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Sample records for dna building blocks

  1. Rapid and annealing-free self-assembly of DNA building blocks for 3D hydrogel chaperoned by cationic comb-type copolymers.

    Science.gov (United States)

    Zhang, Zheng; Wu, Yuyang; Yu, Feng; Niu, Chaoqun; Du, Zhi; Chen, Yong; Du, Jie

    2017-10-01

    The construction and self-assembly of DNA building blocks are the foundation of bottom-up development of three-dimensional DNA nanostructures or hydrogels. However, most self-assembly from DNA components is impeded by the mishybridized intermediates or the thermodynamic instability. To enable rapid production of complicated DNA objects with high yields no need for annealing process, herein different DNA building blocks (Y-shaped, L- and L'-shaped units) were assembled in presence of a cationic comb-type copolymer, poly (L-lysine)-graft-dextran (PLL-g-Dex), under physiological conditions. The results demonstrated that PLL-g-Dex not only significantly promoted the self-assembly of DNA blocks with high efficiency, but also stabilized the assembled multi-level structures especially for promoting the complicated 3D DNA hydrogel formation. This study develops a novel strategy for rapid and high-yield production of DNA hydrogel even derived from instable building blocks at relatively low DNA concentrations, which would endow DNA nanotechnology for more practical applications.

  2. Polymorphic Ring-Shaped Molecular Clusters Made of Shape-Variable Building Blocks

    Directory of Open Access Journals (Sweden)

    Keitel Cervantes-Salguero

    2015-02-01

    Full Text Available Self-assembling molecular building blocks able to dynamically change their shapes, is a concept that would offer a route to reconfigurable systems. Although simulation studies predict novel properties useful for applications in diverse fields, such kinds of building blocks, have not been implemented thus far with molecules. Here, we report shape-variable building blocks fabricated by DNA self-assembly. Blocks are movable enough to undergo shape transitions along geometrical ranges. Blocks connect to each other and assemble into polymorphic ring-shaped clusters via the stacking of DNA blunt-ends. Reconfiguration of the polymorphic clusters is achieved by the surface diffusion on mica substrate in response to a monovalent salt concentration. This work could inspire novel reconfigurable self-assembling systems for applications in molecular robotics.

  3. A new building block for DNA network formation by self-assembly and polymerase chain reaction.

    Science.gov (United States)

    Bußkamp, Holger; Keller, Sascha; Robotta, Marta; Drescher, Malte; Marx, Andreas

    2014-01-01

    The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.

  4. Creating Metamaterial Building Blocks with Directed Photochemical Metallization of Silver onto DNA Origami Templates.

    Science.gov (United States)

    Hossen, Md Mir; Bendickson, Lee; Palo, Pierre; Yao, Zhiqi; Nilsen-Hamilton, Marit; Hillier, Andrew C

    2018-06-07

    DNA origami can be used to create a variety of complex and geometrically unique nanostructures that can be further modified to produce building blocks for applications such as in optical metamaterials. We describe a method for creating metal-coated nanostructures using DNA origami templates and a photochemical metallization technique. Triangular DNA origami were fabricated and coated with a thin metal layer by photochemical silver reduction while either in solution or supported on a surface. The DNA origami template serves as a localized photosensitizer to facilitate reduction of silver ions directly from solution onto the DNA surface. The metallizing process is shown to result in a conformal metal coating, which grows in height to a self-limiting value with increasing photoreduction steps. Although this coating process results in a slight decrease in the triangle dimensions, the overall template shape is retained. Notably, this coating method exhibits characteristics of self-limiting and defect-filling growth, which results in a metal nanostructure that maps the shape of the original origami template with a continuous and uniform metal layer and stops growing once all available DNA sites are exhausted. © 2018 IOP Publishing Ltd.

  5. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

    Science.gov (United States)

    Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

    2015-01-01

    Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.

  6. Hierarchical coassembly of DNA–triptycene hybrid molecular building blocks and zinc protoporphyrin IX

    Directory of Open Access Journals (Sweden)

    Rina Kumari

    2016-05-01

    Full Text Available Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA–DNA building blocks and zinc protoporphyrin IX (Zn PpIX. DNA–organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5′-C12-amine-terminated modified single strand DNA (ssDNA and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE, reverse-phase high-performance liquid chromatography (RP-HPLC and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF. The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA–TPA molecular building blocks as well as a model guest molecule within the DNA–TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD and atomic force microscopy (AFM have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA–TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA–DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA–TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT applications as well as photocatalytic reactions.

  7. Synthesis of a Hoechst 32258 Analogue Amino Acid Building Block for Direct Incorporation of a Fluorescent High-Affinity DNA Binding Motif into Peptides

    DEFF Research Database (Denmark)

    Harrit, Niels; Behrens, Carsten; Nielsen, P. E.

    2001-01-01

    The synthesis of a new versatile "Hoechst 33258-like" Boc-protected amino acid building block for peptide synthesis is described. It is demonstrated that this new ligand is an effective mimic of Hoechst 33258 in terms of DNA affinity and sequence specificity. Furthermore, this minor groove binder...

  8. Toward Applications for DNA Nanotechnology-More Bricks To Build With.

    Science.gov (United States)

    Dietz, Hendrik

    2016-06-16

    Another brick in the wall: DNA nanotechnology has come a long way since its initial beginnings. This would not be possible without the continued development of methods for DNA assembly and new uses for DNA as a material. This Special Issue highlights some of the newest building blocks for nanodevices based on DNA. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. A Novel Tetrathiafulvalene Building Block

    DEFF Research Database (Denmark)

    Jeppesen, Jan Oskar; Takimiya, Kazuo; Thorup, Niels

    1999-01-01

    Efficient synthesis of a novel tetrathiafulvalene building block. 2,3-bis(2-cyanoethylthio)-6,7-bis(thiocyanato-methyl)tetrathiafulv alene (7) useful for stepwise and asymmetrical bis-function-alization is reported.......Efficient synthesis of a novel tetrathiafulvalene building block. 2,3-bis(2-cyanoethylthio)-6,7-bis(thiocyanato-methyl)tetrathiafulv alene (7) useful for stepwise and asymmetrical bis-function-alization is reported....

  10. Building Curriculum during Block Play

    Science.gov (United States)

    Andrews, Nicole

    2015-01-01

    Blocks are not just for play! In this article, Nicole Andrews describes observing the interactions of three young boys enthusiastically engaged in the kindergarten block center of their classroom, using blocks in a building project that displayed their ability to use critical thinking skills, physics exploration, and the development of language…

  11. NANOSTRUCTURED METAL OXIDE CATALYSTS VIA BUILDING BLOCK SYNTHESES

    Energy Technology Data Exchange (ETDEWEB)

    Craig E. Barnes

    2013-03-05

    A broadly applicable methodology has been developed to prepare new single site catalysts on silica supports. This methodology requires of three critical components: a rigid building block that will be the main structural and compositional component of the support matrix; a family of linking reagents that will be used to insert active metals into the matrix as well as cross link building blocks into a three dimensional matrix; and a clean coupling reaction that will connect building blocks and linking agents together in a controlled fashion. The final piece of conceptual strategy at the center of this methodology involves dosing the building block with known amounts of linking agents so that the targeted connectivity of a linking center to surrounding building blocks is obtained. Achieving targeted connectivities around catalytically active metals in these building block matrices is a critical element of the strategy by which single site catalysts are obtained. This methodology has been demonstrated with a model system involving only silicon and then with two metal-containing systems (titanium and vanadium). The effect that connectivity has on the reactivity of atomically dispersed titanium sites in silica building block matrices has been investigated in the selective oxidation of phenols to benezoquinones. 2-connected titanium sites are found to be five times as active (i.e. initial turnover frequencies) than 4-connected titanium sites (i.e. framework titanium sites).

  12. High-Throughput Block Optical DNA Sequence Identification.

    Science.gov (United States)

    Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

    2018-01-01

    Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Building Blocks for Personal Brands

    Science.gov (United States)

    Thomas, Lisa Carlucci

    2011-01-01

    In this article, the author discusses the four essential building blocks for personal brands: (1) name; (2) message; (3) channels; and (4) bridges. However, outstanding building materials can only take a person so far. The author emphasizes that vision, determination, faith, a sense of humor, and humility are also required.

  14. Identification of critical technology building blocks

    DEFF Research Database (Denmark)

    Ravn, Poul Martin; Mortensen, Niels Henrik; Hvam, Lars

    2017-01-01

    on competition, the challenge is to know how to identify and prioritize the development tasks. If possible, an effective strategy can be defined. This article suggests a framework for identification and analysis of a product portfolio, with special emphasis on identifying critical technology building blocks...... development steps. The framework is based on methods and theories in literature. The analysis of the portfolio is carried out through the framework in three steps: by creating an overview of the portfolio encompassing product and technology, assessing the elements in the overview with assessment metrics......, and using property chains to identify critical technology building blocks....

  15. Large N saddle formulation of quadratic building block theories

    International Nuclear Information System (INIS)

    Halpern, M.B.

    1980-01-01

    I develop a large N saddle point formulation for the broad class of 'theories of quadratic building blocks'. Such theories are those on which the sums over internal indices are contained in quadratic building blocks, e.g. PHI 2 = Σsup(N)sub(a-1)PHi sup(a)sup(a). The formulation applies as well to fermions, derivative coupling and non-polynomial interactions. In a related development, closed Schwinger-Dyson equations for Green functions of the building blocks are derived and solved for large N. (orig.)

  16. Sortase-Mediated Ligation of Purely Artificial Building Blocks

    Directory of Open Access Journals (Sweden)

    Xiaolin Dai

    2018-02-01

    Full Text Available Sortase A (SrtA from Staphylococcus aureus has been often used for ligating a protein with other natural or synthetic compounds in recent years. Here we show that SrtA-mediated ligation (SML is universally applicable for the linkage of two purely artificial building blocks. Silica nanoparticles (NPs, poly(ethylene glycol and poly(N-isopropyl acrylamide are chosen as synthetic building blocks. As a proof of concept, NP–polymer, NP–NP, and polymer–polymer structures are formed by SrtA catalysis. Therefore, the building blocks are equipped with the recognition sequence needed for SrtA reaction—the conserved peptide LPETG—and a pentaglycine motif. The successful formation of the reaction products is shown by means of transmission electron microscopy (TEM, matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF MS, and dynamic light scattering (DLS. The sortase catalyzed linkage of artificial building blocks sets the stage for the development of a new approach to link synthetic structures in cases where their synthesis by established chemical methods is complicated.

  17. Single molecule magnets from magnetic building blocks

    Science.gov (United States)

    Kroener, W.; Paretzki, A.; Cervetti, C.; Hohloch, S.; Rauschenbach, S.; Kern, K.; Dressel, M.; Bogani, L.; M&üLler, P.

    2013-03-01

    We provide a basic set of magnetic building blocks that can be rationally assembled, similar to magnetic LEGO bricks, in order to create a huge variety of magnetic behavior. Using rare-earth centers and multipyridine ligands, fine-tuning of intra and intermolecular exchange interaction is demonstrated. We have investigated a series of molecules with monomeric, dimeric and trimeric lanthanide centers using SQUID susceptometry and Hall bar magnetometry. A home-made micro-Hall-probe magnetometer was used to measure magnetic hysteresis loops at mK temperatures and fields up to 17 T. All compounds show hysteresis below blocking temperatures of 3 to 4 K. The correlation of the assembly of the building blocks with the magnetic properties will be discussed.

  18. A Traceless Aryl-Triazene Linker for DNA-Directed Chemistry

    DEFF Research Database (Denmark)

    Hejesen, Christian; Pedersen, Lars Kolster; Gothelf, Kurt Vesterager

    2013-01-01

    DNA-directed synthesis of encoded combinatorial libraries of small organic compounds most often involves transfer of organic building blocks from one DNA strand to another. This requires cleavable linkers to enable cleavage of the link to the original DNA strand from which the building block...... is transferred. Relatively few cleavable linkers are available for DNA-directed synthesis and most often they leave an amino group at the organic molecule. Here we have extended the application of 10 aryltriazenes as traceless linkers for DNA-directed synthesis. After reaction of one building block...

  19. Divergent synthesis and optoelectronic properties of oligodiacetylene building blocks

    NARCIS (Netherlands)

    Pilzak, G.S.; Lagen, van B.; Sudhölter, E.J.R.; Zuilhof, H.

    2008-01-01

    A new and divergent synthetic route to oligodiacetylene (ODA) building blocks has been developed via Sonogashira reactions under a reductive atmosphere. These central building blocks provide a new way for rapid preparation of long ODAs. In addition, we report on their optoelectronic properties which

  20. Customizable Visualizations with Formula-Linked Building Blocks

    DEFF Research Database (Denmark)

    Kuhail, Mohammad Amin; Lauesen, Søren

    different appearance or behavior than what the widgets support. Another approach is to combine primitive graphical elements using traditional programming or visualization toolkits. Traditional programming allows high customizability, but it is time consuming and hard to develop advanced visualizations......One approach to visualization construction is to use complex blocks (widgets) that are tailored for specific visualizations, and customize the visualizations by setting the properties of the widgets. This approach allows fast and easy visualization construction but falls short if the user wants....... Visualization toolkits allow easier visualization creation in some cases, but customization and interaction are tedious. As an alternative, we developed uVis visualization tool that uses spreadsheet-like formulas to connect building blocks. uVis formulas can refer to building blocks and database tables. We...

  1. DNA functionalization by dynamic chemistry

    Directory of Open Access Journals (Sweden)

    Zeynep Kanlidere

    2016-10-01

    Full Text Available Dynamic combinatorial chemistry (DCC is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80% was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.

  2. Characteristics of Recycled Concrete Aggregates from Precast Slab Block Buildings

    Science.gov (United States)

    Venkrbec, Václav; Nováková, Iveta; Henková, Svatava

    2017-10-01

    Precast slab block buildings (PSBB) typically and frequently occur in Central and Eastern Europe, as well as elsewhere in the world. Some of these buildings are currently used beyond their service life capacity. The utilization of recycled materials from these buildings with regard to applying the principles of sustainable construction and using recycled materials will probably be significant in the following years. Documentation from the manufacturing processes of prefabricated blocks for precast slab block buildings is not available, and also it is difficult to declare technological discipline during the construction of these buildings. Therefore, properties of recycled concrete aggregates (RCA) produced from construction and demolition waste (C&DW) of precast slab block buildings build between 1950s to 1990s are not sufficiently known. The demolition of these buildings is very rare today, but it can be assumed an increase in demolitions of these buildings in the future. The use of RCA in new concrete requires verification/testing of the geometrical and physical properties of RCA according to the EN 12 620+A1 standard. The aim of the contribution is to present a case study of the demolition of slab block building with emphasis on RCA usage. The paper presents the results of the tests according to European standards for determining selected geometrical and physical properties of the RCA. The paper describes and evaluates tests such as determination of particle size distribution - Sieve Analysis, content of fine particles, determination of density and water absorption. The results of the properties testing of RCA are compared with the properties of natural aggregate. The general boundary conditions of RCA particular tests are presented.

  3. A droplet-based building block approach for bladder smooth muscle cell (SMC) proliferation

    Energy Technology Data Exchange (ETDEWEB)

    Xu, F; Moon, S J; Emre, A E; Turali, E S; Song, Y S; Hacking, S A; Demirci, U [Department of Medicine, Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Nagatomi, J, E-mail: udemirci@rics.bwh.harvard.ed [Department of Bioengineering, Clemson University, Clemson, SC (United States)

    2010-03-15

    Tissue engineering based on building blocks is an emerging method to fabricate 3D tissue constructs. This method requires depositing and assembling building blocks (cell-laden microgels) at high throughput. The current technologies (e.g., molding and photolithography) to fabricate microgels have throughput challenges and provide limited control over building block properties (e.g., cell density). The cell-encapsulating droplet generation technique has potential to address these challenges. In this study, we monitored individual building blocks for viability, proliferation and cell density. The results showed that (i) SMCs can be encapsulated in collagen droplets with high viability (>94.2 +- 3.2%) for four cases of initial number of cells per building block (i.e. 7 +- 2, 16 +- 2, 26 +- 3 and 37 +- 3 cells/building block). (ii) Encapsulated SMCs can proliferate in building blocks at rates that are consistent (1.49 +- 0.29) across all four cases, compared to that of the controls. (iii) By assembling these building blocks, we created an SMC patch (5 mm x 5 mm x 20 mum), which was cultured for 51 days forming a 3D tissue-like construct. The histology of the cultured patch was compared to that of a native rat bladder. These results indicate the potential of creating 3D tissue models at high throughput in vitro using building blocks.

  4. Solid-phase route to Fmoc-protected cationic amino acid building blocks

    DEFF Research Database (Denmark)

    Clausen, Jacob Dahlqvist; Linderoth, Lars; Nielsen, Hanne Mørck

    2012-01-01

    Diamino acids are commonly found in bioactive compounds, yet only few are commercially available as building blocks for solid-phase peptide synthesis. In the present work a convenient, inexpensive route to multiple-charged amino acid building blocks with varying degree of hydrophobicity...... was developed. A versatile solid-phase protocol leading to selectively protected amino alcohol intermediates was followed by oxidation to yield the desired di- or polycationic amino acid building blocks in gram-scale amounts. The synthetic sequence comprises loading of (S)-1-(p-nosyl)aziridine-2-methanol onto...... of simple neutral amino acids as well as analogs displaying high bulkiness or polycationic side chains was prepared. Two building blocks were incorporated into peptide sequences using microwave-assisted solid-phase peptide synthesis confirming their general utility....

  5. Internet of Things building blocks and business models

    CERN Document Server

    Hussain, Fatima

    2017-01-01

    This book describes the building blocks and introductory business models for Internet of Things (IoT). The author provide an overview of the entire IoT architecture and constituent layers, followed by detail description of each block . Various inter-connecting technologies and sensors are discussed in context of IoT networks. In addition to this, concepts of Big Data and Fog Computing are presented and characterized as per data generated by versatile IoT applications . Smart parking system and context aware services are presented as an hybrid model of cloud and Fog Afterwards, various IoT applications and respective business models are discussed. Finally, author summarizes the IoT building blocks and identify research issues in each, and suggest potential research projects worthy of pursuing. .

  6. Building Blocks: Enmeshing Technology and Creativity with Artistic Pedagogical Technologies

    Science.gov (United States)

    Janzen, Katherine J.; Perry, Beth; Edwards, Margaret

    2017-01-01

    Using the analogy of children's building blocks, the reader is guided through the results of a research study that explored the use of three Artistic Pedagogical Technologies (APTs). "Building blocks" was the major theme that emerged from the data. Sub-themes included developing community, enhancing creativity, and risk taking. The…

  7. Elementary structural building blocks encountered in silicon surface reconstructions

    International Nuclear Information System (INIS)

    Battaglia, Corsin; Monney, Claude; Didiot, Clement; Schwier, Eike Fabian; Garnier, Michael Gunnar; Aebi, Philipp; Gaal-Nagy, Katalin; Onida, Giovanni

    2009-01-01

    Driven by the reduction of dangling bonds and the minimization of surface stress, reconstruction of silicon surfaces leads to a striking diversity of outcomes. Despite this variety even very elaborate structures are generally comprised of a small number of structural building blocks. We here identify important elementary building blocks and discuss their integration into the structural models as well as their impact on the electronic structure of the surface. (topical review)

  8. Tops as building blocks for G 2 manifolds

    Science.gov (United States)

    Braun, Andreas P.

    2017-10-01

    A large number of examples of compact G 2 manifolds, relevant to supersymmetric compactifications of M-Theory to four dimensions, can be constructed by forming a twisted connected sum of two building blocks times a circle. These building blocks, which are appropriate K3-fibred threefolds, are shown to have a natural and elegant construction in terms of tops, which parallels the construction of Calabi-Yau manifolds via reflexive polytopes. In particular, this enables us to prove combinatorial formulas for the Hodge numbers and other relevant topological data.

  9. Two innovative solutions based on fibre concrete blocks designed for building substructure

    Science.gov (United States)

    Pazderka, J.; Hájek, P.

    2017-09-01

    Using of fibers in a high-strength concrete allows reduction of the dimensions of small precast concrete elements, which opens up new ways of solution for traditional construction details in buildings. The paper presents two innovative technical solutions for building substructure: The special shaped plinth block from fibre concrete and the fibre concrete elements for new technical solution of ventilated floor. The main advantages of plinth block from fibre concrete blocks (compared with standard plinth solutions) is: easier and faster assembly, higher durability and thanks to the air cavity between the vertical part of the block, the building substructure reduced moisture level of structures under the waterproofing layer and a comprehensive solution to the final surface of building plinth as well as the surface of adjacent terrain. The ventilated floor based on fibre concrete precast blocks is an attractive structural alternative for tackling the problem of increased moisture in masonry in older buildings, lacking a functional waterproof layer in the substructure.

  10. Essential Building Blocks of Human Nature

    CERN Document Server

    Frey, Ulrich J; Willführ, Kai P

    2011-01-01

    To understand why we humans are as we are, it is necessary to look at the essential building blocks that comprise our nature. The foundations of this structure are our evolutionary origins as primates and our social roots. Upon these rest features such as our emotions, language and aesthetic preferences, with our self-perceptions, self-deceptions and thirst for knowledge right at the top. The unifying force holding these blocks together is evolutionary theory. Evolution provides a deeper understanding of human nature and, in particular, of the common roots of these different perspectives. To build a reliable and coherent model of man, leading authors from fields as diverse as primatology, anthropology, neurobiology and philosophy have joined forces to present essays  each describing their own expert perspective. Together they provide a convincing and complete picture of our own human nature.

  11. Polarizability of DNA Block Copolymer Nanoparticles Observed by Electrostatic Force Microscopy

    NARCIS (Netherlands)

    Sowwan, Mukhles; Faroun, Maryam; Mentovich, Elad; Ibrahim, Imad; Haboush, Shayma; Alemdaroglu, Fikri Emrah; Kwak, Minseok; Richter, Shachar; Herrmann, Andreas

    2010-01-01

    In this study, DNA block copolymer (DBC) micelles with a polystyrene (PS) core and a single-stranded (ss) DNA shell were doped with ferrocene (Fc) molecules. Tapping mode atomic force microscopy (AFM) was used to study the morphology of the doped and undoped block copolymer aggregates. We show that

  12. Principles of DNA architectonics: design of DNA-based nanoobjects

    International Nuclear Information System (INIS)

    Vinogradova, O A; Pyshnyi, D V

    2012-01-01

    The methods of preparation of monomeric DNA blocks that serve as key building units for the construction of complex DNA objects are described. Examples are given of the formation of DNA blocks based on native and modified oligonucleotide components using hydrogen bonding and nucleic acid-specific types of bonding and also some affinity interactions with RNA, proteins, ligands. The static discrete and periodic two- and three-dimensional DNA objects reported to date are described systematically. Methods used to prove the structures of DNA objects and the prospects for practical application of nanostructures based on DNA and its analogues in biology, medicine and biophysics are considered. The bibliography includes 195 references.

  13. Optically controlled three-dimensional assembly of microfabricated building blocks

    DEFF Research Database (Denmark)

    Rodrigo, Peter John; Kelemen, Lorand; Palima, Darwin

    2009-01-01

    We demonstrate a system for constructing reconfigurable microstructures using multiple, real-time configurable counterpropagating-beam traps. We optically assemble geometrically complementary microstructures with complex three-dimensional (3D) topologies produced by two-photon polymerization....... This demonstrates utilization of controllable 3D optical traps for building hierarchical structures from microfabricated building blocks. Optical microassembly with translational and tip-tilt control in 3D achieved by dynamic multiple CB traps can potentially facilitate the construction of functional microdevices...... and may also lead to the future realization of optically actuated micromachines. Fabricating morphologically complex microstructures and then optically manipulating these archetypal building blocks can also be used to construct reconfigurable microenvironments that can aid in understanding cellular...

  14. DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks.

    Science.gov (United States)

    Guyard, Alice; Boyez, Alice; Pujals, Anaïs; Robe, Cyrielle; Tran Van Nhieu, Jeanne; Allory, Yves; Moroch, Julien; Georges, Odette; Fournet, Jean-Christophe; Zafrani, Elie-Serge; Leroy, Karen

    2017-10-01

    Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5.5 years. Quantitation of DNA by fluorimetry showed a 53% decrease in DNA quantity after storage. Quantitative PCR (qPCR) targeting KRAS exon 2 showed delayed amplification of DNA extracted after storage in all samples but one. The qPCR/fluorimetry quantification ratio decreased from 56 to 15% after storage (p DNA analyzable by qPCR represented only 11% of the amount obtained at first extraction. Maximal length of amplifiable DNA fragments assessed with a multiplex PCR was reduced in DNA extracted from stored tissue, indicating that DNA fragmentation had increased in the paraffin blocks during storage. Next-generation sequencing was performed on 12 samples and showed a mean 3.3-fold decrease in library yield and a mean 4.5-fold increase in the number of single-nucleotide variants detected after storage. In conclusion, we observed significant degradation of DNA extracted from the same FFPE block after 4 to 6 years of storage. Better preservation strategies should be considered for storage of FFPE biopsy specimens.

  15. Demand Response Technology Readiness Levels for Energy Management in Blocks of Buildings

    Directory of Open Access Journals (Sweden)

    Tracey Crosbie

    2018-01-01

    Full Text Available Fossil fuels deliver most of the flexibility in contemporary electricity systems. The pressing need to reduce CO2 emissions requires new methods to provide this flexibility. Demand response (DR offers consumers a significant role in the delivery of flexibility by reducing or shifting their electricity usage during periods of stress or constraint. Blocks of buildings offer more flexibility in the timing and use of energy than single buildings, however, and a lack of relevant scalable ICT tools hampers DR in blocks of buildings. To ameliorate this problem, a current innovation project called “Demand Response in Blocks of Buildings” (DR-BoB: www.dr-bob.eu has integrated existing technologies into a scalable cloud-based solution for DR in blocks of buildings. The degree to which the DR-BoB energy management solution can increase the ability of any given site to participate in DR is dependent upon its current energy systems, i.e., the energy metering, the telemetry and control technologies in building management systems, and the existence/capacity of local power generation and storage plants. To encourage the owners and managers of blocks of buildings to participate in DR, a method of assessing and validating the technological readiness to participate in DR energy management solutions at any given site is required. This paper describes the DR-BoB energy management solution and outlines what we have called the demand response technology readiness levels (DRTRLs for the implementation of such a solution in blocks of buildings.

  16. Building Blocks for Sustainable Communities: Assistance from Grantees

    Science.gov (United States)

    EPA awarded Building Blocks for Sustainable Communities grants to four nonprofit organizations with extensive expertise in community sustainability. These organizations deliver technical assistance to communities.

  17. Synthesis of homo- and heteromultivalent carbohydrate-functionalized oligo(amidoamines using novel glyco-building blocks

    Directory of Open Access Journals (Sweden)

    Felix Wojcik

    2013-11-01

    Full Text Available We present the solid phase synthesis of carbohydrate-functionalized oligo(amidoamines with different functionalization patterns utilizing a novel alphabet of six differently glycosylated building blocks. Highly efficient in flow conjugation of thioglycosides to a double-bond presenting diethylentriamine precursor is the key step to prepare these building blocks suitable for fully automated solid-phase synthesis. Introduction of the sugar ligands via functionalized building blocks rather than postfunctionalization of the oligomeric backbone allows for the straightforward synthesis of multivalent glycoligands with full control over monomer sequence and functionalization pattern. We demonstrate the potential of this building-block approach by synthesizing oligomers with different numbers and spacing of carbohydrates and also show the feasibility of heteromultivalent glycosylation patterns by combining building blocks presenting different mono- and disaccharides.

  18. Are lesions induced by ionizing radiation direct blocks to DNA chain elongation

    International Nuclear Information System (INIS)

    Painter, R.B.

    1983-01-01

    Ionizing radiation blocks DNA chain elongation in normal diploid fibroblasts but not in fibroblasts from patients with ataxia-telangiectasia, even though there are no differences in the damage induced between the two cell types. This difference suggests that radiation-induced lesions in DNA are not themselves blocks to chain elongation in ataxia cells and raises the possibility that in normal cells a mediator exists between DNA damage and chain termination

  19. Block assembly for global registration of building scans

    KAUST Repository

    Yan, Feilong; Nan, Liangliang; Wonka, Peter

    2016-01-01

    We propose a framework for global registration of building scans. The first contribution of our work is to detect and use portals (e.g., doors and windows) to improve the local registration between two scans. Our second contribution is an optimization based on a linear integer programming formulation. We abstract each scan as a block and model the blocks registration as an optimization problem that aims at maximizing the overall matching score of the entire scene. We propose an efficient solution to this optimization problem by iteratively detecting and adding local constraints. We demonstrate the effectiveness of the proposed method on buildings of various styles and that our approach is superior to the current state of the art.

  20. Block assembly for global registration of building scans

    KAUST Repository

    Yan, Feilong

    2016-11-11

    We propose a framework for global registration of building scans. The first contribution of our work is to detect and use portals (e.g., doors and windows) to improve the local registration between two scans. Our second contribution is an optimization based on a linear integer programming formulation. We abstract each scan as a block and model the blocks registration as an optimization problem that aims at maximizing the overall matching score of the entire scene. We propose an efficient solution to this optimization problem by iteratively detecting and adding local constraints. We demonstrate the effectiveness of the proposed method on buildings of various styles and that our approach is superior to the current state of the art.

  1. THE USAGE OF FACEBOOK FUNCTIONAL BUILDING BLOCKS IN UNISEL

    Directory of Open Access Journals (Sweden)

    Latifah Abd Latib

    2015-08-01

    Full Text Available The emergence of Internet-based social media has made it possible for a personto communicate with thousands of other people to increase the communicationeffectiveness, collaboration among internal organization and knowledge sharing.By engaging employees through social media such as Facebook as a two-waycommunications tool, employers can reach a larger audience and build credibilitywith techno-savvy workers. Although it is clear that Facebook is a very powerfultool for communication, many employers are unable to identify the functionalityof Facebook in terms of developing strategies and to allocate the resourceseffectively. Taking this into account this study sought to identify the usage ofFacebook Functionality building blocks. This survey involved 55 academic staffsfrom the Faculty of Computer Science and Information Technology, Unisel. Theseven functional building blocks identified were Identity (M=3.39, Relationships(M=3.39, Groups (M=3.6, Presence (M=3.28, Sharing (M=3.06, andConversations (M=2.90, Reputation (M=2.05. This study suggests that theability to identify the functional building blocks itself is very important in anorganization in terms of developing their communication strategies. It is hopedthat the results of the study will be applicable to the instituition, current users,and potential users of Facebook.

  2. Building blocks for modular data acquisition systems

    Energy Technology Data Exchange (ETDEWEB)

    Hoffmann, B

    1996-12-31

    The principles of building blocks for modular data acquisition systems by means of the VIC bus are discussed. Real time operating systems based on the VME environment for program development drastically reducing the time needed to develop a working system. 4 figs.

  3. Building blocks of Collagen based biomaterial devices

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Building blocks of Collagen based biomaterial devices. Collagen as a protein. Collagen in tissues and organs. Stabilizing and cross linking agents. Immunogenicity. Hosts (drugs). Controlled release mechanisms of hosts. Biodegradability, workability into devices ...

  4. Hydration effects on the electronic properties of eumelanin building blocks

    International Nuclear Information System (INIS)

    Assis Oliveira, Leonardo Bruno; Fonseca, Tertius L.; Costa Cabral, Benedito J.; Coutinho, Kaline; Canuto, Sylvio

    2016-01-01

    Theoretical results for the electronic properties of eumelanin building blocks in the gas phase and water are presented. The building blocks presently investigated include the monomeric species DHI (5,6-dihydroxyindole) or hydroquinone (HQ), DHICA (5,6-dihydroxyindole-2-carboxylic acid), indolequinone (IQ), quinone methide (MQ), two covalently bonded dimers [HM ≡ HQ + MQ and IM ≡ IQ + MQ], and two tetramers [HMIM ≡ HQ + IM, IMIM ≡ IM + IM]. The electronic properties in water were determined by carrying out sequential Monte Carlo/time dependent density functional theory calculations. The results illustrate the role played by hydrogen bonding and electrostatic interactions in the electronic properties of eumelanin building blocks in a polar environment. In water, the dipole moments of monomeric species are significantly increased ([54–79]%) relative to their gas phase values. Recently, it has been proposed that the observed enhancement of the higher-energy absorption intensity in eumelanin can be explained by excitonic coupling among eumelanin protomolecules [C.-T. Chen et al., Nat. Commun. 5, 3859 (2014)]. Here, we are providing evidence that for DHICA, IQ, and HMIM, the electronic absorption toward the higher-energy end of the spectrum ([180–220] nm) is enhanced by long-range Coulombic interactions with the water environment. It was verified that by superposing the absorption spectra of different eumelanin building blocks corresponding to the monomers, dimers, and tetramers in liquid water, the behaviour of the experimental spectrum, which is characterised by a nearly monotonic decay from the ultraviolet to the infrared, is qualitatively reproduced. This result is in keeping with a “chemical disorder model,” where the broadband absorption of eumelanin pigments is determined by the superposition of the spectra associated with the monomeric and oligomeric building blocks.

  5. Hydration effects on the electronic properties of eumelanin building blocks

    Energy Technology Data Exchange (ETDEWEB)

    Assis Oliveira, Leonardo Bruno [Instituto de Física da Universidade Federal de Goiás, 74690-900 Goiânia, GO (Brazil); Departamento de Física - CEPAE, Universidade Federal de Goiás, 74690-900 Goiânia, GO (Brazil); Escola de Ciências Exatas e da Computação, Pontifícia Universidade Católica de Goiás, 74605-010 Goiânia, GO (Brazil); Fonseca, Tertius L. [Instituto de Física da Universidade Federal de Goiás, 74690-900 Goiânia, GO (Brazil); Costa Cabral, Benedito J., E-mail: ben@cii.fc.ul.pt [Grupo de Física Matemática da Universidade de Lisboa and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa (Portugal); Coutinho, Kaline; Canuto, Sylvio [Instituto de Física da Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP (Brazil)

    2016-08-28

    Theoretical results for the electronic properties of eumelanin building blocks in the gas phase and water are presented. The building blocks presently investigated include the monomeric species DHI (5,6-dihydroxyindole) or hydroquinone (HQ), DHICA (5,6-dihydroxyindole-2-carboxylic acid), indolequinone (IQ), quinone methide (MQ), two covalently bonded dimers [HM ≡ HQ + MQ and IM ≡ IQ + MQ], and two tetramers [HMIM ≡ HQ + IM, IMIM ≡ IM + IM]. The electronic properties in water were determined by carrying out sequential Monte Carlo/time dependent density functional theory calculations. The results illustrate the role played by hydrogen bonding and electrostatic interactions in the electronic properties of eumelanin building blocks in a polar environment. In water, the dipole moments of monomeric species are significantly increased ([54–79]%) relative to their gas phase values. Recently, it has been proposed that the observed enhancement of the higher-energy absorption intensity in eumelanin can be explained by excitonic coupling among eumelanin protomolecules [C.-T. Chen et al., Nat. Commun. 5, 3859 (2014)]. Here, we are providing evidence that for DHICA, IQ, and HMIM, the electronic absorption toward the higher-energy end of the spectrum ([180–220] nm) is enhanced by long-range Coulombic interactions with the water environment. It was verified that by superposing the absorption spectra of different eumelanin building blocks corresponding to the monomers, dimers, and tetramers in liquid water, the behaviour of the experimental spectrum, which is characterised by a nearly monotonic decay from the ultraviolet to the infrared, is qualitatively reproduced. This result is in keeping with a “chemical disorder model,” where the broadband absorption of eumelanin pigments is determined by the superposition of the spectra associated with the monomeric and oligomeric building blocks.

  6. Molecular Clusters: Nanoscale Building Blocks for Solid-State Materials.

    Science.gov (United States)

    Pinkard, Andrew; Champsaur, Anouck M; Roy, Xavier

    2018-04-17

    The programmed assembly of nanoscale building blocks into multicomponent hierarchical structures is a powerful strategy for the bottom-up construction of functional materials. To develop this concept, our team has explored the use of molecular clusters as superatomic building blocks to fabricate new classes of materials. The library of molecular clusters is rich with exciting properties, including diverse functionalization, redox activity, and magnetic ordering, so the resulting cluster-assembled solids, which we term superatomic crystals (SACs), hold the promise of high tunability, atomic precision, and robust architectures among a diverse range of other material properties. Molecular clusters have only seldom been used as precursors for functional materials. Our team has been at the forefront of new developments in this exciting research area, and this Account focuses on our progress toward designing materials from cluster-based precursors. In particular, this Account discusses (1) the design and synthesis of molecular cluster superatomic building blocks, (2) their self-assembly into SACs, and (3) their resulting collective properties. The set of molecular clusters discussed herein is diverse, with different cluster cores and ligand arrangements to create an impressive array of solids. The cluster cores include octahedral M 6 E 8 and cubane M 4 E 4 (M = metal; E = chalcogen), which are typically passivated by a shell of supporting ligands, a feature upon which we have expanded upon by designing and synthesizing more exotic ligands that can be used to direct solid-state assembly. Building from this library, we have designed whole families of binary SACs where the building blocks are held together through electrostatic, covalent, or van der Waals interactions. Using single-crystal X-ray diffraction (SCXRD) to determine the atomic structure, a remarkable range of compositional variability is accessible. We can also use this technique, in tandem with vibrational

  7. Analog Organic Electronics Building Blocks for Organic Smart Sensor Systems on Foil

    CERN Document Server

    Marien, Hagen; Heremans, Paul

    2013-01-01

     This book provides insight into organic electronics technology and in analog circuit techniques that can be used to increase the performance of both analog and digital organic circuits. It explores the domain of organic electronics technology for analog circuit applications, specifically smart sensor systems.  It focuses on all the building blocks in the data path of an organic sensor system between the sensor and the digital processing block. Sensors, amplifiers, analog-to-digital converters and DC-DC converters are discussed in detail. Coverage includes circuit techniques, circuit implementation, design decisions and measurement results of the building blocks described. Offers readers the first book to focus on analog organic circuit design; Discusses organic electronics technology for analog circuit applications in the context of smart sensor systems; Describes all building blocks necessary for an organic sensor system between the sensor and the digital processing block; Includes circuit techniques, cir...

  8. Building blocks for protein interaction devices

    Science.gov (United States)

    Grünberg, Raik; Ferrar, Tony S.; van der Sloot, Almer M.; Constante, Marco; Serrano, Luis

    2010-01-01

    Here, we propose a framework for the design of synthetic protein networks from modular protein–protein or protein–peptide interactions and provide a starter toolkit of protein building blocks. Our proof of concept experiments outline a general work flow for part–based protein systems engineering. We streamlined the iterative BioBrick cloning protocol and assembled 25 synthetic multidomain proteins each from seven standardized DNA fragments. A systematic screen revealed two main factors controlling protein expression in Escherichia coli: obstruction of translation initiation by mRNA secondary structure or toxicity of individual domains. Eventually, 13 proteins were purified for further characterization. Starting from well-established biotechnological tools, two general–purpose interaction input and two readout devices were built and characterized in vitro. Constitutive interaction input was achieved with a pair of synthetic leucine zippers. The second interaction was drug-controlled utilizing the rapamycin-induced binding of FRB(T2098L) to FKBP12. The interaction kinetics of both devices were analyzed by surface plasmon resonance. Readout was based on Förster resonance energy transfer between fluorescent proteins and was quantified for various combinations of input and output devices. Our results demonstrate the feasibility of parts-based protein synthetic biology. Additionally, we identify future challenges and limitations of modular design along with approaches to address them. PMID:20215443

  9. Automate Your Physical Plant Using the Building Block Approach.

    Science.gov (United States)

    Michaelson, Matt

    1998-01-01

    Illustrates how Mount Saint Vincent University (Halifax), by upgrading the control and monitoring of one building or section of the school at a time, could produce savings in energy and operating costs and improve the environment. Explains a gradual, "building block" approach to facility automation that provides flexibility without a…

  10. Traveling Rocky Roads: The Consequences of Transcription-Blocking DNA Lesions on RNA Polymerase II.

    Science.gov (United States)

    Steurer, Barbara; Marteijn, Jurgen A

    2017-10-27

    The faithful transcription of eukaryotic genes by RNA polymerase II (RNAP2) is crucial for proper cell function and tissue homeostasis. However, transcription-blocking DNA lesions of both endogenous and environmental origin continuously challenge the progression of elongating RNAP2. The stalling of RNAP2 on a transcription-blocking lesion triggers a series of highly regulated events, including RNAP2 processing to make the lesion accessible for DNA repair, R-loop-mediated DNA damage signaling, and the initiation of transcription-coupled DNA repair. The correct execution and coordination of these processes is vital for resuming transcription following the successful repair of transcription-blocking lesions. Here, we outline recent insights into the molecular consequences of RNAP2 stalling on transcription-blocking DNA lesions and how these lesions are resolved to restore mRNA synthesis. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  11. Functional polymers as nanoscopic building blocks

    International Nuclear Information System (INIS)

    Hernandez-Lopez, J.L.; Bauer, R.E.; Chang, W.-S.; Glasser, G.; Grebel-Koehler, D.; Klapper, M.; Kreiter, M.; Leclaire, J.; Majoral, J.-P.; Mittler, S.; Muellen, K.; Vasilev, K.; Weil, T.; Wu, J.; Zhu, T.; Knoll, W.

    2003-01-01

    Polyphenylene dendrimers are introduced as polymeric building blocks--with a strictly monodisperse particle size distribution within the nanometer range--for the construction of nanostructured materials and devices. The possibility for the introduction of different functionalities in the core, the scaffold or the periphery of the dendrimers offer their use as interesting modules for photonic, electronic or bioactive structures and supramolecular functional assemblies. Thus, dendrimers complement the available set of nanoscopic building blocks made from metals, e.g., Au nanoclusters and semiconductors, e.g., luminescent quantum dots. In a first set of experiments, we describe the fabrication of multilayer architectures using dendrimers with chargeable groups at the surface. This way, the polyelectrolyte deposition technique can be applied for the construction of hybrid layered assemblies with a control of the internal supramolecular structure at the nanometer level. Surface plasmon field-enhanced fluorescence spectroscopy is used to monitor the luminescent properties of dendrimers with a phthalocyanine core integrated into such a multilayer assembly. AFM and SEM micrographs demonstrate the use of surface-functionalized dendrimers (exposing sulfur groups at the periphery) in combination with Au nanoparticles for the controlled assembly of hybrid aggregates as nanoscopic functional devices

  12. Origami-inspired building block and parametric design for mechanical metamaterials

    Science.gov (United States)

    Jiang, Wei; Ma, Hua; Feng, Mingde; Yan, Leilei; Wang, Jiafu; Wang, Jun; Qu, Shaobo

    2016-08-01

    An origami-based building block of mechanical metamaterials is proposed and explained by introducing a mechanism model based on its geometry. According to our model, this origami mechanism supports response to uniaxial tension that depends on structure parameters. Hence, its mechanical properties can be tunable by adjusting the structure parameters. Experiments for poly lactic acid (PLA) samples were carried out, and the results are in good agreement with those of finite element analysis (FEA). This work may be useful for designing building blocks of mechanical metamaterials or other complex mechanical structures.

  13. Origami-inspired building block and parametric design for mechanical metamaterials

    International Nuclear Information System (INIS)

    Jiang, Wei; Ma, Hua; Feng, Mingde; Yan, Leilei; Wang, Jiafu; Wang, Jun; Qu, Shaobo

    2016-01-01

    An origami-based building block of mechanical metamaterials is proposed and explained by introducing a mechanism model based on its geometry. According to our model, this origami mechanism supports response to uniaxial tension that depends on structure parameters. Hence, its mechanical properties can be tunable by adjusting the structure parameters. Experiments for poly lactic acid (PLA) samples were carried out, and the results are in good agreement with those of finite element analysis (FEA). This work may be useful for designing building blocks of mechanical metamaterials or other complex mechanical structures. (paper)

  14. Nano matters: building blocks for a precautionary approach

    NARCIS (Netherlands)

    van Broekhuizen, J.C.

    2012-01-01

    ‘Nano matters’ studies the positioning of civil society organisations (CSOs) regarding the responsible development of nanotechnologies and formulates building blocks for a precautionary approach, as to express the CSOs’ demands towards industry and governmental authorities. The study assesses the

  15. An Approach for On-Board Software Building Blocks Cooperation and Interfaces Definition

    Science.gov (United States)

    Pascucci, Dario; Campolo, Giovanni; Candia, Sante; Lisio, Giovanni

    2010-08-01

    This paper provides an insight on the Avionic SW architecture developed by Thales Alenia Space Italy (TAS-I) to achieve structuring of the OBSW as a set of self-standing and re-usable building blocks. It is initially described the underlying framework for building blocks cooperation, which is based on ECSSE-70 packets forwarding (for services request to a building block) and standard parameters exchange for data communication. Subsequently it is discussed the high level of flexibility and scalability of the resulting architecture, reporting as example an implementation of the Failure Detection, Isolation and Recovery (FDIR) function which exploits the proposed architecture. The presented approach evolves from avionic SW architecture developed in the scope of the project PRIMA (Mult-Purpose Italian Re-configurable Platform) and has been adopted for the Sentinel-1 Avionic Software (ASW).

  16. Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

    DEFF Research Database (Denmark)

    Boessenkool, Sanne; Epp, Laura S.; Haile, James Seymour

    2012-01-01

    the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified....

  17. A new fixation strategy for addressable nano-network building blocks

    KAUST Repository

    Lundberg, Erik P.; El-Sagheer, Afaf H.; Kocalka, Petr; Wilhelmsson, L. Marcus; Brown, Tom; Nordé n, Bengt

    2010-01-01

    Rapid controlled self-assembly makes DNA ideal for building nanostructures. A problem using hybridized intermediates in hierarchic assembly is their thermodynamic lability. We demonstrate a click-fixation technology by which robust hexagonal DNA modules can be made. This principle is applicable to a wide variety of DNA nanoconstructs. © 2010 The Royal Society of Chemistry.

  18. Photovoltaic building blocks

    DEFF Research Database (Denmark)

    Hanberg, Peter Jesper; Jørgensen, Anders Michael

    2014-01-01

    efficiency of about 15% for commercial Silicon solar cells there is still much to gain. DTU Danchip provides research facilities, equipment and expertise for the building blocks that comprises fabricating the efficient solar cell. In order to get more of the sun light into the device we provide thin film......Photovoltaics (PV), better known as solar cells, are now a common day sight on many rooftops in Denmark.The installed capacity of PV systems worldwide is growing exponentially1 and is the third most importantrenewable energy source today. The cost of PV is decreasing fast with ~10%/year but to make...... it directcompetitive with fossil energy sources a further reduction is needed. By increasing the efficiency of the solar cells one gain an advantage through the whole chain of cost. So that per produced Watt of power less material is spent, installation costs are lower, less area is used etc. With an average...

  19. Building Blocks for the Development of Electronics Employees ...

    African Journals Online (AJOL)

    Building Blocks for the Development of Electronics Employees Performance Management System. ... West African Journal of Industrial and Academic Research ... Our approach is to determine the extent of effectiveness of the operational Performance Management System (PMS) in the NPS, which the literature identifies as ...

  20. Building block synthesis using the polymerase chain assembly method.

    Science.gov (United States)

    Marchand, Julie A; Peccoud, Jean

    2012-01-01

    De novo gene synthesis allows the creation of custom DNA molecules without the typical constraints of traditional cloning assembly: scars, restriction site incompatibility, and the quest to find all the desired parts to name a few. Moreover, with the help of computer-assisted design, the perfect DNA molecule can be created along with its matching sequence ready to download. The challenge is to build the physical DNA molecules that have been designed with the software. Although there are several DNA assembly methods, this section presents and describes a method using the polymerase chain assembly (PCA).

  1. Quantitative NMR Approach to Optimize the Formation of Chemical Building Blocks from Abundant Carbohydrates

    DEFF Research Database (Denmark)

    Elliot, Samuel Gilbert; Tolborg, Søren; Sádaba, Irantzu

    2017-01-01

    -containing catalysts such as Sn-Beta. These compounds are potential building blocks for polyesters with additional olefin and alcohol functionalities. We employ an NMR approach to identify, quantify and optimize the formation these building blocks in the chemocatalytic transformation of abundant carbohydrates by Sn...

  2. COP9 signalosome: a provider of DNA building blocks

    DEFF Research Database (Denmark)

    Nielsen, Olaf

    2003-01-01

    In fission yeast, the COP9 signalosome is required to activate ribonucleotide reductase for DNA synthesis. This is mediated via the ubiquitin ligase Pcu4, activation of which leads to degradation of the scaffold protein Spd1, which anchors the small ribonucleotide reductase subunit in the nucleus...

  3. Block Copolymer Micellization as a Protection Strategy for DNA Origami.

    Science.gov (United States)

    Agarwal, Nayan P; Matthies, Michael; Gür, Fatih N; Osada, Kensuke; Schmidt, Thorsten L

    2017-05-08

    DNA nanotechnology enables the synthesis of nanometer-sized objects that can be site-specifically functionalized with a large variety of materials. For these reasons, DNA-based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)-polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs). This straightforward, cost-effective, and robust route to protect DNA-based structures could therefore enable applications in biology and nanomedicine where unprotected DNA origami would be degraded. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Controlled Nucleation and Growth of DNA Tile Arrays within Prescribed DNA Origami Frames and Their Dynamics

    Science.gov (United States)

    2015-01-01

    Controlled nucleation of nanoscale building blocks by geometrically defined seeds implanted in DNA nanoscaffolds represents a unique strategy to study and understand the dynamic processes of molecular self-assembly. Here we utilize a two-dimensional DNA origami frame with a hollow interior and selectively positioned DNA hybridization seeds to control the self-assembly of DNA tile building blocks, where the small DNA tiles are directed to fill the interior of the frame through prescribed sticky end interactions. This design facilitates the construction of DNA origami/array hybrids that adopt the overall shape and dimensions of the origami frame, forming a 2D array in the core consisting of a large number of simple repeating DNA tiles. The formation of the origami/array hybrid was characterized with atomic force microscopy, and the nucleation dynamics were monitored by serial AFM scanning and fluorescence spectroscopy, which revealed faster kinetics of growth within the frame as compared to growth without the presence of a frame. Our study provides insight into the fundamental behavior of DNA-based self-assembling systems. PMID:24575893

  5. Development of building blocks using vegetable oil and recycled aggregate

    Directory of Open Access Journals (Sweden)

    Attia Mohamed I.

    2017-01-01

    Full Text Available The primary objective of this research was to contribute towards greater sustainability of the construction industry in the Qatar by proposing methods to reduce its dependency on primary imported materials. In this investigation, recycled and secondary aggregates (RSA were combined with non-traditional binders to develop a unique method of manufacturing construction and building blocks. Following an extensive phase of laboratory trials and experimentation, it was realised that many types of graded mineral aggregates, when mixed with vegetable oils (virgin or waste at optimal proportions, then compacted and thermally cured at elevated temperatures can readily generate hardened composites that have the mechanical characteristics of conventional building blocks. The resultant blocks have been named “Vegeblocks” and are viewed as viable alternatives to conventional concrete blocks. Furthermore, the research has demonstrated the feasibility of producing Vegeblocks composed of 100% recycled aggregate and discarded waste cooking oil. Based on physical and mineralogical properties, each type of aggregate has an optimum oil content for maximum compressive strength, beyond which, any additional oil will result in reduction in mechanical properties. Acceptable compressive strength values were achieved by thermally curing Vegeblocks at of 170 °C for 24 hours.

  6. Gigadalton-scale shape-programmable DNA assemblies

    Science.gov (United States)

    Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik

    2017-12-01

    Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

  7. Amphiphilic building blocks for self-assembly: from amphiphiles to supra-amphiphiles.

    Science.gov (United States)

    Wang, Chao; Wang, Zhiqiang; Zhang, Xi

    2012-04-17

    The process of self-assembly spontaneously creates well-defined structures from various chemical building blocks. Self-assembly can include different levels of complexity: it can be as simple as the dimerization of two small building blocks driven by hydrogen bonding or as complicated as a cell membrane, a remarkable supramolecular architecture created by a bilayer of phospholipids embedded with functional proteins. The study of self-assembly in simple systems provides a fundamental understanding of the driving forces and cooperativity behind these processes. Once the rules are understood, these guidelines can facilitate the research of highly complex self-assembly processes. Among the various components for self-assembly, an amphiphilic molecule, which contains both hydrophilic and hydrophobic parts, forms one of the most powerful building blocks. When amphiphiles are dispersed in water, the hydrophilic component of the amphiphile preferentially interacts with the aqueous phase while the hydrophobic portion tends to reside in the air or in the nonpolar solvent. Therefore, the amphiphiles aggregate to form different molecular assemblies based on the repelling and coordinating forces between the hydrophilic and hydrophobic parts of the component molecules and the surrounding medium. In contrast to conventional amphiphiles, supra-amphiphiles are constructed on the basis of noncovalent interactions or dynamic covalent bonds. In supra-amphiphiles, the functional groups can be attached to the amphiphiles by noncovalent synthesis, greatly speeding their construction. The building blocks for supra-amphiphiles can be either small organic molecules or polymers. Advances in the development of supra-amphiphiles will not only enrich the family of conventional amphiphiles that are based on covalent bonds but will also provide a new kind of building block for the preparation of complex self-assemblies. When polymers are used to construct supra-amphiphiles, the resulting

  8. Fundamental Autopoietic Building Blocks in 4.0 Organization as a Challenge to Humane Organization

    Directory of Open Access Journals (Sweden)

    Tanja Balažic Peček

    2017-12-01

    Full Text Available Research question (RQ: The area of a human, organizations and Organizations is complex and with new aspects of 4.0 organization even more complex. We did an autopoietic outline with horizontal and vertical view of a researcher who sticks to humanity of an individual and organizations. The research question stems from the central study: Which are building blocks of autopoises in a modern and which in 4.0 organization? Purpose: To detect, recognize, research principles of autopoiesis and setting building blocks of autopoiesis in organizations. We are interested in a human in organization, in interpersonal co-dependance on micro and macro level. Inside this more and more virtual organization we are studying a human, humanity and human potential as a creative potential of humane organization. Method: Action research with mixed methods for comprehensive study of autopoietic principle and methodology of setting the autopoietic building blocks. We used Atlas.ti software and methodological informational software »Informational graph of Autopoiesis - IGA«. Validation was carried out with double triangulaton (static and dynamic view. Results: We formed and validated four directional building blocks and 36 process building blocks, which are shown in a human as: emotions, thinking, directing and activity. Significant difference in two process building blocks of autopoiesis in modern and 4.0 organization confirms the set thesis statement that the building blocks of modern and 4.0 organization are different. We detected that in 4.0 organization the process building blocks of self-/co-feeling and self-/co-referencing aregetting weaker. With results we claim that 4.0 organization is oriented mostly towards action and is getting stronger in improved communication. However, it decreases in emotions and thinking of a human in an organization. Organization: Results can serve as a guideline and challenge to humane organizations. We present the challenge how – by

  9. Building Blocks of Psychology: on Remaking the Unkept Promises of Early Schools.

    Science.gov (United States)

    Gozli, Davood G; Deng, Wei Sophia

    2018-03-01

    The appeal and popularity of "building blocks", i.e., simple and dissociable elements of behavior and experience, persists in psychological research. We begin our assessment of this research strategy with an historical review of structuralism (as espoused by E. B. Titchener) and behaviorism (espoused by J. B. Watson and B. F. Skinner), two movements that held the assumption in their attempts to provide a systematic and unified discipline. We point out the ways in which the elementism of the two schools selected, framed, and excluded topics of study. After the historical review, we turn to contemporary literature and highlight the persistence of research into building blocks and the associated framing and exclusions in psychological research. The assumption that complex categories of human psychology can be understood in terms of their elementary components and simplest forms seems indefensible. In specific cases, therefore, reliance on the assumption requires justification. Finally, we review alternative strategies that bypass the commitment to building blocks.

  10. Molecular Building Blocks for Nanotechnology From Diamondoids to Nanoscale Materials and Applications

    CERN Document Server

    Mansoori, G. Ali; Assoufid, Lahsen; Zhang, Guoping

    2007-01-01

    This book is a result of the research and educational activities of a group of outstanding scientists worldwide who have authored the chapters of this book dealing with the behavior of nanoscale building blocks. It contains a variety of subjects covering computational, dry and wet nanotechnology. The state-of-the-art subject matters presented here provide the reader with the latest developments on ongoing nanoscience and nanotechnology research from the bottom-up approach, which starts with with atoms and molecules as molecular building blocks.

  11. The Impact of Individual Differences, Types of Model and Social Settings on Block Building Performance among Chinese Preschoolers.

    Science.gov (United States)

    Tian, Mi; Deng, Zhu; Meng, Zhaokun; Li, Rui; Zhang, Zhiyi; Qi, Wenhui; Wang, Rui; Yin, Tingting; Ji, Menghui

    2018-01-01

    Children's block building performances are used as indicators of other abilities in multiple domains. In the current study, we examined individual differences, types of model and social settings as influences on children's block building performance. Chinese preschoolers ( N = 180) participated in a block building activity in a natural setting, and performance was assessed with multiple measures in order to identify a range of specific skills. Using scores generated across these measures, three dependent variables were analyzed: block building skills, structural balance and structural features. An overall MANOVA showed that there were significant main effects of gender and grade level across most measures. Types of model showed no significant effect in children's block building. There was a significant main effect of social settings on structural features, with the best performance in the 5-member group, followed by individual and then the 10-member block building. These findings suggest that boys performed better than girls in block building activity. Block building performance increased significantly from 1st to 2nd year of preschool, but not from second to third. The preschoolers created more representational constructions when presented with a model made of wooden rather than with a picture. There was partial evidence that children performed better when working with peers in a small group than when working alone or working in a large group. It is suggested that future study should examine other modalities rather than the visual one, diversify the samples and adopt a longitudinal investigation.

  12. Toward a catalytic site in DNA

    DEFF Research Database (Denmark)

    Jakobsen, Ulla; Rohr, Katja; Vogel, Stefan

    2007-01-01

    A number of functionalized polyaza crown ether building blocks have been incorporated into DNA-conjugates as catalytic Cu(2+) binding sites. The effect of the DNA-conjugate catalyst on the stereochemical outcome of a Cu(2+)-catalyzed Diels-Alder reaction will be presented....

  13. Noncanonical self-assembly of multifunctional DNA nanoflowers for biomedical applications.

    Science.gov (United States)

    Zhu, Guizhi; Hu, Rong; Zhao, Zilong; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

    2013-11-06

    DNA nanotechnology has been extensively explored to assemble various functional nanostructures for versatile applications. Mediated by Watson-Crick base-pairing, these DNA nanostructures have been conventionally assembled through hybridization of many short DNA building blocks. Here we report the noncanonical self-assembly of multifunctional DNA nanostructures, termed as nanoflowers (NFs), and the versatile biomedical applications. These NFs were assembled from long DNA building blocks generated via rolling circle replication (RCR) of a designer template. NF assembly was driven by liquid crystallization and dense packaging of building blocks, without relying on Watson-Crick base-pairing between DNA strands, thereby avoiding the otherwise conventional complicated DNA sequence design. NF sizes were readily tunable in a wide range, by simply adjusting such parameters as assembly time and template sequences. NFs were exceptionally resistant to nuclease degradation, denaturation, or dissociation at extremely low concentration, presumably resulting from the dense DNA packaging in NFs. The exceptional biostability is critical for biomedical applications. By rational design, NFs can be readily incorporated with myriad functional moieties. All these properties make NFs promising for versatile applications. As a proof-of-principle demonstration, in this study, NFs were integrated with aptamers, bioimaging agents, and drug loading sites, and the resultant multifunctional NFs were demonstrated for selective cancer cell recognition, bioimaging, and targeted anticancer drug delivery.

  14. The Impact of Individual Differences, Types of Model and Social Settings on Block Building Performance among Chinese Preschoolers

    Directory of Open Access Journals (Sweden)

    Mi Tian

    2018-01-01

    Full Text Available Children’s block building performances are used as indicators of other abilities in multiple domains. In the current study, we examined individual differences, types of model and social settings as influences on children’s block building performance. Chinese preschoolers (N = 180 participated in a block building activity in a natural setting, and performance was assessed with multiple measures in order to identify a range of specific skills. Using scores generated across these measures, three dependent variables were analyzed: block building skills, structural balance and structural features. An overall MANOVA showed that there were significant main effects of gender and grade level across most measures. Types of model showed no significant effect in children’s block building. There was a significant main effect of social settings on structural features, with the best performance in the 5-member group, followed by individual and then the 10-member block building. These findings suggest that boys performed better than girls in block building activity. Block building performance increased significantly from 1st to 2nd year of preschool, but not from second to third. The preschoolers created more representational constructions when presented with a model made of wooden rather than with a picture. There was partial evidence that children performed better when working with peers in a small group than when working alone or working in a large group. It is suggested that future study should examine other modalities rather than the visual one, diversify the samples and adopt a longitudinal investigation.

  15. Oligomers and Polymers Based on Pentacene Building Blocks

    Science.gov (United States)

    Lehnherr, Dan; Tykwinski, Rik R.

    2010-01-01

    Functionalized pentacene derivatives continue to provide unique materials for organic semiconductor applications. Although oligomers and polymers based on pentacene building blocks remain quite rare, recent synthetic achievements have provided a number of examples with varied structural motifs. This review highlights recent work in this area and, when possible, contrasts the properties of defined-length pentacene oligomers to those of mono- and polymeric systems.

  16. The Building Blocks of Life Move from Ground to Tree to Animal and Back to Ground

    Science.gov (United States)

    Davidson, E. A.

    2015-12-01

    I generally use combinations of big words to describe my science, such as biogeochemistry, ecosystem ecology, nutrient cycling, stoichiometry, tropical deforestation, land-use change, agricultural intensification, eutrophication, greenhouse gas emissions, and sustainable development. I didn't expect to use any of these words, but I was surprised that I couldn't use some others that seem simple enough to me, such as farm, plant, soil, and forest. I landed on "building blocks" as my metaphor for the forms of carbon, nitrogen, phosphorus, and other elements that I study as they cycle through and among ecosystems. I study what makes trees and other kinds of life grow. We all know that they need the sun and that they take up water from the ground, but what else do trees need from the ground? What do animals that eat leaves and wood get from the trees? Just as we need building blocks to grow our bodies, trees and animals also need building blocks for growing their bodies. Trees get part of their building blocks from the ground and animals get theirs from what they eat. When animals poop and when leaves fall, some of their building blocks return to the ground. When they die, their building blocks also go back to the ground. I also study what happens to the ground, the water, and the air when we cut down trees, kill or shoo away the animals, and make fields to grow our food. Can we grow enough food and still keep the ground, water, and air clean? I think the answer is yes, but it will take better understanding of how all of those building blocks fit together and move around, from ground to tree to animal and back to ground.

  17. Silicene Flowers: A Dual Stabilized Silicon Building Block for High-Performance Lithium Battery Anodes.

    Science.gov (United States)

    Zhang, Xinghao; Qiu, Xiongying; Kong, Debin; Zhou, Lu; Li, Zihao; Li, Xianglong; Zhi, Linjie

    2017-07-25

    Nanostructuring is a transformative way to improve the structure stability of high capacity silicon for lithium batteries. Yet, the interface instability issue remains and even propagates in the existing nanostructured silicon building blocks. Here we demonstrate an intrinsically dual stabilized silicon building block, namely silicene flowers, to simultaneously address the structure and interface stability issues. These original Si building blocks as lithium battery anodes exhibit extraordinary combined performance including high gravimetric capacity (2000 mAh g -1 at 800 mA g -1 ), high volumetric capacity (1799 mAh cm -3 ), remarkable rate capability (950 mAh g -1 at 8 A g -1 ), and excellent cycling stability (1100 mA h g -1 at 2000 mA g -1 over 600 cycles). Paired with a conventional cathode, the fabricated full cells deliver extraordinarily high specific energy and energy density (543 Wh kg ca -1 and 1257 Wh L ca -1 , respectively) based on the cathode and anode, which are 152% and 239% of their commercial counterparts using graphite anodes. Coupled with a simple, cost-effective, scalable synthesis approach, this silicon building block offers a horizon for the development of high-performance batteries.

  18. Dialkoxybithiazole: a new building block for head-to-head polymer semiconductors.

    Science.gov (United States)

    Guo, Xugang; Quinn, Jordan; Chen, Zhihua; Usta, Hakan; Zheng, Yan; Xia, Yu; Hennek, Jonathan W; Ortiz, Rocío Ponce; Marks, Tobin J; Facchetti, Antonio

    2013-02-06

    Polymer semiconductors have received great attention for organic electronics due to the low fabrication cost offered by solution-based printing techniques. To enable the desired solubility/processability and carrier mobility, polymers are functionalized with hydrocarbon chains by strategically manipulating the alkylation patterns. Note that head-to-head (HH) linkages have traditionally been avoided because the induced backbone torsion leads to poor π-π overlap and amorphous film microstructures, and hence to low carrier mobilities. We report here the synthesis of a new building block for HH linkages, 4,4'-dialkoxy-5,5'-bithiazole (BTzOR), and its incorporation into polymers for high performance organic thin-film transistors. The small oxygen van der Waals radius and intramolecular S(thiazolyl)···O(alkoxy) attraction promote HH macromolecular architectures with extensive π-conjugation, low bandgaps (1.40-1.63 eV), and high crystallinity. In comparison to previously reported 3,3'-dialkoxy-2,2'-bithiophene (BTOR), BTzOR is a promising building block in view of thiazole geometric and electronic properties: (a) replacing (thiophene)C-H with (thiazole)N reduces steric encumbrance in -BTzOR-Ar- dyads by eliminating repulsive C-H···H-C interactions with neighboring arene units, thereby enhancing π-π overlap and film crystallinity; and (b) thiazole electron-deficiency compensates alkoxy electron-donating characteristics, thereby lowering the BTzOR polymer HOMO versus that of the BTOR analogues. Thus, the new BTzOR polymers show substantial hole mobilities (0.06-0.25 cm(2)/(V s)) in organic thin-film transistors, as well as enhanced I(on):I(off) ratios and greater ambient stability than the BTOR analogues. These geometric and electronic properties make BTzOR a promising building block for new classes of polymer semiconductors, and the synthetic route to BTzOR reported here should be adaptable to many other bithiazole-based building blocks.

  19. Building Blocks Of Innovation Within A State-Owned Enterprise (Part Two

    Directory of Open Access Journals (Sweden)

    Betsie van Zyl

    2005-11-01

    Full Text Available In this article (the second part of a two-part study the focus is on establishing a theoretical framework of state owned enterprise (SOE managers’ espoused theory of building blocks of innovation. A qualitative approach, namely Grounded Theory, supported by Theoretical Sampling, was applied in generating the primary data for the study from different management levels in the SOE. The managers’ espoused theory, based on empirical evidence, shows that innovation consisted of five important building blocks, namely contextual setting; strategic enablers; business enablers; foundational enablers; and human resources; each with its own categories and sub-categories. The study also identified barriers to innovation. An innovation diffusion framework, specifically for implementation in a government context, was proposed.

  20. Alq3 nanorods: promising building blocks for optical devices.

    Science.gov (United States)

    Chen, Wei; Peng, Qing; Li, Yadong

    2008-07-17

    Monodisperse Alq3 nanorods with hexagonal-prism-like morphology are produced via a facile, emulsion based synthesis route. The photoluminescence of individual nanorods differs from the bulk material. These nanorods are promising building blocks for novel optical devices. Copyright © 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Oligomers and Polymers Based on Pentacene Building Blocks

    Directory of Open Access Journals (Sweden)

    Dan Lehnherr

    2010-04-01

    Full Text Available Functionalized pentacene derivatives continue to provide unique materials for organic semiconductor applications. Although oligomers and polymers based on pentacene building blocks remain quite rare, recent synthetic achievements have provided a number of examples with varied structural motifs. This review highlights recent work in this area and, when possible, contrasts the properties of defined-length pentacene oligomers to those of mono- and polymeric systems.

  2. The scientific building blocks for business coaching: A literature review

    Directory of Open Access Journals (Sweden)

    Flip Schutte

    2015-03-01

    Contribution: The building blocks for business coaching as a relatively new and emerging science within the field of business leadership have been defined. This will contribute to the articulation of concepts within this discipline by future researchers and practitioners.

  3. Effects of different building blocks designs on the statistical ...

    African Journals Online (AJOL)

    Tholang T. Mokhele

    Enumeration Areas (EAs), Small Area Layers (SALs) and SubPlaces) from the 2001 census data were used as building blocks for the generation of census output areas with AZTool program in both rural and urban areas of South Africa. One way-Analysis of Variance (ANOVA) was also performed to determine statistical ...

  4. In vitro-reconstituted nucleoids can block mitochondrial DNA replication and transcription.

    Science.gov (United States)

    Farge, Géraldine; Mehmedovic, Majda; Baclayon, Marian; van den Wildenberg, Siet M J L; Roos, Wouter H; Gustafsson, Claes M; Wuite, Gijs J L; Falkenberg, Maria

    2014-07-10

    The mechanisms regulating the number of active copies of mtDNA are still unclear. A mammalian cell typically contains 1,000-10,000 copies of mtDNA, which are packaged into nucleoprotein complexes termed nucleoids. The main protein component of these structures is mitochondrial transcription factor A (TFAM). Here, we reconstitute nucleoid-like particles in vitro and demonstrate that small changes in TFAM levels dramatically impact the fraction of DNA molecules available for transcription and DNA replication. Compaction by TFAM is highly cooperative, and at physiological ratios of TFAM to DNA, there are large variations in compaction, from fully compacted nucleoids to naked DNA. In compacted nucleoids, TFAM forms stable protein filaments on DNA that block melting and prevent progression of the replication and transcription machineries. Based on our observations, we suggest that small variations in the TFAM-to-mtDNA ratio may be used to regulate mitochondrial gene transcription and DNA replication. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

    Science.gov (United States)

    Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O'Connor, Mary; Shapiro, Bruce A

    2008-10-01

    One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes.

  6. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler☆

    Science.gov (United States)

    Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O’Connor, Mary; Shapiro, Bruce A.

    2013-01-01

    One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes. PMID:18838281

  7. Synthesis of most polyene natural product motifs using just twelve building blocks and one coupling reaction

    Science.gov (United States)

    Woerly, Eric M.; Roy, Jahnabi; Burke, Martin D.

    2014-01-01

    The inherent modularity of polypeptides, oligonucleotides, and oligosaccharides has been harnessed to achieve generalized building block-based synthesis platforms. Importantly, like these other targets, most small molecule natural products are biosynthesized via iterative coupling of bifunctional building blocks. This suggests that many small molecules also possess inherent modularity commensurate with systematic building block-based construction. Supporting this hypothesis, here we report that the polyene motifs found in >75% of all known polyene natural products can be synthesized using just 12 building blocks and one coupling reaction. Using the same general retrosynthetic algorithm and reaction conditions, this platform enabled the synthesis of a wide range of polyene frameworks covering all of this natural product chemical space, and first total syntheses of the polyene natural products asnipyrone B, physarigin A, and neurosporaxanthin β-D-glucopyranoside. Collectively, these results suggest the potential for a more generalized approach for making small molecules in the laboratory. PMID:24848233

  8. Preons - yet smaller building blocks of matter

    International Nuclear Information System (INIS)

    Schrempp, B.; Schrempp, F.

    1985-01-01

    Are quarks and leptons the elementary building blocks of matter or do they have again a substructure in the form of common constituents, the preons. Is the force which is responsible for the binding of preons in quarks and leptons, arranged in our consisting picture of forces or is a revision required. The background of such questions and possible answers are presented. Two specific preon models serve for the illustration of characteristic signals for substructure which can possibly already soon be detected in the experiment. (orig.) [de

  9. DNA-Controlled Assembly of Soft Nanoparticles

    DEFF Research Database (Denmark)

    Vogel, Stefan

    2015-01-01

    This book covers the emerging topic of DNA nanotechnology and DNA supramolecular chemistry in its broader sense. By taking DNA out of its biological role, this biomolecule has become a very versatile building block in materials chemistry, supramolecular chemistry and bio-nanotechnology. Many nove......-covalent systems, DNA origami, DNA based switches, DNA machines, and alternative structures and templates. This broad coverage is very appealing since it combines both the synthesis of modified DNA as well as designer concepts to successfully plan and make DNA nanostructures....

  10. DNA-templated photonic arrays and assemblies: design principles and future opportunities.

    Science.gov (United States)

    Su, Wu; Bonnard, Vanessa; Burley, Glenn A

    2011-07-11

    Molecular photonics is a rapidly developing and multi-disciplinary field of research involving the construction of molecular assemblies comprising photoactive building blocks that are responsive to a light stimulus. A salient challenge in this field is the controlled assembly of these building blocks with nanoscale precision. DNA exhibits considerable promise as an architecture for the templated assembly of photoactive materials. In this Concept Article we describe the progress that has been made in the area of DNA photonics, in which DNA acts as a platform for the construction of optoelectronic assemblies, thin films and devices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Interlocking Toy Building Blocks as Hands-On Learning Modules for Blind and Visually Impaired Chemistry Students

    Science.gov (United States)

    Melaku, Samuel; Schreck, James O.; Griffin, Kameron; Dabke, Rajeev B.

    2016-01-01

    Interlocking toy building blocks (e.g., Lego) as chemistry learning modules for blind and visually impaired (BVI) students in high school and undergraduate introductory or general chemistry courses are presented. Building blocks were assembled on a baseplate to depict the relative changes in the periodic properties of elements. Modules depicting…

  12. BUILDING BLOCKS: ENMESHING TECHNOLOGY AND CREATIVITY WITH ARTISTIC PEDAGOGICAL TECHNOLOGIES

    Directory of Open Access Journals (Sweden)

    Katherine J.JANZEN

    2017-01-01

    Full Text Available Using the analogy of children’s building blocks, the reader is guided through the results of a research study that explored the use of three Artistic Pedagogical Technologies (APTs. ‘Building blocks’ was the major theme that emerged from the data. Sub-themes included developing community, enhancing creativity, and risk taking. The discourse of the paper centers on how selected APTs stimulate interaction, create social presence, and help develop community in the online post-secondary classroom. Additional findings are discussed and implications are presented.

  13. π-Extended Isoindigo-Based Derivative: A Promising Electron-Deficient Building Block for Polymer Semiconductors.

    Science.gov (United States)

    Xu, Long; Zhao, Zhiyuan; Xiao, Mingchao; Yang, Jie; Xiao, Jian; Yi, Zhengran; Wang, Shuai; Liu, Yunqi

    2017-11-22

    The exploration of novel electron-deficient building blocks is a key task for developing high-performance polymer semiconductors in organic thin-film transistors. In view of the situation of the lack of strong electron-deficient building blocks, we designed two novel π-extended isoindigo-based electron-deficient building blocks, IVI and F 4 IVI. Owing to the strong electron-deficient nature and the extended π-conjugated system of the two acceptor units, their copolymers, PIVI2T and PF 4 IVI2T, containing 2,2'-bithiophene donor units, are endowed with deep-lying highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO) energy levels and strong intermolecular interactions. In comparison to PIVI2T, the fluorinated PF 4 IVI2T exhibits stronger intra- and intermolecular interactions, lower HOMO/LUMO energy levels up to -5.74/-4.17 eV, and more ordered molecular packing with a smaller π-π stacking distance of up to 3.53 Å, resulting in an excellent ambipolar transporting behavior and a promising application in logic circuits for PF 4 IVI2T in ambient with hole and electron mobilities of up to 1.03 and 1.82 cm 2 V -1 s -1 , respectively. The results reveal that F 4 IVI is a promising and strong electron-deficient building unit to construct high-performance semiconducting polymers, which provides an insight into the structure-property relationships for the exploration and molecular engineering of excellent electron-deficient building blocks in the field of organic electronics.

  14. A bipedal DNA motor that travels back and forth between two DNA origami tiles.

    Science.gov (United States)

    Liber, Miran; Tomov, Toma E; Tsukanov, Roman; Berger, Yaron; Nir, Eyal

    2015-02-04

    In this work, the successful operation of a dynamic DNA device constructed from two DNA origami building blocks is reported. The device includes a bipedal walker that strides back and forth between the two origami tiles. Two different DNA origami tiles are first prepared separately; they are then joined together in a controlled manner by a set of DNA strands to form a stable track in high yield as confirmed by single-molecule fluorescence (SMF). Second, a bipedal DNA motor, initially attached to one of the two origami units and operated by sequential interaction with "fuel" and "antifuel" DNA strands, moves from one origami tile to another and then back again. The operational yield, measured by SMF, was similar to that of a motor operating on a similar track embedded in a single origami tile, confirming that the transfer across the junction from one tile to the other does not result in dissociation that is any more than that of steps on a single tile. These results demonstrate that moving parts can reliably travel from one origami unit to another, and it demonstrates the feasibility of dynamic DNA molecular machines that are made of more than a single origami building block. This study is a step toward the development of motors that can stride over micrometer distances. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Fragmented Agrarian Space: Building Blocks and Modernisation Trajectories. The Case of Slovenia

    Directory of Open Access Journals (Sweden)

    Slavič Irma Potočnik

    2017-06-01

    Full Text Available Production, processing and consumption within Slovenian agrarian space are fragmented due to physical constraints (72.4% of the territory categorised as ANC and socio-geographic factors. Based on available data, five essential building blocks of contemporary Slovenian agrarian space (available land, change management, integrated circular economy, adjustable policies, and flexibility of institutions are discussed. Interrelations among the building blocks shape the modernisation trajectories of approx. 70,000 agricultural holdings in Slovenia. The coexistence of three modernisation trajectories, i.e. practised autarky, various forms of pluri-activity, and small-scale intensive and innovative modernisation, creates a complex mosaic. The governance of multifunctional and multi-structured agrarian space is becoming more demanding.

  16. DNA-nanoparticle superlattices formed from anisotropic building blocks

    Science.gov (United States)

    Jones, Matthew R.; Macfarlane, Robert J.; Lee, Byeongdu; Zhang, Jian; Young, Kaylie L.; Senesi, Andrew J.; Mirkin, Chad A.

    2010-11-01

    Directional bonding interactions in solid-state atomic lattices dictate the unique symmetries of atomic crystals, resulting in a diverse and complex assortment of three-dimensional structures that exhibit a wide variety of material properties. Methods to create analogous nanoparticle superlattices are beginning to be realized, but the concept of anisotropy is still largely underdeveloped in most particle assembly schemes. Some examples provide interesting methods to take advantage of anisotropic effects, but most are able to make only small clusters or lattices that are limited in crystallinity and especially in lattice parameter programmability. Anisotropic nanoparticles can be used to impart directional bonding interactions on the nanoscale, both through face-selective functionalization of the particle with recognition elements to introduce the concept of valency, and through anisotropic interactions resulting from particle shape. In this work, we examine the concept of inherent shape-directed crystallization in the context of DNA-mediated nanoparticle assembly. Importantly, we show how the anisotropy of these particles can be used to synthesize one-, two- and three-dimensional structures that cannot be made through the assembly of spherical particles.

  17. Building Blocks for Transport-Class Hybrid and Turboelectric Vehicles

    Science.gov (United States)

    Jankovsky, Amy; Bowman, Cheryl; Jansen, Ralph

    2016-01-01

    NASA has been investing in research efforts to define potential vehicles that use hybrid and turboelectric propulsion to enable savings in fuel burn and carbon usage. This paper overviews the fundamental building blocks that have been derived from those studies and details what key performance parameters have been defined, what key ground and flight tests need to occur, and highlights progress toward each.

  18. Recent advances in synthesis of bacterial rare sugar building blocks and their applications.

    Science.gov (United States)

    Emmadi, Madhu; Kulkarni, Suvarn S

    2014-07-01

    Covering: 1964 to 2013. Bacteria have unusual glycans on their surfaces which distinguish them from the host cells. These unique structures offer avenues for targeting bacteria with specific therapeutics and vaccine. However, these rare sugars are not accessible in acceptable purity and amounts by isolation from natural sources. Thus, procurement of orthogonally protected rare sugar building blocks through efficient chemical synthesis is regarded as a crucial step towards the development of glycoconjugate vaccines. This Highlight focuses on recent advances in the synthesis of the bacterial deoxy amino hexopyranoside building blocks and their application in constructing various biologically important bacterial O-glycans.

  19. Engineering multifunctional protein nanoparticles by in vitro disassembling and reassembling of heterologous building blocks

    Science.gov (United States)

    Unzueta, Ugutz; Serna, Naroa; Sánchez-García, Laura; Roldán, Mónica; Sánchez-Chardi, Alejandro; Mangues, Ramón; Villaverde, Antonio; Vázquez, Esther

    2017-12-01

    The engineering of protein self-assembling at the nanoscale allows the generation of functional and biocompatible materials, which can be produced by easy biological fabrication. The combination of cationic and histidine-rich stretches in fusion proteins promotes oligomerization as stable protein-only regular nanoparticles that are composed by a moderate number of building blocks. Among other applications, these materials are highly appealing as tools in targeted drug delivery once empowered with peptidic ligands of cell surface receptors. In this context, we have dissected here this simple technological platform regarding the controlled disassembling and reassembling of the composing building blocks. By applying high salt and imidazole in combination, nanoparticles are disassembled in a process that is fully reversible upon removal of the disrupting agents. By taking this approach, we accomplish here the in vitro generation of hybrid nanoparticles formed by heterologous building blocks. This fact demonstrates the capability to generate multifunctional and/or multiparatopic or multispecific materials usable in nanomedical applications.

  20. Identification of tumor specimens by DNA analysis in a case of histocytological paraffin tissue block swapping

    Science.gov (United States)

    Raina, Anupuma; Yadav, Bhuvnesh; Ali, Sher; Das Dogra, Tirath

    2011-01-01

    We report on a patient who was diagnosed with high-grade breast carcinoma by all the pre-surgery clinical evidence of malignancy, but histopathological reports did not reveal any such tumor residue in the post-surgical tissue block. This raised a suspicion that either exchange of block, labeling error, or a technical error took place during gross examination of the tissue. The mastectomy residue was unprocurable to sort out the problem. So, two doubtful paraffin blocks were sent for DNA fingerprinting analysis. The partial DNA profiles (8-9/15 loci) were obtained from histocytological blocks. The random matching probability for both the paraffin blocks and the patient’s blood were found to be 1 in 4.43E4, 1.89E6, and 8.83E13, respectively for Asian population. Multiplex short tandem repeat analysis applied in this case determined that the cause of tumor absence was an error in gross examination of the post-surgical tissue. Moreover, the analysis helped in justifying the therapy given to the patient. Thus, with DNA fingerprinting technique, it was concluded that there was no exchange of the blocks between the two patients operated on the same day and the treatment given to the concerned patient was in the right direction. PMID:21674839

  1. Building block method: a bottom-up modular synthesis methodology for distributed compliant mechanisms

    Directory of Open Access Journals (Sweden)

    G. Krishnan

    2012-03-01

    Full Text Available Synthesizing topologies of compliant mechanisms are based on rigid-link kinematic designs or completely automated optimization techniques. These designs yield mechanisms that match the kinematic specifications as a whole, but seldom yield user insight on how each constituent member contributes towards the overall mechanism performance. This paper reviews recent developments in building block based design of compliant mechanisms. A key aspect of such a methodology is formulating a representation of compliance at a (i single unique point of interest in terms of geometric quantities such as ellipses and vectors, and (ii relative compliance between distinct input(s and output(s in terms of load flow. This geometric representation provides a direct mapping between the mechanism geometry and their behavior, and is used to characterize simple deformable members that form a library of building blocks. The design space spanned by the building block library guides the decomposition of a given problem specification into tractable sub-problems that can be each solved from an entry in the library. The effectiveness of this geometric representation aids user insight in design, and enables discovery of trends and guidelines to obtain practical conceptual designs.

  2. Transportable Payload Operations Control Center reusable software: Building blocks for quality ground data systems

    Science.gov (United States)

    Mahmot, Ron; Koslosky, John T.; Beach, Edward; Schwarz, Barbara

    1994-01-01

    The Mission Operations Division (MOD) at Goddard Space Flight Center builds Mission Operations Centers which are used by Flight Operations Teams to monitor and control satellites. Reducing system life cycle costs through software reuse has always been a priority of the MOD. The MOD's Transportable Payload Operations Control Center development team established an extensive library of 14 subsystems with over 100,000 delivered source instructions of reusable, generic software components. Nine TPOCC-based control centers to date support 11 satellites and achieved an average software reuse level of more than 75 percent. This paper shares experiences of how the TPOCC building blocks were developed and how building block developer's, mission development teams, and users are all part of the process.

  3. Sinusoidal oscillators and waveform generators using modern electronic circuit building blocks

    CERN Document Server

    Senani, Raj; Singh, V K; Sharma, R K

    2016-01-01

    This book serves as a single-source reference to sinusoidal oscillators and waveform generators, using classical as well as a variety of modern electronic circuit building blocks. It provides a state-of-the-art review of a large variety of sinusoidal oscillators and waveform generators and includes a catalogue of over 600 configurations of oscillators and waveform generators, describing their relevant design details and salient performance features/limitations. The authors discuss a number of interesting, open research problems and include a comprehensive collection of over 1500 references on oscillators and non-sinusoidal waveform generators/relaxation oscillators. Offers readers a single-source reference to everything connected to sinusoidal oscillators and waveform generators, using classical as well as modern electronic circuit building blocks; Provides a state-of-the-art review of a large variety of sinusoidal oscillators and waveform generators; Includes a catalog of over 600 configurations of oscillato...

  4. Topology Optimization of Building Blocks for Photonic Integrated Circuits

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Sigmund, Ole

    2005-01-01

    Photonic integrated circuits are likely candidates as high speed replacements for the standard electrical integrated circuits of today. However, in order to obtain a satisfactorily performance many design prob- lems that up until now have resulted in too high losses must be resolved. In this work...... we demonstrate how the method of topology optimization can be used to design a variety of high performance building blocks for the future circuits....

  5. Linked supramolecular building blocks for enhanced cluster formation

    DEFF Research Database (Denmark)

    McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.

    2015-01-01

    the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]-arenes and transition metal ions or 3d-4 f combinations......(Figure Presented). Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise...

  6. Fluorinated building blocks for next-generation polymer electrolyte membrane fuel cells

    NARCIS (Netherlands)

    Wadekar, M.N.

    2012-01-01

    The purpose of this thesis is to design, create and study basic building blocks for the construction of self-assembled nanostructured electrodes and membranes for PEMFC. The research described deals with the synthesis of polymerizable fluorosurfactant (1) and its non-polymerizable analogue (2) and

  7. Total synthesis of TMG-chitotriomycin based on an automated electrochemical assembly of a disaccharide building block.

    Science.gov (United States)

    Isoda, Yuta; Sasaki, Norihiko; Kitamura, Kei; Takahashi, Shuji; Manmode, Sujit; Takeda-Okuda, Naoko; Tamura, Jun-Ichi; Nokami, Toshiki; Itoh, Toshiyuki

    2017-01-01

    The total synthesis of TMG-chitotriomycin using an automated electrochemical synthesizer for the assembly of carbohydrate building blocks is demonstrated. We have successfully prepared a precursor of TMG-chitotriomycin, which is a structurally-pure tetrasaccharide with typical protecting groups, through the methodology of automated electrochemical solution-phase synthesis developed by us. The synthesis of structurally well-defined TMG-chitotriomycin has been accomplished in 10-steps from a disaccharide building block.

  8. Enantiopure heterobimetallic single-chain magnets from the chiral Ru(III) building block.

    Science.gov (United States)

    Ru, Jing; Gao, Feng; Wu, Tao; Yao, Min-Xia; Li, Yi-Zhi; Zuo, Jing-Lin

    2014-01-21

    A pair of one-dimensional enantiomers based on the versatile chiral dicyanoruthenate(III) building block have been synthesized and they are chiral single-chain magnets with the effective spin-reversal barrier of 28.2 K.

  9. Measuring the health systems impact of disease control programmes: a critical reflection on the WHO building blocks framework.

    Science.gov (United States)

    Mounier-Jack, Sandra; Griffiths, Ulla K; Closser, Svea; Burchett, Helen; Marchal, Bruno

    2014-03-25

    The WHO health systems Building Blocks framework has become ubiquitous in health systems research. However, it was not developed as a research instrument, but rather to facilitate investments of resources in health systems. In this paper, we reflect on the advantages and limitations of using the framework in applied research, as experienced in three empirical vaccine studies we have undertaken. We argue that while the Building Blocks framework is valuable because of its simplicity and ability to provide a common language for researchers, it is not suitable for analysing dynamic, complex and inter-linked systems impacts. In our three studies, we found that the mechanical segmentation of effects by the WHO building blocks, without recognition of their interactions, hindered the understanding of impacts on systems as a whole. Other important limitations were the artificial equal weight given to each building block and the challenge in capturing longer term effects and opportunity costs. Another criticism is not of the framework per se, but rather how it is typically used, with a focus on the six building blocks to the neglect of the dynamic process and outcome aspects of health systems.We believe the framework would be improved by making three amendments: integrating the missing "demand" component; incorporating an overarching, holistic health systems viewpoint and including scope for interactions between components. If researchers choose to use the Building Blocks framework, we recommend that it be adapted to the specific study question and context, with formative research and piloting conducted in order to inform this adaptation. As with frameworks in general, the WHO Building Blocks framework is valuable because it creates a common language and shared understanding. However, for applied research, it falls short of what is needed to holistically evaluate the impact of specific interventions on health systems. We propose that if researchers use the framework, it

  10. Modeling the building blocks of biodiversity.

    Directory of Open Access Journals (Sweden)

    Lucas N Joppa

    Full Text Available BACKGROUND: Networks of single interaction types, such as plant-pollinator mutualisms, are biodiversity's "building blocks". Yet, the structure of mutualistic and antagonistic networks differs, leaving no unified modeling framework across biodiversity's component pieces. METHODS/PRINCIPAL FINDINGS: We use a one-dimensional "niche model" to predict antagonistic and mutualistic species interactions, finding that accuracy decreases with the size of the network. We show that properties of the modeled network structure closely approximate empirical properties even where individual interactions are poorly predicted. Further, some aspects of the structure of the niche space were consistently different between network classes. CONCLUSIONS/SIGNIFICANCE: These novel results reveal fundamental differences between the ability to predict ecologically important features of the overall structure of a network and the ability to predict pair-wise species interactions.

  11. Technological characteristics of compressed earth blocks for its use as a building material

    Science.gov (United States)

    Gomez-Villalba, Luz Stella; Camacho-Perez, Nancy; Alvarez de Buergo, Monica; Becerra-Becerra, Javier; Esmeralda Corredor-Pulido, Dery; Fort, Rafael

    2013-04-01

    We present here an innovative building technique, which uses ecological, inexpensive and environmentally friendly materials. These compressed earth blocks seem to be very good for building purposes and that is why we have characterized three types of compressed earth blocks (CEB, named by their color as yellow, grey and red) mineralogically by means of X ray diffraction XRD and scanning electron microscopy SEM (both blocks and raw materials), petrographically by polarizing optical light microscopy POLM, and SEM, and, mainly, petrophysically: their hydric, physical and physico-mechanical properties by means of determining their capillary water absorption, porosity (open or accessible to water, pore size distribution and micro/macroporosity), and densities, color and ultrasound velocity (together with anisotropy). The particularities of these analyzed materials show that some varieties are more durable than others, and that all of them can be used as building materials with some restrictions related to their appropriate placing in the structures and the exposure to water. Acknowledgements: This work is supported by the GEOMATERIALES (S2009/MAT-1629) and CONSOLIDER-TCP (CSD2007-0058) programmes. Thanks also to the UCM (Complutense University of Madrid) Research Group "Alteración y conservación de los materiales pétreos del patrimonio" / Alteration and conservation of heritage stone materials (ref. 921349).

  12. A Customizable Quantum-Dot Cellular Automata Building Block for the Synthesis of Classical and Reversible Circuits.

    Science.gov (United States)

    Moustafa, Ahmed; Younes, Ahmed; Hassan, Yasser F

    2015-01-01

    Quantum-dot cellular automata (QCA) are nanoscale digital logic constructs that use electrons in arrays of quantum dots to carry out binary operations. In this paper, a basic building block for QCA will be proposed. The proposed basic building block can be customized to implement classical gates, such as XOR and XNOR gates, and reversible gates, such as CNOT and Toffoli gates, with less cell count and/or better latency than other proposed designs.

  13. Total synthesis of TMG-chitotriomycin based on an automated electrochemical assembly of a disaccharide building block

    Directory of Open Access Journals (Sweden)

    Yuta Isoda

    2017-05-01

    Full Text Available The total synthesis of TMG-chitotriomycin using an automated electrochemical synthesizer for the assembly of carbohydrate building blocks is demonstrated. We have successfully prepared a precursor of TMG-chitotriomycin, which is a structurally-pure tetrasaccharide with typical protecting groups, through the methodology of automated electrochemical solution-phase synthesis developed by us. The synthesis of structurally well-defined TMG-chitotriomycin has been accomplished in 10-steps from a disaccharide building block.

  14. Proteins mediating DNA loops effectively block transcription.

    Science.gov (United States)

    Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

    2017-07-01

    Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  15. Identification of Biomolecular Building Blocks by Recognition Tunneling: Stride towards Nanopore Sequencing of Biomolecules

    Science.gov (United States)

    Sen, Suman

    DNA, RNA and Protein are three pivotal biomolecules in human and other organisms, playing decisive roles in functionality, appearance, diseases development and other physiological phenomena. Hence, sequencing of these biomolecules acquires the prime interest in the scientific community. Single molecular identification of their building blocks can be done by a technique called Recognition Tunneling (RT) based on Scanning Tunneling Microscope (STM). A single layer of specially designed recognition molecule is attached to the STM electrodes, which trap the targeted molecules (DNA nucleoside monophosphates, RNA nucleoside monophosphates or amino acids) inside the STM nanogap. Depending on their different binding interactions with the recognition molecules, the analyte molecules generate stochastic signal trains accommodating their "electronic fingerprints". Signal features are used to detect the molecules using a machine learning algorithm and different molecules can be identified with significantly high accuracy. This, in turn, paves the way for rapid, economical nanopore sequencing platform, overcoming the drawbacks of Next Generation Sequencing (NGS) techniques. To read DNA nucleotides with high accuracy in an STM tunnel junction a series of nitrogen-based heterocycles were designed and examined to check their capabilities to interact with naturally occurring DNA nucleotides by hydrogen bonding in the tunnel junction. These recognition molecules are Benzimidazole, Imidazole, Triazole and Pyrrole. Benzimidazole proved to be best among them showing DNA nucleotide classification accuracy close to 99%. Also, Imidazole reader can read an abasic monophosphate (AP), a product from depurination or depyrimidination that occurs 10,000 times per human cell per day. In another study, I have investigated a new universal reader, 1-(2-mercaptoethyl)pyrene (Pyrene reader) based on stacking interactions, which should be more specific to the canonical DNA nucleosides. In addition

  16. Divide and control: split design of multi-input DNA logic gates.

    Science.gov (United States)

    Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2015-01-18

    Logic gates made of DNA have received significant attention as biocompatible building blocks for molecular circuits. The majority of DNA logic gates, however, are controlled by the minimum number of inputs: one, two or three. Here we report a strategy to design a multi-input logic gate by splitting a DNA construct.

  17. Image Chunking: Defining Spatial Building Blocks for Scene Analysis.

    Science.gov (United States)

    1987-04-01

    mumgs0.USmusa 7.AUWOJO 4. CIUTAC Rm6ANT Wuugme*j James V/. Mlahoney DACA? 6-85-C-00 10 NOQ 1 4-85-K-O 124 Artificial Inteligence Laboratory US USS 545...0197 672 IMAGE CHUWING: DEINING SPATIAL UILDING PLOCKS FOR 142 SCENE ANRLYSIS(U) MASSACHUSETTS INST OF TECH CAIIAIDGE ARTIFICIAL INTELLIGENCE LAO J...Technical Report 980 F-Image Chunking: Defining Spatial Building Blocks for Scene DTm -Analysis S ELECTED James V. Mahoney’ MIT Artificial Intelligence

  18. Building blocks toward contemporary trauma theory: Ferenczi 's paradigm shift.

    Science.gov (United States)

    Mészáros, Judit

    2010-12-01

    In laying down the building blocks of contemporary trauma theory, Ferenczi asserted that trauma is founded on real events and that it occurs in the interpersonal and intersubjective dynamics of object relations. He stressed the significance of the presence or lack of a trusted person in the post-traumatic situation. After the trauma, the loneliness and later the isolation of the victim represent a serious pathogenic source. In the traumatic situation, the victim and the persecutor/aggressor operate differing ego defense mechanisms. Ferenczi was the first to describe the ego defense mechanism of identification with the aggressor. Ferenczi pointed out the characteristic features of the role of analyst/therapist with which (s)he may assist the patient in working through the trauma, among them being the development of a therapeutic atmosphere based on trust, so that the traumatic experiences can be relived, without which effective therapeutic change cannot be achieved. For the analyst, countertransference, as part of authentic communication, is incorporated into the therapeutic process. These are the key building blocks that are laid down by Ferenczi in his writings and appear in later works on trauma theory.

  19. Synthesis of most polyene natural product motifs using just 12 building blocks and one coupling reaction.

    Science.gov (United States)

    Woerly, Eric M; Roy, Jahnabi; Burke, Martin D

    2014-06-01

    The inherent modularity of polypeptides, oligonucleotides and oligosaccharides has been harnessed to achieve generalized synthesis platforms. Importantly, like these other targets, most small-molecule natural products are biosynthesized via iterative coupling of bifunctional building blocks. This suggests that many small molecules also possess inherent modularity commensurate with systematic building block-based construction. Supporting this hypothesis, here we report that the polyene motifs found in >75% of all known polyene natural products can be synthesized using just 12 building blocks and one coupling reaction. Using the same general retrosynthetic algorithm and reaction conditions, this platform enabled both the synthesis of a wide range of polyene frameworks that covered all of this natural-product chemical space and the first total syntheses of the polyene natural products asnipyrone B, physarigin A and neurosporaxanthin b-D-glucopyranoside. Collectively, these results suggest the potential for a more generalized approach to making small molecules in the laboratory.

  20. Block Play and Mathematics Learning in Preschool: The Effects of Building Complexity, Peer and Teacher Interactions in the Block Area, and Replica Play Materials

    Science.gov (United States)

    Trawick-Smith, Jeffrey; Swaminathan, Sudha; Baton, Brooke; Danieluk, Courtney; Marsh, Samantha; Szarwacki, Monika

    2017-01-01

    Block play has been included in early childhood classrooms for over a century, yet few studies have examined its effects on learning. Several previous investigations indicate that the complexity of block building is associated with math ability, but these studies were often conducted in adult-guided, laboratory settings. In the present…

  1. Quantitative NMR Approach to Optimize the Formation of Chemical Building Blocks from Abundant Carbohydrates.

    Science.gov (United States)

    Elliot, Samuel G; Tolborg, Søren; Sádaba, Irantzu; Taarning, Esben; Meier, Sebastian

    2017-07-21

    The future role of biomass-derived chemicals relies on the formation of diverse functional monomers in high yields from carbohydrates. Recently, it has become clear that a series of α-hydroxy acids, esters, and lactones can be formed from carbohydrates in alcohol and water solvents using tin-containing catalysts such as Sn-Beta. These compounds are potential building blocks for polyesters bearing additional olefin and alcohol functionalities. An NMR approach was used to identify, quantify, and optimize the formation of these building blocks in the Sn-Beta-catalyzed transformation of abundant carbohydrates. Record yields of the target molecules can be achieved by obstructing competing reactions through solvent selection. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Anisotropy Spectra for Enantiomeric Differentiation of Biomolecular Building Blocks

    DEFF Research Database (Denmark)

    Evans, Amanda C.; Meinert, Cornelia; Bredehoft, Jan H.

    2013-01-01

    All biopolymers are composed of homochiral building blocks, and both D-sugars and L-amino acids uniquely constitute life on Earth. These monomers were originally enantiomerically differentiated under prebiotic conditions. Particular progress has recently been made in support of the photochemical...... light. This chapter will: (1) present the theory and configuration of anisotropy spectroscopy; (2) explain experimentally recorded anisotropy spectra of selected chiral biomolecules such as amino acids; and (3) discuss the relevance of these spectra for the investigation of the origin of the molecular...

  3. Microbes on building materials - Evaluation of DNA extraction protocols as common basis for molecular analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ettenauer, Joerg D., E-mail: joerg.ettenauer@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Pinar, Guadalupe, E-mail: Guadalupe.Pinar@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Lopandic, Ksenija, E-mail: Ksenija.Lopandic@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Spangl, Bernhard, E-mail: Bernhard.Spangl@boku.ac.at [University of Natural Resources and Life Sciences, Department of Landscape, Spatial and Infrastructure Science, Institute of Applied Statistics and Computing (IASC), Gregor Mendel-Str. 33, A-1180 Vienna (Austria); Ellersdorfer, Guenther, E-mail: Guenther.Ellersdorfer@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Voitl, Christian, E-mail: Christian.Voitl@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria); Sterflinger, Katja, E-mail: Katja.Sterflinger@boku.ac.at [VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 11, A-1190 Vienna (Austria)

    2012-11-15

    The study of microbial life in building materials is an emerging topic concerning biodeterioration of materials as well as health risks in houses and at working places. Biodegradation and potential health implications associated with microbial growth in our residues claim for more precise methods for quantification and identification. To date, cultivation experiments are commonly used to gain insight into the microbial diversity. Nowadays, molecular techniques for the identification of microorganisms provide efficient methods that can be applied in this field. The efficiency of DNA extraction is decisive in order to perform a reliable and reproducible quantification of the microorganisms by qPCR or to characterize the structure of the microbial community. In this study we tested thirteen DNA extraction methods and evaluated their efficiency for identifying (1) the quantity of DNA, (2) the quality and purity of DNA and (3) the ability of the DNA to be amplified in a PCR reaction using three universal primer sets for the ITS region of fungi as well as one primer pair targeting the 16S rRNA of bacteria with three typical building materials - common plaster, red brick and gypsum cardboard. DNA concentration measurements showed strong variations among the tested methods and materials. Measurement of the DNA yield showed up to three orders of magnitude variation from the same samples, whereas A260/A280 ratios often prognosticated biases in the PCR amplifications. Visualization of the crude DNA extracts and the comparison of DGGE fingerprints showed additional drawbacks of some methods. The FastDNA Spin kit for soil showed to be the best DNA extraction method and could provide positive results for all tests with the three building materials. Therefore, we suggest this method as a gold standard for quantification of indoor fungi and bacteria in building materials. -- Highlights: Black-Right-Pointing-Pointer Up to thirteen extraction methods were evaluated with three

  4. Molecular engineering of chiral colloidal liquid crystals using DNA origami

    Science.gov (United States)

    Siavashpouri, Mahsa; Wachauf, Christian H.; Zakhary, Mark J.; Praetorius, Florian; Dietz, Hendrik; Dogic, Zvonimir

    2017-08-01

    Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials.

  5. Silicon-Carbide (SIC) Multichip Power Modules (MCPMS) For Power Building Block Applications, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This Small Business Innovation Research Phase I project seeks to prove the feasibility of developing high power density modular power electronic building blocks...

  6. Stereoselective total synthesis of Oxylipin from open chain gluco-configured building block.

    Science.gov (United States)

    Borkar, Santosh Ramdas; Aidhen, Indrapal Singh

    2017-04-18

    Total synthesis of naturally occurring Oxylipin has been achieved from open chain gluco-configured building block which is readily assembled from inexpensive and commercially available D-(+)-gluconolactone. Grignard reaction and Wittig olefination reactions are key steps for the requisite CC bond formation. Copyright © 2017. Published by Elsevier Ltd.

  7. Preparing a Safety Analysis Report using the building block approach

    International Nuclear Information System (INIS)

    Herrington, C.C.

    1990-01-01

    The credibility of the applicant in a licensing proceeding is severely impacted by the quality of the license application, particularly the Safety Analysis Report. To ensure the highest possible credibility, the building block approach was devised to support the development of a quality Safety Analysis Report. The approach incorporates a comprehensive planning scheme that logically ties together all levels of the investigation and provides the direction necessary to prepare a superior Safety Analysis Report

  8. Benzoylated Uronic Acid Building Blocks and Synthesis of N-Uronate Conjugates of Lamotrigine

    Directory of Open Access Journals (Sweden)

    Bård Helge Hoff

    2012-01-01

    Full Text Available A chemoenzymatic approach towards benzoylated uronic acid building blocks has been investigated starting with benzoylated hexapyranosides using regioselective C-6 enzymatic hydrolysis as the key step. Two of the building blocks were reacted with the antiepileptic drug lamotrigine. Glucuronidation of lamotrigine using methyl (2,3,4-tri-O-benzoyl-α-D-glycopyranosyl bromideuronate proceeded to give the N2-conjugate. However, lamotrigine-N2-glucuronide was most efficiently synthesised from methyl (2,3,4-tri-O-acetyl-α-D-glucopyranosyl bromideuronate. Employing nitromethane as solvent with CdCO3 as a base lamotrigine-N2 glucuronide was prepared in a high yield (41%. Also methyl (2,3-di-O-benzoyl-4-deoxy-4-fluoro-α-D-glucosyl bromideuronate underwent N-glucuronidation, but the product was unstable, eliminating hydrogen fluoride to give the corresponding enoate conjugate.

  9. Microbes on building materials — Evaluation of DNA extraction protocols as common basis for molecular analysis

    International Nuclear Information System (INIS)

    Ettenauer, Jörg D.; Piñar, Guadalupe; Lopandic, Ksenija; Spangl, Bernhard; Ellersdorfer, Günther; Voitl, Christian; Sterflinger, Katja

    2012-01-01

    The study of microbial life in building materials is an emerging topic concerning biodeterioration of materials as well as health risks in houses and at working places. Biodegradation and potential health implications associated with microbial growth in our residues claim for more precise methods for quantification and identification. To date, cultivation experiments are commonly used to gain insight into the microbial diversity. Nowadays, molecular techniques for the identification of microorganisms provide efficient methods that can be applied in this field. The efficiency of DNA extraction is decisive in order to perform a reliable and reproducible quantification of the microorganisms by qPCR or to characterize the structure of the microbial community. In this study we tested thirteen DNA extraction methods and evaluated their efficiency for identifying (1) the quantity of DNA, (2) the quality and purity of DNA and (3) the ability of the DNA to be amplified in a PCR reaction using three universal primer sets for the ITS region of fungi as well as one primer pair targeting the 16S rRNA of bacteria with three typical building materials — common plaster, red brick and gypsum cardboard. DNA concentration measurements showed strong variations among the tested methods and materials. Measurement of the DNA yield showed up to three orders of magnitude variation from the same samples, whereas A260/A280 ratios often prognosticated biases in the PCR amplifications. Visualization of the crude DNA extracts and the comparison of DGGE fingerprints showed additional drawbacks of some methods. The FastDNA Spin kit for soil showed to be the best DNA extraction method and could provide positive results for all tests with the three building materials. Therefore, we suggest this method as a gold standard for quantification of indoor fungi and bacteria in building materials. -- Highlights: ► Up to thirteen extraction methods were evaluated with three building materials.

  10. 25 years and still going strong: 2'-O-(pyren-1-yl)methylribonucleotides - versatile building blocks for applications in molecular biology, diagnostics and materials science.

    Science.gov (United States)

    Hrdlicka, Patrick J; Karmakar, Saswata

    2017-11-29

    Oligonucleotides (ONs) modified with 2'-O-(pyren-1-yl)methylribonucleotides have been explored for a range of applications in molecular biology, nucleic acid diagnostics, and materials science for more than 25 years. The first part of this review provides an overview of synthetic strategies toward 2'-O-(pyren-1-yl)methylribonucleotides and is followed by a summary of biophysical properties of nucleic acid duplexes modified with these building blocks. Insights from structural studies are then presented to rationalize the reported properties. In the second part, applications of ONs modified with 2'-O-(pyren-1-yl)methyl-RNA monomers are reviewed, which include detection of RNA targets, discrimination of single nucleotide polymorphisms, formation of self-assembled pyrene arrays on nucleic acid scaffolds, the study of charge transfer phenomena in nucleic acid duplexes, and sequence-unrestricted recognition of double-stranded DNA. The predictable binding mode of the pyrene moiety, coupled with the microenvironment-dependent properties and synthetic feasibility, render 2'-O-(pyren-1-yl)methyl-RNA monomers as a promising class of pyrene-functionalized nucleotide building blocks for new applications in molecular biology, nucleic acid diagnostics, and materials science.

  11. MECs: "Building Blocks" for Creating Biological and Chemical Instruments.

    Directory of Open Access Journals (Sweden)

    Douglas A Hill

    Full Text Available The development of new biological and chemical instruments for research and diagnostic applications is often slowed by the cost, specialization, and custom nature of these instruments. New instruments are built from components that are drawn from a host of different disciplines and not designed to integrate together, and once built, an instrument typically performs a limited number of tasks and cannot be easily adapted for new applications. Consequently, the process of inventing new instruments is very inefficient, especially for researchers or clinicians in resource-limited settings. To improve this situation, we propose that a family of standardized multidisciplinary components is needed, a set of "building blocks" that perform a wide array of different tasks and are designed to integrate together. Using these components, scientists, engineers, and clinicians would be able to build custom instruments for their own unique needs quickly and easily. In this work we present the foundation of this set of components, a system we call Multifluidic Evolutionary Components (MECs. "Multifluidic" conveys the wide range of fluid volumes MECs operate upon (from nanoliters to milliliters and beyond; "multi" also reflects the multiple disciplines supported by the system (not only fluidics but also electronics, optics, and mechanics. "Evolutionary" refers to the design principles that enable the library of MEC parts to easily grow and adapt to new applications. Each MEC "building block" performs a fundamental function that is commonly found in biological or chemical instruments, functions like valving, pumping, mixing, controlling, and sensing. Each MEC also has a unique symbol linked to a physical definition, which enables instruments to be designed rapidly and efficiently using schematics. As a proof-of-concept, we use MECs to build a variety of instruments, including a fluidic routing and mixing system capable of manipulating fluid volumes over five orders

  12. EDITORIAL: Nature's building blocks Nature's building blocks

    Science.gov (United States)

    Engel, Andreas

    2009-10-01

    The scanning tunnelling microscope (STM), invented by Gerd Binnig and Heinrich Rohrer in the early 1980s in the IBM Laboratory in Zurich, and the atomic force microscope (AFM) that followed shortly afterwards, were key developments that initiated a new era in scientific research: nanotechnology. These and related scanning probe microscopes have become fruitful tools in the study of cells, supramolecular assemblies and single biomolecules, as well as other nanoscale structures. In particular, the ability to investigate living matter in native environments made possible by atomic force microscopy, has allowed pronounced progress in biological research. The journal Nanotechnology was the first to serve as a publication platform for this rapidly developing field of science. The journal celebrates its 20th volume with this special issue, which presents a collection of original research articles in various fields of science, but all with the common feature that the structures, processes and functions all take place at the nanometre scale. Scanning probe microscopes are constantly being devised with increasingly sophisticated sensing and actuating features that optimize their performance. However, while these tools continue to provide impressive and informative images of nanoscale systems and allow single molecules to be manipulated with increasing dexterity, a wider field of research activity stimulated either by or for biology has emerged. The unique properties of matter at the nanoscale, such as localized surface plasmons supported by nanostructures, have been exploited in sensors with unprecedented sensitivity. Nanostructures have also found a profitable role in the encapsulation of molecules for 'smart' drug delivery. The potential application of DNA in the self-assembly of nanostructures guided by molecular recognition is another rapidly advancing area of research. In this issue a group of researchers in Germany report how the addition of copper ions can promote the

  13. Dimeric Building Blocks for Solid-Phase Synthesis of α-Peptide-β-Peptoid Chimeras

    DEFF Research Database (Denmark)

    Seigan, Gitte Bonke; Vedel, Line; Matthias, Witt,

    2008-01-01

    Recently, a novel type of antimicrobial and proteolytically stable peptidomimetic oligomers having an α-peptide-β-peptoid chimeric backbone was reported. The present paper describes efficient protocols for the preparation of a wide range of dimeric building blocks, displaying different types of s...

  14. From synthesis to function via iterative assembly of N-methyliminodiacetic acid boronate building blocks.

    Science.gov (United States)

    Li, Junqi; Grillo, Anthony S; Burke, Martin D

    2015-08-18

    The study and optimization of small molecule function is often impeded by the time-intensive and specialist-dependent process that is typically used to make such compounds. In contrast, general and automated platforms have been developed for making peptides, oligonucleotides, and increasingly oligosaccharides, where synthesis is simplified to iterative applications of the same reactions. Inspired by the way natural products are biosynthesized via the iterative assembly of a defined set of building blocks, we developed a platform for small molecule synthesis involving the iterative coupling of haloboronic acids protected as the corresponding N-methyliminodiacetic acid (MIDA) boronates. Here we summarize our efforts thus far to develop this platform into a generalized and automated approach for small molecule synthesis. We and others have employed this approach to access many polyene-based compounds, including the polyene motifs found in >75% of all polyene natural products. This platform further allowed us to derivatize amphotericin B, the powerful and resistance-evasive but also highly toxic last line of defense in treating systemic fungal infections, and thereby understand its mechanism of action. This synthesis-enabled mechanistic understanding has led us to develop less toxic derivatives currently under evaluation as improved antifungal agents. To access more Csp(3)-containing small molecules, we gained a stereocontrolled entry into chiral, non-racemic α-boryl aldehydes through the discovery of a chiral derivative of MIDA. These α-boryl aldehydes are versatile intermediates for the synthesis of many Csp(3) boronate building blocks that are otherwise difficult to access. In addition, we demonstrated the utility of these types of building blocks in accessing pharmaceutically relevant targets via an iterative Csp(3) cross-coupling cycle. We have further expanded the scope of the platform to include stereochemically complex macrocyclic and polycyclic molecules

  15. Synthesis of orthogonally protected bacterial, rare-sugar and D-glycosamine building blocks.

    Science.gov (United States)

    Emmadi, Madhu; Kulkarni, Suvarn S

    2013-10-01

    Bacterial glycoconjugates comprise atypical deoxy amino sugars that are not present on the human cell surface, making them good targets for drug discovery and carbohydrate-based vaccine development. Unfortunately, they cannot be isolated with sufficient purity in acceptable amounts, and therefore chemical synthesis is a crucial step toward the development of these products. Here we describe a detailed protocol for the synthesis of orthogonally protected bacterial deoxy amino hexopyranoside (2,4-diacetamido-2,4,6-trideoxyhexose (DATDH), D-bacillosamine, D-fucosamine, and 2-acetamido-4-amino-2,4,6-trideoxy-D-galactose (AAT)), D-glucosamine and D-galactosamine building blocks starting from β-D-thiophenylmannoside. Readily available β-D-thiophenylmannoside was first converted into the corresponding 2,4-diols via deoxygenation or silylation at C6, followed by O3 acylation. The 2,4-diols were converted into 2,4-bis-trifluoromethanesulfonates, which underwent highly regioselective, one-pot, double-serial and double-parallel displacements by azide, phthalimide, acetate and nitrite ions as nucleophiles. Thus, D-rhamnosyl- and D-mannosyl 2,4-diols can be efficiently transformed into various rare sugars and D-galactosamine, respectively, as orthogonally protected thioglycoside building blocks on a gram scale in 1-2 d, in 54-85% overall yields, after a single chromatographic purification. This would otherwise take 1-2 weeks. D-Glucosamine building blocks can be prepared from β-D-thiophenylmannoside in four steps via C2 displacement of triflates by azide in 2 d and in 66-70% overall yields. These procedures have been applied to the synthesis of L-serine-linked trisaccharide of Neisseria meningitidis and a rare disaccharide fragment of the zwitterionic polysaccharide (ZPS) A1 (ZPS A1) of Bacteroides fragilis.

  16. LEGO® bricks as building blocks for centimeter-scale biological environments: the case of plants.

    Science.gov (United States)

    Lind, Kara R; Sizmur, Tom; Benomar, Saida; Miller, Anthony; Cademartiri, Ludovico

    2014-01-01

    LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil.

  17. Engineering cell factories for producing building block chemicals for bio-polymer synthesis.

    Science.gov (United States)

    Tsuge, Yota; Kawaguchi, Hideo; Sasaki, Kengo; Kondo, Akihiko

    2016-01-21

    Synthetic polymers are widely used in daily life. Due to increasing environmental concerns related to global warming and the depletion of oil reserves, the development of microbial-based fermentation processes for the production of polymer building block chemicals from renewable resources is desirable to replace current petroleum-based methods. To this end, strains that efficiently produce the target chemicals at high yields and productivity are needed. Recent advances in metabolic engineering have enabled the biosynthesis of polymer compounds at high yield and productivities by governing the carbon flux towards the target chemicals. Using these methods, microbial strains have been engineered to produce monomer chemicals for replacing traditional petroleum-derived aliphatic polymers. These developments also raise the possibility of microbial production of aromatic chemicals for synthesizing high-performance polymers with desirable properties, such as ultraviolet absorbance, high thermal resistance, and mechanical strength. In the present review, we summarize recent progress in metabolic engineering approaches to optimize microbial strains for producing building blocks to synthesize aliphatic and high-performance aromatic polymers.

  18. HARP preferentially co-purifies with RPA bound to DNA-PK and blocks RPA phosphorylation.

    Science.gov (United States)

    Quan, Jinhua; Yusufzai, Timur

    2014-05-01

    The HepA-related protein (HARP/SMARCAL1) is an ATP-dependent annealing helicase that is capable of rewinding DNA structures that are stably unwound due to binding of the single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA). HARP has been implicated in maintaining genome integrity through its role in DNA replication and repair, two processes that generate RPA-coated ssDNA. In addition, mutations in HARP cause a rare disease known as Schimke immuno-osseous dysplasia. In this study, we purified HARP containing complexes with the goal of identifying the predominant factors that stably associate with HARP. We found that HARP preferentially interacts with RPA molecules that are bound to the DNA-dependent protein kinase (DNA-PK). We also found that RPA is phosphorylated by DNA-PK in vitro, while the RPA-HARP complexes are not. Our results suggest that, in addition to its annealing helicase activity, which eliminates the natural binding substrate for RPA, HARP blocks the phosphorylation of RPA by DNA-PK.

  19. Dendrimers and Dendrons as Versatile Building Blocks for the Fabrication of Functional Hydrogels

    Directory of Open Access Journals (Sweden)

    Sadik Kaga

    2016-04-01

    Full Text Available Hydrogels have emerged as a versatile class of polymeric materials with a wide range of applications in biomedical sciences. The judicious choice of hydrogel precursors allows one to introduce the necessary attributes to these materials that dictate their performance towards intended applications. Traditionally, hydrogels were fabricated using either polymerization of monomers or through crosslinking of polymers. In recent years, dendrimers and dendrons have been employed as well-defined building blocks in these materials. The multivalent and multifunctional nature of dendritic constructs offers advantages in either formulation or the physical and chemical properties of the obtained hydrogels. This review highlights various approaches utilized for the fabrication of hydrogels using well-defined dendrimers, dendrons and their polymeric conjugates. Examples from recent literature are chosen to illustrate the wide variety of hydrogels that have been designed using dendrimer- and dendron-based building blocks for applications, such as sensing, drug delivery and tissue engineering.

  20. LEGO® bricks as building blocks for centimeter-scale biological environments: the case of plants.

    Directory of Open Access Journals (Sweden)

    Kara R Lind

    Full Text Available LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil.

  1. Design of fundamental building blocks for fast binary readout CMOS sensors used in high-energy physics experiments

    Energy Technology Data Exchange (ETDEWEB)

    Degerli, Yavuz [CEA Saclay, IRFU/SEDI, 91191 Gif-sur-Yvette Cedex (France)], E-mail: degerli@cea.fr

    2009-04-21

    In this paper, design details of key building blocks for fast binary readout CMOS monolithic active pixel sensors developed for charged particle detection are presented. Firstly, an all-NMOS pixel architecture with in-pixel amplification and reset noise suppression which allows fast readout is presented. This pixel achieves high charge-to-voltage conversion factors (CVF) using a few number of transistors inside the pixel. It uses a pre-amplifying stage close to the detector and a simple double sampling (DS) circuitry to store the reset level of the detector. The DS removes the offset mismatches of amplifiers and the reset noise of the detector. Offset mismatches of the source follower are also corrected by a second column-level DS stage. The second important building block of these sensors, a low-power auto-zeroed column-level discriminator, is also presented. These two blocks transform the charge of the impinging particle into binary data. Finally, some experimental results obtained on CMOS chips designed using these blocks are presented.

  2. Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

    Science.gov (United States)

    Campo, Daniel; García-Vázquez, Eva

    2012-01-01

    The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

  3. Traveling Rocky Roads: The Consequences of Transcription-Blocking DNA Lesions on RNA Polymerase II

    NARCIS (Netherlands)

    B. Steurer (Barbara); J.A. Marteijn (Jurgen)

    2016-01-01

    textabstractThe faithful transcription of eukaryotic genes by RNA polymerase II (RNAP2) is crucial for proper cell function and tissue homeostasis. However, transcription-blocking DNA lesions of both endogenous and environmental origin continuously challenge the progression of elongating RNAP2. The

  4. Multifunctional Nanoparticles Self-Assembled from Small Organic Building Blocks for Biomedicine.

    Science.gov (United States)

    Xing, Pengyao; Zhao, Yanli

    2016-09-01

    Supramolecular self-assembly shows significant potential to construct responsive materials. By tailoring the structural parameters of organic building blocks, nanosystems can be fabricated, whose performance in catalysis, energy storage and conversion, and biomedicine has been explored. Since small organic building blocks are structurally simple, easily modified, and reproducible, they are frequently employed in supramolecular self-assembly and materials science. The dynamic and adaptive nature of self-assembled nanoarchitectures affords an enhanced sensitivity to the changes in environmental conditions, favoring their applications in controllable drug release and bioimaging. Here, recent significant research advancements of small-organic-molecule self-assembled nanoarchitectures toward biomedical applications are highlighted. Functionalized assemblies, mainly including vesicles, nanoparticles, and micelles are categorized according to their topological morphologies and functions. These nanoarchitectures with different topologies possess distinguishing advantages in biological applications, well incarnating the structure-property relationship. By presenting some important discoveries, three domains of these nanoarchitectures in biomedical research are covered, including biosensors, bioimaging, and controlled release/therapy. The strategies regarding how to design and characterize organic assemblies to exhibit biomedical applications are also discussed. Up-to-date research developments in the field are provided and research challenges to be overcome in future studies are revealed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Building blocks for a polarimeter-on-a-chip

    International Nuclear Information System (INIS)

    Stevenson, Thomas R.; Hsieh, W.-T.; Schneider, Gideon; Travers, Douglas; Cao, Nga; Wollack, Edward; Limon, Michele; Kogut, Alan

    2006-01-01

    For the 'Primordial Anisotropy Polarization Pathfinder Array (PAPPA)' balloon flight project, we have designed and made thin-film niobium microstrip circuits as building blocks for a 'polarimeter-on-a-chip' in which superconducting transmission lines are used to couple millimeter wave signals from planar antennas to superconducting transition edge sensor (TES) detectors. Our goal is to demonstrate technology for precision measurements of the polarization of the cosmic microwave background. To enable characterization and verification of our microstrip components, we have incorporated waveguide probes on each chip that can bring millimeter wave signals from a room temperature vector network analyzer to the superconducting circuits on the chip and back again for S-parameter measurements. We have designed a planar antenna and RF choke on the probes to efficiently couple radiation between waveguide and thin-film microstrip. To support the probe antennas in waveguides, we sculpted thin silicon cantilevers that extend from an edge of each silicon chip into a pair of waveguides within a specially designed split-block mount. This technique will allow us to make calibrated measurements at low temperatures of the velocity, impedance, and loss properties of our niobium transmission lines, the frequency response of microstrip filters, hybrid couplers, or terminations, and the performance of integrated detectors

  6. Key Building Blocks via Enzyme-Mediated Synthesis

    Science.gov (United States)

    Fischer, Thomas; Pietruszka, Jörg

    Biocatalytic approaches to valuable building blocks in organic synthesis have emerged as an important tool in the last few years. While first applications were mainly based on hydrolases, other enzyme classes such as oxidoreductases or lyases moved into the focus of research. Nowadays, a vast number of biotransformations can be found in the chemical and pharmaceutical industries delivering fine chemicals or drugs. The mild reaction conditions, high stereo-, regio-, and chemoselectivities, and the often shortened reaction pathways lead to economical and ecological advantages of enzymatic conversions. Due to the enormous number of enzyme-mediated syntheses, the present chapter is not meant to be a complete review, but to deliver comprehensive insights into well established enzymatic systems and recent advances in the application of enzymes in natural product synthesis. Furthermore, it is focused on the most frequently used enzymes or enzyme classes not covered elsewhere in the present volume.

  7. Automated electrochemical assembly of the protected potential TMG-chitotriomycin precursor based on rational optimization of the carbohydrate building block.

    Science.gov (United States)

    Nokami, Toshiki; Isoda, Yuta; Sasaki, Norihiko; Takaiso, Aki; Hayase, Shuichi; Itoh, Toshiyuki; Hayashi, Ryutaro; Shimizu, Akihiro; Yoshida, Jun-ichi

    2015-03-20

    The anomeric arylthio group and the hydroxyl-protecting groups of thioglycosides were optimized to construct carbohydrate building blocks for automated electrochemical solution-phase synthesis of oligoglucosamines having 1,4-β-glycosidic linkages. The optimization study included density functional theory calculations, measurements of the oxidation potentials, and the trial synthesis of the chitotriose trisaccharide. The automated synthesis of the protected potential N,N,N-trimethyl-d-glucosaminylchitotriomycin precursor was accomplished by using the optimized building block.

  8. Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies

    KAUST Repository

    Lundberg, Erik P.

    2011-09-27

    We demonstrate the stepwise assembly of a fully addressable polycyclic DNA hexagon nanonetwork for the preparation of a four-ring system, one of the biggest networks yet constructed from tripodal building blocks. We find that the yield exhibits a distinct upper level <100%, a fundamental problem of thermodynamic DNA assembly that appears to have been overlooked in the DNA nanotechnology literature. A simplistic model based on a single step-yield parameter y can quantitatively describe the total yield of DNA assemblies in one-pot reactions as Y = yduplex n, with n the number of hybridization steps. Experimental errors introducing deviations from perfect stoichiometry and the thermodynamics of hybridization equilibria contribute to decreasing the value of yduplex (on average y = 0.96 for our 10 base pair hybridization). For the four-ring system (n = 31), the total yield is thus less than 30%, which is clearly unsatisfactory if bigger nanoconstructs of this class are to be designed. Therefore, we introduced site-specific click chemistry for making and purifying robust building blocks for future modular constructs of larger assemblies. Although the present yield of this robust module was only about 10%, it demonstrates a first step toward a general fabrication approach. Interestingly, we find that the click yields follow quantitatively a binomial distribution, the predictability of which indicates the usefulness of preparing pools of pure and robust building blocks in this way. The binomial behavior indicates that there is no interference between the six simultaneous click reactions but that step-yield limiting factors such as topological constraints and Cu(I) catalyst concentration are local and independent. © 2011 American Chemical Society.

  9. Synthesis of N-protected Galactosamine Building Blocks from D-Tagatose via the Heyns Rearrangement

    DEFF Research Database (Denmark)

    Wrodnigg, Tanja M.; Lundt, Inge; Stütz, Arnold E.

    2006-01-01

    N-Acetyl-D-galactosamine (11), a very important naturally occurring building block of oligosaccharides, is easily accessible via the Heyns rearrangement of D-tagatose (3) with benzylamine. The short and efficient synthesis of various differently N-protected D-galactosamine derivatives is reported....

  10. DNA origami: a quantum leap for self-assembly of complex structures

    DEFF Research Database (Denmark)

    Tørring, Thomas; Voigt, Niels Vinther; Nangreave, Jeanette

    2011-01-01

    The spatially controlled positioning of functional materials by self-assembly is one of the fundamental visions of nanotechnology. Major steps towards this goal have been achieved using DNA as a programmable building block. This tutorial review will focus on one of the most promising methods: DNA...... origami. The basic design principles, organization of a variety of functional materials and recent implementation of DNA robotics are discussed together with future challenges and opportunities....

  11. Building blocks of the universe

    International Nuclear Information System (INIS)

    Malamud, E.; O'Connor, C.; Cooper, A.

    1990-01-01

    COSI [Ohio's Center for Science and Industry], a well established science center, and SciTech, an emerging one, have formed a collaboration to develop a group of original interactive exhibits conveying to a wide audience the nature of the most fundamental features of the Universe, as revealed in the fascinating world of nuclear and particle science. These new exhibits will add to, and be supported by, the basic science exhibits which have already attracted large numbers of visitors to both centers. The new project, called Building Blocks of the Universe, aims to foster an appreciation of the way all features of the Universe arise from simple, basic rules and to lead the visitor from the perceived complexities of our surroundings, to the unperceived, but simpler features of the sub-nuclear world. It has already become apparent from individual prototypes that these simple but immensely far-reaching ideas can indeed be conveyed by hands-on exhibits. These exhibits will be linked and enhanced by an effective museum environment, using pictorial diagrams, accurate non-technical text, and artistic displays to create an atmosphere in which visitors can learn about phenomena beyond the range of direct perception. This paper describes the goals, content and organization of the exhibition. The authors also outline their experience with prototype exhibits, and thereby invite additional input into the development process

  12. Metal-Organic Frameworks: Building Block Design Strategies for the Synthesis of MOFs.

    KAUST Repository

    Luebke, Ryan

    2014-09-01

    A significant and ongoing challenge in materials chemistry and furthermore solid state chemistry is to design materials with the desired properties and characteristics. The field of Metal-Organic Frameworks (MOFs) offers several strategies to address this challenge and has proven fruitful at allowing some degree of control over the resultant materials synthesized. Several methodologies for synthesis of MOFs have been developed which rely on use of predetermined building blocks. The work presented herein is focused on the utilization of two of these design principles, namely the use of molecular building blocks (MBBs) and supermolecular building blocks (SBBs) to target MOF materials having desired connectivities (topologies). These design strategies also permit the introduction of specific chemical moieties, allowing for modification of the MOFs properties. This research is predominantly focused on two platforms (rht-MOFs and ftw-MOFs) which topologically speaking are edge transitive binodal nets; ftw being a (4,12)-connected net and rht being a (3,24)-connected net. These highly connected nets (at least one node having connectivity greater than eight) have been purposefully targeted to increase the predictability of structural outcome. A general trend in topology is that there is an inverse relationship between the connectivity of the node(s) and the number of topological outcomes. Therefore the key to this research (and to effective use of the SBB and MBB approaches) is identification of conditions which allow for reliable formation of the targeted MBBs and SBBs. In the case of the research presented herein: a 12-connected Group IV or Rare Earth based hexanuclear MBB and a 24-connected transition metal based SBB were successfully targeted and synthesized. These two synthetic platforms will be presented and used as examples of how these design methods have been (and can be further) utilized to modify existing materials or develop new materials for gas storage and

  13. Methods for estimating wake flow and effluent dispersion near simple block-like buildings

    International Nuclear Information System (INIS)

    Hosker, R.P. Jr.

    1981-05-01

    This report is intended as an interim guide for those who routinely face air quality problems associated with near-building exhaust stack placement and height, and the resulting concentration patterns. Available data and methods for estimating wake flow and effluent dispersion near isolated block-like structures are consolidated. The near-building and wake flows are described, and quantitative estimates for frontal eddy size, height and extent of roof and wake cavities, and far wake behavior are provided. Concentration calculation methods for upwind, near-building, and downwind pollutant sources are given. For an upwind source, it is possible to estimate the required stack height, and to place upper limits on the likely near-building concentration. The influences of near-building source location and characteristics relative to the building geometry and orientation are considered. Methods to estimate effective stack height, upper limits for concentration due to flush roof vents, and the effect of changes in rooftop stack height are summarized. Current wake and wake cavity models are presented. Numerous graphs of important expressions have been prepared to facilitate computations and quick estimates of flow patterns and concentration levels for specific simple buildings. Detailed recommendations for additional work are given

  14. DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries.

    Science.gov (United States)

    Franzini, Raphael M; Neri, Dario; Scheuermann, Jörg

    2014-04-15

    DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target

  15. Membrane InP saturable absorbers on silicon as building blocks for transparent optical networks

    NARCIS (Netherlands)

    Raz, O.; Tassaert, M.; Roelkens, G.C.; Dorren, H.J.S.

    2013-01-01

    As silicon photonics continues to gain research and industrial relevance, some of the building blocks in this technology such as modulators and switches still suffer from limitation when it comes to insertion losses and/or extinction ratio. In the past two years we have been investigating a

  16. α-Haloaldehydes: versatile building blocks for natural product synthesis.

    Science.gov (United States)

    Britton, Robert; Kang, Baldip

    2013-02-01

    The diastereoselective addition of organometallic reagents to α-chloroaldehydes was first reported in 1959 and occupies a historically significant role as the prototypical reaction for Cornforth's model of stereoinduction. Despite clear synthetic potential for these reagents, difficulties associated with producing enantiomerically enriched α-haloaldehydes limited their use in natural product synthesis through the latter half of the 20th century. In recent years, however, a variety of robust, organocatalytic processes have been reported that now provide direct access to optically enriched α-haloaldehydes and have motivated renewed interest in their use as building blocks for natural product synthesis. This Highlight summarizes the methods available for the enantioselective preparation of α-haloaldehydes and their stereoselective conversion into natural products.

  17. Engineering cell factories for producing building block chemicals for bio-polymer synthesis

    OpenAIRE

    Tsuge, Yota; Kawaguchi, Hideo; Sasaki, Kengo; Kondo, Akihiko

    2016-01-01

    Synthetic polymers are widely used in daily life. Due to increasing environmental concerns related to global warming and the depletion of oil reserves, the development of microbial-based fermentation processes for the production of polymer building block chemicals from renewable resources is desirable to replace current petroleum-based methods. To this end, strains that efficiently produce the target chemicals at high yields and productivity are needed. Recent advances in metabolic engineerin...

  18. Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing.

    Science.gov (United States)

    Gao, Ru-Ru; Yao, Tian-Ming; Lv, Xiao-Yan; Zhu, Yan-Yan; Zhang, Yi-Wei; Shi, Shuo

    2017-06-01

    To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future.

  19. Catalytic allylic oxidation of internal alkenes to a multifunctional chiral building block

    Science.gov (United States)

    Bayeh, Liela; Le, Phong Q.; Tambar, Uttam K.

    2017-07-01

    The stereoselective oxidation of hydrocarbons is one of the most notable advances in synthetic chemistry over the past fifty years. Inspired by nature, enantioselective dihydroxylations, epoxidations and other oxidations of unsaturated hydrocarbons have been developed. More recently, the catalytic enantioselective allylic carbon-hydrogen oxidation of alkenes has streamlined the production of pharmaceuticals, natural products, fine chemicals and other functional materials. Allylic functionalization provides a direct path to chiral building blocks with a newly formed stereocentre from petrochemical feedstocks while preserving the olefin functionality as a handle for further chemical elaboration. Various metal-based catalysts have been discovered for the enantioselective allylic carbon-hydrogen oxidation of simple alkenes with cyclic or terminal double bonds. However, a general and selective allylic oxidation using the more common internal alkenes remains elusive. Here we report the enantioselective, regioselective and E/Z-selective allylic oxidation of unactivated internal alkenes via a catalytic hetero-ene reaction with a chalcogen-based oxidant. Our method enables non-symmetric internal alkenes to be selectively converted into allylic functionalized products with high stereoselectivity and regioselectivity. Stereospecific transformations of the resulting multifunctional chiral building blocks highlight the potential for rapidly converting internal alkenes into a broad range of enantioenriched structures that can be used in the synthesis of complex target molecules.

  20. Microbial production of building block chemicals and polymers.

    Science.gov (United States)

    Lee, Jeong Wook; Kim, Hyun Uk; Choi, Sol; Yi, Jongho; Lee, Sang Yup

    2011-12-01

    Owing to our increasing concerns on the environment, climate change, and limited natural resources, there has recently been considerable effort exerted to produce chemicals and materials from renewable biomass. Polymers we use everyday can also be produced either by direct fermentation or by polymerization of monomers that are produced by fermentation. Recent advances in metabolic engineering combined with systems biology and synthetic biology are allowing us to more systematically develop superior strains and bioprocesses for the efficient production of polymers and monomers. Here, we review recent trends in microbial production of building block chemicals that can be subsequently used for the synthesis of polymers. Also, recent successful cases of direct one-step production of polymers are reviewed. General strategies for the production of natural and unnatural platform chemicals are described together with representative examples. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Stepwise transformation of the molecular building blocks in a porphyrin-encapsulating metal-organic material

    KAUST Repository

    Zhang, ZhenJie; Wojtas, Łukasz; Eddaoudi, Mohamed; Zaworotko, Michael J.

    2013-01-01

    When immersed in solutions containing Cu(II) cations, the microporous metal-organic material P11 ([Cd4(BPT)4]·[Cd(C 44H36N8)(S)]·[S], BPT = biphenyl-3,4′,5-tricarboxylate) undergoes a transformation of its [Cd 2(COO)6]2- molecular building blocks

  2. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods.

    Science.gov (United States)

    Piñol, J; Mir, G; Gomez-Polo, P; Agustí, N

    2015-07-01

    The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer-template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator-specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 °C annealing temperature and 40 cycles) and high-throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer-template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer-template mismatches explained most of the variation (~3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region. © 2014 John Wiley & Sons Ltd.

  3. Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks.

    Science.gov (United States)

    Chen, Yun; Nielsen, Jens

    2013-12-01

    Bio-based production of chemical building blocks from renewable resources is an attractive alternative to petroleum-based platform chemicals. Metabolic pathway and strain engineering is the key element in constructing robust microbial chemical factories within the constraints of cost effective production. Here we discuss how the development of computational algorithms, novel modules and methods, omics-based techniques combined with modeling refinement are enabling reduction in development time and thus advance the field of industrial biotechnology. We further discuss how recent technological developments contribute to the development of novel cell factories for the production of the building block chemicals: adipic acid, succinic acid and 3-hydroxypropionic acid. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Solution scattering studies on a virus capsid protein as a building block for nanoscale assemblies

    NARCIS (Netherlands)

    Comellas Aragones, M.; Comellas-Aragones, Marta; Sikkema, Friso D.; Delaittre, Guillaume; Terry, Ann E.; King, Stephen M.; Visser, Dirk; Heenan, Richard K.; Nolte, Roeland J.M.; Cornelissen, Jeroen Johannes Lambertus Maria; Feiters, Martin C.

    2011-01-01

    Self-assembled protein cages are versatile building blocks in the construction of biomolecular nanostructures. Because of the defined assembly behaviour the cowpea chlorotic mottle virus (CCMV) protein is often used for such applications. Here we report a detailed solution scattering study of the

  5. A chemical platform approach on cardanol oil: from the synthesis of building blocks to polymer synthesis

    Directory of Open Access Journals (Sweden)

    Jaillet Fanny

    2016-09-01

    Full Text Available This review proposes a platform approach for the synthesis of various building blocks from cardanol oil in one or two-steps synthesis. Cardanol is a natural phenol issued from Cashew nutshell liquid (CNSL. CNSL is a non-edible renewable resource, co-produced from cashew industry in large commercial volumes. Cardanol is non-toxic and particularly suitable as an aromatic renewable resource for polymers and materials. Various routes were used for the synthesis of di- and poly-functional building blocks used thereafter in polymer syntheses. Phenolation was used to dimerize/oligomerize cardanol to propose increase functionality of cardanol. Thio-ene was used to synthesize new reactive amines. Epoxidation and (methacrylation were also used to insert oxirane or (methacrylate groups in order to synthesize polymers and materials.

  6. Prototypic implementations of the building block for component based open Hypermedia systems (BB/CB-OHSs)

    DEFF Research Database (Denmark)

    Mohamed, Omer I. Eldai

    2005-01-01

    In this paper we describe the prototypic implementations of the BuildingBlock (BB/CB-OHSs) that proposed to address some of the Component-based Open Hypermedia Systems (CB-OHSs) issues, including distribution and interoperability [4, 11, 12]. Four service implementations were described below. The...

  7. Theoretical and technological building blocks for an innovation accelerator

    Science.gov (United States)

    van Harmelen, F.; Kampis, G.; Börner, K.; van den Besselaar, P.; Schultes, E.; Goble, C.; Groth, P.; Mons, B.; Anderson, S.; Decker, S.; Hayes, C.; Buecheler, T.; Helbing, D.

    2012-11-01

    Modern science is a main driver of technological innovation. The efficiency of the scientific system is of key importance to ensure the competitiveness of a nation or region. However, the scientific system that we use today was devised centuries ago and is inadequate for our current ICT-based society: the peer review system encourages conservatism, journal publications are monolithic and slow, data is often not available to other scientists, and the independent validation of results is limited. The resulting scientific process is hence slow and sloppy. Building on the Innovation Accelerator paper by Helbing and Balietti [1], this paper takes the initial global vision and reviews the theoretical and technological building blocks that can be used for implementing an innovation (in first place: science) accelerator platform driven by re-imagining the science system. The envisioned platform would rest on four pillars: (i) Redesign the incentive scheme to reduce behavior such as conservatism, herding and hyping; (ii) Advance scientific publications by breaking up the monolithic paper unit and introducing other building blocks such as data, tools, experiment workflows, resources; (iii) Use machine readable semantics for publications, debate structures, provenance etc. in order to include the computer as a partner in the scientific process, and (iv) Build an online platform for collaboration, including a network of trust and reputation among the different types of stakeholders in the scientific system: scientists, educators, funding agencies, policy makers, students and industrial innovators among others. Any such improvements to the scientific system must support the entire scientific process (unlike current tools that chop up the scientific process into disconnected pieces), must facilitate and encourage collaboration and interdisciplinarity (again unlike current tools), must facilitate the inclusion of intelligent computing in the scientific process, must facilitate

  8. RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

    Science.gov (United States)

    Ohno, Hirohisa; Saito, Hirohide

    2016-01-01

    Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Culture's building blocks: investigating cultural evolution in a LEGO construction task.

    Science.gov (United States)

    McGraw, John J; Wallot, Sebastian; Mitkidis, Panagiotis; Roepstorff, Andreas

    2014-01-01

    ONE OF THE MOST ESSENTIAL BUT THEORETICALLY VEXING ISSUES REGARDING THE NOTION OF CULTURE IS THAT OF CULTURAL EVOLUTION AND TRANSMISSION: how a group's accumulated solutions to invariant challenges develop and persevere over time. But at the moment, the notion of applying evolutionary theory to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest challenges for theorists is identifying the appropriate time scales and units of analysis in order to reduce the intractably large and complex phenomenon of "culture" into its component "building blocks." In this paper, we present a model for scientifically investigating cultural processes by analyzing the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development and transmission of culture through the microcosm of interactive LEGO design and assembly.

  10. DNA-Based Single-Molecule Electronics: From Concept to Function

    Science.gov (United States)

    2018-01-01

    Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed. PMID:29342091

  11. DNA-Based Single-Molecule Electronics: From Concept to Function.

    Science.gov (United States)

    Wang, Kun

    2018-01-17

    Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I-V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

  12. Building a DNA barcode library of Alaska's non-marine arthropods.

    Science.gov (United States)

    Sikes, Derek S; Bowser, Matthew; Morton, John M; Bickford, Casey; Meierotto, Sarah; Hildebrandt, Kyndall

    2017-03-01

    Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska - i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.

  13. Determination of lead equivalent thickness to building blocks used in shielding of diagnostic x-ray rooms in Syria

    International Nuclear Information System (INIS)

    Kawash, A.; Khedr, M.; Wannus, K.; Souliman, J.; Al-Oudat, M.

    1998-06-01

    Lead equivalent thicknesses of various kinds of blocks (Hollow core, solid, filled, roof) with different thicknesses were determined. These blocks are widely used for building the diagnostic X-rya departments in Syria. Different applied voltages at X-ray tube (65, 85, 100, 125, 150 KVp) were examined. The results showed that the highest lead equivalent thicknesses for hollow core blocks were at 100 KVp. These equivalent thicknesses were 0.4372, 0.7008 and 0.928 mm for block thicknesses of 10, 15 and 20 cm, respectively. it was also found that, the lead equivalent thicknesses for filled, solid and concrete block were 3.5 to 4 times higher than that of the hollow core block for the same thicknesses and the applied KVp. Values obtained for roof blocks were similar to that of hollow core for the same conditions and geometry. (Author)

  14. Signal replication in a DNA nanostructure

    Science.gov (United States)

    Mendoza, Oscar; Houmadi, Said; Aimé, Jean-Pierre; Elezgaray, Juan

    2017-01-01

    Logic circuits based on DNA strand displacement reaction are the basic building blocks of future nanorobotic systems. The circuits tethered to DNA origami platforms present several advantages over solution-phase versions where couplings are always diffusion-limited. Here we consider a possible implementation of one of the basic operations needed in the design of these circuits, namely, signal replication. We show that with an appropriate preparation of the initial state, signal replication performs in a reproducible way. We also show the existence of side effects concomitant to the high effective concentrations in tethered circuits, such as slow leaky reactions and cross-activation.

  15. Inhibition of polymerases-alpha and -beta completely blocks DNA repair induced by UV irradiation in cultured mouse neuronal cells

    International Nuclear Information System (INIS)

    Licastro, F.; Sarafian, T.; Verity, A.M.; Walford, R.L.

    1985-01-01

    The effects of hydroxyurea, aphidicolin and dideoxythymidine on UV-induced DNA repair of mouse neuronal granular cells were studied. Aphidicolin, which is considered a specific inhibitor of polymerase-alpha, decreased spontaneous DNA synthesis by 93% and totally suppressed DNA repair. Dideoxythymidine, an inhibitor of polymerase-beta, was more potent in decreasing scheduled DNA synthesis than aphidicolin, and also completely blocked the UV-induced DNA repair. Hydroxyurea, a specific inhibitor of ribonucleotide reductase, inhibited scheduled DNA synthesis, but unscheduled DNA synthesis after UV irradiation was always well detectable. Our data suggest that in neuronal cells from 5 to 10 days old mice both polymerases-alpha and -beta are required for both DNA synthesis and repair. These two enzymes may act jointly in filling up the gaps along the DNA molecule and elongating the DNA chain

  16. The mechanism of 2-dimensional manipulation of DNA molecules by water and ethanol flows

    International Nuclear Information System (INIS)

    Shen Zigang; Huang Yibo; Li Bin; Zhang Yi

    2007-01-01

    Due to its unique physical and chemical properties, DNA has recently become a promising material for building blocks in nanofabrication. Many researches focus on how to use DNA molecules as a template for nanowires. Molecular Combing technique is one of important methods to manipulate DNA molecules by using a water meniscus and form specific DNA nano-structures on surfaces. In this paper, by employing a modified molecular combing technique, special patterns of DNA molecules was formed, and the interaction between liquid flows or meniscus and DNA molecules was analyzed, and the mechanism of manipulating DNA molecules by liquid was studied. (authors)

  17. Development of Universal Controller Architecture for SiC Based Power Electronic Building Blocks

    Science.gov (United States)

    2017-10-30

    SiC Based Power Electronic Building Blocks Award Number Title of Research 30 October 2017 SUBMITTED BY D R. HERBERT L. G INN, Pl DEPT. OF...Naval Research , Philadelphia PA, Aug. 2017. • Ginn, H.L. Bakos J., "Development of Universal Controller Architecture for SiC Based Power Electronic...Controller Implementation for MMC Converters", Workshop on Control Architectures for Modular Power Conversion Systems, Office of Naval Research , Arlington VA

  18. DNA-scaffolded nanoparticle structures

    Energy Technology Data Exchange (ETDEWEB)

    Hoegberg, Bjoern; Olin, Haakan [Department of Engineering Physics and Mathematics, Mid Sweden University, SE-851 70 Sundsvall, Sweden (Sweden)

    2007-03-15

    DNA self-assembly is a powerful route to the production of very small, complex structures. When used in combination with nanoparticles it is likely to become a key technology in the production of nanoelectronics in the future. Previously, demonstrated nanoparticle assemblies have mainly been periodic and highly symmetric arrays, unsuited as building blocks for any complex circuits. With the invention of DNA-scaffolded origami reported earlier this year (Rothemund P W K 2006 Nature 440 (7082) 297-302), a new route to complex nanostructures using DNA has been opened. Here, we give a short review of the field and present the current status of our experiments were DNA origami is used in conjunction with nanoparticles. Gold nanoparticles are functionalized with thiolated single stranded DNA. Strands that are complementary to the gold particle strands can be positioned on the self-assembled DNA-structure in arbitrary patterns. This property should allow an accurate positioning of the particles by letting them hybridize on the lattice. We report on our recent experiments on this system and discuss open problems and future applications.

  19. DNA-scaffolded nanoparticle structures

    International Nuclear Information System (INIS)

    Hoegberg, Bjoern; Olin, Haakan

    2007-01-01

    DNA self-assembly is a powerful route to the production of very small, complex structures. When used in combination with nanoparticles it is likely to become a key technology in the production of nanoelectronics in the future. Previously, demonstrated nanoparticle assemblies have mainly been periodic and highly symmetric arrays, unsuited as building blocks for any complex circuits. With the invention of DNA-scaffolded origami reported earlier this year (Rothemund P W K 2006 Nature 440 (7082) 297-302), a new route to complex nanostructures using DNA has been opened. Here, we give a short review of the field and present the current status of our experiments were DNA origami is used in conjunction with nanoparticles. Gold nanoparticles are functionalized with thiolated single stranded DNA. Strands that are complementary to the gold particle strands can be positioned on the self-assembled DNA-structure in arbitrary patterns. This property should allow an accurate positioning of the particles by letting them hybridize on the lattice. We report on our recent experiments on this system and discuss open problems and future applications

  20. The Development of Logico-Mathematical Knowledge in a Block-Building Activity at Ages 1-4

    Science.gov (United States)

    Kamii, Constance; Miyakawa, Yoko; Kato, Yasuhiko

    2004-01-01

    To study the developmental interrelationships among various aspects of logico-mathematical knowledge, 80 one- to 4-year-olds were individually asked to build "something tall" with 20 blocks. Percentages of new and significant behaviors increased with age and were analyzed in terms of the development of logico-mathematical relationships. It was…

  1. Chiral building blocks from biomass: 2,5-Diamino-2,5-dideoxy-1,4-3,6-dianhydroiditol

    NARCIS (Netherlands)

    Thiyagarajan, S.; Gootjes, L.; Vogelzang, W.; Wu, J.; Haveren, van J.; Es, van D.S.

    2011-01-01

    Isohexides (isomannide (endo-endo), isosorbide (endo-exo), and isoidide (exo-exo) are a group of renewable bio-based building blocks that received considerable attention among the polymer industries because these rigid bicyclic diols have several interesting properties in polymer applications.1 We

  2. Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Hobza, Pavel

    2008-01-01

    Roč. 73, č. 2 (2008), s. 161-174 ISSN 0010-0765 R&D Projects: GA MŠk LC512; GA ČR GA203/05/0009; GA ČR(CZ) GD203/05/H001 Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA duplex * interaction energy * stability Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.784, year: 2008

  3. E-Block: A Tangible Programming Tool with Graphical Blocks

    OpenAIRE

    Danli Wang; Yang Zhang; Shengyong Chen

    2013-01-01

    This paper designs a tangible programming tool, E-Block, for children aged 5 to 9 to experience the preliminary understanding of programming by building blocks. With embedded artificial intelligence, the tool defines the programming blocks with the sensors as the input and enables children to write programs to complete the tasks in the computer. The symbol on the programming block's surface is used to help children understanding the function of each block. The sequence information is transfer...

  4. DNA accumulation on ventilation system filters in university buildings in Singapore.

    Science.gov (United States)

    Luhung, Irvan; Wu, Yan; Xu, Siyu; Yamamoto, Naomichi; Chang, Victor Wei-Chung; Nazaroff, William W

    2017-01-01

    Biological particles deposit on air handling system filters as they process air. This study reports and interprets abundance and diversity information regarding biomass accumulation on ordinarily used filters acquired from several locations in a university environment. DNA-based analysis was applied both to quantify (via DNA fluorometry and qPCR) and to characterize (via high-throughput sequencing) the microbial material on filters, which mainly processed recirculated indoor air. Results were interpreted in relation to building occupancy and ventilation system operational parameters. Based on accumulated biomass, average DNA concentrations per AHU filter surface area across nine indoor locations after twelve weeks of filter use were in the respective ranges 1.1 to 41 ng per cm2 for total DNA, 0.02 to 3.3 ng per cm2 for bacterial DNA and 0.2 to 2.0 ng DNA per cm2 for fungal DNA. The most abundant genera detected on the AHU filter samples were Clostridium, Streptophyta, Bacillus, Acinetobacter and Ktedonobacter for bacteria and Aspergillus, Cladosporium, Nigrospora, Rigidoporus and Lentinus for fungi. Conditional indoor airborne DNA concentrations (median (range)) were estimated to be 13 (2.6-107) pg/m3 for total DNA, 0.4 (0.05-8.4) pg/m3 for bacterial DNA and 2.3 (1.0-5.1) pg/m3 for fungal DNA. Conditional airborne concentrations and the relative abundances of selected groups of genera correlate well with occupancy level. Bacterial DNA was found to be more responsive than fungal DNA to differences in occupancy level and indoor environmental conditions.

  5. Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks.

    Science.gov (United States)

    Yeh, Chun-Ting; Brunette, T J; Baker, David; McIntosh-Smith, Simon; Parmeggiani, Fabio

    2018-02-01

    Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (>1000 amino acids) that match three-dimensional geometric descriptions provided by the user. A run time of about 20min on a laptop computer for a 3000 amino acid structure makes Elfin accessible to users with limited computational resources. Protein structures with controlled geometry will allow the systematic study of the effect of spatial arrangement of enzymes and signaling molecules, and provide new scaffolds for functional nanomaterials. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Mucosal delivery of a transmission-blocking DNA vaccine encoding Giardia lamblia CWP2 by Salmonella typhimurium bactofection vehicle.

    Science.gov (United States)

    Abdul-Wahid, Aws; Faubert, Gaétan

    2007-12-05

    In this study, we investigated the use of Salmonella typhimurium (STM1 strain) as a bactofection vehicle to deliver a transmission-blocking DNA vaccine (TBDV) plasmid to the intestinal immune system. The gene encoding the full length cyst wall protein-2 (CWP2) from Giardia lamblia was subcloned into the pCDNA3 mammalian expression vector and stably introduced into S. typhimurium STM1. Eight-week-old female BALB/c mice were orally immunized every 2 weeks, for a total of three immunizations. Vaccinated and control mice were sacrificed 1 week following the last injection. Administration of the DNA vaccine led to the production of CWP2-specific cellular immune responses characterized by a mixed Th1/Th2 response. Using ELISA, antigen-specific IgA and IgG antibodies were detected in intestinal secretions. Moreover, analysis of sera demonstrated that the DNA immunization also stimulated the production of CWP2-specific IgG antibodies that were mainly of the IgG2a isotype. Finally, challenge infection with live Giardia muris cysts revealed that mice receiving the CWP2-encoding DNA vaccine were able to reduce cyst shedding by approximately 60% compared to control mice. These results demonstrate, for the first time, the development of parasite transmission-blocking immunity at the intestinal level following the administration of a mucosal DNA vaccine delivered by S. typhimurium STM1.

  7. A polynomial-chaos-expansion-based building block approach for stochastic analysis of photonic circuits

    Science.gov (United States)

    Waqas, Abi; Melati, Daniele; Manfredi, Paolo; Grassi, Flavia; Melloni, Andrea

    2018-02-01

    The Building Block (BB) approach has recently emerged in photonic as a suitable strategy for the analysis and design of complex circuits. Each BB can be foundry related and contains a mathematical macro-model of its functionality. As well known, statistical variations in fabrication processes can have a strong effect on their functionality and ultimately affect the yield. In order to predict the statistical behavior of the circuit, proper analysis of the uncertainties effects is crucial. This paper presents a method to build a novel class of Stochastic Process Design Kits for the analysis of photonic circuits. The proposed design kits directly store the information on the stochastic behavior of each building block in the form of a generalized-polynomial-chaos-based augmented macro-model obtained by properly exploiting stochastic collocation and Galerkin methods. Using this approach, we demonstrate that the augmented macro-models of the BBs can be calculated once and stored in a BB (foundry dependent) library and then used for the analysis of any desired circuit. The main advantage of this approach, shown here for the first time in photonics, is that the stochastic moments of an arbitrary photonic circuit can be evaluated by a single simulation only, without the need for repeated simulations. The accuracy and the significant speed-up with respect to the classical Monte Carlo analysis are verified by means of classical photonic circuit example with multiple uncertain variables.

  8. Catalytic asymmetric synthesis of enantiopure isoprenoid building blocks : application in the synthesis of apple leafminer pheromones

    NARCIS (Netherlands)

    Summeren, Ruben P. van; Reijmer, Sven J.W.; Minnaard, Adriaan J.; Feringa, Bernard

    2005-01-01

    The first catalytic asymmetric procedure capable of preparing all 4 diastereoisomers (ee > 99%, de > 98%) of a versatile saturated isoprenoid building block was developed and the value of this new method was demonstrated in its application to the concise total synthesis of two pheromones.

  9. Rapid formation of complexity in the total synthesis of natural products enabled by oxabicyclo[2.2.1]heptene building blocks.

    Science.gov (United States)

    Schindler, Corinna S; Carreira, Erick M

    2009-11-01

    This critical review showcases examples of rapid formation of complexity in total syntheses starting from 7-oxabicyclo[2.2.1]hept-5-ene derivatives. An overview of methods allowing synthetic access to these building blocks is provided and their application in recently developed synthetic transformations to structurally complex systems is illustrated. In addition, the facile access to a novel oxabicyclo[2.2.1]heptene derived building block is presented which significantly enlarges the possibilities of previously known chemical transformations and is highlighted in the enantioselective route to the core of the banyaside and suomilide natural products (107 references).

  10. Concept analysis and the building blocks of theory: misconceptions regarding theory development.

    Science.gov (United States)

    Bergdahl, Elisabeth; Berterö, Carina M

    2016-10-01

    The purpose of this article is to discuss the attempts to justify concepts analysis as a way to construct theory - a notion often advocated in nursing. The notion that concepts are the building blocks or threads from which theory is constructed is often repeated. It can be found in many articles and well-known textbooks. However, this notion is seldom explained or defended. The notion of concepts as building blocks has also been questioned by several authors. However, most of these authors seem to agree to some degree that concepts are essential components from which theory is built. Discussion paper. Literature was reviewed to synthesize and debate current knowledge. Our point is that theory is not built by concepts analysis or clarification and we will show that this notion has its basis in some serious misunderstandings. We argue that concept analysis is not a part of sound scientific method and should be abandoned. The current methods of concept analysis in nursing have no foundation in philosophy of science or in language philosophy. The type of concept analysis performed in nursing is not a way to 'construct' theory. Rather, theories are formed by creative endeavour to propose a solution to a scientific and/or practical problem. The bottom line is that the current style and form of concept analysis in nursing should be abandoned in favour of methods in line with modern theory of science. © 2016 John Wiley & Sons Ltd.

  11. Network diversity through two-step crystal engineering of a decorated 6-connected primary molecular building block

    KAUST Repository

    Yang, Qing-Yuan

    2016-10-04

    [Cr3O(nicotinate)6]+ was isolated and then utilised as a new primary molecular building block, PMBB, linked by 2-, 3- and 4-connected metal centres. Five novel metal–organic materials (MOMs) with acs, stp, rtl, fsc and pcu topologies were thereby isolated and characterised.

  12. Network diversity through two-step crystal engineering of a decorated 6-connected primary molecular building block

    KAUST Repository

    Yang, Qing-Yuan; Chen, Kai-Jie; Schoedel, Alexander; Wojtas, Lukasz; Perry IV, John J.; Zaworotko, Michael J.

    2016-01-01

    [Cr3O(nicotinate)6]+ was isolated and then utilised as a new primary molecular building block, PMBB, linked by 2-, 3- and 4-connected metal centres. Five novel metal–organic materials (MOMs) with acs, stp, rtl, fsc and pcu topologies were thereby isolated and characterised.

  13. SNUPPS power block engineering

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, C A [Bechtel Power Corp., San Francisco, Calif. (USA)

    1975-11-01

    The Standard Power Block is based on a modular concept and consists of the following: turbine building, auxiliary building, fuel building, control building, radwaste building, diesel generators building, and outside storage tanks and transformers. Each power block unit includes a Westinghouse pressurized water reactor and has a thermal power rating of 3425 MW(t). The corresponding General Electric turbine generator net electrical output is 1188 MW(e). This standardization approach results in not only a reduction in the costs of engineering, licensing, procurement, and project planning, but should also result in additional savings by the application of experience gained in the construction of the first unit to the following units and early input of construction data to design.

  14. Exploring the building blocks of social cognition: spontaneous agency perception and visual perspective taking in autism.

    Science.gov (United States)

    Zwickel, Jan; White, Sarah J; Coniston, Devorah; Senju, Atsushi; Frith, Uta

    2011-10-01

    Individuals with autism spectrum disorders have highly characteristic impairments in social interaction and this is true also for those with high functioning autism or Asperger syndrome (AS). These social cognitive impairments are far from global and it seems likely that some of the building blocks of social cognition are intact. In our first experiment, we investigated whether high functioning adults who also had a diagnosis of AS would be similar to control participants in terms of their eye movements when watching animated triangles in short movies that normally evoke mentalizing. They were. Our second experiment using the same movies, tested whether both groups would spontaneously adopt the visuo-spatial perspective of a triangle protagonist. They did. At the same time autistic participants differed in their verbal accounts of the story line underlying the movies, confirming their specific difficulties in on-line mentalizing. In spite of this difficulty, two basic building blocks of social cognition appear to be intact: spontaneous agency perception and spontaneous visual perspective taking.

  15. Optimum Compressive Strength of Hardened Sandcrete Building Blocks with Steel Chips

    Directory of Open Access Journals (Sweden)

    Alohan Omoregie

    2013-02-01

    Full Text Available The recycling of steel chips into an environmentally friendly, responsive, and profitable commodity in the manufacturing and construction industries is a huge and difficult challenge. Several strategies designed for the management and processing of this waste in developed countries have been largely unsuccessful in developing countries mainly due to its capital-intensive nature. To this end, this investigation attempts to provide an alternative solution to the recycling of this material by maximizing its utility value in the building construction industry. This is to establish their influence on the compressive strength of sandcrete hollow blocks and solid cubes with the aim of specifying the range percent of steel chips for the sandcrete optimum compressive strength value. This is particularly important for developing countries in sub-Saharan Africa, and even Latin America where most sandcrete blocks exhibit compressive strengths far below standard requirements. Percentages of steel chips relative to the weight of cement were varied and blended with the sand in an attempt to improve the sand grading parameters. The steel chips variations were one, two, three, four, five, ten and fifteen percent respectively. It was confirmed that the grading parameters were improved and there were significant increases in the compressive strength of the blocks and cube samples. The greatest improvement was noticed at four percent steel chips and sand combination. Using the plotted profile, the margin of steel chips additions for the optimum compressive strength was also established. It is recommended that steel chip sandcrete blocks are suitable for both internal load bearing, and non-load bearing walls, in areas where they are not subjected to moisture ingress. However, for external walls, and in areas where they are liable to moisture attack after laying, the surfaces should be well rendered. Below ground level, the surfaces should be coated with a water

  16. NMR characterization of the DNA binding properties of a novel Hoechst 33258 analogue peptide building block

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; Behrens, Carsten; Jacobsen, Jens Peter

    2002-01-01

    A novel aryl-bis-benzimidazole amino acid analogue of the DNA-binding compound Hoechst 33258 has recently been designed for incorporation in peptide combinatorial libraries by replacing the N-methylpiperazine group with a carboxyl group and the hydroxy group with an amino-methyl group. The DNA......-binding properties of the aryl-bis-benzimidazole monomer with the C-terminus derivatized with 3-(dimethylamino)-propylamine has been investigated in this paper by (1)H NMR studies of two different complexes with two different DNA sequences: A(5) d(5'-GCCA(5)CG-3'):d(5'-CGT(5)GGC-3') and A(3)T(3) d(5'-CGA(3)T(3)CG-3...... preference with the bis-benzimidazole moiety displaced toward the 3'-end from the center of the duplex. Two families of models of the complexes with A(5) and A(3)T(3) were derived with restrained molecular dynamics based on a large set of 70 and 61, respectively, intermolecular ligand NOEs. Both models give...

  17. Setting the stage - building and working in an ancient DNA laboratory.

    Science.gov (United States)

    Knapp, Michael; Clarke, Andrew C; Horsburgh, K Ann; Matisoo-Smith, Elizabeth A

    2012-01-20

    With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own species in particular. While the amount of sequence data available from ancient human, other animal and plant remains has increased dramatically over the past five years, some key limitations of ancient DNA research remain. Most notably, reduction of contamination and the authentication of results are of utmost importance. A number of studies have addressed different aspects of sampling, DNA extraction and DNA manipulation in order to establish protocols that most efficiently generate reproducible and authentic results. As increasing numbers of researchers from different backgrounds become interested in using ancient DNA technology to address key questions, the need for practical guidelines on how to construct and use an ancient DNA facility arises. The aim of this article is therefore to provide practical tips for building a state-of-the-art ancient DNA facility. It is intended to help researchers new to the field of ancient DNA research generally, and those considering the application of next generation sequencing, in their planning process. Copyright © 2011 Elsevier GmbH. All rights reserved.

  18. Carborane-linked 2'-deoxyuridine 5'-O-triphosphate as building block for polymerase synthesis of carborane-modified DNA.

    Science.gov (United States)

    Balintová, Jana; Simonova, Anna; Białek-Pietras, Magdalena; Olejniczak, Agnieszka; Lesnikowski, Zbigniew J; Hocek, Michal

    2017-11-01

    5-[(p-Carborane-2-yl)ethynyl]-2'-deoxyuridine 5'-O-triphosphate was synthesized and used as a good substrate in enzymatic construction of carborane-modified DNA or oligonucleotides containing up to 21 carborane moieties in primer extension reactions by DNA polymerases. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Autonomously Self-Adhesive Hydrogels as Building Blocks for Additive Manufacturing.

    Science.gov (United States)

    Deng, Xudong; Attalla, Rana; Sadowski, Lukas P; Chen, Mengsu; Majcher, Michael J; Urosev, Ivan; Yin, Da-Chuan; Selvaganapathy, P Ravi; Filipe, Carlos D M; Hoare, Todd

    2018-01-08

    We report a simple method of preparing autonomous and rapid self-adhesive hydrogels and their use as building blocks for additive manufacturing of functional tissue scaffolds. Dynamic cross-linking between 2-aminophenylboronic acid-functionalized hyaluronic acid and poly(vinyl alcohol) yields hydrogels that recover their mechanical integrity within 1 min after cutting or shear under both neutral and acidic pH conditions. Incorporation of this hydrogel in an interpenetrating calcium-alginate network results in an interfacially stiffer but still rapidly self-adhesive hydrogel that can be assembled into hollow perfusion channels by simple contact additive manufacturing within minutes. Such channels withstand fluid perfusion while retaining their dimensions and support endothelial cell growth and proliferation, providing a simple and modular route to produce customized cell scaffolds.

  20. Building Quality Report Cards for Geriatric Care in The Netherlands: Using Concept Mapping to Identify the Appropriate "Building Blocks" from the Consumer's Perspective

    Science.gov (United States)

    Groenewoud, A. Stef; van Exel, N. Job A.; Berg, Marc; Huijsman, Robbert

    2008-01-01

    Purpose: This article reports on a study to identify "building blocks" for quality report cards for geriatric care. Its aim is to present (a) the results of the study and (b) the innovative step-by-step approach that was developed to arrive at these results. Design and Methods: We used Concept Mapping/Structured Conceptualization to…

  1. Culture’s building blocks: investigating cultural evolution in a LEGO construction task

    Science.gov (United States)

    McGraw, John J.; Wallot, Sebastian; Mitkidis, Panagiotis; Roepstorff, Andreas

    2014-01-01

    One of the most essential but theoretically vexing issues regarding the notion of culture is that of cultural evolution and transmission: how a group’s accumulated solutions to invariant challenges develop and persevere over time. But at the moment, the notion of applying evolutionary theory to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest challenges for theorists is identifying the appropriate time scales and units of analysis in order to reduce the intractably large and complex phenomenon of “culture” into its component “building blocks.” In this paper, we present a model for scientifically investigating cultural processes by analyzing the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development and transmission of culture through the microcosm of interactive LEGO design and assembly. PMID:25309482

  2. Culture’s building blocks: investigating cultural evolution in a LEGO construction task

    Directory of Open Access Journals (Sweden)

    John Joseph Mcgraw

    2014-09-01

    Full Text Available One of the most essential but theoretically vexing issues regarding the notion of culture is that of cultural evolution and transmission: how a group’s accumulated solutions to invariant challenges develop and persevere over time. But at the moment, the notion of applying evolutionary theory to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest challenges for theorists is identifying the appropriate time scales and units of analysis in order to reduce the intractably large and complex phenomenon of culture into its component building blocks. In this paper, we present a model for scientifically investigating cultural processes by analyzing the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development and transmission of culture through the microcosm of interactive LEGO design and assembly.

  3. Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries.

    Science.gov (United States)

    Franzini, Raphael M; Samain, Florent; Abd Elrahman, Maaly; Mikutis, Gediminas; Nauer, Angela; Zimmermann, Mauro; Scheuermann, Jörg; Hall, Jonathan; Neri, Dario

    2014-08-20

    DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.

  4. 324 and 325 Building Hot Cell Cleanout Program: Air lock cover block refurbishment

    International Nuclear Information System (INIS)

    Katayama, Y.B.; Holton, L.K. Jr.; Gale, R.M.

    1989-05-01

    The high-density concrete cover blocks shielding the pipe trench in the hot-cell air lock of the 324 Building Radiochemical Engineering Cells had accumulated fixed radioactivity ranging from 1100 to 22, 000 mrad/hr. A corresponding increase in the radiation exposure to personnel entering the air lock, together with ALARA concerns, led to the removal of the contaminated concrete surface with a hydraulic spaller and the emplacement of a stainless steel covering over a layer of grout. The resultant saving in radiation exposure is estimated to be 7200 mrad for personnel completing burial box runs for the 324 and 325 Building Hot Cell Cleanout Program. Radiation exposure to all staff members entering the air lock is now at least 50% lower. 3 refs., 22 figs., 1 tab

  5. Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase

    OpenAIRE

    Gaur, Vineet; Vyas, Rajan; Fowler, Jason D.; Efthimiopoulos, Georgia; Feng, Joy Y.; Suo, Zucai

    2014-01-01

    Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) a...

  6. Noncanonical ATM Activation and Signaling in Response to Transcription-Blocking DNA Damage.

    Science.gov (United States)

    Marteijn, Jurgen A; Vermeulen, Wim; Tresini, Maria

    2017-01-01

    Environmental genotoxins and metabolic byproducts generate DNA lesions that can cause genomic instability and disrupt tissue homeostasis. To ensure genomic integrity, cells employ mechanisms that convert signals generated by stochastic DNA damage into organized responses, including activation of repair systems, cell cycle checkpoints, and apoptotic mechanisms. DNA damage response (DDR) signaling pathways coordinate these responses and determine cellular fates in part, by transducing signals that modulate RNA metabolism. One of the master DDR coordinators, the Ataxia Telangiectasia Mutated (ATM) kinase, has a fundamental role in mediating DNA damage-induced changes in mRNA synthesis. ATM acts by modulating a variety of RNA metabolic pathways including nascent RNA splicing, a process catalyzed by the spliceosome. Interestingly, ATM and the spliceosome influence each other's activity in a reciprocal manner by a pathway that initiates when transcribing RNA polymerase II (RNAPII) encounters DNA lesions that prohibit forward translocation. In response to stalling of RNAPII assembly of late-stage spliceosomes is disrupted resulting in increased splicing factor mobility. Displacement of spliceosomes from lesion-arrested RNA polymerases facilitates formation of R-loops between the nascent RNA and DNA adjacent to the transcription bubble. R-loops signal for noncanonical ATM activation which in quiescent cells occurs in absence of detectable dsDNA breaks. In turn, activated ATM signals to regulate spliceosome dynamics and AS genome wide.This chapter describes the use of fluorescence microscopy methods that can be used to evaluate noncanonical ATM activation by transcription-blocking DNA damage. First, we present an immunofluorescence-detection method that can be used to evaluate ATM activation by autophosphorylation, in fixed cells. Second, we present a protocol for Fluorescence Recovery After Photobleaching (FRAP) of GFP-tagged splicing factors, a highly sensitive and

  7. Self-assembling peptide-based building blocks in medical applications

    Energy Technology Data Exchange (ETDEWEB)

    Acar, Handan; Srivastava, Samanvaya; Chung, Eun Ji; Schnorenberg, Mathew R.; Barrett, John C.; LaBelle, James L.; Tirrell, Matthew

    2017-02-01

    Peptides and peptide-conjugates, comprising natural and synthetic building blocks, are an increasingly popular class of biomaterials. Self-assembled nanostructures based on peptides and peptide-conjugates offer advantages such as precise selectivity and multifunctionality that can address challenges and limitations in the clinic. In this review article, we discuss recent developments in the design and self-assembly of various nanomaterials based on peptides and peptide-conjugates for medical applications, and categorize them into two themes based on the driving forces of molecular self-assembly. First, we present the self-assembled nanostructures driven by the supramolecular interactions between the peptides, with or without the presence of conjugates. The studies where nanoassembly is driven by the interactions between the conjugates of peptide-conjugates are then presented. Particular emphasis is given to in vivo studies focusing on therapeutics, diagnostics, immune modulation and regenerative medicine. Finally, challenges and future perspectives are presented.

  8. Origami building blocks: Generic and special four-vertices

    Science.gov (United States)

    Waitukaitis, Scott; van Hecke, Martin

    2016-02-01

    Four rigid panels connected by hinges that meet at a point form a four-vertex, the fundamental building block of origami metamaterials. Most materials designed so far are based on the same four-vertex geometry, and little is known regarding how different geometries affect folding behavior. Here we systematically categorize and analyze the geometries and resulting folding motions of Euclidean four-vertices. Comparing the relative sizes of sector angles, we identify three types of generic vertices and two accompanying subtypes. We determine which folds can fully close and the possible mountain-valley assignments. Next, we consider what occurs when sector angles or sums thereof are set equal, which results in 16 special vertex types. One of these, flat-foldable vertices, has been studied extensively, but we show that a wide variety of qualitatively different folding motions exist for the other 15 special and 3 generic types. Our work establishes a straightforward set of rules for understanding the folding motion of both generic and special four-vertices and serves as a roadmap for designing origami metamaterials.

  9. Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization.

    Science.gov (United States)

    Liber, Miran; Tomov, Toma E; Tsukanov, Roman; Berger, Yaron; Popov, Mary; Khara, Dinesh C; Nir, Eyal

    2018-06-01

    Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self-dimerization of the origami monomers, likely via blunt-end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Use of Mixed Micelles for Presentation of Building Blocks in a New Combinatorial Discovery Methodology: Proof-of-Concept Studies

    Directory of Open Access Journals (Sweden)

    Istvan Toth

    2013-03-01

    Full Text Available We describe a new method of combinatorial screening in which building blocks, instead of being linked together chemically, are placed on the surface of nanoparticles. Two- or three-dimensional structures form on the surface of these particles through the close approach of different building blocks, with sufficient flexibility to be able to adapt and interact with putative binding sites in biological systems. The particles assemble without the need for formation of chemical bonds, so libraries comprised of many structures can be prepared rapidly, with large quantities of material available for testing. Screening methods can include solid and solution-phase binding assays, or tissue culture models, for example looking for structures which can change the behaviour of cells in a disease-modifying manner.

  11. The assessment of professional competence: building blocks for theory development.

    Science.gov (United States)

    van der Vleuten, C P M; Schuwirth, L W T; Scheele, F; Driessen, E W; Hodges, B

    2010-12-01

    This article presents lessons learnt from experiences with assessment of professional competence. Based on Miller's pyramid, a distinction is made between established assessment technology for assessing 'knows', 'knowing how' and 'showing how' and more recent developments in the assessment of (clinical) performance at the 'does' level. Some general lessons are derived from research of and experiences with the established assessment technology. Here, many paradoxes are revealed and empirical outcomes are often counterintuitive. Instruments for assessing the 'does' level are classified and described, and additional general lessons for this area of performance assessment are derived. These lessons can also be read as general principles of assessment (programmes) and may provide theoretical building blocks to underpin appropriate and state-of-the-art assessment practices. Copyright © 2010 Elsevier Ltd. All rights reserved.

  12. C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA.

    Science.gov (United States)

    Aschenbrenner, Daniela; Baumann, Fabian; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

    2015-07-20

    Increased thermal or mechanical stability of DNA duplexes is desired for many applications in nanotechnology or -medicine where DNA is used as a programmable building block. Modifications of pyrimidine bases are known to enhance thermal stability and have the advantage of standard base-pairing and easy integration during chemical DNA synthesis. Through single-molecule force spectroscopy experiments with atomic force microscopy and the molecular force assay we investigated the effect of pyrimidines harboring C-5 propynyl modifications on the mechanical stability of double-stranded DNA. Utilizing these complementary techniques, we show that propynyl bases significantly increase the mechanical stability if the DNA is annealed at high temperature. In contrast, modified DNA complexes formed at room temperature and short incubation times display the same stability as non-modified DNA duplexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. The Building Blocks for JWST I and T (Integrations and Test) to Operations - From Simulator to Flight Units

    Science.gov (United States)

    Fatig, Curtis; Ochs, William; Johns, Alan; Seaton, Bonita; Adams, Cynthia; Wasiak, Francis; Jones, Ronald; Jackson, Wallace

    2012-01-01

    The James Webb Space Telescope (JWST) Project has an extended integration and test (I&T) phase due to long procurement and development times of various components as well as recent launch delays. The JWST Ground Segment and Operations group has developed a roadmap of the various ground and flight elements and their use in the various JWST I&T test programs. The JWST Project s building block approach to the eventual operational systems, while not new, is complex and challenging; a large-scale mission like JWST involves international partners, many vendors across the United States, and competing needs for the same systems. One of the challenges is resource balancing so simulators and flight products for various elements congeal into integrated systems used for I&T and flight operations activities. This building block approach to an incremental buildup provides for early problem identification with simulators and exercises the flight operations systems, products, and interfaces during the JWST I&T test programs. The JWST Project has completed some early I&T with the simulators, engineering models and some components of the operational ground system. The JWST Project is testing the various flight units as they are delivered and will continue to do so for the entire flight and operational system. The JWST Project has already and will continue to reap the value of the building block approach on the road to launch and flight operations.

  14. Aminobenzoates as building blocks for natural product assembly lines.

    Science.gov (United States)

    Walsh, Christopher T; Haynes, Stuart W; Ames, Brian D

    2012-01-01

    The ortho-, meta-, and para- regioisomers of aminobenzoate are building blocks for a wide range of microbial natural products. Both the ortho-isomer (anthranilate) and PABA derive from the central shikimate pathway metabolite chorismate while the meta-isomer is not available by that route and starts from UDP-3-aminoglucose. PABA is largely funnelled into folate biosynthesis while anthranilate is the scaffold for biosynthetic elaboration into many natural heterocycles, most notably with its role in indole formation for tryptophan biosynthesis. Anthranilate is also converted to benzodiazepinones, fumiquinazolines, quinoxalines, phenoxazines, benzoxazolinates, quinolones, and phenazines, often with redox enzyme participation. The 5-hydroxy form of 3-aminobenzaote is the starter unit for ansa-bridged rifamycins, ansamitocins, and geldanamycins, whereas regioisomers 2-hydroxy, 4-hydroxy and 2,4-dihydroxy-3-aminobenzoate are key components of antimycin, grixazone, and platencin and platensimycin biosynthesis, respectively. The enzymatic mechanisms for generation of the aminobenzoate regioisomers and their subsequent utilization for diverse heterocycle and macrocycle construction are examined.

  15. STRUCTURAL SOLUTIONS AND SPECIAL FEATURES OF THE THERMAL PROTECTION ANALYSIS OF EXTERIOR WALLS OF BUILDINGS MADE OF AUTOCLAVED GAS-CONCRETE BLOCKS

    Directory of Open Access Journals (Sweden)

    Bedov Anatolij Ivanovich

    2012-10-01

    Full Text Available Relevant structural solutions, physical and mechanical characteristics, coefficients of thermal conductivity for exterior masonry walls made of autoclaved gas-concrete blocks are provided in the article. If a single-layer wall is under consideration, an autoclaved gas-concrete block is capable of performing the two principal functions of a shell structure, including the function of thermal protection and the bearing function. The functions are performed simultaneously. Therefore, the application of the above masonry material means the design development and erection of exterior walls of residential buildings noteworthy for their thermal efficiency. In the event of frameless structures, the height of the residential building in question may be up to 5 stories, while the use of a monolithic or a ready-made frame makes it possible to build high-rise buildings, and the number of stories is not limited in this case. If the average block density is equal to 400…500 kilograms per cubic meter, the designed wall thickness is to be equal to 400 mm. Its thermal resistance may be lower than the one set in the event of the per-element design of the thermal protection (Rreq = 3.41 м2 C/Watt, in Ufa, although it will meet the requirements of the applicable regulations if per-unit power consumption rate is considered.

  16. The asc trinodal platform: Two-step assembly of triangular, tetrahedral, and trigonal-prismatic molecular building blocks

    KAUST Repository

    Schoedel, Alexander; Cairns, Amy; Belmabkhout, Youssef; Wojtas, Łukasz; Mohamed, Mona Hassan; Zhang, ZhenJie; Proserpio, Davide Maria; Eddaoudi, Mohamed; Zaworotko, Michael J.

    2013-01-01

    The self-assembly of triangular, tetrahedral, and trigonal-prismatic molecular building blocks affords the first example of a trinodal family of metal-organic materials. Four examples of isoreticular expanded and functionalized frameworks are detailed. Gas adsorption experiments validated the permanent porosity of the parent structure. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. The asc trinodal platform: Two-step assembly of triangular, tetrahedral, and trigonal-prismatic molecular building blocks

    KAUST Repository

    Schoedel, Alexander

    2013-02-10

    The self-assembly of triangular, tetrahedral, and trigonal-prismatic molecular building blocks affords the first example of a trinodal family of metal-organic materials. Four examples of isoreticular expanded and functionalized frameworks are detailed. Gas adsorption experiments validated the permanent porosity of the parent structure. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Novel DNA materials and their applications.

    Science.gov (United States)

    Yang, Dayong; Campolongo, Michael J; Nhi Tran, Thua Nguyen; Ruiz, Roanna C H; Kahn, Jason S; Luo, Dan

    2010-01-01

    The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials. © 2010 John Wiley & Sons, Inc.

  19. Bottom-up nanoarchitecture of semiconductor nano-building blocks by controllable in situ SEM-FIB thermal soldering method

    KAUST Repository

    Zhang, Xuan; Zheng, Xiujun; Zhang, Hong; Zhang, Junli; Fu, Jiecai; Zhang, Qiang; Peng, Chaoyi; Bai, Feiming; Zhang, Xixiang; Peng, Yong

    2017-01-01

    Here we demonstrate that the building blocks of semiconductor WO3 nanowires can be controllably soldered together by a novel nano-soldering technique of in situ SEM-FIB thermal soldering, in which the soldering temperature can precisely remain in an optimal range to avoid a strong thermal diffusion.

  20. Bottom-up nanoarchitecture of semiconductor nano-building blocks by controllable in situ SEM-FIB thermal soldering method

    KAUST Repository

    Zhang, Xuan

    2017-08-10

    Here we demonstrate that the building blocks of semiconductor WO3 nanowires can be controllably soldered together by a novel nano-soldering technique of in situ SEM-FIB thermal soldering, in which the soldering temperature can precisely remain in an optimal range to avoid a strong thermal diffusion.

  1. Systems thinking in practice: the current status of the six WHO building blocks for health system strengthening in three BHOMA intervention districts of Zambia: a baseline qualitative study.

    Science.gov (United States)

    Mutale, Wilbroad; Bond, Virginia; Mwanamwenge, Margaret Tembo; Mlewa, Susan; Balabanova, Dina; Spicer, Neil; Ayles, Helen

    2013-08-01

    The primary bottleneck to achieving the MDGs in low-income countries is health systems that are too fragile to deliver the volume and quality of services to those in need. Strong and effective health systems are increasingly considered a prerequisite to reducing the disease burden and to achieving the health MDGs. Zambia is one of the countries that are lagging behind in achieving millennium development targets. Several barriers have been identified as hindering the progress towards health related millennium development goals. Designing an intervention that addresses these barriers was crucial and so the Better Health Outcomes through Mentorship (BHOMA) project was designed to address the challenges in the Zambia's MOH using a system wide approach. We applied systems thinking approach to describe the baseline status of the Six WHO building blocks for health system strengthening. A qualitative study was conducted looking at the status of the Six WHO building blocks for health systems strengthening in three BHOMA districts. We conducted Focus group discussions with community members and In-depth Interviews with key informants. Data was analyzed using Nvivo version 9. The study showed that building block specific weaknesses had cross cutting effect in other health system building blocks which is an essential element of systems thinking. Challenges noted in service delivery were linked to human resources, medical supplies, information flow, governance and finance building blocks either directly or indirectly. Several barriers were identified as hindering access to health services by the local communities. These included supply side barriers: Shortage of qualified health workers, bad staff attitude, poor relationships between community and health staff, long waiting time, confidentiality and the gender of health workers. Demand side barriers: Long distance to health facility, cost of transport and cultural practices. Participating communities seemed to lack the capacity

  2. Internet governance and global self regulation: theoretical and empirical building blocks for a general theory of self regulation

    NARCIS (Netherlands)

    Vey Mestdagh, C.; Rijgersberg, R.

    2010-01-01

    The following exposition sets out to identify the basic theoretical and empirical building blocks for a general theory of self-regulation. It uses the Internet as an empirical basis since its global reach and technical characteristics create interdependencies between actors that transcend national

  3. Programmable chemical controllers made from DNA

    Science.gov (United States)

    Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

    2013-10-01

    Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

  4. On the building blocks of the M31 and Milky Way halos

    Directory of Open Access Journals (Sweden)

    Monelli Matteo

    2017-01-01

    Full Text Available We discuss the formation of the halo of M31 and the Milky Way as traced by the population of RR Lyrae stars, in comparison with the population of such stars preent in satellite dwarf galaxies. We find that both halos and the massive dwarf host a population of high amplitude short period RRab stars, absent in low-mass dwarfs. These stars are explained as the metal-rich tail of the RR Lyrae distribution ([Fe/H] ∼ - 1.5, and thus their existence imply fast chemical enrichment in the host system. Their presence in both halos implies that massive building blocks had an important role in their formation.

  5. Current situation of the project finishing of the building of 3 and 4 block of the nuclear power plant Mochovce

    International Nuclear Information System (INIS)

    Niznan, S.

    2005-01-01

    In the contribution there is the basic information mentioned about history of building and the current situation at the finishing of the building of 3 and 4 block of the Nuclear Power Plant Mochovce with the use of project digitization. Further on the contribution shows what kinds of supporting material has been elaborated, what kind of decisions have been issued to the finishing of the building, way of financing and also the assumption of investment return under the defined conditions. An orientation time schedule of the finishing of the building and the crucial steps for its security are presented in the conclusion

  6. InGaN micro-LED-pillar as the building block for high brightness emitters

    KAUST Repository

    Shen, Chao; Cha, Dong Kyu; Ng, Tien Khee; Ooi, Boon S.; Yang, Yang

    2013-01-01

    In summary, we confirmed the improved electrical and optical characteristics, with reduced efficiency droop in InGaN μLED-pillars when these devices were scaled down in size. We demonstrated that strain relief contributed to further improvement in EQE characteristics in small InGaN μLED-pillars (D < 50 μm), apart from the current spreading effect. The μLED-pillar can be deployed as the building block for large effective-area, high brightness emitter. © 2013 IEEE.

  7. Building houses with earth blocks: A guide for upgrading traditional building methods using handmade earth blocks

    CSIR Research Space (South Africa)

    Bolton, M

    2001-01-01

    Full Text Available This report is a guide to building strong earth houses that will last a long time but without having to spend a lot of extra money or hire outside experts to do the building. It supports the process of improving the quality of earth housing...

  8. Hydrotalcite catalysis for the synthesis of new chiral building blocks.

    Science.gov (United States)

    Rodilla, Jesus M; Neves, Patricia P; Pombal, Sofia; Rives, Vicente; Trujillano, Raquel; Díez, David

    2016-01-01

    The use of hydrotalcites for the synthesis of two chiral building blocks in a simple way is described as a new and green methodology. The synthesis of these compounds implies a regioselective Baeyer-Villiger reaction in a very selective way with ulterior opening and lactonisation. This methodology should be considered green for the use of hydrogen peroxide as the only oxidant and hydrotalcites as the catalyst, and because no residues are produced apart from water. The procedure is very adequate for using in gram scale, in order to increase the value of the obtained compounds. The conditions are excellent and can be applied for nonstable compounds, as they are very mild. The synthesised compounds are magnific starting materials for the synthesis of biologically active or natural compounds. The use of a cheap, commercial and chiral compound as carvone disposable in both enantiomeric forms adds an extra value to this methodology.

  9. C–H arylation of unsubstituted furan and thiophene with acceptor bromides: access to donor–acceptor–donor-type building blocks for organic electronics.

    Science.gov (United States)

    Matsidik, Rukiya; Martin, Johannes; Schmidt, Simon; Obermayer, Johannes; Lombeck, Florian; Nübling, Fritz; Komber, Hartmut; Fazzi, Daniele; Sommer, Michael

    2015-01-16

    Pd-catalyzed direct arylation (DA) reaction conditions have been established for unsubstituted furan (Fu) and thiophene (Th) with three popular acceptor building blocks to be used in materials for organic electronics, namely 4,7-dibromo-2,1,3-benzothiadiazole (BTBr2), N,N′-dialkylated 2,6-dibromonaphthalene-1,4,5,8-bis(dicarboximide) (NDIBr2), and 1,4-dibromotetrafluorobenzene (F4Br2). Reactions with BTBr2, F4Br2, and NDIBr2 require different solvents to obtain high yields. The use of dimethylacetamide (DMAc) is essential for the successful coupling of BTBr2 and F4Br2, but detrimental for NDIBr2, as the electron-deficient NDI core is prone to nucleophilic core substitution in DMAc as solvent but not in toluene. NDIFu2 is much more planar compared to NDITh2, resulting in an enhanced charge-transfer character, which makes it an interesting building block for conjugated systems designed for organic electronics. This study highlights direct arylation as a simple and inexpensive method to construct a series of important donor–acceptor–donor building blocks to be further used for the preparation of a variety of conjugated materials.

  10. A cargo-sorting DNA robot.

    Science.gov (United States)

    Thubagere, Anupama J; Li, Wei; Johnson, Robert F; Chen, Zibo; Doroudi, Shayan; Lee, Yae Lim; Izatt, Gregory; Wittman, Sarah; Srinivas, Niranjan; Woods, Damien; Winfree, Erik; Qian, Lulu

    2017-09-15

    Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their destinations allows for a simple robot design: a single-stranded DNA with one leg and two foot domains for walking, and one arm and one hand domain for picking up and dropping off cargos. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers them to specified destinations until all molecules are sorted into two distinct piles. The robot is designed to perform a random walk without any energy supply. Exploiting this feature, a single robot can repeatedly sort multiple cargos. Localization on DNA origami allows for distinct cargo-sorting tasks to take place simultaneously in one test tube or for multiple robots to collectively perform the same task. Copyright © 2017, American Association for the Advancement of Science.

  11. The storage period of the formalin-fixed paraffin-embedded tumor blocks does not influence the concentration and purity of the isolated DNA in a series of 83 renal and thyroid carcinomas.

    Science.gov (United States)

    Nechifor-Boilă, Adela Corina; Loghin, Andrada; Vacariu, Victor; Halaţiu, Vasile Bogdan; Borda, Angela

    2015-01-01

    Optimal recovery of nucleic acids from formalin-fixed paraffin-embedded (FFPE) tissues is highly dependent on a series of pre-extraction steps, mainly related (but not limited) to fixation. The aim of our study was to investigate if the storage period of the FFPE blocks had a significant effect on the isolated DNA. We examined the quantity and purity of the isolated DNA from 83 FFPE blocks, corresponding to malignant thyroid (n=28) and renal (n=55) carcinomas that had been stored in our department for up to eight years. The DNA extraction protocol was based on a precipitation method (MasterPure™ DNA Purification Kit, Epicentre), in accordance to the manufacturer instructions, optimized in our laboratory. A spectrophotometer was used to determine the yield (A260) and purity (A260/A280 ratio) of the isolated DNA. We successfully isolated good DNA quantity and purity from all our study cases (mean concentration: 223.4 ± 104.16 ng/μL; mean A260/A280 ratio: 1.68 ± 0.09). Moreover, no statistically significant differences were observed between tumor blocks stored for 2-3 years and 7-8 years, respectively, both in terms of DNA quantity (p=0.196) and purity (p=0.663). In conclusion, we successfully validated an efficient, reproducible DNA extraction technique that provided a good range of DNA concentrations and purity, regardless the type of tissue (thyroid or kidney). Moreover, we demonstrated that the storage period of the FFPE blocks does not have a significant influence on the DNA quantity and purity.

  12. Damage of DNA by Low Energy Electrons (< 3 eV)

    International Nuclear Information System (INIS)

    Bald, Ilko; Illenberger, Eugen; Kopyra, Janina

    2012-01-01

    Recent experiments on low energy electron attachment to DNA and its components in the condensed phase and in the gas phase are reviewed and analysed. From different condensed phase experiments the sensitivity of DNA towards low energy electrons is well documented and strand breaks in DNA are observed at subexcitation energies (< 3 eV) and also in ultrafast electron transfer experiments involving electrons in presolvated states. Gas phase experiments indicate that all building blocks of DNA (the nucleobases, the sugar and the phosphate moiety) undergo resonant dissociative electron attachment (DEA) in the subexcitation regime which may ultimately lead to strand breaks. From very recent gas phase experiments on an entire nucleotide it can be concluded that most strand breaks result from direct electron attachment to the DNA backbone, but also initial electron capture by the nucleobase following electron transfer to the backbone contributes.

  13. Measurement of soil moisture using gypsum blocks

    DEFF Research Database (Denmark)

    Friis Dela, B.

    the building. Consequently, measuring the moisture of the surrounding soil is of great importance for detecting the source of moisture in a building. Up till now, information has been needed to carry out individual calibrations for the different types of gypsum blocks available on the market and to account......For the past 50 years, gypsum blocks have been used to determine soil moisture content. This report describes a method for calibrating gypsum blocks for soil moisture measurements. Moisture conditions inside a building are strongly influenced by the moisture conditions in the soil surrounding...

  14. Uniparental mitochondrial DNA inheritance is not affected in Ustilago maydis Δatg11 mutants blocked in mitophagy.

    Science.gov (United States)

    Wagner-Vogel, Gaby; Lämmer, Frauke; Kämper, Jörg; Basse, Christoph W

    2015-02-06

    Maternal or uniparental inheritance (UPI) of mitochondria is generally observed in sexual eukaryotes, however, the underlying mechanisms are diverse and largely unknown. Recently, based on the use of mutants blocked in autophagy, it has been demonstrated that autophagy is required for strict maternal inheritance in the nematode Caenorhabditis elegans. Uniparental mitochondrial DNA (mtDNA) inheritance has been well documented for numerous fungal species, and in particular, has been shown to be genetically governed by the mating-type loci in the isogamous species Cryptococcus neoformans, Phycomyces blakesleeanus and Ustilago maydis. Previously, we have shown that the a2 mating-type locus gene lga2 is decisive for UPI during sexual development of U. maydis. In axenic culture, conditional overexpression of lga2 triggers efficient loss of mtDNA as well as mitophagy. To assess a functional relationship, we have investigated UPI in U. maydis Δatg11 mutants, which are blocked in mitophagy. This study has revealed that Δatg11 mutants are not affected in pathogenic development and this has allowed us to analyse UPI under comparable developmental conditions between mating-compatible wild-type and mutant strain combinations. Explicitly, we have examined two independent strain combinations that gave rise to different efficiencies of UPI. We demonstrate that in both cases UPI is atg11-independent, providing evidence that mitophagy is not critical for UPI in U. maydis, even under conditions of strict UPI. Until now, analysis of a role of mitophagy in UPI has not been reported for microbial species. Our study suggests that selective autophagy does not contribute to UPI in U. maydis, but is rather a consequence of selective mtDNA elimination in response to mitochondrial damage.

  15. Avatar DNA Nanohybrid System in Chip-on-a-Phone

    Science.gov (United States)

    Park, Dae-Hwan; Han, Chang Jo; Shul, Yong-Gun; Choy, Jin-Ho

    2014-05-01

    Long admired for informational role and recognition function in multidisciplinary science, DNA nanohybrids have been emerging as ideal materials for molecular nanotechnology and genetic information code. Here, we designed an optical machine-readable DNA icon on microarray, Avatar DNA, for automatic identification and data capture such as Quick Response and ColorZip codes. Avatar icon is made of telepathic DNA-DNA hybrids inscribed on chips, which can be identified by camera of smartphone with application software. Information encoded in base-sequences can be accessed by connecting an off-line icon to an on-line web-server network to provide message, index, or URL from database library. Avatar DNA is then converged with nano-bio-info-cogno science: each building block stands for inorganic nanosheets, nucleotides, digits, and pixels. This convergence could address item-level identification that strengthens supply-chain security for drug counterfeits. It can, therefore, provide molecular-level vision through mobile network to coordinate and integrate data management channels for visual detection and recording.

  16. Systems thinking in practice: the current status of the six WHO building blocks for health system strengthening in three BHOMA intervention districts of Zambia: a baseline qualitative study

    Science.gov (United States)

    2013-01-01

    Background The primary bottleneck to achieving the MDGs in low-income countries is health systems that are too fragile to deliver the volume and quality of services to those in need. Strong and effective health systems are increasingly considered a prerequisite to reducing the disease burden and to achieving the health MDGs. Zambia is one of the countries that are lagging behind in achieving millennium development targets. Several barriers have been identified as hindering the progress towards health related millennium development goals. Designing an intervention that addresses these barriers was crucial and so the Better Health Outcomes through Mentorship (BHOMA) project was designed to address the challenges in the Zambia’s MOH using a system wide approach. We applied systems thinking approach to describe the baseline status of the Six WHO building blocks for health system strengthening. Methods A qualitative study was conducted looking at the status of the Six WHO building blocks for health systems strengthening in three BHOMA districts. We conducted Focus group discussions with community members and In-depth Interviews with key informants. Data was analyzed using Nvivo version 9. Results The study showed that building block specific weaknesses had cross cutting effect in other health system building blocks which is an essential element of systems thinking. Challenges noted in service delivery were linked to human resources, medical supplies, information flow, governance and finance building blocks either directly or indirectly. Several barriers were identified as hindering access to health services by the local communities. These included supply side barriers: Shortage of qualified health workers, bad staff attitude, poor relationships between community and health staff, long waiting time, confidentiality and the gender of health workers. Demand side barriers: Long distance to health facility, cost of transport and cultural practices. Participating

  17. 3D DNA Origami Crystals.

    Science.gov (United States)

    Zhang, Tao; Hartl, Caroline; Frank, Kilian; Heuer-Jungemann, Amelie; Fischer, Stefan; Nickels, Philipp C; Nickel, Bert; Liedl, Tim

    2018-05-18

    3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high rigidity and sufficiently large open guest space. A DNA-origami-based "tensegrity triangle" structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site-specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1.83 × 10 5 nm 3 , which would also suffice to accommodate ribosome-sized macromolecules. The accurate assembly of the DNA origami lattice itself, as well as the precise incorporation of gold particles, is validated by electron microscopy and small-angle X-ray scattering experiments. The results show that it is possible to create DNA building blocks that assemble into lattices with customized geometry. Site-specific hosting of nano objects in the optically transparent DNA lattice sets the stage for metamaterial and structural biology applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Horizontal gene transfer from macrophages to ischemic muscles upon delivery of naked DNA with Pluronic block copolymers.

    Science.gov (United States)

    Mahajan, Vivek; Gaymalov, Zagit; Alakhova, Daria; Gupta, Richa; Zucker, Irving H; Kabanov, Alexander V

    2016-01-01

    Intramuscular administration of plasmid DNA (pDNA) with non-ionic Pluronic block copolymers increases gene expression in injected muscles and lymphoid organs. We studied the role of immune cells in muscle transfection upon inflammation. Local inflammation in murine hind limb ischemia model (MHLIM) drastically increased DNA, RNA and expressed protein levels in ischemic muscles injected with pDNA/Pluronic. The systemic inflammation (MHLIM or peritonitis) also increased expression of pDNA/Pluronic in the muscles. When pDNA/Pluronic was injected in ischemic muscles the reporter gene, Green Fluorescent Protein (GFP) co-localized with desmin(+) muscle fibers and CD11b(+) macrophages (MØs), suggesting transfection of MØs along with the muscle cells. P85 enhanced (∼ 4 orders) transfection of MØs with pDNA in vitro. Moreover, adoptively transferred MØs were shown to pass the transgene to inflamed muscle cells in MHLIM. Using a co-culture of myotubes (MTs) and transfected MØs expressing a reporter gene under constitutive (cmv-luciferase) or muscle specific (desmin-luciferase) promoter we demonstrated that P85 enhances horizontal gene transfer from MØ to MTs. Therefore, MØs can play an important role in muscle transfection with pDNA/Pluronic during inflammation, with both inflammation and Pluronic contributing to the increased gene expression. pDNA/Pluronic has potential for therapeutic gene delivery in muscle pathologies that involve inflammation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters.

    Science.gov (United States)

    Grunseich, Christopher; Wang, Isabel X; Watts, Jason A; Burdick, Joshua T; Guber, Robert D; Zhu, Zhengwei; Bruzel, Alan; Lanman, Tyler; Chen, Kelian; Schindler, Alice B; Edwards, Nancy; Ray-Chaudhury, Abhik; Yao, Jianhua; Lehky, Tanya; Piszczek, Grzegorz; Crain, Barbara; Fischbeck, Kenneth H; Cheung, Vivian G

    2018-02-01

    R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Building blocks of temporal filters in retinal synapses.

    Directory of Open Access Journals (Sweden)

    Bongsoo Suh

    2014-10-01

    Full Text Available Sensory systems must be able to extract features of a stimulus to detect and represent properties of the world. Because sensory signals are constantly changing, a critical aspect of this transformation relates to the timing of signals and the ability to filter those signals to select dynamic properties, such as visual motion. At first assessment, one might think that the primary biophysical properties that construct a temporal filter would be dynamic mechanisms such as molecular concentration or membrane electrical properties. However, in the current issue of PLOS Biology, Baden et al. identify a mechanism of temporal filtering in the zebrafish and goldfish retina that is not dynamic but is in fact a structural building block-the physical size of a synapse itself. The authors observe that small, bipolar cell synaptic terminals are fast and highly adaptive, whereas large ones are slower and adapt less. Using a computational model, they conclude that the volume of the synaptic terminal influences the calcium concentration and the number of available vesicles. These results indicate that the size of the presynaptic terminal is an independent control for the dynamics of a synapse and may reveal aspects of synaptic function that can be inferred from anatomical structure.

  1. Building Blocks of the Universe

    CERN Document Server

    The ATLAS collaboration

    2015-01-01

    This article presents possibilities to impart knowledge of and enthusiasm for particle physics to essentially all non-expert target audiences by the use of LEGO bricks and models of particle physics experiments built from these. Methods of using LEGO models, both as a passive exhibit and as part of interactive outreach events, are presented, along with a historical review of the “Build Your Own Particle Detector” programme and the corresponding idea of hosting competitions in building detector models in LEGO pieces as a perfect setting to grasp people’s attention, get them involved and ultimately convey knowledge in particle physics to them.

  2. Detection of minor and major satellite DNA in cytokinesis-blocked mouse splenocytes by a PRINS tandem labelling approach.

    Science.gov (United States)

    Russo, A; Tommasi, A M; Renzi, L

    1996-11-01

    A protocol for the simultaneous visualization of minor and major satellite DNA by primed in situ DNA synthesis (PRINS) was developed in cytokinesis-blocked murine splenocytes. After individuation of optimal experimental conditions, a micronucleus (MN) test was carried out by treating splenocytes in vitro with the clastogenic agent mitomycin C and the aneugenic compound Colcemid. It was found that PRINS gives highly reproducible results, also comparable with the literature on MN results obtained by fluorescent in situ hybridization (FISH). Therefore the PRINS methodology may be proposed as a fast alternative to FISH for the characterization of induced MN.

  3. E-Block: A Tangible Programming Tool with Graphical Blocks

    Directory of Open Access Journals (Sweden)

    Danli Wang

    2013-01-01

    Full Text Available This paper designs a tangible programming tool, E-Block, for children aged 5 to 9 to experience the preliminary understanding of programming by building blocks. With embedded artificial intelligence, the tool defines the programming blocks with the sensors as the input and enables children to write programs to complete the tasks in the computer. The symbol on the programming block's surface is used to help children understanding the function of each block. The sequence information is transferred to computer by microcomputers and then translated into semantic information. The system applies wireless and infrared technologies and provides user with feedbacks on both screen and programming blocks. Preliminary user studies using observation and user interview methods are shown for E-Block's prototype. The test results prove that E-Block is attractive to children and easy to learn and use. The project also highlights potential advantages of using single chip microcomputer (SCM technology to develop tangible programming tools for children.

  4. Object Use in Children with Autism: Building with Blocks from a Piagetian Perspective

    Directory of Open Access Journals (Sweden)

    Antonio Iannaccone

    2018-02-01

    Full Text Available AimThis study focused on the manipulation of objects by children with suspected autism spectrum disorder. The aim was to demonstrate how objects can be seen as active agents of interpersonal exchange in face-to-face interactions.ParticipantsThree children with suspected autism spectrum disorder (aged 18, 20, and 24 months were selected as representative of the sensorimotor stage of development.MethodsStarting from Piaget’s classical approach to the sensorimotor and symbolic developmental stages, the study moved toward a socio-material interpretation in which some patterns of interaction involving object manipulation seem to create a space that supports adult–child communication. In videotaped observations of verbal and non-verbal signs during an (organized free play session, each child manipulated seven small blocks of colored plastic in the presence of an adult. The observations were informed by a checklist of 14 items, including eye contact and building a tower of toy blocks from section B of the CHAT (CHecklist for Autism in Toddlers instrument.ResultsBased on a broad Piagetian perspective and recent work in the field of socio-materiality, key observations included the following: (1 sensorimotor and realistic play was observed in all three children; (2 there were some intriguing indications that objects serve as concrete mediators in the intersubjective space between adult and child; (3 some of the children’s attention patterns were visibly mediated by the object.Discussion and conclusionAll three children exhibited a particular sequence of actions. First, they manipulated the blocks through active experimentation; second, there was an apparent pause, during which, the children were in fact examining the blocks to determine how best to continue the interaction; and finally, the children monitored adult attention by means of eye contact or by restarting manipulation of the blocks. As this last step in the sequence indicated that the

  5. Building blocks for the development of an interface for high-throughput thin layer chromatography/ambient mass spectrometric analysis: a green methodology.

    Science.gov (United States)

    Cheng, Sy-Chyi; Huang, Min-Zong; Wu, Li-Chieh; Chou, Chih-Chiang; Cheng, Chu-Nian; Jhang, Siou-Sian; Shiea, Jentaie

    2012-07-17

    Interfacing thin layer chromatography (TLC) with ambient mass spectrometry (AMS) has been an important area of analytical chemistry because of its capability to rapidly separate and characterize the chemical compounds. In this study, we have developed a high-throughput TLC-AMS system using building blocks to deal, deliver, and collect the TLC plate through an electrospray-assisted laser desorption ionization (ELDI) source. This is the first demonstration of the use of building blocks to construct and test the TLC-MS interfacing system. With the advantages of being readily available, cheap, reusable, and extremely easy to modify without consuming any material or reagent, the use of building blocks to develop the TLC-AMS interface is undoubtedly a green methodology. The TLC plate delivery system consists of a storage box, plate dealing component, conveyer, light sensor, and plate collecting box. During a TLC-AMS analysis, the TLC plate was sent to the conveyer from a stack of TLC plates placed in the storage box. As the TLC plate passed through the ELDI source, the chemical compounds separated on the plate would be desorbed by laser desorption and subsequently postionized by electrospray ionization. The samples, including a mixture of synthetic dyes and extracts of pharmaceutical drugs, were analyzed to demonstrate the capability of this TLC-ELDI/MS system for high-throughput analysis.

  6. Expedite Protocol for Construction of Chiral Regioselectively N-Protected Monosubstituted Piperazine, 1,4-Diazepane, and 1,4-Diazocane Building Blocks

    DEFF Research Database (Denmark)

    Crestey, François; Witt, Matthias; Jaroszewski, Jerzy W.

    2009-01-01

    This paper describes the first study of solution-phase synthesis of chiral monosubstituted piperazine building blocks from nosylamide-activated aziridines. The protocol, involving aminolysis of the starting aziridines with ω-amino alcohols and subsequent Fukuyama−Mitsunobu cyclization, offers the...

  7. DNA-nanoparticle assemblies go organic: Macroscopic polymeric materials with nanosized features

    Directory of Open Access Journals (Sweden)

    Mentovich Elad D

    2012-05-01

    Full Text Available Abstract Background One of the goals in the field of structural DNA nanotechnology is the use of DNA to build up 2- and 3-D nanostructures. The research in this field is motivated by the remarkable structural features of DNA as well as by its unique and reversible recognition properties. Nucleic acids can be used alone as the skeleton of a broad range of periodic nanopatterns and nanoobjects and in addition, DNA can serve as a linker or template to form DNA-hybrid structures with other materials. This approach can be used for the development of new detection strategies as well as nanoelectronic structures and devices. Method Here we present a new method for the generation of unprecedented all-organic conjugated-polymer nanoparticle networks guided by DNA, based on a hierarchical self-assembly process. First, microphase separation of amphiphilic block copolymers induced the formation of spherical nanoobjects. As a second ordering concept, DNA base pairing has been employed for the controlled spatial definition of the conjugated-polymer particles within the bulk material. These networks offer the flexibility and the diversity of soft polymeric materials. Thus, simple chemical methodologies could be applied in order to tune the network's electrical, optical and mechanical properties. Results and conclusions One- two- and three-dimensional networks have been successfully formed. Common to all morphologies is the integrity of the micelles consisting of DNA block copolymer (DBC, which creates an all-organic engineered network.

  8. DNA-nanoparticle assemblies go organic: macroscopic polymeric materials with nanosized features.

    Science.gov (United States)

    Mentovich, Elad D; Livanov, Konstantin; Prusty, Deepak K; Sowwan, Mukules; Richter, Shachar

    2012-05-30

    One of the goals in the field of structural DNA nanotechnology is the use of DNA to build up 2- and 3-D nanostructures. The research in this field is motivated by the remarkable structural features of DNA as well as by its unique and reversible recognition properties. Nucleic acids can be used alone as the skeleton of a broad range of periodic nanopatterns and nanoobjects and in addition, DNA can serve as a linker or template to form DNA-hybrid structures with other materials. This approach can be used for the development of new detection strategies as well as nanoelectronic structures and devices. Here we present a new method for the generation of unprecedented all-organic conjugated-polymer nanoparticle networks guided by DNA, based on a hierarchical self-assembly process. First, microphase separation of amphiphilic block copolymers induced the formation of spherical nanoobjects. As a second ordering concept, DNA base pairing has been employed for the controlled spatial definition of the conjugated-polymer particles within the bulk material. These networks offer the flexibility and the diversity of soft polymeric materials. Thus, simple chemical methodologies could be applied in order to tune the network's electrical, optical and mechanical properties. One- two- and three-dimensional networks have been successfully formed. Common to all morphologies is the integrity of the micelles consisting of DNA block copolymer (DBC), which creates an all-organic engineered network.

  9. Total synthesis of a CD-ring: side-chain building block for preparing 17-epi-calcitriol derivatives from the Hajos-Parrish dione.

    Science.gov (United States)

    Michalak, Karol; Wicha, Jerzy

    2011-08-19

    An efficient synthesis of the key building block for 17-epi-calctriol from the Hajos-Parrish dione involving a sequence of diastereoselective transformation of the azulene core and the side-chain construction is presented.

  10. Synthesis of 4-Halogenated 3-Fluoro-6-methoxyquinolines: Key Building Blocks for the Synthesis of Antibiotics

    DEFF Research Database (Denmark)

    Flagstad, Thomas; Petersen, Mette Terp; Hinnerfeldt, Daniel Michael

    2014-01-01

    A practical and scalable 4-step route is presented for the synthesis of 4-bromo-3-fluoro-6-methoxyoquinoline and 3-fluoro-4-iodo-6-methoxyoquinoline from readily available 2,4-dichloro-3-fluoroquinoline with an overall yield of 81-85%. Halogenated quinoline building blocks have found much use in ...... in antimicrobial drug discovery, and the method reported here would be useful for the synthesis of these compounds. © Georg Thieme Verlag....

  11. Calcein represses human papillomavirus 16 E1-E2 mediated DNA replication via blocking their binding to the viral origin of replication.

    Science.gov (United States)

    Das, Dipon; Smith, Nathan W; Wang, Xu; Richardson, Stacie L; Hartman, Matthew C T; Morgan, Iain M

    2017-08-01

    Human papillomaviruses are causative agents in several human diseases ranging from genital warts to ano-genital and oropharyngeal cancers. Currently only symptoms of HPV induced disease are treated; there are no antivirals available that directly target the viral life cycle. Previously, we determined that the cellular protein TopBP1 interacts with the HPV16 replication/transcription factor E2. This E2-TopBP1 interaction is essential for optimal E1-E2 DNA replication and for the viral life cycle. The drug calcein disrupts the interaction of TopBP1 with itself and other host proteins to promote cell death. Here we demonstrate that calcein blocks HPV16 E1-E2 DNA replication via blocking the viral replication complex forming at the origin of replication. This occurs at non-toxic levels of calcein and demonstrates specificity as it does not block the ability of E2 to regulate transcription. We propose that calcein or derivatives could be developed as an anti-HPV therapeutic. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Modes of DNA repair and replication

    International Nuclear Information System (INIS)

    Hanawalt, P.; Kondo, S.

    1979-01-01

    Modes of DNA repair and replication require close coordination as well as some overlap of enzyme functions. Some classes of recovery deficient mutants may have defects in replication rather than repair modes. Lesions such as the pyrimidine dimers produced by ultraviolet light irradiation are the blocks to normal DNA replication in vivo and in vitro. The DNA synthesis by the DNA polymerase 1 of E. coli is blocked at one nucleotide away from the dimerized pyrimidines in template strands. Thus, some DNA polymerases seem to be unable to incorporate nucleotides opposite to the non-pairing lesions in template DNA strands. The lesions in template DNA strands may block the sequential addition of nucleotides in the synthesis of daughter strands. Normal replication utilizes a constitutive ''error-free'' mode that copies DNA templates with high fidelity, but which may be totally blocked at a lesion that obscures the appropriate base pairing specificity. It might be expected that modified replication system exhibits generally high error frequency. The error rate of DNA polymerases may be controlled by the degree of phosphorylation of the enzyme. Inducible SOS system is controlled by recA genes that also control the pathways for recombination. It is possible that SOS system involves some process other than the modification of a blocked replication apparatus to permit error-prone transdimer synthesis. (Yamashita, S.)

  13. Building blocks for a clinical imaging informatics environment.

    Science.gov (United States)

    Kohli, Marc D; Warnock, Max; Daly, Mark; Toland, Christopher; Meenan, Chris; Nagy, Paul G

    2014-04-01

    Over the past 20 years, imaging informatics has been driven by the widespread adoption of radiology information and picture archiving and communication and speech recognition systems. These three clinical information systems are commonplace and are intuitive to most radiologists as they replicate familiar paper and film workflow. So what is next? There is a surge of innovation in imaging informatics around advanced workflow, search, electronic medical record aggregation, dashboarding, and analytics tools for quality measures (Nance et al., AJR Am J Roentgenol 200:1064-1070, 2013). The challenge lies in not having to rebuild the technological wheel for each of these new applications but instead attempt to share common components through open standards and modern development techniques. The next generation of applications will be built with moving parts that work together to satisfy advanced use cases without replicating databases and without requiring fragile, intense synchronization from clinical systems. The purpose of this paper is to identify building blocks that can position a practice to be able to quickly innovate when addressing clinical, educational, and research-related problems. This paper is the result of identifying common components in the construction of over two dozen clinical informatics projects developed at the University of Maryland Radiology Informatics Research Laboratory. The systems outlined are intended as a mere foundation rather than an exhaustive list of possible extensions.

  14. Molecular building blocks and their architecture in biologically/environmentally compatible soft matter chemical machinery.

    Science.gov (United States)

    Toyota, Taro; Banno, Taisuke; Nitta, Sachiko; Takinoue, Masahiro; Nomoto, Tomonori; Natsume, Yuno; Matsumura, Shuichi; Fujinami, Masanori

    2014-01-01

    This review briefly summarizes recent developments in the construction of biologically/environmentally compatible chemical machinery composed of soft matter. Since environmental and living systems are open systems, chemical machinery must continuously fulfill its functions not only through the influx and generation of molecules but also via the degradation and dissipation of molecules. If the degradation or dissipation of soft matter molecular building blocks and biomaterial molecules/polymers can be achieved, soft matter particles composed of them can be used to realize chemical machinery such as selfpropelled droplets, drug delivery carriers, tissue regeneration scaffolds, protocell models, cell-/tissuemarkers, and molecular computing systems.

  15. LEP : four building blocks of matter ... times three Conference MT17

    CERN Multimedia

    2001-01-01

    The four building blocks of everyday matter form a family composed of the up-quark, the down-quark, the electron and the electron-neutrino. Similar particles, heavier but otherwise identical, are known to exist - grouped together in two further families. By measuring the number of neutrino types that exist, LEP has shown that there are no more fam-ilies of particles. Nature has chosen the number three. This is an intriguing result, and the reason why there are neither more nor fewer than three particle families is one of the greatest mysteries of modern physics. One important consequence is that we exist. Had there been any fewer than three families of matter particles, the phenomenon known as CP violation - which led to matter dominating anti-matter in the early Universe - would not have occurred. All the matter and antimatter created in the Big Bang would have annihilated.

  16. "Science SQL" as a Building Block for Flexible, Standards-based Data Infrastructures

    Science.gov (United States)

    Baumann, Peter

    2016-04-01

    We have learnt to live with the pain of separating data and metadata into non-interoperable silos. For metadata, we enjoy the flexibility of databases, be they relational, graph, or some other NoSQL. Contrasting this, users still "drown in files" as an unstructured, low-level archiving paradigm. It is time to bridge this chasm which once was technologically induced, but today can be overcome. One building block towards a common re-integrated information space is to support massive multi-dimensional spatio-temporal arrays. These "datacubes" appear as sensor, image, simulation, and statistics data in all science and engineering domains, and beyond. For example, 2-D satellilte imagery, 2-D x/y/t image timeseries and x/y/z geophysical voxel data, and 4-D x/y/z/t climate data contribute to today's data deluge in the Earth sciences. Virtual observatories in the Space sciences routinely generate Petabytes of such data. Life sciences deal with microarray data, confocal microscopy, human brain data, which all fall into the same category. The ISO SQL/MDA (Multi-Dimensional Arrays) candidate standard is extending SQL with modelling and query support for n-D arrays ("datacubes") in a flexible, domain-neutral way. This heralds a new generation of services with new quality parameters, such as flexibility, ease of access, embedding into well-known user tools, and scalability mechanisms that remain completely transparent to users. Technology like the EU rasdaman ("raster data manager") Array Database system can support all of the above examples simultaneously, with one technology. This is practically proven: As of today, rasdaman is in operational use on hundreds of Terabytes of satellite image timeseries datacubes, with transparent query distribution across more than 1,000 nodes. Therefore, Array Databases offering SQL/MDA constitute a natural common building block for next-generation data infrastructures. Being initiator and editor of the standard we present principles

  17. Increased luminance of MEH-PPV and PFO based PLEDs by using salmon DNA as an electron blocking layer

    International Nuclear Information System (INIS)

    Madhwal, Devinder; Rait, S.S.; Verma, A.; Kumar, Amit; Bhatnagar, P.K.; Mathur, P.C.; Onoda, M.

    2010-01-01

    The effect of salmon DNA-CTMA as an electron blocking layer (EBL) has been examined on the performance of MEH-PPV and PFO-based light emitting diodes. Though the turn-on voltage increases with incorporation of EBL, a significant increase in luminance and luminous efficiency for both the devices is observed. The EBL improves the device performance by blocking electrons at the EBL-polymer interface, thereby increasing the recombination probability of electrons and holes. The luminance of the MEH-PPV based Bio-LED increases to 100 cd/m 2 from 30 cd/m 2 while a corresponding increase for the PFO based LED is to 160 cd/m 2 from 80 cd/m 2 with and without EBL, respectively.

  18. Streamlining the Design-to-Build Transition with Build-Optimization Software Tools.

    Science.gov (United States)

    Oberortner, Ernst; Cheng, Jan-Fang; Hillson, Nathan J; Deutsch, Samuel

    2017-03-17

    Scaling-up capabilities for the design, build, and test of synthetic biology constructs holds great promise for the development of new applications in fuels, chemical production, or cellular-behavior engineering. Construct design is an essential component in this process; however, not every designed DNA sequence can be readily manufactured, even using state-of-the-art DNA synthesis methods. Current biological computer-aided design and manufacture tools (bioCAD/CAM) do not adequately consider the limitations of DNA synthesis technologies when generating their outputs. Designed sequences that violate DNA synthesis constraints may require substantial sequence redesign or lead to price-premiums and temporal delays, which adversely impact the efficiency of the DNA manufacturing process. We have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST incorporates knowledge of DNA synthesis success determinants into the design process to output ready-to-build sequences, preempting the need for sequence redesign. The BOOST web application is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable integration into automated, customized DNA design processes. The herein presented results highlight the effectiveness of BOOST in reducing DNA synthesis costs and timelines.

  19. 2-Substituted dATP Derivatives as Building Blocks for Polymerase-Catalyzed Synthesis of DNA Modified in the Minor Groove

    Czech Academy of Sciences Publication Activity Database

    Matyašovský, Ján; Perlíková, Pavla; Malnuit, Vincent; Pohl, Radek; Hocek, Michal

    2016-01-01

    Roč. 55, č. 51 (2016), s. 15856-15859 ISSN 1433-7851 R&D Projects: GA ČR GA14-04289S EU Projects: European Commission(XE) 642023 - ClickGene Institutional support: RVO:61388963 Keywords : bioconjugation * DNA modification * DNA polymerase * nucleotides * fluorescent labelling Subject RIV: CC - Organic Chemistry Impact factor: 11.994, year: 2016 http://onlinelibrary.wiley.com/doi/10.1002/anie.201609007/full

  20. Main-chain supramolecular block copolymers.

    Science.gov (United States)

    Yang, Si Kyung; Ambade, Ashootosh V; Weck, Marcus

    2011-01-01

    Block copolymers are key building blocks for a variety of applications ranging from electronic devices to drug delivery. The material properties of block copolymers can be tuned and potentially improved by introducing noncovalent interactions in place of covalent linkages between polymeric blocks resulting in the formation of supramolecular block copolymers. Such materials combine the microphase separation behavior inherent to block copolymers with the responsiveness of supramolecular materials thereby affording dynamic and reversible materials. This tutorial review covers recent advances in main-chain supramolecular block copolymers and describes the design principles, synthetic approaches, advantages, and potential applications.

  1. Pinenes: Abundant and Renewable Building Blocks for a Variety of Sustainable Polymers.

    Science.gov (United States)

    Winnacker, Malte

    2018-05-14

    Pinenes - a group of monoterpenes containing a double bond - are very suitable renewable building blocks for a variety of sustainable polymers and materials. Their abundance from mainly non-edible parts of plants as well as the feasibility to isolate them render these compounds unique amongst the variety of biomass that is utilizable for novel materials. Accordingly, their use for the synthesis of biobased polymers has been investigated intensively, and strong progress has been made with this especially within the past 2-3 years. Direct cationic or radical polymerization via the double bonds as well as polymerization upon their further functionalization can afford a variety of sustainable polymers suitable for many applications, which is summarized in this article. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

    Directory of Open Access Journals (Sweden)

    Guang Hu

    2017-01-01

    Full Text Available DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs. The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.

  3. The role of DNA dependent protein kinase in synapsis of DNA ends

    NARCIS (Netherlands)

    E.P.W.C. Weterings (Eric); N.S. Verkaik (Nicole); H.T. Brüggenwirth (Hennie); D.C. van Gent (Dik); J.H.J. Hoeijmakers (Jan)

    2003-01-01

    textabstractDNA dependent protein kinase (DNA-PK) plays a central role in the non-homologous end-joining pathway of DNA double strand break repair. Its catalytic subunit (DNA-PK(CS)) functions as a serine/threonine protein kinase. We show that DNA-PK forms a stable complex at DNA termini that blocks

  4. Probing the Conformational Landscape of Polyether Building Blocks in Supersonic Jets

    Science.gov (United States)

    Bocklitz, Sebastian; Hewett, Daniel M.; Zwier, Timothy S.; Suhm, Martin A.

    2016-06-01

    Polyethylene oxides (Polyethylene glycoles) and their phenoxy-capped analogs represent a prominent class of important polymers that are highly used as precursor molecules in supramolecular reactions. After a detailed study on the simplest representative (1,2-dimethoxyethane) [1], we present results on oligoethylene oxides with increasing chain lengths obtained by spontaneous Raman scattering in a supersonic jet. Through variation of stagnation pressure, carrier gas, nozzle distance and temperature we gain information on the conformational landscape as well as the mutual interconversion of low energy conformers. The obtained results are compared to state-of-the-art quantum chemical calculations. Additionally, we present UV as well as IR-UV and UV-UV double resonance studies on 1-methoxy-2-phenoxyethane in a supersonic jet. These complementary techniques allow for conformationally selective electronic and vibrational spectra in a closely related conformational landscape. [1] S. Bocklitz, M. A. Suhm, Constraining the Conformational Landscape of a Polyether Building Block by Raman Jet Spectroscopy, Z. Phys. Chem. 2015, 229, 1625-1648.

  5. Natural supramolecular building blocks: from virus coat proteins to viral nanoparticles.

    Science.gov (United States)

    Liu, Zhi; Qiao, Jing; Niu, Zhongwei; Wang, Qian

    2012-09-21

    Viruses belong to a fascinating class of natural supramolecular structures, composed of multiple copies of coat proteins (CPs) that assemble into different shapes with a variety of sizes from tens to hundreds of nanometres. Because of their advantages including simple/economic production, well-defined structural features, unique shapes and sizes, genetic programmability and robust chemistries, recently viruses and virus-like nanoparticles (VLPs) have been used widely in biomedical applications and materials synthesis. In this critical review, we highlight recent advances in the use of virus coat proteins (VCPs) and viral nanoparticles (VNPs) as building blocks in self-assembly studies and materials development. We first discuss the self-assembly of VCPs into VLPs, which can efficiently incorporate a variety of different materials as cores inside the viral protein shells. Then, the self-assembly of VNPs at surfaces or interfaces is summarized. Finally, we discuss the co-assembly of VNPs with different functional materials (178 references).

  6. Establishing an Appropriate Level of Detail (LoD) for a Building Information Model (BIM) - West Block, Parliament Hill, Ottawa, Canada

    Science.gov (United States)

    Fai, S.; Rafeiro, J.

    2014-05-01

    In 2011, Public Works and Government Services Canada (PWGSC) embarked on a comprehensive rehabilitation of the historically significant West Block of Canada's Parliament Hill. With over 17 thousand square meters of floor space, the West Block is one of the largest projects of its kind in the world. As part of the rehabilitation, PWGSC is working with the Carleton Immersive Media Studio (CIMS) to develop a building information model (BIM) that can serve as maintenance and life-cycle management tool once construction is completed. The scale and complexity of the model have presented many challenges. One of these challenges is determining appropriate levels of detail (LoD). While still a matter of debate in the development of international BIM standards, LoD is further complicated in the context of heritage buildings because we must reconcile the LoD of the BIM with that used in the documentation process (terrestrial laser scan and photogrammetric survey data). In this paper, we will discuss our work to date on establishing appropriate LoD within the West Block BIM that will best serve the end use. To facilitate this, we have developed a single parametric model for gothic pointed arches that can be used for over seventy-five unique window types present in the West Block. Using the AEC (CAN) BIM as a reference, we have developed a workflow to test each of these window types at three distinct levels of detail. We have found that the parametric Gothic arch significantly reduces the amount of time necessary to develop scenarios to test appropriate LoD.

  7. Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world.

    Science.gov (United States)

    Soslau, Gerald

    2018-06-14

    The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang. Perhaps the most important support for the concept comes from the fact that some RNA species possess catalytic activity, ribozymes, and that RNA could be reverse transcribe to DNA. The thrust of numerous papers on this topic has been to explore how the available molecules on Earth, at its birth, gave rise to life as we know it today. This paper focuses more on a reverse view of the topic. The "how" molecular building blocks were synthesized is not addressed nor how the "first" RNA molecules were synthesized. We can clearly speculate on the variable environmental conditions and chemistry available on Earth billions of years ago. However, we can never truly replicate the changing conditions or know the chemical composition of Earth at the beginning of time. We can, however, confirm that over millions, perhaps billions of years the basic building blocks for life accumulated sufficiently to initiate evolution to an RNA world followed by our RNA/DNA world. Here we are attempting to take the information from our current knowledge of biology and by inference and extrapolation work backward to hypothesize biological events in the march forward from RNA to DNA. It is proposed that the primordial replicating RNA cell, the ribocyte, evolved from liposomes encompassing required reactants and products for "life" and that ribonucleopeptide complexes formed membrane pores to support bidirectional ion and molecular transport to maintain biological functions and

  8. Building Numbers from Primes

    Science.gov (United States)

    Burkhart, Jerry

    2009-01-01

    Prime numbers are often described as the "building blocks" of natural numbers. This article shows how the author and his students took this idea literally by using prime factorizations to build numbers with blocks. In this activity, students explore many concepts of number theory, including the relationship between greatest common factors and…

  9. Photodegradable neutral-cationic brush block copolymers for nonviral gene delivery.

    Science.gov (United States)

    Hu, Xianglong; Li, Yang; Liu, Tao; Zhang, Guoying; Liu, Shiyong

    2014-08-01

    We report on the fabrication of a photodegradable gene-delivery vector based on PEO-b-P(GMA-g-PDMAEMA) neutral-cationic brush block copolymers that possess cationic poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA) brushes for DNA compaction, poly(ethylene oxide) (PEO) as a hydrophilic block, and poly(glycidyl methacrylate) (PGMA) as the backbone. The PEO-b-P(GMA-g-PDMAEMA) copolymers were synthesized through the combination of reversible addition-fragmentation transfer (RAFT) polymerization and postmodification. A photocleavable PEO-based macroRAFT agent was first synthesized; next, the PEO-b-PGMA block copolymer was prepared by RAFT polymerization of GMA; this was followed by a click reaction to introduce the RAFT initiators on the side chains of the PGMA block; then, RAFT polymerization of DMAEMA afforded the PEO-b-P(GMA-g-PDMAEMA) copolymer. The obtained neutral-cationic brush block copolymer could effectively complex plasmid DNA (pDNA) into nanoparticles at an N/P ratio (i.e., the number of nitrogen residues per DNA phosphate) of 4. Upon UV irradiation, pDNA could be released owing to cleavage of the pDNA-binding cationic PDMAEMA side chains as well as the nitrobenzyl ester linkages at the diblock junction point. In addition, in vitro gene transfection results demonstrated that the polyplexes could be effectively internalized by cells with good transfection efficiency, and the UV irradiation protocol could considerably enhance the efficiency of gene transfection. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Winter energy behaviour in multi-family block buildings in a temperate-cold climate in Argentina

    Energy Technology Data Exchange (ETDEWEB)

    Filippin, C. [CONICET - CC302, Santa Rosa, 6300 La Pampa (Argentina); Larsen, S. Flores [CONICET - CC302, Santa Rosa, 6300 La Pampa (Argentina); INENCO - Instituto de Investigaciones en Energias No Convencionales, U.N.Sa., CONICET, Avda. Bolivia 5150 - CP 4400, Salta Capital (Argentina); Mercado, V. [LAHV-Laboratorio de Ambienet Humano y Vivienda (INCIHUSA-CCT-CONICET) (Argentina)

    2011-01-15

    This paper analyzes the thermal and energy behaviour of apartments in three-story block buildings located along a NE-SW axis (azimuth = 120 ) in a temperate-cold climate (latitude: 36 57'; longitude: 64 27') in the city of Santa Rosa, La Pampa, central Argentina. Four apartments had been monitored during May and June 2009. Three of them are located in Block 126. Two of these apartments face South: 15 and 23 on the SE end, ground and first floor, respectively; 18 faces N on the second floor. Finally apartment, 12 is located in Block 374, on the first floor, faces N and shows a carpentry-closed balcony. The purpose of this work is - to study the evolution of the indoor temperature in each apartment; to analyze energy consumption and comfort conditions; to study energy potential and energy intervention in order to reduce energy consumption; to analyze bioclimatic alternatives feasibility and the possibility to extrapolate results to all blocks. On the basis of the analysis of natural gas historical consumption records, results showed that regarding heating energy consumption during the period May-June, Apartment 12, facing N, with its only bedroom facing NW and its carpentry-closed, transparent glass balcony, presented a mean temperature of 21.2 C, using a halogen heater for 6 h/day between 9 pm and 2 am (0.16 kWh/day/m{sup 2}). Apartment 15, on the SE end, first floor of the block consumed 22.5 kWh/day (0.43 kWh/day/m{sup 2}) (mean temperature = 22.2 C). Apartment 23, located on the second and top floor (on top of Apartment 15) with higher energy loss, consumed 28 kWh/day (0.54 kWh/day/m{sup 2}) (mean temperature 23.7 C). Apartment 18, also on the second floor and facing N, located in the centre and with its only bedroom facing SE, consumed 18.8 kWh/day (0.48 kWh/day/m{sup 2}) (mean temperature = 22.3 C). Apartment 23, with higher thermal loss through its envelope, but with heat transfer from the apartment located below, is the one that showed the highest

  11. Synthesis of borylated porphyrin and bromo- porphyrin as building blocks for light harvesting antenna molecule

    Science.gov (United States)

    Radzuan, Nuur Haziqah Mohd; Hassan, Nurul Izzaty; Bakar, Muntaz Abu

    2018-04-01

    The building blocks for synthesis of light harvesting antenna which are 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolane)-10,20-diphenylporphyrin, 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolane)-10,20-dihexylporphyrin and 5,10,15,20-tetra-(bromophenyl)porphyrin were synthesized. Borylated porphyrin was synthesized by Suzuki coupling reaction between A2BC bromo-porphyrin and pinacolborane. Whereas 5,10,15,20-tetra-(bromophenyl) porphyrin was synthesized by Lindsey condensation reaction between pyrrole and 4-bromobenzaldehyde. 1H-NMR, 13C-NMR spectroscopy and UV-visible spectroscopy confirmed the successful formation of all compounds.

  12. The Influence of Building Block Play on Mathematics Achievement and Logical and Divergent Thinking in Italian Primary School Mathematics Classes

    Science.gov (United States)

    Pirrone, Concetta; Tienken, Christopher H.; Pagano, Tatiana; Di Nuovo, Santo

    2018-01-01

    In an experimental study to explain the effect of structured Building Block Play with LEGO™ bricks on 6-year-old student mathematics achievement and in the areas of logical thinking, divergent thinking, nonverbal reasoning, and mental imagery, students in the experimental group scored significantly higher (p = 0.05) in mathematics achievement and…

  13. Programmable disorder in random DNA tilings

    Science.gov (United States)

    Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu

    2017-03-01

    Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network—random loops, mazes and trees—on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures.

  14. Life Cycle CO2 Assessment by Block Type Changes of Apartment Housing

    Directory of Open Access Journals (Sweden)

    Cheonghoon Baek

    2016-08-01

    Full Text Available The block type and structural systems in buildings affect the amount of building materials required as well as the CO2 emissions that occur throughout the building life cycle (LCCO2. The purpose of this study was to assess the life cycle CO2 emissions when an apartment housing with ‘flat-type’ blocks (the reference case was replaced with more sustainable ‘T-type’ blocks with fewer CO2 emissions (the alternative case maintaining the same total floor area. The quantity of building materials used and building energy simulations were analyzed for each block type using building information modeling techniques, and improvements in LCCO2 emission were calculated by considering high-strength concrete alternatives. By changing the bearing wall system of the ‘flat-type’ block to the ‘column and beam’ system of the ‘T-type’ block, LCCO2 emissions of the alternative case were 4299 kg-CO2/m2, of which 26% was at the construction stage, 73% was as the operational stage and 1% was at the dismantling and disposal stage. These total LCCO2 emissions were 30% less than the reference case.

  15. Polymers with alternating anthracene and phenylene building blocks linked by ethynylene and/or vinylene units: Studying structure-properties-relationships

    Czech Academy of Sciences Publication Activity Database

    Boudiba, S.; Růžička, Aleš; Ulbricht, C.; Enengl, S.; Enengl, C.; Gasiorowski, J.; Yumusak, C.; Pokorná, Veronika; Výprachtický, Drahomír; Hingerl, K.; Zahn, D. R. T.; Tinti, F.; Camaioni, N.; Bouguessa, S.; Gouasmia, A.; Cimrová, Věra; Egbe, D. A. M.

    2017-01-01

    Roč. 55, č. 1 (2017), s. 129-143 ISSN 0887-624X R&D Projects: GA ČR(CZ) GA13-26542S Institutional support: RVO:61389013 Keywords : anthracene building block * charge transport * conjugated polymers Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 2.952, year: 2016

  16. DENA: A Configurable Microarchitecture and Design Flow for Biomedical DNA-Based Logic Design.

    Science.gov (United States)

    Beiki, Zohre; Jahanian, Ali

    2017-10-01

    DNA is known as the building block for storing the life codes and transferring the genetic features through the generations. However, it is found that DNA strands can be used for a new type of computation that opens fascinating horizons in computational medicine. Significant contributions are addressed on design of DNA-based logic gates for medical and computational applications but there are serious challenges for designing the medium and large-scale DNA circuits. In this paper, a new microarchitecture and corresponding design flow is proposed to facilitate the design of multistage large-scale DNA logic systems. Feasibility and efficiency of the proposed microarchitecture are evaluated by implementing a full adder and, then, its cascadability is determined by implementing a multistage 8-bit adder. Simulation results show the highlight features of the proposed design style and microarchitecture in terms of the scalability, implementation cost, and signal integrity of the DNA-based logic system compared to the traditional approaches.

  17. Expedient Route To Access Rare Deoxy Amino l-Sugar Building Blocks for the Assembly of Bacterial Glycoconjugates.

    Science.gov (United States)

    Sanapala, Someswara Rao; Kulkarni, Suvarn S

    2016-04-13

    Bacterial glycoproteins and oligosaccharides contain several rare deoxy amino l-sugars which are virtually absent in the human cells. This structural difference between the bacterial and host cell surface glycans can be exploited for the development of carbohydrate based vaccines and target specific drugs. However, the unusual deoxy amino l-sugars present in the bacterial glycoconjugates are not available from natural sources. Thus, procurement of orthogonally protected rare l-sugar building blocks through efficient chemical synthesis is a crucial step toward the synthesis of structurally well-defined and homogeneous complex glycans. Herein, we report a general and expedient methodology to access a variety of unusual deoxy amino l-sugars starting from readily available l-rhamnose and l-fucose via highly regioselective, one-pot double serial and double parallel displacements of the corresponding 2,4-bistriflates using azide and nitrite anions as nucleophiles. Alternatively, regioselective monotriflation at O2, O3, and O4 of l-rhamnose/l-fucose allowed selective inversions at respective positions leading to diverse rare sugars. The orthogonally protected deoxy amino l-sugar building blocks could be stereoselectively assembled to obtain biologically relevant bacterial O-glycans, as exemplified by the first total synthesis of the amino linker-attached, conjugation-ready tetrasaccharide of O-PS of Yersinia enterocolitica O:50 strain 3229 and the trisaccharide of Pseudomonas chlororaphis subsp. aureofaciens strain M71.

  18. Core-Shell Particles as Building Blocks for Systems with High Duality Symmetry

    Science.gov (United States)

    Rahimzadegan, Aso; Rockstuhl, Carsten; Fernandez-Corbaton, Ivan

    2018-05-01

    Material electromagnetic duality symmetry requires a system to have equal electric and magnetic responses. Intrinsically dual materials that meet the duality conditions at the level of the constitutive relations do not exist in many frequency bands. Nevertheless, discrete objects like metallic helices and homogeneous dielectric spheres can be engineered to approximate the dual behavior. We exploit the extra degrees of freedom of a core-shell dielectric sphere in a particle optimization procedure. The duality symmetry of the resulting particle is more than 1 order of magnitude better than previously reported nonmagnetic objects. We use T -matrix-based multiscattering techniques to show that the improvement is transferred onto the duality symmetry of composite objects when the core-shell particle is used as a building block instead of homogeneous spheres. These results are relevant for the fashioning of systems with high duality symmetry, which are required for some technologically important effects.

  19. Water-soluble building blocks for terpyridine-containing supramolecular polymers : synthesis, complexation, and pH stability studies of poly(ethylene oxide) moieties

    NARCIS (Netherlands)

    Lohmeijer, B.G.G.; Schubert, U.S.

    2003-01-01

    Poly(ethylene oxide) of various molecular weights ([bar M ]n = 3 000, 5 200, 10 000, 16 500 g · mol-1) has been modified with terpyridine end groups as building blocks for water-soluble metallo-supramolecular polymers. Metallo-supramolecular A-A homopolymers have been prepared and characterized by

  20. From Building Blocks to Architects Empowering Learners for Success

    Directory of Open Access Journals (Sweden)

    Reyes Juana Mahissa

    2002-08-01

    Full Text Available Although our ultimate goal is to enable our learners to become autonomous and efficient in their use of the foreign language, whether or not they have the opportunity to ever live and interact in a foreign language setting, our work as teachers must involve a conscious analysis of the different factors involved in this process, as well as the conscious effort to put all the intervening factors into action. Furthermore, it is our responsibility to develop the learners¿ thinking skills as they increase their competence in the target language and at the same time make them aware of their responsibility for their own processes and success by enhancing their autonomy and making them aware of the value of learning strategies. It is our task as teachers to be present on this journey and guide our learners towards becoming architects and masters of their own foreign language construct. In order for this journey to be a successful one, we must make sure we provide the learner with a correct supply of building blocks. In this paper we present an analysis of the main components comprised in teaching English as a foreign language, including a historical overview of methods, approaches, strategies, the concept of learner¿s autonomy, social and psychological factors, aiming at contributing to every teacher¿s reflection on his/her task in the school context.

  1. Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks

    DEFF Research Database (Denmark)

    Chen, Yun; Nielsen, Jens

    2013-01-01

    Bio-based production of chemical building blocks from renewable resources is an attractive alternative to petroleum-based platform chemicals. Metabolic pathway and strain engineering is the key element in constructing robust microbial chemical factories within the constraints of cost effective...... production. Here we discuss how the development of computational algorithms, novel modules and methods, omics-based techniques combined with modeling refinement are enabling reduction in development time and thus advance the field of industrial biotechnology. We further discuss how recent technological...

  2. Mononuclear, trinuclear, and hetero-trinuclear supramolecular complexes containing a new tri-sulfonate ligand and cobalt(II)/copper(II)-(1,10-phenanthroline) 2 building blocks

    Science.gov (United States)

    Yu, Yunfang; Wei, Yongqin; Broer, Ria; Sa, Rongjian; Wu, Kechen

    2008-03-01

    Novel mononuclear, trinuclear, and hetero-trinuclear supermolecular complexes, [Co(phen) 2(H 2O)(HTST)]·2H 2O ( 1), [Co 3(phen) 6(H 2O) 2(TST) 2]·7H 2O ( 2), and [Co 2Cu(phen) 6(H 2O) 2(TST) 2]·10H 2O ( 3), have been synthesized by the reactions of a new tri-sulfonate ligand (2,4,6-tris(4-sulfophenylamino)-1,3,5-triazine, H 3TST) with the M2+ ( M=Co, Cu) and the second ligand 1,10-phenanthroline (phen). Complex 1 contains a cis-Co(II)(phen) 2 building block and an HTST as monodentate ligand; complex 2 consists of two TST as bidentate ligands connecting one trans- and two cis-Co(II)(phen) 2 building blocks; complex 3 is formed by replacing the trans-Co(II)(phen) 2 in 2 with a trans-Cu(II)(phen) 2, which is the first reported hetero-trinuclear supramolecular complex containing both the Co(II)(phen) 2 and Cu(II)(phen) 2 as building blocks. The study shows the flexible multifunctional self-assembly capability of the H 3TST ligands presenting in these supramolecular complexes through coordinative, H-bonding and even π- π stacking interactions. The photoluminescent optical properties of these complexes are also investigated and discussed as well as the second-order nonlinear optical properties of 1.

  3. CEMENT KILN DUST AS A MATERIAL FOR BUILDING BLOCKS ...

    African Journals Online (AJOL)

    This paper presents the results of a study on the properties of hollow sandcrete blocks with cement kiln dust (CKD) as an additive and as a replacement for ordinary portland cement (OPC). When CKD was used as a replacement for cement, the compressive strength and density of blocks generally decreased with higher ...

  4. Designing Optical Properties in DNA-Programmed Nanoparticle Superlattices

    Science.gov (United States)

    Ross, Michael Brendan

    A grand challenge of modern science has been the ability to predict and design the properties of new materials. This approach to the a priori design of materials presents a number of challenges including: predictable properties of the material building blocks, a programmable means for arranging such building blocks into well understood architectures, and robust models that can predict the properties of these new materials. In this dissertation, we present a series of studies that describe how optical properties in DNA-programmed nanoparticle superlattices can be predicted prior to their synthesis. The first chapter provides a history and introduction to the study of metal nanoparticle arrays. Chapter 2 surveys and compares several geometric models and electrodynamics simulations with the measured optical properties of DNA-nanoparticle superlattices. Chapter 3 describes silver nanoparticle superlattices (rather than gold) and identifies their promise as plasmonic metamaterials. In chapter 4, the concept of plasmonic metallurgy is introduced, whereby it is demonstrated that concepts from materials science and metallurgy can be applied to the optical properties of mixed metallic plasmonic materials, unveiling rich and tunable optical properties such as color and asymmetric reflectivity. Chapter 5 presents a comprehensive theoretical exploration of anisotropy (non-spherical) in nanoparticle superlattice architectures. The role of anisotropy is discussed both on the nanoscale, where several desirable metamaterial properties can be tuned from the ultraviolet to near-infrared, and on the mesoscale, where the size and shape of a superlattice is demonstrated to have a pronounced effect on the observed far-field optical properties. Chapter 6 builds upon those theoretical data presented in chapter 5, including the experimental realization of size and shape dependent properties in DNA-programmed superlattices. Specifically, nanoparticle spacing is explored as a parameter that

  5. A New Modular Approach to Nanoassembly: Stable and Addressable DNA Nanoconstructs via Orthogonal Click Chemistries

    KAUST Repository

    Gerrard, Simon R.

    2012-10-23

    Thermodynamic instability is a problem when assembling and purifying complex DNA nanostructures formed by hybridization alone. To address this issue, we have used photochemical fixation and orthogonal copper-free, ring-strain-promoted, click chemistry for the synthesis of dimeric, trimeric, and oligomeric modular DNA scaffolds from cyclic, double-stranded, 80-mer DNA nanoconstructs. This particular combination of orthogonal click reactions was more effective for nanoassembly than others explored. The complex nanostructures are stable to heat and denaturation agents and can therefore be purified and characterized. They are addressable in a sequence-specific manner by triplex formation, and they can be reversibly and selectively deconstructed. Nanostructures utilizing this orthogonal, chemical fixation methodology can be used as building blocks for nanomachines and functional DNA nanoarchitectures. © 2012 American Chemical Society.

  6. How We Make DNA Origami.

    Science.gov (United States)

    Wagenbauer, Klaus F; Engelhardt, Floris A S; Stahl, Evi; Hechtl, Vera K; Stömmer, Pierre; Seebacher, Fabian; Meregalli, Letizia; Ketterer, Philip; Gerling, Thomas; Dietz, Hendrik

    2017-10-05

    DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage-free preparation of DNA origami. These methods are agarose-gel purification, filtration through molecular cut-off membranes, PEG precipitation, size-exclusion chromatography, and ultracentrifugation-based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Carborane-linked 2'-deoxyuridine 5'-O-triphosphate as building block for polymerase synthesis of carborane-modified DNA

    Czech Academy of Sciences Publication Activity Database

    Balintová, Jana; Simonova, Anna; Bialek-Pietras, M.; Olejniczak, A.; Lesnikowski, Z. J.; Hocek, Michal

    2017-01-01

    Roč. 27, č. 21 (2017), s. 4786-4788 ISSN 0960-894X R&D Projects: GA ČR GBP206/12/G151 Grant - others:AV ČR(CZ) AP1501 Program:Akademická prémie - Praemium Academiae Institutional support: RVO:61388963 Keywords : nucleotides * nucleoside triphosphates * carboranes * DNA polymerase * oligonucleotides Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 2.454, year: 2016

  8. Integration of G-quadruplex and DNA-templated Ag NCs for nonarithmetic information processing† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00361g Click here for additional data file.

    Science.gov (United States)

    Gao, Ru-Ru; Lv, Xiao-Yan; Zhu, Yan-Yan; Zhang, Yi-Wei

    2017-01-01

    To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer. Moreover, a parity checker which is capable of identifying odd and even numbers from natural numbers is constructed conceptually. Finally, a multi-valued logic gate (ternary inhibit gate) is readily achieved by taking this DNA/Ag NC system as a universal platform. All of the above logic circuits share the same building blocks, indicating the great prospects of the assembly of nanomaterials and DNA for biochemical logic devices. Considering its biocompatibility, the novel prototypes developed here may have potential applications in the fields of biological computers and medical diagnosis and serve as a promising proof of principle in the not-too-distant future. PMID:28626564

  9. Quantification of cellular uptake of DNA nanostructures by qPCR.

    Science.gov (United States)

    Okholm, Anders Hauge; Nielsen, Jesper Sejrup; Vinther, Mathias; Sørensen, Rasmus Schøler; Schaffert, David; Kjems, Jørgen

    2014-05-15

    DNA nanostructures facilitating drug delivery are likely soon to be realized. In the past few decades programmed self-assembly of DNA building blocks have successfully been employed to construct sophisticated nanoscale objects. By conjugating functionalities to DNA, other molecules such as peptides, proteins and polymers can be precisely positioned on DNA nanostructures. This exceptional ability to produce modular nanoscale devices with tunable and controlled behavior has initiated an interest in employing DNA nanostructures for drug delivery. However, to obtain this the relationship between cellular interactions and structural and functional features of the DNA delivery device must be thoroughly investigated. Here, we present a rapid and robust method for the precise quantification of the component materials of DNA origami structures capable of entering cells in vitro. The quantification is performed by quantitative polymerase chain reaction, allowing a linear dynamic range of detection of five orders of magnitude. We demonstrate the use of this method for high-throughput screening, which could prove efficient to identify key features of DNA nanostructures enabling cell penetration. The method described here is suitable for quantification of in vitro uptake studies but should easily be extended to quantify DNA nanostructures in blood or tissue samples. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. A DNA-Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition.

    Science.gov (United States)

    Favalli, Nicholas; Biendl, Stefan; Hartmann, Marco; Piazzi, Jacopo; Sladojevich, Filippo; Gräslund, Susanne; Brown, Peter J; Näreoja, Katja; Schüler, Herwig; Scheuermann, Jörg; Franzini, Raphael; Neri, Dario

    2018-06-01

    A DNA-encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5-bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a K d value of 6 nm, while compounds with the same substituents on an equidistant but flexible l-lysine scaffold showed 140-fold lower affinity. A 18 nm tankyrase-1 binder featured l-lysine as linking moiety, while molecules based on d-Lysine or (2S,4S)-amino-l-proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Role of Solvent, pH, and Molecular Size in Excited-State Deactivation of Key Eumelanin Building Blocks: Implications for Melanin Pigment Photostability

    DEFF Research Database (Denmark)

    Gauden, M.; Pezzella, A.; Panzella, L.

    2008-01-01

      Ultrafast time-resolved fluorescence spectroscopy has been used to investigate the excited state dynamics of the basic eumelanin building block 5,6-dihydroxyindole-2-carboxylic acid  (DHICA) its acetylated, methylated and carboxylic ester derivatives as well as two oligomers, a dimer and a trim...

  12. Biorefineries for the production of top building block chemicals and their derivatives.

    Science.gov (United States)

    Choi, Sol; Song, Chan Woo; Shin, Jae Ho; Lee, Sang Yup

    2015-03-01

    Due to the growing concerns on the climate change and sustainability on petrochemical resources, DOE selected and announced the bio-based top 12 building blocks and discussed the needs for developing biorefinery technologies to replace the current petroleum based industry in 2004. Over the last 10 years after its announcement, many studies have been performed for the development of efficient technologies for the bio-based production of these chemicals and derivatives. Now, ten chemicals among these top 12 chemicals, excluding the l-aspartic acid and 3-hydroxybutyrolactone, have already been commercialized or are close to commercialization. In this paper, we review the current status of biorefinery development for the production of these platform chemicals and their derivatives. In addition, current technological advances on industrial strain development for the production of platform chemicals using micro-organisms will be covered in detail with case studies on succinic acid and 3-hydroxypropionic acid as examples. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  13. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

    Science.gov (United States)

    Muto, Yutaka; Yokoyama, Shigeyuki

    2012-01-01

    'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

  14. A Structurally Variable Hinged Tetrahedron Framework from DNA Origami

    Directory of Open Access Journals (Sweden)

    David M. Smith

    2011-01-01

    Full Text Available Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffolds as well as a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75 nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure's surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT.

  15. Building blocks for future detectors: Silicon test masses and 1550 nm laser light

    International Nuclear Information System (INIS)

    Schnabel, R; Britzger, M; Burmeister, O; Danzmann, K; Duck, J; Eberle, T; Friedrich, D; Luck, H; Mehmet, M; Steinlechner, S; Willke, B; Brueckner, F; Nawrodt, R

    2010-01-01

    Current interferometric gravitational wave detectors use the combination of quasi-monochromatic, continuous-wave laser light at 1064 nm and fused silica test masses at room temperature. Detectors of the third generation, such as the Einstein-Telescope, will involve a considerable sensitivity increase. The combination of 1550 nm laser radiation and crystalline silicon test masses at low temperatures might be important ingredients in order to achieve the sensitivity goal. Here we compare some properties of the fused silica and silicon test mass materials relevant for decreasing the thermal noise in future detectors as well as the recent technology achievements in the preparation of laser radiation at 1064 nm and 1550 nm relevant for decreasing the quantum noise. We conclude that silicon test masses and 1550 nm laser light have the potential to form the future building blocks of gravitational wave detection.

  16. Remote stabilization of copper paddlewheel based molecular building blocks in metal-organic frameworks

    KAUST Repository

    Gao, Wenyang

    2015-03-24

    Copper paddlewheel based molecular building blocks (MBBs) are ubiquitous and have been widely employed for the construction of highly porous metal-organic frameworks (MOFs). However, most copper paddlewheel based MOFs fail to retain their structural integrity in the presence of water. This instability is directly correlated to the plausible displacement of coordinating carboxylates in the copper paddlewheel MBB, [Cu2(O2C-)4], by the strongly coordinating water molecules. In this comprehensive study, we illustrate the chemical stability control in the rht-MOF platform via strengthening the coordinating bonds within the triangular inorganic MBB, [Cu3O(N4-x(CH)xC-)3] (x = 0, 1, or 2). Remotely, the chemical stabilization propagated into the paddlewheel MBB to afford isoreticular rht-MOFs with remarkably enhanced water/chemical stabilities compared to the prototypal rht-MOF-1. © 2015 American Chemical Society.

  17. Remote stabilization of copper paddlewheel based molecular building blocks in metal-organic frameworks

    KAUST Repository

    Gao, Wenyang; Cai, Rong; Pham, Tony T.; Forrest, Katherine A.; Hogan, Adam; Nugent, Patrick S.; Williams, Kia R.; Wojtas, Łukasz; Luebke, Ryan; Weselinski, Lukasz Jan; Zaworotko, Michael J.; Space, Brian; Chen, Yusheng; Eddaoudi, Mohamed; Shi, Xiaodong; Ma, Shengqian

    2015-01-01

    Copper paddlewheel based molecular building blocks (MBBs) are ubiquitous and have been widely employed for the construction of highly porous metal-organic frameworks (MOFs). However, most copper paddlewheel based MOFs fail to retain their structural integrity in the presence of water. This instability is directly correlated to the plausible displacement of coordinating carboxylates in the copper paddlewheel MBB, [Cu2(O2C-)4], by the strongly coordinating water molecules. In this comprehensive study, we illustrate the chemical stability control in the rht-MOF platform via strengthening the coordinating bonds within the triangular inorganic MBB, [Cu3O(N4-x(CH)xC-)3] (x = 0, 1, or 2). Remotely, the chemical stabilization propagated into the paddlewheel MBB to afford isoreticular rht-MOFs with remarkably enhanced water/chemical stabilities compared to the prototypal rht-MOF-1. © 2015 American Chemical Society.

  18. Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Anna-Karin Berglund

    2017-02-01

    Full Text Available Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides. Our analyses strongly suggest that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of a mitochondrial ribonucleotide excision repair pathway in human cells. Furthermore, we clearly demonstrate that when dNTP pools are limiting, ribonucleotides serve as a source of building blocks to maintain DNA replication. Increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools may contribute to a pathogenic mechanism that affects mtDNA stability and impair new rounds of mtDNA replication.

  19. Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA.

    Science.gov (United States)

    Berglund, Anna-Karin; Navarrete, Clara; Engqvist, Martin K M; Hoberg, Emily; Szilagyi, Zsolt; Taylor, Robert W; Gustafsson, Claes M; Falkenberg, Maria; Clausen, Anders R

    2017-02-01

    Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA) and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP) pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides. Our analyses strongly suggest that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of a mitochondrial ribonucleotide excision repair pathway in human cells. Furthermore, we clearly demonstrate that when dNTP pools are limiting, ribonucleotides serve as a source of building blocks to maintain DNA replication. Increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools may contribute to a pathogenic mechanism that affects mtDNA stability and impair new rounds of mtDNA replication.

  20. Phosphate-methylated DNA aimed at HIV-1 RNA loops and integrated DNA inhibits viral infectivity

    NARCIS (Netherlands)

    Buck, H. M.; Koole, L. H.; van Genderen, M. H.; Smit, L.; Geelen, J. L.; Jurriaans, S.; Goudsmit, J.

    1990-01-01

    Phosphate-methylated DNA hybridizes strongly and specifically to natural DNA and RNA. Hybridization to single-stranded and double-stranded DNA leads to site-selective blocking of replication and transcription. Phosphate-methylated DNA was used to interrupt the life cycle of the human

  1. Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

    Institute of Scientific and Technical Information of China (English)

    Xiao-Rong Wu; Chen-Wei Wu; Fei Ding; Cheng Tian; Wen Jiang; Cheng-De Mao; Chuan Zhang

    2017-01-01

    Discrete and symmetric three-dimensional (3D) DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization (e.g.dye molecules,proteins,inorganic nanoparticles,etc.) to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA pointstar motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron (E-TET),rhombic dodecahedron (R-DOD),and rhombic triacontahedron (R-TRI) are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis (PAGE),atomic force microscope (AFM) imaging,and cryogenic transmission electron microscope imaging (cryo-TEM) associated with single particle reconstruction.

  2. Block Play: Practical Suggestions for Common Dilemmas

    Science.gov (United States)

    Tunks, Karyn Wellhousen

    2009-01-01

    Learning materials and teaching methods used in early childhood classrooms have fluctuated greatly over the past century. However, one learning tool has stood the test of time: Wood building blocks, often called unit blocks, continue to be a source of pleasure and learning for young children at play. Wood blocks have the unique capacity to engage…

  3. Building a DNA barcode reference library for the true butterflies (Lepidoptera) of Peninsula Malaysia: what about the subspecies?

    Science.gov (United States)

    Wilson, John-James; Sing, Kong-Wah; Sofian-Azirun, Mohd

    2013-01-01

    The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity.

  4. Building a DNA Barcode Reference Library for the True Butterflies (Lepidoptera) of Peninsula Malaysia: What about the Subspecies?

    Science.gov (United States)

    Wilson, John-James; Sing, Kong-Wah; Sofian-Azirun, Mohd

    2013-01-01

    The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity. PMID:24282514

  5. Building a DNA barcode reference library for the true butterflies (Lepidoptera of Peninsula Malaysia: what about the subspecies?

    Directory of Open Access Journals (Sweden)

    John-James Wilson

    Full Text Available The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92% and revealed that most subspecies possessed unique DNA barcodes (84%. In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity.

  6. Electrical detection and quantification of single and mixed DNA nucleotides in suspension

    Science.gov (United States)

    Ahmad, Mahmoud Al; Panicker, Neena G.; Rizvi, Tahir A.; Mustafa, Farah

    2016-09-01

    High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical properties. In this study, the four different types of nucleotides that constitute a DNA molecule were suspended in a buffer followed by performing several types of electrical measurements. These electrical parameters were then used to quantify the suspended DNA nucleotides. Thus, we present a purely electrical counting scheme based on the semiconductor theory that allows one to determine the number of nucleotides in a solution by measuring their capacitance-voltage dependency. The nucleotide count was observed to be similar to the multiplication of the corresponding dopant concentration and debye volume after de-embedding the buffer contribution. The presented approach allows for a fast and label-free quantification of single and mixed nucleotides in a solution.

  7. Lurgi MegaMethanol technology. Delivering the building blocks for the future fuel and monomer demand

    Energy Technology Data Exchange (ETDEWEB)

    Wurzel, T. [Lurgi AG, Frankfurt/Main (Germany)

    2006-07-01

    The paper describes the central role of methanol within a changing environment with respect to feedstock availability as well as steadily growing demand in fuel and monomer demand. The current large-scale production facilities are described with respect to the technological challenges in order to ensure the availability of sufficient methanol for down-stream applications. Different down-stream applications are described which clearly confirm that methanol is the dominant C1-building block due to its chemical flexibility. It is concluded that by means of the implementation of two MTP (Methanol to Propylene) projects in China initiated the era of ''down-stream methanol'' has begun in the industry. (orig.)

  8. Solar thermal electricity production. A building block for the energy turnaround?; Solarthermische Stromerzeugung. Ein Baustein fuer die Energiewende?

    Energy Technology Data Exchange (ETDEWEB)

    Pitz-Paal, Robert [Deutsches Zentrum fuer Luft- und Raumfahrt (DLR) e.V., Koeln (Germany). Inst. fuer Solarforschung

    2012-12-15

    Whereas in Germany enthusiasm for solar thermal power plants has subsided following the inglorious insolvency of Solar Millennium AG, internationally the market is livening up again. This has to do with the fact that many countries have now understood that security of supply cannot be founded on photovoltaics and wind alone in the long term. Solar thermal power could thus yet become an important building block in Germany's energy supply system as it continues to pursue the energy turnaround.

  9. Bifacial DNA origami-directed discrete, three-dimensional, anisotropic plasmonic nanoarchitectures with tailored optical chirality.

    Science.gov (United States)

    Lan, Xiang; Chen, Zhong; Dai, Gaole; Lu, Xuxing; Ni, Weihai; Wang, Qiangbin

    2013-08-07

    Discrete three-dimensional (3D) plasmonic nanoarchitectures with well-defined spatial configuration and geometry have aroused increasing interest, as new optical properties may originate from plasmon resonance coupling within the nanoarchitectures. Although spherical building blocks have been successfully employed in constructing 3D plasmonic nanoarchitectures because their isotropic nature facilitates unoriented localization, it still remains challenging to assemble anisotropic building blocks into discrete and rationally tailored 3D plasmonic nanoarchitectures. Here we report the first example of discrete 3D anisotropic gold nanorod (AuNR) dimer nanoarchitectures formed using bifacial DNA origami as a template, in which the 3D spatial configuration is precisely tuned by rationally shifting the location of AuNRs on the origami template. A distinct plasmonic chiral response was experimentally observed from the discrete 3D AuNR dimer nanoarchitectures and appeared in a spatial-configuration-dependent manner. This study represents great progress in the fabrication of 3D plasmonic nanoarchitectures with tailored optical chirality.

  10. A Thieno[3,2-b][1]benzothiophene Isoindigo Building Block for Additive- and Annealing-Free High-Performance Polymer Solar Cells

    KAUST Repository

    Yue, Wan; Ashraf, Raja Shahid; Nielsen, Christian B.; Collado-Fregoso, Elisa; Niazi, Muhammad Rizwan; Yousaf, Syeda Amber; Kirkus, Mindaugas; Chen, Hung-Yang; Amassian, Aram; Durrant, James R.; McCulloch, Iain

    2015-01-01

    A novel photoactive polymer with two different molecular weights is reported, based on a new building block: thieno[3,2-b][1]benzothiophene isoindigo. Due to the improved crystallinity, optimal blend morphology, and higher charge mobility, solar-cell devices of the high-molecular-weight polymer exhibit a superior performance, affording efficiencies of 9.1% without the need for additives, annealing, or additional extraction layers during device fabrication.

  11. A Thieno[3,2-b][1]benzothiophene Isoindigo Building Block for Additive- and Annealing-Free High-Performance Polymer Solar Cells

    KAUST Repository

    Yue, Wan

    2015-08-20

    A novel photoactive polymer with two different molecular weights is reported, based on a new building block: thieno[3,2-b][1]benzothiophene isoindigo. Due to the improved crystallinity, optimal blend morphology, and higher charge mobility, solar-cell devices of the high-molecular-weight polymer exhibit a superior performance, affording efficiencies of 9.1% without the need for additives, annealing, or additional extraction layers during device fabrication.

  12. Metallothionein blocks oxidative DNA damage induced by acute inorganic arsenic exposure

    Energy Technology Data Exchange (ETDEWEB)

    Qu, Wei, E-mail: qu@niehs.nih.gov; Waalkes, Michael P.

    2015-02-01

    We studied how protein metallothionein (MT) impacts arsenic-induced oxidative DNA damage (ODD) using cells that poorly express MT (MT-I/II double knockout embryonic cells; called MT-null cells) and wild-type (WT) MT competent cells. Arsenic (as NaAsO{sub 2}) was less cytolethal over 24 h in WT cells (LC{sub 50} = 11.0 ± 1.3 μM; mean ± SEM) than in MT-null cells (LC{sub 50} = 5.6 ± 1.2 μM). ODD was measured by the immuno-spin trapping method. Arsenic (1 or 5 μM; 24 h) induced much less ODD in WT cells (121% and 141% of control, respectively) than in MT-null cells (202% and 260%). In WT cells arsenic caused concentration-dependent increases in MT expression (transcript and protein), and in the metal-responsive transcription factor-1 (MTF-1), which is required to induce the MT gene. In contrast, basal MT levels were not detectable in MT-null cells and unaltered by arsenic exposure. Transfection of MT-I gene into the MT-null cells markedly reduced arsenic-induced ODD levels. The transport genes, Abcc1 and Abcc2 were increased by arsenic in WT cells but either showed no or very limited increases in MT-null cells. Arsenic caused increases in oxidant stress defense genes HO-1 and GSTα2 in both WT and MT-null cells, but to much higher levels in WT cells. WT cells appear more adept at activating metal transport systems and oxidant response genes, although the role of MT in these responses is unclear. Overall, MT protects against arsenic-induced ODD in MT competent cells by potential sequestration of scavenging oxidant radicals and/or arsenic. - Highlights: • Metallothionein blocks arsenic toxicity. • Metallothionein reduces arsenic-induced DNA damage. • Metallothionein may bind arsenic or radicals produced by arsenic.

  13. Naphthalene Bis(4,8-diamino-1,5-dicarboxyl)amide Building Block for Semiconducting Polymers.

    Science.gov (United States)

    Eckstein, Brian J; Melkonyan, Ferdinand S; Manley, Eric F; Fabiano, Simone; Mouat, Aidan R; Chen, Lin X; Facchetti, Antonio; Marks, Tobin J

    2017-10-18

    We report a new naphthalene bis(4,8-diamino-1,5-dicarboxyl)amide (NBA) building block for polymeric semiconductors. Computational modeling suggests that regio-connectivity at the 2,6- or 3,7-NBA positions strongly modulates polymer backbone torsion and, therefore, intramolecular π-conjugation and aggregation. Optical, electrochemical, and X-ray diffraction characterization of 3,7- and 2,6-dithienyl-substituted NBA molecules and corresponding isomeric NBA-bithiophene copolymers P1 and P2, respectively, reveals the key role of regio-connectivity. Charge transport measurements demonstrate that while the twisted 3,7-NDA-based P1 is a poor semiconductor, the planar 2,6-functionalized NBA polymers (P2-P4) exhibit ambipolarity, with μ e and μ h of up to 0.39 and 0.32 cm 2 /(V·s), respectively.

  14. Exploring the Chemistry of Bicyclic Isoxazolidines for the Multicomponent Synthesis of Glycomimetic Building Blocks.

    Science.gov (United States)

    Hoogenboom, Jorin; Lutz, Martin; Zuilhof, Han; Wennekes, Tom

    2016-10-07

    Starting from a chiral furanone, the nitrone-olefin [3 + 2] cycloaddition can be used to obtain bicyclic isoxazolidines for which we report a set of reactions to selectively modify each functional position. These synthetically versatile bicyclic isoxazolidines allowed us to obtain complex glycomimetic building blocks, like iminosugars, via multicomponent chemistry. For example, a library of 20 pipecolic acid derivatives, a recurring motif in various prescription drugs, could be obtained via a one-pot Staudinger/aza-Wittig/Ugi three-component reaction of a bicyclic isoxazolidine-derived azido-hemiacetal. Notably, specific pipecolic acids in this library were obtained via hydrolysis of an unique tricyclic imidate side product of the Ugi reaction. The azido-hemiacetal was also converted into an aza-C-glycoside iminosugar via an unprecendented one-pot Staudinger/aza-Wittig/Mannich reaction.

  15. Chiral thiazoline and thiazole building blocks for the synthesis of peptide-derived natural products.

    Science.gov (United States)

    Just-Baringo, Xavier; Albericio, Fernando; Alvarez, Mercedes

    2014-01-01

    Thiazoline and thiazole heterocycles are privileged motifs found in numerous peptide-derived natural products of biological interest. During the last decades, the synthesis of optically pure building blocks has been addressed by numerous groups, which have developed a plethora of strategies to that end. Efficient and reliable methodologies that are compatible with the intricate and capricious architectures of natural products are a must to further develop their science. Structure confirmation, structure-activity relationship studies and industrial production are fields of paramount importance that require these robust methodologies in order to successfully bring natural products into the clinic. Today's chemist toolbox is assorted with many powerful methods for chiral thiazoline and thiazole synthesis. Ranging from biomimetic approaches to stereoselective alkylations, one is likely to find a suitable method for their needs.

  16. Eggshell membrane-templated porous gold membranes using nanoparticles as building blocks

    International Nuclear Information System (INIS)

    Ashraf, S.; Khalid, Z. M.; Hussain, I.

    2013-01-01

    Highly porous gold membrane-like structures are formed using eggshell membrane, as such and heat denatured, as a template and gold nanoparticles as building blocks. Gold nanoparticles were produced in-situ on the eggshell membranes without using additional reducing agents. The morphology and loading of gold nanoparticles can easily be controlled by adjusting the pH and thus the redox potential of eggshell membranes. Lower pH favored the formation of irregularly-shaped but dense gold macro/ nanocrystals whereas higher pH(8-9) favored the formation of fairly uniform but less dense gold nanoparticles onto the eggshell membranes. Heat treatment of eggshell membrane-gold nanoparticle composites formed at pH 8-9 led to the formation of highly porous membrane like gold while mimicking the original structure of eggshell membrane. All these materials have been thoroughly characterized using field emission scanning electron microscopy (FESEM), energy dispersive X-ray spectroscopy (EDX), and inductively coupled plasma - atomic emission spectroscopy (ISP-AES). These highly porous membrane-like gold materials may have potential applications in catalysis, biosensors, electrode materials, optically selective coatings, heat dissipation and biofiltration. (author)

  17. Impacts of city-block-scale countermeasures against urban heat-island phenomena upon a building's energy-consumption for air-conditioning

    Energy Technology Data Exchange (ETDEWEB)

    Kikegawa, Yukihiro [Department of Environmental Systems, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506 (Japan); Genchi, Yutaka [Research Center for Life Cycle Assessment, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan); Kondo, Hiroaki [Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 (Japan); Hanaki, Keisuke [Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)

    2006-06-15

    This study quantifies the possible impacts of urban heat-island countermeasures upon buildings' energy use during summer in Tokyo metropolis. Considering the dependency of the buildings air temperature upon the local urban canopy structure, Tokyo urban canopies were classified in the city-block-scale using the sky-view factor (svf). Then, a multi-scale model system describing the interaction between buildings' energy use and urban meteorological conditions was applied to each classified canopy. In terms of urban warming alleviation and cooling energy saving, simulations suggested that the reduction in the air-conditioning anthropogenic heat could be the most effective measure in office buildings' canopies, and that vegetative fraction increase on the side walls of buildings in residential canopies. Both measures indicated daily and spatially averaged decreases in near-ground summer air temperature of 0.2-1.2{sup o}C. The simulations also suggested these temperature decreases could result in the buildings' cooling energy-savings of 4-40%, indicating remarkable savings in residential canopies. These temperature drops and energy savings tended to increase with the decrease of the svf of urban canopies. (author)

  18. Depth geological model building: application to the 3D high resolution 'ANDRA' seismic block

    International Nuclear Information System (INIS)

    Mari, J.L.; Yven, B.

    2012-01-01

    Document available in extended abstract form only. 3D seismic blocks and logging data, mainly acoustic and density logs, are often used for geological model building in time. The geological model must be then converted from time to depth. Geostatistical approach for time-to-depth conversion of seismic horizons is often used in many geo-modelling projects. From a geostatistical point of view, the time-to-depth conversion of seismic horizons is a classical estimation problem involving one or more secondary variables. Bayesian approach [1] provides an excellent estimator which is more general than the traditional kriging with external drift(s) and fits very well to the needs for time-to-depth conversion of seismic horizons. The time-to-depth conversion of the selected seismic horizons is used to compute a time-to-depth conversion model at the time sampling rate (1 ms). The 3D depth conversion model allows the computation of an interval velocity block which is compared with the acoustic impedance block to estimate a density block as QC. Non realistic density values are edited and the interval velocity block as well as the depth conversion model is updated. The proposed procedure has been applied on a 3D data set. The dataset comes from a High Resolution 3D seismic survey recorded in France at the boundary of the Meuse and Haute-Marne departments in the vicinity of the Andra Center (National radioactive waste management Agency). The 3D design is a cross spread. The active spread is composed of 12 receiver lines with 120 stations each. The source lines are perpendicular to the receiver lines. The receiver and source line spacings are respectively 80 m and 120 m. The receiver and source point spacings are 20 m. The source is a Vibroseis source generating a signal in the 14 - 140 Hz frequency bandwidth.. The bin size is 10 x 10 m 2 . The nominal fold is 60. A conventional seismic sequence was applied to the data set. It includes amplitude recovery, deconvolution and wave

  19. Synthesis and Molecular Modeling of Thermally Stable DNA G-Quadruplexes with Anthraquinone Insertions

    DEFF Research Database (Denmark)

    Gouda, Alaa S.; Amine, Mahasen S.; Pedersen, Erik Bjerregaard

    2017-01-01

    Two new phosphoramidite building blocks for DNA synthesis were synthesized from 1,5- and 2,6-dihydroxyanthraquinones through alkylation with 3-bromo-1-propanol followed by DMT-protection. The novel synthesized 1,5- and 2,6-disubstituted anthraquinone monomers H15 and H26 are incorporated into a G...... anthraquinone-modified quadruplexes revealed no change of the antiparallel structure when compared with the wild type under potassium buffer conditions. The significantly increased thermostabilities were interpreted by molecular modeling of anthraquinone-modified G-quadruplexes....

  20. Hierarchical assembly of inorganic nanostructure building blocks to octahedral superstructures-a true template-free self-assembly

    International Nuclear Information System (INIS)

    Kuchibhatla, Satyanarayana V N T; Karakoti, Ajay S; Seal, Sudipta

    2007-01-01

    A room temperature, template-free, wet chemical synthesis of ceria nanoparticles and their long term ageing characteristics are reported. High resolution transmission electron microscopy and UV-visible spectroscopy techniques are used to observe the variation in size, structure and oxidation state, respectively as a function of time. The morphology variation and the hierarchical assembly (octahedral superstructure) of nanostructures are imputed to the inherent structural aspects of cerium oxide. It is hypothesized that the 3-5 nm individual building blocks will undergo an intra-agglomerate re-orientation to attain the low energy configuration. This communication also emphasizes the need for long term ageing studies of nanomaterials in various solvents for multiple functionalities

  1. Synthesis, activity, and structure--activity relationship studies of novel cationic lipids for DNA transfer.

    Science.gov (United States)

    Byk, G; Dubertret, C; Escriou, V; Frederic, M; Jaslin, G; Rangara, R; Pitard, B; Crouzet, J; Wils, P; Schwartz, B; Scherman, D

    1998-01-15

    We have designed and synthesized original cationic lipids for gene delivery. A synthetic method on solid support allowed easy access to unsymmetrically monofunctionalized polyamine building blocks of variable geometries. These polyamine building blocks were introduced into cationic lipids. To optimize the transfection efficiency in the novel series, we have carried out structure-activity relationship studies by introduction of variable-length lipids, of variable-length linkers between lipid and cationic moiety, and of substituted linkers. We introduce the concept of using the linkers within cationic lipids molecules as carriers of side groups harboring various functionalities (side chain entity), as assessed by the introduction of a library composed of cationic entities, additional lipid chains, targeting groups, and finally the molecular probes rhodamine and biotin for cellular traffic studies. The transfection activity of the products was assayed in vitro on Hela carcinoma, on NIH3T3, and on CV1 fibroblasts and in vivo on the Lewis Lung carcinoma model. Products from the series displayed high transfection activities. Results indicated that the introduction of a targeting side chain moiety into the cationic lipid is permitted. A primary physicochemical characterization of the DNA/lipid complexes was demonstrated with this leading compound. Selected products from the series are currently being developed for preclinical studies, and the labeled lipopolyamines can be used to study the intracellular traffic of DNA/cationic lipid complexes.

  2. The building blocks of drinking experience across men and women: A case study with craft and industrial beers.

    Science.gov (United States)

    Gómez-Corona, Carlos; Escalona-Buendía, Héctor B; Chollet, Sylvie; Valentin, Dominique

    2017-09-01

    In today's market, every product seems to be marked by the label of "experience". It is expected that successful products give the consumer "extraordinary experiences". The research in consumption experience is growing, but much work still needs to be done to understand the food and beverage experience. A qualitative study was conducted using contextual focus groups to explore the building blocks of consumers' drinking experience of industrial and craft beers. The results show that drinking experience is shaped by our cognitive, sensory or affective systems, especially during the core consumption experience. Elements such as attitudes, consumption habits, and individual versus social consumption, shopping experience and product benefits are also responsible for shaping the experience, but are more relevant during the pre-consumption or post-consumption experience. Gender differences occur more frequently in the affective experience, as women search more for relaxation while men for excitement and stimulation while drinking beer. When comparing industrial users versus craft, in the latter the cognitive and shopping experiences are more relevant. Overall, the results showed that the drinking experience of beers can be studied as a function of the salient human system used during product interaction, and this systems act as the building blocks of the drinking experience of beer. This information can be applied in consumer research studies to further study the experiential differences across products and consumers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system.

    Science.gov (United States)

    Inkinen, J; Jayaprakash, B; Santo Domingo, J W; Keinänen-Toivola, M M; Ryu, H; Pitkänen, T

    2016-06-01

    Next-generation sequencing of 16S ribosomal RNA genes (rDNA) and ribosomal RNA (rRNA) was used to characterize water and biofilm microbiome collected from a drinking water distribution system of an office building after its first year of operation. The total bacterial community (rDNA) and active bacterial members (rRNA) sequencing databases were generated by Illumina MiSeq PE250 platform. As estimated by Chao1 index, species richness in cold water system was lower (180-260) in biofilms (Sphingomonas spp., Methylobacterium spp., Limnohabitans spp., Rhizobiales order) than in waters (250-580), (also Methylotenera spp.) (P = 0·005, n = 20). Similarly species richness (Chao1) was slightly higher (210-580) in rDNA libraries compared to rRNA libraries (150-400; P = 0·054, n = 24). Active Mycobacterium spp. was found in cross-linked polyethylene (PEX), but not in corresponding copper pipeline biofilm. Nonpathogenic Legionella spp. was found in rDNA libraries but not in rRNA libraries. Microbial communities differed between water and biofilms, between cold and hot water systems, locations in the building and between water rRNA and rDNA libraries, as shown by clear clusters in principal component analysis (PcoA). By using the rRNA method, we found that not all bacterial community members were active (e.g. Legionella spp.), whereas other members showed increased activity in some locations; for example, Pseudomonas spp. in hot water circulations' biofilm and order Rhizobiales and Limnohabitans spp. in stagnated locations' water and biofilm. rRNA-based methods may be better than rDNA-based methods for evaluating human health implications as rRNA methods can be used to describe the active bacterial fraction. This study indicates that copper as a pipeline material might have an adverse impact on the occurrence of Mycobacterium spp. The activity of Legionella spp. maybe questionable when detected solely by using DNA-based methods. © 2016 The Society for Applied

  4. DNA Topology and the Initiation of Virus DNA Packaging.

    Directory of Open Access Journals (Sweden)

    Choon Seok Oh

    Full Text Available During progeny assembly, viruses selectively package virion genomes from a nucleic acid pool that includes host nucleic acids. For large dsDNA viruses, including tailed bacteriophages and herpesviruses, immature viral DNA is recognized and translocated into a preformed icosahedral shell, the prohead. Recognition involves specific interactions between the viral packaging enzyme, terminase, and viral DNA recognition sites. Generally, viral DNA is recognized by terminase's small subunit (TerS. The large terminase subunit (TerL contains translocation ATPase and endonuclease domains. In phage lambda, TerS binds a sequence repeated three times in cosB, the recognition site. TerS binding to cosB positions TerL to cut the concatemeric DNA at the adjacent nicking site, cosN. TerL introduces staggered nicks in cosN, generating twelve bp cohesive ends. Terminase separates the cohesive ends and remains bound to the cosB-containing end, in a nucleoprotein structure called Complex I. Complex I docks on the prohead's portal vertex and translocation ensues. DNA topology plays a role in the TerSλ-cosBλ interaction. Here we show that a site, I2, located between cosN and cosB, is critically important for an early DNA packaging step. I2 contains a complex static bend. I2 mutations block DNA packaging. I2 mutant DNA is cut by terminase at cosN in vitro, but in vivo, no cos cleavage is detected, nor is there evidence for Complex I. Models for what packaging step might be blocked by I2 mutations are presented.

  5. Studies and mechanical properties of a new type of 'hybrid' ceramic block for buildings in structural masonry

    International Nuclear Information System (INIS)

    Camara, Cassio Freire; Gomes, Uilame Umbelino

    2012-01-01

    This paper presents the development of a hybrid ceramic block to the use of resides in the buildings executed with structural masonry. This work seeking new materials and / or products with the purpose of increasing the compressive strength of the ceramic blocks, without neglecting other properties (water absorption and linear shrinkage). After the obtained material (clay powder and crushed), the packaging (in percentages ranging from 0%, 5%, 10% and 15% substitution of crushed clay powder), the identification and measuring (weights and lengths) of the bodies of the test piece, was performed on the approach characterized by fluorescence, mineralogy and SEM of these materials as well as the characterization (SEM) of ceramic blocks after the sintering (temperature of the 900 deg C, 1000 deg C, and 1100 deg C rate with heating tax of 5 o C/minute and soak for 1 hour). Then the samples were subjected to the tests (compressive strength and water absorption) and the respective calculated linear shrinkage. After conducting the analysis of the results of these tests (according to the criteria and parameters required by the ABNT NBR 15270) was found that the 'hybrid' block with the addition of 10% crushed powder obtained the best results, increasing the compressive strength at 16 % without compromising the other parameters required by the Standard. (author)

  6. Undecylenic acid: a valuable and physiologically active renewable building block from castor oil.

    Science.gov (United States)

    Van der Steen, Marijke; Stevens, Christian V

    2009-01-01

    A lot of attention is currently being paid to the transition to a biobased economy. In this movement, most efforts concentrate on the development of bioenergy applications including bioethanol, biodiesel, thermochemical conversion of biomass, and others. However, in the energy sector other nonbiomass alternatives are known, whereas no valuable alternatives are available when thinking about chemical building blocks. Therefore, it is also essential to develop new routes for the synthesis of bio-based chemicals and materials derived thereof. Such intermediates can originate either from plants or from animals. Castor oil is a non-edible oil extracted from the seeds of the castor bean plant Ricinus communis (Euphorbiaceae), which grows in tropical and subtropical areas. Globally, around one million tons of castor seeds are produced every year, the leading producing areas being India, PR China, and Brazil.2 10-Undecenoic acid or undecylenic acid is a fatty acid derived from castor oil that, owing to its bifunctional nature, has many possibilities to develop sustainable applications.

  7. Developing Key Parameters for Green Performance of Partition Wall Blocks

    Directory of Open Access Journals (Sweden)

    Goh Cheng Siew

    2016-01-01

    Full Text Available To promote sustainable construction, it is important to consider green performance of construction materials throughout the life cycle. Selecting inappropriate materials could not only affect the functional performance but also preclude the achievement of green building performance as a whole. Green performance of construction materials has therefore been one of the primary considerations of green building assessment systems. Using partition wall blocks as an example, this paper examines green performance of building materials primarily from the cradle to gate boundaries. Nine key parameters are proposed for the green performance of partition wall blocks. Apart from environmental features, technical performance of partition wall blocks is also taken into consideration since it is the determinant of the lifecycle performance. This paper offers a roadmap to decision makers to make environmentally responsible choices for their materials of internal walls and partitions, and hence provides a potential sustainable solution for green buildings.

  8. Studies of torsional properties of DNA and nucleosomes using angular optical trapping

    Science.gov (United States)

    Sheinin, Maxim Y.

    DNA in vivo is subjected to torsional stress due to the action of molecular motors and other DNA-binding proteins. Several decades of research have uncovered the fascinating diversity of DNA transformations under torsion and the important role they play in the regulation of vital cellular processes such as transcription and replication. Recent studies have also suggested that torsion can influence the structure and stability of nucleosomes---basic building blocks of the eukaryotic genome. However, our understanding of the impact of torsion is far from being complete due to significant experimental challenges. In this work we have used a powerful single-molecule experimental technique, angular optical trapping, to address several long-standing issues in the field of DNA and nucleosome mechanics. First, we utilized the high resolution and direct torque measuring capability of the angular optical trapping to precisely measure DNA twist-stretch coupling. Second, we characterized DNA melting under tension and torsion. We found that torsionally underwound DNA forms a left-handed structure, significantly more flexible compared to the regular B-DNA. Finally, we performed the first comprehensive investigation of the single nucleosome behavior under torque and force. Importantly, we discovered that positive torque causes significant dimer loss, which can have implications for transcription through chromatin.

  9. An investigation on damaged buildings in Ranau due the 2015 Sabah earthquake

    Science.gov (United States)

    Lim, Yang Soh; Tan, Jun Pin; Chiew, Lerk Qing; Chang, Wai Hoe; Lau, Tze Liang

    2017-10-01

    A magnitude 5.9 earthquake struck near Ranau district in Sabah, Malaysia on June 5, 2015. The epicenter was located 14 km from Ranau. Various buildings were damaged by the earthquake. This paper discusses the extent of the destruction to two severely damaged structures in Ranau. An assessment of damaged buildings in Ranau Hospital using microtremor data was conducted after the earthquake event. The building consists of two identical blocks with similar soft-story structural forms. Two microtremor observations were carried out before and after the repair work. The predominant frequencies of the damaged buildings were determined by using the Nakamura's H/V method. Based on the assumption that both identical blocks of building in Ranau Hospital have similar predominant frequencies due to the same structural design and construction quality, results show that B block of Ranau Hospital suffered more damage compared with another block of the building. The predominant frequency of B block is 10% lower than that of A Block. Results obtained are consistent with the observed building performance during the site reconnaissance. The predominant frequency of both buildings measured after the repair work shows 11% to 21% increment, which implies that the lateral stiffness of both buildings has been improved.

  10. An easy access to 2-Amino-5,6-dihydro-3H-pyrimidin-4-one building blocks: the reaction under conventional and microwave conditions.

    Science.gov (United States)

    Ostras, Konstantin S; Gorobets, Nikolay Yu; Desenko, Sergey M; Musatov, Vladimir I

    2006-08-01

    A new one-stage fast multicomponent synthesis of title compounds leads to products in 21-55% isolated yields under both conventional and microwave conditions. The primary amino group in the building blocks can be easily acylated by various usual electophilic agents that can be utilized in the synthesis of diverse heterocylic compounds libraries.

  11. Nucleic acids and smart materials: advanced building blocks for logic systems.

    Science.gov (United States)

    Pu, Fang; Ren, Jinsong; Qu, Xiaogang

    2014-09-03

    Logic gates can convert input signals into a defined output signal, which is the fundamental basis of computing. Inspired by molecular switching from one state to another under an external stimulus, molecular logic gates are explored extensively and recognized as an alternative to traditional silicon-based computing. Among various building blocks of molecular logic gates, nucleic acid attracts special attention owing to its specific recognition abilities and structural features. Functional materials with unique physical and chemical properties offer significant advantages and are used in many fields. The integration of nucleic acids and functional materials is expected to bring about several new phenomena. In this Progress Report, recent progress in the construction of logic gates by combining the properties of a range of smart materials with nucleic acids is introduced. According to the structural characteristics and composition, functional materials are categorized into three classes: polymers, noble-metal nanomaterials, and inorganic nanomaterials. Furthermore, the unsolved problems and future challenges in the construction of logic gates are discussed. It is hoped that broader interests in introducing new smart materials into the field are inspired and tangible applications for these constructs are found. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Ultraflat Au nanoplates as a new building block for molecular electronics.

    Science.gov (United States)

    Jeong, Wooseok; Lee, Miyeon; Lee, Hyunsoo; Lee, Hyoban; Kim, Bongsoo; Park, Jeong Young

    2016-05-27

    We demonstrate the charge transport properties of a self-assembled organic monolayer on Au nanoplates with conductive probe atomic force microscopy (CP-AFM). Atomically flat Au nanoplates, a few hundred micrometers on each side, that have only (111) surfaces, were synthesized using the chemical vapor transport method; these nanoplates were employed as the substrates for hexadecanethiol (HDT) self-assembled monolayers (SAMs). Atomic-scale high-resolution images show (√3 x √3) R30° molecular periodicity, indicating a well-ordered structure of the HDT on the Au nanoplates. We observed reduced friction and adhesion forces on the HDT SAMs on Au nanoplates, compared with Si substrates, which is consistent with the lubricating nature of HDT SAMs. The electrical properties, such as I-V characteristics and current as a function of load, were measured using CP-AFM. We obtained a tunneling decay constant (β) of 0.57 Å(-1), including through-bond (βtb = 0.99 Å(-1)) and through-space (βts = 1.36 Å(-1)) decay constants for the two-pathway model. This indicates that the charge transport properties of HDT SAMs on Au nanoplates are consistent with those on a Au (111) film, suggesting that SAMs on nanoplates can provide a new building block for molecular electronics.

  13. Filamentous phages as building blocks for reconfigurable and hierarchical self-assembly

    Science.gov (United States)

    Gibaud, Thomas

    2017-12-01

    Filamentous bacteriophages such as fd-like viruses are monodisperse rod-like colloids that have well defined properties of diameter, length, rigidity, charge and chirality. Engineering these viruses leads to a library of colloidal rods, which can be used as building blocks for reconfigurable and hierarchical self-assembly. Their condensation in an aqueous solution with additive polymers, which act as depletants to induce attraction between the rods, leads to a myriad of fluid-like micronic structures ranging from isotropic/nematic droplets, colloid membranes, achiral membrane seeds, twisted ribbons, π-wall, pores, colloidal skyrmions, Möbius anchors, scallop membranes to membrane rafts. These structures, and the way that they shape-shift, not only shed light on the role of entropy, chiral frustration and topology in soft matter, but also mimic many structures encountered in different fields of science. On the one hand, filamentous phages being an experimental realization of colloidal hard rods, their condensation mediated by depletion interactions constitutes a blueprint for the self-assembly of rod-like particles and provides a fundamental foundation for bio- or material-oriented applications. On the other hand, the chiral properties of the viruses restrict the generalities of some results but vastly broaden the self-assembly possibilities.

  14. Impact-Contact Analysis of Prismatic Graphite Blocks Using Abaqus

    International Nuclear Information System (INIS)

    Kang, Ji Ho; Kim, Gyeong Ho; Choi, Woo Seok

    2010-12-01

    Graphite blocks are the important core components of the high temperature gas-cooled reactor. As these blocks are simply stacked in array, collisions among neighboring components may occur during earthquakes or accidents. The final objective of the research project is to develop a reliable seismic model of the stacked graphite blocks from which their behavior can be predicted and, thus, they are designed to have sufficient strength to maintain their structural integrity during the anticipated occurrences. The work summarized in this report is a first step toward the big picture and is dedicated to build a realistic impact-contact dynamics model of the graphite block using a commercial FEM package, Abaqus. The developed model will be further used to assist building a reliable lumped dynamics model of these stacked graphite components

  15. Quantum Simulation with Circuit-QED Lattices: from Elementary Building Blocks to Many-Body Theory

    Science.gov (United States)

    Zhu, Guanyu

    Recent experimental and theoretical progress in superconducting circuits and circuit QED (quantum electrodynamics) has helped to develop high-precision techniques to control, manipulate, and detect individual mesoscopic quantum systems. A promising direction is hence to scale up from individual building blocks to form larger-scale quantum many-body systems. Although realizing a scalable fault-tolerant quantum computer still faces major barriers of decoherence and quantum error correction, it is feasible to realize scalable quantum simulators with state-of-the-art technology. From the technological point of view, this could serve as an intermediate stage towards the final goal of a large-scale quantum computer, and could help accumulating experience with the control of quantum systems with a large number of degrees of freedom. From the physical point of view, this opens up a new regime where condensed matter systems can be simulated and studied, here in the context of strongly correlated photons and two-level systems. In this thesis, we mainly focus on two aspects of circuit-QED based quantum simulation. First, we discuss the elementary building blocks of the quantum simulator, in particular a fluxonium circuit coupled to a superconducting resonator. We show the interesting properties of the fluxonium circuit as a qubit, including the unusual structure of its charge matrix elements. We also employ perturbation theory to derive the effective Hamiltonian of the coupled system in the dispersive regime, where qubit and the photon frequencies are detuned. The observables predicted with our theory, including dispersive shifts and Kerr nonlinearity, are compared with data from experiments, such as homodyne transmission and two-tone spectroscopy. These studies also relate to the problem of detection in a circuit-QED quantum simulator. Second, we study many-body physics of circuit-QED lattices, serving as quantum simulators. In particular, we focus on two different

  16. Non-perturbative topological strings and conformal blocks

    NARCIS (Netherlands)

    Cheng, M.C.N.; Dijkgraaf, R.; Vafa, C.

    2011-01-01

    We give a non-perturbative completion of a class of closed topological string theories in terms of building blocks of dual open strings. In the specific case where the open string is given by a matrix model these blocks correspond to a choice of integration contour. We then apply this definition to

  17. The Role of Repulsion in Colloidal Crystal Engineering with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Soyoung E. [Department; Li, Tao [X-ray; Senesi, Andrew J. [X-ray; Mirkin, Chad A. [Department; Lee, Byeongdu [X-ray

    2017-11-07

    Hybridization interactions between DNA-functionalized nanoparticles (DNA-NPs) can be used to program the crystallization behavior of superlattices, yielding access to complex three-dimensional structures with more than 30 different lattice symmetries. The first superlattice structures using DNA-NPs as building blocks were identified almost two decades ago, yet the role of repulsive interactions in guiding structure formation is still largely unexplored. Here, a com-prehensive approach is taken to study the role of repulsion in the assembly behavior of DNA-NPs, enabling the calculation of interparticle interaction potentials based on experimental results. In this work, we used two different means to assemble DNA-NPs—Watson-Crick base pairing interactions and depletion interactions—and systematically varied the salt concen-tration to study the effective interactions in DNA-NP superlattices. A comparison between the two systems allows us to decouple the repulsive forces from the attractive hybridization interactions that are sensitive to the ionic environment. We find that the gap distance between adjacent DNA-NPs follows a simple power law dependence on solution ionic strength regardless of the type of attractive forces present. This result suggests that the observed trend is driven by repulsive inter-actions. To better understand such behavior, we propose a mean-field model that provides a mathematical description for the observed trend. This model shows that the trend is due to the variation in the effective cross-sectional diameter of DNA duplex and the thickness of DNA shell.

  18. Challenges in Simulating Light-Induced Processes in DNA

    Directory of Open Access Journals (Sweden)

    Philipp Marquetand

    2016-12-01

    Full Text Available In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i stationary quantum chemical computations; (ii the explicit description of the initial excitation of DNA with light; (iii modeling the nonadiabatic excited state dynamics; (iv simulation of the detected experimental observable; and (v the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.

  19. Molecular modeling of the elastomeric properties of repeating units and building blocks of resilin, a disordered elastic protein.

    Science.gov (United States)

    Khandaker, Md Shahriar K; Dudek, Daniel M; Beers, Eric P; Dillard, David A; Bevan, David R

    2016-08-01

    The mechanisms responsible for the properties of disordered elastomeric proteins are not well known. To better understand the relationship between elastomeric behavior and amino acid sequence, we investigated resilin, a disordered rubber-like protein, found in specialized regions of the cuticle of insects. Resilin of Drosophila melanogaster contains Gly-rich repetitive motifs comprised of the amino acids, PSSSYGAPGGGNGGR, which confer elastic properties to resilin. The repetitive motifs of insect resilin can be divided into smaller partially conserved building blocks: PSS, SYGAP, GGGN and GGR. Using molecular dynamics (MD) simulations, we studied the relative roles of SYGAP, and its less common variants SYSAP and TYGAP, on the elastomeric properties of resilin. Results showed that SYGAP adopts a bent structure that is one-half to one-third the end-to-end length of the other motifs having an equal number of amino acids but containing SYSAP or TYGAP substituted for SYGAP. The bent structure of SYGAP forms due to conformational freedom of glycine, and hydrogen bonding within the motif apparently plays a role in maintaining this conformation. These structural features of SYGAP result in higher extensibility compared to other motifs, which may contribute to elastic properties at the macroscopic level. Overall, the results are consistent with a role for the SYGAP building block in the elastomeric properties of these disordered proteins. What we learned from simulating the repetitive motifs of resilin may be applicable to the biology and mechanics of other elastomeric biomaterials, and may provide us the deeper understanding of their unique properties. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. A Cationic Smart Copolymer for DNA Binding

    Directory of Open Access Journals (Sweden)

    Tânia Ribeiro

    2017-11-01

    Full Text Available A new block copolymer with a temperature-responsive block and a cationic block was prepared by reversible addition-fragmentation chain transfer (RAFT polymerization, with good control of its size and composition. The first block is composed by di(ethylene glycol methyl ether methacrylate (DEGMA and oligo(ethylene glycol methyl ether methacrylate (OEGMA, with the ratio DEGMA/OEGMA being used to choose the volume phase transition temperature of the polymer in water, tunable from ca. 25 to above 90 °C. The second block, of trimethyl-2-methacroyloxyethylammonium chloride (TMEC, is positively charged at physiological pH values and is used for DNA binding. The coacervate complexes between the block copolymer and a model single strand DNA are characterized by fluorescence correlation spectroscopy and fluorescence spectroscopy. The new materials offer good prospects for biomedical application, for example in controlled gene delivery.

  1. A tribo-mechanical analysis of PVA-based building-blocks for implementation in a 2-layered skin model.

    Science.gov (United States)

    Morales Hurtado, M; de Vries, E G; Zeng, X; van der Heide, E

    2016-09-01

    Poly(vinyl) alcohol hydrogel (PVA) is a well-known polymer widely used in the medical field due to its biocompatibility properties and easy manufacturing. In this work, the tribo-mechanical properties of PVA-based blocks are studied to evaluate their suitability as a part of a structure simulating the length scale dependence of human skin. Thus, blocks of pure PVA and PVA mixed with Cellulose (PVA-Cel) were synthesised via freezing/thawing cycles and their mechanical properties were determined by Dynamic Mechanical Analysis (DMA) and creep tests. The dynamic tests addressed to elastic moduli between 38 and 50kPa for the PVA and PVA-Cel, respectively. The fitting of the creep compliance tests in the SLS model confirmed the viscoelastic behaviour of the samples with retardation times of 23 and 16 seconds for the PVA and PVA-Cel, respectively. Micro indentation tests were also achieved and the results indicated elastic moduli in the same range of the dynamic tests. Specifically, values between 45-55 and 56-81kPa were obtained for the PVA and PVA-Cel samples, respectively. The tribological results indicated values of 0.55 at low forces for the PVA decreasing to 0.13 at higher forces. The PVA-Cel blocks showed lower friction even at low forces with values between 0.2 and 0.07. The implementation of these building blocks in the design of a 2-layered skin model (2LSM) is also presented in this work. The 2LSM was stamped with four different textures and their surface properties were evaluated. The hydration of the 2LSM was also evaluated with a corneometer and the results indicated a gradient of hydration comparable to the human skin. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Low Molecular Weight pDMAEMA-block-pHEMA Block-Copolymers Synthesized via RAFT-Polymerization: Potential Non-Viral Gene Delivery Agents?

    Directory of Open Access Journals (Sweden)

    Thomas Kissel

    2011-03-01

    Full Text Available The aim of this study was to investigate non-viral pDNA carriers based on diblock-copolymers consisting of poly(2-(dimethyl aminoethyl methacrylate (pDMAEMA and poly(2-hydroxyethyl methacrylate (pHEMA. Specifically the block-lengths and molecular weights were varied to determine the minimal requirements for transfection. Such vectors should allow better transfection at acceptable toxicity levels and the entire diblock-copolymer should be suitable for renal clearance. For this purpose, a library of linear poly(2-(dimethyl aminoethyl methacrylate-block-poly(2-hydroxyl methacrylate (pDMAEMA-block-pHEMA copolymers was synthesized via RAFT (reversible addition-fragmentation chain transfer polymerization in a molecular weight (Mw range of 17–35.7 kDa and analyzed using 1H and 13C NMR (nuclear magnetic resonance, ATR (attenuated total reflectance, GPC (gel permeation chromatography and DSC (differential scanning calorimetry. Copolymers possessing short pDMAEMA-polycation chains were 1.4–9.7 times less toxic in vitro than polyethylenimine (PEI 25 kDa, and complexed DNA into polyplexes of 100–170 nm, favorable for cellular uptake. The DNA-binding affinity and polyplex stability against competing polyanions was comparable with PEI 25 kDa. The zeta-potential of polyplexes of pDMAEMA-grafted copolymers remained positive (+15–30 mV. In comparison with earlier reported low molecular weight homo pDMAEMA vectors, these diblock-copolymers showed enhanced transfection efficacy under in vitro conditions due to their lower cytotoxicity, efficient cellular uptake and DNA packaging. The homo pDMAEMA115 (18.3 kDa self-assembled with DNA into small positively charged polyplexes, but was not able to transfect cells. The grafting of 6 and 57 repeating units of pHEMA (0.8 and 7.4 kDa to pDMAEMA115 increased the transfection efficacy significantly, implying a crucial impact of pHEMA on vector-cell interactions. The intracellular trafficking, in vivo transfection

  3. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  4. Aerial Imagery and LIDAR Data Fusion for Unambiguous Extraction of Adjacent Level-Buildings Footprints

    Science.gov (United States)

    Mola Ebrahimi, S.; Arefi, H.; Rasti Veis, H.

    2017-09-01

    Our paper aims to present a new approach to identify and extract building footprints using aerial images and LiDAR data. Employing an edge detector algorithm, our method first extracts the outer boundary of buildings, and then by taking advantage of Hough transform and extracting the boundary of connected buildings in a building block, it extracts building footprints located in each block. The proposed method first recognizes the predominant leading orientation of a building block using Hough transform, and then rotates the block according to the inverted complement of the dominant line's angle. Therefore the block poses horizontally. Afterwards, by use of another Hough transform, vertical lines, which might be the building boundaries of interest, are extracted and the final building footprints within a block are obtained. The proposed algorithm is implemented and tested on the urban area of Zeebruges, Belgium(IEEE Contest,2015). The areas of extracted footprints are compared to the corresponding areas in the reference data and mean error is equal to 7.43 m2. Besides, qualitative and quantitative evaluations suggest that the proposed algorithm leads to acceptable results in automated precise extraction of building footprints.

  5. Nek1 silencing slows down DNA repair and blocks DNA damage-induced cell cycle arrest.

    Science.gov (United States)

    Pelegrini, Alessandra Luíza; Moura, Dinara Jaqueline; Brenner, Bethânia Luise; Ledur, Pitia Flores; Maques, Gabriela Porto; Henriques, João Antônio Pegas; Saffi, Jenifer; Lenz, Guido

    2010-09-01

    Never in mitosis A (NIMA)-related kinases (Nek) are evolutionarily conserved proteins structurally related to the Aspergillus nidulans mitotic regulator NIMA. Nek1 is one of the 11 isoforms of the Neks identified in mammals. Different lines of evidence suggest the participation of Nek1 in response to DNA damage, which is also supported by the interaction of this kinase with proteins involved in DNA repair pathways and cell cycle regulation. In this report, we show that cells with Nek1 knockdown (KD) through stable RNA interference present a delay in DNA repair when treated with methyl-methanesulfonate (MMS), hydrogen peroxide (H(2)O(2)) and cisplatin (CPT). In particular, interstrand cross links induced by CPT take much longer to be resolved in Nek1 KD cells when compared to wild-type (WT) cells. In KD cells, phosphorylation of Chk1 in response to CPT was strongly reduced. While WT cells accumulate in G(2)/M after DNA damage with MMS and H(2)O(2), Nek1 KD cells do not arrest, suggesting that G(2)/M arrest induced by the DNA damage requires Nek1. Surprisingly, CPT-treated Nek1 KD cells arrest with a 4N DNA content similar to WT cells. This deregulation in cell cycle control in Nek1 KD cells leads to an increased sensitivity to genotoxic agents when compared to WT cells. These results suggest that Nek1 is involved in the beginning of the cellular response to genotoxic stress and plays an important role in preventing cell death induced by DNA damage.

  6. Dynamics of DNA conformations and DNA-protein interaction

    DEFF Research Database (Denmark)

    Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen

    2005-01-01

    Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...... denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed...... in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent...

  7. Gaze Interactive Building Instructions

    DEFF Research Database (Denmark)

    Hansen, John Paulin; Ahmed, Zaheer; Mardanbeigi, Diako

    We combine eye tracking technology and mobile tablets to support hands-free interaction with digital building instructions. As a proof-of-concept we have developed a small interactive 3D environment where one can interact with digital blocks by gaze, keystroke and head gestures. Blocks may be moved...

  8. Isotopic evolution of the protoplanetary disk and the building blocks of Earth and the Moon

    DEFF Research Database (Denmark)

    Schiller, Martin; Bizzarro, Martin; Fernandes, Vera Assis

    2018-01-01

    Nucleosynthetic isotope variability among Solar System objects is often used to probe the genetic relationship between meteorite groups and the rocky planets (Mercury, Venus, Earth and Mars), which, in turn, may provide insights into the building blocks of the Earth-Moon system. Using this approach......, it has been inferred that no primitive meteorite matches the terrestrial composition and the protoplanetary disk material from which Earth and the Moon accreted is therefore largely unconstrained. This conclusion, however, is based on the assumption that the observed nucleosynthetic variability of inner...... into the thermally processed inner protoplanetary disk associated with the accretion of mass to the proto-Sun. The identical calcium isotope composition of Earth and the Moon reported here is a prediction of our model if the Moon-forming impact involved protoplanets or precursors that completed their accretion near...

  9. The building blocks of the full body ownership illusion

    Directory of Open Access Journals (Sweden)

    Antonella eMaselli

    2013-03-01

    Full Text Available Previous work has reported that it is not difficult to give people the illusion of ownership over an artificial body, providing a powerful tool for the investigation of the neural and cognitive mechanisms underlying body perception and self consciousness. We present an experimental study that uses immersive virtual reality focused on identifying the perceptual building blocks of this illusion. We systematically manipulated visuotactile and visual sensorimotor contingencies, visual perspective, and the appearance of the virtual body in order to assess their relative role and mutual interaction. Consistent results from subjective reports and physiological measures showed that a first person perspective over a fake humanoid body is essential for eliciting a body ownership illusion. We found that the level of realism of the virtual body, in particular the realism of skin tone, plays a critical role: when high enough, the illusion can be triggered by the sole effect of the spatial overlap between the real and virtual bodies, providing congruent visuoproprioceptive information, with no need for the additional contribution of congruent visuotactile and/or visual sensorimotor cues. Additionally, we found that the processing of incongruent perceptual cues can be modulated by the level of the illusion: when the illusion is strong, incongruent cues are not experienced as incorrect. Participants exposed to asynchronous visuotactile stimulation can experience the ownership illusion and perceive touch as originating from an object seen to contact the virtual body. Analogously, when the level of realism of the virtual body and/or the spatial overlap of the two bodies is not high enough, the contribution of congruent multisensory and/or sensorimotor cues is required for evoking the illusion. On the basis of these results and inspired by findings from neurophysiological recordings in the monkey, we propose a model that accounts for many of the results reported

  10. The building blocks of the full body ownership illusion

    Science.gov (United States)

    Maselli, Antonella; Slater, Mel

    2013-01-01

    Previous work has reported that it is not difficult to give people the illusion of ownership over an artificial body, providing a powerful tool for the investigation of the neural and cognitive mechanisms underlying body perception and self consciousness. We present an experimental study that uses immersive virtual reality (IVR) focused on identifying the perceptual building blocks of this illusion. We systematically manipulated visuotactile and visual sensorimotor contingencies, visual perspective, and the appearance of the virtual body in order to assess their relative role and mutual interaction. Consistent results from subjective reports and physiological measures showed that a first person perspective over a fake humanoid body is essential for eliciting a body ownership illusion. We found that the illusion of ownership can be generated when the virtual body has a realistic skin tone and spatially substitutes the real body seen from a first person perspective. In this case there is no need for an additional contribution of congruent visuotactile or sensorimotor cues. Additionally, we found that the processing of incongruent perceptual cues can be modulated by the level of the illusion: when the illusion is strong, incongruent cues are not experienced as incorrect. Participants exposed to asynchronous visuotactile stimulation can experience the ownership illusion and perceive touch as originating from an object seen to contact the virtual body. Analogously, when the level of realism of the virtual body is not high enough and/or when there is no spatial overlap between the two bodies, then the contribution of congruent multisensory and/or sensorimotor cues is required for evoking the illusion. On the basis of these results and inspired by findings from neurophysiological recordings in the monkey, we propose a model that accounts for many of the results reported in the literature. PMID:23519597

  11. Hydrodynamic delivery of plasmid DNA encoding human FcγR-Ig dimers blocks immune-complex mediated inflammation in mice.

    Science.gov (United States)

    Shashidharamurthy, R; Machiah, D; Bozeman, E N; Srivatsan, S; Patel, J; Cho, A; Jacob, J; Selvaraj, P

    2012-09-01

    Therapeutic use and function of recombinant molecules can be studied by the expression of foreign genes in mice. In this study, we have expressed human Fcγ receptor-Ig fusion molecules (FcγR-Igs) in mice by administering FcγR-Ig plasmid DNAs hydrodynamically and compared their effectiveness with purified molecules in blocking immune-complex (IC)-mediated inflammation in mice. The concentration of hydrodynamically expressed FcγR-Igs (CD16A(F)-Ig, CD32A(R)-Ig and CD32A(H)-Ig) reached a maximum of 130 μg ml(-1) of blood within 24 h after plasmid DNA administration. The in vivo half-life of FcγR-Igs was found to be 9-16 days and western blot analysis showed that the FcγR-Igs were expressed as a homodimer. The hydrodynamically expressed FcγR-Igs blocked 50-80% of IC-mediated inflammation up to 3 days in a reverse passive Arthus reaction model. Comparative analysis with purified molecules showed that hydrodynamically expressed FcγR-Igs are more efficient than purified molecules in blocking IC-mediated inflammation and had a higher half-life. In summary, these results suggest that the administration of a plasmid vector with the FcγR-Ig gene can be used to study the consequences of blocking IC binding to FcγRs during the development of inflammatory diseases. This approach may have potential therapeutic value in treating IC-mediated inflammatory autoimmune diseases such as lupus, arthritis and autoimmune vasculitis.

  12. Le glycérol « building blocks » majeur de la bioraffinerie oléagineuse

    Directory of Open Access Journals (Sweden)

    Vandeputte Jacky

    2012-01-01

    Full Text Available Biodiesel production increases, and each ton of biodiésel produced leads to about 100 kg of glycerol. Because of increasing amount of generated glycerol, but also according to environmental concerns and scarcity of oil, glycerol is considered as one of the top 10 building block chemicals derived from biomass that can subsequently be converted into a number of high value biobased chemicals. Besides the well established sell of purified glycerine to manufacturers of cosmetics and pharmaceuticals, a variety of novel conversion techniques are introduced. This paper provides an overview of the latest biobased compounds produced from glycerol’s conversion, and of the lower environmental impact of these new ways of production.

  13. Replication of UV-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli: evidence for bypass of pyrimidine photodimers

    International Nuclear Information System (INIS)

    Livneh, Z.

    1986-01-01

    Replication of UV-irradiated circular single-stranded phage M13 DNA by Escherichia coli RNA polymerase (EC 2.7.7.6) and DNA polymerase III holoenzyme (EC 2.7.7.7) in the presence of single-stranded DNA binding protein yielded full-length as well as partially replicated products. A similar result was obtained with phage G4 DNA primed with E. coli DNA primase, and phage phi X174 DNA primed with a synthetic oligonucleotide. The fraction of full-length DNA was several orders of magnitude higher than predicted if pyrimidine photodimers were to constitute absolute blocks to DNA replication. Recent models have suggested that pyrimidine photodimers are absolute blocks to DNA replication and that SOS-induced proteins are required to allow their bypass. Our results demonstrate that, under in vitro replication conditions, E. coli DNA polymerase III holoenzyme can insert nucleotides opposite pyrimidine dimers to a significant extent, even in the absence of SOS-induced proteins

  14. Exploring Integration in Action: Competencies as Building Blocks of Expertise.

    Science.gov (United States)

    Mylopoulos, Maria; Borschel, Debaroti Tina; O'Brien, Tara; Martimianakis, Sofia; Woods, Nicole N

    2017-12-01

    Competency frameworks such as the CanMEDS roles and the ACGME core competencies may lead to the implicit assumption that physicians can learn and practice individual competencies in isolation. In contrast, models of adaptive expertise suggest that the integration of competencies reflects the capabilities of an expert physician. Thus, educational programming aimed at teaching discrete roles or competencies might overlook expert physician capabilities that are central to patient care. To develop expertise, learning opportunities must reflect expert capabilities. To better understand the relationship between competency-based medical education and expert development, the authors sought to explore how integrated competencies are enacted during patient care by postgraduate medical trainees. Using a cognitive ethnographic approach, in 2014-2015 the authors conducted observations and-to refine and elaborate these observations-ad hoc informal interviews with 13 postgraduate trainee participants. Data collection resulted in 92 hours of observation, 26 patient case portraits, and a total of 220 pages of field notes for analysis. Through analysis, the authors identified and examined moments when postgraduate trainees appeared to be simultaneously enacting multiple competencies. The authors identified two key expert capabilities in moments of integrated competence: finding complexity and being patient-centered. They described two mechanisms for these forms of integration: valuing the patient's narrative of their illness, and integrated understanding. Understanding integrated competencies as the building blocks of expert capabilities, along with recognizing the importance of mechanisms that support integration, offers an opportunity to use existing competency-based frameworks to understand and teach adaptive expertise.

  15. Steam-cured stabilised soil blocks for masonry construction

    Energy Technology Data Exchange (ETDEWEB)

    Venkatarama Reddy, B.V. [Indian Inst. of Science, Bangalore (India). Dept. of Civil Engineering; Lokras, S.S. [Indian Inst. of Science, Bangalore (India). ASTRA

    1998-12-01

    Energy-efficient, economical and durable building materials are essential for sustainable construction practices. The paper deals with production and properties of energy-efficient steam-cured stabilised soil blocks used for masonry construction. Problems of mixing expansive soil and lime, and production of blocks using soil-lime mixtures have been discussed briefly. Details of steam curing of stabilised soil blocks and properties of such blocks are given. A comparison of energy content of steam-cured soil blocks and burnt bricks is presented. It has been shown that energy-efficient steam cured soil blocks (consuming 35% less thermal energy compared to burnt clay bricks) having high compressive strength can be easily produced in a decentralised manner. (orig.)

  16. Bark polyflavonoids from Pinus radiata as functional building-blocks for polylactic acid (PLA-based green composites

    Directory of Open Access Journals (Sweden)

    D. E. Garcia

    2016-10-01

    Full Text Available Polylactic acid (PLA was melt-blended with Pinus radiata unmodified and modified (hydroxypropyled bark polyflavonoids in order to use such polyphenolic building-blocks as functional additives for envisaged applications. Rheological, morphological, molecular, thermal, and flexural properties were studied. Polyflavonoids improved blend processability in terms of short-time mixing. Furthermore, hydroxypropylated polyflavonoids improve miscibility in binary and ternary blends. Blend-composition affects crystallization-, melting-, and glass transition-temperature of PLA, as well as thermal resistance, and flexural properties of the blends. Polyflavonoids induced PLA-crystallization, and polymer-chain decomposition. Modified and unmodified bark polyflavonoids from radiata pine can be used successfully in PLA-based green composites beyond the food-packaging applications. The high compatibility between PLA and hydroxypropyled polyflavonoids highlights the potential of such phenolic derivatives for PLA-based material design.

  17. Recovery of DNA synthesis after ultraviolet irradiation of xeroderma pigmentosum cells depends on excision repair and is blocked by caffeine

    International Nuclear Information System (INIS)

    Park, S.D.; Cleaver, J.E.

    1979-01-01

    Normal human and xeroderma pigmentosum (XP, excision-defective group A) cells (both SV40-transformed) pulse-labeled with [ 3 H] thymidine at various times after irradiation with ultraviolet light showed a decline and recovery of both the molecular weights of newly synthesized DNA and the rated of synthesis per cell. At the same ultraviolet dose, both molecular weights and rates of synthesis were inhibited more in XP than in normal cells. This indicates that excision repair plays a role in minimizing the inhibition of chain growth, possibly by excision of dimers ahead of the growing point. The ability to synthesize normal-sized DNA recovered more rapidly than rates of synthesis in normal cells, but both parameters recovered in phase in XP cells. During recovery in normal cells there are therefore fewer actively replicating clusters of replicons because the single-strand breaks involved in the excision of dimers inhibit replicon initiation. XP cells have few excision repair events and therefore fewer breaks to interfere with initiation, but chain growth is blocked by unexcised dimers. In both cell types recovery of the ability to synthesize normal-sized DNA was prevented by growing cells in caffeine after irradiation, possibly because of competition between the DNA binding properties of caffeine and replication proteins. These observations imply that excision repair and semiconservative replication interact strongly in irradiated cells to produce a complex spectrum of changes in DNA replication which may be confused with parts of alternative systems such as post-replication repair. (author)

  18. DNA computing models

    CERN Document Server

    Ignatova, Zoya; Zimmermann, Karl-Heinz

    2008-01-01

    In this excellent text, the reader is given a comprehensive introduction to the field of DNA computing. The book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines.

  19. Dynamics of termination during in vitro replication of ultraviolet-irradiated DNA with DNA polymerase III holoenzyme of Escherichia coli

    International Nuclear Information System (INIS)

    Shwartz, H.; Livneh, Z.

    1987-01-01

    During in vitro replication of UV-irradiated single-stranded DNA with Escherichia coli DNA polymerase III holoenzyme termination frequently occurs at pyrimidine photodimers. The termination stage is dynamic and characterized by at least three different events: repeated dissociation-reinitiation cycles of the polymerase at the blocked termini; extensive hydrolysis of ATP to ADP and inorganic phosphate; turnover of dNTPs into dNMP. The reinitiation events are nonproductive and are not followed by further elongation. The turnover of dNTPs into dNMPs is likely to result from repeated cycles of insertion of dNMP residues opposite the blocking lesions followed by their excision by the 3'----5' exonucleolytic activity of the polymerase. Although all dNTPs are turned over, there is a preference for dATP, indicating that DNA polymerase III holoenzyme has a preference for inserting a dAMP residue opposite blocking pyrimidine photodimers. We suggest that the inability of the polymerase to bypass photodimers during termination is due to the formation of defective initiation-like complexes with reduced stability at the blocked termini

  20. Lifting of a sector block for YE-2 at Kawasaki.

    CERN Multimedia

    R. Loveless/U. of Wisconsin

    2000-01-01

    YE-2 is build from machined sector blocks. Trial assembly is carried out horizontally. This picture represents the lifting of a machined sector block destined to the trial assembly of a half disk YE-2 at Kawasaki (KHI) Kobe, Japan.

  1. Lightweight concrete blocks with EVA recycled aggregate: a contribution to the thermal efficiency of building external walls

    Directory of Open Access Journals (Sweden)

    De Melo, A. B.

    2013-12-01

    Full Text Available The regions with lots of shoe production suffer environmental impacts from waste generation during manufacturing of insoles and outsoles. Research conducted in Brazil has demonstrated the technical feasibility to recycle these wastes, especially Ethylene Vinyl Acetate (EVA, as lightweight aggregate, in the production of non-structural cement blocks. This article presents an evaluation of thermal performance with measurements of temperature variation in mini walls (1 m2 built with different materials, including various kinds of EVA block and ceramic bricks. Tests have shown efficient thermal performance for masonry blocks with EVA. These results and supplementary estimates contribute to add value to the EVA block, considering that there are good expectations that the component, with the new geometry proposed, can contribute to the energy efficiency of buildings, highlighting its suitability to most Brazilian bioclimatic regions.Las regiones con una gran producción de calzado sufren impactos ambientales derivados de la generación de residuos durante la producción de plantillas y suelas. Investigaciones realizadas en Brasil han demostrado la viabilidad técnica para el reciclaje de estos residuos, especialmente el Etileno Vinil Acetato (EVA, como agregado ligero en la fabricación de bloques de hormigón no estructurales. Este trabajo presenta una evaluación del rendimiento térmico, con mediciones de la variación de la temperatura en pequeñas paredes (1 m2 construidas con diversos materiales, incluyendo algunos tipos de bloques EVA y ladrillos de cerámica. Las pruebas demostraron actuaciones térmicas eficientes para las muestras con bloques EVA. Estos resultados y cálculos adicionales contribuyen con un aporte de valor añadido al bloque EVA, considerando que existen buenas expectativas del componente, con una nueva propuesta de geometría, pudiendo contribuir a la eficiencia energética de edificios, especialmente por su adecuación a la

  2. Liquid Metallic Hydrogen: A Building Block for the Liquid Sun

    Directory of Open Access Journals (Sweden)

    Robitaille P.-M.

    2011-07-01

    Full Text Available Liquid metallic hydrogen provides a compelling material for constructing a condensed matter model of the Sun and the photosphere. Like diamond, metallic hydrogen might have the potential to be a metastable substance requiring high pressures for forma- tion. Once created, it would remain stable even at lower pressures. The metallic form of hydrogen was initially conceived in 1935 by Eugene Wigner and Hillard B. Huntington who indirectly anticipated its elevated critical temperature for liquefaction (Wigner E. and Huntington H.B. On the possibility of a metallic modification of hydro- gen. J. Chem. Phys. , 1935, v.3, 764–770. At that time, solid metallic hydrogen was hypothesized to exist as a body centered cubic, although a more energetically accessible layered graphite-like lattice was also envisioned. Relative to solar emission, this struc- tural resemblance between graphite and layered metallic hydrogen should not be easily dismissed. In the laboratory, metallic hydrogen remains an elusive material. However, given the extensive observational evidence for a condensed Sun composed primarily of hydrogen, it is appropriate to consider metallic hydrogen as a solar building block. It is anticipated that solar liquid metallic hydrogen should possess at least some layered order. Since layered liquid metallic hydrogen would be essentially incompressible, its invocation as a solar constituent brings into question much of current stellar physics. The central proof of a liquid state remains the thermal spectrum of the Sun itself. Its proper understanding brings together all the great forces which shaped modern physics. Although other proofs exist for a liquid photosphere, our focus remains solidly on the generation of this light.

  3. Amino propynyl benzoic acid building block in rigid spacers of divalent ligands binding to the Syk SH2 domains with equally high affinity as the natural ligand

    NARCIS (Netherlands)

    Dekker, Frank J; de Mol, Nico J; Fischer, Marcel J E; Liskamp, Rob M J; Dekker, Frank

    2003-01-01

    The construction of rigid spacers composed of amino propynyl benzoic acid building blocks is described. These spacers were used to link two phosphopeptide ligand sites towards obtaining divalent ligands with a high affinity for Syk tandem SH2 domains, which are important in signal transduction. The

  4. Powered Explicit Guidance Modifications and Enhancements for Space Launch System Block-1 and Block-1B Vehicles

    Science.gov (United States)

    Von der Porten, Paul; Ahmad, Naeem; Hawkins, Matt; Fill, Thomas

    2018-01-01

    NASA is currently building the Space Launch System (SLS) Block-1 launch vehicle for the Exploration Mission 1 (EM-1) test flight. NASA is also currently designing the next evolution of SLS, the Block-1B. The Block-1 and Block-1B vehicles will use the Powered Explicit Guidance (PEG) algorithm (of Space Shuttle heritage) for closed loop guidance. To accommodate vehicle capabilities and design for future evolutions of SLS, modifications were made to PEG for Block-1 to handle multi-phase burns, provide PEG updated propulsion information, and react to a core stage engine out. In addition, due to the relatively low thrust-to-weight ratio of the Exploration Upper Stage (EUS) and EUS carrying out Lunar Vicinity and Earth Escape missions, certain enhancements to the Block-1 PEG algorithm are needed to perform Block-1B missions to account for long burn arcs and target translunar and hyperbolic orbits. This paper describes the design and implementation of modifications to the Block-1 PEG algorithm as compared to Space Shuttle. Furthermore, this paper illustrates challenges posed by the Block-1B vehicle and the required PEG enhancements. These improvements make PEG capable for use on the SLS Block-1B vehicle as part of the Guidance, Navigation, and Control (GN&C) System.

  5. Effect of block weight on work demands and physical workload during masonry work

    NARCIS (Netherlands)

    van der Molen, H.F.; Kuijer, P.P.F.; Hopmans, P.P.; Houweling, A.G.; Faber, G.S.; Hoozemans, M.J.M.; Frings-Dresen, M.H.W.

    2007-01-01

    The effect of block weight on work demands and physical workload was determined for masons who laid sandstone building blocks over the course of a full work day. Three groups of five sandstone block masons participated. Each group worked with a different block weight: 11 kg, 14 kg or 16 kg.

  6. Effect of block weight on work demands and physical workload during masonry work.

    NARCIS (Netherlands)

    van der Molen, H.F.; Kuijer, P.P.F.M.; Hopmans, P.P.; Houweling, A.G.; Faber, G.S.; Hoozemans, M.J.M.; Frings-Dresen, M.H.

    2008-01-01

    The effect of block weight on work demands and physical workload was determined for masons who laid sandstone building blocks over the course of a full work day. Three groups of five sandstone block masons participated. Each group worked with a different block weight: 11 kg, 14 kg or 16 kg.

  7. Effect of block weight on work demands and physical workload during masonry work

    NARCIS (Netherlands)

    van der Molen, H. F.; Kuijer, P. P. F. M.; Hopmans, P. P. W.; Houweling, A. G.; Faber, G. S.; Hoozemans, M. J. M.; Frings-Dresen, M. H. W.

    2008-01-01

    The effect of block weight on work demands and physical workload was determined for masons who laid sandstone building blocks over the course of a full work day. Three groups of five sandstone block masons participated. Each group worked with a different block weight: 11 kg, 14 kg or 16 kg.

  8. Evidence Suggesting Absence of Mitochondrial DNA Methylation

    DEFF Research Database (Denmark)

    Mechta, Mie; Ingerslev, Lars R; Fabre, Odile

    2017-01-01

    , 16S, ND5 and CYTB, suggesting that mtDNA supercoiled structure blocks the access to bisulfite conversion. Here, we identified an artifact of mtDNA bisulfite sequencing that can lead to an overestimation of mtDNA methylation levels. Our study supports that cytosine methylation is virtually absent...

  9. Stepwise transformation of the molecular building blocks in a porphyrin-encapsulating metal-organic material

    KAUST Repository

    Zhang, ZhenJie

    2013-04-24

    When immersed in solutions containing Cu(II) cations, the microporous metal-organic material P11 ([Cd4(BPT)4]·[Cd(C 44H36N8)(S)]·[S], BPT = biphenyl-3,4′,5-tricarboxylate) undergoes a transformation of its [Cd 2(COO)6]2- molecular building blocks (MBBs) into novel tetranuclear [Cu4X2(COO)6(S) 2] MBBs to form P11-Cu. The transformation occurs in single-crystal to single-crystal fashion, and its stepwise mechanism was studied by varying the Cd2+/Cu2+ ratio of the solution in which crystals of P11 were immersed. P11-16/1 (Cd in framework retained, Cd in encapsulated porphyrins exchanged) and other intermediate phases were thereby isolated and structurally characterized. P11-16/1 and P11-Cu retain the microporosity of P11, and the relatively larger MBBs in P11-Cu permit a 20% unit cell expansion and afford a higher surface area and a larger pore size. © 2013 American Chemical Society.

  10. Mononuclear, trinuclear, and hetero-trinuclear supramolecular complexes containing a new tri-sulfonate ligand and cobalt(II)/copper(II)-(1,10-phenanthroline)2 building blocks

    International Nuclear Information System (INIS)

    Yu Yunfang; Wei Yongqin; Broer, Ria; Sa Rongjian; Wu Kechen

    2008-01-01

    Novel mononuclear, trinuclear, and hetero-trinuclear supermolecular complexes, [Co(phen) 2 (H 2 O)(HTST)].2H 2 O (1), [Co 3 (phen) 6 (H 2 O) 2 (TST) 2 ].7H 2 O (2), and [Co 2 Cu(phen) 6 (H 2 O) 2 (TST) 2 ].10H 2 O (3), have been synthesized by the reactions of a new tri-sulfonate ligand (2,4,6-tris(4-sulfophenylamino)-1,3,5-triazine, H 3 TST) with the M 2+ (M=Co, Cu) and the second ligand 1,10-phenanthroline (phen). Complex 1 contains a cis-Co(II)(phen) 2 building block and an HTST as monodentate ligand; complex 2 consists of two TST as bidentate ligands connecting one trans- and two cis-Co(II)(phen) 2 building blocks; complex 3 is formed by replacing the trans-Co(II)(phen) 2 in 2 with a trans-Cu(II)(phen) 2 , which is the first reported hetero-trinuclear supramolecular complex containing both the Co(II)(phen) 2 and Cu(II)(phen) 2 as building blocks. The study shows the flexible multifunctional self-assembly capability of the H 3 TST ligands presenting in these supramolecular complexes through coordinative, H-bonding and even π-π stacking interactions. The photoluminescent optical properties of these complexes are also investigated and discussed as well as the second-order nonlinear optical properties of 1. - Graphical abstract: Novel mononuclear, trinuclear, and hetero-trinuclear supermolecular complexes, [Co(phen) 2 (H 2 O)(HTST)].2H 2 O (1), [Co 3 (phen) 6 (H 2 O) 2 (TST) 2 ].7H 2 O (2), and [Co 2 Cu(phen) 6 (H 2 O) 2 (TST) 2 ].10H 2 O (3), have been synthesized by the reactions of a new tri-sulfonate ligand (2,4,6-tris(4-sulfophenylamino)-1,3,5-triazine, H 3 TST) with the M 2+ (M=Co, Cu) and the second ligand 1,10-phenanthroline (phen). The study shows the flexible multifunctional self-assembly capability of H 3 TST ligand presenting in these supramolecular complexes

  11. Forensic intelligence framework. Part II: Study of the main generic building blocks and challenges through the examples of illicit drugs and false identity documents monitoring.

    Science.gov (United States)

    Baechler, Simon; Morelato, Marie; Ribaux, Olivier; Beavis, Alison; Tahtouh, Mark; Kirkbride, K Paul; Esseiva, Pierre; Margot, Pierre; Roux, Claude

    2015-05-01

    The development of forensic intelligence relies on the expression of suitable models that better represent the contribution of forensic intelligence in relation to the criminal justice system, policing and security. Such models assist in comparing and evaluating methods and new technologies, provide transparency and foster the development of new applications. Interestingly, strong similarities between two separate projects focusing on specific forensic science areas were recently observed. These observations have led to the induction of a general model (Part I) that could guide the use of any forensic science case data in an intelligence perspective. The present article builds upon this general approach by focusing on decisional and organisational issues. The article investigates the comparison process and evaluation system that lay at the heart of the forensic intelligence framework, advocating scientific decision criteria and a structured but flexible and dynamic architecture. These building blocks are crucial and clearly lay within the expertise of forensic scientists. However, it is only part of the problem. Forensic intelligence includes other blocks with their respective interactions, decision points and tensions (e.g. regarding how to guide detection and how to integrate forensic information with other information). Formalising these blocks identifies many questions and potential answers. Addressing these questions is essential for the progress of the discipline. Such a process requires clarifying the role and place of the forensic scientist within the whole process and their relationship to other stakeholders. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Balancing Pathways in DNA Double Strand Break Repair

    NARCIS (Netherlands)

    I. Brandsma (Inger)

    2016-01-01

    markdownabstractAll information a cell needs to live and survive is stored in the genomic DNA. Maintenance of an intact and uncompromised genome is of vital importance for cell survival. Damaged DNA can block transcription and replication, processes essential for cell viability. Persistent DNA

  13. Online design of Matlab/Simulink block schemes

    Directory of Open Access Journals (Sweden)

    Zoltán Janík

    2011-04-01

    Full Text Available The paper presents a new online tool that enables to build a Matlab/Simulink block scheme in the Internet environment. The block scheme can be designed in similar manner as it is offered by local installation of Simulink. The application was created by widely used technologies as XHTML, CSS, JavaScript, PHP together with AJAX approach. The created application can be used as a supporting tool in virtual and remote laboratories.

  14. Building an organic block storage service at CERN with Ceph

    Science.gov (United States)

    van der Ster, Daniel; Wiebalck, Arne

    2014-06-01

    Emerging storage requirements, such as the need for block storage for both OpenStack VMs and file services like AFS and NFS, have motivated the development of a generic backend storage service for CERN IT. The goals for such a service include (a) vendor neutrality, (b) horizontal scalability with commodity hardware, (c) fault tolerance at the disk, host, and network levels, and (d) support for geo-replication. Ceph is an attractive option due to its native block device layer RBD which is built upon its scalable, reliable, and performant object storage system, RADOS. It can be considered an "organic" storage solution because of its ability to balance and heal itself while living on an ever-changing set of heterogeneous disk servers. This work will present the outcome of a petabyte-scale test deployment of Ceph by CERN IT. We will first present the architecture and configuration of our cluster, including a summary of best practices learned from the community and discovered internally. Next the results of various functionality and performance tests will be shown: the cluster has been used as a backend block storage system for AFS and NFS servers as well as a large OpenStack cluster at CERN. Finally, we will discuss the next steps and future possibilities for Ceph at CERN.

  15. Introduction of Molecular Building Blocks to Improve the Stability of Metal-Organic Frameworks for Efficient Mercury Removal.

    Science.gov (United States)

    Jiang, Shu-Yi; He, Wen-Wen; Li, Shun-Li; Su, Zhong-Min; Lan, Ya-Qian

    2018-05-08

    With expanding human needs, many heavy metals were mined, smelted, processed, and manufactured for commercialization, which caused serious environmental pollutions. Currently, many adsorption materials are applied in the field of adsorption of heavy metals. Among them, the principle of many mercury adsorbents is based on the interaction between mercury and sulfur. Here, a S-containing metal-organic framework NENU-400 was synthesized for effective mercury extraction. Unfortunately, the skeleton of NENU-400 collapsed easily when exposed to the mercury liquid solution. To improve the stability, a synthetic strategy installing molecular building blocks (MBBs) into the channels was used. Modified by the MBBs, a more stable nanoporous framework was synthesized, which not only exhibits a high capacity of saturation mercury uptake but also shows high selectivity and efficient recyclability.

  16. Mechanisms of mutagenesis: DNA replication in the presence of DNA damage.

    Science.gov (United States)

    Liu, Binyan; Xue, Qizhen; Tang, Yong; Cao, Jia; Guengerich, F Peter; Zhang, Huidong

    2016-01-01

    Environmental mutagens cause DNA damage that disturbs replication and produces mutations, leading to cancer and other diseases. We discuss mechanisms of mutagenesis resulting from DNA damage, from the level of DNA replication by a single polymerase to the complex DNA replisome of some typical model organisms (including bacteriophage T7, T4, Sulfolobus solfataricus, Escherichia coli, yeast and human). For a single DNA polymerase, DNA damage can affect replication in three major ways: reducing replication fidelity, causing frameshift mutations, and blocking replication. For the DNA replisome, protein interactions and the functions of accessory proteins can yield rather different results even with a single DNA polymerase. The mechanism of mutation during replication performed by the DNA replisome is a long-standing question. Using new methods and techniques, the replisomes of certain organisms and human cell extracts can now be investigated with regard to the bypass of DNA damage. In this review, we consider the molecular mechanism of mutagenesis resulting from DNA damage in replication at the levels of single DNA polymerases and complex DNA replisomes, including translesion DNA synthesis. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. The role of DNA dependent protein kinase in synapsis of DNA ends.

    Science.gov (United States)

    Weterings, Eric; Verkaik, Nicole S; Brüggenwirth, Hennie T; Hoeijmakers, Jan H J; van Gent, Dik C

    2003-12-15

    DNA dependent protein kinase (DNA-PK) plays a central role in the non-homologous end-joining pathway of DNA double strand break repair. Its catalytic subunit (DNA-PK(CS)) functions as a serine/threonine protein kinase. We show that DNA-PK forms a stable complex at DNA termini that blocks the action of exonucleases and ligases. The DNA termini become accessible after autophosphorylation of DNA-PK(CS), which we demonstrate to require synapsis of DNA ends. Interestingly, the presence of DNA-PK prevents ligation of the two synapsed termini, but allows ligation to another DNA molecule. This alteration of the ligation route is independent of the type of ligase that we used, indicating that the intrinsic architecture of the DNA-PK complex itself is not able to support ligation of the synapsed DNA termini. We present a working model in which DNA-PK creates a stable molecular bridge between two DNA ends that is remodeled after DNA-PK autophosphorylation in such a way that the extreme termini become accessible without disrupting synapsis. We infer that joining of synapsed DNA termini would require an additional protein factor.

  18. High-definition polymeric membranes: construction of 3D lithographed channel arrays through control of natural building blocks dynamics.

    Science.gov (United States)

    Speranza, Valentina; Trotta, Francesco; Drioli, Enrico; Gugliuzza, Annarosa

    2010-02-01

    The fabrication of well-defined interfaces is in high demand in many fields of biotechnologies. Here, high-definition membrane-like arrays are developed through the self-assembly of water droplets, which work as natural building blocks for the construction of ordered channels. Solution viscosity together with the dynamics of the water droplets can decide the final formation of three-dimensional well-ordered patterns resembling anodic structures, especially because solvents denser than water are used. Particularly, the polymer solution viscosity is demonstrated to be a powerful tool for control of the mobility of submerged droplets during the microfabrication process. The polymeric patterns are structured at very high levels of organization and exhibit well-established transport-surface property relationships, considered basics for any types of advanced biotechnologies.

  19. Region 9 Census Block 2010

    Science.gov (United States)

    Geography:The TIGER Line Files are feature classes and related database files (.) that are an extract of selected geographic and cartographic information from the U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB). The MTDB represents a seamless national file with no overlaps or gaps between parts, however, each TIGER Line File is designed to stand alone as an independent data set, or they can be combined to cover the entire nation. Census Blocks are statistical areas bounded on all sides by visible features, such as streets, roads, streams, and railroad tracks, and/or by non visible boundaries such as city, town, township, and county limits, and short line-of-sight extensions of streets and roads. Census blocks are relatively small in area; for example, a block in a city bounded by streets. However, census blocks in remote areas are often large and irregular and may even be many square miles in area. A common misunderstanding is that data users think census blocks are used geographically to build all other census geographic areas, rather all other census geographic areas are updated and then used as the primary constraints, along with roads and water features, to delineate the tabulation blocks. As a result, all 2010 Census blocks nest within every other 2010 Census geographic area, so that Census Bureau statistical data can be tabulated at the block level and aggregated up t

  20. Building an organic block storage service at CERN with Ceph

    International Nuclear Information System (INIS)

    Ster, Daniel van der; Wiebalck, Arne

    2014-01-01

    Emerging storage requirements, such as the need for block storage for both OpenStack VMs and file services like AFS and NFS, have motivated the development of a generic backend storage service for CERN IT. The goals for such a service include (a) vendor neutrality, (b) horizontal scalability with commodity hardware, (c) fault tolerance at the disk, host, and network levels, and (d) support for geo-replication. Ceph is an attractive option due to its native block device layer RBD which is built upon its scalable, reliable, and performant object storage system, RADOS. It can be considered an 'organic' storage solution because of its ability to balance and heal itself while living on an ever-changing set of heterogeneous disk servers. This work will present the outcome of a petabyte-scale test deployment of Ceph by CERN IT. We will first present the architecture and configuration of our cluster, including a summary of best practices learned from the community and discovered internally. Next the results of various functionality and performance tests will be shown: the cluster has been used as a backend block storage system for AFS and NFS servers as well as a large OpenStack cluster at CERN. Finally, we will discuss the next steps and future possibilities for Ceph at CERN.

  1. Perspectives of 99mTc chemistry and radiopharmacy: strategies, building blocks and targets

    International Nuclear Information System (INIS)

    Alberto, R.

    2007-01-01

    Technetium chemistry, both fundamental and applied are required to a larger extent in order to keep the essential role of this element in radiopharmacy alive. After an introduction, highlighting the situation in general from research and market aspects, new strategies will be proposed in which technetium and rhenium play an essential role which can not be taken over by other radionuclides such as 11 C or 18 F. Furthermore, currently available and potential future building blocks in technetium chemistry and their relationship to the new strategies as well as characteristics of new precursors will be discussed and compared to each other. Targets and targeting molecules, again in the context of strategies unique for technetium (and rhenium) are in the focus of the last part. With respect of retaining a unique role, it is obvious that any future technetium or rhenium labelled biomolecule should have potential to therapy or be applied in the immediate context of therapy, as e.g. for the early assessment of success in chemotherapy. All these aspects emphasize a role of inorganic technetium chemistry which goes far beyond simple labelling strategies. To underline the importance of fundamental chemistry, we will present and discuss some examples with nuclear targeting agents, amino acids and vitamin B12. (author)

  2. Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor.

    Science.gov (United States)

    Levy, Yaakov

    2017-09-26

    Proteins, like other biomolecules, have a modular and hierarchical structure. Various building blocks are used to construct proteins of high structural complexity and diverse functionality. In multidomain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO brick metaphor is justified as a means of simplifying the complexity of three-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talk that are essential to protein function. In this work, we illustrate recently reported protein behavior in multidomain proteins that deviates from the LEGO brick analogy. While earlier studies showed that a protein domain is often unaffected by being fused to another domain or becomes more stable following the formation of a new interface between the tethered domains, destabilization due to tethering has been reported for several systems. We illustrate that tethering may sometimes result in a multidomain protein behaving as "less than the sum of its parts". We survey these cases for which structure additivity does not guarantee thermodynamic additivity. Protein destabilization due to fusion to other domains may be linked in some cases to biological function and should be taken into account when designing large assemblies.

  3. Seismic proof test of shielding block walls

    International Nuclear Information System (INIS)

    Ohte, Yukio; Watanabe, Takahide; Watanabe, Hiroyuki; Maruyama, Kazuhide

    1989-01-01

    Most of the shielding block walls used for building nuclear facilities are built by dry process. When a nuclear facility is designed, seismic waves specific at each site are set as input seismic motions and they are adopted in the design. Therefore, it is necessary to assure safety of the shielding block walls for earthquake by performing anti-seismic experiments under the conditions at each site. In order to establish the normal form that can be applied to various seismic conditions in various areas, Shimizu Corp. made an actual-size test samples for the shielding block wall and confirmed the safety for earthquake and validity of normalization. (author)

  4. Blocking CHK1 Expression Induces Apoptosis and Abrogates the G2 Checkpoint Mechanism

    Directory of Open Access Journals (Sweden)

    Yan Luo

    2001-01-01

    Full Text Available Checkpoint kinase 1 (Chki is a checkpoint gene that is activated after DNA damage. It phosphorylates and inactivates the Cdc2 activating phosphatase Cdc25C. This in turn inactivates Cdc2, which leads to G2/M arrest. We report that blocking Chki expression by antisense or ribozymes in mammalian cells induces apoptosis and interferes with the G2/M arrest induced by adriamycin. The Chki inhibitor UCN-01 also blocks the G2 arrest after DNA damage and renders cells more susceptible to adriamycin. These results indicate that Chki is an essential gene for the checkpoint mechanism during normal cell proliferation as well as in the DNA damage response.

  5. The dynamic interplay between DNA topoisomerases and DNA topology.

    Science.gov (United States)

    Seol, Yeonee; Neuman, Keir C

    2016-11-01

    Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

  6. Regulation of the DNA Damage Response by DNA-PKcs Inhibitory Phosphorylation of ATM.

    Science.gov (United States)

    Zhou, Yi; Lee, Ji-Hoon; Jiang, Wenxia; Crowe, Jennie L; Zha, Shan; Paull, Tanya T

    2017-01-05

    Ataxia-telangiectasia mutated (ATM) regulates the DNA damage response as well as DNA double-strand break repair through homologous recombination. Here we show that ATM is hyperactive when the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is chemically inhibited or when the DNA-PKcs gene is deleted in human cells. Pre-incubation of ATM protein with active DNA-PKcs also significantly reduces ATM activity in vitro. We characterize several phosphorylation sites in ATM that are targets of DNA-PKcs and show that phospho-mimetic mutations at these residues significantly inhibit ATM activity and impair ATM signaling upon DNA damage. In contrast, phospho-blocking mutations at one cluster of sites increase the frequency of apoptosis during normal cell growth. DNA-PKcs, which is integral to the non-homologous end joining pathway, thus negatively regulates ATM activity through phosphorylation of ATM. These observations illuminate an important regulatory mechanism for ATM that also controls DNA repair pathway choice. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. The building blocks of a 'Liveable Neighbourhood': Identifying the key performance indicators for walking of an operational planning policy in Perth, Western Australia.

    Science.gov (United States)

    Hooper, Paula; Knuiman, Matthew; Foster, Sarah; Giles-Corti, Billie

    2015-11-01

    Planning policy makers are requesting clearer guidance on the key design features required to build neighbourhoods that promote active living. Using a backwards stepwise elimination procedure (logistic regression with generalised estimating equations adjusting for demographic characteristics, self-selection factors, stage of construction and scale of development) this study identified specific design features (n=16) from an operational planning policy ("Liveable Neighbourhoods") that showed the strongest associations with walking behaviours (measured using the Neighbourhood Physical Activity Questionnaire). The interacting effects of design features on walking behaviours were also investigated. The urban design features identified were grouped into the "building blocks of a Liveable Neighbourhood", reflecting the scale, importance and sequencing of the design and implementation phases required to create walkable, pedestrian friendly developments. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: the case of Ag2Te–PbTe

    International Nuclear Information System (INIS)

    Cadavid, Doris; Ibáñez, Maria; Gorsse, Stéphane; López, Antonio M.; Cirera, Albert; Morante, Joan Ramon; Cabot, Andreu

    2012-01-01

    Nanocomposites are highly promising materials to enhance the efficiency of current thermoelectric devices. A straightforward and at the same time highly versatile and controllable approach to produce nanocomposites is the assembly of solution-processed nanocrystal building blocks. The convenience of this bottom-up approach to produce nanocomposites with homogeneous phase distributions and adjustable composition is demonstrated here by blending Ag 2 Te and PbTe colloidal nanocrystals to form Ag 2 Te–PbTe bulk nanocomposites. The thermoelectric properties of these nanocomposites are analyzed in the temperature range from 300 to 700 K. The evolution of their electrical conductivity and Seebeck coefficient is discussed in terms of the blend composition and the characteristics of the constituent materials.

  9. Building a Phylogenetic Tree of the Human and Ape Superfamily Using DNA-DNA Hybridization Data

    Science.gov (United States)

    Maier, Caroline Alexander

    2004-01-01

    The study describes the process of DNA-DNA hybridization and the history of its use by Sibley and Alquist in simple, straightforward, and interesting language that students easily understand to create their own phylogenetic tree of the hominoid superfamily. They calibrate the DNA clock and use it to estimate the divergence dates of the various…

  10. Fluorinated cyclohexanes: Synthesis of amine building blocks of the all-cis 2,3,5,6-tetrafluorocyclohexylamine motif

    Directory of Open Access Journals (Sweden)

    Tetiana Bykova

    2017-04-01

    Full Text Available This paper reports the synthesis of three amine stereoisomers 5a–c of the tetrafluorocyclohexyl ring system, as building blocks for discovery chemistry programmes. The synthesis starts from a Birch reduction of benzonitrile, followed by an in situ methyl iodide quench. The resultant 2,5-cyclohexadiene was progressed via double epoxidations and then hydrofluorination ring opening reactions. The resultant fluorohydrin moieties were then converted to different stereoisomers of the tetrafluorocyclohexyl ring system, and then reductive hydrogenation of the nitrile delivered three amine stereoisomers. It proved necessary to place a methyl group on the cyclohexane ring in order to stabilise the compound against subsequent HF elimination. The two all-cis tetrafluorocyclohexyl isomers 5a and 5b constitute facially polarized cyclohexane rings, with fluorines on the electronegative face and hydrogens on the electropositive face.

  11. Small Buildings in Earthquake Areas. Educational Building Digest 2.

    Science.gov (United States)

    Mooij, D.

    This booklet is intended for builders and others who actually construct small buildings in earthquake areas and not for professionally qualified architects or engineers. In outline form with sketches the following topics are discussed: general construction and design principles; foundations; earth walls; brick, block, and stone walls; timber frame…

  12. DNMT1-interacting RNAs block gene specific DNA methylation

    Science.gov (United States)

    Di Ruscio, Annalisa; Ebralidze, Alexander K.; Benoukraf, Touati; Amabile, Giovanni; Goff, Loyal A.; Terragni, Joylon; Figueroa, Maria Eugenia; De Figureido Pontes, Lorena Lobo; Alberich-Jorda, Meritxell; Zhang, Pu; Wu, Mengchu; D’Alò, Francesco; Melnick, Ari; Leone, Giuseppe; Ebralidze, Konstantin K.; Pradhan, Sriharsa; Rinn, John L.; Tenen, Daniel G.

    2013-01-01

    Summary DNA methylation was described almost a century ago. However, the rules governing its establishment and maintenance remain elusive. Here, we present data demonstrating that active transcription regulates levels of genomic methylation. We identified a novel RNA arising from the CEBPA gene locus critical in regulating the local DNA methylation profile. This RNA binds to DNMT1 and prevents CEBPA gene locus methylation. Deep sequencing of transcripts associated with DNMT1 combined with genome-scale methylation and expression profiling extended the generality of this finding to numerous gene loci. Collectively, these results delineate the nature of DNMT1-RNA interactions and suggest strategies for gene selective demethylation of therapeutic targets in disease. PMID:24107992

  13. Triazole: a unique building block for the construction of functional materials.

    Science.gov (United States)

    Juríček, Michal; Kouwer, Paul H J; Rowan, Alan E

    2011-08-21

    Over the past 50 years, numerous roads towards carbon-based materials have been explored, all of them being paved using mainly one functional group as the brick: acetylene. The acetylene group, or the carbon-carbon triple bond, is one of the oldest and simplest functional groups in chemistry, and although not present in any of the naturally occurring carbon allotropes, it is an essential tool to access their synthetic carbon-rich family. In general, two strategies towards the synthesis of π-conjugated carbon-rich structures can be employed: (a) either the acetylene group serves as a building block to access acetylene-derived structures or (b) it serves as a synthetic tool to provide other, usually benzenoid, structures. The recently discovered copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction, however, represents a new powerful alternative: it transforms the acetylene group into a five-membered heteroaromatic 1H-1,2,3-triazole (triazole) ring and this gives rise to new opportunities. Compared with all-carbon aromatic non-functional rings, the triazole ring possesses three nitrogen atoms and, thus, can serve as a ligand to coordinate metals, or as a hydrogen bond acceptor and donor. This Feature Article summarises examples of using the triazole ring to construct conjugation- and/or function-related heteroaromatic materials, such as tuneable multichromophoric covalent ensembles, macrocyclic receptors or responsive foldamers. These recent examples, which open a new sub-field within organic materials, started to appear only few years ago and represent "a few more bricks" on the road to carbon-rich functional materials. This journal is © The Royal Society of Chemistry 2011

  14. In vitro-reconstituted nucleoids can block mitochondrial DNA replication and transcription

    NARCIS (Netherlands)

    Farge, Géraldine; Mehmedovic, Majda; Baclayon, Marian; van den Wildenberg, Siet M J L; Roos, Wouter H; Gustafsson, Claes M; Wuite, Gijs J L; Falkenberg, Maria

    2014-01-01

    The mechanisms regulating the number of active copies of mtDNA are still unclear. A mammalian cell typically contains 1,000-10,000 copies of mtDNA, which are packaged into nucleoprotein complexes termed nucleoids. The main protein component of these structures is mitochondrial transcription factor A

  15. Locked nucleic acid inhibits amplification of contaminating DNA in real-time PCR

    DEFF Research Database (Denmark)

    Hummelshoj, Lone; Ryder, Lars P; Madsen, Hans O

    2005-01-01

    and real-time PCR, the addition of LNA showed blocking of the amplification of genomic XBP1 but not cDNA XBP1. To test the effect of melting temperature (Tm) on the LNA, we investigated the number of LNA nucleotides that could be replaced with DNA nucleotides and still retain the blocking activity. More...

  16. A Rewritable, Random-Access DNA-Based Storage System.

    Science.gov (United States)

    Yazdi, S M Hossein Tabatabaei; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

    2015-09-18

    We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

  17. DNA replication stress restricts ribosomal DNA copy number.

    Science.gov (United States)

    Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

    2017-09-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  18. DNA replication stress restricts ribosomal DNA copy number

    Science.gov (United States)

    Salim, Devika; Bradford, William D.; Freeland, Amy; Cady, Gillian; Wang, Jianmin

    2017-01-01

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number. PMID:28915237

  19. DNA replication stress restricts ribosomal DNA copy number.

    Directory of Open Access Journals (Sweden)

    Devika Salim

    2017-09-01

    Full Text Available Ribosomal RNAs (rRNAs in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  20. The Building Blocks of User-Focused 3D City Models

    Directory of Open Access Journals (Sweden)

    Isabel Sargent

    2015-12-01

    Full Text Available At Ordnance Survey, GB, we have taken an incremental approach to creating our 3D geospatial database. Research at Ordnance Survey has focused not only on methods for deriving 3D data, but also on the needs of the user in terms of the actual tasks they perform. This provides insights into the type and quality of the data required and how its quality is conveyed. In 2007, using task analysis and user-centred design, we derived a set of geometric characteristics of building exteriors that are relevant to one or more use contexts. This work has been valuable for guiding which building data to collect and how to augment our products. In 2014, we began to supply building height attributes as an alpha-release enhancement to our 2D topography data, OS MasterMap® Topography Layer. This is the first in a series of enhancements of our 2D data that forms part of a road map that will ultimately lead to a full range of 3D products. This paper outlines our research journey from the understanding of the key 3D building characteristics to the development of geo-spatial products and the specification of research. There remains a rich seam of research into methods for capturing user-focused, geo-spatial data to enable visualisation and analysis in three dimensions. Because the process of informing and designing a product is necessarily focused on the practicalities of production, storage and distribution, this paper is presented as a case report, as we believe our journey will be of interest to others involved in the capture of 3D buildings at a national level.

  1. Developing Verification Systems for Building Information Models of Heritage Buildings with Heterogeneous Datasets

    Science.gov (United States)

    Chow, L.; Fai, S.

    2017-08-01

    The digitization and abstraction of existing buildings into building information models requires the translation of heterogeneous datasets that may include CAD, technical reports, historic texts, archival drawings, terrestrial laser scanning, and photogrammetry into model elements. In this paper, we discuss a project undertaken by the Carleton Immersive Media Studio (CIMS) that explored the synthesis of heterogeneous datasets for the development of a building information model (BIM) for one of Canada's most significant heritage assets - the Centre Block of the Parliament Hill National Historic Site. The scope of the project included the development of an as-found model of the century-old, six-story building in anticipation of specific model uses for an extensive rehabilitation program. The as-found Centre Block model was developed in Revit using primarily point cloud data from terrestrial laser scanning. The data was captured by CIMS in partnership with Heritage Conservation Services (HCS), Public Services and Procurement Canada (PSPC), using a Leica C10 and P40 (exterior and large interior spaces) and a Faro Focus (small to mid-sized interior spaces). Secondary sources such as archival drawings, photographs, and technical reports were referenced in cases where point cloud data was not available. As a result of working with heterogeneous data sets, a verification system was introduced in order to communicate to model users/viewers the source of information for each building element within the model.

  2. Engineering artificial machines from designable DNA materials for biomedical applications.

    Science.gov (United States)

    Qi, Hao; Huang, Guoyou; Han, Yulong; Zhang, Xiaohui; Li, Yuhui; Pingguan-Murphy, Belinda; Lu, Tian Jian; Xu, Feng; Wang, Lin

    2015-06-01

    Deoxyribonucleic acid (DNA) emerges as building bricks for the fabrication of nanostructure with complete artificial architecture and geometry. The amazing ability of DNA in building two- and three-dimensional structures raises the possibility of developing smart nanomachines with versatile controllability for various applications. Here, we overviewed the recent progresses in engineering DNA machines for specific bioengineering and biomedical applications.

  3. Phase-assisted synthesis and DNA unpacking evaluation of biologically inspired metallo nanocomplexes using peptide as unique building block.

    Science.gov (United States)

    Raman, N; Sudharsan, S

    2011-12-01

    The goal of nanomaterials' surface modification using a biomaterial is to preserve the materials' bulk properties while modifying only their surface to possess desired recognition and specificity. Here, we have developed a phase-assisted, modified Brust-Schiffrin methodological synthesis of metallo nanocomplexes anchored by a peptide, N,N'-(1,3-propylene)-bis-hippuricamide. The spectral, thermal and morphological characterizations assure the formation of nanocomplexes. Therapeutic behavior of all the nanocomplexes has been well sighted by evaluating their DNA unpacking skills. In addition, we demonstrate their biological inspiration by targeting few bacterial and fungal strains. The in vitro antimicrobial investigation reports that all the nanocomplexes disrupt microbial cell walls/membranes efficiently and inhibit the growth of microbes. These sorts of nanocomplexes synthesized in large quantities and at low cost, deliver versatile biomedical applications, and can be used to treat various diseases which may often cause high mortality. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Ligation bias in Illumina next-generation DNA libraries

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel

    2013-01-01

    Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products,...... for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.......Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by......-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate...

  5. Human CD4+ T cells require exogenous cystine for glutathione and DNA synthesis

    DEFF Research Database (Denmark)

    Levring, Trine B; Kongsbak-Wismann, Martin; Rode, Anna Kathrine Obelitz

    2015-01-01

    . The aim of this study was to elucidate why activated human T cells require exogenous Cys2 in order to proliferate. We activated purified naïve human CD4+ T cells and found that glutathione (GSH) levels and DNA synthesis were dependent on Cys2 and increased in parallel with increasing concentrations of Cys......Adaptive immune responses require activation and expansion of antigen-specific T cells. Whereas early T cell activation is independent of exogenous cystine (Cys2), T cell proliferation is dependent of Cys2. However, the exact roles of Cys2 in T cell proliferation still need to be determined...... for the activity of ribonucleotide reductase (RNR), the enzyme responsible for generation of the deoxyribonucleotide DNA building blocks. In conclusion, we show that activated human T cells require exogenous Cys2 to proliferate and that this is partly explained by the fact that Cys2 is required for production...

  6. Developing DNA nanotechnology using single-molecule fluorescence.

    Science.gov (United States)

    Tsukanov, Roman; Tomov, Toma E; Liber, Miran; Berger, Yaron; Nir, Eyal

    2014-06-17

    CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and

  7. Proposed and existing passive and inherent safety-related structures, systems, and components (building blocks) for advanced light-water reactors

    International Nuclear Information System (INIS)

    Forsberg, C.W.; Moses, D.L.; Lewis, E.B.; Gibson, R.; Pearson, R.; Reich, W.J.; Murphy, G.A.; Staunton, R.H.; Kohn, W.E.

    1989-10-01

    A nuclear power plant is composed of many structures, systems, and components (SSCs). Examples include emergency core cooling systems, feedwater systems, and electrical systems. The design of a reactor consists of combining various SSCs (building blocks) into an integrated plant design. A new reactor design is the result of combining old SSCs in new ways or use of new SSCs. This report identifies, describes, and characterizes SSCs with passive and inherent features that can be used to assure safety in light-water reactors. Existing, proposed, and speculative technologies are described. The following approaches were used to identify the technologies: world technical literature searches, world patent searches, and discussions with universities, national laboratories and industrial vendors. 214 refs., 105 figs., 26 tabs

  8. Proposed and existing passive and inherent safety-related structures, systems, and components (building blocks) for advanced light-water reactors

    Energy Technology Data Exchange (ETDEWEB)

    Forsberg, C.W.; Moses, D.L.; Lewis, E.B.; Gibson, R.; Pearson, R.; Reich, W.J.; Murphy, G.A.; Staunton, R.H.; Kohn, W.E.

    1989-10-01

    A nuclear power plant is composed of many structures, systems, and components (SSCs). Examples include emergency core cooling systems, feedwater systems, and electrical systems. The design of a reactor consists of combining various SSCs (building blocks) into an integrated plant design. A new reactor design is the result of combining old SSCs in new ways or use of new SSCs. This report identifies, describes, and characterizes SSCs with passive and inherent features that can be used to assure safety in light-water reactors. Existing, proposed, and speculative technologies are described. The following approaches were used to identify the technologies: world technical literature searches, world patent searches, and discussions with universities, national laboratories and industrial vendors. 214 refs., 105 figs., 26 tabs.

  9. Overproduction of the poly(ADP-ribose)polymerase DNA-binding domain blocks alkylation-induced DNA repair synthesis in mammalian cells.

    NARCIS (Netherlands)

    M. Molinete; W. Vermeulen (Wim); A. Bürkle; J. Mé nissier-de Murcia; J.H. Küpper; J.H.J. Hoeijmakers (Jan); G. de Murcia

    1993-01-01

    textabstractThe zinc-finger DNA-binding domain (DBD) of poly (ADP-ribose) polymerase (PARP, EC 2.4.2.30) specifically recognizes DNA strand breaks induced by various DNA-damaging agents in eukaryotes. This, in turn, triggers the synthesis of polymers of ADP-ribose linked to nuclear proteins during

  10. Toward three-dimensional microelectronic systems: directed self-assembly of silicon microcubes via DNA surface functionalization.

    Science.gov (United States)

    Lämmerhardt, Nico; Merzsch, Stephan; Ledig, Johannes; Bora, Achyut; Waag, Andreas; Tornow, Marc; Mischnick, Petra

    2013-07-02

    The huge and intelligent processing power of three-dimensional (3D) biological "processors" like the human brain with clock speeds of only 0.1 kHz is an extremely fascinating property, which is based on a massively parallel interconnect strategy. Artificial silicon microprocessors are 7 orders of magnitude faster. Nevertheless, they do not show any indication of intelligent processing power, mostly due to their very limited interconnectivity. Massively parallel interconnectivity can only be realized in three dimensions. Three-dimensional artificial processors would therefore be at the root of fabricating artificially intelligent systems. A first step in this direction would be the self-assembly of silicon based building blocks into 3D structures. We report on the self-assembly of such building blocks by molecular recognition, and on the electrical characterization of the formed assemblies. First, planar silicon substrates were functionalized with self-assembling monolayers of 3-aminopropyltrimethoxysilane for coupling of oligonucleotides (single stranded DNA) with glutaric aldehyde. The oligonucleotide immobilization was confirmed and quantified by hybridization with fluorescence-labeled complementary oligonucleotides. After the individual processing steps, the samples were analyzed by contact angle measurements, ellipsometry, atomic force microscopy, and fluorescence microscopy. Patterned DNA-functionalized layers were fabricated by microcontact printing (μCP) and photolithography. Silicon microcubes of 3 μm edge length as model objects for first 3D self-assembly experiments were fabricated out of silicon-on-insulator (SOI) wafers by a combination of reactive ion etching (RIE) and selective wet etching. The microcubes were then surface-functionalized using the same protocol as on planar substrates, and their self-assembly was demonstrated both on patterned silicon surfaces (88% correctly placed cubes), and to cube aggregates by complementary DNA

  11. Genetic exchanges caused by ultraviolet photoproducts in phage lamda DNA molecules: the role of DNA replication

    International Nuclear Information System (INIS)

    Lin, P.F.; Howard-Flanders, P.; Yale Univ., New Haven, Conn.

    1976-01-01

    Genetic recombination induced by structural damage in DNA molecules was investigated in E. coli K12(lamda) lysogens infected with genetically marked phage lamda. Photoproducts were induced in the phage DNA before infection by exposing them either to 313 nm light in the presence of acetophenone or to 254 nm light. To test the role of the replication of the damage phage DNA on the frequency of the induced recombination , both heteroimmune and homoimmune crosses were performed, and scored for P + recombinants. In heteroimmune crosses, recombination was less frequent in infected cells exposed to visible light and in wild type cells able to perform excision repair than in excision-defective lysogens. Therefore, much of the induced recombination can be attributed to the pyrimidine dimers in the phage DNA. In homoimmune crosses, replication of the phage DNA containing ultraviolet photoproducts was represented by lamda immunity, and was further blocked by the lack of the P gene product needed for replication. The 254 nm photoproducts increased the frequency of recombination in these homoimmune crosses, even though phage DNA replication was blocked. Irradiation with 313 nm light and acetophenone M, which produces dimers and unknown photoproducts, was not as effective per dimer as the 254 nm light. It is concluded from these results that certain unidentified 254 nm photoproducts can cause recombination even in the absence of DNA replication. They are not pyrimidine dimers, as they are not susceptible to excision repair or photoreactivation. In contrast, pyrimidine dimers appear to cause recombination only when the DNA containing them undergoes replication. (orig./MG) [de

  12. Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: the case of Ag{sub 2}Te-PbTe

    Energy Technology Data Exchange (ETDEWEB)

    Cadavid, Doris [Catalonia Institute for Energy Research, IREC (Spain); Ibanez, Maria [Universitat de Barcelona, Departament d' Electronica (Spain); Gorsse, Stephane [Universite de Bordeaux, ICMCB, CNRS (France); Lopez, Antonio M. [Universitat Politecnica de Catalunya, Departament d' Enginyeria Electronica (Spain); Cirera, Albert [Universitat de Barcelona, Departament d' Electronica (Spain); Morante, Joan Ramon; Cabot, Andreu, E-mail: acabot@irec.cat [Catalonia Institute for Energy Research, IREC (Spain)

    2012-12-15

    Nanocomposites are highly promising materials to enhance the efficiency of current thermoelectric devices. A straightforward and at the same time highly versatile and controllable approach to produce nanocomposites is the assembly of solution-processed nanocrystal building blocks. The convenience of this bottom-up approach to produce nanocomposites with homogeneous phase distributions and adjustable composition is demonstrated here by blending Ag{sub 2}Te and PbTe colloidal nanocrystals to form Ag{sub 2}Te-PbTe bulk nanocomposites. The thermoelectric properties of these nanocomposites are analyzed in the temperature range from 300 to 700 K. The evolution of their electrical conductivity and Seebeck coefficient is discussed in terms of the blend composition and the characteristics of the constituent materials.

  13. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  14. [DNA complexes, formed on aqueous phase surfaces: new planar polymeric and composite nanostructures].

    Science.gov (United States)

    Antipina, M N; Gaĭnutdinov, R V; Rakhnianskaia, A A; Sergeev-Cherenkov, A N; Tolstikhina, A L; Iurova, T V; Kislov, V V; Khomutov, G B

    2003-01-01

    The formation of DNA complexes with Langmuir monolayers of the cationic lipid octadecylamine (ODA) and the new amphiphilic polycation poly-4-vinylpyridine with 16% of cetylpyridinium groups (PVP-16) on the surface of an aqueous solution of native DNA of low ionic strength was studied. Topographic images of Langmuir-Blodgett films of DNA/ODA and DNA/PVP-16 complexes applied to micaceous substrates were investigated by the method of atomic force microscopy. It was found that films of the amphiphilic polycation have an ordered planar polycrystalline structure. The morphology of planar DNA complexes with the amphiphilic cation substantially depended on the incubation time and the phase state of the monolayer on the surface of the aqueous DNA solution. Complex structures and individual DNA molecules were observed on the surface of the amphiphilic monolayer. Along with quasi-linear individual bound DNA molecules, characteristic extended net-like structures and quasi-circular toroidal condensed conformations of planar DNA complexes were detected. Mono- and multilayer films of DNA/PVP-16 complexes were used as templates and nanoreactors for the synthesis of inorganic nanostructures via the binding of metal cations from the solution and subsequent generation of the inorganic phase. As a result, ultrathin polymeric composite films with integrated DNA building blocks and quasi-linear arrays of inorganic semiconductor (CdS) and iron oxide nanoparticles and nanowires were obtained. The nanostructures obtained were characterized by scanning probe microscopy and transmission electron microscopy techniques. The methods developed are promising for investigating the mechanisms of structural organization and transformation in DNA and polyelectrolyte complexes at the gas-liquid interface and for the design of new extremely thin highly ordered planar polymeric and composite materials, films, and coatings with controlled ultrastructure for applications in nanoelectronics and

  15. Rockfall vulnerability assessment for reinforced concrete buildings

    Science.gov (United States)

    Mavrouli, O.; Corominas, J.

    2010-10-01

    The vulnerability of buildings to the impact of rockfalls is a topic that has recently attracted increasing attention in the scientific literature. The quantification of the vulnerability, when based on empirical or heuristic approaches requires data recorded from historical rockfalls, which are not always available. This is the reason why appropriate alternatives are required. The use of analytical and numerical models can be one of them. In this paper, a methodology is proposed for the analytical evaluation of the vulnerability of reinforced concrete buildings. The vulnerability is included in the risk equation by incorporating the uncertainty of the impact location of the rock block and the subsequent damage level. The output is a weighted vulnerability that ranges from 0 to 1 and expresses the potential damage that a rock block causes to a building in function of its velocity and size. The vulnerability is calculated by the sum of the products of the probability of block impact on each element of the building and its associated damage state, the latter expressed in relative recovery cost terms. The probability of exceeding a specific damage state such as non-structural, local, partial, extensive or total collapse is also important for the quantification of risk and to this purpose, several sets of fragility curves for various rock diameters and increasing velocities have been prepared. An example is shown for the case of a simple reinforced concrete building and impact energies from 0 to 4075 kJ.

  16. Strength of masonry blocks made with recycled concrete aggregates

    Science.gov (United States)

    Matar, Pierre; Dalati, Rouba El

    The idea of recycling concrete of demolished buildings aims at preserving the environment. Indeed, the reuse of concrete as aggregate in new concrete mixes helped to reduce the expenses related to construction and demolition (C&D) waste management and, especially, to protect the environment by reducing the development rate of new quarries. This paper presents the results of an experimental study conducted on masonry blocks containing aggregates resulting from concrete recycling. The purpose of this study is to investigate the effect of recycled aggregates on compressive strength of concrete blocks. Tests were performed on series of concrete blocks: five series each made of different proportions of recycled aggregates, and one series of reference blocks exclusively composed of natural aggregates. Tests showed that using recycled aggregates with addition of cement allows the production of concrete blocks with compressive strengths comparable to those obtained on concrete blocks made exclusively of natural aggregates.

  17. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    Energy Technology Data Exchange (ETDEWEB)

    Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Waleń, Tomasz [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); University of Warsaw, Banacha 2, 02-097 Warsaw (Poland); Piątkowski, Paweł; Potrzebowski, Wojciech [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Bujnicki, Janusz M. [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Adam Mickiewicz University, Umultowska 89, 61-614 Poznan (Poland)

    2015-03-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

  18. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    International Nuclear Information System (INIS)

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-01-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx

  19. Multiple conformational states of DnaA protein regulate its interaction with DnaA boxes in the initiation of DNA replication.

    Science.gov (United States)

    Patel, Meera J; Bhatia, Lavesh; Yilmaz, Gulden; Biswas-Fiss, Esther E; Biswas, Subhasis B

    2017-09-01

    DnaA protein is the initiator of genomic DNA replication in prokaryotes. It binds to specific DNA sequences in the origin of DNA replication and unwinds small AT-rich sequences downstream for the assembly of the replisome. The mechanism of activation of DnaA that enables it to bind and organize the origin DNA and leads to replication initiation remains unclear. In this study, we have developed double-labeled fluorescent DnaA probes to analyze conformational states of DnaA protein upon binding DNA, nucleotide, and Soj sporulation protein using Fluorescence Resonance Energy Transfer (FRET). Our studies demonstrate that DnaA protein undergoes large conformational changes upon binding to substrates and there are multiple distinct conformational states that enable it to initiate DNA replication. DnaA protein adopted a relaxed conformation by expanding ~15Å upon binding ATP and DNA to form the ATP·DnaA·DNA complex. Hydrolysis of bound ATP to ADP led to a contraction of DnaA within the complex. The relaxed conformation of DnaA is likely required for the formation of the multi-protein ATP·DnaA·DNA complex. In the initiation of sporulation, Soj binding to DnaA prevented relaxation of its conformation. Soj·ADP appeared to block the activation of DnaA, suggesting a mechanism for Soj·ADP in switching initiation of DNA replication to sporulation. Our studies demonstrate that multiple conformational states of DnaA protein regulate its binding to DNA in the initiation of DNA replication. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Synthesis of acetylene linked double-nucleobase nucleos(t)ide building blocks and polymerase construction of DNA containing cytosines in the major groove

    Czech Academy of Sciences Publication Activity Database

    Kielkowski, Pavel; Pohl, Radek; Hocek, Michal

    2011-01-01

    Roč. 76, č. 9 (2011), s. 3457-3462 ISSN 0022-3263 R&D Projects: GA MŠk LC512; GA ČR GA203/09/0317 Institutional research plan: CEZ:AV0Z40550506 Keywords : nucleoside triphosphates * functionalized DNA * cross - coupling reactions * nucleic-acids Subject RIV: CC - Organic Chemistry Impact factor: 4.450, year: 2011

  1. Water versus DNA: new insights into proton track-structure modelling in radiobiology and radiotherapy.

    Science.gov (United States)

    Champion, C; Quinto, M A; Monti, J M; Galassi, M E; Weck, P F; Fojón, O A; Hanssen, J; Rivarola, R D

    2015-10-21

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.

  2. Binding Blocks: Building the Universe One Nucleus at a Time

    Science.gov (United States)

    Diget, C. Aa.; Pastore, A.; Leech, K.; Haylett, T.; Lock, S.; Sanders, T.; Shelley, M.; Willett, H. V.; Keegans, J.; Sinclair, L.; Simpson, E. C.

    2017-01-01

    We present a new teaching and outreach activity based around the construction of a three-dimensional chart of isotopes using LEGO® bricks. The activity, "binding blocks", demonstrates nuclear and astrophysical processes through a seven-meter chart of all nuclear isotopes, built from over 26000 LEGO® bricks. It integrates A-Level and GCSE…

  3. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    International Nuclear Information System (INIS)

    Swasey, Steven M; Gwinn, Elisabeth G

    2016-01-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson–Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag + , as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag + –DNA nanostructures. Our studies of Ag + -induced assembly of non-complementary DNA oligomers employ strands of 2–24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag + can be achieved by optimizing solution conditions. These Ag + -mediated duplexes are stable to at least 60 mM Mg 2+ , higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag + -mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag + -mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’. (paper)

  4. DEVELOPING VERIFICATION SYSTEMS FOR BUILDING INFORMATION MODELS OF HERITAGE BUILDINGS WITH HETEROGENEOUS DATASETS

    Directory of Open Access Journals (Sweden)

    L. Chow

    2017-08-01

    Full Text Available The digitization and abstraction of existing buildings into building information models requires the translation of heterogeneous datasets that may include CAD, technical reports, historic texts, archival drawings, terrestrial laser scanning, and photogrammetry into model elements. In this paper, we discuss a project undertaken by the Carleton Immersive Media Studio (CIMS that explored the synthesis of heterogeneous datasets for the development of a building information model (BIM for one of Canada’s most significant heritage assets – the Centre Block of the Parliament Hill National Historic Site. The scope of the project included the development of an as-found model of the century-old, six-story building in anticipation of specific model uses for an extensive rehabilitation program. The as-found Centre Block model was developed in Revit using primarily point cloud data from terrestrial laser scanning. The data was captured by CIMS in partnership with Heritage Conservation Services (HCS, Public Services and Procurement Canada (PSPC, using a Leica C10 and P40 (exterior and large interior spaces and a Faro Focus (small to mid-sized interior spaces. Secondary sources such as archival drawings, photographs, and technical reports were referenced in cases where point cloud data was not available. As a result of working with heterogeneous data sets, a verification system was introduced in order to communicate to model users/viewers the source of information for each building element within the model.

  5. Embodied Energy and CO2 Analyses of Mud-brick and Cement-block Houses

    Directory of Open Access Journals (Sweden)

    Abanda F.Henry

    2014-01-01

    Full Text Available In building projects, the extraction of vast quantities of materials is too common. The extraction of materials and the erection of buildings consume embodied energy and emit carbon dioxide (CO2 that impact negatively on the environment. Therefore it is necessary to consider embodied energy and CO2 amongst other factors in selecting building materials for use in building projects. In most developing countries, building environmental performance analysis has yet to gain interest from the construction community. However, with recent increase in sustainability awareness, both developed and developing nations have engaged in efforts to tackle this challenge. Embodied energy and CO2 are among the leading parameters in assessing environmental building performance. In Cameroon, studies about the assessment of embodied energy and CO2 of building projects are scarce. Hence, professionals find it difficult to make alternative choices for building materials to use in their different building projects. This study uses a detailed process analysis approach supported by two popular housing types in Cameroon (mud-brick and cement-block houses to assess the embodied energy and CO2 impacts from building materials. The emerging Building Information Modelling (BIM tool was used to validate the computational results of the process analysis method. The findings revealed the embodied energy and CO2 for the mud-brick houses are 137934.91 MJ (2007.8 MJ/m2 and 15665.56 Kg CO2 (228.03 Kg CO2/m2; the cement-block houses are 292326.81 MJ (3065.51 MJ/m2 and 37829.19 Kg CO2 (396.7 Kg CO2/m2 respectively. Thus, the cement-block house expends at least 1.5 times more embodied energy and emits at least 1.7 times more embodied CO2 than mud-brick house. Although these findings cannot be generalized, they nonetheless indicate the importance of considering embodied energy and CO2 in making alternative choices for use in different building projects.

  6. BUILDING FAÇADE SEPARATION IN VERTICAL AERIAL IMAGES

    Directory of Open Access Journals (Sweden)

    P. Meixner

    2012-07-01

    Full Text Available Three-dimensional models of urban environments have great appeal and offer promises of interesting applications. While initially it was of interest to just have such 3D data, it increasingly becomes evident that one really would like to have interpreted urban objects. To be able to interpret buildings we have to split a visible whole building block into its different single buildings. Usually this is done using cadastral information to divide the single land parcels. The problem in this case is that sometimes the building boundaries derived from the cadastre are insufficiently accurate due to several reasons like old databases with lower accuracies or inaccuracies due to transformation between two coordinate systems. For this reason it can happen that a cadastral boundary coming from an old map is displaced by up to several meters and therefore divides two buildings incorrectly. To overcome such problems we incorporate the information from vertical aerial images. We introduce a façade separation method that is able to find individual building façades using multi view stereo. The purpose is to identify the individual façades and separate them from one another before on proceeds with the analysis of a façade's details. The source was a set of overlapping, thus "redundant" vertical aerial images taken by an UltraCam digital aerial camera. Therefore in a first step we determine the building block outlines using the building classification and use the height values from the Digital Surface Model (DSM to determine approximate "façade quadrilaterals". We also incorporate height discontinuities using the height profiles along the building outlines to enhance our façade separation. In a next step we detect repeated pattern in these "façade images" and use them to separate the façades respectively building blocks from one another. We show that this method can be successfully used to separate building façades using vertical aerial images with a

  7. Comparison of checkpoint responses triggered by DNA polymerase inhibition versus DNA damaging agents

    International Nuclear Information System (INIS)

    Liu, J.-S.; Kuo, S.-R.; Melendy, Thomas

    2003-01-01

    To better understand the different cellular responses to replication fork pausing versus blockage, early DNA damage response markers were compared after treatment of cultured mammalian cells with agents that either inhibit DNA polymerase activity (hydroxyurea (HU) or aphidicolin) or selectively induce S-phase DNA damage responses (the DNA alkylating agents, methyl methanesulfonate (MMS) and adozelesin). These agents were compared for their relative abilities to induce phosphorylation of Chk1, H2AX, and replication protein A (RPA), and intra-nuclear focalization of γ-H2AX and RPA. Treatment by aphidicolin and HU resulted in phosphorylation of Chk1, while HU, but not aphidicolin, induced focalization of γ-H2AX and RPA. Surprisingly, pre-treatment with aphidicolin to stop replication fork progression, did not abrogate HU-induced γ-H2AX and RPA focalization. This suggests that HU may act on the replication fork machinery directly, such that fork progression is not required to trigger these responses. The DNA-damaging fork-blocking agents, adozelesin and MMS, both induced phosphorylation and focalization of H2AX and RPA. Unlike adozelesin and HU, the pattern of MMS-induced RPA focalization did not match the BUdR incorporation pattern and was not blocked by aphidicolin, suggesting that MMS-induced damage is not replication fork-dependent. In support of this, MMS was the only reagent used that did not induce phosphorylation of Chk1. These results indicate that induction of DNA damage checkpoint responses due to adozelesin is both replication fork and fork progression dependent, induction by HU is replication fork dependent but progression independent, while induction by MMS is independent of both replication forks and fork progression

  8. Comparison of checkpoint responses triggered by DNA polymerase inhibition versus DNA damaging agents

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.-S.; Kuo, S.-R.; Melendy, Thomas

    2003-11-27

    To better understand the different cellular responses to replication fork pausing versus blockage, early DNA damage response markers were compared after treatment of cultured mammalian cells with agents that either inhibit DNA polymerase activity (hydroxyurea (HU) or aphidicolin) or selectively induce S-phase DNA damage responses (the DNA alkylating agents, methyl methanesulfonate (MMS) and adozelesin). These agents were compared for their relative abilities to induce phosphorylation of Chk1, H2AX, and replication protein A (RPA), and intra-nuclear focalization of {gamma}-H2AX and RPA. Treatment by aphidicolin and HU resulted in phosphorylation of Chk1, while HU, but not aphidicolin, induced focalization of {gamma}-H2AX and RPA. Surprisingly, pre-treatment with aphidicolin to stop replication fork progression, did not abrogate HU-induced {gamma}-H2AX and RPA focalization. This suggests that HU may act on the replication fork machinery directly, such that fork progression is not required to trigger these responses. The DNA-damaging fork-blocking agents, adozelesin and MMS, both induced phosphorylation and focalization of H2AX and RPA. Unlike adozelesin and HU, the pattern of MMS-induced RPA focalization did not match the BUdR incorporation pattern and was not blocked by aphidicolin, suggesting that MMS-induced damage is not replication fork-dependent. In support of this, MMS was the only reagent used that did not induce phosphorylation of Chk1. These results indicate that induction of DNA damage checkpoint responses due to adozelesin is both replication fork and fork progression dependent, induction by HU is replication fork dependent but progression independent, while induction by MMS is independent of both replication forks and fork progression.

  9. Transcriptional blockages in a cell-free system by sequence-selective DNA alkylating agents.

    Science.gov (United States)

    Ferguson, L R; Liu, A P; Denny, W A; Cullinane, C; Talarico, T; Phillips, D R

    2000-04-14

    There is considerable interest in DNA sequence-selective DNA-binding drugs as potential inhibitors of gene expression. Five compounds with distinctly different base pair specificities were compared in their effects on the formation and elongation of the transcription complex from the lac UV5 promoter in a cell-free system. All were tested at drug levels which killed 90% of cells in a clonogenic survival assay. Cisplatin, a selective alkylator at purine residues, inhibited transcription, decreasing the full-length transcript, and causing blockage at a number of GG or AG sequences, making it probable that intrastrand crosslinks are the blocking lesions. A cyclopropylindoline known to be an A-specific alkylator also inhibited transcription, with blocks at adenines. The aniline mustard chlorambucil, that targets primarily G but also A sequences, was also effective in blocking the formation of full-length transcripts. It produced transcription blocks either at, or one base prior to, AA or GG sequences, suggesting that intrastrand crosslinks could again be involved. The non-alkylating DNA minor groove binder Hoechst 33342 (a bisbenzimidazole) blocked formation of the full-length transcript, but without creating specific blockage sites. A bisbenzimidazole-linked aniline mustard analogue was a more effective transcription inhibitor than either chlorambucil or Hoechst 33342, with different blockage sites occurring immediately as compared with 2 h after incubation. The blockages were either immediately prior to AA or GG residues, or four to five base pairs prior to such sites, a pattern not predicted from in vitro DNA-binding studies. Minor groove DNA-binding ligands are of particular interest as inhibitors of gene expression, since they have the potential ability to bind selectively to long sequences of DNA. The results suggest that the bisbenzimidazole-linked mustard does cause alkylation and transcription blockage at novel DNA sites. in addition to sites characteristic of

  10. Buildings vs. ballistics: Quantifying the vulnerability of buildings to volcanic ballistic impacts using field studies and pneumatic cannon experiments

    Science.gov (United States)

    Williams, G. T.; Kennedy, B. M.; Wilson, T. M.; Fitzgerald, R. H.; Tsunematsu, K.; Teissier, A.

    2017-09-01

    Recent casualties in volcanic eruptions due to trauma from blocks and bombs necessitate more rigorous, ballistic specific risk assessment. Quantitative assessments are limited by a lack of experimental and field data on the vulnerability of buildings to ballistic hazards. An improved, quantitative understanding of building vulnerability to ballistic impacts is required for informing appropriate life safety actions and other risk reduction strategies. We assessed ballistic impacts to buildings from eruptions at Usu Volcano and Mt. Ontake in Japan and compiled available impact data from eruptions elsewhere to identify common damage patterns from ballistic impacts to buildings. We additionally completed a series of cannon experiments which simulate ballistic block impacts to building claddings to investigate their performance over a range of ballistic projectile velocities, masses and energies. Our experiments provide new insights by quantifying (1) the hazard associated with post-impact shrapnel from building and rock fragments; (2) the effect of impact obliquity on damage; and (3) the additional impact resistance buildings possess when claddings are struck in areas directly supported by framing components. This was not well identified in previous work which may have underestimated building vulnerability to ballistic hazards. To improve assessment of building vulnerability to ballistics, we use our experimental and field data to develop quantitative vulnerability models known as fragility functions. Our fragility functions and field studies show that although unreinforced buildings are highly vulnerable to large ballistics (> 20 cm diameter), they can still provide shelter, preventing death during eruptions.

  11. DNMT1-interacting RNAs block gene-specific DNA methylation

    Czech Academy of Sciences Publication Activity Database

    Di Ruscio, A.; Ebralidze, A.; Benoukraf, T.; Amabile, G.; Goff, L.A.; Terragni, J.; Figueroa, M.E.; Pontes, L.L.D.; Alberich-Jorda, Meritxell; Zhang, P.; Wu, M.C.; D´Alo, F.; Melnick, A.; Leone, G.; Ebralidze, K.K.; Pradhan, S.; Rinn, J.L.; Tenen, D.G.

    2013-01-01

    Roč. 503, č. 7476 (2013), s. 371-376 ISSN 0028-0836 R&D Projects: GA MŠk LK21307 Institutional support: RVO:68378050 Keywords : DNA methylation * non-coding RNA * DNMT1 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 42.351, year: 2013

  12. High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

    International Nuclear Information System (INIS)

    Chou, Shanho; Flynn, P.; Wang, A.; Reid, B.

    1991-01-01

    Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies

  13. Comparison of Dynamic Characteristics of Two Instrumented Tall Buildings

    DEFF Research Database (Denmark)

    Ventura, C.; Laverick, B.; Brincker, Rune

    2003-01-01

    attention to the three-dimensional nonlinear dynamic behaviour of tall buildings, so there is a need for these types of studies. The purpose of this paper is to study the dynamic properties of two well-instrumented tall steel frame buildings in Los Angeles, California. These building are within a few blocks...

  14. Sensitization of Tumor to 212Pb Radioimmunotherapy by Gemcitabine Involves Initial Abrogation of G2 Arrest and Blocked DNA Damage Repair by Interference With Rad51

    International Nuclear Information System (INIS)

    Yong, Kwon Joong; Milenic, Diane E.; Baidoo, Kwamena E.; Brechbiel, Martin W.

    2013-01-01

    Purpose: To elucidate the mechanism of the therapeutic efficacy of targeted α-particle radiation therapy using 212 Pb-TCMC-trastuzumab together with gemcitabine for treatment of disseminated peritoneal cancers. Methods and Materials: Mice bearing human colon cancer LS-174T intraperitoneal xenografts were pretreated with gemcitabine, followed by 212 Pb-TCMC-trastuzumab and compared with controls. Results: Treatment with 212 Pb-TCMC-trastuzumab increased the apoptotic rate in the S-phase-arrested tumors induced by gemcitabine at earlier time points (6 to 24 hours). 212 Pb-TCMC-trastuzumab after gemcitabine pretreatment abrogated G2/M arrest at the same time points, which may be associated with the inhibition of Chk1 phosphorylation and, in turn, cell cycle perturbation, resulting in apoptosis. 212 Pb-TCMC-trastuzumab treatment after gemcitabine pretreatment caused depression of DNA synthesis, DNA double-strand breaks, accumulation of unrepaired DNA, and down-regulation of Rad51 protein, indicating that DNA damage repair was blocked. In addition, modification in the chromatin structure of p21 may be associated with transcriptionally repressed chromatin states, indicating that the open structure was delayed at earlier time points. Conclusion: These findings suggest that the cell-killing efficacy of 212 Pb-TCMC-trastuzumab after gemcitabine pretreatment may be associated with abrogation of the G2/M checkpoint, inhibition of DNA damage repair, and chromatin remodeling

  15. Modulation of radiation-induced apoptosis and G2/M block in murine T-lymphoma cells

    International Nuclear Information System (INIS)

    Palayoor, S.T.; Macklis, R.M.; Bump, E.A.; Coleman, C.N.

    1995-01-01

    Radiation-induced apoptosis in lymphocyte-derived cell lines is characterized by endonucleolytic cleavage of cellular DNA within hours after radiation exposure. We have studied this phenomenon qualitatively (DNA gel electrophoresis) and quantitatively (diphenylamine reagent assay) in murine EL4 T-lymphoma cells exposed to 137 Cs γ irradiation. Fragmentation was discernible within 18-24 h after exposure. It increased with time and dose and reached a plateau after 8 Gy of γ radiation. We studied the effect of several pharmacological agents on the radiation-induced G 2 /M block and DNA fragmentation. The agents which reduced the radiation-induced G 2 /M-phase arrest (caffeine, theobromine, theophylline and 2-aminopurine) enhanced the degree of DNA fragmentation at 24 h. In contrast, the agents which sustained the radiation-induced G 2 /M-phase arrest (TPA, DBcAMP, IBMX and 3-aminobenzamide) inhibited the DNA fragmentation at 24 h. These studies on EL4 lymphoma cells are consistent with the hypothesis that cells with radiation-induced genetic damage are eliminated by apoptosis subsequent to a G 2 /M block. Furthermore, it may be possible to modulate the process of radiation-induced apoptosis in lymphoma cells with pharmacological agents that modify the radiation-induced G 2 /M block, and to use this effect in the treatment of patients with malignant disease. 59 refs., 7 figs

  16. Effects of inhibitors of DNA synthesis and protein synthesis on the rate of DNA synthesis after exposure of mammalian cells to ultraviolet light

    International Nuclear Information System (INIS)

    Griffiths, T.D.; Dahle, D.B.; Meechan, P.J.; Carpenter, J.G.

    1981-01-01

    Chinese hamster V-79 cells were treated with metabolic inhibitors of DNA or protein synthesis for various intervals of time after exposure of 3.0 or 5.0 J m -2 . After removal of the metabolic block(s) the rate of DNA synthesis was followed by measuring the incorporation of [ 14 C]thymidine into acid-insoluble material. A 2.5 or 5.0h incubation with cycloheximide or hydroxyurea was effective in delaying the onset of the recovery in the rate of DNA synthesis that normally becomes evident several hours after exposure to ultraviolet light. By using concentrations of cycloheximide or hydroxyurea that inhibit DNA synthesis by a similar amount (70%), but protein synthesis by vastly different amounts (95% for cycloheximide; 0% for hydroxyurea), it was apparent that the delay in recovery caused by the treatment of the cells with cycloheximide could be accounted for entirely by its inhibitory effect on DNA synthesis. This suggests that the recovery in DNA synthetic rates following exposure of V-79 cells to ultraviolet light does not appear to require de novo protein synthesis, and therefore does not appear to require the involvement of an inducible DNA repair process. (Auth.)

  17. Novel fundamental building blocks and site dependent isomorphism in the first actinide borophosphates.

    Science.gov (United States)

    Wu, Shijun; Polinski, Matthew J; Malcherek, Thomas; Bismayer, Ulrich; Klinkenberg, Martina; Modolo, Giuseppe; Bosbach, Dirk; Depmeier, Wulf; Albrecht-Schmitt, Thomas E; Alekseev, Evgeny V

    2013-07-15

    Three novel uranyl borophosphates, Ag2(NH4)3[(UO2)2{B3O(PO4)4(PO4H)2}]H2O (AgNBPU-1), Ag(2-x)(NH4)3[(UO2)2{B2P5O(20-x)(OH)x}] (x = 1.26) (AgNBPU-2), and Ag(2-x)(NH4)3[(UO2)2{B2P(5-y)AsyO(20-x)(OH)x}] (x = 1.43, y = 2.24) (AgNBPU-3), have been prepared by the H3BO3-NH4H2PO4/NH4H2AsO4 flux method. The structure of AgNBPU-1 has an unprecedented fundamental building block (FBB), composed of three BO4 and six PO4 tetrahedra which can be written as 9□:[Φ] □□|□□|□□|. Two Ag atoms are linearly coordinated; the coordination of a third one is T-shaped. AgNBPU-2 and AgNBPU-3 are isostructural and possess a FBB of two BO4 and five TO4 (T = P, As) tetrahedra (7□:□□|□). AgNBPU-3 is a solid solution with some PO4 tetrahedra of the AgNBPU-2 end-member being substituted by AsO4. Only two out of the three independent P positions are partially occupied by As, resulting in site dependent isomorphism. The three compounds represent the first actinide borophosphates.

  18. An Overview of Metallic Nanowire Networks, Promising Building Blocks for Next Generation Transparent Conductors: Emergence, Fundamentals and Challenges

    Science.gov (United States)

    Pirsalami, Sedigheh; Zebarjad, Seyed Mojtaba; Daneshmanesh, Habib

    2017-08-01

    Transparent conductors (TCs) have a wide range of applications in numerous electronic and optoelectronic devices. This review provides an overview of the emergence of metallic nanowire networks (MNNs) as promising building blocks for the next generation transparent conductors. The fundamental aspects, structure-property relations, fabrication techniques and the corresponding challenges are reviewed. Theoretical and experimental researches suggest that nanowires with smaller diameter, longer length and higher aspect ratio have higher performance. Yet, the development of an efficient synthesis technique for the production of MNNs has remained a challenge. The synthesis method is also crucial to the scalability and the commercial potential of these emerging TCs. The most promising techniques for the synthesis together with their advantages, limitations and the recent findings are here discussed. Finally, we will try to show the promising future research trends in MNNs to have an approach to design the next generation TCs.

  19. DNA Nanotechnology for Cancer Therapy

    Science.gov (United States)

    Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

    2016-01-01

    DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients. PMID:27022418

  20. Inhibition and recovery of the replication of depurinated parvovirus DNA in mouse fibroblasts

    International Nuclear Information System (INIS)

    Vos, J.M.; Avalosse, B.; Su, Z.Z.; Rommelaere, J.

    1984-01-01

    Apurinic sites were introduced in the single-stranded DNA of parvovirus minute-virus-of-mice (MVM) and their effect on viral DNA synthesis was measured in mouse fibroblasts. Approximately one apurinic site per viral genome, is sufficient to block its replication in untreated cells. The exposure of host cells to a sublethal dose of UV-light 15 hours prior to virus infection, enhances their ability to support the replication of depurinated MVM. Cell preirradiation induces the apparent overcome of 10-15% of viral DNA replication blocks. These results indicate that apurinic sites prevent mammalian cells from replicating single-stranded DNA unless a recovery process is activated by cell UV-irradiation

  1. (tek) block for housing provision and construction in ghana

    African Journals Online (AJOL)

    User

    is strongly associated with traditional unstabi- ... of reducing cost of housing development and to ... lised-earth floors were used to provide low cost ..... system. Even though some of the buildings have been transformed from TEK blocks into.

  2. An efficient, block-by-block algorithm for inverting a block tridiagonal, nearly block Toeplitz matrix

    International Nuclear Information System (INIS)

    Reuter, Matthew G; Hill, Judith C

    2012-01-01

    We present an algorithm for computing any block of the inverse of a block tridiagonal, nearly block Toeplitz matrix (defined as a block tridiagonal matrix with a small number of deviations from the purely block Toeplitz structure). By exploiting both the block tridiagonal and the nearly block Toeplitz structures, this method scales independently of the total number of blocks in the matrix and linearly with the number of deviations. Numerical studies demonstrate this scaling and the advantages of our method over alternatives.

  3. Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Chad R.; Zhang, Fei; MacCulloch, Tara; Fahmi, Noureddine; Stephanopoulos, Nicholas; Liu, Yan; Seeman, Nadrian C. [Department; Yan, Hao

    2017-08-02

    The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.

  4. Building-Up of a DNA Barcode Library for True Bugs (Insecta: Hemiptera: Heteroptera) of Germany Reveals Taxonomic Uncertainties and Surprises

    Science.gov (United States)

    Raupach, Michael J.; Hendrich, Lars; Küchler, Stefan M.; Deister, Fabian; Morinière, Jérome; Gossner, Martin M.

    2014-01-01

    During the last few years, DNA barcoding has become an efficient method for the identification of species. In the case of insects, most published DNA barcoding studies focus on species of the Ephemeroptera, Trichoptera, Hymenoptera and especially Lepidoptera. In this study we test the efficiency of DNA barcoding for true bugs (Hemiptera: Heteroptera), an ecological and economical highly important as well as morphologically diverse insect taxon. As part of our study we analyzed DNA barcodes for 1742 specimens of 457 species, comprising 39 families of the Heteroptera. We found low nucleotide distances with a minimum pairwise K2P distance 2.2% were detected for 16 traditionally recognized and valid species. With a successful identification rate of 91.5% (418 species) our study emphasizes the use of DNA barcodes for the identification of true bugs and represents an important step in building-up a comprehensive barcode library for true bugs in Germany and Central Europe as well. Our study also highlights the urgent necessity of taxonomic revisions for various taxa of the Heteroptera, with a special focus on various species of the Miridae. In this context we found evidence for on-going hybridization events within various taxonomically challenging genera (e.g. Nabis Latreille, 1802 (Nabidae), Lygus Hahn, 1833 (Miridae), Phytocoris Fallén, 1814 (Miridae)) as well as the putative existence of cryptic species (e.g. Aneurus avenius (Duffour, 1833) (Aradidae) or Orius niger (Wolff, 1811) (Anthocoridae)). PMID:25203616

  5. Unscheduled synthesis of DNA and poly(ADP-ribose) in human fibroblasts following DNA damage

    International Nuclear Information System (INIS)

    McCurry, L.S.; Jacobson, M.K.

    1981-01-01

    Unscheduled DNA synthesis has been measured in human fibroblasts under conditions of reduced rates of conversion of NAD to poly)ADP-ribose). Cells heterozygous for the xeroderma pigmentosum genotype showed normal rates of uv induced unscheduled DNA synthesis under conditions in which the rate of poly(ADP-ribose) synthesis was one-half the rate of normal cells. The addition of theophylline, a potent inhibitor of poly(ADP-ribose) polymerase, to the culture medium of normal cells blocked over 90% of the conversion of NAD to poly(ADP-ribose) following treatment with uv or N-methyl-N'-nitro-N-nitro-soguanidine but did not affect the rate of unscheduled DNA synthesis

  6. Blocking of Single α-Hemolysin Pore by Rhodamine Derivatives.

    Science.gov (United States)

    Rokitskaya, Tatyana I; Nazarov, Pavel A; Golovin, Andrey V; Antonenko, Yuri N

    2017-06-06

    Measurements of ion conductance through α-hemolysin pore in a bilayer lipid membrane revealed blocking of the ion channel by a series of rhodamine 19 and rhodamine B esters. The longest dwell closed time of the blocking was observed with rhodamine 19 butyl ester (C4R1), whereas the octyl ester (C8R1) was of poor effect. Voltage asymmetry in the binding kinetics indicated that rhodamine derivatives bound to the stem part of the aqueous pore lumen. The binding frequency was proportional to a quadratic function of rhodamine concentrations, thereby showing that the dominant binding species were rhodamine dimers. Two levels of the pore conductance and two dwell closed times of the pore were found. The dwell closed times lengthened as the voltage increased, suggesting impermeability of the channel for the ligands. Molecular docking analysis revealed two distinct binding sites within the lumen of the stem of the α-hemolysin pore for the C4R1 dimer, but only one binding site for the C8R1 dimer. The blocking of the α-hemolysin nanopore by rhodamines could be utilized in DNA sequencing as additional optical sensing owing to bright fluorescence of rhodamines if used for DNA labeling. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  7. Modulation of radiation-induced apoptosis and G{sub 2}/M block in murine T-lymphoma cells

    Energy Technology Data Exchange (ETDEWEB)

    Palayoor, S.T.; Macklis, R.M.; Bump, E.A.; Coleman, C.N. [Harvard Medical School, Boston, MA (United States)

    1995-03-01

    Radiation-induced apoptosis in lymphocyte-derived cell lines is characterized by endonucleolytic cleavage of cellular DNA within hours after radiation exposure. We have studied this phenomenon qualitatively (DNA gel electrophoresis) and quantitatively (diphenylamine reagent assay) in murine EL4 T-lymphoma cells exposed to {sup 137}Cs {gamma} irradiation. Fragmentation was discernible within 18-24 h after exposure. It increased with time and dose and reached a plateau after 8 Gy of {gamma} radiation. We studied the effect of several pharmacological agents on the radiation-induced G{sub 2}/M block and DNA fragmentation. The agents which reduced the radiation-induced G{sub 2}/M-phase arrest (caffeine, theobromine, theophylline and 2-aminopurine) enhanced the degree of DNA fragmentation at 24 h. In contrast, the agents which sustained the radiation-induced G{sub 2}/M-phase arrest (TPA, DBcAMP, IBMX and 3-aminobenzamide) inhibited the DNA fragmentation at 24 h. These studies on EL4 lymphoma cells are consistent with the hypothesis that cells with radiation-induced genetic damage are eliminated by apoptosis subsequent to a G{sub 2}/M block. Furthermore, it may be possible to modulate the process of radiation-induced apoptosis in lymphoma cells with pharmacological agents that modify the radiation-induced G{sub 2}/M block, and to use this effect in the treatment of patients with malignant disease. 59 refs., 7 figs.

  8. ASSESSING THE COSTS OF THE THERMAL REHABILITATIONS OF A STUDIO BLOCK ENVELOPE

    Directory of Open Access Journals (Sweden)

    DINU R.C.

    2017-06-01

    Full Text Available A view to reducing thermal energy consumption for a block of studios, this paper presents an assessment of the costs of energy efficient building materials used for the thermal rehabilitation of the analyzed building’s tire. Based on information obtained from the evaluation of heat energy consumption and of the actual heat balance of the studios block, resulted the necessity for thermal rehabilitation. These works aimed equally both exterior walls as well as exterior windows and doors and involves a certain level of initial costs wich will be recovered through lower cost of the consumed thermal energy after thermal rehabilitation of the building tire.

  9. The antimetabolite ara-CTP blocks long-term memory of conditioned taste aversion.

    Science.gov (United States)

    Wang, Jianpeng; Ren, Keqin; Pérez, Javier; Silva, Alcino J; Peña de Ortiz, Sandra

    2003-01-01

    We examined the hypothesis that processes related to DNA recombination and repair are involved in learning and memory. Rats received intracerebroventricular (i.c.v.) infusions of the antimetabolite 1-beta-D-arabinofuranosylcytosine triphosphate (ara-CTP) or its precursor cytosine arabinoside (ara-C) 30 min prior to conditioned taste aversion (CTA) training. Both ara-CTP and ara-C caused significant impairments in long-term memory (LTM) of CTA. Control experiments indicate that the effect of ara-CTP on CTA memory is related to interference with learning. Furthermore, as it was previously demonstrated for the protein synthesis inhibitor anisomycin, ara-CTP had no effect on CTA memory when it was injected 1 h after training. Importantly, although both ara-CTP and anisomycin significantly blocked LTM in the task, short-term memory (STM) measured 1 h after training was not affected by either of the drugs. Finally, ara-CTP had no effect on in vitro transcription, but it did effectively block nonhomologous DNA end joining (NHEJ) activity of brain protein extracts. We suggest that DNA ligase-mediated DNA recombination and repair processes are necessary for the expression of LTM in the brain.

  10. Sensitization of Tumor to {sup 212}Pb Radioimmunotherapy by Gemcitabine Involves Initial Abrogation of G2 Arrest and Blocked DNA Damage Repair by Interference With Rad51

    Energy Technology Data Exchange (ETDEWEB)

    Yong, Kwon Joong; Milenic, Diane E.; Baidoo, Kwamena E. [Radioimmune and Inorganic Chemistry Section, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (United States); Brechbiel, Martin W., E-mail: martinwb@mail.nih.gov [Radioimmune and Inorganic Chemistry Section, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (United States)

    2013-03-15

    Purpose: To elucidate the mechanism of the therapeutic efficacy of targeted α-particle radiation therapy using {sup 212}Pb-TCMC-trastuzumab together with gemcitabine for treatment of disseminated peritoneal cancers. Methods and Materials: Mice bearing human colon cancer LS-174T intraperitoneal xenografts were pretreated with gemcitabine, followed by {sup 212}Pb-TCMC-trastuzumab and compared with controls. Results: Treatment with {sup 212}Pb-TCMC-trastuzumab increased the apoptotic rate in the S-phase-arrested tumors induced by gemcitabine at earlier time points (6 to 24 hours). {sup 212}Pb-TCMC-trastuzumab after gemcitabine pretreatment abrogated G2/M arrest at the same time points, which may be associated with the inhibition of Chk1 phosphorylation and, in turn, cell cycle perturbation, resulting in apoptosis. {sup 212}Pb-TCMC-trastuzumab treatment after gemcitabine pretreatment caused depression of DNA synthesis, DNA double-strand breaks, accumulation of unrepaired DNA, and down-regulation of Rad51 protein, indicating that DNA damage repair was blocked. In addition, modification in the chromatin structure of p21 may be associated with transcriptionally repressed chromatin states, indicating that the open structure was delayed at earlier time points. Conclusion: These findings suggest that the cell-killing efficacy of {sup 212}Pb-TCMC-trastuzumab after gemcitabine pretreatment may be associated with abrogation of the G2/M checkpoint, inhibition of DNA damage repair, and chromatin remodeling.

  11. Radiological evaluation of building materials used in Malumfashi ...

    African Journals Online (AJOL)

    ... in building materials (sand, cement, blocks, granite, and paints) used in the construction of buildings in Malumfashi local Government area of Katsina state, Nigeria were determined by means of a gamma-ray spectrometry system using Sodium Iodide thallium activated (NaI(Tl)) detector in a low background configuration.

  12. DNA replication and repair of Tilapia cells: Pt. 2

    International Nuclear Information System (INIS)

    Chen, J.D.; Yew, F.H.

    1988-01-01

    TO-2 is a fish cell line derived from the Tilapia ovary. It grows over a wide range of temperature (15-34 0 C). We report the effects of temperature on DNA replication and u.v. repair in TO-2 cells. When the cells were moved from 31 0 C to the sublethal high temperature of 37 0 C, the rate of DNA synthesis first decreased to 60%, then speedy recovery soon set in, and after 8h at 37 0 C the rate of DNA synthesis overshot the 31 0 C control level by 180%. When moved to low temperature (18 0 C) Tilapia cells also showed an initial suppression of DNA synthesis before settling at 30% of the control level. U.V. reduced but could not block DNA synthesis completely. The inhibition was overcome in 3h at 37, 31 and 25 0 C, but not at 18 0 C. Initiation of nascent DNA synthesis was blocked at 4Jm -2 in TO-2 cells compared with ≤ 1Jm -2 in mammalian cells. After 9Jm -2 u.v. irradiation, low molecular weight DNA replication intermediates started to accumulate. TO-2 cells showed low levels of u.v.-induced excision repair. (author)

  13. Passive solar design studies for non-domestic buildings. Case studies

    Energy Technology Data Exchange (ETDEWEB)

    1988-01-01

    Of the passive solar designs reported, those for a light industrial building, a nurses hostel and a low rise office block were considered to be clearly cost effective. A retrofit study of a secondary school showed that incorporating passive solar measures into refurbishment could be cost effective. Designs for a sports hall and medium rise office block were considered to be only marginally cost effective and those for a hotel bedroom block and DIY superstore were judged not to be cost effective. The maximization of daylight penetration coupled with controls on the lighting systems produced the main energy saving. This orientation, built form, fenestration, window shape, perimeter (and overhead) daylight and atria were primary solar features. Direct gain considered in conjunction with building weight/response factor could contribute to a lesser degree. Trombe walls were shown to be generally uneconomic for this type of building and conservatories contributed to amenity value more than to savings.

  14. Manipulation of partially oriented hydroxyapatite building blocks to form flowerlike bundles without acid-base regulation.

    Science.gov (United States)

    Wen, Zhenliang; Wang, Zihao; Chen, Jingdi; Zhong, Shengnan; Hu, Yimin; Wang, Jianhua; Zhang, Qiqing

    2016-06-01

    The application of hydroxyapatite (HAP) in different fields depends greatly on its morphology, composition and structure. Besides, the main inorganic building blocks of human bones and teeth are also HAP. Therefore, accurate shape and aggregation control and of hydroxyapatite particles will be of great interest. Herein, oriented bundles of flowerlike HAP nanorods were successfully prepared through hydrothermal treatment without acid-base regulation, with the mono-alkyl phosphate (MAP) and sodium citrate as surfactant and chelating agent, respectively. The prepared samples were characterized by the X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM) and zeta potential, the pH value and conductivity value of suspension were characterized by pH meter and conductivity measurement. The results showed that the MAP and citrate play an important role in assembly of HAP nanorods without acid-base regulation. Citrate calcium complex could decompose slowly and release citrate ions at hydrothermal conditions. Besides, the further decomposition of citrate ions could release aconitic acid as the reaction time prolongs. Moreover, the possible scheme for the formation process was discussed in detail. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Block-free optical quantum Banyan network based on quantum state fusion and fission

    International Nuclear Information System (INIS)

    Zhu Chang-Hua; Meng Yan-Hong; Quan Dong-Xiao; Zhao Nan; Pei Chang-Xing

    2014-01-01

    Optical switch fabric plays an important role in building multiple-user optical quantum communication networks. Owing to its self-routing property and low complexity, a banyan network is widely used for building switch fabric. While, there is no efficient way to remove internal blocking in a banyan network in a classical way, quantum state fusion, by which the two-dimensional internal quantum states of two photons could be combined into a four-dimensional internal state of a single photon, makes it possible to solve this problem. In this paper, we convert the output mode of quantum state fusion from spatial-polarization mode into time-polarization mode. By combining modified quantum state fusion and quantum state fission with quantum Fredkin gate, we propose a practical scheme to build an optical quantum switch unit which is block free. The scheme can be extended to building more complex units, four of which are shown in this paper. (general)

  16. Chemoenzymatic synthesis of statine side chain building blocks and application in the total synthesis of the cholesterol-lowering compound solistatin.

    Science.gov (United States)

    Rieder, Oliver; Wolberg, Michael; Foegen, Silke E; Müller, Michael

    2017-09-20

    The synthesis and enzymatic reduction of several 6-substituted dioxohexanoates are presented. Two-step syntheses of tert-butyl 6-bromo-3,5-dioxohexanoate and the corresponding 6-hydroxy compound have been achieved in 89% and 59% yield, respectively. Regio- and enantioselective reduction of these diketones and of the 6-chloro derivative with alcohol dehydrogenase from Lactobacillus brevis (LBADH) gave the (5S)-5-hydroxy-3-oxo products with enantiomeric excesses of 91%, 98.4%, and >99.5%, respectively. Chain elongation of the reduction products by one carbon via cyanide addition, and by more than one carbon by Julia-Kocienski olefination, gave access to well-established statine side-chain building blocks. Application in the synthesis of the cholesterol-lowering natural compound solistatin is given. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. 47 CFR 27.1330 - Local public safety build-out and operation.

    Science.gov (United States)

    2010-10-01

    ... public safety build-out and operation. (a) The Upper 700 MHz D Block licensee and the Operating Company... exclusive right to build and operate the Shared Wireless Broadband Network. (b) Rights to early build-out in... transfer and compensation to occur prior to the scheduled build out date for such network in the NSA. (ii...

  18. 47 CFR 90.1430 - Local public safety build-out and operation.

    Science.gov (United States)

    2010-10-01

    ... public safety build-out and operation. (a) The Upper 700 MHz D Block licensee and the Operating Company... exclusive right to build and operate the Shared Wireless Broadband Network. (b) Rights to early build-out in... transfer and compensation to occur prior to the scheduled build out date for such network in the NSA. (ii...

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    DNA interstrand cross-links (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. We devised ...

  20. Pyrimidine dimers block simian virus 40 replication forks

    International Nuclear Information System (INIS)

    Berger, C.A.; Edenberg, H.J.

    1986-01-01

    UV light produces lesions, predominantly pyrimidine dimers, which inhibit DNA replication in mammalian cells. The mechanism of inhibition is controversial: is synthesis of a daughter strand halted at a lesion while the replication fork moves on and reinitiates downstream, or is fork progression itself blocked for some time at the site of a lesion? We directly addressed this question by using electron microscopy to examine the distances of replication forks from the origin in unirradiated and UV-irradiated simian virus 40 chromosomes. If UV lesions block replication fork progression, the forks should be asymmetrically located in a large fraction of the irradiated molecules; if replication forks move rapidly past lesions, the forks should be symmetrically located. A large fraction of the simian virus 40 replication forks in irradiated molecules were asymmetrically located, demonstrating that UV lesions present at the frequency of pyrimidine dimers block replication forks. As a mechanism for this fork blockage, we propose that polymerization of the leading strand makes a significant contribution to the energetics of fork movement, so any lesion in the template for the leading strand which blocks polymerization should also block fork movement

  1. [Construction of porous hydroxyapatite (HA) block loaded with cultured chondrocytes].

    Science.gov (United States)

    Yan, M; Dang, G

    1999-07-01

    To construct a kind of bone healing enhancing implant with cultured chondrocytes bound to hydroxyapatite (HA). Chondrocytes were obtained from the costicartilage of rat and were cultured on the porous HA blocks, 3 mm x 3 mm x 4 mm size, for three and seven days. Scanning electron micrograph was taken to show whether the cells grew outside and inside the pore of HA block. The cells cultured on tiny glass sheet for 2 days were used to prove where the cells come from by in situ hybridization technique with alpha1 (II) cDNA probe. Scanning electron micrographs showed that the pores of the HA surface and inside of the blocks are filled with cultured cells, especially the longer cultured block. The cells were chondrocytes confirmed by in situ hybridization. The porous HA can be used as cell cultured substrate and chondrocyte can adhere and proliferate inside the porous HA block.

  2. RELATIVE DISTANCE: THE KEY TO THE SHAPE OF HEPATIC BUILDING BLOCKS

    Directory of Open Access Journals (Sweden)

    Jan M Ruijter

    2011-05-01

    Full Text Available The delineation and the shape of the smallest structural units of the liver is still the subject of debate. However,the blood flow from an upstream terminal branch of the portal vein to a downstream central vein is thought to induce a functional zonation in hepatocyte gene expression. This property was used to determine boundary conditions for the shape of the hepatic building blocks. Histochemical techniques that specifically label periportally or pericentrally expressed enzymes can be used to distinguish periportal and pericentral areas in a liver section. Pairs of images from aligned serial sections, one stained for a portal and the next for a central enzyme, are used. Segmentation and skeletonisation of these images results in the skeletons of the portal and central areas. Distance transformation with respect to these skeletons gives for each point in the image pair the distance to the nearest terminal branches of the portal vein and the central vein. For each point the relative position on the porto-central radius can then be calculated as its distance to a portal vein divided by the sum of its portal and its central distance. In the resulting relative radius image, the area occupied by 'zones' of equivalent relative radius can be measured. According to the principle of Delesse the relative area of a zone in the image is equal to the relative volume of that zone in the tissue. For structural units of plate-like, cylindrical or spherical shape, the relative volume of a zone is equal to the relative radius of that zone to the power 1, 2 or 3, respectively. Thus, the exponent in the relative area - relative radius relation gives information on the shape of the structural unit. Measurement of the areas of each relative radius zone and determination of the area - radius relation in images of random sections of adult mouse liver results in an exponent of 1.1. This suggests that the smallest structural unit of the mouse liver has the shape of a

  3. Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route.

    Science.gov (United States)

    Penocchio, Emanuele; Piccardo, Matteo; Barone, Vincenzo

    2015-10-13

    The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.

  4. Surface tectonics of nanoporous networks of melamine-capped molecular building blocks formed through interface Schiff-base reactions.

    Science.gov (United States)

    Liu, Xuan-He; Wang, Dong; Wan, Li-Jun

    2013-10-01

    Control over the assembly of molecules on a surface is of great importance for the fabrication of molecule-based miniature devices. Melamine (MA) and molecules with terminal MA units are promising candidates for supramolecular interfacial packing patterning, owing to their multiple hydrogen-bonding sites. Herein, we report the formation of self-assembled structures of MA-capped molecules through a simple on-surface synthetic route. MA terminal groups were successfully fabricated onto rigid molecular cores with 2-fold and 3-fold symmetry through interfacial Schiff-base reactions between MA and aldehyde groups. Sub-molecular scanning tunneling microscopy (STM) imaging of the resultant adlayer revealed the formation of nanoporous networks. Detailed structural analysis indicated that strong hydrogen-bonding interactions between the MA groups persistently drove the formation of nanoporous networks. Herein, we demonstrate that functional groups with strong hydrogen-bond-formation ability are promising building blocks for the guided assembly of nanoporous networks and other hierarchical 2D assemblies. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Theoretical insights into the photo-protective mechanisms of natural biological sunscreens: building blocks of eumelanin and pheomelanin.

    Science.gov (United States)

    Marchetti, Barbara; Karsili, Tolga N V

    2016-02-07

    Eumelanin (EM) and pheomelanin (PM) are ubiquitous in mammalian skin and hair--protecting against harmful radiation from the sun. Their primary roles are to absorb solar radiation and efficiently dissipate the excess excited state energy in the form of heat without detriment to the polymeric structure. EU and PM exist as polymeric chains consisting of exotic arrangements of functionalised heteroaromatic molecules. Here we have used state-of-the-art electronic structure calculations and on-the-fly surface hopping molecular dynamics simulations to study the intrinsic deactivation paths of various building blocks of EU and PM. Ultrafast excited state decay, via electron-driven proton transfer (in EU and PM) and proton-transfer coupled ring-opening (in PM) reactions, have been identified to proceed along hitherto unknown charge-separated states in EU and PM oligomers. These results shed light on the possible relaxation pathways that dominate the photochemistry of natural skin melanins. Extrapolation of such findings could provide a gateway into engineering more effective molecular constituents in commercial sunscreens--with reduced phototoxicity.

  6. Use of shock block transmitters in the structural rehabilitation of historical buildings in Calabria and Sicily

    International Nuclear Information System (INIS)

    Bianco, Alessia; Candela, Michele; Fonti, Roberta

    2008-01-01

    Many old and historical masonry buildings, located in the Calabrian and Sicilian areas near the strait of Messina, are affected by typical pattern of cracks, which are not produced by previous earthquakes. These cracks in the masonry walls are characterized by a quasi-vertical trend with constant width. The careful examination of the crack distribution allows to clearly identify the diagnosis: the damage is caused by the sinking due to a horizontal movement of translation of the ground, which is an evident effect of creep phenomena in the soil, so-called 'solifluxion'. This paper, after showing this geological pathology, proposes an innovative strategy of intervention, which consists of the use of 'oleo-dynamic' devices, so-called shock block transmitters, providing different degrees of restraint, according to the loading conditions. In addition, in case of earthquake, an important part of the in-put seismic energy can be dissipated. The strategy of application of this system to the building consists of the subdivision of each masonry wall in two different parts, which are physically separated by the cracks. Each wall portion must be consolidated separately and the different parts of walls behave as statically independent each other, so that they can move independently during the serviceability conditions. The connection among the walls composing the whole structural organism is given by metal tie-rods equipped with 'oleo dynamic' devices, which allows, in a given range, the horizontal sliding in case of slow movement due to the phenomenon of 'solifluxion'. Contrary, in case of dynamic and fast movements, such as the ones produced by an earthquake, each 'oleo dynamic' device provides a fully restraint effect and, as a consequence, the tie-rods behave in the classical way

  7. Retinal bipolar cells: elementary building blocks of vision.

    Science.gov (United States)

    Euler, Thomas; Haverkamp, Silke; Schubert, Timm; Baden, Tom

    2014-08-01

    Retinal bipolar cells are the first ‘projection neurons’ of the vertebrate visual system—all of the information needed for vision is relayed by this intraretinal connection. Each of the at least 13 distinct types of bipolar cells systematically transforms the photoreceptor input in a different way, thereby generating specific channels that encode stimulus properties, such as polarity, contrast, temporal profile and chromatic composition. As a result, bipolar cell output signals represent elementary ‘building blocks’ from which the microcircuits of the inner retina derive a feature-oriented description of the visual world.

  8. Enantioselective ProPhenol-catalyzed addition of 1,3-diynes to aldehydes to generate synthetically versatile building blocks and diyne natural products.

    Science.gov (United States)

    Trost, Barry M; Chan, Vincent S; Yamamoto, Daisuke

    2010-04-14

    A highly enantioselective method for the catalytic addition of terminal 1,3-diynes to aldehydes was developed using our dinuclear zinc ProPhenol (1) system. Furthermore, triphenylphosphine oxide was found to interact synergistically with the catalyst to substantially enhance the chiral recognition. The generality of this catalytic transformation was demonstrated with aryl, alpha,beta-unsaturated and saturated aldehydes, of which the latter were previously limited in alkynyl zinc additions. The chiral diynol products are also versatile building blocks that can be readily elaborated; this was illustrated through highly selective trans-hydrosilylations, which enabled the synthesis of a beta-hydroxyketone and enyne. Additionally, the development of this method allowed for the rapid total syntheses of several biologically important diynol-containing natural products.

  9. Modified Proofreading PCR for Detection of Point Mutations, Insertions and Deletions Using a ddNTP-Blocked Primer

    Science.gov (United States)

    Chen, Qianqian; Chen, Xiaoxiang; Zhang, Sichao; Lan, Ke; Lu, Jian; Zhang, Chiyu

    2015-01-01

    The development of simple, accurate, rapid and cost-effective technologies for mutation detection is crucial to the early diagnosis and prevention of numerous genetic diseases, pharmacogenetics, and drug resistance. Proofreading PCR (PR-PCR) was developed for mutation detection in 1998 but is rarely applied due to its low efficiency in allele discrimination. Here we developed a modified PR-PCR method using a ddNTP-blocked primer and a mixture of DNA polymerases with and without the 3'-5' proofreading function. The ddNTP-blocked primer exhibited the best blocking efficiency to avoid nonspecific primer extension while the mixture of a tiny amount of high-fidelity DNA polymerase with a routine amount of Taq DNA polymerase provided the best discrimination and amplification effects. The modified PR-PCR method is quite capable of detecting various mutation types, including point mutations and insertions/deletions (indels), and allows discrimination amplification when the mismatch is located within the last eight nucleotides from the 3'-end of the ddNTP-blocked primer. The modified PR-PCR has a sensitivity of 1-5 × 102 copies and a selectivity of 5 × 10-5 mutant among 107 copies of wild-type DNA. It showed a 100% accuracy rate in the detection of P72R germ-line mutation in the TP53 gene among 60 clinical blood samples, and a high potential to detect rifampin-resistant mutations at low frequency in Mycobacterium tuberculosis using an adaptor and a fusion-blocked primer. These results suggest that the modified PR-PCR technique is effective in detection of various mutations or polymorphisms as a simple, sensitive and promising approach. PMID:25915410

  10. BUILDING BLOCKS IN THE FOREIGN LANGUAGE CLASSROOM (PILARES BÁSICOS EN EL AULA DE IDIOMAS

    Directory of Open Access Journals (Sweden)

    Coto Keith Rossina

    2010-12-01

    presents each separately, giving the idea that only one or two can be used in the language classroom, thus missing some important matters. The point of this article is that in order to be more effective, Learning Styles, Multiple Intelligences and Language Learning Strategies must intertwine, so as to create a solid building block. The author first gives an overview of each of these areas. She then explains in the review of the literature how they should be used as a closely-knit unit. Next, she provides an example of this integration through a lesson plan on the topic of environmental conservation for an Oral Communication course for English majors at School of Modern Languages, University of Costa Rica. Finally, some advice is given to instructors on the incorporation of each of these building blocks.

  11. DNA replication and repair of Tilapia cells: Pt. 2. Effects of temperature on DNA replication and ultraviolet repair in Tilapia ovary cells

    Energy Technology Data Exchange (ETDEWEB)

    Chen, J.D.; Yew, F.H.

    1988-02-01

    TO-2 is a fish cell line derived from the Tilapia ovary. It grows over a wide range of temperature (15-34/sup 0/C). We report the effects of temperature on DNA replication and u.v. repair in TO-2 cells. When the cells were moved from 31/sup 0/C to the sublethal high temperature of 37/sup 0/C, the rate of DNA synthesis first decreased to 60%, then speedy recovery soon set in, and after 8h at 37/sup 0/C the rate of DNA synthesis overshot the 31/sup 0/C control level by 180%. When moved to low temperature (18/sup 0/C) Tilapia cells also showed an initial suppression of DNA synthesis before settling at 30% of the control level. U.V. reduced but could not block DNA synthesis completely. The inhibition was overcome in 3h at 37, 31 and 25/sup 0/C, but not at 18/sup 0/C. Initiation of nascent DNA synthesis was blocked at 4Jm/sup -2/ in TO-2 cells compared with less than or equal to 1Jm/sup -2/ in mammalian cells. After 9Jm/sup -2/ u.v. irradiation, low molecular weight DNA replication intermediates started to accumulate. TO-2 cells showed low levels of u.v.-induced excision repair.

  12. Clay characterization for making pressed and burned blocks

    International Nuclear Information System (INIS)

    Alexandre, J.; Silva, C.L. de A.P. e

    2012-01-01

    The municipality of Campos dos Goytacazes, located in the state of Rio de Janeiro, at 275 km from the capital, are the largest industrial ceramic state and he has over 100 unionized industries. The production of these industries is based on tiles, building blocks and bricks. Seeking the improvement and diversification of production, the North Fluminense State University has 18 years working in partnership with local industry, with students and teachers. One of the researches is the production of blocks pressed and burned. In this work are presented in many lab tests performed, morphology and some of technological properties. (author)

  13. Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription*

    Science.gov (United States)

    Nadkarni, Aditi; Burns, John A.; Gandolfi, Alberto; Chowdhury, Moinuddin A.; Cartularo, Laura; Berens, Christian; Geacintov, Nicholas E.; Scicchitano, David A.

    2016-01-01

    DNA adducts derived from carcinogenic polycyclic aromatic hydrocarbons like benzo[a]pyrene (B[a]P) and benzo[c]phenanthrene (B[c]Ph) impede replication and transcription, resulting in aberrant cell division and gene expression. Global nucleotide excision repair (NER) and transcription-coupled DNA repair (TCR) are among the DNA repair pathways that evolved to maintain genome integrity by removing DNA damage. The interplay between global NER and TCR in repairing the polycyclic aromatic hydrocarbon-derived DNA adducts (+)-trans-anti-B[a]P-N6-dA, which is subject to NER and blocks transcription in vitro, and (+)-trans-anti-B[c]Ph-N6-dA, which is a poor substrate for NER but also blocks transcription in vitro, was tested. The results show that both adducts inhibit transcription in human cells that lack both NER and TCR. The (+)-trans-anti-B[a]P-N6-dA lesion exhibited no detectable effect on transcription in cells proficient in NER but lacking TCR, indicating that NER can remove the lesion in the absence of TCR, which is consistent with in vitro data. In primary human cells lacking NER, (+)-trans-anti-B[a]P-N6-dA exhibited a deleterious effect on transcription that was less severe than in cells lacking both pathways, suggesting that TCR can repair the adduct but not as effectively as global NER. In contrast, (+)-trans-anti-B[c]Ph-N6-dA dramatically reduces transcript production in cells proficient in global NER but lacking TCR, indicating that TCR is necessary for the removal of this adduct, which is consistent with in vitro data showing that it is a poor substrate for NER. Hence, both global NER and TCR enhance the recovery of gene expression following DNA damage, and TCR plays an important role in removing DNA damage that is refractory to NER. PMID:26559971

  14. Power Block Geometry Applied to the Building of Power Electronics Converters

    Science.gov (United States)

    dos Santos, E. C., Jr.; da Silva, E. R. C.

    2013-01-01

    This paper proposes a new methodology, Power Block Geometry (PBG), for the presentation of power electronics topologies that process ac voltage. PBG's strategy uses formal methods based on a geometrical representation with particular rules and defines a universe with axioms and conjectures to establish a formation law. It allows power…

  15. DNA Block Copolymers : Functional Materials for Nanoscience and Biomedicine

    NARCIS (Netherlands)

    Schnitzler, Tobias; Herrmann, Andreas

    2012-01-01

    We live in a world full of synthetic materials, and the development of new technologies builds on the design and synthesis of new chemical structures, such as polymers. Synthetic macromolecules have changed the world and currently play a major role in all aspects of daily life. Due to their

  16. A patch-clamp ASIC for nanopore-based DNA analysis.

    Science.gov (United States)

    Kim, Jungsuk; Maitra, Raj; Pedrotti, Kenneth D; Dunbar, William B

    2013-06-01

    In this paper, a fully integrated high-sensitivity patch-clamp system is proposed for single-molecule deoxyribonucleic acid (DNA) analysis using a nanopore sensor. This system is composed of two main blocks for amplification and compensation. The amplification block is composed of three stages: 1) a headstage, 2) a voltage-gain difference amplifier, and 3) a track-and-hold circuit, that amplify a minute ionic current variation sensed by the nanopore while the compensation block avoids the headstage saturation caused by the input parasitic capacitances during sensing. By employing design techniques novel for this application, such as an instrumentation--amplifier topology and a compensation switch, we minimize the deleterious effects of the input-offset voltage and the input parasitic capacitances while attaining hardware simplicity. This system is fabricated in a 0.35 μm 4M2P CMOS process and is demonstrated using an α-hemolysin protein nanopore for detection of individual molecules of single-stranded DNA that pass through the 1.5 nm-diameter pore. In future work, the refined system will functionalize single and multiple solid-state nanopores formed in integrated microfluidic devices for advanced DNA analysis, in scientific and diagnostic applications.

  17. Drosophila mutations at the mei-9 and mus(2)201 loci which block excision of thymine dimers also block induction of unscheluded DNA synthesis by methyl methanesulfonate, ethyl methanesulfonate, N-methyl-N-nitrosourea, UV light and X-rays

    International Nuclear Information System (INIS)

    Dusenbery, R.L.; McCormick, S.C.; Smith, P.D.

    1983-01-01

    The mei-9 and mus(2)201 mutants of Drosophila melanogaster were identified as mutagen-sensitive mutants on the basis of larval hypersensitivity to methyl methanesulfonate and characterized as excision repair-deficient on the basis of a greatly reduced capacity to excise thymine dimers from cellular DNA. The high degree of larval cytotoxicity observed with a variety of other chemical and physical agents indicated that these mutants may be unable to excise other important classes of DNA adducts. We have measured the ability of the single mutants and the double mutant combination mei-9;mus(2)201 to perform the resynthesis step in excision repair by means of an autoradiographic analysis of unscheduled DNA synthesis (UDS) induced in a mixed population of primary cells in culture. The 3 strains exhibit no detectable UDS activity in response to applied doses of 1.5-6.0 mM methyl methanesulfonate, 1.0-4.5 nM N-methyl-N-nitrosourea or 10-40 J/m 2 254-nm UV light, dose ranges in which control cells exhibit a strong dose-dependent UDS response. The mei-9 and mei-9;mus(2)201 mutants also have no detectable UDS response to X-ray doses of 300-1.800 rad, whereas the mus(2)201 mutant exhibits a reduced, but dose-dependent, response over this range. These data correlate well with the degree of larval hypersensitivity of the strains and suggest that mutations at both loci block the excision repair of a wide variety of DNA damage prior to the resynthesis step. (orig.)

  18. Use of (S)-trans-gamma-monocyclofarnesol as a useful chiral building block for the stereoselective synthesis of diterpenic natural products.

    Science.gov (United States)

    Serra, Stefano; Cominetti, Alessandra A; Lissoni, Veronica

    2014-03-01

    A comprehensive study of the exploitation of (S)-trans-gamma-monocyclofarnesol as a useful chiral building block for the stereoselective synthesis of natural diterpene derivatives is here described. The farnesol derivative (+)-1 was used as starting material in the preparation of the diterpenes (S)-dehydroambliol-A and (S)-trixagol, as well as for the syntheses of the dinorditerpene (S)-dinortrixagone and of the guanidine-interrupted terpenoid (S)-dotofide. Key steps of the presented syntheses were the cross-coupling between an allyl acetate and a Grignard reagent, the Wittig reaction, the selective preparation ofa diacylguanidine derivative and the alkylation of a sulfone derivative, followed by the reductive removal of the same functional group. It is worth noting that the natural products (+)-8, (+)-12 and (+)-15 were prepared stereoselectively for the first time, thus allowing the unambiguous assignment of their absolute configuration.

  19. The inhibition of anti-DNA binding to DNA by nucleic acid binding polymers.

    Directory of Open Access Journals (Sweden)

    Nancy A Stearns

    Full Text Available Antibodies to DNA (anti-DNA are the serological hallmark of systemic lupus erythematosus (SLE and can mediate disease pathogenesis by the formation of immune complexes. Since blocking immune complex formation can attenuate disease manifestations, the effects of nucleic acid binding polymers (NABPs on anti-DNA binding in vitro were investigated. The compounds tested included polyamidoamine dendrimer, 1,4-diaminobutane core, generation 3.0 (PAMAM-G3, hexadimethrine bromide, and a β-cylodextrin-containing polycation. As shown with plasma from patients with SLE, NABPs can inhibit anti-DNA antibody binding in ELISA assays. The inhibition was specific since the NABPs did not affect binding to tetanus toxoid or the Sm protein, another lupus autoantigen. Furthermore, the polymers could displace antibody from preformed complexes. Together, these results indicate that NABPs can inhibit the formation of immune complexes and may represent a new approach to treatment.

  20. optimizing compressive strength characteristics of hollow building

    African Journals Online (AJOL)

    eobe

    Keywords: hollow building Blocks, granite dust, sand, partial replacement, compressive strength. 1. INTRODUCTION ... exposed to extreme climate. The physical ... Sridharan et al [13] conducted shear strength studies on soil-quarry dust.

  1. DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae

    Science.gov (United States)

    Boiteux, Serge; Jinks-Robertson, Sue

    2013-01-01

    DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage. PMID:23547164

  2. DNA Based Electrochromic and Photovoltaic Cells

    Science.gov (United States)

    2012-01-01

    using deoxyribonucleic acid complex as an electron blocking layer App. Phys. Lett. 88 (2006) 171109. 23. F.H.C. Crick , J.D. Watson . The complementary...9550-09-1-0647 final 01-09-2009 ; 30-11-2011 DNA Based Electrochromic and Photovoltaic Cells FA 9550-09-1-0647 Pawlicka, Agnieszka, J. Instituto de...Available. DNA is an abundant natural product with very good biodegradation properties and can be used to obtain gel polymer electrolytes (GPEs) with high

  3. Comprehensive assessment of the efficiency of high-rise construction projects in the form of urban blocks

    Science.gov (United States)

    Orlov, Alexandr; Chubarkina, Irina

    2018-03-01

    The paper is dedicated to main modern trends in the area of high-rise construction. The classification of buildings and structures by height is given. Functional distribution by the height of buildings is presented. A review of positive and negative aspects of high-rise construction from the economic point of view is given. On the basis of the data obtained, it is proposed to build up residential microdistricts in the form of urban blocks. A plan of microdistricts development is presented. It takes into account urban blocks and includes their main characteristics. An economic and mathematical model was developed to carry out a comprehensive assessment of the effectiveness of high-rise construction projects.

  4. Compressive Strength Of Rice Husk Ash-Cement Sandcrete Blocks ...

    African Journals Online (AJOL)

    There is growing demand for alternative, low-cost building material in developing countries. The effect of partial substitution of ordinary Portland cement with Rice Husk Ash (RHA) on the compressive strength of hollow sandcrete block was investigated through laboratory experimental procedures. The specific gravity, initial ...

  5. quality assessment of sandcrete blocks produced in adeta, kwara

    African Journals Online (AJOL)

    HOD

    This research assessed the quality of blocks produced in. Adeta, Ilorin West ... compared with the Nigerian Industrial Standards (NIS) specifications. ... to provide aesthetics to buildings and serve as control ... Cement is a construction material used in bonding with ... calculated as a percentage of the total sample weight.

  6. Well-defined block copolymers for gene delivery to dendritic cells: probing the effect of polycation chain-length.

    Science.gov (United States)

    Tang, Rupei; Palumbo, R Noelle; Nagarajan, Lakshmi; Krogstad, Emily; Wang, Chun

    2010-03-03

    The development of safe and efficient polymer carriers for DNA vaccine delivery requires mechanistic understanding of structure-function relationship of the polymer carriers and their interaction with antigen-presenting cells. Here we have synthesized a series of diblock copolymers with well-defined chain-length using atom transfer radical polymerization and characterized the influence of polycation chain-length on the physico-chemical properties of the polymer/DNA complexes as well as the interaction with dendritic cells. The copolymers consist of a hydrophilic poly(ethylene glycol) block and a cationic poly(aminoethyl methacrylate) (PAEM) block. The average degree of polymerization (DP) of the PAEM block was varied among 19, 39, and 75, with nearly uniform distribution. With increasing PAEM chain-length, polyplexes formed by the diblock copolymers and plasmid DNA had smaller average particle size and showed higher stability against electrostatic destabilization by salt and heparin. The polymers were not toxic to mouse dendritic cells (DCs) and only displayed chain-length-dependent toxicity at a high concentration (1mg/mL). In vitro gene transfection efficiency and polyplex uptake in DCs were also found to correlate with chain-length of the PAEM block with the longer polymer chain favoring transfection and cellular uptake. The polyplexes induced a modest up-regulation of surface markers for DC maturation that was not significantly dependent on PAEM chain-length. Finally, the polyplex prepared from the longest PAEM block (DP of 75) achieved an average of 20% enhancement over non-condensed anionic dextran in terms of uptake by DCs in the draining lymph nodes 24h after subcutaneous injection into mice. Insights gained from studying such structurally well-defined polymer carriers and their interaction with dendritic cells may contribute to improved design of practically useful DNA vaccine delivery systems. Copyright 2009 Elsevier B.V. All rights reserved.

  7. Linking dwarf galaxies to halo building blocks with the most metal-poor star in Sculptor.

    Science.gov (United States)

    Frebel, Anna; Kirby, Evan N; Simon, Joshua D

    2010-03-04

    Current cosmological models indicate that the Milky Way's stellar halo was assembled from many smaller systems. On the basis of the apparent absence of the most metal-poor stars in present-day dwarf galaxies, recent studies claimed that the true Galactic building blocks must have been vastly different from the surviving dwarfs. The discovery of an extremely iron-poor star (S1020549) in the Sculptor dwarf galaxy based on a medium-resolution spectrum cast some doubt on this conclusion. Verification of the iron-deficiency, however, and measurements of additional elements, such as the alpha-element Mg, are necessary to demonstrate that the same type of stars produced the metals found in dwarf galaxies and the Galactic halo. Only then can dwarf galaxy stars be conclusively linked to early stellar halo assembly. Here we report high-resolution spectroscopic abundances for 11 elements in S1020549, confirming its iron abundance of less than 1/4,000th that of the Sun, and showing that the overall abundance pattern follows that seen in low-metallicity halo stars, including the alpha-elements. Such chemical similarity indicates that the systems destroyed to form the halo billions of years ago were not fundamentally different from the progenitors of present-day dwarfs, and suggests that the early chemical enrichment of all galaxies may be nearly identical.

  8. Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function

    Energy Technology Data Exchange (ETDEWEB)

    Lassila, JK; Bernstein, SL; Kinney, JN; Axen, SD; Kerfeld, CA

    2014-05-29

    Bacterial microconnpartnnents (BMCs) sequester enzymes from the cytoplasmic environment by encapsulation inside a selectively permeable protein shell. Bioinformatic analyses indicate that many bacteria encode BMC clusters of unknown function and with diverse combinations of shell proteins. The genome of the halophilic myxobacterium Haliangium ochraceum encodes one of the most atypical sets of shell proteins in terms of composition and primary structure. We found that microconnpartnnent shells could be purified in high yield when all seven H. ochraceum BMC shell genes were expressed from a synthetic operon in Escherichia coll. These shells differ substantially from previously isolated shell systems in that they are considerably smaller and more homogeneous, with measured diameters of 39 2 nm. The size and nearly uniform geometry allowed the development of a structural model for the shells composed of 260 hexagonal units and 13 hexagons per icosahedral face. We found that new proteins could be recruited to the shells by fusion to a predicted targeting peptide sequence, setting the stage for the use of these remarkably homogeneous shells for applications such as three-dimensional scaffolding and the construction of synthetic BMCs. Our results demonstrate the value of selecting from the diversity of BMC shell building blocks found in genomic sequence data for the construction of novel compartments. (C) 2014 Elsevier Ltd. All rights reserved.

  9. Science Support: The Building Blocks of Active Data Curation

    Science.gov (United States)

    Guillory, A.

    2013-12-01

    While the scientific method is built on reproducibility and transparency, and results are published in peer reviewed literature, we have come to the digital age of very large datasets (now of the order of petabytes and soon exabytes) which cannot be published in the traditional way. To preserve reproducibility and transparency, active curation is necessary to keep and protect the information in the long term, and 'science support' activities provide the building blocks for active data curation. With the explosive growth of data in all fields in recent years, there is a pressing urge for data centres to now provide adequate services to ensure long-term preservation and digital curation of project data outputs, however complex those may be. Science support provides advice and support to science projects on data and information management, from file formats through to general data management awareness. Another purpose of science support is to raise awareness in the science community of data and metadata standards and best practice, engendering a culture where data outputs are seen as valued assets. At the heart of Science support is the Data Management Plan (DMP) which sets out a coherent approach to data issues pertaining to the data generating project. It provides an agreed record of the data management needs and issues within the project. The DMP is agreed upon with project investigators to ensure that a high quality documented data archive is created. It includes conditions of use and deposit to clearly express the ownership, responsibilities and rights associated with the data. Project specific needs are also identified for data processing, visualization tools and data sharing services. As part of the National Centre for Atmospheric Science (NCAS) and National Centre for Earth Observation (NCEO), the Centre for Environmental Data Archival (CEDA) fulfills this science support role of facilitating atmospheric and Earth observation data generating projects to ensure

  10. DNA as an Optical Material

    Science.gov (United States)

    2011-07-01

    the electron blocking function of the DNA layer; electroluminescence occurs in either the AlQ3 (green) or NPB layer (blue) layers. Source: J. A...been observed for sev- eral fluorescent materials with different HOMO/LUMO levels, including AlQ3 (green emission) and NPB (blue emission). OLEDs

  11. Cationic polymers for DNA origami coating - examining their binding efficiency and tuning the enzymatic reaction rates

    Science.gov (United States)

    Kiviaho, Jenny K.; Linko, Veikko; Ora, Ari; Tiainen, Tony; Järvihaavisto, Erika; Mikkilä, Joona; Tenhu, Heikki; Nonappa, Affc; Kostiainen, Mauri A.

    2016-06-01

    DNA origamis are fully tailored, programmable, biocompatible and readily functionalizable nanostructures that provide an excellent foundation for the development of sophisticated drug-delivery systems. However, the DNA origami objects suffer from certain drawbacks such as low cell-transfection rates and low stability. A great deal of studies on polymer-based transfection agents, mainly focusing on polyplex formation and toxicity, exists. In this study, the electrostatic binding between a brick-like DNA origami and cationic block-copolymers was explored. The effect of the polymer structure on the binding was investigated and the toxicity of the polymer-origami complexes evaluated. The study shows that all of the analyzed polymers had a suitable binding efficiency irrespective of the block structure. It was also observed that the toxicity of polymer-origami complexes was insignificant at the biologically relevant concentration levels. Besides brick-like DNA origamis, tubular origami carriers equipped with enzymes were also coated with the polymers. By adjusting the amount of cationic polymers that cover the DNA structures, we showed that it is possible to control the enzyme kinetics of the complexes. This work gives a starting point for further development of biocompatible and effective polycation-based block copolymers that can be used in coating different DNA origami nanostructures for various bioapplications.DNA origamis are fully tailored, programmable, biocompatible and readily functionalizable nanostructures that provide an excellent foundation for the development of sophisticated drug-delivery systems. However, the DNA origami objects suffer from certain drawbacks such as low cell-transfection rates and low stability. A great deal of studies on polymer-based transfection agents, mainly focusing on polyplex formation and toxicity, exists. In this study, the electrostatic binding between a brick-like DNA origami and cationic block-copolymers was explored. The

  12. DNA synthesis in irradiated mammalian cells

    International Nuclear Information System (INIS)

    Painter, R.B.; California Univ., San Francisco; Young, B.R.

    1987-01-01

    One of the first responses observed in S phase mammalian cells that have suffered DNA damage is the inhibition of initiation of DNA replicons. In cells exposed to ionizing radiation, a single-strand break appears to be the stimulus for this effect, whereby the initiation of many adjacent replicons (a replicon cluster) is blocked by a single-strand break in any one of them. In cells exposed to ultraviolet light (u.v.), replicon initiation is blocked at fluences that induce about one pyrimidine dimer per replicon. The inhibition of replicon initiation by u.v. in Chinese hamster cells that are incapable of excising pyrimidine dimers from their DNA is virtually the same as in cells that are proficient in dimer excision. Therefore, a single-strand break formed during excision repair of pyrimidine dimers is not the stimulus for inhibition of replicon initiation in u.v.-irradiated cells. Considering this fact, as well as the comparative insensitivity of human ataxia telangiectasia cells to u.v.-induced inhibition of replicon initiation, we propose that a relatively rare lesion is the stimulus for u.v. -induced inhibition of replicon initiation. (author

  13. Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases

    OpenAIRE

    Maxwell, Brian A.; Suo, Zucai

    2014-01-01

    The kinetic mechanisms by which DNA polymerases catalyze DNA replication and repair have long been areas of active research. Recently discovered Y-family DNA polymerases catalyze the bypass of damaged DNA bases that would otherwise block replicative DNA polymerases and stall replication forks. Unlike DNA polymerases from the five other families, the Y-family DNA polymerases have flexible, solvent-accessible active sites that are able to tolerate various types of damaged template bases and all...

  14. Membrane-Assisted Growth of DNA Origami Nanostructure Arrays

    Science.gov (United States)

    2015-01-01

    Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors—a three-layered rectangular block and a Y-shaped DNA structure—to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes. PMID:25734977

  15. Membrane-assisted growth of DNA origami nanostructure arrays.

    Science.gov (United States)

    Kocabey, Samet; Kempter, Susanne; List, Jonathan; Xing, Yongzheng; Bae, Wooli; Schiffels, Daniel; Shih, William M; Simmel, Friedrich C; Liedl, Tim

    2015-01-01

    Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors--a three-layered rectangular block and a Y-shaped DNA structure--to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.

  16. Polyaza crown ether as non-nucleosidic building blocks in DNA-conjugates

    DEFF Research Database (Denmark)

    Jakobsen, Ulla; Rohr, Katja; Madsen, Rasmus K

    2007-01-01

    The synthesis of amphiphilic polyaza crown ether monomers X (palmityl-substituted), Y (cholesteryl-substituted) and Z (dipalmityl-subtituted) and their incorporation into oligonucleotides are described. Their effects on thermal duplex stability were investigated by UV melting curve analysis. Ther...

  17. Bidirectional cross metathesis and ring-closing metathesis/ring opening of a C2-symmetric building block: a strategy for the synthesis of decanolide natural products

    Directory of Open Access Journals (Sweden)

    Bernd Schmidt

    2013-11-01

    Full Text Available Starting from the conveniently available ex-chiral pool building block (R,R-hexa-1,5-diene-3,4-diol, the ten-membered ring lactones stagonolide E and curvulide A were synthesized using a bidirectional olefin-metathesis functionalization of the terminal double bonds. Key steps are (i a site-selective cross metathesis, (ii a highly diastereoselective extended tethered RCM to furnish a (Z,E-configured dienyl carboxylic acid and (iii a Ru–lipase-catalyzed dynamic kinetic resolution to establish the desired configuration at C9. Ring closure was accomplished by macrolactonization. Curvulide A was synthesized from stagonolide E through Sharpless epoxidation.

  18. Bidirectional cross metathesis and ring-closing metathesis/ring opening of a C 2-symmetric building block: a strategy for the synthesis of decanolide natural products.

    Science.gov (United States)

    Schmidt, Bernd; Kunz, Oliver

    2013-01-01

    Starting from the conveniently available ex-chiral pool building block (R,R)-hexa-1,5-diene-3,4-diol, the ten-membered ring lactones stagonolide E and curvulide A were synthesized using a bidirectional olefin-metathesis functionalization of the terminal double bonds. Key steps are (i) a site-selective cross metathesis, (ii) a highly diastereoselective extended tethered RCM to furnish a (Z,E)-configured dienyl carboxylic acid and (iii) a Ru-lipase-catalyzed dynamic kinetic resolution to establish the desired configuration at C9. Ring closure was accomplished by macrolactonization. Curvulide A was synthesized from stagonolide E through Sharpless epoxidation.

  19. Identification of a residue critical for the excision of 3′-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family

    Science.gov (United States)

    Castillo-Acosta, Víctor M.; Ruiz-Pérez, Luis M.; Yang, Wei; González-Pacanowska, Dolores; Vidal, Antonio E.

    2009-01-01

    DNA single-strand breaks containing 3′-blocking groups are generated from attack of the sugar backbone by reactive oxygen species or after base excision by DNA glycosylase/apurinic/apyrimidinic (AP) lyases. In human cells, APE1 excises sugar fragments that block the 3′-ends thus facilitating DNA repair synthesis. In Leishmania major, the causal agent of leishmaniasis, the APE1 homolog is the class II AP endonuclease LMAP. Expression of LMAP but not of APE1 reverts the hypersensitivity of a xth nfo repair-deficient Escherichia coli strain to the oxidative compound hydrogen peroxide (H2O2). To identify the residues specifically involved in the repair of oxidative DNA damage, we generated random mutations in the ape1 gene and selected those variants that conferred protection against H2O2. Among the resistant clones, we isolated a mutant in the nuclease domain of APE1 (D70A) with an increased capacity to remove 3′-blocking ends in vitro. D70 of APE1 aligns with A138 of LMAP and mutation of the latter to aspartate significantly reduces its 3′-phosphodiesterase activity. Kinetic analysis shows a novel role of residue D70 in the excision rate of 3′-blocking ends. The functional and structural differences between the parasite and human enzymes probably reflect a divergent molecular evolution of their DNA repair responses to oxidative damage. PMID:19181704

  20. UVB DNA dosimeters analyzed by polymerase chain reactors

    International Nuclear Information System (INIS)

    Yoshida, Hiroko; Regan, J.D.; Florida Inst. of Tech., Melbourne, FL

    1997-01-01

    Purified bacteriophage λ DNA was dried on a UV-transparent polymer film and served as a UVB dosimeter for personal and ecological applications. Bacteriophage λ DNA was chosen because it is commercially available and inexpensive, and its entire sequence is known. Each dosimeter contained two sets of DNA sandwiched between UV-transparent polymer films, one exposed to solar radiation (experimental) and another protected from UV radiation by black paper (control). The DNA dosimeter was then analyzed by a polymerase chain reaction (PCR) that amplifies a 500 base pair specific region of λ DNA. Photoinduced damage in DNA blocks polymerase from synthesizing a new strand; therefore, the amount of amplified product in UV-exposed DNA was reduced from that found in control DNA. The dried λ DNA dosimeter is compact, robust, safe and transportable, stable over long storage times and provides the total UVB dose integrated over the exposure time. (author)