, Afshin; Akbarizadeh, Amin Reza; Delju, Fatemeh; Rannug, Agneta

    2016-05-25

    The aim of this study was to gain more information about the mechanisms that regulate expression of the aryl hydrocarbon receptor (AHR) target gene CYP1A1. Human hepatoma cells (HepG2 and Huh7) and human immortalized keratinocytes (HaCaT) were treated with different concentrations of the dietary polyphenolic compound curcumin (CUR) alone or in combination with the natural AHR agonist 6-formylindolo[3,2-b]carbazole (FICZ). In an earlier study, we described that CUR can activate the AHR indirectly by inhibiting metabolic clearance of FICZ. Here, we measured cell viability, activation of AHR signaling, oxidative stress and histone modifying activities in response to CUR at concentrations ranging from 0.1 to 50 μM. We observed apparent non-linear responses on cell viability and activation of AHR signaling. The CYP1A1 expression and the CYP1A1 enzyme activity in the presence of CUR reflected the histone acetylation efficiency observed in nuclear extracts. At the lowest concentration, CUR significantly decreased histone deacetylase activity and increased the FICZ-induced CYP1A1 activity. In contrast, at the highest concentration, CUR increased the formation of reactive oxygen species, significantly inhibited histone acetylation, and temporally decreased FICZ-induced CYP1A1 activity. The results suggest that CUR can both increase and decrease the accessibility of DNA and thereby influence transcriptional responses to the ligand-activated AHR. This suggestion was supported by the fact that chromatin remodeling treatments with trichostatin A, p300, or 5-aza-dC increased CYP1A1 transcription. We conclude that the AHR-dependent transcriptional efficiency is modified by factors that influence the cellular redox status and the chromatin structure. PMID:27041069

  1. Architectural geometry

    KAUST Repository

    Pottmann, Helmut

    2014-11-26

    Around 2005 it became apparent in the geometry processing community that freeform architecture contains many problems of a geometric nature to be solved, and many opportunities for optimization which however require geometric understanding. This area of research, which has been called architectural geometry, meanwhile contains a great wealth of individual contributions which are relevant in various fields. For mathematicians, the relation to discrete differential geometry is significant, in particular the integrable system viewpoint. Besides, new application contexts have become available for quite some old-established concepts. Regarding graphics and geometry processing, architectural geometry yields interesting new questions but also new objects, e.g. replacing meshes by other combinatorial arrangements. Numerical optimization plays a major role but in itself would be powerless without geometric understanding. Summing up, architectural geometry has become a rewarding field of study. We here survey the main directions which have been pursued, we show real projects where geometric considerations have played a role, and we outline open problems which we think are significant for the future development of both theory and practice of architectural geometry.

  2. IAIMS architecture.

    Science.gov (United States)

    Hripcsak, G

    1997-01-01

    An information system architecture defines the components of a system and the interfaces among the components. A good architecture is essential for creating an Integrated Advanced Information Management System (IAIMS) that works as an integrated whole yet is flexible enough to accommodate many users and roles, multiple applications, changing vendors, evolving user needs, and advancing technology. Modularity and layering promote flexibility by reducing the complexity of a system and by restricting the ways in which components may interact. Enterprise-wide mediation promotes integration by providing message routing, support for standards, dictionary-based code translation, a centralized conceptual data schema, business rule implementation, and consistent access to databases. Several IAIMS sites have adopted a client-server architecture, and some have adopted a three-tiered approach, separating user interface functions, application logic, and repositories. PMID:9067884

  3. Architectural Anthropology

    DEFF Research Database (Denmark)

    Stender, Marie

    Architecture and anthropology have always had a common focus on dwelling, housing, urban life and spatial organisation. Current developments in both disciplines make it even more relevant to explore their boundaries and overlaps. Architects are inspired by anthropological insights and methods......, while recent material and spatial turns in anthropology have also brought an increasing interest in design, architecture and the built environment. Understanding the relationship between the social and the physical is at the heart of both disciplines, and they can obviously benefit from further...... collaboration: How can qualitative anthropological approaches contribute to contemporary architecture? And just as importantly: What can anthropologists learn from architects’ understanding of spatial and material surroundings? Recent theoretical developments in anthropology stress the role of materials and...

  4. Architectural Narratives

    DEFF Research Database (Denmark)

    Kiib, Hans

    2010-01-01

    In this essay, I focus on the combination of programs and the architecture of cultural projects that have emerged within the last few years. These projects are characterized as “hybrid cultural projects,” because they intend to combine experience with entertainment, play, and learning. This essay...... identifies new rationales related to this development, and it argues that “cultural planning” has increasingly shifted its focus from a cultural institutional approach to a more market-oriented strategy that integrates art and business. The role of architecture has changed, too. It not only provides a...... functional framework for these concepts, but tries increasingly to endow the main idea of the cultural project with a spatially aesthetic expression - a shift towards “experience architecture.” A great number of these projects typically recycle and reinterpret narratives related to historical buildings and...

  5. Architectural Theatricality

    DEFF Research Database (Denmark)

    Tvedebrink, Tenna Doktor Olsen

    initiatives in Aalborg Hospital to overcome patient undernutrition by refurbishing eating environments, this thesis engages in an investigation of the interior architectural qualities of patient eating environments. The relevance for this holistic perspective, synthesizing health, food and architecture...... environments and a knowledge gap therefore exists in present hospital designs. Consequently, the purpose of this thesis has been to investigate if any research-based knowledge exist supporting the hypothesis that the interior architectural qualities of eating environments influence patient food intake, health...... such as a literature review, timeline and historical outline to create a “knowledge map”, which in an eclectic manner merges the positive, normative and polemical knowledge rooted in research, objects and writings. The results of these investigations show that sparse researchbased knowledge exist directly taking...

  6. Differential Response of Human Hepatocyte Chromatin to HDAC Inhibitors as a Function of Microenvironmental Glucose Level.

    Science.gov (United States)

    Felisbino, Marina Barreto; Alves da Costa, Thiago; Gatti, Maria Silvia Viccari; Mello, Maria Luiza Silveira

    2016-10-01

    Diabetes is a complex multifactorial disorder characterized by chronic hyperglycemia due to impaired insulin secretion. Recent observations suggest that the complexity of the disease cannot be entirely accounted for genetic predisposition and a compelling argument for an epigenetic component is rapidly emerging. The use of histone deacetylase inhibitor (HDACi) in clinical setting is an emerging area of investigation. In this study, we have aimed to understand and compare the response of hepatocyte chromatin to valproic acid (VPA) and trichostatin A (TSA) treatments under normoglycemic or hyperglycemic conditions to expand our knowledge about the consequences of HDACi treatment in a diabetes cell model. Under normoglycemic conditions, these treatments promoted chromatin remodeling, as assessed by image analysis and H3K9ac and H3K9me2 abundance. Simultaneously, H3K9ac marks shifted to the nuclear periphery accompanied by HP1 dissociation from the heterochromatin and a G1 cell cycle arrest. More striking changes in the cell cycle progression and mitotic ratios required drastic treatment. Under hyperglycemic conditions, high glucose per se promoted chromatin changes similar to those promoted by VPA and TSA. Nonetheless, these results were not intensified in cells treated with HDACis under hyperglycemic conditions. Despite the absence of morphological changes being promoted, HDACi treatment seems to confer a physiological meaning, ameliorating the cellular hyperglycemic state through reduction of glucose production. These observations allow us to conclude that the glucose level to which the hepatocytes are subjected affects how chromatin responds to HDACi and their action under high-glucose environment might not reflect on chromatin remodeling. J. Cell. Physiol. 231: 2257-2265, 2016. © 2016 Wiley Periodicals, Inc. PMID:26888775

  7. Prevalence of X-chromatin in Jordanian women

    International Nuclear Information System (INIS)

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

  8. Architectural Anthropology

    DEFF Research Database (Denmark)

    Stender, Marie

    and other spaces that architects are preoccupied with. On the other hand, the distinction between architecture and design is not merely one of scale. Design and architecture represent – at least in Denmark – also quite different disciplinary traditions and methods. Where designers develop prototypes......, architects tend to work with models and plans that are not easily understood by lay people. Further, many architects are themselves sceptical towards notions of user-involvement and collaborative design. They fear that the imagination of citizens and users is restricted to what they are already familiar with...

  9. Reframing Architecture

    DEFF Research Database (Denmark)

    Riis, Søren

    2013-01-01

    I would like to thank Prof. Stephen Read (2011) and Prof. Andrew Benjamin (2011) for both giving inspiring and elaborate comments on my article “Dwelling in-between walls: the architectural surround”. As I will try to demonstrate below, their two different responses not only supplement my article...... focuses on how the absence of an initial distinction might threaten the endeavour of my paper. In my reply to Read and Benjamin, I will discuss their suggestions and arguments, while at the same time hopefully clarifying the postphenomenological approach to architecture....

  10. Multithreading architecture

    CERN Document Server

    Nemirovsky, Mario

    2013-01-01

    Multithreaded architectures now appear across the entire range of computing devices, from the highest-performing general purpose devices to low-end embedded processors. Multithreading enables a processor core to more effectively utilize its computational resources, as a stall in one thread need not cause execution resources to be idle. This enables the computer architect to maximize performance within area constraints, power constraints, or energy constraints. However, the architectural options for the processor designer or architect looking to implement multithreading are quite extensive and

  11. Long Noncoding RNAs, Chromatin, and Development

    Directory of Open Access Journals (Sweden)

    Daniel P. Caley

    2010-01-01

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

  12. Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes

    OpenAIRE

    Arifulin E. A.

    2015-01-01

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

  13. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

    OpenAIRE

    Cieślik, Marcin; Bekiranov, Stefan

    2014-01-01

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

  14. Single-epitope recognition imaging of native chromatin

    OpenAIRE

    Wang Hongda; Dalal Yamini; Henikoff Steven; Lindsay Stuart

    2008-01-01

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

  15. Hydrogen peroxide mediates higher order chromatin degradation.

    Science.gov (United States)

    Bai, H; Konat, G W

    2003-01-01

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

  16. From green architecture to architectural green

    DEFF Research Database (Denmark)

    Earon, Ofri

    2011-01-01

    The paper investigates the topic of green architecture from an architectural point of view and not an energy point of view. The purpose of the paper is to establish a debate about the architectural language and spatial characteristics of green architecture. In this light, green becomes an adjective...... that describes the architectural exclusivity of this particular architecture genre. The adjective green expresses architectural qualities differentiating green architecture from none-green architecture. Currently, adding trees and vegetation to the building’s facade is the main architectural characteristics...... of green architecture. The paper argues that this greenification of facades is insufficient. The green is only a skin cladding the exterior envelope without having a spatial significance. Through the paper it is proposed to flip the order of words from green architecture to architectural green...

  17. Religious Architecture

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The main religions of ancient China were Buddhism,Taoism and Islam, of which Buddhism was the most widespread. As a result, Buddhist temples and towers are found all over China, and have become important components of the country's ancient architecture.

  18. Reflective Teaching

    Science.gov (United States)

    Farrell, Thomas S. C.

    2013-01-01

    Thomas Farrell's "Reflective Teaching" outlines four principles that take teachers from just doing reflection to making it a way of being. Using the four principles, Reflective Practice Is Evidence Based, Reflective Practice Involves Dialogue, Reflective Practice Links Beliefs and Practices, and Reflective Practice Is a Way of Life,…

  19. Performative Urban Architecture

    DEFF Research Database (Denmark)

    Thomsen, Bo Stjerne; Jensen, Ole B.

    The paper explores how performative urban architecture can enhance community-making and public domain using socio-technical systems and digital technologies to constitute an urban reality. Digital medias developed for the web are now increasingly occupying the urban realm as a tool for navigating...... discusses the perspectives of using interactive technologies for performative objects, which are able to register the impulses of urban activity and reproduce the contexts of the city. In this way the performative environment is established as an event setting providing an embodied experience as a ‘quasi......-object' that can couple relationships between architecture, humans and society. These performative relationships between digital and physical environments are seen as illustrative of the social production of space by performance and the creative production of identity. The paper reflects on the perspectives of...

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

    Science.gov (United States)

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

    2002-01-01

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

  1. Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster.

    Science.gov (United States)

    Tsai, Yu-Cheng; Cooke, Nancy E; Liebhaber, Stephen A

    2016-06-01

    The relationships of higher order chromatin organization to mammalian gene expression remain incompletely defined. The human Growth Hormone (hGH) multigene cluster contains five gene paralogs. These genes are selectively activated in either the pituitary or the placenta by distinct components of a remote locus control region (LCR). Prior studies have revealed that appropriate activation of the placental genes is dependent not only on the actions of the LCR, but also on the multigene composition of the cluster itself. Here, we demonstrate that the hGH LCR 'loops' over a distance of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes in the cluster. This long-range interaction sequesters the GH genes from the three hCS genes which co-assemble into a tightly packed 'hCS chromatin hub'. Elimination of the long-range looping, via specific deletion of the placental LCR components, triggers a dramatic disruption of the hCS chromatin hub. These data reveal a higher-order structural pathway by which long-range looping from an LCR impacts on local chromatin architecture that is linked to tissue-specific gene regulation within a multigene cluster. PMID:26893355

  2. Kosmos = architecture

    Directory of Open Access Journals (Sweden)

    Tine Kurent

    2015-10-01

    Full Text Available The old Greek word "kosmos" means not only "cosmos", but also "the beautiful order", "the way of building", "building", "scenography", "mankind", and, in the time of the New Testament, also "pagans". The word "arhitekton", meaning first the "master of theatrical scenography", acquired the meaning of "builder", when the words "kosmos" and ~kosmetes" became pejorative. The fear that architecture was not considered one of the arts before Renaissance, since none of the Muses supervised the art of building, results from the misunderstanding of the word "kosmos". Urania was the Goddes of the activity implied in the verb "kosmein", meaning "to put in the beautiful order" - everything, from the universe to the man-made space, i. e. the architecture.

  3. MUF architecture /art London

    DEFF Research Database (Denmark)

    Svenningsen Kajita, Heidi

    2009-01-01

    Om MUF architecture samt interview med Liza Fior og Katherine Clarke, partnere i muf architecture/art......Om MUF architecture samt interview med Liza Fior og Katherine Clarke, partnere i muf architecture/art...

  4. The AID-induced DNA damage response in chromatin

    DEFF Research Database (Denmark)

    Daniel, Jeremy A; Nussenzweig, André

    2013-01-01

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

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    OpenAIRE

    Meshorer, Eran; Herrmann, Harald; Raška, Ivan

    2011-01-01

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

  10. THE DYNAMICS OF THE FORM OF NUSANTARA MOSQUE: ARCHITECTURAL HOMOGENEITY VIS A VIS ARCHITECTURAL HYBRIDITY

    Directory of Open Access Journals (Sweden)

    Pudji Pratitis Wismantara

    2012-09-01

    Full Text Available There are two points of departure in the design of mosque architecture in Nusantara, namely architectural homogeneity and architectural hybridity. Each provides the legitimacy of the architecture of identity formation. This paper seeks to explore the comparative, the concept of homogeneity and hybridity architecture, with a critical theory approach. The  results of this search is, the concept of architectural homogeneity establishing assumption that certain architectural forms are supposed to represent "universal identity and modernity" of Muslim architecture. Meanwhile, the concept of architectural hybridity to show enrichment architecture identity because of the attempt to combine aspects of the universality of Islam with locality of Nusantara. Both these aspects can be positioned as the two subjects of mutual dialogue in a parallel position. As architecture strategy, the concept of hybridity reflects the effort or ijtihad in interpreting local and universal contextuality in the contemporary conditions that are constantly evolving and open.Keywords: Nusantara mosque, hybridity of architecture, homogeneity of architecture, architecture strategy

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

    Science.gov (United States)

    Green, G R

    2001-01-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

  13. Chromatin structure near transcriptionally active genes

    International Nuclear Information System (INIS)

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

  14. HJURP is involved in the expansion of centromeric chromatin.

    Science.gov (United States)

    Perpelescu, Marinela; Hori, Tetsuya; Toyoda, Atsushi; Misu, Sadahiko; Monma, Norikazu; Ikeo, Kazuho; Obuse, Chikashi; Fujiyama, Asao; Fukagawa, Tatsuo

    2015-08-01

    The CENP-A-specific chaperone HJURP mediates CENP-A deposition at centromeres. The N-terminal region of HJURP is responsible for binding to soluble CENP-A. However, it is unclear whether other regions of HJURP have additional functions for centromere formation and maintenance. In this study, we generated chicken DT40 knockout cell lines and gene replacement constructs for HJURP to assess the additional functions of HJURP in vivo. Our analysis revealed that the middle region of HJURP associates with the Mis18 complex protein M18BP1/KNL2 and that the HJURP-M18BP1 association is required for HJURP function. In addition, on the basis of the analysis of artificial centromeres induced by ectopic HJURP localization, we demonstrate that HJURP exhibits a centromere expansion activity that is separable from its CENP-A-binding activity. We also observed centromere expansion surrounding natural centromeres after HJURP overexpression. We propose that this centromere expansion activity reflects the functional properties of HJURP, which uses this activity to contribute to the plastic establishment of a centromeric chromatin structure. PMID:26063729

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

    OpenAIRE

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

    2012-01-01

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

  16. Reflection, Reflective Practice and Embodied Reflective Practice

    OpenAIRE

    Leigh, Jennifer S; Bailey, Richard

    2013-01-01

    Although widely employed in professional practice of all kinds, ‘reflection’ and ‘reflective practice’ can be considered ‘success words’. That is, they elicit positive and supportive responses and yet the concepts are vague, ill-defined, contradictory and reflective skills can be hard to teach. Using examples from education and somatic movement therapy, we argue that a purely analytical approach to reflective practice that involves reflecting on thoughts alone is likely to lead into a negativ...

  17. Haptic architecture becomes architectural hap

    OpenAIRE

    Herssens, Jasmien; Heylighen, Ann

    2007-01-01

    Universal Design is a recent design paradigm which aims at handicap elimination in the physical environment and strives for a more humanized architecture. After pointing out the value of Universal Design, the paper advances human centred design as a possible methodology to make this paradigm operational. Key to this methodology is the explicit attention for cognitive human factors in experiencing space and—the focus of this paper—for the role played by the sense of tou...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  19. Reflection Coefficients.

    Science.gov (United States)

    Greenslade, Thomas B., Jr.

    1994-01-01

    Discusses and provides an example of reflectivity approximation to determine whether reflection will occur. Provides a method to show thin-film interference on a projection screen. Also applies the reflectivity concepts to electromagnetic wave systems. (MVL)

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

    Science.gov (United States)

    Hirakawa, Takeshi; Matsunaga, Sachihiro

    2016-01-01

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

  1. Textile Architecture

    DEFF Research Database (Denmark)

    Heimdal, Elisabeth Jacobsen

    2010-01-01

    Textiles can be used as building skins, adding new aesthetic and functional qualities to architecture. Just like we as humans can put on a coat, buildings can also get dressed. Depending on our mood, or on the weather, we can change coat, and so can the building. But the idea of using textiles...... to create human habitation is not new. As Diether S. Hope phrases it, referring to tents: The history of development of humanity would be barely conceivable without free spanning textile membrane structures....

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

    Science.gov (United States)

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

    2010-11-01

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

  3. Characteristics of thymine dimer excision from xeroderma pigmentosum chromatin

    International Nuclear Information System (INIS)

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

  4. Anti-chromatin antibodies in juvenile rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    V. Gerloni

    2011-09-01

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

  5. PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

    KAUST Repository

    Bahabri, Rihab R.

    2013-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Timsy Uppal

    2015-01-01

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

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

    International Nuclear Information System (INIS)

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

  8. CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

    Science.gov (United States)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Hinde Elizabeth

    2012-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-14

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

  11. Nucleosome positioning and composition modulate in silico chromatin flexibility

    Science.gov (United States)

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

    2015-02-01

    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

  12. Promoter architectures and developmental gene regulation.

    Science.gov (United States)

    Haberle, Vanja; Lenhard, Boris

    2016-09-01

    Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation. Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development. This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation. PMID:26783721

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

    OpenAIRE

    Borochov, N; Ausio, J; Eisenberg, H

    1984-01-01

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

  14. The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide

    OpenAIRE

    Mukhopadhyay, Rituparna; Yu, Wenqiang; Whitehead, Joanne; Xu, Junwang; Lezcano, Magda; Pack, Svetlana; Kanduri, Chandrasekhar; Kanduri, Meena; Ginjala, Vasudeva; Vostrov, Alexander; Quitschke, Wolfgang; Chernukhin, Igor; Klenova, Elena; Lobanenkov, Victor; Ohlsson, Rolf

    2004-01-01

    All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified...

  15. 夏热冬冷地区建筑反射隔热涂料应用的技术要点%The Technical Points of Application for the Architectural Reflective Thermal Insulation Coatings in Hot Summer and Cold Winter Zone

    Institute of Scientific and Technical Information of China (English)

    薛黎明

    2011-01-01

    介绍了建筑反射隔热涂料在工程应用中的主要技术问题和实施要点,包括建筑反射隔热涂料的应用特点、应用方式、涂层构造和技术指标要求,以及设计要点和施工技术等。其主要应用方式是建筑反射隔热涂料一无机保温砂浆外墙外保温体系,以及建筑反射隔热涂料一保温腻子层体系两种方式。设计中,首先应满足建筑节能规定的建筑物传热阻值,并将涂料等效热阻考虑到设计中;涂膜最小厚度和变形缝的设置等也是设计中应当考虑的问题。%The main technical insulation coatings in the enginee problem and implementation points of the architectural reflective thermal ring application were introduced. These contents were included: the application characteristics, the application way, the coating structure, the technical index requests, and the main pionts for design and the construction technology etc. The main application way were the architectural reflective thermal insulating coatings-inorganic thermal insulation mortar system, and the architectural reflective thermal insulating coatings-thermal insulation p energy-saving design was satisfie system. d, and In the the eq thickness of the film and setting deformation design, the thermal resistance of the building regulated in build uivalent thermal resistance of coatings was calculated. The least int were also considered in the design.

  16. Replication domains are self-interacting structural chromatin units of human chromosomes

    Science.gov (United States)

    Arneodo, Alain

    2011-03-01

    In higher eukaryotes, the absence of specific sequence motifs marking the origins of replication has been a serious hindrance to the understanding of the mechanisms that regulate the initiation and the maintenance of the replication program in different cell types. In silico analysis of nucleotide compositional skew has predicted the existence, in the germline, of replication N-domains bordered by putative replication origins and where the skew decreases rather linearly as the signature of a progressive inversion of the average fork polarity. Here, from the demonstration that the average fork polarity can be directly extracted from the derivative of replication timing profiles, we develop a wavelet-based pattern recognition methodology to delineate replication U-domains where the replication timing profile is shaped as a U and its derivative as a N. Replication U-domains are robustly found in seven cell lines as covering a significant portion (40-50%) of the human genome where the replication timing data actually displays some plasticity between cell lines. The early replication initiation zones at U-domains borders are found to be hypersensitive to DNase I cleavage, to be associated with transcriptional activity and to present a significant enrichment in insular-binding proteins CTCF, the hallmark of an open chromatin structure. A comparative analysis of genome-wide chromatin interaction (HiC) data shows that replication-U domains correspond to self-interacting structural high order chromatin units of megabase characteristic size. Taken together, these findings provide evidence that the epigenetic compartmentalization of the human genome into autonomous replication U-domains comes along with an extensive remodelling of the threedimensional chromosome architecture during development or in specific diseases. The observed cell specific conservation of the replication timing between the human and mouse genomes strongly suggests that this chromosome organization into

  17. Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization

    Energy Technology Data Exchange (ETDEWEB)

    Costes, Sylvain V; Chiolo, Irene; Pluth, Janice M.; Barcellos-Hoff, Mary Helen; Jakob, Burkhard

    2009-09-15

    DNA damage sensing proteins have been shown to localize to the sites of DSB within seconds to minutes following ionizing radiation (IR) exposure, resulting in the formation of microscopically visible nuclear domains referred to as radiation-induced foci (RIF). This review characterizes the spatio-temporal properties of RIF at physiological doses, minutes to hours following exposure to ionizing radiation, and it proposes a model describing RIF formation and resolution as a function of radiation quality and nuclear densities. Discussion is limited to RIF formed by three interrelated proteins ATM (Ataxia telangiectasia mutated), 53BP1 (p53 binding protein 1) and ?H2AX (phosphorylated variant histone H2AX). Early post-IR, we propose that RIF mark chromatin reorganization, leading to a local nuclear scaffold rigid enough to keep broken DNA from diffusing away, but open enough to allow the repair machinery. We review data indicating clear kinetic and physical differences between RIF emerging from dense and uncondensed regions of the nucleus. At later time post-IR, we propose that persistent RIF observed days following exposure to ionizing radiation are nuclear ?scars? marking permanent disruption of the chromatin architecture. When DNA damage is resolved, such chromatin modifications should not necessarily lead to growth arrest and it has been shown that persistent RIF can replicate during mitosis. Thus, heritable persistent RIF spanning over tens of Mbp may affect the transcriptome of a large progeny of cells. This opens the door for a non DNA mutation-based mechanism of radiation-induced phenotypes.

  18. Lamin C and chromatin organization in Drosophila

    Indian Academy of Sciences (India)

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

    2010-04-01

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

  19. Centromeric chromatin and its dynamics in plants.

    Science.gov (United States)

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

    2015-07-01

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

  20. DNA-Protein interactions in nucleosomes and in Chromatin

    International Nuclear Information System (INIS)

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

  1. Probing Chromatin-modifying Enzymes with Chemical Tools

    KAUST Repository

    Fischle, Wolfgang

    2016-02-04

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

  2. Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin.

    Science.gov (United States)

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

    2016-02-11

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

  3. Neutron scattering studies on chromatin higher-order structure

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

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

  4. Insights into Chromatin Structure and Dynamics in Plants

    Directory of Open Access Journals (Sweden)

    Stefanie Rosa

    2013-11-01

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

  5. Does seminal fluid viscosity influence sperm chromatin integrity?

    Science.gov (United States)

    Gopalkrishnan, K; Padwal, V; Balaiah, D

    2000-01-01

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

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

    Science.gov (United States)

    Gay, Sophie; Foiani, Marco

    2015-01-01

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

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

    OpenAIRE

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

    1997-01-01

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

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

    Science.gov (United States)

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

    2012-05-01

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

  9. Higher order chromatin structure: bridging physics and biology

    OpenAIRE

    Fudenberg, Geoffrey; Mirny, Leonid A.

    2012-01-01

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

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

    OpenAIRE

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

    2004-01-01

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

  11. Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire

    Directory of Open Access Journals (Sweden)

    Lindsey Montefiori

    2016-02-01

    Full Text Available Early B cell development is characterized by large-scale Igh locus contraction prior to V(DJ recombination to facilitate a highly diverse Ig repertoire. However, an understanding of the molecular architecture that mediates locus contraction remains unclear. We have combined high-resolution chromosome conformation capture (3C techniques with 3D DNA FISH to identify three conserved topological subdomains. Each of these topological folds encompasses a major VH gene family that become juxtaposed in pro-B cells via megabase-scale chromatin looping. The transcription factor Pax5 organizes the subdomain that spans the VHJ558 gene family. In its absence, the J558 VH genes fail to associate with the proximal VH genes, thereby providing a plausible explanation for reduced VHJ558 gene rearrangements in Pax5-deficient pro-B cells. We propose that Igh locus contraction is the cumulative effect of several independently controlled chromatin subdomains that provide the structural infrastructure to coordinate optimal antigen receptor assembly.

  12. Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).

    Science.gov (United States)

    Ouma, Wilberforce Zachary; Mejia-Guerra, Maria Katherine; Yilmaz, Alper; Pareja-Tobes, Pablo; Li, Wei; Doseff, Andrea I; Grotewold, Erich

    2015-01-01

    Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs). ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-wide binding sites of a particular TF. However, in all organisms investigated an average of 40% of reads fail to align to the corresponding genome, with some datasets having as much as 80% of reads failing to align. We describe here the provenance of previously unaligned reads in ChIP-Seq experiments from animals and plants. We show that a substantial portion corresponds to sequences of bacterial and metazoan origin, irrespective of the ChIP-Seq chromatin source. Unforeseen was the finding that 30%-40% of unaligned reads were actually alignable. To validate these observations, we investigated the characteristics of the previously unaligned reads corresponding to TAL1, a human TF involved in lineage specification of hemopoietic cells. We show that, while unmapped ChIP-Seq read datasets contain foreign DNA sequences, additional TFBSs can be identified from the previously unaligned ChIP-Seq reads. Our results indicate that the re-evaluation of previously unaligned reads from ChIP-Seq experiments will significantly contribute to TF target identification and determination of emerging properties of GRNs. PMID:25727450

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

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

  15. Decoding the architectural theory

    Institute of Scientific and Technical Information of China (English)

    Gu Mengchao

    2008-01-01

    Starting from the illustration of the definition and concept of the architectural theory, the author established his unique understanding about the framework of the architectural theory and the innovation of the architectural theory underlined by Chinese characteristics.

  16. Preserving Architectural Decisions through Architectural Patterns

    OpenAIRE

    Thon That, Minh Tu; Sadou, Salah; Oquendo, F.; Fleurquin, R

    2014-01-01

    International audience Architectural decisions have emerged as a means to maintain the quality of the architecture during its evolution. One of the most important de-cisions made by architects are those about the design approach such as the use of patterns or styles in the architecture. The structural nature of this type of decisions give them the potential to be controlled systematically. In the litera-ture, there are some works on the automation of architectural decision violation checki...

  17. Impact of Pdx1-associated chromatin modifiers on islet β-cells.

    Science.gov (United States)

    Spaeth, J M; Walker, E M; Stein, R

    2016-09-01

    Diabetes mellitus arises from insufficient insulin secretion from pancreatic islet β-cells. In type 2 diabetes (T2D), β-cell dysfunction is associated with inactivation and/or loss of transcription factor (TF) activity, including Pdx1. Notably, this particular TF is viewed as a master regulator of pancreas development and islet β-cell formation, identity and function. TFs, like Pdx1, recruit coregulators to transduce activating and/or repressing signals to the general transcriptional machinery for controlling gene expression, including modifiers of DNA, histones and nucleosome architecture. These coregulators impart a secondary layer of control that can be exploited to modulate TF activity. In this review, we describe Pdx1-recruited coregulators that impact chromatin structure, consequently influencing normal β-cell function and likely Pdx1 activity in pathophysiological settings. PMID:27615141

  18. Software Architecture Simulation

    OpenAIRE

    Mårtensson, Frans; Jönsson, Per

    2002-01-01

    A software architecture is one of the first steps towards a software system. A software architecture can be designed in different ways. During the design phase, it is important to select the most suitable design of the architecture, in order to create a good foundation for the system. The selection process is performed by evaluating architecture alternatives against each other. We investigate the use of continuous simulation of a software architecture as a support tool for architecture evalua...

  19. De lo con-céntrico a lo des-centrado. Reflexiones sobre el lugar y el no-lugar en la arquitectura. / From the concentric to the off-center. Reflections on the place and the non-place in architecture.

    Directory of Open Access Journals (Sweden)

    Laura Gallardo Frías

    2012-06-01

    Full Text Available Se propone, a través de la figura del círculo, abrir una reflexión sobre sus propiedades, su presencia y permanencia lo largo de la historia así como en nuestros días. Se invita al lector a un paseo por diferentes propuestas arquitectónicas y pensamientos paraexplorar el paso de lo con-céntrico a lo des-centrado, revisando las nociones de lugar, no-lugar y sus relaciones con la arquitectura. Poniendo de relieve la importancia del proyecto arquitectónico capaz de conformar centros donde el ser humano sea uno consigo mismo y loque le rodea, produciendo una profunda resonancia./ It is proposed, through the figure of the circle, opening a reflection on their properties, their presence and permanence throughout history and today. It invites the reader on a tour of different architectural proposals and thoughts to explore the transition from the con-centric to the ec-centric, reviewing the notions of place, non-place andits relationship with architecture. Emphasizing the importance of architecture as capable of forming centers where a human being with himself and his surroundings to produce a deep resonance.

  20. Architectures of prototypes and architectural prototyping

    DEFF Research Database (Denmark)

    Hansen, Klaus Marius; Christensen, Michael; Sandvad, Elmer;

    1998-01-01

    sessions with users, - evolve over a long period of time to contain more functionality - allow for 6-7 developers working intensively in parallel. Explicit focus on the software architecture and letting the architecture evolve with the prototype played a major role in resolving these conflicting...... constraints. Specifically allowing explicit restructuring phases when the architecture became problematic showed to be crucial.  ...

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

    Science.gov (United States)

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

    2015-01-01

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

  2. Software architecture 2

    CERN Document Server

    Oussalah, Mourad Chabanne

    2014-01-01

    Over the past 20 years, software architectures have significantly contributed to the development of complex and distributed systems. Nowadays, it is recognized that one of the critical problems in the design and development of any complex software system is its architecture, i.e. the organization of its architectural elements. Software Architecture presents the software architecture paradigms based on objects, components, services and models, as well as the various architectural techniques and methods, the analysis of architectural qualities, models of representation of architectural templa

  3. Lightweight enterprise architectures

    CERN Document Server

    Theuerkorn, Fenix

    2004-01-01

    STATE OF ARCHITECTUREArchitectural ChaosRelation of Technology and Architecture The Many Faces of Architecture The Scope of Enterprise Architecture The Need for Enterprise ArchitectureThe History of Architecture The Current Environment Standardization Barriers The Need for Lightweight Architecture in the EnterpriseThe Cost of TechnologyThe Benefits of Enterprise Architecture The Domains of Architecture The Gap between Business and ITWhere Does LEA Fit? LEA's FrameworkFrameworks, Methodologies, and Approaches The Framework of LEATypes of Methodologies Types of ApproachesActual System Environmen

  4. Software architecture 1

    CERN Document Server

    Oussalah , Mourad Chabane

    2014-01-01

    Over the past 20 years, software architectures have significantly contributed to the development of complex and distributed systems. Nowadays, it is recognized that one of the critical problems in the design and development of any complex software system is its architecture, i.e. the organization of its architectural elements. Software Architecture presents the software architecture paradigms based on objects, components, services and models, as well as the various architectural techniques and methods, the analysis of architectural qualities, models of representation of architectural template

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

    Science.gov (United States)

    Bakkenist, Christopher J; Kastan, Michael B

    2015-12-01

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

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

    Science.gov (United States)

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

    2016-03-29

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

  7. Chromatin condensation and differential sensitivity of mammalian and insect cells to DNA strand breaks induced by bleomycin

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Larraza, Daniel M. [IMBICE, C.C. 403, 1900 La Plata (Argentina)]. E-mail: danielop@imbice.org.ar; Padron, Juan [IMBICE, C.C. 403, 1900 La Plata (Argentina); Ronci, Natalia E. [IMBICE, C.C. 403, 1900 La Plata (Argentina); Vidal Rioja, Lidia A. [IMBICE, C.C. 403, 1900 La Plata (Argentina)

    2006-08-30

    Bleomycin (BLM) induces DNA damage in living cells. In this report we analyzed the role of chromatin compactness in the differential response of mosquito (ATC-15) and mammalian (CHO) cells to DNA strand breaks induced by BLM. We used cells unexposed and exposed to sodium butyrate (NaB), which induces chromatin decondensation. By nucleoid sedimentation assay and digestions of nuclei with DNAse I, untreated mosquito cells (no BLM; no NaB) were shown to have more chromatin condensation than untreated CHO cells. By alkaline unwinding ATC-15 cells treated with NaB showed more BLM-induced DNA strand breaks than NaB-untreated CHO cells. The time-course of BLM-induced DNA damage to nuclear DNA was similar for NaB-untreated mammalian and insect cells, but with mosquito cells showing less DNA strand breaks, both at physiological temperatures and at 4 {sup o}C. However, when DNA repair was inhibited by low temperatures and chromatin was decondensed by NaB treatments, differences in BLM-induced DNA damage between these cells lines were no longer observed. In both cell lines, NaB did not affect BLM action on cell growth and viability. On the other hand, the low sensitivity of ATC-15 cells to BLM was reflected in their better growth efficiency. These cells exhibited a satisfactory growth at BLM doses that produced a permanent arrest of growth in CHO cells. The data suggest that mosquito cells might have linker DNAs shorter than those of mammalian cells, which would result in the observed both greater chromatin condensation and greater resistance to DNA damage induced by BLM as compared to CHO cells.

  8. Building science of indian temple architecture

    OpenAIRE

    Vardia, Shweta

    2008-01-01

    Master’s Thesis Structural Analysis of Monuments and Historical Constructions Every style of building construction reflects a clearly distinctive basic principle that represents a particular culture and era. In this context the Indian Hindu temple architecture are not only the abode of God and place of worship, but they are also the cradle of knowledge, art, architecture and culture. The practices and traditions of temples exist not only in history but also in present time which g...

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

    OpenAIRE

    Lai, F; Ørom, U.; M. Cesaroni; Beringer, M.; Taatjes, D.; Blobel, G; Shiekhattar, R.

    2013-01-01

    Recent advances in genomic research have revealed the existence of a large number of transcripts devoid of protein-coding potential in multiple organisms 1-8 . While the functional role for long non-coding RNAs (lncRNAs) has been best defined in epigenetic phenomena such as X inactivation and imprinting, different classes of lncRNAs may have varied biological functions 8-13 . We and others have identified a class of lncRNAs, termed ncRNA-activating (ncRNA-a), that function to activate their n...

  10. Information architecture. Volume 1, The foundations

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-03-01

    The Information Management Planning and Architecture Coordinating Team was formed to establish an information architecture framework to meet DOE`s current and future information needs. This department- wide activity was initiated in accordance with the DOE Information Management Strategic Plan; it also supports the Departmental Strategic Plan. It recognizes recent changes in emphasis as reflected in OMB Circular A-130 and the Information Resources Management Planning Process Improvement Team recommendations. Sections of this document provides the foundation for establishing DOE`s Information Architecture: Background, Business Case (reduced duplication of effort, increased integration of activities, improved operational capabilities), Baseline (technology baseline currently in place within DOE), Vision (guiding principles for future DOE Information Architecture), Standards Process, Policy and Process Integration (describes relations between information architecture and business processes), and Next Steps. Following each section is a scenario. A glossary of terms is provided.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Olins, D E

    1977-01-01

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

  13. Creating product line architectures

    OpenAIRE

    Bayer, J.; Flege, O.; Gacek, C.

    2000-01-01

    The creation and validation of product line software architectures are inherently more complex than those of software architectures for single systems. This paper compares a process for creating and evaluating a traditional, one-of-a- kind software architecture with one for a reference software architecture. The comparison is done in the context of PuLSE-DSSA, a customizable process that integrates both product line architecture creation and evaluation.

  14. ESA: Enterprise Service Architecture

    OpenAIRE

    2010-01-01

    The Service oriented perspective is emerging as an important view both for business architecture and IT architecture in the overall context of enterprise architectures. Many existing enterprise architecture frameworks like DODAF, MODAF and NAF have lately been extended with service-oriented views. The UPDM UML Profile and Metamodel for DODAF and MODAF has thus included various service-oriented views. This thesis proposes a new enterprise architecture framework ESA Enterprise Service Arch...

  15. Phenotypic plasticity in Drosophila pigmentation caused by temperature sensitivity of a chromatin regulator network.

    Directory of Open Access Journals (Sweden)

    Jean-Michel Gibert

    2007-02-01

    Full Text Available Phenotypic plasticity is the ability of a genotype to produce contrasting phenotypes in different environments. Although many examples have been described, the responsible mechanisms are poorly understood. In particular, it is not clear how phenotypic plasticity is related to buffering, the maintenance of a constant phenotype against genetic or environmental variation. We investigate here the genetic basis of a particularly well described plastic phenotype: the abdominal pigmentation in female Drosophila melanogaster. Cold temperature induces a dark pigmentation, in particular in posterior segments, while higher temperature has the opposite effect. We show that the homeotic gene Abdominal-B (Abd-B has a major role in the plasticity of pigmentation in the abdomen. Abd-B plays opposite roles on melanin production through the regulation of several pigmentation enzymes. This makes the control of pigmentation very unstable in the posterior abdomen, and we show that the relative spatio-temporal expression of limiting pigmentation enzymes in this region of the body is thermosensitive. Temperature acts on melanin production by modulating a chromatin regulator network, interacting genetically with the transcription factor bric-à-brac (bab, a target of Abd-B and Hsp83, encoding the chaperone Hsp90. Genetic disruption of this chromatin regulator network increases the effect of temperature and the instability of the pigmentation pattern in the posterior abdomen. Colocalizations on polytene chromosomes suggest that BAB and these chromatin regulators cooperate in the regulation of many targets, including several pigmentation enzymes. We show that they are also involved in sex comb development in males and that genetic destabilization of this network is also strongly modulated by temperature for this phenotype. Thus, we propose that phenotypic plasticity of pigmentation is a side effect reflecting a global impact of temperature on epigenetic mechanisms

  16. Oxidative stress signaling to chromatin in health and disease

    KAUST Repository

    Kreuz, Sarah

    2016-06-20

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

  17. Sliding and peeling of histone during chromatin remodelling

    CERN Document Server

    Garai, Ashok; Chowdhury, Debashish

    2011-01-01

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

  18. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis

    Directory of Open Access Journals (Sweden)

    Jialei Hu

    2015-12-01

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

  19. 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

  20. Reflection groups

    International Nuclear Information System (INIS)

    In 2005, PISA organised proactive meetings of reflection groups on involvement in decision making, expert culture and ethical aspects of radiation protection.All reflection group meetings address particular targeted audiences while the output publication in book form is put forward

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

    Directory of Open Access Journals (Sweden)

    Grøntved Lars

    2012-06-01

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

  2. Single-epitope recognition imaging of native chromatin

    Directory of Open Access Journals (Sweden)

    Wang Hongda

    2008-12-01

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

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

    OpenAIRE

    Názer, Ezequiel; Lei, Elissa P.

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Laugesen, Anne; Helin, Kristian

    2014-01-01

    The chromatin environment is essential for the correct specification and preservation of cell identity through modulation and maintenance of transcription patterns. Many chromatin regulators are required for development, stem cell maintenance, and differentiation. Here, we review the roles of the...... polycomb repressive complexes, PRC1 and PRC2, and the HDAC1- and HDAC2-containing complexes, NuRD, Sin3, and CoREST, in stem cells, development, and cancer, as well as the ongoing efforts to develop therapies targeting these complexes in human cancer. Furthermore, we discuss the role of repressive...... complexes in modulating thresholds for gene activation and their importance for specification and maintenance of cell fate....

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

    Science.gov (United States)

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

    2015-01-01

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

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

    OpenAIRE

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

    2015-01-01

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

  7. E-Business Security Architectures

    Directory of Open Access Journals (Sweden)

    2009-01-01

    Full Text Available By default the Internet is an open high risk environment and also the main place where the e-business is growing. As result of this fact, the paper aims to highlight the security aspects that relate to distributed applications [3], with reference to the concept of e-business. In this direction will analyze the quality characteristics, considered to be important by the author. Based on these and on existing e-business architectures will be presented a particularly diagram which will reflect a new approach to the concept of future e-business. The development of the new architecture will have its stands based on technologies that are used to build the applications of tomorrow.

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

    DEFF Research Database (Denmark)

    Lichota, J.; Grasser, Klaus D.

    2003-01-01

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

  9. Linking Morphogen and Chromatin in the Hair Follicle

    OpenAIRE

    Mesa, Kailin R; Greco, Valentina

    2013-01-01

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

  10. ATP independent and ATP dependent chromatin remodeling in wheat

    International Nuclear Information System (INIS)

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

  11. Chromatin remodelers in the DNA double strand break response

    NARCIS (Netherlands)

    Smeenk, Godelieve

    2012-01-01

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

  12. Chromatin-regulating proteins as targets for cancer therapy

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2014-07-01

    Chromatin-regulating proteins represent a large class of novel targets for cancer therapy. In the context of radiotherapy, acetylation and deacetylation of histones by histone acetyltransferases (HATs) and histone deacetylases (HDACs) play important roles in the repair of DNA double-strand breaks generated by ionizing irradiation, and are therefore attractive targets for radiosensitization. Small-molecule inhibitors of HATs (garcinol, anacardic acid and curcumin) and HDACs (vorinostat, sodium butyrate and valproic acid) have been shown to sensitize cancer cells to ionizing irradiation in preclinical models, and some of these molecules are being tested in clinical trials, either alone or in combination with radiotherapy. Meanwhile, recent large-scale genome analyses have identified frequent mutations in genes encoding chromatin-regulating proteins, especially in those encoding subunits of the SWI/SNF chromatin-remodeling complex, in various human cancers. These observations have driven researchers toward development of targeted therapies against cancers carrying these mutations. DOT1L inhibition in MLL-rearranged leukemia, EZH2 inhibition in EZH2-mutant or MLL-rearranged hematologic malignancies and SNF5-deficient tumors, BRD4 inhibition in various hematologic malignancies, and BRM inhibition in BRG1-deficient tumors have demonstrated promising anti-tumor effects in preclinical models, and these strategies are currently awaiting clinical application. Overall, the data collected so far suggest that targeting chromatin-regulating proteins is a promising strategy for tomorrow's cancer therapy, including radiotherapy and molecularly targeted chemotherapy. PMID:24522270

  14. Effect of triiodothyronine on rat liver chromatin protein kinase

    International Nuclear Information System (INIS)

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

  15. Control of the Transition to Flowering by Chromatin Modifications

    Institute of Scientific and Technical Information of China (English)

    Yuehui He

    2009-01-01

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

  16. Rhein-Ruhr architecture

    DEFF Research Database (Denmark)

    2002-01-01

    katalog til udstillingen 'Rhein - Ruhr architecture' Meldahls smedie, 15. marts - 28. april 2002. 99 sider......katalog til udstillingen 'Rhein - Ruhr architecture' Meldahls smedie, 15. marts - 28. april 2002. 99 sider...

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

    OpenAIRE

    Martínez Redondo, Paloma

    2014-01-01

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

  18. Bioclimatism in vernacular architecture

    OpenAIRE

    Coch Roura, Helena

    1998-01-01

    Any analysis of the role played by energy in architecture is faced with serious limitations due to the lack of studies in the architectural bibliography, especially studies of popular architecture. An awareness of these limitations will allow us to understand better why architects have paid little attention to the interaction of form and energy, and to the bioclimatic approach in contemporary architecture in general. The first limitation stems from the very essence of bioclimatic analysis; en...

  19. Controller Architectures for Switching

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Poulsen, Niels Kjølstad

    2009-01-01

    This paper investigate different controller architectures in connection with controller switching. The controller switching is derived by using the Youla-Jabr-Bongiorno-Kucera (YJBK) parameterization. A number of different architectures for the implementation of the YJBK parameterization are...... described and applied in connection with controller switching. An architecture that does not include inversion of the coprime factors is introduced. This architecture will make controller switching particular simple....

  20. Neuronal accumulation of unrepaired DNA in a novel specific chromatin domain: structural, molecular and transcriptional characterization.

    Science.gov (United States)

    Mata-Garrido, Jorge; Casafont, Iñigo; Tapia, Olga; Berciano, Maria T; Lafarga, Miguel

    2016-01-01

    There is growing evidence that defective DNA repair in neurons with accumulation of DNA lesions and loss of genome integrity underlies aging and many neurodegenerative disorders. An important challenge is to understand how neurons can tolerate the accumulation of persistent DNA lesions without triggering the apoptotic pathway. Here we study the impact of the accumulation of unrepaired DNA on the chromatin architecture, kinetics of the DNA damage response and transcriptional activity in rat sensory ganglion neurons exposed to 1-to-3 doses of ionizing radiation (IR). In particular, we have characterized the structural, molecular and transcriptional compartmentalization of unrepaired DNA in persistent DNA damaged foci (PDDF). IR induced the formation of numerous transient foci, which repaired DNA within the 24 h post-IR, and a 1-to-3 PDDF. The latter concentrate DNA damage signaling and repair factors, including γH2AX, pATM, WRAP53 and 53BP1. The number and size of PDDF was dependent on the doses of IR administered. The proportion of neurons carrying PDDF decreased over time of post-IR, indicating that a slow DNA repair occurs in some foci. The fine structure of PDDF consisted of a loose network of unfolded 30 nm chromatin fiber intermediates, which may provide a structural scaffold accessible for DNA repair factors. Furthermore, the transcription assay demonstrated that PDDF are transcriptionally silent, although transcription occurred in flanking euchromatin. Therefore, the expression of γH2AX can be used as a reliable marker of gene silencing in DNA damaged neurons. Moreover, PDDF were located in repressive nuclear environments, preferentially in the perinucleolar domain where they were frequently associated with Cajal bodies or heterochromatin clumps forming a structural triad. We propose that the sequestration of unrepaired DNA in discrete PDDF and the transcriptional silencing can be essential to preserve genome stability and prevent the synthesis of

  1. Minimalist Architecture; Discussion of Its Sustainability in Indonesia

    OpenAIRE

    Silfia Mona Aryani

    2011-01-01

    Architecture develops along with particular society changing. In the period of modern, some traditional architecture with their complex rules become considered old fashioned. It was not implemented in modern buildings. When functionality becomes priority, minimalist architecture, recognized as Neo-Modernism, spreads and offers reflection of modern lifestyle. However, every style is not always suitable for each circumstance. The unconditional application of style can create another problem ins...

  2. An event-based architecture for solving constraint satisfaction problems

    OpenAIRE

    Mostafa, Hesham; Müller, Lorenz K.; Indiveri, Giacomo

    2015-01-01

    Constraint satisfaction problems (CSPs) are typically solved using conventional von Neumann computing architectures. However, these architectures do not reflect the distributed nature of many of these problems and are thus ill-suited to solving them. In this paper we present a hybrid analog/digital hardware architecture specifically designed to solve such problems. We cast CSPs as networks of stereotyped multi-stable oscillatory elements that communicate using digital pulses, or events. The o...

  3. Tourists' Transformation Experience: From Destination Architecture to Identity Formation

    DEFF Research Database (Denmark)

    Ye, Helen Yi; Tussyadiah, Iis

    2010-01-01

    Today’s tourists seek unique destinations that could associate with their self identity in a profound way. It is meaningful for destinations to design unique physical elements that offer transformational travel experiences. This study aims at identifying how tourists encounter architecture in a...... destination and if architecture facilitates tourists’ self transformation. Based on narrative structure analysis by deconstruction of travel blog posts, the results suggest that tourists perceive architectural landscape as an important feature that reflects destinations’ identity. Four different interaction...

  4. School of Architecture + Design establishes Virginia Tech architecture publications

    OpenAIRE

    Chadwick, Heather Riley

    2007-01-01

    Virginia Tech's School of Architecture + Design, in the College of Architecture and Urban Studies, with the initiative of Markus Breitschmid, assistant professor of architecture, has established Virginia Tech Architecture Publications.

  5. Citrullination regulates pluripotency and histone H1 binding to chromatin

    Science.gov (United States)

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

    2014-03-01

    Citrullination is the post-translational conversion of an arginine residue within a protein to the non-coded amino acid citrulline. This modification leads to the loss of a positive charge and reduction in hydrogen-bonding ability. It is carried out by a small family of tissue-specific vertebrate enzymes called peptidylarginine deiminases (PADIs) and is associated with the development of diverse pathological states such as autoimmunity, cancer, neurodegenerative disorders, prion diseases and thrombosis. Nevertheless, the physiological functions of citrullination remain ill-defined, although citrullination of core histones has been linked to transcriptional regulation and the DNA damage response. PADI4 (also called PAD4 or PADV), the only PADI with a nuclear localization signal, was previously shown to act in myeloid cells where it mediates profound chromatin decondensation during the innate immune response to infection. Here we show that the expression and enzymatic activity of Padi4 are also induced under conditions of ground-state pluripotency and during reprogramming in mouse. Padi4 is part of the pluripotency transcriptional network, binding to regulatory elements of key stem-cell genes and activating their expression. Its inhibition lowers the percentage of pluripotent cells in the early mouse embryo and significantly reduces reprogramming efficiency. Using an unbiased proteomic approach we identify linker histone H1 variants, which are involved in the generation of compact chromatin, as novel PADI4 substrates. Citrullination of a single arginine residue within the DNA-binding site of H1 results in its displacement from chromatin and global chromatin decondensation. Together, these results uncover a role for citrullination in the regulation of pluripotency and provide new mechanistic insights into how citrullination regulates chromatin compaction.

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

    Science.gov (United States)

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

    1991-10-01

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

  7. Architectural Knitted Surfaces

    DEFF Research Database (Denmark)

    Mossé, Aurélie

    2010-01-01

    WGSN reports from the Architectural Knitted Surfaces workshop recently held at ShenkarCollege of Engineering and Design, Tel Aviv, which offered a cutting-edge insight into interactive knitted surfaces. With the increasing role of smart textiles in architecture, the Architectural Knitted Surfaces...

  8. Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Jamy C.

    2007-05-05

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

  9. Language-based support for service oriented architectures

    DEFF Research Database (Denmark)

    Giambiagi, Pablo; Owe, Olaf; Ravn, Anders Peter;

    2006-01-01

    The fast evolution of the Internet has popularized service-oriented architectures (SOA) with their promise of dynamic IT-supported inter-business collaborations. Yet this popularity does not reflect on the number of actual applications using the architecture. Programming models in use today make ...

  10. Reflective State Pattern with Dynamic Constructiveness

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    After discussing the reflective method of structure and behaviorin th e State design pattern based on Role Object pattern and the Reflective pattern o f software architecture, this paper proposes a reflective state pattern with dyn amic constructiveness. This paper explains the meta level and the base level, wh ich are two levels of this pattern, and specifies the relation of two levels by using Meta Object Protocol (MOP). Then it discusses mechanism of interception an d reification for reflecting base object from Meta object. Finally this paper g ives an example of network server for applying the Reflective State pattern

  11. Software Architecture Viewpoint Models: A Short Survey

    Directory of Open Access Journals (Sweden)

    Seyyed Ali Razavi Ebrahimi

    2013-11-01

    Full Text Available A software architecture is a complex entity that cannot be described in a simple one-dimensional fashion. The architecture views used to describe software provide the architect with a means of explaining the architecture to stakeholders. Each view presents different aspects of the system that fulfill functional and non-functional requirements. A view of a system is a representation of the system from the perspective of a viewpoint. Architecture viewpoints in software products provide guidelines to describe uniformly the total system and its subsystems. It defines the stakeholders whose concerns are reflected in the viewpoint and the guidelines, principles, and template models for constructing its views. The results of this study may serve as a roadmap to the software developers and architects in helping them select the appropriate viewpoint model based on the stakeholders and concerns that need to be covered by views.

  12. Evolution of plant genome architecture.

    Science.gov (United States)

    Wendel, Jonathan F; Jackson, Scott A; Meyers, Blake C; Wing, Rod A

    2016-01-01

    We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement. PMID:26926526

  13. Reflective optics

    CERN Document Server

    Korsch, Dietrich

    1991-01-01

    This is the first book dedicated exclusively to all-reflective imaging systems. It is a teaching tool as well as a practical design tool for anyone who specializes in optics, particularly for those interested in telescopes, infrared, and grazing-incidence systems. The first part of the book describes a unified geometric optical theory of all-reflective imaging systems (from near-normal to grazing incidence) developed from basic principles. The second part discusses correction methods and a multitude of closed-form solutions of well-corrected systems, supplemented with many conventional and unc

  14. Software architecture evolution

    DEFF Research Database (Denmark)

    Barais, Olivier; Le Meur, Anne-Francoise; Duchien, Laurence;

    2008-01-01

    Software architectures must frequently evolve to cope with changing requirements, and this evolution often implies integrating new concerns. Unfortunately, when the new concerns are crosscutting, existing architecture description languages provide little or no support for this kind of evolution....... The software architect must modify multiple elements of the architecture manually, which risks introducing inconsistencies. This chapter provides an overview, comparison and detailed treatment of the various state-of-the-art approaches to describing and evolving software architectures. Furthermore, we...... discuss one particular framework named Tran SAT, which addresses the above problems of software architecture evolution. Tran SAT provides a new element in the software architecture descriptions language, called an architectural aspect, for describing new concerns and their integration into an existing...

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

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Griffith, J

    1977-01-01

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

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

    Science.gov (United States)

    Wolf, G; Beil, M; Guski, H

    1995-02-01

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

  17. Proteomics and the genetics of sperm chromatin condensation

    Institute of Scientific and Technical Information of China (English)

    Rafael Oliva; Judit Castillo

    2011-01-01

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

  18. Integrative annotation of chromatin elements from ENCODE data

    OpenAIRE

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

    2012-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

  20. Effect of saffron on rat sperm chromatin integrity

    OpenAIRE

    Mohammad Mardani; Ahmad Vaez; Shahnaz Razavi

    2014-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  2. 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...

  3. Chromatin-regulating proteins as targets for cancer therapy

    OpenAIRE

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

    2014-01-01

    Chromatin-regulating proteins represent a large class of novel targets for cancer therapy. In the context of radiotherapy, acetylation and deacetylation of histones by histone acetyltransferases (HATs) and histone deacetylases (HDACs) play important roles in the repair of DNA double-strand breaks generated by ionizing irradiation, and are therefore attractive targets for radiosensitization. Small-molecule inhibitors of HATs (garcinol, anacardic acid and curcumin) and HDACs (vorinostat, sodium...

  4. Chaperone-mediated assembly of centromeric chromatin in vitro

    OpenAIRE

    Furuyama, Takehito; Dalal, Yamini; Henikoff, Steven

    2006-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2009-01-01

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

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

    OpenAIRE

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

    1999-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

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

  8. Transcription within Condensed Chromatin: Steric Hindrance Facilitates Elongation

    OpenAIRE

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

    2010-01-01

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

  9. Quality of histone modification antibodies undermines chromatin biology research

    OpenAIRE

    Goran Kungulovski; Albert Jeltsch

    2015-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

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

    OpenAIRE

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

    2009-01-01

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

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

    Science.gov (United States)

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

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model. PMID:662693

  13. Modular Architecture for the Measurement of Space Radiation

    Science.gov (United States)

    Delaune, Paul; Turner, Kathryn; Holland, S. Douglas; Carson, William R.; Riman, Fadi

    2007-01-01

    A modular architecture has been conceived for the design of radiation-monitoring instruments used aboard spacecraft and in planetary-exploration settings. This architecture reflects lessons learned from experience with prior radiation-monitoring instruments. A prototype instrument that embodies the architecture has been developed as part of the Mars Advanced Radiation Acquisition (MARA) project. The architecture is also applicable on Earth for radiation-monitoring instruments in research of energetic electrically charged particles and instruments monitoring radiation for purposes of safety, military defense, and detection of hidden nuclear devices and materials.

  14. Minimalist Architecture; Discussion of Its Sustainability in Indonesia

    Directory of Open Access Journals (Sweden)

    Silfia Mona Aryani

    2011-01-01

    Full Text Available Architecture develops along with particular society changing. In the period of modern, some traditional architecture with their complex rules become considered old fashioned. It was not implemented in modern buildings. When functionality becomes priority, minimalist architecture, recognized as Neo-Modernism, spreads and offers reflection of modern lifestyle. However, every style is not always suitable for each circumstance. The unconditional application of style can create another problem instead of a solution. This essay will discuss the existence of minimalism in architecture; its historical relationship with modernism, the theoretical reviews which underpin the discussion and the appropriate adaptations need to be made to fit in tropical climate.

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

    Science.gov (United States)

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

    2013-03-01

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

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

    Science.gov (United States)

    Gonzales, G F; Sánchez, A

    1994-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ivo A. Hendriks

    2015-03-01

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

  18. Architecture and Stages

    DEFF Research Database (Denmark)

    Kiib, Hans

    2009-01-01

    future. But this is not enough. The agenda is to develop architectural spaces, where social interaction and learning are enhanced by art and fun. How can we develop new architectural designs in our inner cities and waterfronts where eventscapes, learning labs and temporal use are merged with everyday......Architecture and Art as Fuel New development zones for shopping and entertainment and space for festivals inside the city CAN be coupled with art and architecture and become ‘open minded' public domains based on cultural exchange and mutual learning. This type of space could be labelled as...... "experiencescape" - a space between tourism, culture, learning and economy. Strategies related to these challenges involve new architectural concepts and art as ‘engines' for a change. New expressive architecture and old industrial buildings are often combined into hybrid narratives, linking the past with the...

  19. Research on the Contemporary Japanese Architectural Creation and its Special Aesthetical Taste of Nationality

    Directory of Open Access Journals (Sweden)

    Shan Linlin

    2013-08-01

    Full Text Available Contemporary Japanese architecture has achieved great success and has been widely accepted by the whole architectural field. What is the driving force for the contemporary Japanese architectural creation is worth of thinking carefully about. In this study, some famous Japanese architects, including Toyo Ito, Tadao Ando, Arata Isozaki, Kengo Kuma, Kazuyo Sejima and Ryue Nishizawa and their architectural studiess are analyzed and studied from the angle of nationality. These architects keep up with the step of the world architecture and always pursuit the aesthetical taste of nationality. They proposed some special architectural theories that profoundly reflect the nationality of Japanese and make great influence on the architectural forms, architectural space and architectural aesthetics of Contemporary Japanese architecture. In the architectural form, they pursuit the simplicity, pureness, lightness and finesses; in the architectural space and behavior, they pursuit the shadow of the ma space and nature existence; in the architectural aesthetics, they pursuit the beauty of animism, dreariness and substance sadness. Through conjoint analysis of the architectural examples and the theory of nationality, this study proposed that the contemporary Japanese architectural creation is directly derived from the profound traditional culture and firm nationality and nationality is the cornerstone of the Japanese architecture and always promotes the progress of the Japanese architecture.

  20. Molecular Mechanisms of Processing Proteome Reorganization of Interphase Chromatin During Stress and Adaptation to Winter in Wheat

    Directory of Open Access Journals (Sweden)

    Ivanov R.S.

    2015-06-01

    Full Text Available Research of fundamental molecular and genetic processes of plant interaction with the environment, is a progressive field of understanding the fundamental problems of stress supramolecular biochemistry of developmental biology. The purpose of the work was the analysis of localization shielded to protease processing proteins of suprastructures of interphase chromatin matrix in the conditions of adaptation during vegetative phase of wheat to stressful environment factors. It is shown that in the conditions of perennial adaptation to cold shock of wheat at the level of chromatin suprastructures tightly bound to the nuclear matrix there is a total shielding of arginine-X sites to protease-processing. Perhaps these are zones that affect to the architecture organization of the cell nucleus that can help to survive in complex environmental conditions. According to the priorities in the study of agricultural plants, put forward by EPIC (The Epigenomics of Plants International Consortium in 2011 for the next decade, was included the point of necessity to understand the molecular basis of the interactions of genotype and environment that change the characteristics of plants in different conditions of the environment. These data will be useful for those who involved in the development of mathematical logic schemes of the theory and practice of biological specificity, and it could be included in the ontology of the stages plant growth and development.

  1. Sustained activation of STAT5 is essential for chromatin remodeling and maintenance of mammary-specific function

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Ren; Nelson, Celeste M.; Muschler, John L.; Veiseh, Mandana; Vonderhaar, Barbara K.; Bissell, Mina J.

    2009-06-03

    Epithelial cells, once dissociated and placed in two-dimensional (2D) cultures, rapidly lose tissue-specific functions. We showed previously that in addition to prolactin, signaling by laminin-111 was necessary to restore functional differentiation of mammary epithelia. Here, we elucidate two additional aspects of laminin-111 action. We show that in 2D cultures, the prolactin receptor is basolaterally localized and physically segregated from its apically placed ligand. Detachment of the cells exposes the receptor to ligation by prolactin leading to signal transducers and activators of transcription protein 5 (STAT5) activation, but only transiently and not sufficiently for induction of milk protein expression. We show that laminin-111 reorganizes mammary cells into polarized acini, allowing both the exposure of the prolactin receptor and sustained activation of STAT5. The use of constitutively active STAT5 constructs showed that the latter is necessary and sufficient for chromatin reorganization and {beta}-casein transcription. These results underscore the crucial role of continuous laminin signaling and polarized tissue architecture in maintenance of transcription factor activation, chromatin organization, and tissue-specific gene expression.

  2. Architecture humanitarian emergencies

    DEFF Research Database (Denmark)

    Gomez-Guillamon, Maria; Eskemose Andersen, Jørgen; Contreras, Jorge Lobos;

    2013-01-01

    Introduced by scientific articles conserning architecture and human rights in light of cultures, emergencies, social equality and sustainability, democracy, economy, artistic development and science into architecture. Concluding in definition of needs for new roles, processes and education of...... architecture. Followed by articles focusing on interdisciplinary research and design of emergency shelters as well as educational environments. Finally concretized in 35 studies from international workshops arranged globally on and by different architect schools: Royal Danish Academy of Fine Arts in Denmark...

  3. Discovery Food - Culinary Architecture

    OpenAIRE

    Buettner-Graefenhain, Christine

    2005-01-01

    What keeps places unique in times of globalization? If information, goods, food, architecture are the same everywhere, what`s the difference between places? What are people identifying with? Eating habits are a main factor of cultural identification. How can architecture contribute to these feelings of belonging, self awareness and joy? How can it teach something about the place and the people living there? What if a new kind of culinary architecture can help opening people`s e...

  4. An Architecture for Autonomy

    OpenAIRE

    Alami, Rachid; Chatila, Raja; Fleury, Sara; Ghallab, Malik; Ingrand, Félix

    1998-01-01

    International audience An autonomous robot offers a challenging and ideal field for the study of intelligent architectures. Autonomy within a rational behavior could be evaluated by the robot's effectiveness and robustness in carrying out tasks in different and ill-known environments_ It raises major requirements on the control architecture. Furthermore, a robot as a programmable machine brings up other architectural needs, such as the ease and quality of its speci_cation and programming. ...

  5. Architecture Criticism Blindfolded

    OpenAIRE

    Ann Heylighen; Jasmien Herssens; Hubert Froyen

    2009-01-01

    The paper reports on a recent Belgian initiative targeting architectural practice through the professional press. Architecture critics were invited to revisit an exemplary public building while being blindfolded and guided by persons who are visually impaired. Afterwards, they were asked to report on this visit in an article for an architectural magazine. The initiative aimed at drawing the attention of the critics—and, by extension, the readers of their articles—to the need for accessibil...

  6. Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

    OpenAIRE

    Phillips-Cremins, Jennifer E.; Sauria, Michael E. G.; Sanyal, Amartya; Gerasimova, Tatiana I; Lajoie, Bryan R.; Bell, Joshua S. K.; Ong, Chin-Tong; Hookway, Tracy A.; Guo, Changying; Sun, Yuhua; Bland, Michael J.; Wagstaff, William; Dalton, Stephen; McDevitt, Todd C.; Sen, Ranjan

    2013-01-01

    Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread...

  7. Architecture of Network Systems

    CERN Document Server

    Serpanos, Dimitrios

    2011-01-01

    Network systems require technical skills in computer architecture, design methodologies, algorithm design, and networking. Architecture of Network Systems explains the practice and methodologies that will allow you to solve a broad range of problems in system design, including problems related to security, quality of service, performance, manageability, and more. Leading researchers Dimitrios Serpanos and Tilman Wolf develop architectures for all network sub-systems, bridging the gap between operation and VLSI. Discussing the major challenges in the design of networks and the architectures tha

  8. IT Architecture For Dummies

    CERN Document Server

    Hausman, Kalani Kirk

    2010-01-01

    A solid introduction to the practices, plans, and skills required for developing a smart system architecture. Information architecture combines IT skills with business skills in order to align the IT structure of an organization with the mission, goals, and objectives of its business. This friendly introduction to IT architecture walks you through the myriad issues and complex decisions that many organizations face when setting up IT systems to work in sync with business procedures. Veteran IT professional and author Kirk Hausman explains the business value behind IT architecture and provides

  9. Grid Architecture 2

    Energy Technology Data Exchange (ETDEWEB)

    Taft, Jeffrey D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-01-01

    The report describes work done on Grid Architecture under the auspices of the Department of Electricity Office of Electricity Delivery and Reliability in 2015. As described in the first Grid Architecture report, the primary purpose of this work is to provide stakeholder insight about grid issues so as to enable superior decision making on their part. Doing this requires the creation of various work products, including oft-times complex diagrams, analyses, and explanations. This report provides architectural insights into several important grid topics and also describes work done to advance the science of Grid Architecture as well.

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

    DEFF Research Database (Denmark)

    Alexiadis, V; Waldmann, T; Andersen, Jens S.; Mann, M; Knippers, R; Gruss, C

    2000-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Antonio Rodríguez-Campos

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

  12. Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster.

    Science.gov (United States)

    Lee, Hangnoh; Cho, Dong-Yeon; Whitworth, Cale; Eisman, Robert; Phelps, Melissa; Roote, John; Kaufman, Thomas; Cook, Kevin; Russell, Steven; Przytycka, Teresa; Oliver, Brian

    2016-09-01

    Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies of the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of gene regulation due to altered nuclear architecture are rare. These rare cases include trans de-repression when deficiencies delete chromatin characterized as repressive in other studies. Generally, effects of breakpoints on expression are promoter proximal (~100bp) or in the gene body. Effects of deficiencies genome-wide are in genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds. PMID:27599372

  13. Digitally-Driven Architecture

    Directory of Open Access Journals (Sweden)

    Henriette Bier

    2010-06-01

    Full Text Available The shift from mechanical to digital forces architects to reposition themselves: Architects generate digital information, which can be used not only in designing and fabricating building components but also in embedding behaviours into buildings. This implies that, similar to the way that industrial design and fabrication with its concepts of standardisation and serial production influenced modernist architecture, digital design and fabrication influences contemporary architecture. While standardisa­tion focused on processes of rationalisation of form, mass-customisation as a new paradigm that replaces mass-production, addresses non-standard, complex, and flexible designs. Furthermore, knowledge about the designed object can be encoded in digital data pertaining not just to the geometry of a design but also to its physical or other behaviours within an environment. Digitally-driven architecture implies, therefore, not only digitally-designed and fabricated architecture, it also implies architecture – built form – that can be controlled, actuated, and animated by digital means. In this context, this sixth Footprint issue examines the influence of digital means as prag­matic and conceptual instruments for actuating architecture. The focus is not so much on computer-based systems for the development of architectural designs, but on architecture incorporating digital control, sens­ing, actuating, or other mechanisms that enable buildings to inter­act with their users and surroundings in real time in the real world through physical or sensory change and variation.

  14. Digitally-Driven Architecture

    Directory of Open Access Journals (Sweden)

    Henriette Bier

    2014-07-01

    Full Text Available The shift from mechanical to digital forces architects to reposition themselves: Architects generate digital information, which can be used not only in designing and fabricating building components but also in embedding behaviours into buildings. This implies that, similar to the way that industrial design and fabrication with its concepts of standardisation and serial production influenced modernist architecture, digital design and fabrication influences contemporary architecture. While standardisation focused on processes of rationalisation of form, mass-customisation as a new paradigm that replaces mass-production, addresses non-standard, complex, and flexible designs. Furthermore, knowledge about the designed object can be encoded in digital data pertaining not just to the geometry of a design but also to its physical or other behaviours within an environment. Digitally-driven architecture implies, therefore, not only digitally-designed and fabricated architecture, it also implies architecture – built form – that can be controlled, actuated, and animated by digital means.In this context, this sixth Footprint issue examines the influence of digital means as pragmatic and conceptual instruments for actuating architecture. The focus is not so much on computer-based systems for the development of architectural designs, but on architecture incorporating digital control, sens­ing, actuating, or other mechanisms that enable buildings to inter­act with their users and surroundings in real time in the real world through physical or sensory change and variation.

  15. Clinical document architecture.

    Science.gov (United States)

    Heitmann, Kai

    2003-01-01

    The Clinical Document Architecture (CDA), a standard developed by the Health Level Seven organisation (HL7), is an ANSI approved document architecture for exchange of clinical information using XML. A CDA document is comprised of a header with associated vocabularies and a body containing the structural clinical information. PMID:15061557

  16. Software Architecture Evolution

    Science.gov (United States)

    Barnes, Jeffrey M.

    2013-01-01

    Many software systems eventually undergo changes to their basic architectural structure. Such changes may be prompted by new feature requests, new quality attribute requirements, changing technology, or other reasons. Whatever the causes, architecture evolution is commonplace in real-world software projects. Today's software architects, however,…

  17. Towards a Media Architecture

    DEFF Research Database (Denmark)

    Ebsen, Tobias

    2010-01-01

    This text explores the concept of media architecture as a phenomenon of visual culture that describes the use of screen-technology in new spatial configurations in practices of architecture and art. I shall argue that this phenomenon is not necessarily a revolutionary new approach, but rather...

  18. Workflow automation architecture standard

    Energy Technology Data Exchange (ETDEWEB)

    Moshofsky, R.P.; Rohen, W.T. [Boeing Computer Services Co., Richland, WA (United States)

    1994-11-14

    This document presents an architectural standard for application of workflow automation technology. The standard includes a functional architecture, process for developing an automated workflow system for a work group, functional and collateral specifications for workflow automation, and results of a proof of concept prototype.

  19. Architecture or Sculpture?

    DEFF Research Database (Denmark)

    Baumeister, Ruth

    Jørn Utzon´s museum design for Asger Jorn´s collection in Silkeborg contextualized in the postwar context of an organic architecture.......Jørn Utzon´s museum design for Asger Jorn´s collection in Silkeborg contextualized in the postwar context of an organic architecture....

  20. Architecture and energy

    DEFF Research Database (Denmark)

    Marsh, Rob; Lauring, Michael

    2011-01-01

    Traditional low-energy architecture has not necessarily led to reduced energy consumption. A paradigm shift is proposed promoting pluralistic energy-saving strategies.......Traditional low-energy architecture has not necessarily led to reduced energy consumption. A paradigm shift is proposed promoting pluralistic energy-saving strategies....

  1. A catalog of architectural primitives for modeling architectural patterns

    NARCIS (Netherlands)

    Zdun, Uwe; Avgeriou, Paris

    2008-01-01

    Architectural patterns are a fundamental aspect of the architecting process and subsequently the architectural documentation. Unfortunately, there is only poor support for modeling architectural patterns for two reasons. First, patterns describe recurring design solutions and hence do not directly m

  2. The architecture of neutrophil extracellular traps investigated by atomic force microscopy

    Science.gov (United States)

    Pires, Ricardo H.; Felix, Stephan B.; Delcea, Mihaela

    2016-07-01

    Neutrophils are immune cells that engage in a suicidal pathway leading to the release of partially decondensed chromatin, or neutrophil extracellular traps (NETs). NETs behave as a double edged sword; they can bind to pathogens thereby ensnaring them and limiting their spread during infection; however, they may bind to host circulating materials and trigger thrombotic events, and are associated with autoimmune disorders. Despite the fundamental role of NETs as part of an immune system response, there is currently a very poor understanding of how their nanoscale properties are reflected in their macroscopic impact. In this work, using a combination of fluorescence and atomic force microscopy, we show that NETs appear as a branching filament network that results in a substantially organized porous structure with openings with 0.03 +/- 0.04 μm2 on average and thus in the size range of small pathogens. Topological profiles typically up to 3 +/- 1 nm in height are compatible with a ``beads on a string'' model of nucleosome chromatin. Typical branch lengths of 153 +/- 103 nm appearing as rigid rods and height profiles of naked DNA in NETs of 1.2 +/- 0.5 nm are indicative of extensive DNA supercoiling throughout NETs. The presence of DNA duplexes could also be inferred from force spectroscopy and the occurrence of force plateaus that ranged from ~65 pN to 300 pN. Proteolytic digestion of NETs resulted in widespread disassembly of the network structure and considerable loss of mechanical properties. Our results suggest that the underlying structure of NETs is considerably organized and that part of its protein content plays an important role in maintaining its mesh architecture. We anticipate that NETs may work as microscopic mechanical sieves with elastic properties that stem from their DNA-protein composition, which is able to segregate particles also as a result of their size. Such a behavior may explain their participation in capturing pathogens and their association

  3. Product Architecture Modularity Strategies

    DEFF Research Database (Denmark)

    Mikkola, Juliana Hsuan

    2003-01-01

    The focus of this paper is to integrate various perspectives on product architecture modularity into a general framework, and also to propose a way to measure the degree of modularization embedded in product architectures. Various trade-offs between modular and integral product architectures and...... how components and interfaces influence the degree of modularization are considered. In order to gain a better understanding of product architecture modularity as a strategy, a theoretical framework and propositions are drawn from various academic literature sources. Based on the literature review......, the following key elements of product architecture are identified: components (standard and new-to-the-firm), interfaces (standardization and specification), degree of coupling, and substitutability. A mathematical function, termed modularization function, is introduced to measure the degree of...

  4. Inspiring Reflections

    DEFF Research Database (Denmark)

    Muchie, Mammo

    2011-01-01

    life is not free from fluctuations, cycles, disruptions, crises and destructions both human and ecological. Innovation research ought to position itself to address environmental, financial and economic crises. The third is innovation research for development by addressing not only poverty erdaication......A numberof Chris Freeman's colleagues were asked to reflect on what they thought describes his life and work in a few words. Some of the colleagues replied including former SPRU students that were taught or supervised by Chris Freeman. Their views on what they thought were Chris Freeman's defining...... contributions have been put together. There are a number of ways to continue Chris Freeman's legacy on innovation research. The first is to build in a critical tradition in the economics of innovation research by introducing fearlessly emancipatory epistemology. Second the economic system that dominates social...

  5. ARCHITECTURE IN THE ISLAMIC CIVILIZATION: MUSLIM BUILDING OR ISLAMIC ARCHITECTURE

    OpenAIRE

    Ayat Ali Yassin; Dr. Nangkula Utaberta

    2012-01-01

    The main problem of the theory in the arena of islamic architecture is affected by some of its Westernthoughts, and stereotyping the islamic architecture according to Western thoughts; this leads to the breakdownof the foundations in the islamic architecture. It is a myth that islamic architecture is subjected to theinfluence from foreign architectures. This paper will highlight the dialectical concept of islamic architecture ormuslim buildings and the areas of recognition in islamic architec...

  6. Analysis of Architecture Pattern Usage in Legacy System Architecture Documentation

    OpenAIRE

    Harrison, Neil B.; Avgeriou, Paris

    2008-01-01

    Architecture patterns are an important tool in architectural design. However, while many architecture patterns have been identified, there is little in-depth understanding of their actual use in software architectures. For instance, there is no overview of how many patterns are used per system or which patterns are the most common or most important for particular domains. In addition, little is known of how architecture patterns may interact with each other. We studied architecture documentat...

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

    Science.gov (United States)

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

    2012-10-01

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

  8. 30 nm染色质的体外组装和电镜分析%In vitro Assembly and Electron Microscopic Analysis of 30 nm Chromatin Fibers

    Institute of Scientific and Technical Information of China (English)

    孙大鹏; 宋峰; 黄丽; 张阔; 季刚; 陈萍; 朱平

    2013-01-01

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

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

    OpenAIRE

    Roopa, T.; Shivashankar, G. V.

    2006-01-01

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

  10. Chromatin preparation and ChIP from Drosophila brain and discs tissues

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Constance Richter, Katarzyna Oktaba, Juerg Mueller & Juergen A. Knoblich ### Abstract Chromatin preparation and chromatin immunoprecipitation (ChIP) protocol as described in Oktaba et al., 2008, Dev Cell, 15, 877-89. The protocol includes description of chromatin preparation from larval tissues, ChIP and quantitative analysis of ChIP material. ### Procedure **1. First “fast” dissection**: Dissect for 20 minutes third instar larvae in ice-cold PBS and remove gu...

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

    OpenAIRE

    Soldi, Monica; Bonaldi, Tiziana

    2013-01-01

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

  12. A chromatin activity based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing

    OpenAIRE

    Liu, Cui; Yu, Yanbao; Liu, Feng; Wei, Xin; Wrobel, John A; Gunawardena, Harsha P.; Zhou, Li; Jin, Jian; Chen, Xian

    2014-01-01

    Immune cells develop endotoxin tolerance (ET) after prolonged stimulation. ET increases the level of a repression mark H3K9me2 in the transcriptional-silent chromatin specifically associated with pro-inflammatory genes. However, it is not clear what proteins are functionally involved in this process. Here we show that a novel chromatin activity based chemoproteomic (ChaC) approach can dissect the functional chromatin protein complexes that regulate ET-associated inflammation. Using UNC0638 th...

  13. A critical role for chromatin in mounting a synergistic transcriptional response to GAL4-VP16.

    OpenAIRE

    Chang, C; Gralla, J D

    1994-01-01

    The role of chromatin in mounting a synergistic transcriptional response to GAL4-VP16 was investigated. Strong synergy was observed when chromatin templates were used in vitro. The synergy was severely reduced when naked DNA templates were transcribed. In vivo synergy was strong when nonreplicating templates were used. However, the use of replicating templates, which involved transient disruptions of chromatin, led to strong reductions in synergy. In both of these low-synergy responses, trans...

  14. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species

    OpenAIRE

    Lee, Hye-Ran; Zhang, Wenli; Langdon, Tim; Jin, Weiwei; Yan, Huihuang; Cheng, Zhukuan; Jiang, Jiming

    2005-01-01

    The functional centromeres of rice (Oryza sativa, AA genome) chromosomes contain two key DNA components: the CRR centromeric retrotransposons and a 155-bp satellite repeat, CentO. However, several wild Oryza species lack the CentO repeat. We developed a chromatin immunoprecipitation-based technique to clone DNA fragments derived from chromatin containing the centromeric histone H3 variant CenH3. Chromatin immunoprecipitation cloning was carried out in the CentO-less species Oryza rhizomatis (...

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

    OpenAIRE

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

    2007-01-01

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

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

    OpenAIRE

    Monica Soldi; Alessandro Cuomo; Michael Bremang; Tiziana Bonaldi

    2013-01-01

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

  17. Architecture in the Experience City

    DEFF Research Database (Denmark)

    Kiib, Hans

    narratives related to historical buildings and architectural heritage; another group tries to embed new performative technologies in expressive architectural representation. The article provides a theoretical framework for the analysis of the political rationales of these projects and for the architectural...

  18. Evolution of histone 2A for chromatin compaction in eukaryotes

    OpenAIRE

    Macadangdang, Benjamin R; Oberai, Amit; Spektor, Tanya; Campos, Oscar A; Sheng, Fang; Carey, Michael F.; Vogelauer, Maria; Kurdistani, Siavash K

    2014-01-01

    eLife digest There are up to three meters of DNA in a human cell. To fit this length into the cell's nucleus in an organized manner, DNA is wrapped around proteins called histones and then tightly packaged to form a structure called chromatin. The interaction between the histones and the DNA is helped by certain amino acids on the surface of the histones fitting snugly into the DNA molecule. Plants and animals have genomes that are significantly larger than those of single-celled organisms. H...

  19. Effects of nuclear isolation on psoralen affinity for chromatin

    International Nuclear Information System (INIS)

    We have tested the effects of nuclear isolation on intercalation of TMP (a psoralen) at specific sequences and in total DNA of cultured human cells. DNA in nuclei photobound about 20% more TMP than in cells and about 10% as much as purified DNA. In contrast, a transcribed ras gene and a randomly selected polymorphic sequence each bound about 20% more TMP than total DNA in cells. However, in nuclei, as in purified DNA, both sequences were just as sensitive as total DNA. Apparently, chromatin in cells exists within diverse TMP-binding environments and some of this diversity was lost upon nuclear isolation

  20. Chromatin immunoselection defines a TAL-1 target gene.

    OpenAIRE

    Cohen-Kaminsky, S; Maouche-Chrétien, L; Vitelli, L; Vinit, M A; Blanchard, I; M. Yamamoto; Peschle, C; Roméo, P H

    1998-01-01

    Despite the major functions of the basic helix-loop-helix transcription factor TAL-1 in hematopoiesis and T-cell leukemogenesis, no TAL-1 target gene has been identified. Using immunoprecipitation of genomic fragments bound to TAL-1 in the chromatin of murine erythro-leukemia (MEL) cells, we found that 10% of the immunoselected fragments contained a CAGATG or a CAGGTG E-box, followed by a GATA site. We studied one of these fragments containing two E-boxes, CAGATG and CAGGTC, followed by a GAT...

  1. Evaluation of sperm chromatin structure in boar semen

    Directory of Open Access Journals (Sweden)

    Banaszewska Dorota

    2015-06-01

    Full Text Available This study was an attempt to evaluate sperm chromatin structure in the semen of insemination boars. Preparations of semen were stained with acridine orange, aniline blue, and chromomycin A3. Abnormal protamination occurred more frequently in young individuals whose sexual development was not yet complete, but may also be an individual trait. This possibility is important to factor into the decision regarding further exploitation of insemination boars. Thus a precise assessment of abnormalities in the protamination process would seem to be expedient as a tool supplementing morphological and molecular evaluation of semen. Disruptions in nucleoprotein structure can be treated as indicators of the biological value of sperm cells.

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

    Science.gov (United States)

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

    2005-01-01

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

  3. Erythroid-specific gene chromatin has an altered association with linker histones.

    OpenAIRE

    Ridsdale, J A; Rattner, J.B.; Davie, J R

    1988-01-01

    The chromatin of several genes was assayed for sensitivity to DNAase I and for solubility as polynucleosomes in 0.15 M NaCl. The degree of solubility of chromatin fragments as polynucleosomes in 0.15 M NaCl correlates well with the sensitivity to DNAase I for several genes. Chromatin of repressed, housekeeping and erythroid-specific genes can be distinguished as distinct groups by the degree to which they display these properties. NaCl precipitation of chromatin fragments stripped and then re...

  4. Evolution of contemporary museum architecture

    OpenAIRE

    Bilous, Yulia

    2013-01-01

    This article deals with the development of museum architecture from the formation of the classic building architecture to the establishment of the contemporary museum architecture. Changes in the museum building architecture and displaying principles have been analysed. The 19th century was defined by the emergence of a vast number of museums serving through present as examples of the contemporary museum architecture. New styles are tried in the museum architecture alo...

  5. Hybrid architecture: object, landscape, infrastructure

    OpenAIRE

    Pinto de Freitas, Rita

    2011-01-01

    The concept of "hybrid architecture" developed in this study considers hybrid all architecture that is at once object, landscape and infrastructure. Hybrid architecture, pushed by the fact that it concentrates in a single architectural intervention a triple object-, landscape- and infrastructure-related nature, generates architectural answers with very specific features, and its study achieves following goals: 1: Clarify the term hybrid related to architectural intervention; 2: Tran...

  6. Business Capabilities Centric Enterprise Architecture

    OpenAIRE

    Barroero, Thiago; Motta, Gianmario; Pignatelli, Giovanni

    2010-01-01

    In the field of Enterprise Architecture, The Open Group Architecture Framework (TOGAF) is a well known framework, that links Business Architecture, Data Architecture, Application Architecture, Technology. A key concept within Business Architecture domain is Business Capabilities, that are delivered by Business Component (BC). A BC is a business unit that encompasses a coherent set of activities, supported by assets including people, processes and technology. Current TOGAF version recognizes t...

  7. Data-Centric Enterprise Architecture

    OpenAIRE

    Zeinab Rajabi; Maryam Nooraei Abade

    2012-01-01

    Enterprises choose Enterprise Architecture (EA) solution, in order to overcome dynamic business challenges and in coordinate various enterprise elements. In this article, a solution is suggested for the Enterprise Architecture development. The solution focuses on architecture data in the Enterprise Architecture development process. Data-centric architecture approach is preferred product-centric architecture approach. We suggest using Enterprise Ontology (EO) as context for collecting architec...

  8. Initial steps of the base excision repair pathway within the nuclear architecture

    International Nuclear Information System (INIS)

    Oxidative stress induced lesions threaten aerobic organisms by representing a major cause of genomic instability. A common product of guanine oxidation, 8-oxo-guanine (8- oxoG) is particularly mutagenic by provoking G to T transversions. Removal of oxidised bases from DNA is initiated by the recognition and excision of the damaged base by a DNA glycosylase, initiating the base excision repair (BER) pathway. In mammals, 8-oxoG is processed by the 8-oxoG-DNA-glycosylase I (OGG1), which biochemical mechanisms has been well characterised in vitro. However how and where this enzyme finds the modified base within the complex chromatin architecture is not yet understood. We show that upon induction of 8-oxoG, OGG1, together with at least two other proteins involved in BER, is recruited from a soluble fraction to chromatin. Formation kinetics of this patches correlates with 8-oxoG excision, suggesting a direct link between presence of this chromatin-associated complexes and 8-oxoG repair. More precisely, these repair patches are specifically directed to euchromatin regions, and completely excluded from heterochromatin regions. Inducing of artificial chromatin compaction results in a complete inhibition of the in vivo repair of 8-oxoG, probably by impeding the access of OGG1 to the lesion. Using OGG1 mutants, we show that OGG1 direct recognition of 8-oxoG did not trigger its re-localisation to the chromatin. We conclude that in response to the induction of oxidative DNA damage, the DNA glycosylase is actively recruited to regions of open chromatin allowing the access of the BER machinery to the lesions. (author)

  9. On Detailing in Contemporary Architecture

    DEFF Research Database (Denmark)

    Kristensen, Claus; Kirkegaard, Poul Henning

    Details in architecture have a significant influence on how architecture is experienced. One can touch the materials and analyse the detailing - thus details give valuable information about the architectural scheme as a whole. The absence of perceptual stimulation like details and materiality...... / tactility can blur the meaning of the architecture and turn it into an empty statement. The present paper will outline detailing in contemporary architecture and discuss the issue with respect to architectural quality. Architectural cases considered as sublime piece of architecture will be presented and...... discussed with respect to the meaning of detailing....

  10. Integrated Data Assimilation Architecture Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Integrated Data Assimilation Architecture (IDAA) is a middleware architecture that facilitates the incorporation of heterogeneous sensing and control devices...

  11. Avionics Architecture for Exploration Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Avionics Architectures for Exploration Project team will develop a system level environment and architecture that will accommodate equipment from multiple...

  12. Computer architecture technology trends

    CERN Document Server

    1991-01-01

    Please note this is a Short Discount publication. This year's edition of Computer Architecture Technology Trends analyses the trends which are taking place in the architecture of computing systems today. Due to the sheer number of different applications to which computers are being applied, there seems no end to the different adoptions which proliferate. There are, however, some underlying trends which appear. Decision makers should be aware of these trends when specifying architectures, particularly for future applications. This report is fully revised and updated and provides insight in

  13. Architecture, energy and climate

    DEFF Research Database (Denmark)

    Lauring, Michael

    2010-01-01

    Architecture has always had to relate to climatic conditions while providing shelter from the sun, the rain, the winds or the cold. This is a main purpose of buildings: To establish an indoor climate different from the outdoor. In the Nordic countries fuels for heating buildings has been a vital...... cases been to search for traditional and pre-industrialized ways of building and settlement. The idea of this theme number is not to flee from modern life and approaches, but instead to face modern conditions relevant in achieving sustainable urban development and sustainable architecture, the only...... truly modern architecture that exists....

  14. Architecture for Verifiable Software

    Science.gov (United States)

    Reinholtz, William; Dvorak, Daniel

    2005-01-01

    Verifiable MDS Architecture (VMA) is a software architecture that facilitates the construction of highly verifiable flight software for NASA s Mission Data System (MDS), especially for smaller missions subject to cost constraints. More specifically, the purpose served by VMA is to facilitate aggressive verification and validation of flight software while imposing a minimum of constraints on overall functionality. VMA exploits the state-based architecture of the MDS and partitions verification issues into elements susceptible to independent verification and validation, in such a manner that scaling issues are minimized, so that relatively large software systems can be aggressively verified in a cost-effective manner.

  15. RECONSTRUCTING DECONSTRUCTION IN ARCHITECTURE

    Directory of Open Access Journals (Sweden)

    IDHAM Noor Cholis

    2013-01-01

    Full Text Available This paper examines deconstruction in architecture and forms used, which triggered by dispute of form and its scientification claimed by deconstructivists. Deconstruction terminologyis studied in the first part related to architecture field as a base knowledge. Some sample works of known deconstructionist architects are assessed in order to understand how their building is deconstructed and what forms they used. Discussion about form and its relation to other fields is then pursued by discussing the involvement of terminology of science, aesthetic pattern, and human life. The results of this discussion give clear understanding how form related to deconstruction in architecture are used.

  16. Mixed Reality Architecture: a dynamic architectural topology

    OpenAIRE

    Schnädelbach, H.; A Penn; Steadman, P.

    2007-01-01

    Architecture can be shown to structure patterns of co-presence and in turn to be structured itself by the rules and norms of the society present within it. This two-way relationship exists in a surprisingly stable framework, as fundamental changes to buildings are slow and costly. At the same time, change within organisations is increasingly rapid and buildings are used to accommodate some of that change. This adaptation can be supported by the use of telecommunication technolo...

  17. Chromatin Assembly at Kinetochores Is Uncoupled from DNA Replication

    Science.gov (United States)

    Shelby, Richard D.; Monier, Karine; Sullivan, Kevin F.

    2000-01-01

    The specification of metazoan centromeres does not depend strictly on centromeric DNA sequences, but also requires epigenetic factors. The mechanistic basis for establishing a centromeric “state” on the DNA remains unclear. In this work, we have directly examined replication timing of the prekinetochore domain of human chromosomes. Kinetochores were labeled by expression of epitope-tagged CENP-A, which stably marks prekinetochore domains in human cells. By immunoprecipitating CENP-A mononucleosomes from synchronized cells pulsed with [3H]thymidine we demonstrate that CENP-A–associated DNA is replicated in mid-to-late S phase. Cytological analysis of DNA replication further demonstrated that centromeres replicate asynchronously in parallel with numerous other genomic regions. In contrast, quantitative Western blot analysis demonstrates that CENP-A protein synthesis occurs later, in G2. Quantitative fluorescence microscopy and transient transfection in the presence of aphidicolin, an inhibitor of DNA replication, show that CENP-A can assemble into centromeres in the absence of DNA replication. Thus, unlike most genomic chromatin, histone synthesis and assembly are uncoupled from DNA replication at the kinetochore. Uncoupling DNA replication from CENP-A synthesis suggests that regulated chromatin assembly or remodeling could play a role in epigenetic centromere propagation. PMID:11086012

  18. Chromatin factors affecting DNA repair in mammalian cell nuclei

    International Nuclear Information System (INIS)

    We are investigating chromatin factors that participate in the incision step of DNA repair in eukaryotic cells. Localization of repair activity within nuclei, the stability and extractability of activity, the specificity for recognizing damage in chromatin or purified DNA as substrates are of interest in this investigation of human cells, CHO cells, and their radiation sensitive mutants. We have developed procedures that provide nuclei in which their DNA behaves as a collection of circular molecules. The integrity of the DNA in human nuclei can be maintained during incubation in appropriate buffers for as long as 60 minutes. When cells or nuclei are exposed to uv light prior to incubation, incisions presumably associated with DNA repair can be demonstrated. Incision activity is stable to prior extraction of nuclei with 0.6 M NaCl, which removes many nonhistone proteins. Our studies are consistent with an hypothesis that factors responsible for initiating DNA repair are localized in the nuclear matrix. 18 references, 3 figures

  19. SF3B1 Association with Chromatin Determines Splicing Outcomes

    Directory of Open Access Journals (Sweden)

    Nir Kfir

    2015-04-01

    Full Text Available Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. One probable explanation lies in differences in chromatin organization between exons and introns. Proteomic, co-immunoprecipitation, and sedimentation analyses described here indicate that SF3B1, an essential splicing component of the U2 snRNP complex, is strongly associated with nucleosomes. ChIP-seq and RNA-seq analyses reveal that SF3B1 specifically binds nucleosomes located at exonic positions. SF3B1 binding is enriched at nucleosomes positioned over short exons flanked by long introns that are also characterized by differential GC content between exons and introns. Disruption of SF3B1 binding to such nucleosomes affects splicing of these exons similarly to SF3B1 knockdown. Our findings suggest that the association of SF3B1 with nucleosomes is functionally important for splice-site recognition and that SF3B1 conveys splicing-relevant information embedded in chromatin structure.

  20. Robot Electronics Architecture

    Science.gov (United States)

    Garrett, Michael; Magnone, Lee; Aghazarian, Hrand; Baumgartner, Eric; Kennedy, Brett

    2008-01-01

    An electronics architecture has been developed to enable the rapid construction and testing of prototypes of robotic systems. This architecture is designed to be a research vehicle of great stability, reliability, and versatility. A system according to this architecture can easily be reconfigured (including expanded or contracted) to satisfy a variety of needs with respect to input, output, processing of data, sensing, actuation, and power. The architecture affords a variety of expandable input/output options that enable ready integration of instruments, actuators, sensors, and other devices as independent modular units. The separation of different electrical functions onto independent circuit boards facilitates the development of corresponding simple and modular software interfaces. As a result, both hardware and software can be made to expand or contract in modular fashion while expending a minimum of time and effort.

  1. DSP Architecture Design Essentials

    CERN Document Server

    Marković, Dejan

    2012-01-01

    In DSP Architecture Design Essentials, authors Dejan Marković and Robert W. Brodersen cover a key subject for the successful realization of DSP algorithms for communications, multimedia, and healthcare applications. The book addresses the need for DSP architecture design that maps advanced DSP algorithms to hardware in the most power- and area-efficient way. The key feature of this text is a design methodology based on a high-level design model that leads to hardware implementation with minimum power and area. The methodology includes algorithm-level considerations such as automated word-length reduction and intrinsic data properties that can be leveraged to reduce hardware complexity. From a high-level data-flow graph model, an architecture exploration methodology based on linear programming is used to create an array of architectural solutions tailored to the underlying hardware technology. The book is supplemented with online material: bibliography, design examples, CAD tutorials and custom software.

  2. Greek architecture now

    DEFF Research Database (Denmark)

    Skousbøll, Karin Merete

    2006-01-01

    With the author's Scandinavian viewpoint the aim of this book has been an investigation into contemporary Greek architecture and at the same time providing an understanding for its essential characteristics based on the historic, cultural heritage of Hellas....

  3. Analyzing architecture articles

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In the present study, we express the quality, function, and characteristics of architecture to help people comprehensively understand what architecture is. We also reveal the problems and conflict found in population, land, water resources, pollution, energy, and the organization systems in construction. China’s economy is transforming. We should focus on the cities, architectural environment, energy conservation, emission-reduction, and low-carbon output that will result in successful green development. We should macroscopically and microscopically analyze the development, from the natural environment to the artificial environment; from the relationship between human beings and nature to the combination of social ecology in cities, and farmlands. We must learn to develop and control them harmoniously and scientifically to provide a foundation for the methods used in architecture research.

  4. Adaptive Architectural Envelope

    DEFF Research Database (Denmark)

    Foged, Isak Worre; Kirkegaard, Poul Henning

    2010-01-01

    Recent years have seen an increasing variety of applications of adaptive architectural structures for improvement of structural performance by recognizing changes in their environments and loads, adapting to meet goals, and using past events to improve future performance or maintain serviceability....... The general scopes of this paper are to develop a new adaptive kinetic architectural structure, particularly a reconfigurable architectural structure which can transform body shape from planar geometries to hyper-surfaces using different control strategies, i.e. a transformation into more than one or...... two different shape alternatives. The adaptive structure is a proposal for a responsive building envelope which is an idea of a first level operational framework for present and future investigations towards performance based responsive architectures through a set of responsive typologies. A mock- up...

  5. Architectural Competition and BIM

    DEFF Research Database (Denmark)

    Sørensen, Nils Lykke; Frandsen, Anne Kathrine; Øien, Turid Borgestrand

    2015-01-01

    on architecturalcompetitions, a series of interviews was conducted with building clients as well as architects, focusing on the impact of the above-mentioned changes within the building sector on architectural competitions as an institution. In the interviews, ICT and notleast BIM was a recurring...... clients, architects and client consultants) and the applied technologies (competition forms, ICT tools, directives) in architectural competitions in a theoretical actor-network perspective. The diverging understandings of the role of BIM are demonstrating one of many negotiations in progress in the...... network of architectural competitions. BIM is transformed from an inscription device visually representing the competition proposals to form an actant that challenges the very concept of architectural competition. The objective of the paper is to contribute to theunderstanding of BIM used in the kind of...

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

    Directory of Open Access Journals (Sweden)

    Mora Xavier

    2007-05-01

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

  7. Analysis of Architecture Pattern Usage in Legacy System Architecture Documentation

    NARCIS (Netherlands)

    Harrison, Neil B.; Avgeriou, Paris

    2008-01-01

    Architecture patterns are an important tool in architectural design. However, while many architecture patterns have been identified, there is little in-depth understanding of their actual use in software architectures. For instance, there is no overview of how many patterns are used per system or wh

  8. Redesigning architecture through photography

    OpenAIRE

    Germen, Murat

    2008-01-01

    Abstract – This paper focuses on the possibility of (re)designing architecture virtually with the help of one of the most important representation tools: Photography. Various digital processes like stitching multiple photos together and mirroring images in image editing software like Photoshop, allow this virtual architecture to take place in virtual environments. Photography can be utilized in the process of ‘constructing’ a new space --that we can call ‘narrative space’-- from an existing s...

  9. Essential software architecture

    CERN Document Server

    Gorton, Ian

    2011-01-01

    Job titles like ""Technical Architect"" and ""Chief Architect"" nowadays abound in software industry, yet many people suspect that ""architecture"" is one of the most overused and least understood terms in professional software development. Gorton's book tries to resolve this dilemma. It concisely describes the essential elements of knowledge and key skills required to be a software architect. The explanations encompass the essentials of architecture thinking, practices, and supporting technologies. They range from a general understanding of structure and quality attributes through technical i

  10. Generic Distributed Simulation Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Booker, C.P.

    1999-05-14

    A Generic Distributed Simulation Architecture is described that allows a simulation to be automatically distributed over a heterogeneous network of computers and executed with very little human direction. A prototype Framework is presented that implements the elements of the Architecture and demonstrates the feasibility of the concepts. It provides a basis for a future, improved Framework that will support legacy models. Because the Framework is implemented in Java, it may be installed on almost any modern computer system.

  11. Pushing architectural quality further

    OpenAIRE

    Laverge, Jelle; Van Den Bossche, Nathan; Janssens, Arnold

    2008-01-01

    In this paper, the intentions thriving the implementation of computational modeling of building physics as it is approached in the Architectural engineering courses at Ghent University are discussed. During the bachelor degree, courses focus mainly on integration of basic building physics feasibility in the architectural conceptualization. During the final bachelor year, students program their own simplified 2D models for internal condensation and thermal bridges in a spreadsheet, based on...

  12. Climate and architecture

    DEFF Research Database (Denmark)

    Tind Kristensen, Eva; Friis Møller, Winnie; Rotne, Georg;

    2010-01-01

    Climate and Architecture analyserer klimaets rolle i arkitekturen. Intentionen med bogen er at pege på nogle af de mange muligheder for bygningers klimaregulering, som et mere detaljeret studie af de lokale klimatiske forhold og den stedlige byggeskik tilbyder.......Climate and Architecture analyserer klimaets rolle i arkitekturen. Intentionen med bogen er at pege på nogle af de mange muligheder for bygningers klimaregulering, som et mere detaljeret studie af de lokale klimatiske forhold og den stedlige byggeskik tilbyder....

  13. Digitally-Driven Architecture

    OpenAIRE

    Henriette Bier; Terry Knight

    2014-01-01

    The shift from mechanical to digital forces architects to reposition themselves: Architects generate digital information, which can be used not only in designing and fabricating building components but also in embedding behaviours into buildings. This implies that, similar to the way that industrial design and fabrication with its concepts of standardisation and serial production influenced modernist architecture, digital design and fabrication influences contemporary architecture. While stan...

  14. Models of Architecture

    OpenAIRE

    Pelcat, Maxime; Desnos, Karol; Maggiani, Luca; Liu, Yanzhou; Heulot, Julien; Nezan, Jean-François; Bhattacharyya, Shuvra S.

    2015-01-01

    The current trend in high performance and embedded computing consists of designing increasingly complex heterogeneous hardware architectures with non-uniform communication resources. In order to take hardware and software design decisions, early evaluations of the system non-functional properties are needed. These evaluations of system efficiency require high-level information on both the algorithms and the architecture. In state of the art Model Driven Engineering (MDE) methods, different co...

  15. Aesthetics of sustainable architecture

    OpenAIRE

    Lee, S.

    2011-01-01

    The purpose of this book is to reveal, explore and further the debate on the aesthetic potentials of sustainable architecture and its practice. This book opens a new area of scholarship and discourse in the design and production of sustainable architecture, one that is based in aesthetics. The chapters in this book have been compiled from architects and scholars working in diverse research and practice areas in North America, Europe, the Middle East and Asia. While they approach the subject m...

  16. Artificial cognition architectures

    CERN Document Server

    Crowder, James A; Friess, Shelli A

    2013-01-01

    The goal of this book is to establish the foundation, principles, theory, and concepts that are the backbone of real, autonomous Artificial Intelligence. Presented here are some basic human intelligence concepts framed for Artificial Intelligence systems. These include concepts like Metacognition and Metamemory, along with architectural constructs for Artificial Intelligence versions of human brain functions like the prefrontal cortex. Also presented are possible hardware and software architectures that lend themselves to learning, reasoning, and self-evolution

  17. ARCHITECTURE IN THE ISLAMIC CIVILIZATION: MUSLIM BUILDING OR ISLAMIC ARCHITECTURE

    Directory of Open Access Journals (Sweden)

    Ayat Ali Yassin

    2012-12-01

    Full Text Available The main problem of the theory in the arena of islamic architecture is affected by some of its Westernthoughts, and stereotyping the islamic architecture according to Western thoughts; this leads to the breakdownof the foundations in the islamic architecture. It is a myth that islamic architecture is subjected to theinfluence from foreign architectures. This paper will highlight the dialectical concept of islamic architecture ormuslim buildings and the areas of recognition in islamic architecture. It will also widen the knowledge in thecharacteristics of each point in time according to the stages of islamic architecture from the prophetic agemoving through the architecture outside the city of Medina, the Caliphs, the Umayyad, Abbasid, andarchitectural models by spatial and time periods, taking Iraq as the example to explain how the Islam influentson architecture and vice versa.

  18. Utilizing the Central Courtyard of Traditional Architecture in Modern Architecture

    OpenAIRE

    Javad Samadi

    2014-01-01

    The purpose of this study is utilizing the central courtyard of traditional architecture in modern architecture. Since the nineteenth century, the traditional architecture has been more taken into account. From this time period, the sixties century is significantly important. The studies on the traditional architecture were conducted and followed in this period with the new objective and attitude. Until the early sixties century, most of the studies on the traditional architecture were briefl...

  19. Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 - 15, 2016 - Strasbourg, France.

    Science.gov (United States)

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

    2016-08-01

    In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meeting to remember. In this article we summarize some of the new insights into chromatin, epigenetics, and epigenomics research and highlight nascent ideas and emerging concepts in this exciting area of research. PMID:27184433

  20. Discussing performance management architecture in public service broadcasting

    DEFF Research Database (Denmark)

    Tambo, Torben; Gabel, Ole Dahl

    2014-01-01

    Purpose: To demonstrate design of Performance Management (PM) processes in highly complex, non-profit, culture-producing organisations specifically the shift from Performance Management Systems (PMS) to Performance Management Architectures (PMA) specifically using Danish Broadcasting Corporation...... metrics, reflected in an architecture, raises the certainty and level of organisational consensus. Research limitations/implications: DR is unique as the largest cultural institution in the Danish language area backed by a political consensus, strong popular support, high level of funding and a...

  1. Second International Workshop on Variability in Software Architecture

    OpenAIRE

    Galster, Matthias; Avgeriou, Paris; Weyns, Danny; Becker, Martin

    2012-01-01

    Variability is the ability of a software system or artifact to be adapted for specific contexts, in a preplanned manner. Many of today's software systems are built with variability in mind, e.g., product lines and families, self-adaptive systems, open platforms, or service-based systems that support dynamic runtime composition of web services. Variability is reflected in and facilitated through the software architecture. Also, as the software architecture is a reference point for many develop...

  2. The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide.

    Science.gov (United States)

    Mukhopadhyay, Rituparna; Yu, WenQiang; Whitehead, Joanne; Xu, JunWang; Lezcano, Magda; Pack, Svetlana; Kanduri, Chandrasekhar; Kanduri, Meena; Ginjala, Vasudeva; Vostrov, Alexander; Quitschke, Wolfgang; Chernukhin, Igor; Klenova, Elena; Lobanenkov, Victor; Ohlsson, Rolf

    2004-08-01

    All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states. PMID:15256511

  3. The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide

    Science.gov (United States)

    Mukhopadhyay, Rituparna; Yu, WenQiang; Whitehead, Joanne; Xu, JunWang; Lezcano, Magda; Pack, Svetlana; Kanduri, Chandrasekhar; Kanduri, Meena; Ginjala, Vasudeva; Vostrov, Alexander; Quitschke, Wolfgang; Chernukhin, Igor; Klenova, Elena; Lobanenkov, Victor; Ohlsson, Rolf

    2004-01-01

    All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states. PMID:15256511

  4. New Energy Architecture. Myanmar

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-06-15

    A global transition towards a new energy architecture is under way, driven by countries' need to respond to the changing dynamics of economic growth, environmental sustainability and energy security. The World Economic Forum, in collaboration with Accenture, has created the New Energy Architecture Initiative to address and accelerate this transition. The Initiative supports the development of national strategies and policy frameworks as countries seek to achieve the combined goals of energy security and access, sustainability, and economic growth and development. The World Economic Forum has formed a partnership with the Ministry of Energy of Myanmar to help apply the Initiative's approach to this developing and resource-rich nation. The Asian Development Bank and the World Economic Forum's Project Adviser, Accenture, have collaborated with the Forum on this consultation process, and have been supported by relevant government, industry and civil society stakeholders. The consultation process aims to understand the nation's current energy architecture challenges and provide an overview of a path to a New Energy Architecture through a series of insights. These insights could form the basis for a long-term multistakeholder roadmap to build Myanmar's energy sector in a way that is secure and sustainable, and promotes economic growth as the country makes its democratic transition. While not all recommendations can be implemented in the near term, they do provide options for creating a prioritized roadmap for Myanmar's energy transition. This report is the culmination of a nine-month multistakeholder process investigating Myanmar's energy architecture. Over the course of many visits to the country, the team has conducted numerous interviews, multistakeholder workshops, and learning and data-gathering exercises to ensure a comprehensive range of information and views. The team has also engaged with a variety of stakeholders to better

  5. Time · Space · Architecture

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In the 20th century a Swiss writer wrote a book titled Time, Space and Architecture, in which he discussed the relationship between architecture and the times. Fifty years after that, this paper adopts the same title, hoping to deepen the understanding of the space-time structure in architecture and contribute to the new exploration of architectural forms.

  6. Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications

    Directory of Open Access Journals (Sweden)

    Wang Jiang

    2009-07-01

    Full Text Available Abstract Background ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated. Results In this paper, we have developed a computational method to generate the first genome-wide landscape of interactions between ATP-dependent chromatin remodeling and the covalent modification of histones in Saccharomyces cerevisiae. Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. Our results also demonstrate that most chromatin remodeling-modification interactions act via interactions of remodelers with both histone-modifying enzymes and histone residues. We also found that the co-occurrence of both modification and remodeling has significantly different influences on multiple gene features (e.g. nucleosome occupancy compared with the presence of either one. Conclusion We gave the first genome-wide picture of ATP-dependent chromatin remodeling-histone modification interactions. We also revealed how these two activities work together to regulate chromatin structure and function. Our results suggest that distinct strategies for regulating chromatin activity are selectively employed by genes with different properties.

  7. Radiolysis of chromatin extracted from cultured mammalian cells: formation of DNA-protein cross links

    International Nuclear Information System (INIS)

    Chromatin extracted from Chinese hamster lung fibroblasts has been examined for the formation of radiation-induced DNA-protein cross links, using a membrane filter assay. The relative efficiencies of the aqueous radical intermediates, 0H., esub(aq)- and 02-, were investigated. Cross links were found in gamma-irradiated isolated chromatin and in chromatin irradiated in the cell before isolation. When isolated chromatin was irradiated under conditions in which the chromosomal proteins were dissociated from the DNA, no cross links were detectable. The most efficient radical for the production of cross links in irradiated, isolated chromatin was found to be the hydroxyl radical, whereas, the superoxide radical was essentially ineffective. For chromatin irradiated in the cell before isolation, the greatest effect was seen for cells irradiated in an atmosphere of nitrous oxide, suggesting the hydroxyl radical may be involved in the formation of cross links in intact cells also. The formation of cross links in chromatin irradiated in cells before isolation was considerably less efficient than in irradiated, isolated chromatin. (author)

  8. Induction of stable protein-deoxyribonucleic acid adducts in Chinese hamster cell chromatin by ultraviolet light

    International Nuclear Information System (INIS)

    Ultraviolet (uv)-light-mediated formation of protein-DNA adducts in Chinese hamster cell chromatin was investigated in an attempt to compare chromatin alterations induced in vitro with those observed in vivo. Three independent methods of analysis indicated stable protein-DNA associations: a membrane filter assay which retained DNA on the filter in the presence of high salt-detergent; a Sepharose 4B column assay in which protein eluted coincident with DNA; and a CsCl density gradient equilibrium assay which showed both protein and DNA banding at densities other than their respective native densities. Treatment of the irradiated chromatin with DNase provided further evidence that protein--DNA and not protein-protein adducts were being observed in the column assay. There is a fluence-dependent response of protein-DNA adduct formation when the chromatin is irradiated at low ionic strength and is linear for protein over the range studied. When the chromatin is exposed to differing conditions of pH, ionic strength, or divalent metal ion concentration, the quantity of adduct formed upon uv irradiation varies. Susceptibility to adduct formation can be partially explained in terms of the condensation state of the chromatin and other factors such as rearrangement, denaturation, and dissociation of the chromatin components. Besides providing information on the biological significance of these types of uv-induced lesions, this technique may be useful as a probe of chromatin structure

  9. Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Waterfall, Joshua J; Kim, Dong Wook;

    2015-01-01

    facilitates recruitment of co-activators to activate transcription. Here we show that in addition to hormone-independent TR occupancy, ChIP-seq against endogenous TR in mouse liver tissue demonstrates considerable hormone-induced TR recruitment to chromatin associated with chromatin remodelling and activated...

  10. Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Persson, Jenna [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); Ekwall, Karl, E-mail: karl.ekwall@ki.se [Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet (Sweden); School of Life Sciences, University College Sodertorn, NOVUM, Huddinge (Sweden)

    2010-05-01

    Eukaryotic DNA is packaged around octamers of histone proteins into nucleosomes, the basic unit of chromatin. In addition to enabling meters of DNA to fit within the confines of a nucleus, the structure of chromatin has functional implications for cell identity. Covalent chemical modifications to the DNA and to histones, histone variants, ATP-dependent chromatin remodelers, small noncoding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. The great diversity of epigenomes that can arise from a single genome permits a single, totipotent cell to generate the hundreds of distinct cell types found in humans. Two recent studies in mouse and in fly have highlighted the importance of Chd1 chromatin remodelers for maintaining an open, active chromatin state. Based on evidence from fission yeast as a model system, we speculate that Chd1 remodelers are involved in the disassembly of nucleosomes at promoter regions, thus promoting active transcription and open chromatin. It is likely that these nucleosomes are specifically marked for disassembly by the histone variant H2A.Z.

  11. A Testis-Specific Chaperone and the Chromatin Remodeler ISWI Mediate Repackaging of the Paternal Genome

    Directory of Open Access Journals (Sweden)

    Cécile M. Doyen

    2015-11-01

    Full Text Available During spermatogenesis, the paternal genome is repackaged into a non-nucleosomal, highly compacted chromatin structure. Bioinformatic analysis revealed that Drosophila sperm chromatin proteins are characterized by a motif related to the high-mobility group (HMG box, which we termed male-specific transcript (MST-HMG box. MST77F is a MST-HMG-box protein that forms an essential component of sperm chromatin. The deposition of MST77F onto the paternal genome requires the chaperone function of tNAP, a testis-specific NAP protein. MST77F, in turn, enables the stable incorporation of MST35Ba and MST35Bb into sperm chromatin. Following MST-HMG-box protein deposition, the ATP-dependent chromatin remodeler ISWI mediates the appropriate organization of sperm chromatin. Conversely, at fertilization, maternal ISWI targets the paternal genome and drives its repackaging into de-condensed nucleosomal chromatin. Failure of this transition in ISWI mutant embryos is followed by mitotic defects, aneuploidy, and haploid embryonic divisions. Thus, ISWI enables bi-directional transitions between two fundamentally different forms of chromatin.

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

    Directory of Open Access Journals (Sweden)

    Shao-Jun Tang

    2012-03-01

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

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

    DEFF Research Database (Denmark)

    Jasencakova, Zusana; Groth, Anja

    2010-01-01

    In dividing cells genome stability and function rely on faithful transmission of both DNA sequence and its organization into chromatin. In the course of DNA replication chromatin undergoes transient genome-wide disruption followed by restoration on new DNA. This involves tight coordination of DNA...

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

    NARCIS (Netherlands)

    Mlynárová, Ludmila; Loonen, Annelies; Mietkiewska, Elzbieta; Jansen, Ritsert C.; Nap, Jan-Peter

    2002-01-01

    The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli β-glucuronidase gene and the firefly luciferase gene, driven by different prom

  15. A Reflective Look at Reflecting Teams

    Science.gov (United States)

    Pender, Rebecca L.; Stinchfield, Tracy

    2012-01-01

    This article reviewed existing literature and research on the reflecting team process. There is a dearth of empirical research that explores the reflecting team process and the outcome of counseling that uses reflecting teams. Implications of using reflecting teams for counselors, counselor educators, and clients will be discussed. A call for…

  16. Data-Centric Enterprise Architecture

    Directory of Open Access Journals (Sweden)

    Zeinab Rajabi

    2012-08-01

    Full Text Available Enterprises choose Enterprise Architecture (EA solution, in order to overcome dynamic business challenges and in coordinate various enterprise elements. In this article, a solution is suggested for the Enterprise Architecture development. The solution focuses on architecture data in the Enterprise Architecture development process. Data-centric architecture approach is preferred product-centric architecture approach. We suggest using Enterprise Ontology (EO as context for collecting architecture data; Enterprise Ontology enhances quality of architecture data and lead to effective architecture results for decision-making. First, Enterprise is modeled using the ontology. Then how collecting Enterprise Architecture data based on the Enterprise Ontology is explained. Finally, the results and advantages of the solution are demonstrated.

  17. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination

    Directory of Open Access Journals (Sweden)

    Pedro P. Rocha

    2016-06-01

    Full Text Available During class switch recombination (CSR, B cells replace the Igh Cμ or δ exons with another downstream constant region exon (CH, altering the antibody isotype. CSR occurs through the introduction of AID-mediated double-strand breaks (DSBs in switch regions and subsequent ligation of broken ends. Here, we developed an assay to investigate the dynamics of DSB formation in individual cells. We demonstrate that the upstream switch region Sμ is first targeted during recombination and that the mechanism underlying this control relies on 53BP1. Surprisingly, regulation of break order occurs through residual binding of 53BP1 to chromatin before the introduction of damage and independent of its established role in DNA repair. Using chromosome conformation capture, we show that 53BP1 mediates changes in chromatin architecture that affect break order. Finally, our results explain how changes in Igh architecture in the absence of 53BP1 could promote inversional rearrangements that compromise CSR.

  18. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination.

    Science.gov (United States)

    Rocha, Pedro P; Raviram, Ramya; Fu, Yi; Kim, JungHyun; Luo, Vincent M; Aljoufi, Arafat; Swanzey, Emily; Pasquarella, Alessandra; Balestrini, Alessia; Miraldi, Emily R; Bonneau, Richard; Petrini, John; Schotta, Gunnar; Skok, Jane A

    2016-06-28

    During class switch recombination (CSR), B cells replace the Igh Cμ or δ exons with another downstream constant region exon (CH), altering the antibody isotype. CSR occurs through the introduction of AID-mediated double-strand breaks (DSBs) in switch regions and subsequent ligation of broken ends. Here, we developed an assay to investigate the dynamics of DSB formation in individual cells. We demonstrate that the upstream switch region Sμ is first targeted during recombination and that the mechanism underlying this control relies on 53BP1. Surprisingly, regulation of break order occurs through residual binding of 53BP1 to chromatin before the introduction of damage and independent of its established role in DNA repair. Using chromosome conformation capture, we show that 53BP1 mediates changes in chromatin architecture that affect break order. Finally, our results explain how changes in Igh architecture in the absence of 53BP1 could promote inversional rearrangements that compromise CSR. PMID:27320916

  19. Herpes simplex virus 1 induces egress channels through marginalized host chromatin.

    Science.gov (United States)

    Myllys, Markko; Ruokolainen, Visa; Aho, Vesa; Smith, Elizabeth A; Hakanen, Satu; Peri, Piritta; Salvetti, Anna; Timonen, Jussi; Hukkanen, Veijo; Larabell, Carolyn A; Vihinen-Ranta, Maija

    2016-01-01

    Lytic infection with herpes simplex virus type 1 (HSV-1) induces profound modification of the cell nucleus including formation of a viral replication compartment and chromatin marginalization into the nuclear periphery. We used three-dimensional soft X-ray tomography, combined with cryogenic fluorescence, confocal and electron microscopy, to analyse the transformation of peripheral chromatin during HSV-1 infection. Our data showed an increased presence of low-density gaps in the marginalized chromatin at late infection. Advanced data analysis indicated the formation of virus-nucleocapsid-sized (or wider) channels extending through the compacted chromatin of the host. Importantly, confocal and electron microscopy analysis showed that these gaps frequently contained viral nucleocapsids. These results demonstrated that HSV-1 infection induces the formation of channels penetrating the compacted layer of cellular chromatin and allowing for the passage of progeny viruses to the nuclear envelope, their site of nuclear egress. PMID:27349677

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  1. Probing nuclear dynamics and architecture using single-walled carbon nanotubes

    Science.gov (United States)

    Jung, Yoon; Li, Junang; Fakhri, Nikta

    Chromatin is a multiscale dynamic architecture that acts as a template for many biochemical processes such as transcription and DNA replication. Recent developments such as Hi-C technology enable an identification of chromatin interactions across an entire genome. However, a single cell dynamic view of chromatin organization is far from understood. We discuss a new live cell imaging technique to probe the dynamics of the nucleus at a single cell level using single-walled carbon nanotubes (SWNTs). SWNTs are non-perturbing rigid rods (diameter of 1 nm and length of roughly 100 nm) that fluoresce in the near infrared region. Due to their high aspect ratio, they can diffuse in tight spaces and report on the architecture and dynamics of the nucleoplasm. We develop 3D imaging and tracking of SWNTs in the volume of the nucleus using double helix point spread function microscopy (DH-PSF) and discuss the capabilities of the DH-PSF for inferring the 3D orientation of nanotubes based on vectorial diffraction theory.

  2. Educating ecological architecture – ecological educational architecture

    OpenAIRE

    Costa Santos, Sandra; Klein, Gerald; Despang, Martin

    2010-01-01

    “Sustainability,” being the buzzword of the 21st century, is particularly challenging to the current generation, now in their early teens, which grew up with a childhood of lackadaisical use of fossil energy. This generation, which will soon be leading the world, has been inappropriately labeled the “generation me” and is expected to prove its successful transitioning into “generation p[ostfossil].” If the young emerging architectural professionals choose, they can be the mission group in hel...

  3. Virtual architecture: reconstructing architecture through photography

    OpenAIRE

    Germen, Murat

    2007-01-01

    The concept of construction in architectural design process is a temporary action that exists for a while and transforms itself into another product; i.e. the final building to be inhabited. Construction site can be taken as a podium where a play-to-remain-incomplete is being staged. The incompleteness causes us to dream, due to the fact that a complete building loses its narrative potential as it informs us about all the necessary pieces that constitute the whole: There is no puzzle to solve...

  4. Context-free pragmatism in Danish campus architecture

    DEFF Research Database (Denmark)

    Knudsen, Lars Emmerik Damgaard

    The idea of new pragmatism has inspired a new Danish wave in architecture that since 2012 has had enormous influence on the design of campus buildings in the professional education sector in Denmark. In arguing for a no-nonsense approach to architecture representatives of new pragmatism refers to...... reflects an educational ideal that also seem to lack a sense of context, and hence both the architecture and the educational structuring in Campus Roskilde can be understood as a context free pragmatism. I analyze this tendency with references to Dewey’s own work on the meaning of the educational...

  5. Perceived benefits from enterprise architecture

    OpenAIRE

    Plessius, Henk; Steenbergen, Marlies van; Slot, Raymond

    2014-01-01

    Enterprise Architecture has been developed in order to optimize the alignment between business needs and the (rapidly changing) possibilities of information technology. But do organizations indeed benefit from the application of Enterprise Architecture according to those who are in any way involved in architecture? To answer this question, a model has been developed (the Enterprise Architecture Value Framework) to organize the benefits of Enterprise Architecture. Based on this model, a survey...

  6. Assembly of telomeric chromatin to create ALTernative endings.

    Science.gov (United States)

    O'Sullivan, Roderick J; Almouzni, Genevieve

    2014-11-01

    Circumvention of the telomere length-dependent mechanisms that control the upper boundaries of cellular proliferation is necessary for the unlimited growth of cancer. Most cancer cells achieve cellular immortality by up-regulating the expression of telomerase to extend and maintain their telomere length. However, a small but significant number of cancers do so via the exchange of telomeric DNA between chromosomes in a pathway termed alternative lengthening of telomeres, or ALT. Although it remains to be clarified why a cell chooses the ALT pathway and how ALT is initiated, recently identified mutations in factors that shape the chromatin and epigenetic landscape of ALT telomeres are shedding light on these mechanisms. In this review, we examine these recent findings and integrate them into the current models of the ALT mechanism. PMID:25172551

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

    Directory of Open Access Journals (Sweden)

    Daniël P. Melters

    2015-08-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    protein- protein interaction network. We determined the Haspin consensus motif and the co-crystal structure of the kinase with the histone H3 tail. The structure revealed a unique bent substrate binding mode positioning the histone H3 residues Arg2 and Lys4 adjacent to the Haspin phosphorylated threonine......Recent discoveries have highlighted the importance of Haspin kinase activity for the correct positioning of the kinase Aurora B at the centromere. Haspin phosphorylates Thr3 of the histone H3 (H3), which provides a signal for Aurora B to localize to the centromere of mitotic chromosomes. To date......, histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin- associated proteins and identified a Haspin...

  9. Impact of sperm DNA chromatin in the clinic.

    Science.gov (United States)

    Ioannou, Dimitrios; Miller, David; Griffin, Darren K; Tempest, Helen G

    2016-02-01

    The paternal contribution to fertilization and embryogenesis is frequently overlooked as the spermatozoon is often considered to be a silent vessel whose only function is to safely deliver the paternal genome to the maternal oocyte. In this article, we hope to demonstrate that this perception is far from the truth. Typically, infertile men have been unable to conceive naturally (or through regular IVF), and therefore, a perturbation of the genetic integrity of sperm heads in infertile males has been under-considered. The advent of intracytoplasmic sperm injection (ICSI) however has led to very successful treatment of male factor infertility and subsequent widespread use in IVF clinics worldwide. Until recently, little concern has been raised about the genetic quality of sperm in ICSI patients or the impact genetic aberrations could have on fertility and embryogenesis. This review highlights the importance of chromatin packaging in the sperm nucleus as essential for the establishment and maintenance of a viable pregnancy. PMID:26678492

  10. H3K9 acetylation and radial chromatin positioning

    Czech Academy of Sciences Publication Activity Database

    Strašák, Luděk; Bártová, Eva; Harničarová, Andrea; Galiová-Šustáčková, Gabriela; Krejčí, Jana; Kozubek, Stanislav

    2009-01-01

    Roč. 220, č. 1 (2009), s. 91-101. ISSN 0021-9541 R&D Projects: GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535; GA AV ČR(CZ) 1QS500040508; GA AV ČR(CZ) IAA5004306; GA ČR(CZ) GA204/06/0978 Grant ostatní: GA ČR(CZ) GP310/07/P480 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : chromatin structure * RIDGE and anti-RIDGE regions * H3K9 acetylation Subject RIV: BO - Biophysics Impact factor: 4.586, year: 2009

  11. Mutations in chromatin machinery and pediatric high-grade glioma.

    Science.gov (United States)

    Lulla, Rishi R; Saratsis, Amanda Muhs; Hashizume, Rintaro

    2016-03-01

    Pediatric central nervous system tumors are the most common solid tumor of childhood. Of these, approximately one-third are gliomas that exhibit diverse biological behaviors in the unique context of the developing nervous system. Although low-grade gliomas predominate and have favorable outcomes, up to 20% of pediatric gliomas are high-grade. These tumors are a major contributor to cancer-related morbidity and mortality in infants, children, and adolescents, with long-term survival rates of only 10 to 15%. The recent discovery of somatic oncogenic mutations affecting chromatin regulation in pediatric high-grade glioma has markedly improved our understanding of disease pathogenesis, and these findings have stimulated the development of novel therapeutic approaches targeting epigenetic regulators for disease treatment. We review the current perspective on pediatric high-grade glioma genetics and epigenetics, and discuss the emerging and experimental therapeutics targeting the unique molecular abnormalities present in these deadly childhood brain tumors. PMID:27034984

  12. Quantitative Immunofluorescence Analysis of Nucleolus-Associated Chromatin.

    Science.gov (United States)

    Dillinger, Stefan; Németh, Attila

    2016-01-01

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

  13. FASHION AND ARCHITECTURE

    Directory of Open Access Journals (Sweden)

    Hatice Harmankaya

    2014-04-01

    Full Text Available Fashion and architecture fields as non-verbal expression languages are affected by social, cultural, economic and historical factors and shaped around creativity. In both disciplines, based on human scales, employed material is brought dimension in the scope of math. Hue, texture, material, rate-ratio, line, form and shape are common design components of both fashion and architecture. Especially it is possible to see the accrued interactions in terms of pattern, form and decoration throughout the history. The aim of this survey is determining the common grounds, similarities, and interactions of clothing and architectural design that cover to protect the human body based on housing instinct. Descriptive method is used in the survey that examines the subject in depth. In the survey, that structural constitutions constructed on human body are studied in both fields in extent of art, status of fashion designers are affected from architecture is examined. New approaches are exhibited by giving examples of clothing designs in accordance with architectural principles.

  14. The Simulation Intranet Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Holmes, V.P.; Linebarger, J.M.; Miller, D.J.; Vandewart, R.L.

    1998-12-02

    The Simdarion Infranet (S1) is a term which is being used to dcscribc one element of a multidisciplinary distributed and distance computing initiative known as DisCom2 at Sandia National Laboratory (http ct al. 1998). The Simulation Intranet is an architecture for satisfying Sandia's long term goal of providing an end- to-end set of scrviccs for high fidelity full physics simu- lations in a high performance, distributed, and distance computing environment. The Intranet Architecture group was formed to apply current distributed object technologies to this problcm. For the hardware architec- tures and software models involved with the current simulation process, a CORBA-based architecture is best suited to meet Sandia's needs. This paper presents the initial desi-a and implementation of this Intranct based on a three-tier Network Computing Architecture(NCA). The major parts of the architecture include: the Web Cli- ent, the Business Objects, and Data Persistence.

  15. Genomic aberrations frequently alter chromatin regulatory genes in chordoma.

    Science.gov (United States)

    Wang, Lu; Zehir, Ahmet; Nafa, Khedoudja; Zhou, Nengyi; Berger, Michael F; Casanova, Jacklyn; Sadowska, Justyna; Lu, Chao; Allis, C David; Gounder, Mrinal; Chandhanayingyong, Chandhanarat; Ladanyi, Marc; Boland, Patrick J; Hameed, Meera

    2016-07-01

    Chordoma is a rare primary bone neoplasm that is resistant to standard chemotherapies. Despite aggressive surgical management, local recurrence and metastasis is not uncommon. To identify the specific genetic aberrations that play key roles in chordoma pathogenesis, we utilized a genome-wide high-resolution SNP-array and next generation sequencing (NGS)-based molecular profiling platform to study 24 patient samples with typical histopathologic features of chordoma. Matching normal tissues were available for 16 samples. SNP-array analysis revealed nonrandom copy number losses across the genome, frequently involving 3, 9p, 1p, 14, 10, and 13. In contrast, copy number gain is uncommon in chordomas. Two minimum deleted regions were observed on 3p within a ∼8 Mb segment at 3p21.1-p21.31, which overlaps SETD2, BAP1 and PBRM1. The minimum deleted region on 9p was mapped to CDKN2A locus at 9p21.3, and homozygous deletion of CDKN2A was detected in 5/22 chordomas (∼23%). NGS-based molecular profiling demonstrated an extremely low level of mutation rate in chordomas, with an average of 0.5 mutations per sample for the 16 cases with matched normal. When the mutated genes were grouped based on molecular functions, many of the mutation events (∼40%) were found in chromatin regulatory genes. The combined copy number and mutation profiling revealed that SETD2 is the single gene affected most frequently in chordomas, either by deletion or by mutations. Our study demonstrated that chordoma belongs to the C-class (copy number changes) tumors whose oncogenic signature is non-random multiple copy number losses across the genome and genomic aberrations frequently alter chromatin regulatory genes. © 2016 Wiley Periodicals, Inc. PMID:27072194

  16. Plasticity of Fission Yeast CENP-A Chromatin Driven by Relative Levels of Histone H3 and H4

    OpenAIRE

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

    2007-01-01

    The histone H3 variant CENP-A assembles into chromatin exclusively at centromeres. The process of CENP-A chromatin assembly is epigenetically regulated. Fission yeast centromeres are composed of a central kinetochore domain on which CENP-A chromatin is assembled, and this is flanked by heterochromatin. Marker genes are silenced when placed within kinetochore or heterochromatin domains. It is not known if fission yeast CENP-A(Cnp1) chromatin is confined to specific sequences or whether histone...

  17. Theory of Traditional Chinese Aesthetic Thoughts Influence on Ancient Chinese Architectural Style

    Institute of Scientific and Technical Information of China (English)

    吴静

    2014-01-01

    the Chinese tradition of Confucianism, Taoism and Buddhism thought influence the design style of the building. Confu-cian, Taoist thought of"the doctrine of the mean"of"nature and humanity"ideology, traditional Confucian thought on the forma-tion of the traditional architectural style vital role. Of ancient Chinese architecture is harmonious and peaceful feelings, Confucian, Taoist, buddhist thought deeply, meanwhile, reflect the hand, reasonable aspiration is dependent of the aesthetic, the emotion affects the ancient Chinese architecture planning, layout and construction, formed the ancient Chinese architecture unique architectural style and artistic style and features.

  18. Software Architecture Design Reasoning

    Science.gov (United States)

    Tang, Antony; van Vliet, Hans

    Despite recent advancements in software architecture knowledge management and design rationale modeling, industrial practice is behind in adopting these methods. The lack of empirical proofs and the lack of a practical process that can be easily incorporated by practitioners are some of the hindrance for adoptions. In particular, the process to support systematic design reasoning is not available. To rectify this issue, we propose a design reasoning process to help architects cope with an architectural design environment where design concerns are cross-cutting and diversified.We use an industrial case study to validate that the design reasoning process can help improve the quality of software architecture design. The results have indicated that associating design concerns and identifying design options are important steps in design reasoning.

  19. Avionics System Architecture Tool

    Science.gov (United States)

    Chau, Savio; Hall, Ronald; Traylor, marcus; Whitfield, Adrian

    2005-01-01

    Avionics System Architecture Tool (ASAT) is a computer program intended for use during the avionics-system-architecture- design phase of the process of designing a spacecraft for a specific mission. ASAT enables simulation of the dynamics of the command-and-data-handling functions of the spacecraft avionics in the scenarios in which the spacecraft is expected to operate. ASAT is built upon I-Logix Statemate MAGNUM, providing a complement of dynamic system modeling tools, including a graphical user interface (GUI), modeling checking capabilities, and a simulation engine. ASAT augments this with a library of predefined avionics components and additional software to support building and analyzing avionics hardware architectures using these components.

  20. Persian architecture and mathematics

    CERN Document Server

    2012-01-01

    This volulme features eight original papers dedicated to the theme “Persian Architecture and Mathematics,” guest edited by Reza Sarhangi. All papers were approved through a rigorous process of blind peer review and edited by an interdisciplinary scientific editorial committee. Topics range from symmetry in ancient Persian architecture to the elaborate geometric patterns and complex three-dimensional structures of standing monuments of historical periods, from the expression of mathematical ideas to architectonic structures, and from decorative ornament to the representation of modern group theory and quasi-crystalline patterns. The articles discuss unique monuments Persia, including domed structures and two-dimensional patterns, which have received significant scholarly attention in recent years. This book is a unique contribution to studies of Persian architecture in relation to mathematics.

  1. Architecture of Environmental Engineering

    DEFF Research Database (Denmark)

    Wenzel, Henrik; Alting, Leo

    2006-01-01

    An architecture of Environmental Engineering has been developed comprising the various disciplines and tools involved. It identifies industry as the major actor and target group, and it builds on the concept of Eco-efficiency. To improve Eco-efficiency, there is a limited number of intervention......-efficiency is the aim of Environmental Engineering, the discipline of synthesis – design and creation of solutions – will form a core pillar of the architecture. Other disciplines of Environmental Engineering exist forming the necessary background and frame for the synthesis. Environmental Engineering, thus, in...... essence comprise the disciplines of: management, system description & inventory, analysis & assessment, prioritisation, synthesis, and communication, each existing at all levels of intervention. The developed architecture of Environmental Engineering, thus, consists of thirty individual disciplines...

  2. Architecture of Environmental Engineering

    DEFF Research Database (Denmark)

    Wenzel, Henrik; Alting, Leo

    2004-01-01

    An architecture of Environmental Engineering has been developed comprising the various disciplines and tools involved. It identifies industry as the major actor and target group, and it builds on the concept of Eco-efficiency. To improve Eco-efficiency, there is a limited number of intervention...... of Eco-efficiency is the aim of Environmental Engineering, the discipline of synthesis – design and creation of solutions – will form a core pillar of the architecture. Other disciplines of Environmental Engineering exist forming the necessary background and frame for the synthesis. Environmental...... Engineering, thus, in essence comprise the disciplines of: management, system description & inventory, analysis & assessment, prioritisation, synthesis, and communication, each existing at all levels of intervention. The developed architecture of Environmental Engineering, thus, consists of thirty individual...

  3. Towards an Architectural Anthropology

    DEFF Research Database (Denmark)

    Stender, Marie

    2016-01-01

    Architecture and anthropology have always had overlapping interests regarding issues such as spatial organisation, forms of human dwellings and the interplay between social life and physical surroundings. Recent developments in both disciplines make it even more relevant to explore and evolve their...... overlaps and collaboration. However, there are also challenging differences to take into account regarding disciplinary traditions of e.g. communication, temporality and normativity. This article explores the potentials and challenges of architectural anthropology as a distinct sub-discipline, and outlines...

  4. Synergetics and architecture

    Science.gov (United States)

    Maslov, V. P.; Maslova, T. V.

    2008-03-01

    A series of phenomena pertaining to economics, quantum physics, language, literary criticism, and especially architecture is studied from the standpoint of synergetics (the study of self-organizing complex systems). It turns out that a whole series of concrete formulas describing these phenomena is identical in these different situations. This is the case of formulas relating to the Bose-Einstein distribution of particles and the distribution of words from a frequency dictionary. This also allows to apply a "quantized" from of the Zipf law to the problem of the authorship of Quiet Flows the Don and to the "blending in" of new architectural structures in an existing environment.

  5. Reframing information architecture

    CERN Document Server

    Resmini, Andrea

    2014-01-01

    Information architecture has changed dramatically since the mid-1990s and earlier conceptions of the world and the internet being different and separate have given way to a much more complex scenario in the present day. In the post-digital world that we now inhabit the digital and the physical blend easily and our activities and usage of information takes place through multiple contexts and via multiple devices and unstable, emergent choreographies. Information architecture now is steadily growing into a channel- or medium-specific multi-disciplinary framework, with contributions coming from a

  6. Interactive Architecture #1

    OpenAIRE

    Oosterhuis, K.; X. Xia

    2007-01-01

    The iA bookzine series will consist of twelve issues, bi-annually published over a period of six years under the supervision of Prof. ir. Kas Oosterhuis, director of the Hperbody at the Delft University of Technology. Interactive Architecture - from here on abbreviated as iA - is NOT simply architecture that is responsive or adaptive to changing circumstances. On the contrary, iA is based on the concept of bi-directional communication, which requires two active parties. Naturally, communicati...

  7. Radio-Communications Architectures

    OpenAIRE

    Diet, Antoine; Villegas, Martine; Baudoin, Genevieve; Robert, Fabien

    2010-01-01

    The goal of this chapter is to demonstrate the absolute need of matching the architecture design and the signal carrying the information. In section 1 and 2, considerations about current users' needs helped to identify three types of carrier signals in the context of radio-communications: NB-CW, WB-CW and IR. A separation between CW and IR signals is unavoidable because it drives us to a different technological design. Basic blocks of transmitter architecture are optimized in function with th...

  8. Information architecture. Volume 3: Guidance

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-04-01

    The purpose of this document, as presented in Volume 1, The Foundations, is to assist the Department of Energy (DOE) in developing and promulgating information architecture guidance. This guidance is aimed at increasing the development of information architecture as a Departmentwide management best practice. This document describes departmental information architecture principles and minimum design characteristics for systems and infrastructures within the DOE Information Architecture Conceptual Model, and establishes a Departmentwide standards-based architecture program. The publication of this document fulfills the commitment to address guiding principles, promote standard architectural practices, and provide technical guidance. This document guides the transition from the baseline or defacto Departmental architecture through approved information management program plans and budgets to the future vision architecture. This document also represents another major step toward establishing a well-organized, logical foundation for the DOE information architecture.

  9. Biomedical laboratories: architecture and radioprotection principles

    International Nuclear Information System (INIS)

    In institutions where biological research are made and some technologies make use of radioisotope, the radiation protection is an issue of biosecurity for conceptual reasons. In the process of architectural design of Biomedical Laboratories, engineering and architecture reveal interfaces with other areas of knowledge and specific concepts. Exploring the role of architectural design in favor of personal and environmental protection in biological containment laboratories that handle non-sealed sources in research, the work discusses the triad that compose the principle of containment in health environments: best practices, protective equipment, physical facilities, with greater emphasis on the latter component. The shortcomings of the design process are reflected in construction and in use-operation and maintenance of these buildings, with direct consequences on the occupational health and safety, environmental and credibility of work processes. In this context, the importance of adoption of alternatives to improve the design process is confirmed, taking into account the early consideration of several variables involved and providing subsidies to the related laboratories . The research, conducted at FIOCRUZ - a Brazilian health institution, developed from the analysis of the participants in the architectural project, aiming at the formulation of design guidelines which could contribute to the rationalisation of this kind of building construction

  10. Chromatin Targeting of de Novo DNA Methyltransferases by the PWWP Domain

    Institute of Scientific and Technical Information of China (English)

    Ying-ZiGe; Min-TiePu; HumairaGowher; Hai-PingWu; Jian-PingDing; AlbertJeltsch; Guo-LiangXu

    2005-01-01

    DNA methylation patterns of mammalian genomes are generated in gametogenesis and early embryonic development. Two de novo DNA methyltransferases, Dnmt3a and Dnmt3b, are responsible for the process. Both en-zymes contain a long N-terminal regulatory region linked to a conserved C-terminal domain responsible forthe catalytic activity. Although a PWWP domain in the N-terminal region has been shown to bind DNA in vitro, it is unclear how the DNA methyltransferases access their substrate in chromatin in vivo. We show here that the two proteins are associated with chromatin including mitotic chromosomes in mammalian cells, and the PWWP domain is essential for the chromatin targeting of the enzymes. The functional significance of PWWPmediated chromatin targeting is suggested by the fact that a missense mutation in this domain of human DNMT3B causes immunodeficiency, centromeric heterochromatin instability, facial anomalies (ICF) syndrome, which is characterized by loss of methylation insatellite DNA, pericentromeric instability, and immunodeficiency. We demonstrate that the mutant protein completely loses its chromatin targeting capacity. Our data establish the PWWP domain as a novel chromatin/chromosome-targeting module and suggest that the PWWP-mediated chromatin association is essential for the function of the de novo methyltransferases during development.

  11. Non coding RNA: sequence-specific guide for chromatin modification and DNA damage signaling

    Directory of Open Access Journals (Sweden)

    Sofia eFrancia

    2015-11-01

    Full Text Available Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports suggest that ncRNAs are involved in DDR signaling and homology-mediated DNA repair. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.

  12. Discrete optimization in architecture architectural & urban layout

    CERN Document Server

    Zawidzki, Machi

    2016-01-01

    This book presents three projects that demonstrate the fundamental problems of architectural design and urban composition – the layout design, evaluation and optimization. Part I describes the functional layout design of a residential building, and an evaluation of the quality of a town square (plaza). The algorithm for the functional layout design is based on backtracking using a constraint satisfaction approach combined with coarse grid discretization. The algorithm for the town square evaluation is based on geometrical properties derived directly from its plan. Part II introduces a crowd-simulation application for the analysis of escape routes on floor plans, and optimization of a floor plan for smooth crowd flow. The algorithms presented employ agent-based modeling and cellular automata.

  13. Hadl: HUMS Architectural Description Language

    Science.gov (United States)

    Mukkamala, R.; Adavi, V.; Agarwal, N.; Gullapalli, S.; Kumar, P.; Sundaram, P.

    2004-01-01

    Specification of architectures is an important prerequisite for evaluation of architectures. With the increase m the growth of health usage and monitoring systems (HUMS) in commercial and military domains, the need far the design and evaluation of HUMS architectures has also been on the increase. In this paper, we describe HADL, HUMS Architectural Description Language, that we have designed for this purpose. In particular, we describe the features of the language, illustrate them with examples, and show how we use it in designing domain-specific HUMS architectures. A companion paper contains details on our design methodology of HUMS architectures.

  14. Architecture Descriptions. A Contribution to Modeling of Production System Architecture

    DEFF Research Database (Denmark)

    Jepsen, Allan Dam; Hvam, Lars

    operational design and handling of production system architecture, research is conducted into the description of production system architecture, including what an architecture description contains in general and what it should describe for production systems specifically. The contribution in this area of...... research consists of three parts. First, a conceptual model of architecture descriptions is established based on the ISO/IEC/IEEE 42010 standard. Secondly, the stakeholders and architecture related concerns of relevance for descriptions of production system architectures are investigated, and requirements......The subject of this PhD dissertation is architecture-centric design and the description of production system architecture. Companies are facing demands for the development and production of new products at an ever increasing rate, as the market life of products decreases and the rate at which...

  15. American School & University Architectural Portfolio 2000 Awards: Landscape Architecture.

    Science.gov (United States)

    American School & University, 2000

    2000-01-01

    Presents photographs and basic information on architectural design, costs, square footage, and principle designers of the award winning school landscaping projects that competed in the American School & University Architectural Portfolio 2000. (GR)

  16. High-resolution mapping reveals links of HP1 with active and inactive chromatin components.

    Directory of Open Access Journals (Sweden)

    Elzo de Wit

    2007-03-01

    Full Text Available Heterochromatin protein 1 (HP1 is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. To obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1-binding sites on Chromosomes 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DNA adenine methyltransferase identification (DamID technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5' regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2, which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5' ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

  17. Graduate transfer exam (DGS and architecture program: Example of Selcuk University, department of architecture

    Directory of Open Access Journals (Sweden)

    Mehmet Uysal

    2011-02-01

    offered. Another program that is not compatible with undergraduate architecture education is vocational program of Restoration and Conservation. Vocational program in “Construction Draft” provides the best match for and is mostly compatible with architecture education. This program offers courses pertaining to four different fields of architecture. Due to the distribution pattern of the vocational programs, both quantitative and qualitative problems are observed in view of teaching staff and curriculum. The adaptation period which is precisely deliberated under law needs to be extended for architecture and similar academic fields. It has been observed that those students transferred to Selcuk University, Department of Architecture through DGS face many problems of academic achievement in design related courses due to the lack of design courses in their previous academic disciplines, the short duration of adaptation period, and the inability to compensate for the lack of design education in such short periods. Although these students manage to complete their undergraduate education, they suffer the lack of design education especially during the earlier semesters and generally become insufficient in reflecting the understanding of architectural design. ConclusionIt is an undisputed fact that vocational and technical education and training is important for Turkey. The present and planned regulations point at an increasing number of students to be admitted to two-year degree programs and even more students admitted to undergraduate programs in different fields. Hence, the education of transfer students through DGS becomes more and more important. Evaluating the present situation and programs of vocational training, it is recommended that further Construction Draft Departments shall be opened and transfers from these departments should be encouraged. Restoration departments might be converted to architectural restoration departments considering the quantity and quality of

  18. Robustness via Diffractal Architectures

    CERN Document Server

    Moocarme, Matthew

    2015-01-01

    When plane waves diffract through fractal-patterned apertures, the resulting far-field profiles or diffractals also exhibit iterated, self-similar features. Here we show that this specific architecture enables robust signal processing and spatial multiplexing: arbitrary parts of a diffractal contain sufficient information to recreate the entire original sparse signal.

  19. Embedded instrumentation systems architecture

    Science.gov (United States)

    Visnevski, Nikita A.

    2007-04-01

    This paper describes the operational concept of the Embedded Instrumentation Systems Architecture (EISA) that is being developed for Test and Evaluation (T&E) applications. The architecture addresses such future T&E requirements as interoperability, flexibility, and non-intrusiveness. These are the ultimate requirements that support continuous T&E objectives. In this paper, we demonstrate that these objectives can be met by decoupling the Embedded Instrumentation (EI) system into an on-board and an off-board component. An on-board component is responsible for sampling, pre-processing, buffering, and transmitting data to the off-board component. The latter is responsible for aggregating, post-processing, and storing test data as well as providing access to the data via a clearly defined interface including such aspects as security, user authentication and access control. The power of the EISA architecture approach is in its inherent ability to support virtual instrumentation as well as enabling interoperability with such important T&E systems as Integrated Network-Enhanced Telemetry (iNET), Test and Training Enabling Architecture (TENA) and other relevant Department of Defense initiatives.

  20. Sun, space and architecture

    Energy Technology Data Exchange (ETDEWEB)

    Iyama, Takeshi

    1987-01-01

    Several projects being performed in Japan on the relationship between architectural space and solar energy are briefly described. The experimental buildings under investigation include the Matsumoto house, the Maruyama house, a tropical dome, the Teraoka Windhouse restaurant, a cross-cultural building blueprint, the Hirata town hall blueprint, the Kijo Alumni hall plan and the 'Ever-Spring' house.

  1. Architectural workshop Tyre3

    OpenAIRE

    Vasa J. Perović; Aljoša Dekleva; Anja Vidic

    2012-01-01

    The workshop deals with and researches three topics: space, user and material. The topics are developed in a parallel and mutually interrelated way, with the final intention being to undertake an architectural intervention on 1:1 scale within a specific public space for a specific user.

  2. Robotically Driven Architectural Production

    OpenAIRE

    Bier, H.H.

    2014-01-01

    Robotically driven architectural production advances seamless, computer-numerically controlled (CNC) and robotically supported design to production and operation processes enabling im-plementation of robotically driven buildings from conceptualisation to use. It enables production of free-formed, heterogeneous, optimized structures in order to address specific requirements in terms of properties (density, consistency, rigidity, etc.) and behaviours (re-configurability, responsiveness, etc.) i...

  3. Architecture Sauvage

    DEFF Research Database (Denmark)

    Baumeister, Ruth

    Danish artist Asger Jorn (1914-1973) is internationally renowed as a proponent of Nordic art and for his activities as a member of Cobra and the Situationist International. Quite apart from his art, Jorn produced a remarkable quantity of writing on art, architecture and urbanism and engaged in...

  4. Enterprise Architecture Evaluation

    DEFF Research Database (Denmark)

    Andersen, Peter; Carugati, Andrea

    2014-01-01

    By being holistically preoccupied with coherency among organizational elements such as organizational strategy, business needs and the IT functions role in supporting the business, enterprise architecture (EA) has grown to become a core competitive advantage. Though EA is a maturing research area...

  5. Future Network Architectures

    DEFF Research Database (Denmark)

    Wessing, Henrik; Bozorgebrahimi, Kurosh; Belter, Bartosz;

    2015-01-01

    This study identifies key requirements for NRENs towards future network architectures that become apparent as users become more mobile and have increased expectations in terms of availability of data. In addition, cost saving requirements call for federated use of, in particular, the optical...

  6. Drawing Music, Playing Architecture

    OpenAIRE

    Makrinos, George Adam

    2005-01-01

    ARCHITECTURE AND MUSIC SHARE INTRINSIC MEANINGS GENERATED BY A CONSTANT STREAM OF METAPHORS WHICH ARE FORMS OF POETIC TRANSFORMATIONS. This thesis sought to challange the present way an architect-musician makes drawings through the exploration of multimedia possibilities at hand. The drawings are composed using Macromedia Flash MX. OPEN HOMEPAGE.EXE To download flash player, click here: Download flash Player

  7. Architecture, constraints, and behavior

    OpenAIRE

    Doyle, John C.; Csete, Marie

    2011-01-01

    This paper aims to bridge progress in neuroscience involving sophisticated quantitative analysis of behavior, including the use of robust control, with other relevant conceptual and theoretical frameworks from systems engineering, systems biology, and mathematics. Familiar and accessible case studies are used to illustrate concepts of robustness, organization, and architecture (modularity and protocols) that are central to understanding complex networks. These essential organizational feature...

  8. Architecture and Energy

    DEFF Research Database (Denmark)

    Lauring, Michael; Marsh, Rob

    2009-01-01

    , and where the transition from an industrial to an information- or knowledge-based society is well-developed. The last three decades of the 20th century show many conscientious - both governmental and architectural - Danish attempts at creating buildings with lower heat consumption. The lower U...

  9. Architectural Creation of Light

    DEFF Research Database (Denmark)

    Bülow, Katja

    2015-01-01

    Bidraget "Architectural Creation of Light" indgår sammen med 108 andre bidrag i bogen "You Say Light, I Think Shadow". Bogens indhold undersøger: "Hvad er lys". I dette bidrag besvares spørgsmålet gennem iagttagelser af arkitektstuderendes undersøgelser af lyset i deres arbejdsmodeller i...

  10. Smart Grid Architectures

    DEFF Research Database (Denmark)

    Dondossola, Giovanna; Terruggia, Roberta; Bessler, Sandford;

    2014-01-01

    The scope of this paper is to address the evolution of distribution grid architectures following the widespread introduction of renewable energy sources. The increasing connection of distributed resources has a strong impact on the topology and the control functionality of the current distribution...

  11. Enterprise Architecture (EA) Roadmap

    Data.gov (United States)

    Office of Personnel Management — The Enterprise Roadmap reflects the information technology (IT) investment priorities established in agency PortfolioStat reviews, as well as IT program decisions...

  12. Architecture of Institution & Home. Architecture as Cultural Medium

    OpenAIRE

    Robinson, J W

    2004-01-01

    This dissertation addresses how architecture functions as a cultural medium. It does so by by investigating how the architecture of institution and home each construct and support different cultural practices. By studying the design of ordinary settings in terms of how qualitative differences in architectural environments affect those who use them, this study exemplifies architectural research directed toward constructive cultural change. In the United States, ordinary people often describe h...

  13. Structural hierarchy of chromatin in chicken erythrocyte nuclei based on small-angle neutron scattering: Fractal nature of the large-scale chromatin organization

    International Nuclear Information System (INIS)

    The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 x 10-1 to 10-4 A-1 with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 μm and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm

  14. Geometric Rationalization for Freeform Architecture

    KAUST Repository

    jiang, caigui

    2016-06-20

    The emergence of freeform architecture provides interesting geometric challenges with regards to the design and manufacturing of large-scale structures. To design these architectural structures, we have to consider two types of constraints. First, aesthetic constraints are important because the buildings have to be visually impressive. Sec- ond, functional constraints are important for the performance of a building and its e cient construction. This thesis contributes to the area of architectural geometry. Specifically, we are interested in the geometric rationalization of freeform architec- ture with the goal of combining aesthetic and functional constraints and construction requirements. Aesthetic requirements typically come from designers and architects. To obtain visually pleasing structures, they favor smoothness of the building shape, but also smoothness of the visible patterns on the surface. Functional requirements typically come from the engineers involved in the construction process. For exam- ple, covering freeform structures using planar panels is much cheaper than using non-planar ones. Further, constructed buildings have to be stable and should not collapse. In this thesis, we explore the geometric rationalization of freeform archi- tecture using four specific example problems inspired by real life applications. We achieve our results by developing optimization algorithms and a theoretical study of the underlying geometrical structure of the problems. The four example problems are the following: (1) The design of shading and lighting systems which are torsion-free structures with planar beams based on quad meshes. They satisfy the functionality requirements of preventing light from going inside a building as shad- ing systems or reflecting light into a building as lighting systems. (2) The Design of freeform honeycomb structures that are constructed based on hex-dominant meshes with a planar beam mounted along each edge. The beams intersect without

  15. 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

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

    Science.gov (United States)

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

    2015-09-15

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

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

    Directory of Open Access Journals (Sweden)

    Fan-Tso Chien

    2014-12-01

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

  18. Genome-wide profiling of salt fractions maps physical properties of chromatin

    OpenAIRE

    Henikoff, Steven; Henikoff, Jorja G.; Sakai, Akiko; Loeb, Gabriel B.; Ahmad, Kami

    2009-01-01

    We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical “active” chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA ...

  19. Urban planning, architecture, landscape architecture projects underway for Roanoke

    OpenAIRE

    Chadwick, Heather Riley

    2009-01-01

    Faculty and students in the College of Architecture and Urban Studies at Virginia Tech bring expertise and solutions to communities all around the world. Currently, the college is working on six different urban planning, architecture, and landscape architecture projects in Roanoke, Va.

  20. ACOUSTICS IN ARCHITECTURAL DESIGN, AN ANNOTATED BIBLIOGRAPHY ON ARCHITECTURAL ACOUSTICS.

    Science.gov (United States)

    DOELLE, LESLIE L.

    THE PURPOSE OF THIS ANNOTATED BIBLIOGRAPHY ON ARCHITECTURAL ACOUSTICS WAS--(1) TO COMPILE A CLASSIFIED BIBLIOGRAPHY, INCLUDING MOST OF THOSE PUBLICATIONS ON ARCHITECTURAL ACOUSTICS, PUBLISHED IN ENGLISH, FRENCH, AND GERMAN WHICH CAN SUPPLY A USEFUL AND UP-TO-DATE SOURCE OF INFORMATION FOR THOSE ENCOUNTERING ANY ARCHITECTURAL-ACOUSTIC DESIGN…