WorldWideScience

Sample records for chromatin architecture exploring

  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. 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...

  3. 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...

  4. Exploring Enterprise Architecture Evaluation Practices

    DEFF Research Database (Denmark)

    Andersen, Peter; Carugati, Andrea; Grue Sørensen, Morten

    2015-01-01

    using empirical and practical studies. This paper presents the findings from a case study exploring how enterprise architecture (EA) evaluation takes place in practice. The aim of the case study is to explore EA evaluation from the practical view of primarily enterprise architects and project managers......EA evaluation has received very little attention in academic publications on EA. While EA evaluation to some extent has been described in the literature, the different ways of evaluating architecture have mainly used a top-down approach deriving measures from theory rather than a bottom-up approach...

  5. 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....

  6. Generic Design Space Exploration for Reconfigurable Architectures

    OpenAIRE

    Bossuet, Lilian; Gogniat, Guy; Philippe, Jean Luc

    2005-01-01

    We propose in this paper an original design space exploration method for reconfigurable architectures adapted to fine and coarse grain resources. The exploration flow deals with communication hierarchical distribution and processing resources use rate for the architecture under exploration. With this information, designer can explore the architectural design space to define a power-efficient architecture. Exploration results for image computing and cryptography applications are provided to de...

  7. 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.

  8. 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

  9. 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.

  10. Exploration of Heterogeneous FPGA Architectures

    Directory of Open Access Journals (Sweden)

    Umer Farooq

    2011-01-01

    mesh and tree-based architectures are evaluated for three sets of benchmark circuits. Experimental results show that a more flexible floor-planning in mesh-based FPGA gives better results as compared to the column-based floor-planning. Also it is shown that compared to different floor-plannings of mesh-based FPGA, tree-based architecture gives better area, performance, and power results.

  11. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-08-21

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

  13. Exploring the Materials of Architectural Development

    OpenAIRE

    Ditcher, Kamille

    2012-01-01

    A factory inspired exploration in the architectural potential of space, material, sound, and light. This thesis is divided into chapters of the media types used for design. Primarily, the materials include photography, drawing, and modeling. The process yields overlap and interchange in ways of design that alter the ways of seeing and of advancing the work. Consequently, divisions of the book reoccur throughout the course of the thesis.

  14. 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

  15. 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.

  16. 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...

  17. Design space exploration in the microthreaded many-core architecture

    OpenAIRE

    Uddin, Irfan

    2013-01-01

    Design space exploration is commonly performed in embedded system, where the architecture is a complicated piece of engineering. With the current trend of many-core systems, design space exploration in general-purpose computers can no longer be avoided. Microgrid is a complicated architecture, and therefor we need to perform design space exploration. Generally, simulators are used for the design space exploration of an architecture. Different simulators with different levels of complexity, si...

  18. Functional Interface Considerations within an Exploration Life Support System Architecture

    Science.gov (United States)

    Perry, Jay L.; Sargusingh, Miriam J.; Toomarian, Nikzad

    2016-01-01

    As notional life support system (LSS) architectures are developed and evaluated, myriad options must be considered pertaining to process technologies, components, and equipment assemblies. Each option must be evaluated relative to its impact on key functional interfaces within the LSS architecture. A leading notional architecture has been developed to guide the path toward realizing future crewed space exploration goals. This architecture includes atmosphere revitalization, water recovery and management, and environmental monitoring subsystems. Guiding requirements for developing this architecture are summarized and important interfaces within the architecture are discussed. The role of environmental monitoring within the architecture is described.

  19. Communication-Oriented Design Space Exploration for Reconfigurable Architectures

    Directory of Open Access Journals (Sweden)

    Gogniat Guy

    2007-01-01

    Full Text Available Many academic works in computer engineering focus on reconfigurable architectures and associated tools. Fine-grain architectures, field programmable gate arrays (FPGAs, are the most well-known structures of reconfigurable hardware. Dedicated tools (generic or specific allow for the exploration of their design space to choose the best architecture characteristics and/or to explore the application characteristics. The aim is to increase the synergy between the application and the architecture in order to get the best performance. However, there is no generic tool to perform such an exploration for coarse-grain or heterogeneous-grain architectures, just a small number of very specific tools are able to explore a limited set of architectures. To address this major lack, in this paper we propose a new design space exploration approach adapted to fine- and coarse-grain granularities. Our approach combines algorithmic and architecture explorations. It relies on an automatic estimation tool which computes the communication hierarchical distribution and the architectural processing resources use rate for the architecture under exploration. Such an approach forwards the rapid definition of efficient reconfigurable architectures dedicated to one or several applications.

  20. Communication-Oriented Design Space Exploration for Reconfigurable Architectures

    Directory of Open Access Journals (Sweden)

    Lilian Bossuet

    2007-03-01

    Full Text Available Many academic works in computer engineering focus on reconfigurable architectures and associated tools. Fine-grain architectures, field programmable gate arrays (FPGAs, are the most well-known structures of reconfigurable hardware. Dedicated tools (generic or specific allow for the exploration of their design space to choose the best architecture characteristics and/or to explore the application characteristics. The aim is to increase the synergy between the application and the architecture in order to get the best performance. However, there is no generic tool to perform such an exploration for coarse-grain or heterogeneous-grain architectures, just a small number of very specific tools are able to explore a limited set of architectures. To address this major lack, in this paper we propose a new design space exploration approach adapted to fine- and coarse-grain granularities. Our approach combines algorithmic and architecture explorations. It relies on an automatic estimation tool which computes the communication hierarchical distribution and the architectural processing resources use rate for the architecture under exploration. Such an approach forwards the rapid definition of efficient reconfigurable architectures dedicated to one or several applications.

  1. Avionics Architectures for Exploration: Wireless Technologies and Human Spaceflight

    Science.gov (United States)

    Goforth, Montgomery B.; Ratliff, James E.; Barton, Richard J.; Wagner, Raymond S.; Lansdowne, Chatwin

    2014-01-01

    The authors describe ongoing efforts by the Avionics Architectures for Exploration (AAE) project chartered by NASA's Advanced Exploration Systems (AES) Program to evaluate new avionics architectures and technologies, provide objective comparisons of them, and mature selected technologies for flight and for use by other AES projects. The AAE project team includes members from most NASA centers and from industry. This paper provides an overview of recent AAE efforts, with particular emphasis on the wireless technologies being evaluated under AES to support human spaceflight.

  2. Operational Concepts for a Generic Space Exploration Communication Network Architecture

    Science.gov (United States)

    Ivancic, William D.; Vaden, Karl R.; Jones, Robert E.; Roberts, Anthony M.

    2015-01-01

    This document is one of three. It describes the Operational Concept (OpsCon) for a generic space exploration communication architecture. The purpose of this particular document is to identify communication flows and data types. Two other documents accompany this document, a security policy profile and a communication architecture document. The operational concepts should be read first followed by the security policy profile and then the architecture document. The overall goal is to design a generic space exploration communication network architecture that is affordable, deployable, maintainable, securable, evolvable, reliable, and adaptable. The architecture should also require limited reconfiguration throughout system development and deployment. System deployment includes: subsystem development in a factory setting, system integration in a laboratory setting, launch preparation, launch, and deployment and operation in space.

  3. The Evolution of Mission Architectures for Human Lunar Exploration

    Science.gov (United States)

    Everett, S. F.

    1995-01-01

    Defining transportation architectures for the human exploration of the Moon is a complex task due to the multitude of mission scenarios available. The mission transportation architecture recently proposed for the First Lunar Outpost (FLO) was not designed from carefully predetermined mission requirements and goals, but evolved from an initial set of requirements, which were continually modified as studies revealed that some early assumptions were not optimal. This paper focuses on the mission architectures proposed for FLO and investigates how these transportation architectures evolved. A comparison of the strengths and weaknesses of the three distinct mission architectures are discussed, namely (1) Lunar Orbit Rendezvous, (2) staging from the Cislunar Libration Point, and (3) direct to the lunar surface. In addition, several new and revolutionary architectures are discussed.

  4. Robotic lunar exploration: Architectures, issues and options

    Science.gov (United States)

    Mankins, John C.; Valerani, Ernesto; Della Torre, Alberto

    2007-06-01

    The US ‘vision for space exploration’ articulated at the beginning of 2004 encompasses a broad range of human and robotic space missions, including missions to the Moon, Mars and destinations beyond. It establishes clear goals and objectives, yet sets equally clear budgetary ‘boundaries’ by stating firm priorities, including ‘tough choices’ regarding current major NASA programs. The new vision establishes as policy the goals of pursuing commercial and international collaboration in realizing future space exploration missions. Also, the policy envisions that advances in human and robotic mission technologies will play a key role—both as enabling and as a major public benefit that will result from implementing that vision. In pursuing future international space exploration goals, the exploration of the Moon during the coming decades represents a particularly appealing objective. The Moon provides a unique venue for exploration and discovery—including the science of the Moon (e.g., geological studies), science from the Moon (e.g., astronomical observatories), and science on the Moon (including both basic research, such as biological laboratory science, and applied research and development, such as the use of the Moon as a test bed for later exploration). The Moon may also offer long-term opportunties for utilization—including Earth observing applications and commercial developments. During the coming decade, robotic lunar exploration missions will play a particularly important role, both in their own right and as precursors to later, more ambitious human and robotic exploration and development efforts. The following paper discusses some of the issues and opportunities that may arise in establishing plans for future robotic lunar exploration. Particular emphasis is placed on four specific elements of future robotic infrastructure: Earth Moon in-space transportation systems; lunar orbiters; lunar descent and landing systems; and systems for long

  5. System-Level Design Space Exploration of Reconfigurable Architectures

    OpenAIRE

    Sigdel, K.

    2011-01-01

    Reconfigurable architectures are becoming increasingly popular as they bear a promise of combining the flexibility of software with the performance of hardware. Nevertheless, such architectures are subject to numerous constraints, such as performance, memory requirements, chip area, and power consumption. To create an efficient design, performing Design Space Exploration (DSE) at various stages is essential in order to effectively appraise several design alternatives. DSE at early design stages...

  6. Exploring Socio-material Orderings in Ethnography of Architectural Design

    DEFF Research Database (Denmark)

    Lotz, Katrine; Stang Våland, Marianne

    2012-01-01

    recognized to cause displacements – some of them deliberately installed to do so - in established architectural practice: The attempts to regulate and homogenize project-information in digital 3D/4D-models from very early stages of the planning; the manifest tendency of involving an increased number of...... in contemporary architectural design. We attempt to follow the actors in detail through their socio-material involvements and ‘architectural inventions’ such as visualized motives of space, materials, atmospheres, buildingparts and -components, and to explore how relations continuously tie and untie...

  7. 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.

  8. 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

  9. Exploration Space Suit Architecture: Destination Environmental-Based Technology Development

    Science.gov (United States)

    Hill, Terry R.

    2010-01-01

    This paper picks up where EVA Space Suit Architecture: Low Earth Orbit Vs. Moon Vs. Mars (Hill, Johnson, IEEEAC paper #1209) left off in the development of a space suit architecture that is modular in design and interfaces and could be reconfigured to meet the mission or during any given mission depending on the tasks or destination. This paper will walk though the continued development of a space suit system architecture, and how it should evolve to meeting the future exploration EVA needs of the United States space program. In looking forward to future US space exploration and determining how the work performed to date in the CxP and how this would map to a future space suit architecture with maximum re-use of technology and functionality, a series of thought exercises and analysis have provided a strong indication that the CxP space suit architecture is well postured to provide a viable solution for future exploration missions. Through the destination environmental analysis that is presented in this paper, the modular architecture approach provides the lowest mass, lowest mission cost for the protection of the crew given any human mission outside of low Earth orbit. Some of the studies presented here provide a look and validation of the non-environmental design drivers that will become every-increasingly important the further away from Earth humans venture and the longer they are away. Additionally, the analysis demonstrates a logical clustering of design environments that allows a very focused approach to technology prioritization, development and design that will maximize the return on investment independent of any particular program and provide architecture and design solutions for space suit systems in time or ahead of being required for any particular manned flight program in the future. The new approach to space suit design and interface definition the discussion will show how the architecture is very adaptable to programmatic and funding changes with

  10. Service-Oriented Architecture for Space Exploration Robotic Rover Systems

    CERN Document Server

    Bassil, Youssef

    2012-01-01

    Currently, industrial sectors are transforming their business processes into e-services and component-based architectures to build flexible, robust, and scalable systems, and reduce integration-related maintenance and development costs. Robotics is yet another promising and fast-growing industry that deals with the creation of machines that operate in an autonomous fashion and serve for various applications including space exploration, weaponry, laboratory research, and manufacturing. It is in space exploration that the most common type of robots is the planetary rover which moves across the surface of a planet and conducts a thorough geological study of the celestial surface. This type of rover system is still ad-hoc in that it incorporates its software into its core hardware making the whole system cohesive, tightly-coupled, more susceptible to shortcomings, less flexible, hard to be scaled and maintained, and impossible to be adapted to other purposes. This paper proposes a service-oriented architecture fo...

  11. Exploration and Planning in a Three-Level Cognitive Architecture

    DEFF Research Database (Denmark)

    Kraft, Dirk; Baseski, Emre; Popovic, Mila;

    2008-01-01

    We describe an embodied cognitive system based on a three-level architecture that includes a sensorimotor layer, a mid-level layer that stores and reasons about object-action episodes, and a high-level symbolic planner that creates abstract action plans to be realised and possibly further specified...... by the lower levels. The system works in two modes, exploration and plan execution, that both make use of the same architecture. We give results of different sub-processes as well as their interaction. In particular, we describe the generation and execution of plans as well as a set of learning...... processes that take place independently of, or in parallel with, plan execution....

  12. Software Architecture of Sensor Data Distribution In Planetary Exploration

    Science.gov (United States)

    Lee, Charles; Alena, Richard; Stone, Thom; Ossenfort, John; Walker, Ed; Notario, Hugo

    2006-01-01

    Data from mobile and stationary sensors will be vital in planetary surface exploration. The distribution and collection of sensor data in an ad-hoc wireless network presents a challenge. Irregular terrain, mobile nodes, new associations with access points and repeaters with stronger signals as the network reconfigures to adapt to new conditions, signal fade and hardware failures can cause: a) Data errors; b) Out of sequence packets; c) Duplicate packets; and d) Drop out periods (when node is not connected). To mitigate the effects of these impairments, a robust and reliable software architecture must be implemented. This architecture must also be tolerant of communications outages. This paper describes such a robust and reliable software infrastructure that meets the challenges of a distributed ad hoc network in a difficult environment and presents the results of actual field experiments testing the principles and actual code developed.

  13. 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

  14. 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

  15. Modular production line optimization: The exPLORE architecture

    Directory of Open Access Journals (Sweden)

    Spinellis Diomidis D.

    2000-01-01

    Full Text Available The general design problem in serial production lines concerns the allocation of resources such as the number of servers, their service rates, and buffers given production-specific constraints, associated costs, and revenue projections. We describe the design of exPLOre: a modular, object-oriented, production line optimization software architecture. An abstract optimization module can be instantiated using a variety of stochastic optimization methods such as simulated annealing and genetic algorithms. Its search space is constrained by a constraint checker while its search direction is guided by a cost analyser which combines the output of a throughput evaluator with the business model. The throughput evaluator can be instantiated using Markovian, generalised queueing network methods, a decomposition, or an expansion method algorithm.

  16. Modular production line optimization: The exPLORE architecture

    Directory of Open Access Journals (Sweden)

    Diomidis D. Spinellis

    2001-01-01

    Full Text Available The general design problem in serial production lines concerns the allocation of resources such as the number of servers, their service rates, and buffers given production-specific constraints, associated costs, and revenue projections. We describe the design of exPLOre: a modular, object-oriented, production line optimization software architecture. An abstract optimization module can be instantiated using a variety of stochastic optimization methods such as simulated annealing and genetic algorithms. Its search space is constrained by a constraint checker while its search direction is guided by a cost analyser which combines the output of a throughput evaluator with the business model. The throughput evaluator can be instantiated using Markovian, generalised queueing network methods, a decomposition, or an expansion method algorithm.

  17. Avionics Architectures for Exploration: Ongoing Efforts in Human Spaceflight

    Science.gov (United States)

    Goforth, Montgomery B.; Ratliff, James E.; Hames, Kevin L.; Vitalpur, Sharada V.; Woodman, Keith L.

    2014-01-01

    The field of Avionics is advancing far more rapidly in terrestrial applications than in spaceflight applications. Spaceflight Avionics are not keeping pace with expectations set by terrestrial experience, nor are they keeping pace with the need for increasingly complex automation and crew interfaces as we move beyond Low Earth Orbit. NASA must take advantage of the strides being made by both space-related and terrestrial industries to drive our development and sustaining costs down. This paper describes ongoing efforts by the Avionics Architectures for Exploration (AAE) project chartered by NASA's Advanced Exploration Systems (AES) Program to evaluate new avionic architectures and technologies, provide objective comparisons of them, and mature selected technologies for flight and for use by other AES projects. The AAE project team includes members from most NASA centers, and from industry. It is our intent to develop a common core avionic system that has standard capabilities and interfaces, and contains the basic elements and functionality needed for any spacecraft. This common core will be scalable and tailored to specific missions. It will incorporate hardware and software from multiple vendors, and be upgradeable in order to infuse incremental capabilities and new technologies. It will maximize the use of reconfigurable open source software (e.g., Goddard Space Flight Center's (GSFC's) Core Flight Software (CFS)). Our long-term focus is on improving functionality, reliability, and autonomy, while reducing size, weight, and power. Where possible, we will leverage terrestrial commercial capabilities to drive down development and sustaining costs. We will select promising technologies for evaluation, compare them in an objective manner, and mature them to be available for future programs. The remainder of this paper describes our approach, technical areas of emphasis, integrated test experience and results as of mid-2014, and future plans. As a part of the AES

  18. Tree-based Heterogeneous FPGA Architectures Application Specific Exploration and Optimization

    CERN Document Server

    Farooq, Umer; Mehrez, Habib

    2012-01-01

    This book presents a new FPGA architecture known as tree-based FPGA architecture, due to its hierarchical nature. This type of architecture has been relatively unexplored despite their better performance and predictable routing behavior, as compared to mesh-based FPGA architectures. In this book, we explore and optimize the tree-based architecture and we evaluate it by comparing it to equivalent mesh-based FPGA architectures. Provides a single-source reference, surveying and comparing mesh and tree-based FPGA architectures, including exploration of a number of techniques for both architectures and comparison using a large set of benchmarks; Describes in detail Computer-Aided-Design (CAD) flow of FPGAs which is used to map different circuits; Includes a survey of the current and future trends in FPGA design.

  19. 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.

  20. Exploring Life Support Architectures for Evolution of Deep Space Human Exploration

    Science.gov (United States)

    Anderson, Molly S.; Stambaugh, Imelda C.

    2015-01-01

    Life support system architectures for long duration space missions are often explored analytically in the human spaceflight community to find optimum solutions for mass, performance, and reliability. But in reality, many other constraints can guide the design when the life support system is examined within the context of an overall vehicle, as well as specific programmatic goals and needs. Between the end of the Constellation program and the development of the "Evolvable Mars Campaign", NASA explored a broad range of mission possibilities. Most of these missions will never be implemented but the lessons learned during these concept development phases may color and guide future analytical studies and eventual life support system architectures. This paper discusses several iterations of design studies from the life support system perspective to examine which requirements and assumptions, programmatic needs, or interfaces drive design. When doing early concept studies, many assumptions have to be made about technology and operations. Data can be pulled from a variety of sources depending on the study needs, including parametric models, historical data, new technologies, and even predictive analysis. In the end, assumptions must be made in the face of uncertainty. Some of these may introduce more risk as to whether the solution for the conceptual design study will still work when designs mature and data becomes available.

  1. SENSES OF DARKNESS: AN EXPLORATION OF BLIND NAVIGATION THROUGH ARCHITECTURE

    OpenAIRE

    Wojno, Alexandra

    2013-01-01

    Based on the principle of sequential lessons for teaching orienteering, the program is a center that teaches navigation to people who are blind, located in the remains of the Chesapeake and Ohio Canal in Harpers Ferry, West Virginia. Through the use of materials, light, and this program of sequential patterns, the architecture focuses on heightening the working senses of the occupants using the progression throughout the building. This connection of the body and mind to architecture creates a...

  2. Architecture Exploration Based on GA-PSO Optimization, ANN Modeling, and Static Scheduling

    OpenAIRE

    Ahmed Elhossini; Shawki Areibi; Robert Dony

    2013-01-01

    Embedded systems are widely used today in different digital signal processing (DSP) applications that usually require high computation power and tight constraints. The design space to be explored depends on the application domain and the target platform. A tool that helps explore different architectures is required to design such an efficient system. This paper proposes an architecture exploration framework for DSP applications based on Particle Swarm Optimization (PSO) and genetic algorithms...

  3. 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

  4. 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...

  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. metaphor(m)-an exploration of the simultaneous absence and presence in architecture and landscape

    OpenAIRE

    McGrath, Patrick Ryan

    2013-01-01

    An exploration of simultaneous presence and absence in Architecture and Landscape. The site of memory as metaphor[m] and narrative. Architecture persists the metapsyche glimpse into the infinite. A gestalt of space and time relative to an obscur sensory perspective. Architecture defines place within space. That the vague sphere of mental and psychological perception extends infinite past any boundary. It is these boundaries that awaken the thought of a simultaneous absence and presence wi...

  7. 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

  8. Hinge Dimension: An Exploration of Enaction in Architecture

    DEFF Research Database (Denmark)

    Franinovic, Karmen; Wilson, Alexander

    2007-01-01

    In this paper, we address issues of technologically mediated enactive experience with and within architectural contexts, and the ways in which it may affect our relationships to constructed surroundings. We present the conceptual ideas and design development of the Hinge Dimension project, an...

  9. Exploration Architecture with Quantum Inertial Gravimetry and In Situ ChipSat Sensors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This will study an exploration architecture combining remote survey with in situ sampling, with example missions to Europa and a Near Earth Object. In particular...

  10. Exploring architectures displaying multimeric presentations of a trihydroxypiperidine iminosugar

    Directory of Open Access Journals (Sweden)

    Camilla Matassini

    2015-12-01

    Full Text Available The synthesis of new multivalent architectures based on a trihydroxypiperidine α-fucosidase inhibitor is reported herein. Tetravalent and nonavalent dendrimers were obtained by means of the click chemistry approach involving the copper azide-alkyne-catalyzed cycloaddition (CuAAC between suitable scaffolds bearing terminal alkyne moieties and an azido-functionalized piperidine as the bioactive moiety. A preliminary biological investigation is also reported towards commercially available and human glycosidases.

  11. Exploring architectures displaying multimeric presentations of a trihydroxypiperidine iminosugar

    Science.gov (United States)

    Matassini, Camilla; Mirabella, Stefania; Goti, Andrea; Robina, Inmaculada; Moreno-Vargas, Antonio J

    2015-01-01

    Summary The synthesis of new multivalent architectures based on a trihydroxypiperidine α-fucosidase inhibitor is reported herein. Tetravalent and nonavalent dendrimers were obtained by means of the click chemistry approach involving the copper azide-alkyne-catalyzed cycloaddition (CuAAC) between suitable scaffolds bearing terminal alkyne moieties and an azido-functionalized piperidine as the bioactive moiety. A preliminary biological investigation is also reported towards commercially available and human glycosidases. PMID:26734108

  12. An Agent-Based Dynamic Model for Analysis of Distributed Space Exploration Architectures

    Science.gov (United States)

    Sindiy, Oleg V.; DeLaurentis, Daniel A.; Stein, William B.

    2009-07-01

    A range of complex challenges, but also potentially unique rewards, underlie the development of exploration architectures that use a distributed, dynamic network of resources across the solar system. From a methodological perspective, the prime challenge is to systematically model the evolution (and quantify comparative performance) of such architectures, under uncertainty, to effectively direct further study of specialized trajectories, spacecraft technologies, concept of operations, and resource allocation. A process model for System-of-Systems Engineering is used to define time-varying performance measures for comparative architecture analysis and identification of distinguishing patterns among interoperating systems. Agent-based modeling serves as the means to create a discrete-time simulation that generates dynamics for the study of architecture evolution. A Solar System Mobility Network proof-of-concept problem is introduced representing a set of longer-term, distributed exploration architectures. Options within this set revolve around deployment of human and robotic exploration and infrastructure assets, their organization, interoperability, and evolution, i.e., a system-of-systems. Agent-based simulations quantify relative payoffs for a fully distributed architecture (which can be significant over the long term), the latency period before they are manifest, and the up-front investment (which can be substantial compared to alternatives). Verification and sensitivity results provide further insight on development paths and indicate that the framework and simulation modeling approach may be useful in architectural design of other space exploration mass, energy, and information exchange settings.

  13. Exploring Textiles in Architecture through Tangible Three-Dimensional Sketching Tools

    DEFF Research Database (Denmark)

    Heimdal, Elisabeth Jacobsen; Lenau, Torben Anker; O'Mahony, Marie

    This paper argues that tangible three dimensional sketching with textiles makes it more likely that these materials will be used when creating architectural spaces. Our research contributes to the more general idea that innovation in architecture and design can be stimulated by the exploration of...... new materials. With tangible three dimensional sketching, we mean an iterative process of physical model making. In two experiments with architectural students, all textile novices, spaces were modelled using a three dimensional sketching tool consisting of textiles, cardboard support and tools for...

  14. Rule-based graph theory to enable exploration of the space system architecture design space

    Science.gov (United States)

    Arney, Dale Curtis

    The primary goal of this research is to improve upon system architecture modeling in order to enable the exploration of design space options. A system architecture is the description of the functional and physical allocation of elements and the relationships, interactions, and interfaces between those elements necessary to satisfy a set of constraints and requirements. The functional allocation defines the functions that each system (element) performs, and the physical allocation defines the systems required to meet those functions. Trading the functionality between systems leads to the architecture-level design space that is available to the system architect. The research presents a methodology that enables the modeling of complex space system architectures using a mathematical framework. To accomplish the goal of improved architecture modeling, the framework meets five goals: technical credibility, adaptability, flexibility, intuitiveness, and exhaustiveness. The framework is technically credible, in that it produces an accurate and complete representation of the system architecture under consideration. The framework is adaptable, in that it provides the ability to create user-specified locations, steady states, and functions. The framework is flexible, in that it allows the user to model system architectures to multiple destinations without changing the underlying framework. The framework is intuitive for user input while still creating a comprehensive mathematical representation that maintains the necessary information to completely model complex system architectures. Finally, the framework is exhaustive, in that it provides the ability to explore the entire system architecture design space. After an extensive search of the literature, graph theory presents a valuable mechanism for representing the flow of information or vehicles within a simple mathematical framework. Graph theory has been used in developing mathematical models of many transportation and

  15. Exploring the Architectural Tradespace of Severe Weather Monitoring Nanosatellite Constellations

    Science.gov (United States)

    Hitomi, N.; Selva, D.; Blackwell, W. J.

    2014-12-01

    MicroMAS-1, a 3U nanosatellite developed by MIT/LL, MIT/SSL, and University of Massachusetts, was launched on July 13, 2014 and is scheduled for deployment from the International Space Station in September. The development of MicroMAS motivates an architectural analysis of a constellation of nanosatellites with the goal of drastically reducing the cost of observing severe storms compared with current monolithic missions such as the Precision and All-Weather Temperature and Humidity (PATH) mission from the NASA Decadal Survey. Our goal is to evolve the instrument capability on weather monitoring nanosatellites to achieve higher performance and better satisfy stakeholder needs. Clear definitions of performance requirements are critical in the conceptual design phase when much of the project's lifecycle cost and performance will be fixed. Ability to perform trade studies and optimization of performance needs with instrument capability will enable design teams to focus on key technologies that will introduce high value and high return on investment. In this work, we approach the significant trades and trends of constellations for monitoring severe storms by applying our rule-based decision support tool. We examine a subset of stakeholder groups listed in the OSCAR online database (e.g., weather, climate) that would benefit from severe storm weather data and their respective observation requirements (e.g. spatial resolution, accuracy). We use ten parameters in our analysis, including atmospheric temperature, humidity, and precipitation. We compare the performance and cost of thousands of different possible constellations. The constellations support hyperspectral sounders that cover different portions of the millimeter-wave spectrum (50-60 GHz, 118GHz, 183GHz) in different orbits, and the performance results are compared against those of the monolithic PATH mission. Our preliminary results indicate that constellations using the hyperspectral millimeter wave sounders can

  16. A Low Cost Spacecraft Architecture for Robotic Lunar Exploration Projects

    Science.gov (United States)

    Lemke, Lawrence G.; Gonzales, Andrew A.

    2006-01-01

    A program of frequent, capable, but affordable lunar robotic missions prior to return of humans to the moon can contribute to the Vision for Space Exploration (VSE) NASA is tasked to execute. The Lunar Reconnaissance Orbiter (LRO) and its secondary payload are scheduled to orbit the moon, and impact it, respectively, in 2008. It is expected that the sequence of missions occurring for approximately the decade after 2008 will place an increasing emphasis on soft landed payloads. These missions are requited to explore intrinsic characteristics of the moon, such as hydrogen distribution in the regolith, and levitated dust, to demonstrate the ability to access and process in-situ resources, and to demonstrate functions critical to supporting human presence, such as automated precision navigation and landing. Additional factors governing the design of spacecraft to accomplish this diverse set of objectives are: operating within a relatively modest funding profile, the need tb visit multiple sites (both polar and equatorial) repeatedly, and to use the current generation of launch vehicles. In the US, this implies use of the Evolved Expendable Launch Vehicles, or EELVs, although this design philosophy may be extended to launch vehicles of other nations, as well. Many of these factors are seemingly inconsistent with each other. For example, the cost of a spacecraft usually increases with mass; therefore the desire to fly frequent, modestly priced spacecraft seems to imply small spacecraft (autonomous navigation and soft landing) also usually increases cost. A strategy for spacecraft design that meets these conflicting requirements is presented. Taken together, spacecraft structure and propulsion subsystems constitute the majority of spacecraft mass; saving development and integration cost on these elements is critical to controlling cost. Therefore, a low cost, modular design for spacecraft structure and propulsion subsystems is presented which may be easily scaled up or

  17. Exploring the architectural trade space of NASAs Space Communication and Navigation Program

    Science.gov (United States)

    Sanchez, M.; Selva, D.; Cameron, B.; Crawley, E.; Seas, A.; Seery, B.

    NASAs Space Communication and Navigation (SCaN) Program is responsible for providing communication and navigation services to space missions and other users in and beyond low Earth orbit. The current SCaN architecture consists of three independent networks: the Space Network (SN), which contains the TDRS relay satellites in GEO; the Near Earth Network (NEN), which consists of several NASA owned and commercially operated ground stations; and the Deep Space Network (DSN), with three ground stations in Goldstone, Madrid, and Canberra. The first task of this study is the stakeholder analysis. The goal of the stakeholder analysis is to identify the main stakeholders of the SCaN system and their needs. Twenty-one main groups of stakeholders have been identified and put on a stakeholder map. Their needs are currently being elicited by means of interviews and an extensive literature review. The data will then be analyzed by applying Cameron and Crawley's stakeholder analysis theory, with a view to highlighting dominant needs and conflicting needs. The second task of this study is the architectural tradespace exploration of the next generation TDRSS. The space of possible architectures for SCaN is represented by a set of architectural decisions, each of which has a discrete set of options. A computational tool is used to automatically synthesize a very large number of possible architectures by enumerating different combinations of decisions and options. The same tool contains models to evaluate the architectures in terms of performance and cost. The performance model uses the stakeholder needs and requirements identified in the previous steps as inputs, and it is based in the VASSAR methodology presented in a companion paper. This paper summarizes the current status of the MIT SCaN architecture study. It starts by motivating the need to perform tradespace exploration studies in the context of relay data systems through a description of the history NASA's space communicati

  18. Exploration Space Suit Architecture and Destination Environmental-Based Technology Development

    Science.gov (United States)

    Hill, Terry R.; McFarland, Shane M.; Korona, F. Adam

    2013-01-01

    This paper continues forward where EVA Space Suit Architecture: Low Earth Orbit Vs. Moon Vs. Mars left off in the development of a space suit architecture that is modular in design and could be reconfigured prior to launch or during any given mission depending on the tasks or destination. This space suit system architecture and technologies required based on human exploration (EVA) destinations will be discussed, and how these systems should evolve to meet the future exploration EVA needs of the US human space flight program. A series of exercises and analyses provided a strong indication that the Constellation Program space suit architecture, with its maximum reuse of technology and functionality across a range of mission profiles and destinations, is postured to provide a viable solution for future space exploration missions. The destination environmental analysis demonstrates that the modular architecture approach could provide the lowest mass and mission cost for the protection of the crew, given any human mission outside of low-Earth orbit. Additionally, some of the high-level trades presented here provide a review of the environmental and nonenvironmental design drivers that will become increasingly important as humans venture farther from Earth. The presentation of destination environmental data demonstrates a logical clustering of destination design environments that allows a focused approach to technology prioritization, development, and design that will maximize the return on investment, largely independent of any particular design reference mission.

  19. An Object-Oriented Software Architecture for the Explorer-2 Knowledge Management Environment

    OpenAIRE

    Tarabar, David B.; Greenes, Robert A; Slosser, Eric T.

    1989-01-01

    Explorer-2 is a workstation based environment to facilitate knowledge management. It provides consistent access to a broad range of knowledge on the basis of purpose, not type. We have developed a software architecture based on Object-Oriented programming for Explorer-2. We have defined three classes of program objects: Knowledge ViewFrames, Knowledge Resources, and Knowledge Bases. This results in knowledge management at three levels: the screen level, the disk level and the meta-knowledge l...

  20. Explorations in Teaching Sustainable Design: A Studio Experience in Interior Design/Architecture

    Science.gov (United States)

    Gurel, Meltem O.

    2010-01-01

    This article argues that a design studio can be a dynamic medium to explore the creative potential of the complexity of sustainability from its technological to social ends. The study seeks to determine the impact of an interior design/architecture studio experience that was initiated to teach diverse meanings of sustainability and to engage the…

  1. Exploring Architectures for Fast and Easy Development of Immersive Learning Scenarios

    NARCIS (Netherlands)

    Nadolski, Rob; Slootmaker, Aad; Hummel, Hans

    2009-01-01

    Nadolski, R. J., Slootmaker, A., & Hummel, H. G. K. (2009). Exploring Architectures for Fast and Easy Development of Immersive Learning Scenarios. Presentation given at Online Educa. December, 3-4, 2009, Berlin, Germany. [For Powerpoint-version of this presentation. Please see http://www.slideshare.

  2. NASA Langley Research Center Systems Analysis & Concepts Directorate Participation in the Exploration Systems Architecture Study

    Science.gov (United States)

    Keyes, Jennifer; Troutman, Patrick A.; Saucillo, Rudolph; Cirillo, William M.; Cavanaugh, Steve; Stromgren, Chel

    2006-01-01

    The NASA Langley Research Center (LaRC) Systems Analysis & Concepts Directorate (SACD) began studying human exploration missions beyond low Earth orbit (LEO) in the year 1999. This included participation in NASA s Decadal Planning Team (DPT), the NASA Exploration Team (NExT), Space Architect studies and Revolutionary Aerospace Systems Concepts (RASC) architecture studies that were used in formulating the new Vision for Space Exploration. In May of 2005, NASA initiated the Exploration Systems Architecture Study (ESAS). The primary outputs of the ESAS activity were concepts and functional requirements for the Crewed Exploration Vehicle (CEV), its supporting launch vehicle infrastructure and identification of supporting technology requirements and investments. An exploration systems analysis capability has evolved to support these functions in the past and continues to evolve to support anticipated future needs. SACD had significant roles in supporting the ESAS study team. SACD personnel performed the liaison function between the ESAS team and the Shuttle/Station Configuration Options Team (S/SCOT), an agency-wide team charged with using the Space Shuttle to complete the International Space Station (ISS) by the end of Fiscal Year (FY) 2010. The most significant of the identified issues involved the ability of the Space Shuttle system to achieve the desired number of flights in the proposed time frame. SACD with support from the Kennedy Space Center performed analysis showing that, without significant investments in improving the shuttle processing flow, that there was almost no possibility of completing the 28-flight sequence by the end of 2010. SACD performed numerous Lunar Surface Access Module (LSAM) trades to define top level element requirements and establish architecture propellant needs. Configuration trades were conducted to determine the impact of varying degrees of segmentation of the living capabilities of the combined descent stage, ascent stage, and other

  3. The Potential of Subjective Semantic Methods in Exploring the Perception of Architecture

    Directory of Open Access Journals (Sweden)

    Vyrva A.U.,

    2016-01-01

    Full Text Available This research focuses on empirical explorations of psychological features and mechanisms of the percep¬tion of urban architecture and on the specifics of the perception of buildings of various architectural styles. The techniques employed included those of personality and architectural semantic differential and the Value Spectrum technique. Four factors were found to have a significant impact on an individual’s percep¬tion and understanding of architectural space: ‘passive-active’, ‘whole-split’, ‘open-closed’, and ‘expressive’. People tend to attribute more semantic features and values to listed buildings or buildings that bear witness of a certain historical period than to those buildings that look alike and represent a typical example of mass housing. No significant sex differences were found in the individuals’ evaluations of buildings. Consistent quantitative differences were revealed between the images of listed buildings and of mass housing. The paper describes the relevance of various research methods in explorations of architectural images.

  4. Autonomy Software Architecture for LORAX (Life On ice Robotic Antarctic eXplorer)

    Science.gov (United States)

    Jonsson, Ari; McGann, Conor; Pedersen, Liam; Iatauro, Michael; Rajagopalan, Srikanth

    2005-01-01

    LORAX is a robotic astrobiological study of the ice field surrounding the Carapace Nunatak near the Allan Hills in Antarctica. The study culminates in a l00km traverse, sampling the ice at various depths (from surface to 10cm) at over 100 sites to survey microbial ecology and to record environmental parameters. The autonomy requirements from LORAX are shared by many robotic exploration tasks. Consequently, the LORAX autonomy architecture is a general architecture for on-board planning and execution in environments where science return is to be maximized against resource limitations and other constraints.

  5. Avionics Architectures for Exploration: Building a Better Approach for (Human) Spaceflight Avionics

    Science.gov (United States)

    Goforth, Montgomery B.; Ratliff, James E.; Hames, Kevin L.; Vitalpur, Sharada V.

    2014-01-01

    The field of Avionics is advancing far more rapidly in terrestrial applications than in space flight applications. Spaceflight Avionics are not keeping pace with expectations set by terrestrial experience, nor are they keeping pace with the need for increasingly complex automation and crew interfaces as we move beyond Low Earth Orbit. NASA must take advantage of the strides being made by both space-related and terrestrial industries to drive our development and sustaining costs down. This paper describes ongoing efforts by the Avionics Architectures for Exploration (AAE) project chartered by NASA's Advanced Exploration Systems (AES) Program to evaluate new avionic architectures and technologies, provide objective comparisons of them, and mature selected technologies for flight and for use by other AES projects. Results from the AAE project's FY13 efforts are discussed, along with the status of FY14 efforts and future plans.

  6. Architectural Design Space Exploration of an FPGA-based Compressed Sampling Engine

    DEFF Research Database (Denmark)

    El-Sayed, Mohammad; Koch, Peter; Le Moullec, Yannick

    2015-01-01

    We present the architectural design space exploration of a compressed sampling engine for use in a wireless heart-rate monitoring system. We show how parallelism affects execution time at the register transfer level. Furthermore, two example solutions (modified semi-parallel and full......-parallel) selected from the design space are prototyped on an Altera Cyclone III FPGA platform; in both cases the FPGA resource usage is less than 1% and the maximum frequency is 250 MHz....

  7. Earth Orbiting Support Systems for commercial low Earth orbit data relay: Assessing architectures through tradespace exploration

    Science.gov (United States)

    Palermo, Gianluca; Golkar, Alessandro; Gaudenzi, Paolo

    2015-06-01

    As small satellites and Sun Synchronous Earth Observation systems are assuming an increased role in nowadays space activities, including commercial investments, it is of interest to assess how infrastructures could be developed to support the development of such systems and other spacecraft that could benefit from having a data relay service in Low Earth Orbit (LEO), as opposed to traditional Geostationary relays. This paper presents a tradespace exploration study of the architecture of such LEO commercial satellite data relay systems, here defined as Earth Orbiting Support Systems (EOSS). The paper proposes a methodology to formulate architectural decisions for EOSS constellations, and enumerate the corresponding tradespace of feasible architectures. Evaluation metrics are proposed to measure benefits and costs of architectures; lastly, a multicriteria Pareto criterion is used to downselect optimal architectures for subsequent analysis. The methodology is applied to two case studies for a set of 30 and 100 customer-spacecraft respectively, representing potential markets for LEO services in Exploration, Earth Observation, Science, and CubeSats. Pareto analysis shows how increased performance of the constellation is always achieved by an increased node size, as measured by the gain of the communications antenna mounted on EOSS spacecraft. On the other hand, nonlinear trends in optimal orbital altitude, number of satellites per plane, and number of orbital planes, are found in both cases. An upward trend in individual node memory capacity is found, although never exceeding 256 Gbits of onboard memory for both cases that have been considered, assuming the availability of a polar ground station for EOSS data downlink. System architects can use the proposed methodology to identify optimal EOSS constellations for a given service pricing strategy and customer target, thus identifying alternatives for selection by decision makers.

  8. Exploring Heterogeneous NoC Design Space in Heterogeneous GPU-CPU Architectures

    Institute of Scientific and Technical Information of China (English)

    方娟; 姚治成; 冷镇宇; 隋秀峰; 刘思彤

    2015-01-01

    Computer architecture is transiting from the multicore era into the heterogeneous era in which heterogeneous architectures use on-chip networks to access shared resources and how a network is configured will likely have a significant impact on overall performance and power consumption. Recently, heterogeneous network on chip (NoC) has been proposed not only to achieve performance comparable to that of the NoCs with buffered routers but also to reduce buffer cost and energy consumption. However, heterogeneous NoC design for heterogeneous GPU-CPU architectures has not been studied in depth. This paper first evaluates the performance and power consumption of a variety of static hot-potato based heterogeneous NoCs with different buffered and bufferless router placements, which is helpful to explore the design space for heterogeneous GPU-CPU interconnection. Then it proposes Unidirectional Flow Control (UFC), a simple credit-based flow control mechanism for heterogeneous NoC in GPU-CPU architectures to control network congestion. UFC can guarantee that there are always unoccupied entries in buffered routers to receive flits coming from adjacent bufferless routers. Our evaluations show that when compared to hot-potato routing, UFC improves performance by an average of 14.1%with energy increased by an average of 5.3%only.

  9. 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...

  10. Exploring simple assessment methods for lighting quality with architecture and design students

    DEFF Research Database (Denmark)

    Madsen, Merete

    2006-01-01

    Schools of Architecture in Copenhagen and Victoria University of Wellington (New Zealand). The authors explore two approaches to teaching students simple assessment methods that can contribute to making more informed decisions about the luminous environment and its quality. One approach deals with the......Architecture and design students are frequently required to establish suitable lighting conditions for the buildings and spaces they design as part of their studio courses. While lighting design guidelines are avaiilable, students find out quickly, that lighting quality is a complex issue that...... cannot be assessed by simple equations or rules-of-thumb. Balancing the many an often contradictory aspects of energy efficiency and high quality lighting design is a complex undertaking not just for students. The work described in this paper is one result of an academic staff exchange between the...

  11. A Sustainable Architecture for Lunar Resource Prospecting from an EML-based Exploration Platform

    Science.gov (United States)

    Klaus, K.; Post, K.; Lawrence, S. J.

    2012-12-01

    Introduction - We present a point of departure architecture for prospecting for Lunar Resources from an Exploration Platform at the Earth - Moon Lagrange points. Included in our study are launch vehicle, cis-lunar transportation architecture, habitat requirements and utilization, lander/rover concepts and sample return. Different transfer design techniques can be explored by mission designers, testing various propulsive systems, maneuvers, rendezvous, and other in-space and surface operations. Understanding the availability of high and low energy trajectory transfer options opens up the possibility of exploring the human and logistics support mission design space and deriving solutions never before contemplated. For sample return missions from the lunar surface, low-energy transfers could be utilized between EML platform and the surface as well as return of samples to EML-based spacecraft. Human Habitation at the Exploration Platform - Telerobotic and telepresence capabilities are considered by the agency to be "grand challenges" for space technology. While human visits to the lunar surface provide optimal opportunities for field geologic exploration, on-orbit telerobotics may provide attractive early opportunities for geologic exploration, resource prospecting, and other precursor activities in advance of human exploration campaigns and ISRU processing. The Exploration Platform provides a perfect port for a small lander which could be refueled and used for multiple missions including sample return. The EVA and robotic capabilities of the EML Exploration Platform allow the lander to be serviced both internally and externally, based on operational requirements. The placement of the platform at an EML point allows the lander to access any site on the lunar surface, thus providing the global lunar surface access that is commonly understood to be required in order to enable a robust lunar exploration program. Designing the sample return lander for low

  12. Requirements for Designing Life Support System Architectures for Crewed Exploration Missions Beyond Low-Earth Orbit

    Science.gov (United States)

    Howard, David; Perry,Jay; Sargusingh, Miriam; Toomarian, Nikzad

    2016-01-01

    NASA's technology development roadmaps provide guidance to focus technological development on areas that enable crewed exploration missions beyond low-Earth orbit. Specifically, the technology area roadmap on human health, life support and habitation systems describes the need for life support system (LSS) technologies that can improve reliability and in-situ maintainability within a minimally-sized package while enabling a high degree of mission autonomy. To address the needs outlined by the guiding technology area roadmap, NASA's Advanced Exploration Systems (AES) Program has commissioned the Life Support Systems (LSS) Project to lead technology development in the areas of water recovery and management, atmosphere revitalization, and environmental monitoring. A notional exploration LSS architecture derived from the International Space has been developed and serves as the developmental basis for these efforts. Functional requirements and key performance parameters that guide the exploration LSS technology development efforts are presented and discussed. Areas where LSS flight operations aboard the ISS afford lessons learned that are relevant to exploration missions are highlighted.

  13. Advanced Avionics and Processor Systems for a Flexible Space Exploration Architecture

    Science.gov (United States)

    Keys, Andrew S.; Adams, James H.; Smith, Leigh M.; Johnson, Michael A.; Cressler, John D.

    2010-01-01

    The Advanced Avionics and Processor Systems (AAPS) project, formerly known as the Radiation Hardened Electronics for Space Environments (RHESE) project, endeavors to develop advanced avionic and processor technologies anticipated to be used by NASA s currently evolving space exploration architectures. The AAPS project is a part of the Exploration Technology Development Program, which funds an entire suite of technologies that are aimed at enabling NASA s ability to explore beyond low earth orbit. NASA s Marshall Space Flight Center (MSFC) manages the AAPS project. AAPS uses a broad-scoped approach to developing avionic and processor systems. Investment areas include advanced electronic designs and technologies capable of providing environmental hardness, reconfigurable computing techniques, software tools for radiation effects assessment, and radiation environment modeling tools. Near-term emphasis within the multiple AAPS tasks focuses on developing prototype components using semiconductor processes and materials (such as Silicon-Germanium (SiGe)) to enhance a device s tolerance to radiation events and low temperature environments. As the SiGe technology will culminate in a delivered prototype this fiscal year, the project emphasis shifts its focus to developing low-power, high efficiency total processor hardening techniques. In addition to processor development, the project endeavors to demonstrate techniques applicable to reconfigurable computing and partially reconfigurable Field Programmable Gate Arrays (FPGAs). This capability enables avionic architectures the ability to develop FPGA-based, radiation tolerant processor boards that can serve in multiple physical locations throughout the spacecraft and perform multiple functions during the course of the mission. The individual tasks that comprise AAPS are diverse, yet united in the common endeavor to develop electronics capable of operating within the harsh environment of space. Specifically, the AAPS tasks for

  14. 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

  15. A Sustainable, Reliable Mission-Systems Architecture that Supports a System of Systems Approach to Space Exploration

    Science.gov (United States)

    Watson, Steve; Orr, Jim; O'Neil, Graham

    2004-01-01

    A mission-systems architecture based on a highly modular "systems of systems" infrastructure utilizing open-standards hardware and software interfaces as the enabling technology is absolutely essential for an affordable and sustainable space exploration program. This architecture requires (a) robust communication between heterogeneous systems, (b) high reliability, (c) minimal mission-to-mission reconfiguration, (d) affordable development, system integration, and verification of systems, and (e) minimum sustaining engineering. This paper proposes such an architecture. Lessons learned from the space shuttle program are applied to help define and refine the model.

  16. 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.

  17. A Reliable Service-Oriented Architecture for NASA's Mars Exploration Rover Mission

    Science.gov (United States)

    Mak, Ronald; Walton, Joan; Keely, Leslie; Hehner, Dennis; Chan, Louise

    2005-01-01

    The Collaborative Information Portal (CIP) was enterprise software developed jointly by the NASA Ames Research Center and the Jet Propulsion Laboratory (JPL) for NASA's highly successful Mars Exploration Rover (MER) mission. Both MER and CIP have performed far beyond their original expectations. Mission managers and engineers ran CIP inside the mission control room at JPL, and the scientists ran CIP in their laboratories, homes, and offices. All the users connected securely over the Internet. Since the mission ran on Mars time, CIP displayed the current time in various Mars and Earth time zones, and it presented staffing and event schedules with Martian time scales. Users could send and receive broadcast messages, and they could view and download data and image files generated by the rovers' instruments. CIP had a three-tiered, service-oriented architecture (SOA) based on industry standards, including J2EE and web services, and it integrated commercial off-the-shelf software. A user's interactions with the graphical interface of the CIP client application generated web services requests to the CIP middleware. The middleware accessed the back-end data repositories if necessary and returned results for these requests. The client application could make multiple service requests for a single user action and then present a composition of the results. This happened transparently, and many users did not even realize that they were connecting to a server. CIP performed well and was extremely reliable; it attained better than 99% uptime during the course of the mission. In this paper, we present overviews of the MER mission and of CIP. We show how CIP helped to fulfill some of the mission needs and how people used it. We discuss the criteria for choosing its architecture, and we describe how the developers made the software so reliable. CIP's reliability did not come about by chance, but was the result of several key design decisions. We conclude with some of the important

  18. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

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

  19. 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

  20. Exploring business model innovation in professional service firms: Insights from architecture

    OpenAIRE

    Lieftink, B.; Bos-De Vos, M.; Lauche, K.; Smits, A

    2014-01-01

    Business model innovation may be a significant source of competitive advantage and firm performance. New ways of doing business have become increasingly important in the professional service sector. This research specifically focuses on business model innovation by architecture firms, which are suffering from the current financial crisis and changes in the architecture, engineering and construction industry. Architecture firms need to innovate not only their services, but also make more funda...

  1. 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

  2. Leading Praxis: Exploring Educational Leadership through the Lens of Practice Architectures

    Science.gov (United States)

    Wilkinson, Jane; Olin, Anette; Lund, Torbjorn; Ahlberg, Ann; Nyvaller, Monica

    2010-01-01

    In this article we investigate educational leadership as a site of practice, utilising the notion of "practice architectures" as our lens. The latter shifts Etienne Wenger's more individualising notion of 'learning architectures' to a broader study of the systems and organisations that prefigure educational practices and potentially, leading…

  3. 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...

  4. How toExplore Golden Ratio in Architecture and Designing City

    Directory of Open Access Journals (Sweden)

    Wezha Hawez Baiz

    2016-08-01

    Full Text Available In architecture, there are many different standards and rules to design buildings, urban and planning and principles and proportion are the clear limitations among the main standards. Golden ratio or golden section is considered as a clear proportion in the architecturaldesign. Severalacademic researches and studies can befound that talk about the golden ratio. This ratio also can be seen in natural division, arts, music and architecture. It is measured as a standard for the aesthetic and beauty of the architectural appearance. Thepresent paperdiscusses the golden ratio in general, its history that shows first use and understandingsand related to which ancient civilization. Furthermore, it explains the position of the golden ratio in architecture principles. Following that, this paper discoversa number of case studies that designed with this ratio existed around the world. Also, itdemonstratesthat,how it can be applicable in architecture field today? Then there isa summaryof the research inthe conclusion.

  5. 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

  6. 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...

  7. 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...

  8. Exploring multiple feature combination strategies with a recurrent neural network architecture for off-line handwriting recognition

    Science.gov (United States)

    Mioulet, L.; Bideault, G.; Chatelain, C.; Paquet, T.; Brunessaux, S.

    2015-01-01

    The BLSTM-CTC is a novel recurrent neural network architecture that has outperformed previous state of the art algorithms in tasks such as speech recognition or handwriting recognition. It has the ability to process long term dependencies in temporal signals in order to label unsegmented data. This paper describes different ways of combining features using a BLSTM-CTC architecture. Not only do we explore the low level combination (feature space combination) but we also explore high level combination (decoding combination) and mid-level (internal system representation combination). The results are compared on the RIMES word database. Our results show that the low level combination works best, thanks to the powerful data modeling of the LSTM neurons.

  9. Exploring the Applications of Bio-Eco Architecture for Sustainable Design and Construction process

    Directory of Open Access Journals (Sweden)

    M. M. Naguib

    2013-04-01

    Full Text Available It has been commonly noted that the main perception of nature influenced forms isbasically aesthetic while little concern is given to the importance of inspiring from naturein the construction and structural performance of buildings as well as in the naturalecological architectural solutions, thus, this paper will focus on bio-inspired architectureapproach which embraces the eco-friendly practices of sustainable construction, the useof natural materials and the energy conservation by mimicking the natural life.A number of bio-inspired architectural designs will be illustrated presenting acomprehensive analysis of bio-inspired role to be played in developing the concept ofecological sustainable design and construction in contemporary architecture.Building must teach the society with new ecological moral, thus, a better understanding ofbiological morphogenesis can usefully inspire architectural design to resolve challengesthat have already been resolved by nature that will not only help in creating a healthyenvironment but will also produce positive environmental impacts.Bio-Eco Architecture harnesses and replicates the principles found in nature in order tocreate built environment which benefit people and other living creatures as well as safe-guarding the biodiversity; thus, Biomimetics in architecture will help develop a culture ofactive environmental design.

  10. Evolutionary Space Communications Architectures for Human/Robotic Exploration and Science Missions

    Science.gov (United States)

    Bhasin, Kul; Hayden, Jeffrey L.

    2004-01-01

    NASA enterprises have growing needs for an advanced, integrated, communications infrastructure that will satisfy the capabilities needed for multiple human, robotic and scientific missions beyond 2015. Furthermore, the reliable, multipoint infrastructure is required to provide continuous, maximum coverage of areas of concentrated activities, such as around Earth and in the vicinity of the Moon or Mars, with access made available on demand of the human or robotic user. As a first step, the definitions of NASA's future space communications and networking architectures are underway. Architectures that describe the communications and networking needed between the nodal regions consisting of Earth, Moon, Lagrange points, Mars, and the places of interest within the inner and outer solar system have been laid out. These architectures will need the modular flexibility that must be included in the communication and networking technologies to enable the infrastructure to grow in capability with time and to transform from supporting robotic missions in the solar system to supporting human ventures to Mars, Jupiter, Jupiter's moons, and beyond. The protocol-based networking capability seamlessly connects the backbone, access, inter-spacecraft and proximity network elements of the architectures employed in the infrastructure. In this paper, we present the summary of NASA's near and long term needs and capability requirements that were gathered by participative methods. We describe an integrated architecture concept and model that will enable communications for evolutionary robotic and human science missions. We then define the communication nodes, their requirements, and various options to connect them.

  11. 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...

  12. 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...

  13. Prenucleosomes and Active Chromatin

    Science.gov (United States)

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

    2016-01-01

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

  14. Architecture-Level Exploration of Alternative Interconnection Schemes Targeting 3D FPGAs: A Software-Supported Methodology

    Directory of Open Access Journals (Sweden)

    Kostas Siozios

    2008-01-01

    Full Text Available In current reconfigurable architectures, the interconnection structures increasingly contribute more to the delay and power consumption. The demand for increased clock frequencies and logic density (smaller area footprint makes the problem even more important. Three-dimensional (3D architectures are able to alleviate this problem by accommodating a number of functional layers, each of which might be fabricated in different technology. However, the benefits of such integration technology have not been sufficiently explored yet. In this paper, we propose a software-supported methodology for exploring and evaluating alternative interconnection schemes for 3D FPGAs. In order to support the proposed methodology, three new CAD tools were developed (part of the 3D MEANDER Design Framework. During our exploration, we study the impact of vertical interconnection between functional layers in a number of design parameters. More specifically, the average gains in operation frequency, power consumption, and wirelength are 35%, 32%, and 13%, respectively, compared to existing 2D FPGAs with identical logic resources. Also, we achieve higher utilization ratio for the vertical interconnections compared to existing approaches by 8% for designing 3D FPGAs, leading to cheaper and more reliable devices.

  15. Exploring Sustainable Industrial Software System Development : within the Software Architecture Environment

    OpenAIRE

    Stoll, Pia

    2009-01-01

    This thesis describes how sustainable development definitions can be transposed to the software architecture environment for the industrial software system domain. In a case study, sustainable development concerns from three companies are investigated for their influence on the dimensions of sustainable development: economical, environmental, and social sustainability. Classifying the case study’s concerns, in the thesis’s Software Engineering taxonomy, shows that the software development con...

  16. Exploring the Applications of Bio-Eco Architecture for Sustainable Design and Construction process

    OpenAIRE

    M. M. Naguib,M; A. M Hanafi

    2013-01-01

    It has been commonly noted that the main perception of nature influenced forms isbasically aesthetic while little concern is given to the importance of inspiring from naturein the construction and structural performance of buildings as well as in the naturalecological architectural solutions, thus, this paper will focus on bio-inspired architectureapproach which embraces the eco-friendly practices of sustainable construction, the useof natural materials and the energy conservation by mimickin...

  17. Control System Architectures, Technologies and Concepts for Near Term and Future Human Exploration of Space

    Science.gov (United States)

    Boulanger, Richard; Overland, David

    2004-01-01

    Technologies that facilitate the design and control of complex, hybrid, and resource-constrained systems are examined. This paper focuses on design methodologies, and system architectures, not on specific control methods that may be applied to life support subsystems. Honeywell and Boeing have estimated that 60-80Y0 of the effort in developing complex control systems is software development, and only 20-40% is control system development. It has also been shown that large software projects have failure rates of as high as 50-65%. Concepts discussed include the Unified Modeling Language (UML) and design patterns with the goal of creating a self-improving, self-documenting system design process. Successful architectures for control must not only facilitate hardware to software integration, but must also reconcile continuously changing software with much less frequently changing hardware. These architectures rely on software modules or components to facilitate change. Architecting such systems for change leverages the interfaces between these modules or components.

  18. 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...

  19. Adaptive Multiclient Network-on-Chip Memory Core: Hardware Architecture, Software Abstraction Layer, and Application Exploration

    OpenAIRE

    Diana Göhringer; Lukas Meder; Stephan Werner; Oliver Oey; Jürgen Becker; Michael Hübner

    2012-01-01

    This paper presents the hardware architecture and the software abstraction layer of an adaptive multiclient Network-on-Chip (NoC) memory core. The memory core supports the flexibility of a heterogeneous FPGA-based runtime adaptive multiprocessor system called RAMPSoC. The processing elements, also called clients, can access the memory core via the Network-on-Chip (NoC). The memory core supports a dynamic mapping of an address space for the different clients as well as different data transfer ...

  20. Outlook of possible European contributions to future exploration scenarios and architectures

    Science.gov (United States)

    Perino, M. A.; Fenoglio, F.; Pelle, S.; Couzin, P.; Thaeter, J.; Eilingsfeld, F.; Hufenbach, B.; Bergamasco, A.

    2013-07-01

    Building upon the important experience acquired with the development of the International Space Station, the major spacefaring countries are working within the International Space Exploration Coordination Group (ISECG) at the definition of a coordinated framework for expanding the human presence beyond the Low Earth Orbit, the Global Exploration Roadmap (GER). The GER defines a long-range strategy for global exploration and include three major elements. Common goals of ISECG participating agencies for space exploration. Notional mission scenarios which are technically feasible and programmatically implementable. Two mission scenarios were defined in the 1st iteration of the GER: the "Asteroid Next" and the "Moon Next" mission scenarios. Identification of near-term opportunities for coordination and cooperation related to e.g. the development of technologies, the implementation of robotic missions to destination of interest for closing strategic knowledge gaps which need to be addressed prior to human missions as well as the utilization of ISS for demonstration of exploration enabling capabilities. In 2009 two studies have been awarded by ESA to Industrial Teams led by Thales Alenia Space—Italy and by Astrium—Germany to define, analyze and assess optional European scenarios for future human spaceflight and exploration activities, and to derive the required capabilities for the investigated timeframe until the year 2033. Work on the European scenarios has been aligned with and informed by the international work on the GER. A conceptual design of different Building Block Elements, representing critical contributions to international Design Reference Missions (DRM's) included in the ISECG GER, has been performed and analyzed with respect to programmatic risks, budgets and required technologies. Key driving requirements for the analyzed Building Block elements have been derived from the international DRM's included in the GER. The interim outcomes of the human

  1. Assertion-Based Design Exploration of DVS in Network Processor Architectures

    CERN Document Server

    Yu, Jia; Chen, Xi; Hsieh, Harry; Yang, Jun; Balarin, Felice

    2011-01-01

    With the scaling of technology and higher requirements on performance and functionality, power dissipation is becoming one of the major design considerations in the development of network processors. In this paper, we use an assertion-based methodology for system-level power/performance analysis to study two dynamic voltage scaling (DVS) techniques, traffic-based DVS and execution-based DVS, in a network processor model. Using the automatically generated distribution analyzers, we analyze the power and performance distributions and study their trade-offs for the two DVS policies with different parameter settings such as threshold values and window sizes. We discuss the optimal configurations of the two DVS policies under different design requirements. By a set of experiments, we show that the assertion-based trace analysis methodology is an efficient tool that can help a designer easily compare and study optimal architectural configurations in a large design space.

  2. Hierarchical video surveillance architecture: a chassis for video big data analytics and exploration

    Science.gov (United States)

    Ajiboye, Sola O.; Birch, Philip; Chatwin, Christopher; Young, Rupert

    2015-03-01

    There is increasing reliance on video surveillance systems for systematic derivation, analysis and interpretation of the data needed for predicting, planning, evaluating and implementing public safety. This is evident from the massive number of surveillance cameras deployed across public locations. For example, in July 2013, the British Security Industry Association (BSIA) reported that over 4 million CCTV cameras had been installed in Britain alone. The BSIA also reveal that only 1.5% of these are state owned. In this paper, we propose a framework that allows access to data from privately owned cameras, with the aim of increasing the efficiency and accuracy of public safety planning, security activities, and decision support systems that are based on video integrated surveillance systems. The accuracy of results obtained from government-owned public safety infrastructure would improve greatly if privately owned surveillance systems `expose' relevant video-generated metadata events, such as triggered alerts and also permit query of a metadata repository. Subsequently, a police officer, for example, with an appropriate level of system permission can query unified video systems across a large geographical area such as a city or a country to predict the location of an interesting entity, such as a pedestrian or a vehicle. This becomes possible with our proposed novel hierarchical architecture, the Fused Video Surveillance Architecture (FVSA). At the high level, FVSA comprises of a hardware framework that is supported by a multi-layer abstraction software interface. It presents video surveillance systems as an adapted computational grid of intelligent services, which is integration-enabled to communicate with other compatible systems in the Internet of Things (IoT).

  3. 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.

  4. 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.

  5. 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,…

  6. 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

  7. Phenotypic and genotypic data integration and exploration through a web-service architecture

    Directory of Open Access Journals (Sweden)

    Bellazzi Riccardo

    2009-10-01

    Full Text Available Abstract Background Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in particular studies aimed at the analysis of complex traits, which require the definition of multifaceted phenotypes and the integration genotypic information to discover the most prevalent diseases, is a paradigmatic goal of Biomedical Informatics. This paper describes the use of Information Technology methods and tools to develop a system for the management, inspection and integration of phenotypic and genotypic data. Results We present the design and architecture of the Phenotype Miner, a software system able to flexibly manage phenotypic information, and its extended functionalities to retrieve genotype information from external repositories and to relate it to phenotypic data. For this purpose we developed a module to allow customized data upload by the user and a SOAP-based communications layer to retrieve data from existing biomedical knowledge management tools. In this paper we also demonstrate the system functionality by an example application of the system in which we analyze two related genomic datasets. Conclusion In this paper we show how a comprehensive, integrated and automated workbench for genotype and phenotype integration can facilitate and improve the hypothesis generation process underlying modern genetic studies.

  8. 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.

  9. Hyper-interspersed NANO/MEMS - Architecture design for new concepts in miniature robotics for space exploration

    Science.gov (United States)

    Santoli, Salvatore

    1999-05-01

    Launch weight and volume requirements are substantially decreased by reduction of probe size in exploration mission systems, as mass and volume both scale as the third power of system size. Accordingly, the already quite developed MEMS (Micro Electro Mechanical System) technology, that offers low cost, small, light weight, and increasingly reliable devices through durability and redundancy, is strongly attractive as a near-term technology for significantly reducing the cost to launch and operate space systems. It is shown that the final goal of MEMS technology, i.e. the merging through solid state microdcvices of the functions of sensing, computation, communication and actuation, can lead to a new, biomimetic kind of miniature robotics, particularly suitable for planetary exploration, through molecular mono- electronics/MEMS integration jointly with a hyper-interspersed architecture made up of autonomous units embodying sensors, information processors and actuators. The problem tackled here concerns the basic design of such miniature robots, from some μm to insect size, featuring finely structured intelligent autonomous parts as smart skins, sensory and manipulating members working on the analogue external reality and communicating with their inner molecular level nondiscrete pseudo-analogue information processing networks. The (mesoscopic network)/MEMS units are shown to embody a quantum mechanical/macroscopic world connection, in which the nondiscrete molecular devices allow the automaton parts to perform very complex, fast information processing operations as metaphores of bionic functions like learning, attention, and decision making under uncertain conditions, this last due to the stochasticity inherent in the quantum network. Flexible architectures instead of von Neumann type rigid architectures in addition to hyper-interspersion of autonomous units can be realized through such nano/MEMS devices, and the μm — cm size of the whole robots and their organs

  10. 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.

  11. Galaxy Evolution Spectroscopic Explorer (GESE): Science Rationale, Optical Design, and Telescope Architecture

    Science.gov (United States)

    Heap, Sara R.; Gong, Qian; Hull, Tony; Purves, Lloyd

    2014-01-01

    One of the key goals of NASA’s astrophysics program is to answer the question: How did galaxies evolve into the spiral, elliptical, and irregular galaxies that we see today? We describe a space mission concept called Galaxy Evolution Spectroscopic Explorer (GESE) to help address this question by making a large ultraviolet spectroscopic survey of galaxies at a redshift, z approximately 1 (look-back time of approximately 8 billion years). GESE is a 1.5-m space telescope with an near-ultraviolet (NUV) multi-object slit spectrograph covering the spectral range, 0.2-0.4 micrometers (0.1-0.2 micrometers as emitted by galaxies at a redshift, z approximately 1) at a spectral resolution of delta lambda=6 A.

  12. Inter-organizational design: exploring the relationship between formal architecture and ICT investments

    Science.gov (United States)

    Iubatti, Daniela; Masciarelli, Francesca; Simboli, Alberto

    This chapter aims to explore how the information-processing capabilities that emerge from a network structure affect the diffusion of innovation in a multidivisional organization. In particular, this study analyzes the role of firm investments in ICT to facilitate communication and knowledge diffusion. Using a qualitative approach, we investigate the behavior of an Italian multinational firm, Engineering S.p.A., analyzing our data using a content analysis procedure. Our results show the limited role of ICT in favoring knowledge exchange both inside and outside the firm's divisions: traditional communication patterns are generally preferred over the use of technologies for information sharing. Additionally, we find that key individuals who play a central role in the firm's communication network are unable to use ICTs for knowledge transfer. We conclude that this is the result of a strategic decision to keep top management practically unchanged since the firm was established. Therefore, key individuals act as filters to knowledge flows. Knowledge, in particular tacit knowledge, is transferred from key individuals to other actors through face-to-face contacts, thereby creating a diseconomy for the organization.

  13. Conceptual Design and Architecture of Mars Exploration Rover (MER) for Seismic Experiments Over Martian Surfaces

    Science.gov (United States)

    Garg, Akshay; Singh, Amit

    2012-07-01

    Keywords: MER, Mars, Rover, Seismometer Mars has been a subject of human interest for exploration missions for quite some time now. Both rover as well as orbiter missions have been employed to suit mission objectives. Rovers have been preferentially deployed for close range reconnaissance and detailed experimentation with highest accuracy. However, it is essential to strike a balance between the chosen science objectives and the rover operations as a whole. The objective of this proposed mechanism is to design a vehicle (MER) to carry out seismic studies over Martian surface. The conceptual design consists of three units i.e. Mother Rover as a Surrogate (Carrier) and Baby Rovers (two) as seeders for several MEMS-based accelerometer / seismometer units (Nodes). Mother Rover can carry these Baby Rovers, having individual power supply with solar cells and with individual data transmission capabilities, to suitable sites such as Chasma associated with Valles Marineris, Craters or Sand Dunes. Mother rover deploys these rovers in two opposite direction and these rovers follow a triangulation pattern to study shock waves generated through firing tungsten carbide shells into the ground. Till the time of active experiments Mother Rover would act as a guiding unit to control spatial spread of detection instruments. After active shock experimentation, the babies can still act as passive seismometer units to study and record passive shocks from thermal quakes, impact cratering & landslides. Further other experiments / payloads (XPS / GAP / APXS) can also be carried by Mother Rover. Secondary power system consisting of batteries can also be utilized for carrying out further experiments over shallow valley surfaces. The whole arrangement is conceptually expected to increase the accuracy of measurements (through concurrent readings) and prolong life cycle of overall experimentation. The proposed rover can be customised according to the associated scientific objectives and further

  14. Exploring Venus with high-altitude balloons: Science objectives and mission architectures

    Science.gov (United States)

    Baines, Kevin; Limaye, Sanjay; Zahnle, Kevin; Atreya, Sushil K.

    Following the trailblazing flights of the 1985 twin Soviet VEGA balloons, missions to fly in the high atmosphere of Venus near 55 km altitude have been proposed to both NASA's Discovery Program and ESA's Cosmic Vision. Such missions would address a variety of fundamental science issues highlighted in a variety of high-level NASA-authorized science documents in recent years, including the Decadal Study, various NASA roadmaps, and recommendations coming out of the Venus Exploration Analysis Group (VEXAG). Such missions would in particular address key questions of Venus's origin, evolution, and current state, including detailed measurements of (1) trace gases associated with Venus's active photoand thermo-chemistry and (2) measurements of vertical motions and local temperature which characterize convective and wave processes. As an example of what can be done with a small mission (less than 500M US dollars), the Venus Aerostatic-Lift Observatories for in-situ Research (VALOR) Discovery mission will be discussed. This mission would fly twin balloon-borne aerostats over temperate and polar latitudes, sampling rare gases, chemicals and dynamics in two distinct latitude regions for several days. A variety of scenarios for the origin, formation, and evolution of Venus would be tested by sampling all the noble gases and their isotopes, especially the heaviest elements never reliably measured previously: xenon and krypton. Riding the gravity and planetary waves of Venus, the VALOR balloons would sample the chemistry, meteorology and dynamics of Venus's sulfur-cloud region. Tracked by an array of Earth-based telescopes, zonal, meridional, and vertical winds would be measured with unprecedented precision. Such measurements would help to develop a fundamental understanding of (1) the circulation of Venus, especially its enigmatic super-rotation, (2) the nature of Venus's sulfur cycle, key to Venus's current climate, and (3) how Venus formed and evolved over the aeons.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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...

  5. 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

  6. 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....

  7. 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)

  8. Architecture-Level Exploration of Alternative Interconnection Schemes Targeting 3D FPGAs: A Software-Supported Methodology

    OpenAIRE

    Dimitrios Soudris; Alexandros Bartzas; Kostas Siozios

    2008-01-01

    In current reconfigurable architectures, the interconnection structures increasingly contribute more to the delay and power consumption. The demand for increased clock frequencies and logic density (smaller area footprint) makes the problem even more important. Three-dimensional (3D) architectures are able to alleviate this problem by accommodating a number of functional layers, each of which might be fabricated in different technology. However, the benefits of such integration technology hav...

  9. 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.

  10. 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

  11. Exploration

    Science.gov (United States)

    Wilburn, D.R.; Porter, K.E.

    1999-01-01

    This summary of international nonfuel mineral exploration activities for 1998 draws on available data from literature, industry and US Geological Survey (USGS) specialists. Data on exploration budgets by region and commodity are reported, significant mineral discoveries and exploration target areas are identified and government programs affecting the mineral exploration industry are discussed. Inferences and observations on mineral industry direction are drawn from these data and discussions.

  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. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  17. Preliminary Exploration of Next Generation Network Architecture%下一代网络体系结构初探

    Institute of Scientific and Technical Information of China (English)

    张炜; 陈晨

    2013-01-01

    This paper introduces the developement history and current situation of the Internet architecture. Then it makes a de scription and comparison of the research direction of the next internet architecture.At last it proposes a metheod based on net work service model to design the next internet architecture and also gives the model and the requirement. Re sult shows that Ipv6 maybe the core of the next internet architecture .%该文首先介绍了互联网体系结构的发展历程和现状,其次对下一代互联网体系结构的研究方向进行了阐述和比较.最后提出基于网络使用模型这一方式来进行互联网体系结构的设计,并给出了模型和要求,得出IPv6可能是下一代互联网体系结构的核心.

  18. 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

  19. Using Computer Modelling and Virtual Reality to Explore the Ideological Dimensions of Thule Whalebone Architecture in Arctic Canada

    Directory of Open Access Journals (Sweden)

    Peter C. Dawson

    2005-09-01

    Full Text Available Arctic archaeologists have long suspected that the whalebones used to construct semi-subterranean winter houses by Thule culture peoples were symbolically resonant. These assumptions are based on observations of the non-utilitarian use of jaw bones and crania in Thule house ruins, and ethnographic descriptions of architectural symbolism relating to the whale hunt in Historic Alaskan Inupiat houses. In this paper, we use a 3-dimensional computer reconstruction of a semi-subterranean whalebone house to search for visual expressions of whaling-related ritual in Thule architecture. Results suggest that the whalebone superstructure may have been designed to evoke important themes when viewed from specific locations within the house, and under different lighting conditions. These themes, which appear in Inupiat myths and stories, involve the belief that women transform houses into living whales during the time of the hunt.

  20. 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

  1. 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.

  2. 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 ...

  3. 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

  4. 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...

  5. highFAR建筑设计生成方法探索%Exploration of Generative Method Based on MAS for Architectural Design: highFAR

    Institute of Scientific and Technical Information of China (English)

    李飚; 钱敬平

    2011-01-01

    highFAR生成工具是东南大学建筑学院2007年毕业班建筑生成设计研究组的生成设计教学系列探索之一.通过highFAR基于多智能体系统数字生成工具的程序开发研究,尝试高层建筑高密度布局的新途径,为同类建筑应用程序开发提供必要的算法参考.%This paper presents one of the teaching explorations of Generative Design Group ( 2007 ) in School of Architecture. Southeast University. Based on the multi-agent systems and computer programming, the group explores a new method of layout of high-rise building with high-density by digital too! named highFAR. HighFAR provides necessary references tor the development of congener architectural application software.

  6. 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...

  7. Exploration

    International Nuclear Information System (INIS)

    Oil and gas exploration is a unique kind of business. Businesses providing a vast and ever-changing panoply of products to markets are a focus of several disciplines' energetic study and analysis. The product inventory problem is robust, pertinent, and meaningful, and it merits the voluminous and protracted attention received from keen business practitioners. Prototypical business practitioners, be they trained by years of business hurly-burly, or sophisticated MBAs with arrays of mathematical algorithms and computers, are not normally prepared, however, to recognize the unique nature of exploration's inventories. Put together such a business practitioner with an explorationist and misunderstandings, hidden and open, are inevitable and predictably rife. The first purpose of this paper is to articulate the inherited inventory handling paradigms of business practitioners in relation to exploration's inventories. To do so, standard pedagogy in business administration is used and a case study of an exploration venture is presented. A second purpose is to show the burdens that the misunderstandings create. The result is not just business plans that go awry, but public policies that have effects opposite from those intended

  8. 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...

  9. 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....

  10. 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...

  11. 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...

  12. 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.

  13. 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.

  14. 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...

  15. 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.

  16. 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.

  17. 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...

  18. 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...

  19. Exploring the future role of Asia utilizing a Scenario Matrix Architecture and Shared Socio-economic Pathways

    International Nuclear Information System (INIS)

    We explore the implications that alternative pathways for human population and economic development have for the role of Asia in reference no-climate-policy scenarios and scenarios in which climate forcing is limited. We consider three different pathways of socioeconomic development, which we refer to as Shared Socio-economic Pathways (SSPs) and four different levels of limitation on climate forcing, which we refer to as Shared Climate Policy Assumptions (SPAs). SSPs are differentiated by population and economic growth assumptions, while SPAs are differentiated on the level of radiative forcing in the year 2100. Regardless of the scenarios we examined Asia plays a central role in shaping the world's future with nearly half of the world's people and more than half of the world's economic activity and energy consumption. The future of Asia and the world are dramatically different across the various combinations of SSPs and SPAs. High population worlds place significant stress on Asian resources and ecosystems. In high population SSPs the poorest members of the population face high energy and food prices and the more stringent the level of emissions mitigation, the more stress poor populations experience, though the more stringent the emissions mitigation, the larger the area of unmanaged ecosystems that are preserved. - Highlights: ► We explore the implications of alternative population and economic pathways for the role of Asia. ► High population world places significant stress on Asian resources and ecosystems. ► In high population world, the poorest members of the population face high energy and food prices. ► The greater level of emissions mitigation, the more stress poor people experience. ► The greater the emissions mitigation, the larger the area of unmanaged ecosystems preserved.

  20. 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)

  1. 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

  2. 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...

  3. Live visualization of chromatin dynamics with fluorescent TALEs.

    Science.gov (United States)

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

    2013-11-01

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

  4. 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...

  5. Computational strategies to address chromatin structure problems.

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-01-01

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

  6. 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

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Aguilar, Carlos A.; Craighead, Harold G.

    2013-10-01

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

  10. 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....

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

    OpenAIRE

    Pudji Pratitis Wismantara

    2012-01-01

    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...

  12. 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.

  13. 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.

  14. 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.

  15. 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

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

    Science.gov (United States)

    Luque, Antoni; Ozer, Gungor; Schlick, Tamar

    2016-06-01

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

  19. 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

  20. 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.

  1. Time·Space·Architecture

    Institute of Scientific and Technical Information of China (English)

    QI Kang

    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.

  2. Architectural Prototyping in Industrial Practice

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak; Hansen, Klaus Marius

    2008-01-01

    Architectural prototyping is the process of using executable code to investigate stakeholders’ software architecture concerns with respect to a system under development. Previous work has established this as a useful and cost-effective way of exploration and learning of the design space of a system......, in addressing issues regarding quality attributes, in addressing architectural risks, and in addressing the problem of knowledge transfer and conformance. Little work has been reported so far on the actual industrial use of architectural prototyping. In this paper, we report from an ethnographical...... study and focus group involving architects from four companies in which we have focused on architectural prototypes. Our findings conclude that architectural prototypes play an important role in resolving problems experimentally, but less so in exploring alternative solutions. Furthermore, architectural...

  3. 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...

  4. 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...

  5. 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...

  6. 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.

  7. 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…

  8. 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.

  9. 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

  10. 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)

  11. 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.

  12. Neutron-scattering studies of chromatin

    International Nuclear Information System (INIS)

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

  13. 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.

  14. 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...

  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. 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...

  20. 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...

  1. 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

  2. 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.

  3. 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...

  4. 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

  5. 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...

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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 ...

  11. 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...

  12. 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,

  13. 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...

  14. 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

  15. Exploration of a Capability-Focused Aerospace System of Systems Architecture Alternative with Bilayer Design Space, Based on RST-SOM Algorithmic Methods

    OpenAIRE

    2014-01-01

    In defense related programs, the use of capability-based analysis, design, and acquisition has been significant. In order to confront one of the most challenging features of a huge design space in capability based analysis (CBA), a literature review of design space exploration was first examined. Then, in the process of an aerospace system of systems design space exploration, a bilayer mapping method was put forward, based on the existing experimental and operating data. Finally, the feasibil...

  16. 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...

  17. Molecular rheology of branched polymers: Decoding and exploring the role of architectural dispersity through a synergy of anionic synthesis, interaction chromatography, rheometry and modeling

    KAUST Repository

    Van Ruymbeke, Evelyne

    2014-01-01

    An emerging challenge in polymer physics is the quantitative understanding of the influence of a macromolecular architecture (i.e., branching) on the rheological response of entangled complex polymers. Recent investigations of the rheology of well-defined architecturally complex polymers have determined the composition in the molecular structure and identified the role of side-products in the measured samples. The combination of different characterization techniques, experimental and/or theoretical, represents the current state-of-the-art. Here we review this interdisciplinary approach to molecular rheology of complex polymers, and show the importance of confronting these different tools for ensuring an accurate characterization of a given polymeric sample. We use statistical tools in order to relate the information available from the synthesis protocols of a sample and its experimental molar mass distribution (typically obtained from size exclusion chromatography), and hence obtain precise information about its structural composition, i.e. enhance the existing sensitivity limit. We critically discuss the use of linear rheology as a reliable quantitative characterization tool, along with the recently developed temperature gradient interaction chromatography. The latter, which has emerged as an indispensable characterization tool for branched architectures, offers unprecedented sensitivity in detecting the presence of different molecular structures in a sample. Combining these techniques is imperative in order to quantify the molecular composition of a polymer and its consequences on the macroscopic properties. We validate this approach by means of a new model asymmetric comb polymer which was synthesized anionically. It was thoroughly characterized and its rheology was carefully analyzed. The main result is that the rheological signal reveals fine molecular details, which must be taken into account to fully elucidate the viscoelastic response of entangled branched

  18. 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

  19. Diversity in the organization of centromeric chromatin.

    Science.gov (United States)

    Steiner, Florian A; Henikoff, Steven

    2015-04-01

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

  20. 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

  1. An architectural approach to level design

    CERN Document Server

    Totten, Christopher W

    2014-01-01

    Explore Level Design through the Lens of Architectural and Spatial Experience TheoryWritten by a game developer and professor trained in architecture, An Architectural Approach to Level Design is one of the first books to integrate architectural and spatial design theory with the field of level design. It explores the principles of level design through the context and history of architecture, providing information useful to both academics and game development professionals.Understand Spatial Design Principles for Game Levels in 2D, 3D, and Multiplayer ApplicationsThe book presents architectura

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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 ...

  8. 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...

  9. 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...

  10. 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...

  11. 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)

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

    Directory of Open Access Journals (Sweden)

    Justin W Walley

    2008-12-01

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

  13. PTEN Interacts with Histone H1 and Controls Chromatin Condensation

    Directory of Open Access Journals (Sweden)

    Zhu Hong Chen

    2014-09-01

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

  14. 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.

  15. 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

  16. 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...

  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. 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...

  19. 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.

  20. 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)

  1. 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...

  2. 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....

  3. 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

  4. 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.

  5. 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...

  6. Hydrogen peroxide mediates higher order chromatin degradation.

    Science.gov (United States)

    Bai, H; Konat, G W

    2003-01-01

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

  7. 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...

  8. 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.

  9. Lived modernism: when architecture transforms

    OpenAIRE

    le Roux, Hannah

    2014-01-01

    Lived modernism explores the moments when architecture changes. Inspired by my first hand experience of the contemporary reuse, in Africa and beyond, of spaces constructed during modernism, specifically from 1945 to 1975, it works to extract approaches and concepts applicable to the contemporary practice of architecture. Modernist space, despite its deterministic intentions, becomes open at the moment of appropriation by emergent social practices. This lived modernism can find an analogy in d...

  10. 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

  11. Flightless I (Drosophila) homolog facilitates chromatin accessibility of the estrogen receptor α target genes in MCF-7 breast cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kwang Won, E-mail: kwjeong@gachon.ac.kr

    2014-04-04

    Highlights: • H3K4me3 and Pol II binding at TFF1 promoter were reduced in FLII-depleted MCF-7 cells. • FLII is required for chromatin accessibility of the enhancer of ERalpha target genes. • Depletion of FLII causes inhibition of proliferation of MCF-7 cells. - Abstract: The coordinated activities of multiple protein complexes are essential to the remodeling of chromatin structure and for the recruitment of RNA polymerase II (Pol II) to the promoter in order to facilitate the initiation of transcription in nuclear receptor-mediated gene expression. Flightless I (Drosophila) homolog (FLII), a nuclear receptor coactivator, is associated with the SWI/SNF-chromatin remodeling complex during estrogen receptor (ER)α-mediated transcription. However, the function of FLII in estrogen-induced chromatin opening has not been fully explored. Here, we show that FLII plays a critical role in establishing active histone modification marks and generating the open chromatin structure of ERα target genes. We observed that the enhancer regions of ERα target genes are heavily occupied by FLII, and histone H3K4me3 and Pol II binding induced by estrogen are decreased in FLII-depleted MCF-7 cells. Furthermore, formaldehyde-assisted isolation of regulatory elements (FAIRE)-quantitative polymerase chain reaction (qPCR) experiments showed that depletion of FLII resulted in reduced chromatin accessibility of multiple ERα target genes. These data suggest FLII as a key regulator of ERα-mediated transcription through its role in regulating chromatin accessibility for the binding of RNA Polymerase II and possibly other transcriptional coactivators.

  12. Flightless I (Drosophila) homolog facilitates chromatin accessibility of the estrogen receptor α target genes in MCF-7 breast cancer cells

    International Nuclear Information System (INIS)

    Highlights: • H3K4me3 and Pol II binding at TFF1 promoter were reduced in FLII-depleted MCF-7 cells. • FLII is required for chromatin accessibility of the enhancer of ERalpha target genes. • Depletion of FLII causes inhibition of proliferation of MCF-7 cells. - Abstract: The coordinated activities of multiple protein complexes are essential to the remodeling of chromatin structure and for the recruitment of RNA polymerase II (Pol II) to the promoter in order to facilitate the initiation of transcription in nuclear receptor-mediated gene expression. Flightless I (Drosophila) homolog (FLII), a nuclear receptor coactivator, is associated with the SWI/SNF-chromatin remodeling complex during estrogen receptor (ER)α-mediated transcription. However, the function of FLII in estrogen-induced chromatin opening has not been fully explored. Here, we show that FLII plays a critical role in establishing active histone modification marks and generating the open chromatin structure of ERα target genes. We observed that the enhancer regions of ERα target genes are heavily occupied by FLII, and histone H3K4me3 and Pol II binding induced by estrogen are decreased in FLII-depleted MCF-7 cells. Furthermore, formaldehyde-assisted isolation of regulatory elements (FAIRE)-quantitative polymerase chain reaction (qPCR) experiments showed that depletion of FLII resulted in reduced chromatin accessibility of multiple ERα target genes. These data suggest FLII as a key regulator of ERα-mediated transcription through its role in regulating chromatin accessibility for the binding of RNA Polymerase II and possibly other transcriptional coactivators

  13. Architectural Exploration and Design of Time-Interleaved SAR Arrays for Low-Power and High Speed A/D Converters

    Science.gov (United States)

    Saponara, Sergio; Nuzzo, Pierluigi; Nani, Claudio; van der Plas, Geert; Fanucci, Luca

    Time-interleaved (TI) analog-to-digital converters (ADCs) are frequently advocated as a power-efficient solution to realize the high sampling rates required in single-chip transceivers for the emerging communication schemes: ultra-wideband, fast serial links, cognitive-radio and software-defined radio. However, the combined effects of multiple distortion sources due to channel mismatches (bandwidth, offset, gain and timing) severely affect system performance and power consumption of a TI ADC and need to be accounted for since the earlier design phases. In this paper, system-level design of TI ADCs is addressed through a platform-based methodology, enabling effective investigation of different speed/resolution scenarios as well as the impact of parallelism on accuracy, yield, sampling-rate, area and power consumption. Design space exploration of a TI successive approximation ADC is performed top-down via Monte Carlo simulations, by exploiting behavioral models built bottom-up after characterizing feasible implementations of the main building blocks in a 90-nm 1-V CMOS process. As a result, two implementations of the TI ADC are proposed that are capable to provide an outstanding figure-of-merit below 0.15pJ/conversion-step.

  14. 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

  15. 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.

  16. 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...

  17. 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...

  18. 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...

  19. 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

  20. 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...

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  2. 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.

  3. 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

  4. 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

  5. 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...

  6. Dance Architecture Spatiality

    OpenAIRE

    Renard, Johanna

    2014-01-01

    L’ouvrage rassemble les traces visuelles et textuelles du programme intensif européen DAS (Dance Architecture Spatiality), coordonné par Frédérique Villemur, qui s’est déroulé en 2012 à Athènes, sur les collines face à l’Acropole. Guidés par Patrice Barthès, chorégraphe en résidence à l’ENSAM de Montpellier, une vingtaine d’étudiants en architecture, esthétique et design ont explorés les interactions entre le geste dansé et les temporalités architecturales et paysagères. Accueilli par l’Isado...

  7. 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

  8. 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...

  9. Aerobot Autonomy Architecture

    Science.gov (United States)

    Elfes, Alberto; Hall, Jeffery L.; Kulczycki, Eric A.; Cameron, Jonathan M.; Morfopoulos, Arin C.; Clouse, Daniel S.; Montgomery, James F.; Ansar, Adnan I.; Machuzak, Richard J.

    2009-01-01

    An architecture for autonomous operation of an aerobot (i.e., a robotic blimp) to be used in scientific exploration of planets and moons in the Solar system with an atmosphere (such as Titan and Venus) is undergoing development. This architecture is also applicable to autonomous airships that could be flown in the terrestrial atmosphere for scientific exploration, military reconnaissance and surveillance, and as radio-communication relay stations in disaster areas. The architecture was conceived to satisfy requirements to perform the following functions: a) Vehicle safing, that is, ensuring the integrity of the aerobot during its entire mission, including during extended communication blackouts. b) Accurate and robust autonomous flight control during operation in diverse modes, including launch, deployment of scientific instruments, long traverses, hovering or station-keeping, and maneuvers for touch-and-go surface sampling. c) Mapping and self-localization in the absence of a global positioning system. d) Advanced recognition of hazards and targets in conjunction with tracking of, and visual servoing toward, targets, all to enable the aerobot to detect and avoid atmospheric and topographic hazards and to identify, home in on, and hover over predefined terrain features or other targets of scientific interest. The architecture is an integrated combination of systems for accurate and robust vehicle and flight trajectory control; estimation of the state of the aerobot; perception-based detection and avoidance of hazards; monitoring of the integrity and functionality ("health") of the aerobot; reflexive safing actions; multi-modal localization and mapping; autonomous planning and execution of scientific observations; and long-range planning and monitoring of the mission of the aerobot. The prototype JPL aerobot (see figure) has been tested extensively in various areas in the California Mojave desert.

  10. 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...

  11. 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...

  12. 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.

  13. 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

  14. 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....

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. Product architecture, modularity and product market internationalisation

    OpenAIRE

    Burton, Nicholas; Nyuur, Richard

    2015-01-01

    The product modularity literature has burgeoned in recent years. However, there has been limited focus on how product modularity may potentially facilitate product market internationalisation strategies. The focus of this conceptual paper is in exploring whether open and modular product architectures may be associated with increasing product market internationalisation, and whether therefore the relationship between product architecture and product market internationalisation can be hypothesi...

  6. Avionics System Architecture for NASA Orion Vehicle

    Science.gov (United States)

    Baggerman, Clint

    2010-01-01

    This viewgraph presentation reviews the Orion Crew Exploration Vehicle avionics architecture. The contents include: 1) What is Orion?; 2) Orion Concept of Operations; 3) Orion Subsystems; 4) Orion Avionics Architecture; 5) Orion Avionics-Network; 6) Orion Network Unification; 7) Orion Avionics-Integrity; 8) Orion Avionics-Partitioning; and 9) Orion Avionics-Redundancy.

  7. 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 ...

  8. Increased exchange rate of histone H1 on chromatin by exogenous myogenin expression

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    To explore the molecular mechanism of chromatin remodeling involved in the regulation of transcriptionalactivation of specific genes by a myogenic regulatory factor Myogenin, we used NIH3T3 fibroblasts with astably integrated H1.1-GFP fusion protein to monitor histone H1 movement directly by fluorescence recov-ery after photobleaching (FRAP) in living cells. The observation from FRAP experiments with myogenintransfected fibroblasts showed that the exchange rate of histone H1 in chromatin was obviously increased,indicating that forced expression of exogenous Myogenin can induce chromatin remodeling. The hyper-acetylation of histones H3 and H4 from myogenin transfected fibroblasts was detected by triton-acid-urea(TAU)/SDS (2-D) electrophoresis and Western blot with specific antibodies against acetylated N-termini ofhistones H3 and H4. RT-PCR analysis indicated that the nAChR α-subunit gene was expressed in the trans-fected fibroblasts. These results suggest that the expression of exogenous Myogenin can induce chromatinremodeling and activate the transcription of Myogenin-targeted gene in non-muscle cells.

  9. Memory architecture exploration for programmable embedded systems

    CERN Document Server

    Grun, Peter; Nicolau, Alexandru

    2007-01-01

    From the reviews:""This book considers the opportunities and discusses the challenges in designing embedded memory system … . The book is well organized, up-to-date and easy to follow for self-study. … In general the book has high educational value. … The book is really interesting both for specialists in the topic, and graduate students … . The reviewer rates this book highly and recommends it to graduate students, researchers and practicing engineers in embedded systems design. Overall, the authors have done a commendable job … ."" (Mile Stojcev, Microelectronics Reliability, Vol. 47, 2004)

  10. Radio Wavelength Observatories within the Exploration Architecture

    CERN Document Server

    Lazio, J; Burns, J; Demaio, L; Jones, D L; Weiler, K W

    2007-01-01

    Observations at radio wavelengths address key problems in astrophysics, astrobiology, and lunar structure including the first light in the Universe (the Epoch of Reionization), the presence of magnetic fields around extrasolar planets, particle acceleration mechanisms, and the structure of the lunar ionosphere. Moreover, achieving the performance needed to address these scientific questions demands observations at wavelengths longer than those that penetrate the Earth's ionosphere, observations in extremely "radio quiet" locations such as the Moon's far side, or both. We describe a series of lunar-based radio wavelength interferometers of increasing capability. The Radio Observatory for Lunar Sortie Science (ROLSS) is an array designed to be deployed during the first lunar sorties (or even before via robotic rovers) and addressing particle acceleration and the lunar ionosphere. Future arrays would be larger, more capable, and deployed as experience is gained in working on the lunar surface.

  11. Multi-Robot Planetary Exploration Architectures Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Space policy direction is shifting, particularly with respect to human goals. Given the uncertainty of future missions to the moon, Mars, and other bodies, a tool...

  12. Exploring Processor and Memory Architectures for Multimedia

    OpenAIRE

    Iranpour, Ali

    2012-01-01

    Multimedia has become one of the cornerstones of our 21st century society and, when combined with mobility, has enabled a tremendous evolution of our society. However, joining these two concepts introduces many technical challenges. These range from having sufficient performance for handling multimedia content to having the battery stamina for acceptable mobile usage. When taking a projection of where we are heading, we see these issues becoming ever more challenging by increased mobility as ...

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.)

  18. 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.

  19. 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

  20. Neutron scattering studies on chromatin higher-order structure

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

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

  1. 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.

  2. 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

  3. 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

  4. 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...

  5. 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

  6. 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...

  7. 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 ...

  8. 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.

  9. 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

  10. ATP-Dependent Chromatin Remodeling Factors and Their Roles in Affecting Nucleosome Fiber Composition

    Directory of Open Access Journals (Sweden)

    Alexandra Lusser

    2011-10-01

    Full Text Available ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.

  11. 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.

  12. 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.

  13. 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...

  14. 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

  15. 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...

  16. An empirical investigation of architectural prototyping

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak; Hansen, Klaus Marius

    2010-01-01

    Architectural prototyping is the process of using executable code to investigate stakeholders’ software architecture concerns with respect to a system under development. Previous work has established this as a useful and cost-effective way of exploration and learning of the design space of a system...... prototyping in practice. First, we report findings from an ethnographic study of practicing software architects. Secondly, we report from a focus group on architectural prototyping involving architects from four companies. And, thirdly, we report from a survey study of 20 practicing software architects and...... software developers. Our findings indicate that architectural prototyping plays an important and frequent role in resolving problems experimentally, but less so in exploring alternative solutions. Furthermore, architectural prototypes include end-user or business related functionality rather than purely...

  17. Computer organization, design, and architecture

    CERN Document Server

    Shiva, Sajjan G

    2007-01-01

    Suitable for a one- or two-semester undergraduate or beginning graduate course in computer science and computer engineering, Computer Organization, Design, and Architecture, Fourth Edition presents the operating principles, capabilities, and limitations of digital computers to enable development of complex yet efficient systems. With 40% updated material and four new chapters, this edition takes students through a solid, up-to-date exploration of single- and multiple-processor systems, embedded architectures, and performance evaluation. New to the Fourth Edition Additional material that cove

  18. Computer Architecture A Quantitative Approach

    CERN Document Server

    Hennessy, John L

    2007-01-01

    The era of seemingly unlimited growth in processor performance is over: single chip architectures can no longer overcome the performance limitations imposed by the power they consume and the heat they generate. Today, Intel and other semiconductor firms are abandoning the single fast processor model in favor of multi-core microprocessors--chips that combine two or more processors in a single package. In the fourth edition of Computer Architecture, the authors focus on this historic shift, increasing their coverage of multiprocessors and exploring the most effective ways of achieving parallelis

  19. 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.  ...

  20. 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

  1. 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

  2. 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

  3. Assessment of Chromatin Maturity in Human Spermatozoa: Useful Aniline Blue Assay for Routine Diagnosis of Male Infertility

    Directory of Open Access Journals (Sweden)

    Afifa Sellami

    2013-01-01

    Full Text Available During spermatogenesis, sperm chromatin undergoes structural changes and results in a high condensation. This nuclear compaction would be useful as a predictor of sperm fertilization capacity and pregnancy outcome. We purpose to evaluate firstly the relationship among chromatin maturity assessed by aniline blue staining (AB and the semen parameters in infertile men. Secondly, we analyzed whether the sperm gradient density centrifugation is effective to select mature spermatozoa. Fifty-one ejaculates were investigated by semen analysis and stained for chromatin condensation with AB to distinguish between unstained mature sperm and stained immature sperm. AB was applied also on 12 ejaculates which proceeded by density gradient centrifugation to compare the rates of immature sperm before and after selection. Neat semen were divided into two groups: G1 (: immature sperm <20% and G2 (: immature sperm ≥20%. No significant differences were detected in sperm concentration, motility, and normal morphology between G1 and G2. However, the rates of some morphology abnormalities were higher in G2: head abnormalities ( and microcephalic sperm (. We founded significant correlation between sperm immaturity and acrosome abnormalities (; . Sperm selection has significantly reduced the rates of immature sperm. A better understanding of chromatin structure and its impact on the sperm potential is needed to explore male infertility.

  4. 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

  5. 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

  6. Healing Architecture

    DEFF Research Database (Denmark)

    Folmer, Mette Blicher; Mullins, Michael; Frandsen, Anne Kathrine

    2012-01-01

    ’s backstage-frontstage theory and Lawsons ‘Language of Space’ is used. Data is analyzed in accordance with principles describes in Robert Yin’s ‘Case Study Research’. The goal of the project is to create new knowledge which can contribute to new ways to design, plan and organize the hospital and qualify....... The project is an explorative case study and consists of systematic observations, interviews and photo documentation. The aim is to collect different kinds of data on: 1. Relatives’ behavior 2. Relatives’ experience and 3. Environment. In order to guide the collection of data and the analysis of them Goffman...

  7. Exploration architecturale pour la conception d'un système sur puce de vision robotique, adéquation algorithme-architecture d'un système embarqué temps-réel

    OpenAIRE

    Lefebvre, Thomas

    2012-01-01

    This Ph.D Thesis stands at the crossroads of three scientific domains : algorithm-architecture adequacy, bio-inspired vision systems in mobile robotics, and image processing.The goal is to make a robot autonomous in its visual perception, by the integration to the robot of this cognitive task, usually executed on remote processing servers.To achieve this goal, the design approach follows a path of algorithm architecture adequacy, where the different image processing steps of the vision system...

  8. Codesign Lessons Learned from Implementing Graph Matching on Multithreaded Architectures

    Energy Technology Data Exchange (ETDEWEB)

    Halappanavar, Mahantesh; Pothen, Alex; Azad, Md Ariful; Manne, Fredrik; Langguth, Johannes; Khan, Arif

    2015-08-12

    Co-design of algorithms and architectures is an effective way to address the performance of irregular applications on multithreaded architectures. We explore the interplay between algorithm design and architectural features using graph matching as a case study. We present the key lessons that we have learnt as a means to influence co-design of algorithms and architecture for execution of data-intensive irregular workloads.

  9. Archexplorer for automatic design space exploration

    OpenAIRE

    Desmet, V; Girbal, Sylvain; Ramírez Bellido, Alejandro; Temam, Olivier; Vega, Augusto

    2010-01-01

    Growing architectural complexity and stringent time-to-market constraints suggest the need to move architecture design beyond parametric exploration to structural exploration. ArchExplorer is a Web-based permanent and open design-space exploration framework that lets researchers compare their designs against others. The authors demonstrate their approach by exploring the design space of an on-chip memory subsystem and a multicore processor.

  10. 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...

  11. Choreographing the double strand break response: Ubiquitin and SUMO control of nuclear architecture

    Directory of Open Access Journals (Sweden)

    Shane M Harding

    2016-06-01

    Full Text Available The cellular response to DNA double strand breaks (DSBs is a multifaceted signaling program that centers on post-translational modifications including phosphorylation, ubiquitylation and SUMOylation. In this review we discuss how ubiquitin and SUMO orchestrate the recognition of DSBs and explore how this influences chromatin organization. We discuss functional outcomes of this response including transcriptional silencing and how pre-existing chromatin states may control the DSB response and the maintenance of genomic stability.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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...

  17. Naval open systems architecture

    Science.gov (United States)

    Guertin, Nick; Womble, Brian; Haskell, Virginia

    2013-05-01

    For the past 8 years, the Navy has been working on transforming the acquisition practices of the Navy and Marine Corps toward Open Systems Architectures to open up our business, gain competitive advantage, improve warfighter performance, speed innovation to the fleet and deliver superior capability to the warfighter within a shrinking budget1. Why should Industry care? They should care because we in Government want the best Industry has to offer. Industry is in the business of pushing technology to greater and greater capabilities through innovation. Examples of innovations are on full display at this conference, such as exploring the impact of difficult environmental conditions on technical performance. Industry is creating the tools which will continue to give the Navy and Marine Corps important tactical advantages over our adversaries.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Chromatin structure and evolution in the human genome

    Directory of Open Access Journals (Sweden)

    Dunlop Malcolm G

    2007-05-01

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

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

    OpenAIRE

    Názer, Ezequiel; Lei, Elissa P.

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Laugesen, Anne; Helin, Kristian

    2014-01-01

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

  6. Module Architecture for in Situ Space Laboratories

    Science.gov (United States)

    Sherwood, Brent

    2010-01-01

    The paper analyzes internal outfitting architectures for space exploration laboratory modules. ISS laboratory architecture is examined as a baseline for comparison; applicable insights are derived. Laboratory functional programs are defined for seven planet-surface knowledge domains. Necessary and value-added departures from the ISS architecture standard are defined, and three sectional interior architecture options are assessed for practicality and potential performance. Contemporary guidelines for terrestrial analytical laboratory design are found to be applicable to the in-space functional program. Densepacked racks of system equipment, and high module volume packing ratios, should not be assumed as the default solution for exploration laboratories whose primary activities include un-scriptable investigations and experimentation on the system equipment itself.

  7. Sequence and chromatin determinants of cell-type-specific transcription factor binding.

    Science.gov (United States)

    Arvey, Aaron; Agius, Phaedra; Noble, William Stafford; Leslie, Christina

    2012-09-01

    Gene regulatory programs in distinct cell types are maintained in large part through the cell-type-specific binding of transcription factors (TFs). The determinants of TF binding include direct DNA sequence preferences, DNA sequence preferences of cofactors, and the local cell-dependent chromatin context. To explore the contribution of DNA sequence signal, histone modifications, and DNase accessibility to cell-type-specific binding, we analyzed 286 ChIP-seq experiments performed by the ENCODE Consortium. This analysis included experiments for 67 transcriptional regulators, 15 of which were profiled in both the GM12878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines. To model TF-bound regions, we trained support vector machines (SVMs) that use flexible k-mer patterns to capture DNA sequence signals more accurately than traditional motif approaches. In addition, we trained SVM spatial chromatin signatures to model local histone modifications and DNase accessibility, obtaining significantly more accurate TF occupancy predictions than simpler approaches. Consistent with previous studies, we find that DNase accessibility can explain cell-line-specific binding for many factors. However, we also find that of the 10 factors with prominent cell-type-specific binding patterns, four display distinct cell-type-specific DNA sequence preferences according to our models. Moreover, for two factors we identify cell-specific binding sites that are accessible in both cell types but bound only in one. For these sites, cell-type-specific sequence models, rather than DNase accessibility, are better able to explain differential binding. Our results suggest that using a single motif for each TF and filtering for chromatin accessible loci is not always sufficient to accurately account for cell-type-specific binding profiles. PMID:22955984

  8. Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus.

    Science.gov (United States)

    Nakaoka, Hirofumi; Gurumurthy, Aishwarya; Hayano, Takahide; Ahmadloo, Somayeh; Omer, Waleed H; Yoshihara, Kosuke; Yamamoto, Akihito; Kurose, Keisuke; Enomoto, Takayuki; Akira, Shigeo; Hosomichi, Kazuyoshi; Inoue, Ituro

    2016-04-01

    Genome-wide association studies (GWASs) have discovered numerous single nucleotide polymorphisms (SNPs) associated with human complex disorders. However, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a SNP on chromosome 9p21 associated with endometriosis by leveraging "allele-specific" functional genomic approaches. By re-sequencing 1.29 Mb of 9p21 region and scrutinizing DNase-seq data from the ENCODE project, we prioritized rs17761446 as a candidate functional variant that was in perfect linkage disequilibrium with the original GWAS SNP (rs10965235) and located on DNase I hypersensitive site. Chromosome conformation capture followed by high-throughput sequencing revealed that the protective G allele of rs17761446 exerted stronger chromatin interaction with ANRIL promoter. We demonstrated that the protective allele exhibited preferential binding affinities to TCF7L2 and EP300 by bioinformatics and chromatin immunoprecipitation (ChIP) analyses. ChIP assays for histone H3 lysine 27 acetylation and RNA polymerase II reinforced the enhancer activity of the SNP site. The allele specific expression analysis for eutopic endometrial tissues and endometrial carcinoma cell lines showed that rs17761446 was a cis-regulatory variant where G allele was associated with increased ANRIL expression. Our work illuminates the allelic imbalances in a series of transcriptional regulation from factor binding to gene expression mediated by chromatin interaction underlie the molecular mechanism of 9p21 endometriosis risk locus. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage. PMID:27055116

  9. Chromatin landscaping in algae reveals novel regulation pathway for biofuels production

    Energy Technology Data Exchange (ETDEWEB)

    Ngan, Chew Yee; Wong, Chee-Hong; Choi, Cindy; Pratap, Abhishek; Han, James; Wei, Chia-Lin

    2013-02-19

    The diminishing reserve of fossil fuels calls for the development of biofuels. Biofuels are produced from renewable resources, including photosynthetic organisms, generating clean energy. Microalgae is one of the potential feedstock for biofuels production. It grows easily even in waste water, and poses no competition to agricultural crops for arable land. However, little is known about the algae lipid biosynthetic regulatory mechanisms. Most studies relied on the homology to other plant model organisms, in particular Arabidopsis or through low coverage expression analysis to identify key enzymes. This limits the discovery of new components in the biosynthetic pathways, particularly the genetic regulators and effort to maximize the production efficiency of algal biofuels. Here we report an unprecedented and de novo approach to dissect the algal lipid pathways through disclosing the temporal regulations of chromatin states during lipid biosynthesis. We have generated genome wide chromatin maps in chlamydomonas genome using ChIP-seq targeting 7 histone modifications and RNA polymerase II in a time-series manner throughout conditions activating lipid biosynthesis. To our surprise, the combinatory profiles of histone codes uncovered new regulatory mechanism in gene expression in algae. Coupled with matched RNA-seq data, chromatin changes revealed potential novel regulators and candidate genes involved in the activation of lipid accumulations. Genetic perturbation on these candidate regulators further demonstrated the potential to manipulate the regulatory cascade for lipid synthesis efficiency. Exploring epigenetic landscape in microalgae shown here provides powerful tools needed in improving biofuel production and new technology platform for renewable energy generation, global carbon management, and environmental survey.

  10. Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus

    Science.gov (United States)

    Nakaoka, Hirofumi; Gurumurthy, Aishwarya; Hayano, Takahide; Ahmadloo, Somayeh; Omer, Waleed H; Yoshihara, Kosuke; Yamamoto, Akihito; Kurose, Keisuke; Enomoto, Takayuki; Akira, Shigeo; Hosomichi, Kazuyoshi; Inoue, Ituro

    2016-01-01

    Genome-wide association studies (GWASs) have discovered numerous single nucleotide polymorphisms (SNPs) associated with human complex disorders. However, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a SNP on chromosome 9p21 associated with endometriosis by leveraging “allele-specific” functional genomic approaches. By re-sequencing 1.29 Mb of 9p21 region and scrutinizing DNase-seq data from the ENCODE project, we prioritized rs17761446 as a candidate functional variant that was in perfect linkage disequilibrium with the original GWAS SNP (rs10965235) and located on DNase I hypersensitive site. Chromosome conformation capture followed by high-throughput sequencing revealed that the protective G allele of rs17761446 exerted stronger chromatin interaction with ANRIL promoter. We demonstrated that the protective allele exhibited preferential binding affinities to TCF7L2 and EP300 by bioinformatics and chromatin immunoprecipitation (ChIP) analyses. ChIP assays for histone H3 lysine 27 acetylation and RNA polymerase II reinforced the enhancer activity of the SNP site. The allele specific expression analysis for eutopic endometrial tissues and endometrial carcinoma cell lines showed that rs17761446 was a cis-regulatory variant where G allele was associated with increased ANRIL expression. Our work illuminates the allelic imbalances in a series of transcriptional regulation from factor binding to gene expression mediated by chromatin interaction underlie the molecular mechanism of 9p21 endometriosis risk locus. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage. PMID:27055116

  11. 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, ...

  12. Integration of architectural design in the landscape

    OpenAIRE

    Dimoska, Aleksandra; Mitanoska, Ana; Sandeva, Vaska; Despot, Katerina; Mitev, Trajce

    2012-01-01

    This paper focuses on integration of the architectural form in the landscape, a topic that is related to the conservation of the environment with ecological and bioclimatic architecture. This report explores the forerunners of sustainable development, energy saving and environmental adaptation, and research developed within the subterranean living to large projects, with particular attention to the formal and practical potential of land use. The paper contains both, modern and historica...

  13. Sustainable, Reliable Mission-Systems Architecture

    Science.gov (United States)

    O'Neil, Graham; Orr, James K.; Watson, Steve

    2007-01-01

    A mission-systems architecture, based on a highly modular infrastructure utilizing: open-standards hardware and software interfaces as the enabling technology is essential for affordable and sustainable space exploration programs. This mission-systems architecture requires (a) robust communication between heterogeneous system, (b) high reliability, (c) minimal mission-to-mission reconfiguration, (d) affordable development, system integration, and verification of systems, and (e) minimal sustaining engineering. This paper proposes such an architecture. Lessons learned from the Space Shuttle program and Earthbound complex engineered system are applied to define the model. Technology projections reaching out 5 years are mde to refine model details.

  14. Planetary cubesats - mission architectures

    Science.gov (United States)

    Bousquet, Pierre W.; Ulamec, Stephan; Jaumann, Ralf; Vane, Gregg; Baker, John; Clark, Pamela; Komarek, Tomas; Lebreton, Jean-Pierre; Yano, Hajime

    2016-07-01

    Miniaturisation of technologies over the last decade has made cubesats a valid solution for deep space missions. For example, a spectacular set 13 cubesats will be delivered in 2018 to a high lunar orbit within the frame of SLS' first flight, referred to as Exploration Mission-1 (EM-1). Each of them will perform autonomously valuable scientific or technological investigations. Other situations are encountered, such as the auxiliary landers / rovers and autonomous camera that will be carried in 2018 to asteroid 1993 JU3 by JAXA's Hayabusas 2 probe, and will provide complementary scientific return to their mothership. In this case, cubesats depend on a larger spacecraft for deployment and other resources, such as telecommunication relay or propulsion. For both situations, we will describe in this paper how cubesats can be used as remote observatories (such as NEO detection missions), as technology demonstrators, and how they can perform or contribute to all steps in the Deep Space exploration sequence: Measurements during Deep Space cruise, Body Fly-bies, Body Orbiters, Atmospheric probes (Jupiter probe, Venus atmospheric probes, ..), Static Landers, Mobile landers (such as balloons, wheeled rovers, small body rovers, drones, penetrators, floating devices, …), Sample Return. We will elaborate on mission architectures for the most promising concepts where cubesat size devices offer an advantage in terms of affordability, feasibility, and increase of scientific return.

  15. 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...

  16. 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.

  17. 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

  18. 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.

  19. 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)

  20. 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

  1. 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.)

  2. Control of the Transition to Flowering by Chromatin Modifications

    Institute of Scientific and Technical Information of China (English)

    Yuehui He

    2009-01-01

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

  3. 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...

  4. 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...

  5. 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...

  6. 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....

  7. 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

  8. 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.

  9. 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.

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

    Science.gov (United States)

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

    1991-10-01

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

  11. 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...

  12. 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

  13. 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....

  14. Exploration architecturale pour la conception d'un système sur puce de vision robotique, adéquation algorithme-architecture d'un système embarqué temps-réel

    OpenAIRE

    Lefebvre, Thomas

    2012-01-01

    This Ph.D Thesis stands at the crossroads of three scientific domains : algorithmarchitecture adequacy, bio-inspired vision systems in mobile robotics, and image processing. The goal is to make a robot autonomous in its visual perception, by the integration to the robot of this cognitive task, usually executed on remote processing servers. To achieve this goal, the design approach follows a path of algorithm architecture adequacy, where the different image processing steps of the vision syste...

  15. Constellation Architecture and System Margins Strategy

    Science.gov (United States)

    Muirhead, Brian

    2008-01-01

    NASA's Constellation Program (CxP) is responsible for the definition, design, development, and operations of the flight, ground, and mission operations elements being developed by the United States for the human exploration of the Moon, Mars, and beyond. This paper provides an overview of the latest CxP technical architecture baseline, driving requirements, and reference missions for initial capability to fly to the International Space Station (ISS) and to the Moon. The results of the most recent design decisions and analyses supporting the architecture, including the Ares I, Ares V, Orion crew exploration vehicle, and the Altair lunar lander will be presented.

  16. 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...

  17. 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....

  18. An Embodied Architecture

    Directory of Open Access Journals (Sweden)

    Frances Downing

    2012-10-01

    Full Text Available An architecture of the body is emerging out of theories of biology, complexity, and systems through the use of an evolving organism as its metaphor. Autopoiesis is the term used by biologists to describe the realm of existence for a living organism as it slides between the interchange of structure and information. Incoming information is filtered through the organism for its usefulness in the art of staying alive. Structural or organizational changes evolve as the organism adjusts to new information. To remain a viable organism—to survive—means that an entity must keep evolving without surrendering identity. Humans must maintain an embodied identity, often referred to as an organized self (Maturana & Varela, 1980, 1987, while viably exchanging information with other entities and the environment. This operation creates a topological boundary across which the communication takes place. Cognitive theorists and researchers have proposed that the animal condition is one of Embodied Realism; that is, animals such as we humans, are embodied, using our bodies to create basic metaphors, and, that we do this in a“real” world. The role of cognition in this equation is to allow humans the use of embodiment to explore abstract ideas through metaphor—such as “grasping an idea” (Lakoff &Johnson, 2003. In doing so, it allows the invention of an evolving language that refers to things “outside” our skin,like other entities and places. Autopoiesis describes the activities at the “edge” or boundary of an organism. The linguistic act can, therefore, be identified as fundamental medium for communication in the edge, between inside and outside, that assures the autopoiesis of place.In our own bodies, flesh is the biological manifest of the edge or boundary condition. Our understanding of flesh is that it is another of our organs; and at the same time, all organs are also bounded by flesh. It serves as a porous filter, delicate and complicated

  19. 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

  20. 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.

  1. 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...

  2. 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/...

  3. 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...

  4. 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

  5. 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...

  6. 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...

  7. 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....

  8. 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

  9. 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...

  10. 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

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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

  16. Reference Avionics Architecture for Lunar Surface Systems

    Science.gov (United States)

    Somervill, Kevin M.; Lapin, Jonathan C.; Schmidt, Oron L.

    2010-01-01

    Developing and delivering infrastructure capable of supporting long-term manned operations to the lunar surface has been a primary objective of the Constellation Program in the Exploration Systems Mission Directorate. Several concepts have been developed related to development and deployment lunar exploration vehicles and assets that provide critical functionality such as transportation, habitation, and communication, to name a few. Together, these systems perform complex safety-critical functions, largely dependent on avionics for control and behavior of system functions. These functions are implemented using interchangeable, modular avionics designed for lunar transit and lunar surface deployment. Systems are optimized towards reuse and commonality of form and interface and can be configured via software or component integration for special purpose applications. There are two core concepts in the reference avionics architecture described in this report. The first concept uses distributed, smart systems to manage complexity, simplify integration, and facilitate commonality. The second core concept is to employ extensive commonality between elements and subsystems. These two concepts are used in the context of developing reference designs for many lunar surface exploration vehicles and elements. These concepts are repeated constantly as architectural patterns in a conceptual architectural framework. This report describes the use of these architectural patterns in a reference avionics architecture for Lunar surface systems elements.

  17. The Mothership Mission Architecture

    Science.gov (United States)

    Ernst, S. M.; DiCorcia, J. D.; Bonin, G.; Gump, D.; Lewis, J. S.; Foulds, C.; Faber, D.

    2015-12-01

    The Mothership is considered to be a dedicated deep space carrier spacecraft. It is currently being developed by Deep Space Industries (DSI) as a mission concept that enables a broad participation in the scientific exploration of small bodies - the Mothership mission architecture. A Mothership shall deliver third-party nano-sats, experiments and instruments to Near Earth Asteroids (NEOs), comets or moons. The Mothership service includes delivery of nano-sats, communication to Earth and visuals of the asteroid surface and surrounding area. The Mothership is designed to carry about 10 nano-sats, based upon a variation of the Cubesat standard, with some flexibility on the specific geometry. The Deep Space Nano-Sat reference design is a 14.5 cm cube, which accommodates the same volume as a traditional 3U CubeSat. To reduce cost, Mothership is designed as a secondary payload aboard launches to GTO. DSI is offering slots for nano-sats to individual customers. This enables organizations with relatively low operating budgets to closely examine an asteroid with highly specialized sensors of their own choosing and carry out experiments in the proximity of or on the surface of an asteroid, while the nano-sats can be built or commissioned by a variety of smaller institutions, companies, or agencies. While the overall Mothership mission will have a financial volume somewhere between a European Space Agencies' (ESA) S- and M-class mission for instance, it can be funded through a number of small and individual funding sources and programs, hence avoiding the processes associated with traditional space exploration missions. DSI has been able to identify a significant interest in the planetary science and nano-satellite communities.

  18. Multiple-Morphs Adaptive Stream Architecture

    Institute of Scientific and Technical Information of China (English)

    Mei Wen; Nan Wu; Hai-Yan Li; Chun-Yuan Zhang

    2005-01-01

    In modern VLSI technology, hundreds of thousands of arithmetic units fit on a 1cm2 chip. The challenge is supplying them with instructions and data. Stream architecture is able to solve the problem well. However, the applications suited for typical stream architecture are limited. This paper presents the definition of regular stream and irregular stream,and then describes MASA (Multiple-morphs Adaptive Stream Architecture) prototype system which supports different execution models according to applications' stream characteristics. This paper first discusses MASA architecture and stream model, and then explores the features and advantages of MASA through mapping stream applications to hardware.Finally MASA is evaluated by ten benchmarks. The result is encouraging.

  19. Generation of non-overlapping fiber architecture

    DEFF Research Database (Denmark)

    Chapelle, Lucie; Lévesque, M.; Brøndsted, Povl;

    2015-01-01

    Numerical models generating actual fiber architecture by including parameters such as the fiber geometry and arrangement are a powerful tool to explore the relation between the fiber architecture and mechanical properties. The generation of virtual architectures of fibrous materials is the first...... step toward the computation of their physical properties. In this work, a realistic 3D model is developed to describe the architecture of a complex fiber structure. The domain of application of the model could include natural fibers composites, wood fibers materials, papers, mineral and steel wools...... and polymer networks. The model takes into account the complex geometry of the fiber arrangement in which a fiber can be modeled with a certain degree of bending while keeping a main fiber orientation. The model is built in two steps. First, fibers are generated as a chain of overlapping spheres or as a chain...

  20. Relationship between Meaning and Expression in Architecture Design

    Institute of Scientific and Technical Information of China (English)

    LiKun

    2002-01-01

    During the evolvement of architecture,the research on architectural form and structure as well as different ways to express and realize architectural thoughts is constantly the focus of many architects,This paper illustrates the mutual influence of the ways of expression and design of architecture to people's understanding of the meaning of architecture throughout the history of their efforts and exploration.the paper also discusses the extensive usage of virtual-realith approach through computer technology,It points out that the traditional architectural standpoint will undergo breakthrough by the emergence of new expression and design method.In this way,people's understanding of architecture will be more profound and lasting.

  1. Semantic Relations between Words in Naval Architecture and Maritime Languages

    OpenAIRE

    Anca TRIȘCĂ

    2014-01-01

    The present article aims at identifying the semantic relations that occur between words in naval architecture and maritime languages. For this purpose several specialized dictionaries as well as various textbooks and specific naval architecture documents were explored. Both the naval architecture and maritime field-specific lexis consist of few genuinely ‘unique’ words and of a large number of items, not ‘unique’ in and by themselves, which have migrated from everyday language to become ‘t...

  2. A Network Software Architecture Suitable for Service Customization

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper explores the service customization in the view of network software architectures. The authors first abstract a network system into a framework that consists of several layered basic systems and then propose a component-based network software architecture for one basic system of network software, which is suitable for service customization. The network software architecture is formalized with the theory of Communicating Sequential Process and show its possible applications in areas of personal service environment and service customization.

  3. Advanced Topology Optimization Methods for Conceptual Architectural Design

    DEFF Research Database (Denmark)

    Aage, Niels; Amir, Oded; Clausen, Anders;

    2014-01-01

    This paper presents a series of new, advanced topology optimization methods, developed specifically for conceptual architectural design of structures. The proposed computational procedures are implemented as components in the framework of a Grasshopper plugin, providing novel capacities in...... frames are implemented. The developed procedures allow for the exploration of new territories in optimization of architectural structures, and offer new methodological strategies for bridging conceptual gaps between optimization and architectural practice....

  4. The Legal Environment for Landscape Architecture in Utah

    OpenAIRE

    Scarborough, Jeffrey J.

    1996-01-01

    This paper explores and delineates the legal environment for the practice of landscape architecture in Utah. The national, state, and local (city and county), codes that apply to landscape architecture and the related professions of architecture, engineering, and land surveying are documented, as is pertinent case law. Figures allow comparisons to be made between the various government levels to demonstrate contradictions and congruencies, as well as the clarity of the ordinances. Major findi...

  5. An Application Framework for a Power-Aware Processor Architecture

    OpenAIRE

    Mandlekar, Anup Shrikant

    2012-01-01

    The instruction-set based general purpose processors are not energy-efficient for event-driven applications. The E-textiles group at Virginia Tech proposed a novel data-flow processor architecture design to bridge the gap between event-driven applications and the target architecture. The architecture, although promising in terms of performance and energy-efficiency, was explored for limited number of applications. This thesis presents a model-driven approach for the design of an applicatio...

  6. 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.

  7. 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

  8. 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.

  9. 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...

  10. A Summary of NASA Architecture Studies Utilizing Fission Surface Power Technology

    Science.gov (United States)

    Mason, Lee S.; Poston, David I.

    2011-01-01

    Beginning with the Exploration Systems Architecture Study in 2005, NASA has conducted various mission architecture studies to evaluate implementation options for the U.S. Space Policy. Several of the studies examined the use of Fission Surface Power (FSP) systems for human missions to the lunar and Martian surface. This paper summarizes the FSP concepts developed under four different NASA-sponsored architecture studies: Lunar Architecture Team, Mars Architecture Team, Lunar Surface Systems/Constellation Architecture Team, and International Architecture Working Group-Power Function Team.

  11. 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.

  12. 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.

  13. 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...

  14. 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...

  15. 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. ...

  16. 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...

  17. 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...

  18. Computer Architecture A Quantitative Approach

    CERN Document Server

    Hennessy, John L

    2011-01-01

    The computing world today is in the middle of a revolution: mobile clients and cloud computing have emerged as the dominant paradigms driving programming and hardware innovation today. The Fifth Edition of Computer Architecture focuses on this dramatic shift, exploring the ways in which software and technology in the cloud are accessed by cell phones, tablets, laptops, and other mobile computing devices. Each chapter includes two real-world examples, one mobile and one datacenter, to illustrate this revolutionary change.Updated to cover the mobile computing revolutionEmphasizes the two most im

  19. 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

  20. 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

  1. 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.

  2. 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...

  3. Process-driven architecture: design techniques and methods

    NARCIS (Netherlands)

    Jaskiewicz, T.

    2007-01-01

    This paper explores the notion of process-driven architecture and, as a consequence, application of complex systems in the newly defined area of digital process-driven architectural design in order to formulate a suitable design method. Protospace software environment and SwarmCAD software applicati

  4. Transformation of Minarets in Contemporary Mosque Architecture in Turkey

    OpenAIRE

    Özgür Ürey

    2013-01-01

    This study aims to explore the usage, the formal and functional transformation of minarets in contemporary mosque architecture in Turkey, through a survey of the selected cases. The selected cases are the outstanding examples of Turkish contemporary mosque architecture. Their architects are innovative in their design decisions and displayed their own design approach and interpretation outside the main stream contemporary mosque design in T...

  5. Dendronized Polymer Architectures for Fuel Cell Membranes

    DEFF Research Database (Denmark)

    Nielsen, Mads Møller; Dimitrov, Ivaylo; Takamuku, S.;

    2013-01-01

    evaluated as PEMs for use in fuel cells by proton conductivity measurements, and in the case of dendronized architectures: thermal stability. The proposed synthetic strategy facilitates exploration of a non‐fluorous system with various flexible side chains where IEC is tunable by the degree of substitution....

  6. Digital architecture, wearable computers and providing affinity

    DEFF Research Database (Denmark)

    Guglielmi, Michel; Johannesen, Hanne Louise

    2005-01-01

    paper will, through research, a workshop and participation in a cumulus competition, focus on the exploration of boundaries between digital architecture, performative space and wearable computers. Our design method in general focuses on the interplay between the performing body and the environment...

  7. Nuclear Architecture: Past and Future Tense.

    Science.gov (United States)

    Gasser, Susan M

    2016-07-01

    The architecture of the interphase nucleus remains a treasure trove for explorers of the 3D folding of macromolecules, like DNA, and of their related functions. Only recently has there been insight into how transient interactions of the genome and its associated proteins, in space and time, facilitate transcription, replication, and repair. PMID:27177990

  8. Software Architecture : Framing Stakeholders' Concerns introduction

    NARCIS (Netherlands)

    Lago, Patricia; Avgeriou, Paris; Hilliard, Rich

    2010-01-01

    As noted earlier, some stakeholder concerns are well-served today by available architecture viewpoints, frameworks, or ADLs, while others aren't expressible with available, off-the-shelf approaches. Hence the theme of this special issue: exploring the space of architecting in the face of multiple st

  9. 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.

  10. 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

  11. HTLV-1 Tax mediated downregulation of miRNAs associated with chromatin remodeling factors in T cells with stably integrated viral promoter.

    Directory of Open Access Journals (Sweden)

    Saifur Rahman

    Full Text Available RNA interference (RNAi is a natural cellular mechanism to silence gene expression and is predominantly mediated by microRNAs (miRNAs that target messenger RNA. Viruses can manipulate the cellular processes necessary for their replication by targeting the host RNAi machinery. This study explores the effect of human T-cell leukemia virus type 1 (HTLV-1 transactivating protein Tax on the RNAi pathway in the context of a chromosomally integrated viral long terminal repeat (LTR using a CD4(+ T-cell line, Jurkat. Transcription factor profiling of the HTLV-1 LTR stably integrated T-cell clone transfected with Tax demonstrates increased activation of substrates and factors associated with chromatin remodeling complexes. Using a miRNA microarray and bioinformatics experimental approach, Tax was also shown to downregulate the expression of miRNAs associated with the translational regulation of factors required for chromatin remodeling. These observations were validated with selected miRNAs and an HTLV-1 infected T cells line, MT-2. miR-149 and miR-873 were found to be capable of directly targeting p300 and p/CAF, chromatin remodeling factors known to play critical role in HTLV-1 pathogenesis. Overall, these results are first in line establishing HTLV-1/Tax-miRNA-chromatin concept and open new avenues toward understanding retroviral latency and/or replication in a given cell type.

  12. Architecture Framework for Fault Management Assessment And Design (AFFMAD) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Architecture Framework for Fault Management Assessment And Design (AFFMAD) is a constraint-checking system for FM trade space exploration that provides rigorous...

  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. 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.

  18. 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....

  19. 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....

  20. 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

  1. 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.

  2. 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...

  3. 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...

  4. 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...

  5. Non-Toxic Ionic Liquid Fuels for Exploration Applications Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Challenges arise in the propulsion systems for the new exploration architecture. The currently operational and proven storable hypergolic systems raise toxicity...

  6. 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.

  7. Comparative Study of Bio-implantable Acoustic Generator Architectures

    Science.gov (United States)

    Christensen, D.; Roundy, S.

    2013-12-01

    This paper is a comparative study of the design spaces of two bio-implantable acoustically excited generator architectures: the thickness-stretch-mode circular piezoelectric plate and the bending-mode unimorph piezoelectric diaphragm. The generators are part of an acoustic power transfer system for implanted sensors and medical devices such as glucose monitors, metabolic monitors, drug delivery systems, etc. Our studies indicate that at small sizes the diaphragm architecture outperforms the plate architecture. This paper will present the results of simulation studies and initial experiments that explore the characteristics of the two architectures and compare their performance.

  8. The Architectural Practice of Regeneration

    Directory of Open Access Journals (Sweden)

    Tom Van Malderen

    2013-09-01

    Full Text Available In form and in content, cities are the epitome of diversity. This state is the result of the accumulation of layers of history, of construction, of demolition and reconstruction cycles. These tensions are the catalyst for the emergence of new urban forms and participate in the construction of heritage. As such they should be encouraged. As important as the existing fabric of the city is, its evolution to accommodate the ever-changing needs and fashions of its inhabitants is paramount. For regeneration to be successful it must inscribe itself in this process and it must be driven by an understanding of the environment where it occurs. This paper explores, through the lens of an architectural practice, some design processes and architectural proposals that have been generated by working on the Valletta harbours. It also discusses the necessary dynamics required to accommodate stakeholder engagement and planning policy while ensuring design quality and the perpetuation of the creative process inherent to the city. Finally, the paper introduces, as a possible future, the experiments and studies of the practice on the wider Valletta, putting into perspective the benefits of theoretical research combined with formal and aesthetic explorations of the harbour region.

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

    Institute of Scientific and Technical Information of China (English)

    孙大鹏; 宋峰; 黄丽; 张阔; 季刚; 陈萍; 朱平

    2013-01-01

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

  10. 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...

  11. 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...

  12. 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 ...

  13. 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...

  14. 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...

  15. 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 (...

  16. 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...

  17. 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...

  18. 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...

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

    OpenAIRE

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

    2014-01-01

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

  20. Effects of nuclear isolation on psoralen affinity for chromatin

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

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

    1998-01-01

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

  2. Evaluation of sperm chromatin structure in boar semen

    Directory of Open Access Journals (Sweden)

    Banaszewska Dorota

    2015-06-01

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

  3. 工程造价专业“建筑结构”课程改革的探索%Exploration into the Course Reform of Architectural Structure for Engineering Cost Specialty

    Institute of Scientific and Technical Information of China (English)

    史晓燕; 王兵

    2011-01-01

    根据专业特色,从教学内容、教学方法和实践性环节三个方面对建筑结构课程进行改革。工程造价专业的建筑结构课程内容主要包括钢筋砼结构设计、砌体结构设计、铜结构设计和建筑结构抗震基本知识。根据工程造价专业学生未来岗位关键能力的要求,建筑结构课程除了讲授基本构件的设计理论知识外,还要求学生熟悉常见结构类型的特点、不同结构类型的计算简图和构造知识。课程讲授除采用传统板书教学外,还可采用多媒体课件和现场情境式教学相结合的模式。建筑结构课程的实践性环节主要包括钢筋砼楼盖课程设计和建筑结构施工图识图模拟实训。%Based on the speciality characteristics, this paper makes the course reform on Architectural Structure from three aspects such as the teaching content, the teaching method and practical teaching. In addition to the design and calculation of the basic elements, the knowledge of structure construction is supplemented. In accordance with the characteristics of Engineering Cost Specialty, curriculum reform is carried out in theory teaching and practical teaching, through which the students can grasp the basic principles of architectural structure design and methods. And it can lay a good foundation for studying the follow-up courses and skill requirements of future career jobs.

  4. Extra sex combs, chromatin, and cancer: Exploring epigenetic regulation and tumorigenesis in Drosophila

    Institute of Scientific and Technical Information of China (English)

    Can Zhang; Bo Liu; Guangyao Li; Lei Zhou

    2011-01-01

    Developmental genetic studies in Drosophila unraveled the importance of Polycomb group (PcG) and Trithorax group (TrxG) genes in controlling cellular identity.PcG and TrxG proteins form histone modifying complexes that catalyze repressive or activating histone modifications,respectively,and thus maintaining the expression status of homeotic genes.Human orthologs of PcG and TrxG genes are implicated in tumorigenesis as well as in determining the prognosis of individual cancers.Recent whole genome analyses of cancers also highlighted the importance of histone modifying proteins in controlling tumorigenesis.Comprehensive understanding of the mechanistic relationship between histone regulation and tumorigenesis holds the promise of significantly advancing our understanding and management of cancer.It is anticipated that Drosophila melanogaster,the model organism that contributed significantly to our understanding of the functional role of histone regulation in development,could also provide unique insight for our understanding of how histone dysregulation can lead to cancer.In this review,we will discuss several recent advances in this regard.

  5. 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

  6. 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...

  7. Homeowner's Architectural Responses to Crime in Dar Es Salaan : Its impacts and implications to urban architecture, urban design and urban management

    OpenAIRE

    Bulamile, Ludigija Boniface

    2009-01-01

    HTML clipboardThis study is about Homeowner’s architectural responses to crime in Dar es Salaam Tanzania: its impacts and implications to urban architecture, urban design and urban management. The study explores and examines the processes through which homeowners respond to crimes of burglary, home robbery and fear of it using architectural or physical elements. The processes are explored and examined using case study methodology in three cases in Dar es Salaam. The cases are residentia...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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)

  13. Plastic Super Models: aesthetics, architecture and the model of emergence

    Directory of Open Access Journals (Sweden)

    Pia Ednie-Brown

    2008-01-01

    Full Text Available Modelling is at the core of what architects do, rendering the discipline especially fragile and sensitive to shifts in the nature of models and modelling. A digitally-based, explorative architectural milieu has been actively modelling in tune with a socio-cultural paradigm related to the concept of emergence, presenting numerous challenges to a range of assumptions about the activity of architectural design. This paper explores how this milieu has acted to unsettle the cool containments of architectural composure by bringing affective activity emphatically to the foreground.

  14. HERACLES Concept - An International Lunar Exploration Study

    Science.gov (United States)

    Landgraf, M.; Carpenter, J.; Sawada, H.

    2015-10-01

    HERACLES is an ESA-led architecture study by various agency members of the ISECG to define an end-to-end scenario of human-robotic lunar exploration. The architecture has the objective to prepare human missions and to perform science.

  15. 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....

  16. 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...

  17. Conceptual service architecture for adaptive mobile location services

    DEFF Research Database (Denmark)

    Schou, Saowanee

    This paper presents a conceptual service architecture for adaptive mobile location services designed to be used on the next generation wireless network. The developed service architecture consists of a set of concepts, principles, rules and guidelines for constructing, deploying, and operating the...... mobile location services. The service architecture identifies the components required to build the mobile location services and describes how these components are combined and how they should interact. As a means of exploring the developed conceptual service architecture, an illustrative case study of a...... new-concept tracking service is chosen to demonstrate the applicability of the architecture. Through the case study, the service request and response processes will be illustrated. New possible service functions provided by the developed service architecture will be examined and discussed in...

  18. Landscape architecture as an entity of property development in Wilayah Persekutuan, Putrajaya

    OpenAIRE

    Ahmad Nasyution bin Abdul Razak; Anuar bin Alias

    2015-01-01

    This study explores the relationship between landscape architecture and property development. Landscape architecture emphasizes the nature of conservation, development of public parks, city parks, local parks, artificial forests, lakes, recreational areas, outdoor recreation centers, open space systems and other components of landscape architecture in providing opportunities and benefits for real estate development. Backed by ample literature review, this study reveals the significant relatio...

  19. 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

  20. 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....

  1. 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.

  2. 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.

  3. 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...

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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....

  9. 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.

  10. 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...

  11. 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...

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

    Directory of Open Access Journals (Sweden)

    Mora Xavier

    2007-05-01

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

  13. 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

  14. 论知识管理和信息构建%On Knowledge Management & Information Architecture

    Institute of Scientific and Technical Information of China (English)

    张新民; 梁战平

    2003-01-01

    The paper outlines the concept and implementation process of knowledge management, introduces a new domain of study in information science, that is, the concept, composition and process of information architecture, and explores the relationship between knowledge aumagement and information architecture.

  15. 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...

  16. 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

  17. 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.

  18. 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...

  19. 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....

  20. 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...